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Allow PBC in just some directions

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-07-08 02:30:03 +02:00
parent 32836eebcb
commit 814f561993
5 changed files with 91 additions and 60 deletions
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3
data/dem/mdbench_params.conf
View File

@ -1,3 +1,6 @@
pbc_x 0
pbc_y 0
pbc_z 0
ntimes 200 ntimes 200
dt 0.001 dt 0.001
reneigh_every 20 reneigh_every 20

54
lammps/atom.c
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@ -448,32 +448,37 @@ int readAtom_in(Atom* atom, Parameter* param) {
return -1; return -1;
} }
fgets(line, MAXLINE, fp);
natoms = atoi(strtok(line, " "));
atom->Natoms = natoms;
atom->Nlocal = natoms;
atom->ntypes = 1; atom->ntypes = 1;
while(!feof(fp)) {
while(atom->Nlocal >= atom->Nmax) {
growAtom(atom);
}
for(int i = 0; i < natoms; i++) {
fgets(line, MAXLINE, fp); fgets(line, MAXLINE, fp);
natoms = atoi(line);
for(int i = 0; i < natoms; i++) {
fgets(line, MAXLINE, fp);
// TODO: store mass per atom // TODO: store mass per atom
char *s_mass = strtok(line, " "); char *s_mass = strtok(line, " ");
if(strncmp(s_mass, "inf", 3) == 0) { if(strncmp(s_mass, "inf", 3) == 0) {
// Set atom's mass to INFINITY // Set atom's mass to INFINITY
} else { } else {
param->mass = atof(s_mass); param->mass = atof(s_mass);
}
atom->radius[atom_id] = atof(strtok(NULL, " "));
atom_x(atom_id) = atof(strtok(NULL, " "));
atom_y(atom_id) = atof(strtok(NULL, " "));
atom_z(atom_id) = atof(strtok(NULL, " "));
atom_vx(atom_id) = atof(strtok(NULL, " "));
atom_vy(atom_id) = atof(strtok(NULL, " "));
atom_vz(atom_id) = atof(strtok(NULL, " "));
atom->type[atom_id] = 0;
atom->ntypes = MAX(atom->type[atom_id], atom->ntypes);
atom_id++;
} }
atom->radius[atom_id] = atof(strtok(NULL, " "));
atom_x(atom_id) = atof(strtok(NULL, " "));
atom_y(atom_id) = atof(strtok(NULL, " "));
atom_z(atom_id) = atof(strtok(NULL, " "));
atom_vx(atom_id) = atof(strtok(NULL, " "));
atom_vy(atom_id) = atof(strtok(NULL, " "));
atom_vz(atom_id) = atof(strtok(NULL, " "));
atom->type[atom_id] = 0;
atom->ntypes = MAX(atom->type[atom_id], atom->ntypes);
atom_id++;
} }
if(!natoms) { if(!natoms) {
@ -517,9 +522,8 @@ void growAtom(Atom *atom) {
atom->fz = (MD_FLOAT*) reallocate(atom->fz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT)); atom->fz = (MD_FLOAT*) reallocate(atom->fz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
#endif #endif
atom->type = (int *) reallocate(atom->type, ALIGNMENT, atom->Nmax * sizeof(int), nold * sizeof(int)); atom->type = (int *) reallocate(atom->type, ALIGNMENT, atom->Nmax * sizeof(int), nold * sizeof(int));
#ifdef DEM // DEM
atom->radius = (int *) reallocate(atom->radius, ALIGNMENT, atom->Nmax * sizeof(int), nold * sizeof(int)); atom->radius = (MD_FLOAT *) reallocate(atom->radius, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->av = (MD_FLOAT*) reallocate(atom->av, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT) * 3, nold * sizeof(MD_FLOAT) * 3); atom->av = (MD_FLOAT*) reallocate(atom->av, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT) * 3, nold * sizeof(MD_FLOAT) * 3);
atom->r = (MD_FLOAT*) reallocate(atom->r, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT) * 4, nold * sizeof(MD_FLOAT) * 4); atom->r = (MD_FLOAT*) reallocate(atom->r, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT) * 4, nold * sizeof(MD_FLOAT) * 4);
#endif
} }

1
lammps/includes/parameter.h
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@ -53,6 +53,7 @@ typedef struct {
MD_FLOAT cutforce; MD_FLOAT cutforce;
MD_FLOAT cutneigh; MD_FLOAT cutneigh;
int nx, ny, nz; int nx, ny, nz;
int pbc_x, pbc_y, pbc_z;
MD_FLOAT lattice; MD_FLOAT lattice;
MD_FLOAT xlo, xhi, ylo, yhi, zlo, zhi; MD_FLOAT xlo, xhi, ylo, yhi, zlo, zhi;
MD_FLOAT xprd, yprd, zprd; MD_FLOAT xprd, yprd, zprd;

