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lammps/src/USER-SMD/atom_vec_smd.cpp
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atom_vec_smd.cpp
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/* ----------------------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
* This file is part of the USER-SMD package for LAMMPS.
* Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de
* Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI,
* Eckerstrasse 4, D-79104 Freiburg i.Br, Germany.
*
* ----------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "atom_vec_smd.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "force.h"
#include "fix.h"
#include "fix_adapt.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define NMAT_FULL 9
#define NMAT_SYMM 6
/* ---------------------------------------------------------------------- */
AtomVecSMD::AtomVecSMD(LAMMPS *lmp) :
AtomVec(lmp) {
molecular = 0;
comm_x_only = 0;
comm_f_only = 0;
size_forward = 6; // variables that are changed by time integration
size_reverse = 4; // f[3] + de
size_border = 31;
size_velocity = 6; // v + vest
size_data_atom = 13; // 7 + 3 x0 + 3 x
size_data_vel = 4;
xcol_data = 11;
atom->radius_flag = 1;
atom->rmass_flag = 1;
atom->vfrac_flag = 1;
atom->contact_radius_flag = 1;
atom->molecule_flag = 1;
atom->smd_data_9_flag = 1;
atom->e_flag = 1;
atom->vest_flag = 1;
atom->smd_stress_flag = 1;
atom->eff_plastic_strain_flag = 1;
atom->x0_flag = 1;
atom->damage_flag = 1;
atom->eff_plastic_strain_rate_flag = 1;
forceclearflag = 1;
atom->smd_flag = 1;
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::init() {
AtomVec::init();
// do nothing here
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecSMD::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");
//printf("in grow, nmax is now %d\n", nmax);
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");
de = memory->grow(atom->de, nmax * comm->nthreads, "atom:de");
vfrac = memory->grow(atom->vfrac, nmax, "atom:vfrac");
rmass = memory->grow(atom->rmass, nmax, "atom:rmass");
x0 = memory->grow(atom->x0, nmax, 3, "atom:x0");
radius = memory->grow(atom->radius, nmax, "atom:radius");
contact_radius = memory->grow(atom->contact_radius, nmax, "atom:contact_radius");
molecule = memory->grow(atom->molecule, nmax, "atom:molecule");
smd_data_9 = memory->grow(atom->smd_data_9, nmax, NMAT_FULL, "atom:defgrad_old");
e = memory->grow(atom->e, nmax, "atom:e");
vest = memory->grow(atom->vest, nmax, 3, "atom:vest");
tlsph_stress = memory->grow(atom->smd_stress, nmax, NMAT_SYMM, "atom:tlsph_stress");
eff_plastic_strain = memory->grow(atom->eff_plastic_strain, nmax, "atom:eff_plastic_strain");
eff_plastic_strain_rate = memory->grow(atom->eff_plastic_strain_rate, nmax, "atom:eff_plastic_strain_rate");
damage = memory->grow(atom->damage, nmax, "atom:damage");
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 AtomVecSMD::grow_reset() {
tag = atom->tag;
type = atom->type;
mask = atom->mask;
image = atom->image;
x = atom->x;
v = atom->v;
f = atom->f;
radius = atom->radius;
rmass = atom->rmass;
vfrac = atom->vfrac;
x0 = atom->x0;
contact_radius = atom->contact_radius;
molecule = atom->molecule;
smd_data_9 = atom->smd_data_9;
e = atom->e;
de = atom->de;
tlsph_stress = atom->smd_stress;
eff_plastic_strain = atom->eff_plastic_strain;
eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
damage = atom->damage;
vest = atom->vest;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void AtomVecSMD::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];
vfrac[j] = vfrac[i];
rmass[j] = rmass[i];
x0[j][0] = x0[i][0];
x0[j][1] = x0[i][1];
x0[j][2] = x0[i][2];
radius[j] = radius[i];
contact_radius[j] = contact_radius[i];
molecule[j] = molecule[i];
e[j] = e[i];
eff_plastic_strain[j] = eff_plastic_strain[i];
eff_plastic_strain_rate[j] = eff_plastic_strain_rate[i];
vest[j][0] = vest[i][0];
vest[j][1] = vest[i][1];
vest[j][2] = vest[i][2];
for (int k = 0; k < NMAT_FULL; k++) {
smd_data_9[j][k] = smd_data_9[i][k];
}
for (int k = 0; k < NMAT_SYMM; k++) {
tlsph_stress[j][k] = tlsph_stress[i][k];
}
damage[j] = damage[i];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i, j, delflag);
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
return -1;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_comm_vel(int n, int *list, double *buf, int pbc_flag, int *pbc) {
// communicate quantities to ghosts, which are changed by time-integration AND are required on ghost atoms.
