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all of remaining USER package styles except AWPMD

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This commit is contained in:
Steve Plimpton
2019-12-03 11:15:16 -07:00
parent ccca80a6a5
commit 9e52980aaa
16 changed files with 368 additions and 4077 deletions
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12
src/SPIN/atom_vec_spin.cpp
View File

@ -62,14 +62,16 @@ AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp)
}
/* ----------------------------------------------------------------------
clear all forces (mechanical and magnetic)
clear extra forces starting at atom N
nbytes = # of bytes to clear for a per-atom vector
include f b/c this is invoked from within SPIN pair styles
------------------------------------------------------------------------- */
void AtomVecSpin::force_clear(int /*n*/, size_t nbytes)
void AtomVecSpin::force_clear(int n, size_t nbytes)
{
memset(&atom->f[0][0],0,3*nbytes);
memset(&atom->fm[0][0],0,3*nbytes);
memset(&atom->fm_long[0][0],0,3*nbytes);
memset(&atom->f[n][0],0,3*nbytes);
memset(&atom->fm[n][0],0,3*nbytes);
memset(&atom->fm_long[n][0],0,3*nbytes);
}
/* ----------------------------------------------------------------------

17
src/USER-EFF/atom_vec_electron.cpp
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@ -18,14 +18,8 @@
#include "atom_vec_electron.h"
#include <cstring>
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -46,6 +40,8 @@ AtomVecElectron::AtomVecElectron(LAMMPS *lmp) : AtomVec(lmp)
{
if (lmp->citeme) lmp->citeme->add(cite_user_eff_package);
mass_type = 1;
molecular = 0;
forceclearflag = 1;
atom->ecp_flag = 0;
@ -75,11 +71,14 @@ AtomVecElectron::AtomVecElectron(LAMMPS *lmp) : AtomVec(lmp)
setup_fields();
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
clear extra forces starting at atom N
nbytes = # of bytes to clear for a per-atom vector
------------------------------------------------------------------------- */
void AtomVecElectron::force_clear(int /*n*/, size_t nbytes)
void AtomVecElectron::force_clear(int n, size_t nbytes)
{
memset(&atom->erforce[0],0,nbytes);
memset(&atom->erforce[n],0,nbytes);
}
/* ----------------------------------------------------------------------

20
src/USER-MESO/atom_vec_edpd.cpp
View File

@ -29,9 +29,6 @@ using namespace LAMMPS_NS;
AtomVecEDPD::AtomVecEDPD(LAMMPS *lmp) : AtomVec(lmp)
{
if (strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style edpd requires lj units");
molecular = 0;
mass_type = 1;
forceclearflag = 1;
@ -62,9 +59,22 @@ AtomVecEDPD::AtomVecEDPD(LAMMPS *lmp) : AtomVec(lmp)
/* ---------------------------------------------------------------------- */
void AtomVecEDPD::force_clear(int /*n*/, size_t nbytes)
void AtomVecEDPD::init()
{
memset(&atom->edpd_flux[0],0,nbytes);
AtomVec::init();
if (strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style edpd requires lj units");
}
/* ----------------------------------------------------------------------
clear extra forces starting at atom N
nbytes = # of bytes to clear for a per-atom vector
------------------------------------------------------------------------- */
void AtomVecEDPD::force_clear(int n, size_t nbytes)
{
memset(&atom->edpd_flux[n],0,nbytes);
}
/* ----------------------------------------------------------------------

1
src/USER-MESO/atom_vec_edpd.h
View File

@ -27,6 +27,7 @@ namespace LAMMPS_NS {
class AtomVecEDPD : public AtomVec {
public:
AtomVecEDPD(class LAMMPS *);
void init();
void force_clear(int, size_t);
void create_atom_post(int);
void data_atom_post(int);

