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fix_qeq.cpp
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Thu, Jun 27, 23:30

fix_qeq.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 author: Ray Shan (Sandia)
Based on fix qeq/reax by H. Metin Aktulga
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "fix_qeq.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "force.h"
#include "kspace.h"
#include "group.h"
#include "pair.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace FixConst;
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 8) error->all(FLERR,"Illegal fix qeq command");
nevery = force->inumeric(FLERR,arg[3]);
cutoff = force->numeric(FLERR,arg[4]);
tolerance = force->numeric(FLERR,arg[5]);
maxiter = force->inumeric(FLERR,arg[6]);
alpha = 0.20;
swa = 0.0;
swb = cutoff;
shld = NULL;
n = n_cap = 0;
N = nmax = 0;
m_fill = m_cap = 0;
pack_flag = 0;
s = NULL;
t = NULL;
nprev = 5;
Hdia_inv = NULL;
b_s = NULL;
b_t = NULL;
b_prc = NULL;
b_prm = NULL;
// CG
p = NULL;
q = NULL;
r = NULL;
d = NULL;
// H matrix
H.firstnbr = NULL;
H.numnbrs = NULL;
H.jlist = NULL;
H.val = NULL;
// others
cutoff_sq = cutoff*cutoff;
chizj = NULL;
qf = NULL;
q1 = NULL;
q2 = NULL;
comm_forward = comm_reverse = 1;
// perform initial allocation of atom-based arrays
// register with Atom class
s_hist = t_hist = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
for( int i = 0; i < atom->nmax; i++ )
for (int j = 0; j < nprev; ++j )
s_hist[i][j] = t_hist[i][j] = 0;
read_file(arg[7]);
}
/* ---------------------------------------------------------------------- */
FixQEq::~FixQEq()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
memory->destroy(s_hist);
memory->destroy(t_hist);
deallocate_storage();
deallocate_matrix();
memory->destroy(shld);
memory->destroy(chi);
memory->destroy(eta);
memory->destroy(gamma);
memory->destroy(zeta);
memory->destroy(zcore);
}
/* ---------------------------------------------------------------------- */
int FixQEq::setmask()
{
int mask = 0;
mask |= PRE_FORCE;
mask |= MIN_PRE_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixQEq::allocate_storage()
{
nmax = atom->nmax;
memory->create(s,nmax,"qeq:s");
memory->create(t,nmax,"qeq:t");
memory->create(Hdia_inv,nmax,"qeq:Hdia_inv");
memory->create(b_s,nmax,"qeq:b_s");
memory->create(b_t,nmax,"qeq:b_t");
memory->create(b_prc,nmax,"qeq:b_prc");
memory->create(b_prm,nmax,"qeq:b_prm");
memory->create(p,nmax,"qeq:p");
memory->create(q,nmax,"qeq:q");
memory->create(r,nmax,"qeq:r");
memory->create(d,nmax,"qeq:d");
memory->create(chizj,nmax,"qeq:chizj");
memory->create(qf,nmax,"qeq:qf");
memory->create(q1,nmax,"qeq:q1");
memory->create(q2,nmax,"qeq:q2");
}
/* ---------------------------------------------------------------------- */
void FixQEq::deallocate_storage()
{
memory->destroy(s);
memory->destroy(t);
memory->destroy( Hdia_inv );
memory->destroy( b_s );
memory->destroy( b_t );
memory->destroy( b_prc );
memory->destroy( b_prm );
memory->destroy( p );
memory->destroy( q );
memory->destroy( r );
memory->destroy( d );
memory->destroy( chizj );
memory->destroy( qf );
memory->destroy( q1 );
memory->destroy( q2 );
}
/* ---------------------------------------------------------------------- */
