From 37993fc4e10f629d70b6814ff174be8819c8b29d Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Fri, 8 Feb 2019 21:49:18 +0100
Subject: [PATCH] gmx 2018.5
---
.../{gromacs-2018.4.config => gromacs-2018.5.config} | 0
.../src/gromacs/CMakeLists.txt | 0
.../src/gromacs/CMakeLists.txt.preplumed | 0
.../src/gromacs/mdlib/force.cpp | 0
.../src/gromacs/mdlib/force.cpp.preplumed | 0
.../src/gromacs/mdlib/minimize.cpp | 0
.../src/gromacs/mdlib/minimize.cpp.preplumed | 0
.../src/programs/mdrun/md.cpp | 12 +++++++++---
.../src/programs/mdrun/md.cpp.preplumed | 12 +++++++++---
.../src/programs/mdrun/mdrun.cpp | 0
.../src/programs/mdrun/mdrun.cpp.preplumed | 0
.../src/programs/mdrun/repl_ex.cpp | 0
.../src/programs/mdrun/repl_ex.cpp.preplumed | 0
.../src/programs/mdrun/repl_ex.h | 0
.../src/programs/mdrun/repl_ex.h.preplumed | 0
.../src/programs/mdrun/runner.cpp | 0
.../src/programs/mdrun/runner.cpp.preplumed | 0
.../src/programs/mdrun/runner.h | 0
.../src/programs/mdrun/runner.h.preplumed | 0
19 files changed, 18 insertions(+), 6 deletions(-)
rename patches/{gromacs-2018.4.config => gromacs-2018.5.config} (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/gromacs/CMakeLists.txt (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/gromacs/CMakeLists.txt.preplumed (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/gromacs/mdlib/force.cpp (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/gromacs/mdlib/force.cpp.preplumed (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/gromacs/mdlib/minimize.cpp (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/gromacs/mdlib/minimize.cpp.preplumed (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/md.cpp (99%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/md.cpp.preplumed (99%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/mdrun.cpp (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/mdrun.cpp.preplumed (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/repl_ex.cpp (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/repl_ex.cpp.preplumed (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/repl_ex.h (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/repl_ex.h.preplumed (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/runner.cpp (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/runner.cpp.preplumed (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/runner.h (100%)
rename patches/{gromacs-2018.4.diff => gromacs-2018.5.diff}/src/programs/mdrun/runner.h.preplumed (100%)
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 31f271a63..341584928 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 de5a7031f..e77170a9c 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
--
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