Skip to content
Snippets Groups Projects
Commit edfed6c0 authored by Giovanni Bussi's avatar Giovanni Bussi
Browse files

Merge branch 'v2.4-namd-patches' into v2.4

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