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lammps/src/REAXFF/fix_acks2_reaxff.cpp
Axel Kohlmeyer 98cdfa1016 fix bug detected by coverity scan
2021-10-15 09:29:47 -04:00

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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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: Stan Moore (Sandia)
------------------------------------------------------------------------- */
#include "fix_acks2_reaxff.h"
#include "atom.h"
#include "citeme.h"
#include "comm.h"
#include "error.h"
#include "fix_efield.h"
#include "force.h"
#include "group.h"
#include "memory.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "pair.h"
#include "pair_reaxff.h"
#include "reaxff_api.h"
#include "respa.h"
#include "text_file_reader.h"
#include "update.h"
#include "utils.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
class parser_error : public std::exception {
std::string message;
public:
parser_error(const std::string &mesg) { message = mesg; }
const char *what() const noexcept { return message.c_str(); }
};
static const char cite_fix_acks2_reax[] =
"fix acks2/reaxff command:\n\n"
"@Article{O'Hearn2020,\n"
" author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},\n"
" title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},\n"
" journal = {SIAM J. Sci. Comput.},\n"
" year = 2020,\n"
" volume = 42,\n"
" pages = {1--22}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
FixACKS2ReaxFF::FixACKS2ReaxFF(LAMMPS *lmp, int narg, char **arg) :
FixQEqReaxFF(lmp, narg, arg)
{
bcut = nullptr;
X_diag = nullptr;
Xdia_inv = nullptr;
// BiCGStab
g = nullptr;
q_hat = nullptr;
r_hat = nullptr;
y = nullptr;
z = nullptr;
// X matrix
X.firstnbr = nullptr;
X.numnbrs = nullptr;
X.jlist = nullptr;
X.val = nullptr;
// Update comm sizes for this fix
comm_forward = comm_reverse = 2;
s_hist_X = s_hist_last = nullptr;
last_rows_rank = 0;
last_rows_flag = (comm->me == last_rows_rank);
}
/* ---------------------------------------------------------------------- */
FixACKS2ReaxFF::~FixACKS2ReaxFF()
{
if (copymode) return;
memory->destroy(bcut);
if (!reaxflag)
memory->destroy(bcut_acks2);
memory->destroy(s_hist_X);
memory->destroy(s_hist_last);
deallocate_storage();
deallocate_matrix();
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::post_constructor()
{
if (lmp->citeme) lmp->citeme->add(cite_fix_acks2_reax);
memory->create(s_hist_last,2,nprev,"acks2/reax:s_hist_last");
for (int i = 0; i < 2; i++)
for (int j = 0; j < nprev; ++j)
s_hist_last[i][j] = 0.0;
grow_arrays(atom->nmax);
for (int i = 0; i < atom->nmax; i++)
for (int j = 0; j < nprev; ++j)
s_hist[i][j] = s_hist_X[i][j] = 0.0;
pertype_parameters(pertype_option);
if (dual_enabled)
error->all(FLERR,"Dual keyword only supported with fix qeq/reax/omp");
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::pertype_parameters(char *arg)
{
// match either new keyword "reaxff" or old keyword "reax/c"
if (utils::strmatch(arg,"^reax..$")) {
reaxflag = 1;
Pair *pair = force->pair_match("^reax..",0);
if (!pair) error->all(FLERR,"No reaxff pair style for fix qeq/reaxff");