7
lammps/parameter.c
View File

@ -42,6 +42,9 @@ void initParameter(Parameter *param) {
param->nx = 32; param->nx = 32;
param->ny = 32; param->ny = 32;
param->nz = 32; param->nz = 32;
param->pbc_x = 1;
param->pbc_y = 1;
param->pbc_z = 1;
param->cutforce = 2.5; param->cutforce = 2.5;
param->skin = 0.3; param->skin = 0.3;
param->cutneigh = param->cutforce + param->skin; param->cutneigh = param->cutforce + param->skin;
@ -116,6 +119,9 @@ void readParameter(Parameter *param, const char *filename) {
PARSE_INT(nx); PARSE_INT(nx);
PARSE_INT(ny); PARSE_INT(ny);
PARSE_INT(nz); PARSE_INT(nz);
PARSE_INT(pbc_x);
PARSE_INT(pbc_y);
PARSE_INT(pbc_z);
PARSE_INT(nstat); PARSE_INT(nstat);
PARSE_INT(reneigh_every); PARSE_INT(reneigh_every);
PARSE_INT(x_out_every); PARSE_INT(x_out_every);
@ -147,6 +153,7 @@ void printParameter(Parameter *param) {
printf("\tForce field: %s\n", ff2str(param->force_field)); printf("\tForce field: %s\n", ff2str(param->force_field));
printf("\tUnit cells (nx, ny, nz): %d, %d, %d\n", param->nx, param->ny, param->nz); printf("\tUnit cells (nx, ny, nz): %d, %d, %d\n", param->nx, param->ny, param->nz);
printf("\tDomain box sizes (x, y, z): %e, %e, %e\n", param->xprd, param->yprd, param->zprd); printf("\tDomain box sizes (x, y, z): %e, %e, %e\n", param->xprd, param->yprd, param->zprd);
printf("\tPeriodic (x, y, z): %d, %d, %d\n", param->pbc_x, param->pbc_y, param->pbc_z);
printf("\tLattice size: %e\n", param->lattice); printf("\tLattice size: %e\n", param->lattice);
printf("\tEpsilon: %e\n", param->epsilon); printf("\tEpsilon: %e\n", param->epsilon);
printf("\tSigma: %e\n", param->sigma); printf("\tSigma: %e\n", param->sigma);

