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Wed, Nov 13, 09:46

pair_awpmd_cut.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: Ilya Valuev (JIHT, Moscow, Russia)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_awpmd_cut.h"
#include "atom.h"
#include "update.h"
#include "min.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "TCP/wpmd_split.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairAWPMDCut::PairAWPMDCut(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
nmax = 0;
min_var = NULL;
min_varforce = NULL;
nextra = 4;
pvector = new double[nextra];
ermscale=1.;
width_pbc=0.;
wpmd= new AWPMD_split();
half_box_length=0;
}
/* ---------------------------------------------------------------------- */
PairAWPMDCut::~PairAWPMDCut()
{
delete [] pvector;
memory->destroy(min_var);
memory->destroy(min_varforce);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
}
delete wpmd;
}
struct cmp_x{
double **xx;
double tol;
cmp_x(double **xx_=NULL, double tol_=1e-12):xx(xx_),tol(tol_){}
bool operator()(const pair<int,int> &left, const pair<int,int> &right) const {
if(left.first==right.first){
double d=xx[left.second][0]-xx[right.second][0];
if(d<-tol)
return true;
else if(d>tol)
return false;
d=xx[left.second][1]-xx[right.second][1];
if(d<-tol)
return true;
else if(d>tol)
return false;
d=xx[left.second][2]-xx[right.second][2];
if(d<-tol)
return true;
else
return false;
}
else
return left.first<right.first;
}
};
/* ---------------------------------------------------------------------- */
void PairAWPMDCut::compute(int eflag, int vflag)
{
// pvector = [KE, Pauli, ecoul, radial_restraint]
for (int i=0; i<4; i++) pvector[i] = 0.0;
if (eflag || vflag)
ev_setup(eflag,vflag);
else
evflag = vflag_fdotr = 0; //??
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *spin = atom->spin;
int *type = atom->type;
int *etag = atom->etag;
double **v = atom->v;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int ntot=nlocal+nghost;
int newton_pair = force->newton_pair;
int inum = list->inum;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// width pbc
if(width_pbc<0)
wpmd->Lextra=2*half_box_length;
else
wpmd->Lextra=width_pbc;
wpmd->newton_pair=newton_pair;
# if 1
// mapping of the LAMMPS numbers to the AWPMC numbers
vector<int> gmap(ntot,-1);
for (int ii = 0; ii < inum; ii++) {
int i = ilist[ii];
// local particles are all there
gmap[i]=0;
Vector_3 ri=Vector_3(x[i][0],x[i][1],x[i][2]);
int itype = type[i];
int *jlist = firstneigh[i];
int jnum = numneigh[i];
for (int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
j &= NEIGHMASK;
if(j>=nlocal){ // this is a ghost
Vector_3 rj=Vector_3(x[j][0],x[j][1],x[j][2]);
int jtype = type[j];
double rsq=(ri-rj).norm2();
if (rsq < cutsq[itype][jtype])
gmap[j]=0; //bingo, this ghost is really needed
}
}
}
# else // old mapping
// mapping of the LAMMPS numbers to the AWPMC numbers
vector<int> gmap(ntot,-1);
// map for filtering the clones out: [tag,image] -> id
typedef map< pair<int,int>, int, cmp_x > map_t;
cmp_x cmp(x);
map_t idmap(cmp);
for (int ii = 0; ii < inum; ii++) {
int i = ilist[ii];
// local particles are all there
idmap[make_pair(atom->tag[i],i)]=i;
bool i_local= i<nlocal ? true : false;
if(i_local)
gmap[i]=0;
else if(gmap[i]==0) // this is a ghost which already has been tested
continue;
Vector_3 ri=Vector_3(x[i][0],x[i][1],x[i][2]);
int itype = type[i];
int *jlist = firstneigh[i];
int jnum = numneigh[i];
for (int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
j &= NEIGHMASK;
pair<map_t::iterator,bool> res=idmap.insert(make_pair(make_pair(atom->tag[j],j),j));
bool have_it=!res.second;
if(have_it){ // the clone of this particle is already listed
if(res.first->second!=j) // check that was not the very same particle
gmap[j]=-1; // filter out
continue;
}
bool j_local= j<nlocal ? true : false;
if((i_local && !j_local) || (j_local && !i_local)){ // some of them is a ghost
Vector_3 rj=Vector_3(x[j][0],x[j][1],x[j][2]);
int jtype = type[j];
double rsq=(ri-rj).norm2();
if (rsq < cutsq[itype][jtype]){
if(!i_local){
gmap[i]=0; //bingo, this ghost is really needed
break; // don't need to continue j loop
}
else
gmap[j]=0; //bingo, this ghost is really needed
}
}
}
}
# endif
// prepare the solver object
wpmd->reset();
map<int,vector<int> > etmap;