903
src/USER-MESO/atom_vec_mdpd.cpp
View File

@ -14,14 +14,8 @@
#include "atom_vec_mdpd.h"
#include <cstring>
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -29,865 +23,63 @@ using namespace LAMMPS_NS;
AtomVecMDPD::AtomVecMDPD(LAMMPS *lmp) : AtomVec(lmp)
{
if(strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style mdpd requires lj units");
molecular = 0;
mass_type = 1;
forceclearflag = 1;
comm_x_only = comm_f_only = 0;
comm->ghost_velocity = 1;
size_forward = 3 + 4; // 3 + rho + vest[3], that means we may only communicate 4 in hybrid
size_reverse = 3 + 1; // 3 + drho
size_border = 6 + 4; // 6 + rho + vest[3]
size_velocity = 3;
size_data_atom = 6;
size_data_vel = 4;
xcol_data = 4;
atom->rho_flag = 1;
atom->vest_flag = 1;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rho drho vest";
fields_copy = (char *) "rho drho vest";
fields_comm = (char *) "rho vest";
fields_comm_vel = (char *) "rho vest";
fields_reverse = (char *) "drho";
fields_border = (char *) "rho vest";
fields_border_vel = (char *) "rho vest";
fields_exchange = (char *) "rho vest";
fields_restart = (char * ) "rho vest";
fields_create = (char *) "rho drho vest";
fields_data_atom = (char *) "id type rho x";
fields_data_vel = (char *) "id v";
setup_fields();
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void AtomVecMDPD::grow(int n)
void AtomVecMDPD::init()
{
if (n == 0) grow_nmax();
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one(FLERR,"Per-processor system is too big");
tag = memory->grow(atom->tag, nmax, "atom:tag");
type = memory->grow(atom->type, nmax, "atom:type");
mask = memory->grow(atom->mask, nmax, "atom:mask");
image = memory->grow(atom->image, nmax, "atom:image");
x = memory->grow(atom->x, nmax, 3, "atom:x");
v = memory->grow(atom->v, nmax, 3, "atom:v");
f = memory->grow(atom->f, nmax*comm->nthreads, 3, "atom:f");
rho = memory->grow(atom->rho, nmax, "atom:rho");
drho = memory->grow(atom->drho, nmax*comm->nthreads, "atom:drho");
vest = memory->grow(atom->vest, nmax, 3, "atom:vest");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
if (strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style mdpd requires lj units");
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecMDPD::grow_reset() {
tag = atom->tag;
type = atom->type;
mask = atom->mask;
image = atom->image;
x = atom->x;
v = atom->v;
f = atom->f;
rho = atom->rho;
drho = atom->drho;
vest = atom->vest;
}
/* ---------------------------------------------------------------------- */
void AtomVecMDPD::copy(int i, int j, int delflag) {
//printf("in AtomVecMDPD::copy\n");
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
rho[j] = rho[i];
drho[j] = drho[i];
vest[j][0] = vest[i][0];
vest[j][1] = vest[i][1];
vest[j][2] = vest[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i, j,delflag);
}
/* ---------------------------------------------------------------------- */
clear extra forces starting at atom N
nbytes = # of bytes to clear for a per-atom vector
------------------------------------------------------------------------- */
void AtomVecMDPD::force_clear(int n, size_t nbytes)
{
memset(&drho[n],0,nbytes);
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::pack_comm_hybrid(int n, int *list, double *buf) {
//printf("in AtomVecMDPD::pack_comm_hybrid\n");
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::unpack_comm_hybrid(int n, int first, double *buf) {
//printf("in AtomVecMDPD::unpack_comm_hybrid\n");
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
rho[i] = buf[m++];
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::pack_border_hybrid(int n, int *list, double *buf) {
//printf("in AtomVecMDPD::pack_border_hybrid\n");
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::unpack_border_hybrid(int n, int first, double *buf) {
//printf("in AtomVecMDPD::unpack_border_hybrid\n");
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
rho[i] = buf[m++];
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::pack_reverse_hybrid(int n, int first, double *buf) {
//printf("in AtomVecMDPD::pack_reverse_hybrid\n");
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = drho[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::unpack_reverse_hybrid(int n, int *list, double *buf) {
//printf("in AtomVecMDPD::unpack_reverse_hybrid\n");
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
drho[j] += buf[m++];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::pack_comm(int n, int *list, double *buf, int pbc_flag,
int *pbc) {
//printf("in AtomVecMDPD::pack_comm\n");
int i, j, m;
double dx, dy, dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0] * domain->xprd;
dy = pbc[1] * domain->yprd;
dz = pbc[2] * domain->zprd;
} else {
dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
dz = pbc[2] * domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::pack_comm_vel(int n, int *list, double *buf, int pbc_flag,
int *pbc) {
//printf("in AtomVecMDPD::pack_comm_vel\n");
int i, j, m;
double dx, dy, dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0] * domain->xprd;
dy = pbc[1] * domain->yprd;
dz = pbc[2] * domain->zprd;
} else {
dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
dz = pbc[2] * domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecMDPD::unpack_comm(int n, int first, double *buf) {
//printf("in AtomVecMDPD::unpack_comm\n");
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
rho[i] = buf[m++];
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecMDPD::unpack_comm_vel(int n, int first, double *buf) {
//printf("in AtomVecMDPD::unpack_comm_vel\n");
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
rho[i] = buf[m++];
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::pack_reverse(int n, int first, double *buf) {
//printf("in AtomVecMDPD::pack_reverse\n");
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
buf[m++] = drho[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecMDPD::unpack_reverse(int n, int *list, double *buf) {
//printf("in AtomVecMDPD::unpack_reverse\n");
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
drho[j] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::pack_border(int n, int *list, double *buf, int pbc_flag,
int *pbc) {
//printf("in AtomVecMDPD::pack_border\n");
int i, j, m;
double dx, dy, dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0] * domain->xprd;
dy = pbc[1] * domain->yprd;
dz = pbc[2] * domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::pack_border_vel(int n, int *list, double *buf, int pbc_flag,
int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0] * domain->xprd;
dy = pbc[1] * domain->yprd;
dz = pbc[2] * domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
} else {
dvx = pbc[0] * h_rate[0] + pbc[5] * h_rate[5] + pbc[4] * h_rate[4];