//no need to pack stress or defgrad information here, as these quantities are not required for ghost atoms.
// Inside pair_style tlsph, these quantities are computed and communicated to ghosts.
// no need to communicate x0 here, as it is not changed by time integration
// if x0 is changed when the ref config is updated, this communication is performed in the fix_integrate/tlsph
// similarily, rmass could be removed here.
// radius should be communicated here for future time-integration of the radius with ulsph (not implemented yet)
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]; //3
buf[m++] = radius[j];
buf[m++] = vfrac[j]; // 5
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2]; // 8
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2]; // 11
buf[m++] = e[j]; // 12
}
} 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++] = radius[j];
buf[m++] = vfrac[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2]; // 8
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2]; // 11
buf[m++] = e[j]; // 12
}
} 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];
// printf("\ndvx = %f, dvy=%f, dvz=%f\n", dvx, dvy, dvz);
// printf("dx = %f, dy=%f, dz=%f\n", dx, dy, dz);
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++] = radius[j];
buf[m++] = vfrac[j];
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++] = 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]; // 8
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2]; // 11
}
buf[m++] = e[j]; // 12
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_comm_hybrid(int n, int *list, double *buf) {
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = radius[j];
buf[m++] = vfrac[j];
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2];
buf[m++] = e[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::unpack_comm(int n, int first, double *buf) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::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++]; //3
radius[i] = buf[m++];
vfrac[i] = buf[m++]; // 5
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++]; // 8
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++]; // 11
e[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::unpack_comm_hybrid(int n, int first, double *buf) {
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
radius[i] = buf[m++];
vfrac[i] = buf[m++];
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++];
e[i] = buf[m++];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_reverse(int n, int first, double *buf) {
int i, m, last;
printf("in pack_reverse\n");
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++] = de[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_reverse_hybrid(int n, int first, double *buf) {
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = de[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::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++];
de[j] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::unpack_reverse_hybrid(int n, int *list, double *buf) {
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
de[j] += buf[m++];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
return -1;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::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;
//printf("AtomVecSMD::pack_border_vel\n");
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]; // 3
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2]; // 6
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d; // 10
buf[m++] = radius[j];
buf[m++] = rmass[j];
buf[m++] = vfrac[j];
buf[m++] = contact_radius[j];
buf[m++] = e[j];
buf[m++] = eff_plastic_strain[j]; // 16
for (int k = 0; k < NMAT_FULL; k++) {
buf[m++] = smd_data_9[j][k];
} // 25
for (int k = 0; k < NMAT_SYMM; k++) {
buf[m++] = tlsph_stress[j][k];
