diff --git a/CHANGES/v2.3.md b/CHANGES/v2.3.md index 6aa9d2b73665ac986b85e66688d5baf494aa0ea0..a4719b06638d70ebf59be9925a200590426214c2 100644 --- a/CHANGES/v2.3.md +++ b/CHANGES/v2.3.md @@ -232,6 +232,7 @@ For developers: For users: - Fixed a problem leading to NaN derivatives of \ref switchingfunction `Q` when distance between two atoms is large. +- GROMACS patch updated to gromacs-2016.5. For developers: - Fixed small issue in debug options of \ref driver (see \issue{245}). diff --git a/patches/gromacs-2016.4.config b/patches/gromacs-2016.5.config similarity index 100% rename from patches/gromacs-2016.4.config rename to patches/gromacs-2016.5.config diff --git a/patches/gromacs-2016.4.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-2016.5.diff/src/gromacs/CMakeLists.txt similarity index 100% rename from patches/gromacs-2016.4.diff/src/gromacs/CMakeLists.txt rename to patches/gromacs-2016.5.diff/src/gromacs/CMakeLists.txt diff --git a/patches/gromacs-2016.4.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-2016.5.diff/src/gromacs/CMakeLists.txt.preplumed similarity index 100% rename from patches/gromacs-2016.4.diff/src/gromacs/CMakeLists.txt.preplumed rename to patches/gromacs-2016.5.diff/src/gromacs/CMakeLists.txt.preplumed diff --git a/patches/gromacs-2016.4.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2016.5.diff/src/gromacs/mdlib/force.cpp similarity index 100% rename from patches/gromacs-2016.4.diff/src/gromacs/mdlib/force.cpp rename to patches/gromacs-2016.5.diff/src/gromacs/mdlib/force.cpp diff --git a/patches/gromacs-2016.4.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-2016.5.diff/src/gromacs/mdlib/force.cpp.preplumed similarity index 100% rename from patches/gromacs-2016.4.diff/src/gromacs/mdlib/force.cpp.preplumed rename to patches/gromacs-2016.5.diff/src/gromacs/mdlib/force.cpp.preplumed diff --git a/patches/gromacs-2016.4.diff/src/gromacs/mdlib/minimize.cpp b/patches/gromacs-2016.5.diff/src/gromacs/mdlib/minimize.cpp similarity index 100% rename from patches/gromacs-2016.4.diff/src/gromacs/mdlib/minimize.cpp rename to patches/gromacs-2016.5.diff/src/gromacs/mdlib/minimize.cpp diff --git a/patches/gromacs-2016.4.diff/src/gromacs/mdlib/minimize.cpp.preplumed b/patches/gromacs-2016.5.diff/src/gromacs/mdlib/minimize.cpp.preplumed similarity index 100% rename from patches/gromacs-2016.4.diff/src/gromacs/mdlib/minimize.cpp.preplumed rename to patches/gromacs-2016.5.diff/src/gromacs/mdlib/minimize.cpp.preplumed diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp b/patches/gromacs-2016.5.diff/src/programs/mdrun/md.cpp similarity index 100% rename from patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp rename to patches/gromacs-2016.5.diff/src/programs/mdrun/md.cpp diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp.preplumed b/patches/gromacs-2016.5.diff/src/programs/mdrun/md.cpp.preplumed similarity index 100% rename from patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp.preplumed rename to patches/gromacs-2016.5.diff/src/programs/mdrun/md.cpp.preplumed diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-2016.5.diff/src/programs/mdrun/mdrun.cpp similarity index 100% rename from patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp rename to patches/gromacs-2016.5.diff/src/programs/mdrun/mdrun.cpp diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp.preplumed b/patches/gromacs-2016.5.diff/src/programs/mdrun/mdrun.cpp.preplumed similarity index 100% rename from patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp.preplumed rename to patches/gromacs-2016.5.diff/src/programs/mdrun/mdrun.cpp.preplumed diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.cpp similarity index 100% rename from patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp rename to patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.cpp diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp.preplumed b/patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.cpp.preplumed similarity index 100% rename from patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp.preplumed rename to patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.cpp.preplumed diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h b/patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.h similarity index 100% rename from patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h rename to patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.h diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h.preplumed b/patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.h.preplumed similarity index 100% rename from patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h.preplumed rename to patches/gromacs-2016.5.diff/src/programs/mdrun/repl_ex.h.preplumed diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/runner.cpp b/patches/gromacs-2016.5.diff/src/programs/mdrun/runner.cpp similarity index 99% rename from patches/gromacs-2016.4.diff/src/programs/mdrun/runner.cpp rename to patches/gromacs-2016.5.diff/src/programs/mdrun/runner.cpp index f3e0e4eceae9e64016c949876d76ce2053d6694f..b5eafe37dd2fb7008696fd02b07475843c14509d 100644 --- a/patches/gromacs-2016.4.diff/src/programs/mdrun/runner.cpp +++ b/patches/gromacs-2016.5.diff/src/programs/mdrun/runner.cpp @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by + * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, 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. @@ -526,7 +526,7 @@ static void increase_nstlist(FILE *fp, t_commrec *cr, gmx_warning(!bBox ? box_err : dd_err); if (fp != NULL) { - fprintf(fp, "\n%s\n", bBox ? box_err : dd_err); + fprintf(fp, "\n%s\n", !bBox ? box_err : dd_err); } ir->nstlist = nstlist_orig; } diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/runner.cpp.preplumed b/patches/gromacs-2016.5.diff/src/programs/mdrun/runner.cpp.preplumed similarity index 99% rename from patches/gromacs-2016.4.diff/src/programs/mdrun/runner.cpp.preplumed rename to patches/gromacs-2016.5.diff/src/programs/mdrun/runner.cpp.preplumed index 560b923ba600d4304b2eea72a1a5d76b7a1f6bfa..ad3998103aca3abc52a8e81e6b52e352924f8446 100644 --- a/patches/gromacs-2016.4.diff/src/programs/mdrun/runner.cpp.preplumed +++ b/patches/gromacs-2016.5.diff/src/programs/mdrun/runner.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) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by + * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, 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. @@ -520,7 +520,7 @@ static void increase_nstlist(FILE *fp, t_commrec *cr, gmx_warning(!bBox ? box_err : dd_err); if (fp != NULL) { - fprintf(fp, "\n%s\n", bBox ? box_err : dd_err); + fprintf(fp, "\n%s\n", !bBox ? box_err : dd_err); } ir->nstlist = nstlist_orig; }