int tmp;
chi = (double *) pair->extract("chi",tmp);
eta = (double *) pair->extract("eta",tmp);
gamma = (double *) pair->extract("gamma",tmp);
bcut_acks2 = (double *) pair->extract("bcut_acks2",tmp);
double* bond_softness_ptr = (double *) pair->extract("bond_softness",tmp);
if (chi == nullptr || eta == nullptr || gamma == nullptr ||
bcut_acks2 == nullptr || bond_softness_ptr == nullptr)
error->all(FLERR,
"Fix acks2/reaxff could not extract params from pair reaxff");
bond_softness = *bond_softness_ptr;
return;
}
reaxflag = 0;
const int ntypes = atom->ntypes;
memory->create(chi,ntypes+1,"acks2/reaxff:chi");
memory->create(eta,ntypes+1,"acks2/reaxff:eta");
memory->create(gamma,ntypes+1,"acks2/reaxff:gamma");
memory->create(bcut_acks2,ntypes+1,"acks2/reaxff:bcut_acks2");
if (comm->me == 0) {
bond_softness = chi[0] = eta[0] = gamma[0] = 0.0;
try {
TextFileReader reader(arg,"acks2/reaxff parameter");
reader.ignore_comments = false;
const char *line = reader.next_line();
if (!line)
throw parser_error("Invalid parameter file for fix acks2/reaxff");
ValueTokenizer values(line);
if (values.count() != 1)
throw parser_error("Fix acks2/reaxff: Incorrect format of parameter file");
bond_softness = values.next_double();
for (int i = 1; i <= ntypes; i++) {
const char *line = reader.next_line();
if (!line)
throw parser_error("Invalid parameter file for fix acks2/reaxff");
ValueTokenizer values(line);
if (values.count() != 5)
throw parser_error("Fix acks2/reaxff: Incorrect format of parameter file");
int itype = values.next_int();
if ((itype < 1) || (itype > ntypes))
throw parser_error("Fix acks2/reaxff: invalid atom type in parameter file");
chi[itype] = values.next_double();
eta[itype] = values.next_double();
gamma[itype] = values.next_double();
bcut_acks2[itype] = values.next_double();
}
} catch (std::exception &e) {
error->one(FLERR,e.what());
}
}
MPI_Bcast(chi,ntypes+1,MPI_DOUBLE,0,world);
MPI_Bcast(eta,ntypes+1,MPI_DOUBLE,0,world);
MPI_Bcast(gamma,ntypes+1,MPI_DOUBLE,0,world);
MPI_Bcast(bcut_acks2,ntypes+1,MPI_DOUBLE,0,world);
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::allocate_storage()
{
nmax = atom->nmax;
int size = nmax*2 + 2;
// 0 to nn-1: owned atoms related to H matrix
// nn to NN-1: ghost atoms related to H matrix
// NN to NN+nn-1: owned atoms related to X matrix
// NN+nn to 2*NN-1: ghost atoms related X matrix
// 2*NN to 2*NN+1: last two rows, owned by proc 0
memory->create(s,size,"acks2:s");
memory->create(b_s,size,"acks2:b_s");
memory->create(Hdia_inv,nmax,"acks2:Hdia_inv");
memory->create(chi_field,nmax,"acks2:chi_field");
memory->create(X_diag,nmax,"acks2:X_diag");
memory->create(Xdia_inv,nmax,"acks2:Xdia_inv");
memory->create(p,size,"acks2:p");
memory->create(q,size,"acks2:q");
memory->create(r,size,"acks2:r");
memory->create(d,size,"acks2:d");
memory->create(g,size,"acks2:g");
memory->create(q_hat,size,"acks2:q_hat");
memory->create(r_hat,size,"acks2:r_hat");
memory->create(y,size,"acks2:y");
memory->create(z,size,"acks2:z");
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::deallocate_storage()
{