dvy = pbc[1] * h_rate[1] + pbc[3] * h_rate[3];
dvz = pbc[2] * h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
buf[m++] = rho[j];
buf[m++] = vest[j][0] + dvx;
buf[m++] = vest[j][1] + dvy;
buf[m++] = vest[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = rho[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
}
}
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecMDPD::unpack_border(int n, int first, double *buf) {
//printf("in AtomVecMDPD::unpack_border\n");
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax)
grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
rho[i] = buf[m++];
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->
unpack_border(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
void AtomVecMDPD::unpack_border_vel(int n, int first, double *buf) {
//printf("in AtomVecMDPD::unpack_border_vel\n");
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax)
grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
rho[i] = buf[m++];
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->
unpack_border(n,first,&buf[m]);
memset(&atom->drho[n],0,nbytes);
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecMDPD::pack_exchange(int i, double *buf) {
//printf("in AtomVecMDPD::pack_exchange\n");
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = ubuf(tag[i]).d;
buf[m++] = ubuf(type[i]).d;
buf[m++] = ubuf(mask[i]).d;
buf[m++] = ubuf(image[i]).d;
buf[m++] = rho[i];
buf[m++] = vest[i][0];
buf[m++] = vest[i][1];
buf[m++] = vest[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i, &buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMDPD::unpack_exchange(double *buf) {
//printf("in AtomVecMDPD::unpack_exchange\n");
int nlocal = atom->nlocal;
if (nlocal == nmax)
grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
rho[nlocal] = buf[m++];
vest[nlocal][0] = buf[m++];
vest[nlocal][1] = buf[m++];
vest[nlocal][2] = buf[m++];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]-> unpack_exchange(nlocal,
&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecMDPD::size_restart() {
int i;
int nlocal = atom->nlocal;
int n = 15 * nlocal; // 11 + rho + vest[3]
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecMDPD::pack_restart(int i, double *buf) {
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = ubuf(tag[i]).d;
buf[m++] = ubuf(type[i]).d;
buf[m++] = ubuf(mask[i]).d;
buf[m++] = ubuf(image[i]).d;
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = rho[i];
buf[m++] = vest[i][0];
buf[m++] = vest[i][1];
buf[m++] = vest[i][2];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i, &buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecMDPD::unpack_restart(double *buf) {
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
memory->grow(atom->extra, nmax, atom->nextra_store, "atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
rho[nlocal] = buf[m++];
vest[nlocal][0] = buf[m++];
vest[nlocal][1] = buf[m++];
vest[nlocal][2] = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++)
extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecMDPD::create_atom(int itype, double *coord) {
int nlocal = atom->nlocal;
if (nlocal == nmax)
grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
rho[nlocal] = 0.0;
vest[nlocal][0] = 0.0;
vest[nlocal][1] = 0.0;
vest[nlocal][2] = 0.0;
drho[nlocal] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecMDPD::data_atom(double *coord, imageint imagetmp, char **values) {
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp);
type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
vest[nlocal][0] = 0.0;
vest[nlocal][1] = 0.0;
vest[nlocal][2] = 0.0;
rho[nlocal] = utils::numeric(FLERR,values[2],true,lmp);
drho[nlocal] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecMDPD::data_atom_hybrid(int nlocal, char **values)
{
rho[nlocal] = utils::numeric(FLERR,values[0],true,lmp);
return 3;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
modify what AtomVec::data_atom() just unpacked
or initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecMDPD::pack_data(double **buf)
void AtomVecMDPD::data_atom_post(int ilocal)
{
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(tag[i]).d;
buf[i][1] = ubuf(type[i]).d;
buf[i][2] = rho[i];
buf[i][3] = x[i][0];
buf[i][4] = x[i][1];
buf[i][5] = x[i][2];
buf[i][6] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
buf[i][7] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][8] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
}
}
/* ----------------------------------------------------------------------
pack hybrid atom info for data file
------------------------------------------------------------------------- */
int AtomVecMDPD::pack_data_hybrid(int i, double *buf)
{
buf[0] = rho[i];
return 3;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecMDPD::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %-1.16e "
"%d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4],buf[i][5],
(int) ubuf(buf[i][6]).i,(int) ubuf(buf[i][7]).i,
(int) ubuf(buf[i][8]).i);
}
/* ----------------------------------------------------------------------
write hybrid atom info to data file
------------------------------------------------------------------------- */
int AtomVecMDPD::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %-1.16e",buf[0]);
return 3;
atom->drho[ilocal] = 0.0;
atom->vest[ilocal][0] = 0.0;
atom->vest[ilocal][1] = 0.0;
atom->vest[ilocal][2] = 0.0;
}
/* ----------------------------------------------------------------------
@ -912,15 +104,17 @@ void AtomVecMDPD::pack_property_atom(int index, double *buf,
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
int n = 0;
int n = 0;
if (index == 0) {
double *rho = atom->rho;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = rho[i];
else buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
double *drho = atom->drho;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = drho[i];
else buf[n] = 0.0;
@ -928,24 +122,3 @@ void AtomVecMDPD::pack_property_atom(int index, double *buf,
}
}
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecMDPD::memory_usage() {
bigint bytes = 0;
if (atom->memcheck("tag")) bytes += memory->usage(tag, nmax);
if (atom->memcheck("type")) bytes += memory->usage(type, nmax);
if (atom->memcheck("mask")) bytes += memory->usage(mask, nmax);
if (atom->memcheck("image")) bytes += memory->usage(image, nmax);
if (atom->memcheck("x")) bytes += memory->usage(x, nmax, 3);
if (atom->memcheck("v")) bytes += memory->usage(v, nmax, 3);
if (atom->memcheck("f")) bytes += memory->usage(f, nmax*comm->nthreads, 3);
if (atom->memcheck("rho")) bytes += memory->usage(rho, nmax);
if (atom->memcheck("drho")) bytes += memory->usage(drho, nmax*comm->nthreads);
if (atom->memcheck("vest")) bytes += memory->usage(vest, nmax, 3);
return bytes;
}

