From 83b14b962031cc3d5df12960991986ccde173ef6 Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Sat, 12 Nov 2016 13:54:56 +0100
Subject: [PATCH] GMX2016.1: patch updated
---
CHANGES/v2.3.txt | 1 +
patches/{gromacs-2016.config => gromacs-2016.1.config} | 5 ++++-
.../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 | 0
.../src/programs/mdrun/md.cpp.preplumed | 0
.../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/runner.cpp | 0
.../src/programs/mdrun/runner.cpp.preplumed | 0
16 files changed, 5 insertions(+), 1 deletion(-)
rename patches/{gromacs-2016.config => gromacs-2016.1.config} (95%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/gromacs/CMakeLists.txt (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/gromacs/CMakeLists.txt.preplumed (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/gromacs/mdlib/force.cpp (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/gromacs/mdlib/force.cpp.preplumed (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/gromacs/mdlib/minimize.cpp (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/gromacs/mdlib/minimize.cpp.preplumed (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/programs/mdrun/md.cpp (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/programs/mdrun/md.cpp.preplumed (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/programs/mdrun/mdrun.cpp (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/programs/mdrun/mdrun.cpp.preplumed (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/programs/mdrun/repl_ex.cpp (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/programs/mdrun/repl_ex.cpp.preplumed (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/programs/mdrun/runner.cpp (100%)
rename patches/{gromacs-2016.diff => gromacs-2016.1.diff}/src/programs/mdrun/runner.cpp.preplumed (100%)
diff --git a/CHANGES/v2.3.txt b/CHANGES/v2.3.txt
index 7b21c4c52..02812fa5a 100644
--- a/CHANGES/v2.3.txt
+++ b/CHANGES/v2.3.txt
@@ -127,6 +127,7 @@ Fixes since 2.3b. Relevant things could be merged in the changelog above when we
- \ref PUCKERING now supports 6 membered rings.
- Tutorials have been (partially) updated to reflect some of the changes in the syntax
- gromacs 5.1.x patch updated to 5.1.4
+- gromacs 2016.x patch updated to 2016.1
- LAMMPS patch updated to support multiple walkers and report plumed bias to LAMMPS (thanks to Pablo Piaggi).
- When using \ref METAD with file-based multple walkers and parallel jobs (i.e. mpirun) extra suffix is not added (thanks to Marco De La Pierre).
- Parser now reports errors when passing numbers that cannot be parsed instead of silently replacing their default value. See \issue{104}.
diff --git a/patches/gromacs-2016.config b/patches/gromacs-2016.1.config
similarity index 95%
rename from patches/gromacs-2016.config
rename to patches/gromacs-2016.1.config
index ef1f89565..4348d93fd 100644
--- a/patches/gromacs-2016.config
+++ b/patches/gromacs-2016.1.config
@@ -7,7 +7,6 @@ function plumed_preliminary_test(){
function plumed_patch_info(){
cat << EOF
-
PLUMED can be incorporated into gromacs using the standard patching procedure.
Patching must be done in the gromacs root directory _before_ the cmake command is invoked.
