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pair_lj_cut_hars_at.cpp
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Sat, Nov 16, 06:25

pair_lj_cut_hars_at.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: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_cut_hars_at.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "domain.h"
#include "fix.h"
#include "fix_lambdah_calc.h"
#include "modify.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define BIG MAXTAGINT
/* ---------------------------------------------------------------------- */
PairLJCutHARSAT::PairLJCutHARSAT(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 1;
writedata = 1;
AT_massproc_H = NULL;
AT_masstotal_H = NULL;
AT_molmap_H = NULL;
AT_mol_f_H = NULL;
AT_mol_f_all_H = NULL;
Comp_Energy_Num_H = NULL;
Comp_Energy_Num_all_H = NULL;
Int_Mean_Energy_H = NULL;
Mean_Energy_H = NULL;
Comp_Energy_H = NULL;
Comp_Energy_all_H = NULL;
Mean_Comp_Energy_H = NULL;
AT_molmap_H = NULL;
nmolecules = molecules_in_group(idlo,idhi);
H_AdResS_allocated = 0;
AT_Pressure_Compensation_Run = 0;
Comp_Counter_H = 0;
memory->create(AT_massproc_H,nmolecules,"pair:AT_massproc_H");
memory->create(AT_masstotal_H,nmolecules,"pair:AT_masstotal_H");
memory->create(AT_mol_f_H,nmolecules,3,"pair:AT_mol_f_H");
memory->create(AT_mol_f_all_H,nmolecules,3,"pair:AT_mol_f_all_H");
// compute masstotal for each molecule
MPI_Comm_rank(world, &me);
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
tagint imol;
double massone;
for (int i = 0; i < nmolecules; i++) AT_massproc_H[i] = 0.0;
for (int i = 0; i < nlocal; i++)
{
// if (mask[i] & groupbit) {
if (mask[i]) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
imol = molecule[i];
if (AT_molmap_H) imol = AT_molmap_H[imol-idlo];
else imol--;
AT_massproc_H[imol] += massone;
}
}
MPI_Allreduce(AT_massproc_H,AT_masstotal_H,nmolecules,MPI_DOUBLE,MPI_SUM,world);
}
/* ---------------------------------------------------------------------- */
PairLJCutHARSAT::~PairLJCutHARSAT()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(offset);
memory->destroy(AT_massproc_H);
memory->destroy(AT_masstotal_H);
memory->destroy(AT_molmap_H);
memory->destroy(AT_mol_f_H);
memory->destroy(AT_mol_f_all_H);
memory->destroy(Comp_Energy_Num_H);
memory->destroy(Comp_Energy_Num_all_H);
memory->destroy(Int_Mean_Energy_H);
memory->destroy(Mean_Energy_H);
memory->destroy(Comp_Energy_H);
memory->destroy(Comp_Energy_all_H);
memory->destroy(Mean_Comp_Energy_H);
}
}
/* ---------------------------------------------------------------------- */
void PairLJCutHARSAT::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj, factor_lj,Vij;
int *ilist,*jlist,*numneigh,**firstneigh;
int imoltypeH,jmoltypeH;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *lambdaH = atom->lambdaH;
double **gradlambdaH = atom->gradlambdaH;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
int imol,jmol;
tagint *molecule = atom->molecule;
double *mass = atom->mass;
int *replambdaH = atom->replambdaH;
int *moltypeH = atom->moltypeH;
int ibin, jbin;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
//if(update->ntimestep<3)return;
double iLambda, jLambda, ijLambda;
int This_Step = update->ntimestep;
