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Tue, May 28, 00:55

pair_reax_c.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: Hasan Metin Aktulga, Purdue University
------------------------------------------------------------------------- */
#include "pair_reax_c.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "modify.h"
#include "fix.h"
#include "fix_reax_c.h"
#include "memory.h"
#include "error.h"
#include "reaxc_types.h"
#include "reaxc_allocate.h"
#include "reaxc_control.h"
#include "reaxc_ffield.h"
#include "reaxc_forces.h"
#include "reaxc_init_md.h"
#include "reaxc_io_tools.h"
#include "reaxc_list.h"
#include "reaxc_lookup.h"
#include "reaxc_reset_tools.h"
#include "reaxc_traj.h"
#include "reaxc_vector.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairReaxC::PairReaxC(LAMMPS *lmp) : Pair(lmp)
{
system = (reax_system *)
memory->smalloc(sizeof(reax_system),"reax:system");
control = (control_params *)
memory->smalloc(sizeof(control_params),"reax:control");
data = (simulation_data *)
memory->smalloc(sizeof(simulation_data),"reax:data");
workspace = (storage *)
memory->smalloc(sizeof(storage),"reax:storage");
lists = (reax_list *)
memory->smalloc(LIST_N * sizeof(reax_list),"reax:lists");
out_control = (output_controls *)
memory->smalloc(sizeof(output_controls),"reax:out_control");
mpi_data = (mpi_datatypes *)
memory->smalloc(sizeof(mpi_datatypes),"reax:mpi");
MPI_Comm_rank(world,&system->my_rank);
system->my_coords[0] = 0;
system->my_coords[1] = 0;
system->my_coords[2] = 0;
system->num_nbrs = 0;
system->n = 0; // my atoms
system->N = 0; // mine + ghosts
system->bigN = 0; // all atoms in the system
system->local_cap = 0;
system->total_cap = 0;
system->gcell_cap = 0;
system->bndry_cuts.ghost_nonb = 0;
system->bndry_cuts.ghost_hbond = 0;
system->bndry_cuts.ghost_bond = 0;
system->bndry_cuts.ghost_cutoff = 0;
system->my_atoms = NULL;
fix_reax = NULL;
nextra = 14;
pvector = new double[nextra];
setup_flag = 0;
}
/* ---------------------------------------------------------------------- */
PairReaxC::~PairReaxC()
{
if (fix_reax) modify->delete_fix("REAXC");
Close_Output_Files( system, control, out_control, mpi_data );
// deallocate reax data-structures
if( control->tabulate ) Deallocate_Lookup_Tables( system );
if( control->hbond_cut > 0 ) Delete_List( lists+HBONDS, world );
Delete_List( lists+BONDS, world );
Delete_List( lists+THREE_BODIES, world );
Delete_List( lists+FAR_NBRS, world );
// fprintf( stderr, "3\n" );
DeAllocate_Workspace( control, workspace );
DeAllocate_System( system );
//fprintf( stderr, "4\n" );
memory->destroy( system );
memory->destroy( control );
memory->destroy( data );
memory->destroy( workspace );
memory->destroy( lists );
memory->destroy( out_control );
memory->destroy( mpi_data );
//fprintf( stderr, "5\n" );
// deallocate interface storage
if( allocated ) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
delete [] chi;
delete [] eta;
delete [] gamma;
}
delete [] pvector;
//fprintf( stderr, "6\n" );
}
/* ---------------------------------------------------------------------- */
void PairReaxC::allocate( )
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
map = new int[n+1];
chi = new double[n+1];
eta = new double[n+1];
gamma = new double[n+1];
}
/* ---------------------------------------------------------------------- */
void PairReaxC::settings(int narg, char **arg)
{
if (narg != 1 && narg != 3) error->all("Illegal pair_style command");
// read name of control file or use default controls
if (strcmp(arg[0],"NULL") == 0) {
