jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1192 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-11-30 21:49:20 +00:00
parent 5d0e722080
commit d9df67ded2
9 changed files with 17 additions and 1558 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
src/GRANULAR/Install.csh
View File

@ -6,7 +6,6 @@ if ($1 == 1) then
cp atom_vec_granular.cpp ..
cp fix_freeze.cpp ..
cp fix_gran_diag.cpp ..
cp fix_nve_gran.cpp ..
cp fix_pour.cpp ..
cp fix_wall_gran.cpp ..
@ -16,7 +15,6 @@ if ($1 == 1) then
cp atom_vec_granular.h ..
cp fix_freeze.h ..
cp fix_gran_diag.h ..
cp fix_nve_gran.h ..
cp fix_pour.h ..
cp fix_wall_gran.h ..
@ -31,7 +29,6 @@ else if ($1 == 0) then
rm ../atom_vec_granular.cpp
rm ../fix_freeze.cpp
rm ../fix_gran_diag.cpp
rm ../fix_nve_gran.cpp
rm ../fix_pour.cpp
rm ../fix_wall_gran.cpp
@ -41,7 +38,6 @@ else if ($1 == 0) then
rm ../atom_vec_granular.h
rm ../fix_freeze.h
rm ../fix_gran_diag.h
rm ../fix_nve_gran.h
rm ../fix_pour.h
rm ../fix_wall_gran.h

1009
src/GRANULAR/fix_gran_diag.cpp
View File

File diff suppressed because it is too large Load Diff

60
src/GRANULAR/fix_gran_diag.h
View File

@ -1,60 +0,0 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifndef FIX_GRAN_DIAG_H
#define FIX_GRAN_DIAG_H
#include "stdio.h"
#include "fix.h"
namespace LAMMPS_NS {
class FixGranDiag : public Fix {
public:
FixGranDiag(class LAMMPS *, int, char **);
~FixGranDiag();
int setmask();
void init();
void setup();
void end_of_step();
private:
int me,first,pairstyle,nlayers,maxlayers,dim;
FILE *fpden,*fpvel,*fpstr;
double step,stepinv,boxlo,PI;
double dt,xkk,xkkt,xmu,gamman_dl,gammas_dl;
int freeze_group_bit;
int *numdens;
double *dendens;
double *velx,*vely,*velz;
double *velxx,*velyy,*velzz,*velxy,*velxz,*velyz;
double *sigxx,*sigyy,*sigzz,*sigxy,*sigxz,*sigyz;
double *velx11,*vely11,*velz11;
double *velxx11,*velyy11,*velzz11,*velxy11,*velxz11,*velyz11;
double *velfxx,*velfyy,*velfzz,*velfxy,*velfxz,*velfyz;
double *sigx2,*sigy2,*sigz2,*sigxy2,*sigxz2,*sigyz2;
class Pair *pair;
class NeighList *list,*listgran;
void allocate();
void deallocate();
void stress_no_history();
void stress_history();
void stress_hertzian();
};
}
#endif

2
src/GRANULAR/style_granular.h
View File

@ -21,7 +21,6 @@ AtomStyle(granular,AtomVecGranular)
#ifdef FixInclude
#include "fix_freeze.h"
#include "fix_gran_diag.h"
#include "fix_nve_gran.h"
#include "fix_pour.h"
#include "fix_shear_history.h"
@ -30,7 +29,6 @@ AtomStyle(granular,AtomVecGranular)
#ifdef FixClass
FixStyle(freeze,FixFreeze)
FixStyle(gran/diag,FixGranDiag)
FixStyle(nve/gran,FixNVEGran)
FixStyle(pour,FixPour)
FixStyle(SHEAR_HISTORY,FixShearHistory)

