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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11463 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-02-04 01:16:32 +00:00
parent 45bcc86602
commit fc5f92579d
13 changed files with 1352 additions and 26 deletions
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15
src/PERI/compute_damage_atom.cpp
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@ -100,23 +100,22 @@ void ComputeDamageAtom::compute_peratom()
if (mask[i] & groupbit) {
jnum = npartner[i];
damage_temp = 0.0;
for (jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
// look up local index of this partner particle
// skip if particle is "lost"
j = atom->map(partner[i][jj]);
if (j < 0) continue;
damage_temp += vfrac[j];
}
}
else damage_temp = vinter[i];
if (vinter[i] != 0.0) damage[i] = 1.0 - damage_temp/vinter[i];
else damage[i] = 0.0;
if (vinter[i] != 0.0) damage[i] = 1.0 - damage_temp/vinter[i];
else damage[i] = 0.0;
} else damage[i] = 0.0;
}
}

127
src/PERI/compute_dilatation_atom.cpp Normal file
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@ -0,0 +1,127 @@
/* ----------------------------------------------------------------------
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: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_dilatation_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "comm.h"
#include "force.h"
#include "pair.h"
#include "pair_peri_lps.h"
#include "pair_peri_pmb.h"
#include "pair_peri_ves.h"
#include "pair_peri_eps.h"
#include "fix_peri_neigh.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeDilatationAtom::
ComputeDilatationAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute Dilatation/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
nmax = 0;
dilatation = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeDilatationAtom::~ComputeDilatationAtom()
{
memory->destroy(dilatation);
}
/* ---------------------------------------------------------------------- */
void ComputeDilatationAtom::init()
{
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"dilatation/peri") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute dilatation/atom");
// check PD pair style
isPMB = isLPS = isVES = isEPS = 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;
if (force->pair_match("peri/eps",1)) isEPS = 1;
if (isPMB)
error->all(FLERR,"Compute dilatation/atom cannot be used "
"with this pair style");
// find associated PERI_NEIGH fix that must exist
int ifix_peri = -1;
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,"Compute dilatation/atom requires Peridynamic pair style");
}
/* ---------------------------------------------------------------------- */
void ComputeDilatationAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow dilatation array if necessary
if (atom->nlocal > nmax) {
memory->destroy(dilatation);
nmax = atom->nmax;
memory->create(dilatation,nmax,"dilatation/atom:dilatation");
vector_atom = dilatation;
}
// extract dilatation for each atom in group
double *theta;
Pair *anypair = force->pair_match("peri",0);
if (isLPS) theta = ((PairPeriLPS *) anypair)->theta;
if (isVES) theta = ((PairPeriVES *) anypair)->theta;
if (isEPS) theta = ((PairPeriEPS *) anypair)->theta;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) dilatation[i] = theta[i];
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeDilatationAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}

48
src/PERI/compute_dilatation_atom.h Normal file
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@ -0,0 +1,48 @@
/* ----------------------------------------------------------------------
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 COMPUTE_CLASS
ComputeStyle(dilatation/atom,ComputeDilatationAtom)
#else
#ifndef LMP_COMPUTE_DILATATION_ATOM_H
#define LMP_COMPUTE_DILATATION_ATOM_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeDilatationAtom : public Compute {
friend class PairPeriPMB;
friend class PairPeriLPS;
friend class PairPeriVES;
friend class PairPeriEPS;
public:
ComputeDilatationAtom(class LAMMPS *, int, char **);
~ComputeDilatationAtom();
void init();
void compute_peratom();
double memory_usage();
private:
int nmax;
double *dilatation;
int isPMB,isLPS,isVES,isEPS;
};
}
#endif
#endif