43
src/USER-MESO/atom_vec_mdpd.h
View File

@ -27,50 +27,11 @@ namespace LAMMPS_NS {
class AtomVecMDPD : public AtomVec {
public:
AtomVecMDPD(class LAMMPS *);
~AtomVecMDPD() {}
void grow(int);
void grow_reset();
void copy(int, int, int);
void init();
void force_clear(int, size_t);
int pack_comm(int, int *, double *, int, int *);
int pack_comm_vel(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
void unpack_comm_vel(int, int, double *);
int pack_reverse(int, int, double *);
void unpack_reverse(int, int *, double *);
int pack_comm_hybrid(int, int *, double *);
int unpack_comm_hybrid(int, int, double *);
int pack_border_hybrid(int, int *, double *);
int unpack_border_hybrid(int, int, double *);
int pack_reverse_hybrid(int, int, double *);
int unpack_reverse_hybrid(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, imageint, char **);
int data_atom_hybrid(int, char **);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);
int write_data_hybrid(FILE *, double *);
void data_atom_post(int);
int property_atom(char *);
void pack_property_atom(int, double *, int, int);
bigint memory_usage();
private:
tagint *tag;
int *type,*mask;
imageint *image;
double **x,**v,**f;
double *rho, *drho;
double **vest; // estimated velocity during force computation
};
}

