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sjplimp
2016-06-16 15:46:02 +00:00
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src/MISC/fix_orient_bcc.cpp Normal file
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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)
Modification for bcc provided by: Tegar Wicaksono (UBC)
For a tutorial, please see "Order parameters of crystals in LAMMPS"
(https://dx.doi.org/10.6084/m9.figshare.1488628.v1
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include <mpi.h>
#include "fix_orient_bcc.h"
#include "atom.h"
#include "update.h"
#include "respa.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "comm.h"
#include "output.h"
#include "force.h"
#include "math_const.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
#define BIG 1000000000
static const char cite_fix_orient_bcc[] =
"fix orient/bcc command:\n\n"
"@Article{Wicaksono16,\n"
" author = {A. T. Wicaksono, C. W. Sinclair, M. Militzer},\n"
" title = {An atomistic study of the correlation between the migration of planar and curved grain boundaries},\n"
" journal = {Computational Materials Science},\n"
" year = 2016,\n"
" volume = 117,\n"
" pages = {397--405}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
FixOrientBCC::FixOrientBCC(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_orient_bcc);
MPI_Comm_rank(world,&me);
if (narg != 11) error->all(FLERR,"Illegal fix orient/bcc command");
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
peratom_flag = 1;
size_peratom_cols = 2;
peratom_freq = 1;
nstats = force->inumeric(FLERR,arg[3]);
direction_of_motion = force->inumeric(FLERR,arg[4]);
a = force->numeric(FLERR,arg[5]);
Vxi = force->numeric(FLERR,arg[6]);
uxif_low = force->numeric(FLERR,arg[7]);
uxif_high = force->numeric(FLERR,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(FLERR,"Illegal fix orient/bcc command");
// initializations
half_bcc_nn = 4;
use_xismooth = false;
double xicutoff = 1.57;
xicutoffsq = xicutoff * xicutoff;
cutsq = 0.75 * a*a*xicutoffsq;
nmax = 0;
// read xi and chi reference orientations from files
if (me == 0) {
char line[IMGMAX];
char *result;
int count;
FILE *infile = fopen(xifilename,"r");
if (infile == NULL) error->one(FLERR,"Fix orient/bcc file open failed");
for (int i = 0; i < 4; i++) {
result = fgets(line,IMGMAX,infile);
if (!result) error->one(FLERR,"Fix orient/bcc file read failed");
count = sscanf(line,"%lg %lg %lg",&Rxi[i][0],&Rxi[i][1],&Rxi[i][2]);
if (count != 3) error->one(FLERR,"Fix orient/bcc file read failed");
}
fclose(infile);
infile = fopen(chifilename,"r");
if (infile == NULL) error->one(FLERR,"Fix orient/bcc file open failed");
for (int i = 0; i < 4; i++) {
result = fgets(line,IMGMAX,infile);
if (!result) error->one(FLERR,"Fix orient/bcc file read failed");
count = sscanf(line,"%lg %lg %lg",&Rchi[i][0],&Rchi[i][1],&Rchi[i][2]);
if (count != 3) error->one(FLERR,"Fix orient/bcc 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 < 4; 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 8 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 < 4; 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 /= 8.0;
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;
added_energy = 0.0;
nmax = atom->nmax;
nbr = (Nbr *) memory->smalloc(nmax*sizeof(Nbr),"orient/bcc:nbr");
memory->create(order,nmax,2,"orient/bcc:order");
array_atom = order;
// zero the array since a variable may access it before first run
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) order[i][0] = order[i][1] = 0.0;
}
/* ---------------------------------------------------------------------- */
FixOrientBCC::~FixOrientBCC()
{
delete [] xifilename;
delete [] chifilename;
memory->sfree(nbr);
memory->destroy(order);
}
/* ---------------------------------------------------------------------- */
int FixOrientBCC::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixOrientBCC::init()
{
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
// need a full neighbor list, built whenever re-neighboring occurs
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
/* ---------------------------------------------------------------------- */
void FixOrientBCC::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void FixOrientBCC::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixOrientBCC::post_force(int vflag)
{
int i,j,k,ii,jj,inum,jnum,m,n,nn,nsort;
tagint id_self;
int *ilist,*jlist,*numneigh,**firstneigh;
double edelta,omega;
double dx,dy,dz,rsq,xismooth,xi_sq,duxi,duxi_other;
double dxi[3];
double *dxiptr;
bool found_myself;
// set local ptrs
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// insure nbr and order data structures are adequate size
if (nall > nmax) {
nmax = nall;
memory->destroy(nbr);
memory->destroy(order);
nbr = (Nbr *) memory->smalloc(nmax*sizeof(Nbr),"orient/bcc:nbr");
memory->create(order,nmax,2,"orient/bcc:order");
array_atom = order;
}
// loop over owned atoms and build Nbr data structure of neighbors
// use full neighbor list
added_energy = 0.0;
int count = 0;
int mincount = BIG;
int maxcount = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jlist = firstneigh[i];
jnum = numneigh[i];
if (jnum < mincount) mincount = jnum;
if (jnum > maxcount) {
if (maxcount) delete [] sort;
sort = new Sort[jnum];
maxcount = jnum;
}
// 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 (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
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 - 4.0*rsq/(3.0*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 <= 8
if (nsort > 8) qsort(sort,nsort,sizeof(Sort),compare);
// copy up to 8 nearest neighbors into nbr data structure
