diff --git a/CHANGES/Unreleased.txt b/CHANGES/Unreleased.txt
index 83a43603efa2d7ade39b2ea0f2d557eb8524f13a..67196435854aa70aa764c792e5c4fb63a0dbfb58 100644
--- a/CHANGES/Unreleased.txt
+++ b/CHANGES/Unreleased.txt
@@ -28,6 +28,7 @@ Changes from version 2.2 which are relevant for users:
\ref REWEIGHT_METAD. These actions calculate the quantities that were calculated using the keywords REWEIGHT_BIAS and REWEIGHT_TEMP that
used to appear in the old HISTOGRAM method. Now those these methods can be used in any methods that calculate ensemble averages for
example \ref HISTOGRAM and \ref AVERAGE
+ - Manual is now build with locally compiled plumed
- New actions:
- \ref FIXEDATOM
- \ref HBOND_MATRIX
@@ -66,5 +67,7 @@ Changes from version 2.2 which are relevant for users:
- \ref driver now allows --trajectory-stride to be set to zero when reading with --ixtc/--itrr. In this case, step number is read from the trajectory file.
- MetaD and PBMetaD can now be restarted from a GRID
- Added keywords TARGET and DAMPFACTOR in \ref METAD
+- Other features:
+ - Added a plumed-config command line tool. Can be used to inspect configuration also when cross compiling.
*/
diff --git a/CHANGES/v2.2.txt b/CHANGES/v2.2.txt
index 11ff0c90c20d4ddf92e0fd696f9ed264a3095730..cbb22ca2a6c9c9be5745a2945eed40c909ef1a28 100644
--- a/CHANGES/v2.2.txt
+++ b/CHANGES/v2.2.txt
@@ -146,6 +146,8 @@ For users:
- When looking for a value outside the GRID now the error include the name of the responsible
collective variable
- Numerical check in LatticeReduction made less picky.
+- Added --disable-dependency-tracking to ./configure
+- \ref LOAD now works also when plumed is installed with a suffix.
For developers:
diff --git a/Makefile b/Makefile
index 4c2be18b962e61753df2b9dcd8f677a5104b9912..d9d1476ce4a257b0a562eeb3ee6c2adbe8436700 100644
--- a/Makefile
+++ b/Makefile
@@ -9,7 +9,7 @@ SUBDIRS := $(SRCDIRS) user-doc developer-doc regtest
SUBDIRSCLEAN:=$(addsuffix .clean,$(SUBDIRS))
-.PHONY: all lib clean $(SRCDIRS) doc docclean check cppcheck distclean
+.PHONY: all lib clean $(SRCDIRS) doc docclean check cppcheck distclean all_plus_docs
# if machine dependent configuration has been found:
ifdef GCCDEP
@@ -17,6 +17,12 @@ all:
$(MAKE) lib
$(MAKE) -C vim
+# target useful for macports
+# it builds the code then the documentation
+all_plus_docs:
+ $(MAKE) all
+ $(MAKE) docs
+
lib:
$(MAKE) -C src
diff --git a/Makefile.conf.in b/Makefile.conf.in
index b525a10a4916aed8b4a6c789858b7e107629e704..9059e0c269af3cee4543fdb860baec7c70b0f989 100644
--- a/Makefile.conf.in
+++ b/Makefile.conf.in
@@ -13,6 +13,7 @@ SOEXT=@SOEXT@
LD=@LD@
LDSO=@LDSO@
GCCDEP=@CXX@
+disable_dependency_tracking=@disable_dependency_tracking@
prefix=@prefix@
program_name=@program_name@
program_transform_name=@program_transform_name@
diff --git a/configure b/configure
index 54434ece1578311ad0c3ed956d35ebd50b1e681f..96ca564153ae5389ece0186dc8ce06cdda91af22 100755
--- a/configure
+++ b/configure
@@ -625,6 +625,7 @@ program_name
LD_RO
program_can_run_mpi
program_can_run
+disable_dependency_tracking
xxd
make_pdfdoc
dot
@@ -700,6 +701,7 @@ enable_basic_warnings
enable_fussy
enable_debug_glibcxx
enable_shared
+enable_dependency_tracking
enable_cxx_exceptions
enable_ld_r
enable_mpi
@@ -1362,6 +1364,8 @@ Optional Features:
--enable-fussy enable fussy warnings, default: no
--enable-debug-glibcxx enable enable boundary check, default: no
--enable-shared enable shared libs, default: yes
+ --enable-dependency-tracking
+ enable dependency tracking, default: yes
--enable-cxx-exceptions enable c++ exceptions, default: no
--enable-ld-r enable group object files, default: yes
--enable-mpi enable search for mpi, default: yes
@@ -2528,6 +2532,24 @@ fi
+dependency_tracking=
+# Check whether --enable-dependency-tracking was given.
+if test "${enable_dependency_tracking+set}" = set; then :
+ enableval=$enable_dependency_tracking; case "${enableval}" in
+ (yes) dependency_tracking=true ;;
+ (no) dependency_tracking=false ;;
+ (*) as_fn_error $? "wrong argument to --enable-dependency-tracking" "$LINENO" 5 ;;
+ esac
+else
+ case "yes" in
+ (yes) dependency_tracking=true ;;
+ (no) dependency_tracking=false ;;
