diff --git a/.travis.yml b/.travis.yml
index 388892a3c807c0ec9108c0c669b20d374e52c30d..3723bc969eec3100213188993e13bf7cce28c284 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -25,7 +25,7 @@ matrix:
- os: linux
dist: trusty
sudo: required
- env: CPPCHECK=yes CPPCHECK_VERSION=1.85
+ env: CPPCHECK=yes CPPCHECK_VERSION=1.87
# then check with different optimization flags
- os: linux
dist: trusty
diff --git a/CHANGES/v2.3.md b/CHANGES/v2.3.md
index d6e37d2177247d90f202d4348601c9b91849549e..afb48298f23198f780c80ba7268780e534840ecf 100644
--- a/CHANGES/v2.3.md
+++ b/CHANGES/v2.3.md
@@ -254,13 +254,15 @@ For users:
- Fixed flag DETAILED_TIMERS in \ref DEBUG (flag was ignored and detailed timers always written).
- Small fix in \ref DUMPMASSCHARGE (atoms are now correctly requested only at first step).
-## Version 2.3.8 ()
+## Version 2.3.8 (Dec 19, 2018)
\plumednotmaintained
For users:
- Fixed some openMP regression (some related to the whole codes and some specifics for Coordination and Multicolvar), this were compiler dependent so not all users may have experienced them
- Fixed an issue with \ref CS2BACKBONE when more than 2 chains were used
+- Fixed memory leak in \ref RDC.
+- Fixed segmentation fault with more than two CVs in reweighting \ref METAD (see \issue{399}, thanks to fiskissimo).
For developers:
- Small fix in LDFLAGS when enabling coverage.
diff --git a/CHANGES/v2.4.md b/CHANGES/v2.4.md
index ae03f3e0e325d10354d2cbbf06871fda15262422..080763a0eb889551d87b7d557abe2bedbc17ad51 100644
--- a/CHANGES/v2.4.md
+++ b/CHANGES/v2.4.md
@@ -201,15 +201,39 @@ For users:
- Module VES: Fixed a bug in TD_GRID for 2D grids where the grid spacing is not the same for both dimensions.
- GROMACS patch for gromacs-2018.3.
-## Version 2.4.4 (to be released)
+## Version 2.4.4 (Dec 19, 2018)
For users:
- Fixed some performances regression issue with OpenMP
- Updated NAMD patches to version 2.12 and 2.13. Old patches have been removed.
- GROMACS patch for gromacs-2018.4.
- - Fixed a bug in CS2BACKBONE when using more than 2 chains
+ - Fixed a threadsafety issue using forces on \ref HISTOGRAM
+ - Fixed error message suggesting wrong actions (see \issue{421}).
For developers:
- All fixed done in version 2.3.8
- CPPCHECK updated to 1.85
+## Version 2.4.5 (Apr 1, 2019)
+
+\plumednotmaintained
+
+For users:
+ - Fixed an inconsistency in parsing of braces.
+ It is now possible to pass individual options
+ including spaces (e.g. with `FILE={/path with space/file}`). Notice
+ that this invalidates syntax such as `ATOMS={1}{2}{3}{4}`. See more
+ at \issue{434}.
+ - Fixed \ref simplemd so as to call "runFinalJobs" at the end of the simulation.
+ - GROMACS patch for gromacs-2016.6.
+ - GROMACS patch for gromacs-2018.6.
+ - Added aliases for some actions/options containing dashes (`-`) in their name. This will improve
+ backward compatibility when these actions/options will be removed (see \issue{449}).
+
+## Version 2.4.6 ()
+
+For users:
+ - Fixed a bug in \ref COORDINATIONNUMBER where derivatives were wrong when using R_POWER > 2, thanks to @MoleOrbitalHybridAnalyst for spotting and fixing
+ - Fixed a bug in library search, possibly affecting linked blas/lapack on OSX (see \issue{476}).
+ - Fixed a bug in \ref METAD with `TARGET` and `GRID_SPARSE` (see \issue{467}).
+
diff --git a/VERSION b/VERSION
index 8239574498acf5389999716f1539cd94567733f1..453f773d3e9f62bd1c2478400142a683177d26d0 100644
--- a/VERSION
+++ b/VERSION
@@ -5,4 +5,4 @@
# (this is same as gromacs)
# Notice that "plumed info --version" will return only 2.X
# and "plumed info --long-version" will return the full string
-2.4.3
+2.4.5
diff --git a/configure b/configure
index 375c1f0126d5046c48b79458bc856f18c80f66c8..f44bfbb3337fe0d47785865022e57110e5a1daeb 100755
--- a/configure
+++ b/configure
@@ -5687,6 +5687,66 @@ fi
# first look for blas
if test "$external_blas" == true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether dgemv can be linked with no library" >&5
+$as_echo_n "checking whether dgemv can be linked with no library... " >&6; }
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dgemv ();
+int
+main ()
+{
+return dgemv ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ blas_found=nounderscore
+
+else
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether dgemv_ can be linked with no library" >&5
+$as_echo_n "checking whether dgemv_ can be linked with no library... " >&6; }
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dgemv_ ();
+int
+main ()
+{
+return dgemv_ ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ blas_found=underscore
+
+else
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
if test "${libsearch}" == true ; then
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dgemv" >&5
@@ -6044,6 +6104,14 @@ fi
fi
+
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
fi
# if not found, then use internal lapack and blas
diff --git a/configure.ac b/configure.ac
index 23484c27ed76d3bddeef5058b3b37dbfbae1f7e6..81e38cb273e5b60d1b44ae0e93c1428db50f884d 100644
--- a/configure.ac
+++ b/configure.ac
@@ -428,8 +428,22 @@ fi
# first look for blas
if test "$external_blas" == true ; then
- PLUMED_SEARCH_LIBS([dgemv],[blas],[blas_found=nounderscore], [
- PLUMED_SEARCH_LIBS([dgemv_],[blas],[blas_found=underscore])
+ AC_MSG_CHECKING([whether dgemv can be linked with no library])
+ AC_LINK_IFELSE([AC_LANG_CALL([], [dgemv])],[
+ AC_MSG_RESULT([yes])
+ blas_found=nounderscore
+ ],[
+ AC_MSG_RESULT([no])
+ AC_MSG_CHECKING([whether dgemv_ can be linked with no library])
+ AC_LINK_IFELSE([AC_LANG_CALL([], [dgemv_])],[
+ AC_MSG_RESULT([yes])
+ blas_found=underscore
+ ],[
+ AC_MSG_RESULT([no])
+ PLUMED_SEARCH_LIBS([dgemv],[blas],[blas_found=nounderscore],[
+ PLUMED_SEARCH_LIBS([dgemv_],[blas],[blas_found=underscore])
+ ])
+ ])
])
fi
diff --git a/patches/gromacs-2016.5.config b/patches/gromacs-2016.6.config
similarity index 100%
rename from patches/gromacs-2016.5.config
rename to patches/gromacs-2016.6.config
diff --git a/patches/gromacs-2016.5.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-2016.6.diff/src/gromacs/CMakeLists.txt
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/gromacs/CMakeLists.txt
rename to patches/gromacs-2016.6.diff/src/gromacs/CMakeLists.txt
diff --git a/patches/gromacs-2016.5.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-2016.6.diff/src/gromacs/CMakeLists.txt.preplumed
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/gromacs/CMakeLists.txt.preplumed
rename to patches/gromacs-2016.6.diff/src/gromacs/CMakeLists.txt.preplumed
diff --git a/patches/gromacs-2016.5.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2016.6.diff/src/gromacs/mdlib/force.cpp
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/gromacs/mdlib/force.cpp
rename to patches/gromacs-2016.6.diff/src/gromacs/mdlib/force.cpp
diff --git a/patches/gromacs-2016.5.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-2016.6.diff/src/gromacs/mdlib/force.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/gromacs/mdlib/force.cpp.preplumed
rename to patches/gromacs-2016.6.diff/src/gromacs/mdlib/force.cpp.preplumed
diff --git a/patches/gromacs-2016.5.diff/src/gromacs/mdlib/minimize.cpp b/patches/gromacs-2016.6.diff/src/gromacs/mdlib/minimize.cpp
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/gromacs/mdlib/minimize.cpp
rename to patches/gromacs-2016.6.diff/src/gromacs/mdlib/minimize.cpp
diff --git a/patches/gromacs-2016.5.diff/src/gromacs/mdlib/minimize.cpp.preplumed b/patches/gromacs-2016.6.diff/src/gromacs/mdlib/minimize.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/gromacs/mdlib/minimize.cpp.preplumed
rename to patches/gromacs-2016.6.diff/src/gromacs/mdlib/minimize.cpp.preplumed
diff --git a/patches/gromacs-2016.5.diff/src/programs/mdrun/md.cpp b/patches/gromacs-2016.6.diff/src/programs/mdrun/md.cpp
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/programs/mdrun/md.cpp
rename to patches/gromacs-2016.6.diff/src/programs/mdrun/md.cpp
diff --git a/patches/gromacs-2016.5.diff/src/programs/mdrun/md.cpp.preplumed b/patches/gromacs-2016.6.diff/src/programs/mdrun/md.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/programs/mdrun/md.cpp.preplumed
rename to patches/gromacs-2016.6.diff/src/programs/mdrun/md.cpp.preplumed
diff --git a/patches/gromacs-2016.5.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-2016.6.diff/src/programs/mdrun/mdrun.cpp
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/programs/mdrun/mdrun.cpp
rename to patches/gromacs-2016.6.diff/src/programs/mdrun/mdrun.cpp
diff --git a/patches/gromacs-2016.5.diff/src/programs/mdrun/mdrun.cpp.preplumed b/patches/gromacs-2016.6.diff/src/programs/mdrun/mdrun.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/programs/mdrun/mdrun.cpp.preplumed
rename to patches/gromacs-2016.6.diff/src/programs/mdrun/mdrun.cpp.preplumed
diff --git a/patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-2016.6.diff/src/programs/mdrun/repl_ex.cpp
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.cpp
rename to patches/gromacs-2016.6.diff/src/programs/mdrun/repl_ex.cpp
diff --git a/patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.cpp.preplumed b/patches/gromacs-2016.6.diff/src/programs/mdrun/repl_ex.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.cpp.preplumed
rename to patches/gromacs-2016.6.diff/src/programs/mdrun/repl_ex.cpp.preplumed
diff --git a/patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.h b/patches/gromacs-2016.6.diff/src/programs/mdrun/repl_ex.h
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.h
rename to patches/gromacs-2016.6.diff/src/programs/mdrun/repl_ex.h
diff --git a/patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.h.preplumed b/patches/gromacs-2016.6.diff/src/programs/mdrun/repl_ex.h.preplumed
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.h.preplumed
rename to patches/gromacs-2016.6.diff/src/programs/mdrun/repl_ex.h.preplumed
diff --git a/patches/gromacs-2016.5.diff/src/programs/mdrun/runner.cpp b/patches/gromacs-2016.6.diff/src/programs/mdrun/runner.cpp
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/programs/mdrun/runner.cpp
rename to patches/gromacs-2016.6.diff/src/programs/mdrun/runner.cpp
diff --git a/patches/gromacs-2016.5.diff/src/programs/mdrun/runner.cpp.preplumed b/patches/gromacs-2016.6.diff/src/programs/mdrun/runner.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.5.diff/src/programs/mdrun/runner.cpp.preplumed
rename to patches/gromacs-2016.6.diff/src/programs/mdrun/runner.cpp.preplumed
diff --git a/patches/gromacs-2018.4.config b/patches/gromacs-2018.6.config
similarity index 100%
rename from patches/gromacs-2018.4.config
rename to patches/gromacs-2018.6.config
diff --git a/patches/gromacs-2018.4.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-2018.6.diff/src/gromacs/CMakeLists.txt
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/gromacs/CMakeLists.txt
rename to patches/gromacs-2018.6.diff/src/gromacs/CMakeLists.txt
diff --git a/patches/gromacs-2018.4.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-2018.6.diff/src/gromacs/CMakeLists.txt.preplumed
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/gromacs/CMakeLists.txt.preplumed
rename to patches/gromacs-2018.6.diff/src/gromacs/CMakeLists.txt.preplumed
diff --git a/patches/gromacs-2018.4.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2018.6.diff/src/gromacs/mdlib/force.cpp
similarity index 99%
rename from patches/gromacs-2018.4.diff/src/gromacs/mdlib/force.cpp
rename to patches/gromacs-2018.6.diff/src/gromacs/mdlib/force.cpp
index 07e1337af3e096184aa387b5d6caf66748fca510..6279fa85dab4112c1d627bbd8128591e16d12c7e 100644
--- a/patches/gromacs-2018.4.diff/src/gromacs/mdlib/force.cpp
+++ b/patches/gromacs-2018.6.diff/src/gromacs/mdlib/force.cpp
@@ -3,7 +3,7 @@
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
@@ -824,7 +824,7 @@ void sum_dhdl(gmx_enerdata_t *enerd, gmx::ArrayRef<const real> lambda, t_lambda
enerpart_lambda += dlam*enerd->term[F_DVDL_CONSTR];
}
- if (j == efptMASS)
+ if (j == efptMASS && !fepvals->separate_dvdl[j])
{
enerpart_lambda += dlam*enerd->term[F_DKDL];
}
diff --git a/patches/gromacs-2018.4.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-2018.6.diff/src/gromacs/mdlib/force.cpp.preplumed
similarity index 99%
rename from patches/gromacs-2018.4.diff/src/gromacs/mdlib/force.cpp.preplumed
rename to patches/gromacs-2018.6.diff/src/gromacs/mdlib/force.cpp.preplumed
index c939c4e8a7f13553ec52fde621a8812dc35727b7..4332b3f99d31ab5ebf6f5cd66f1b321d73d66c87 100644
--- a/patches/gromacs-2018.4.diff/src/gromacs/mdlib/force.cpp.preplumed
+++ b/patches/gromacs-2018.6.diff/src/gromacs/mdlib/force.cpp.preplumed
@@ -3,7 +3,7 @@
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
@@ -810,7 +810,7 @@ void sum_dhdl(gmx_enerdata_t *enerd, gmx::ArrayRef<const real> lambda, t_lambda
enerpart_lambda += dlam*enerd->term[F_DVDL_CONSTR];
}
- if (j == efptMASS)
+ if (j == efptMASS && !fepvals->separate_dvdl[j])
{
enerpart_lambda += dlam*enerd->term[F_DKDL];
}
diff --git a/patches/gromacs-2018.4.diff/src/gromacs/mdlib/minimize.cpp b/patches/gromacs-2018.6.diff/src/gromacs/mdlib/minimize.cpp
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/gromacs/mdlib/minimize.cpp
rename to patches/gromacs-2018.6.diff/src/gromacs/mdlib/minimize.cpp
diff --git a/patches/gromacs-2018.4.diff/src/gromacs/mdlib/minimize.cpp.preplumed b/patches/gromacs-2018.6.diff/src/gromacs/mdlib/minimize.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/gromacs/mdlib/minimize.cpp.preplumed
rename to patches/gromacs-2018.6.diff/src/gromacs/mdlib/minimize.cpp.preplumed
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/md.cpp b/patches/gromacs-2018.6.diff/src/programs/mdrun/md.cpp
similarity index 99%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/md.cpp
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/md.cpp
index 31f271a63de7822c7e4931635ef4361c8bbef70c..3415849286aeffa54cf9f19ae9062302ce1c1692 100644
--- a/patches/gromacs-2018.4.diff/src/programs/mdrun/md.cpp
+++ b/patches/gromacs-2018.6.diff/src/programs/mdrun/md.cpp
@@ -620,9 +620,15 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
/* Update mdebin with energy history if appending to output files */
if (continuationOptions.appendFiles)
{
- restore_energyhistory_from_state(mdebin, observablesHistory->energyHistory.get());
+ /* If no history is available (because a checkpoint is from before
+ * it was written) make a new one later, otherwise restore it.
+ */
+ if (observablesHistory->energyHistory)
+ {
+ restore_energyhistory_from_state(mdebin, observablesHistory->energyHistory.get());
+ }
}
- else if (observablesHistory->energyHistory.get() != nullptr)
+ else if (observablesHistory->energyHistory)
{
/* We might have read an energy history from checkpoint.
* As we are not appending, we want to restart the statistics.
@@ -631,7 +637,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
observablesHistory->energyHistory = {};
}
}
- if (observablesHistory->energyHistory.get() == nullptr)
+ if (!observablesHistory->energyHistory)
{
observablesHistory->energyHistory = std::unique_ptr<energyhistory_t>(new energyhistory_t {});
}
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/md.cpp.preplumed b/patches/gromacs-2018.6.diff/src/programs/mdrun/md.cpp.preplumed
similarity index 99%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/md.cpp.preplumed
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/md.cpp.preplumed
index de5a7031ff1093334ca547c574fdf64d5596c6ac..e77170a9c870af3a909d6cd3ce3a986d6b683226 100644
--- a/patches/gromacs-2018.4.diff/src/programs/mdrun/md.cpp.preplumed
+++ b/patches/gromacs-2018.6.diff/src/programs/mdrun/md.cpp.preplumed
@@ -603,9 +603,15 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
/* Update mdebin with energy history if appending to output files */
if (continuationOptions.appendFiles)
{
- restore_energyhistory_from_state(mdebin, observablesHistory->energyHistory.get());
+ /* If no history is available (because a checkpoint is from before
+ * it was written) make a new one later, otherwise restore it.
+ */
+ if (observablesHistory->energyHistory)
+ {
+ restore_energyhistory_from_state(mdebin, observablesHistory->energyHistory.get());
+ }
}
- else if (observablesHistory->energyHistory.get() != nullptr)
+ else if (observablesHistory->energyHistory)
{
/* We might have read an energy history from checkpoint.
* As we are not appending, we want to restart the statistics.
@@ -614,7 +620,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
observablesHistory->energyHistory = {};
}
}
- if (observablesHistory->energyHistory.get() == nullptr)
+ if (!observablesHistory->energyHistory)
{
observablesHistory->energyHistory = std::unique_ptr<energyhistory_t>(new energyhistory_t {});
}
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-2018.6.diff/src/programs/mdrun/mdrun.cpp
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/mdrun.cpp
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/mdrun.cpp
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/mdrun.cpp.preplumed b/patches/gromacs-2018.6.diff/src/programs/mdrun/mdrun.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/mdrun.cpp.preplumed
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/mdrun.cpp.preplumed
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-2018.6.diff/src/programs/mdrun/repl_ex.cpp
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/repl_ex.cpp
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/repl_ex.cpp
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/repl_ex.cpp.preplumed b/patches/gromacs-2018.6.diff/src/programs/mdrun/repl_ex.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/repl_ex.cpp.preplumed
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/repl_ex.cpp.preplumed
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/repl_ex.h b/patches/gromacs-2018.6.diff/src/programs/mdrun/repl_ex.h
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/repl_ex.h
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/repl_ex.h
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/repl_ex.h.preplumed b/patches/gromacs-2018.6.diff/src/programs/mdrun/repl_ex.h.preplumed
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/repl_ex.h.preplumed
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/repl_ex.h.preplumed
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/runner.cpp b/patches/gromacs-2018.6.diff/src/programs/mdrun/runner.cpp
similarity index 99%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/runner.cpp
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/runner.cpp
index 16653a0ca85223a99770e0349c21ab35c4ddfd52..f8a336a638e6e3c0f11e89df143be3730b159b82 100644
--- a/patches/gromacs-2018.4.diff/src/programs/mdrun/runner.cpp
+++ b/patches/gromacs-2018.6.diff/src/programs/mdrun/runner.cpp
@@ -1337,6 +1337,18 @@ int Mdrunner::mdrunner()
fr->cginfo_mb);
}
+ /* PLUMED */
+ if(plumedswitch){
+ /* detect plumed API version */
+ int pversion=0;
+ plumed_cmd(plumedmain,"getApiVersion",&pversion);
+ if(pversion>5) {
+ int nth = gmx_omp_nthreads_get(emntDefault);
+ if(pversion>5) plumed_cmd(plumedmain,"setNumOMPthreads",&nth);
+ }
+ }
+ /* END PLUMED */
+
/* Now do whatever the user wants us to do (how flexible...) */
my_integrator(inputrec->eI) (fplog, cr, mdlog, nfile, fnm,
oenv,
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/runner.cpp.preplumed b/patches/gromacs-2018.6.diff/src/programs/mdrun/runner.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/runner.cpp.preplumed
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/runner.cpp.preplumed
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/runner.h b/patches/gromacs-2018.6.diff/src/programs/mdrun/runner.h
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/runner.h
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/runner.h
diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/runner.h.preplumed b/patches/gromacs-2018.6.diff/src/programs/mdrun/runner.h.preplumed
similarity index 100%
rename from patches/gromacs-2018.4.diff/src/programs/mdrun/runner.h.preplumed
rename to patches/gromacs-2018.6.diff/src/programs/mdrun/runner.h.preplumed
diff --git a/regtest/basic/rt-close-structure/plumed.dat b/regtest/basic/rt-close-structure/plumed.dat
index 381ce05df6b631030bdd0e8ba9ad5c7d5154cc11..eaa25efa87d4cbb1d56b5e64b5622b6d759b9d5e 100644
--- a/regtest/basic/rt-close-structure/plumed.dat
+++ b/regtest/basic/rt-close-structure/plumed.dat
@@ -1,4 +1,5 @@
-p2: PROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087 EPSILON=0.001 LOG-CLOSE=1 DEBUG-CLOSE=1
+# LOG_CLOSE and DEBUG_CLOSE are synonym of CLOSE and DEBUG-CLOSE
+p2: PROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087 EPSILON=0.001 LOG_CLOSE=1 DEBUG_CLOSE=1
p3: PROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=5 EPSILON=0.001 LOG-CLOSE=1 DEBUG-CLOSE=1
PRINT ARG=p2.X,p2.Y,p2.zzz,p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.2f
DUMPDERIVATIVES ARG=p2.X,p2.Y,p2.zzz,p3.X,p3.Y,p3.zzz STRIDE=1 FILE=deriv FMT=%8.2f
diff --git a/regtest/basic/rt-multirmsd/plumed.dat b/regtest/basic/rt-multirmsd/plumed.dat
index 3b8dc02bda0a21f80f217382327f1c9fef644ab6..92c1a3b972486864fa67312a52518a68a8b50202 100644
--- a/regtest/basic/rt-multirmsd/plumed.dat
+++ b/regtest/basic/rt-multirmsd/plumed.dat
@@ -1,4 +1,5 @@
-rmsd0: MULTI-RMSD TYPE=MULTI-OPTIMAL REFERENCE=test0.pdb
+# MULTI_RMSD is a synonym of MULTI-RMSD
+rmsd0: MULTI_RMSD TYPE=MULTI-OPTIMAL REFERENCE=test0.pdb
rmsds1: MULTI-RMSD TYPE=MULTI-SIMPLE REFERENCE=test1.pdb
drmsd1: MULTI-RMSD TYPE=MULTI-DRMSD REFERENCE=test2.pdb
diff --git a/regtest/basic/rt65/TARGET2.reference b/regtest/basic/rt65/TARGET2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..ce46b0755d184a396760a5143b08b3a0596a1d22
--- /dev/null
+++ b/regtest/basic/rt65/TARGET2.reference
@@ -0,0 +1,13 @@
+#! FIELDS time e1 sigma_e1 height biasf
+#! SET multivariate false
+#! SET min_e1 -pi
+#! SET max_e1 pi
+ 0.002 -1.903205551688819 0.15 9.109750009330055e-06 -1
+ 0.004 -2.96314509497333 0.15 1.185709146847737e-05 -1
+ 0.006 -2.563611512401551 0.15 3.459682279642131e-06 -1
+ 0.008 -3.120966152841994 0.15 2.627063088737373e-05 -1
+ 0.01 -2.640309461910613 0.15 3.857669512410835e-06 -1
+ 0.012 -2.981598623047649 0.15 1.18570902777194e-05 -1
+ 0.014 -1.30629526983071 0.15 2.684491613922633e-05 -1
+ 0.016 -2.503951571795555 0.15 3.399120208955464e-06 -1
+ 0.018 -3.014247277468189 0.15 1.387646340580046e-05 -1
diff --git a/regtest/basic/rt65/plumed.dat b/regtest/basic/rt65/plumed.dat
index 6365032dc62d4fff4c1c610882c68db40f51791b..78ec0359b1253edbd41bfc3915b35f5e28b58a58 100644
--- a/regtest/basic/rt65/plumed.dat
+++ b/regtest/basic/rt65/plumed.dat
