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fix_srp.cpp
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Mon, Nov 11, 03:21

fix_srp.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF)
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include "fix_srp.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "neighbor.h"
#include "atom_vec.h"
#include "modify.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixSRP::FixSRP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
// settings
nevery=1;
peratom_freq = 1;
time_integrate = 0;
create_attribute = 0;
comm_border = 2;
// restart settings
restart_global = 1;
restart_peratom = 1;
restart_pbc = 1;
// per-atom array width 2
peratom_flag = 1;
size_peratom_cols = 2;
// initial allocation of atom-based array
// register with Atom class
array = NULL;
grow_arrays(atom->nmax);
// extends pack_exchange()
atom->add_callback(0);
atom->add_callback(1); // restart
atom->add_callback(2);
// initialize to illegal values so we capture
btype = -1;
bptype = -1;
// zero
for (int i = 0; i < atom->nmax; i++)
for (int m = 0; m < 3; m++)
array[i][m] = 0.0;
}
/* ---------------------------------------------------------------------- */
FixSRP::~FixSRP()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
atom->delete_callback(id,1);
atom->delete_callback(id,2);
memory->destroy(array);
}
/* ---------------------------------------------------------------------- */
int FixSRP::setmask()
{
int mask = 0;
mask |= PRE_FORCE;
mask |= PRE_EXCHANGE;
mask |= POST_RUN;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixSRP::init()
{
if (force->pair_match("hybrid",1) == NULL)
error->all(FLERR,"Cannot use pair srp without pair_style hybrid");
if ((bptype < 1) || (bptype > atom->ntypes))
error->all(FLERR,"Illegal bond particle type");
// fix SRP should be the first fix running at the PRE_EXCHANGE step.
// Otherwise it might conflict with, e.g. fix deform
if (modify->n_pre_exchange > 1) {
char *first = modify->fix[modify->list_pre_exchange[0]]->id;
if ((comm->me == 0) && (strcmp(id,first) != 0))
error->warning(FLERR,"Internal fix for pair srp defined too late."
" May lead to incorrect behavior.");
}
// setup neigh exclusions for diff atom types
// bond particles do not interact with other types
// type bptype only interacts with itself
char* arg1[4];
arg1[0] = (char *) "exclude";
arg1[1] = (char *) "type";
char c0[20];
char c1[20];
for(int z = 1; z < atom->ntypes; z++) {
if(z == bptype)
continue;
sprintf(c0, "%d", z);
arg1[2] = c0;
sprintf(c1, "%d", bptype);
arg1[3] = c1;
neighbor->modify_params(4, arg1);
}
}
/* ----------------------------------------------------------------------
insert bond particles
------------------------------------------------------------------------- */
void FixSRP::setup_pre_force(int zz)
{
double **x = atom->x;
double **xold;
tagint *tag = atom->tag;
tagint *tagold;
int *type = atom->type;
int* dlist;
AtomVec *avec = atom->avec;
int **bondlist = neighbor->bondlist;
int nlocal, nlocal_old;
nlocal = nlocal_old = atom->nlocal;
bigint nall = atom->nlocal + atom->nghost;
int nbondlist = neighbor->nbondlist;
int i,j,n;
// make a copy of all coordinates and tags
// that is consistent with the bond list as
// atom->x will be affected by creating/deleting atoms.
// also compile list of local atoms to be deleted.