+ esac
+
+fi
+
+
+
cxx_exceptions=
# Check whether --enable-cxx-exceptions was given.
if test "${enable_cxx_exceptions+set}" = set; then :
@@ -6916,6 +6938,18 @@ then
fi
+if test "$dependency_tracking" = true
+then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: dependency tracking enabled" >&5
+$as_echo "$as_me: dependency tracking enabled" >&6;}
+ disable_dependency_tracking=no
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: dependency tracking disabled" >&5
+$as_echo "$as_me: dependency tracking disabled" >&6;}
+ disable_dependency_tracking=yes
+fi
+
+
program_can_run=""
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a program can be run on this machine" >&5
$as_echo_n "checking whether a program can be run on this machine... " >&6; }
@@ -7139,6 +7173,9 @@ fi
if test "$(echo "$program_name" | tr 'A-Z' 'a-z')" != "$(echo "$program_name" | tr 'A-Z' 'a-z' | sed 's/-patch$//')" ; then
as_fn_error $? "$program_name is not a valid program name (should not terminate with -patch)" "$LINENO" 5
fi
+if test "$(echo "$program_name" | tr 'A-Z' 'a-z')" != "$(echo "$program_name" | tr 'A-Z' 'a-z' | sed 's/-config$//')" ; then
+ as_fn_error $? "$program_name is not a valid program name (should not terminate with -config)" "$LINENO" 5
+fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: **** PLUMED will be installed using the following paths:" >&5
$as_echo "$as_me: **** PLUMED will be installed using the following paths:" >&6;}
diff --git a/configure.ac b/configure.ac
index cd09cf4e1ceadb16305f4f32211ddc4597b97895..4305c4c68af95c6c9416d11048043f2203ecf0ed 100644
--- a/configure.ac
+++ b/configure.ac
@@ -163,6 +163,7 @@ PLUMED_CONFIG_ENABLE([basic_warnings],[basic-warnings],[basic warnings],[yes])
PLUMED_CONFIG_ENABLE([fussy],[fussy],[fussy warnings],[no])
PLUMED_CONFIG_ENABLE([debug_glibcxx],[debug-glibcxx],[enable boundary check],[no])
PLUMED_CONFIG_ENABLE([shared],[shared],[shared libs],[yes])
+PLUMED_CONFIG_ENABLE([dependency_tracking],[dependency-tracking],[dependency tracking],[yes])
PLUMED_CONFIG_ENABLE([cxx_exceptions],[cxx-exceptions],[c++ exceptions],[no])
PLUMED_CONFIG_ENABLE([ld_r],[ld-r],[group object files],[yes])
PLUMED_CONFIG_ENABLE([mpi],[mpi],[search for mpi],[yes])
@@ -598,6 +599,16 @@ then
AC_MSG_ERROR([xxd should be installed for PLUMED to compile properly])
fi
+AC_SUBST(disable_dependency_tracking)
+if test "$dependency_tracking" = true
+then
+ AC_MSG_NOTICE([dependency tracking enabled])
+ disable_dependency_tracking=no
+else
+ AC_MSG_NOTICE([dependency tracking disabled])
+ disable_dependency_tracking=yes
+fi
+
AC_SUBST(program_can_run)
program_can_run=""
AC_MSG_CHECKING([whether a program can be run on this machine])
@@ -768,6 +779,9 @@ fi
if test "$(echo "$program_name" | tr '[A-Z]' '[a-z]')" != "$(echo "$program_name" | tr '[A-Z]' '[a-z]' | sed 's/-patch$//')" ; then
AC_MSG_ERROR([$program_name is not a valid program name (should not terminate with -patch)])
fi
+if test "$(echo "$program_name" | tr '[A-Z]' '[a-z]')" != "$(echo "$program_name" | tr '[A-Z]' '[a-z]' | sed 's/-config$//')" ; then
+ AC_MSG_ERROR([$program_name is not a valid program name (should not terminate with -config)])
+fi
AC_MSG_NOTICE([**** PLUMED will be installed using the following paths:])
AC_MSG_NOTICE([**** prefix: $prefix])
diff --git a/developer-doc/go-doxygen b/developer-doc/go-doxygen
index 398f1044a835463fcfceef1cc6edeb2161409002..363a9d6b6c7048a2b4312cce70a04698bb2c4c26 100755
--- a/developer-doc/go-doxygen
+++ b/developer-doc/go-doxygen
@@ -1,8 +1,10 @@
#! /bin/bash
+source ../sourceme.sh
+
{
cat Doxyfile
- echo "PROJECT_NUMBER = \"$(plumed --no-mpi info --version)\""
+ echo "PROJECT_NUMBER = \"$(../src/lib/plumed --no-mpi info --version)\""
echo "INPUT+=" ../src/*/ ../src/*/*/ ../.github/*.md
echo "REFERENCES_RELATION=NO"
echo "REFERENCED_BY_RELATION=NO"
diff --git a/regtest/multicolvar/rt-histogram/Makefile b/regtest/multicolvar/rt-histogram/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/multicolvar/rt-histogram/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/multicolvar/rt-histogram/analysis.0.density.reference b/regtest/multicolvar/rt-histogram/analysis.0.density.reference
new file mode 100644
index 0000000000000000000000000000000000000000..a41defa4d599244318dabf402912067033619c10
--- /dev/null
+++ b/regtest/multicolvar/rt-histogram/analysis.0.density.reference
@@ -0,0 +1,207 @@
+#! FIELDS c1 h dh_c1
+#! SET normalisation 2.0000
+#! SET min_c1 0
+#! SET max_c1 10
+#! SET nbins_c1 200
+#! SET periodic_c1 false
+ 0.0000 0.0001 0.0050
+ 0.0500 0.0009 0.0324
+ 0.1000 0.0050 0.1620
+ 0.1500 0.0224 0.6164
+ 0.2000 0.0783 1.7663
+ 0.2500 0.2135 3.7483
+ 0.3000 0.4533 5.6924
+ 0.3500 0.7495 5.6656
+ 0.4000 0.9652 2.4702
+ 0.4500 0.9681 -2.3629
+ 0.5000 0.7562 -5.6266
+ 0.5500 0.4600 -5.7228
+ 0.6000 0.2179 -3.8010
+ 0.6500 0.0804 -1.8045
+ 0.7000 0.0231 -0.6341
+ 0.7500 0.0052 -0.1678
+ 0.8000 0.0009 -0.0337
+ 0.8500 0.0002 0.0081
+ 0.9000 0.0014 0.0497
+ 0.9500 0.0074 0.2323
+ 1.0000 0.0313 0.8241
+ 1.0500 0.1030 2.1951
+ 1.1000 0.2638 4.3026
+ 1.1500 0.5262 5.9506
+ 1.2000 0.8174 5.1565
+ 1.2500 0.9889 1.2938
+ 1.3000 0.9317 -3.4393
+ 1.3500 0.6836 -5.9417
+ 1.4000 0.3906 -5.3486
+ 1.4500 0.1739 -3.2497
+ 1.5000 0.0603 -1.4276
+ 1.5500 0.0163 -0.4667
+ 1.6000 0.0034 -0.1152
+ 1.6500 0.0006 -0.0217
+ 1.7000 0.0000 0.0000
+ 1.7500 0.0000 0.0000
+ 1.8000 0.0000 0.0000
+ 1.8500 0.0000 0.0000
+ 1.9000 0.0000 0.0000
+ 1.9500 0.0000 0.0000