@@ -28,3 +27,7 @@ For more information on gromacs you should visit http://www.gromacs.org
EOF
}
+plumed_before_patch(){
+ plumed_patch_info
+}
+
diff --git a/patches/gromacs-2016.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-2016.1.diff/src/gromacs/CMakeLists.txt
similarity index 100%
rename from patches/gromacs-2016.diff/src/gromacs/CMakeLists.txt
rename to patches/gromacs-2016.1.diff/src/gromacs/CMakeLists.txt
diff --git a/patches/gromacs-2016.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-2016.1.diff/src/gromacs/CMakeLists.txt.preplumed
similarity index 100%
rename from patches/gromacs-2016.diff/src/gromacs/CMakeLists.txt.preplumed
rename to patches/gromacs-2016.1.diff/src/gromacs/CMakeLists.txt.preplumed
diff --git a/patches/gromacs-2016.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2016.1.diff/src/gromacs/mdlib/force.cpp
similarity index 100%
rename from patches/gromacs-2016.diff/src/gromacs/mdlib/force.cpp
rename to patches/gromacs-2016.1.diff/src/gromacs/mdlib/force.cpp
diff --git a/patches/gromacs-2016.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-2016.1.diff/src/gromacs/mdlib/force.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.diff/src/gromacs/mdlib/force.cpp.preplumed
rename to patches/gromacs-2016.1.diff/src/gromacs/mdlib/force.cpp.preplumed
diff --git a/patches/gromacs-2016.diff/src/gromacs/mdlib/minimize.cpp b/patches/gromacs-2016.1.diff/src/gromacs/mdlib/minimize.cpp
similarity index 100%
rename from patches/gromacs-2016.diff/src/gromacs/mdlib/minimize.cpp
rename to patches/gromacs-2016.1.diff/src/gromacs/mdlib/minimize.cpp
diff --git a/patches/gromacs-2016.diff/src/gromacs/mdlib/minimize.cpp.preplumed b/patches/gromacs-2016.1.diff/src/gromacs/mdlib/minimize.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.diff/src/gromacs/mdlib/minimize.cpp.preplumed
rename to patches/gromacs-2016.1.diff/src/gromacs/mdlib/minimize.cpp.preplumed
diff --git a/patches/gromacs-2016.diff/src/programs/mdrun/md.cpp b/patches/gromacs-2016.1.diff/src/programs/mdrun/md.cpp
similarity index 100%
rename from patches/gromacs-2016.diff/src/programs/mdrun/md.cpp
rename to patches/gromacs-2016.1.diff/src/programs/mdrun/md.cpp
diff --git a/patches/gromacs-2016.diff/src/programs/mdrun/md.cpp.preplumed b/patches/gromacs-2016.1.diff/src/programs/mdrun/md.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.diff/src/programs/mdrun/md.cpp.preplumed
rename to patches/gromacs-2016.1.diff/src/programs/mdrun/md.cpp.preplumed
diff --git a/patches/gromacs-2016.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-2016.1.diff/src/programs/mdrun/mdrun.cpp
similarity index 100%
rename from patches/gromacs-2016.diff/src/programs/mdrun/mdrun.cpp
rename to patches/gromacs-2016.1.diff/src/programs/mdrun/mdrun.cpp
diff --git a/patches/gromacs-2016.diff/src/programs/mdrun/mdrun.cpp.preplumed b/patches/gromacs-2016.1.diff/src/programs/mdrun/mdrun.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.diff/src/programs/mdrun/mdrun.cpp.preplumed
rename to patches/gromacs-2016.1.diff/src/programs/mdrun/mdrun.cpp.preplumed
diff --git a/patches/gromacs-2016.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-2016.1.diff/src/programs/mdrun/repl_ex.cpp
similarity index 100%
rename from patches/gromacs-2016.diff/src/programs/mdrun/repl_ex.cpp
rename to patches/gromacs-2016.1.diff/src/programs/mdrun/repl_ex.cpp
diff --git a/patches/gromacs-2016.diff/src/programs/mdrun/repl_ex.cpp.preplumed b/patches/gromacs-2016.1.diff/src/programs/mdrun/repl_ex.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.diff/src/programs/mdrun/repl_ex.cpp.preplumed
rename to patches/gromacs-2016.1.diff/src/programs/mdrun/repl_ex.cpp.preplumed
diff --git a/patches/gromacs-2016.diff/src/programs/mdrun/runner.cpp b/patches/gromacs-2016.1.diff/src/programs/mdrun/runner.cpp
similarity index 100%
rename from patches/gromacs-2016.diff/src/programs/mdrun/runner.cpp
rename to patches/gromacs-2016.1.diff/src/programs/mdrun/runner.cpp
diff --git a/patches/gromacs-2016.diff/src/programs/mdrun/runner.cpp.preplumed b/patches/gromacs-2016.1.diff/src/programs/mdrun/runner.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016.diff/src/programs/mdrun/runner.cpp.preplumed
rename to patches/gromacs-2016.1.diff/src/programs/mdrun/runner.cpp.preplumed
--
GitLab