strcpy( control->sim_name, "simulate" );
control->ensemble = 0;
out_control->energy_update_freq = 0;
control->tabulate = 0;
control->reneighbor = 1;
control->vlist_cut = control->nonb_cut;
control->bond_cut = 5.;
control->hbond_cut = 7.50;
control->thb_cut = 0.001;
out_control->write_steps = 0;
out_control->traj_method = 0;
strcpy( out_control->traj_title, "default_title" );
out_control->atom_info = 0;
out_control->bond_info = 0;
out_control->angle_info = 0;
} else Read_Control_File(arg[0], control, out_control);
// default values
qeqflag = 1;
// process optional keywords
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"checkqeq") == 0) {
if (iarg+2 > narg) error->all("Illegal pair_style reax/c command");
if (strcmp(arg[iarg+1],"yes") == 0) qeqflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) qeqflag = 0;
else error->all("Illegal pair_style reax/c command");
iarg += 2;
} else error->all("Illegal pair_style reax/c command");
}
// LAMMPS is responsible for generating nbrs
control->reneighbor = 1;
}
/* ---------------------------------------------------------------------- */
void PairReaxC::coeff( int nargs, char **args )
{
if (!allocated) allocate();
if (nargs != 3 + atom->ntypes)
error->all("Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(args[0],"*") != 0 || strcmp(args[1],"*") != 0)
error->all("Incorrect args for pair coefficients");
// read ffield file
Read_Force_Field(args[2], &(system->reax_param), control);
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
int itmp;
int nreax_types = system->reax_param.num_atom_types;
for (int i = 3; i < nargs; i++) {
if (strcmp(args[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
itmp = atoi(args[i]) - 1;
map[i-2] = itmp;
// error check
if (itmp < 0 || itmp >= nreax_types)
error->all("Non-existent ReaxFF type");
}
int n = atom->ntypes;
int count = 0;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++) {
setflag[i][j] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ---------------------------------------------------------------------- */
void PairReaxC::init_style( )
{
if (!atom->q_flag) error->all("Pair reax/c requires atom attribute q");
firstwarn = 1;
int iqeq;
for (iqeq = 0; iqeq < modify->nfix; iqeq++)
if (strcmp(modify->fix[iqeq]->style,"qeq/reax") == 0) break;
if (iqeq == modify->nfix && qeqflag == 1)
error->all("Pair reax/c requires use of fix qeq/reax");
system->n = atom->nlocal; // my atoms
system->N = atom->nlocal + atom->nghost; // mine + ghosts
system->bigN = static_cast<int> (atom->natoms); // all atoms in the system
system->wsize = comm->nprocs;
system->big_box.V = 0;
system->big_box.box_norms[0] = 0;
system->big_box.box_norms[1] = 0;
system->big_box.box_norms[2] = 0;
if (atom->tag_enable == 0)
error->all("Pair style reax/c requires atom IDs");
if (force->newton_pair == 0)
error->all("Pair style reax/c requires newton pair on");
// need a half neighbor list w/ Newton off
// built whenever re-neighboring occurs
int irequest = neighbor->request(this);
neighbor->requests[irequest]->newton = 2;
cutmax = MAX3(control->nonb_cut, control->hbond_cut, 2*control->bond_cut);
for( int i = 0; i < LIST_N; ++i )
lists[i].allocated = 0;
if (fix_reax == NULL) {
char **fixarg = new char*[3];
fixarg[0] = (char *) "REAXC";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "REAXC";
modify->add_fix(3,fixarg);
delete [] fixarg;
fix_reax = (FixReaxC *) modify->fix[modify->nfix-1];
}
}
/* ---------------------------------------------------------------------- */
void PairReaxC::setup( )
{
int oldN;
system->n = atom->nlocal; // my atoms
