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Merge pull request #796 from akohlmey/create-bonds-sanity-check

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Sanity check on created/read-in bonds/angles/dihedrals/impropers
This commit is contained in:
Steve Plimpton
2018-02-02 14:46:46 -07:00
committed by GitHub
parent f4a79b4d8e 38715d7f85
commit 196b3c81ef
2 changed files with 25 additions and 13 deletions
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31
src/atom.cpp
View File

@ -1031,8 +1031,8 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
}
itype += type_offset;
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max)
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) || (atom1 == atom2))
error->one(FLERR,"Invalid atom ID in Bonds section of data file");
if (itype <= 0 || itype > nbondtypes)
error->one(FLERR,"Invalid bond type in Bonds section of data file");
@ -1085,9 +1085,10 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
}
itype += type_offset;
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max)
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) ||
(atom3 <= 0) || (atom3 > map_tag_max) ||
(atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3))
error->one(FLERR,"Invalid atom ID in Angles section of data file");
if (itype <= 0 || itype > nangletypes)
error->one(FLERR,"Invalid angle type in Angles section of data file");
@ -1156,10 +1157,12 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
}
itype += type_offset;
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
atom4 <= 0 || atom4 > map_tag_max)
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) ||
(atom3 <= 0) || (atom3 > map_tag_max) ||
(atom4 <= 0) || (atom4 > map_tag_max) ||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR,"Invalid atom ID in Dihedrals section of data file");
if (itype <= 0 || itype > ndihedraltypes)
error->one(FLERR,
@ -1243,10 +1246,12 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
}
itype += type_offset;
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
atom4 <= 0 || atom4 > map_tag_max)
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) ||
(atom3 <= 0) || (atom3 > map_tag_max) ||
(atom4 <= 0) || (atom4 > map_tag_max) ||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR,"Invalid atom ID in Impropers section of data file");
if (itype <= 0 || itype > nimpropertypes)
error->one(FLERR,

7
src/create_bonds.cpp
View File

@ -75,6 +75,8 @@ void CreateBonds::command(int narg, char **arg)
btype = force->inumeric(FLERR,arg[1]);
batom1 = force->tnumeric(FLERR,arg[2]);
batom2 = force->tnumeric(FLERR,arg[3]);
if (batom1 == batom2)
error->all(FLERR,"Illegal create_bonds command");
iarg = 4;
} else if (strcmp(arg[0],"single/angle") == 0) {
style = SANGLE;
@ -83,6 +85,8 @@ void CreateBonds::command(int narg, char **arg)
aatom1 = force->tnumeric(FLERR,arg[2]);
aatom2 = force->tnumeric(FLERR,arg[3]);
aatom3 = force->tnumeric(FLERR,arg[4]);
if ((aatom1 == aatom2) || (aatom1 == aatom3) || (aatom2 == aatom3))
error->all(FLERR,"Illegal create_bonds command");
iarg = 5;
} else if (strcmp(arg[0],"single/dihedral") == 0) {
style = SDIHEDRAL;
@ -92,6 +96,9 @@ void CreateBonds::command(int narg, char **arg)
datom2 = force->tnumeric(FLERR,arg[3]);
datom3 = force->tnumeric(FLERR,arg[4]);
datom4 = force->tnumeric(FLERR,arg[5]);
if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) ||
(datom2 == datom3) || (datom2 == datom4) || (datom3 == datom4))
error->all(FLERR,"Illegal create_bonds command");
iarg = 6;
} else error->all(FLERR,"Illegal create_bonds command");