FixQEqReaxFF::deallocate_storage();
memory->destroy(X_diag);
memory->destroy(Xdia_inv);
memory->destroy(g);
memory->destroy(q_hat);
memory->destroy(r_hat);
memory->destroy(y);
memory->destroy(z);
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::allocate_matrix()
{
FixQEqReaxFF::allocate_matrix();
X.n = n_cap;
X.m = m_cap;
memory->create(X.firstnbr,n_cap,"acks2:X.firstnbr");
memory->create(X.numnbrs,n_cap,"acks2:X.numnbrs");
memory->create(X.jlist,m_cap,"acks2:X.jlist");
memory->create(X.val,m_cap,"acks2:X.val");
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::deallocate_matrix()
{
FixQEqReaxFF::deallocate_matrix();
memory->destroy(X.firstnbr);
memory->destroy(X.numnbrs);
memory->destroy(X.jlist);
memory->destroy(X.val);
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::init()
{
FixQEqReaxFF::init();
init_bondcut();
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::init_bondcut()
{
int i,j;
int ntypes;
ntypes = atom->ntypes;
if (bcut == nullptr)
memory->create(bcut,ntypes+1,ntypes+1,"acks2:bondcut");
for (i = 1; i <= ntypes; ++i)
for (j = 1; j <= ntypes; ++j) {
bcut[i][j] = 0.5*(bcut_acks2[i] + bcut_acks2[j]);
}
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::init_storage()
{
if (efield) get_chi_field();
for (int ii = 0; ii < NN; ii++) {
int i = ilist[ii];
if (atom->mask[i] & groupbit) {
b_s[i] = -chi[atom->type[i]];
if (efield) b_s[i] -= chi_field[i];
b_s[NN + i] = 0.0;
s[i] = 0.0;
s[NN + i] = 0.0;
}
}
for (int i = 0; i < 2; i++) {
b_s[2*NN + i] = 0.0;
s[2*NN + i] = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::pre_force(int /*vflag*/)
{
if (update->ntimestep % nevery) return;
int n = atom->nlocal;
if (reaxff) {
nn = reaxff->list->inum;
NN = reaxff->list->inum + reaxff->list->gnum;
ilist = reaxff->list->ilist;
numneigh = reaxff->list->numneigh;
firstneigh = reaxff->list->firstneigh;
} else {
nn = list->inum;
NN = list->inum + list->gnum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
}
// grow arrays if necessary
// need to be atom->nmax in length
if (atom->nmax > nmax) reallocate_storage();
if (n > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE)
reallocate_matrix();
if (efield) get_chi_field();
init_matvec();
matvecs = BiCGStab(b_s, s); // BiCGStab on s - parallel
calculate_Q();
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::init_matvec()
{
/* fill-in H matrix */
compute_H();
/* fill-in X matrix */
compute_X();
pack_flag = 4;
comm->reverse_comm_fix(this); //Coll_Vector(X_diag);
int ii, i;
for (ii = 0; ii < nn; ++ii) {
if (X_diag[ii] == 0.0)
Xdia_inv[ii] = 1.0;
else
Xdia_inv[ii] = 1.0 / X_diag[ii];
i = ilist[ii];
if (atom->mask[i] & groupbit) {
/* init pre-conditioner for H and init solution vectors */
Hdia_inv[i] = 1. / eta[atom->type[i]];
b_s[i] = -chi[atom->type[i]];
if (efield) b_s[i] -= chi_field[i];
b_s[NN+i] = 0.0;
/* cubic extrapolation for s from previous solutions */
s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]);
s[NN+i] = 4*(s_hist_X[i][0]+s_hist_X[i][2])-(6*s_hist_X[i][1]+s_hist_X[i][3]);
}
}
// last two rows
if (last_rows_flag) {
for (i = 0; i < 2; i++) {
b_s[2*NN+i] = 0.0;
