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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10430 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-07-26 16:53:49 +00:00
parent 0a1c74ef9e
commit 4aecc6eaf0
7 changed files with 928 additions and 125 deletions
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104
src/PERI/fix_peri_neigh.cpp
View File

@ -12,13 +12,14 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Parks (SNL)
Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA)
------------------------------------------------------------------------- */
#include "math.h"
#include "fix_peri_neigh.h"
#include "pair_peri_pmb.h"
#include "pair_peri_lps.h"
#include "pair_peri_ves.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
@ -40,6 +41,11 @@ using namespace FixConst;
FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
Fix(lmp, narg, arg)
{
isPMB = isLPS = isVES = 0;
if (force->pair_match("peri/pmb",1)) isPMB = 1;
if (force->pair_match("peri/lps",1)) isLPS = 1;
if (force->pair_match("peri/ves",1)) isVES = 1;
restart_global = 1;
restart_peratom = 1;
first = 1;
@ -51,6 +57,8 @@ FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
maxpartner = 1;
npartner = NULL;
partner = NULL;
deviatorextention = NULL;
deviatorBackextention = NULL;
r0 = NULL;
vinter = NULL;
wvolume = NULL;
@ -82,6 +90,8 @@ FixPeriNeigh::~FixPeriNeigh()
memory->destroy(npartner);
memory->destroy(partner);
memory->destroy(deviatorextention);
memory->destroy(deviatorBackextention);
memory->destroy(r0);
memory->destroy(vinter);
memory->destroy(wvolume);
@ -195,12 +205,16 @@ void FixPeriNeigh::setup(int vflag)
// realloc arrays with correct value for maxpartner
memory->destroy(partner);
memory->destroy(deviatorextention);
memory->destroy(deviatorBackextention);
memory->destroy(r0);
memory->destroy(npartner);
npartner = NULL;
partner = NULL;
r0 = NULL;
deviatorextention = NULL;
deviatorBackextention = NULL;
r0 = NULL;
grow_arrays(atom->nmax);
// create partner list and r0 values from neighbor list
@ -233,7 +247,10 @@ void FixPeriNeigh::setup(int vflag)
if (rsq <= cutsq[itype][jtype]) {
partner[i][npartner[i]] = tag[j];
r0[i][npartner[i]] = sqrt(rsq);
if (isVES)
deviatorextention[i][npartner[i]] =
deviatorBackextention[i][npartner[i]] = 0.0;
r0[i][npartner[i]] = sqrt(rsq);
npartner[i]++;
vinter[i] += vfrac[j];
}
@ -263,6 +280,8 @@ void FixPeriNeigh::setup(int vflag)
double vfrac_scale;
PairPeriLPS *pairlps = static_cast<PairPeriLPS*>(anypair);
PairPeriPMB *pairpmb = static_cast<PairPeriPMB*>(anypair);
PairPeriVES *pairves = static_cast<PairPeriVES*>(anypair);
for (i = 0; i < nlocal; i++) {
double xtmp0 = x0[i][0];
double ytmp0 = x0[i][1];
@ -301,12 +320,16 @@ void FixPeriNeigh::setup(int vflag)
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
if (pairpmb != NULL) // define influence function to be 1.0
wvolume[i] += 1.0 * rsq0 * vfrac[j] * vfrac_scale;
else if (pairlps != NULL) // call the PairPeriLPS influence function
// for PMB, influence = 1.0, otherwise invoke influence function
if (isPMB)
wvolume[i] += 1.0 * rsq0 * vfrac[j] * vfrac_scale;
else if (isLPS)
wvolume[i] += pairlps->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
else if (isVES)
wvolume[i] += pairves->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
}
}
@ -340,14 +363,18 @@ void FixPeriNeigh::setup(int vflag)
------------------------------------------------------------------------- */
double FixPeriNeigh::memory_usage()
{
{
int nmax = atom->nmax;
int bytes = nmax * sizeof(int);
bytes += nmax*maxpartner * sizeof(int);
bytes += nmax*maxpartner * sizeof(double);
if (isVES) {
bytes += nmax*maxpartner * sizeof(double);
bytes += nmax*maxpartner * sizeof(double);
}
bytes += nmax * sizeof(double);
bytes += nmax * sizeof(double);
return bytes;
return bytes;
}