@@ -3,3 +3,6 @@ MOLINFO STRUCTURE=AA.pdb MOLTYPE=rna
e1: TORSION ATOMS=@epsilon-1
t: METAD ARG=e1 SIGMA=0.15 PACE=1 TAU=200 DAMPFACTOR=100 TARGET=tgt_e1 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=200 FILE=TARGET TEMP=300
+
+t2: METAD ARG=e1 SIGMA=0.15 PACE=1 TAU=200 DAMPFACTOR=100 TARGET=tgt_e2 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=200 FILE=TARGET2 TEMP=300 GRID_SPARSE
+
diff --git a/regtest/basic/rt65/tgt_e2 b/regtest/basic/rt65/tgt_e2
new file mode 100644
index 0000000000000000000000000000000000000000..49b5f58a4bbe55af7e4f08d83e64d10697aa4a38
--- /dev/null
+++ b/regtest/basic/rt65/tgt_e2
@@ -0,0 +1,205 @@
+#! FIELDS e1 t2.target der_e1
+#! SET min_e1 -pi
+#! SET max_e1 pi
+#! SET nbins_e1 200
+#! SET periodic_e1 true
+ -3.14159 5.10076 -12.70892
+ -3.11018 4.70239 -12.67962
+ -3.07876 4.30407 -12.68027
+ -3.04734 3.90566 -12.65820
+ -3.01593 3.50873 -12.56070
+ -2.98451 3.11645 -12.34584
+ -2.95310 2.73302 -11.98905
+ -2.92168 2.36315 -11.48303
+ -2.89026 2.01152 -10.83462
+ -2.85885 1.68239 -10.06301
+ -2.82743 1.37924 -9.19536
+ -2.79602 1.10463 -8.25853
+ -2.76460 0.86035 -7.27827
+ -2.73319 0.64733 -6.27846
+ -2.70177 0.46586 -5.27871
+ -2.67035 0.31565 -4.29520
+ -2.63894 0.19598 -3.33913
+ -2.60752 0.10585 -2.41815
+ -2.57611 0.04405 -1.53788
+ -2.54469 0.00922 -0.70101
+ -2.51327 0.00000 0.09104
+ -2.48186 0.01494 0.83725
+ -2.45044 0.05261 1.53656
+ -2.41903 0.11149 2.18707
+ -2.38761 0.19002 2.78648
+ -2.35619 0.28657 3.33221
+ -2.32478 0.39939 3.82147
+ -2.29336 0.52667 4.25183
+ -2.26195 0.66654 4.62342
+ -2.23053 0.81717 4.93553
+ -2.19911 0.97665 5.18839
+ -2.16770 1.14317 5.38294
+ -2.13628 1.31487 5.51695
+ -2.10487 1.48981 5.58462
+ -2.07345 1.66576 5.57692
+ -2.04203 1.84022 5.48097
+ -2.01062 2.01014 5.28380
+ -1.97920 2.17221 4.97850
+ -1.94779 2.32295 4.56436
+ -1.91637 2.45899 4.05604
+ -1.88496 2.57780 3.48558
+ -1.85354 2.67800 2.90046
+ -1.82212 2.76004 2.35978
+ -1.79071 2.82627 1.92248
+ -1.75929 2.88083 1.64450
+ -1.72788 2.92960 1.56915
+ -1.69646 2.97943 1.71195
+ -1.66504 3.03716 2.07025
+ -1.63363 3.10950 2.62387
+ -1.60221 3.20203 3.33816
+ -1.57080 3.31925 4.17143
+ -1.53938 3.46413 5.07054
+ -1.50796 3.63784 5.97985
+ -1.47655 3.83984 6.84656
+ -1.44513 4.06801 7.62050
+ -1.41372 4.31866 8.25743
+ -1.38230 4.58685 8.73061
+ -1.35088 4.86722 9.03758
+ -1.31947 5.15470 9.20074
+ -1.28805 5.44532 9.27486
+ -1.25664 5.73745 9.33973
+ -1.22522 6.03215 9.47554
+ -1.19381 6.33282 9.75711
+ -1.16239 6.64521 10.22904
+ -1.13097 6.97553 10.90943
+ -1.09956 7.33067 11.77148
+ -1.06814 7.71514 12.75565
+ -1.03673 8.13212 13.79332
+ -1.00531 8.58181 14.77995
+ -0.97389 9.06078 15.61190
+ -0.94248 9.56273 16.16983
+ -0.91106 10.07676 16.32518
+ -0.87965 10.58848 16.02464
+ -0.84823 11.08362 15.28715
+ -0.81681 11.54900 14.17647
+ -0.78540 11.97436 12.86211
+ -0.75398 12.35715 11.57633
+ -0.72257 12.70172 10.55300
+ -0.69115 13.02022 9.88103
+ -0.65973 13.32257 9.50496
+ -0.62832 13.61742 9.40240
+ -0.59690 13.91333 9.43842
+ -0.56549 14.21046 9.44831
+ -0.53407 14.50698 9.34280
+ -0.50265 14.79749 9.04752
+ -0.47124 15.07546 8.52664
+ -0.43982 15.33323 7.74502
+ -0.40841 15.56209 6.80145
+ -0.37699 15.76058 5.80952
+ -0.34558 15.92712 4.90263
+ -0.31416 16.06862 4.15626
+ -0.28274 16.18826 3.55378
+ -0.25133 16.29191 2.98214
+ -0.21991 16.37564 2.29118
+ -0.18850 16.43587 1.31572
+ -0.15708 16.45830 -0.09998
+ -0.12566 16.42959 -1.82144
+ -0.09425 16.34386 -3.60730
+ -0.06283 16.20294 -5.18707
+ -0.03142 16.01795 -6.30761
+ 0.00000 15.80662 -6.83201
+ 0.03142 15.58868 -6.76985
+ 0.06283 15.38125 -6.23660
+ 0.09425 15.19682 -5.36388
+ 0.12566 15.04423 -4.28282
+ 0.15708 14.92772 -3.11155
+ 0.18850 14.84872 -1.93712
+ 0.21991 14.80601 -0.84119
+ 0.25133 14.79587 0.12393
+ 0.28274 14.81380 0.87287
+ 0.31416 14.85071 1.34688
+ 0.34558 14.89842 1.51588
+ 0.37699 14.94596 1.30661
+ 0.40841 14.98052 0.68187
+ 0.43982 14.98880 -0.32791
+ 0.47124 14.95992 -1.69025
+ 0.50265 14.88260 -3.29052
+ 0.53407 14.75317 -4.96947
+ 0.56549 14.57036 -6.58050
+ 0.59690 14.33970 -7.94522
+ 0.62832 14.07115 -8.95276
+ 0.65973 13.77719 -9.54424
+ 0.69115 13.47147 -9.71559
+ 0.72257 13.16674 -9.52214
+ 0.75398 12.87318 -9.04455
+ 0.78540 12.59845 -8.35746
+ 0.81681 12.34806 -7.53288
+ 0.84823 12.12515 -6.63737
+ 0.87965 11.93102 -5.70555
+ 0.91106 11.76666 -4.77067
+ 0.94248 11.63127 -3.85511
+ 0.97389 11.52443 -2.96150
+ 1.00531 11.44519 -2.10886
+ 1.03673 11.39193 -1.30973
+ 1.06814 11.36290 -0.57795
+ 1.09956 11.35562 0.06564
+ 1.13097 11.36702 0.60908
+ 1.16239 11.39388 1.04956
+ 1.19381 11.43297 1.39725
+ 1.22522 11.48168 1.67383
+ 1.25664 11.53814 1.91235
+ 1.28805 11.60183 2.15400
+ 1.31947 11.67348 2.43040
+ 1.35088 11.75454 2.78076
+ 1.38230 11.84820 3.21639
+ 1.41372 11.95663 3.73112
+ 1.44513 12.08264 4.31252
+ 1.47655 12.22760 4.93997
+ 1.50796 12.39302 5.59522
+ 1.53938 12.57915 6.22538
+ 1.57080 12.78417 6.81465
+ 1.60221 13.00733 7.31439
+ 1.63363 13.24375 7.69216
+ 1.66504 13.49064 7.92523
+ 1.69646 13.74171 7.96631
+ 1.72788 13.99118 7.82705
+ 1.75929 14.23350 7.52661
+ 1.79071 14.46409 7.07963
+ 1.82212 14.67832 6.56183
+ 1.85354 14.87639 6.02293
+ 1.88496 15.05676 5.48870
+ 1.91637 15.22125 4.97648
+ 1.94779 15.36943 4.47050
+ 1.97920 15.50214 3.93312
+ 2.01062 15.61656 3.25777
+ 2.04203 15.70683 2.41601
+ 2.07345 15.76836 1.35324
+ 2.10487 15.79186 0.07937
+ 2.13628 15.77335 -1.32078
+ 2.16770 15.70887 -2.78132
+ 2.19911 15.59859 -4.15591
+ 2.23053 15.44775 -5.35838
+ 2.26195 15.26192 -6.29576
+ 2.29336 15.05217 -6.91512
+ 2.32478 14.82742 -7.29068
+ 2.35619 14.59409 -7.47898
+ 2.38761 14.35751 -7.52943
+ 2.41903 14.12100 -7.53571
+ 2.45044 13.88403 -7.59844
+ 2.48186 13.64358 -7.73822
+ 2.51327 13.39782 -7.97864
+ 2.54469 13.14226 -8.41694
+ 2.57611 12.86897 -9.08704
+ 2.60752 12.57131 -9.95794
+ 2.63894 12.24329 -11.01270
+ 2.67035 11.87936 -12.16703
+ 2.70177 11.47881 -13.30580
+ 2.73319 11.04332 -14.32339
+ 2.76460 10.57884 -15.12139
+ 2.79602 10.09323 -15.64548
+ 2.82743 9.59582 -15.88386
+ 2.85885 9.09522 -15.86574
+ 2.89026 8.59895 -15.63372
+ 2.92168 8.11292 -15.24911
+ 2.95310 7.64082 -14.77260
+ 2.98451 7.18473 -14.26221
+ 3.01593 6.74469 -13.77231
+ 3.04734 6.31939 -13.34976
+ 3.07876 5.90590 -13.02634
+ 3.11018 5.50091 -12.81419
diff --git a/regtest/basic/rt67-mpi/COLVAR.reference b/regtest/basic/rt67-mpi/COLVAR.reference
index 7d00a355feca39f9bec7a530282a1b70349104d2..2f9cce0086b9293399fcf1e494ad3111e8f91a6b 100644
--- a/regtest/basic/rt67-mpi/COLVAR.reference
+++ b/regtest/basic/rt67-mpi/COLVAR.reference
@@ -14,13 +14,13 @@
8.000000 -1.8429 1.3293 0.6692 0.5800 0.1025
9.000000 -2.2424 2.6059 0.0000 -0.1025 0.1109
10.000000 -1.1482 0.5350 1.8435 1.7326 0.1281
- 11.000000 -1.7580 2.0752 0.0012 -0.1269 0.1367
- 12.000000 -1.3186 3.0997 0.0000 -0.1367 0.1443
- 13.000000 -2.9911 2.8991 0.0000 -0.1443 0.1524
- 14.000000 -1.4112 0.0028 0.0285 -0.1239 0.1614
- 15.000000 -2.5995 2.6683 0.3230 0.1616 0.1714
- 16.000000 -1.4608 0.2622 0.9676 0.7962 0.1856
- 17.000000 -1.3791 1.1576 3.0484 2.8628 0.2090
- 18.000000 -1.6771 0.9078 1.5947 1.3857 0.2309
- 19.000000 -1.5241 1.2623 4.1823 3.9513 0.2607
- 20.000000 -1.1997 0.9529 3.1902 2.9295 0.2924
+ 11.000000 -1.7580 2.0752 0.0012 -0.1269 0.1368
+ 12.000000 -1.3186 3.0997 0.0000 -0.1368 0.1451
+ 13.000000 -2.9911 2.8991 0.0000 -0.1451 0.1534
+ 14.000000 -1.4112 0.0028 0.0285 -0.1250 0.1625
+ 15.000000 -2.5995 2.6683 0.3230 0.1606 0.1725
+ 16.000000 -1.4608 0.2622 0.9676 0.7951 0.1867
+ 17.000000 -1.3791 1.1576 3.0484 2.8617 0.2101
+ 18.000000 -1.6771 0.9078 1.5947 1.3846 0.2320
+ 19.000000 -1.5241 1.2623 4.1823 3.9503 0.2617
+ 20.000000 -1.1997 0.9529 3.1902 2.9285 0.2935
diff --git a/regtest/basic/rt67/COLVAR.reference b/regtest/basic/rt67/COLVAR.reference
index 7d00a355feca39f9bec7a530282a1b70349104d2..2f9cce0086b9293399fcf1e494ad3111e8f91a6b 100644
--- a/regtest/basic/rt67/COLVAR.reference
+++ b/regtest/basic/rt67/COLVAR.reference
@@ -14,13 +14,13 @@
8.000000 -1.8429 1.3293 0.6692 0.5800 0.1025
9.000000 -2.2424 2.6059 0.0000 -0.1025 0.1109
10.000000 -1.1482 0.5350 1.8435 1.7326 0.1281
- 11.000000 -1.7580 2.0752 0.0012 -0.1269 0.1367
- 12.000000 -1.3186 3.0997 0.0000 -0.1367 0.1443
- 13.000000 -2.9911 2.8991 0.0000 -0.1443 0.1524
- 14.000000 -1.4112 0.0028 0.0285 -0.1239 0.1614
- 15.000000 -2.5995 2.6683 0.3230 0.1616 0.1714
- 16.000000 -1.4608 0.2622 0.9676 0.7962 0.1856
- 17.000000 -1.3791 1.1576 3.0484 2.8628 0.2090
- 18.000000 -1.6771 0.9078 1.5947 1.3857 0.2309
- 19.000000 -1.5241 1.2623 4.1823 3.9513 0.2607
- 20.000000 -1.1997 0.9529 3.1902 2.9295 0.2924
+ 11.000000 -1.7580 2.0752 0.0012 -0.1269 0.1368
+ 12.000000 -1.3186 3.0997 0.0000 -0.1368 0.1451
+ 13.000000 -2.9911 2.8991 0.0000 -0.1451 0.1534
+ 14.000000 -1.4112 0.0028 0.0285 -0.1250 0.1625
+ 15.000000 -2.5995 2.6683 0.3230 0.1606 0.1725
+ 16.000000 -1.4608 0.2622 0.9676 0.7951 0.1867
+ 17.000000 -1.3791 1.1576 3.0484 2.8617 0.2101
+ 18.000000 -1.6771 0.9078 1.5947 1.3846 0.2320
+ 19.000000 -1.5241 1.2623 4.1823 3.9503 0.2617
+ 20.000000 -1.1997 0.9529 3.1902 2.9285 0.2935
diff --git a/regtest/multicolvar/rt-coordination-powers/derivatives.reference b/regtest/multicolvar/rt-coordination-powers/derivatives.reference
index 5c4c73cea81fa7347ec6155c6957d0c3f1685312..b11b9df8d68e66c188553105d0846adeb6e75270 100644
--- a/regtest/multicolvar/rt-coordination-powers/derivatives.reference
+++ b/regtest/multicolvar/rt-coordination-powers/derivatives.reference
@@ -1,196 +1,196 @@
#! FIELDS time parameter c1.mean c1num.mean
- 0.000000 0 0.3371 0.3371
- 0.000000 1 0.2309 0.2309
- 0.000000 2 0.1160 0.1160
- 0.000000 3 -0.3510 -0.3510
- 0.000000 4 0.3400 0.3400
- 0.000000 5 0.0247 0.0247
- 0.000000 6 -0.2278 -0.2278
- 0.000000 7 -0.3331 -0.3331
- 0.000000 8 0.1718 0.1718
- 0.000000 9 0.3076 0.3076
- 0.000000 10 -0.3590 -0.3590
- 0.000000 11 0.0586 0.0586
- 0.000000 12 0.3427 0.3427
- 0.000000 13 0.3101 0.3101
- 0.000000 14 -0.0220 -0.0220
- 0.000000 15 -0.3300 -0.3300
- 0.000000 16 0.2127 0.2127
- 0.000000 17 -0.1563 -0.1563
- 0.000000 18 -0.3289 -0.3289
- 0.000000 19 -0.3330 -0.3330
- 0.000000 20 -0.0762 -0.0762
- 0.000000 21 0.2298 0.2298
- 0.000000 22 -0.3172 -0.3171
- 0.000000 23 -0.1589 -0.1589
- 0.000000 24 0.2379 0.2379
- 0.000000 25 0.1246 0.1246
- 0.000000 26 -0.0916 -0.0916
- 0.000000 27 -0.2175 -0.2175
- 0.000000 28 0.1238 0.1238
- 0.000000 29 0.1339 0.1339
- 0.000000 30 1.2686 1.2686
- 0.000000 31 0.0008 0.0008
- 0.000000 32 -0.0777 -0.0777
- 0.000000 33 0.0008 0.0008
- 0.000000 34 1.1233 1.1233
- 0.000000 35 0.0031 0.0031
- 0.000000 36 -0.0777 -0.0777
- 0.000000 37 0.0031 0.0031
- 0.000000 38 2.5446 2.5446
- 0.005000 0 0.3287 0.3287
- 0.005000 1 0.2323 0.2323
- 0.005000 2 0.1100 0.1100
- 0.005000 3 -0.3587 -0.3587
- 0.005000 4 0.3367 0.3367
- 0.005000 5 0.0181 0.0181
- 0.005000 6 -0.2232 -0.2232
- 0.005000 7 -0.3296 -0.3296
- 0.005000 8 0.1699 0.1699
- 0.005000 9 0.2908 0.2908
- 0.005000 10 -0.3585 -0.3585
- 0.005000 11 0.0690 0.0690
- 0.005000 12 0.3444 0.3444
- 0.005000 13 0.2895 0.2895
- 0.005000 14 -0.0237 -0.0237
- 0.005000 15 -0.3163 -0.3163
- 0.005000 16 0.1948 0.1948
- 0.005000 17 -0.1722 -0.1722
- 0.005000 18 -0.3261 -0.3261
- 0.005000 19 -0.3198 -0.3198
- 0.005000 20 -0.0941 -0.0941
- 0.005000 21 0.2273 0.2273
- 0.005000 22 -0.2878 -0.2878
- 0.005000 23 -0.1523 -0.1523
- 0.005000 24 0.2355 0.2355
- 0.005000 25 0.1149 0.1149
- 0.005000 26 -0.0652 -0.0652
- 0.005000 27 -0.2023 -0.2023
- 0.005000 28 0.1276 0.1276
- 0.005000 29 0.1406 0.1406
- 0.005000 30 1.2983 1.2983
- 0.005000 31 0.0074 0.0074
- 0.005000 32 -0.0442 -0.0442
- 0.005000 33 0.0074 0.0074
- 0.005000 34 1.0616 1.0616
- 0.005000 35 0.0049 0.0049
- 0.005000 36 -0.0442 -0.0442
- 0.005000 37 0.0049 0.0049
- 0.005000 38 2.4949 2.4949
- 0.010000 0 0.3057 0.3057
- 0.010000 1 0.2219 0.2219
- 0.010000 2 0.1123 0.1123
- 0.010000 3 -0.3610 -0.3610
- 0.010000 4 0.3207 0.3207
- 0.010000 5 0.0249 0.0249
- 0.010000 6 -0.2431 -0.2431
- 0.010000 7 -0.3227 -0.3227
- 0.010000 8 0.1861 0.1861
- 0.010000 9 0.3110 0.3110
- 0.010000 10 -0.3230 -0.3230
- 0.010000 11 0.0536 0.0536
- 0.010000 12 0.3321 0.3321
- 0.010000 13 0.2460 0.2460
- 0.010000 14 -0.0204 -0.0204
- 0.010000 15 -0.3035 -0.3035
- 0.010000 16 0.1750 0.1750
- 0.010000 17 -0.1895 -0.1895
- 0.010000 18 -0.3215 -0.3215
- 0.010000 19 -0.3011 -0.3011
- 0.010000 20 -0.0991 -0.0991
- 0.010000 21 0.2342 0.2342
- 0.010000 22 -0.2677 -0.2677
- 0.010000 23 -0.1512 -0.1512
- 0.010000 24 0.2325 0.2325
- 0.010000 25 0.1200 0.1200
- 0.010000 26 -0.0458 -0.0458
- 0.010000 27 -0.1864 -0.1864
- 0.010000 28 0.1309 0.1309
- 0.010000 29 0.1290 0.1290
- 0.010000 30 1.3546 1.3546
- 0.010000 31 -0.0010 -0.0010
- 0.010000 32 -0.0324 -0.0324
- 0.010000 33 -0.0010 -0.0010
- 0.010000 34 0.9469 0.9469
- 0.010000 35 0.0118 0.0118
- 0.010000 36 -0.0324 -0.0324
- 0.010000 37 0.0118 0.0118
- 0.010000 38 2.4485 2.4485
- 0.015000 0 0.2784 0.2784
- 0.015000 1 0.2040 0.2040
- 0.015000 2 0.0909 0.0909
- 0.015000 3 -0.3455 -0.3455
- 0.015000 4 0.2867 0.2867
- 0.015000 5 0.0230 0.0230
- 0.015000 6 -0.2596 -0.2596
- 0.015000 7 -0.3044 -0.3044
- 0.015000 8 0.2036 0.2036
- 0.015000 9 0.3216 0.3216
- 0.015000 10 -0.2752 -0.2752
- 0.015000 11 0.0411 0.0411
- 0.015000 12 0.3142 0.3142
- 0.015000 13 0.1924 0.1924
- 0.015000 14 -0.0163 -0.0163
- 0.015000 15 -0.2939 -0.2939
- 0.015000 16 0.1585 0.1585
- 0.015000 17 -0.2068 -0.2068
- 0.015000 18 -0.3090 -0.3090
- 0.015000 19 -0.2674 -0.2674
- 0.015000 20 -0.0777 -0.0777
- 0.015000 21 0.2317 0.2317
- 0.015000 22 -0.2560 -0.2560
- 0.015000 23 -0.1327 -0.1327
- 0.015000 24 0.2310 0.2310
- 0.015000 25 0.1252 0.1252
- 0.015000 26 -0.0350 -0.0350
- 0.015000 27 -0.1689 -0.1689
- 0.015000 28 0.1363 0.1363
- 0.015000 29 0.1099 0.1099
- 0.015000 30 1.3937 1.3937
- 0.015000 31 -0.0040 -0.0040
- 0.015000 32 -0.0365 -0.0365
- 0.015000 33 -0.0040 -0.0040
- 0.015000 34 0.8269 0.8269
- 0.015000 35 -0.0103 -0.0103
- 0.015000 36 -0.0365 -0.0365
- 0.015000 37 -0.0103 -0.0103
- 0.015000 38 2.3510 2.3510
- 0.020000 0 0.2666 0.2666
- 0.020000 1 0.1869 0.1869
- 0.020000 2 0.0703 0.0703
- 0.020000 3 -0.3255 -0.3255
- 0.020000 4 0.2692 0.2692
- 0.020000 5 0.0102 0.0102
- 0.020000 6 -0.2645 -0.2645
- 0.020000 7 -0.2835 -0.2835
- 0.020000 8 0.2141 0.2141
- 0.020000 9 0.3166 0.3166
- 0.020000 10 -0.2635 -0.2635
- 0.020000 11 0.0653 0.0653
- 0.020000 12 0.3024 0.3024
- 0.020000 13 0.1976 0.1976
- 0.020000 14 -0.0355 -0.0355
- 0.020000 15 -0.2931 -0.2931
- 0.020000 16 0.1405 0.1405
- 0.020000 17 -0.2155 -0.2155
- 0.020000 18 -0.2977 -0.2977
- 0.020000 19 -0.2589 -0.2589
- 0.020000 20 -0.0579 -0.0579
- 0.020000 21 0.2223 0.2223
- 0.020000 22 -0.2595 -0.2595
- 0.020000 23 -0.1251 -0.1251
- 0.020000 24 0.2263 0.2263
- 0.020000 25 0.1348 0.1348
- 0.020000 26 -0.0242 -0.0242
- 0.020000 27 -0.1535 -0.1535
- 0.020000 28 0.1365 0.1365
- 0.020000 29 0.0982 0.0982
- 0.020000 30 1.3942 1.3942
- 0.020000 31 0.0116 0.0116
- 0.020000 32 -0.0319 -0.0319
- 0.020000 33 0.0116 0.0116
- 0.020000 34 0.8066 0.8066
- 0.020000 35 -0.0388 -0.0388
- 0.020000 36 -0.0319 -0.0319
- 0.020000 37 -0.0388 -0.0388
- 0.020000 38 2.2840 2.2840
+ 0.000000 0 0.2576 0.2576
+ 0.000000 1 0.1784 0.1784
+ 0.000000 2 0.1148 0.1148
+ 0.000000 3 -0.2848 -0.2848
+ 0.000000 4 0.2573 0.2573
+ 0.000000 5 0.0311 0.0311
+ 0.000000 6 -0.1602 -0.1602
+ 0.000000 7 -0.2576 -0.2576
+ 0.000000 8 0.1443 0.1443
+ 0.000000 9 0.2195 0.2195
+ 0.000000 10 -0.2827 -0.2827
+ 0.000000 11 0.0801 0.0801
+ 0.000000 12 0.2542 0.2542
+ 0.000000 13 0.2204 0.2204
+ 0.000000 14 -0.0389 -0.0389
+ 0.000000 15 -0.2562 -0.2562
+ 0.000000 16 0.1441 0.1441
+ 0.000000 17 -0.1263 -0.1263
+ 0.000000 18 -0.2496 -0.2496
+ 0.000000 19 -0.2380 -0.2380
+ 0.000000 20 -0.0968 -0.0968
+ 0.000000 21 0.1800 0.1800
+ 0.000000 22 -0.2248 -0.2248
+ 0.000000 23 -0.1502 -0.1502
+ 0.000000 24 0.2051 0.2051
+ 0.000000 25 0.0951 0.0951
+ 0.000000 26 -0.0616 -0.0616
+ 0.000000 27 -0.1656 -0.1656
+ 0.000000 28 0.1078 0.1078
+ 0.000000 29 0.1035 0.1035
+ 0.000000 30 0.9771 0.9771
+ 0.000000 31 -0.0025 -0.0025
+ 0.000000 32 -0.0434 -0.0434
+ 0.000000 33 -0.0025 -0.0025
+ 0.000000 34 0.8416 0.8416
+ 0.000000 35 0.0170 0.0170
+ 0.000000 36 -0.0434 -0.0434
+ 0.000000 37 0.0170 0.0170
+ 0.000000 38 2.5110 2.5110
+ 0.005000 0 0.2556 0.2556
+ 0.005000 1 0.1841 0.1841
+ 0.005000 2 0.1225 0.1225
+ 0.005000 3 -0.3096 -0.3096
+ 0.005000 4 0.2536 0.2536
+ 0.005000 5 0.0116 0.0116
+ 0.005000 6 -0.1518 -0.1518
+ 0.005000 7 -0.2632 -0.2632
+ 0.005000 8 0.1297 0.1297
+ 0.005000 9 0.2044 0.2044
+ 0.005000 10 -0.2823 -0.2823
+ 0.005000 11 0.0947 0.0947
+ 0.005000 12 0.2620 0.2620
+ 0.005000 13 0.1952 0.1952
+ 0.005000 14 -0.0426 -0.0426
+ 0.005000 15 -0.2497 -0.2497
+ 0.005000 16 0.1184 0.1184
+ 0.005000 17 -0.1320 -0.1320
+ 0.005000 18 -0.2566 -0.2566
+ 0.005000 19 -0.2169 -0.2169
+ 0.005000 20 -0.1139 -0.1139
+ 0.005000 21 0.1797 0.1797
+ 0.005000 22 -0.1888 -0.1888
+ 0.005000 23 -0.1530 -0.1530
+ 0.005000 24 0.2132 0.2132
+ 0.005000 25 0.0817 0.0817
+ 0.005000 26 -0.0227 -0.0227
+ 0.005000 27 -0.1472 -0.1472
+ 0.005000 28 0.1180 0.1180
+ 0.005000 29 0.1056 0.1056
+ 0.005000 30 1.0253 1.0253
+ 0.005000 31 0.0065 0.0065
+ 0.005000 32 0.0105 0.0105
+ 0.005000 33 0.0065 0.0065
+ 0.005000 34 0.7862 0.7862
+ 0.005000 35 0.0302 0.0302
+ 0.005000 36 0.0105 0.0105
+ 0.005000 37 0.0302 0.0302
+ 0.005000 38 2.4682 2.4682
+ 0.010000 0 0.2377 0.2377
+ 0.010000 1 0.1684 0.1684
+ 0.010000 2 0.1429 0.1429
+ 0.010000 3 -0.3273 -0.3273
+ 0.010000 4 0.2339 0.2339
+ 0.010000 5 0.0073 0.0073
+ 0.010000 6 -0.1809 -0.1809
+ 0.010000 7 -0.2617 -0.2617
+ 0.010000 8 0.1499 0.1499
+ 0.010000 9 0.2401 0.2401
+ 0.010000 10 -0.2325 -0.2325
+ 0.010000 11 0.0678 0.0678
+ 0.010000 12 0.2520 0.2520
+ 0.010000 13 0.1286 0.1286
+ 0.010000 14 -0.0378 -0.0378
+ 0.010000 15 -0.2463 -0.2463
+ 0.010000 16 0.0987 0.0987
+ 0.010000 17 -0.1384 -0.1384
+ 0.010000 18 -0.2558 -0.2558
+ 0.010000 19 -0.1817 -0.1817
+ 0.010000 20 -0.1166 -0.1166
+ 0.010000 21 0.1873 0.1873
+ 0.010000 22 -0.1756 -0.1756
+ 0.010000 23 -0.1491 -0.1491
+ 0.010000 24 0.2139 0.2139
+ 0.010000 25 0.0968 0.0968
+ 0.010000 26 -0.0203 -0.0203
+ 0.010000 27 -0.1205 -0.1205
+ 0.010000 28 0.1250 0.1250
+ 0.010000 29 0.0945 0.0945
+ 0.010000 30 1.1005 1.1005
+ 0.010000 31 -0.0026 -0.0026
+ 0.010000 32 0.0195 0.0195
+ 0.010000 33 -0.0026 -0.0026
+ 0.010000 34 0.6764 0.6764
+ 0.010000 35 0.0390 0.0390
+ 0.010000 36 0.0195 0.0195
+ 0.010000 37 0.0390 0.0390
+ 0.010000 38 2.4056 2.4056
+ 0.015000 0 0.2201 0.2201
+ 0.015000 1 0.1468 0.1468
+ 0.015000 2 0.1232 0.1232
+ 0.015000 3 -0.3255 -0.3255
+ 0.015000 4 0.1931 0.1931
+ 0.015000 5 -0.0015 -0.0015
+ 0.015000 6 -0.2162 -0.2162
+ 0.015000 7 -0.2551 -0.2551
+ 0.015000 8 0.1767 0.1767
+ 0.015000 9 0.2721 0.2721
+ 0.015000 10 -0.1773 -0.1773
+ 0.015000 11 0.0444 0.0444
+ 0.015000 12 0.2404 0.2404
+ 0.015000 13 0.0659 0.0659
+ 0.015000 14 -0.0348 -0.0348
+ 0.015000 15 -0.2492 -0.2492
+ 0.015000 16 0.0911 0.0911
+ 0.015000 17 -0.1519 -0.1519
+ 0.015000 18 -0.2516 -0.2516
+ 0.015000 19 -0.1356 -0.1356
+ 0.015000 20 -0.0847 -0.0847
+ 0.015000 21 0.1922 0.1922
+ 0.015000 22 -0.1733 -0.1733
+ 0.015000 23 -0.1152 -0.1152
+ 0.015000 24 0.2141 0.2141
+ 0.015000 25 0.1112 0.1112
+ 0.015000 26 -0.0339 -0.0339
+ 0.015000 27 -0.0963 -0.0963
+ 0.015000 28 0.1333 0.1333
+ 0.015000 29 0.0776 0.0776
+ 0.015000 30 1.1799 1.1799
+ 0.015000 31 -0.0010 -0.0010
+ 0.015000 32 -0.0029 -0.0029
+ 0.015000 33 -0.0010 -0.0010
+ 0.015000 34 0.5770 0.5770
+ 0.015000 35 -0.0037 -0.0037
+ 0.015000 36 -0.0029 -0.0029
+ 0.015000 37 -0.0037 -0.0037
+ 0.015000 38 2.2992 2.2992
+ 0.020000 0 0.2204 0.2204
+ 0.020000 1 0.1243 0.1243
+ 0.020000 2 0.0996 0.0996
+ 0.020000 3 -0.3153 -0.3153
+ 0.020000 4 0.1757 0.1757
+ 0.020000 5 -0.0146 -0.0146
+ 0.020000 6 -0.2366 -0.2366
+ 0.020000 7 -0.2451 -0.2451
+ 0.020000 8 0.1915 0.1915
+ 0.020000 9 0.2832 0.2832
+ 0.020000 10 -0.1666 -0.1666
+ 0.020000 11 0.0758 0.0758
+ 0.020000 12 0.2393 0.2393
+ 0.020000 13 0.0789 0.0789
+ 0.020000 14 -0.0617 -0.0617
+ 0.020000 15 -0.2540 -0.2540
+ 0.020000 16 0.0820 0.0820
+ 0.020000 17 -0.1645 -0.1645
+ 0.020000 18 -0.2546 -0.2546
+ 0.020000 19 -0.1308 -0.1308
+ 0.020000 20 -0.0623 -0.0623
+ 0.020000 21 0.1886 0.1886
+ 0.020000 22 -0.1836 -0.1836
+ 0.020000 23 -0.1014 -0.1014
+ 0.020000 24 0.2077 0.2077
+ 0.020000 25 0.1270 0.1270
+ 0.020000 26 -0.0371 -0.0371
+ 0.020000 27 -0.0787 -0.0787
+ 0.020000 28 0.1383 0.1383
+ 0.020000 29 0.0747 0.0747
+ 0.020000 30 1.2233 1.2233
+ 0.020000 31 0.0214 0.0214
+ 0.020000 32 -0.0092 -0.0092
+ 0.020000 33 0.0214 0.0214
+ 0.020000 34 0.5735 0.5735
+ 0.020000 35 -0.0503 -0.0503
+ 0.020000 36 -0.0092 -0.0092
+ 0.020000 37 -0.0503 -0.0503
+ 0.020000 38 2.2551 2.2551
diff --git a/regtest/multicolvar/rt-coordination-powers/plumed.dat b/regtest/multicolvar/rt-coordination-powers/plumed.dat
index ec3e4821ca5de2b98285b66e9ea0dad56959f3c9..74f3664294456c84bafa9c9fff4c13cba25a89f8 100644
--- a/regtest/multicolvar/rt-coordination-powers/plumed.dat
+++ b/regtest/multicolvar/rt-coordination-powers/plumed.dat
@@ -1,3 +1,3 @@
-COORDINATIONNUMBER SPECIES=1-10 R_0=1 R_POWER=2 LABEL=c1 MEAN
-COORDINATIONNUMBER SPECIES=1-10 R_0=1 NUMERICAL_DERIVATIVES R_POWER=2 LABEL=c1num MEAN
+COORDINATIONNUMBER SPECIES=1-10 R_0=1 R_POWER=3 LABEL=c1 MEAN
+COORDINATIONNUMBER SPECIES=1-10 R_0=1 NUMERICAL_DERIVATIVES R_POWER=3 LABEL=c1num MEAN
DUMPDERIVATIVES ARG=c1.*,c1num.* STRIDE=1 FILE=derivatives FMT=%8.4f
diff --git a/regtest/multicolvar/rt25/derivatives.reference b/regtest/multicolvar/rt25/derivatives.reference
index 10e58b83c011b08740ae51bf94def9247b5c04fc..d0cb13b2f5ad38a82bde4fdfa1bc20696a776816 100644
--- a/regtest/multicolvar/rt25/derivatives.reference
+++ b/regtest/multicolvar/rt25/derivatives.reference
@@ -1,526 +1,526 @@
-#! FIELDS time parameter c1 c1num
- 0.000000 0 -0.0023 -0.0023
- 0.000000 1 0.0023 0.0023
- 0.000000 2 0.0008 0.0008
- 0.000000 3 -0.0027 -0.0027
- 0.000000 4 -0.0030 -0.0030
- 0.000000 5 -0.0010 -0.0010
- 0.000000 6 0.0126 0.0126
- 0.000000 7 0.0021 0.0021
- 0.000000 8 0.0006 0.0006
- 0.000000 9 -0.0076 -0.0076
- 0.000000 10 -0.0014 -0.0014
- 0.000000 11 -0.0004 -0.0004
- 0.000000 12 -0.1068 -0.1068
- 0.000000 13 -0.0978 -0.0978
- 0.000000 14 0.0943 0.0943
- 0.000000 15 0.0592 0.0592
- 0.000000 16 -0.0011 -0.0011
- 0.000000 17 -0.0556 -0.0556
- 0.000000 18 0.0234 0.0234
- 0.000000 19 0.1834 0.1834
- 0.000000 20 -0.0108 -0.0108
- 0.000000 21 0.0243 0.0243
- 0.000000 22 -0.0845 -0.0845
- 0.000000 23 -0.0279 -0.0279
- 0.000000 24 0.0377 0.0377
- 0.000000 25 -0.1134 -0.1134
- 0.000000 26 -0.0379 -0.0379
- 0.000000 27 0.0123 0.0123
- 0.000000 28 0.0956 0.0956