111
src/PERI/compute_plasticity_atom.cpp Normal file
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@ -0,0 +1,111 @@
/* ----------------------------------------------------------------------
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: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_plasticity_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "comm.h"
#include "force.h"
#include "pair_peri_pmb.h"
#include "fix_peri_neigh.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputePlasticityAtom::
ComputePlasticityAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute plasticity/atom command");
if (!force->pair_match("peri/eps",1))
error->all(FLERR,"Compute plasticity/atom cannot be used "
"with this pair style");
peratom_flag = 1;
size_peratom_cols = 0;
nmax = 0;
plasticity = NULL;
}
/* ---------------------------------------------------------------------- */
ComputePlasticityAtom::~ComputePlasticityAtom()
{
memory->destroy(plasticity);
}
/* ---------------------------------------------------------------------- */
void ComputePlasticityAtom::init()
{
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"plasticity/peri") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute plasticity/atom");
// find associated PERI_NEIGH fix that must exist
ifix_peri = -1;
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,"Compute plasticity/atom requires Peridynamic pair style");
}
/* ---------------------------------------------------------------------- */
void ComputePlasticityAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow damage array if necessary
if (atom->nlocal > nmax) {
memory->destroy(plasticity);
nmax = atom->nmax;
memory->create(plasticity,nmax,"plasticity/atom:plasticity");
vector_atom = plasticity;
}
// extract plasticity for each atom in group
double *lambdaValue = ((FixPeriNeigh *) modify->fix[ifix_peri])->lambdaValue;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) plasticity[i] = lambdaValue[i];
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputePlasticityAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}

44
src/PERI/compute_plasticity_atom.h Normal file
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@ -0,0 +1,44 @@
/* ----------------------------------------------------------------------
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 COMPUTE_CLASS
ComputeStyle(plasticity/atom,ComputePlasticityAtom)
#else
#ifndef LMP_COMPUTE_PLASTICITY_ATOM_H
#define LMP_COMPUTE_PLASTICITY_ATOM_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputePlasticityAtom : public Compute {
public:
ComputePlasticityAtom(class LAMMPS *, int, char **);
~ComputePlasticityAtom();
void init();
void compute_peratom();
double memory_usage();
private:
int nmax;
double *plasticity;
int ifix_peri;
};
}
#endif
#endif

