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Commit f7212846 authored by Giovanni Bussi's avatar Giovanni Bussi
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Merge branch 'v2.4-namd-patches3' into v2.4

parents 9ebbcdde 9ac9284f
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patches/namd-2.12.diff
+ 35
− 39
View file @ f7212846
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
@@ -359,13 +359,15 @@ @@ -439,10 +439,15 @@
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) CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS)
CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS) CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS)
CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS) CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS)
CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS) CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS)
CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS) CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS)
+include .rootdir/Plumed.inc +include .rootdir/Plumed.inc
+PLUMED_PREFIX=-Wl,
+PLUMED_LOAD1=$(patsubst "%.so",$(PLUMED_PREFIX)"%.so",$(PLUMED_LOAD))
+PLUMED_LOAD2=$(patsubst "%.dylib",$(PLUMED_PREFIX)"%.dylib",$(PLUMED_LOAD1))
+ +
CXXCOLVARFLAGS = $(CXXBASEFLAGS) $(CXXCOLVAROPTS) 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) @@ -479,10 +484,11 @@
SBGCCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(CUDALIB) \
@@ -394,13 +396,14 @@ $(DPMTALIB) \
$(CUDAOBJS) \ $(DPMELIB) \
$(CUDALIB) \ $(FMMLIB) \
$(DPMTALIB) \ $(TCLLIB) \
$(DPMELIB) \ + $(PLUMED_LOAD2) \
$(FMMLIB) \ $(PYTHONLIB) \
$(TCLLIB) \ $(FFTLIB) \
+ $(PLUMED_LOAD) \ $(PLUGINLIB) \
$(PYTHONLIB) \ $(SBLIB) \
$(FFTLIB) \ $(CHARMOPTS) \
$(PLUGINLIB) \
$(SBLIB) \
$(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 -N --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
--- ./src/ComputeMgr.C.preplumed --- ./src/ComputeMgr.C.preplumed
+++ ./src/ComputeMgr.C +++ ./src/ComputeMgr.C
@@ -80,12 +80,135 @@ @@ -92,12 +92,135 @@
#include "GlobalMasterSMD.h" #include "GlobalMasterSMD.h"
#include "GlobalMasterTMD.h" #include "GlobalMasterTMD.h"
#include "GlobalMasterSymmetry.h" #include "GlobalMasterSymmetry.h"
...@@ -168,11 +165,11 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF ...@@ -168,11 +165,11 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
+ } + }
+}; +};
ComputeMgr::ComputeMgr() #include "ComputeNonbondedMICKernel.h"
{
CkpvAccess(BOCclass_group).computeMgr = thisgroup; #include "DeviceCUDA.h"
computeGlobalObject = 0; #ifdef NAMD_CUDA
@@ -785,10 +908,15 @@ @@ -922,10 +1045,15 @@
masterServerObject->addClient(new GlobalMasterSymmetry()); masterServerObject->addClient(new GlobalMasterSymmetry());
if (simParams->TMDOn) if (simParams->TMDOn)
masterServerObject->addClient(new GlobalMasterTMD()); masterServerObject->addClient(new GlobalMasterTMD());
...@@ -189,10 +186,10 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF ...@@ -189,10 +186,10 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
masterServerObject->addClient(new GlobalMasterColvars()); masterServerObject->addClient(new GlobalMasterColvars());
EOF_EOF EOF_EOF
patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF patch -u -l -b -F 5 -N --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
--- ./src/SimParameters.C.preplumed --- ./src/SimParameters.C.preplumed
+++ ./src/SimParameters.C +++ ./src/SimParameters.C
@@ -1324,10 +1324,17 @@ @@ -1603,10 +1603,17 @@
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?",
...@@ -210,21 +207,20 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF ...@@ -210,21 +207,20 @@ 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",
@@ -4299,12 +4307,12 @@ @@ -5128,11 +5135,11 @@
}
// Global forces configuration // Global forces configuration
globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn || globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
(IMDon && ! IMDignore) || SMDOn || TMDOn || (IMDon && ! IMDignore) || SMDOn || TMDOn ||
- colvarsOn || symmetryOn || qmForcesOn ); - colvarsOn || symmetryOn || qmForcesOn );
+ colvarsOn || symmetryOn || qmForcesOn || plumedOn ); + colvarsOn || symmetryOn || qmForcesOn || plumedOn );
if (tclForcesOn) if (tclForcesOn)
{ {
iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n"; iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n";
@@ -4384,10 +4391,25 @@ @@ -5213,10 +5220,25 @@
} }
iout << endi; iout << endi;
...@@ -251,10 +247,10 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF ...@@ -251,10 +247,10 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
iout << iINFO << "INTERACTIVE MD PORT " << IMDport << "\n"; iout << iINFO << "INTERACTIVE MD PORT " << IMDport << "\n";
iout << iINFO << "INTERACTIVE MD FREQ " << IMDfreq << "\n"; iout << iINFO << "INTERACTIVE MD FREQ " << IMDfreq << "\n";
EOF_EOF EOF_EOF
patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF patch -u -l -b -F 5 -N --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF
--- ./src/SimParameters.h.preplumed --- ./src/SimParameters.h.preplumed
+++ ./src/SimParameters.h +++ ./src/SimParameters.h
@@ -430,10 +430,13 @@ @@ -522,10 +522,13 @@
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?