/* ----------------------------------------------------------------------
@ -356,22 +383,32 @@ double FixPeriNeigh::memory_usage()
void FixPeriNeigh::grow_arrays(int nmax)
{
memory->grow(npartner,nmax,"peri_neigh:npartner");
memory->grow(partner,nmax,maxpartner,"peri_neigh:partner");
memory->grow(r0,nmax,maxpartner,"peri_neigh:r0");
memory->grow(vinter,nmax,"peri_neigh:vinter");
memory->grow(wvolume,nmax,"peri_neigh:wvolume");
memory->grow(npartner,nmax,"peri_neigh:npartner");
memory->grow(partner,nmax,maxpartner,"peri_neigh:partner");
if (isVES) {
memory->grow(deviatorextention,nmax,maxpartner,
"peri_neigh:deviatorextention");
memory->grow(deviatorBackextention,nmax,maxpartner,
"peri_neigh:deviatorBackextention");
}
memory->grow(r0,nmax,maxpartner,"peri_neigh:r0");
memory->grow(vinter,nmax,"peri_neigh:vinter");
memory->grow(wvolume,nmax,"peri_neigh:wvolume");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixPeriNeigh::copy_arrays(int i, int j, int delflag)
void FixPeriNeigh::copy_arrays(int i, int j)
{
npartner[j] = npartner[i];
for (int m = 0; m < npartner[j]; m++) {
partner[j][m] = partner[i][m];
if (isVES) {
deviatorextention[j][m] = deviatorextention[i][m];
deviatorBackextention[j][m] = deviatorBackextention[i][m];
}
r0[j][m] = r0[i][m];
}
vinter[j] = vinter[i];
@ -391,10 +428,14 @@ int FixPeriNeigh::pack_exchange(int i, double *buf)
for (int n = 0; n < npartner[i]; n++) {
if (partner[i][n] == 0) continue;
buf[m++] = partner[i][n];
if (isVES) {
buf[m++] = deviatorextention[i][n];
buf[m++] = deviatorBackextention[i][n];
}
buf[m++] = r0[i][n];
}
buf[0] = m/2;
if (isVES) buf[0] = m/4;
else buf[0] = m/2;
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
return m;
@ -410,7 +451,11 @@ int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
npartner[nlocal] = static_cast<int> (buf[m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
partner[nlocal][n] = static_cast<int> (buf[m++]);
r0[nlocal][n] = buf[m++];
if (isVES) {
deviatorextention[nlocal][n] = buf[m++];
deviatorBackextention[nlocal][n] = buf[m++];
}
r0[nlocal][n] = buf[m++];
}
vinter[nlocal] = buf[m++];
wvolume[nlocal] = buf[m++];
@ -486,15 +531,21 @@ void FixPeriNeigh::restart(char *buf)
int FixPeriNeigh::pack_restart(int i, double *buf)
{
int m = 0;
buf[m++] = 2*npartner[i] + 4;
if (isVES) buf[m++] = 4*npartner[i] + 4;
else buf[m++] = 2*npartner[i] + 4;
buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) {
buf[m++] = partner[i][n];
if (isVES) {
buf[m++] = deviatorextention[i][n];
buf[m++] = deviatorBackextention[i][n];
}
buf[m++] = r0[i][n];
}
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
return m;
return m;
}
/* ----------------------------------------------------------------------
@ -503,6 +554,7 @@ int FixPeriNeigh::pack_restart(int i, double *buf)
void FixPeriNeigh::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
@ -514,10 +566,14 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)
npartner[nlocal] = static_cast<int> (extra[nlocal][m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
partner[nlocal][n] = static_cast<int> (extra[nlocal][m++]);
if (isVES) {
deviatorextention[nlocal][n] = extra[nlocal][m++];
deviatorBackextention[nlocal][n] = extra[nlocal][m++];
}
r0[nlocal][n] = extra[nlocal][m++];
}
vinter[nlocal] = extra[nlocal][m++];
wvolume[nlocal] = extra[nlocal][m++];
wvolume[nlocal] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
@ -526,7 +582,8 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)
int FixPeriNeigh::maxsize_restart()
{
return 2*maxpartner + 4;
if (isVES) return 4*maxpartner + 4;
return 2*maxpartner + 4;
}
/* ----------------------------------------------------------------------
@ -535,5 +592,6 @@ int FixPeriNeigh::maxsize_restart()
int FixPeriNeigh::size_restart(int nlocal)
{
return 2*npartner[nlocal] + 4;
if (isVES) return 4*npartner[nlocal] + 4;
