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fix_orient_fcc.cpp
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Wed, Oct 16, 15:33

fix_orient_fcc.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: Koenraad Janssens and David Olmsted (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "mpi.h"
#include "fix_orient_fcc.h"
#include "atom.h"
#include "update.h"
#include "respa.h"
#include "neighbor.h"
#include "comm.h"
#include "output.h"
#include "error.h"
using namespace LAMMPS_NS;
#define BIG 1000000000
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
MPI_Comm_rank(world,&me);
if (narg != 11) error->all("Illegal fix orient/fcc command");
neigh_full_every = 1;
nstats = atoi(arg[3]);
direction_of_motion = atoi(arg[4]);
a = atof(arg[5]);
Vxi = atof(arg[6]);
uxif_low = atof(arg[7]);
uxif_high = atof(arg[8]);
if (direction_of_motion == 0) {
int n = strlen(arg[9]) + 1;
chifilename = new char[n];
strcpy(chifilename,arg[9]);
n = strlen(arg[10]) + 1;
xifilename = new char[n];
strcpy(xifilename,arg[10]);
} else if (direction_of_motion == 1) {
int n = strlen(arg[9]) + 1;
xifilename = new char[n];
strcpy(xifilename,arg[9]);
n = strlen(arg[10]) + 1;
chifilename = new char[n];
strcpy(chifilename,arg[10]);
} else error->all("Illegal fix orient/fcc command");
// initializations
PI = 4.0*atan(1.0);
half_fcc_nn = 6;
use_xismooth = false;
double xicutoff = 1.57;
xicutoffsq = xicutoff * xicutoff;
cutsq = 0.5 * a*a*xicutoffsq;
nmax = 0;
// read xi and chi reference orientations from files
if (me == 0) {
char line[512];
char *result;
int count;
FILE *infile = fopen(xifilename,"r");
if (infile == NULL) error->one("Fix orient/fcc file open failed");
for (int i = 0; i < 6; i++) {
result = fgets(line,512,infile);
if (!result) error->one("Fix orient/fcc file read failed");
count = sscanf(line,"%lg %lg %lg",&Rxi[i][0],&Rxi[i][1],&Rxi[i][2]);
if (count != 3) error->one("Fix orient/fcc file read failed");
}
fclose(infile);
infile = fopen(chifilename,"r");
if (infile == NULL) error->one("Fix orient/fcc file open failed");
for (int i = 0; i < 6; i++) {
result = fgets(line,512,infile);
if (!result) error->one("Fix orient/fcc file read failed");
count = sscanf(line,"%lg %lg %lg",&Rchi[i][0],&Rchi[i][1],&Rchi[i][2]);
if (count != 3) error->one("Fix orient/fcc file read failed");
}
fclose(infile);
}
MPI_Bcast(&Rxi[0][0],18,MPI_DOUBLE,0,world);
MPI_Bcast(&Rchi[0][0],18,MPI_DOUBLE,0,world);
// make copy of the reference vectors
for (int i = 0; i < 6; i++)
for (int j = 0; j < 3; j++) {
half_xi_chi_vec[0][i][j] = Rxi[i][j];
half_xi_chi_vec[1][i][j] = Rchi[i][j];
}
// compute xiid,xi0,xi1 for all 12 neighbors
// xi is the favored crystal
// want order parameter when actual is Rchi
double xi_sq,dxi[3],rchi[3];
xiid = 0.0;
for (int i = 0; i < 6; i++) {
rchi[0] = Rchi[i][0];
rchi[1] = Rchi[i][1];
rchi[2] = Rchi[i][2];
find_best_ref(rchi,0,xi_sq,dxi);
xiid += sqrt(xi_sq);
for (int j = 0; j < 3; j++) rchi[j] = -rchi[j];
find_best_ref(rchi,0,xi_sq,dxi);
xiid += sqrt(xi_sq);
}
xiid /= 12.0;
xi0 = uxif_low * xiid;
xi1 = uxif_high * xiid;
// set comm size needed by this Fix
// NOTE: doesn't seem that use_xismooth is ever true
if (use_xismooth) comm_forward = 62;
else comm_forward = 50;
}
/* ---------------------------------------------------------------------- */
FixOrientFCC::~FixOrientFCC()
{
delete [] xifilename;
delete [] chifilename;
if (nmax) delete [] nbr;
}
/* ---------------------------------------------------------------------- */
int FixOrientFCC::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixOrientFCC::init()
{
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixOrientFCC::setup()
{
eflag_enable = 1;
if (strcmp(update->integrate_style,"verlet") == 0)
post_force(1);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(1,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
eflag_enable = 0;
}
/* ---------------------------------------------------------------------- */
void FixOrientFCC::post_force(int vflag)
{
int i,j,k,m,n,nn,nsort,id_self;
int *neighs;
double edelta,added_energy,omega;