25
src/MEAM/pair_meam.cpp
View File

@ -122,6 +122,15 @@ void PairMEAM::compute(int eflag, int vflag)
int *ilist_half,*jlist_half,*numneigh_half,**firstneigh_half;
int *numneigh_full,**firstneigh_full;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
// error check (for now)
if (eflag_atom || vflag_atom)
error->all("Pair style meam does not yet support peratom energy/virial");
// grow local arrays if necessary
if (atom->nmax > nmax) {
@ -176,7 +185,7 @@ void PairMEAM::compute(int eflag, int vflag)
// check size of scrfcn based on half neighbor list
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int nall = nlocal + atom->nghost;
n = 0;
for (ii = 0; ii < inum_half; ii++) n += numneigh_half[ilist_half[ii]];
@ -194,9 +203,6 @@ void PairMEAM::compute(int eflag, int vflag)
(double *) memory->smalloc(maxneigh*sizeof(double),"pair:fcpair");
}
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
// zero out local arrays
for (i = 0; i < nall; i++) {
@ -229,7 +235,7 @@ void PairMEAM::compute(int eflag, int vflag)
for (ii = 0; ii < inum_half; ii++) {
i = ilist_half[ii];
ifort = i+1;
meam_dens_init_(&ifort,&nmax,&eflag,&eng_vdwl,&ntype,type,fmap,&x[0][0],
meam_dens_init_(&ifort,&nmax,&eflag,&evdwl,&ntype,type,fmap,&x[0][0],
&numneigh_half[i],firstneigh_half[i],
&numneigh_full[i],firstneigh_full[i],
&scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
@ -246,7 +252,7 @@ void PairMEAM::compute(int eflag, int vflag)
reverse_flag = 0;
comm->reverse_comm_pair(this);
meam_dens_final_(&nlocal,&nmax,&eflag,&eng_vdwl,&ntype,type,fmap,
meam_dens_final_(&nlocal,&nmax,&eflag,&evdwl,&ntype,type,fmap,
&arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],
&arho3b[0][0],&t_ave[0][0],gamma,dgamma1,
dgamma2,dgamma3,rho,rho0,rho1,rho2,rho3,frhop,&errorflag);
@ -263,7 +269,7 @@ void PairMEAM::compute(int eflag, int vflag)
for (ii = 0; ii < inum_half; ii++) {
i = ilist_half[ii];
ifort = i+1;
meam_force_(&ifort,&nmax,&eflag,&eng_vdwl,&ntype,type,fmap,&x[0][0],
meam_force_(&ifort,&nmax,&eflag,&evdwl,&ntype,type,fmap,&x[0][0],
&numneigh_half[i],firstneigh_half[i],
&numneigh_full[i],firstneigh_full[i],
&scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
@ -286,7 +292,10 @@ void PairMEAM::compute(int eflag, int vflag)
neigh_f2c(inum_half,ilist_half,numneigh_half,firstneigh_half);
neigh_f2c(inum_half,ilist_half,numneigh_full,firstneigh_full);
if (vflag == 2) virial_compute();
// just sum global energy (for now)
if (evflag) ev_tally(0,0,nlocal,newton_pair,evdwl,0.0,0.0,0.0,0.0);
if (vflag_fdotr) virial_compute();
}
/* ---------------------------------------------------------------------- */

166
src/compute_ebond_atom.cpp
View File

@ -1,166 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_ebond_atom.h"
#include "atom.h"
#include "neighbor.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "bond.h"
#include "modify.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
ComputeEbondAtom::ComputeEbondAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal compute ebond/atom command");
peratom_flag = 1;
size_peratom = 0;
comm_reverse = 1;
nmax = 0;
energy = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeEbondAtom::~ComputeEbondAtom()
{
memory->sfree(energy);
}
/* ---------------------------------------------------------------------- */
void ComputeEbondAtom::init()
{
if (force->bond == NULL)
error->all("Bond style does not support computing per-atom bond energy");
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"ebond/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning("More than one compute ebond/atom");
}
/* ---------------------------------------------------------------------- */
void ComputeEbondAtom::compute_peratom()
{
int i,n,i1,i2,type,iflag,jflag;
double delx,dely,delz,rsq,fforce,eng;
// grow energy array if necessary
if (atom->nmax > nmax) {
memory->sfree(energy);
nmax = atom->nmax;
energy = (double *)
memory->smalloc(nmax*sizeof(double),"compute/epair/atom:energy");
scalar_atom = energy;
}
// clear energy array
// n includes ghosts only if newton_bond flag is set
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
if (newton_bond) n = nlocal + atom->nghost;
else n = nlocal;
for (i = 0; i < n; i++) energy[i] = 0.0;
// compute bond energy for atoms via bond->single()
// if neither atom is in compute group, skip that bond
// only add energy to atoms in group
double **x = atom->x;
int *mask = atom->mask;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
iflag = mask[i1] & groupbit;
jflag = mask[i2] & groupbit;
if (iflag == 0 && jflag == 0) continue;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
force->bond->single(type,rsq,i1,i2,1,fforce,eng);
if (iflag) energy[i1] += eng;
if (jflag && (newton_bond || i2 < nlocal)) energy[i2] += eng;
}
// communicate energy between neigchbor procs
if (newton_bond) comm->reverse_comm_compute(this);
// remove double counting of per-atom energy
for (i = 0; i < nlocal; i++) energy[i] *= 0.5;
}
/* ---------------------------------------------------------------------- */
int ComputeEbondAtom::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) buf[m++] = energy[i];
return 1;
}
/* ---------------------------------------------------------------------- */
void ComputeEbondAtom::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
energy[j] += buf[m++];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeEbondAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}

