Unverified Commit 196b3c81 authored by Steve Plimpton's avatar Steve Plimpton Committed by GitHub
Browse files

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

Sanity check on created/read-in bonds/angles/dihedrals/impropers
parents f4a79b4d 38715d7f

src/atom.cpp

+18 −13
Original line number Diff line number Diff line
@@ -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,

src/create_bonds.cpp

+7 −0
Original line number Diff line number Diff line
@@ -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");

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