} // 31
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2]; // 34
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2]; // 37
}
} 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) {
//printf("dx = %f\n", dx);
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; // 3
buf[m++] = x0[j][0]; // this is correct
buf[m++] = x0[j][1];
buf[m++] = x0[j][2]; // 6
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d; // 10
buf[m++] = radius[j];
buf[m++] = rmass[j];
buf[m++] = vfrac[j];
buf[m++] = contact_radius[j];
buf[m++] = e[j];
buf[m++] = eff_plastic_strain[j]; // 17
for (int k = 0; k < NMAT_FULL; k++) {
buf[m++] = smd_data_9[j][k];
} // 26
for (int k = 0; k < NMAT_SYMM; k++) {
buf[m++] = tlsph_stress[j][k];
} // 32
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2]; // 35
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2]; // 38
}
} 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];
// printf("\ndvx = %f, dvy=%f, dvz=%f\n", dvx, dvy, dvz);
// printf("dx = %f, dy=%f, dz=%f\n", dx, dy, dz);
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; // 3
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2]; // 6
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d; // 10
buf[m++] = radius[j];
buf[m++] = rmass[j];
buf[m++] = vfrac[j];
buf[m++] = contact_radius[j];
buf[m++] = e[j];
buf[m++] = eff_plastic_strain[j]; // 16
for (int k = 0; k < NMAT_FULL; k++) {
buf[m++] = smd_data_9[j][k];
} // 25
for (int k = 0; k < NMAT_SYMM; k++) {
buf[m++] = tlsph_stress[j][k];
} // 31
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz; // 34
buf[m++] = vest[j][0] + dvx;
buf[m++] = vest[j][1] + dvy;
buf[m++] = vest[j][2] + dvz; // 37
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2]; // 34
buf[m++] = vest[j][0];
buf[m++] = vest[j][1];
buf[m++] = vest[j][2]; // 37
}
}
}
}
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 AtomVecSMD::pack_border_hybrid(int n, int *list, double *buf) {
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2]; // 3
buf[m++] = ubuf(molecule[j]).d; // 4
buf[m++] = radius[j];
buf[m++] = rmass[j];
buf[m++] = vfrac[j];
buf[m++] = contact_radius[j];
buf[m++] = e[j];
buf[m++] = eff_plastic_strain[j]; // 11
for (int k = 0; k < NMAT_FULL; k++) {
buf[m++] = smd_data_9[j][k];
} // 20
for (int k = 0; k < NMAT_SYMM; k++) {
buf[m++] = tlsph_stress[j][k];
} // 26
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::unpack_border(int n, int first, double *buf) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::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++]; // 3
x0[i][0] = buf[m++];
x0[i][1] = buf[m++];
x0[i][2] = buf[m++]; // 6
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i; // 10
radius[i] = buf[m++];
rmass[i] = buf[m++];
vfrac[i] = buf[m++];
contact_radius[i] = buf[m++];
e[i] = buf[m++];
eff_plastic_strain[i] = buf[m++]; // 16
for (int k = 0; k < NMAT_FULL; k++) {
smd_data_9[i][k] = buf[m++];
} // 25
for (int k = 0; k < NMAT_SYMM; k++) {
tlsph_stress[i][k] = buf[m++];
} // 31
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++]; // 34
vest[i][0] = buf[m++];
vest[i][1] = buf[m++];
vest[i][2] = buf[m++]; // 37
}
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]);
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::unpack_border_hybrid(int n, int first, double *buf) {
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x0[i][0] = buf[m++];
x0[i][1] = buf[m++];
x0[i][2] = buf[m++]; // 3
molecule[i] = (tagint) ubuf(buf[m++]).i; // 4
radius[i] = buf[m++];
rmass[i] = buf[m++];
vfrac[i] = buf[m++];
contact_radius[i] = buf[m++];
e[i] = buf[m++];
eff_plastic_strain[i] = buf[m++]; // 11
for (int k = 0; k < NMAT_FULL; k++) {
smd_data_9[i][k] = buf[m++];
} // 20
for (int k = 0; k < NMAT_SYMM; k++) {
tlsph_stress[i][k] = buf[m++];
} // 26
}