38
src/compute_ebond_atom.h
View File

@ -1,38 +0,0 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifndef COMPUTE_EBOND_ATOM_H
#define COMPUTE_EBOND_ATOM_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeEbondAtom : public Compute {
public:
ComputeEbondAtom(class LAMMPS *, int, char **);
~ComputeEbondAtom();
void init();
void compute_peratom();
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
private:
int nmax;
double *energy;
};
}
#endif

231
src/compute_epair_atom.cpp
View File

@ -1,231 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_epair_atom.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "modify.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
ComputeEpairAtom::ComputeEpairAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal compute epair/atom command");
peratom_flag = 1;
size_peratom = 0;
comm_reverse = 1;
nmax = 0;
energy = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeEpairAtom::~ComputeEpairAtom()
{
memory->sfree(energy);
}
/* ---------------------------------------------------------------------- */
void ComputeEpairAtom::init()
{
if (force->pair == NULL || force->pair->single_enable == 0)
error->all("Pair style does not support computing per-atom energy");
// need an occasional half neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
if (force->pair_match("eam")) eamstyle = 1;
else eamstyle = 0;
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"epair/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning("More than one compute epair/atom");
}
/* ---------------------------------------------------------------------- */
void ComputeEpairAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeEpairAtom::compute_peratom()
{
int i,j,ii,jj,n,inum,jnum,itype,jtype,iflag,jflag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double factor_coul,factor_lj,eng;
int *ilist,*jlist,*numneigh,**firstneigh;
Pair::One one;
// grow energy array if necessary
if (atom->nmax > nmax) {
memory->sfree(energy);
nmax = atom->nmax;
energy = (double *)
memory->smalloc(nmax*sizeof(double),"compute/epair/atom:energy");
scalar_atom = energy;
}
// clear energy array
// n includes ghosts only if newton_pair flag is set
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
if (newton_pair) n = nlocal + atom->nghost;
else n = nlocal;
for (i = 0; i < n; i++) energy[i] = 0.0;
// invoke half neighbor list (will copy or build if necessary)
neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// compute pairwise energy for atoms via pair->single()
// if neither atom is in compute group, skip that pair
// only add energy to atoms in group
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double **cutsq = force->pair->cutsq;
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int nall = nlocal + atom->nghost;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
iflag = mask[i] & groupbit;
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
jflag = mask[j] & groupbit;
if (iflag == 0 && jflag == 0) continue;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,1,one);
eng = one.eng_coul + one.eng_vdwl;
if (iflag) energy[i] += eng;
if (jflag && (newton_pair || j < nlocal)) energy[j] += eng;
}
}
}
// communicate energy between neigchbor procs
if (newton_pair) comm->reverse_comm_compute(this);
// remove double counting of per-atom energy
for (i = 0; i < nlocal; i++) energy[i] *= 0.5;
// for EAM, include embedding function contribution to energy
// only for atoms in compute group
if (eamstyle) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
force->pair->single_embed(i,type[i],eng);
energy[i] += eng;
}
}
}
}
/* ---------------------------------------------------------------------- */
int ComputeEpairAtom::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) buf[m++] = energy[i];
return 1;
}
/* ---------------------------------------------------------------------- */
void ComputeEpairAtom::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
energy[j] += buf[m++];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeEpairAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}

40
src/compute_epair_atom.h
View File

@ -1,40 +0,0 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifndef COMPUTE_EPAIR_ATOM_H
#define COMPUTE_EPAIR_ATOM_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeEpairAtom : public Compute {
public:
ComputeEpairAtom(class LAMMPS *, int, char **);
~ComputeEpairAtom();
void init();
void init_list(int, class NeighList *);
void compute_peratom();
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
private:
int nmax,eamstyle;
class NeighList *list;
double *energy;
};
}
#endif