// add particles to the AWPMD solver object
for (int i = 0; i < ntot; i++) {
//int i = ilist[ii];
if(gmap[i]<0) // this particle was filtered out
continue;
if(spin[i]==0) // this is an ion
gmap[i]=wpmd->add_ion(q[i], Vector_3(x[i][0],x[i][1],x[i][2]),i<nlocal ? atom->tag[i] : -atom->tag[i]);
else if(spin[i]==1 || spin[i]==-1){ // electron, sort them according to the tag
etmap[etag[i]].push_back(i);
}
else
error->all(FLERR,fmt("Invalid spin value (%d) for particle %d !",spin[i],i));
}
// ion force vector
Vector_3 *fi=NULL;
if(wpmd->ni)
fi= new Vector_3[wpmd->ni];
// adding electrons
for(map<int,vector<int> >::iterator it=etmap.begin(); it!= etmap.end(); ++it){
vector<int> &el=it->second;
if(!el.size()) // should not happen
continue;
int s=spin[el[0]] >0 ? 0 : 1;
wpmd->add_electron(s); // starts adding the spits
for(size_t k=0;k<el.size();k++){
int i=el[k];
if(spin[el[0]]!=spin[i])
error->all(FLERR,fmt("WP splits for one electron should have the same spin (at particles %d, %d)!",el[0],i));
double m= atom->mass ? atom->mass[type[i]] : force->e_mass;
Vector_3 xx=Vector_3(x[i][0],x[i][1],x[i][2]);
Vector_3 rv=m*Vector_3(v[i][0],v[i][1],v[i][2]);
double pv=ermscale*m*atom->ervel[i];
Vector_2 cc=Vector_2(atom->cs[2*i],atom->cs[2*i+1]);
gmap[i]=wpmd->add_split(xx,rv,atom->eradius[i],pv,cc,1.,atom->q[i],i<nlocal ? atom->tag[i] : -atom->tag[i]);
// resetting for the case constraints were applied
v[i][0]=rv[0]/m;
v[i][1]=rv[1]/m;
v[i][2]=rv[2]/m;
atom->ervel[i]=pv/(m*ermscale);
}
}
wpmd->set_pbc(NULL); // not required for LAMMPS
wpmd->interaction(0x1|0x4|0x10,fi);
// get forces from the AWPMD solver object
for (int ii = 0; ii < inum; ii++) {
int i = ilist[ii];
if(gmap[i]<0) // this particle was filtered out
continue;
if(spin[i]==0){ // this is an ion, copying forces
int ion=gmap[i];
f[i][0]=fi[ion][0];
f[i][0]=fi[ion][1];
f[i][0]=fi[ion][2];
}
else { // electron
int iel=gmap[i];
int s=spin[i] >0 ? 0 : 1;
wpmd->get_wp_force(s,iel,(Vector_3 *)f[i],(Vector_3 *)(atom->vforce+3*i),atom->erforce+i,atom->ervelforce+i,(Vector_2 *)(atom->csforce+2*i));
}
}
if(fi)
delete [] fi;
// update LAMMPS energy
if (eflag_either) {
if (eflag_global){
eng_coul+= wpmd->get_energy();
// pvector = [KE, Pauli, ecoul, radial_restraint]
pvector[0] = wpmd->Ee[0]+wpmd->Ee[1];
pvector[2] = wpmd->Eii+wpmd->Eei[0]+wpmd->Eei[1]+wpmd->Eee;
pvector[1] = pvector[0] + pvector[2] - wpmd->Edk - wpmd->Edc - wpmd->Eii; // All except diagonal terms
pvector[3] = wpmd->Ew;
}
if (eflag_atom) {
// transfer per-atom energies here
for (int i = 0; i < ntot; i++) {
if(gmap[i]<0) // this particle was filtered out
continue;
if(spin[i]==0){
eatom[i]=wpmd->Eiep[gmap[i]]+wpmd->Eiip[gmap[i]];
}
else {
int s=spin[i] >0 ? 0 : 1;
eatom[i]=wpmd->Eep[s][gmap[i]]+wpmd->Eeip[s][gmap[i]]+wpmd->Eeep[s][gmap[i]]+wpmd->Ewp[s][gmap[i]];
}
}
}
}
if (vflag_fdotr) {
virial_fdotr_compute();
if (flexible_pressure_flag)
virial_eradius_compute();
}
}
/* ----------------------------------------------------------------------
electron width-specific contribution to global virial
------------------------------------------------------------------------- */
void PairAWPMDCut::virial_eradius_compute()
{
double *eradius = atom->eradius;
double *erforce = atom->erforce;
double e_virial;
int *spin = atom->spin;
// sum over force on all particles including ghosts
if (neighbor->includegroup == 0) {
int nall = atom->nlocal + atom->nghost;
for (int i = 0; i < nall; i++) {
if (spin[i]) {
e_virial = erforce[i]*eradius[i]/3;
virial[0] += e_virial;
virial[1] += e_virial;
virial[2] += e_virial;
}
}
// neighbor includegroup flag is set
// sum over force on initial nfirst particles and ghosts
} else {
int nall = atom->nfirst;
for (int i = 0; i < nall; i++) {
if (spin[i]) {
e_virial = erforce[i]*eradius[i]/3;
virial[0] += e_virial;
virial[1] += e_virial;
virial[2] += e_virial;
}
}
nall = atom->nlocal + atom->nghost;
for (int i = atom->nlocal; i < nall; i++) {
if (spin[i]) {
e_virial = erforce[i]*eradius[i]/3;
virial[0] += e_virial;
virial[1] += e_virial;
virial[2] += e_virial;
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairAWPMDCut::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
}
/* ---------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
// the format is: pair_style awpmd/cut [<global_cutoff|-1> [command1] [command2] ...]