+ 2.0000 0.0000 0.0000
+ 2.0500 0.0000 0.0000
+ 2.1000 0.0000 0.0000
+ 2.1500 0.0000 0.0000
+ 2.2000 0.0000 0.0000
+ 2.2500 0.0000 0.0000
+ 2.3000 0.0000 0.0000
+ 2.3500 0.0000 0.0000
+ 2.4000 0.0000 0.0000
+ 2.4500 0.0003 0.0109
+ 2.5000 0.0018 0.0641
+ 2.5500 0.0095 0.2918
+ 2.6000 0.0390 1.0057
+ 2.6500 0.1255 2.6341
+ 2.7000 0.3189 5.2098
+ 2.7500 0.6458 7.7105
+ 2.8000 1.0587 8.3640
+ 2.8500 1.4334 6.1545
+ 2.9000 1.6365 1.7228
+ 2.9500 1.5956 -3.3127
+ 3.0000 1.3249 -7.1765
+ 3.0500 0.9219 -8.4493
+ 3.1000 0.5261 -7.0148
+ 3.1500 0.2417 -4.3082
+ 3.2000 0.0882 -1.9870
+ 3.2500 0.0253 -0.6936
+ 3.3000 0.0057 -0.1820
+ 3.3500 0.0010 -0.0372
+ 3.4000 0.0000 0.0000
+ 3.4500 0.0000 0.0000
+ 3.5000 0.0000 0.0000
+ 3.5500 0.0000 0.0000
+ 3.6000 0.0000 0.0000
+ 3.6500 0.0000 0.0000
+ 3.7000 0.0000 0.0000
+ 3.7500 0.0000 0.0000
+ 3.8000 0.0000 0.0000
+ 3.8500 0.0000 0.0000
+ 3.9000 0.0000 0.0000
+ 3.9500 0.0000 0.0000
+ 4.0000 0.0000 0.0000
+ 4.0500 0.0000 0.0000
+ 4.1000 0.0000 0.0000
+ 4.1500 0.0000 0.0000
+ 4.2000 0.0000 0.0000
+ 4.2500 0.0000 0.0000
+ 4.3000 0.0000 0.0000
+ 4.3500 0.0000 0.0000
+ 4.4000 0.0000 0.0000
+ 4.4500 0.0000 0.0000
+ 4.5000 0.0000 0.0000
+ 4.5500 0.0000 0.0000
+ 4.6000 0.0000 0.0000
+ 4.6500 0.0000 0.0000
+ 4.7000 0.0000 0.0000
+ 4.7500 0.0000 0.0000
+ 4.8000 0.0000 0.0000
+ 4.8500 0.0000 0.0000
+ 4.9000 0.0000 0.0000
+ 4.9500 0.0000 0.0000
+ 5.0000 0.0000 0.0000
+ 5.0500 0.0000 0.0000
+ 5.1000 0.0000 0.0000
+ 5.1500 0.0000 0.0000
+ 5.2000 0.0000 0.0000
+ 5.2500 0.0000 0.0000
+ 5.3000 0.0000 0.0000
+ 5.3500 0.0000 0.0000
+ 5.4000 0.0000 0.0000
+ 5.4500 0.0000 0.0000
+ 5.5000 0.0000 0.0000
+ 5.5500 0.0000 0.0000
+ 5.6000 0.0000 0.0000
+ 5.6500 0.0000 0.0000
+ 5.7000 0.0000 0.0000
+ 5.7500 0.0000 0.0000
+ 5.8000 0.0000 0.0000
+ 5.8500 0.0000 0.0000
+ 5.9000 0.0000 0.0000
+ 5.9500 0.0000 0.0000
+ 6.0000 0.0000 0.0000
+ 6.0500 0.0000 0.0000
+ 6.1000 0.0000 0.0000
+ 6.1500 0.0000 0.0000
+ 6.2000 0.0000 0.0000
+ 6.2500 0.0000 0.0000
+ 6.3000 0.0000 0.0000
+ 6.3500 0.0000 0.0000
+ 6.4000 0.0000 0.0000
+ 6.4500 0.0000 0.0000
+ 6.5000 0.0000 0.0000
+ 6.5500 0.0000 0.0000
+ 6.6000 0.0000 0.0000
+ 6.6500 0.0000 0.0000
+ 6.7000 0.0000 0.0000
+ 6.7500 0.0000 0.0000
+ 6.8000 0.0000 0.0000
+ 6.8500 0.0000 0.0000
+ 6.9000 0.0000 0.0000
+ 6.9500 0.0000 0.0000
+ 7.0000 0.0000 0.0000
+ 7.0500 0.0000 0.0000
+ 7.1000 0.0000 0.0000
+ 7.1500 0.0000 0.0000
+ 7.2000 0.0000 0.0000
+ 7.2500 0.0000 0.0000
+ 7.3000 0.0000 0.0000
+ 7.3500 0.0000 0.0000
+ 7.4000 0.0000 0.0000
+ 7.4500 0.0000 0.0000
+ 7.5000 0.0000 0.0000
+ 7.5500 0.0000 0.0000
+ 7.6000 0.0000 0.0000
+ 7.6500 0.0000 0.0000
+ 7.7000 0.0000 0.0000
+ 7.7500 0.0000 0.0000
+ 7.8000 0.0000 0.0000
+ 7.8500 0.0000 0.0000
+ 7.9000 0.0000 0.0000
+ 7.9500 0.0000 0.0000
+ 8.0000 0.0000 0.0000
+ 8.0500 0.0000 0.0000
+ 8.1000 0.0000 0.0000
+ 8.1500 0.0000 0.0000
+ 8.2000 0.0000 0.0000
+ 8.2500 0.0000 0.0000
+ 8.3000 0.0000 0.0000
+ 8.3500 0.0000 0.0000
+ 8.4000 0.0000 0.0000
+ 8.4500 0.0000 0.0000
+ 8.5000 0.0000 0.0000
+ 8.5500 0.0000 0.0000
+ 8.6000 0.0000 0.0000
+ 8.6500 0.0000 0.0000
+ 8.7000 0.0000 0.0000
+ 8.7500 0.0000 0.0000
+ 8.8000 0.0000 0.0000
+ 8.8500 0.0000 0.0000
+ 8.9000 0.0000 0.0000
+ 8.9500 0.0000 0.0000
+ 9.0000 0.0000 0.0000
+ 9.0500 0.0000 0.0000
+ 9.1000 0.0000 0.0000
+ 9.1500 0.0000 0.0000
+ 9.2000 0.0000 0.0000
+ 9.2500 0.0000 0.0000
+ 9.3000 0.0000 0.0000
+ 9.3500 0.0000 0.0000
+ 9.4000 0.0000 0.0000
+ 9.4500 0.0000 0.0000
+ 9.5000 0.0000 0.0000
+ 9.5500 0.0000 0.0000
+ 9.6000 0.0000 0.0000
+ 9.6500 0.0000 0.0000
+ 9.7000 0.0000 0.0000
+ 9.7500 0.0000 0.0000
+ 9.8000 0.0000 0.0000
+ 9.8500 0.0000 0.0000
+ 9.9000 0.0000 0.0000
+ 9.9500 0.0000 0.0000
+ 10.0000 0.0000 0.0000
diff --git a/regtest/multicolvar/rt-histogram/config b/regtest/multicolvar/rt-histogram/config
new file mode 100644
index 0000000000000000000000000000000000000000..0a3f96138a109d8802b16620c5c6c48534bbf82b
--- /dev/null
+++ b/regtest/multicolvar/rt-histogram/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
diff --git a/regtest/multicolvar/rt-histogram/density.reference b/regtest/multicolvar/rt-histogram/density.reference
new file mode 100644
index 0000000000000000000000000000000000000000..721bb5dc5f9d58027fd39b2b5fd96e342f85691e
--- /dev/null
+++ b/regtest/multicolvar/rt-histogram/density.reference
@@ -0,0 +1,207 @@
+#! FIELDS c1 h dh_c1
+#! SET normalisation 4.0000
+#! SET min_c1 0
+#! SET max_c1 10
+#! SET nbins_c1 200
+#! SET periodic_c1 false
+ 0.0000 0.0001 0.0025
+ 0.0500 0.0004 0.0162
+ 0.1000 0.0025 0.0810
+ 0.1500 0.0112 0.3082
+ 0.2000 0.0391 0.8832
+ 0.2500 0.1067 1.8742
+ 0.3000 0.2266 2.8462
+ 0.3500 0.3748 2.8349
+ 0.4000 0.4830 1.2491
+ 0.4500 0.4862 -1.1096
+ 0.5000 0.3881 -2.5335
+ 0.5500 0.2657 -2.0409
+ 0.6000 0.2084 -0.1153
+ 0.6500 0.2555 1.8884
+ 0.7000 0.3748 2.5746
+ 0.7500 0.4799 1.3290
+ 0.8000 0.4889 -1.0132
+ 0.8500 0.3894 -2.7346
+ 0.9000 0.2425 -2.8733
+ 0.9500 0.1221 -1.8172
+ 1.0000 0.0676 -0.3234
+ 1.0500 0.0948 1.4873
+ 1.1000 0.2258 3.8354
+ 1.1500 0.4793 6.1958
+ 1.2000 0.8188 6.9797
+ 1.2500 1.1283 4.9161
+ 1.3000 1.2739 0.7187
+ 1.3500 1.2013 -3.4327
+ 1.4000 0.9607 -5.8303
+ 1.4500 0.6540 -6.1152
+ 1.5000 0.3752 -4.8567
+ 1.5500 0.1780 -3.0156
+ 1.6000 0.0685 -1.4591
+ 1.6500 0.0211 -0.5460
+ 1.7000 0.0050 -0.1515
+ 1.7500 0.0010 -0.0342
+ 1.8000 0.0000 0.0000
+ 1.8500 0.0000 0.0000
+ 1.9000 0.0000 0.0000
+ 1.9500 0.0001 0.0036
+ 2.0000 0.0006 0.0222
+ 2.0500 0.0033 0.1056