...@@ -265,7 +261,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF ...@@ -265,7 +261,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF
+ +
Bool fixedAtomsOn; // Are there fixed atoms? Bool fixedAtomsOn; // Are there fixed atoms?
Bool fixedAtomsForces; // Calculate forces anyway? Bool fixedAtomsForces; // Calculate forces anyway?
Bool fixedAtomsForceOutput; // Output fixed forces?
Bool langevinOn; // Flag TRUE-> langevin dynamics active Bool langevinOnAtStartup; // Ensure that langevin is set up properly
BigReal langevinTemp; // Temperature for Langevin dynamics
EOF_EOF EOF_EOF
patches/namd-2.13.diff
+ 36
− 45
View file @ f7212846
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
@@ -359,16 +359,18 @@ @@ -438,10 +438,15 @@
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) CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS)
CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS) CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS)
CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS) CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS)
CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS) CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS)
CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS) CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS)
+include .rootdir/Plumed.inc +include .rootdir/Plumed.inc
+PLUMED_PREFIX=-Wl,
+PLUMED_LOAD1=$(patsubst "%.so",$(PLUMED_PREFIX)"%.so",$(PLUMED_LOAD))
+PLUMED_LOAD2=$(patsubst "%.dylib",$(PLUMED_PREFIX)"%.dylib",$(PLUMED_LOAD1))
+ +
COLVARSCXXFLAGS = $(CXXBASEFLAGS) $(CXXCOLVAROPTS) $(COPTI)$(LEPTONINCDIR) -DLEPTON -DLEPTON_USE_STATIC_LIBRARIES COLVARSCXXFLAGS = $(CXXBASEFLAGS) $(CXXCOLVAROPTS) $(COPTI)$(LEPTONINCDIR) -DLEPTON -DLEPTON_USE_STATIC_LIBRARIES
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) @@ -481,10 +486,11 @@
SBGCCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(CUDALIB) \
COLVARSGXXFLAGS= $(GXXFLAGS) $(DPMTALIB) \
LEPTONGCCFLAGS= $(COPTI)$(LEPTONINCDIR) $(DPMELIB) \
LEPTONCXXFLAGS=$(CXXBASEFLAGS) $(COPTI)$(LEPTONINCDIR) -DLEPTON_BUILDING_STATIC_LIBRARY $(FMMLIB) \
@@ -394,15 +396,16 @@ $(TCLLIB) \
$(CUDAOBJS) \ + $(PLUMED_LOAD2) \
$(CUDALIB) \ $(PYTHONLIB) \
$(DPMTALIB) \ $(FFTLIB) \
$(DPMELIB) \ $(PLUGINLIB) \
$(FMMLIB) \ $(SBLIB) \
$(TCLLIB) \ $(COLVARSLIB) \
+ $(PLUMED_LOAD) \
$(PYTHONLIB) \
$(FFTLIB) \
$(PLUGINLIB) \
$(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 -N --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
--- ./src/ComputeMgr.C.preplumed --- ./src/ComputeMgr.C.preplumed
+++ ./src/ComputeMgr.C +++ ./src/ComputeMgr.C
@@ -80,12 +80,135 @@ @@ -92,12 +92,135 @@
#include "GlobalMasterSMD.h" #include "GlobalMasterSMD.h"
#include "GlobalMasterTMD.h" #include "GlobalMasterTMD.h"
#include "GlobalMasterSymmetry.h" #include "GlobalMasterSymmetry.h"
...@@ -173,11 +165,11 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF ...@@ -173,11 +165,11 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
+ } + }
+}; +};
ComputeMgr::ComputeMgr() #include "ComputeNonbondedMICKernel.h"
{
CkpvAccess(BOCclass_group).computeMgr = thisgroup; #include "DeviceCUDA.h"
computeGlobalObject = 0; #ifdef NAMD_CUDA
@@ -785,10 +908,15 @@ @@ -1048,10 +1171,15 @@