// commands:
// [hartree|dproduct|uhf] -- quantum approximation level (default is hartree)
// [free|pbc <length|-1>|fix <w0|-1>|relax|harm <w0>] -- width restriction (default is free)
// [ermscale <number>] -- scaling factor between electron mass and effective width mass (used for equations of motion only) (default is 1)
// [flex_press] -- set flexible pressure flag
// -1 for length means default setting (L/2 for cutoff and L for width PBC)
void PairAWPMDCut::settings(int narg, char **arg){
if (narg < 1) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
ermscale=1.;
width_pbc=0.;
for(int i=1;i<narg;i++){
// reading commands
if(!strcmp(arg[i],"hartree"))
wpmd->approx=AWPMD::HARTREE;
else if(!strcmp(arg[i],"dproduct"))
wpmd->approx=AWPMD::DPRODUCT;
else if(!strcmp(arg[i],"uhf"))
wpmd->approx=AWPMD::UHF;
else if(!strcmp(arg[i],"free"))
wpmd->constraint=AWPMD::NONE;
else if(!strcmp(arg[i],"fix")){
wpmd->constraint=AWPMD::FIX;
i++;
if(i>=narg)
error->all(FLERR,"Setting 'fix' should be followed by a number in awpmd/cut");
wpmd->w0=force->numeric(FLERR,arg[i]);
}
else if(!strcmp(arg[i],"harm")){
wpmd->constraint=AWPMD::HARM;
i++;
if(i>=narg)
error->all(FLERR,"Setting 'harm' should be followed by a number in awpmd/cut");
wpmd->w0=force->numeric(FLERR,arg[i]);
wpmd->set_harm_constr(wpmd->w0);
}
else if(!strcmp(arg[i],"pbc")){
i++;
if(i>=narg)
error->all(FLERR,"Setting 'pbc' should be followed by a number in awpmd/cut");
width_pbc=force->numeric(FLERR,arg[i]);
}
else if(!strcmp(arg[i],"relax"))
wpmd->constraint=AWPMD::RELAX;
else if(!strcmp(arg[i],"ermscale")){
i++;
if(i>=narg)
error->all(FLERR,"Setting 'ermscale' should be followed by a number in awpmd/cut");
ermscale=force->numeric(FLERR,arg[i]);
}
else if(!strcmp(arg[i],"flex_press"))
flexible_pressure_flag = 1;
}
// reset cutoffs that have been explicitly set
/*
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}*/
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
// pair settings are as usual
void PairAWPMDCut::coeff(int narg, char **arg)
{
if (narg < 2 || narg > 3) error->all(FLERR,"Incorrect args for pair coefficients");
/*if(domain->xperiodic == 1 || domain->yperiodic == 1 ||
domain->zperiodic == 1) {*/
double delx = domain->boxhi[0]-domain->boxlo[0];
double dely = domain->boxhi[1]-domain->boxlo[1];
double delz = domain->boxhi[2]-domain->boxlo[2];
half_box_length = 0.5 * MIN(delx, MIN(dely, delz));
//}
if(cut_global<0)
cut_global=half_box_length;
if (!allocated)
allocate();
else{
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double cut_one = cut_global;
if (narg == 3) cut_one = force->numeric(FLERR,arg[2]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairAWPMDCut::init_style()
{
// error and warning checks
if (!atom->q_flag || !atom->spin_flag ||
!atom->eradius_flag || !atom->erforce_flag ) // TO DO: adjust this to match approximation used
error->all(FLERR,"Pair awpmd/cut requires atom attributes "
"q, spin, eradius, erforce");
/*
if(vflag_atom){ // can't compute virial per atom
//warning->
error->all(FLERR,"Pair style awpmd can't compute per atom virials");
}*/
// add hook to minimizer for eradius and erforce
if (update->whichflag == 2)
int ignore = update->minimize->request(this,1,0.01);
// make sure to use the appropriate timestep when using real units
/*if (update->whichflag == 1) {
if (force->qqr2e == 332.06371 && update->dt == 1.0)
error->all(FLERR,"You must lower the default real units timestep for pEFF ");
}*/
// need a half neigh list and optionally a granular history neigh list
//int irequest = neighbor->request(this,instance_me);
//if (atom->tag_enable == 0)
// error->all(FLERR,"Pair style reax requires atom IDs");
//if (force->newton_pair == 0)
//error->all(FLERR,"Pair style awpmd requires newton pair on");
//if (strcmp(update->unit_style,"real") != 0 && comm->me == 0)
//error->warning(FLERR,"Not using real units with pair reax");
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->newton = 2;
if(force->e_mass==0. || force->hhmrr2e==0. || force->mvh2r==0.)