48
src/PERI/fix_peri_neigh.cpp
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@ -20,6 +20,7 @@
#include "pair_peri_pmb.h"
#include "pair_peri_lps.h"
#include "pair_peri_ves.h"
#include "pair_peri_eps.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
@ -41,10 +42,11 @@ using namespace FixConst;
FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
Fix(lmp, narg, arg)
{
isPMB = isLPS = isVES = 0;
isPMB = isLPS = isVES = isEPS = 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;
if (force->pair_match("peri/eps",1)) isEPS = 1;
restart_global = 1;
restart_peratom = 1;
@ -59,6 +61,8 @@ FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
partner = NULL;
deviatorextention = NULL;
deviatorBackextention = NULL;
deviatorPlasticextension = NULL;
lambdaValue = NULL;
r0 = NULL;
vinter = NULL;
wvolume = NULL;
@ -92,6 +96,8 @@ FixPeriNeigh::~FixPeriNeigh()
memory->destroy(partner);
memory->destroy(deviatorextention);
memory->destroy(deviatorBackextention);
memory->destroy(deviatorPlasticextension);
memory->destroy(lambdaValue);
memory->destroy(r0);
memory->destroy(vinter);
memory->destroy(wvolume);
@ -218,6 +224,8 @@ void FixPeriNeigh::setup(int vflag)
memory->destroy(partner);
memory->destroy(deviatorextention);
memory->destroy(deviatorBackextention);
memory->destroy(deviatorPlasticextension);
memory->destroy(lambdaValue);
memory->destroy(r0);
memory->destroy(npartner);
@ -225,6 +233,8 @@ void FixPeriNeigh::setup(int vflag)
partner = NULL;
deviatorextention = NULL;
deviatorBackextention = NULL;
deviatorPlasticextension = NULL;
lambdaValue = NULL;
r0 = NULL;
grow_arrays(atom->nmax);
@ -235,6 +245,7 @@ void FixPeriNeigh::setup(int vflag)
npartner[i] = 0;
vinter[i] = 0.0;
wvolume[i] = 0.0;
if (isEPS) lambdaValue[i] = 0.0;
}
for (ii = 0; ii < inum; ii++) {
@ -261,6 +272,8 @@ void FixPeriNeigh::setup(int vflag)
if (isVES)
deviatorextention[i][npartner[i]] =
deviatorBackextention[i][npartner[i]] = 0.0;
if (isEPS)
deviatorPlasticextension[i][npartner[i]] = 0.0;
r0[i][npartner[i]] = sqrt(rsq);
npartner[i]++;
vinter[i] += vfrac[j];
@ -292,6 +305,7 @@ void FixPeriNeigh::setup(int vflag)
PairPeriLPS *pairlps = static_cast<PairPeriLPS*>(anypair);
PairPeriPMB *pairpmb = static_cast<PairPeriPMB*>(anypair);
PairPeriVES *pairves = static_cast<PairPeriVES*>(anypair);
PairPeriEPS *paireps = static_cast<PairPeriEPS*>(anypair);
for (i = 0; i < nlocal; i++) {
double xtmp0 = x0[i][0];
@ -319,6 +333,7 @@ void FixPeriNeigh::setup(int vflag)
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];
@ -332,7 +347,6 @@ void FixPeriNeigh::setup(int vflag)
else vfrac_scale = 1.0;
// for PMB, influence = 1.0, otherwise invoke influence function
if (isPMB)
wvolume[i] += 1.0 * rsq0 * vfrac[j] * vfrac_scale;
else if (isLPS)
@ -341,6 +355,9 @@ void FixPeriNeigh::setup(int vflag)
else if (isVES)
wvolume[i] += pairves->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
else if (isEPS)
wvolume[i] += paireps->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
}
}
@ -377,12 +394,16 @@ double FixPeriNeigh::memory_usage()
{
int nmax = atom->nmax;
int bytes = nmax * sizeof(int);
bytes += nmax*maxpartner * sizeof(int);
bytes += nmax*maxpartner * sizeof(tagint);
bytes += nmax*maxpartner * sizeof(double);
if (isVES) {
bytes += nmax*maxpartner * sizeof(double);
bytes += nmax*maxpartner * sizeof(double);
}
if (isEPS) {
bytes += nmax*maxpartner * sizeof(double);
bytes += nmax * sizeof(double);
}
bytes += nmax * sizeof(double);
bytes += nmax * sizeof(double);
return bytes;
@ -402,7 +423,10 @@ void FixPeriNeigh::grow_arrays(int nmax)
memory->grow(deviatorBackextention,nmax,maxpartner,
"peri_neigh:deviatorBackextention");
}
if (isEPS) memory->grow(deviatorPlasticextension,nmax,maxpartner,
"peri_neigh:deviatorPlasticextension");
memory->grow(r0,nmax,maxpartner,"peri_neigh:r0");
if (isEPS) memory->grow(lambdaValue,nmax,"peri_neigh:lambdaValue");
memory->grow(vinter,nmax,"peri_neigh:vinter");
memory->grow(wvolume,nmax,"peri_neigh:wvolume");
}
@ -420,8 +444,11 @@ void FixPeriNeigh::copy_arrays(int i, int j, int delflag)
deviatorextention[j][m] = deviatorextention[i][m];
deviatorBackextention[j][m] = deviatorBackextention[i][m];
}
if (isEPS)
deviatorPlasticextension[j][m] = deviatorPlasticextension[i][m];
r0[j][m] = r0[i][m];
}
if (isEPS) lambdaValue[j] = lambdaValue[i];
vinter[j] = vinter[i];
wvolume[j] = wvolume[i];
}
@ -443,10 +470,13 @@ int FixPeriNeigh::pack_exchange(int i, double *buf)
buf[m++] = deviatorextention[i][n];
buf[m++] = deviatorBackextention[i][n];
}
if (isEPS) buf[m++] = deviatorPlasticextension[i][n];
buf[m++] = r0[i][n];
}
if (isVES) buf[0] = m/4;
else buf[0] = m/2;
else if (isEPS) buf[0] = m/3;
else buf[0] = m/2;
if (isEPS) buf[m++] = lambdaValue[i];
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
return m;
@ -466,8 +496,10 @@ int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
deviatorextention[nlocal][n] = buf[m++];
deviatorBackextention[nlocal][n] = buf[m++];
}
if (isEPS) deviatorPlasticextension[nlocal][n] = buf[m++];
r0[nlocal][n] = buf[m++];
}
if (isEPS) lambdaValue[nlocal] = buf[m++];
vinter[nlocal] = buf[m++];
wvolume[nlocal] = buf[m++];
return m;
@ -543,8 +575,8 @@ int FixPeriNeigh::pack_restart(int i, double *buf)
{
int m = 0;
if (isVES) buf[m++] = 4*npartner[i] + 4;
else if (isEPS) buf[m++] = 3*npartner[i] + 5;
else buf[m++] = 2*npartner[i] + 4;
buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) {
buf[m++] = partner[i][n];
@ -552,8 +584,10 @@ int FixPeriNeigh::pack_restart(int i, double *buf)
buf[m++] = deviatorextention[i][n];
buf[m++] = deviatorBackextention[i][n];
}
if (isEPS) buf[m++] = deviatorPlasticextension[i][n];
buf[m++] = r0[i][n];
}
if (isEPS) buf[m++] = lambdaValue[i];
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
return m;
@ -581,8 +615,10 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)
deviatorextention[nlocal][n] = extra[nlocal][m++];
deviatorBackextention[nlocal][n] = extra[nlocal][m++];
}
if (isEPS) deviatorPlasticextension[nlocal][n] = extra[nlocal][m++];
r0[nlocal][n] = extra[nlocal][m++];
}
if (isEPS) lambdaValue[nlocal] = extra[nlocal][m++];
vinter[nlocal] = extra[nlocal][m++];
wvolume[nlocal] = extra[nlocal][m++];
}
@ -594,6 +630,7 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)
int FixPeriNeigh::maxsize_restart()
{
if (isVES) return 4*maxpartner + 4;
if (isEPS) return 3*maxpartner + 5;
return 2*maxpartner + 4;
}
@ -604,5 +641,6 @@ int FixPeriNeigh::maxsize_restart()
int FixPeriNeigh::size_restart(int nlocal)
{
if (isVES) return 4*npartner[nlocal] + 4;
if (isEPS) return 3*npartner[nlocal] + 5;
return 2*npartner[nlocal] + 4;
}