s[2*NN+i] = 4*(s_hist_last[i][0]+s_hist_last[i][2])-(6*s_hist_last[i][1]+s_hist_last[i][3]);
}
}
pack_flag = 2;
comm->forward_comm_fix(this); //Dist_vector(s);
more_forward_comm(s);
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::compute_X()
{
int jnum;
int i, j, ii, jj, flag;
double dx, dy, dz, r_sqr;
const double SMALL = 0.0001;
int *type = atom->type;
tagint *tag = atom->tag;
double **x = atom->x;
int *mask = atom->mask;
memset(X_diag,0.0,atom->nmax*sizeof(double));
// fill in the X matrix
m_fill = 0;
r_sqr = 0;
for (ii = 0; ii < nn; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
jlist = firstneigh[i];
jnum = numneigh[i];
X.firstnbr[i] = m_fill;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
dx = x[j][0] - x[i][0];
dy = x[j][1] - x[i][1];
dz = x[j][2] - x[i][2];
r_sqr = SQR(dx) + SQR(dy) + SQR(dz);
flag = 0;
if (r_sqr <= SQR(swb)) {
if (j < atom->nlocal) flag = 1;
else if (tag[i] < tag[j]) flag = 1;
else if (tag[i] == tag[j]) {
if (dz > SMALL) flag = 1;
else if (fabs(dz) < SMALL) {
if (dy > SMALL) flag = 1;
else if (fabs(dy) < SMALL && dx > SMALL)
flag = 1;
}
}
}
if (flag) {
double bcutoff = bcut[type[i]][type[j]];
double bcutoff2 = bcutoff*bcutoff;
if (r_sqr <= bcutoff2) {
X.jlist[m_fill] = j;
double X_val = calculate_X(sqrt(r_sqr), bcutoff);
X.val[m_fill] = X_val;
X_diag[i] -= X_val;
X_diag[j] -= X_val;
m_fill++;
}
}
}
X.numnbrs[i] = m_fill - X.firstnbr[i];
}
}
if (m_fill >= X.m)
error->all(FLERR,"Fix acks2/reaxff has insufficient ACKS2 X matrix size: m_fill={} X.m={}\n",m_fill,X.m);
}
/* ---------------------------------------------------------------------- */
double FixACKS2ReaxFF::calculate_X(double r, double bcut)
{
double d = r/bcut;
double d3 = d*d*d;
double omd = 1.0 - d;
double omd2 = omd*omd;
double omd6 = omd2*omd2*omd2;
return bond_softness*d3*omd6;
}
/* ---------------------------------------------------------------------- */
int FixACKS2ReaxFF::BiCGStab(double *b, double *x)
{
int i, j;
double tmp, alpha, beta, omega, sigma, rho, rho_old, rnorm, bnorm;
int jj;
sparse_matvec_acks2(&H, &X, x, d);
pack_flag = 1;
comm->reverse_comm_fix(this); //Coll_Vector(d);
more_reverse_comm(d);
vector_sum(r , 1., b, -1., d, nn);
bnorm = parallel_norm(b, nn);
rnorm = parallel_norm(r, nn);
if (bnorm == 0.0) bnorm = 1.0;
vector_copy(r_hat, r, nn);
omega = 1.0;
rho = 1.0;
for (i = 1; i < imax && rnorm / bnorm > tolerance; ++i) {
rho = parallel_dot(r_hat, r, nn);
if (rho == 0.0) break;
if (i > 1) {
beta = (rho / rho_old) * (alpha / omega);
vector_sum(q , 1., p, -omega, z, nn);
vector_sum(p , 1., r, beta, q, nn);
} else {
vector_copy(p, r, nn);
}
// pre-conditioning
for (jj = 0; jj < nn; ++jj) {
j = ilist[jj];
if (atom->mask[j] & groupbit) {
d[j] = p[j] * Hdia_inv[j];
d[NN+j] = p[NN+j] * Xdia_inv[j];
}
}
// last two rows
if (last_rows_flag) {
d[2*NN] = p[2*NN];
d[2*NN + 1] = p[2*NN + 1];
}
pack_flag = 1;
comm->forward_comm_fix(this); //Dist_vector(d);
more_forward_comm(d);
sparse_matvec_acks2(&H, &X, d, z);
pack_flag = 2;
comm->reverse_comm_fix(this); //Coll_vector(z);
more_reverse_comm(z);
tmp = parallel_dot(r_hat, z, nn);