void FixQEq::reallocate_storage()
{
deallocate_storage();
allocate_storage();
init_storage();
}
/* ---------------------------------------------------------------------- */
void FixQEq::allocate_matrix()
{
int i,ii,inum,m;
int *ilist, *numneigh;
int mincap;
double safezone;
mincap = MIN_CAP;
safezone = SAFE_ZONE;
n = atom->nlocal;
n_cap = MAX( (int)(n * safezone), mincap );
N = atom->nlocal + atom->nghost;
// determine the total space for the H matrix
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
m = 0;
for( ii = 0; ii < inum; ii++ ) {
i = ilist[ii];
m += numneigh[i];
}
m_cap = MAX( (int)(m * safezone), mincap * MIN_NBRS );
H.n = n_cap;
H.m = m_cap;
memory->create(H.firstnbr,n_cap,"qeq:H.firstnbr");
memory->create(H.numnbrs,n_cap,"qeq:H.numnbrs");
memory->create(H.jlist,m_cap,"qeq:H.jlist");
memory->create(H.val,m_cap,"qeq:H.val");
}
/* ---------------------------------------------------------------------- */
void FixQEq::deallocate_matrix()
{
memory->destroy( H.firstnbr );
memory->destroy( H.numnbrs );
memory->destroy( H.jlist );
memory->destroy( H.val );
}
/* ---------------------------------------------------------------------- */
void FixQEq::reallocate_matrix()
{
deallocate_matrix();
allocate_matrix();
}
/* ---------------------------------------------------------------------- */
void FixQEq::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void FixQEq::setup_pre_force(int vflag)
{
neighbor->build_one(list);
deallocate_storage();
allocate_storage();
init_storage();
deallocate_matrix();
allocate_matrix();
pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixQEq::setup_pre_force_respa(int vflag, int ilevel)
{
if (ilevel < nlevels_respa-1) return;
setup_pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixQEq::min_setup_pre_force(int vflag)
{
setup_pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixQEq::init_storage()
{
int N = atom->nlocal + atom->nghost;
for( int i = 0; i < N; i++ ) {
Hdia_inv[i] = 1. / eta[atom->type[i]];
b_s[i] = -chi[atom->type[i]];
b_t[i] = -1.0;
b_prc[i] = 0;
b_prm[i] = 0;
s[i] = t[i] = 0;
chizj[i] = 0.0;
qf[i] = 0.0;
q1[i] = 0.0;
q2[i] = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void FixQEq::pre_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixQEq::min_pre_force(int vflag)
{
pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
int FixQEq::CG( double *b, double *x )
{
int i, j;
double tmp, alfa, beta, b_norm;
double sig_old, sig_new;
int nn, jj;
int *ilist;
nn = list->inum;
ilist = list->ilist;
pack_flag = 1;
sparse_matvec( &H, x, q );
comm->reverse_comm_fix( this ); //Coll_Vector( q );
vector_sum( r , 1., b, -1., q, nn );
for( jj = 0; jj < nn; ++jj ) {
j = ilist[jj];
if (atom->mask[j] & groupbit)
d[j] = r[j] * Hdia_inv[j]; //pre-condition
}
b_norm = parallel_norm( b, nn );
sig_new = parallel_dot( r, d, nn);
for( i = 1; i < maxiter && sqrt(sig_new) / b_norm > tolerance; ++i ) {
comm->forward_comm_fix(this); //Dist_vector( d );
sparse_matvec( &H, d, q );
comm->reverse_comm_fix(this); //Coll_vector( q );
tmp = parallel_dot( d, q, nn);
alfa = sig_new / tmp;
vector_add( x, alfa, d, nn );
vector_add( r, -alfa, q, nn );
// pre-conditioning
for( jj = 0; jj < nn; ++jj ) {
j = ilist[jj];
if (atom->mask[j] & groupbit)
