Merge pull request #977 from akohlmey/collected-small-changes (c3fe26a6) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -941,7 +941,7 @@ endforeach()
		string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
		get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
		include(FeatureSummary)
		feature_summary(DEFAULT_DESCRIPTION WHAT PACKAGES_FOUND)
		feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND)
		message(STATUS "<<< Build configuration >>>
		Build type ${CMAKE_BUILD_TYPE}
		Install path ${CMAKE_INSTALL_PREFIX}

doc/src/dump_modify.txt

+3 −3

Original line number	Diff line number	Diff line
		@@ -600,13 +600,13 @@ included.)

		region foo sphere 10 20 10 15
		variable inregion atom rmask(foo)
		dump_modify ... thresh v_inregion \|^ LAST
		dump_modify ... thresh v_inregion \|^ LAST :pre

		This will dump atoms which crossed the boundary of the spherical
		region since the last dump.

		variable charge atom "(q > 0.5) \|\| (q < -0.5)"
		dump_modify ... thresh v_charge \|^ LAST
		dump_modify ... thresh v_charge \|^ LAST :pre

		This will dump atoms whose charge has changed from an absolute value
		less than 1/2 to greater than 1/2 (or vice versa) since the last dump.

src/LATTE/fix_latte.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -62,7 +62,7 @@ FixLatte::FixLatte(LAMMPS lmp, int narg, char *arg) :
		if (comm->nprocs != 1)
		error->all(FLERR,"Fix latte currently runs only in serial");

		if (latte_abiversion() != ABIVERSION)
		if (LATTE_ABIVERSION != latte_abiversion())
		error->all(FLERR,"LAMMPS is linked against incompatible LATTE library");

		if (narg != 4) error->all(FLERR,"Illegal fix latte command");

src/USER-MISC/compute_entropy_atom.cpp

+13 −11

Original line number	Diff line number	Diff line
		@@ -59,11 +59,11 @@ ComputeEntropyAtom(LAMMPS lmp, int narg, char *arg) :
		// the g(r)

		sigma = force->numeric(FLERR,arg[3]);
		if (sigma < 0.0) error->all(FLERR,"Illegal compute entropy/atom"
		" command; negative sigma");
		if (sigma <= 0.0) error->all(FLERR,"Illegal compute entropy/atom"
		" command; sigma must be positive");
		cutoff = force->numeric(FLERR,arg[4]);
		if (cutoff < 0.0) error->all(FLERR,"Illegal compute entropy/atom"
		" command; negative cutoff");
		if (cutoff <= 0.0) error->all(FLERR,"Illegal compute entropy/atom"
		" command; cutoff must be positive");

		avg_flag = 0;
		local_flag = 0;
		@@ -121,7 +121,7 @@ ComputeEntropyAtom::~ComputeEntropyAtom()
		void ComputeEntropyAtom::init()
		{
		if (force->pair == NULL)
		error->all(FLERR,"Compute centro/atom requires a pair style be"
		error->all(FLERR,"Compute entropy/atom requires a pair style be"
		" defined");

		if ( (cutoff+cutoff2) > (force->pair->cutforce + neighbor->skin) )
		@@ -163,7 +163,8 @@ void ComputeEntropyAtom::compute_peratom()
		int i,j,ii,jj,inum,jnum;
		double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
		int ilist,jlist,numneigh,*firstneigh;
		double rbin[nbin], rbinsq[nbin];
		double *rbin = new double[nbin];
		double *rbinsq = new double[nbin];

		invoked_peratom = update->ntimestep;

		@@ -207,6 +208,8 @@ void ComputeEntropyAtom::compute_peratom()

		double **x = atom->x;
		int *mask = atom->mask;
		double *gofr = new double[nbin];
		double *integrand = new double[nbin];

		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		@@ -235,7 +238,6 @@ void ComputeEntropyAtom::compute_peratom()
		// loop over list of all neighbors within force cutoff

		// initialize gofr
		double gofr[nbin];
		for(int k=0;k<nbin;++k) gofr[k]=0.;

		for (jj = 0; jj < jnum; jj++) {
		@@ -265,7 +267,6 @@ void ComputeEntropyAtom::compute_peratom()
		}

		// Calculate integrand
		double integrand[nbin];
		for(int k=0;k<nbin;++k){
		if (gofr[k]<1.e-10) {
		integrand[k] = rbinsq[k];
		@@ -284,10 +285,10 @@ void ComputeEntropyAtom::compute_peratom()
		value *= deltar;

		pair_entropy[i] = -2MY_PIdensity*value;

		}
		}

		delete [] gofr;
		delete [] integrand;

		if (avg_flag) {
		for (ii = 0; ii < inum; ii++) {
		@@ -320,7 +321,8 @@ void ComputeEntropyAtom::compute_peratom()
		}
		}
		}

		delete [] rbin;
		delete [] rbinsq;
		}

src/USER-MISC/compute_entropy_atom.h

+0 −1

Original line number	Diff line number	Diff line
		@@ -41,7 +41,6 @@ class ComputeEntropyAtom : public Compute {
		double cutsq, cutsq2;
		double deltar;
		int deltabin;
		double invNormConstantBase;
		int avg_flag;
		int local_flag;
		};

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