double dx,dy,dz,rsq,xismooth,xi_sq,duxi,duxi_other;
double dxi[3];
double *dxiptr;
bool found_myself;
bool eflag = false;
if (eflag_enable) eflag = true;
else if (output->next_thermo == update->ntimestep) eflag = true;
// set local ptrs
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int *tag = atom->tag;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
// insure nbr data structure is adequate size
if (nall > nmax) {
if (nmax) delete [] nbr;
nbr = new Nbr[nall];
nmax = nall;
}
// loop over owned atoms and build Nbr data structure of neighbors
// use full neighbor list
if (eflag) added_energy = 0.0;
int count = 0;
int mincount = BIG;
int maxcount = 0;
for (i = 0; i < nlocal; i++) {
neighs = neighbor->firstneigh_full[i];
n = neighbor->numneigh_full[i];
if (n < mincount) mincount = n;
if (n > maxcount) {
if (maxcount) delete [] sort;
sort = new Sort[n];
maxcount = n;
}
// loop over all neighbors of atom i
// for those within cutsq, build sort data structure
// store local id, rsq, delta vector, xismooth (if included)
nsort = 0;
for (k = 0; k < n; k++) {
j = neighs[k];
count++;
dx = x[i][0] - x[j][0];
dy = x[i][1] - x[j][1];
dz = x[i][2] - x[j][2];
rsq = dx*dx + dy*dy + dz*dz;
if (rsq < cutsq) {
sort[nsort].id = j;
sort[nsort].rsq = rsq;
sort[nsort].delta[0] = dx;
sort[nsort].delta[1] = dy;
sort[nsort].delta[2] = dz;
if (use_xismooth) {
xismooth = (xicutoffsq - 2.0*rsq/(a*a)) / (xicutoffsq - 1.0);
sort[nsort].xismooth = 1.0 - fabs(1.0-xismooth);
}
nsort++;
}
}
// sort neighbors by rsq distance
// no need to sort if nsort <= 12
if (nsort > 12) qsort(sort,nsort,sizeof(Sort),compare);
// copy up to 12 nearest neighbors into nbr data structure
// operate on delta vector via find_best_ref() to compute dxi
n = MIN(12,nsort);
nbr[i].n = n;
if (n == 0) continue;
double xi_total = 0.0;
for (j = 0; j < n; j++) {
find_best_ref(sort[j].delta,0,xi_sq,dxi);
xi_total += sqrt(xi_sq);
nbr[i].id[j] = sort[j].id;
nbr[i].dxi[j][0] = dxi[0]/n;
nbr[i].dxi[j][1] = dxi[1]/n;
nbr[i].dxi[j][2] = dxi[2]/n;
if (use_xismooth) nbr[i].xismooth[j] = sort[j].xismooth;
}
xi_total /= n;
// compute potential derivative to xi
if (xi_total < xi0) {
nbr[i].duxi = 0.0;
if (eflag) edelta = 0.0;
} else if (xi_total > xi1) {
nbr[i].duxi = 0.0;
if (eflag) edelta = Vxi;
} else {
omega = (0.5*PI)*(xi_total-xi0) / (xi1-xi0);
nbr[i].duxi = PI*Vxi*sin(2.0*omega) / (2.0*(xi1-xi0));
if (eflag) edelta = Vxi*(1 - cos(2.0*omega)) / 2.0;
}
if (eflag) added_energy += edelta;
}
if (maxcount) delete [] sort;
// communicate to acquire nbr data for ghost atoms
comm->comm_fix(this);
// compute grain boundary force on each owned atom
// skip atoms not in group
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
n = nbr[i].n;
duxi = nbr[i].duxi;
for (j = 0; j < n; j++) {
dxiptr = &nbr[i].dxi[j][0];
if (use_xismooth) {
xismooth = nbr[i].xismooth[j];
f[i][0] += duxi * dxiptr[0] * xismooth;
f[i][1] += duxi * dxiptr[1] * xismooth;
f[i][2] += duxi * dxiptr[2] * xismooth;
} else {
f[i][0] += duxi * dxiptr[0];
f[i][1] += duxi * dxiptr[1];
f[i][2] += duxi * dxiptr[2];
}
// m = local index of neighbor
// id_self = ID for atom I in atom M's neighbor list
// if M is local atom, id_self will be local ID of atom I
// if M is ghost atom, id_self will be global ID of atom I
m = nbr[i].id[j];
if (m < nlocal) id_self = i;
else id_self = tag[i];
found_myself = false;
nn = nbr[m].n;
for (k = 0; k < nn; k++) {
if (id_self == nbr[m].id[k]) {
if (found_myself) error->one("Fix orient/fcc found self twice");
found_myself = true;
duxi_other = nbr[m].duxi;
dxiptr = &nbr[m].dxi[k][0];
if (use_xismooth) {
xismooth = nbr[m].xismooth[k];
f[i][0] -= duxi_other * dxiptr[0] * xismooth;
f[i][1] -= duxi_other * dxiptr[1] * xismooth;
f[i][2] -= duxi_other * dxiptr[2] * xismooth;
} else {
f[i][0] -= duxi_other * dxiptr[0];
f[i][1] -= duxi_other * dxiptr[1];
f[i][2] -= duxi_other * dxiptr[2];
}
}
}
}
}
// sum energy across procs
if (eflag)
MPI_Allreduce(&added_energy,&total_added_e,1,MPI_DOUBLE,MPI_SUM,world);
// print statistics every nstats timesteps
if (nstats && update->ntimestep % nstats == 0) {