- 0.000000 29 -0.0118 -0.0118
- 0.000000 30 0.0879 0.0879
- 0.000000 31 -0.1220 -0.1220
- 0.000000 32 -0.0879 -0.0879
- 0.000000 33 -0.1379 -0.1379
- 0.000000 34 0.1399 0.1399
- 0.000000 35 0.1376 0.1376
- 0.000000 36 -0.1868 -0.1868
- 0.000000 37 0.1816 0.1816
- 0.000000 38 0.2145 0.2145
- 0.000000 39 -0.0037 -0.0037
- 0.000000 40 0.0112 0.0112
- 0.000000 41 -0.1880 -0.1880
- 0.000000 42 -0.0093 -0.0093
- 0.000000 43 0.0195 0.0195
- 0.000000 44 -0.2515 -0.2515
- 0.000000 45 0.1999 0.1999
- 0.000000 46 -0.2123 -0.2123
- 0.000000 47 0.2250 0.2250
- 0.000000 48 0.0481 0.0481
- 0.000000 49 -0.1259 -0.1259
- 0.000000 50 0.0384 0.0384
- 0.000000 51 -0.1440 -0.1440
- 0.000000 52 0.2683 0.2683
- 0.000000 53 -0.1172 -0.1172
- 0.000000 54 -0.0504 -0.0504
- 0.000000 55 0.0087 0.0087
- 0.000000 56 -0.0429 -0.0429
- 0.000000 57 0.1463 0.1463
- 0.000000 58 -0.1512 -0.1512
- 0.000000 59 0.1218 0.1218
- 0.000000 60 -0.0873 -0.0873
- 0.000000 61 -0.0686 -0.0686
- 0.000000 62 0.2131 0.2131
- 0.000000 63 0.0814 0.0814
- 0.000000 64 0.0863 0.0863
- 0.000000 65 -0.2416 -0.2416
- 0.000000 66 -0.1096 -0.1096
- 0.000000 67 0.0507 0.0507
- 0.000000 68 0.0043 0.0043
- 0.000000 69 0.1156 0.1156
- 0.000000 70 -0.0684 -0.0684
- 0.000000 71 0.0242 0.0242
- 0.000000 72 -0.9759 -0.9759
- 0.000000 73 -0.0191 -0.0191
- 0.000000 74 0.0303 0.0303
- 0.000000 75 1.3232 1.3232
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- 0.000000 78 -0.6202 -0.6202
- 0.000000 79 -0.0184 -0.0184
- 0.000000 80 0.0024 0.0024
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- 0.000000 82 0.0135 0.0135
- 0.000000 83 0.0136 0.0136
- 0.000000 84 -0.2793 -0.2793
- 0.000000 85 -0.2587 -0.2587
- 0.000000 86 0.1898 0.1898
- 0.000000 87 0.4427 0.4427
- 0.000000 88 0.3809 0.3809
- 0.000000 89 -0.2772 -0.2772
- 0.000000 90 -0.3711 -0.3711
- 0.000000 91 -0.1266 -0.1266
- 0.000000 92 0.0760 0.0760
- 0.000000 93 0.2077 0.2077
- 0.000000 94 0.0044 0.0044
- 0.000000 95 0.0114 0.0114
- 0.000000 96 0.6933 0.6933
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- 0.000000 99 -0.0140 -0.0140
- 0.000000 100 -0.1875 -0.1875
- 0.000000 101 0.1721 0.1721
- 0.000000 102 -0.4462 -0.4462
- 0.000000 103 0.1721 0.1721
- 0.000000 104 -0.5058 -0.5058
- 0.005000 0 -0.0357 -0.0357
- 0.005000 1 0.0361 0.0361
- 0.005000 2 0.0121 0.0121
- 0.005000 3 -0.0497 -0.0497
- 0.005000 4 -0.0589 -0.0589
- 0.005000 5 -0.0187 -0.0187
- 0.005000 6 0.2092 0.2092
- 0.005000 7 0.0610 0.0610
- 0.005000 8 0.0181 0.0181
- 0.005000 9 -0.1238 -0.1238
- 0.005000 10 -0.0383 -0.0383
- 0.005000 11 -0.0114 -0.0114
- 0.005000 12 -0.0925 -0.0925
- 0.005000 13 -0.0866 -0.0866
- 0.005000 14 0.0795 0.0795
- 0.005000 15 0.0436 0.0436
- 0.005000 16 -0.0012 -0.0012
- 0.005000 17 -0.0413 -0.0413
- 0.005000 18 0.0315 0.0315
- 0.005000 19 0.1598 0.1598
- 0.005000 20 -0.0150 -0.0150
- 0.005000 21 0.0174 0.0174
- 0.005000 22 -0.0721 -0.0721
- 0.005000 23 -0.0232 -0.0232
- 0.005000 24 0.0415 0.0415
- 0.005000 25 -0.1253 -0.1253
- 0.005000 26 -0.0411 -0.0411
- 0.005000 27 0.0128 0.0128
- 0.005000 28 0.0978 0.0978
- 0.005000 29 -0.0114 -0.0114
- 0.005000 30 0.0953 0.0953
- 0.005000 31 -0.1353 -0.1353
- 0.005000 32 -0.0930 -0.0930
- 0.005000 33 -0.1495 -0.1495
- 0.005000 34 0.1628 0.1628
- 0.005000 35 0.1455 0.1455
- 0.005000 36 -0.1637 -0.1637
- 0.005000 37 0.1539 0.1539
- 0.005000 38 0.2042 0.2042
- 0.005000 39 -0.0092 -0.0092
- 0.005000 40 0.0225 0.0225
- 0.005000 41 -0.1675 -0.1675
- 0.005000 42 -0.0029 -0.0029
- 0.005000 43 0.0232 0.0232
- 0.005000 44 -0.2600 -0.2600
- 0.005000 45 0.1758 0.1758
- 0.005000 46 -0.1997 -0.1997
- 0.005000 47 0.2233 0.2233
- 0.005000 48 0.0603 0.0603
- 0.005000 49 -0.1435 -0.1435
- 0.005000 50 0.0408 0.0408
- 0.005000 51 -0.1671 -0.1671
- 0.005000 52 0.3054 0.3054
- 0.005000 53 -0.1170 -0.1170
- 0.005000 54 -0.0508 -0.0508
- 0.005000 55 0.0091 0.0091
- 0.005000 56 -0.0390 -0.0390
- 0.005000 57 0.1576 0.1576
- 0.005000 58 -0.1711 -0.1711
- 0.005000 59 0.1151 0.1151
- 0.005000 60 -0.1012 -0.1012
- 0.005000 61 -0.0710 -0.0710
- 0.005000 62 0.2224 0.2224
- 0.005000 63 0.0955 0.0955
- 0.005000 64 0.0843 0.0843
- 0.005000 65 -0.2424 -0.2424
- 0.005000 66 -0.1189 -0.1189
- 0.005000 67 0.0594 0.0594
- 0.005000 68 -0.0067 -0.0067
- 0.005000 69 0.1245 0.1245
- 0.005000 70 -0.0727 -0.0727
- 0.005000 71 0.0267 0.0267
- 0.005000 72 -1.2302 -1.2302
- 0.005000 73 0.0179 0.0179
- 0.005000 74 0.1828 0.1828
- 0.005000 75 1.6774 1.6774
- 0.005000 76 -0.0317 -0.0317
- 0.005000 77 -0.2673 -0.2673
- 0.005000 78 -0.7339 -0.7339
- 0.005000 79 -0.0097 -0.0097
- 0.005000 80 0.0588 0.0588
- 0.005000 81 0.2867 0.2867
- 0.005000 82 0.0235 0.0235
- 0.005000 83 0.0257 0.0257
- 0.005000 84 -0.2659 -0.2659
- 0.005000 85 -0.2550 -0.2550
- 0.005000 86 0.1537 0.1537
- 0.005000 87 0.4281 0.4281
- 0.005000 88 0.3637 0.3637
- 0.005000 89 -0.2142 -0.2142
- 0.005000 90 -0.3759 -0.3759
- 0.005000 91 -0.1141 -0.1141
- 0.005000 92 0.0422 0.0422
- 0.005000 93 0.2137 0.2137
- 0.005000 94 0.0055 0.0055
- 0.005000 95 0.0182 0.0182
- 0.005000 96 0.7206 0.7206
- 0.005000 97 0.0406 0.0406
- 0.005000 98 -0.4108 -0.4108
- 0.005000 99 0.0406 0.0406
- 0.005000 100 -0.1644 -0.1644
- 0.005000 101 0.1748 0.1748
- 0.005000 102 -0.4108 -0.4108
- 0.005000 103 0.1748 0.1748
- 0.005000 104 -0.5562 -0.5562
- 0.010000 0 -0.0878 -0.0878
- 0.010000 1 0.0941 0.0941
- 0.010000 2 0.0293 0.0293
- 0.010000 3 -0.1396 -0.1396
- 0.010000 4 -0.2010 -0.2010
- 0.010000 5 -0.0619 -0.0619
- 0.010000 6 0.5550 0.5550
- 0.010000 7 0.2748 0.2748
- 0.010000 8 0.0840 0.0840
- 0.010000 9 -0.3276 -0.3276
- 0.010000 10 -0.1680 -0.1680
- 0.010000 11 -0.0513 -0.0513
- 0.010000 12 -0.0737 -0.0737
- 0.010000 13 -0.0790 -0.0790
- 0.010000 14 0.0692 0.0692
- 0.010000 15 0.0283 0.0283
- 0.010000 16 0.0040 0.0040
- 0.010000 17 -0.0286 -0.0286
- 0.010000 18 0.0321 0.0321
- 0.010000 19 0.1328 0.1328
- 0.010000 20 -0.0225 -0.0225
- 0.010000 21 0.0134 0.0134
- 0.010000 22 -0.0577 -0.0577
- 0.010000 23 -0.0182 -0.0182
- 0.010000 24 0.0392 0.0392
- 0.010000 25 -0.1362 -0.1362
- 0.010000 26 -0.0422 -0.0422
- 0.010000 27 0.0200 0.0200
- 0.010000 28 0.0971 0.0971
- 0.010000 29 -0.0148 -0.0148
- 0.010000 30 0.0947 0.0947
- 0.010000 31 -0.1522 -0.1522
- 0.010000 32 -0.0947 -0.0947
- 0.010000 33 -0.1540 -0.1540
- 0.010000 34 0.1914 0.1914
- 0.010000 35 0.1516 0.1516
- 0.010000 36 -0.1499 -0.1499
- 0.010000 37 0.1475 0.1475
- 0.010000 38 0.1960 0.1960
- 0.010000 39 -0.0286 -0.0286
- 0.010000 40 0.0465 0.0465
- 0.010000 41 -0.1645 -0.1645
- 0.010000 42 0.0153 0.0153
- 0.010000 43 0.0061 0.0061
- 0.010000 44 -0.2523 -0.2523
- 0.010000 45 0.1633 0.1633
- 0.010000 46 -0.2001 -0.2001
- 0.010000 47 0.2208 0.2208
- 0.010000 48 0.0664 0.0664
- 0.010000 49 -0.1581 -0.1581
- 0.010000 50 0.0474 0.0474
- 0.010000 51 -0.1797 -0.1797
- 0.010000 52 0.3399 0.3399
- 0.010000 53 -0.1327 -0.1327
- 0.010000 54 -0.0480 -0.0480
- 0.010000 55 0.0176 0.0176
- 0.010000 56 -0.0391 -0.0391
- 0.010000 57 0.1612 0.1612
- 0.010000 58 -0.1994 -0.1994
- 0.010000 59 0.1245 0.1245
- 0.010000 60 -0.0725 -0.0725
- 0.010000 61 -0.0708 -0.0708
- 0.010000 62 0.2184 0.2184
- 0.010000 63 0.0633 0.0633
- 0.010000 64 0.0837 0.0837
- 0.010000 65 -0.2366 -0.2366
- 0.010000 66 -0.1075 -0.1075
- 0.010000 67 0.0513 0.0513
- 0.010000 68 -0.0042 -0.0042
- 0.010000 69 0.1167 0.1167
- 0.010000 70 -0.0642 -0.0642
- 0.010000 71 0.0223 0.0223
- 0.010000 72 0.2882 0.2882
- 0.010000 73 0.0151 0.0151
- 0.010000 74 -0.0540 -0.0540
- 0.010000 75 -0.1914 -0.1914
- 0.010000 76 -0.0155 -0.0155
- 0.010000 77 0.0481 0.0481
- 0.010000 78 0.0790 0.0790
- 0.010000 79 -0.0143 -0.0143
- 0.010000 80 0.0262 0.0262
- 0.010000 81 -0.1757 -0.1757
- 0.010000 82 0.0147 0.0147
- 0.010000 83 -0.0202 -0.0202
- 0.010000 84 -0.2260 -0.2260
- 0.010000 85 -0.2493 -0.2493
- 0.010000 86 0.1549 0.1549
- 0.010000 87 0.3591 0.3591
- 0.010000 88 0.3498 0.3498
- 0.010000 89 -0.2123 -0.2123
- 0.010000 90 -0.3374 -0.3374
- 0.010000 91 -0.1078 -0.1078
- 0.010000 92 0.0378 0.0378
- 0.010000 93 0.2044 0.2044
- 0.010000 94 0.0073 0.0073
- 0.010000 95 0.0195 0.0195
- 0.010000 96 0.3275 0.3275
- 0.010000 97 0.1241 0.1241
- 0.010000 98 -0.4037 -0.4037
- 0.010000 99 0.1241 0.1241
- 0.010000 100 0.0089 0.0089
- 0.010000 101 0.1813 0.1813
- 0.010000 102 -0.4037 -0.4037
- 0.010000 103 0.1813 0.1813
- 0.010000 104 -0.3364 -0.3364
- 0.015000 0 -0.1535 -0.1535
- 0.015000 1 0.1803 0.1803
- 0.015000 2 0.0500 0.0500
- 0.015000 3 -0.2381 -0.2381
- 0.015000 4 -0.5263 -0.5263
- 0.015000 5 -0.1521 -0.1521
- 0.015000 6 0.9632 0.9632
- 0.015000 7 0.8844 0.8844
- 0.015000 8 0.2606 0.2606
- 0.015000 9 -0.5716 -0.5716
- 0.015000 10 -0.5385 -0.5385
- 0.015000 11 -0.1585 -0.1585
- 0.015000 12 -0.0624 -0.0624
- 0.015000 13 -0.0749 -0.0749
- 0.015000 14 0.0649 0.0649
- 0.015000 15 0.0176 0.0176
- 0.015000 16 0.0062 0.0062
- 0.015000 17 -0.0192 -0.0192
- 0.015000 18 0.0342 0.0342
- 0.015000 19 0.1168 0.1168
- 0.015000 20 -0.0307 -0.0307
- 0.015000 21 0.0107 0.0107
- 0.015000 22 -0.0481 -0.0481
- 0.015000 23 -0.0150 -0.0150
- 0.015000 24 0.0328 0.0328
- 0.015000 25 -0.1462 -0.1462
- 0.015000 26 -0.0414 -0.0414
- 0.015000 27 0.0294 0.0294
- 0.015000 28 0.0888 0.0888
- 0.015000 29 -0.0208 -0.0208
- 0.015000 30 0.0855 0.0855
- 0.015000 31 -0.1693 -0.1693
- 0.015000 32 -0.0921 -0.0921
- 0.015000 33 -0.1477 -0.1477
- 0.015000 34 0.2267 0.2267
- 0.015000 35 0.1543 0.1543
- 0.015000 36 -0.1412 -0.1412
- 0.015000 37 0.1563 0.1563
- 0.015000 38 0.1875 0.1875
- 0.015000 39 -0.0493 -0.0493
- 0.015000 40 0.0707 0.0707
- 0.015000 41 -0.1724 -0.1724
- 0.015000 42 0.0328 0.0328
- 0.015000 43 -0.0229 -0.0229
- 0.015000 44 -0.2415 -0.2415
- 0.015000 45 0.1577 0.1577
- 0.015000 46 -0.2041 -0.2041
- 0.015000 47 0.2264 0.2264
- 0.015000 48 0.0653 0.0653
- 0.015000 49 -0.1604 -0.1604
- 0.015000 50 0.0531 0.0531
- 0.015000 51 -0.1803 -0.1803
- 0.015000 52 0.3532 0.3532
- 0.015000 53 -0.1526 -0.1526
- 0.015000 54 -0.0428 -0.0428
- 0.015000 55 0.0255 0.0255
- 0.015000 56 -0.0402 -0.0402
- 0.015000 57 0.1578 0.1578
- 0.015000 58 -0.2183 -0.2183
- 0.015000 59 0.1398 0.1398
- 0.015000 60 -0.0302 -0.0302
- 0.015000 61 -0.0650 -0.0650
- 0.015000 62 0.1977 0.1977
- 0.015000 63 0.0179 0.0179
- 0.015000 64 0.0801 0.0801
- 0.015000 65 -0.2225 -0.2225
- 0.015000 66 -0.0904 -0.0904
- 0.015000 67 0.0344 0.0344
- 0.015000 68 0.0104 0.0104
- 0.015000 69 0.1028 0.1028
- 0.015000 70 -0.0494 -0.0494
- 0.015000 71 0.0144 0.0144
- 0.015000 72 0.2761 0.2761
- 0.015000 73 0.0238 0.0238
- 0.015000 74 -0.0571 -0.0571
- 0.015000 75 -0.1910 -0.1910
- 0.015000 76 -0.0225 -0.0225
- 0.015000 77 0.0519 0.0519
- 0.015000 78 0.0731 0.0731
- 0.015000 79 -0.0147 -0.0147
- 0.015000 80 0.0284 0.0284
- 0.015000 81 -0.1582 -0.1582
- 0.015000 82 0.0134 0.0134
- 0.015000 83 -0.0232 -0.0232
- 0.015000 84 -0.1886 -0.1886
- 0.015000 85 -0.2341 -0.2341
- 0.015000 86 0.1574 0.1574
- 0.015000 87 0.2953 0.2953
- 0.015000 88 0.3230 0.3230
- 0.015000 89 -0.2125 -0.2125
- 0.015000 90 -0.2987 -0.2987
- 0.015000 91 -0.0966 -0.0966
- 0.015000 92 0.0352 0.0352
- 0.015000 93 0.1920 0.1920
- 0.015000 94 0.0076 0.0076
- 0.015000 95 0.0199 0.0199
- 0.015000 96 0.0805 0.0805
- 0.015000 97 0.1377 0.1377
- 0.015000 98 -0.4185 -0.4185
- 0.015000 99 0.1377 0.1377
- 0.015000 100 0.2115 0.2115
- 0.015000 101 0.1624 0.1624
- 0.015000 102 -0.4185 -0.4185
- 0.015000 103 0.1624 0.1624
- 0.015000 104 -0.2920 -0.2920
- 0.020000 0 -0.2027 -0.2027
- 0.020000 1 0.2564 0.2564
- 0.020000 2 0.0632 0.0632
- 0.020000 3 -0.1626 -0.1626
- 0.020000 4 -0.9163 -0.9163
- 0.020000 5 -0.2431 -0.2431
- 0.020000 6 0.8925 0.8925
- 0.020000 7 1.6918 1.6918
- 0.020000 8 0.4605 0.4605
- 0.020000 9 -0.5272 -0.5272
- 0.020000 10 -1.0320 -1.0320
- 0.020000 11 -0.2806 -0.2806
- 0.020000 12 -0.0683 -0.0683
- 0.020000 13 -0.0827 -0.0827
- 0.020000 14 0.0756 0.0756
- 0.020000 15 0.0153 0.0153
- 0.020000 16 0.0064 0.0064
- 0.020000 17 -0.0177 -0.0177
- 0.020000 18 0.0412 0.0412
- 0.020000 19 0.1278 0.1278
- 0.020000 20 -0.0410 -0.0410
- 0.020000 21 0.0118 0.0118
- 0.020000 22 -0.0516 -0.0516
- 0.020000 23 -0.0169 -0.0169
- 0.020000 24 0.0325 0.0325
- 0.020000 25 -0.1489 -0.1489
- 0.020000 26 -0.0383 -0.0383
- 0.020000 27 0.0296 0.0296
- 0.020000 28 0.0777 0.0777
- 0.020000 29 -0.0248 -0.0248
- 0.020000 30 0.0807 0.0807
- 0.020000 31 -0.1714 -0.1714
- 0.020000 32 -0.0858 -0.0858
- 0.020000 33 -0.1429 -0.1429
- 0.020000 34 0.2426 0.2426
- 0.020000 35 0.1489 0.1489
- 0.020000 36 -0.1241 -0.1241
- 0.020000 37 0.1558 0.1558
- 0.020000 38 0.1741 0.1741
- 0.020000 39 -0.0543 -0.0543
- 0.020000 40 0.0705 0.0705
- 0.020000 41 -0.1847 -0.1847
- 0.020000 42 0.0351 0.0351
- 0.020000 43 -0.0425 -0.0425
- 0.020000 44 -0.2183 -0.2183
- 0.020000 45 0.1433 0.1433
- 0.020000 46 -0.1839 -0.1839
- 0.020000 47 0.2288 0.2288
- 0.020000 48 0.0562 0.0562
- 0.020000 49 -0.1493 -0.1493
- 0.020000 50 0.0525 0.0525
- 0.020000 51 -0.1626 -0.1626
- 0.020000 52 0.3303 0.3303
- 0.020000 53 -0.1629 -0.1629
- 0.020000 54 -0.0384 -0.0384
- 0.020000 55 0.0320 0.0320
- 0.020000 56 -0.0434 -0.0434
- 0.020000 57 0.1448 0.1448
- 0.020000 58 -0.2130 -0.2130
- 0.020000 59 0.1538 0.1538
- 0.020000 60 -0.0027 -0.0027
- 0.020000 61 -0.0548 -0.0548
- 0.020000 62 0.1651 0.1651
- 0.020000 63 -0.0126 -0.0126
- 0.020000 64 0.0708 0.0708
- 0.020000 65 -0.1933 -0.1933
- 0.020000 66 -0.0731 -0.0731
- 0.020000 67 0.0237 0.0237
- 0.020000 68 0.0207 0.0207
- 0.020000 69 0.0884 0.0884
- 0.020000 70 -0.0397 -0.0397
- 0.020000 71 0.0076 0.0076
- 0.020000 72 0.2868 0.2868
- 0.020000 73 0.0276 0.0276
- 0.020000 74 -0.0545 -0.0545
- 0.020000 75 -0.2066 -0.2066
- 0.020000 76 -0.0254 -0.0254
- 0.020000 77 0.0507 0.0507
- 0.020000 78 0.0782 0.0782
- 0.020000 79 -0.0140 -0.0140
- 0.020000 80 0.0296 0.0296
- 0.020000 81 -0.1585 -0.1585
- 0.020000 82 0.0118 0.0118
- 0.020000 83 -0.0258 -0.0258
- 0.020000 84 -0.1759 -0.1759
- 0.020000 85 -0.2245 -0.2245
- 0.020000 86 0.1480 0.1480
- 0.020000 87 0.2912 0.2912
- 0.020000 88 0.3104 0.3104
- 0.020000 89 -0.1981 -0.1981
- 0.020000 90 -0.3037 -0.3037
- 0.020000 91 -0.0940 -0.0940
- 0.020000 92 0.0306 0.0306
- 0.020000 93 0.1884 0.1884
- 0.020000 94 0.0081 0.0081
- 0.020000 95 0.0195 0.0195
- 0.020000 96 -0.0480 -0.0480
- 0.020000 97 0.0463 0.0463
- 0.020000 98 -0.4386 -0.4386
- 0.020000 99 0.0463 0.0463
- 0.020000 100 0.2798 0.2798
- 0.020000 101 0.1279 0.1279
- 0.020000 102 -0.4386 -0.4386
- 0.020000 103 0.1279 0.1279
- 0.020000 104 -0.2318 -0.2318
+#! FIELDS time parameter c1
+ 0.000000 0 -0.0023
+ 0.000000 1 0.0023
+ 0.000000 2 0.0008
+ 0.000000 3 -0.0027
+ 0.000000 4 -0.0030
+ 0.000000 5 -0.0010
+ 0.000000 6 0.0126
+ 0.000000 7 0.0021
+ 0.000000 8 0.0006
+ 0.000000 9 -0.0076
+ 0.000000 10 -0.0014
+ 0.000000 11 -0.0004
+ 0.000000 12 -0.1068
+ 0.000000 13 -0.0978
+ 0.000000 14 0.0943
+ 0.000000 15 0.0592
+ 0.000000 16 -0.0011
+ 0.000000 17 -0.0556
+ 0.000000 18 0.0234
+ 0.000000 19 0.1834
+ 0.000000 20 -0.0108
+ 0.000000 21 0.0243
+ 0.000000 22 -0.0845
+ 0.000000 23 -0.0279
+ 0.000000 24 0.0377
+ 0.000000 25 -0.1134
+ 0.000000 26 -0.0379
+ 0.000000 27 0.0123
+ 0.000000 28 0.0956
+ 0.000000 29 -0.0118
+ 0.000000 30 0.0879
+ 0.000000 31 -0.1220
+ 0.000000 32 -0.0879
+ 0.000000 33 -0.1379
+ 0.000000 34 0.1399
+ 0.000000 35 0.1376
+ 0.000000 36 -0.1868
+ 0.000000 37 0.1816
+ 0.000000 38 0.2145
+ 0.000000 39 -0.0037
+ 0.000000 40 0.0112
+ 0.000000 41 -0.1880
+ 0.000000 42 -0.0093
+ 0.000000 43 0.0195
+ 0.000000 44 -0.2515
+ 0.000000 45 0.1999
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diff --git a/regtest/multicolvar/rt25/plumed.dat b/regtest/multicolvar/rt25/plumed.dat
index a9fc93f014db3711a545e77e12569b9915a14888..ed370346031a361290ed3f767105e1650efd7fc3 100644
--- a/regtest/multicolvar/rt25/plumed.dat
+++ b/regtest/multicolvar/rt25/plumed.dat
@@ -10,20 +10,7 @@ ATOMS8=2,4,17,9
REFERENCE=1
LABEL=c1
...
-ALPHABETA ...
-REFERENCE=1
-NUMERICAL_DERIVATIVES
-LABEL=c1num
-ATOMS1=1,3,6,10
-ATOMS2=2,4,7,9
-ATOMS3=3,5,6,7
-ATOMS4=2,1,3,4
-ATOMS5=12,14,17,19
-ATOMS6=22,24,27,29
-ATOMS7=21,20,5,9
-ATOMS8=2,4,17,9
-...
-DUMPDERIVATIVES ARG=c1.*,c1num.* STRIDE=1 FILE=derivatives FMT=%8.4f
+DUMPDERIVATIVES ARG=c1.* STRIDE=1 FILE=derivatives FMT=%8.4f
RESTRAINT ARG=c1 AT=-2 KAPPA=0 SLOPE=1
diff --git a/src/adjmat/ActionWithInputMatrix.cpp b/src/adjmat/ActionWithInputMatrix.cpp
index cbb2e18313ad294b4153e4e90b09e89eca0866a6..30df6fa7e4283f5e74944477a79802d9745159b8 100644
--- a/src/adjmat/ActionWithInputMatrix.cpp
+++ b/src/adjmat/ActionWithInputMatrix.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ActionWithInputMatrix.h b/src/adjmat/ActionWithInputMatrix.h
index 2911c267a099c2275df82d972c98ce4e29ff1d57..7443c5654ceec9d1580ecc5979d85736804c49c3 100644
--- a/src/adjmat/ActionWithInputMatrix.h
+++ b/src/adjmat/ActionWithInputMatrix.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/AdjacencyMatrixBase.cpp b/src/adjmat/AdjacencyMatrixBase.cpp
index 457b08791fd6d7bba8eaa9b1056cda261204974a..8ebb296a39ed3002da4c2d6249f6ed05e20b4636 100644
--- a/src/adjmat/AdjacencyMatrixBase.cpp
+++ b/src/adjmat/AdjacencyMatrixBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/AdjacencyMatrixBase.h b/src/adjmat/AdjacencyMatrixBase.h
index 45f8d4674404fdd74548a1e114854b9e6551b7ce..76823ed429a5282bdc4b5b02cd11c4871ca2fbf5 100644
--- a/src/adjmat/AdjacencyMatrixBase.h
+++ b/src/adjmat/AdjacencyMatrixBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/AdjacencyMatrixVessel.cpp b/src/adjmat/AdjacencyMatrixVessel.cpp
index 668ee7287cef3e3800ddd6f35eb601b64ccefc34..6adc5b7e46627a3dbd4883367ba3003fe504cb3b 100644
--- a/src/adjmat/AdjacencyMatrixVessel.cpp
+++ b/src/adjmat/AdjacencyMatrixVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/AdjacencyMatrixVessel.h b/src/adjmat/AdjacencyMatrixVessel.h
index 754da5d5a4dcb982dd55a8cf737b37f8794d7572..ce951670d3b1b7a5bc8968187525e8d591dae739 100644
--- a/src/adjmat/AdjacencyMatrixVessel.h
+++ b/src/adjmat/AdjacencyMatrixVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/AlignedMatrixBase.cpp b/src/adjmat/AlignedMatrixBase.cpp
index 73c5869dec5e4bb5b9ba95017f5d814821164b81..1fa3f069f952d7ceff97a84155168a5f0a8823e7 100644
--- a/src/adjmat/AlignedMatrixBase.cpp
+++ b/src/adjmat/AlignedMatrixBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/AlignedMatrixBase.h b/src/adjmat/AlignedMatrixBase.h
index 10f58d6071e9490f14ef08ecef6d95ca16131534..71336d92382c88a89d9d84da7e2b935879df2762 100644
--- a/src/adjmat/AlignedMatrixBase.h
+++ b/src/adjmat/AlignedMatrixBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ClusterAnalysisBase.cpp b/src/adjmat/ClusterAnalysisBase.cpp
index 3e8429d3d5387e51453a36ed8461c85a09a9bace..250a9c7bff621a5918c1797b4a412fba164bb389 100644
--- a/src/adjmat/ClusterAnalysisBase.cpp
+++ b/src/adjmat/ClusterAnalysisBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ClusterAnalysisBase.h b/src/adjmat/ClusterAnalysisBase.h
index 942e14101db7e2946576c0db1e47fc83142d5c78..b11dc63209a74e0c86f6f433ca96a44b13e65719 100644
--- a/src/adjmat/ClusterAnalysisBase.h
+++ b/src/adjmat/ClusterAnalysisBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ClusterDiameter.cpp b/src/adjmat/ClusterDiameter.cpp
index 10be1fde5ddc7e204d4dd923b1451532c707439a..da11fe2faf718426c2187c0375133399c13ba202 100644
--- a/src/adjmat/ClusterDiameter.cpp
+++ b/src/adjmat/ClusterDiameter.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ClusterDistribution.cpp b/src/adjmat/ClusterDistribution.cpp
index 5f1c84068c0ace67b11c77396dad7270d96c1e8f..c1c06ccc85c0297e35b8ce8199970477f9f4168d 100644
--- a/src/adjmat/ClusterDistribution.cpp
+++ b/src/adjmat/ClusterDistribution.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ClusterProperties.cpp b/src/adjmat/ClusterProperties.cpp
index d708ae2e84d61162d8aeb5949151799091ca2d24..aa4a6899a15ec8336cd3bdf9a1a475694e552c3e 100644
--- a/src/adjmat/ClusterProperties.cpp
+++ b/src/adjmat/ClusterProperties.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ClusterSize.cpp b/src/adjmat/ClusterSize.cpp
index af1eed8eb687350a3072f667db104f66dbc8026c..a65f596fef455e6b32cd13c8daebc386d6dc49e7 100644
--- a/src/adjmat/ClusterSize.cpp
+++ b/src/adjmat/ClusterSize.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ClusterWithSurface.cpp b/src/adjmat/ClusterWithSurface.cpp
index a3e010e5afca900cf7eb1e0f48e78c82b2551293..48403dc6c52d2dcc670aaff52a8da32853ac24a7 100644
--- a/src/adjmat/ClusterWithSurface.cpp
+++ b/src/adjmat/ClusterWithSurface.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ClusteringBase.cpp b/src/adjmat/ClusteringBase.cpp
index 7b7b9da55dbead0dc603c4c67d66e995ebcfd73f..75ae7066a2b47d7e1e0db4787e5567ef93101345 100644
--- a/src/adjmat/ClusteringBase.cpp
+++ b/src/adjmat/ClusteringBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ClusteringBase.h b/src/adjmat/ClusteringBase.h
index 006c67941616ae40d4c8f69c18df36687177c9c9..b560fafabd5b3674d49595da4f71c421216044ef 100644
--- a/src/adjmat/ClusteringBase.h
+++ b/src/adjmat/ClusteringBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ContactAlignedMatrix.cpp b/src/adjmat/ContactAlignedMatrix.cpp
index b23de0af2122d6909b1497a6cc089ec379964849..10314c8d632d6b9efdba691a8d274bd8fb93a33f 100644
--- a/src/adjmat/ContactAlignedMatrix.cpp
+++ b/src/adjmat/ContactAlignedMatrix.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/ContactMatrix.cpp b/src/adjmat/ContactMatrix.cpp
index 0fa2aecc5bba0e792ff66e497427372b4a8c3ce9..6b161c586745a8d7e9aae77d79cbfbf489cf6693 100644
--- a/src/adjmat/ContactMatrix.cpp
+++ b/src/adjmat/ContactMatrix.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/DFSClustering.cpp b/src/adjmat/DFSClustering.cpp
index 82017a971abfcfc4543fa78613e0d8ec6191c55d..21e1126ba013d4ab411e03b9e4f8148e72f762d6 100644
--- a/src/adjmat/DFSClustering.cpp
+++ b/src/adjmat/DFSClustering.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/DumpGraph.cpp b/src/adjmat/DumpGraph.cpp
index eea1eb0d703819196a9fbb02ae7bdfc576f8d2e0..94696a5277ba732a43e9776c8f8793788ae56b82 100644
--- a/src/adjmat/DumpGraph.cpp
+++ b/src/adjmat/DumpGraph.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/HbondMatrix.cpp b/src/adjmat/HbondMatrix.cpp
index 3bdc06e712b9531f05fd01200a45d85a72905380..14c838606e54d8b71d6f1c047af0e40b121e6578 100644
--- a/src/adjmat/HbondMatrix.cpp
+++ b/src/adjmat/HbondMatrix.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/MatrixColumnSums.cpp b/src/adjmat/MatrixColumnSums.cpp
index 4ff47ab2068afd09a88c1de5a61e39db551e3367..4a7d62dc5bc1ce8fb568f1ec8dc0e73b7722ae19 100644
--- a/src/adjmat/MatrixColumnSums.cpp
+++ b/src/adjmat/MatrixColumnSums.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -76,7 +76,7 @@ PLUMED_REGISTER_ACTION(MatrixColumnSums,"COLUMNSUMS")
void MatrixColumnSums::registerKeywords( Keywords& keys ) {
ActionWithInputMatrix::registerKeywords( keys );