+ 2.1000 0.0143 0.3818
+ 2.1500 0.0479 1.0371
+ 2.2000 0.1248 2.0772
+ 2.2500 0.2531 2.9478
+ 2.3000 0.3999 2.6572
+ 2.3500 0.4920 0.8093
+ 2.4000 0.4714 -1.5815
+ 2.4500 0.3519 -2.9334
+ 2.5000 0.2053 -2.6980
+ 2.5500 0.0973 -1.5523
+ 2.6000 0.0521 -0.2588
+ 2.6500 0.0717 1.0632
+ 2.7000 0.1613 2.5411
+ 2.7500 0.3232 3.8430
+ 2.8000 0.5293 4.1820
+ 2.8500 0.7167 3.0772
+ 2.9000 0.8183 0.8614
+ 2.9500 0.7978 -1.6564
+ 3.0000 0.6625 -3.5882
+ 3.0500 0.4609 -4.2246
+ 3.1000 0.2631 -3.5074
+ 3.1500 0.1209 -2.1541
+ 3.2000 0.0441 -0.9935
+ 3.2500 0.0127 -0.3468
+ 3.3000 0.0028 -0.0910
+ 3.3500 0.0005 -0.0186
+ 3.4000 0.0000 0.0000
+ 3.4500 0.0000 0.0000
+ 3.5000 0.0000 0.0000
+ 3.5500 0.0000 0.0000
+ 3.6000 0.0000 0.0000
+ 3.6500 0.0000 0.0000
+ 3.7000 0.0000 0.0000
+ 3.7500 0.0000 0.0000
+ 3.8000 0.0000 0.0000
+ 3.8500 0.0000 0.0000
+ 3.9000 0.0000 0.0000
+ 3.9500 0.0000 0.0000
+ 4.0000 0.0000 0.0000
+ 4.0500 0.0000 0.0000
+ 4.1000 0.0000 0.0000
+ 4.1500 0.0000 0.0000
+ 4.2000 0.0000 0.0000
+ 4.2500 0.0000 0.0000
+ 4.3000 0.0000 0.0000
+ 4.3500 0.0000 0.0000
+ 4.4000 0.0000 0.0000
+ 4.4500 0.0000 0.0000
+ 4.5000 0.0000 0.0000
+ 4.5500 0.0000 0.0000
+ 4.6000 0.0000 0.0000
+ 4.6500 0.0000 0.0000
+ 4.7000 0.0000 0.0000
+ 4.7500 0.0000 0.0000
+ 4.8000 0.0000 0.0000
+ 4.8500 0.0000 0.0000
+ 4.9000 0.0000 0.0000
+ 4.9500 0.0000 0.0000
+ 5.0000 0.0000 0.0000
+ 5.0500 0.0000 0.0000
+ 5.1000 0.0000 0.0000
+ 5.1500 0.0000 0.0000
+ 5.2000 0.0000 0.0000
+ 5.2500 0.0000 0.0000
+ 5.3000 0.0000 0.0000
+ 5.3500 0.0000 0.0000
+ 5.4000 0.0000 0.0000
+ 5.4500 0.0000 0.0000
+ 5.5000 0.0000 0.0000
+ 5.5500 0.0000 0.0000
+ 5.6000 0.0000 0.0000
+ 5.6500 0.0000 0.0000
+ 5.7000 0.0000 0.0000
+ 5.7500 0.0000 0.0000
+ 5.8000 0.0000 0.0000
+ 5.8500 0.0000 0.0000
+ 5.9000 0.0000 0.0000
+ 5.9500 0.0000 0.0000
+ 6.0000 0.0000 0.0000
+ 6.0500 0.0000 0.0000
+ 6.1000 0.0000 0.0000
+ 6.1500 0.0000 0.0000
+ 6.2000 0.0000 0.0000
+ 6.2500 0.0000 0.0000
+ 6.3000 0.0000 0.0000
+ 6.3500 0.0000 0.0000
+ 6.4000 0.0000 0.0000
+ 6.4500 0.0000 0.0000
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diff --git a/regtest/multicolvar/rt-histogram/plumed.dat b/regtest/multicolvar/rt-histogram/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..357ff4f2613dcd62f23889a921a4a21deb98e0e8
--- /dev/null
+++ b/regtest/multicolvar/rt-histogram/plumed.dat
@@ -0,0 +1,3 @@
+c1: COORDINATIONNUMBER SPECIESA=1,2 SPECIESB=1-200 SWITCH={RATIONAL R_0=1.0}
+h: MULTICOLVARHISTOGRAM DATA=c1 GRID_BIN=200 GRID_MIN=0 GRID_MAX=10 BANDWIDTH=0.1
+DUMPGRID GRID=h STRIDE=20 FILE=density FMT=%8.4f
diff --git a/regtest/multicolvar/rt-histogram/trajectory.xyz b/regtest/multicolvar/rt-histogram/trajectory.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..13fdd1145b035bccce5f23b233adf6afe3b7099f
--- /dev/null
+++ b/regtest/multicolvar/rt-histogram/trajectory.xyz
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+Ar 5.60079 2.5502 1.13809
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+Ar 6.55088 0.616576 2.78534
+Ar 1.88598 7.69475 5.67168
+Ar 6.47486 3.03928 1.09507
+Ar 4.7741 8.22263 7.81637
+Ar 4.67219 5.55962 0.577062
+Ar 2.12326 5.69258 5.24466
+Ar 1.13544 3.34053 4.33406
+Ar 4.29996 9.34654 7.28091
+Ar 8.37924 9.93932 0.116003
+Ar 3.85205 1.44965 4.19509
+Ar 7.23612 7.55002 3.13938
+Ar 6.55743 0.648518 9.64876
+Ar 5.7365 3.36003 2.04684
+Ar 5.40897 8.60198 3.3941
+Ar 8.8512 2.10176 4.25653
+Ar 8.37896 5.1477 7.42059
+Ar 2.43862 5.87741 1.59926
+Ar 0.857514 2.23809 5.65975
+Ar 5.20599 7.00215 5.14985
+Ar 2.245 1.74703 2.32142
+Ar 8.19193 1.72719 8.80939
+Ar 1.92166 7.2765 6.12871
+Ar 9.60594 7.0251 0.783787
+Ar 7.49085 8.79009 5.01202
+Ar 5.12531 1.03312 3.61994
+Ar 6.68699 8.23934 8.65404
+Ar 5.85407 9.37865 6.91885
+Ar 8.28803 6.91793 9.71231
+Ar 0.154994 4.99089 1.81561
+Ar 7.47213 4.11338 3.59508
+Ar 4.94654 6.47822 9.44509
+Ar 5.0936 8.16921 9.92238
+Ar 1.06304 6.57717 2.5574
+Ar 6.40198 8.14627 4.44098
+Ar 4.90826 3.16757 7.38135
+Ar 8.95555 6.00488 4.08592
+Ar 3.95336 4.17199 8.71278
+Ar 5.47846 6.40654 4.7525
+Ar 7.36347 7.83685 3.85437
+Ar 8.27623 8.65346 8.70981
+Ar 1.6617 8.19874 6.1984
+Ar 4.50241 2.00458 0.971449
+Ar 7.76135 5.04448 2.63619
+Ar 8.71161 6.07659 9.21288
+Ar 6.76582 3.08604 7.01563
+Ar 9.21579 9.78598 2.96539
+Ar 0.855888 4.90513 0.457679
+Ar 8.2507 9.56063 5.59129
+Ar 2.08136 1.42156 2.19529
+Ar 7.70847 6.17798 3.27745
+Ar 0.754502 0.909584 7.37261
+Ar 9.43419 0.423678 0.760008
+Ar 5.435 6.11527 9.33427
+Ar 8.02994 9.2571 4.03267
+Ar 0.606574 4.6945 0.383465
+Ar 9.35323 9.74732 3.19666
+Ar 6.36671 5.22578 9.74157
+Ar 5.95597 1.91401 8.77683
+Ar 1.40332 5.56064 7.74702
+Ar 6.30169 2.42405 1.04518
+Ar 2.34835 8.69722 4.20179
+Ar 0.670357 6.6892 5.34706
+Ar 8.63881 2.45052 5.89593
+Ar 1.26038 3.14406 2.16308
+Ar 1.58515 1.54755 9.59656
+Ar 7.05547 1.25183 9.5881
+Ar 3.01513 5.25619 0.776404
+Ar 2.64111 9.14238 6.04527
+Ar 6.33888 7.62816 6.48992
+Ar 5.49963 2.2152 0.907294
+Ar 7.72449 5.53304 3.83241
+Ar 4.46581 6.90197 1.34986
+Ar 7.2834 2.1483 6.41683
+Ar 9.77827 3.36416 1.43895
+Ar 3.87117 2.67413 4.07172
+Ar 6.46873 9.92897 6.25149
+Ar 0.268344 0.0617421 7.69979
+Ar 8.13526 9.23425 0.117487
+Ar 9.51619 8.66444 3.31978
+Ar 2.70354 8.34826 9.27735
+Ar 3.98257 4.97261 4.6757
diff --git a/scripts/config.sh b/scripts/config.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2f68e6b2b64fe2d7d68ec9772dad352ff1ee3221
--- /dev/null
+++ b/scripts/config.sh
@@ -0,0 +1,90 @@
+#! /bin/bash
+