14
src/PERI/fix_peri_neigh.h
View File

@ -28,9 +28,11 @@ class FixPeriNeigh : public Fix {
friend class PairPeriPMB;
friend class PairPeriPMBOMP;
friend class PairPeriLPS;
friend class PairPeriVES; //NEW
friend class PairPeriVES;
friend class PairPeriEPS;
friend class PairPeriLPSOMP;
friend class ComputeDamageAtom;
friend class ComputePlasticityAtom;
public:
FixPeriNeigh(class LAMMPS *,int, char **);
@ -63,14 +65,14 @@ class FixPeriNeigh : public Fix {
tagint **partner; // neighs for each atom, stored as global IDs
double **deviatorextention; // Deviatoric extention
double **deviatorBackextention; // Deviatoric back extention
double **deviatorPlasticextension; // Deviatoric plastic extension
double *lambdaValue;
double **r0; // initial distance to partners
double **r1; // Instanteneous distance to partners *** NEW ***
double *thetaOld; // Dilatation Old one
double **r1; // instanteneous distance to partners
double *thetaValue; // dilatation
double *vinter; // sum of vfrac for bonded neighbors
double *wvolume; // weighted volume of particle
int isPMB;
int isLPS;
int isVES;
int isPMB,isLPS,isVES,isEPS; // which flavor of PD
class NeighList *list;
};

