add groups to molecule templates (337cee7b) · Commits · 郑智淋 / lammps

src/molecule.cpp

+59 −2

Original line number	Diff line number	Diff line
		@@ -46,7 +46,7 @@ Molecule::Molecule(LAMMPS lmp, int narg, char *arg, int &index) :
		improper_atom3(NULL), improper_atom4(NULL), nspecial(NULL), special(NULL),
		shake_flag(NULL), shake_atom(NULL), shake_type(NULL), avec_body(NULL), ibodyparams(NULL),
		dbodyparams(NULL), dx(NULL), dxcom(NULL), dxbody(NULL), quat_external(NULL),
		fp(NULL), count(NULL)
		fp(NULL), count(NULL), groupmask(NULL)
		{
		me = comm->me;

		@@ -447,6 +447,9 @@ void Molecule::read(int flag)
		} else if (strstr(line,"impropers")) {
		nmatch = sscanf(line,"%d",&nimpropers);
		nwant = 1;
		} else if (strstr(line,"groups")) {
		nmatch = sscanf(line,"%d",&ngroups);
		nwant = 1;
		} else if (strstr(line,"mass")) {
		massflag = 1;
		nmatch = sscanf(line,"%lg",&masstotal);
		@@ -523,6 +526,10 @@ void Molecule::read(int flag)
		moleculeflag = 1;
		if (flag) molecules(line);
		else skip_lines(natoms,line);
		} else if (strcmp(keyword,"Groups") == 0) {
		groupflag = 1;
		if (flag) groups(line);
		else skip_lines(ngroups,line);
		} else if (strcmp(keyword,"Charges") == 0) {
		qflag = 1;
		if (flag) charges(line);
		@@ -721,6 +728,35 @@ void Molecule::molecules(char *line)
		nmolecules = MAX(nmolecules,molecule[i]);
		}

		/* ----------------------------------------------------------------------
		read groups from file
		------------------------------------------------------------------------- */

		void Molecule::groups(char *line)
		{
		int n,m,atomID,nwords;
		char *words = new char[natoms+1];

		for (int i = 0; i < ngroups; i++) {
		readline(line);
		nwords = parse(line,words,natoms+1);
		if (nwords > natoms+1)
		error->all(FLERR,"Invalid atom ID in Groups section of molecule file");
		n = strlen(words[0]) + 1;
		groupnames[i] = new char[n];
		strcpy(groupnames[i],words[0]);

		for (m = 1; m < nwords; m++) {
		atomID = atoi(words[m]);
		if (atomID <= 0 \|\| atomID > natoms)
		error->all(FLERR,"Invalid atom ID in Groups section of molecule file");
		groupmask[i][atomID-1] = 1;
		}
		}

		delete [] words;
		}

		/* ----------------------------------------------------------------------
		read charges from file
		------------------------------------------------------------------------- */
		@@ -1386,6 +1422,17 @@ void Molecule::body(int flag, int pflag, char *line)
		}
		}

		/* ----------------------------------------------------------------------
		return group index if name matches existing group, -1 if no such group
		------------------------------------------------------------------------- */

		int Molecule::findgroup(const char *name)
		{
		for (int igroup = 0; igroup < ngroups; igroup++)
		if (groupnames[igroup] && strcmp(name,groupnames[igroup]) == 0) return igroup;
		return -1;
		}

		/* ----------------------------------------------------------------------
		error check molecule attributes and topology against system settings
		flag = 0, just check this molecule
		@@ -1466,7 +1513,7 @@ void Molecule::initialize()
		bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
		maxspecial = 0;

		xflag = typeflag = moleculeflag = qflag = radiusflag = rmassflag = 0;
		xflag = typeflag = moleculeflag = groupflag = qflag = radiusflag = rmassflag = 0;
		bondflag = angleflag = dihedralflag = improperflag = 0;
		nspecialflag = specialflag = 0;
		shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
		@@ -1522,6 +1569,10 @@ 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 (groupflag) groupnames = new char*[ngroups];
		if (groupflag) memory->create(groupmask,ngroups,natoms,"molecule:groupmask");
		for (int i = 0; i < ngroups; i++)
		for (int j = 0; j < natoms; j++) groupmask[i][j] = 0;
		if (qflag) memory->create(q,natoms,"molecule:q");
		if (radiusflag) memory->create(radius,natoms,"molecule:radius");
		if (rmassflag) memory->create(rmass,natoms,"molecule:rmass");
		@@ -1614,6 +1665,12 @@ void Molecule::deallocate()
		memory->destroy(radius);
		memory->destroy(rmass);

		memory->destroy(groupmask);
		if (groupflag) {
		for (int i = 0; i < ngroups; i++) delete [] groupnames[i];
		delete [] groupnames;
		}

		memory->destroy(num_bond);
		memory->destroy(bond_type);
		memory->destroy(bond_atom);

src/molecule.h

+8 −2

Original line number	Diff line number	Diff line
		@@ -30,10 +30,14 @@ class Molecule : protected Pointers {

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

		// group info
		char **groupnames;
		int **groupmask; // ngroups by natoms

		// max bond,angle,etc per atom

		int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
		@@ -41,7 +45,7 @@ class Molecule : protected Pointers {

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

		int xflag,typeflag,moleculeflag,qflag,radiusflag,rmassflag;
		int xflag,typeflag,moleculeflag,groupflag,qflag,radiusflag,rmassflag;
		int bondflag,angleflag,dihedralflag,improperflag;
		int nspecialflag,specialflag;
		int shakeflag,shakeflagflag,shakeatomflag,shaketypeflag;
		@@ -119,6 +123,7 @@ class Molecule : protected Pointers {
		void compute_mass();
		void compute_com();
		void compute_inertia();
		int findgroup(const char *);
		void check_attributes(int);

		private:
		@@ -133,6 +138,7 @@ class Molecule : protected Pointers {
		void coords(char *);
		void types(char *);
		void molecules(char *);
		void groups(char *);
		void charges(char *);
		void diameters(char *);
		void masses(char *);

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