diff --git a/CHANGES/v2.5.md b/CHANGES/v2.5.md index e16cc58fce8cfc173ed30e4f69871c553d778961..5f588ff6bd2e7df74f79bf5366b7d56faa56c3e4 100644 --- a/CHANGES/v2.5.md +++ b/CHANGES/v2.5.md @@ -177,5 +177,5 @@ For users: For users: - New shortcuts are available for selecting protein atoms: `@chi2-#`, `@chi3-#`,`@chi4-#` and `@chi5-#` - Fixed performance of \ref CUSTOM when having zero derivatives with respect to some arguments. -- New patch for GROMACS 2019.1 +- New patch for GROMACS 2019.2 - Module VES: Fixed performance of \ref BF_CUSTOM for basis functions with linear terms (e.g. having zero derivatives). diff --git a/patches/gromacs-2019.1.config b/patches/gromacs-2019.2.config similarity index 100% rename from patches/gromacs-2019.1.config rename to patches/gromacs-2019.2.config diff --git a/patches/gromacs-2019.1.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-2019.2.diff/src/gromacs/CMakeLists.txt similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/CMakeLists.txt rename to patches/gromacs-2019.2.diff/src/gromacs/CMakeLists.txt diff --git a/patches/gromacs-2019.1.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-2019.2.diff/src/gromacs/CMakeLists.txt.preplumed similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/CMakeLists.txt.preplumed rename to patches/gromacs-2019.2.diff/src/gromacs/CMakeLists.txt.preplumed diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2019.2.diff/src/gromacs/mdlib/force.cpp similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp rename to patches/gromacs-2019.2.diff/src/gromacs/mdlib/force.cpp diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-2019.2.diff/src/gromacs/mdlib/force.cpp.preplumed similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/mdlib/force.cpp.preplumed rename to patches/gromacs-2019.2.diff/src/gromacs/mdlib/force.cpp.preplumed diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.cpp similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.cpp diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.h similarity index 98% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.h index 01454f92678bc800038d22a31654b84518a0e6c2..019a12439e4f9cf6031b8d82ca17f3d6426015c2 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h +++ b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.h @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018,2019, 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. @@ -252,7 +252,7 @@ class LegacyMdrunOptions { "-append", FALSE, etBOOL, {&bTryToAppendFiles}, "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" }, { "-nsteps", FALSE, etINT64, {&mdrunOptions.numStepsCommandline}, - "Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" }, + "Run this number of steps (-1 means infinite, -2 means use mdp option, smaller is invalid)" }, { "-maxh", FALSE, etREAL, {&mdrunOptions.maximumHoursToRun}, "Terminate after 0.99 times this time (hours)" }, { "-replex", FALSE, etINT, {&replExParams.exchangeInterval}, diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed similarity index 98% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed index 637cd2a6b93dabe9fd632d92e30794922c3a8fec..27a6de629a3ef033a86802560cbb175e748ee4c9 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed +++ b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018,2019, 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. @@ -241,7 +241,7 @@ class LegacyMdrunOptions { "-append", FALSE, etBOOL, {&bTryToAppendFiles}, "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" }, { "-nsteps", FALSE, etINT64, {&mdrunOptions.numStepsCommandline}, - "Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" }, + "Run this number of steps (-1 means infinite, -2 means use mdp option, smaller is invalid)" }, { "-maxh", FALSE, etREAL, {&mdrunOptions.maximumHoursToRun}, "Terminate after 0.99 times this time (hours)" }, { "-replex", FALSE, etINT, {&replExParams.exchangeInterval}, diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/md.cpp b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/md.cpp similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/md.cpp rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/md.cpp diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/md.cpp.preplumed b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/md.cpp.preplumed similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/md.cpp.preplumed rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/md.cpp.preplumed diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/minimize.cpp b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.cpp similarity index 99% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/minimize.cpp rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.cpp index e677e23f36ee59f95c5a170e417c12d744716035..6fb913acdf7fda216bd50c6a63cb04f973064344 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/minimize.cpp +++ b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.