- keys.use("ALT_MIN"); keys.use("LOWEST"); keys.use("HIGHEST"); keys.use("MEAN");
+ keys.use("ALT_MIN"); keys.use("LOWEST"); keys.use("HIGHEST");
keys.use("MEAN"); keys.use("MIN"); keys.use("MAX"); keys.use("LESS_THAN");
keys.use("MORE_THAN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
}
diff --git a/src/adjmat/MatrixRowSums.cpp b/src/adjmat/MatrixRowSums.cpp
index add4b0cf067ce0b384d363a17de50ad3e72590db..fb60b8b31e25124e906fa25381d41e4412298963 100644
--- a/src/adjmat/MatrixRowSums.cpp
+++ b/src/adjmat/MatrixRowSums.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -76,7 +76,7 @@ PLUMED_REGISTER_ACTION(MatrixRowSums,"ROWSUMS")
void MatrixRowSums::registerKeywords( Keywords& keys ) {
ActionWithInputMatrix::registerKeywords( keys );
- keys.use("ALT_MIN"); keys.use("LOWEST"); keys.use("HIGHEST"); keys.use("MEAN");
+ keys.use("ALT_MIN"); keys.use("LOWEST"); keys.use("HIGHEST");
keys.use("MEAN"); keys.use("MIN"); keys.use("MAX"); keys.use("LESS_THAN");
keys.use("MORE_THAN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
}
diff --git a/src/adjmat/OutputCluster.cpp b/src/adjmat/OutputCluster.cpp
index 66c58da608961a84dd96bcedd4ae495aec76d805..c5c867c668d04c8cbfc5da07c220a004dba6ff62 100644
--- a/src/adjmat/OutputCluster.cpp
+++ b/src/adjmat/OutputCluster.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/SMACMatrix.cpp b/src/adjmat/SMACMatrix.cpp
index 25d6f69347ed936c3817a5ec2b72aa8c9ec99dd8..b0d1e83455b48c78f98ec5184ec82c8d62f8b8e0 100644
--- a/src/adjmat/SMACMatrix.cpp
+++ b/src/adjmat/SMACMatrix.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/Sprint.cpp b/src/adjmat/Sprint.cpp
index 4c167801c2b7a0685c86c4768180e04c94aed280..b4b91a74d0c8877afe29a34ae0888621ceaaec95 100644
--- a/src/adjmat/Sprint.cpp
+++ b/src/adjmat/Sprint.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/adjmat/TopologyMatrix.cpp b/src/adjmat/TopologyMatrix.cpp
index 0b4de263ec7dd1afc908fbb80b195672042ecfef..b0c214ca940d5b3312f261f97bbb366442d2313d 100644
--- a/src/adjmat/TopologyMatrix.cpp
+++ b/src/adjmat/TopologyMatrix.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/Analysis.cpp b/src/analysis/Analysis.cpp
index 088d2e76c60f387b3ab01dd41e21b4cef40bd65c..9d6409e277a22a1e58a28f78afb59257c885c2b2 100644
--- a/src/analysis/Analysis.cpp
+++ b/src/analysis/Analysis.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/Analysis.h b/src/analysis/Analysis.h
index 61405e41b6ac74db5d4b28803085ad7605ffb833..5ef938cfaea7607a7b883f2000cb73a9dec4010b 100644
--- a/src/analysis/Analysis.h
+++ b/src/analysis/Analysis.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/AnalysisWithLandmarks.cpp b/src/analysis/AnalysisWithLandmarks.cpp
index f6a37baa83e1973caba76d6911a89fd9f68bc204..73545cebb9a8e95a5d91267a1a14c1f4fe68e0bf 100644
--- a/src/analysis/AnalysisWithLandmarks.cpp
+++ b/src/analysis/AnalysisWithLandmarks.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/AnalysisWithLandmarks.h b/src/analysis/AnalysisWithLandmarks.h
index 9c260bceb325647096c5fd457607523c7cc84756..32598c4391d835df0012433e6cc730bbc48b6e97 100644
--- a/src/analysis/AnalysisWithLandmarks.h
+++ b/src/analysis/AnalysisWithLandmarks.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/Average.cpp b/src/analysis/Average.cpp
index e2e61b2f91def9f49d8f07804f52c244e9b00b46..4b244782015c18dd2ebaf6aad65d1adb27d6aa1e 100644
--- a/src/analysis/Average.cpp
+++ b/src/analysis/Average.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/AverageVessel.cpp b/src/analysis/AverageVessel.cpp
index 5b54f91ae52c0cf5549eda37e7d13fc45434d959..42384e30e2d7a1a55d179f6997f0c9811d254681 100644
--- a/src/analysis/AverageVessel.cpp
+++ b/src/analysis/AverageVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/AverageVessel.h b/src/analysis/AverageVessel.h
index d465a4ac7ce9a03508e8b5001ec85535ea1dc003..15eae68bde2500b4c47c6d0f385a891aed599d48 100644
--- a/src/analysis/AverageVessel.h
+++ b/src/analysis/AverageVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/ClassicalMultiDimensionalScaling.cpp b/src/analysis/ClassicalMultiDimensionalScaling.cpp
index 3a3e412578af5578b3d74406e488eaa45e805448..810657bb4a483484c6ddb7eaded9c055d3153d23 100644
--- a/src/analysis/ClassicalMultiDimensionalScaling.cpp
+++ b/src/analysis/ClassicalMultiDimensionalScaling.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/ClassicalScaling.cpp b/src/analysis/ClassicalScaling.cpp
index f1ac0821c29012bdcd0f972b1970d6f0e73378b3..b1dc5d8f35a9519854610d4d7f5b7148920d801b 100644
--- a/src/analysis/ClassicalScaling.cpp
+++ b/src/analysis/ClassicalScaling.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/ClassicalScaling.h b/src/analysis/ClassicalScaling.h
index c3f7893315023c355a8418d1882a18ca3d49a21a..79e199ec7995a4bbfff157f10e971571ddd9092f 100644
--- a/src/analysis/ClassicalScaling.h
+++ b/src/analysis/ClassicalScaling.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/Committor.cpp b/src/analysis/Committor.cpp
index 5dfeddb5e4d720b7bf80323e85f4f29bd4c824ec..4f76bd583416038897b19c7dc54f18015bc6c6c6 100644
--- a/src/analysis/Committor.cpp
+++ b/src/analysis/Committor.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index 826c459d32403765cb886632c5663e98ac279ed5..914a37ed5b7cffeaf2f7bf917123ad7dde157b1a 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/LandmarkRegister.cpp b/src/analysis/LandmarkRegister.cpp
index e8fde312c562a703fbb8a00cd8c8ecfd4c48b6ff..7dff13e46b7ee4d802d9869735a9615dfb0327fa 100644
--- a/src/analysis/LandmarkRegister.cpp
+++ b/src/analysis/LandmarkRegister.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/LandmarkRegister.h b/src/analysis/LandmarkRegister.h
index f6d2593f19dbeccdbfa8a969a3db66d2d955cc1c..794bd56668df23dd35b3436105acb930df3d21da 100644
--- a/src/analysis/LandmarkRegister.h
+++ b/src/analysis/LandmarkRegister.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/LandmarkSelectionBase.cpp b/src/analysis/LandmarkSelectionBase.cpp
index 69438b95d1e30c26e126b92c50cf382f95518270..2e73c05484c3210b6420512efce6b97a33fbd804 100644
--- a/src/analysis/LandmarkSelectionBase.cpp
+++ b/src/analysis/LandmarkSelectionBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/LandmarkSelectionBase.h b/src/analysis/LandmarkSelectionBase.h
index a8b9079b2f61bdff43f8837be83f900773672b75..2b31975a468430f09eec7b602cde2b434a948562 100644
--- a/src/analysis/LandmarkSelectionBase.h
+++ b/src/analysis/LandmarkSelectionBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/PCA.cpp b/src/analysis/PCA.cpp
index c0dfda76cdb8e1cd94819c81475c505541d967c3..f4bb9304d626925b1912c63793a88e9845fa4099 100644
--- a/src/analysis/PCA.cpp
+++ b/src/analysis/PCA.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/analysis/SelectAllFrames.cpp b/src/analysis/SelectAllFrames.cpp
index cf0e45cb1b93a5644618291f408209145554ac1b..41754c0faf554a0253faf58db47d1cb20747a6cf 100644
--- a/src/analysis/SelectAllFrames.cpp
+++ b/src/analysis/SelectAllFrames.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/ABMD.cpp b/src/bias/ABMD.cpp
index 5d0c401722c878ac9da51c119636f4eae04f0075..fea11b2a30db289e5fc4186a5a039505fc8eb58a 100644
--- a/src/bias/ABMD.cpp
+++ b/src/bias/ABMD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/ActionRegister.h b/src/bias/ActionRegister.h
index 792b889e8a9da9a288f3571da62795646e177d02..97d1d0d96e81eb133ca03b3fd41f4a9dcb897a53 100644
--- a/src/bias/ActionRegister.h
+++ b/src/bias/ActionRegister.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/Bias.cpp b/src/bias/Bias.cpp
index 99e5844eade821e85d2792c2b871b8312f701e95..94d7f6f58118cb4cceff3e5205bc8083d1c53af8 100644
--- a/src/bias/Bias.cpp
+++ b/src/bias/Bias.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/Bias.h b/src/bias/Bias.h
index 22337457a77d2e1bd35b300d7fe99ebb578b9400..0b846eb75a75066d81ba6454b1c20c624b3a1dab 100644
--- a/src/bias/Bias.h
+++ b/src/bias/Bias.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/BiasValue.cpp b/src/bias/BiasValue.cpp
index 1a2b6a4eef7337eb67c418a6d94455b7644510b0..cb96b05f331fea85b8313fdc744c444c1c3328ef 100644
--- a/src/bias/BiasValue.cpp
+++ b/src/bias/BiasValue.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/ExtendedLagrangian.cpp b/src/bias/ExtendedLagrangian.cpp
index a8e08bf780210dfe4dff8262b7fba93950b16f58..52b41ae8c7b2b0c9cab0faccde7edd6e541d3ce8 100644
--- a/src/bias/ExtendedLagrangian.cpp
+++ b/src/bias/ExtendedLagrangian.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index 8610493531cac2d5294917a647f9c589553db03f..d5f98efef9d4a7e458528ec56f361ea56c8411f0 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/LWalls.cpp b/src/bias/LWalls.cpp
index 58dc9db42aa1b7cc516da33b84791734e4ae618a..e7c58bc7f57876b3ed2e995a396f8eb90a66bfa5 100644
--- a/src/bias/LWalls.cpp
+++ b/src/bias/LWalls.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/MaxEnt.cpp b/src/bias/MaxEnt.cpp
index a66794bf08030d94320184c17e1ac5ce294c918f..a4a8908de3073ad61ea32c73b7b444b76e8f008e 100644
--- a/src/bias/MaxEnt.cpp
+++ b/src/bias/MaxEnt.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index 9367a13545b19c6c1b016ca9a98be8de25b8da9b..cc207b2aef1bf951cb953c383c55395f1eac48b7 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -1862,8 +1862,8 @@ void MetaD::computeReweightingFactor()
for(unsigned i=rank; i<ntotgrid; i+=stride) {
t_index[0]=(i%rewf_grid_[0]);
unsigned kk=i;
- for(unsigned j=1; j<ncv-1; ++j) { kk=(kk-t_index[j-1])/rewf_grid_[i-1]; t_index[j]=(kk%rewf_grid_[i]); }
- if( ncv>=2 ) t_index[ncv-1]=((kk-t_index[ncv-1])/rewf_grid_[ncv-2]);
+ for(unsigned j=1; j<ncv-1; ++j) { kk=(kk-t_index[j-1])/rewf_grid_[j-1]; t_index[j]=(kk%rewf_grid_[j]); }
+ if( ncv>=2 ) t_index[ncv-1]=((kk-t_index[ncv-2])/rewf_grid_[ncv-2]);
for(unsigned j=0; j<ncv; ++j) vals[j]=dmin[j] + t_index[j]*grid_spacing[j];
diff --git a/src/bias/MovingRestraint.cpp b/src/bias/MovingRestraint.cpp
index b58ea675b4dfe28757f9706adc77eea28472386d..24305270850c3321655a1cd5a801fc6056a5c60b 100644
--- a/src/bias/MovingRestraint.cpp
+++ b/src/bias/MovingRestraint.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/PBMetaD.cpp b/src/bias/PBMetaD.cpp
index 41bb543412df2d393927238f650703cbad62de41..a77cb42be99de7ca69284d864e907a0987eb6085 100644
--- a/src/bias/PBMetaD.cpp
+++ b/src/bias/PBMetaD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/Restraint.cpp b/src/bias/Restraint.cpp
index a7a97b1096a589b7ed18f034c7c2a79447ae9b1f..207ebbde1acb7548a9c42907c02cb2e1a14a0134 100644
--- a/src/bias/Restraint.cpp
+++ b/src/bias/Restraint.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/ReweightBase.cpp b/src/bias/ReweightBase.cpp
index ea8099ead785836a4a5a74f9cf9de126d1e980db..6ca81e8225532afd2d40ddc3f2a003c215f211f4 100644
--- a/src/bias/ReweightBase.cpp
+++ b/src/bias/ReweightBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/ReweightBase.h b/src/bias/ReweightBase.h
index de172a328514ea81ec858bc5b484f0cbb02d87ba..cb553ff7f88589ac28d2f2a3802762b8eb90b149 100644
--- a/src/bias/ReweightBase.h
+++ b/src/bias/ReweightBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/ReweightBias.cpp b/src/bias/ReweightBias.cpp
index 34cf09ea6a0f1c2bb8553ad2fe14e35c2559327c..9fac4153857616102736f9837848e9824ca7f76b 100644
--- a/src/bias/ReweightBias.cpp
+++ b/src/bias/ReweightBias.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/ReweightMetad.cpp b/src/bias/ReweightMetad.cpp
index 234f4aae24faa9955caf0852196e481fcd3f2ac2..759a4903809e45ba8741bf89ded84340dbcae67d 100644
--- a/src/bias/ReweightMetad.cpp
+++ b/src/bias/ReweightMetad.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/ReweightTemperature.cpp b/src/bias/ReweightTemperature.cpp
index 2450e9d59f8f11564e71061c154dccd02d884b82..db1683a612d2a50ff4c23cdf3c2768d898d3a854 100644
--- a/src/bias/ReweightTemperature.cpp
+++ b/src/bias/ReweightTemperature.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/bias/UWalls.cpp b/src/bias/UWalls.cpp
index 2c867517f20c7feece37442ea447f5b6116cc6be..c866c087ab0d6e5d12de3c28d4ce493d2298eeb5 100644
--- a/src/bias/UWalls.cpp
+++ b/src/bias/UWalls.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/CLTool.cpp b/src/cltools/CLTool.cpp
index 161b5a5d522f48bfa7558ec003669558a5346e79..b75dd0c76d6b6fda68aebf79122fd65d06120898 100644
--- a/src/cltools/CLTool.cpp
+++ b/src/cltools/CLTool.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/CLTool.h b/src/cltools/CLTool.h
index 52d181bc3a5a2dbe416533ac63d47c8af8d132ad..f17873b8062f6fbc24d3e499fea21466dcce0224 100644
--- a/src/cltools/CLTool.h
+++ b/src/cltools/CLTool.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/CLToolRegister.h b/src/cltools/CLToolRegister.h
index efb440659a79bd758563a31f77bfc8ff7077fcc8..2f116969f9cdfee81e6608372df7637fc9bcbb68 100644
--- a/src/cltools/CLToolRegister.h
+++ b/src/cltools/CLToolRegister.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
index fa9149934b26573113fbcd02de1963dce28fba05..5d31302ee0c9aeba323f6b7f2fbe53b4b952e874 100644
--- a/src/cltools/Driver.cpp
+++ b/src/cltools/Driver.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/DriverDouble.cpp b/src/cltools/DriverDouble.cpp
index 073502a4b18cae83b2e57e37947b3d70242c5363..afd50fc28ab2de4d5612a3f1503b85c869f8eda5 100644
--- a/src/cltools/DriverDouble.cpp
+++ b/src/cltools/DriverDouble.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/DriverFloat.cpp b/src/cltools/DriverFloat.cpp
index 299bc537e97b09c30228933ce14a67d5f3d20210..69a3ee59a0ce15edd2eea934b7956f13cc2092aa 100644
--- a/src/cltools/DriverFloat.cpp
+++ b/src/cltools/DriverFloat.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/GenTemplate.cpp b/src/cltools/GenTemplate.cpp
index 28ed043b2a51af8a041b44498a15f6a3d9925630..0b35d2f166fe373820352ff45807398f6f0d9ab1 100644
--- a/src/cltools/GenTemplate.cpp
+++ b/src/cltools/GenTemplate.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/Info.cpp b/src/cltools/Info.cpp
index 0b6fe00784bfd94cfca8525ec04e76a5e25ed70b..404c725ef766b2474906e776dcd04904584dcf87 100644
--- a/src/cltools/Info.cpp
+++ b/src/cltools/Info.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/Manual.cpp b/src/cltools/Manual.cpp
index 9d4b509fef8a1b4b4ff5bb364f84cba7c427201c..38959c59d1bbe26dd58086bcdf404c5edf7c4d51 100644
--- a/src/cltools/Manual.cpp
+++ b/src/cltools/Manual.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/SimpleMD.cpp b/src/cltools/SimpleMD.cpp
index 5cc429f94ec17ea65c77e3823cf9cc2d04b9d0bf..4adcae7f5b45d77acd5fb6861b5e9a5c82393b10 100644
--- a/src/cltools/SimpleMD.cpp
+++ b/src/cltools/SimpleMD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -602,6 +602,9 @@ private:
}
+// call final plumed jobs
+ plumed->cmd("runFinalJobs");
+
// write final positions
write_final_positions(outputfile,natoms,positions,cell,wrapatoms);
diff --git a/src/cltools/SumHills.cpp b/src/cltools/SumHills.cpp
index 03ede3a6b1cd5178287b68501f5f6d9cc89af0a8..1dc00aa06ff13a4682c3af2c2123b673030efb55 100644
--- a/src/cltools/SumHills.cpp
+++ b/src/cltools/SumHills.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/kT.cpp b/src/cltools/kT.cpp
index 358087657f38a2fa701a721821ab98da13e84285..3c88da51d78ee38d5082bcdedc431d2765cac8be 100644
--- a/src/cltools/kT.cpp
+++ b/src/cltools/kT.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/cltools/pesmd.cpp b/src/cltools/pesmd.cpp
index a7bef02b3c413cc8e725fd8841e2a7b965a4a58c..3357002605a6cd7adb947f3ed1082ec23d7d8145 100644
--- a/src/cltools/pesmd.cpp
+++ b/src/cltools/pesmd.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -243,7 +243,7 @@ public:
double lrand=sqrt((1.-lscale*lscale)*temp);
for(unsigned j=0; j<nat; ++j) {
for(unsigned k=0; k<3; ++k) {
- if( 3*j+k>dim ) break;
+ if( 3*j+k>dim-1 ) break;
therm_eng=therm_eng+0.5*velocities[j][k]*velocities[j][k];
velocities[j][k]=lscale*velocities[j][k]+lrand*random.Gaussian();
therm_eng=therm_eng-0.5*velocities[j][k]*velocities[0][k];
@@ -253,7 +253,7 @@ public:
// First step of velocity verlet
for(unsigned j=0; j<nat; ++j) {
for(unsigned k=0; k<3; ++k) {
- if( 3*j+k>dim ) break;
+ if( 3*j+k>dim-1 ) break;
velocities[j][k] = velocities[j][k] + 0.5*tstep*forces[1+j][k];
positions[1+j][k] = positions[1+j][k] + tstep*velocities[j][k];
// Apply pbc
@@ -279,7 +279,7 @@ public:
// Second step of velocity verlet
for(unsigned j=0; j<nat; ++j) {
for(unsigned k=0; k<3; ++k) {
- if( 3*j+k>dim ) break;
+ if( 3*j+k>dim-1 ) break;
velocities[j][k] = velocities[j][k] + 0.5*tstep*forces[1+j][k];
}
}
@@ -289,7 +289,7 @@ public:
lrand=sqrt((1.-lscale*lscale)*temp);
for(unsigned j=0; j<nat; ++j) {
for(unsigned k=0; k<3; ++k) {
- if( 3*j+k>dim ) break;
+ if( 3*j+k>dim-1 ) break;
therm_eng=therm_eng+0.5*velocities[j][k]*velocities[j][k];
velocities[j][k]=lscale*velocities[j][k]+lrand*random.Gaussian();
therm_eng=therm_eng-0.5*velocities[j][k]*velocities[j][k];
@@ -299,7 +299,7 @@ public:
tke=0;
for(unsigned i=0; i<nat; ++i) {
for(unsigned j=0; j<3; ++j) {
- if( 3*i+j>dim ) break;
+ if( 3*i+j>dim-1 ) break;
tke += 0.5*velocities[i][j]*velocities[i][j];
}
}
diff --git a/src/colvar/ActionRegister.h b/src/colvar/ActionRegister.h
index fa3362968912c4c77720c9b1c56484cae199a9ea..5e4b9f96719d310c45731fb5fb0f6fd254ccb648 100644
--- a/src/colvar/ActionRegister.h
+++ b/src/colvar/ActionRegister.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Angle.cpp b/src/colvar/Angle.cpp
index 9403d9c52c5834a63ff642125c1b797d58fbe577..976656560f6b3c420d92a5fa63cee9c0f2878d6a 100644
--- a/src/colvar/Angle.cpp
+++ b/src/colvar/Angle.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Cell.cpp b/src/colvar/Cell.cpp
index 77de19912395fcf2efa01615faab327c1d90aae3..d3b756875394f79f5aa1e28e28e21f0c2b919e77 100644
--- a/src/colvar/Cell.cpp
+++ b/src/colvar/Cell.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Colvar.cpp b/src/colvar/Colvar.cpp
index f68aa3f2d9cd4655dac985822aa0e21a2f9e133e..24febc4dd2155593932b3ff254c9d1a22178a3d9 100644
--- a/src/colvar/Colvar.cpp
+++ b/src/colvar/Colvar.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Colvar.h b/src/colvar/Colvar.h
index 5b0069436245a634125764f82543ec034b6af7fa..b5fb645e530f9dee9b21ac7c08827236c43e756b 100644
--- a/src/colvar/Colvar.h
+++ b/src/colvar/Colvar.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Constant.cpp b/src/colvar/Constant.cpp
index 13164b9b93f0a40e9301391a6edc44a3deb2b7f5..685e0fe6081e1ddc25c9bc4e1a03b645e76ad0eb 100644
--- a/src/colvar/Constant.cpp
+++ b/src/colvar/Constant.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/ContactMap.cpp b/src/colvar/ContactMap.cpp
index 07fda44d747db13541bec406c37585ad9b644d9d..fc23ae36129cc07824e14a5659068bd0e062df06 100644
--- a/src/colvar/ContactMap.cpp
+++ b/src/colvar/ContactMap.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -271,8 +271,8 @@ void ContactMap::calculate() {
Tensor virial;
std::vector<Vector> deriv(getNumberOfAtoms());
- unsigned stride=comm.Get_size();
- unsigned rank=comm.Get_rank();
+ unsigned stride;
+ unsigned rank;
if(serial) {
// when using components the parallelisation do not work
stride=1;
diff --git a/src/colvar/Coordination.cpp b/src/colvar/Coordination.cpp
index 2247c828fe21957bc8ab152c6d21ce5ceb4586e0..bd968a460d76354e6dd237c49e15e5912e134739 100644
--- a/src/colvar/Coordination.cpp
+++ b/src/colvar/Coordination.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/CoordinationBase.cpp b/src/colvar/CoordinationBase.cpp
index 75040505ae7ab4f2f7c666769f4d371f6945a83e..fb1a21bb35cfdaf1aa55f376355f4f8e1e2eb0f6 100644
--- a/src/colvar/CoordinationBase.cpp
+++ b/src/colvar/CoordinationBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -140,8 +140,8 @@ void CoordinationBase::calculate()
nl->update(getPositions());
}
- unsigned stride=comm.Get_size();
- unsigned rank=comm.Get_rank();
+ unsigned stride;
+ unsigned rank;
if(serial) {
stride=1;
rank=0;
diff --git a/src/colvar/CoordinationBase.h b/src/colvar/CoordinationBase.h
index 20653942959cfa0bea2cf0a6105ff6131c972e2d..b816e2de1d6c2d19338dcad51fec14fed1ee5f81 100644
--- a/src/colvar/CoordinationBase.h
+++ b/src/colvar/CoordinationBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/DHEnergy.cpp b/src/colvar/DHEnergy.cpp
index 4d53b195562018a5804ac8ebb8dcc0b53d7c5f7e..da7b6c5c7f1e487e75c3e3e4175e07963086ff7b 100644
--- a/src/colvar/DHEnergy.cpp
+++ b/src/colvar/DHEnergy.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/DRMSD.cpp b/src/colvar/DRMSD.cpp
index 166685df30318082739cf2ea38addd4c546b7875..7495d38e07fd205b1d600730941832f413e555aa 100644
--- a/src/colvar/DRMSD.cpp
+++ b/src/colvar/DRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Dimer.cpp b/src/colvar/Dimer.cpp
index 4cd5d1c075b0a6e0dcd7a115f3c8e45533c8234c..c5ce2ea34b15f3f7e346714b608d0059796ddf84 100644
--- a/src/colvar/Dimer.cpp
+++ b/src/colvar/Dimer.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Dipole.cpp b/src/colvar/Dipole.cpp
index 8f327448bf0c1267e3aec5d1833fd9a03afb35f8..eba428a892049b794d0c1be50c37d5041a215d26 100644
--- a/src/colvar/Dipole.cpp
+++ b/src/colvar/Dipole.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Distance.cpp b/src/colvar/Distance.cpp
index ec6a81c309146a1c109d659b4a65b8efc6e9feb6..9dd0fb6c4813870ed19c6bcf9ca4471f31da5278 100644
--- a/src/colvar/Distance.cpp
+++ b/src/colvar/Distance.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/EEFSolv.cpp b/src/colvar/EEFSolv.cpp
index 2a6ec617648a7e317cb07e62b45469f264a8d945..7666e3bf112025a1baef7b659836b579cf577c22 100644
--- a/src/colvar/EEFSolv.cpp
+++ b/src/colvar/EEFSolv.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/ERMSD.cpp b/src/colvar/ERMSD.cpp
index cdac3cd3306f3c85ca176807598d66321850349d..c8cfe2d5191b2e383c32dd583a797c475d5831be 100644
--- a/src/colvar/ERMSD.cpp
+++ b/src/colvar/ERMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Energy.cpp b/src/colvar/Energy.cpp
index c8007854543c91acfe80a23ede72c74a681f71b8..10e19d5cbe8a0c22ba43b8608e1ad15aff99d483 100644
--- a/src/colvar/Energy.cpp
+++ b/src/colvar/Energy.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Fake.cpp b/src/colvar/Fake.cpp
index 2edfce0d83fafccc5e6b43747b2defdc733665e6..a9ea001f071998531a0b106393c8a558e2f95c27 100644
--- a/src/colvar/Fake.cpp
+++ b/src/colvar/Fake.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Gyration.cpp b/src/colvar/Gyration.cpp
index 8ce4c2be301ebf9b40f15d35d4799dd48f2cc38b..84ef970e86f611ae9c72a013a1b95ffbd3a7f116 100644
--- a/src/colvar/Gyration.cpp
+++ b/src/colvar/Gyration.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/MultiRMSD.cpp b/src/colvar/MultiRMSD.cpp
index 3ff3a21b1ed42e47f1a65a1089aaf5055be66da5..1a45aecd9698ff0542f62599ff03fbc8abc841a4 100644
--- a/src/colvar/MultiRMSD.cpp
+++ b/src/colvar/MultiRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -148,6 +148,28 @@ END
PLUMED_REGISTER_ACTION(MultiRMSD,"MULTI-RMSD")
+//+PLUMEDOC DCOLVAR MULTI_RMSD
+/*
+An alias to the \ref MULTI-RMSD function.
