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adjust comments in source files

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This commit is contained in:
Steve Plimpton
2024-07-01 14:41:31 -06:00
parent 8ec5d83540
commit 489e80151a
3 changed files with 14 additions and 62 deletions
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69
src/GRANSURF/fix_surface_global.cpp
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@ -52,6 +52,9 @@ FixSurfaceGlobal::FixSurfaceGlobal(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[4],"hooke") == 0) pairstyle = HOOKE;
else if (strcmp(arg[4],"hooke/history") == 0) pairstyle = HOOKE_HISTORY;
// NOTE: hertz/history not yet supported ?
else if (strcmp(arg[4],"hertz/history") == 0) pairstyle = HERTZ_HISTORY;
else error->all(FLERR,"Invalid fix surface/global interaction style");
@ -156,39 +159,6 @@ FixSurfaceGlobal::FixSurfaceGlobal(LAMMPS *lmp, int narg, char **arg) :
if (dimension == 3) nsurf = ntris;
set_attributes();
/*
for (int i = 0; i < nlines; i++) {
printf("Connect %d:\n",i);
printf(" points: %d %d flags %d\n",
connect3d[i].neigh_p1,
connect3d[i].neigh_p2,
connect3d[i].flags);
}
*/
/*
for (int i = 0; i < ntris; i++) {
printf("Connect %d:\n",i);
printf(" edges: %d %d %d flags %d\n",
connect3d[i].neigh_e1,
connect3d[i].neigh_e2,
connect3d[i].neigh_e3,
connect3d[i].flags);
printf(" corner1: %d:",connect3d[i].nc1);
for (int j = 0; j < connect3d[i].nc1; j++)
printf(" %d",connect3d[i].neigh_c1[j]);
printf("\n");
printf(" corner2: %d:",connect3d[i].nc2);
for (int j = 0; j < connect3d[i].nc2; j++)
printf(" %d",connect3d[i].neigh_c2[j]);
printf("\n");
printf(" corner3: %d:",connect3d[i].nc3);
for (int j = 0; j < connect3d[i].nc3; j++)
printf(" %d",connect3d[i].neigh_c3[j]);
printf("\n");
}
*/
}
/* ---------------------------------------------------------------------- */
@ -1623,26 +1593,11 @@ int FixSurfaceGlobal::corner_neigh_check(int i, int j, int jflag)
/* ----------------------------------------------------------------------
extract points,line,surfs from molecule ID for one or more mol files
concatenate into single list of points,lines,tris
each proc owns copy of all points,lines,tris
------------------------------------------------------------------------- */
void FixSurfaceGlobal::extract_from_molecules(char *molID)
{
// check that no line/tri particles already exist
// no connectivity would be produced for them
int *surf = atom->line;
if (dimension == 3) surf = atom->tri;
int nlocal = atom->nlocal;
int flag = 0;
for (int i = 0; i < nlocal; i++)
if (surf[i] >= 0) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
if (flagall)
error->all(FLERR,"Fix surface local molecule file "
"when surfaces already exist");
// populate global point/line/tri data structs
points = NULL;
@ -1654,8 +1609,12 @@ void FixSurfaceGlobal::extract_from_molecules(char *molID)
if (imol == -1)
error->all(FLERR,"Molecule template ID for "
"fix surface/global does not exist");
// loop over one or more molecules in mol-ID
Molecule **onemols = &atom->molecules[imol];
int nmol = onemols[0]->nset;
for (int m = 0; m < nmol; m++) {
if (onemols[m]->pointflag == 0)
error->all(FLERR,"Fix surface/global molecule must have points");
@ -1666,13 +1625,6 @@ void FixSurfaceGlobal::extract_from_molecules(char *molID)
if (onemols[m]->triflag == 0)
error->all(FLERR,"Fix surface/global molecule must have triangles");
// NOTE: anything else about molfile surf to check?
// e.g. are types within bounds?
// or did Molecule check at read?
// NOTE: for nmol = 1, could just set points,lines,tris to pt
// to chunk of 2d data in molfile arrays
int np = onemols[m]->npoints;
int nl = onemols[m]->nlines;
int nt = onemols[m]->ntris;
@ -1696,7 +1648,8 @@ void FixSurfaceGlobal::extract_from_molecules(char *molID)
j++;
}
// need to offset line/tri index lists by previous npoints & subtract one
// offset line/tri index lists by previous npoints
// subtract one to give C-style index into points vector
if (dimension == 2) {
int *molline = onemols[m]->molline;
@ -1748,7 +1701,7 @@ void FixSurfaceGlobal::connectivity2d_global()
connect2d[i].flags = 0;
}
// create ptflag = pair of flags for each point
// create ptflag[2] = pair of flags for each point
// 1st index:
// 0 if pt not in line
// 1 if 1st point in one line, 2 if 2nd point in one line

6
src/GRANSURF/fix_surface_global.h
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@ -86,13 +86,13 @@ class FixSurfaceGlobal : public Fix {
};
struct Line {
int mol,type; // molID and type of the element
int mol,type; // molID and type of the line
int p1,p2; // indices of points in line segment
// rhand rule: Z x (p2-p1) = outward normal
};
struct Tri {
int mol,type; // modID and type of the element
int mol,type; // modID and type of the triangle
int p1,p2,p3; // indices of points in triangle
// rhand rule: (p2-p1) x (p3-p1) = outward normal
double norm[3]; // unit normal to tri plane
@ -102,7 +102,7 @@ class FixSurfaceGlobal : public Fix {
Line *lines; // global list of lines
Tri *tris; // global list of tris
int npoints,nlines,ntris; // count of each
int nsurf; // lines or tris for 2d/3d
int nsurf; // count of lines or tris for 2d/3d
int **clist; // ragged 2d array for global corner pt lists

1
src/molecule.cpp
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@ -44,7 +44,6 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
radius(nullptr), rmass(nullptr), mu(nullptr),
points(nullptr), lines(nullptr), tris(nullptr),
molline(nullptr), typeline(nullptr), moltri(nullptr), typetri(nullptr),
num_bond(nullptr), bond_type(nullptr),
bond_atom(nullptr), num_angle(nullptr), angle_type(nullptr), angle_atom1(nullptr),
angle_atom2(nullptr), angle_atom3(nullptr), num_dihedral(nullptr), dihedral_type(nullptr),