if(This_Step >= AT_Update_Time_Begin && This_Step < AT_Update_Time_End && AT_Pressure_Comp_Flag != 0) AT_Pressure_Compensation_Run = 1;
for (int i = 0; i < nmolecules; i++) {
AT_mol_f_H[i][0] = AT_mol_f_H[i][1] = AT_mol_f_H[i][2] = 0;
AT_mol_f_all_H[i][0] = AT_mol_f_all_H[i][1] = AT_mol_f_all_H[i][2] = 0;
}
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
imoltypeH = moltypeH[i];
jlist = firstneigh[i];
jnum = numneigh[i];
iLambda = lambdaH[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
jLambda = lambdaH[j];
if(iLambda==0 && jLambda==0 && AllAtomistic!=1)continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
jmoltypeH = moltypeH[j];
imol = molecule[i];
jmol = molecule[j];
if (AT_molmap_H) {
imol = AT_molmap_H[imol-idlo];
jmol = AT_molmap_H[jmol-idlo];
}
else {
imol--;
jmol--;
}
if (rsq < cutsq[itype][jtype] && lj1[itype][jtype] != 0 && (imol != jmol)) {
if(((iLambda==1 && jLambda==1) || AllAtomistic)){
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
else if(iLambda !=0 || jLambda != 0){
ijLambda = 0.5 * (iLambda + jLambda);
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*(forcelj*ijLambda)*r2inv;
Vij = 0.5*(r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype]);
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
ibin = floor(iLambda/AT_lambda_Increment);
if(ibin==AT_Bin_Num)ibin = AT_Bin_Num - 1;
if(AT_Pressure_Compensation_Run != 0 && iLambda != 0 && iLambda != 1)Comp_Energy_H[ibin][imoltypeH-1] += Vij;
AT_mol_f_H[imol][0] += -Vij*gradlambdaH[i][0];
AT_mol_f_H[imol][1] += -Vij*gradlambdaH[i][1];
AT_mol_f_H[imol][2] += -Vij*gradlambdaH[i][2];
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
jbin = floor(jLambda/AT_lambda_Increment);
if(jbin==AT_Bin_Num)jbin = AT_Bin_Num - 1;
if(AT_Pressure_Compensation_Run != 0 && jLambda != 0 && jLambda != 1)Comp_Energy_H[jbin][jmoltypeH-1] += Vij;
AT_mol_f_H[jmol][0] += -Vij*gradlambdaH[j][0];
AT_mol_f_H[jmol][1] += -Vij*gradlambdaH[j][1];
AT_mol_f_H[jmol][2] += -Vij*gradlambdaH[j][2];
}
if (eflag) {
evdwl = ijLambda*Vij*2.0;
evdwl *= factor_lj;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
MPI_Allreduce(&AT_mol_f_H[0][0],&AT_mol_f_all_H[0][0],3*nmolecules,MPI_DOUBLE,MPI_SUM,world);
if(AT_Pressure_Compensation_Run != 0 && AT_Pressure_Comp_Flag != 0){
for (int i = 0; i < nlocal; i++){
iLambda = lambdaH[i];
if(replambdaH[i]!=0 && iLambda != 0 && iLambda != 1){
ibin = floor(iLambda/AT_lambda_Increment);
if(ibin==AT_Bin_Num)ibin = AT_Bin_Num - 1;
imoltypeH = moltypeH[i]-1;
Comp_Energy_Num_H[ibin][imoltypeH]++;
}
}
if(This_Step % AT_Update_Frequency == 0 && This_Step > AT_Update_Time_Begin)AT_Update_Compensation_Energy();
}
if(This_Step == AT_Update_Time_End && AT_Pressure_Compensation_Run != 0)AT_Print_Compensation_Energy();
double mol_mass,mass_frac;
if(AllAtomistic != 1){
if(AT_Pressure_Comp_Flag != 0){
for (int i = 0; i < nlocal; i++){
iLambda = lambdaH[i];
if(iLambda != 0 && iLambda != 1){
imol = molecule[i];
if (AT_molmap_H)imol = AT_molmap_H[imol-idlo];
else imol--;
mol_mass = AT_masstotal_H[imol];
mass_frac = mass[type[i]] / mol_mass;
ibin = floor(iLambda/AT_lambda_Increment);
imoltypeH = moltypeH[i] - 1;
f[i][0] += mass_frac*(AT_mol_f_all_H[imol][0]+gradlambdaH[i][0]*Mean_Comp_Energy_H[ibin][imoltypeH]);
f[i][1] += mass_frac*(AT_mol_f_all_H[imol][1]+gradlambdaH[i][1]*Mean_Comp_Energy_H[ibin][imoltypeH]);
