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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4465 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2010-08-07 22:41:39 +00:00
parent 74105f61e8
commit 26f888dd14
6 changed files with 979 additions and 12 deletions
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4
src/PERI/Install.sh
View File

@ -4,11 +4,13 @@ if (test $1 = 1) then
cp atom_vec_peri.cpp ..
cp pair_peri_pmb.cpp ..
cp pair_peri_lps.cpp ..
cp fix_peri_neigh.cpp ..
cp compute_damage_atom.cpp ..
cp atom_vec_peri.h ..
cp pair_peri_pmb.h ..
cp pair_peri_lps.h ..
cp fix_peri_neigh.h ..
cp compute_damage_atom.h ..
@ -16,11 +18,13 @@ elif (test $1 = 0) then
rm -f ../atom_vec_peri.cpp
rm -f ../pair_peri_pmb.cpp
rm -f ../pair_peri_lps.cpp
rm -f ../fix_peri_neigh.cpp
rm -f ../compute_damage_atom.cpp
rm -f ../atom_vec_peri.h
rm -f ../pair_peri_pmb.h
rm -f ../pair_peri_lps.h
rm -f ../fix_peri_neigh.h
rm -f ../compute_damage_atom.h

166
src/PERI/fix_peri_neigh.cpp
View File

@ -17,18 +17,21 @@
#include "math.h"
#include "fix_peri_neigh.h"
#include "pair_peri_pmb.h"
#include "pair_peri_lps.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "update.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "pair.h"
#include "lattice.h"
#include "memory.h"
#include "error.h"
#include "comm.h"
#include "update.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
@ -39,6 +42,7 @@ using namespace LAMMPS_NS;
FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
Fix(lmp, narg, arg)
{
restart_global = 1;
restart_peratom = 1;
first = 1;
@ -51,6 +55,7 @@ FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
partner = NULL;
r0 = NULL;
vinter = NULL;
wvolume = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
@ -60,6 +65,10 @@ FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) npartner[i] = 0;
// set comm sizes needed by this fix
comm_forward = 1;
}
/* ---------------------------------------------------------------------- */
@ -78,6 +87,7 @@ FixPeriNeigh::~FixPeriNeigh()
memory->destroy_2d_int_array(partner);
memory->destroy_2d_double_array(r0);
memory->sfree(vinter);
memory->sfree(wvolume);
}
/* ---------------------------------------------------------------------- */
@ -92,6 +102,8 @@ int FixPeriNeigh::setmask()
void FixPeriNeigh::init()
{
if (!first) return;
// need a full neighbor list once
int irequest = neighbor->request((void *) this);
@ -127,7 +139,7 @@ void FixPeriNeigh::setup(int vflag)
int *tag = atom->tag;
int nlocal = atom->nlocal;
// only build list of bonds on very first run
// only build list of bonds on very first run
if (!first) return;
first = 0;
@ -190,6 +202,7 @@ void FixPeriNeigh::setup(int vflag)
for (i = 0; i < nlocal; i++) {
npartner[i] = 0;
vinter[i] = 0.0;
wvolume[i] = 0.0;
}
for (ii = 0; ii < inum; ii++) {
@ -211,14 +224,74 @@ void FixPeriNeigh::setup(int vflag)
jtype = type[j];
if (rsq <= cutsq[itype][jtype]) {
partner[i][npartner[i]] = tag[j];
r0[i][npartner[i]] = sqrt(rsq);
npartner[i]++;
partner[i][npartner[i]] = tag[j];
r0[i][npartner[i]] = sqrt(rsq);
npartner[i]++;
vinter[i] += vfrac[j];
}
}
}
// compute wvolume for each atom
double **x0 = atom->x0;
double half_lc = 0.5*(domain->lattice->xlattice);
double vfrac_scale;
PairPeriLPS *pairlps = dynamic_cast<PairPeriLPS*>(anypair);
PairPeriPMB *pairpmb = dynamic_cast<PairPeriPMB*>(anypair);
for (i = 0; i < nlocal; i++) {
double xtmp0 = x0[i][0];
double ytmp0 = x0[i][1];
double ztmp0 = x0[i][2];
jnum = npartner[i];
itype = type[i];
// loop over partners of particle i
for (jj = 0; jj < jnum; jj++) {
// if bond already broken, skip this partner
if (partner[i][jj] == 0) continue;