memory->create(xold,nall,3,"fix_srp:xold");
memory->create(tagold,nall,"fix_srp:tagold");
memory->create(dlist,nall,"fix_srp:dlist");
for (i = 0; i < nall; i++){
xold[i][0] = x[i][0];
xold[i][1] = x[i][1];
xold[i][2] = x[i][2];
tagold[i]=tag[i];
dlist[i] = (type[i] == bptype) ? 1 : 0;
for (n = 0; n < 3; n++)
array[i][n] = 0.0;
}
// delete local atoms flagged in dlist
i = 0;
int ndel = 0;
while (i < nlocal) {
if (dlist[i]) {
avec->copy(nlocal-1,i,1);
dlist[i] = dlist[nlocal-1];
nlocal--;
ndel++;
} else i++;
}
atom->nlocal = nlocal;
memory->destroy(dlist);
int nadd = 0;
double rsqold = 0.0;
double delx, dely, delz, rmax, rsq, rsqmax;
double xone[3];
for (n = 0; n < nbondlist; n++) {
// consider only the user defined bond type
// btype of zero considers all bonds
if(btype > 0 && bondlist[n][2] != btype)
continue;
i = bondlist[n][0];
j = bondlist[n][1];
// position of bond i
xone[0] = (xold[i][0] + xold[j][0])*0.5;
xone[1] = (xold[i][1] + xold[j][1])*0.5;
xone[2] = (xold[i][2] + xold[j][2])*0.5;
// record longest bond
// this used to set ghost cutoff
delx = xold[j][0] - xold[i][0];
dely = xold[j][1] - xold[i][1];
delz = xold[j][2] - xold[i][2];
rsq = delx*delx + dely*dely + delz*delz;
if(rsq > rsqold) rsqold = rsq;
// make one particle for each bond
// i is local
// if newton bond, always make particle
// if j is local, always make particle
// if j is ghost, decide from tag
if ((force->newton_bond) || (j < nlocal_old) || (tagold[i] > tagold[j])) {
atom->natoms++;
avec->create_atom(bptype,xone);
// pack tag i/j into buffer for comm
array[atom->nlocal-1][0] = static_cast<double>(tagold[i]);
array[atom->nlocal-1][1] = static_cast<double>(tagold[j]);
nadd++;
}
}
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
// free temporary storage
memory->destroy(xold);
memory->destroy(tagold);
char str[128];
int nadd_all = 0, ndel_all = 0;
MPI_Allreduce(&ndel,&ndel_all,1,MPI_INT,MPI_SUM,world);
MPI_Allreduce(&nadd,&nadd_all,1,MPI_INT,MPI_SUM,world);
if(comm->me == 0){
sprintf(str, "Removed/inserted %d/%d bond particles.", ndel_all,nadd_all);
error->message(FLERR,str);
}
// check ghost comm distances
// warn and change if shorter from estimate
// ghost atoms must be present for bonds on edge of neighbor cutoff
// extend cutghost slightly more than half of the longest bond
MPI_Allreduce(&rsqold,&rsqmax,1,MPI_DOUBLE,MPI_MAX,world);
rmax = sqrt(rsqmax);
double cutneighmax_srp = neighbor->cutneighmax + 0.51*rmax;
// find smallest cutghost
double cutghostmin = comm->cutghost[0];
if (cutghostmin > comm->cutghost[1])
cutghostmin = comm->cutghost[1];
if (cutghostmin > comm->cutghost[2])
cutghostmin = comm->cutghost[2];
// reset cutghost if needed
if (cutneighmax_srp > cutghostmin){
if(comm->me == 0){
sprintf(str, "Extending ghost comm cutoff. New %f, old %f.", cutneighmax_srp, cutghostmin);
error->message(FLERR,str);
}
// cutghost updated by comm->setup
comm->cutghostuser = cutneighmax_srp;
}
// assign tags for new atoms, update map
atom->tag_extend();
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
// put new particles in the box before exchange
// move owned to new procs
// get ghosts
// build neigh lists again
// if triclinic, lambda coords needed for pbc, exchange, borders
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
if (atom->sortfreq > 0) atom->sort();
comm->borders();
// back to box coords
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
neighbor->build();
neighbor->ncalls = 0;
// new atom counts
nlocal = atom->nlocal;
nall = atom->nlocal + atom->nghost;
// zero all forces
for(i = 0; i < nall; i++)
atom->f[i][0] = atom->f[i][1] = atom->f[i][2] = 0.0;
// do not include bond particles in thermo output
// remove them from all groups. set their velocity to zero.
