Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F120277373
atom_vec_smd.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Jul 3, 05:05
Size
35 KB
Mime Type
text/x-c
Expires
Sat, Jul 5, 05:05 (2 d)
Engine
blob
Format
Raw Data
Handle
26779337
Attached To
rLAMMPS lammps
atom_vec_smd.cpp
View Options
/* ----------------------------------------------------------------------
*
* *** 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);
}
Event Timeline
Log In to Comment