+
+\par Examples
+
+Just replace \ref MULTI-RMSD with \ref MULTI_RMSD
+
+\plumedfile
+MULTI_RMSD REFERENCE=file.pdb TYPE=MULTI-DRMSD
+\endplumedfile
+
+*/
+//+ENDPLUMEDOC
+
+class Multi_RMSD :
+ public MultiRMSD {
+};
+
+PLUMED_REGISTER_ACTION(MultiRMSD,"MULTI_RMSD")
+
+
void MultiRMSD::registerKeywords(Keywords& keys) {
Colvar::registerKeywords(keys);
keys.add("compulsory","REFERENCE","a file in pdb format containing the reference structure and the atoms involved in the CV.");
diff --git a/src/colvar/PCARMSD.cpp b/src/colvar/PCARMSD.cpp
index 74efe902dc1fcb92a59f28cbf8fb20a0ab252457..561464a4185f8cc01a460d5e8af97c5ff6c0af27 100644
--- a/src/colvar/PCARMSD.cpp
+++ b/src/colvar/PCARMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -76,6 +76,7 @@ void PCARMSD::registerKeywords(Keywords& keys) {
keys.addOutputComponent("eig","default","the projections on each eigenvalue are stored on values labeled eig-1, eig-2, ...");
keys.addOutputComponent("residual","default","the distance of the present configuration from the configuration supplied as AVERAGE in terms of MSD after optimal alignment ");
keys.addFlag("SQUARED-ROOT",false," This should be setted if you want RMSD instead of MSD ");
+ keys.addFlag("SQUARED_ROOT",false," Same as SQUARED-ROOT");
}
PCARMSD::PCARMSD(const ActionOptions&ao):
@@ -88,6 +89,7 @@ PCARMSD::PCARMSD(const ActionOptions&ao):
string f_eigenvectors;
parse("EIGENVECTORS",f_eigenvectors);
bool sq; parseFlag("SQUARED-ROOT",sq);
+ if(!sq) parseFlag("SQUARED_ROOT",sq);
if (sq) { squared=false; }
checkRead();
diff --git a/src/colvar/PathMSD.cpp b/src/colvar/PathMSD.cpp
index 9162a5b589a57df00bc93c9f0165268b5294927d..85d8e557986c537e80ab112ebc681c5f10f050ed 100644
--- a/src/colvar/PathMSD.cpp
+++ b/src/colvar/PathMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/PathMSDBase.cpp b/src/colvar/PathMSDBase.cpp
index d7bd006eaf805ba05d1060e498cba667cb51fc2a..de184c3110f634c0c62d6c5561ad21931f25f303 100644
--- a/src/colvar/PathMSDBase.cpp
+++ b/src/colvar/PathMSDBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -44,6 +44,8 @@ void PathMSDBase::registerKeywords(Keywords& keys) {
keys.add("optional", "EPSILON", "(default=-1) the maximum distance between the close and the current structure, the positive value turn on the close structure method");
keys.add("optional", "LOG-CLOSE", "(default=0) value 1 enables logging regarding the close structure");
keys.add("optional", "DEBUG-CLOSE", "(default=0) value 1 enables extensive debugging info regarding the close structure, the simulation will run much slower");
+ keys.add("optional", "LOG_CLOSE", "same as LOG-CLOSE");
+ keys.add("optional", "DEBUG_CLOSE", "same as DEBUG-CLOSE");
}
PathMSDBase::PathMSDBase(const ActionOptions&ao):
@@ -62,7 +64,9 @@ PathMSDBase::PathMSDBase(const ActionOptions&ao):
parse("REFERENCE",reference);
parse("EPSILON", epsilonClose);
parse("LOG-CLOSE", logClose);
+ if(!logClose) parse("LOG_CLOSE", logClose);
parse("DEBUG-CLOSE", debugClose);
+ if(!debugClose) parse("DEBUG_CLOSE",debugClose);
// open the file
FILE* fp=fopen(reference.c_str(),"r");
diff --git a/src/colvar/PathMSDBase.h b/src/colvar/PathMSDBase.h
index 027f17977bfd04a69ada601d9a831a8c34ad6946..4e2a465c65ede199bc293f1ede5205f38ab00e8f 100644
--- a/src/colvar/PathMSDBase.h
+++ b/src/colvar/PathMSDBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Position.cpp b/src/colvar/Position.cpp
index efa757edc57b8f86059d12a139fd24892f0678b3..b06806299d802eea07609044abc38c8b71c88412 100644
--- a/src/colvar/Position.cpp
+++ b/src/colvar/Position.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/PropertyMap.cpp b/src/colvar/PropertyMap.cpp
index 4f222aa85cc4c7304f80f7ee4ad7496d868c61bf..3a4380bd4370d152e6a89ac6b5a476a00a312c84 100644
--- a/src/colvar/PropertyMap.cpp
+++ b/src/colvar/PropertyMap.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Puckering.cpp b/src/colvar/Puckering.cpp
index 13b00856b9e9845f7f6220cba35841c9ae3c2bee..0eb27f0dedd36b53695fd6471ddf5868da4a6919 100644
--- a/src/colvar/Puckering.cpp
+++ b/src/colvar/Puckering.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/RMSD.cpp b/src/colvar/RMSD.cpp
index aad563350325c1f1e98d67ec60110a5efc9375c9..a4f68c00cd4f54a19ea3703af7c025ad9a44f775 100644
--- a/src/colvar/RMSD.cpp
+++ b/src/colvar/RMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Template.cpp b/src/colvar/Template.cpp
index cbb1665343cad16cc80ab540b8f0df6fb27d0a1f..2a3c884b56b4d60ba1115d517975759eadded4fe 100644
--- a/src/colvar/Template.cpp
+++ b/src/colvar/Template.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Torsion.cpp b/src/colvar/Torsion.cpp
index 0d1fed867f533830706685ec168287bb0d95d115..5c9b17a08cfccfc611bad7e139d30b866a2bc49e 100644
--- a/src/colvar/Torsion.cpp
+++ b/src/colvar/Torsion.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/colvar/Volume.cpp b/src/colvar/Volume.cpp
index f4dfb1a2019fa1d54eef1c41f4840b4553328a79..69823edda28258bc44a7b073ede2b89e6e03bf36 100644
--- a/src/colvar/Volume.cpp
+++ b/src/colvar/Volume.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/config/Config.cpp b/src/config/Config.cpp
index cd3bc1597be6eac0f962f684059d54a89f4941e4..253b869f7128967cf220f0594bf203100e45f19c 100644
--- a/src/config/Config.cpp
+++ b/src/config/Config.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/config/Config.h b/src/config/Config.h
index 1f2b94f4b017299e0d877fd1efced590c5638ccb..92786bcfe2a0cddd68fb9b8da16a1ccfb46aca2a 100644
--- a/src/config/Config.h
+++ b/src/config/Config.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/config/Config.inc.in b/src/config/Config.inc.in
index a4bc8a6dfe5e53acb3dcb75140085df145b7e015..f75ba84aa3660c200af51513d45cf8350b508ea6 100644
--- a/src/config/Config.inc.in
+++ b/src/config/Config.inc.in
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/config/ConfigInstall.cpp b/src/config/ConfigInstall.cpp
index d1d0915bde98ecddee985203a6ab3561986447c4..d71f74b8de236f596a9094071971e5276f1dc0bb 100644
--- a/src/config/ConfigInstall.cpp
+++ b/src/config/ConfigInstall.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/Action.cpp b/src/core/Action.cpp
index 6f7fff33a055826dfa5d5b09f9f017f10ecf0949..d55c7addc36d8ec988916cd3b60558e8eb32d0ef 100644
--- a/src/core/Action.cpp
+++ b/src/core/Action.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/Action.h b/src/core/Action.h
index ad0e42e9a1166d3d4bf8fa843bb1ed143795b6b0..efd2136ef0872e6ac43ad2067a3e86018ebf5ff7 100644
--- a/src/core/Action.h
+++ b/src/core/Action.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionAtomistic.cpp b/src/core/ActionAtomistic.cpp
index a848da3538764a2814a4d831b78f0935616e7761..ac3b35813626e65a5012091d563bd3a42dee6ca7 100644
--- a/src/core/ActionAtomistic.cpp
+++ b/src/core/ActionAtomistic.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionAtomistic.h b/src/core/ActionAtomistic.h
index 5fe38dc2dfc4c474b687c1260ebe0dcde1249ec5..905b0efec48ba0a89fd0d5e087e188cf04498df9 100644
--- a/src/core/ActionAtomistic.h
+++ b/src/core/ActionAtomistic.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionPilot.cpp b/src/core/ActionPilot.cpp
index 58ad723d86cc04d652e7a88dfa7e14d869916fac..01bf786005b9d7390e6502f20e7370e61d2bfc1f 100644
--- a/src/core/ActionPilot.cpp
+++ b/src/core/ActionPilot.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionPilot.h b/src/core/ActionPilot.h
index e1f70192344f1efe22fe514104e4ccb47b1cd0d8..ea9420ac7fc754f3edcd4ba13600d8a3b93262f9 100644
--- a/src/core/ActionPilot.h
+++ b/src/core/ActionPilot.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionRegister.cpp b/src/core/ActionRegister.cpp
index 732e9e9bc7ba60a763667d8c8a6f6b53f36fa01b..c3999211f88356be6361dee0e6bdb6022116359b 100644
--- a/src/core/ActionRegister.cpp
+++ b/src/core/ActionRegister.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionRegister.h b/src/core/ActionRegister.h
index 8fb35565cb949f4123e93013a78f262e2b95397d..891b88056db6382ededfa2a7aa71d99ef017c41a 100644
--- a/src/core/ActionRegister.h
+++ b/src/core/ActionRegister.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionSet.cpp b/src/core/ActionSet.cpp
index da711c95d70b0fc7b9d0ce33033aa5313c79cf85..e7ac6e347fed93ef77189b060a0ff94eef2a9394 100644
--- a/src/core/ActionSet.cpp
+++ b/src/core/ActionSet.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -40,23 +40,4 @@ void ActionSet::clearDelete() {
}
-std::string ActionSet::getLabelList() const {
- std::string outlist;
- for(const auto & p : (*this)) {
- outlist+=dynamic_cast<Action*>(p)->getLabel()+" ";
- };
- return outlist;
-}
-
-std::vector<std::string> ActionSet::getLabelVector() const {
- std::vector<std::string> outlist;
- for(const auto & p : (*this)) {
- outlist.push_back(dynamic_cast<Action*>(p)->getLabel());
- };
- return outlist;
-}
-
-
-
-
}
diff --git a/src/core/ActionSet.h b/src/core/ActionSet.h
index 3d5ea6fc7805f3203e49736733aee4e5a93c55d1..0c15dedda78648788052bfef23d7dd21de3e4887 100644
--- a/src/core/ActionSet.h
+++ b/src/core/ActionSet.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -61,8 +61,12 @@ public:
template <class T>
T selectWithLabel(const std::string&s)const;
/// get the labels in the list of actions in form of a string (useful to debug)
+/// Only classes that can be dynamic casted to T are reported
+ template <class T>
std::string getLabelList() const;
/// get the labels in the form of a vector of strings
+/// Only classes that can be dynamic casted to T are reported
+ template <class T>
std::vector<std::string> getLabelVector() const;
};
@@ -98,6 +102,27 @@ std::vector<Action*> ActionSet::selectNot()const {
return ret;
}
+template <class T>
+std::string ActionSet::getLabelList() const {
+ std::string outlist;
+ for(const auto & p : (*this)) {
+ if(dynamic_cast<T>(p)) outlist+=p->getLabel()+" ";
+ };
+ return outlist;
+}
+
+
+template <class T>
+std::vector<std::string> ActionSet::getLabelVector() const {
+ std::vector<std::string> outlist;
+ for(const auto & p : (*this)) {
+ if(dynamic_cast<T>(p)) outlist.push_back(p->getLabel());
+ };
+ return outlist;
+}
+
+
+
}
#endif
diff --git a/src/core/ActionSetup.cpp b/src/core/ActionSetup.cpp
index a15290ff2d89d7524960a4f7a920b40640471b16..3d621102604d63e22ab83539b23ab362f27703b0 100644
--- a/src/core/ActionSetup.cpp
+++ b/src/core/ActionSetup.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionSetup.h b/src/core/ActionSetup.h
index a2fbb241d208366630ba1c78e6975a973558d1b7..42ef01b10ad5b558ed5ee63cfc2c1e66edcea499 100644
--- a/src/core/ActionSetup.h
+++ b/src/core/ActionSetup.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionWithArguments.cpp b/src/core/ActionWithArguments.cpp
index 5865375d89d95c2b9f9ef1daec91595926ff7478..ac0623dc103823e428570f01de2bfc8ea50d2c56 100644
--- a/src/core/ActionWithArguments.cpp
+++ b/src/core/ActionWithArguments.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -148,8 +148,8 @@ void ActionWithArguments::interpretArgumentList(const std::vector<std::string>&
// Take all the values from an action with a specific name
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(a);
if(!action) {
- std::string str=" (hint! the actions in this ActionSet are: ";
- str+=plumed.getActionSet().getLabelList()+")";
+ std::string str=" (hint! the actions with value in this ActionSet are: ";
+ str+=plumed.getActionSet().getLabelList<ActionWithValue*>()+")";
error("cannot find action named " + a + str);
}
if( action->getNumberOfComponents()==0 ) error("found " + a +".* indicating use all components calculated by action with label " + a + " but this action has no components");
@@ -168,8 +168,8 @@ void ActionWithArguments::interpretArgumentList(const std::vector<std::string>&
// Take values with a specific name
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(a);
if(!action) {
- std::string str=" (hint! the actions in this ActionSet are: ";
- str+=plumed.getActionSet().getLabelList()+")";
+ std::string str=" (hint! the actions with value in this ActionSet are: ";
+ str+=plumed.getActionSet().getLabelList<ActionWithValue*>()+")";
error("cannot find action named " + a +str);
}
if( !(action->exists(c[i])) ) {
@@ -190,8 +190,8 @@ void ActionWithArguments::interpretArgumentList(const std::vector<std::string>&
} else {
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(c[i]);
if(!action) {
- std::string str=" (hint! the actions in this ActionSet are: ";
- str+=plumed.getActionSet().getLabelList()+")";
+ std::string str=" (hint! the actions with value in this ActionSet are: ";
+ str+=plumed.getActionSet().getLabelList<ActionWithValue*>()+")";
error("cannot find action named " + c[i] + str );
}
if( !(action->exists(c[i])) ) {
diff --git a/src/core/ActionWithArguments.h b/src/core/ActionWithArguments.h
index 8784c05ff5aa8ce8674c45d0d718e92e2b940902..40b816cddf380287c39990e8244a8296d0a9a4a4 100644
--- a/src/core/ActionWithArguments.h
+++ b/src/core/ActionWithArguments.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionWithValue.cpp b/src/core/ActionWithValue.cpp
index 3106b8f699d73cd6c063b7eb0e70bdf22d8007bd..285f4ac622090e6d0209905833144803706ed535 100644
--- a/src/core/ActionWithValue.cpp
+++ b/src/core/ActionWithValue.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionWithValue.h b/src/core/ActionWithValue.h
index 765378a64690027b6f493f0e3b67acfd211304a4..68d0006602a34b1627d3cc81b5faf63ce4f93606 100644
--- a/src/core/ActionWithValue.h
+++ b/src/core/ActionWithValue.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionWithVirtualAtom.cpp b/src/core/ActionWithVirtualAtom.cpp
index 1073b46e653174ece1797551053ee4a7018ae616..a8a1732ad2b7b6c2cb63586567f6c8f38e90455e 100644
--- a/src/core/ActionWithVirtualAtom.cpp
+++ b/src/core/ActionWithVirtualAtom.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ActionWithVirtualAtom.h b/src/core/ActionWithVirtualAtom.h
index dad85fddac9b750a0bf0981965225d46719789f5..973ea0b1826704bbf7e07c0308933a257954370e 100644
--- a/src/core/ActionWithVirtualAtom.h
+++ b/src/core/ActionWithVirtualAtom.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/Atoms.cpp b/src/core/Atoms.cpp
index ce1caa17648fe42590bc209d6454631fea89099c..b7b0d57db78e415d2595447a32d6a6f0d6121935 100644
--- a/src/core/Atoms.cpp
+++ b/src/core/Atoms.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/Atoms.h b/src/core/Atoms.h
index 7312a7d37b683003cf9af00b4defe687c62e9919..17dca03263fa2fc8a637ba298d25e0c308b0fd0e 100644
--- a/src/core/Atoms.h
+++ b/src/core/Atoms.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/CLTool.cpp b/src/core/CLTool.cpp
index fd4222f34bb47a09bff85c36d8f2fdf2607dd772..c029e42dfa290a17d39f841eac2bf252de4a1f88 100644
--- a/src/core/CLTool.cpp
+++ b/src/core/CLTool.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/CLTool.h b/src/core/CLTool.h
index 9fd6374cedb6fec23baf85d03ade96de9c825ae1..d05d60352c1bffaf925859e766f32cb71d629d29 100644
--- a/src/core/CLTool.h
+++ b/src/core/CLTool.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/CLToolMain.cpp b/src/core/CLToolMain.cpp
index 2c1d25f8a0eb113cb64e0e9065d2a531059bda5f..f91d057dd2fdff56985620dc04c68e966e967487 100644
--- a/src/core/CLToolMain.cpp
+++ b/src/core/CLToolMain.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/CLToolMain.h b/src/core/CLToolMain.h
index 19f89f79ac631c963452147a178619a21c67c0a4..8a8378b28c962a5a049407fb13817d7fd8bd4d19 100644
--- a/src/core/CLToolMain.h
+++ b/src/core/CLToolMain.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/CLToolRegister.cpp b/src/core/CLToolRegister.cpp
index 77873797bd5f8225d9c051f2b1ff323d176296ea..d0f3cbfd4cd6ecc2cc1be1a546d1fc38ebb7b6f6 100644
--- a/src/core/CLToolRegister.cpp
+++ b/src/core/CLToolRegister.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/CLToolRegister.h b/src/core/CLToolRegister.h
index ae4a9b66c222666bce2a2d333dc18aab4100b32b..d1adcfa5082b9e361a3059e7101697e4c8ea4b1a 100644
--- a/src/core/CLToolRegister.h
+++ b/src/core/CLToolRegister.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/Colvar.cpp b/src/core/Colvar.cpp
index d04592e67a69e33abf94af1fbce50a8328ef79f5..797cc9397b9168e03ee9402800939f017b973d47 100644
--- a/src/core/Colvar.cpp
+++ b/src/core/Colvar.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/Colvar.h b/src/core/Colvar.h
index 914f1bbfceaa022cf48fa10c4674e91bdd2bcefb..5aef9873d4f44938af3a68b4840b0f4026c22254 100644
--- a/src/core/Colvar.h
+++ b/src/core/Colvar.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ExchangePatterns.cpp b/src/core/ExchangePatterns.cpp
index a5e4d7ab35d02dbd9da6b61433f43c2708c9e221..859311d29be0b61fe1df59b7ef7571ad6c2742d5 100644
--- a/src/core/ExchangePatterns.cpp
+++ b/src/core/ExchangePatterns.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/ExchangePatterns.h b/src/core/ExchangePatterns.h
index 8dc6302e1b3175b9a22c9083dda570c92f89fa2f..6379472eb7c6aa958bd0018135fe8c5a902463ff 100644
--- a/src/core/ExchangePatterns.h
+++ b/src/core/ExchangePatterns.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/FlexibleBin.cpp b/src/core/FlexibleBin.cpp
index 19fe135a0e02b4a6d2f8b480f0f76682e83e7eae..c2f83313c310bf8598ed2697c5b7b700c1abe755 100644
--- a/src/core/FlexibleBin.cpp
+++ b/src/core/FlexibleBin.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/FlexibleBin.h b/src/core/FlexibleBin.h
index 216849560eb3c91b014252ec2d66a4a3124b6781..19a4a0314e7d26e011a2da7bdf189e1203462394 100644
--- a/src/core/FlexibleBin.h
+++ b/src/core/FlexibleBin.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/GREX.cpp b/src/core/GREX.cpp
index 775320410ba05a578abc455a2cfd32c75c81b5ea..4e254f72357370ee015aff21539fd234fad18fe9 100644
--- a/src/core/GREX.cpp
+++ b/src/core/GREX.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/GREX.h b/src/core/GREX.h
index e386fb6d8584f45edd33fcb761b4ec53927fbcb1..ba818c9473141f284684bb4311465a4a9b87dfac 100644
--- a/src/core/GREX.h
+++ b/src/core/GREX.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/MDAtoms.cpp b/src/core/MDAtoms.cpp
index 3e88f50e3ec72bc442ce4477be810790f934da75..8782677b2910bbcffccdbe6fcd4f854cdf84b586 100644
--- a/src/core/MDAtoms.cpp
+++ b/src/core/MDAtoms.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/MDAtoms.h b/src/core/MDAtoms.h
index 2e6a55072697fa06d8b5ef06249fa3e3b6d7ad2c..e74554144af892f1a14866759cae37e890025c9f 100644
--- a/src/core/MDAtoms.h
+++ b/src/core/MDAtoms.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index c13ff34b1ba97cbcb45490f53d00683894b134e5..31ccfa7bf4f5a8c4a167fc0fef242742123a2108 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/PlumedMain.h b/src/core/PlumedMain.h
index 06425a5f7e6ef132141924401d0d9d428a3b2358..72ca280e6bafdeaa8ec8c2273c5f690e0254dec4 100644
--- a/src/core/PlumedMain.h
+++ b/src/core/PlumedMain.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/PlumedMainInitializer.cpp b/src/core/PlumedMainInitializer.cpp
index a3f4892b590d61b4a5aa29d1347622c8a32d36ba..6e3b8704dbbefa15949b285bb09c0ee66fe8e408 100644
--- a/src/core/PlumedMainInitializer.cpp
+++ b/src/core/PlumedMainInitializer.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/SetupMolInfo.cpp b/src/core/SetupMolInfo.cpp
index 0b58600e6414603809ce352106af361c894cc0f7..8ad049113d4d363a9c1344466fdd049732b3acc7 100644
--- a/src/core/SetupMolInfo.cpp
+++ b/src/core/SetupMolInfo.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/SetupMolInfo.h b/src/core/SetupMolInfo.h
index b434c5e46f2c15442c88d64c560172e1096fb331..9a3206d53f1e442ed5d9c77ec6b45a97eab064b5 100644
--- a/src/core/SetupMolInfo.h
+++ b/src/core/SetupMolInfo.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/TargetDist.cpp b/src/core/TargetDist.cpp
index 57ce577a02e4c0f723ff82206cc4facb6827c686..25aa5ce133877dc5df9907c5c7f856be6db8983f 100644
--- a/src/core/TargetDist.cpp
+++ b/src/core/TargetDist.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/TargetDist.h b/src/core/TargetDist.h
index c60d24a036d826fc9ede6d25d2f5e1b9c37817c2..2c92a105f083c926caca6f7e60c788d1635c4f9c 100644
--- a/src/core/TargetDist.h
+++ b/src/core/TargetDist.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/Value.cpp b/src/core/Value.cpp
index 806187247be6d091e275d3b86df794667369a810..0c6f426aa25d11f2480ad276d04943a6932db6ff 100644
--- a/src/core/Value.cpp
+++ b/src/core/Value.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/Value.h b/src/core/Value.h
index 158d3519d1ac5a72a373e2e56d426d64b47114b3..6a1e5b2f24dd9f7edf301a76f4e05806d05548ae 100644
--- a/src/core/Value.h
+++ b/src/core/Value.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/WithCmd.cpp b/src/core/WithCmd.cpp
index d8762643e58bb3f01ff0fc4181ea40cbcc0e3431..b92ba559a8fafb864ddb59adb5e3854018d740f5 100644
--- a/src/core/WithCmd.cpp
+++ b/src/core/WithCmd.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/core/WithCmd.h b/src/core/WithCmd.h
index d60805887aae816af1571ece44add9b7670bba0a..61e2f12fa954856dd78b64493cc51523003a8ac9 100644
--- a/src/core/WithCmd.h
+++ b/src/core/WithCmd.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/BondOrientation.cpp b/src/crystallization/BondOrientation.cpp
index 4c822dadeab8974512a999126dc287a366f58de9..49fec36fc19e80b736561a16b3caa7d4f8d4d302 100644
--- a/src/crystallization/BondOrientation.cpp
+++ b/src/crystallization/BondOrientation.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/CubicHarmonicBase.cpp b/src/crystallization/CubicHarmonicBase.cpp
index 38f326598a52aaf765d5e80a4e2ef4dd9663cb41..4001fec3c6e41bf862abf8e87f2e5657f0fc501c 100644
--- a/src/crystallization/CubicHarmonicBase.cpp
+++ b/src/crystallization/CubicHarmonicBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/CubicHarmonicBase.h b/src/crystallization/CubicHarmonicBase.h
index 72d87f5f9d64ab2dac8d53ebf214abde5f4a387e..60ca73b47ee21b940900577cfae7b98fbdc79c26 100644
--- a/src/crystallization/CubicHarmonicBase.h
+++ b/src/crystallization/CubicHarmonicBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/Fccubic.cpp b/src/crystallization/Fccubic.cpp
index 80f9cb19e476c69a41b6ec39a26b58e4a6acb01f..e887ba2290436d8cc3de5ec2f8e3cf194a198924 100644
--- a/src/crystallization/Fccubic.cpp
+++ b/src/crystallization/Fccubic.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/Gradient.cpp b/src/crystallization/Gradient.cpp
index e59b78908da0b53723961dfe4afca0ce1042a186..a2feb733c58fa4290457e8b3c23574bc3aa3af67 100644
--- a/src/crystallization/Gradient.cpp
+++ b/src/crystallization/Gradient.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/Gradient.h b/src/crystallization/Gradient.h
index d4bec24746df206954667e4e50c44af82b1e8809..11039484b635bdf7922a6add3b6a55ff16ac7896 100644
--- a/src/crystallization/Gradient.h
+++ b/src/crystallization/Gradient.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/GradientVessel.cpp b/src/crystallization/GradientVessel.cpp
index 32827665e19b971672e38c8fb812dabcf86fb50f..0fb69e8a00e4cb236e548104f6d5534379cf60b0 100644
--- a/src/crystallization/GradientVessel.cpp
+++ b/src/crystallization/GradientVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/InterMolecularTorsions.cpp b/src/crystallization/InterMolecularTorsions.cpp
index ff2fff1754b3ff4750b05f1989d53cce90bf6a45..07370a0d1345361b54ec07ef38008598c48a27a1 100644
--- a/src/crystallization/InterMolecularTorsions.cpp
+++ b/src/crystallization/InterMolecularTorsions.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/LocalSteinhardt.cpp b/src/crystallization/LocalSteinhardt.cpp
index 26ee18a95436b583c01202484093127e372c061d..d45daa20d0dfb667189af1612bc2c8fb6d8987ba 100644
--- a/src/crystallization/LocalSteinhardt.cpp
+++ b/src/crystallization/LocalSteinhardt.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/LocalSteinhardt.h b/src/crystallization/LocalSteinhardt.h
index e7b03a889c7f5b5ebcc1af32afe19fc63fa5aec2..2aeb76b62b5f7295a08b2265a0248dabb756820b 100644
--- a/src/crystallization/LocalSteinhardt.h
+++ b/src/crystallization/LocalSteinhardt.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/MoleculeOrientation.cpp b/src/crystallization/MoleculeOrientation.cpp
index 4b573e9f6553c9ee3405380ead449a2607f866b5..8112b9a563691bac74212a38b6a939aa1ccbafeb 100644
--- a/src/crystallization/MoleculeOrientation.cpp
+++ b/src/crystallization/MoleculeOrientation.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/MoleculePlane.cpp b/src/crystallization/MoleculePlane.cpp
index 1376d77107de962fb77b4d153160d3d8bdd1f9bf..aea8b6a9bb89994904c3e39fafe83e2dead589ac 100644
--- a/src/crystallization/MoleculePlane.cpp
+++ b/src/crystallization/MoleculePlane.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/OrientationSphere.cpp b/src/crystallization/OrientationSphere.cpp
index e1af69d80529f1918a4b23539b59f197e46dc8a0..7035b3926551cbcee5a857e304d74adfbf9891fb 100644
--- a/src/crystallization/OrientationSphere.cpp
+++ b/src/crystallization/OrientationSphere.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/OrientationSphere.h b/src/crystallization/OrientationSphere.h
index aee464ca394b72da6df79b5923efbf7b89edf463..a920766387ef82e2de4dca7ed91c1cb91404e77b 100644
--- a/src/crystallization/OrientationSphere.h
+++ b/src/crystallization/OrientationSphere.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/PolymerAngles.cpp b/src/crystallization/PolymerAngles.cpp
index 15ef06f494e4e3437811dbf0a0ba057cb1134849..6361fb45b0c3d258f6122178e55ae11a79b87077 100644
--- a/src/crystallization/PolymerAngles.cpp
+++ b/src/crystallization/PolymerAngles.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/Q3.cpp b/src/crystallization/Q3.cpp
index e9deaddd559a0e17066f312a422438e0f596bdf7..61a8ffa42542f10ea208c5c34b217409bab0d5bc 100644
--- a/src/crystallization/Q3.cpp
+++ b/src/crystallization/Q3.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/Q4.cpp b/src/crystallization/Q4.cpp
index 3f453a3250ddee3dedc7d27e23f6c3b69fe6ee8b..90f08c5efbf65233ad0f5af7acb70eadc4da0a35 100644
--- a/src/crystallization/Q4.cpp
+++ b/src/crystallization/Q4.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/Q6.cpp b/src/crystallization/Q6.cpp
index 431f67ed05b406de5bbf13323fa046cc8977a8c8..bd5f48592f613e60ddb25caf367b7cefe2e99955 100644
--- a/src/crystallization/Q6.cpp
+++ b/src/crystallization/Q6.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/SMAC.cpp b/src/crystallization/SMAC.cpp
index d76c0322df143c9c10d0a810f73144193ddce50f..c5e3d79f54ff47743bd3407cf16b1206a9458ad8 100644
--- a/src/crystallization/SMAC.cpp
+++ b/src/crystallization/SMAC.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/SimpleCubic.cpp b/src/crystallization/SimpleCubic.cpp
index e573472965c68fba270ec49c8203e499a642b3f0..484c00e7be4704d48a3a1fc76fc0e07362fa101e 100644
--- a/src/crystallization/SimpleCubic.cpp
+++ b/src/crystallization/SimpleCubic.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/Steinhardt.cpp b/src/crystallization/Steinhardt.cpp
index 30c31b671428978bce4ca10761ae609bdc5644bd..62ef68f11045298f1a3148bcb3fd1aa790e44a91 100644
--- a/src/crystallization/Steinhardt.cpp
+++ b/src/crystallization/Steinhardt.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/Steinhardt.h b/src/crystallization/Steinhardt.h
index b7d021dd606306fc70485eb91f4a6aef252f6ad6..dd2efe94d4eede03cb1948d252669be1d637f973 100644
--- a/src/crystallization/Steinhardt.h
+++ b/src/crystallization/Steinhardt.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/Tetrahedral.cpp b/src/crystallization/Tetrahedral.cpp
index 3deac51d399985c0ae9bd80d6b466b4ab7b2c027..53f5fe5056a2f5a902c14637b0b9170d9f88c5cb 100644
--- a/src/crystallization/Tetrahedral.cpp
+++ b/src/crystallization/Tetrahedral.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/VectorMean.cpp b/src/crystallization/VectorMean.cpp
index b151dbd8f475477739f49d2c19a74c144d9eba19..d769c5a223c2bdb5a2c5414777f325f3dd1a6507 100644
--- a/src/crystallization/VectorMean.cpp
+++ b/src/crystallization/VectorMean.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/VectorMultiColvar.cpp b/src/crystallization/VectorMultiColvar.cpp
index 7bb57762e59de1c9a897c1f10298f96dc681a916..e4dc5e98a6a47e2616f7c3cae139bc01f7fcd170 100644
--- a/src/crystallization/VectorMultiColvar.cpp
+++ b/src/crystallization/VectorMultiColvar.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/VectorMultiColvar.h b/src/crystallization/VectorMultiColvar.h
index 7c9e00b956e740e2bdd4a6c04b14b0ee81d34086..614e897feaf8469a68fd24612fc7d3930ec4cd71 100644
--- a/src/crystallization/VectorMultiColvar.h
+++ b/src/crystallization/VectorMultiColvar.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/crystallization/VectorSum.cpp b/src/crystallization/VectorSum.cpp
index 15c99a895b327c7e58ae6bc8e53f5054f8b1fabd..20af8936351cb07073e96c2b2efc771a9231d948 100644
--- a/src/crystallization/VectorSum.cpp
+++ b/src/crystallization/VectorSum.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/ActionRegister.h b/src/function/ActionRegister.h
index d7872a4fac35c087a901a3c0a74c224b23128579..1d08ac735ec57dd63f10d6807903242e02ea4542 100644
--- a/src/function/ActionRegister.h
+++ b/src/function/ActionRegister.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/Combine.cpp b/src/function/Combine.cpp
index 97e2bdf51ceae3e1a3e9c73d37d2da40f10de582..51d2268564df94ceb77dc7dfd26faa57dfda611d 100644
--- a/src/function/Combine.cpp
+++ b/src/function/Combine.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/Ensemble.cpp b/src/function/Ensemble.cpp
index f5ef0800128ddb649ac2050ec44efeea79203d88..90a41e0dd973da7200df7d693ae8217bba7c758c 100644
--- a/src/function/Ensemble.cpp
+++ b/src/function/Ensemble.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/FuncPathMSD.cpp b/src/function/FuncPathMSD.cpp
index d765f00822daca4e45c9b81518c3a590fb1e8533..f214dcb44a8734ec4bc98bc8119f826c45821709 100644
--- a/src/function/FuncPathMSD.cpp
+++ b/src/function/FuncPathMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/FuncSumHills.cpp b/src/function/FuncSumHills.cpp
index 99e34bd5fa7fae0d7ea3bfd35b4f99c3c10b7933..ba4cb167c605eff33d8b6fa004bdf04714f67e7a 100644
--- a/src/function/FuncSumHills.cpp
+++ b/src/function/FuncSumHills.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/Function.cpp b/src/function/Function.cpp
index f965b2ad9266d4c11bff18631ed8c3ffe13b2596..33fab335edc5844c4c9f7c6c7e30c865dedffd20 100644
--- a/src/function/Function.cpp
+++ b/src/function/Function.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/Function.h b/src/function/Function.h
index 593b074168fe1bc9f1e1496e47c0a4ea8664f761..9c513bca1f2d32d97c1bd827708d17b9f2950302 100644