843
src/PERI/pair_peri_eps.cpp Normal file
View File

@ -0,0 +1,843 @@
/* ----------------------------------------------------------------------
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: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "pair_peri_eps.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;
/* ---------------------------------------------------------------------- */
PairPeriEPS::PairPeriEPS(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_yieldstress = NULL;
// set comm size needed by this Pair
// comm_reverse not needed
comm_forward = 1;
}
/* ---------------------------------------------------------------------- */
PairPeriEPS::~PairPeriEPS()
{
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_yieldstress);
memory->destroy(theta);
memory->destroy(s0_new);
}
}
/* ---------------------------------------------------------------------- */
void PairPeriEPS::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,rkNew,evdwl,fpair,fbond;
double ed,fbondElastoPlastic,fbondFinal;
double deltalambda,edpNp1;
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 **deviatorPlasticextension =
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorPlasticextension;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
double *lambdaValue = ((FixPeriNeigh *) modify->fix[ifix_peri])->lambdaValue;
// 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
int maxpartner = 0;
for (i = 0; i < nlocal; i++) maxpartner = MAX(maxpartner,npartner[i]);
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");
}
// ******** temp array to store Plastic extension *********** ///
double deviatorPlasticExtTemp[nlocal][maxpartner];
for (int ii = 0; ii < nlocal; ii++) {
for (int kk = 0; kk < maxpartner; kk++) {
deviatorPlasticExtTemp[ii][kk] = 0.0;
}
}
// ******** temp array to store Plastic extension *********** ///
// 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, omega;
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;
double yieldStress = m_yieldstress[itype][itype];
double horizon = cut[itype][itype];
double tdnorm = compute_DeviatoricForceStateNorm(i);
double pointwiseYieldvalue = 25.0 * yieldStress *
yieldStress / 8 / M_PI / pow(horizon,5);
double fsurf = (tdnorm * tdnorm)/2 - pointwiseYieldvalue;
bool elastic = true;
double alphavalue = (15 * shearmodulus[itype][itype]) /wvolume[i];
if (fsurf>0) {
elastic = false;
deltalambda = ((tdnorm /sqrt(2.0 * pointwiseYieldvalue)) - 1.0) / alphavalue;
double templambda = lambdaValue[i];
lambdaValue[i] = templambda + deltalambda;
}
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);
//Elastic Part
rk = ((3.0 * bulkmodulus[itype][itype]) * ( (omega_plus * theta[i] / wvolume[i]) +
( omega_minus * theta[j] / wvolume[j] ) ) ) * r0[i][jj];
if (r > 0.0) fbond = -((rk/r) * vfrac[j] * vfrac_scale);
else fbond = 0.0;
//Plastic part
double deviatoric_extension = dr - (theta[i]* r0[i][jj] / 3.0);
edpNp1 = deviatorPlasticextension[i][jj];
double tdtrialValue = ( 15 * shearmodulus[itype][itype]) *
( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
(deviatoric_extension - edpNp1);
if(elastic) {
rkNew = tdtrialValue;
}
else {
rkNew = (sqrt(2.0*pointwiseYieldvalue) * tdtrialValue) / tdnorm;
deviatorPlasticExtTemp[i][jj] = edpNp1 + rkNew * deltalambda;
}
if (r > 0.0) fbondElastoPlastic = -((rkNew/r) * vfrac[j] * vfrac_scale);
else fbondElastoPlastic = 0.0;
// total Force state: elastic + plastic
fbondFinal=fbond+fbondElastoPlastic;
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 - edpNp1) *
(deviatoric_extension-edpNp1)) * 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
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];
for (i = 0; i < nlocal; i++) {
jnum = npartner[i];
for (jj = 0; jj < jnum; jj++) {
double temp_data = deviatorPlasticExtTemp[i][jj];
deviatorPlasticextension[i][jj] = temp_data;
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairPeriEPS::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_yieldstress,n+1,n+1,"pair:m_yieldstress");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairPeriEPS::settings(int narg, char **arg)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairPeriEPS::coeff(int narg, char **arg)
{
if (narg != 8) 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 myieldstress_one = atof(arg[7]);
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_yieldstress[i][j] = myieldstress_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 PairPeriEPS::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_yieldstress[j][i] = m_yieldstress[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairPeriEPS::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 PairPeriEPS::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_yieldstress[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairPeriEPS::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_yieldstress[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_yieldstress[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairPeriEPS::memory_usage()
{
double bytes = 2 * nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
influence function definition
------------------------------------------------------------------------- */
double PairPeriEPS::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");
omega = 1.0/r;
return omega;
}
/* ---------------------------------------------------------------------- */
void PairPeriEPS::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;
tagint **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;
}
}
/* ---------------------------------------------------------------------- */
double PairPeriEPS::compute_DeviatoricForceStateNorm(int i)
{
int 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 tdtrial;
double norm = 0.0;
double **x = atom->x;
int *type = atom->type;
double **x0 = atom->x0;
double *s0 = atom->s0;
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;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
double **deviatorPlasticextension =
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorPlasticextension;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
// compute the dilatation theta
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];
itype = type[i];
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;
}
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;
// scale vfrac[j] if particle j near the horizon
double vfrac_scale;
jtype = type[j];
double 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;
double ed = dr - (theta[i] * r0[i][jj])/3;
double edPNP1 = deviatorPlasticextension[i][jj];
jtype = type[j];
delta = cut[itype][jtype];
double omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
double omega_minus = influence_function(delx0,dely0,delz0);
double stretch = dr / r0[i][jj];
tdtrial = ( 15 * shearmodulus[itype][itype]) *
((omega_plus * theta[i] / wvolume[i]) +
( omega_minus * theta[j] / wvolume[j] ) ) * (ed - edPNP1);
norm += tdtrial * tdtrial * vfrac[j] * vfrac_scale;
}
return sqrt(norm);
}
/* ----------------------------------------------------------------------
communication routines
---------------------------------------------------------------------- */
int PairPeriEPS::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 PairPeriEPS::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++];
}
}

