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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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2
doc/src/dump_image.rst
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@ -44,7 +44,7 @@ Syntax
color = *type* color = *type*
bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
*fix* = fixID color fflag1 fflag2 *fix* = fixID color fflag1 fflag2
fixID = ID of fix that generates objects to dray fixID = ID of fix that generates objects to draw
color = *type* color = *type*
fflag1,fflag2 = 2 numeric flags to affect how fix objects are drawn fflag1,fflag2 = 2 numeric flags to affect how fix objects are drawn
*size* values = width height = size of images *size* values = width height = size of images

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); ntype = utils::inumeric(FLERR, arg[0], false, lmp);
const char *meshfile; const char *meshfile;
double radiusscale = 1.0; radthresh = 1.0;
int iarg; int iarg;
if (strcmp(arg[1], "box") == 0) { if (strcmp(arg[1], "box") == 0) {
style = BOX; style = BOX;
@ -146,6 +146,8 @@ void CreateAtoms::command(int narg, char **arg)
int subsetseed; int subsetseed;
overlapflag = 0; overlapflag = 0;
maxtry = DEFAULT_MAXTRY; maxtry = DEFAULT_MAXTRY;
radscale = 1.0;
radthresh = domain->lattice->xlattice;
nbasis = domain->lattice->nbasis; nbasis = domain->lattice->nbasis;
basistype = new int[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); maxtry = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (maxtry <= 0) error->all(FLERR, "Illegal create_atoms command"); if (maxtry <= 0) error->all(FLERR, "Illegal create_atoms command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "radiusscale") == 0) { } else if (strcmp(arg[iarg], "radscale") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_atoms radiusscale", error); if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_atoms radscale", error);
if (style != MESH) 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) if (!atom->radius_flag)
error->all(FLERR, "Must have atom attribute radius to set radiusscale factor"); error->all(FLERR, "Must have atom attribute radius to set radscale factor");
radiusscale = utils::numeric(FLERR, arg[iarg + 1], false, lmp); 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; iarg += 2;
} else } else
error->all(FLERR, "Illegal create_atoms command option {}", arg[iarg]); 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) else if (style == RANDOM)
add_random(); add_random();
else if (style == MESH) else if (style == MESH)
add_mesh(meshfile, radiusscale); add_mesh(meshfile);
else else
add_lattice(); add_lattice();
@ -841,9 +849,8 @@ void CreateAtoms::add_random()
or split into two halves along the longest side and recurse 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]; double center[3], temp[3];
MathExtra::add3(vert[0], vert[1], center); 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 // lattice parameter, the triangle is split it in half along its longest side
int ilocal = 0; int ilocal = 0;
if (ravg > xlat) { if (ravg > radthresh) {
double vert1[3][3], vert2[3][3], side[3][3]; 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[0], vert[1], side[0]);
MathExtra::sub3(vert[1], vert[2], side[1]); MathExtra::sub3(vert[1], vert[2], side[1]);
MathExtra::sub3(vert[2], vert[0], side[2]); MathExtra::sub3(vert[2], vert[0], side[2]);
// determine longest side
const double l1 = MathExtra::len3(side[0]); const double l1 = MathExtra::len3(side[0]);
const double l2 = MathExtra::len3(side[1]); const double l2 = MathExtra::len3(side[1]);
const double l3 = MathExtra::len3(side[2]); 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(vert1, molid);
ilocal += add_tricenter(vert2, molid, radiusscale); ilocal += add_tricenter(vert2, molid);
} else { } 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])) { (center[1] < subhi[1]) && (center[2] >= sublo[2]) && (center[2] < subhi[2])) {
atom->avec->create_atom(ntype, center); atom->avec->create_atom(ntype, center);
int idx = atom->nlocal-1; int idx = atom->nlocal - 1;
if (atom->radius_flag) atom->radius[idx] = ravg * radiusscale; if (atom->radius_flag) atom->radius[idx] = ravg * radscale;
if (atom->molecule_flag) atom->molecule[idx] = molid; if (atom->molecule_flag) atom->molecule[idx] = molid;
++ilocal; ++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 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]; double vert[3][3];
tagint *mol = atom->molecule; 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 // 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 // or splitting recursively into halves as needed to get the desired density
++ntriangle; ++ntriangle;
atomlocal += add_tricenter(vert, molid, radiusscale); atomlocal += add_tricenter(vert, molid);
} }
} catch (std::exception &e) { } catch (std::exception &e) {
error->all(FLERR, "Error reading triangles from file {}: {}", filename, e.what()); error->all(FLERR, "Error reading triangles from file {}: {}", filename, e.what());

5
src/create_atoms.h
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@ -41,6 +41,7 @@ class CreateAtoms : public Command {
double subsetfrac; double subsetfrac;
int *basistype; int *basistype;
double xone[3], quatone[4]; double xone[3], quatone[4];
double radthresh, radscale;
int varflag, vvar, xvar, yvar, zvar; int varflag, vvar, xvar, yvar, zvar;
char *vstr, *xstr, *ystr, *zstr; char *vstr, *xstr, *ystr, *zstr;
@ -64,8 +65,8 @@ class CreateAtoms : public Command {
void add_single(); void add_single();
void add_random(); void add_random();
void add_mesh(const char *, double); void add_mesh(const char *);
int add_tricenter(const double [3][3], tagint, double); int add_tricenter(const double [3][3], tagint);
void add_lattice(); void add_lattice();
void loop_lattice(int); void loop_lattice(int);
void add_molecule(double *); void add_molecule(double *);