86
lammps/pbc.c
View File

@ -35,8 +35,7 @@ static int *PBCx, *PBCy, *PBCz;
static void growPbc(Atom*); static void growPbc(Atom*);
/* exported subroutines */ /* exported subroutines */
void initPbc(Atom* atom) void initPbc(Atom* atom) {
{
NmaxGhost = 0; NmaxGhost = 0;
atom->border_map = NULL; atom->border_map = NULL;
PBCx = NULL; PBCy = NULL; PBCz = NULL; PBCx = NULL; PBCy = NULL; PBCz = NULL;
@ -44,8 +43,7 @@ void initPbc(Atom* atom)
/* update coordinates of ghost atoms */ /* update coordinates of ghost atoms */
/* uses mapping created in setupPbc */ /* uses mapping created in setupPbc */
void updatePbc(Atom *atom, Parameter *param) void updatePbc(Atom *atom, Parameter *param) {
{
int *border_map = atom->border_map; int *border_map = atom->border_map;
int nlocal = atom->Nlocal; int nlocal = atom->Nlocal;
MD_FLOAT xprd = param->xprd; MD_FLOAT xprd = param->xprd;
@ -61,8 +59,7 @@ void updatePbc(Atom *atom, Parameter *param)
/* relocate atoms that have left domain according /* relocate atoms that have left domain according
* to periodic boundary conditions */ * to periodic boundary conditions */
void updateAtomsPbc(Atom *atom, Parameter *param) void updateAtomsPbc(Atom *atom, Parameter *param) {
{
MD_FLOAT xprd = param->xprd; MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd; MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd; MD_FLOAT zprd = param->zprd;
@ -101,8 +98,7 @@ void updateAtomsPbc(Atom *atom, Parameter *param)
PBCz[Nghost] = dz; \ PBCz[Nghost] = dz; \
atom->type[atom->Nlocal + Nghost] = atom->type[i] atom->type[atom->Nlocal + Nghost] = atom->type[i]
void setupPbc(Atom *atom, Parameter *param) void setupPbc(Atom *atom, Parameter *param) {
{
int *border_map = atom->border_map; int *border_map = atom->border_map;
MD_FLOAT xprd = param->xprd; MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd; MD_FLOAT yprd = param->yprd;
@ -111,10 +107,10 @@ void setupPbc(Atom *atom, Parameter *param)
int Nghost = -1; int Nghost = -1;
for(int i = 0; i < atom->Nlocal; i++) { for(int i = 0; i < atom->Nlocal; i++) {
if (atom->Nlocal + Nghost + 7 >= atom->Nmax) { if (atom->Nlocal + Nghost + 7 >= atom->Nmax) {
growAtom(atom); growAtom(atom);
} }
if (Nghost + 7 >= NmaxGhost) { if (Nghost + 7 >= NmaxGhost) {
growPbc(atom); growPbc(atom);
border_map = atom->border_map; border_map = atom->border_map;
@ -126,34 +122,54 @@ void setupPbc(Atom *atom, Parameter *param)
/* Setup ghost atoms */ /* Setup ghost atoms */
/* 6 planes */ /* 6 planes */
if (x < Cutneigh) { ADDGHOST(+1,0,0); } if(param->pbc_x != 0) {
if (x >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); } if (x < Cutneigh) { ADDGHOST(+1,0,0); }
if (y < Cutneigh) { ADDGHOST(0,+1,0); } if (x >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); }
if (y >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); } }
if (z < Cutneigh) { ADDGHOST(0,0,+1); }
if (z >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); } if(param->pbc_y != 0) {
if (y < Cutneigh) { ADDGHOST(0,+1,0); }
if (y >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); }
}
if(param->pbc_z != 0) {
if (z < Cutneigh) { ADDGHOST(0,0,+1); }
if (z >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); }
}
/* 8 corners */ /* 8 corners */
if (x < Cutneigh && y < Cutneigh && z < Cutneigh) { ADDGHOST(+1,+1,+1); } if(param->pbc_x != 0 && param->pbc_y != 0 && param->pbc_z != 0) {
if (x < Cutneigh && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(+1,-1,+1); } if (x < Cutneigh && y < Cutneigh && z < Cutneigh) { ADDGHOST(+1,+1,+1); }
if (x < Cutneigh && y >= Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); } if (x < Cutneigh && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(+1,-1,+1); }
if (x < Cutneigh && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); } if (x < Cutneigh && y >= Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); }
if (x >= (xprd-Cutneigh) && y < Cutneigh && z < Cutneigh) { ADDGHOST(-1,+1,+1); } if (x < Cutneigh && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); }
if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,-1,+1); } if (x >= (xprd-Cutneigh) && y < Cutneigh && z < Cutneigh) { ADDGHOST(-1,+1,+1); }
if (x >= (xprd-Cutneigh) && y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); } if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,-1,+1); }
if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); } if (x >= (xprd-Cutneigh) && y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); }
if (x >= (xprd-Cutneigh) && y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); }
}
/* 12 edges */ /* 12 edges */
if (x < Cutneigh && z < Cutneigh) { ADDGHOST(+1,0,+1); } if(param->pbc_x != 0 && param->pbc_z != 0) {
if (x < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); } if (x < Cutneigh && z < Cutneigh) { ADDGHOST(+1,0,+1); }
if (x >= (xprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,0,+1); } if (x < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); }
if (x >= (xprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); } if (x >= (xprd-Cutneigh) && z < Cutneigh) { ADDGHOST(-1,0,+1); }
if (y < Cutneigh && z < Cutneigh) { ADDGHOST(0,+1,+1); } if (x >= (xprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); }
if (y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); } }
if (y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(0,-1,+1); }
if (y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); } if(param->pbc_y != 0 && param->pbc_z != 0) {
if (y < Cutneigh && x < Cutneigh) { ADDGHOST(+1,+1,0); } if (y < Cutneigh && z < Cutneigh) { ADDGHOST(0,+1,+1); }
if (y < Cutneigh && x >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); } if (y < Cutneigh && z >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); }
if (y >= (yprd-Cutneigh) && x < Cutneigh) { ADDGHOST(+1,-1,0); } if (y >= (yprd-Cutneigh) && z < Cutneigh) { ADDGHOST(0,-1,+1); }
if (y >= (yprd-Cutneigh) && x >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); } if (y >= (yprd-Cutneigh) && z >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); }
}
if(param->pbc_x != 0 && param->pbc_y != 0) {
if (y < Cutneigh && x < Cutneigh) { ADDGHOST(+1,+1,0); }
if (y < Cutneigh && x >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); }
if (y >= (yprd-Cutneigh) && x < Cutneigh) { ADDGHOST(+1,-1,0); }
if (y >= (yprd-Cutneigh) && x >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); }
}
} }
// increase by one to make it the ghost atom count // increase by one to make it the ghost atom count
atom->Nghost = Nghost + 1; atom->Nghost = Nghost + 1;