return 2*npartner[nlocal] + 4;
}

10
src/PERI/fix_peri_neigh.h
View File

@ -28,6 +28,7 @@ class FixPeriNeigh : public Fix {
friend class PairPeriPMB;
friend class PairPeriPMBOMP;
friend class PairPeriLPS;
friend class PairPeriVES; //NEW
friend class PairPeriLPSOMP;
friend class ComputeDamageAtom;
@ -42,7 +43,7 @@ class FixPeriNeigh : public Fix {
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int, int);
void copy_arrays(int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
void write_restart(FILE *);
@ -60,9 +61,16 @@ class FixPeriNeigh : public Fix {
int maxpartner; // max # of peridynamic neighs for any atom
int *npartner; // # of neighbors for each atom
int **partner; // neighs for each atom, stored as global IDs
double **deviatorextention; // Deviatoric extention
double **deviatorBackextention; // Deviatoric back extention
double **r0; // initial distance to partners
double **r1; // Instanteneous distance to partners *** NEW ***
double *thetaOld; // Dilatation Old one
double *vinter; // sum of vfrac for bonded neighbors
double *wvolume; // weighted volume of particle
int isPMB;
int isLPS;
int isVES;
class NeighList *list;
};

97
src/PERI/pair_peri_lps.cpp
View File

@ -42,6 +42,7 @@ PairPeriLPS::PairPeriLPS(LAMMPS *lmp) : Pair(lmp)
{
for (int i = 0; i < 6; i++) virial[i] = 0.0;
no_virial_fdotr_compute = 1;
single_enable = 0;
ifix_peri = -1;
@ -503,102 +504,6 @@ void PairPeriLPS::read_restart(FILE *fp)
}
}
/* ---------------------------------------------------------------------- */
double PairPeriLPS::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double delx0,dely0,delz0,rsq0;
double d_ij,r,dr,rk,vfrac_scale;
double *vfrac = atom->vfrac;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
int **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
double kshort;
delx0 = x0[i][0] - x0[j][0];
dely0 = x0[i][1] - x0[j][1];
delz0 = x0[i][2] - x0[j][2];
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
d_ij = MIN(0.9*sqrt(rsq0),1.35*lc);
r = sqrt(rsq);
double energy = 0.0;
fforce = 0.0;
if (r < d_ij) {
dr = r - d_ij;
// kshort resembles short-range force constant of bond-based theory in 3d
kshort = (15.0 * 18.0 * bulkmodulus[itype][itype]) /
( 3.141592653589793 * cutsq[itype][jtype] * cutsq[itype][jtype]);
rk = ( kshort * vfrac[j]) * (dr / sqrt(cutsq[itype][jtype]));
if (r > 0.0) fforce += -(rk/r);
energy += 0.5*rk*dr;
}
if (atom->nmax > nmax) {
memory->destroy(theta);
nmax = atom->nmax;
memory->create(theta,nmax,"pair:theta");
}
// Compute the dilatation on each particle
compute_dilatation();
// communicate dilatation (theta) of each particle
comm->forward_comm_pair(this);
// communicate wighted volume (wvolume) upon every reneighbor
if (neighbor->ago == 0)
comm->forward_comm_fix(modify->fix[ifix_peri]);
double omega_plus, omega_minus;
int jnum = npartner[i];
for (int jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
if (j < 0) continue;
if (j == atom->map(partner[i][jj])) {
dr = r - r0[i][jj];
if (fabs(dr) < 2.2204e-016) dr = 0.0;
// scale vfrac[j] if particle j near the horizon
if ( (fabs(r0[i][jj] - sqrt(cutsq[itype][jtype]))) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((sqrt(cutsq[itype][jtype]) - half_lc)/(2*half_lc)));
else vfrac_scale = 1.0;
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
rk = (3.0* bulkmodulus[itype][itype] -5.0 * shearmodulus[itype][itype]) *
vfrac[j] * vfrac_scale * ( (omega_plus * theta[i] / wvolume[i]) +
(omega_minus * theta[j] / wvolume[j])) *
r0[i][jj];
rk += 15.0 * ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
if (r > 0.0) fforce += -(rk/r);
energy += 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
omega_plus * ( dr - theta[i]* r0[i][jj] / 3.0 ) *
( dr - theta[i]* r0[i][jj] / 3.0 ) * vfrac[j] * vfrac_scale;
}
}
return energy;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */

1