p[j] = r[j] * Hdia_inv[j];
}
sig_old = sig_new;
sig_new = parallel_dot( r, p, nn);
beta = sig_new / sig_old;
vector_sum( d, 1., p, beta, d, nn );
}
if (i >= maxiter && comm->me == 0) {
char str[128];
sprintf(str,"Fix qeq CG convergence failed (%g) after %d iterations "
"at " BIGINT_FORMAT " step",sqrt(sig_new) / b_norm,i,update->ntimestep);
error->warning(FLERR,str);
}
return i;
}
/* ---------------------------------------------------------------------- */
void FixQEq::sparse_matvec( sparse_matrix *A, double *x, double *b )
{
int i, j, itr_j;
int nn, NN;
int *ilist;
nn = atom->nlocal;
NN = atom->nlocal + atom->nghost;
ilist = list->ilist;
for( i = 0; i < nn; ++i ) {
if (atom->mask[i] & groupbit)
b[i] = eta[ atom->type[i] ] * x[i];
}
for( i = nn; i < NN; ++i ) {
if (atom->mask[i] & groupbit)
b[i] = 0;
}
for( i = 0; i < nn; ++i ) {
if (atom->mask[i] & groupbit) {
for( itr_j=A->firstnbr[i]; itr_j<A->firstnbr[i]+A->numnbrs[i]; itr_j++) {
j = A->jlist[itr_j];
b[i] += A->val[itr_j] * x[j];
b[j] += A->val[itr_j] * x[i];
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixQEq::calculate_Q()
{
int i, k;
double u, s_sum, t_sum;
double *q = atom->q;
int nn, ii;
int *ilist;
nn = list->inum;
ilist = list->ilist;
s_sum = parallel_vector_acc( s, nn );
t_sum = parallel_vector_acc( t, nn);
u = s_sum / t_sum;
for( ii = 0; ii < nn; ++ii ) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
q[i] = s[i] - u * t[i];
/* backup s & t */
for( k = 4; k > 0; --k ) {
s_hist[i][k] = s_hist[i][k-1];
t_hist[i][k] = t_hist[i][k-1];
}
s_hist[i][0] = s[i];
t_hist[i][0] = t[i];
}
}
pack_flag = 4;
comm->forward_comm_fix( this ); //Dist_vector( atom->q );
}
/* ---------------------------------------------------------------------- */
int FixQEq::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int m;
if( pack_flag == 1)
for(m = 0; m < n; m++) buf[m] = d[list[m]];
else if( pack_flag == 2 )
for(m = 0; m < n; m++) buf[m] = s[list[m]];
else if( pack_flag == 3 )
for(m = 0; m < n; m++) buf[m] = t[list[m]];
else if( pack_flag == 4 )
for(m = 0; m < n; m++) buf[m] = atom->q[list[m]];
return n;
}
/* ---------------------------------------------------------------------- */
void FixQEq::unpack_forward_comm(int n, int first, double *buf)
{
int i, m;
if( pack_flag == 1)
for(m = 0, i = first; m < n; m++, i++) d[i] = buf[m];
else if( pack_flag == 2)
for(m = 0, i = first; m < n; m++, i++) s[i] = buf[m];
else if( pack_flag == 3)
for(m = 0, i = first; m < n; m++, i++) t[i] = buf[m];
else if( pack_flag == 4)
for(m = 0, i = first; m < n; m++, i++) atom->q[i] = buf[m];
}
/* ---------------------------------------------------------------------- */
int FixQEq::pack_reverse_comm(int n, int first, double *buf)
{
int i, m;
for(m = 0, i = first; m < n; m++, i++) buf[m] = q[i];
return n;
}
/* ---------------------------------------------------------------------- */
void FixQEq::unpack_reverse_comm(int n, int *list, double *buf)
{
int m;
for(m = 0; m < n; m++) q[list[m]] += buf[m];
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixQEq::memory_usage()
{
double bytes;
bytes = atom->nmax*nprev*2 * sizeof(double); // s_hist & t_hist
bytes += atom->nmax*11 * sizeof(double); // storage
bytes += n_cap*2 * sizeof(int); // matrix...