858
src/USER-MESO/atom_vec_tdpd.cpp
View File

@ -14,12 +14,7 @@
#include "atom_vec_tdpd.h"
#include <cstring>
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
@ -29,29 +24,30 @@ using namespace LAMMPS_NS;
AtomVecTDPD::AtomVecTDPD(LAMMPS *lmp) : AtomVec(lmp)
{
if(strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style edpd requires lj units");
molecular = 0;
mass_type = 1;
forceclearflag = 1;
comm_x_only = comm_f_only = 0;
comm->ghost_velocity = 1;
cc_species = 0; // for now, reset in process_args()
size_forward = 3 + cc_species + 3; //vest[3]
size_reverse = 3 + cc_species;
size_border = 6 + cc_species + 3; //vest[3]
size_velocity = 3;
// for data_atom, we read id + type + xyz[3] + cc[i] where i=1,cc_species
size_data_atom = 5 + cc_species;
size_data_vel = 4;
xcol_data = 3;
atom->tdpd_flag = 1;
atom->vest_flag = 1;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "cc cc_flux vest";
fields_copy = (char *) "cc vest";
fields_comm = (char *) "cc vest";
fields_comm_vel = (char *) "cc vest";
fields_reverse = (char *) "cc_flux";
fields_border = (char *) "cc vest";
fields_border_vel = (char *) "cc vest";
fields_exchange = (char *) "cc vest";
fields_restart = (char * ) "cc vest";
fields_create = (char *) "cc vest";
fields_data_atom = (char *) "id type x cc";
fields_data_vel = (char *) "id v";
}
/* ----------------------------------------------------------------------
@ -66,812 +62,42 @@ void AtomVecTDPD::process_args(int narg, char **arg)
atom->cc_species = utils::inumeric(FLERR,arg[0],false,lmp);
cc_species = atom->cc_species;
// reset sizes that depend on cc_species
atom->add_peratom_change_columns("cc",cc_species);
atom->add_peratom_change_columns("cc_species",cc_species);
size_forward = 3 + cc_species + 3;
size_reverse = 3 + cc_species;
size_border = 6 + cc_species + 3;
size_data_atom = 5 + cc_species;
// delay setting up of fields until now
setup_fields();
}
/* ---------------------------------------------------------------------- */
void AtomVecTDPD::init()
{
AtomVec::init();
if (strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style tdpd requires lj units");
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
clear extra forces starting at atom N
nbytes = # of bytes to clear for a per-atom vector
------------------------------------------------------------------------- */
void AtomVecTDPD::grow(int n)
{
if (n == 0) grow_nmax();
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one(FLERR,"Per-processor system is too big");
tag = memory->grow(atom->tag,nmax,"atom:tag");
type = memory->grow(atom->type,nmax,"atom:type");
mask = memory->grow(atom->mask,nmax,"atom:mask");
image = memory->grow(atom->image,nmax,"atom:image");
x = memory->grow(atom->x,nmax,3,"atom:x");
v = memory->grow(atom->v,nmax,3,"atom:v");
f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f");
cc = memory->grow(atom->cc,nmax*comm->nthreads,cc_species,"atom:cc");
cc_flux = memory->grow(atom->cc_flux,nmax*comm->nthreads,cc_species,
"atom:cc_flux");
vest = memory->grow(atom->vest, nmax, 3, "atom:vest");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecTDPD::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
cc = atom->cc; cc_flux = atom->cc_flux;
vest = atom->vest;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void AtomVecTDPD::copy(int i, int j, int delflag)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
for(int k = 0; k < cc_species; k++)
cc[j][k] = cc[i][k];
vest[j][0] = vest[i][0];
vest[j][1] = vest[i][1];
vest[j][2] = vest[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
}
void AtomVecTDPD::force_clear(int n, size_t nbytes)
{
memset(&cc_flux[n][0],0,cc_species*nbytes);
}
/* ---------------------------------------------------------------------- */
int AtomVecTDPD::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
for(k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
for(k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecTDPD::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz,dvx,dvy,dvz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
for(k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
for(k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
for(k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecTDPD::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
for(int k = 0; k < cc_species; k++)
cc[i][k] = buf[m++];
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecTDPD::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
for(int k = 0; k < cc_species; k++)
cc[i][k] = buf[m++];
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecTDPD::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
for(int k = 0; k < cc_species; k++)
buf[m++] = cc_flux[i][k];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecTDPD::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
for(int k = 0; k < cc_species; k++)
cc_flux[j][k] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecTDPD::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
for(int k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
for(int k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecTDPD::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
for(int k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
for(int k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
for(int k = 0; k < cc_species; k++)
buf[m++] = cc[j][k];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
}
}
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecTDPD::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
for(int k = 0; k < cc_species; k++)
cc[i][k] = buf[m++];
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->
unpack_border(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
void AtomVecTDPD::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
for(int k = 0; k < cc_species; k++)
cc[i][k] = buf[m++];
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->
unpack_border(n,first,&buf[m]);
memset(&atom->cc_flux[n][0],0,cc_species*nbytes);
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
modify what AtomVec::data_atom() just unpacked
or initialize other atom quantities
------------------------------------------------------------------------- */
int AtomVecTDPD::pack_exchange(int i, double *buf)
void AtomVecTDPD::data_atom_post(int ilocal)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = ubuf(tag[i]).d;
buf[m++] = ubuf(type[i]).d;
buf[m++] = ubuf(mask[i]).d;
buf[m++] = ubuf(image[i]).d;
for(int k = 0; k < cc_species; k++)
buf[m++] = cc[i][k];
buf[m++] = vest[i][0];
buf[m++] = vest[i][1];
buf[m++] = vest[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecTDPD::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
for(int k = 0; k < cc_species; k++)
cc[nlocal][k] = buf[m++];
vest[nlocal][0] = buf[m++];
vest[nlocal][1] = buf[m++];
vest[nlocal][2] = buf[m++];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecTDPD::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = (11 + cc_species + 3) * nlocal; // 11 + cc[i] + vest[3]
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecTDPD::pack_restart(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = ubuf(tag[i]).d;
buf[m++] = ubuf(type[i]).d;
buf[m++] = ubuf(mask[i]).d;
buf[m++] = ubuf(image[i]).d;
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
for(int k = 0; k < cc_species; k++)
buf[m++] = cc[i][k];
buf[m++] = vest[i][0];
buf[m++] = vest[i][1];
buf[m++] = vest[i][2];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecTDPD::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
for(int k = 0; k < cc_species; k++)
cc[nlocal][k] = buf[m++];
vest[nlocal][0] = buf[m++];
vest[nlocal][1] = buf[m++];
vest[nlocal][2] = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecTDPD::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
for(int k = 0; k < cc_species; k++)
cc[nlocal][k] = 0.0;
vest[nlocal][0] = 0.0;
vest[nlocal][1] = 0.0;
vest[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecTDPD::data_atom(double *coord, imageint imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp);
type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
for(int k = 0; k < cc_species; k++)
cc[nlocal][k] = utils::numeric(FLERR,values[5+k],true,lmp);
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
vest[nlocal][0] = 0.0;
vest[nlocal][1] = 0.0;
vest[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecTDPD::pack_data(double **buf)
{
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(tag[i]).d;
buf[i][1] = ubuf(type[i]).d;
buf[i][2] = x[i][0];
buf[i][3] = x[i][1];
buf[i][4] = x[i][2];
buf[i][5] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
buf[i][6] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][7] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
for(int k = 0; k < cc_species; k++)
buf[i][8+k] = cc[i][k];
}
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecTDPD::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++){
fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e %d %d %d",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4],
(int) ubuf(buf[i][5]).i,(int) ubuf(buf[i][6]).i,
(int) ubuf(buf[i][7]).i);
for(int k = 0; k < cc_species; k++)
fprintf(fp," %-1.16e",buf[i][8+k]);
fprintf(fp,"\n");
}
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecTDPD::memory_usage()
{
bigint bytes = 0;
if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3);
if (atom->memcheck("cc")) bytes += memory->usage(cc,nmax*comm->nthreads,cc_species);
if (atom->memcheck("cc_flux")) bytes += memory->usage(cc_flux,nmax*comm->nthreads,cc_species);
if (atom->memcheck("vest")) bytes += memory->usage(vest, nmax);
return bytes;
atom->vest[ilocal][0] = 0.0;
atom->vest[ilocal][1] = 0.0;
atom->vest[ilocal][2] = 0.0;
}

