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exclude_cutoff to exclude_radius

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This commit is contained in:
Eugen Rožić
2022-02-03 21:58:14 +01:00
parent 1da12feafc
commit b06d4a3300
2 changed files with 36 additions and 16 deletions
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50
src/create_atoms.cpp
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@ -14,7 +14,7 @@
/* ----------------------------------------------------------------------
Contributing author (ratio and subset) : Jake Gissinger (U Colorado)
Contributing author (exclude and maxtries) : Eugen Rozic (IRB, Zagreb)
Contributing author (maxtries & exclude) : Eugen Rozic (IRB, Zagreb)
------------------------------------------------------------------------- */
#include "create_atoms.h"
@ -230,15 +230,6 @@ void CreateAtoms::command(int narg, char **arg)
if (nsubset <= 0 || subsetseed <= 0)
error->all(FLERR,"Illegal create_atoms command");
iarg += 3;
} else if (strcmp(arg[iarg],"exclude") == 0) {
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_cutoff = force->numeric(FLERR,arg[iarg+1]);
if (exclude_cutoff <= 0)
error->all(FLERR,"Illegal create_atoms command");
excludeflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"maxtries") == 0) {
if (style != RANDOM) error->all(FLERR,"Illegal create_atoms command: "
"'maxtries' can only be combined with 'random' style!");
@ -247,6 +238,15 @@ void CreateAtoms::command(int narg, char **arg)
if (maxtries <= 0)
error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"exclude") == 0) {
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]);
if (exclude_radius <= 0)
error->all(FLERR,"Illegal create_atoms command");
excludeflag = 1;
iarg += 2;
} else error->all(FLERR,"Illegal create_atoms command");
}
@ -673,6 +673,17 @@ void CreateAtoms::add_random()
double lamda[3],*coord;
double *boxlo,*boxhi;
if (excludeflag) {
int nlocal = atom->nlocal;
double **x = atom->x;
double delx, dely, delz, distsq;
double 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;
}
// random number generator, same for all procs
// warm up the generator 30x to avoid correlations in first-particle
// positions if runs are repeated with consecutive seeds
@ -708,7 +719,9 @@ void CreateAtoms::add_random()
}
// generate random positions for each new atom/molecule within bounding box
// iterate until atom is within region, variable, and triclinic simulation box
// iterate until atom is within region, variable, triclinic simulation box
// and outside the exclusion area of other atoms, or if maximum number
// of attempts (maxtries) have been exceeded for any atom/molecule.
// if final atom position is in my subbox, create it
if (xlo > xhi || ylo > yhi || zlo > zhi)
@ -737,11 +750,18 @@ void CreateAtoms::add_random()
gen_mol_coords(xone, quatone);
if (excludeflag) {
if (mode == ATOM) {
//TODO check fox xone... if not OK: continue;
} else {
//TODO check for each temp_mol_coord... if not OK: continue;
int reject = 0;
for (int i = 0; i < nlocal; i++){
delx = xone[0] - x[i][0];
dely = xone[1] - x[i][1];
delz = xone[2] - x[i][2];
distsq = delx*delx + dely*dely + delz*delz;
if (distsq < excutsq){
reject = 1;
break;
}
}
if (reject) continue;
}
if (triclinic) {