--- a/src/function/Function.h
+++ b/src/function/Function.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/LocalEnsemble.cpp b/src/function/LocalEnsemble.cpp
index 6470f29c24cfeb18eba53bfcabf7d7cebe9a58a3..1c680a965db4c7ae1cba4468da1b69eb168d596d 100644
--- a/src/function/LocalEnsemble.cpp
+++ b/src/function/LocalEnsemble.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/Matheval.cpp b/src/function/Matheval.cpp
index cf1ce84b10787b1cd1a5470b1b62b9e03270e1cb..4db00f6986b78953600ff964f7e7ece19aa5d259 100644
--- a/src/function/Matheval.cpp
+++ b/src/function/Matheval.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/Piecewise.cpp b/src/function/Piecewise.cpp
index a98b94b80c0bc141a768427fbdeeb90e56e4e86b..3702ce6e233d0c59ee6b53a3da63350592a4f828 100644
--- a/src/function/Piecewise.cpp
+++ b/src/function/Piecewise.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/Sort.cpp b/src/function/Sort.cpp
index 108f453a9cbbbf4cb0e83105b3f93f07defe9251..24d90a8b8721538587df354e89701b7b7cdfb389 100644
--- a/src/function/Sort.cpp
+++ b/src/function/Sort.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/Stats.cpp b/src/function/Stats.cpp
index 49825ddfe761c08ef78ae1b4da546b93711a56f1..26101a302bd248d02261317cd434568543d1d1d5 100644
--- a/src/function/Stats.cpp
+++ b/src/function/Stats.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/function/Target.cpp b/src/function/Target.cpp
index fbd728319fbe412a687be840ef5f1306b5fb8c9c..ce19f2b52df8be4dc8f48666520c7583bf1c34e8 100644
--- a/src/function/Target.cpp
+++ b/src/function/Target.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/Debug.cpp b/src/generic/Debug.cpp
index d2856a10ab8b223f8888e6fca5c3b825fbc8512d..b18928d0877c7cb7a8cb6b6f2409f8ed2c551688 100644
--- a/src/generic/Debug.cpp
+++ b/src/generic/Debug.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/DumpAtoms.cpp b/src/generic/DumpAtoms.cpp
index bda4dc57624efbcd890b801b61e8cc6968e0624c..2fc58f1c6f2f69dcb24e58701d90ae8408daed8b 100644
--- a/src/generic/DumpAtoms.cpp
+++ b/src/generic/DumpAtoms.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/DumpDerivatives.cpp b/src/generic/DumpDerivatives.cpp
index 9c82729af90cee3d5010bebac722b91a8a28d758..153f76f601daf6999cfb6ccb76ec57e41e99141c 100644
--- a/src/generic/DumpDerivatives.cpp
+++ b/src/generic/DumpDerivatives.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/DumpForces.cpp b/src/generic/DumpForces.cpp
index a7202353bf6bce0a5acfec577a2cb81cab965360..33ec80b8033e0ee969e1f541c1a179ec201fe910 100644
--- a/src/generic/DumpForces.cpp
+++ b/src/generic/DumpForces.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/DumpMassCharge.cpp b/src/generic/DumpMassCharge.cpp
index 8aaa462aa50f79730258f4ba4501127dde7a3127..8a923d093c1654ce1401fba6311512725ef92def 100644
--- a/src/generic/DumpMassCharge.cpp
+++ b/src/generic/DumpMassCharge.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/DumpProjections.cpp b/src/generic/DumpProjections.cpp
index 3e4926fd39af5f2cb10b27ac96a0335e41970ebf..46275a120d6bcb2ff0eabbb1d01ad43a7a35733d 100644
--- a/src/generic/DumpProjections.cpp
+++ b/src/generic/DumpProjections.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/EffectiveEnergyDrift.cpp b/src/generic/EffectiveEnergyDrift.cpp
index f4185c0fc638f2603c5ef5637f6f2e176e95dc11..750a2f824e935f6d1e6e9c160168461c2d82c62b 100644
--- a/src/generic/EffectiveEnergyDrift.cpp
+++ b/src/generic/EffectiveEnergyDrift.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -222,8 +222,6 @@ void EffectiveEnergyDrift::update() {
pNLocalAtoms = pGatindex.size();
pPositions=positions;
pForces=forces;
- pPositions=positions;
- pForces=forces;
pbox=box;
pfbox=fbox;
initialBias=plumed.getBias();
diff --git a/src/generic/EndPlumed.cpp b/src/generic/EndPlumed.cpp
index be2a4c53bff396959b93e4d47b77d78332d55dab..71ad70cf50d462fbffdd4b54c2c57e8f37ef929c 100644
--- a/src/generic/EndPlumed.cpp
+++ b/src/generic/EndPlumed.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/FitToTemplate.cpp b/src/generic/FitToTemplate.cpp
index 7598e632d2b7f51a979ea5ab814a3a927c26865d..f2d94f37fd2c4518ce771fa41e0ce1794be9aab5 100644
--- a/src/generic/FitToTemplate.cpp
+++ b/src/generic/FitToTemplate.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/Flush.cpp b/src/generic/Flush.cpp
index 1a2460cf11d1e56d693f7343d02a9cb3ffb43bb5..6a6a8f5036a7dd0d3a647236185e3669fd35c208 100644
--- a/src/generic/Flush.cpp
+++ b/src/generic/Flush.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/Group.cpp b/src/generic/Group.cpp
index e540acfb2e50702e2db271faa1b0af56f14ed999..26b56a9c1b7fed99cc1ff3bb9e54e8f7e37fbd75 100644
--- a/src/generic/Group.cpp
+++ b/src/generic/Group.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/Include.cpp b/src/generic/Include.cpp
index 46c7b96920d3f27a0d3ef8543067d1730c155e85..e26354c3a97c8a471c9b5374b7ddaa8546b0f3eb 100644
--- a/src/generic/Include.cpp
+++ b/src/generic/Include.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/Print.cpp b/src/generic/Print.cpp
index babf1239d05e79af87176d56b2c67e12cf9fe32d..4cdaf39b5a5a52e7e7c69ded2ac6aa12614fc4bc 100644
--- a/src/generic/Print.cpp
+++ b/src/generic/Print.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/RandomExchanges.cpp b/src/generic/RandomExchanges.cpp
index 71a449a8f29b9a3119f7038dd6ba2e04d07d22bb..3d7e6a6f4ea431ca0b0b6b1e1c6a9529c46f80ae 100644
--- a/src/generic/RandomExchanges.cpp
+++ b/src/generic/RandomExchanges.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/Read.cpp b/src/generic/Read.cpp
index f158464dd9220a1c79f63f130a05ae2791cdb4c8..82ff12dcfbb9547b4780c659f242263834fcc9ce 100644
--- a/src/generic/Read.cpp
+++ b/src/generic/Read.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/ResetCell.cpp b/src/generic/ResetCell.cpp
index 40caea04b4d22f3c18812e7f3c707791832f128e..dc98ccb85c30da8c054d539e02e5aa8f872fb36e 100644
--- a/src/generic/ResetCell.cpp
+++ b/src/generic/ResetCell.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/Time.cpp b/src/generic/Time.cpp
index 309d10359746e2d292387e0f447f3f96f2479446..d7fd630672e8346e4acff64217562f4757530686 100644
--- a/src/generic/Time.cpp
+++ b/src/generic/Time.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/UpdateIf.cpp b/src/generic/UpdateIf.cpp
index 758f75bc55414ff83b87149cb05928355ff2c719..acd44f61123e468f81402f1e9d798e0d37e4c2e6 100644
--- a/src/generic/UpdateIf.cpp
+++ b/src/generic/UpdateIf.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/WholeMolecules.cpp b/src/generic/WholeMolecules.cpp
index 4fee06bb3bddacbf08d6752d0a88c1a472fa7f3a..b9da8935a2ebd77d59f5c5e79f4c62c6a073944a 100644
--- a/src/generic/WholeMolecules.cpp
+++ b/src/generic/WholeMolecules.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/generic/WrapAround.cpp b/src/generic/WrapAround.cpp
index 9b8712a086e7daf3614e7e4333414df1dff3e689..8d927cded511fd636992552a7392553d5d214848 100644
--- a/src/generic/WrapAround.cpp
+++ b/src/generic/WrapAround.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/ActionWithGrid.cpp b/src/gridtools/ActionWithGrid.cpp
index 44d51dbcb1e9bdd87d84ca518518d5b0c96ec4a8..56ac87d4897cd4978127c7e9cf4fbf337d1c6202 100644
--- a/src/gridtools/ActionWithGrid.cpp
+++ b/src/gridtools/ActionWithGrid.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/ActionWithGrid.h b/src/gridtools/ActionWithGrid.h
index 86e676a5963b1da180efc80ce5a339c18a2553b4..70926ff7a6652c53490556e87f9a5a42150e60b4 100644
--- a/src/gridtools/ActionWithGrid.h
+++ b/src/gridtools/ActionWithGrid.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/ActionWithInputGrid.cpp b/src/gridtools/ActionWithInputGrid.cpp
index 8a46e72937e1d3d79df1806308a973581468ee31..41ea5c3db2d36cf3ff0f31e155c2c8a12123417c 100644
--- a/src/gridtools/ActionWithInputGrid.cpp
+++ b/src/gridtools/ActionWithInputGrid.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/ActionWithInputGrid.h b/src/gridtools/ActionWithInputGrid.h
index f0cf496d00865c6b796c10eb4c738d33d88eac92..bf595a58f5f066cddaaded25d880151f67a4917b 100644
--- a/src/gridtools/ActionWithInputGrid.h
+++ b/src/gridtools/ActionWithInputGrid.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/ActionWithIntegral.cpp b/src/gridtools/ActionWithIntegral.cpp
index 85e1a11ffd3e71eaa629ef108d27d0519ac6e0f6..340a2511abf6028fa426570279dddfe374225c44 100644
--- a/src/gridtools/ActionWithIntegral.cpp
+++ b/src/gridtools/ActionWithIntegral.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/ActionWithIntegral.h b/src/gridtools/ActionWithIntegral.h
index 775a8c3e82ddb65e0eeceec4a6ea753a56c2edb9..d666ea4c1707e0d67f1c70ccd631fd224d31b027 100644
--- a/src/gridtools/ActionWithIntegral.h
+++ b/src/gridtools/ActionWithIntegral.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/AverageOnGrid.cpp b/src/gridtools/AverageOnGrid.cpp
index 7a993ca78f691ee1dec9799fe552ada50d8609d9..03980f88eba31704e6f08913475ca80847eedd96 100644
--- a/src/gridtools/AverageOnGrid.cpp
+++ b/src/gridtools/AverageOnGrid.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/AverageOnGrid.h b/src/gridtools/AverageOnGrid.h
index 76ce44e0ceea2bf6f7d8f7536e455a20a40c2e3a..16b1154a581078a880257cd5e1c26af603814d63 100644
--- a/src/gridtools/AverageOnGrid.h
+++ b/src/gridtools/AverageOnGrid.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/ContourFindingBase.cpp b/src/gridtools/ContourFindingBase.cpp
index 011e2ba5f81062339a3bf50fbebf87d712fc12c6..d9a752f3be161f3507e571c285ce0ba06fafa1cb 100644
--- a/src/gridtools/ContourFindingBase.cpp
+++ b/src/gridtools/ContourFindingBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/ContourFindingBase.h b/src/gridtools/ContourFindingBase.h
index 8b82b7689779e2e02d96966b758ac07c8dba747f..4309cd87d12b874f11160c6ed848bf4506159c22 100644
--- a/src/gridtools/ContourFindingBase.h
+++ b/src/gridtools/ContourFindingBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/ConvertToFES.cpp b/src/gridtools/ConvertToFES.cpp
index 989e5e4f0c9bc3f94ac2dac10ed1aadf88360e8a..eb027a76197a2ed5e68847e278dbddfa74231634 100644
--- a/src/gridtools/ConvertToFES.cpp
+++ b/src/gridtools/ConvertToFES.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/DumpCube.cpp b/src/gridtools/DumpCube.cpp
index 7238f043556755275d5de64a5c2a49a7b0fff11b..fe1f0eb984be9caa8bda982f7c0f60ec47b9ba28 100644
--- a/src/gridtools/DumpCube.cpp
+++ b/src/gridtools/DumpCube.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/DumpGrid.cpp b/src/gridtools/DumpGrid.cpp
index 60924878cf271f96b1a85a97b2198bec07977ca5..8054950ad00471cba921f8f494026409c86d3d30 100644
--- a/src/gridtools/DumpGrid.cpp
+++ b/src/gridtools/DumpGrid.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/FindContour.cpp b/src/gridtools/FindContour.cpp
index e11ed7e4a06b422e2389fb6e0bbe095c61eb148d..89a4e52112f11ed8ae8e28477ab71725418e5a1b 100644
--- a/src/gridtools/FindContour.cpp
+++ b/src/gridtools/FindContour.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/FindContourSurface.cpp b/src/gridtools/FindContourSurface.cpp
index 2d7524a728d91902e1e67f8ab49b3b0574c9dac0..fba19e0b785e7fb6eded6bdbbbc7c8975f81dda9 100644
--- a/src/gridtools/FindContourSurface.cpp
+++ b/src/gridtools/FindContourSurface.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/FindSphericalContour.cpp b/src/gridtools/FindSphericalContour.cpp
index 72e256b98b13367c14b9a410b43a4ca588658aa5..ad7480805d1acd9238191d0f0204a11f6bdb397a 100644
--- a/src/gridtools/FindSphericalContour.cpp
+++ b/src/gridtools/FindSphericalContour.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/FourierTransform.cpp b/src/gridtools/FourierTransform.cpp
index 05f4d9724efc8d0ba5f411f09d9ff72f879e642b..f5222528c80279b6d86ace7b93a99cd30344f39f 100644
--- a/src/gridtools/FourierTransform.cpp
+++ b/src/gridtools/FourierTransform.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/GridPrintingBase.cpp b/src/gridtools/GridPrintingBase.cpp
index 82521b5a169f96703c6999528f7647ac1801f696..81960444a9a2969b04f68988caf5ce05be383c63 100644
--- a/src/gridtools/GridPrintingBase.cpp
+++ b/src/gridtools/GridPrintingBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/GridPrintingBase.h b/src/gridtools/GridPrintingBase.h
index 2b97194c44840ec4b0f5814bc7c5608d781223db..4c6dedd21cc2d0af0af7ae08e969f6710c4ab4c6 100644
--- a/src/gridtools/GridPrintingBase.h
+++ b/src/gridtools/GridPrintingBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/GridToXYZ.cpp b/src/gridtools/GridToXYZ.cpp
index fd22d2a88f651dac39c5a6cebc7d81eaff43d9bd..6715fe514586beaced21799df4134f20492f4f8e 100644
--- a/src/gridtools/GridToXYZ.cpp
+++ b/src/gridtools/GridToXYZ.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -97,7 +97,8 @@ void GridToXYZ::printGrid( OFile& ofile ) const {
ofile.printf("Grid converted to xyz file \n");
for(unsigned i=0; i<ingrid->getNumberOfPoints(); ++i) {
ingrid->getGridPointCoordinates( i, point );
- ofile.printf("X"); double val=ingrid->getGridElement( i, 0 );
+ ofile.printf("X");
+ double val;
if( ingrid->getType()=="flat" ) val=1.0;
else val=ingrid->getGridElement( i, 0 );
for(unsigned j=0; j<3; ++j) { ofile.printf( (" " + fmt).c_str(), val*lenunit*point[j] ); }
diff --git a/src/gridtools/GridVessel.cpp b/src/gridtools/GridVessel.cpp
index 3bacfa1b8980c38b7b1463014fd38073b2bfa633..e83b371d6e6af5f03b39712f714ca927a36af950 100644
--- a/src/gridtools/GridVessel.cpp
+++ b/src/gridtools/GridVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/GridVessel.h b/src/gridtools/GridVessel.h
index c0e0cb5d22eaef3a7d4e950d46432a34f1a59b9c..71d2a020c3b29ed96009720ca9d84bd47df8403e 100644
--- a/src/gridtools/GridVessel.h
+++ b/src/gridtools/GridVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/HistogramOnGrid.cpp b/src/gridtools/HistogramOnGrid.cpp
index 3e9a04a92aa813671b6c4d5fdc9e803dcc7b3d24..0eade88ca14da496f5f2a5064ed87c972f61e404 100644
--- a/src/gridtools/HistogramOnGrid.cpp
+++ b/src/gridtools/HistogramOnGrid.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/HistogramOnGrid.h b/src/gridtools/HistogramOnGrid.h
index 1684c2200f4767e27597a3b2997f3532cc77c1e3..ff52897fc660bfc070dcd152e75a531c2468ef0f 100644
--- a/src/gridtools/HistogramOnGrid.h
+++ b/src/gridtools/HistogramOnGrid.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/IntegrateGrid.cpp b/src/gridtools/IntegrateGrid.cpp
index d6a86ef4525aa4df3f1fdc550696c34a2f353011..43580bf2a2fcfff69da166469db1f8bb158ecbec 100644
--- a/src/gridtools/IntegrateGrid.cpp
+++ b/src/gridtools/IntegrateGrid.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/gridtools/InterpolateGrid.cpp b/src/gridtools/InterpolateGrid.cpp
index fc1d98c1dd4047bae7422f31503c7931893108f6..a1c3c340be3d42f96f69221b5df8b951b2235745 100644
--- a/src/gridtools/InterpolateGrid.cpp
+++ b/src/gridtools/InterpolateGrid.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/CS2Backbone.cpp b/src/isdb/CS2Backbone.cpp
index 4b82fc760d27c5e44687749f2dd50813be4599e4..fd7fb019205bfcc374d704b348cb327b173c96c6 100644
--- a/src/isdb/CS2Backbone.cpp
+++ b/src/isdb/CS2Backbone.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/EMMI.cpp b/src/isdb/EMMI.cpp
index 1ccf5b4826bbc385d790145adb1900cd99249ede..00ec876fa9a5411d881cdb1531072619f10e310a 100644
--- a/src/isdb/EMMI.cpp
+++ b/src/isdb/EMMI.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/FretEfficiency.cpp b/src/isdb/FretEfficiency.cpp
index 0950e01e9f731c06a6141a55f6459f9f1d777812..43fd30e59081d5066143462b81523018cb405b7d 100644
--- a/src/isdb/FretEfficiency.cpp
+++ b/src/isdb/FretEfficiency.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/Jcoupling.cpp b/src/isdb/Jcoupling.cpp
index 1666abc1351144ef0175495ec26708307f1dbf71..3228747937bd50c1fbb4ae6703e6cc3e18282e7b 100644
--- a/src/isdb/Jcoupling.cpp
+++ b/src/isdb/Jcoupling.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/Metainference.cpp b/src/isdb/Metainference.cpp
index da31be589cf803bee8f26c48e1f3e49c186e9f74..c4e22a4927d5ae3e7b44d9a8586e0058a38e4996 100644
--- a/src/isdb/Metainference.cpp
+++ b/src/isdb/Metainference.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/MetainferenceBase.cpp b/src/isdb/MetainferenceBase.cpp
index 42dd24e3aea513a0e77601e71b8362314ef025a4..4746d89f44829731772123188e51186fb21ccfa5 100644
--- a/src/isdb/MetainferenceBase.cpp
+++ b/src/isdb/MetainferenceBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/MetainferenceBase.h b/src/isdb/MetainferenceBase.h
index b5b651d292186fcc5f657f64adcb98b7855575f1..07d071ffb0b202de6fc1abc4be01c1729e2f4dba 100644
--- a/src/isdb/MetainferenceBase.h
+++ b/src/isdb/MetainferenceBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/NOE.cpp b/src/isdb/NOE.cpp
index 8c7d64916db021f91a1331dd9b5519e5504a072d..7e698a022804457010e8471671d7a2f9bcc2855e 100644
--- a/src/isdb/NOE.cpp
+++ b/src/isdb/NOE.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/PRE.cpp b/src/isdb/PRE.cpp
index 4afb203d3f928424ccb2cd90a0275a438e4a3448..d1fbc0d1b42f5736dcd71edb57132fd7e8e48d8a 100644
--- a/src/isdb/PRE.cpp
+++ b/src/isdb/PRE.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/RDC.cpp b/src/isdb/RDC.cpp
index 735a4a675ebea4f63ec23619fba5bd8f655946c6..049fb3a6e3b981a2396eedbcaa84b9cf71d90830 100644
--- a/src/isdb/RDC.cpp
+++ b/src/isdb/RDC.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -407,6 +407,7 @@ void RDC::do_svd()
}
gsl_matrix_free(coef_mat);
gsl_matrix_free(A);
+ gsl_matrix_free(V);
gsl_vector_free(rdc_vec);
gsl_vector_free(bc);
gsl_vector_free(Stmp);
diff --git a/src/isdb/Rescale.cpp b/src/isdb/Rescale.cpp
index 5c7a0c361ce9785b6cb909e43263287362c986ed..38828686e9c8e84d8c43f9904d54c0ac818e5fa8 100644
--- a/src/isdb/Rescale.cpp
+++ b/src/isdb/Rescale.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/SAXS.cpp b/src/isdb/SAXS.cpp
index 7afd67ac4f0a16e56d64d1566946f7b731f8028e..785a34a2a9472fa98b9ad12106c40403a44fc1f1 100644
--- a/src/isdb/SAXS.cpp
+++ b/src/isdb/SAXS.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/Select.cpp b/src/isdb/Select.cpp
index 7decf3112cb681b72fb41dc6236cdcafa3956b3a..4ec39dba664bc65e7454fcc6b9cae436f250ddac 100644
--- a/src/isdb/Select.cpp
+++ b/src/isdb/Select.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/isdb/Selector.cpp b/src/isdb/Selector.cpp
index 5b0287540f2c19b9fc31f113b391e3d220968472..8676463b62d334f2e11d596ac6620d5735ee8390 100644
--- a/src/isdb/Selector.cpp
+++ b/src/isdb/Selector.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/main/main.cpp b/src/main/main.cpp
index c5a79f81fbb87e76fbcbddd35e4231e3fece3941..233786931d1009487c1f6a6641336234658a30e4 100644
--- a/src/main/main.cpp
+++ b/src/main/main.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/manyrestraints/LWalls.cpp b/src/manyrestraints/LWalls.cpp
index f560c24e76b484cb54454e1ae14d5328bfc43399..1a5819607266af90c12d7a91f94da6e539849915 100644
--- a/src/manyrestraints/LWalls.cpp
+++ b/src/manyrestraints/LWalls.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/manyrestraints/ManyRestraintsBase.cpp b/src/manyrestraints/ManyRestraintsBase.cpp
index a85fc6db0cfe3aae3eb923fdb6b925766d4ffce4..1ea5e647857c5e665edfe18f1e6b0f89daf57884 100644
--- a/src/manyrestraints/ManyRestraintsBase.cpp
+++ b/src/manyrestraints/ManyRestraintsBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/manyrestraints/ManyRestraintsBase.h b/src/manyrestraints/ManyRestraintsBase.h
index c01a2223321cdacc6e201c313526c1a9850065f9..e39599f5e2388e5758d5f28aace7791f191aafbc 100644
--- a/src/manyrestraints/ManyRestraintsBase.h
+++ b/src/manyrestraints/ManyRestraintsBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/manyrestraints/UWalls.cpp b/src/manyrestraints/UWalls.cpp
index 5776d94a90ab28ea382c653fa87dae59ecf61ae2..299b3094274968d60c7e411fc7ede493f2344925 100644
--- a/src/manyrestraints/UWalls.cpp
+++ b/src/manyrestraints/UWalls.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/AdaptivePath.cpp b/src/mapping/AdaptivePath.cpp
index 1f4d710c80d524fa504856e1b123a5f966d30057..f1f85c404987ce0abc1b07df7601492589f7a0d9 100644
--- a/src/mapping/AdaptivePath.cpp
+++ b/src/mapping/AdaptivePath.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/Mapping.cpp b/src/mapping/Mapping.cpp
index 5e73d6d10ad8f55a942d6691bf0e4572f9205606..3f845c7ed3785def725f4a639ce8a7f2c75088d6 100644
--- a/src/mapping/Mapping.cpp
+++ b/src/mapping/Mapping.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/Mapping.h b/src/mapping/Mapping.h
index 42037a354b6299fa74cb7c2d12c5abdb48eeaee1..07454866cd7a54c240ca39efde089d9f8381ee2c 100644
--- a/src/mapping/Mapping.h
+++ b/src/mapping/Mapping.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/PCAVars.cpp b/src/mapping/PCAVars.cpp
index 762089c367a04a60e2da66333d5839e829163f49..e99f78c8f59b940c940bf4df8a573fece9c3377b 100644
--- a/src/mapping/PCAVars.cpp
+++ b/src/mapping/PCAVars.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/Path.cpp b/src/mapping/Path.cpp
index 8f81d4a07b501a8ecdb0dca01bdab473b8fac372..cc7b0469f07dc385340de338d582cf280eea60e4 100644
--- a/src/mapping/Path.cpp
+++ b/src/mapping/Path.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/PathBase.cpp b/src/mapping/PathBase.cpp
index 34833884ffb1bd410ffd7de21089928ad4a2384c..35f64d7c5c7229ccb2c2723ed0de59a07ca2f37c 100644
--- a/src/mapping/PathBase.cpp
+++ b/src/mapping/PathBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/PathBase.h b/src/mapping/PathBase.h
index 8b78534d9973709f6e75ddcff4f0d80c80e382bb..e2109b7805b3f63edb5633d9e82238b82df26622 100644
--- a/src/mapping/PathBase.h
+++ b/src/mapping/PathBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/PathReparameterization.cpp b/src/mapping/PathReparameterization.cpp
index 4eb343815b0821a9050f0d37af5e56f1aa41e518..14b1c9c5185c413d21feac45eea5093af1949b13 100644
--- a/src/mapping/PathReparameterization.cpp
+++ b/src/mapping/PathReparameterization.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/PathReparameterization.h b/src/mapping/PathReparameterization.h
index 5ad8d46feba4a80e8451008977ec69653be34fc6..c80366fa885cac6bf8ea1673e2097f48f019dd80 100644
--- a/src/mapping/PathReparameterization.h
+++ b/src/mapping/PathReparameterization.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/PathTools.cpp b/src/mapping/PathTools.cpp
index 69a450ab3a8b4c7ac4a7b0009b59e5a22646c9ba..3e0b40428766a41e8965a7a01641f0319e0831bf 100644
--- a/src/mapping/PathTools.cpp
+++ b/src/mapping/PathTools.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/PropertyMap.cpp b/src/mapping/PropertyMap.cpp
index 751d78edc2224b5effeafc1a00260fcba759379d..6bb66a931585910fdf6c3a20117a8ae4332b45bf 100644
--- a/src/mapping/PropertyMap.cpp
+++ b/src/mapping/PropertyMap.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/SpathVessel.cpp b/src/mapping/SpathVessel.cpp
index 9805b36d91a2791273188d3ac8a081c4fae2556d..67e61b292740eca04b6a8c8d71f0981491d40205 100644
--- a/src/mapping/SpathVessel.cpp
+++ b/src/mapping/SpathVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/TrigonometricPathVessel.cpp b/src/mapping/TrigonometricPathVessel.cpp
index 3ba8f8088ba072da1c5e1f0e8be36301024c6da2..7faf13cc388ec0c4eded228deb1e0901080487a0 100644
--- a/src/mapping/TrigonometricPathVessel.cpp
+++ b/src/mapping/TrigonometricPathVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/TrigonometricPathVessel.h b/src/mapping/TrigonometricPathVessel.h
index f6cd4c8c68ed8b916d52c05ddfab29f0b27adee1..a2e7ef69105b522466891b1a1ea73cc2a58db5d4 100644
--- a/src/mapping/TrigonometricPathVessel.h
+++ b/src/mapping/TrigonometricPathVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/mapping/ZpathVessel.cpp b/src/mapping/ZpathVessel.cpp
index 31460ac44842bf34bfde76c081c7dd6cf3721eb1..28b2d867652c2ec41734808f223088d2ec15e9b5 100644
--- a/src/mapping/ZpathVessel.cpp
+++ b/src/mapping/ZpathVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/ActionVolume.cpp b/src/multicolvar/ActionVolume.cpp
index 3b3ed947e002ebdcb64b3d6efd7a6d442b7235b2..cc06ffa5fe35e3a0c22c4e64bc4546367165f8d2 100644
--- a/src/multicolvar/ActionVolume.cpp
+++ b/src/multicolvar/ActionVolume.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/ActionVolume.h b/src/multicolvar/ActionVolume.h
index 733ab1e2d19de6d2f11c6afca6b7980a40b92b24..a8f86cc8d0680e1e77f9c0d2ae71e8ec8bc250ce 100644
--- a/src/multicolvar/ActionVolume.h
+++ b/src/multicolvar/ActionVolume.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/AlphaBeta.cpp b/src/multicolvar/AlphaBeta.cpp
index af82f68a4b160e30e840011f085e6f88d9418246..e72f7ff765928c6b299be9be06ef99df2d3060e7 100644
--- a/src/multicolvar/AlphaBeta.cpp
+++ b/src/multicolvar/AlphaBeta.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/Angles.cpp b/src/multicolvar/Angles.cpp
index 7aedd6cda46602d2d6990dab990e1fc4286b14a6..99c55a5ef9fa7e07099c293c001991cc700315d4 100644
--- a/src/multicolvar/Angles.cpp
+++ b/src/multicolvar/Angles.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/AtomValuePack.cpp b/src/multicolvar/AtomValuePack.cpp
index 7579c432c307f4f9353cc09fdc88d61e854be735..c274d8cef8c867e1b36850fbcb80b5330d6b345d 100644
--- a/src/multicolvar/AtomValuePack.cpp
+++ b/src/multicolvar/AtomValuePack.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/AtomValuePack.h b/src/multicolvar/AtomValuePack.h
index 2257df558f9318c91186563fa4638445e3eb059d..fab70f3f1cb93a0a253568d815b2bd10f28da5ae 100644
--- a/src/multicolvar/AtomValuePack.h
+++ b/src/multicolvar/AtomValuePack.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/Bridge.cpp b/src/multicolvar/Bridge.cpp
index f3fdae0777b19780f4944497587ee84b1dbc6306..44b7d509fc532d9fac08d43dd49e15fe3af005ce 100644
--- a/src/multicolvar/Bridge.cpp
+++ b/src/multicolvar/Bridge.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/BridgedMultiColvarFunction.cpp b/src/multicolvar/BridgedMultiColvarFunction.cpp
index a952fa85c7985c561b5e86c54213c0c85ca5bd9e..606f7482752ae4fb99b53b4de33d113dfe522426 100644
--- a/src/multicolvar/BridgedMultiColvarFunction.cpp
+++ b/src/multicolvar/BridgedMultiColvarFunction.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/BridgedMultiColvarFunction.h b/src/multicolvar/BridgedMultiColvarFunction.h
index 8ab8354adce8603811de182b361160b38daa03e7..25b33f78292a95edb371715e1a6f8cad6753fa1b 100644
--- a/src/multicolvar/BridgedMultiColvarFunction.h
+++ b/src/multicolvar/BridgedMultiColvarFunction.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/CatomPack.cpp b/src/multicolvar/CatomPack.cpp
index 8dc43888fc44cd32e05a9b188cc09ea07b591829..2eb98d32be35cccc948618a7239dcfa080302ae6 100644
--- a/src/multicolvar/CatomPack.cpp
+++ b/src/multicolvar/CatomPack.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/CatomPack.h b/src/multicolvar/CatomPack.h
index 96021ad073ab901125733df74aa5065b8e60dba6..0eff7d11b7a20628db312d073d29de961687647d 100644
--- a/src/multicolvar/CatomPack.h
+++ b/src/multicolvar/CatomPack.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/CenterOfMultiColvar.cpp b/src/multicolvar/CenterOfMultiColvar.cpp
index 1cd66672b95c02f1e14384a361f8506826b48ab6..3c7cd65f13f02656e833d89eedeaa67190ec107b 100644
--- a/src/multicolvar/CenterOfMultiColvar.cpp
+++ b/src/multicolvar/CenterOfMultiColvar.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/CoordinationNumbers.cpp b/src/multicolvar/CoordinationNumbers.cpp
index 0d4d3649fd96bb4cf9e23f935a14601419686ec5..3995a6f4f020650e9d8586537b6e0af9a2acd2b9 100644
--- a/src/multicolvar/CoordinationNumbers.cpp
+++ b/src/multicolvar/CoordinationNumbers.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -170,8 +170,8 @@ double CoordinationNumbers::compute( const unsigned& tindex, AtomValuePack& myat
if(r_power > 0) {
d = sqrt(d2); raised = pow( d, r_power - 1 );
accumulateSymmetryFunction( 1, i, sw * raised * d,
- (dfunc * d * raised + sw * r_power) * distance,
- (-dfunc * d * raised - sw * r_power) * Tensor(distance, distance),
+ (dfunc * d * raised + sw * r_power * raised / d) * distance,
+ (-dfunc * d * raised - sw * r_power * raised / d) * Tensor(distance, distance),
myatoms );
} else {
accumulateSymmetryFunction( 1, i, sw, (dfunc)*distance, (-dfunc)*Tensor(distance,distance), myatoms );
diff --git a/src/multicolvar/Density.cpp b/src/multicolvar/Density.cpp
index 5a8a14d754d17bea41dc3b29c42b2992afcecaac..8b7e527376ae153d19db00c55181e3ee3aa6c41a 100644
--- a/src/multicolvar/Density.cpp
+++ b/src/multicolvar/Density.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/DihedralCorrelation.cpp b/src/multicolvar/DihedralCorrelation.cpp
index ba9094f3de445b98c66fb1af9b101bec80f5c4c3..629d91451a2d978bdfb199c4516b7a510041b35c 100644
--- a/src/multicolvar/DihedralCorrelation.cpp
+++ b/src/multicolvar/DihedralCorrelation.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/DistanceFromContour.cpp b/src/multicolvar/DistanceFromContour.cpp
index 6e4ce6161cdfd288ab2873cb8fe92b6075877b1c..de44580141a878251b31599e46b71c1438b9c9c2 100644
--- a/src/multicolvar/DistanceFromContour.cpp
+++ b/src/multicolvar/DistanceFromContour.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/Distances.cpp b/src/multicolvar/Distances.cpp
index 99b95061deff58358d7e2b86d052479a1f182feb..392c2d5f2b200ecf9dbdfc89e60bc047b062edba 100644
--- a/src/multicolvar/Distances.cpp
+++ b/src/multicolvar/Distances.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/DumpMultiColvar.cpp b/src/multicolvar/DumpMultiColvar.cpp
index fb6f53344d5270b49e4597437799cf002e4b2e45..045cdf628bb6b27da3467400d583d6f5b1e2afce 100644
--- a/src/multicolvar/DumpMultiColvar.cpp
+++ b/src/multicolvar/DumpMultiColvar.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/FilterBetween.cpp b/src/multicolvar/FilterBetween.cpp
index 20f42a1cf60cc78e76efec07dec968d9fefe33cd..b526c756acae1c7069325b06d266ed3c386bcf25 100644
--- a/src/multicolvar/FilterBetween.cpp
+++ b/src/multicolvar/FilterBetween.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/FilterLessThan.cpp b/src/multicolvar/FilterLessThan.cpp
index 23a9603d561dad2f97c39da7dc352499e444b7df..8e4341c42cf92aa736b01ee0776ca01ac2cf4b52 100644
--- a/src/multicolvar/FilterLessThan.cpp
+++ b/src/multicolvar/FilterLessThan.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/FilterMoreThan.cpp b/src/multicolvar/FilterMoreThan.cpp
index bfca0d218af8932852ba90929b7618f0576634dc..52120769cd55829560ca6ce00a5029d47adf259a 100644
--- a/src/multicolvar/FilterMoreThan.cpp
+++ b/src/multicolvar/FilterMoreThan.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/InPlaneDistances.cpp b/src/multicolvar/InPlaneDistances.cpp
index a1fc79cdb8d03165a6b0b42de7452ec148c26524..423c72719fde75d48044acbf5bfc4c5d80ae9928 100644