src/PERI/pair_peri_lps.h
View File

@ -40,7 +40,6 @@ class PairPeriLPS : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *) {}
void read_restart_settings(FILE *) {}
double single(int, int, int, int, double, double, double, double &);
double memory_usage();
double influence_function(double, double, double);
void compute_dilatation();

8
src/PERI/pair_peri_pmb.h
View File

@ -83,6 +83,10 @@ E: Pair peri requires an atom map, see atom_modify
Even for atomic systems, an atom map is required to find Peridynamic
bonds. Use the atom_modify command to define one.
E: Pair peri requires a lattice be defined
Use the lattice command for this purpose.
E: Pair peri lattice is not identical in x, y, and z
The lattice defined by the lattice command must be cubic.
@ -91,8 +95,4 @@ E: Fix peri neigh does not exist
Somehow a fix that the pair style defines has been deleted.
U: Pair peri requires a lattice be defined
Use the lattice command for this purpose.
*/

724
src/PERI/pair_peri_ves.cpp Normal file
View File

@ -0,0 +1,724 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Ezwanur Rahman, J.T. Foster (UTSA)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "pair_peri_ves.h"
#include "atom.h"
#include "domain.h"
#include "lattice.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "fix_peri_neigh.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "update.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairPeriVES::PairPeriVES(LAMMPS *lmp) : Pair(lmp)
{
for (int i = 0; i < 6; i++) virial[i] = 0.0;
no_virial_fdotr_compute = 1;
single_enable = 0;
ifix_peri = -1;
nmax = 0;
s0_new = NULL;
theta = NULL;
bulkmodulus = NULL;
shearmodulus = NULL;
s00 = alpha = NULL;
cut = NULL;
m_lambdai = NULL;
m_taubi = NULL;
// set comm size needed by this Pair
// comm_reverse not needed
comm_forward = 1;
}
/* ---------------------------------------------------------------------- */
PairPeriVES::~PairPeriVES()
{
if (ifix_peri >= 0) modify->delete_fix("PERI_NEIGH");
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(bulkmodulus);
memory->destroy(shearmodulus);
memory->destroy(s00);
memory->destroy(alpha);
memory->destroy(cut);
memory->destroy(m_lambdai);
memory->destroy(m_taubi);
memory->destroy(theta);
memory->destroy(s0_new);
}
}
/* ---------------------------------------------------------------------- */
void PairPeriVES::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0,rsq0;
double rsq,r,dr,dr1,rk,evdwl,fpair,fbond;
double deltaed,fbondViscoElastic,fbondFinal;
double decay,betai,lambdai,edbNp1,rkNew;
int *ilist,*jlist,*numneigh,**firstneigh;
double d_ij,delta,stretch;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
double timestepsize = update->dt;
double *vfrac = atom->vfrac;
double *s0 = atom->s0;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
double **deviatorextention =
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorextention;
double **deviatorBackextention =
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorBackextention;
int **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
// lc = lattice constant
// init_style guarantees it's the same in x, y, and z
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
double vfrac_scale = 1.0;
// short-range forces
int newton_pair = force->newton_pair;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
// need minimg() for x0 difference since not ghosted
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
r = sqrt(rsq);
// short-range interaction distance based on initial particle position
// 0.9 and 1.35 are constants
d_ij = MIN(0.9*sqrt(rsq0),1.35*lc);
// short-range contact forces
// 15 is constant taken from the EMU Theory Manual
// Silling, 12 May 2005, p 18
if (r < d_ij) {
dr = r - d_ij;
// kshort based upon short-range force constant
// of the bond-based theory used in PMB model