111
src/PERI/pair_peri_eps.h Normal file
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@ -0,0 +1,111 @@
/* ----------------------------------------------------------------------
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/eps,PairPeriEPS)
#else
#ifndef LMP_PAIR_PERI_EPS_H
#define LMP_PAIR_PERI_EPS_H
#include "pair.h"
namespace LAMMPS_NS {
class PairPeriEPS : public Pair {
public:
double *theta;
PairPeriEPS(class LAMMPS *);
virtual ~PairPeriEPS();
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();
double compute_DeviatoricForceStateNorm(int);
protected:
int ifix_peri;
double **bulkmodulus;
double **shearmodulus;
double **s00, **alpha;
double **cut, **m_yieldstress; //NEW: **m_yieldstress
double *s0_new;
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.
*/

3
src/PERI/pair_peri_lps.cpp
View File

@ -620,12 +620,11 @@ void PairPeriLPS::compute_dilatation()
/* ----------------------------------------------------------------------
communication routines
---------------------------------------------------------------------- */
---------------------------------------------------------------------- */
int PairPeriLPS::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;

5
src/PERI/pair_peri_lps.h
View File

@ -26,6 +26,8 @@ namespace LAMMPS_NS {
class PairPeriLPS : public Pair {
public:
double *theta;
PairPeriLPS(class LAMMPS *);
virtual ~PairPeriLPS();
int pack_comm(int, int *, double *, int, int *);
@ -48,11 +50,10 @@ class PairPeriLPS : public Pair {
int ifix_peri;
double **bulkmodulus;
double **shearmodulus;
double **s00, **alpha;
double **s00,**alpha;
double **cut;
double *s0_new;
double *theta;
int nmax;
void allocate();

2
src/PERI/pair_peri_ves.cpp
View File

@ -260,7 +260,7 @@ void PairPeriVES::compute(int eflag, int vflag)
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]);

7
src/PERI/pair_peri_ves.h
View File

@ -26,6 +26,8 @@ namespace LAMMPS_NS {
class PairPeriVES : public Pair {
public:
double *theta;
PairPeriVES(class LAMMPS *);
virtual ~PairPeriVES();
int pack_comm(int, int *, double *, int, int *);
@ -49,10 +51,11 @@ class PairPeriVES : public Pair {
double **bulkmodulus;
double **shearmodulus;
double **s00, **alpha;
double **cut, **m_lambdai, **m_taubi; //NEW: **m_lambdai,**m_taubi
double **cut;
double **m_lambdai;
double **m_taubi;
double *s0_new;
double *theta;
int nmax;
void allocate();