+MANUAL="\
+
+Options:
+ -h, --help
+ print this help and exit
+ -q, --quiet
+ don't write anything, just return true of false
+ show
+ dump a full configuration file
+ has [word1 [word2]..]
+ check if plumed has features words
+ module [word1 [word2]..]
+ check if plumed has enables modules words
+
+Examples:
+
+Check if plumed as xdrfile enabled
+> plumed config has xdrfile
+Check if plumed as xdrfile AND zlib enabled
+> plumed config has xdrfile zlib
+Check if plumed as module colvar active
+> plumed config module colvar
+"
+
+configfile="$(cat "$PLUMED_ROOT"/src/config/config.txt)"
+
+quiet=no
+list=no
+checklist=""
+for opt
+do
+ case "$opt" in
+ (--help|-h) echo "$MANUAL" ; exit ;;
+ (--description)
+ echo "inquire plumed about how it was configure"
+ exit 0
+ ;;
+ (--quiet|-q) quiet=yes ;;
+ (--version|-v) action=version ;;
+ (show)
+ echo "$configfile"
+ exit 0
+ ;;
+ (has) action=has ;;
+ (module) action=module ;;
+ (*)
+ checklist="$checklist $opt"
+ esac
+done
+
+if test -z "$checklist" && ( test "$action" = show || test "$action" = has || test "$action" = module)
+then
+ test "$quiet" = no && echo "nothing to do"
+ exit 1
+fi
+
+case $action in
+(has|module)
+ retval=0
+ for check in $checklist
+ do
+
+ ff=$(
+ echo "$configfile" |
+ awk -v action="$action" -v check="$check" '{ if($1==action && $2==check){ print $3;exit } }'
+ )
+
+ if test "$ff" = on ; then
+ test "$quiet" = no && echo "$check on"
+ elif test "$ff" = off ; then
+ test "$quiet" = no && echo "$check off"
+ retval=1
+ else
+ test "$quiet" = no && echo "$check not found"
+ retval=1
+ fi
+
+ done
+
+ exit $retval
+ ;;
+(version)
+ long=$(echo "$configfile" | grep -v \# | awk '{ if($1=="version" && $2=="long") print $3 }')
+ git=$(echo "$configfile" | grep -v \# | awk '{ if($1=="version" && $2=="git") print $3 }')
+ echo "Version: $long (git: $git)"
+ ;;
+esac
+
diff --git a/src/config/.gitignore b/src/config/.gitignore
index 8888415d5f98916205a5e5e7e99c0e4b510542e3..68b4c544bf0dd97e6eb2d9f14d17fc1a696af017 100644
--- a/src/config/.gitignore
+++ b/src/config/.gitignore
@@ -3,3 +3,4 @@
/ConfigInstall.cpp
/install*
/version.h
+/config.txt
diff --git a/src/config/Makefile b/src/config/Makefile
index bdcddde9374f78c189d45469c4e9b9606e361db3..23ec182622ccee9638093b93a2559ad0f6ed511f 100644
--- a/src/config/Makefile
+++ b/src/config/Makefile
@@ -16,11 +16,15 @@ endif
# default target
all:
- $(MAKE) PLUMED_FORCE=yes ConfigInstall.cpp Config.cpp version.h
+ $(MAKE) PLUMED_FORCE=yes ConfigInstall.cpp Config.cpp version.h config.txt
$(MAKE) Config.o ConfigInstall.o compile_options.sh
obj: all
+config.txt: ../../Makefile.conf
+ @echo "Updating config.txt file"
+ @ ../maketools/update-config-txt.sh config.txt $(CPPFLAGS)
+
version.h:
@echo "Updating version.h"
@ ../maketools/update-version.sh version.h
@@ -68,7 +72,7 @@ compile_options.sh:
.PHONY: clean
clean:
- rm -f Config.cpp compile_options.sh Makefile_conf version.h
+ rm -f Config.cpp compile_options.sh Makefile_conf version.h config.txt
rm -fr deps
rm -f Config.cpp ConfigInstall.cpp compile_options.sh install.conf
rm -f $(CLEANLIST)
diff --git a/src/core/CLToolMain.cpp b/src/core/CLToolMain.cpp
index e5eb16190b36e104c2b4de80f6d4c14cd3c0bd28..198d49d40b9281a472c45c19a83a219fabc520db 100644
--- a/src/core/CLToolMain.cpp
+++ b/src/core/CLToolMain.cpp
@@ -243,8 +243,12 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,Communicator& pc){
plumed_massert(out==stdout,"shell tools can only work on stdin");
string cmd=config::getEnvCommand()+" \""+root+"/scripts/"+command+".sh\"";
for(int j=i+1;j<argc;j++) cmd+=string(" ")+argv[j];
- system(cmd.c_str());
- return 0;
+ int r=system(cmd.c_str());
+// this is necessary since system seems to return numbers which are multiple
+// of 256. this would make the interpretation by the shell wrong
+// I just return 1 in case of failure and 0 in case of success
+ if(r!=0) return 1;
+ else return 0;
}
string msg="ERROR: unknown command " + command + ". Use 'plumed help' for help";
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index e425b7cd99a0cca10ba871ea1ef0f751d590ff2d..0fe1d5dbf07cfbb23ee7b89fbd0f9640ffed2dc8 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -753,7 +753,10 @@ void PlumedMain::load(const std::string& ss){
if(n!=std::string::npos && n<s.length()-1) extension=s.substr(n+1);
if(n!=std::string::npos && n<s.length()) base=s.substr(0,n);
if(extension=="cpp"){
- string cmd="plumed mklib "+s;
+// full path command, including environment setup
+// this will work even if plumed is not in the execution path or if it has been
+// installed with a name different from "plumed"
+ string cmd=config::getEnvCommand()+" \""+config::getPlumedRoot()+"\"/scripts/mklib.sh "+s;
log<<"Executing: "<<cmd;
if(comm.Get_size()>0) log<<" (only on master node)";
log<<"\n";
diff --git a/src/lib/Makefile b/src/lib/Makefile
index 3b6ff35daa7146fe4eb75981a8832ebe4ed691e1..d9c18b2f48fbf48bf0e41d7ff64adc2aa17a7453 100644
--- a/src/lib/Makefile
+++ b/src/lib/Makefile
@@ -162,6 +162,8 @@ endif
cp ../colvar/Template.cpp "$(DESTDIR)$(libdir)/$(program_name)/src/colvar/"
# copy compile_options.sh file (we leave it in src/colvar/ for backward compatibility)
cp ../config/compile_options.sh "$(DESTDIR)$(libdir)/$(program_name)/src/config/compile_options.sh"
+# copy config.txt file (we leave it in src/colvar/ for backward compatibility)
+ cp ../config/config.txt "$(DESTDIR)$(libdir)/$(program_name)/src/config/config.txt"
ifdef LD_RO
