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bond/react: check for valid IDs in map file

This commit is contained in:
jrgissing 2020-01-21 23:21:41 -07:00
parent 683d6ce9b3
commit d897949ff8
2 changed files with 22 additions and 0 deletions
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18
src/USER-REACTION/fix_bond_react.cpp
View File

@ -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];

4
src/USER-REACTION/fix_bond_react.h
View File

@ -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