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compatible to lammps stable_29Oct2020 #302

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Dec 1, 2020
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compatible to lammps stable_29Oct2020 #302

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4 changes: 2 additions & 2 deletions source/lmp/pair_nnp.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -816,8 +816,8 @@ void PairNNP::coeff(int narg, char **arg)
ihi = n;
jhi = n;
if (narg == 2) {
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
if (ilo != 1 || jlo != 1 || ihi != n || jhi != n) {
error->all(FLERR,"deepmd requires that the scale should be set to all atom types, i.e. pair_coeff * *.");
}
Expand Down
75 changes: 23 additions & 52 deletions source/lmp/pppm_dplr.cpp
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, [email protected]

Copyright (2003) Sandia Corporation. Under the terms of Contract
Expand Down Expand Up @@ -38,6 +38,7 @@ enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM};
#define ONEF 1.0
#endif


/* ---------------------------------------------------------------------- */

#ifdef OLD_LMP_PPPM
Expand Down Expand Up @@ -68,7 +69,6 @@ void PPPMDPLR::init()
fill(fele.begin(), fele.end(), 0.0);
}


/* ----------------------------------------------------------------------
compute the PPPM long-range force, energy, virial
------------------------------------------------------------------------- */
Expand All @@ -80,15 +80,9 @@ void PPPMDPLR::compute(int eflag, int vflag)
// set energy/virial flags
// invoke allocate_peratom() if needed for first time

if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = evflag_atom = eflag_global = vflag_global =
eflag_atom = vflag_atom = 0;
ev_init(eflag,vflag);

if (evflag_atom && !peratom_allocate_flag) {
allocate_peratom();
cg_peratom->ghost_notify();
cg_peratom->setup();
}
if (evflag_atom && !peratom_allocate_flag) allocate_peratom();

// if atom count has changed, update qsum and qsqsum

Expand Down Expand Up @@ -127,7 +121,8 @@ void PPPMDPLR::compute(int eflag, int vflag)
// to fully sum contribution in their 3d bricks
// remap from 3d decomposition to FFT decomposition

cg->reverse_comm(this,REVERSE_RHO);
gc->reverse_comm_kspace(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
brick2fft();

// compute potential gradient on my FFT grid and
Expand All @@ -140,16 +135,22 @@ void PPPMDPLR::compute(int eflag, int vflag)
// all procs communicate E-field values
// to fill ghost cells surrounding their 3d bricks

if (differentiation_flag == 1) cg->forward_comm(this,FORWARD_AD);
else cg->forward_comm(this,FORWARD_IK);
if (differentiation_flag == 1)
gc->forward_comm_kspace(this,1,sizeof(FFT_SCALAR),FORWARD_AD,
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
else
gc->forward_comm_kspace(this,3,sizeof(FFT_SCALAR),FORWARD_IK,
gc_buf1,gc_buf2,MPI_FFT_SCALAR);

// extra per-atom energy/virial communication

if (evflag_atom) {
if (differentiation_flag == 1 && vflag_atom)
cg_peratom->forward_comm(this,FORWARD_AD_PERATOM);
gc->forward_comm_kspace(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM,
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
else if (differentiation_flag == 0)
cg_peratom->forward_comm(this,FORWARD_IK_PERATOM);
gc->forward_comm_kspace(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM,
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
}

// calculate the force on my particles
Expand Down Expand Up @@ -183,14 +184,6 @@ void PPPMDPLR::compute(int eflag, int vflag)
MPI_Allreduce(virial,virial_all,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) virial[i] = 0.5*qscale*volume*virial_all[i];
}
// std::cout<< "energy in pppm -------------------" << std::endl;
// std::cout << energy << " "
// << std::endl;
// std::cout<< "virial in pppm -------------------" << std::endl;
// for (int ii = 0; ii < 6; ++ii){
// std::cout << virial[ii] << " " ;
// }
// std::cout << std::endl;

// per-atom energy/virial
// energy includes self-energy correction
Expand Down Expand Up @@ -227,10 +220,10 @@ void PPPMDPLR::compute(int eflag, int vflag)
if (triclinic) domain->lamda2x(atom->nlocal);
}


/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles for ik
------------------------------------------------------------------------- */

void PPPMDPLR::fieldforce_ik()
{
int i,l,m,n,nx,ny,nz,mx,my,mz;
Expand Down Expand Up @@ -288,21 +281,6 @@ void PPPMDPLR::fieldforce_ik()
fele[i*3+1] += qfactor*eky;
if (slabflag != 2) fele[i*3+2] += qfactor*ekz;
}

// vector<FLOAT_PREC> dcoord(nall*3), dbox(9);
// vector<int> dtype(nall);
// {
// double ** xx = atom->x;
// for(int ii = 0; ii < nall; ++ii){
// for (int dd = 0; dd < 3; +=dd){
// dcoord[ii*3+dd] = xx[ii][dd];
// }
// }
// int *type = atom->type;
// for (int ii = 0; ii < nall; ++ii){
// dtype[ii] = type[ii] - 1;
// }
// }
}

/* ----------------------------------------------------------------------
Expand Down Expand Up @@ -335,11 +313,14 @@ void PPPMDPLR::fieldforce_ad()

double *q = atom->q;
double **x = atom->x;
double **f = atom->f;
// double **f = atom->f;

int nlocal = atom->nlocal;
int nghost = atom->nghost;
int nall = nlocal + nghost;

vector<double > fele(nlocal, 0.0);
fele.resize(nlocal*3);
fill(fele.begin(), fele.end(), 0.0);

for (i = 0; i < nlocal; i++) {
nx = part2grid[i][0];
Expand Down Expand Up @@ -369,7 +350,7 @@ void PPPMDPLR::fieldforce_ad()
eky *= hy_inv;
ekz *= hz_inv;

// convert E-field to force and substract self forces
// convert E-field to force and subtract self forces

const double qfactor = qqrd2e * scale;

Expand All @@ -392,15 +373,5 @@ void PPPMDPLR::fieldforce_ad()
sf *= 2*q[i]*q[i];
if (slabflag != 2) fele[i*3+2] += qfactor*(ekz*q[i] - sf);
}

// for (int ii = 0; ii < nlocal; ++ii){
// cout << ii << "\t ";
// for (int dd = 0; dd < 3; ++dd){
// cout << fele[ii*3+dd] << " " ;
// }
// cout << endl;
// }
}