32
src/USER-MESO/atom_vec_tdpd.h
View File

@ -27,40 +27,12 @@ namespace LAMMPS_NS {
class AtomVecTDPD : public AtomVec {
public:
AtomVecTDPD(class LAMMPS *);
virtual ~AtomVecTDPD() {}
void process_args(int, char **);
void grow(int);
void grow_reset();
void copy(int, int, int);
void init();
void force_clear(int, size_t);
virtual int pack_comm(int, int *, double *, int, int *);
virtual int pack_comm_vel(int, int *, double *, int, int *);
virtual void unpack_comm(int, int, double *);
virtual void unpack_comm_vel(int, int, double *);
int pack_reverse(int, int, double *);
void unpack_reverse(int, int *, double *);
virtual int pack_border(int, int *, double *, int, int *);
virtual int pack_border_vel(int, int *, double *, int, int *);
virtual void unpack_border(int, int, double *);
virtual void unpack_border_vel(int, int, double *);
virtual int pack_exchange(int, double *);
virtual int unpack_exchange(double *);
int size_restart();
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, imageint, char **);
void pack_data(double **);
void write_data(FILE *, int, double **);
bigint memory_usage();
void data_atom_post(int);
protected:
tagint *tag;
int *type,*mask;
imageint *image;
double **x,**v,**f;
double **vest; // store intermediate velocity for using mvv integrator
double **cc,**cc_flux;
int cc_species;
};

1296
src/USER-SMD/atom_vec_smd.cpp
View File

File diff suppressed because it is too large Load Diff

59
src/USER-SMD/atom_vec_smd.h
View File

@ -9,7 +9,6 @@
*
* ----------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
@ -39,63 +38,9 @@ namespace LAMMPS_NS {
class AtomVecSMD : public AtomVec {
public:
AtomVecSMD(class LAMMPS *);
~AtomVecSMD() {}
void init();
void grow(int);
void grow_reset();
void copy(int, int, int);
void force_clear(int, size_t);
int pack_comm(int, int *, double *, int, int *);
int pack_comm_vel(int, int *, double *, int, int *);
int pack_comm_hybrid(int, int *, double *);
void unpack_comm(int, int, double *);
void unpack_comm_vel(int, int, double *);
int unpack_comm_hybrid(int, int, double *);
int pack_reverse(int, int, double *);
int pack_reverse_hybrid(int, int, double *);
void unpack_reverse(int, int *, double *);
int unpack_reverse_hybrid(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, imageint, char **);
int data_atom_hybrid(int, char **);
void data_vel(int, char **);
int data_vel_hybrid(int, char **);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);
int write_data_hybrid(FILE *, double *);
void pack_vel(double **);
int pack_vel_hybrid(int, double *);
void write_vel(FILE *, int, double **);
int write_vel_hybrid(FILE *, double *);
bigint memory_usage();
private:
tagint *tag;
int *type,*mask;
imageint *image;
double **x,**v,**f;
double *radius,*rmass;
tagint *molecule;
double *vfrac,**x0,*contact_radius, **smd_data_9, *e, *de, **vest;
double **tlsph_stress;
double *eff_plastic_strain;
double *damage;
double *eff_plastic_strain_rate;
void create_atom_post(int);
void data_atom_post(int);
};
}