return m;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecSMD::pack_exchange(int i, double *buf) {
int m = 1;
//printf("in AtomVecSMD::pack_exchange tag %d\n", tag[i]);
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2]; // 3
buf[m++] = x0[i][0];
buf[m++] = x0[i][1];
buf[m++] = x0[i][2]; // 6
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++] = ubuf(molecule[i]).d; // 11
buf[m++] = radius[i];
buf[m++] = rmass[i];
buf[m++] = vfrac[i];
buf[m++] = contact_radius[i];
buf[m++] = e[i];
buf[m++] = eff_plastic_strain[i]; // 18
buf[m++] = eff_plastic_strain_rate[i]; // 19
for (int k = 0; k < NMAT_FULL; k++) {
buf[m++] = smd_data_9[i][k];
} // 27
for (int k = 0; k < NMAT_SYMM; k++) {
buf[m++] = tlsph_stress[i][k];
} // 33
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2]; // 36
buf[m++] = vest[i][0];
buf[m++] = vest[i][1];
buf[m++] = vest[i][2]; // 39
buf[m++] = damage[i];
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 AtomVecSMD::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++]; // 3
x0[nlocal][0] = buf[m++];
x0[nlocal][1] = buf[m++];
x0[nlocal][2] = buf[m++]; // 6
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;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i; // 11
radius[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
vfrac[nlocal] = buf[m++];
contact_radius[nlocal] = buf[m++];
e[nlocal] = buf[m++];
eff_plastic_strain[nlocal] = buf[m++]; // 18
eff_plastic_strain_rate[nlocal] = buf[m++]; // 19
for (int k = 0; k < NMAT_FULL; k++) {
smd_data_9[nlocal][k] = buf[m++];
} // 27
for (int k = 0; k < NMAT_SYMM; k++) {
tlsph_stress[nlocal][k] = buf[m++];
} // 33
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++]; // 36
vest[nlocal][0] = buf[m++];
vest[nlocal][1] = buf[m++];
vest[nlocal][2] = buf[m++]; // 39
damage[nlocal] = buf[m++]; //40
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 AtomVecSMD::size_restart() {
int i;
int nlocal = atom->nlocal;
int n = 43 * nlocal; // count pack_restart + 1 (size of buffer)
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 AtomVecSMD::pack_restart(int i, double *buf) {
int m = 1; // 1
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2]; // 4
buf[m++] = x0[i][0];
buf[m++] = x0[i][1];
buf[m++] = x0[i][2]; // 7
buf[m++] = ubuf(tag[i]).d;
buf[m++] = ubuf(type[i]).d;
buf[m++] = ubuf(mask[i]).d; // 10
buf[m++] = ubuf(image[i]).d;
buf[m++] = ubuf(molecule[i]).d;
buf[m++] = radius[i];
buf[m++] = rmass[i];
buf[m++] = vfrac[i]; // 15
buf[m++] = contact_radius[i];
buf[m++] = e[i];
buf[m++] = eff_plastic_strain[i];
buf[m++] = eff_plastic_strain_rate[i]; // 19
for (int k = 0; k < NMAT_FULL; k++) {
buf[m++] = smd_data_9[i][k];
} // 28
for (int k = 0; k < NMAT_SYMM; k++) {
buf[m++] = tlsph_stress[i][k];
} // 34
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2]; // 37
buf[m++] = vest[i][0];
buf[m++] = vest[i][1];
buf[m++] = vest[i][2]; // 40
buf[m++] = damage[i]; // 41
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 AtomVecSMD::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++]; // 3
x0[nlocal][0] = buf[m++];
x0[nlocal][1] = buf[m++];
x0[nlocal][2] = buf[m++]; // 6
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;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i; // 11
radius[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
vfrac[nlocal] = buf[m++]; //14
contact_radius[nlocal] = buf[m++]; //15
e[nlocal] = buf[m++];
eff_plastic_strain[nlocal] = buf[m++]; // 18
eff_plastic_strain_rate[nlocal] = buf[m++]; // 29
for (int k = 0; k < NMAT_FULL; k++) {
smd_data_9[nlocal][k] = buf[m++];
} // 28
for (int k = 0; k < NMAT_SYMM; k++) {
tlsph_stress[nlocal][k] = buf[m++];
} // 34
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++]; // 37
vest[nlocal][0] = buf[m++];
vest[nlocal][1] = buf[m++];
vest[nlocal][2] = buf[m++]; // 40