f[i][2] += mass_frac*(AT_mol_f_all_H[imol][2]+gradlambdaH[i][2]*Mean_Comp_Energy_H[ibin][imoltypeH]);
if (evflag) ev_tally(i,i,nlocal,newton_pair,
-0.5*Int_Mean_Energy_H[ibin][imoltypeH],0.0,0.0,0.0,0.0,0.0);
}
}
}
else{
for (int i = 0; i < nlocal; i++){
iLambda = lambdaH[i];
if(iLambda != 0 && iLambda != 1){
imol = molecule[i];
if (AT_molmap_H)imol = AT_molmap_H[imol-idlo];
else imol--;
mol_mass = AT_masstotal_H[imol];
mass_frac = mass[type[i]] / mol_mass;
ibin = floor(iLambda/AT_lambda_Increment);
f[i][0] += mass_frac*(AT_mol_f_all_H[imol][0]);
f[i][1] += mass_frac*(AT_mol_f_all_H[imol][1]);
f[i][2] += mass_frac*(AT_mol_f_all_H[imol][2]);
}
}
}
}
if(This_Step == AT_Update_Time_End)AT_Pressure_Compensation_Run = 0;
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairLJCutHARSAT::compute_inner()
{
error->all(FLERR,"Rrespa has not been included!");
}
/* ---------------------------------------------------------------------- */
void PairLJCutHARSAT::compute_middle()
{
error->all(FLERR,"Rrespa has not been included!");
}
/* ---------------------------------------------------------------------- */
void PairLJCutHARSAT::compute_outer(int eflag, int vflag)
{
error->all(FLERR,"Rrespa has not been included!");
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJCutHARSAT::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pairLJHAT: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,"pairLJHAT:cutsq");
memory->create(cut,n+1,n+1,"pairLJHAT:cut");
memory->create(epsilon,n+1,n+1,"pairLJHAT:epsilon");
memory->create(sigma,n+1,n+1,"pairLJHAT:sigma");
memory->create(lj1,n+1,n+1,"pairLJHAT:lj1");
memory->create(lj2,n+1,n+1,"pairLJHAT:lj2");
memory->create(lj3,n+1,n+1,"pairLJHAT:lj3");
memory->create(lj4,n+1,n+1,"pairLJHAT:lj4");
memory->create(offset,n+1,n+1,"pairLJHAT:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJCutHARSAT::settings(int narg, char **arg)
{
if (narg != 3) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
// reset cutoffs that have been explicitly set
AllAtomistic = force->numeric(FLERR,arg[1]);
Load_File_Flag = force->numeric(FLERR,arg[2]);
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
------------------------------------------------------------------------- */
void PairLJCutHARSAT::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double epsilon_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double cut_one = cut_global;
if (narg == 5) cut_one = force->numeric(FLERR,arg[4]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
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 PairLJCutHARSAT::init_style()
{
// request regular or rRESPA neighbor lists
if(me == 0){
if (screen)fprintf(screen,"AT_H_AdResS_allocated flag = %d\n",H_AdResS_allocated);
if (logfile)fprintf(logfile,"AT_H_AdResS_allocated flag = %d\n",H_AdResS_allocated);
}
if(!H_AdResS_allocated)H_AdResS_Allocation();
int This_Step = update->ntimestep;
if((This_Step > AT_Update_Time_Begin || Load_File_Flag) && AT_Pressure_Comp_Flag != 0)Load_Compensation_Pressure();
if(This_Step < AT_Update_Time_End && This_Step >= AT_Update_Time_Begin)Comp_Counter_H = floor((This_Step-AT_Update_Time_Begin)/AT_Update_Frequency);
if(me==0 && This_Step < AT_Update_Time_End && This_Step > AT_Update_Time_Begin){