for(i=0; i< nlocal; i++)
if(atom->type[i] == bptype) {
atom->mask[i] = 0;
atom->v[i][0] = atom->v[i][1] = atom->v[i][2] = 0.0;
}
}
/* ----------------------------------------------------------------------
set position of bond particles
------------------------------------------------------------------------- */
void FixSRP::pre_exchange()
{
// update ghosts
comm->forward_comm();
// reassign bond particle coordinates to midpoint of bonds
// only need to do this before neigh rebuild
double **x=atom->x;
int i,j;
int nlocal = atom->nlocal;
for(int ii = 0; ii < nlocal; ii++){
if(atom->type[ii] != bptype) continue;
i = atom->map(static_cast<tagint>(array[ii][0]));
if(i < 0) error->all(FLERR,"Fix SRP failed to map atom");
i = domain->closest_image(ii,i);
j = atom->map(static_cast<tagint>(array[ii][1]));
if(j < 0) error->all(FLERR,"Fix SRP failed to map atom");
j = domain->closest_image(ii,j);
// position of bond particle ii
atom->x[ii][0] = (x[i][0] + x[j][0])*0.5;
atom->x[ii][1] = (x[i][1] + x[j][1])*0.5;
atom->x[ii][2] = (x[i][2] + x[j][2])*0.5;
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double FixSRP::memory_usage()
{
double bytes = atom->nmax*2 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void FixSRP::grow_arrays(int nmax)
{
memory->grow(array,nmax,2,"fix_srp:array");
array_atom = array;
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
called when move to new proc
------------------------------------------------------------------------- */
void FixSRP::copy_arrays(int i, int j, int delflag)
{
for (int m = 0; m < 2; m++)
array[j][m] = array[i][m];
}
/* ----------------------------------------------------------------------
initialize one atom's array values
called when atom is created
------------------------------------------------------------------------- */
void FixSRP::set_arrays(int i)
{
array[i][0] = -1;
array[i][1] = -1;
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixSRP::pack_exchange(int i, double *buf)
{
for (int m = 0; m < 2; m++) buf[m] = array[i][m];
return 2;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixSRP::unpack_exchange(int nlocal, double *buf)
{
for (int m = 0; m < 2; m++) array[nlocal][m] = buf[m];
return 2;
}
/* ----------------------------------------------------------------------
pack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixSRP::pack_border(int n, int *list, double *buf)
{
// pack buf for border com
int i,j;
int m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = array[j][0];
buf[m++] = array[j][1];
}
return m;
}
/* ----------------------------------------------------------------------
unpack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixSRP::unpack_border(int n, int first, double *buf)
{
// unpack buf into array
int i,last;
int m = 0;
last = first + n;
for (i = first; i < last; i++){
array[i][0] = buf[m++];
array[i][1] = buf[m++];
}
return m;
}
/* ----------------------------------------------------------------------
remove particles after run
------------------------------------------------------------------------- */
void FixSRP::post_run()
{
// all bond particles are removed after each run
// useful for write_data and write_restart commands
// since those commands occur between runs
bigint natoms_previous = atom->natoms;
int nlocal = atom->nlocal;
int* dlist;
memory->create(dlist,nlocal,"fix_srp:dlist");
for (int i = 0; i < nlocal; i++){
if(atom->type[i] == bptype)
dlist[i] = 1;
else
dlist[i] = 0;
}
// delete local atoms flagged in dlist
// reset nlocal
AtomVec *avec = atom->avec;
int i = 0;
while (i < nlocal) {
if (dlist[i]) {
avec->copy(nlocal-1,i,1);
dlist[i] = dlist[nlocal-1];
nlocal--;
} else i++;
}
atom->nlocal = nlocal;
memory->destroy(dlist);
// reset atom->natoms
// reset atom->map if it exists
// set nghost to 0 so old ghosts won't be mapped
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
// print before and after atom count
bigint ndelete = natoms_previous - atom->natoms;
if (comm->me == 0) {
if (screen) fprintf(screen,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (logfile) fprintf(logfile,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
}
// verlet calls box_too_small_check() in post_run
// this check maps all bond partners
// therefore need ghosts
// need to convert to lambda coords before apply pbc
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
comm->setup();
comm->exchange();
if (atom->sortfreq > 0) atom->sort();
comm->borders();
// change back to box coordinates
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixSRP::pack_restart(int i, double *buf)
{
int m = 0;
buf[m++] = 3;
buf[m++] = array[i][0];
buf[m++] = array[i][1];
return m;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixSRP::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++){
m += extra[nlocal][m];
}
m++;
array[nlocal][0] = extra[nlocal][m++];
array[nlocal][1] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixSRP::maxsize_restart()
{
return 3;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixSRP::size_restart(int nlocal)
{
return 3;
}
/* ----------------------------------------------------------------------
pack global state of Fix
------------------------------------------------------------------------- */
void FixSRP::write_restart(FILE *fp)
{
int n = 0;
double list[3];
list[n++] = comm->cutghostuser;
list[n++] = btype;
list[n++] = bptype;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixSRP::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
comm->cutghostuser = static_cast<double> (list[n++]);
btype = static_cast<int> (list[n++]);
bptype = static_cast<int> (list[n++]);
}
/* ----------------------------------------------------------------------
interface with pair class
pair srp sets the bond type in this fix
------------------------------------------------------------------------- */
int FixSRP::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"btype") == 0) {
btype = atoi(arg[1]);
return 2;
}
if (strcmp(arg[0],"bptype") == 0) {
bptype = atoi(arg[1]);
return 2;
}
return 0;
}

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