sync with GH (d58e8662) · Commits · 郑智淋 / lammps

doc/Makefile

+8 −4

Original line number	Diff line number	Diff line
		@@ -8,13 +8,15 @@ VENV = $(BUILDDIR)/docenv
		TXT2RST = $(VENV)/bin/txt2rst

		PYTHON = $(shell which python3)
		HAS_PYTHON3 = NO
		HAS_VIRTUALENV = NO

		ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 1)
		$(error Python3 was not found! Please check README.md for further instructions)
		ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
		HAS_PYTHON3 = YES
		endif

		ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 1)
		$(error virtualenv was not found! Please check README.md for further instructions)
		ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
		HAS_VIRTUALENV = YES
		endif

		SOURCES=$(wildcard src/*.txt)
		@@ -109,6 +111,8 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
		)

		$(VENV):
		@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
		@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
		@( \
		virtualenv -p $(PYTHON) $(VENV); \
		. $(VENV)/bin/activate; \

python/lammps.py

+14 −7

Original line number	Diff line number	Diff line
		@@ -58,6 +58,13 @@ class lammps(object):
		# determine module location

		modpath = dirname(abspath(getsourcefile(lambda:0)))
		self.lib = None

		# if a pointer to a LAMMPS object is handed in, all symbols should already be available.
		try:
		if ptr: self.lib = CDLL("",RTLD_GLOBAL)
		except:
		self.lib = None

		# load liblammps.so unless name is given.
		# e.g. if name = "g++", load liblammps_g++.so
		@@ -66,7 +73,7 @@ class lammps(object):
		# does not need to be set for regular installations.
		# fall back to loading with a relative path, which typically
		# requires LD_LIBRARY_PATH to be set appropriately.

		if not self.lib:
		try:
		if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL)
		else: self.lib = CDLL(join(modpath,"liblammps_%s.so" % name),RTLD_GLOBAL)

src/USER-DPD/fix_rx.cpp

+10 −28

Original line number	Diff line number	Diff line
		@@ -642,15 +642,9 @@ void FixRX::setup_pre_force(int vflag)
		int ii;

		if(localTempFlag){
		if (newton_pair) {
		dpdThetaLocal = new double[nlocal+nghost];
		for (ii = 0; ii < nlocal+nghost; ii++)
		dpdThetaLocal[ii] = 0.0;
		} else {
		dpdThetaLocal = new double[nlocal];
		for (ii = 0; ii < nlocal; ii++)
		dpdThetaLocal[ii] = 0.0;
		}
		int count = nlocal + (newton_pair ? nghost : 0);
		dpdThetaLocal = new double[count];
		memset(dpdThetaLocal, 0, sizeof(double)*count);
		computeLocalTemperature();
		}

		@@ -690,15 +684,9 @@ void FixRX::pre_force(int vflag)
		double theta;

		if(localTempFlag){
		if (newton_pair) {
		dpdThetaLocal = new double[nlocal+nghost];
		for (ii = 0; ii < nlocal+nghost; ii++)
		dpdThetaLocal[ii] = 0.0;
		} else {
		dpdThetaLocal = new double[nlocal];
		for (ii = 0; ii < nlocal; ii++)
		dpdThetaLocal[ii] = 0.0;
		}
		int count = nlocal + (newton_pair ? nghost : 0);
		dpdThetaLocal = new double[count];
		memset(dpdThetaLocal, 0, sizeof(double)*count);
		computeLocalTemperature();
		}

		@@ -1677,16 +1665,10 @@ void FixRX::computeLocalTemperature()
		double wij=0.0;
		double *dpdTheta = atom->dpdTheta;

		// Initialize the local density and local temperature arrays
		if (newton_pair) {
		sumWeights = new double[nlocal+nghost];
		for (ii = 0; ii < nlocal+nghost; ii++)
		sumWeights[ii] = 0.0;
		} else {
		sumWeights = new double[nlocal];
		for (ii = 0; ii < nlocal; ii++)
		dpdThetaLocal[ii] = 0.0;
		}
		// Initialize the local temperature weight array
		int sumWeightsCt = nlocal + (newton_pair ? nghost : 0);
		sumWeights = new double[sumWeightsCt];
		memset(sumWeights, 0, sizeof(double)*sumWeightsCt);

		inum = pairDPDE->list->inum;
		ilist = pairDPDE->list->ilist;

Admin message