damage[nlocal] = buf[m++]; //41
//printf("nlocal in restart is %d\n", nlocal);
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++;
//printf("returning m=%d in unpack_restart\n", m);
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecSMD::create_atom(int itype, double *coord) {
int nlocal = atom->nlocal;
if (nlocal == nmax) {
printf("nlocal = %d, nmax = %d, calling grow\n", nlocal, nmax);
grow(0);
printf("... finished growing\n");
}
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
x0[nlocal][0] = coord[0];
x0[nlocal][1] = coord[1];
x0[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;
vest[nlocal][0] = 0.0;
vest[nlocal][1] = 0.0;
vest[nlocal][2] = 0.0;
vfrac[nlocal] = 1.0;
rmass[nlocal] = 1.0;
radius[nlocal] = 0.5;
contact_radius[nlocal] = 0.5;
molecule[nlocal] = 1;
e[nlocal] = 0.0;
eff_plastic_strain[nlocal] = 0.0;
eff_plastic_strain_rate[nlocal] = 0.0;
for (int k = 0; k < NMAT_FULL; k++) {
smd_data_9[nlocal][k] = 0.0;
}
smd_data_9[nlocal][0] = 1.0; // xx
smd_data_9[nlocal][4] = 1.0; // yy
smd_data_9[nlocal][8] = 1.0; // zz
for (int k = 0; k < NMAT_SYMM; k++) {
tlsph_stress[nlocal][k] = 0.0;
}
damage[nlocal] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) {
int nlocal = atom->nlocal;
if (nlocal == nmax)
grow(0);
tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR, "Invalid atom type in Atoms section of data file");
molecule[nlocal] = ATOTAGINT(values[2]);
if (molecule[nlocal] <= 0)
error->one(FLERR, "Invalid molecule in Atoms section of data file");
vfrac[nlocal] = atof(values[3]);
if (vfrac[nlocal] < 0.0)
error->one(FLERR, "Invalid volume in Atoms section of data file");
rmass[nlocal] = atof(values[4]);
if (rmass[nlocal] == 0.0)
error->one(FLERR, "Invalid mass in Atoms section of data file");
radius[nlocal] = atof(values[5]);
if (radius[nlocal] < 0.0)
error->one(FLERR, "Invalid radius in Atoms section of data file");
contact_radius[nlocal] = atof(values[6]);
if (contact_radius[nlocal] < 0.0)
error->one(FLERR, "Invalid contact radius in Atoms section of data file");
e[nlocal] = 0.0;
x0[nlocal][0] = atof(values[7]);
x0[nlocal][1] = atof(values[8]);
x0[nlocal][2] = atof(values[9]);
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;
damage[nlocal] = 0.0;
eff_plastic_strain[nlocal] = 0.0;
eff_plastic_strain_rate[nlocal] = 0.0;
for (int k = 0; k < NMAT_FULL; k++) {
smd_data_9[nlocal][k] = 0.0;
}
for (int k = 0; k < NMAT_SYMM; k++) {
tlsph_stress[nlocal][k] = 0.0;
}
smd_data_9[nlocal][0] = 1.0; // xx
smd_data_9[nlocal][4] = 1.0; // yy
smd_data_9[nlocal][8] = 1.0; // zz
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecSMD::data_atom_hybrid(int nlocal, char **values) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
return -1;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecSMD::data_vel(int m, char **values) {
v[m][0] = atof(values[0]);
v[m][1] = atof(values[1]);
v[m][2] = atof(values[2]);
vest[m][0] = atof(values[0]);
vest[m][1] = atof(values[1]);
vest[m][2] = atof(values[2]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int AtomVecSMD::data_vel_hybrid(int m, char **values) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
return 0;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecSMD::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] = ubuf(molecule[i]).d;
buf[i][3] = vfrac[i];
buf[i][4] = rmass[i];
buf[i][5] = radius[i];
buf[i][6] = contact_radius[i];
buf[i][7] = x[i][0];
buf[i][8] = x[i][1];
buf[i][9] = x[i][2];
buf[i][10] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
buf[i][11] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][12] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
}
}
/* ----------------------------------------------------------------------
pack hybrid atom info for data file
------------------------------------------------------------------------- */