--- a/src/multicolvar/InPlaneDistances.cpp
+++ b/src/multicolvar/InPlaneDistances.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/LocalAverage.cpp b/src/multicolvar/LocalAverage.cpp
index bbcf17ba4bc1f48c1e45a929c94cb326e35dac25..206893244d3fa3cf04de5b6d185e4cb293127d61 100644
--- a/src/multicolvar/LocalAverage.cpp
+++ b/src/multicolvar/LocalAverage.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/MultiColvarBase.cpp b/src/multicolvar/MultiColvarBase.cpp
index b926997cac8a15550fc892b096966379eedb97d9..2ea9426f7ebb1dbaafb7a1181efcc35ab39f977b 100644
--- a/src/multicolvar/MultiColvarBase.cpp
+++ b/src/multicolvar/MultiColvarBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/MultiColvarBase.h b/src/multicolvar/MultiColvarBase.h
index bbae961767730833e46cd3e7fc434de5624315ab..b24191932179be49d4db6b5b6450b6fc405990b1 100644
--- a/src/multicolvar/MultiColvarBase.h
+++ b/src/multicolvar/MultiColvarBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/MultiColvarCombine.cpp b/src/multicolvar/MultiColvarCombine.cpp
index c947268f3ce3f45b453aa1b8ce2f5dd0580b7d98..607ed6437375c489aa26d62447ea4f96c55c152e 100644
--- a/src/multicolvar/MultiColvarCombine.cpp
+++ b/src/multicolvar/MultiColvarCombine.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -56,7 +56,7 @@ void MultiColvarCombine::registerKeywords( Keywords& keys ) {
MultiColvarBase::registerKeywords( keys );
keys.add("compulsory","DATA","the multicolvars you are calculating linear combinations for");
keys.add("compulsory","COEFFICIENTS","1.0","the coeficients to use for the various multicolvars");
- keys.use("MEAN"); keys.use("MORE_THAN"); keys.use("SUM"); keys.use("LESS_THAN"); keys.use("HISTOGRAM"); keys.use("HISTOGRAM");
+ keys.use("MEAN"); keys.use("MORE_THAN"); keys.use("SUM"); keys.use("LESS_THAN"); keys.use("HISTOGRAM");
keys.use("MIN"); keys.use("MAX"); keys.use("LOWEST"); keys.use("HIGHEST"); keys.use("ALT_MIN"); keys.use("BETWEEN"); keys.use("MOMENTS");
}
diff --git a/src/multicolvar/MultiColvarDensity.cpp b/src/multicolvar/MultiColvarDensity.cpp
index b2941aa577f021368f599934cbdbeb36d31fe01e..a71ace110411f5e533270ad23cf80ed02523a298 100644
--- a/src/multicolvar/MultiColvarDensity.cpp
+++ b/src/multicolvar/MultiColvarDensity.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/MultiColvarFilter.cpp b/src/multicolvar/MultiColvarFilter.cpp
index 45f33efff5d002cd6a9efe6e6cea50590f27265d..61a978728fe97f1f44c22e84c065782ed7e1e5ce 100644
--- a/src/multicolvar/MultiColvarFilter.cpp
+++ b/src/multicolvar/MultiColvarFilter.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/MultiColvarFilter.h b/src/multicolvar/MultiColvarFilter.h
index 1daecc18ac2949f24810163c192734e12f17b1b9..eb4c1372dc0fa5719019755fb1f7fcd388050b2d 100644
--- a/src/multicolvar/MultiColvarFilter.h
+++ b/src/multicolvar/MultiColvarFilter.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/MultiColvarProduct.cpp b/src/multicolvar/MultiColvarProduct.cpp
index ee2b2e7f036be74d4031acf7398f4d75a6173c75..32748fed6bb5c7db33f92a7c7856826161f2896e 100644
--- a/src/multicolvar/MultiColvarProduct.cpp
+++ b/src/multicolvar/MultiColvarProduct.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -54,7 +54,7 @@ PLUMED_REGISTER_ACTION(MultiColvarProduct,"MCOLV_PRODUCT")
void MultiColvarProduct::registerKeywords( Keywords& keys ) {
MultiColvarBase::registerKeywords( keys );
keys.add("compulsory","DATA","the multicolvars you are calculating the product of");
- keys.use("MEAN"); keys.use("MORE_THAN"); keys.use("SUM"); keys.use("LESS_THAN"); keys.use("HISTOGRAM"); keys.use("HISTOGRAM");
+ keys.use("MEAN"); keys.use("MORE_THAN"); keys.use("SUM"); keys.use("LESS_THAN"); keys.use("HISTOGRAM");
keys.use("MIN"); keys.use("MAX"); keys.use("LOWEST"); keys.use("HIGHEST"); keys.use("ALT_MIN"); keys.use("BETWEEN"); keys.use("MOMENTS");
}
diff --git a/src/multicolvar/NumberOfLinks.cpp b/src/multicolvar/NumberOfLinks.cpp
index 3b930b0e269b0560f0ef2bf98f909bd739180c36..0b657af8bd827142436fd8dac213e97133b69123 100644
--- a/src/multicolvar/NumberOfLinks.cpp
+++ b/src/multicolvar/NumberOfLinks.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/Torsions.cpp b/src/multicolvar/Torsions.cpp
index 8d490962ae613ab3d2d05b74850bd9ff4cc5b022..5bc7ee0832016e037b255a4433c9d588760aa181 100644
--- a/src/multicolvar/Torsions.cpp
+++ b/src/multicolvar/Torsions.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/VolumeAround.cpp b/src/multicolvar/VolumeAround.cpp
index 4d9b54f8901ee7f169dd35742500387f927bafb1..06bd7632f5258c345e492276ce9afd7a529619f9 100644
--- a/src/multicolvar/VolumeAround.cpp
+++ b/src/multicolvar/VolumeAround.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/VolumeBetweenContours.cpp b/src/multicolvar/VolumeBetweenContours.cpp
index 5b53a36b9d969a8ceae29c7a0988c2f4a3b49087..b9b56368a838ef2ef6c103b35edb2adf1cbee92e 100644
--- a/src/multicolvar/VolumeBetweenContours.cpp
+++ b/src/multicolvar/VolumeBetweenContours.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2017,2018 The plumed team
+ Copyright (c) 2017-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/VolumeCavity.cpp b/src/multicolvar/VolumeCavity.cpp
index 44215c605c1f6ecf6b8156f4d3b4a269c92388cf..5823d50d0b1e103f68eb443f15f7dd6ca793ad48 100644
--- a/src/multicolvar/VolumeCavity.cpp
+++ b/src/multicolvar/VolumeCavity.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/VolumeGradientBase.cpp b/src/multicolvar/VolumeGradientBase.cpp
index 37e45cf8841d0f3c1fb55e7346646dd9030f146e..bb0841e65605e3a53f0684671dc9b3292190e202 100644
--- a/src/multicolvar/VolumeGradientBase.cpp
+++ b/src/multicolvar/VolumeGradientBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/VolumeGradientBase.h b/src/multicolvar/VolumeGradientBase.h
index bc3cf37f61e312377008b05320261ebac36ba32a..ccb7f5f394f09d15c7db1c2fe3af39074fa2480f 100644
--- a/src/multicolvar/VolumeGradientBase.h
+++ b/src/multicolvar/VolumeGradientBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/VolumeInCylinder.cpp b/src/multicolvar/VolumeInCylinder.cpp
index 0db39116976cdb9ff1131ebe4317d50baef661ab..368d027d11394dca2ef5687447ade2e1889961c6 100644
--- a/src/multicolvar/VolumeInCylinder.cpp
+++ b/src/multicolvar/VolumeInCylinder.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/VolumeInSphere.cpp b/src/multicolvar/VolumeInSphere.cpp
index ff7d23d2344a857b5806ff8b9e622357f43ca341..6ebb097bc4aad6fdff9d9e93a16d1dbd0af6a9f3 100644
--- a/src/multicolvar/VolumeInSphere.cpp
+++ b/src/multicolvar/VolumeInSphere.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/VolumeTetrapore.cpp b/src/multicolvar/VolumeTetrapore.cpp
index 5e92018e93f89731d90d766d9ebe89ee5557736f..f763bd975db54680aadfb2cdecfaf91cd93bfd0e 100644
--- a/src/multicolvar/VolumeTetrapore.cpp
+++ b/src/multicolvar/VolumeTetrapore.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/XAngle.cpp b/src/multicolvar/XAngle.cpp
index 35fbf838c89ee77ba21dce16a4e64f4198f9de5e..f58440636233b227397ca250154af4f26c7a6fdf 100644
--- a/src/multicolvar/XAngle.cpp
+++ b/src/multicolvar/XAngle.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/XDistances.cpp b/src/multicolvar/XDistances.cpp
index 9f3ef5049e825628c84cfa78382ad3e438f1bfe6..432cbfba2c364b74e2be67e656741c4f292a90b3 100644
--- a/src/multicolvar/XDistances.cpp
+++ b/src/multicolvar/XDistances.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/XYDistances.cpp b/src/multicolvar/XYDistances.cpp
index 9da8fd943709cbb26394ef4aa6811a985fe50f5e..2781a74996ab2387b10e658a6d993716bf0e4c9d 100644
--- a/src/multicolvar/XYDistances.cpp
+++ b/src/multicolvar/XYDistances.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/multicolvar/XYTorsion.cpp b/src/multicolvar/XYTorsion.cpp
index 48c956644e3e8cd84c251c34f20345425d8f89b1..64fc978003c7a310880aed5a9a91feee59723913 100644
--- a/src/multicolvar/XYTorsion.cpp
+++ b/src/multicolvar/XYTorsion.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/ArgumentOnlyDistance.cpp b/src/reference/ArgumentOnlyDistance.cpp
index d1e5439a3fe227a4637029c94211b2128d11ee09..bc513e5b07663e263c6274467420e7702cbe6889 100644
--- a/src/reference/ArgumentOnlyDistance.cpp
+++ b/src/reference/ArgumentOnlyDistance.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/ArgumentOnlyDistance.h b/src/reference/ArgumentOnlyDistance.h
index 0ebe06a9a6ff54f8891e22e78b4ad635bd679808..eaa83d86cf1595822a957dafa35a0c75573dffb6 100644
--- a/src/reference/ArgumentOnlyDistance.h
+++ b/src/reference/ArgumentOnlyDistance.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/DRMSD.cpp b/src/reference/DRMSD.cpp
index ed5ca5be82b0a9686203bcd80ce5680924d200c0..9aa65d9ea6abdadbee3f8531f078abc7bf0c8122 100644
--- a/src/reference/DRMSD.cpp
+++ b/src/reference/DRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/DRMSD.h b/src/reference/DRMSD.h
index fd59f412454b0383822ada7950692483b083bea7..aa3ae94a5708c23cc2aff8394e715fbe15094820 100644
--- a/src/reference/DRMSD.h
+++ b/src/reference/DRMSD.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/Direction.cpp b/src/reference/Direction.cpp
index 3f55a8e59c007f7d89c4615075331c22e9e74b68..27568f9c8dbd10351e02fbcf559acdcecbc4cefd 100644
--- a/src/reference/Direction.cpp
+++ b/src/reference/Direction.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/Direction.h b/src/reference/Direction.h
index b2418fc5fdadf8824e265a8c2203048ebc335b86..fe2d0146637987b235460b832a8d76a7bc048f19 100644
--- a/src/reference/Direction.h
+++ b/src/reference/Direction.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/DotProductDistance.cpp b/src/reference/DotProductDistance.cpp
index 9eb830ecaa0be7581f0257c49ad3e91b0cfd24ef..5ffc149196a5326022d3a7e86b39c9164770ab60 100644
--- a/src/reference/DotProductDistance.cpp
+++ b/src/reference/DotProductDistance.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/EuclideanDistance.cpp b/src/reference/EuclideanDistance.cpp
index 5213e845a63f0b9a394879d791f2c04eb619f7a4..2dfe392a40c376469684312cabffae5a4b9a6bb3 100644
--- a/src/reference/EuclideanDistance.cpp
+++ b/src/reference/EuclideanDistance.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/FakeFrame.cpp b/src/reference/FakeFrame.cpp
index 758e97e55d667954d1cc76055dadf1e9a35a4e81..7466ea765e3a2871f3d799c0dbd63d7c09af7812 100644
--- a/src/reference/FakeFrame.cpp
+++ b/src/reference/FakeFrame.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/FakeFrame.h b/src/reference/FakeFrame.h
index 9ddbb9a22660561ccdd27cfecb9a76121c7c4426..df0bbc1d90972152ffebadbbcff96faa4ce35f8d 100644
--- a/src/reference/FakeFrame.h
+++ b/src/reference/FakeFrame.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/IntermolecularDRMSD.cpp b/src/reference/IntermolecularDRMSD.cpp
index a9a0e546c7d0559ffc51ef82d2b63ee67522c480..f7e1bffd2fb8526bd44eb1501b57128016f0294e 100644
--- a/src/reference/IntermolecularDRMSD.cpp
+++ b/src/reference/IntermolecularDRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/IntramolecularDRMSD.cpp b/src/reference/IntramolecularDRMSD.cpp
index 710e37ba8c08c2f571200efe69540ab5af4ebfa8..7fa030ca4b1e605c7fe2e7a7bc2afe572328762e 100644
--- a/src/reference/IntramolecularDRMSD.cpp
+++ b/src/reference/IntramolecularDRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/MahalanobisDistance.cpp b/src/reference/MahalanobisDistance.cpp
index 262e8f1c70315128fd7bcba8225de5aa920c22ac..55053f0b53fa29cdb0e5c5c3527e52b154e28a4c 100644
--- a/src/reference/MahalanobisDistance.cpp
+++ b/src/reference/MahalanobisDistance.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/MetricRegister.cpp b/src/reference/MetricRegister.cpp
index 557741e9a3d83b6558c70d2417d5d59aa5408f09..ce99f291f4dd1ed1cc88d50ca752b00928123d70 100644
--- a/src/reference/MetricRegister.cpp
+++ b/src/reference/MetricRegister.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/MetricRegister.h b/src/reference/MetricRegister.h
index ce9d293da8bce92fb8a5be78c8197c04da6961d7..92f4a2711cf3870a0a4a1c01a0aa2666da0386a0 100644
--- a/src/reference/MetricRegister.h
+++ b/src/reference/MetricRegister.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/MultiDomainRMSD.cpp b/src/reference/MultiDomainRMSD.cpp
index b3961a61c24af8c3efece49c29c329850ee666fd..907067abc7c831cbab92df47b49b1a4dc1275fa3 100644
--- a/src/reference/MultiDomainRMSD.cpp
+++ b/src/reference/MultiDomainRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/MultiDomainRMSD.h b/src/reference/MultiDomainRMSD.h
index 5207da6085a36b70e020ef84cb3bf4e875c02560..149c613714c4b8ac1a25d1c4420f0a26845dcaae 100644
--- a/src/reference/MultiDomainRMSD.h
+++ b/src/reference/MultiDomainRMSD.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/MultiReferenceBase.cpp b/src/reference/MultiReferenceBase.cpp
index d6aae1d0e58494193408b139da75341a5b39a2cf..8c6126ba8803110e2e8578b9792b4c74419c197b 100644
--- a/src/reference/MultiReferenceBase.cpp
+++ b/src/reference/MultiReferenceBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/MultiReferenceBase.h b/src/reference/MultiReferenceBase.h
index 39c9e9bfd1ae7fda1d542f92003d2ce1b797c2c4..cb92bd547896b18bc92299a12c1584c0e38520a7 100644
--- a/src/reference/MultiReferenceBase.h
+++ b/src/reference/MultiReferenceBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/NormalizedEuclideanDistance.cpp b/src/reference/NormalizedEuclideanDistance.cpp
index 677d4f56f18f6c9de07ce762b7c8caf1e204c75c..7491e2834bcb225258fd75b0f7052cc444da1442 100644
--- a/src/reference/NormalizedEuclideanDistance.cpp
+++ b/src/reference/NormalizedEuclideanDistance.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/OptimalRMSD.cpp b/src/reference/OptimalRMSD.cpp
index 67815278a782e3e3cc5954c13c37bf47fc03bfb5..88194f45fc2dad0b7ccb01e64809e2f46dbdfe84 100644
--- a/src/reference/OptimalRMSD.cpp
+++ b/src/reference/OptimalRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/PointWiseMapping.cpp b/src/reference/PointWiseMapping.cpp
index 6e3d9c95e44fecf4816212ddcb7e8ae3b420e24f..8f3521683532c7c2e93fda5ca9ca0b5b897b8d66 100644
--- a/src/reference/PointWiseMapping.cpp
+++ b/src/reference/PointWiseMapping.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/PointWiseMapping.h b/src/reference/PointWiseMapping.h
index e283eb600830c9d5921b6048f319e32c8f2946f8..abfb8dfaa9e95321fd8bfdfa7fe89e0de5884965 100644
--- a/src/reference/PointWiseMapping.h
+++ b/src/reference/PointWiseMapping.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/RMSDBase.cpp b/src/reference/RMSDBase.cpp
index e641fe24b4bb8e614b2de2ceb420a66ffe1ca7dc..87e19615a14c5c74cc80c62acdc08e7b06ffdc8b 100644
--- a/src/reference/RMSDBase.cpp
+++ b/src/reference/RMSDBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/RMSDBase.h b/src/reference/RMSDBase.h
index 58871c80a2e102b6b572430891debacfc4cd7716..ef28e75c3bd95cff6d139459d2ce7556f17b307d 100644
--- a/src/reference/RMSDBase.h
+++ b/src/reference/RMSDBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/ReferenceArguments.cpp b/src/reference/ReferenceArguments.cpp
index 0609048f79b5efae115895a0d776fcf3e77ce0f4..a001f2421adc809df43c552a751023a3d0cde766 100644
--- a/src/reference/ReferenceArguments.cpp
+++ b/src/reference/ReferenceArguments.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/ReferenceArguments.h b/src/reference/ReferenceArguments.h
index 6444291ab6195a55defb214e77de74686815bc11..c29b1a90fe6cb824ea2679dd623c41e22757b5b8 100644
--- a/src/reference/ReferenceArguments.h
+++ b/src/reference/ReferenceArguments.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/ReferenceAtoms.cpp b/src/reference/ReferenceAtoms.cpp
index d562a601a253ccd658509413add263b112ce309c..5d751f26470cf4520951ef25e356d70b9765568a 100644
--- a/src/reference/ReferenceAtoms.cpp
+++ b/src/reference/ReferenceAtoms.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/ReferenceAtoms.h b/src/reference/ReferenceAtoms.h
index d063e14c0c9a4c9845e4f54ad558328e3baa579b..71592aa1d9ca61d27801a7791acb3a22f52eecea 100644
--- a/src/reference/ReferenceAtoms.h
+++ b/src/reference/ReferenceAtoms.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/ReferenceConfiguration.cpp b/src/reference/ReferenceConfiguration.cpp
index 420230408dff80edc9bf0a9c4f7aec97b1cad11c..d773cc02b1f803a816a5bc28bc776979007d0884 100644
--- a/src/reference/ReferenceConfiguration.cpp
+++ b/src/reference/ReferenceConfiguration.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/ReferenceConfiguration.h b/src/reference/ReferenceConfiguration.h
index 2776ffdee8a89d960c797c08f8affdb77dd29f43..a9ae446559cb603765b200825b2ba02362005dd4 100644
--- a/src/reference/ReferenceConfiguration.h
+++ b/src/reference/ReferenceConfiguration.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/ReferenceValuePack.cpp b/src/reference/ReferenceValuePack.cpp
index 32752f604f97428e57bedbb3ebec5af97cdf44a5..4c196c56cab5c8a9decd24937357e58c591abcab 100644
--- a/src/reference/ReferenceValuePack.cpp
+++ b/src/reference/ReferenceValuePack.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/ReferenceValuePack.h b/src/reference/ReferenceValuePack.h
index c98ca5ad117ae98da5e19fc347edd577ca64c3e5..bcc01d7140114d0cae58eeaff4f405070a99353b 100644
--- a/src/reference/ReferenceValuePack.h
+++ b/src/reference/ReferenceValuePack.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/SimpleRMSD.cpp b/src/reference/SimpleRMSD.cpp
index 6045d3211e9079068b60eaaa332a4fa8fbff6a68..5edc34d6f59b994bd0b575d3a8e42987b5fd710d 100644
--- a/src/reference/SimpleRMSD.cpp
+++ b/src/reference/SimpleRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/SingleDomainRMSD.cpp b/src/reference/SingleDomainRMSD.cpp
index 57e39a2c111acb3af9e51f5b02592d14ca75d68b..99efa284dfa9acd771ab1f2ae6b676badbbf10c2 100644
--- a/src/reference/SingleDomainRMSD.cpp
+++ b/src/reference/SingleDomainRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/reference/SingleDomainRMSD.h b/src/reference/SingleDomainRMSD.h
index f034a0b496c23e314aeb8059710f9550f2ed0a8d..82f81ebab3eae90a92883443620cd4741c706f3f 100644
--- a/src/reference/SingleDomainRMSD.h
+++ b/src/reference/SingleDomainRMSD.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/secondarystructure/AlphaRMSD.cpp b/src/secondarystructure/AlphaRMSD.cpp
index 4e22785ced881efde41bd1b38605b555acc77871..41d1f58d82695d0faf687ee9c5a0112aff6a9c96 100644
--- a/src/secondarystructure/AlphaRMSD.cpp
+++ b/src/secondarystructure/AlphaRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/secondarystructure/AntibetaRMSD.cpp b/src/secondarystructure/AntibetaRMSD.cpp
index 92263a43f5597551b5b162c1f9858c75dd26ca78..e762dc05f88f0aae1669672dc727af53b082576a 100644
--- a/src/secondarystructure/AntibetaRMSD.cpp
+++ b/src/secondarystructure/AntibetaRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/secondarystructure/ParabetaRMSD.cpp b/src/secondarystructure/ParabetaRMSD.cpp
index 02dd6c260e505bf891c48407094b328b82d66685..a3cddb2d659c294b1d179f2827030e1c5192844b 100644
--- a/src/secondarystructure/ParabetaRMSD.cpp
+++ b/src/secondarystructure/ParabetaRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/secondarystructure/SecondaryStructureRMSD.cpp b/src/secondarystructure/SecondaryStructureRMSD.cpp
index 380ff3ed234138e72c2d089d2ceaae3b25467a6c..5aab56367f6167f69f242d8713e308eb9bc4d162 100644
--- a/src/secondarystructure/SecondaryStructureRMSD.cpp
+++ b/src/secondarystructure/SecondaryStructureRMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/secondarystructure/SecondaryStructureRMSD.h b/src/secondarystructure/SecondaryStructureRMSD.h
index 2b27febebb96f98dd925374d588c0f3fceb7ebb5..f963b24eae0a15759586b42e3394e522dd9dd2e6 100644
--- a/src/secondarystructure/SecondaryStructureRMSD.h
+++ b/src/secondarystructure/SecondaryStructureRMSD.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/setup/ActionSetup.h b/src/setup/ActionSetup.h
index 9a3fdbf915170d9d97406c42a3f38db33d839f9c..8c9970ddcda78f6e468e57f2d4d394899abd0372 100644
--- a/src/setup/ActionSetup.h
+++ b/src/setup/ActionSetup.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/setup/Load.cpp b/src/setup/Load.cpp
index ce70a519cc173523bb18e6fe0f68cb7d0dce763e..4a99d2cf12d09160c815032fd75c2dbda47c121c 100644
--- a/src/setup/Load.cpp
+++ b/src/setup/Load.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/setup/MolInfo.cpp b/src/setup/MolInfo.cpp
index 5395a80608d7e14785637847a000423fbec1ec21..12861daac0f4f457d3612b593beb2dc9ad2d37c7 100644
--- a/src/setup/MolInfo.cpp
+++ b/src/setup/MolInfo.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/setup/Restart.cpp b/src/setup/Restart.cpp
index 5af05ede9a365577099558b1995797d8b0328c8b..376c39469ba6f3818d3df7e082336882fcb9dd12 100644
--- a/src/setup/Restart.cpp
+++ b/src/setup/Restart.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/setup/Units.cpp b/src/setup/Units.cpp
index b47dda7049b613a1f45226a84532b3215b332ab4..8087a85ca84c45a7eb190ba673ac109f0b74d2eb 100644
--- a/src/setup/Units.cpp
+++ b/src/setup/Units.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Angle.cpp b/src/tools/Angle.cpp
index 5e5f106803169bb61e56ed98a30a9ef690d54f02..7f5c1fbd184ee8a1e0dd75f0be7441eecc191973 100644
--- a/src/tools/Angle.cpp
+++ b/src/tools/Angle.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Angle.h b/src/tools/Angle.h
index 4c6b7dab9e5f4bb9aeeb2501a9e3ea1f1a0042fc..79d7e468457d6c32a22817bd00f287e1a33db6f6 100644
--- a/src/tools/Angle.h
+++ b/src/tools/Angle.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/AtomNumber.cpp b/src/tools/AtomNumber.cpp
index e13e5454d9e38611754b4f6352233045e8a43ad5..887bb911372637a74a886dc4a802d4429d978b87 100644
--- a/src/tools/AtomNumber.cpp
+++ b/src/tools/AtomNumber.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/AtomNumber.h b/src/tools/AtomNumber.h
index 65b682ad0bfaff2f01b775ff08c6caab1c8c0cf4..2059ed7350167df8195412bfbd88372a17ccbfcd 100644
--- a/src/tools/AtomNumber.h
+++ b/src/tools/AtomNumber.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/BiasRepresentation.cpp b/src/tools/BiasRepresentation.cpp
index f12f0bc1f5f542571a74fd06656a7c4f85af5b8e..771d9558c2e1af5a30bf4acaba56b090669002cb 100644
--- a/src/tools/BiasRepresentation.cpp
+++ b/src/tools/BiasRepresentation.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/BiasRepresentation.h b/src/tools/BiasRepresentation.h
index 50a41b0ab488b95bb3a8c772aa476079fc4456d8..4b6a287971a93727d35b4fe8688deb5a03ae3f09 100644
--- a/src/tools/BiasRepresentation.h
+++ b/src/tools/BiasRepresentation.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Brent1DRootSearch.cpp b/src/tools/Brent1DRootSearch.cpp
index f862832391c42d827881218eb93c14e8e43c57c0..ba485ffc23aaac9c4e2f9e75dc32e27ba189a50a 100644
--- a/src/tools/Brent1DRootSearch.cpp
+++ b/src/tools/Brent1DRootSearch.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Brent1DRootSearch.h b/src/tools/Brent1DRootSearch.h
index 7aee0daa5716e99290ea0e3524b9443848400f1d..1ae4035f887c6509e7bf9c9ba02db2a9b94f8429 100644
--- a/src/tools/Brent1DRootSearch.h
+++ b/src/tools/Brent1DRootSearch.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Citations.cpp b/src/tools/Citations.cpp
index e3064012d7fc53a587467fadbb5871cf1f35ee97..aecf9982d0ee13586ce88ef8098f0fd592e69c25 100644
--- a/src/tools/Citations.cpp
+++ b/src/tools/Citations.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Citations.h b/src/tools/Citations.h
index 2f6fe8d3c41e152868bf099619e3f47004cd0b4a..2650e3f6e3746c0cc7a6d047c4be38eaa1bea3ea 100644
--- a/src/tools/Citations.h
+++ b/src/tools/Citations.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Communicator.cpp b/src/tools/Communicator.cpp
index 48acdd3458f9f7c5667bcf8e98c7a84e4141359a..f8d9491b8666f7d9e3d57662fa4d21be71ca2c89 100644
--- a/src/tools/Communicator.cpp
+++ b/src/tools/Communicator.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -34,20 +34,12 @@ Communicator::Communicator()
{
}
-// cppcheck complains about this:
-// Member variable 'Communicator::communicator' is not initialized in the constructor
-// this is a false positive so I suppress it
-// cppcheck-suppress uninitMemberVar
Communicator::Communicator(const Communicator&pc) {
Set_comm(pc.communicator);
}
Communicator::Status Communicator::StatusIgnore;
-// cppcheck complains about this:
-// Member variable 'Communicator::communicator' is not assigned a value in 'Communicator::operator='
-// this is a false positive so I suppress it
-// cppcheck-suppress operatorEqVarError
Communicator& Communicator::operator=(const Communicator&pc) {
if (this != &pc) {
Set_comm(pc.communicator);
diff --git a/src/tools/Communicator.h b/src/tools/Communicator.h
index b28056c20619fe834ec4d38dc439d0cca29a59e0..ea407838fd2b21151f2bbb516607359b6f59b4d0 100644
--- a/src/tools/Communicator.h
+++ b/src/tools/Communicator.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/DLLoader.cpp b/src/tools/DLLoader.cpp
index 289ceba1574b31ae75edb2a047be5c52a8dbb151..89ef9680c59c58c7d372c7d432f83584124e7782 100644
--- a/src/tools/DLLoader.cpp
+++ b/src/tools/DLLoader.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/DLLoader.h b/src/tools/DLLoader.h
index 791a0f51a7d33d03bd938671f7b1913b3b75c53b..81b45476cca9e55715e280ac5844a5b6363efd79 100644
--- a/src/tools/DLLoader.h
+++ b/src/tools/DLLoader.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/DynamicList.cpp b/src/tools/DynamicList.cpp
index 4fea15d20233b4dfc67c05c41431821d8e9d1517..555b77c35c177bbfa66eec190fca9e791d902d2f 100644
--- a/src/tools/DynamicList.cpp
+++ b/src/tools/DynamicList.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/DynamicList.h b/src/tools/DynamicList.h
index 3a461a89d50fce88a3073045d1e05fbaa4794d2d..c7f017e6bf06822670ae059131abea27e5a1042e 100644
--- a/src/tools/DynamicList.h
+++ b/src/tools/DynamicList.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/ERMSD.cpp b/src/tools/ERMSD.cpp
index e39cf925c04ced35f90da362aa9106da88b0f333..831237ee9fb258e37309ac0d59322d511d7fba93 100644
--- a/src/tools/ERMSD.cpp
+++ b/src/tools/ERMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/ERMSD.h b/src/tools/ERMSD.h
index b37d48dccdc6e4545a96c72aadc61ca54940666f..836148968e77de163a1bc091877eb579b401263f 100644
--- a/src/tools/ERMSD.h
+++ b/src/tools/ERMSD.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Exception.cpp b/src/tools/Exception.cpp
index ccd3ad418937c69fe778c28d76794c815e5b1a0c..c79d13b4a01637074fe15b31732df0d0154cd504 100644
--- a/src/tools/Exception.cpp
+++ b/src/tools/Exception.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Exception.h b/src/tools/Exception.h
index 054f0e81720ff04b7ed12676741f20f4d21780fc..678ccf3a786bc24d56aba6afa42b03a9ba6cd54e 100644
--- a/src/tools/Exception.h
+++ b/src/tools/Exception.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/File.h b/src/tools/File.h
index 156311cbaa382ed7c5c9f675eb19a24f74e683da..8a1525177bdb27ff32eb51f2d7355f8d65e9646d 100644
--- a/src/tools/File.h
+++ b/src/tools/File.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/FileBase.cpp b/src/tools/FileBase.cpp
index ca55a572c7cfdbfdcf406c97ba1daf8a6acffae1..a7995ead114795b32c0c7cf1808b82cdc2a6eced 100644
--- a/src/tools/FileBase.cpp
+++ b/src/tools/FileBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/FileBase.h b/src/tools/FileBase.h
index 52e5fd649b361c5ca8fc21699038d92aa8f0217b..b9bf29183e8de9b0229f7d4d13906b0028fc60c5 100644
--- a/src/tools/FileBase.h
+++ b/src/tools/FileBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Grid.cpp b/src/tools/Grid.cpp
index e2a304b38935742e9de85a39e94e49ebca787501..02f562901ae6abd3fadaae8e8564f1ad1f64d30f 100644
--- a/src/tools/Grid.cpp
+++ b/src/tools/Grid.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -821,6 +821,24 @@ void SparseGrid::writeToFile(OFile& ofile) {
}
}
+double SparseGrid::getMinValue() const {
+ double minval;
+ minval=0.0;
+ for(auto const & i : map_) {
+ if(i.second<minval) minval=i.second;
+ }
+ return minval;
+}
+
+double SparseGrid::getMaxValue() const {
+ double maxval;
+ maxval=0.0;
+ for(auto const & i : map_) {
+ if(i.second>maxval) maxval=i.second;
+ }
+ return maxval;
+}
+
void Grid::projectOnLowDimension(double &val, std::vector<int> &vHigh, WeightBase * ptr2obj ) {
unsigned i=0;
diff --git a/src/tools/Grid.h b/src/tools/Grid.h
index 48678419ccee08ba57f7bf55d2debb40912e351d..6b73550c8d330d462e260b62e4375cf24c3d5fe3 100644
--- a/src/tools/Grid.h
+++ b/src/tools/Grid.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -271,6 +271,10 @@ public:
void writeToFile(OFile&);
virtual ~SparseGrid() {}
+
+ virtual double getMaxValue() const;
+ virtual double getMinValue() const;
+
};
}
diff --git a/src/tools/HistogramBead.cpp b/src/tools/HistogramBead.cpp
index 3c17ce1442445716ee25296074c80f5c5e3e3d1b..15cbba7cd7e8e8d0c44a9fb67012e03dbe639772 100644
--- a/src/tools/HistogramBead.cpp
+++ b/src/tools/HistogramBead.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -139,7 +139,10 @@ void HistogramBead::generateBins( const std::string& params, std::vector<std::st
void HistogramBead::set( const std::string& params, std::string& errormsg ) {
std::vector<std::string> data=Tools::getWords(params);
- if(data.size()<1) errormsg="No input has been specified";
+ if(data.size()<1) {
+ errormsg="No input has been specified";
+ return;
+ }
std::string name=data[0]; const double DP2CUTOFF=6.25;
if(name=="GAUSSIAN") { type=gaussian; cutoff=sqrt(2.0*DP2CUTOFF); }
diff --git a/src/tools/HistogramBead.h b/src/tools/HistogramBead.h
index a3a58a6fc3cc102ac2145d4230f77dff7f33d9b2..4eb88b3297c21306aef6c71ccfbf3c44307473b5 100644
--- a/src/tools/HistogramBead.h
+++ b/src/tools/HistogramBead.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/IFile.cpp b/src/tools/IFile.cpp
index 7cb119d2266fa85dba54aa1670bc7b90899cbcc2..44a0b976603a721d8f9b608a5870cc5728693a1b 100644
--- a/src/tools/IFile.cpp
+++ b/src/tools/IFile.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -64,7 +64,8 @@ IFile& IFile::advanceField() {
bool done=false;
while(!done) {
getline(line);
- if(!*this) {return *this;}
+// using explicit conversion not to confuse cppcheck 1.86
+ if(!bool(*this)) {return *this;}
std::vector<std::string> words=Tools::getWords(line);
if(words.size()>=2 && words[0]=="#!" && words[1]=="FIELDS") {
fields.clear();
@@ -124,7 +125,8 @@ IFile& IFile::open(const std::string&path) {
IFile& IFile::scanFieldList(std::vector<std::string>&s) {
if(!inMiddleOfField) advanceField();
- if(!*this) return *this;
+// using explicit conversion not to confuse cppcheck 1.86
+ if(!bool(*this)) return *this;
s.clear();
for(unsigned i=0; i<fields.size(); i++)
s.push_back(fields[i].name);