alpha = rho / tmp;
vector_sum(q , 1., r, -alpha, z, nn);
tmp = parallel_dot(q, q, nn);
// early convergence check
if (tmp < tolerance) {
vector_add(x, alpha, d, nn);
break;
}
// pre-conditioning
for (jj = 0; jj < nn; ++jj) {
j = ilist[jj];
if (atom->mask[j] & groupbit) {
q_hat[j] = q[j] * Hdia_inv[j];
q_hat[NN+j] = q[NN+j] * Xdia_inv[j];
}
}
// last two rows
if (last_rows_flag) {
q_hat[2*NN] = q[2*NN];
q_hat[2*NN + 1] = q[2*NN + 1];
}
pack_flag = 3;
comm->forward_comm_fix(this); //Dist_vector(q_hat);
more_forward_comm(q_hat);
sparse_matvec_acks2(&H, &X, q_hat, y);
pack_flag = 3;
comm->reverse_comm_fix(this); //Dist_vector(y);
more_reverse_comm(y);
sigma = parallel_dot(y, q, nn);
tmp = parallel_dot(y, y, nn);
omega = sigma / tmp;
vector_sum(g , alpha, d, omega, q_hat, nn);
vector_add(x, 1., g, nn);
vector_sum(r , 1., q, -omega, y, nn);
rnorm = parallel_norm(r, nn);
if (omega == 0) break;
rho_old = rho;
}
if (comm->me == 0) {
if (omega == 0 || rho == 0) {
error->warning(FLERR,"Fix acks2/reaxff BiCGStab numerical breakdown, omega = {:.8}, rho = {:.8}",
omega,rho);
} else if (i >= imax) {
error->warning(FLERR,"Fix acks2/reaxff BiCGStab convergence failed after {} iterations "
"at step {}", i, update->ntimestep);
}
}
return i;
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::sparse_matvec_acks2(sparse_matrix *H, sparse_matrix *X, double *x, double *b)
{
int i, j, itr_j;
int ii;
for (ii = 0; ii < nn; ++ii) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
b[i] = eta[atom->type[i]] * x[i];
b[NN + i] = X_diag[i] * x[NN + i];
}
}
for (ii = nn; ii < NN; ++ii) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
b[i] = 0;
b[NN + i] = 0;
}
}
// last two rows
b[2*NN] = 0;
b[2*NN + 1] = 0;
for (ii = 0; ii < nn; ++ii) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
// H Matrix
for (itr_j=H->firstnbr[i]; itr_j<H->firstnbr[i]+H->numnbrs[i]; itr_j++) {
j = H->jlist[itr_j];
b[i] += H->val[itr_j] * x[j];
b[j] += H->val[itr_j] * x[i];
}
// X Matrix
for (itr_j=X->firstnbr[i]; itr_j<X->firstnbr[i]+X->numnbrs[i]; itr_j++) {
j = X->jlist[itr_j];
b[NN + i] += X->val[itr_j] * x[NN + j];
b[NN + j] += X->val[itr_j] * x[NN + i];
}
// Identity Matrix
b[NN + i] += x[i];
b[i] += x[NN + i];
// Second-to-last row/column
b[2*NN] += x[NN + i];
b[NN + i] += x[2*NN];
// Last row/column
b[2*NN + 1] += x[i];
b[i] += x[2*NN + 1];
}
}
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::calculate_Q()
{
int i, k;
for (int ii = 0; ii < nn; ++ii) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
/* backup s */
for (k = nprev-1; k > 0; --k) {
s_hist[i][k] = s_hist[i][k-1];
s_hist_X[i][k] = s_hist_X[i][k-1];
}
s_hist[i][0] = s[i];
s_hist_X[i][0] = s[NN+i];
}
}
// last two rows
if (last_rows_flag) {
for (int i = 0; i < 2; ++i) {
for (k = nprev-1; k > 0; --k)
s_hist_last[i][k] = s_hist_last[i][k-1];
s_hist_last[i][0] = s[2*NN+i];
}
}
pack_flag = 2;
comm->forward_comm_fix(this); //Dist_vector(s);
for (int ii = 0; ii < NN; ++ii) {
i = ilist[ii];
if (atom->mask[i] & groupbit)
atom->q[i] = s[i];
}
}
/* ---------------------------------------------------------------------- */