int AtomVecSMD::pack_data_hybrid(int i, double *buf) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
return -1;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecSMD::write_data(FILE *fp, int n, double **buf) {
for (int i = 0; i < n; i++)
fprintf(fp,
TAGINT_FORMAT
" %d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", (tagint) ubuf(buf[i][0]).i,
(int) ubuf(buf[i][1]).i, (int) ubuf(buf[i][2]).i, buf[i][3], buf[i][4], buf[i][5], buf[i][6], buf[i][7], buf[i][8],
buf[i][9], (int) ubuf(buf[i][7]).i, (int) ubuf(buf[i][8]).i, (int) ubuf(buf[i][9]).i);
}
/* ----------------------------------------------------------------------
write hybrid atom info to data file
------------------------------------------------------------------------- */
int AtomVecSMD::write_data_hybrid(FILE *fp, double *buf) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
return -1;
}
/* ----------------------------------------------------------------------
pack velocity info for data file
------------------------------------------------------------------------- */
void AtomVecSMD::pack_vel(double **buf) {
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(tag[i]).d;
buf[i][1] = v[i][0];
buf[i][2] = v[i][1];
buf[i][3] = v[i][2];
}
}
/* ----------------------------------------------------------------------
pack hybrid velocity info for data file
------------------------------------------------------------------------- */
int AtomVecSMD::pack_vel_hybrid(int i, double *buf) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
return 0;
}
/* ----------------------------------------------------------------------
write velocity info to data file
------------------------------------------------------------------------- */
void AtomVecSMD::write_vel(FILE *fp, int n, double **buf) {
for (int i = 0; i < n; i++)
fprintf(fp, TAGINT_FORMAT
" %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n", (tagint) ubuf(buf[i][0]).i, buf[i][1], buf[i][2], buf[i][3],
buf[i][4], buf[i][5], buf[i][6]);
}
/* ----------------------------------------------------------------------
write hybrid velocity info to data file
------------------------------------------------------------------------- */
int AtomVecSMD::write_vel_hybrid(FILE *fp, double *buf) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph");
return 3;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecSMD::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("molecule"))
bytes += memory->usage(molecule, 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("vest"))
bytes += memory->usage(vest, nmax, 3);
if (atom->memcheck("f"))
bytes += memory->usage(f, nmax * comm->nthreads, 3);
if (atom->memcheck("radius"))
bytes += memory->usage(radius, nmax);
if (atom->memcheck("contact_radius"))
bytes += memory->usage(contact_radius, nmax);
if (atom->memcheck("vfrac"))
bytes += memory->usage(vfrac, nmax);
if (atom->memcheck("rmass"))
bytes += memory->usage(rmass, nmax);
if (atom->memcheck("eff_plastic_strain"))
bytes += memory->usage(eff_plastic_strain, nmax);
if (atom->memcheck("eff_plastic_strain_rate"))
bytes += memory->usage(eff_plastic_strain_rate, nmax);
if (atom->memcheck("e"))
bytes += memory->usage(e, nmax);
if (atom->memcheck("de"))
bytes += memory->usage(de, nmax);
if (atom->memcheck("smd_data_9"))
bytes += memory->usage(smd_data_9, nmax, NMAT_FULL);
if (atom->memcheck("tlsph_stress"))
bytes += memory->usage(tlsph_stress, nmax, NMAT_SYMM);
if (atom->memcheck("damage"))
bytes += memory->usage(damage, nmax);
return bytes;
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::force_clear(int n, size_t nbytes) {
//printf("clearing force on atom %d", n);
memset(&de[n], 0, nbytes);
memset(&f[0][0], 0, 3 * nbytes);
}
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