// lookup local index of partner particle
j = atom->map(partner[i][jj]);
// skip if particle is "lost"
if (j < 0) continue;
double delx0 = xtmp0 - x0[j][0];
double dely0 = ytmp0 - x0[j][1];
double delz0 = ztmp0 - x0[j][2];
double rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
double delta = sqrt(cutsq[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;
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
wvolume[i] += pairlps->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
else
error->all("Unknown peridynamic pair style in FixPeriNeigh.");
}
}
// communicate wvolume to ghosts
comm->forward_comm_fix(this);
// bond statistics
int n = 0;
@ -251,6 +324,7 @@ double FixPeriNeigh::memory_usage()
bytes += nmax*maxpartner * sizeof(int);
bytes += nmax*maxpartner * sizeof(double);
bytes += nmax * sizeof(double);
bytes += nmax * sizeof(double);
return bytes;
}
@ -267,6 +341,8 @@ void FixPeriNeigh::grow_arrays(int nmax)
r0 = memory->grow_2d_double_array(r0,nmax,maxpartner,"peri_neigh:r0");
vinter = (double *) memory->srealloc(vinter,nmax*sizeof(double),
"peri_neigh:vinter");
wvolume = (double *) memory->srealloc(wvolume,nmax*sizeof(double),
"peri_neigh:wvolume");
}
/* ----------------------------------------------------------------------
@ -281,6 +357,7 @@ void FixPeriNeigh::copy_arrays(int i, int j)
r0[j][m] = r0[i][m];
}
vinter[j] = vinter[i];
wvolume[j] = wvolume[i];
}
/* ----------------------------------------------------------------------
@ -301,6 +378,7 @@ int FixPeriNeigh::pack_exchange(int i, double *buf)
buf[0] = m/2;
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
return m;
}
@ -317,9 +395,73 @@ int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
r0[nlocal][n] = buf[m++];
}
vinter[nlocal] = buf[m++];
wvolume[nlocal] = buf[m++];
return m;
}
/* ---------------------------------------------------------------------- */
int FixPeriNeigh::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++] = wvolume[j];
}
return 1;
}
/* ---------------------------------------------------------------------- */
void FixPeriNeigh::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
wvolume[i] = buf[m++];
}
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixPeriNeigh::write_restart(FILE *fp)
{
int n = 0;
double list[2];
list[n++] = first;
list[n++] = maxpartner;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixPeriNeigh::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
first = static_cast<int> (list[n++]);
maxpartner = static_cast<int> (list[n++]);
// grow 2D arrays now, cannot change size of 2nd array index later
grow_arrays(atom->nmax);
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
@ -327,13 +469,14 @@ int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
int FixPeriNeigh::pack_restart(int i, double *buf)
{
int m = 0;
buf[m++] = 2*npartner[i] + 2;
buf[m++] = 2*npartner[i] + 4;
buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) {
buf[m++] = partner[i][n];
buf[m++] = r0[i][n];
}
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
return m;
}
@ -357,6 +500,7 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)
r0[nlocal][n] = extra[nlocal][m++];
}
vinter[nlocal] = extra[nlocal][m++];
wvolume[nlocal] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
@ -365,7 +509,7 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)
int FixPeriNeigh::maxsize_restart()
{
return 2*maxpartner + 3;
return 2*maxpartner + 4;
}
/* ----------------------------------------------------------------------
@ -374,5 +518,5 @@ int FixPeriNeigh::maxsize_restart()
int FixPeriNeigh::size_restart(int nlocal)
{
return 2*npartner[nlocal] + 3;
return 2*npartner[nlocal] + 4;
}