double kshort = (15.0 * 18.0 * bulkmodulus[itype][itype]) /
(3.141592653589793 * cutsq[itype][jtype] * cutsq[itype][jtype]);
rk = (kshort * vfrac[j]) * (dr / cut[itype][jtype]);
if (r > 0.0) fpair = -(rk/r);
else fpair = 0.0;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) evdwl = 0.5*rk*dr;
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,
fpair*vfrac[i],delx,dely,delz);
}
}
}
// grow bond forces array if necessary
if (atom->nmax > nmax) {
memory->destroy(s0_new);
memory->destroy(theta);
nmax = atom->nmax;
memory->create(s0_new,nmax,"pair:s0_new");
memory->create(theta,nmax,"pair:theta");
}
// compute the dilatation on each particle
compute_dilatation();
// communicate dilatation (theta) of each particle
comm->forward_comm_pair(this);
// communicate weighted volume (wvolume) upon every reneighbor
if (neighbor->ago == 0)
comm->forward_comm_fix(modify->fix[ifix_peri]);
// volume-dependent part of the energy
if (eflag) {
for (i = 0; i < nlocal; i++) {
itype = type[i];
if (eflag_global)
eng_vdwl += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
if (eflag_atom)
eatom[i] += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
}
}
// loop over my particles and their partners
// partner list contains all bond partners, so I-J appears twice
// if bond already broken, skip this partner
// first = true if this is first neighbor of particle i
bool first;
double omega_minus, omega_plus;
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
itype = type[i];
jnum = npartner[i];
first = true;
for (jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
j = atom->map(partner[i][jj]);
// check if lost a partner without first breaking bond
if (j < 0) {
partner[i][jj] = 0;
continue;
}
// compute force density, add to PD equation of motion
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
jtype = type[j];
delta = cut[itype][jtype];
r = sqrt(rsq);
dr = r - r0[i][jj];
// avoid roundoff errors
if (fabs(dr) < 2.2204e-016) dr = 0.0;
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
rk = ( (3.0 * bulkmodulus[itype][itype]) * vfrac[j] * vfrac_scale *
( (omega_plus * theta[i] / wvolume[i]) +
( omega_minus * theta[j] / wvolume[j] ) ) ) * r0[i][jj];
if (r > 0.0) fbond = -(rk/r);
else fbond = 0.0;
// for viscoelasticity
lambdai=m_lambdai[itype][itype];
double taui = m_taubi[itype][itype];
double c1 = taui/timestepsize;
decay=exp(-1.0/c1);
betai=1.-c1*(1.-decay);
double deviatoric_extension =
dr - (theta[i]* r0[i][jj] / 3.0);
deltaed = deviatoric_extension-deviatorextention[i][jj];
// back extention at current step
edbNp1 = deviatorextention[i][jj]*(1-decay) +
deviatorBackextention[i][jj]*decay+betai*deltaed;
rkNew = ((1-lambdai)*15.0) *
( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
deviatoric_extension;
rkNew += (lambdai*15.0) *
( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
(deviatoric_extension-edbNp1);
if (r > 0.0) fbondViscoElastic = -(rkNew/r);
else fbondViscoElastic = 0.0;
// total Force: elastic + viscoelastic
fbondFinal=fbond+fbondViscoElastic;
fbond=fbondFinal;
f[i][0] += delx*fbond;
f[i][1] += dely*fbond;
f[i][2] += delz*fbond;
// since I-J is double counted, set newton off & use 1/2 factor and I,I
if (eflag) evdwl = (0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
omega_plus * deviatoric_extension *
deviatoric_extension) +
(0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
omega_plus * (deviatoric_extension-edbNp1) *
(deviatoric_extension-edbNp1)) * vfrac[j] * vfrac_scale;
if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,
0.5*fbond*vfrac[i],delx,dely,delz);
// find stretch in bond I-J and break if necessary
// use s0 from previous timestep
// store current deviatoric extention
deviatorextention[i][jj]=deviatoric_extension;
deviatorBackextention[i][jj]=edbNp1;
stretch = dr / r0[i][jj];
if (stretch > MIN(s0[i],s0[j])) partner[i][jj] = 0;