cp install/kernel.o "$(DESTDIR)$(libdir)/$(program_name)/obj/kernel.o"
else
@@ -175,6 +177,8 @@ endif
cp install/plumed "$(DESTDIR)$(bindir)/$(program_name)"
# patch file for cross compiling
cp install/plumed-patch "$(DESTDIR)$(bindir)/$(program_name)-patch"
+# config file for cross compiling
+ cp install/plumed-patch "$(DESTDIR)$(bindir)/$(program_name)-config"
# copy include files for cmake and make
# we leave it in src/lib/ for backward compatibility
cp install/Plumed.cmake* "$(DESTDIR)$(libdir)/$(program_name)/src/lib/"
@@ -223,6 +227,7 @@ endif
@echo $(includedir)/$(program_name)
@echo $(bindir)/$(program_name)
@echo $(bindir)/$(program_name)-patch
+ @echo $(bindir)/$(program_name)-config
ifdef SOEXT
@echo $(libdir)/lib$(program_name).$(SOEXT)
@echo $(libdir)/lib$(program_name)Kernel.$(SOEXT)
@@ -236,6 +241,7 @@ endif
ifeq ($(program_can_run),no)
@echo "WARNING: $(program_name) executable will not run on this machine"
@echo "WARNING: to patch an MD code use 'plumed-patch'"
+ @echo "WARNING: to verify configuration use 'plumed-config'"
@echo "WARNING: a few other command line tools are avalable as $(libdir)/$(program_name)/plumed-*"
else ifeq ($(program_can_run_mpi),no)
@echo "WARNING: $(program_name) executable will not run on this machine"
@@ -255,6 +261,7 @@ uninstall:
@echo "$(DESTDIR)$(includedir)/$(program_name)"
@echo "$(DESTDIR)$(bindir)/$(program_name)"
@echo "$(DESTDIR)$(bindir)/$(program_name)-patch"
+ @echo "$(DESTDIR)$(bindir)/$(program_name)-config"
@echo "$(DESTDIR)$(libdir)/lib$(program_name).$(SOEXT)"
@echo "$(DESTDIR)$(libdir)/lib$(program_name)Kernel.$(SOEXT)"
../maketools/confirm_uninstall
@@ -264,6 +271,7 @@ uninstall:
rm -fr "$(DESTDIR)$(includedir)/$(program_name)"
rm -f "$(DESTDIR)$(bindir)/$(program_name)"
rm -f "$(DESTDIR)$(bindir)/$(program_name)-patch"
+ rm -f "$(DESTDIR)$(bindir)/bin/$(program_name)-config"
rm -f "$(DESTDIR)$(libdir)/lib$(program_name).$(SOEXT)"
rm -f "$(DESTDIR)$(libdir)/lib$(program_name)Kernel.$(SOEXT)"
diff --git a/src/maketools/make.module b/src/maketools/make.module
index 31771e44c39ed894e5080f5692b954a3d306719f..e92fda70874e7ba6c2d2ff716068145733718174 100644
--- a/src/maketools/make.module
+++ b/src/maketools/make.module
@@ -47,7 +47,9 @@ lib:
install:
cd ../lib ; make install
+ifneq ($(disable_dependency_tracking),yes)
-include $(DEP)
+endif
# if machine dependent configuration has not been found:
else
diff --git a/src/maketools/make.rules b/src/maketools/make.rules
index cea71aae3d7a20975241eff85f72bc434301d283..2d3155e89aa7b392e4658e78f03891bf7320b87e 100644
--- a/src/maketools/make.rules
+++ b/src/maketools/make.rules
@@ -12,13 +12,15 @@ endif
# rule for c++
%.o: %.cpp
@echo "compiling " $*.cpp
+ @-test -d deps || mkdir deps
+ifneq ($(disable_dependency_tracking),yes)
$(AT)$(CXXDEP) -c -MM -MF$*.d $(CPPFLAGS) $(ADDCPPFLAGS) $(CXXFLAGS) $*.cpp
@cp -f $*.d $*.d.tmp
- @-test -d deps || mkdir deps
@sed -e 's/.*://' -e 's/\\$$//' < $*.d.tmp | fmt -1 | \
sed -e 's/^ *//' -e 's/$$/:/' >> $*.d
@mv $*.d deps/$*.d
@rm -f $*.d.tmp
+endif
ifndef XLF
$(AT)$(CXX) -c $(CPPFLAGS) $(ADDCPPFLAGS) $(CXXFLAGS) $*.cpp -o $*.o
endif
@@ -26,13 +28,15 @@ endif
# rule for c
%.o: %.c
@echo "compiling " $*.c
+ @-test -d deps || mkdir deps
+ifneq ($(disable_dependency_tracking),yes)
$(AT)$(CXXDEP) -c -MM -MF$*.d $(CPPFLAGS) $(ADDCPPFLAGS) $(CFLAGS) $*.c -o $*.o
@cp -f $*.d $*.d.tmp
- @-test -d deps || mkdir deps
@sed -e 's/.*://' -e 's/\\$$//' < $*.d.tmp | fmt -1 | \
sed -e 's/^ *//' -e 's/$$/:/' >> $*.d
@mv $*.d deps/$*.d
@rm -f $*.d.tmp
+endif
ifndef XLF
$(AT)$(CC) -c $(CPPFLAGS) $(ADDCPPFLAGS) $(CFLAGS) $*.c -o $*.o
endif
diff --git a/src/maketools/update-config-txt.sh b/src/maketools/update-config-txt.sh
new file mode 100755
index 0000000000000000000000000000000000000000..7e8050588375f6c84eba837cee45e99237588bfc
--- /dev/null
+++ b/src/maketools/update-config-txt.sh
@@ -0,0 +1,142 @@
+#! /bin/bash
+
+# first argument is name of txt file to be updated
+file="$1"
+
+# version strings:
+version=$(
+echo "version short $(
+ if test -f ../../VERSION ; then
+ grep -v "#" ../../VERSION | sed 's/^\([0-9][0-9]*\.[0-9][0-9]*\).*/\1/'
+ else
+ echo "Unknown"
+ fi
+)"
+
+echo "version long $(
+ if test -f ../../VERSION ; then
+ grep -v "#" ../../VERSION
+ else
+ echo "Unknown"
+ fi
+)"
+
+echo "version git $(
+ if test -d ../../.git && hash git 2> /dev/null ; then
+# describe --tags gives a nice name
+# in case it does not work, fallback to normal hash (12 char long)
+ git describe --long --tags --dirty --always || git rev-parse --short=12 HEAD
+ else
+ echo "Unknown"
+ fi
+)"
+
+)
+
+
+
+# first get full list of possible defines from configure.ac and .h
+list="$(
+ {
+ cat ../../configure.ac
+ grep -E "^#" ../*/*.h ../*/*.cpp
+ } |
+ grep -o "__PLUMED_HAS_[A-Z_]*" |
+ sed "s/__PLUMED_HAS_//" | sort | uniq | tr A-Z a-z)"
+
+# now get list of -D__PLUMED_HAS flags in Makefile.conf
+has="$(
+for flag
+do
+ case "$flag" in
+ (-D__PLUMED_HAS_*=0) ;;
+ (-D__PLUMED_HAS_*=*) echo ${flag#-D} | sed "s/=.*//" ;;
+ (-D__PLUMED_HAS_*) echo ${flag#-D} ;;
+ (*) ;;
+ esac
+done | sed "s/__PLUMED_HAS_//" | sort | uniq | tr A-Z a-z
+)"
+
+# now get a list of other defines in Makefile.conf
+def="$(
+for flag
+do
+ case "$flag" in
+ (-D__PLUMED_HAS_*) ;;
+ (-D*) echo "define ${flag#-D}" ;;
+ (*) ;;
+ esac
+done | sort | uniq
+)"
+
+modules=$(
+cd ../
+for dir in *
+do
+ if test -f $dir/module.type
+ then
+ mtype="$(cat "$dir/module.type")"
+ is=""
