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make radscale and radthresh class members

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This commit is contained in:
Axel Kohlmeyer
2022-05-07 23:04:34 -04:00
parent e9b1ca16a3
commit e0bb27dbb2
3 changed files with 29 additions and 20 deletions
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42
src/create_atoms.cpp
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@ -86,7 +86,7 @@ void CreateAtoms::command(int narg, char **arg)
ntype = utils::inumeric(FLERR, arg[0], false, lmp);
const char *meshfile;
double radiusscale = 1.0;
radthresh = 1.0;
int iarg;
if (strcmp(arg[1], "box") == 0) {
style = BOX;
@ -146,6 +146,8 @@ void CreateAtoms::command(int narg, char **arg)
int subsetseed;
overlapflag = 0;
maxtry = DEFAULT_MAXTRY;
radscale = 1.0;
radthresh = domain->lattice->xlattice;
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
@ -255,13 +257,19 @@ void CreateAtoms::command(int narg, char **arg)
maxtry = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (maxtry <= 0) error->all(FLERR, "Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg], "radiusscale") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_atoms radiusscale", error);
} else if (strcmp(arg[iarg], "radscale") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_atoms radscale", error);
if (style != MESH)
error->all(FLERR, "Create_atoms radiusscale can only be used with mesh style");
error->all(FLERR, "Create_atoms radscale can only be used with mesh style");
if (!atom->radius_flag)
error->all(FLERR, "Must have atom attribute radius to set radiusscale factor");
radiusscale = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
error->all(FLERR, "Must have atom attribute radius to set radscale factor");
radscale = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "radthresh") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_atoms radthresh", error);
if (style != MESH)
error->all(FLERR, "Create_atoms radthresh can only be used with mesh style");
radthresh = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else
error->all(FLERR, "Illegal create_atoms command option {}", arg[iarg]);
@ -437,7 +445,7 @@ void CreateAtoms::command(int narg, char **arg)
else if (style == RANDOM)
add_random();
else if (style == MESH)
add_mesh(meshfile, radiusscale);
add_mesh(meshfile);
else
add_lattice();
@ -841,9 +849,8 @@ void CreateAtoms::add_random()
or split into two halves along the longest side and recurse
------------------------------------------------------------------------- */
int CreateAtoms::add_tricenter(const double vert[3][3], tagint molid, double radiusscale)
int CreateAtoms::add_tricenter(const double vert[3][3], tagint molid)
{
const double xlat = domain->lattice->xlattice;
double center[3], temp[3];
MathExtra::add3(vert[0], vert[1], center);
@ -862,14 +869,15 @@ int CreateAtoms::add_tricenter(const double vert[3][3], tagint molid, double rad
// lattice parameter, the triangle is split it in half along its longest side
int ilocal = 0;
if (ravg > xlat) {
if (ravg > radthresh) {
double vert1[3][3], vert2[3][3], side[3][3];
// determine side vectors and longest side
// determine side vectors
MathExtra::sub3(vert[0], vert[1], side[0]);
MathExtra::sub3(vert[1], vert[2], side[1]);
MathExtra::sub3(vert[2], vert[0], side[2]);
// determine longest side
const double l1 = MathExtra::len3(side[0]);
const double l2 = MathExtra::len3(side[1]);
const double l3 = MathExtra::len3(side[2]);
@ -894,8 +902,8 @@ int CreateAtoms::add_tricenter(const double vert[3][3], tagint molid, double rad
}
}
ilocal = add_tricenter(vert1, molid, radiusscale);
ilocal += add_tricenter(vert2, molid, radiusscale);
ilocal = add_tricenter(vert1, molid);
ilocal += add_tricenter(vert2, molid);
} else {
/*
@ -908,8 +916,8 @@ int CreateAtoms::add_tricenter(const double vert[3][3], tagint molid, double rad
(center[1] < subhi[1]) && (center[2] >= sublo[2]) && (center[2] < subhi[2])) {
atom->avec->create_atom(ntype, center);
int idx = atom->nlocal-1;
if (atom->radius_flag) atom->radius[idx] = ravg * radiusscale;
int idx = atom->nlocal - 1;
if (atom->radius_flag) atom->radius[idx] = ravg * radscale;
if (atom->molecule_flag) atom->molecule[idx] = molid;
++ilocal;
}
@ -921,7 +929,7 @@ int CreateAtoms::add_tricenter(const double vert[3][3], tagint molid, double rad
add atoms at center of triangulated mesh
------------------------------------------------------------------------- */
void CreateAtoms::add_mesh(const char *filename, double radiusscale)
void CreateAtoms::add_mesh(const char *filename)
{
double vert[3][3];
tagint *mol = atom->molecule;
@ -985,7 +993,7 @@ void CreateAtoms::add_mesh(const char *filename, double radiusscale)
// now we have three vertices ... proceed with adding atom in center of triangle
// or splitting recursively into halves as needed to get the desired density
++ntriangle;
atomlocal += add_tricenter(vert, molid, radiusscale);
atomlocal += add_tricenter(vert, molid);
}
} catch (std::exception &e) {
error->all(FLERR, "Error reading triangles from file {}: {}", filename, e.what());