int FixACKS2ReaxFF::pack_forward_comm(int n, int *list, double *buf,
int /*pbc_flag*/, int * /*pbc*/)
{
int m = 0;
if (pack_flag == 1) {
for(int i = 0; i < n; i++) {
int j = list[i];
buf[m++] = d[j];
buf[m++] = d[NN+j];
}
} else if (pack_flag == 2) {
for(int i = 0; i < n; i++) {
int j = list[i];
buf[m++] = s[j];
buf[m++] = s[NN+j];
}
} else if (pack_flag == 3) {
for(int i = 0; i < n; i++) {
int j = list[i];
buf[m++] = q_hat[j];
buf[m++] = q_hat[NN+j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::unpack_forward_comm(int n, int first, double *buf)
{
int i, m;
int last = first + n;
m = 0;
if (pack_flag == 1) {
for(i = first; i < last; i++) {
d[i] = buf[m++];
d[NN+i] = buf[m++];
}
} else if (pack_flag == 2) {
for(i = first; i < last; i++) {
s[i] = buf[m++];
s[NN+i] = buf[m++];
}
} else if (pack_flag == 3) {
for(i = first; i < last; i++) {
q_hat[i] = buf[m++];
q_hat[NN+i] = buf[m++];
}
}
}
/* ---------------------------------------------------------------------- */
int FixACKS2ReaxFF::pack_reverse_comm(int n, int first, double *buf)
{
int i, m;
m = 0;
int last = first + n;
if (pack_flag == 1) {
for(i = first; i < last; i++) {
buf[m++] = d[i];
buf[m++] = d[NN+i];
}
} else if (pack_flag == 2) {
for(i = first; i < last; i++) {
buf[m++] = z[i];
buf[m++] = z[NN+i];
}
} else if (pack_flag == 3) {
for(i = first; i < last; i++) {
buf[m++] = y[i];
buf[m++] = y[NN+i];
}
} else if (pack_flag == 4) {
for(i = first; i < last; i++)
buf[m++] = X_diag[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::unpack_reverse_comm(int n, int *list, double *buf)
{
int j;
int m = 0;
if (pack_flag == 1) {
for(int i = 0; i < n; i++) {
j = list[i];
d[j] += buf[m++];
d[NN+j] += buf[m++];
}
} else if (pack_flag == 2) {
for(int i = 0; i < n; i++) {
j = list[i];
z[j] += buf[m++];
z[NN+j] += buf[m++];
}
} else if (pack_flag == 3) {
for(int i = 0; i < n; i++) {
j = list[i];
y[j] += buf[m++];
y[NN+j] += buf[m++];
}
} else if (pack_flag == 4) {
for(int i = 0; i < n; i++) {
j = list[i];
X_diag[j] += buf[m++];
}
}
}
/* ----------------------------------------------------------------------
one proc broadcasts last two rows of vector to everyone else
------------------------------------------------------------------------- */
void FixACKS2ReaxFF::more_forward_comm(double *vec)
{
MPI_Bcast(&vec[2*NN],2,MPI_DOUBLE,last_rows_rank,world);
}
/* ----------------------------------------------------------------------
reduce last two rows of vector and give to one proc
------------------------------------------------------------------------- */
void FixACKS2ReaxFF::more_reverse_comm(double *vec)
{
if (last_rows_flag)
MPI_Reduce(MPI_IN_PLACE,&vec[2*NN],2,MPI_DOUBLE,MPI_SUM,last_rows_rank,world);
else
MPI_Reduce(&vec[2*NN],nullptr,2,MPI_DOUBLE,MPI_SUM,last_rows_rank,world);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixACKS2ReaxFF::memory_usage()
{
double bytes;
const double size = 2.0*nmax + 2.0;
bytes = size*nprev * sizeof(double); // s_hist
bytes += nmax*4.0 * sizeof(double); // storage
bytes += size*11.0 * sizeof(double); // storage
bytes += n_cap*4.0 * sizeof(int); // matrix...