+ case "$mtype" in
+ (always) is=on ;;
+ (default-on)
+ if test -f $dir.off ; then
+ is=off
+ else
+ is=on
+ fi ;;
+ (default-off)
+ if test -f $dir.on ; then
+ is=on
+ else
+ is=off
+ fi ;;
+ esac
+ echo "module $dir $is ($mtype)"
+ fi
+done
+)
+
+{
+echo "# version strings"
+echo "# syntax: version short/long/git number"
+echo "$version"
+echo
+echo "# list of 'has' options"
+echo "# syntax: has name on/of"
+echo "# if option xx is on then plumed has beeen compiled with -D__PLUMED_HAS_XX"
+{
+ for d in $has
+ do
+ echo "has $d on"
+ done
+ for u in $list
+ do
+ found=ko
+ for d in $has
+ do
+ if test "$d" = "$u" ; then
+ found=ok
+ fi
+ done
+ if test "$found" = ko ; then
+ echo "has $u off"
+ fi
+ done
+} | sort
+echo
+echo "# other defines"
+echo "# syntax: define name=value"
+echo "$def"
+echo
+echo "# list of modules"
+echo "# syntax: module name on/off (default-on/default-off/always)"
+echo "$modules" | sort
+
+}> $file~
+
+cmp -s $file~ $file || cp $file~ $file
+rm $file~
+
+
+
diff --git a/src/multicolvar/MultiColvarHistogram.cpp b/src/multicolvar/MultiColvarHistogram.cpp
index 393d2fc7f890f55772acfeee15c19d2c8a3d79d6..65ee77ddb05521d1d56036775733d684550fb128 100644
--- a/src/multicolvar/MultiColvarHistogram.cpp
+++ b/src/multicolvar/MultiColvarHistogram.cpp
@@ -31,7 +31,7 @@ namespace PLMD
{
namespace multicolvar {
-//+PLUMEDOC ANALYSIS MULTIHISTOGRAM
+//+PLUMEDOC ANALYSIS MULTICOLVARHISTOGRAM
/*
Evaluate the histogram for a particular multicolvar
@@ -43,12 +43,15 @@ Evaluate the histogram for a particular multicolvar
class MultiColvarHistogram : public gridtools::ActionWithGrid {
private:
+ double ww;
MultiColvarBase* mycolv;
vesselbase::StoreDataVessel* stash;
public:
explicit MultiColvarHistogram(const ActionOptions&);
static void registerKeywords( Keywords& keys );
+ unsigned getNumberOfQuantities() const ;
bool isPeriodic(){ return false; }
+ void prepareForAveraging();
void compute( const unsigned& current, MultiValue& myvals ) const ;
};
@@ -56,6 +59,7 @@ PLUMED_REGISTER_ACTION(MultiColvarHistogram,"MULTICOLVARHISTOGRAM")
void MultiColvarHistogram::registerKeywords( Keywords& keys ){
gridtools::ActionWithGrid::registerKeywords( keys );
+ keys.add("compulsory","DATA","the multicolvar which you would like to calculate a histogram for");
keys.add("compulsory","GRID_MIN","the lower bounds for the grid");
keys.add("compulsory","GRID_MAX","the upper bounds for the grid");
keys.add("optional","GRID_BIN","the number of bins for the grid");
@@ -72,34 +76,28 @@ MultiColvarHistogram::MultiColvarHistogram(const ActionOptions&ao):
stash = mycolv->buildDataStashes( NULL );
// Read stuff for grid
- std::vector<std::string> gmin( getNumberOfArguments() ), gmax( getNumberOfArguments() );
+ std::vector<std::string> gmin( 1 ), gmax( 1 );
parseVector("GRID_MIN",gmin); parseVector("GRID_MAX",gmax);
std::vector<unsigned> nbin; parseVector("GRID_BIN",nbin);
std::vector<double> gspacing; parseVector("GRID_SPACING",gspacing);
- if( nbin.size()!=getNumberOfArguments() && gspacing.size()!=getNumberOfArguments() ){
+ if( nbin.size()!=1 && gspacing.size()!=1 ){
error("GRID_BIN or GRID_SPACING must be set");
}
// Input of name and labels
std::string vstring="COMPONENTS=" + getLabel();
- vstring += " COORDINATES=" + getPntrToArgument(0)->getName();
- for(unsigned i=1;i<getNumberOfArguments();++i) vstring += "," + getPntrToArgument(i)->getName();
+ vstring += " COORDINATES=" + mycolv->getLabel();
// Input for PBC
- if( getPntrToArgument(0)->isPeriodic() ) vstring+=" PBC=T";
+ if( mycolv->isPeriodic() ) vstring+=" PBC=T";
else vstring+=" PBC=F";
- for(unsigned i=1;i<getNumberOfArguments();++i){
- if( getPntrToArgument(i)->isPeriodic() ) vstring+=",T";
- else vstring+=",F";
- }
// And create the grid
createGrid( "histogram", vstring );
mygrid->setBounds( gmin, gmax, nbin, gspacing );
- // And finish the grid setup
- setAveragingAction( mygrid, false );
// Create a task list
for(unsigned i=0;i<mycolv->getFullNumberOfTasks();++i) addTaskToList(i);
- setAveragingAction( mygrid, false ); checkRead();
+ // And finish the grid setup
+ setAveragingAction( mygrid, true ); checkRead();
log.printf(" for colvars calculated by action %s \n",mycolv->getLabel().c_str() );
checkRead();
@@ -107,10 +105,24 @@ MultiColvarHistogram::MultiColvarHistogram(const ActionOptions&ao):
addDependency( mycolv );
}
+void MultiColvarHistogram::prepareForAveraging(){
+ deactivateAllTasks(); double norm=0;
+ std::vector<double> cvals( mycolv->getNumberOfQuantities() );
+ for(unsigned i=0;i<stash->getNumberOfStoredValues();++i){
+ taskFlags[i]=1; stash->retrieveSequentialValue(i, false, cvals );
+ norm += cvals[0];
+ }
+ lockContributors(); ww = 1.0 / norm;
+}
+
+unsigned MultiColvarHistogram::getNumberOfQuantities() const {
+ return 3;
+}
+
void MultiColvarHistogram::compute( const unsigned& current, MultiValue& myvals ) const {
std::vector<double> cvals( mycolv->getNumberOfQuantities() );
stash->retrieveSequentialValue( current, false, cvals );
- myvals.setValue( 0, cvals[0] ); myvals.setValue( 1, cvals[1] );
+ myvals.setValue( 0, cvals[0] ); myvals.setValue( 1, cvals[1] ); myvals.setValue( 2, ww );
}
}
diff --git a/user-doc/extract b/user-doc/extract
index 1a72f4a0ea74467cc414cf4c6f344dc206d105f7..04dbae63f3c1e7164ccb02aedc4275b52131dec3 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -1,28 +1,14 @@
#! /bin/bash
-# Making sure that plumed executable is available
-echo -n "Searching for plumed ..."