7
src/PERI/fix_peri_neigh.h
View File

@ -26,6 +26,7 @@ namespace LAMMPS_NS {
class FixPeriNeigh : public Fix {
friend class PairPeriPMB;
friend class PairPeriLPS;
friend class ComputeDamageAtom;
public:
@ -41,10 +42,15 @@ class FixPeriNeigh : public Fix {
void copy_arrays(int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
void write_restart(FILE *);
void restart(char *);
int pack_restart(int, double *);
void unpack_restart(int, int);
int size_restart(int);
int maxsize_restart();
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
private:
int first; // flag for first time initialization
@ -53,6 +59,7 @@ class FixPeriNeigh : public Fix {
int **partner; // neighs for each atom, stored as global IDs
double **r0; // initial distance to partners
double *vinter; // sum of vfrac for bonded neighbors
double *wvolume; // weighted volume of particle
class NeighList *list;
};

745
src/PERI/pair_peri_lps.cpp Normal file
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@ -0,0 +1,745 @@
/* ----------------------------------------------------------------------
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 author: Mike Parks (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "values.h"
#include "stdlib.h"
#include "string.h"
#include "pair_peri_lps.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;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PairPeriLPS::PairPeriLPS(LAMMPS *lmp) : Pair(lmp)
{
for (int i = 0; i < 6; i++) virial[i] = 0.0;
ifix_peri = -1;
nmax = 0;
s0_new = NULL;
theta = NULL;
bulkmodulus = NULL;
shearmodulus = NULL;
s00 = alpha = NULL;
cut = NULL;
// set comm size needed by this Pair
// comm_reverse not needed
comm_forward = 1; // For passing dilatation (theta)
}
/* ---------------------------------------------------------------------- */
PairPeriLPS::~PairPeriLPS()
{
if (ifix_peri >= 0) modify->delete_fix("PERI_NEIGH");
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(bulkmodulus);
memory->destroy_2d_double_array(shearmodulus);
memory->destroy_2d_double_array(s00);
memory->destroy_2d_double_array(alpha);
memory->destroy_2d_double_array(cut);
memory->sfree(theta);
memory->sfree(s0_new);
}
}
/* ---------------------------------------------------------------------- */
void PairPeriLPS::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,rk,evdwl,fpair,fbond;
int *ilist,*jlist,*numneigh,**firstneigh;
double d_ij,delta,stretch;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
double *vfrac = atom->vfrac;
double *s0 = atom->s0;
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;
// 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 nall = atom->nlocal + atom->nghost;
int newton_pair = force->newton_pair;
int nonperiodic = domain->nonperiodic;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
double dt = update->dt;
// 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 %= nall;
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 (nonperiodic == 0) 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 / sqrt(cutsq[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,delx,dely,delz);
}
}
}
// grow bond forces array if necessary
if (atom->nmax > nmax) {
memory->sfree(s0_new);
memory->sfree(theta);
nmax = atom->nmax;
s0_new = (double *) memory->smalloc(nmax*sizeof(double),"pair:s0_new");
theta = (double *) memory->smalloc(nmax*sizeof(double),"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]);
// Volume-dependent part of the energy
for (i = 0; i < nlocal; i++) {
itype = type[i];
if (eflag) {
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 (nonperiodic == 0) 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 (nonperiodic == 0) domain->minimum_image(delx0,dely0,delz0);
jtype = type[j];
delta = sqrt(cutsq[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]) - (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) fbond = -(rk/r);
else fbond = 0.0;
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
double deviatoric_extension = dr - (theta[i]* r0[i][jj] / 3.0);
if (eflag) evdwl = 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) * omega_plus * ( deviatoric_extension * deviatoric_extension ) * vfrac[j] * vfrac_scale;
if (evflag) ev_tally(i,i,nlocal,0,
0.5*evdwl,0.0,0.5*fbond,delx,dely,delz);
// find stretch in bond I-J and break if necessary
// use s0 from previous timestep
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;
}
}
if (vflag_fdotr) virial_compute();
// store new s0
for (i = 0; i < nlocal; i++) s0[i] = s0_new[i];
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairPeriLPS::allocate()
{
allocated = 1;
int n = atom->ntypes;
setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
bulkmodulus = memory->create_2d_double_array(n+1,n+1,"pair:bulkmodulus");
shearmodulus = memory->create_2d_double_array(n+1,n+1,"pair:shearmodulus");