@@ -141,7 +143,8 @@ bool IFile::FieldExist(const std::string& s) {
IFile& IFile::scanField(const std::string&name,std::string&str) {
if(!inMiddleOfField) advanceField();
- if(!*this) return *this;
+// using explicit conversion not to confuse cppcheck 1.86
+ if(!bool(*this)) return *this;
unsigned i=findField(name);
str=fields[i].value;
fields[i].read=true;
diff --git a/src/tools/IFile.h b/src/tools/IFile.h
index 419221fe6268d9f92d3b117dda061cffd7d52316..3a465d2eef42c61a3efee77b7bb3ae2bb0af0bfc 100644
--- a/src/tools/IFile.h
+++ b/src/tools/IFile.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/KernelFunctions.cpp b/src/tools/KernelFunctions.cpp
index f2242bf59f0aeebeefae89bbb1f7c180c678a588..4d24efe56e31ddf775319f903508af0ea3930895 100644
--- a/src/tools/KernelFunctions.cpp
+++ b/src/tools/KernelFunctions.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/KernelFunctions.h b/src/tools/KernelFunctions.h
index ec209e103b1403676fdfd322f7504dc6418399f5..2446270fa999cf6817aa5b7256d33043a7b955e5 100644
--- a/src/tools/KernelFunctions.h
+++ b/src/tools/KernelFunctions.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Keywords.cpp b/src/tools/Keywords.cpp
index 8e451a28397a75429472dff049ad3236e0f7c7b6..e67547875cef0a760f50ca5b7f6fb67a195d4204 100644
--- a/src/tools/Keywords.cpp
+++ b/src/tools/Keywords.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Keywords.h b/src/tools/Keywords.h
index a8e69121d514f7a126d5eafc6174806b0343518e..48d0db8c32e9b2abd3aa78d32f0c55f4aee82554 100644
--- a/src/tools/Keywords.h
+++ b/src/tools/Keywords.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/LatticeReduction.cpp b/src/tools/LatticeReduction.cpp
index 60bbe5bee0898079c12a8e5241904f07bf9db9d0..85a8ed7bb893d788215f588b4d0182e4779606e1 100644
--- a/src/tools/LatticeReduction.cpp
+++ b/src/tools/LatticeReduction.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/LatticeReduction.h b/src/tools/LatticeReduction.h
index 699f52c5aff8b6042262fb209f6b74bf53dcfd79..48c9af90fc457a8ff360a11c7e4eac9202405b0b 100644
--- a/src/tools/LatticeReduction.h
+++ b/src/tools/LatticeReduction.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/LinkCells.cpp b/src/tools/LinkCells.cpp
index ef02ebc21b704d93355c3fd51d043b22fefb4a1a..60cf941876cb076dfc1c8b6b587ebf919caed42a 100644
--- a/src/tools/LinkCells.cpp
+++ b/src/tools/LinkCells.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/LinkCells.h b/src/tools/LinkCells.h
index b3b396f6ec8465c5951c3a008bc4388aa05e715b..2b17b16c4cac8ec00568064ee0a609c80426072a 100644
--- a/src/tools/LinkCells.h
+++ b/src/tools/LinkCells.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Log.cpp b/src/tools/Log.cpp
index 6bde8f69c30b5e0adb6afb58066726c7d235e8e5..634caa381fe768b12ee58e88785c8c4b98ef4164 100644
--- a/src/tools/Log.cpp
+++ b/src/tools/Log.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Log.h b/src/tools/Log.h
index b91c34e24c54b03567ad99ce420eec104a694224..d17e6add0f207714b82b01a5e9d33bdac5741460 100644
--- a/src/tools/Log.h
+++ b/src/tools/Log.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/LoopUnroller.cpp b/src/tools/LoopUnroller.cpp
index f63169b0eabe05fa765c3a68492e6b38ff9b8164..62d966c84a3d51aba9c4dabfd9b024404955cc6e 100644
--- a/src/tools/LoopUnroller.cpp
+++ b/src/tools/LoopUnroller.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/LoopUnroller.h b/src/tools/LoopUnroller.h
index 4074ce082fbbcdc765a016ed98af9648422bd614..96c3f2269f97db39f86af810e60a05f79135f12b 100644
--- a/src/tools/LoopUnroller.h
+++ b/src/tools/LoopUnroller.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Matrix.cpp b/src/tools/Matrix.cpp
index e170959ef322681893da8ba923b9770294411c5c..4aec8525f579c6d28c1ee550c4a5eba9710ca6b7 100644
--- a/src/tools/Matrix.cpp
+++ b/src/tools/Matrix.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Matrix.h b/src/tools/Matrix.h
index 5865bc9689db3221f319fdc09aa2d9fcf511459a..1b255b45fb00c921fa38e9d07a031b23c2109dce 100644
--- a/src/tools/Matrix.h
+++ b/src/tools/Matrix.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/MatrixSquareBracketsAccess.cpp b/src/tools/MatrixSquareBracketsAccess.cpp
index cb180f6e7a26b78a92060c48dcd963916f4fcb3c..7d431e10bc6cbe871fa91743ec607a70fb55a5c7 100644
--- a/src/tools/MatrixSquareBracketsAccess.cpp
+++ b/src/tools/MatrixSquareBracketsAccess.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/MatrixSquareBracketsAccess.h b/src/tools/MatrixSquareBracketsAccess.h
index 780f8aaf0281f082fb66366a6888eb077c680a47..2ffa52ce35b395fd1349fa8b342c2e2b3561704f 100644
--- a/src/tools/MatrixSquareBracketsAccess.h
+++ b/src/tools/MatrixSquareBracketsAccess.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Minimise1DBrent.cpp b/src/tools/Minimise1DBrent.cpp
index 9a5c410e9d814b91498bcc94348cf04468147b6d..42ed057b9163e5860bdadfd26139851025f19ead 100644
--- a/src/tools/Minimise1DBrent.cpp
+++ b/src/tools/Minimise1DBrent.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Minimise1DBrent.h b/src/tools/Minimise1DBrent.h
index b0b1e0b21b3298b4b15169398bcdef33710b25eb..9a2423757b201661b6fc6a54c60a1602e225fc59 100644
--- a/src/tools/Minimise1DBrent.h
+++ b/src/tools/Minimise1DBrent.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/MinimiseBase.cpp b/src/tools/MinimiseBase.cpp
index 531a0cdb97204f1be4843bdd89959043062f5379..440606c8c126a47f7199280d5bcab7e6074b2b4b 100644
--- a/src/tools/MinimiseBase.cpp
+++ b/src/tools/MinimiseBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/MinimiseBase.h b/src/tools/MinimiseBase.h
index 7eb85e82ef5e63ea83d1d1eb8044ab88d96d30dd..163511ab7aceeecfa4852317e7ca5910fe724241 100644
--- a/src/tools/MinimiseBase.h
+++ b/src/tools/MinimiseBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/MolDataClass.cpp b/src/tools/MolDataClass.cpp
index 107ed2ee3d5725d2d54308a2f8e92e0da785653c..3c4d4684af17febd9b22579ce640134daede6c24 100644
--- a/src/tools/MolDataClass.cpp
+++ b/src/tools/MolDataClass.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -206,7 +206,6 @@ void MolDataClass::specialSymbol( const std::string& type, const std::string& sy
std::string chainid;
if(firstnum==dash+1) {
Tools::convert( symbol.substr(dash+1), resnum );
- resname= mypdb.getResidueName(resnum);
chainid="*"; // this is going to match the first chain
} else {
// if chain id is provided:
diff --git a/src/tools/MolDataClass.h b/src/tools/MolDataClass.h
index 141a9b51b715bc8dbad0dde2e00e20404e57bf30..c5d91056dc5a4889a4c566e10da4f889c752dce1 100644
--- a/src/tools/MolDataClass.h
+++ b/src/tools/MolDataClass.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/MultiValue.cpp b/src/tools/MultiValue.cpp
index f50ad3897732de9d621bc93d117e84413bbea172..21a005448a41adbf5999c26f8f56fe66be9799c1 100644
--- a/src/tools/MultiValue.cpp
+++ b/src/tools/MultiValue.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/MultiValue.h b/src/tools/MultiValue.h
index f9974f998cfe5e9fae7544b6203ab7cf07bbe0d3..75a026598e32cb23b908ccb30b1ed1810f8afbc4 100644
--- a/src/tools/MultiValue.h
+++ b/src/tools/MultiValue.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/NeighborList.cpp b/src/tools/NeighborList.cpp
index 55f2240a9c4b0eb21ab8074d83921e951ddd80fe..589af62c9a29c4b8219e7b56822ff14d9260d7c5 100644
--- a/src/tools/NeighborList.cpp
+++ b/src/tools/NeighborList.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/NeighborList.h b/src/tools/NeighborList.h
index 91441c666351768bf1c7f21b79f6463553a5ccbe..88c9299e86be652ffdfc7b496ad11190d5b28ddc 100644
--- a/src/tools/NeighborList.h
+++ b/src/tools/NeighborList.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/OFile.cpp b/src/tools/OFile.cpp
index 27a2650e85af69927629736494e9b14619f7bf74..029bf888d981339ba5ed44cab8df10ae4d097ee2 100644
--- a/src/tools/OFile.cpp
+++ b/src/tools/OFile.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/OFile.h b/src/tools/OFile.h
index 0baedb8698a37b085ad8c9fedd1622347cf9c39f..3e4a508904a0979d077e3ebf4398dd8dfe09c305 100644
--- a/src/tools/OFile.h
+++ b/src/tools/OFile.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/OpenMP.cpp b/src/tools/OpenMP.cpp
index 9d61de34504f9f57d4ad3b72db6bad38aeb10b2a..531e1be6d1b78c0e1104f36a64ee3164edf21d23 100644
--- a/src/tools/OpenMP.cpp
+++ b/src/tools/OpenMP.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/OpenMP.h b/src/tools/OpenMP.h
index c36d13873314f474c948e1c75833a0505c88ce82..bfe600b2c1f123f86d8335f9a57674c0a8704ae4 100644
--- a/src/tools/OpenMP.h
+++ b/src/tools/OpenMP.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/PDB.cpp b/src/tools/PDB.cpp
index b9ef44f58a1b75840e146bac548e6ff1cf7423b6..e1fc571431c511212c62151f4ae19ecd6dd9cdf4 100644
--- a/src/tools/PDB.cpp
+++ b/src/tools/PDB.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/PDB.h b/src/tools/PDB.h
index a5d3a2c145441676a8c4f1f67adea2f50c86902a..936b9da3e8d04ace63d1a9102dd4e03e83b40187 100644
--- a/src/tools/PDB.h
+++ b/src/tools/PDB.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Pbc.cpp b/src/tools/Pbc.cpp
index f0bad097c1d9c77482b9bff72ac71cdb7b8a4fc3..f5f5595f79eed31926ce6b607f7cbd7ad7da909a 100644
--- a/src/tools/Pbc.cpp
+++ b/src/tools/Pbc.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Pbc.h b/src/tools/Pbc.h
index aa27f7fd1e3cd7a5e112baf08edf10efa3caedb5..05cae54b76fec37f5757929ea604da84495dee42 100644
--- a/src/tools/Pbc.h
+++ b/src/tools/Pbc.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/RMSD.cpp b/src/tools/RMSD.cpp
index a897471902edc61d0039d60821e5d4253d57385c..ad9a744aba1cc684d567e3e62b69ac0314f0f1db 100644
--- a/src/tools/RMSD.cpp
+++ b/src/tools/RMSD.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/RMSD.h b/src/tools/RMSD.h
index 09fd1c5b687fc64e3d9c0120a3f9bb84212b7652..1d35683a9509bc3639c14fee4cae7b1d1f45d103 100644
--- a/src/tools/RMSD.h
+++ b/src/tools/RMSD.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Random.cpp b/src/tools/Random.cpp
index 8b8dcdd3005cad035119c57e9899cfb56588f9b9..530bae72c7c6d1b3640899db73d8a8665cfcbc25 100644
--- a/src/tools/Random.cpp
+++ b/src/tools/Random.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Random.h b/src/tools/Random.h
index c7cbd8b9ce65cd36db20810b5ba486329437fdb7..eebcba0f2ffbea6dc58a1fbc644d40ed6cfd1f34 100644
--- a/src/tools/Random.h
+++ b/src/tools/Random.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/RootFindingBase.cpp b/src/tools/RootFindingBase.cpp
index d687f9e7c0b981c8470589ff9c2eda5ff926a556..081827ce709b10abb6480b430c1cbc177e10d0a1 100644
--- a/src/tools/RootFindingBase.cpp
+++ b/src/tools/RootFindingBase.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/RootFindingBase.h b/src/tools/RootFindingBase.h
index 768aab3808156121f2d2b45b9cf8ffa06cc08636..4da2b56a87737956681b935f1910bd04ab9f7946 100644
--- a/src/tools/RootFindingBase.h
+++ b/src/tools/RootFindingBase.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Stopwatch.cpp b/src/tools/Stopwatch.cpp
index 9169e86409ca01ef0f3525edf2eae550780ae5ba..f5029aa21de8b5d8a457e7a3fcacfa22b959ab07 100644
--- a/src/tools/Stopwatch.cpp
+++ b/src/tools/Stopwatch.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Stopwatch.h b/src/tools/Stopwatch.h
index 7c653e39be9a2a6bccfb07dd95363273cf1ec9d3..1bcebc524b96af3dfe7ac0ebdf44df0a872c17af 100644
--- a/src/tools/Stopwatch.h
+++ b/src/tools/Stopwatch.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/SwitchingFunction.cpp b/src/tools/SwitchingFunction.cpp
index 0ede2392482610d9115b76af668b6cf508c47d14..e5e400dde20abb08f6a3deba129cbe97b4c35d6b 100644
--- a/src/tools/SwitchingFunction.cpp
+++ b/src/tools/SwitchingFunction.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -186,7 +186,10 @@ void SwitchingFunction::registerKeywords( Keywords& keys ) {
void SwitchingFunction::set(const std::string & definition,std::string& errormsg) {
vector<string> data=Tools::getWords(definition);
- if( data.size()<1 ) errormsg="missing all input for switching function";
+ if( data.size()<1 ) {
+ errormsg="missing all input for switching function";
+ return;
+ }
string name=data[0];
data.erase(data.begin());
invr0=0.0;
diff --git a/src/tools/SwitchingFunction.h b/src/tools/SwitchingFunction.h
index 3a7759463b37a6b04b293f9d22ea16eadef7c0da..16c1bcef105b3a56dea34a25e98f0a7671d439ea 100644
--- a/src/tools/SwitchingFunction.h
+++ b/src/tools/SwitchingFunction.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Tensor.cpp b/src/tools/Tensor.cpp
index 767f0b30ee93c38d3b1c8e96091e8e249f103579..adf6a36fd5b2149faa9647c24d53c3f4fabab988 100644
--- a/src/tools/Tensor.cpp
+++ b/src/tools/Tensor.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Tensor.h b/src/tools/Tensor.h
index cb25e4566a3ed1b8604103f35a1a1f5daa2cfb9f..08c138a112f03294d71668275074e7ec4b3bbb06 100644
--- a/src/tools/Tensor.h
+++ b/src/tools/Tensor.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Tools.cpp b/src/tools/Tools.cpp
index 0a24ca7d0baba3794367ab680fdf982608531ae5..1420978ee8d8a615ea2b4dc091b712fe0ea33d3a 100644
--- a/src/tools/Tools.cpp
+++ b/src/tools/Tools.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
@@ -158,7 +158,7 @@ vector<string> Tools::getWords(const string & line,const char* separators,int *
if(parenthesisLevel==0) for(unsigned j=0; j<sep.length(); j++) if(line[i]==sep[j]) found=true;
// If at parenthesis level zero (outer)
if(!(parenthesisLevel==0 && (found||onParenthesis))) word.push_back(line[i]);
- if(onParenthesis) word.push_back(' ');
+ //if(onParenthesis) word.push_back(' ');
if(line[i]==openpar) parenthesisLevel++;
if(found && word.length()>0) {
if(!parlevel) plumed_massert(parenthesisLevel==0,"Unmatching parenthesis in '" + line + "'");
diff --git a/src/tools/Tools.h b/src/tools/Tools.h
index dbd901aebe5fc25077170d8cbbeb83d9b4121b4f..6802142956ac01954341432eb543fcd8a5aacfd4 100644
--- a/src/tools/Tools.h
+++ b/src/tools/Tools.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Torsion.cpp b/src/tools/Torsion.cpp
index d92fc9c0c232712a1ff9e9d53595f22d98e89154..438b60fc81ac79acad0cf97c200304b65b842c92 100644
--- a/src/tools/Torsion.cpp
+++ b/src/tools/Torsion.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Torsion.h b/src/tools/Torsion.h
index e60c0a6b9e6fc403f4c90a3cbd12ae424369fd54..b3b83f4eaaa9611c78bf95873623ea282b6d73fd 100644
--- a/src/tools/Torsion.h
+++ b/src/tools/Torsion.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Units.cpp b/src/tools/Units.cpp
index 1389b7dfb9a658fdfe1e50f87edc958209596801..c3b8d7839553b58a2d4ba92a702f0935108eb9a4 100644
--- a/src/tools/Units.cpp
+++ b/src/tools/Units.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Units.h b/src/tools/Units.h
index dd35cddbcfd18a7a436446f5cd58a094adf466da..7b4d6a794e3caa5592e892d2429bcddb6fdd14dd 100644
--- a/src/tools/Units.h
+++ b/src/tools/Units.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Vector.cpp b/src/tools/Vector.cpp
index aa29eb11687b227769bdbd75410cb766e0bce1eb..6bd80c8d88decf5517c6238fc09f96460e38ba98 100644
--- a/src/tools/Vector.cpp
+++ b/src/tools/Vector.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/tools/Vector.h b/src/tools/Vector.h
index 655a006e206f3c885bad8e147660f03fa798cefc..1ba4889d77941eb9842cd488eb29e2e447ccf3ff 100644
--- a/src/tools/Vector.h
+++ b/src/tools/Vector.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vatom/ActionRegister.h b/src/vatom/ActionRegister.h
index 47fee8965387730c4682cbe247add1a9537bf06a..9ad157024576b7c20875cb99000c2fdced998aa3 100644
--- a/src/vatom/ActionRegister.h
+++ b/src/vatom/ActionRegister.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vatom/ActionWithVirtualAtom.cpp b/src/vatom/ActionWithVirtualAtom.cpp
index 5a457f6dc4339c5e77ad22c4946f5c3c8fac8819..6cb8cc40dce6e2ad93de911e7e9485426bb75d6d 100644
--- a/src/vatom/ActionWithVirtualAtom.cpp
+++ b/src/vatom/ActionWithVirtualAtom.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vatom/ActionWithVirtualAtom.h b/src/vatom/ActionWithVirtualAtom.h
index c656e362232dcbd8fcd7a9522cfcbf08bc57f040..4b7f747c1d87d6846c9ed23ac54c79268c265128 100644
--- a/src/vatom/ActionWithVirtualAtom.h
+++ b/src/vatom/ActionWithVirtualAtom.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vatom/COM.cpp b/src/vatom/COM.cpp
index 6cdabbcb2b0b2d02f90172546a1ee9e1d9d8375e..ee24a8de6765d5ec54d565f4018f24bdf98512fb 100644
--- a/src/vatom/COM.cpp
+++ b/src/vatom/COM.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vatom/Center.cpp b/src/vatom/Center.cpp
index ca054a09697b7d27b917019c023348edfbcab469..8281ee73e2d69ad7530e028506495606b225d62b 100644
--- a/src/vatom/Center.cpp
+++ b/src/vatom/Center.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vatom/FixedAtom.cpp b/src/vatom/FixedAtom.cpp
index 8a8546104cc2926f6926445e588e8f508a32bd28..ec774509c2f62734b271583dd2092e65bfeb29f0 100644
--- a/src/vatom/FixedAtom.cpp
+++ b/src/vatom/FixedAtom.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vatom/Ghost.cpp b/src/vatom/Ghost.cpp
index 7d57c89699e1d7755435ea692bd161643d5e161a..955182bf9197938977d27e4f0f8adf12af032c85 100644
--- a/src/vatom/Ghost.cpp
+++ b/src/vatom/Ghost.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/ves/FermiSwitchingFunction.cpp b/src/ves/FermiSwitchingFunction.cpp
index a53ab6f6a3f444ab6a2886dd1a761c00ccab97a0..f0695c4e801f206936cfe3f7a5a4457afc1432d9 100644
--- a/src/ves/FermiSwitchingFunction.cpp
+++ b/src/ves/FermiSwitchingFunction.cpp
@@ -41,7 +41,10 @@ void FermiSwitchingFunction::registerKeywords( Keywords& keys ) {
void FermiSwitchingFunction::set(const std::string& definition,std::string& errormsg) {
std::vector<std::string> data=Tools::getWords(definition);
- if( data.size()<1 ) errormsg="missing all input for switching function";
+ if( data.size()<1 ) {
+ errormsg="missing all input for switching function";
+ return;
+ }
std::string name=data[0];
data.erase(data.begin());
if(name!="FERMI") {errormsg="only FERMI is supported";}
diff --git a/src/ves/MD_LinearExpansionPES.cpp b/src/ves/MD_LinearExpansionPES.cpp
index d44f0767d63071dfb9efc96e5af5fe19aafdb6cd..f73489b113d241c166171b353b08794677285b4d 100644
--- a/src/ves/MD_LinearExpansionPES.cpp
+++ b/src/ves/MD_LinearExpansionPES.cpp
@@ -236,8 +236,8 @@ int MD_LinearExpansionPES::main( FILE* in, FILE* out, PLMD::Communicator& pc) {
parse("nstep",nsteps);
double tstep;
parse("tstep",tstep);
- //
- double temp;
+ // initialize to solve a cppcheck 1.86 warning
+ double temp=0.0;
std::vector<double> temps_vec(0);
parseVector("temperature",temps_vec);
if(temps_vec.size()==1) {
diff --git a/src/vesselbase/ActionWithAveraging.cpp b/src/vesselbase/ActionWithAveraging.cpp
index 9a43b25e97f55074637eec762651d267cc5959a9..a14f35cafb34ede71b96fbb21d03464277bb68c9 100644
--- a/src/vesselbase/ActionWithAveraging.cpp
+++ b/src/vesselbase/ActionWithAveraging.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/ActionWithAveraging.h b/src/vesselbase/ActionWithAveraging.h
index 45ded46bce81924455fdd56345d96a856dea8dca..8c2583f9fa98a4f6fb976d4fde084cd6376ff047 100644
--- a/src/vesselbase/ActionWithAveraging.h
+++ b/src/vesselbase/ActionWithAveraging.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/ActionWithInputVessel.cpp b/src/vesselbase/ActionWithInputVessel.cpp
index 412550cdce5df90dba3d18ed73852a36695bf261..d1b1a3e15542aa8b53747d3a34800a2b2a9abb3f 100644
--- a/src/vesselbase/ActionWithInputVessel.cpp
+++ b/src/vesselbase/ActionWithInputVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/ActionWithInputVessel.h b/src/vesselbase/ActionWithInputVessel.h
index 9ca6bdc1c9ad2e6321d50eacb78c91b4ac7e5e93..9484500ea4ed70da76980c444131dd44f5399160 100644
--- a/src/vesselbase/ActionWithInputVessel.h
+++ b/src/vesselbase/ActionWithInputVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/ActionWithVessel.cpp b/src/vesselbase/ActionWithVessel.cpp
index 0a692fc779ed11d828fa33354f939f17fbf9139f..04fc2beb1e6931baefff1c9152e6b39afcf17238 100644
--- a/src/vesselbase/ActionWithVessel.cpp
+++ b/src/vesselbase/ActionWithVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/ActionWithVessel.h b/src/vesselbase/ActionWithVessel.h
index f9f479ddf4e0bee703356fd466932bb828d3faad..ebacc8a34c0f7aa69e1c9fd86ceee100b9f41c22 100644
--- a/src/vesselbase/ActionWithVessel.h
+++ b/src/vesselbase/ActionWithVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/AltMin.cpp b/src/vesselbase/AltMin.cpp
index 1559ebbc7eb4defff3c4f5a9330c395879403bdb..a9e1f02e940d3d9d768b786480d6c53be7cfd0bb 100644
--- a/src/vesselbase/AltMin.cpp
+++ b/src/vesselbase/AltMin.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/AveragingVessel.cpp b/src/vesselbase/AveragingVessel.cpp
index c635ea131ee69606c635563c13a717e6e0f86227..a05f2a7f0a8ad78e676c900eba0a49a0efe64a81 100644
--- a/src/vesselbase/AveragingVessel.cpp
+++ b/src/vesselbase/AveragingVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/AveragingVessel.h b/src/vesselbase/AveragingVessel.h
index bec574c3e0c2623c3323160d2d265d44340a25eb..021b859d8088dac802614158cc595f4339cdf163 100644
--- a/src/vesselbase/AveragingVessel.h
+++ b/src/vesselbase/AveragingVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2016-2018 The plumed team
+ Copyright (c) 2016-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Between.cpp b/src/vesselbase/Between.cpp
index 6b1685cdcd41fe4c79ad4f04eb82d2aa4db1c1c6..d650cf35a935c8802929472c36fb020f709f6e34 100644
--- a/src/vesselbase/Between.cpp
+++ b/src/vesselbase/Between.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Between.h b/src/vesselbase/Between.h
index 126960e3ee132380150e71d364032f4ec896c10a..6b66e9333515cb49eb6d8210c8f0e3ecd7e22da2 100644
--- a/src/vesselbase/Between.h
+++ b/src/vesselbase/Between.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/BridgeVessel.cpp b/src/vesselbase/BridgeVessel.cpp
index 7bc5ddc0eb97d0377420b83075c893026c540f9d..e9c0d672f068d4762591894461f5ddb32211649e 100644
--- a/src/vesselbase/BridgeVessel.cpp
+++ b/src/vesselbase/BridgeVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/BridgeVessel.h b/src/vesselbase/BridgeVessel.h
index 427147899123b7f60b54f1e7c48bb7fcd95b291b..a1950ba07d1001d1d21674f4bd9bdd1e0a31e550 100644
--- a/src/vesselbase/BridgeVessel.h
+++ b/src/vesselbase/BridgeVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/FunctionVessel.cpp b/src/vesselbase/FunctionVessel.cpp
index 2a923028c5c6e20dc0dd7c11ca9bf4df697b71f5..e3d0c932b90195b053f56893a39c0552601f78ed 100644
--- a/src/vesselbase/FunctionVessel.cpp
+++ b/src/vesselbase/FunctionVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/FunctionVessel.h b/src/vesselbase/FunctionVessel.h
index 8ac82da113b565dab652f94e0e7d6127cb6ce4e3..4ac3cf6f17edb1c496db78c9b00f2b13a8ec3592 100644
--- a/src/vesselbase/FunctionVessel.h
+++ b/src/vesselbase/FunctionVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Highest.cpp b/src/vesselbase/Highest.cpp
index 2e6c897df0eaf2ac54d9ae98be735df1ce9dd020..bfd36bc782212b880a90e8662684102a606d975e 100644
--- a/src/vesselbase/Highest.cpp
+++ b/src/vesselbase/Highest.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Histogram.cpp b/src/vesselbase/Histogram.cpp
index c2a05b34935a9afa46947f350f4430beb06eed7f..5869c2ec74cf2e61fa22e4464dd0ddf0fd78f6b0 100644
--- a/src/vesselbase/Histogram.cpp
+++ b/src/vesselbase/Histogram.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/LessThan.cpp b/src/vesselbase/LessThan.cpp
index 32f46be0da3f3811328d34e2bf4f1b16b802ef39..73e75694d43546cab3d082a4d7659823e6a54d3b 100644
--- a/src/vesselbase/LessThan.cpp
+++ b/src/vesselbase/LessThan.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/LessThan.h b/src/vesselbase/LessThan.h
index cfd60dafb59e5f76be580cdb9303467083e36f9f..860403f013f965a6d113888284d42dcc9ddeb123 100644
--- a/src/vesselbase/LessThan.h
+++ b/src/vesselbase/LessThan.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2014-2018 The plumed team
+ Copyright (c) 2014-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Lowest.cpp b/src/vesselbase/Lowest.cpp
index c6ee2e518a32c32ac7eba47b0a2fa218744bc8b3..11e6cfa8169e6fc70b537b659e39976ada5fd277 100644
--- a/src/vesselbase/Lowest.cpp
+++ b/src/vesselbase/Lowest.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Max.cpp b/src/vesselbase/Max.cpp
index 7d791bf4ad818e229e1ac237028b70ab2622fdc7..94955b311bd79ff7f41983fb97911d097c05eea9 100644
--- a/src/vesselbase/Max.cpp
+++ b/src/vesselbase/Max.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Mean.cpp b/src/vesselbase/Mean.cpp
index cb3ab202ae49a62f739a3103ce01841b6688bf33..b9da1b39f205c8968b1c9298ae7afef5a60ecd21 100644
--- a/src/vesselbase/Mean.cpp
+++ b/src/vesselbase/Mean.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Min.cpp b/src/vesselbase/Min.cpp
index f83821a194cb19a270f0407a540c03634c5ccbad..ae33c0a39f1642be16216b5846f18b221e4ae528 100644
--- a/src/vesselbase/Min.cpp
+++ b/src/vesselbase/Min.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Moments.cpp b/src/vesselbase/Moments.cpp
index 6f1b2a33d59950d1ee70adf0f0a4eb5646a8ecea..e854009c444ed3b51731adefaaeef5b8c538d793 100644
--- a/src/vesselbase/Moments.cpp
+++ b/src/vesselbase/Moments.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/MoreThan.cpp b/src/vesselbase/MoreThan.cpp
index 94f0adaa2921fc726e86cd1d36636fe2ec2670ae..4e7af91c44b92fe0cb1223a9f66712c4a3b43597 100644
--- a/src/vesselbase/MoreThan.cpp
+++ b/src/vesselbase/MoreThan.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/OrderingVessel.cpp b/src/vesselbase/OrderingVessel.cpp
index 37305cbf09ba3d27878994b7122de0a70e25175f..94220ff2bb5736382066bf223aaea2912cd01c55 100644
--- a/src/vesselbase/OrderingVessel.cpp
+++ b/src/vesselbase/OrderingVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/OrderingVessel.h b/src/vesselbase/OrderingVessel.h
index 906f915cfc23dc84513ab7306019726a35582325..d1114f109d6f0d1a5e1128b504423452203595ee 100644
--- a/src/vesselbase/OrderingVessel.h
+++ b/src/vesselbase/OrderingVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/ShortcutVessel.cpp b/src/vesselbase/ShortcutVessel.cpp
index 9a9fe6801af9a765024eeaef1573ce8a69de46da..6d463a42ea8a5fb09b21f201c1ca8fe385d20ccf 100644
--- a/src/vesselbase/ShortcutVessel.cpp
+++ b/src/vesselbase/ShortcutVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/ShortcutVessel.h b/src/vesselbase/ShortcutVessel.h
index 91bb44d6c4109e303c25b6d48cc3b362d88f2f0b..a0dc51fcc1afd70f7f9730b471fbf5006e3ba9bd 100644
--- a/src/vesselbase/ShortcutVessel.h
+++ b/src/vesselbase/ShortcutVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/StoreDataVessel.cpp b/src/vesselbase/StoreDataVessel.cpp
index e3c72aab72975a8716d2ffd7b5651b288463629a..499dea85530e96492f3b7620399931675d0d21e4 100644
--- a/src/vesselbase/StoreDataVessel.cpp
+++ b/src/vesselbase/StoreDataVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/StoreDataVessel.h b/src/vesselbase/StoreDataVessel.h
index b54e46ffad2e059e0f032826ea4cab70c89cacfe..2775a80f61a3cce6e578bc870fdaafd8b969ae11 100644
--- a/src/vesselbase/StoreDataVessel.h
+++ b/src/vesselbase/StoreDataVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Sum.cpp b/src/vesselbase/Sum.cpp
index 529ad4a9feed2149aec2ac332c0d82680346e0b0..1f460a548a3a2e2934d850ea2dcd9530822a0e58 100644
--- a/src/vesselbase/Sum.cpp
+++ b/src/vesselbase/Sum.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2018 The plumed team
+ Copyright (c) 2013-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/ValueVessel.cpp b/src/vesselbase/ValueVessel.cpp
index 25fbf40239c7b34fde2f567e5ad35a979f236c5a..40d6504abb070dac401dde683c92e6bb9a193c53 100644
--- a/src/vesselbase/ValueVessel.cpp
+++ b/src/vesselbase/ValueVessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/ValueVessel.h b/src/vesselbase/ValueVessel.h
index ead67d95cb080c13ce81f10d31142a2f3b448d5b..a322e54c119b86b7ea70a4d94bd714c5f04ba30c 100644
--- a/src/vesselbase/ValueVessel.h
+++ b/src/vesselbase/ValueVessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2015-2018 The plumed team
+ Copyright (c) 2015-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Vessel.cpp b/src/vesselbase/Vessel.cpp
index 8bb4a85e6be77d9f6633dde10cfb695d9df9983f..e5a4fab4c5b82bbeb884b9fb66a5aa116fa6e011 100644
--- a/src/vesselbase/Vessel.cpp
+++ b/src/vesselbase/Vessel.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/Vessel.h b/src/vesselbase/Vessel.h
index 62f181852648ff1b3d32bce2b8aae331ac01f95e..51b497e7e8d9f1be911b1c7a0c1009569f4371dd 100644
--- a/src/vesselbase/Vessel.h
+++ b/src/vesselbase/Vessel.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/VesselRegister.cpp b/src/vesselbase/VesselRegister.cpp
index 2bdfdf7afa1bdf5c6703abadb048f02021c518f9..dff90a4b25d847d6abd89ab6ea6ffd622a65c48e 100644
--- a/src/vesselbase/VesselRegister.cpp
+++ b/src/vesselbase/VesselRegister.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/vesselbase/VesselRegister.h b/src/vesselbase/VesselRegister.h
index b589f7936ac8facaaf4c6b0b82287905b74966c5..2953c2fe01fb5f378b7aaeb3ecb111d98cd0bc5f 100644
--- a/src/vesselbase/VesselRegister.h
+++ b/src/vesselbase/VesselRegister.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2018 The plumed team
+ Copyright (c) 2012-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/wrapper/Plumed.c b/src/wrapper/Plumed.c
index 40fb1ae0177a628369bbf11917f305aa6cd704cd..d70dc23eec7a97e7b6d5fad7b0ff481855b668f9 100644
--- a/src/wrapper/Plumed.c
+++ b/src/wrapper/Plumed.c
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/wrapper/Plumed.h b/src/wrapper/Plumed.h
index 89836006ca096084aba7a6afb5c7ec96d5b921d4..6f0ba213428489a4f7e49ee3001a7be3fb87c695 100644
--- a/src/wrapper/Plumed.h
+++ b/src/wrapper/Plumed.h
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/src/wrapper/PlumedStatic.cpp b/src/wrapper/PlumedStatic.cpp
index 144b47dfd0a4bbc80ce8f647be210f0f7b4f3465..588d084b6b840b3bd9ada969c9763608dfe05581 100644
--- a/src/wrapper/PlumedStatic.cpp
+++ b/src/wrapper/PlumedStatic.cpp
@@ -1,5 +1,5 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2018 The plumed team
+ Copyright (c) 2011-2019 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed.org for more information.
diff --git a/user-doc/extract b/user-doc/extract
index 8e0b9e1a2a5dd69fc0c3b3bb9f2ebf14e88b66ec..13848a90c24f5d5d30a8242108ce9b8b7a85d3e4 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -48,7 +48,7 @@ EOF
cat << EOF
-\note This command line tool is implemented as a shell script. It's help message is pasted below:
+\note This command line tool is implemented as a shell script. Its help message is pasted below:
\verbatim
EOF