int total;
MPI_Allreduce(&count,&total,1,MPI_INT,MPI_SUM,world);
double ave = total/atom->natoms;
int min,max;
MPI_Allreduce(&mincount,&min,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&maxcount,&max,1,MPI_INT,MPI_MAX,world);
if (me == 0) {
if (screen) {
fprintf(screen,"orient step %d: %g atoms have %d neighbors\n",
update->ntimestep,atom->natoms,total);
fprintf(screen," neighs: min = %d, max = %d, ave = %g\n",
min,max,ave);
}
if (logfile) {
fprintf(logfile,"orient step %d: %g atoms have %d neighbors\n",
update->ntimestep,atom->natoms,total);
fprintf(logfile," neighs: min = %d, max = %d, ave = %g\n",
min,max,ave);
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixOrientFCC::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
double FixOrientFCC::thermo(int n)
{
if (n == 0) return total_added_e;
else return 0.0;
}
/* ---------------------------------------------------------------------- */
int FixOrientFCC::pack_comm(int n, int *list, double *buf, int *pbc_flags)
{
int i,j,k,id,num;
int *tag = atom->tag;
int nlocal = atom->nlocal;
int m = 0;
for (i = 0; i < n; i++) {
k = list[i];
num = nbr[k].n;
buf[m++] = static_cast<double> (num);
buf[m++] = nbr[k].duxi;
for (j = 0; j < num; j++) {
if (use_xismooth) buf[m++] = nbr[m].xismooth[j];
buf[m++] = nbr[k].dxi[j][0];
buf[m++] = nbr[k].dxi[j][1];
buf[m++] = nbr[k].dxi[j][2];
// id stored in buf needs to be global ID
// if k is a local atom, it stores local IDs, so convert to global
// if k is a ghost atom (already comm'd), its IDs are already global
id = nbr[k].id[j];
if (k < nlocal) id = tag[id];
buf[m++] = static_cast<double> (id);
}
m += (12-num) * 3;
if (use_xismooth) m += 12-num;
}
if (use_xismooth) return 62;
return 50;
}
/* ---------------------------------------------------------------------- */
void FixOrientFCC::unpack_comm(int n, int first, double *buf)
{
int i,j,num;
int last = first + n;
int m = 0;
for (i = first; i < last; i++) {
nbr[i].n = num = static_cast<int> (buf[m++]);
nbr[i].duxi = buf[m++];
for (j = 0; j < num; j++) {
if (use_xismooth) nbr[i].xismooth[j] = buf[m++];
nbr[i].dxi[j][0] = buf[m++];
nbr[i].dxi[j][1] = buf[m++];
nbr[i].dxi[j][2] = buf[m++];
nbr[i].id[j] = static_cast<int> (buf[m++]);
}
m += (12-num) * 3;
if (use_xismooth) m += 12-num;
}
}
/* ---------------------------------------------------------------------- */
void FixOrientFCC::find_best_ref(double *displs, int which_crystal,
double &xi_sq, double *dxi)
{
int i;
double dot,tmp;
double best_dot = -1.0; // best is biggest (smallest angle)
int best_i = -1;
int best_sign = 0;
for (i = 0; i < half_fcc_nn; i++) {
dot = displs[0] * half_xi_chi_vec[which_crystal][i][0] +
displs[1] * half_xi_chi_vec[which_crystal][i][1] +
displs[2] * half_xi_chi_vec[which_crystal][i][2];
if (fabs(dot) > best_dot) {
best_dot = fabs(dot);
best_i = i;
if (dot < 0.0) best_sign = -1;
else best_sign = 1;
}
}
xi_sq = 0.0;
for (i = 0; i < 3; i++) {
tmp = displs[i] - best_sign * half_xi_chi_vec[which_crystal][best_i][i];
xi_sq += tmp*tmp;
}
if (xi_sq > 0.0) {
double xi = sqrt(xi_sq);
for (i = 0; i < 3; i++)
dxi[i] = (best_sign * half_xi_chi_vec[which_crystal][best_i][i] -
displs[i]) / xi;
} else dxi[0] = dxi[1] = dxi[2] = 0.0;
}
/* ----------------------------------------------------------------------
compare two neighbors I and J in sort data structure
called via qsort in post_force() method
is a static method so can't access sort data structure directly
return -1 if I < J, 0 if I = J, 1 if I > J
do comparison based on rsq distance
------------------------------------------------------------------------- */
int FixOrientFCC::compare(const void *pi, const void *pj)
{
FixOrientFCC::Sort *ineigh = (FixOrientFCC::Sort *) pi;
FixOrientFCC::Sort *jneigh = (FixOrientFCC::Sort *) pj;
if (ineigh->rsq < jneigh->rsq) return -1;
else if (ineigh->rsq > jneigh->rsq) return 1;
return 0;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
int FixOrientFCC::memory_usage()
{
int bytes = atom->nmax * sizeof(Nbr);
return bytes;
}

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