-if plumed --no-mpi 2>/dev/null 1>/dev/null ; then
- echo " found"
-else
- echo " not found"
- echo -n "Sourcing sourceme.sh and searching again ..."
- if source ../sourceme.sh && plumed --no-mpi 2>/dev/null 1>/dev/null ; then
- echo " found"
- else
- echo "ERROR: you should compile plumed first!"
- exit 1
- fi
-fi
-
+source ../sourceme.sh
# initial cleanup
rm -f errors
rm -rf automatic
mkdir automatic
-long_version="$(plumed --no-mpi info --long-version)"
-git_version="$(plumed --no-mpi info --git-version)"
+long_version="$(../src/lib/plumed --no-mpi info --long-version)"
+git_version="$(../src/lib/plumed --no-mpi info --git-version)"
cat > automatic/version.tmp << EOF
This manual has been compiled from PLUMED version <b> $long_version </b>
@@ -78,7 +64,7 @@ do
echo "- \subpage $mytag " >> automatic/codes.list
echo "/**" >> automatic/$myengine.txt
echo "\page $mytag $myengine" >> automatic/$myengine.txt
- plumed --no-mpi patch -e $myengine -i -q >> automatic/$myengine.txt
+ ../src/lib/plumed --no-mpi patch -e $myengine -i -q >> automatic/$myengine.txt
echo "*/" >> automatic/$myengine.txt
done
@@ -231,7 +217,7 @@ do
if grep -q '//+PLUMEDOC INTERNAL' $file 1>/dev/null 2>/dev/null ; then
cp $file automatic/$flag.txt
else
- if ! plumed --no-mpi manual --action=$flag > automatic/$flag.man 2> /dev/null ; then
+ if ! ../src/lib/plumed --no-mpi manual --action=$flag > automatic/$flag.man 2> /dev/null ; then
echo Full manual for action $flag will not be generated as you are building the manual from a code where this action was not compiled >> errors
elif ! grep -q "\par Examples" $file 1>/dev/null 2>/dev/null
then
diff --git a/user-doc/go-doxygen b/user-doc/go-doxygen
index edf3465a2de246b1e63c2cfdd32c2c67960130ac..ecc848e66664f64bd17fefa589d8fe6cf7f4e3e3 100755
--- a/user-doc/go-doxygen
+++ b/user-doc/go-doxygen
@@ -1,19 +1,6 @@
#! /bin/bash
-# Making sure that plumed executable is available
-echo -n "Searching for plumed ..."
-if plumed --no-mpi 2>/dev/null 1>/dev/null ; then
- echo " found"
-else
- echo " not found"
- echo -n "Sourcing sourceme.sh and searching again ..."
- if source ../sourceme.sh && plumed --no-mpi 2>/dev/null 1>/dev/null ; then
- echo " found"
- else
- echo "ERROR: you should compile plumed first!"
- exit 1
- fi
-fi
+source ../sourceme.sh
LIST="
IntroPP.txt ../CHANGES InstallationPP.txt SyntaxPP.txt ColvarPP.txt GroupPP.txt FunctionsPP.txt AnalysisPP.txt
@@ -21,13 +8,13 @@ LIST="
{
cat Doxyfile
- echo "PROJECT_NUMBER = \"$(plumed --no-mpi info --long-version)\""
+ echo "PROJECT_NUMBER = \"$(../src/lib/plumed --no-mpi info --long-version)\""
echo "INPUT+=" $LIST
# add this to manually control layout:
# echo "LAYOUT_FILE=PlumedLayout.xml"
} | doxygen -
-version=v$(plumed --no-mpi info --version)
+version=v$(../src/lib/plumed --no-mpi info --version)
# in the online manual better to put the branch name
# which is available through the TRAVIS_BRANCH env var
diff --git a/vim/vimsyntax.sh b/vim/vimsyntax.sh
index b0d04cf26bf63d2c4b68a742bcaa30bfb8d0501b..559c46e3b11ab706929cece665fbdee8c8b6627e 100755
--- a/vim/vimsyntax.sh
+++ b/vim/vimsyntax.sh
@@ -1,19 +1,6 @@
#! /bin/bash
-# Making sure that plumed executable is available
-echo -n "Searching for plumed ..."
-if plumed --no-mpi 2>/dev/null 1>/dev/null ; then
- echo " found"
-else
- echo " not found"
- echo -n "Sourcing sourceme.sh and searching again ..."
- if source ../sourceme.sh && plumed --no-mpi 2>/dev/null 1>/dev/null ; then
- echo " found"
- else
- echo "ERROR: you should compile plumed first!"
- exit 1
- fi
-fi
+source ../sourceme.sh
mkdir -p syntax help
@@ -115,7 +102,7 @@ EOF
actions=$(
-plumed --no-mpi manual --action 2>&1 | awk '{
+../src/lib/plumed --no-mpi manual --action 2>&1 | awk '{
if(NR==1) next;
if(NF!=1) exit;
print $1
@@ -127,7 +114,7 @@ actions="$(
for a in $actions
do
-plumed --no-mpi manual --action $a --vim 2>/dev/null | head -n 1
+../src/lib/plumed --no-mpi manual --action $a --vim 2>/dev/null | head -n 1
done
)"
@@ -174,7 +161,7 @@ action_name_=$(echo $action_name | sed s/-/_/g)
echo "****************************************"
echo "Short helpfile for action $action_name"
echo "****************************************"
-plumed --no-mpi manual --action $action_name --vim 2>/dev/null | awk '{if(NR>1) print}'
+../src/lib/plumed --no-mpi manual --action $action_name --vim 2>/dev/null | awk '{if(NR>1) print}'
} > help/$action_name.txt
dictionary='{"word":"LABEL=","menu":"(label)"}'