bytes += m_cap*2.0 * sizeof(int);
bytes += m_cap*2.0 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate solution history array
------------------------------------------------------------------------- */
void FixACKS2ReaxFF::grow_arrays(int nmax)
{
memory->grow(s_hist,nmax,nprev,"acks2:s_hist");
memory->grow(s_hist_X,nmax,nprev,"acks2:s_hist_X");
}
/* ----------------------------------------------------------------------
copy values within solution history array
------------------------------------------------------------------------- */
void FixACKS2ReaxFF::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nprev; m++) {
s_hist[j][m] = s_hist[i][m];
s_hist_X[j][m] = s_hist_X[i][m];
}
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixACKS2ReaxFF::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] = s_hist_X[i][m];
return nprev*2;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixACKS2ReaxFF::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++) s_hist_X[nlocal][m] = buf[nprev+m];
return nprev*2;
}
/* ---------------------------------------------------------------------- */
double FixACKS2ReaxFF::parallel_norm(double *v, int n)
{
int i;
double my_sum, norm_sqr;
int ii;
my_sum = 0.0;
norm_sqr = 0.0;
for (ii = 0; ii < n; ++ii) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
my_sum += SQR(v[i]);
my_sum += SQR(v[NN+i]);
}
}
// last two rows
if (last_rows_flag) {
my_sum += SQR(v[2*NN]);
my_sum += SQR(v[2*NN + 1]);
}
MPI_Allreduce(&my_sum, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world);
return sqrt(norm_sqr);
}
/* ---------------------------------------------------------------------- */
double FixACKS2ReaxFF::parallel_dot(double *v1, double *v2, int n)
{
int i;
double my_dot, res;
int ii;
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];
my_dot += v1[NN+i] * v2[NN+i];
}
}
// last two rows
if (last_rows_flag) {
my_dot += v1[2*NN] * v2[2*NN];
my_dot += v1[2*NN + 1] * v2[2*NN + 1];
}
MPI_Allreduce(&my_dot, &res, 1, MPI_DOUBLE, MPI_SUM, world);
return res;
}
/* ---------------------------------------------------------------------- */
double FixACKS2ReaxFF::parallel_vector_acc(double *v, int n)
{
int i;
double my_acc, res;
int ii;
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];
my_acc += v[NN+i];
}
}
// last two rows
if (last_rows_flag) {
my_acc += v[2*NN];
my_acc += v[2*NN + 1];
}
MPI_Allreduce(&my_acc, &res, 1, MPI_DOUBLE, MPI_SUM, world);
return res;
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::vector_sum(double* dest, double c, double* v,
double d, double* y, int k)
{
int kk;
for (--k; k>=0; --k) {
kk = ilist[k];
if (atom->mask[kk] & groupbit) {
dest[kk] = c * v[kk] + d * y[kk];
dest[NN + kk] = c * v[NN + kk] + d * y[NN + kk];
}
}
// last two rows
if (last_rows_flag) {
dest[2*NN] = c * v[2*NN] + d * y[2*NN];
dest[2*NN + 1] = c * v[2*NN + 1] + d * y[2*NN + 1];
}
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::vector_add(double* dest, double c, double* v, int k)
{
int kk;
for (--k; k>=0; --k) {
kk = ilist[k];
if (atom->mask[kk] & groupbit) {
dest[kk] += c * v[kk];
dest[NN + kk] += c * v[NN + kk];
}
}
// last two rows
if (last_rows_flag) {
dest[2*NN] += c * v[2*NN];
dest[2*NN + 1] += c * v[2*NN + 1];
}
}
/* ---------------------------------------------------------------------- */
void FixACKS2ReaxFF::vector_copy(double* dest, double* v, int k)
{
int kk;
for (--k; k>=0; --k) {
kk = ilist[k];
if (atom->mask[kk] & groupbit) {
dest[kk] = v[kk];
dest[NN + kk] = v[NN + kk];
}
}
// last two rows
if (last_rows_flag) {
dest[2*NN] = v[2*NN];
dest[2*NN + 1] = v[2*NN + 1];
}
}
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