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. @@ -2218,15 +2218,15 @@ Integrator::do_lbfgs() { /* Replace c endpoint with b */ c = b; - /* swap states b and c */ - swap_em_state(&sb, &sc); + /* copy state b to c */ + *sc = *sb; } else { /* Replace a endpoint with b */ a = b; - /* swap states a and b */ - swap_em_state(&sa, &sb); + /* copy state b to a */ + *sa = *sb; } /* @@ -2428,7 +2428,7 @@ Integrator::do_lbfgs() } // Reset stepsize in we are doing more iterations - stepsize = 1.0/ems.fnorm; + stepsize = 1.0; /* Stop when the maximum force lies below tolerance. * If we have reached machine precision, converged is already set to true. diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/minimize.cpp.preplumed b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.cpp.preplumed similarity index 99% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/minimize.cpp.preplumed rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.cpp.preplumed index eb8e910468fd99643d8d9f5aa061caa7a10c13ab..77421a32af2150f87ad728007fa66bd100d3a98c 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/minimize.cpp.preplumed +++ b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.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. @@ -2143,15 +2143,15 @@ Integrator::do_lbfgs() { /* Replace c endpoint with b */ c = b; - /* swap states b and c */ - swap_em_state(&sb, &sc); + /* copy state b to c */ + *sc = *sb; } else { /* Replace a endpoint with b */ a = b; - /* swap states a and b */ - swap_em_state(&sa, &sb); + /* copy state b to a */ + *sa = *sb; } /* @@ -2353,7 +2353,7 @@ Integrator::do_lbfgs() } // Reset stepsize in we are doing more iterations - stepsize = 1.0/ems.fnorm; + stepsize = 1.0; /* Stop when the maximum force lies below tolerance. * If we have reached machine precision, converged is already set to true. diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.cpp b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.cpp similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.cpp rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.cpp diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.h b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.h similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.h rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.h diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.h.preplumed b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.h.preplumed similarity index 100% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.h.preplumed rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.h.preplumed diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/runner.cpp b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/runner.cpp similarity index 99% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/runner.cpp rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/runner.cpp index 39608a5f8f748cace878c131e23736bed38cd75a..ac29a3926d13b7b311cda18900a94aa5f3ffadba 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/runner.cpp +++ b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/runner.cpp @@ -855,6 +855,15 @@ int Mdrunner::mdrunner() */ gmx_bool bReadEkin; + if (mdrunOptions.numStepsCommandline > -2) + { + /* Temporarily set the number of steps to unmlimited to avoid + * triggering the nsteps check in load_checkpoint(). + * This hack will go away soon when the -nsteps option is removed. + */ + inputrec->nsteps = -1; + } + load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr), logFileHandle, cr, domdecOptions.numCells, diff --git a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/runner.cpp.preplumed b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/runner.cpp.preplumed similarity index 99% rename from patches/gromacs-2019.1.diff/src/gromacs/mdrun/runner.cpp.preplumed rename to patches/gromacs-2019.2.diff/src/gromacs/mdrun/runner.cpp.preplumed index ae158a4984deefd1d61ca9e2a912143db1c75e05..370cff95f94c657027b79afd16368f194ac41918 100644 --- a/patches/gromacs-2019.1.diff/src/gromacs/mdrun/runner.cpp.preplumed +++ b/patches/gromacs-2019.2.diff/src/gromacs/mdrun/runner.cpp.preplumed @@ -855,6 +855,15 @@ int Mdrunner::mdrunner() */ gmx_bool bReadEkin; + if (mdrunOptions.numStepsCommandline > -2) + { + /* Temporarily set the number of steps to unmlimited to avoid + * triggering the nsteps check in load_checkpoint(). + * This hack will go away soon when the -nsteps option is removed. + */ + inputrec->nsteps = -1; + } + load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr), logFileHandle, cr, domdecOptions.numCells,