Merge pull request #1340 from akohlmey/bonus-data-checks (eb39866e) · Commits · 郑智淋 / lammps

src/atom.cpp

+40 −0

Original line number	Diff line number	Diff line
		@@ -58,6 +58,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
		natoms = 0;
		nlocal = nghost = nmax = 0;
		ntypes = 0;
		nellipsoids = nlines = ntris = nbodies = 0;
		nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
		nbonds = nangles = ndihedrals = nimpropers = 0;

		@@ -738,6 +739,45 @@ int Atom::tag_consecutive()
		return 1;
		}

		/* ----------------------------------------------------------------------
		check that bonus data settings are valid
		error if number of atoms with ellipsoid/line/tri/body flags
		are consistent with global setting.
		------------------------------------------------------------------------- */

		void Atom::bonus_check()
		{
		bigint local_ellipsoids = 0, local_lines = 0, local_tris = 0;
		bigint local_bodies = 0, num_global;

		for (int i = 0; i < nlocal; ++i) {
		if (ellipsoid && (ellipsoid[i] >=0)) ++local_ellipsoids;
		if (line && (line[i] >=0)) ++local_lines;
		if (tri && (tri[i] >=0)) ++local_tris;
		if (body && (body[i] >=0)) ++local_bodies;
		}

		MPI_Allreduce(&local_ellipsoids,&num_global,1,MPI_LMP_BIGINT,MPI_MIN,world);
		if (nellipsoids != num_global)
		error->all(FLERR,"Inconsistent 'ellipsoids' header value and number of "
		"atoms with enabled ellipsoid flags");

		MPI_Allreduce(&local_lines,&num_global,1,MPI_LMP_BIGINT,MPI_MIN,world);
		if (nlines != num_global)
		error->all(FLERR,"Inconsistent 'lines' header value and number of "
		"atoms with enabled line flags");

		MPI_Allreduce(&local_tris,&num_global,1,MPI_LMP_BIGINT,MPI_MIN,world);
		if (ntris != num_global)
		error->all(FLERR,"Inconsistent 'tris' header value and number of "
		"atoms with enabled tri flags");

		MPI_Allreduce(&local_bodies,&num_global,1,MPI_LMP_BIGINT,MPI_MIN,world);
		if (nbodies != num_global)
		error->all(FLERR,"Inconsistent 'bodies' header value and number of "
		"atoms with enabled body flags");
		}

		/* ----------------------------------------------------------------------
		count and return words in a single line
		make copy of line before using strtok so as not to change line

src/atom.h

+6 −0

Original line number	Diff line number	Diff line
		@@ -34,6 +34,10 @@ class Atom : protected Pointers {
		int tag_enable; // 0/1 if atom ID tags are defined
		int molecular; // 0 = atomic, 1 = standard molecular system,
		// 2 = molecule template system
		bigint nellipsoids; // number of ellipsoids
		bigint nlines; // number of lines
		bigint ntris; // number of triangles
		bigint nbodies; // number of bodies

		bigint nbonds,nangles,ndihedrals,nimpropers;
		int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
		@@ -233,6 +237,8 @@ class Atom : protected Pointers {
		void tag_extend();
		int tag_consecutive();

		void bonus_check();

		int parse_data(const char *);
		int count_words(const char *);
		int count_words(const char , char );

src/atom_vec_body.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -1286,7 +1286,7 @@ void AtomVecBody::data_atom(double coord, imageint imagetmp, char *values)
		body[nlocal] = atoi(values[2]);
		if (body[nlocal] == 0) body[nlocal] = -1;
		else if (body[nlocal] == 1) body[nlocal] = 0;
		else error->one(FLERR,"Invalid atom type in Atoms section of data file");
		else error->one(FLERR,"Invalid bodyflag in Atoms section of data file");

		rmass[nlocal] = atof(values[3]);
		if (rmass[nlocal] <= 0.0)

src/atom_vec_body.h

+3 −1

Original line number	Diff line number	Diff line
		@@ -92,6 +92,8 @@ class AtomVecBody : public AtomVec {
		double radius_body(int, int, int , double );
		void set_quat(int, double *);

		int nlocal_bonus;

		private:
		tagint *tag;
		int type,mask;
		@@ -102,7 +104,7 @@ class AtomVecBody : public AtomVec {
		double angmom,torque;
		int *body;

		int nlocal_bonus,nghost_bonus,nmax_bonus;
		int nghost_bonus,nmax_bonus;
		int intdoubleratio; // sizeof(double) / sizeof(int)

		MyPoolChunk<int> *icp;

src/atom_vec_ellipsoid.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -1148,7 +1148,7 @@ void AtomVecEllipsoid::data_atom(double *coord, imageint imagetmp,
		ellipsoid[nlocal] = atoi(values[2]);
		if (ellipsoid[nlocal] == 0) ellipsoid[nlocal] = -1;
		else if (ellipsoid[nlocal] == 1) ellipsoid[nlocal] = 0;
		else error->one(FLERR,"Invalid atom type in Atoms section of data file");
		else error->one(FLERR,"Invalid ellipsoidflag in Atoms section of data file");

		rmass[nlocal] = atof(values[3]);
		if (rmass[nlocal] <= 0.0)

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