// operate on delta vector via find_best_ref() to compute dxi
n = MIN(8,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;
order[i][0] = xi_total;
// compute potential derivative to xi
if (xi_total < xi0) {
nbr[i].duxi = 0.0;
edelta = 0.0;
order[i][1] = 0.0;
} else if (xi_total > xi1) {
nbr[i].duxi = 0.0;
edelta = Vxi;
order[i][1] = 1.0;
} else {
omega = MY_PI2*(xi_total-xi0) / (xi1-xi0);
nbr[i].duxi = MY_PI*Vxi*sin(2.0*omega) / (2.0*(xi1-xi0));
edelta = Vxi*(1 - cos(2.0*omega)) / 2.0;
order[i][1] = omega / MY_PI2;
}
added_energy += edelta;
}
if (maxcount) delete [] sort;
// communicate to acquire nbr data for ghost atoms
comm->forward_comm_fix(this);
// compute grain boundary force on each owned atom
// skip atoms not in group
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
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(FLERR,"Fix orient/bcc 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];
}
}
}
}
}
// 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 = static_cast<double>(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 " BIGINT_FORMAT ": " BIGINT_FORMAT
" atoms have %d neighbors\n",
update->ntimestep,atom->natoms,total);
if (logfile) fprintf(logfile,
"orient step " BIGINT_FORMAT ": " BIGINT_FORMAT
" atoms have %d neighbors\n",
update->ntimestep,atom->natoms,total);
if (screen)
fprintf(screen," neighs: min = %d, max = %d, ave = %g\n",
min,max,ave);
if (logfile)
fprintf(logfile," neighs: min = %d, max = %d, ave = %g\n",
min,max,ave);
}
}
}
/* ---------------------------------------------------------------------- */
void FixOrientBCC::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
double FixOrientBCC::compute_scalar()
{
double added_energy_total;
MPI_Allreduce(&added_energy,&added_energy_total,1,MPI_DOUBLE,MPI_SUM,world);
return added_energy_total;
}
/* ---------------------------------------------------------------------- */
int FixOrientBCC::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,num;
tagint id;
tagint *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++] = num;
buf[m++] = nbr[k].duxi;
for (j = 0; j < num; j++) {
if (use_xismooth) buf[m++] = nbr[k].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++] = id;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixOrientBCC::unpack_forward_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<tagint> (buf[m++]);
}
}
}
/* ---------------------------------------------------------------------- */
void FixOrientBCC::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_bcc_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 FixOrientBCC::compare(const void *pi, const void *pj)
{
FixOrientBCC::Sort *ineigh = (FixOrientBCC::Sort *) pi;
FixOrientBCC::Sort *jneigh = (FixOrientBCC::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
------------------------------------------------------------------------- */
double FixOrientBCC::memory_usage()
{
double bytes = nmax * sizeof(Nbr);
bytes += 2*nmax * sizeof(double);
return bytes;
}

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/* -*- c++ -*- ----------------------------------------------------------
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 FIX_CLASS
FixStyle(orient/bcc,FixOrientBCC)
#else
#ifndef LMP_FIX_ORIENT_BCC_H
#define LMP_FIX_ORIENT_BCC_H
#include "fix.h"
namespace LAMMPS_NS {
class FixOrientBCC : public Fix {
public:
struct Nbr { // neighbor info for each owned and ghost atom
int n; // # of closest neighbors (up to 8)
tagint id[8]; // IDs of each neighbor
// if center atom is owned, these are local IDs
// if center atom is ghost, these are global IDs
double xismooth[8]; // distance weighting factor for each neighbors
double dxi[8][3]; // d order-parameter / dx for each neighbor
double duxi; // d Energy / d order-parameter for atom
};
struct Sort { // data structure for sorting to find 8 closest
int id; // local ID of neighbor atom
double rsq; // distance between center and neighbor atom
double delta[3]; // displacement between center and neighbor atom
double xismooth; // distance weighting factor
};
FixOrientBCC(class LAMMPS *, int, char **);
~FixOrientBCC();
int setmask();
void init();
void init_list(int, class NeighList *);
void setup(int);
void post_force(int);
void post_force_respa(int, int, int);
double compute_scalar();
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
double memory_usage();
private:
int me;
int nlevels_respa;
int direction_of_motion; // 1 = center shrinks, 0 = center grows
int nstats; // stats output every this many steps
double a; // lattice parameter
double Vxi; // potential value
double uxif_low; // cut-off fraction, low order parameter
double uxif_high; // cut-off fraction, high order parameter
char *xifilename, *chifilename; // file names for 2 crystal orientations
bool use_xismooth;
double Rxi[8][3],Rchi[8][3],half_xi_chi_vec[2][4][3];
double xiid,xi0,xi1,xicutoffsq,cutsq,added_energy;
int half_bcc_nn;
int nmax; // expose 2 per-atom quantities
double **order; // order param and normalized order param
Nbr *nbr;
Sort *sort;
class NeighList *list;
void find_best_ref(double *, int, double &, double *);
static int compare(const void *, const void *);
};
}
#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: Fix orient/bcc file open failed
The fix orient/bcc command could not open a specified file.
E: Fix orient/bcc file read failed
The fix orient/bcc command could not read the needed parameters from a
specified file.
E: Fix orient/bcc found self twice
The neighbor lists used by fix orient/bcc are messed up. If this
error occurs, it is likely a bug, so send an email to the
"developers"_http://lammps.sandia.gov/authors.html.
*/