// update s0 for next timestep
if (first)
s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
else
s0_new[i] = MAX(s0_new[i],s00[itype][jtype] -
(alpha[itype][jtype] * stretch));
first = false;
}
}
// store new s0
for (i = 0; i < nlocal; i++) s0[i] = s0_new[i];
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairPeriVES::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(bulkmodulus,n+1,n+1,"pair:bulkmodulus");
memory->create(shearmodulus,n+1,n+1,"pair:shearmodulus");
memory->create(s00,n+1,n+1,"pair:s00");
memory->create(alpha,n+1,n+1,"pair:alpha");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(m_lambdai,n+1,n+1,"pair:m_lambdai");
memory->create(m_taubi,n+1,n+1,"pair:m_taubi");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairPeriVES::settings(int narg, char **arg)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairPeriVES::coeff(int narg, char **arg)
{
if (narg != 9) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double bulkmodulus_one = atof(arg[2]);
double shearmodulus_one = atof(arg[3]);
double cut_one = atof(arg[4]);
double s00_one = atof(arg[5]);
double alpha_one = atof(arg[6]);
double mlambdai_one = atof(arg[7]);
double mtaui_one = atof(arg[8]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
bulkmodulus[i][j] = bulkmodulus_one;
shearmodulus[i][j] = shearmodulus_one;
cut[i][j] = cut_one;
s00[i][j] = s00_one;
alpha[i][j] = alpha_one;
m_lambdai[i][j] = mlambdai_one;
m_taubi[i][j] = mtaui_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairPeriVES::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
bulkmodulus[j][i] = bulkmodulus[i][j];
shearmodulus[j][i] = shearmodulus[i][j];
s00[j][i] = s00[i][j];
alpha[j][i] = alpha[i][j];
cut[j][i] = cut[i][j];
m_lambdai[j][i] = m_lambdai[i][j];
m_taubi[j][i] = m_taubi[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairPeriVES::init_style()
{
// error checks
if (!atom->peri_flag)
error->all(FLERR,"Pair style peri requires atom style peri");
if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
if (domain->lattice == NULL)
error->all(FLERR,"Pair peri requires a lattice be defined");
if (domain->lattice->xlattice != domain->lattice->ylattice ||
domain->lattice->xlattice != domain->lattice->zlattice ||
domain->lattice->ylattice != domain->lattice->zlattice)
error->all(FLERR,"Pair peri lattice is not identical in x, y, and z");
// if first init, create Fix needed for storing fixed neighbors
if (ifix_peri == -1) {
char **fixarg = new char*[3];
fixarg[0] = (char *) "PERI_NEIGH";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "PERI_NEIGH";
modify->add_fix(3,fixarg);
delete [] fixarg;
}
// find associated PERI_NEIGH fix that must exist
// could have changed locations in fix list since created
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist");
neighbor->request(this);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairPeriVES::write_restart(FILE *fp)
{
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&bulkmodulus[i][j],sizeof(double),1,fp);
fwrite(&shearmodulus[i][j],sizeof(double),1,fp);
fwrite(&s00[i][j],sizeof(double),1,fp);
fwrite(&alpha[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&m_lambdai[i][j],sizeof(double),1,fp);
fwrite(&m_taubi[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairPeriVES::read_restart(FILE *fp)
{
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&bulkmodulus[i][j],sizeof(double),1,fp);
fread(&shearmodulus[i][j],sizeof(double),1,fp);
fread(&s00[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
fread(&m_lambdai[i][j],sizeof(double),1,fp);
fread(&m_taubi[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&m_lambdai[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&m_taubi[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairPeriVES::memory_usage()
{