error->all(FLERR,"Pair style awpmd requires e_mass and conversions hhmrr2e, mvh2r to be properly set for unit system");
wpmd->me=force->e_mass;
wpmd->h2_me=force->hhmrr2e/force->e_mass;
wpmd->one_h=force->mvh2r;
wpmd->coul_pref=force->qqrd2e;
wpmd->calc_ii=1;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairAWPMDCut::init_one(int i, int j)
{
if (setflag[i][j] == 0)
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairAWPMDCut::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairAWPMDCut::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) fread(&cut[i][j],sizeof(double),1,fp);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairAWPMDCut::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairAWPMDCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
returns pointers to the log() of electron radius and corresponding force
minimizer operates on log(radius) so radius never goes negative
these arrays are stored locally by pair style
------------------------------------------------------------------------- */
void PairAWPMDCut::min_xf_pointers(int ignore, double **xextra, double **fextra)
{
// grow arrays if necessary
// need to be atom->nmax in length
int nvar=atom->nmax*(3+1+1+2); // w(1), vel(3), pw(1), cs(2)
if (nvar > nmax) {
memory->destroy(min_var);
memory->destroy(min_varforce);
nmax = nvar;
memory->create(min_var,nmax,"pair:min_var");
memory->create(min_varforce,nmax,"pair:min_varforce");
}
*xextra = min_var;
*fextra = min_varforce;
}
/* ----------------------------------------------------------------------
minimizer requests the log() of electron radius and corresponding force
calculate and store in min_eradius and min_erforce
------------------------------------------------------------------------- */
void PairAWPMDCut::min_xf_get(int ignore)
{
double *eradius = atom->eradius;
double *erforce = atom->erforce;
double **v=atom->v;
double *vforce=atom->vforce;
double *ervel=atom->ervel;
double *ervelforce=atom->ervelforce;
double *cs=atom->cs;
double *csforce=atom->csforce;
int *spin = atom->spin;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (spin[i]) {
min_var[7*i] = log(eradius[i]);
min_varforce[7*i] = eradius[i]*erforce[i];
for(int j=0;j<3;j++){
min_var[7*i+1+3*j] = v[i][j];
min_varforce[7*i+1+3*j] = vforce[3*i+j];
}
min_var[7*i+4] = ervel[i];
min_varforce[7*i+4] = ervelforce[i];
min_var[7*i+5] = cs[2*i];
min_varforce[7*i+5] = csforce[2*i];
min_var[7*i+6] = cs[2*i+1];
min_varforce[7*i+6] = csforce[2*i+1];
} else {
for(int j=0;j<7;j++)
min_var[7*i+j] = min_varforce[7*i+j] = 0.0;
}
}
/* ----------------------------------------------------------------------
propagate the minimizer values to the atom values
------------------------------------------------------------------------- */
void PairAWPMDCut::min_x_set(int ignore)
{
double *eradius = atom->eradius;
double **v=atom->v;
double *ervel=atom->ervel;
double *cs=atom->cs;
int *spin = atom->spin;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (spin[i]){
eradius[i]=exp(min_var[7*i]);
for(int j=0;j<3;j++)
v[i][j]=min_var[7*i+1+3*j];
ervel[i]=min_var[7*i+4];
cs[2*i]=min_var[7*i+5];
cs[2*i+1]=min_var[7*i+6];
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairAWPMDCut::memory_usage()
{
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
bytes += 2 * nmax * sizeof(double);
return bytes;
}

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