if(screen)fprintf(screen,"AT_Pressure componsation forces are again being updated after previous %d times\n",Comp_Counter_H);
if(logfile)fprintf(logfile,"AT_Pressure componsation forces are again being updated after previous %d times\n",Comp_Counter_H);
}
int irequest;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
if (respa == 0) irequest = neighbor->request(this,instance_me);
else if (respa == 1) {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
} else {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 2;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respamiddle = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
}
} else {
irequest = neighbor->request(this,instance_me);
}
// set rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
((Respa *) update->integrate)->level_inner >= 0)
cut_respa = ((Respa *) update->integrate)->cutoff;
else cut_respa = NULL;
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
regular or rRESPA
------------------------------------------------------------------------- */
void PairLJCutHARSAT::init_list(int id, NeighList *ptr)
{
if (id == 0) list = ptr;
else if (id == 1) listinner = ptr;
else if (id == 2) listmiddle = ptr;
else if (id == 3) listouter = ptr;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJCutHARSAT::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
if (offset_flag) {
double ratio = sigma[i][j] / cut[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
offset[j][i] = offset[i][j];
// check interior rRESPA cutoff
if (cut_respa && cut[i][j] < cut_respa[3])
error->all(FLERR,"Pair cutoff < Respa interior cutoff");
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
int nlocal = atom->nlocal;
double count[2],all[2];
count[0] = count[1] = 0.0;
for (int k = 0; k < nlocal; k++) {
if (type[k] == i) count[0] += 1.0;
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
}
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCutHARSAT::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(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCutHARSAT::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(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCutHARSAT::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);
fwrite(&tail_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCutHARSAT::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_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);
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJCutHARSAT::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJCutHARSAT::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJCutHARSAT::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fforce = factor_lj*forcelj*r2inv;
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
return factor_lj*philj;
}
/* ---------------------------------------------------------------------- */
void *PairLJCutHARSAT::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
if (strcmp(str,"sigma") == 0) return (void *) sigma;
return NULL;
}
int PairLJCutHARSAT::molecules_in_group(tagint &idlo, tagint &idhi)
{
int i;
memory->destroy(AT_molmap_H);
AT_molmap_H = NULL;
// find lo/hi molecule ID for any atom in group
// warn if atom in group has ID = 0
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;