977
src/USER-SPH/atom_vec_meso.cpp
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File diff suppressed because it is too large Load Diff

43
src/USER-SPH/atom_vec_meso.h
View File

@ -27,50 +27,11 @@ namespace LAMMPS_NS {
class AtomVecMeso : public AtomVec {
public:
AtomVecMeso(class LAMMPS *);
~AtomVecMeso() {}
void grow(int);
void grow_reset();
void copy(int, int, int);
void force_clear(int, size_t);
int pack_comm(int, int *, double *, int, int *);
int pack_comm_vel(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
void unpack_comm_vel(int, int, double *);
int pack_reverse(int, int, double *);
void unpack_reverse(int, int *, double *);
int pack_comm_hybrid(int, int *, double *);
int unpack_comm_hybrid(int, int, double *);
int pack_border_hybrid(int, int *, double *);
int unpack_border_hybrid(int, int, double *);
int pack_reverse_hybrid(int, int, double *);
int unpack_reverse_hybrid(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, imageint, char **);
int data_atom_hybrid(int, char **);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);
int write_data_hybrid(FILE *, double *);
void create_atom_post(int);
void data_atom_post(int);
int property_atom(char *);
void pack_property_atom(int, double *, int, int);
bigint memory_usage();
private:
tagint *tag;
int *type,*mask;
imageint *image;
double **x,**v,**f;
double *rho, *drho, *e, *de, *cv;
double **vest; // estimated velocity during force computation
};
}

128
src/atom.cpp
View File

@ -81,50 +81,21 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
image = NULL;
x = v = f = NULL;
molecule = NULL;
molindex = molatom = NULL;
// charged and dipolar particles
q = NULL;
mu = NULL;
// finite-size particles
omega = angmom = torque = NULL;
radius = rmass = NULL;
ellipsoid = line = tri = body = NULL;
vfrac = s0 = NULL;
x0 = NULL;
// molecular systems
spin = NULL;
eradius = ervel = erforce = NULL;
cs = csforce = vforce = ervelforce = NULL;
etag = NULL;
rho = drho = e = de = cv = NULL;
vest = NULL;
// SPIN package
sp = fm = fm_long = NULL;
// USER-DPD
uCond = uMech = uChem = uCG = uCGnew = NULL;
duChem = NULL;
dpdTheta = NULL;
// USER-MESO
cc = cc_flux = NULL;
edpd_temp = edpd_flux = edpd_cv = NULL;
// USER-SMD
contact_radius = NULL;
smd_data_9 = NULL;
smd_stress = NULL;
eff_plastic_strain = NULL;
eff_plastic_strain_rate = NULL;
damage = NULL;
// molecular info
molecule = NULL;
molindex = molatom = NULL;
bond_per_atom = extra_bond_per_atom = 0;
num_bond = NULL;
@ -150,6 +121,47 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
nspecial = NULL;
special = NULL;
// PERI package
vfrac = s0 = NULL;
x0 = NULL;
// SPIN package
sp = fm = fm_long = NULL;
// USER-EFF and USER-AWPMD packages
spin = NULL;
eradius = ervel = erforce = NULL;
ervelforce = cs = csforce = NULL;
vforce = NULL;
etag = NULL;
// USER-DPD package
uCond = uMech = uChem = uCG = uCGnew = NULL;
duChem = dpdTheta = NULL;
// USER-MESO package
cc = cc_flux = NULL;
edpd_temp = edpd_flux = edpd_cv = NULL;
// USER-SMD package
contact_radius = NULL;
smd_data_9 = NULL;
smd_stress = NULL;
eff_plastic_strain = NULL;
eff_plastic_strain_rate = NULL;
damage = NULL;
// USER-SPH package
rho = drho = e = de = cv = NULL;
vest = NULL;
// user-defined molecules
nmolecule = 0;
@ -532,9 +544,16 @@ void Atom::peratom_create()
add_peratom("ervel",&ervel,DOUBLE,0);
add_peratom("erforce",&erforce,DOUBLE,0,1); // set per-thread flag
// USER-AWPMD package
add_peratom("cs",&cs,DOUBLE,0);
add_peratom("csforce",&csforce,DOUBLE,0);
add_peratom("vforce",&vforce,DOUBLE,3);
add_peratom("ervelforce",&ervelforce,DOUBLE,0);
add_peratom("etag",&etag,INT,0);
// USER-DPD package
add_peratom("rho",&eradius,DOUBLE,0);
add_peratom("dpdTheta",&dpdTheta,DOUBLE,0);
add_peratom("uCond",&uCond,DOUBLE,0);
add_peratom("uMech",&uMech,DOUBLE,0);
@ -548,7 +567,26 @@ void Atom::peratom_create()
add_peratom("edpd_cv",&edpd_cv,DOUBLE,0);
add_peratom("edpd_temp",&edpd_temp,DOUBLE,0);
add_peratom("edpd_flux",&edpd_flux,DOUBLE,0,1); // set per-thread flag
add_peratom("vest",&vest,DOUBLE,4);
add_peratom("cc",&cc,DOUBLE,1);
add_peratom("cc_flux",&cc_flux,DOUBLE,1,1); // set per-thread flag
// USER-SPH package
add_peratom("rho",&rho,DOUBLE,0);
add_peratom("drho",&drho,DOUBLE,0,1); // set per-thread flag
add_peratom("e",&e,DOUBLE,0);
add_peratom("de",&de,DOUBLE,0,1); // set per-thread flag
add_peratom("vest",&vest,DOUBLE,3);
add_peratom("cv",&cv,DOUBLE,0);
// USER-SMD package
add_peratom("contact_radius",&contact_radius,DOUBLE,0);
add_peratom("smd_data_9",&smd_data_9,DOUBLE,1);
add_peratom("smd_stress",&smd_stress,DOUBLE,1);
add_peratom("eff_plastic_strain",&eff_plastic_strain,DOUBLE,0);
add_peratom("eff_plastic_strain_rate",&eff_plastic_strain_rate,DOUBLE,0);
add_peratom("damage",&damage,DOUBLE,0);
}
/* ----------------------------------------------------------------------
@ -579,6 +617,18 @@ void Atom::add_peratom(const char *name, void *address,
nperatom++;
}
/* ----------------------------------------------------------------------
change the column count fof an existing peratom array entry
allows atom_style to specify column count as an argument
see atom_style tdpd as an example
------------------------------------------------------------------------- */
void Atom::add_peratom_change_columns(const char *name, int cols)
{
for (int i = 0; i < nperatom; i++)
if (strcmp(name,peratom[i].name) == 0) peratom[i].cols = cols;
}
/* ----------------------------------------------------------------------
add info for a single per-atom array to PerAtom data struct
cols = address of int variable with max columns per atom

