add molecule IDs to molecule templates (90bfa6b7) · Commits · 郑智淋 / lammps

src/molecule.cpp

+34 −5

Original line number	Diff line number	Diff line
		@@ -146,19 +146,19 @@ Molecule::Molecule(LAMMPS lmp, int narg, char *arg, int &index) :

		if (me == 0) {
		if (screen)
		fprintf(screen,"Read molecule %s:\n"
		fprintf(screen,"Read molecule template %s:\n %d molecules\n"
		" %d atoms with max type %d\n %d bonds with max type %d\n"
		" %d angles with max type %d\n %d dihedrals with max type %d\n"
		" %d impropers with max type %d\n",
		id,natoms,ntypes,
		id,nmolecules,natoms,ntypes,
		nbonds,nbondtypes,nangles,nangletypes,
		ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
		if (logfile)
		fprintf(logfile,"Read molecule %s:\n"
		fprintf(logfile,"Read molecule template %s:\n %d molecules\n"
		" %d atoms with max type %d\n %d bonds with max type %d\n"
		" %d angles with max type %d\n %d dihedrals with max type %d\n"
		" %d impropers with max type %d\n",
		id,natoms,ntypes,
		id,nmolecules,natoms,ntypes,
		nbonds,nbondtypes,nangles,nangletypes,
		ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
		}
		@@ -519,6 +519,10 @@ void Molecule::read(int flag)
		typeflag = 1;
		if (flag) types(line);
		else skip_lines(natoms,line);
		} else if (strcmp(keyword,"Molecules") == 0) {
		moleculeflag = 1;
		if (flag) molecules(line);
		else skip_lines(natoms,line);
		} else if (strcmp(keyword,"Charges") == 0) {
		qflag = 1;
		if (flag) charges(line);
		@@ -694,6 +698,29 @@ void Molecule::types(char *line)
		ntypes = MAX(ntypes,type[i]);
		}

		/* ----------------------------------------------------------------------
		read molecules from file
		set nmolecules = max of any molecule type
		------------------------------------------------------------------------- */

		void Molecule::molecules(char *line)
		{
		int tmp;
		for (int i = 0; i < natoms; i++) {
		readline(line);
		if (2 != sscanf(line,"%d %d",&tmp,&molecule[i]))
		error->all(FLERR,"Invalid Molecules section in molecule file");
		// molecule[i] += moffset; // placeholder for possible molecule offset
		}

		for (int i = 0; i < natoms; i++)
		if (molecule[i] <= 0)
		error->all(FLERR,"Invalid molecule ID in molecule file");

		for (int i = 0; i < natoms; i++)
		nmolecules = MAX(nmolecules,molecule[i]);
		}

		/* ----------------------------------------------------------------------
		read charges from file
		------------------------------------------------------------------------- */
		@@ -1432,13 +1459,14 @@ void Molecule::initialize()
		natoms = 0;
		nbonds = nangles = ndihedrals = nimpropers = 0;
		ntypes = 0;
		nmolecules = 1;
		nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
		nibody = ndbody = 0;

		bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
		maxspecial = 0;

		xflag = typeflag = qflag = radiusflag = rmassflag = 0;
		xflag = typeflag = moleculeflag = qflag = radiusflag = rmassflag = 0;
		bondflag = angleflag = dihedralflag = improperflag = 0;
		nspecialflag = specialflag = 0;
		shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
		@@ -1493,6 +1521,7 @@ void Molecule::allocate()
		{
		if (xflag) memory->create(x,natoms,3,"molecule:x");
		if (typeflag) memory->create(type,natoms,"molecule:type");
		if (moleculeflag) memory->create(molecule,natoms,"molecule:molecule");
		if (qflag) memory->create(q,natoms,"molecule:q");
		if (radiusflag) memory->create(radius,natoms,"molecule:radius");
		if (rmassflag) memory->create(rmass,natoms,"molecule:rmass");

src/molecule.h

+4 −2

Original line number	Diff line number	Diff line
		@@ -30,7 +30,7 @@ class Molecule : protected Pointers {

		int natoms;
		int nbonds,nangles,ndihedrals,nimpropers;
		int ntypes;
		int ntypes,nmolecules;
		int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
		int nibody,ndbody;

		@@ -41,7 +41,7 @@ class Molecule : protected Pointers {

		// 1 if attribute defined in file, 0 if not

		int xflag,typeflag,qflag,radiusflag,rmassflag;
		int xflag,typeflag,moleculeflag,qflag,radiusflag,rmassflag;
		int bondflag,angleflag,dihedralflag,improperflag;
		int nspecialflag,specialflag;
		int shakeflag,shakeflagflag,shakeatomflag,shaketypeflag;
		@@ -59,6 +59,7 @@ class Molecule : protected Pointers {

		double **x; // displacement of each atom from origin
		int *type; // type of each atom
		tagint *molecule; // molecule of each atom
		double *q; // charge on each atom
		double *radius; // radius of each atom
		double *rmass; // mass of each atom
		@@ -131,6 +132,7 @@ class Molecule : protected Pointers {
		void read(int);
		void coords(char *);
		void types(char *);
		void molecules(char *);
		void charges(char *);
		void diameters(char *);
		void masses(char *);

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