masterServerObject->addClient(new GlobalMasterSymmetry()); masterServerObject->addClient(new GlobalMasterSymmetry());
if (simParams->TMDOn) if (simParams->TMDOn)
masterServerObject->addClient(new GlobalMasterTMD()); masterServerObject->addClient(new GlobalMasterTMD());
...@@ -194,10 +186,10 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF ...@@ -194,10 +186,10 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
masterServerObject->addClient(new GlobalMasterColvars()); masterServerObject->addClient(new GlobalMasterColvars());
EOF_EOF EOF_EOF
patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF patch -u -l -b -F 5 -N --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
--- ./src/SimParameters.C.preplumed --- ./src/SimParameters.C.preplumed
+++ ./src/SimParameters.C +++ ./src/SimParameters.C
@@ -1324,10 +1324,17 @@ @@ -1778,10 +1778,17 @@
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?",
...@@ -215,21 +207,20 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF ...@@ -215,21 +207,20 @@ 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",
@@ -4299,12 +4307,12 @@ @@ -5447,11 +5454,11 @@
}
// Global forces configuration // Global forces configuration
globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn || globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
(IMDon && ! (IMDignore || IMDignoreForces)) || SMDOn || TMDOn || (IMDon && ! (IMDignore || IMDignoreForces)) || SMDOn || TMDOn ||
- colvarsOn || symmetryOn || qmForcesOn ); - colvarsOn || symmetryOn || qmForcesOn );
+ colvarsOn || symmetryOn || qmForcesOn || plumedOn ); + colvarsOn || symmetryOn || qmForcesOn || plumedOn );
if (tclForcesOn) if (tclForcesOn)
{ {
iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n"; iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n";
@@ -4384,10 +4391,25 @@ @@ -5532,10 +5539,25 @@
} }
iout << endi; iout << endi;
...@@ -256,10 +247,10 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF ...@@ -256,10 +247,10 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
iout << iINFO << "INTERACTIVE MD PORT " << IMDport << "\n"; iout << iINFO << "INTERACTIVE MD PORT " << IMDport << "\n";
iout << iINFO << "INTERACTIVE MD FREQ " << IMDfreq << "\n"; iout << iINFO << "INTERACTIVE MD FREQ " << IMDfreq << "\n";
EOF_EOF EOF_EOF
patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF patch -u -l -b -F 5 -N --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF
--- ./src/SimParameters.h.preplumed --- ./src/SimParameters.h.preplumed
+++ ./src/SimParameters.h +++ ./src/SimParameters.h
@@ -430,10 +430,13 @@ @@ -547,10 +547,13 @@
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?
...@@ -270,7 +261,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF ...@@ -270,7 +261,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF
+ +
Bool fixedAtomsOn; // Are there fixed atoms? Bool fixedAtomsOn; // Are there fixed atoms?
Bool fixedAtomsForces; // Calculate forces anyway? Bool fixedAtomsForces; // Calculate forces anyway?
Bool fixedAtomsForceOutput; // Output fixed forces?
Bool langevinOn; // Flag TRUE-> langevin dynamics active Bool langevinOnAtStartup; // Ensure that langevin is set up properly
BigReal langevinTemp; // Temperature for Langevin dynamics
EOF_EOF EOF_EOF
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