tagint lo = BIG;
tagint hi = -BIG;
int flag = 0;
for (i = 0; i < nlocal; i++)
{
// if (mask[i] & groupbit) {
if (mask[i]) {
if (molecule[i] == 0) flag = 1;
lo = MIN(lo,molecule[i]);
hi = MAX(hi,molecule[i]);
}
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning(FLERR,"Atom with molecule ID = 0 included in "
"compute molecule group");
MPI_Allreduce(&lo,&idlo,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&hi,&idhi,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (idlo == BIG) return 0;
// molmap = vector of length nlen
// set to 1 for IDs that appear in group across all procs, else 0
tagint nlen_tag = idhi-idlo+1;
if (nlen_tag > MAXSMALLINT)
error->all(FLERR,"Too many molecules for compute");
int nlen = (int) nlen_tag;
memory->create(AT_molmap_H,nlen,"pair:molmap_H");
for (i = 0; i < nlen; i++) AT_molmap_H[i] = 0;
for (i = 0; i < nlocal; i++)
// if (mask[i] & groupbit)
if (mask[i])
AT_molmap_H[molecule[i]-idlo] = 1;
int *AT_molmapall;
memory->create(AT_molmapall,nlen,"pair:AT_molmapall");
MPI_Allreduce(AT_molmap_H,AT_molmapall,nlen,MPI_INT,MPI_MAX,world);
// nmolecules = # of non-zero IDs in molmap
// molmap[i] = index of molecule, skipping molecules not in group with -1
int nmolecules = 0;
for (i = 0; i < nlen; i++)
if (AT_molmapall[i]) AT_molmap_H[i] = nmolecules++;
else AT_molmap_H[i] = -1;
memory->destroy(AT_molmapall);
// warn if any molecule has some atoms in group and some not in group
flag = 0;
for (i = 0; i < nlocal; i++) {
// if (mask[i] & groupbit) continue;
if (mask[i]) continue;
if (molecule[i] < idlo || molecule[i] > idhi) continue;
if (AT_molmap_H[molecule[i]-idlo] >= 0) flag = 1;
}
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning(FLERR,
"One or more compute molecules has atoms not in group");
// if molmap simply stores 1 to Nmolecules, then free it
if (idlo == 1 && idhi == nmolecules && nlen == nmolecules) {
memory->destroy(AT_molmap_H);
AT_molmap_H = NULL;
}
return nmolecules;
}
void PairLJCutHARSAT::AT_Print_Compensation_Energy(){
FILE *fp1;
fp1 = fopen("Mean_Comp_Energy_AT.txt","w");
if (fp1 == NULL) {
char str[128];
sprintf(str,"Cannot open Mean_Comp_Energy_AT.txt file %s","Mean_Comp_Energy_AT.txt");
error->one(FLERR,str);
}
for(int i = 0;i < AT_Bin_Num; i++){
fprintf(fp1,"%d",i+1);
for(int j = 0; j < atom->nmoltypesH; j++){
fprintf(fp1,"\t%.10f",Mean_Comp_Energy_H[i][j]);
}
fprintf(fp1,"\n");
}
fclose(fp1);
}
void PairLJCutHARSAT::AT_Update_Compensation_Energy(){
MPI_Allreduce(&Comp_Energy_H[0][0],&Comp_Energy_all_H[0][0],AT_Bin_Num*atom->nmoltypesH,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&Comp_Energy_Num_H[0][0],&Comp_Energy_Num_all_H[0][0],AT_Bin_Num*atom->nmoltypesH,MPI_INT,MPI_SUM,world);
for(int j = 0;j < atom->nmoltypesH; j++){
for(int i = 0;i < AT_Bin_Num; i++){
Mean_Energy_H[i][j] = Comp_Energy_all_H[i][j] / Comp_Energy_Num_all_H[i][j];
Mean_Comp_Energy_H[i][j] = (Comp_Counter_H * Mean_Comp_Energy_H[i][j] + Mean_Energy_H[i][j]) / (Comp_Counter_H + 1);
Int_Mean_Energy_H[i][j]=0;
}
}
Comp_Counter_H++;
for(int j = 0;j < atom->nmoltypesH; j++){
for(int i = 0;i < AT_Bin_Num; i++){
Comp_Energy_Num_H[i][j] = 0;
Comp_Energy_Num_all_H[i][j] = 0;
Comp_Energy_H[i][j] = 0;
Comp_Energy_all_H[i][j] =0;
}
}
if (me == 0)AT_Print_Compensation_Energy();