system->N = atom->nlocal + atom->nghost; // mine + ghosts
oldN = system->N;
system->bigN = static_cast<int> (atom->natoms); // all atoms in the system
if (setup_flag == 0) {
setup_flag = 1;
int *num_bonds = fix_reax->num_bonds;
int *num_hbonds = fix_reax->num_hbonds;
control->vlist_cut = neighbor->cutneighmax;
// determine the local and total capacity
system->local_cap = MAX( (int)(system->n * SAFE_ZONE), MIN_CAP );
system->total_cap = MAX( (int)(system->N * SAFE_ZONE), MIN_CAP );
// initialize my data structures
PreAllocate_Space( system, control, workspace, world );
write_reax_atoms();
int num_nbrs = estimate_reax_lists();
if(!Make_List(system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
lists+FAR_NBRS, world))
error->all("Pair reax/c problem in far neighbor list");
write_reax_lists();
Initialize( system, control, data, workspace, &lists, out_control,
mpi_data, world );
for( int k = 0; k < system->N; ++k ) {
num_bonds[k] = system->my_atoms[k].num_bonds;
num_hbonds[k] = system->my_atoms[k].num_hbonds;
}
} else {
// fill in reax datastructures
write_reax_atoms();
// reset the bond list info for new atoms
for(int k = oldN; k < system->N; ++k)
Set_End_Index( k, Start_Index( k, lists+BONDS ), lists+BONDS );
// check if I need to shrink/extend my data-structs
ReAllocate( system, control, data, workspace, &lists, mpi_data );
}
}
/* ---------------------------------------------------------------------- */
double PairReaxC::init_one(int i, int j)
{
return cutmax;
}
/* ---------------------------------------------------------------------- */
void PairReaxC::compute(int eflag, int vflag)
{
double evdwl,ecoul;
double t_start, t_end;
// communicate num_bonds once every reneighboring
// 2 num arrays stored by fix, grab ptr to them
if (neighbor->ago == 0) comm->forward_comm_fix(fix_reax);
int *num_bonds = fix_reax->num_bonds;
int *num_hbonds = fix_reax->num_hbonds;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = vflag_global = 0;
if ((eflag_atom || vflag_atom) && firstwarn) {
firstwarn = 0;
if (comm->me == 0)
error->warning("Pair reax/c cannot yet compute "
"per-atom energy or stress");
}
if (vflag_global) control->virial = 1;
else control->virial = 0;
system->n = atom->nlocal; // my atoms
system->N = atom->nlocal + atom->nghost; // mine + ghosts
system->bigN = static_cast<int> (atom->natoms); // all atoms in the system
system->big_box.V = 0;
system->big_box.box_norms[0] = 0;
system->big_box.box_norms[1] = 0;
system->big_box.box_norms[2] = 0;
if( comm->me == 0 ) t_start = MPI_Wtime();
// setup data structures
setup();
Reset( system, control, data, workspace, &lists, world );
workspace->realloc.num_far = write_reax_lists();
// timing for filling in the reax lists
if( comm->me == 0 ) {
t_end = MPI_Wtime();
data->timing.nbrs = t_end - t_start;
}
// forces
Compute_Forces(system,control,data,workspace,&lists,out_control,mpi_data);
read_reax_forces();
for(int k = 0; k < system->N; ++k) {
num_bonds[k] = system->my_atoms[k].num_bonds;
num_hbonds[k] = system->my_atoms[k].num_hbonds;
}
// energies and pressure
if (eflag_global) {
evdwl += data->my_en.e_bond;
evdwl += data->my_en.e_ov;
evdwl += data->my_en.e_un;
evdwl += data->my_en.e_lp;
evdwl += data->my_en.e_ang;
evdwl += data->my_en.e_pen;
evdwl += data->my_en.e_coa;
evdwl += data->my_en.e_hb;
evdwl += data->my_en.e_tor;
evdwl += data->my_en.e_con;
evdwl += data->my_en.e_vdW;
ecoul += data->my_en.e_ele;
ecoul += data->my_en.e_pol;
eng_vdwl += evdwl;
eng_coul += ecoul;
// Store the different parts of the energy
// in a list for output by compute pair command
