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Commit edfed6c0 authored by Giovanni Bussi's avatar Giovanni Bussi
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Merge branch 'v2.4-namd-patches' into v2.4

parents ab505515 b1d6aead
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patches/namd-2.9.config → patches/namd-2.12.config
+ 0
− 0
View file @ edfed6c0
File moved
patches/namd-2.9.diff → patches/namd-2.12.diff
+ 27
− 20
View file @ edfed6c0
patch -u -l -b -F 5 -N --suffix=.preplumed "./Makefile" << \EOF_EOF
--- ./Makefile.preplumed
+++ ./Makefile
@@ -359,10 +359,12 @@
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(FFT) $(CUDA) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA)
@@ -359,13 +359,15 @@
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(PYTHON) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA) $(CKLOOP)
CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS)
CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS)
CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS)
CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS)
CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS)
+include .rootdir/Plumed.inc
+
CXXCOLVARFLAGS = $(CXXBASEFLAGS) $(CXXCOLVAROPTS)
GXXFLAGS = $(CXXBASEFLAGS) -DNO_STRSTREAM_H
CFLAGS = $(COPTI)$(SRCDIR) $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
PLUGINGCCFLAGS = $(COPTI)$(PLUGINSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN
PLUGINCFLAGS = $(PLUGINGCCFLAGS) $(COPTS)
SBCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
@@ -394,10 +396,11 @@
$(CUDAOBJS) \
$(CUDALIB) \
$(DPMTALIB) \
$(DPMELIB) \
$(TCLLIB) \
SBGCCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
@@ -394,13 +396,14 @@
$(CUDAOBJS) \
$(CUDALIB) \
$(DPMTALIB) \
$(DPMELIB) \
$(FMMLIB) \
$(TCLLIB) \
+ $(PLUMED_LOAD) \
$(FFTLIB) \
$(PLUGINLIB) \
$(CHARMOPTS) \
$(EXTRALINKLIBS) \
-lm -o namd2
$(PYTHONLIB) \
$(FFTLIB) \
$(PLUGINLIB) \
$(SBLIB) \
$(CHARMOPTS) \
$(EXTRALINKLIBS) \
-lm -o namd2
EOF_EOF
patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
--- ./src/ComputeMgr.C.preplumed
......@@ -204,16 +210,17 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
opts.optional("GBIS", "intrinsicRadiusOffset",
"Coulomb Radius Offset", &coulomb_radius_offset, 0.09);
opts.optional("GBIS", "ionConcentration",
@@ -4299,11 +4306,11 @@
@@ -4299,12 +4307,12 @@
}
// Global forces configuration
globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
- (IMDon && ! IMDignore) || SMDOn || TMDOn || colvarsOn || symmetryOn );
+ (IMDon && ! IMDignore) || SMDOn || TMDOn || colvarsOn || symmetryOn || plumedOn );
(IMDon && ! IMDignore) || SMDOn || TMDOn ||
- colvarsOn || symmetryOn || qmForcesOn );
+ colvarsOn || symmetryOn || qmForcesOn || plumedOn );
if (tclForcesOn)
{
iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n";
......
patches/namd-2.8.config → patches/namd-2.13.config
+ 1
− 0
View file @ edfed6c0
......@@ -27,3 +27,4 @@ EOF
}
plumed_ignore_mpi=yes
patches/namd-2.8.diff → patches/namd-2.13.diff
+ 47
− 37
View file @ edfed6c0
patch -u -l -b -F 5 -N --suffix=.preplumed "./Makefile" << \EOF_EOF
--- ./Makefile.preplumed
+++ ./Makefile
@@ -358,10 +358,12 @@
cat $(BUILDINFO).C; \
$(CXX) $(CXXFLAGS) $(COPTO)$(BUILDINFO).o $(COPTC) $(BUILDINFO).C
all: $(BINARIES) $(LIBCUDARTSO)
@@ -359,16 +359,18 @@
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTI)$(COLVARSINCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(PYTHON) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA) $(CKLOOP)
CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS)
CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS)
CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS)
CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS)
CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS)