bytes += m_cap * sizeof(int);
bytes += m_cap * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate fictitious charge arrays
------------------------------------------------------------------------- */
void FixQEq::grow_arrays(int nmax)
{
memory->grow(s_hist,nmax,nprev,"qeq:s_hist");
memory->grow(t_hist,nmax,nprev,"qeq:t_hist");
}
/* ----------------------------------------------------------------------
copy values within fictitious charge arrays
------------------------------------------------------------------------- */
void FixQEq::copy_arrays(int i, int j, int delflag)
{
for (int m = 0; m < nprev; m++) {
s_hist[j][m] = s_hist[i][m];
t_hist[j][m] = t_hist[i][m];
}
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixQEq::pack_exchange(int i, double *buf)
{
for (int m = 0; m < nprev; m++) buf[m] = s_hist[i][m];
for (int m = 0; m < nprev; m++) buf[nprev+m] = t_hist[i][m];
return nprev*2;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixQEq::unpack_exchange(int nlocal, double *buf)
{
for (int m = 0; m < nprev; m++) s_hist[nlocal][m] = buf[m];
for (int m = 0; m < nprev; m++) t_hist[nlocal][m] = buf[nprev+m];
return nprev*2;
}
/* ---------------------------------------------------------------------- */
double FixQEq::parallel_norm( double *v, int n )
{
int i;
double my_sum, norm_sqr;
int ii;
int *ilist;
ilist = list->ilist;
my_sum = 0.0;
norm_sqr = 0.0;
for( ii = 0; ii < n; ++ii ) {
i = ilist[ii];
if (atom->mask[i] & groupbit)
my_sum += v[i]*v[i];
}
MPI_Allreduce( &my_sum, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world );
return sqrt( norm_sqr );
}
/* ---------------------------------------------------------------------- */
double FixQEq::parallel_dot( double *v1, double *v2, int n)
{
int i;
double my_dot, res;
int ii;
int *ilist;
ilist = list->ilist;
my_dot = 0.0;
res = 0.0;
for( ii = 0; ii < n; ++ii ) {
i = ilist[ii];
if (atom->mask[i] & groupbit)
my_dot += v1[i] * v2[i];
}
MPI_Allreduce( &my_dot, &res, 1, MPI_DOUBLE, MPI_SUM, world );
return res;
}
/* ---------------------------------------------------------------------- */
double FixQEq::parallel_vector_acc( double *v, int n )
{
int i;
double my_acc, res;
int ii;
int *ilist;
ilist = list->ilist;
my_acc = 0.0;
res = 0.0;
for( ii = 0; ii < n; ++ii ) {
i = ilist[ii];
if (atom->mask[i] & groupbit)
my_acc += v[i];
}
MPI_Allreduce( &my_acc, &res, 1, MPI_DOUBLE, MPI_SUM, world );
return res;
}
/* ---------------------------------------------------------------------- */
void FixQEq::vector_sum( double* dest, double c, double* v,
double d, double* y, int k )
{
int kk;
int *ilist;
ilist = list->ilist;
for( --k; k>=0; --k ) {
kk = ilist[k];
if (atom->mask[kk] & groupbit)
dest[kk] = c * v[kk] + d * y[kk];
}
}
/* ---------------------------------------------------------------------- */
void FixQEq::vector_add( double* dest, double c, double* v, int k )
{
int kk;
int *ilist;
ilist = list->ilist;
for( --k; k>=0; --k ) {
kk = ilist[k];
if (atom->mask[kk] & groupbit)
dest[kk] += c * v[kk];
}
}
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void FixQEq::read_file(char *file)
{
int i,itype,ntypes;
int params_per_line = 6;
char **words = new char*[params_per_line+1];
ntypes = atom->ntypes;
memory->create(chi,ntypes+1,"qeq:chi");
memory->create(eta,ntypes+1,"qeq:eta");
memory->create(gamma,ntypes+1,"qeq:gamma");
memory->create(zeta,ntypes+1,"qeq:zeta");
memory->create(zcore,ntypes+1,"qeq:zcore");
// open file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open Tersoff potential file %s",file);
error->one(FLERR,str);
}
}
// read each line out of file, skipping blank lines or leading '#'
// store line of params if all 3 element tags are in element list
int n,nwords,ielement,eof;
char line[MAXLINE],*ptr;
eof = ielement = 0;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
ielement ++;
if (ielement > ntypes)
error->all(FLERR,"Invalid fix qeq parameter file");
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
itype = atoi(words[0]);
chi[itype] = atof(words[1]);
eta[itype] = atof(words[2]);
gamma[itype] = atof(words[3]);
zeta[itype] = atof(words[4]);
zcore[itype] = atof(words[5]);
}
delete [] words;
}

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