16
src/atom.h
View File

@ -60,6 +60,8 @@ class Atom : protected Pointers {
imageint *image;
double **x,**v,**f;
// charged and dipolar particles
double *rmass;
double *q,**mu;
@ -69,7 +71,7 @@ class Atom : protected Pointers {
double **omega,**angmom,**torque;
int *ellipsoid,*line,*tri,*body;
// MOLECULE package
// molecular systems
tagint *molecule;
int *molindex,*molatom;
@ -101,15 +103,14 @@ class Atom : protected Pointers {
// SPIN package
double **sp;
double **fm;
double **fm_long;
double **sp,**fm,**fm_long;
// USER-AWPMD and USER_EFF packages
// USER_EFF and USER-AWPMD packages
int *spin;
double *eradius,*ervel,*erforce,*ervelforce;
double *cs,*csforce,*vforce;
double *eradius,*ervel,*erforce;
double *ervelforce,*cs,*csforce;
double **vforce;
int *etag;
// USER-DPD package
@ -261,6 +262,7 @@ class Atom : protected Pointers {
void settings(class Atom *);
void peratom_create();
void add_peratom(const char *, void *, int, int, int threadflag=0);
void add_peratom_change_columns(const char *, int);
void add_peratom_vary(const char *, void *, int, int *,
void *, int collength=0);
void create_avec(const char *, int, char **, int);

5
src/atom_vec_hybrid.h
View File

@ -57,11 +57,6 @@ class AtomVecHybrid : public AtomVec {
void pack_data_pre(int);
void pack_data_post(int);
//void create_atom_post(int);
//void data_atom_post(int);
//void pack_data_pre(int);
//void pack_data_post(int);
int property_atom(char *);
void pack_property_atom(int, double *, int, int);

7
src/atom_vec_sphere.cpp
View File

@ -28,6 +28,7 @@ using namespace MathConst;
AtomVecSphere::AtomVecSphere(LAMMPS *lmp) : AtomVec(lmp)
{
mass_type = 0;
molecular = 0;
atom->sphere_flag = 1;
@ -51,8 +52,6 @@ AtomVecSphere::AtomVecSphere(LAMMPS *lmp) : AtomVec(lmp)
fields_create = (char *) "radius rmass omega";
fields_data_atom = (char *) "id type radius rmass x";
fields_data_vel = (char *) "id v omega";
setup_fields();
}
/* ----------------------------------------------------------------------
@ -74,6 +73,10 @@ void AtomVecSphere::process_args(int narg, char **arg)
fields_comm = (char *) "radius rmass";
fields_comm_vel = (char *) "radius rmass omega";
// delay setting up of fields until now
setup_fields();
}
/* ---------------------------------------------------------------------- */