+include .rootdir/Plumed.inc
+
namd2: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
$(MAKEBUILDINFO)
$(CHARMC) -verbose -ld++-option \
"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
-module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -language charm++ \
@@ -371,10 +373,11 @@
$(CUDALIB) \
$(DPMTALIB) \
$(DPMELIB) \
$(TCLLIB) \
$(FFTLIB) \
COLVARSCXXFLAGS = $(CXXBASEFLAGS) $(CXXCOLVAROPTS) $(COPTI)$(LEPTONINCDIR) -DLEPTON -DLEPTON_USE_STATIC_LIBRARIES
GXXFLAGS = $(CXXBASEFLAGS) -DNO_STRSTREAM_H
CFLAGS = $(COPTI)$(SRCDIR) $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
PLUGINGCCFLAGS = $(COPTI)$(PLUGINSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN
PLUGINCFLAGS = $(PLUGINGCCFLAGS) $(COPTS)
SBCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
SBGCCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
COLVARSGXXFLAGS= $(GXXFLAGS)
LEPTONGCCFLAGS= $(COPTI)$(LEPTONINCDIR)
LEPTONCXXFLAGS=$(CXXBASEFLAGS) $(COPTI)$(LEPTONINCDIR) -DLEPTON_BUILDING_STATIC_LIBRARY
@@ -394,15 +396,16 @@
$(CUDAOBJS) \
$(CUDALIB) \
$(DPMTALIB) \
$(DPMELIB) \
$(FMMLIB) \
$(TCLLIB) \
+ $(PLUMED_LOAD) \
$(PLUGINLIB) \
$(CHARMOPTS) \
$(EXTRALINKLIBS) \
-lm -o namd2
$(PYTHONLIB) \
$(FFTLIB) \
$(PLUGINLIB) \
$(SBLIB) \
$(COLVARSLIB) \
$(LEPTONOBJS) \
$(CHARMOPTS) \
$(EXTRALINKLIBS) \
$(MATHLIBS) -o namd2
EOF_EOF
patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
--- ./src/ComputeMgr.C.preplumed
+++ ./src/ComputeMgr.C
@@ -77,13 +77,137 @@
@@ -80,12 +80,135 @@
#include "GlobalMasterSMD.h"
#include "GlobalMasterTMD.h"
#include "GlobalMasterSymmetry.h"
......@@ -41,7 +52,6 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
+// END PLUMED
#include "GlobalMasterFreeEnergy.h"
#include "GlobalMasterColvars.h"
+class GlobalMasterPlumed:
+ public GlobalMasterEasy,
+ private PLMD::Plumed
......@@ -162,13 +172,12 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
+
+ }
+};
+
ComputeMgr::ComputeMgr()
{
CkpvAccess(BOCclass_group).computeMgr = thisgroup;
computeGlobalObject = 0;
computeDPMEObject = 0;
@@ -743,10 +867,15 @@
@@ -785,10 +908,15 @@
masterServerObject->addClient(new GlobalMasterSymmetry());
if (simParams->TMDOn)
masterServerObject->addClient(new GlobalMasterTMD());
......@@ -188,7 +197,7 @@ EOF_EOF
patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
--- ./src/SimParameters.C.preplumed
+++ ./src/SimParameters.C
@@ -1231,10 +1231,17 @@
@@ -1324,10 +1324,17 @@
opts.optionalB("main", "GBIS", "Use GB implicit solvent?",
&GBISOn, FALSE);
opts.optionalB("main", "GBISSer", "Use GB implicit solvent?",
......@@ -206,20 +215,21 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
opts.optional("GBIS", "intrinsicRadiusOffset",
"Coulomb Radius Offset", &coulomb_radius_offset, 0.09);
opts.optional("GBIS", "ionConcentration",
@@ -4103,11 +4110,11 @@
@@ -4299,12 +4307,12 @@
}
// Global forces configuration
globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
- (IMDon) || SMDOn || TMDOn || colvarsOn || symmetryOn );
+ (IMDon) || SMDOn || TMDOn || colvarsOn || symmetryOn || plumedOn );
(IMDon && ! (IMDignore || IMDignoreForces)) || SMDOn || TMDOn ||
- colvarsOn || symmetryOn || qmForcesOn );
+ colvarsOn || symmetryOn || qmForcesOn || plumedOn );
if (tclForcesOn)
{
iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n";
@@ -4188,10 +4195,25 @@
@@ -4384,10 +4391,25 @@
}
iout << endi;
......@@ -249,7 +259,7 @@ EOF_EOF
patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF
--- ./src/SimParameters.h.preplumed
+++ ./src/SimParameters.h
@@ -401,10 +401,13 @@
@@ -430,10 +430,13 @@
char tclBCArgs[128]; // Extra args for calcforces command
Bool freeEnergyOn; // Doing free energy perturbation?
Bool miscForcesOn; // Using misc forces?
......
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