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bugfixes

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This commit is contained in:
Eugen Rožić
2022-02-08 02:13:42 +01:00
parent 330dd6a7a8
commit 78cf0365e6
1 changed files with 13 additions and 11 deletions
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24
src/create_atoms.cpp
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@ -234,7 +234,7 @@ void CreateAtoms::command(int narg, char **arg)
if (style != RANDOM) error->all(FLERR,"Illegal create_atoms command: "
"'maxtries' can only be combined with 'random' style!");
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
maxtries = force->numeric(FLERR,arg[iarg+1]);
maxtries = utils::inumeric(FLERR,arg[iarg+1],false, lmp);
if (maxtries <= 0)
error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
@ -242,7 +242,7 @@ void CreateAtoms::command(int narg, char **arg)
if (style != RANDOM) error->all(FLERR,"Illegal create_atoms command: "
"'exclude' can only be combined with 'random' style!");
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
exclude_radius = force->numeric(FLERR,arg[iarg+1]);
exclude_radius = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (exclude_radius <= 0)
error->all(FLERR,"Illegal create_atoms command");
excludeflag = 1;
@ -253,7 +253,7 @@ void CreateAtoms::command(int narg, char **arg)
// error checks and further setup for mode = MOLECULE
if (mode == ATOM) {
if (ntype <= 0 || ntype > atom->ntypes))
if (ntype <= 0 || ntype > atom->ntypes)
error->all(FLERR,"Invalid atom type in create_atoms command");
} else if (mode == MOLECULE) {
if (onemol->xflag == 0)
@ -274,7 +274,7 @@ void CreateAtoms::command(int narg, char **arg)
ranmol = new RanMars(lmp, molseed+me);
// a bit of memory for tries to create molecules (if exclude/maxtries)
memory->create(temp_mol_coords, natoms, 3, "create_atoms:temp_mol_coords");
memory->create(temp_mol_coords, onemol->natoms, 3, "create_atoms:temp_mol_coords");
}
ranlatt = nullptr;
@ -673,15 +673,17 @@ void CreateAtoms::add_random()
double lamda[3],*coord;
double *boxlo,*boxhi;
// stuff needed for the exclude option
int nlocal = atom->nlocal;
double **x = atom->x;
double delx, dely, delz, distsq;
double excut, excutsq;
if (excludeflag) {
int nlocal = atom->nlocal;
double **x = atom->x;
double delx, dely, delz, distsq;
double excut = exclude_radius;
excut = exclude_radius;
// exclude option takes into account the radius of the molecule
// but not the radius of a single atom (even if it is defined)
if (mode == MOLECULE) excut += onemol->molradius;
double excutsq = exclude_radius*exclude_radius;
excutsq = excut*excut;
}
// random number generator, same for all procs
@ -1014,7 +1016,7 @@ void CreateAtoms::loop_lattice(int action)
------------------------------------------------------------------------- */
void CreateAtoms::gen_mol_coords(double *center, double *quat_user)
{
double quat[4], rotmat[3][3];
double r[3], quat[4], rotmat[3][3];
int randrot = 1;
if (quat_user) {
for (int i=0; i<4; i++) {
@ -1062,7 +1064,7 @@ void CreateAtoms::create_mol()
// reset in caller after all molecules created by all procs
// pass add_molecule_atom an offset of 0 since don't know
// max tag of atoms in previous molecules at this point
int natoms = onemol->natoms;
int n, natoms = onemol->natoms;
for (int m = 0; m < natoms; m++) {
atom->avec->create_atom(ntype+onemol->type[m], temp_mol_coords[m]);
n = atom->nlocal - 1;