pvector[0] = data->my_en.e_bond;
pvector[1] = data->my_en.e_ov + data->my_en.e_un;
pvector[2] = data->my_en.e_lp;
pvector[3] = 0.0;
pvector[4] = data->my_en.e_ang;
pvector[5] = data->my_en.e_pen;
pvector[6] = data->my_en.e_coa;
pvector[7] = data->my_en.e_hb;
pvector[8] = data->my_en.e_tor;
pvector[9] = data->my_en.e_con;
pvector[10] = data->my_en.e_vdW;
pvector[11] = data->my_en.e_ele;
pvector[12] = 0.0;
pvector[13] = data->my_en.e_pol;
}
if (vflag_fdotr) virial_fdotr_compute();
// #if defined(LOG_PERFORMANCE)
// if( comm->me == 0 && fix_qeq != NULL ) {
// data->timing.s_matvecs += fix_qeq->matvecs;
// data->timing.qEq += fix_qeq->qeq_time;
// }
// #endif
Output_Results( system, control, data, &lists, out_control, mpi_data );
++data->step;
}
/* ---------------------------------------------------------------------- */
void PairReaxC::write_reax_atoms()
{
int *num_bonds = fix_reax->num_bonds;
int *num_hbonds = fix_reax->num_hbonds;
for( int i = 0; i < system->N; ++i ){
system->my_atoms[i].orig_id = atom->tag[i];
system->my_atoms[i].type = map[atom->type[i]];
system->my_atoms[i].x[0] = atom->x[i][0];
system->my_atoms[i].x[1] = atom->x[i][1];
system->my_atoms[i].x[2] = atom->x[i][2];
system->my_atoms[i].q = atom->q[i];
system->my_atoms[i].num_bonds = num_bonds[i];
system->my_atoms[i].num_hbonds = num_hbonds[i];
}
}
/* ---------------------------------------------------------------------- */
void PairReaxC::get_distance( rvec xj, rvec xi, double *d_sqr, rvec *dvec )
{
(*dvec)[0] = xj[0] - xi[0];
(*dvec)[1] = xj[1] - xi[1];
(*dvec)[2] = xj[2] - xi[2];
*d_sqr = SQR((*dvec)[0]) + SQR((*dvec)[1]) + SQR((*dvec)[2]);
}
/* ---------------------------------------------------------------------- */
void PairReaxC::set_far_nbr( far_neighbor_data *fdest,
int j, double d, rvec dvec )
{
fdest->nbr = j;
fdest->d = d;
rvec_Copy( fdest->dvec, dvec );
ivec_MakeZero( fdest->rel_box );
}
/* ---------------------------------------------------------------------- */
int PairReaxC::estimate_reax_lists()
{
int itr_i, itr_j, itr_g, i, j, g;
int nlocal, nghost, num_nbrs, num_marked;
int *ilist, *jlist, *numneigh, **firstneigh, *marked;
double d_sqr, g_d_sqr;
rvec dvec, g_dvec;
double *dist, **x;
reax_list *far_nbrs;
far_neighbor_data *far_list;
x = atom->x;
nlocal = atom->nlocal;
nghost = atom->nghost;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
far_nbrs = lists + FAR_NBRS;
far_list = far_nbrs->select.far_nbr_list;
num_nbrs = 0;
num_marked = 0;
marked = (int*) calloc( system->N, sizeof(int) );
dist = (double*) calloc( system->N, sizeof(double) );
for( itr_i = 0; itr_i < list->inum; ++itr_i ){
i = ilist[itr_i];
marked[i] = 1;
++num_marked;
jlist = firstneigh[i];
for( itr_j = 0; itr_j < numneigh[i]; ++itr_j ){
j = jlist[itr_j];
j &= NEIGHMASK;
get_distance( x[j], x[i], &d_sqr, &dvec );
dist[j] = sqrt(d_sqr);
if( dist[j] <= control->nonb_cut )
++num_nbrs;
}
// compute the nbrs among ghost atoms
for( itr_j = 0; itr_j < numneigh[i]; ++itr_j ){
j = jlist[itr_j];
j &= NEIGHMASK;
if( j >= nlocal && !marked[j] &&
dist[j] <= (control->vlist_cut - control->bond_cut) ){
marked[j] = 1;
++num_marked;
for( itr_g = 0; itr_g < numneigh[i]; ++itr_g ){
g = jlist[itr_g];
g &= NEIGHMASK;
if( g >= nlocal && !marked[g] ){
get_distance( x[g], x[j], &g_d_sqr, &g_dvec );
//g_dvec[0] = x[g][0] - x[j][0];
//g_dvec[1] = x[g][1] - x[j][1];
//g_dvec[2] = x[g][2] - x[j][2];
//g_d_sqr = SQR(g_dvec[0]) + SQR(g_dvec[1]) + SQR(g_dvec[2]);
if( g_d_sqr <= SQR(control->bond_cut) )
++num_nbrs;
}
}
}
}
}
for( i = 0; i < system->N; ++i )
if( !marked[i] ) {