}
void PairLJCutHARSAT::Load_Compensation_Pressure(){
if(me == 0){
FILE *fp1;
char str[128];
fp1 = fopen("Mean_Comp_Energy_AT.txt","r");
if (fp1 == NULL) {
sprintf(str,"Cannot open fix Mean_Comp_Energy_AT.txt file %s","Mean_Comp_Energy_AT.txt");
error->one(FLERR,str);
}
int i1;
float f1;
while (!feof(fp1)){
fscanf (fp1,"%d",&i1);
for(int j=0;j<atom->nmoltypesH;j++){
fscanf (fp1,"\t%f",&f1);
Mean_Comp_Energy_H[i1-1][j] = f1;
}
fscanf (fp1,"\n");
if(i1 > AT_Bin_Num){
sprintf(str,"At drift force compensation bin number mismatches %d != %d",AT_Bin_Num,i1);
error->one(FLERR,str);
}
}
fclose(fp1);
if(me==0){
if(screen)fprintf(screen,"AT_Pressure componsation forces distributed successfully!\n");
if(logfile)fprintf(logfile,"AT_Pressure componsation forces distributed successfully!\n");
}
}
MPI_Bcast(Mean_Comp_Energy_H,AT_Bin_Num,MPI_DOUBLE,0,world);
}
void PairLJCutHARSAT::H_AdResS_Allocation(){
for (int i = 0; i < modify->nfix; i++){
if (strcmp(modify->fix[i]->style,"lambdah/calc") == 0){
lambda_H_fix = (FixLambdaHCalc *) modify->fix[i];
AT_lambda_Increment = lambda_H_fix->Pressure_lambda_Increment;
AT_Bin_Num = lambda_H_fix->Pressure_Bin_Num;
AT_Update_Frequency = lambda_H_fix->Pressure_Update_Frequency;
AT_Update_Time_Begin = lambda_H_fix->Pressure_Update_Time_Begin;
AT_Update_Time_End = lambda_H_fix->Pressure_Update_Time_End;
AT_Pressure_Comp_Flag = lambda_H_fix->Pressure_Comp_Flag;
AT_center_box = lambda_H_fix->center_box;
AT_Hybrid_Style = lambda_H_fix->Hybrid_Style;
}
}
if(me == 0){
if (screen){
fprintf(screen,"AT_lambda_Increment= %f\n",AT_lambda_Increment);
fprintf(screen,"AT_Bin_Num= %d\n",AT_Bin_Num);
fprintf(screen,"AT_Update_Frequency= %d\n",AT_Update_Frequency);
fprintf(screen,"AT_Update_Time_Begin= %d\n",AT_Update_Time_Begin);
fprintf(screen,"AT_Update_Time_End= %d\n",AT_Update_Time_End);
fprintf(screen,"AT_Pressure_Comp_Flag= %d\n",AT_Pressure_Comp_Flag);
}
if (logfile){
fprintf(logfile,"AT_lambda_Increment= %f\n",AT_lambda_Increment);
fprintf(logfile,"AT_Bin_Num= %d\n",AT_Bin_Num);
fprintf(logfile,"AT_Update_Frequency= %d\n",AT_Update_Frequency);
fprintf(logfile,"AT_Update_Time_Begin= %d\n",AT_Update_Time_Begin);
fprintf(logfile,"AT_Update_Time_End= %d\n",AT_Update_Time_End);
fprintf(logfile,"AT_Pressure_Comp_Flag= %d\n",AT_Pressure_Comp_Flag);
}
}
memory->create(Comp_Energy_Num_H,AT_Bin_Num,atom->nmoltypesH,"pairLJHAT:Comp_Energy_Num_H");
memory->create(Comp_Energy_Num_all_H,AT_Bin_Num,atom->nmoltypesH,"pairLJHAT:Comp_Energy_Num_all_H");
memory->create(Int_Mean_Energy_H,AT_Bin_Num,atom->nmoltypesH,"pairLJHAT:Int_Mean_Energy_H");
memory->create(Comp_Energy_H,AT_Bin_Num,atom->nmoltypesH,"pairLJHAT:Comp_Energy_H");
memory->create(Comp_Energy_all_H,AT_Bin_Num,atom->nmoltypesH,"pairLJHAT:Comp_Energy_all_H");
memory->create(Mean_Comp_Energy_H,AT_Bin_Num,atom->nmoltypesH,"pairLJHAT:Mean_Comp_Energy_H");
memory->create(Mean_Energy_H,AT_Bin_Num,atom->nmoltypesH,"pairLJHAT:Mean_Energy_H");
for(int j=0;j<atom->nmoltypesH;j++){
for(int i = 0;i < AT_Bin_Num; i++){
Int_Mean_Energy_H[i][j]=0;
Comp_Energy_H[i][j]=0;
Comp_Energy_all_H[i][j]=0;
Mean_Comp_Energy_H[i][j]=0;
Comp_Energy_Num_H[i][j] = 0;
Comp_Energy_Num_all_H[i][j] = 0;
}
}
H_AdResS_allocated = 1;
}

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