s00 = memory->create_2d_double_array(n+1,n+1,"pair:s00");
alpha = memory->create_2d_double_array(n+1,n+1,"pair:alpha");
cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairPeriLPS::settings(int narg, char **arg)
{
if (narg) error->all("Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairPeriLPS::coeff(int narg, char **arg)
{
if (narg != 7) error->all("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]);
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;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairPeriLPS::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all("All pair coeffs are not set");
cutsq[i][j] = cut[i][j] * cut[i][j];
cutsq[j][i] = cutsq[i][j];
// set other j,i parameters
bulkmodulus[j][i] = bulkmodulus[i][j];
shearmodulus[j][i] = shearmodulus[i][j];
s00[j][i] = s00[i][j];
alpha[j][i] = alpha[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairPeriLPS::init_style()
{
// error checks
if (atom->map_style == 0)
error->all("Pair peri requires an atom map, see atom_modify");
if (atom->style_match("peri") == 0)
error->all("Pair style peri_lps requires atom style peri");
if (domain->lattice == NULL)
error->all("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("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("Fix peri neigh does not exist");
int irequest = neighbor->request(this);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairPeriLPS::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);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairPeriLPS::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);
}
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);
}
}
}
/* ---------------------------------------------------------------------- */
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];
if (domain->nonperiodic == 0) 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 the short-range force constant of the bond-based theory in 3-D !
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->sfree(theta);
nmax = atom->nmax;
theta = (double *) memory->smalloc(nmax*sizeof(double),"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
------------------------------------------------------------------------- */
double PairPeriLPS::memory_usage()
{
double bytes = 2 * nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
Influence function definition
------------------------------------------------------------------------- */
double PairPeriLPS::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("pair_peri_lps - influence_function: Divide by 0");
omega = 1.0/r;
return omega;
}
/* ---------------------------------------------------------------------- */
void PairPeriLPS::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 nonperiodic = domain->nonperiodic;
// compute the dilatation theta
// loop over my particles
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];
// loop over partners of particle 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 (nonperiodic == 0) 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 (nonperiodic == 0) 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 = sqrt(cutsq[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;
} // end loop over all neighbors jj
// If wvolume[i] is zero, then particle i has no bonds. Therefore, the dilatation is set to 0.
if (wvolume[i] != 0.0) theta[i] = (3.0/wvolume[i]) * theta[i];
else theta[i] = 0;
} // end loop over all particles i
}
/* ----------------------------------------------------------------------
communication routines
---------------------------------------------------------------------- */
int PairPeriLPS::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 PairPeriLPS::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++];
}
}

65
src/PERI/pair_peri_lps.h Normal file
View File

@ -0,0 +1,65 @@
/* ----------------------------------------------------------------------
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/lps,PairPeriLPS)
#else
#ifndef LMP_PAIR_PERI_LPS_H
#define LMP_PAIR_PERI_LPS_H
#include "pair.h"
namespace LAMMPS_NS {
class PairPeriLPS : public Pair {
public:
PairPeriLPS(class LAMMPS *);
~PairPeriLPS();
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
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 single(int, int, int, int, double, double, double, double &);
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;
double *s0_new;
double *theta;
int nmax;
void allocate();
};
}
#endif
#endif

2
src/PERI/pair_peri_pmb.cpp
View File

@ -31,6 +31,7 @@
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
@ -399,6 +400,7 @@ void PairPeriPMB::init_style()
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("Fix peri neigh does not exist");
int irequest = neighbor->request(this);
}