double bytes = 2 * nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
influence function definition
------------------------------------------------------------------------- */
double PairPeriVES::influence_function(double xi_x, double xi_y, double xi_z)
{
double r = sqrt(xi_x*xi_x + xi_y*xi_y + xi_z*xi_z);
double omega;
if (fabs(r) < 2.2204e-016)
error->one(FLERR,"Divide by 0 in influence function of pair peri/lps");
omega = 1.0/r;
return omega;
}
/* ---------------------------------------------------------------------- */
void PairPeriVES::compute_dilatation()
{
int i,j,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0;
double rsq,r,dr;
double delta;
double **x = atom->x;
int *type = atom->type;
double **x0 = atom->x0;
int nlocal = atom->nlocal;
double *vfrac = atom->vfrac;
double vfrac_scale = 1.0;
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
int **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
// compute the dilatation theta
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
jnum = npartner[i];
theta[i] = 0.0;
itype = type[i];
for (jj = 0; jj < jnum; jj++) {
// if bond already broken, skip this partner
if (partner[i][jj] == 0) continue;
// look up local index of this partner particle
j = atom->map(partner[i][jj]);
// skip if particle is "lost"
if (j < 0) continue;
// compute force density and add to PD equation of motion
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
r = sqrt(rsq);
dr = r - r0[i][jj];
if (fabs(dr) < 2.2204e-016) dr = 0.0;
jtype = type[j];
delta = cut[itype][jtype];
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
theta[i] += influence_function(delx0, dely0, delz0) * r0[i][jj] * dr *
vfrac[j] * vfrac_scale;
}
// if wvolume[i] is zero, then particle i has no bonds
// therefore, the dilatation is set to
if (wvolume[i] != 0.0) theta[i] = (3.0/wvolume[i]) * theta[i];
else theta[i] = 0;
}
}
/* ----------------------------------------------------------------------
communication routines
---------------------------------------------------------------------- */
int PairPeriVES::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = theta[j];
}
return 1;
}
/* ---------------------------------------------------------------------- */
void PairPeriVES::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
theta[i] = buf[m++];
}
}

109
src/PERI/pair_peri_ves.h Normal file
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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(peri/ves,PairPeriVES)
#else
#ifndef LMP_PAIR_PERI_VES_H
#define LMP_PAIR_PERI_VES_H
#include "pair.h"
namespace LAMMPS_NS {
class PairPeriVES : public Pair {
public:
PairPeriVES(class LAMMPS *);
virtual ~PairPeriVES();
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void init_style();
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *) {}
void read_restart_settings(FILE *) {}
double memory_usage();
double influence_function(double, double, double);
void compute_dilatation();
protected:
int ifix_peri;
double **bulkmodulus;
double **shearmodulus;
double **s00, **alpha;
double **cut, **m_lambdai, **m_taubi; //NEW: **m_lambdai,**m_taubi
double *s0_new;
double *theta;
int nmax;
void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Pair style peri requires atom style peri
Self-explanatory.
E: Pair peri requires an atom map, see atom_modify
Even for atomic systems, an atom map is required to find Peridynamic
bonds. Use the atom_modify command to define one.
E: Pair peri requires a lattice be defined
Use the lattice command for this purpose.
E: Pair peri lattice is not identical in x, y, and z
The lattice defined by the lattice command must be cubic.
E: Fix peri neigh does not exist
Somehow a fix that the pair style defines has been deleted.
E: Divide by 0 in influence function of pair peri/lps
This should not normally occur. It is likely a problem with your
model.
*/