diff --git a/patches/gromacs-2018.4.config b/patches/gromacs-2018.5.config similarity index 100% rename from patches/gromacs-2018.4.config rename to patches/gromacs-2018.5.config diff --git a/patches/gromacs-2018.4.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-2018.5.diff/src/gromacs/CMakeLists.txt similarity index 100% rename from patches/gromacs-2018.4.diff/src/gromacs/CMakeLists.txt rename to patches/gromacs-2018.5.diff/src/gromacs/CMakeLists.txt diff --git a/patches/gromacs-2018.4.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-2018.5.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-2018.5.diff/src/gromacs/CMakeLists.txt.preplumed diff --git a/patches/gromacs-2018.4.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2018.5.diff/src/gromacs/mdlib/force.cpp similarity index 100% rename from patches/gromacs-2018.4.diff/src/gromacs/mdlib/force.cpp rename to patches/gromacs-2018.5.diff/src/gromacs/mdlib/force.cpp diff --git a/patches/gromacs-2018.4.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-2018.5.diff/src/gromacs/mdlib/force.cpp.preplumed similarity index 100% rename from patches/gromacs-2018.4.diff/src/gromacs/mdlib/force.cpp.preplumed rename to patches/gromacs-2018.5.diff/src/gromacs/mdlib/force.cpp.preplumed diff --git a/patches/gromacs-2018.4.diff/src/gromacs/mdlib/minimize.cpp b/patches/gromacs-2018.5.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-2018.5.diff/src/gromacs/mdlib/minimize.cpp diff --git a/patches/gromacs-2018.4.diff/src/gromacs/mdlib/minimize.cpp.preplumed b/patches/gromacs-2018.5.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-2018.5.diff/src/gromacs/mdlib/minimize.cpp.preplumed diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/md.cpp b/patches/gromacs-2018.5.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-2018.5.diff/src/programs/mdrun/md.cpp index 31f271a63de7822c7e4931635ef4361c8bbef70c..3415849286aeffa54cf9f19ae9062302ce1c1692 100644 --- a/patches/gromacs-2018.4.diff/src/programs/mdrun/md.cpp +++ b/patches/gromacs-2018.5.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-2018.5.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-2018.5.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-2018.5.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-2018.5.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-2018.5.diff/src/programs/mdrun/mdrun.cpp diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/mdrun.cpp.preplumed b/patches/gromacs-2018.5.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-2018.5.diff/src/programs/mdrun/mdrun.cpp.preplumed diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-2018.5.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-2018.5.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-2018.5.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-2018.5.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-2018.5.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-2018.5.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-2018.5.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-2018.5.diff/src/programs/mdrun/repl_ex.h.preplumed diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/runner.cpp b/patches/gromacs-2018.5.diff/src/programs/mdrun/runner.cpp similarity index 100% rename from patches/gromacs-2018.4.diff/src/programs/mdrun/runner.cpp rename to patches/gromacs-2018.5.diff/src/programs/mdrun/runner.cpp diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/runner.cpp.preplumed b/patches/gromacs-2018.5.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-2018.5.diff/src/programs/mdrun/runner.cpp.preplumed diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/runner.h b/patches/gromacs-2018.5.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-2018.5.diff/src/programs/mdrun/runner.h diff --git a/patches/gromacs-2018.4.diff/src/programs/mdrun/runner.h.preplumed b/patches/gromacs-2018.5.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-2018.5.diff/src/programs/mdrun/runner.h.preplumed