import template atom ID check from PR #1822 (40e0e78a) · Commits · 郑智淋 / lammps

doc/src/Errors_messages.rst

+3 −0

Original line number	Diff line number	Diff line
		@@ -486,6 +486,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
		Only systems with bonds that can be changed can be used. Atom\_style
		template does not qualify.

		Bond/react: Invalid template atom ID in map file
		Atom IDs in molecule templates range from 1 to the number of atoms in the template.

		Bond/react: Rmax cutoff is longer than pairwise cutoff
		This is not allowed because bond creation is done using the pairwise
		neighbor list.

src/USER-MISC/fix_bond_react.cpp

+18 −0

Original line number	Diff line number	Diff line
		@@ -2946,8 +2946,12 @@ void FixBondReact::read(int myrxn)
		bondflag = 1;
		readline(line);
		sscanf(line,"%d",&ibonding[myrxn]);
		if (ibonding[myrxn] > onemol->natoms)
		error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
		readline(line);
		sscanf(line,"%d",&jbonding[myrxn]);
		if (jbonding[myrxn] > onemol->natoms)
		error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
		} else if (strcmp(keyword,"EdgeIDs") == 0) {
		EdgeIDs(line, myrxn);
		} else if (strcmp(keyword,"Equivalences") == 0) {
		@@ -2987,6 +2991,8 @@ void FixBondReact::EdgeIDs(char *line, int myrxn)
		for (int i = 0; i < nedge; i++) {
		readline(line);
		sscanf(line,"%d",&tmp);
		if (tmp > onemol->natoms)
		error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
		edge[tmp-1][myrxn] = 1;
		}
		}
		@@ -2998,6 +3004,8 @@ void FixBondReact::Equivalences(char *line, int myrxn)
		for (int i = 0; i < nequivalent; i++) {
		readline(line);
		sscanf(line,"%d %d",&tmp1,&tmp2);
		if (tmp1 > onemol->natoms \|\| tmp2 > onemol->natoms)
		error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
		//equivalences is-> clmn 1: post-reacted, clmn 2: pre-reacted
		equivalences[tmp2-1][0][myrxn] = tmp2;
		equivalences[tmp2-1][1][myrxn] = tmp1;
		@@ -3017,6 +3025,8 @@ void FixBondReact::CustomEdges(char *line, int myrxn)
		for (int i = 0; i < ncustom; i++) {
		readline(line);
		sscanf(line,"%d %s",&tmp,edgemode);
		if (tmp > onemol->natoms)
		error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
		if (strcmp(edgemode,"none") == 0)
		custom_edges[tmp-1][myrxn] = 0;
		else if (strcmp(edgemode,"charges") == 0)
		@@ -3033,6 +3043,8 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn)
		for (int i = 0; i < ndelete; i++) {
		readline(line);
		sscanf(line,"%d",&tmp);
		if (tmp > onemol->natoms)
		error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
		delete_atoms[tmp-1][myrxn] = 1;
		}
		}
		@@ -3043,6 +3055,8 @@ void FixBondReact::ChiralCenters(char *line, int myrxn)
		for (int i = 0; i < nchiral; i++) {
		readline(line);
		sscanf(line,"%d",&tmp);
		if (tmp > onemol->natoms)
		error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
		chiral_atoms[tmp-1][0][myrxn] = 1;
		if (onemol->xflag == 0)
		error->one(FLERR,"Bond/react: Molecule template 'Coords' section required for chiralIDs keyword");
		@@ -3080,6 +3094,8 @@ void FixBondReact::Constraints(char *line, int myrxn)
		if (strcmp(constraint_type,"distance") == 0) {
		constraints[nconstraints][1] = DISTANCE;
		sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]);
		if (tmp[0] > onemol->natoms \|\| tmp[1] > onemol->natoms)
		error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
		constraints[nconstraints][2] = tmp[0];
		constraints[nconstraints][3] = tmp[1];
		constraints[nconstraints][4] = tmp[2]*tmp[2]; // using square of distance
		@@ -3087,6 +3103,8 @@ void FixBondReact::Constraints(char *line, int myrxn)
		} else if (strcmp(constraint_type,"angle") == 0) {
		constraints[nconstraints][1] = ANGLE;
		sscanf(line,"%*s %lg %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3],&tmp[4]);
		if (tmp[0] > onemol->natoms \|\| tmp[1] > onemol->natoms \|\| tmp[2] > onemol->natoms)
		error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
		constraints[nconstraints][2] = tmp[0];
		constraints[nconstraints][3] = tmp[1];
		constraints[nconstraints][4] = tmp[2];

src/USER-MISC/fix_bond_react.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -232,6 +232,10 @@ E: Bond/react: Unknown section in map file

		Please ensure reaction map files are properly formatted.

		E: Bond/react: Invalid template atom ID in map file

		Atom IDs in molecule templates range from 1 to the number of atoms in the template.

		E or W: Bond/react: Atom affected by reaction %s too close to template edge

		This means an atom which changes type or connectivity during the

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