marked[i] = 1;
++num_marked;
for( j = i+1; j < system->N; ++j )
if( !marked[j] ) {
get_distance( x[j], x[i], &d_sqr, &dvec );
if( d_sqr <= SQR(control->bond_cut) )
++num_nbrs;
}
}
free( marked );
free( dist );
return static_cast<int> (MAX( num_nbrs*SAFE_ZONE, MIN_CAP*MIN_NBRS ));
}
/* ---------------------------------------------------------------------- */
int PairReaxC::write_reax_lists()
{
int itr_i, itr_j, itr_g, i, j, g;
int nlocal, nghost, num_nbrs;
int *ilist, *jlist, *numneigh, **firstneigh, *marked;
double d_sqr, g_d, g_d_sqr;
rvec dvec, g_dvec;
double *dist, **x;
reax_list *far_nbrs;
far_neighbor_data *far_list;
x = atom->x;
nlocal = atom->nlocal;
nghost = atom->nghost;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
far_nbrs = lists + FAR_NBRS;
far_list = far_nbrs->select.far_nbr_list;
num_nbrs = 0;
marked = (int*) calloc( system->N, sizeof(int) );
dist = (double*) calloc( system->N, sizeof(double) );
for( itr_i = 0; itr_i < list->inum; ++itr_i ){
i = ilist[itr_i];
marked[i] = 1;
jlist = firstneigh[i];
Set_Start_Index( i, num_nbrs, far_nbrs );
for( itr_j = 0; itr_j < numneigh[i]; ++itr_j ){
j = jlist[itr_j];
j &= NEIGHMASK;
get_distance( x[j], x[i], &d_sqr, &dvec );
dist[j] = sqrt( d_sqr );
if( dist[j] <= control->nonb_cut ){
set_far_nbr( &far_list[num_nbrs], j, dist[j], dvec );
++num_nbrs;
}
}
Set_End_Index( i, num_nbrs, far_nbrs );
// compute the nbrs among ghost atoms
for( itr_j = 0; itr_j < numneigh[i]; ++itr_j ){
j = jlist[itr_j];
j &= NEIGHMASK;
if( j >= nlocal && !marked[j] &&
dist[j] <= (control->vlist_cut - control->bond_cut) ){
marked[j] = 1;
Set_Start_Index( j, num_nbrs, far_nbrs );
for( itr_g = 0; itr_g < numneigh[i]; ++itr_g ){
g = jlist[itr_g];
g &= NEIGHMASK;
if( g >= nlocal && !marked[g] ){
get_distance( x[g], x[j], &g_d_sqr, &g_dvec );
if( g_d_sqr <= SQR(control->bond_cut) ){
g_d = sqrt( g_d_sqr );
set_far_nbr( &far_list[num_nbrs], g, g_d, g_dvec );
++num_nbrs;
}
}
}
Set_End_Index( j, num_nbrs, far_nbrs );
}
}
}
for( i = 0; i < system->N; ++i )
if( !marked[i] ) {
marked[i] = 1;
Set_Start_Index( i, num_nbrs, far_nbrs );
for( j = i+1; j < system->N; ++j )
if( !marked[j] ) {
get_distance( x[j], x[i], &d_sqr, &dvec );
if( d_sqr <= SQR(control->bond_cut) ) {
set_far_nbr( &far_list[num_nbrs], j, sqrt(d_sqr), dvec );
++num_nbrs;
}
}
Set_End_Index( i, num_nbrs, far_nbrs );
}
free( marked );
free( dist );
return num_nbrs;
}
/* ---------------------------------------------------------------------- */
void PairReaxC::read_reax_forces()
{
for( int i = 0; i < system->N; ++i ) {
system->my_atoms[i].f[0] = workspace->f[i][0];
system->my_atoms[i].f[1] = workspace->f[i][1];
system->my_atoms[i].f[2] = workspace->f[i][2];
atom->f[i][0] = -workspace->f[i][0];
atom->f[i][1] = -workspace->f[i][1];
atom->f[i][2] = -workspace->f[i][2];
}
}
/* ---------------------------------------------------------------------- */
void *PairReaxC::extract(char *str, int &dim)
{
dim = 1;
if (strcmp(str,"chi") == 0 && chi) {
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) chi[i] = system->reax_param.sbp[map[i]].chi;
else chi[i] = 0.0;
return (void *) chi;
}
if (strcmp(str,"eta") == 0 && eta) {
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) eta[i] = system->reax_param.sbp[map[i]].eta;
else eta[i] = 0.0;
return (void *) eta;
}
if (strcmp(str,"gamma") == 0 && gamma) {
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) gamma[i] = system->reax_param.sbp[map[i]].gamma;
else gamma[i] = 0.0;
return (void *) gamma;
}
return NULL;
}

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