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lammps/src/ML-SNAP/compute_snap.cpp
Aidan Thompson 44436c0eb6 Cleaned up programming style
2022-06-17 17:24:34 -06:00

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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.
------------------------------------------------------------------------- */
#include "compute_snap.h"
#include "sna.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include <cstring>
using namespace LAMMPS_NS;
enum{SCALAR,VECTOR,ARRAY};
#define SNAPCOMPUTENAME "snap"
ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snap(nullptr),
snapall(nullptr), snap_peratom(nullptr), radelem(nullptr), wjelem(nullptr),
sinnerelem(nullptr), dinnerelem(nullptr), snaptr(nullptr)
{
array_flag = 1;
extarray = 0;
// code common to all SNAP computes
double rfac0, rmin0;
int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
int ntypes = atom->ntypes;
int nargmin = 6 + 2 * ntypes;
if (narg < nargmin) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
// default values
rmin0 = 0.0;
switchflag = 1;
bzeroflag = 1;
quadraticflag = 0;
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 0;
nelements = 1;
// process required arguments
memory->create(radelem, ntypes + 1, "snap:radelem"); // offset by 1 to match up with types
memory->create(wjelem, ntypes + 1, "snap:wjelem");
rcutfac = utils::numeric(FLERR, arg[3], false, lmp);
rfac0 = utils::numeric(FLERR, arg[4], false, lmp);
twojmax = utils::inumeric(FLERR, arg[5], false, lmp);
for (int i = 0; i < ntypes; i++)
radelem[i + 1] =
utils::numeric(FLERR, arg[6 + i], false, lmp);
for (int i = 0; i < ntypes; i++)
wjelem[i + 1] =
utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp);
// construct cutsq
double cut;
cutmax = 0.0;
memory->create(cutsq, ntypes + 1, ntypes + 1, "snap:cutsq");
for (int i = 1; i <= ntypes; i++) {
cut = 2.0 * radelem[i] * rcutfac;
if (cut > cutmax) cutmax = cut;
cutsq[i][i] = cut * cut;
for (int j = i + 1; j <= ntypes; j++) {
cut = (radelem[i] + radelem[j]) * rcutfac;
cutsq[i][j] = cutsq[j][i] = cut * cut;
}
}
// set local input checks
int sinnerflag = 0;
int dinnerflag = 0;
// process optional args
int iarg = nargmin;
while (iarg < narg) {
if (strcmp(arg[iarg], "rmin0") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
rmin0 = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "switchflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
switchflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "bzeroflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
bzeroflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "quadraticflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
quadraticflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "chem") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
chemflag = 1;
memory->create(map, ntypes + 1, "compute_sna_grid:map");
nelements = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
for (int i = 0; i < ntypes; i++) {
int jelem = utils::inumeric(FLERR, arg[iarg + 2 + i], false, lmp);
if (jelem < 0 || jelem >= nelements) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
map[i + 1] = jelem;
}
iarg += 2 + ntypes;
} else if (strcmp(arg[iarg], "bnormflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
bnormflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "wselfallflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
wselfallflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "switchinnerflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
switchinnerflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "sinner") == 0) {
iarg++;
if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
memory->create(sinnerelem, ntypes + 1, "snap:sinnerelem");
for (int i = 0; i < ntypes; i++)
sinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
sinnerflag = 1;
iarg += ntypes;
} else if (strcmp(arg[iarg], "dinner") == 0) {
iarg++;
if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
memory->create(dinnerelem, ntypes + 1, "snap:dinnerelem");
for (int i = 0; i < ntypes; i++)
dinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
dinnerflag = 1;
iarg += ntypes;
} else
error->all(FLERR, "Illegal compute ", SNAPCOMPUTENAME, " command");
}
if (switchinnerflag && !(sinnerflag && dinnerflag))
error->all(
FLERR,
"Illegal compute ", SNAPCOMPUTENAME, " command: switchinnerflag = 1, missing sinner/dinner keyword");
if (!switchinnerflag && (sinnerflag || dinnerflag))
error->all(
FLERR,
"Illegal compute ", SNAPCOMPUTENAME, " command: switchinnerflag = 0, unexpected sinner/dinner keyword");
snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag,
wselfallflag, nelements, switchinnerflag);
ncoeff = snaptr->ncoeff;
nvalues = ncoeff;
if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2;
// end code common to all SNAP computes
ndims_force = 3;
ndims_virial = 6;
yoffset = nvalues;
zoffset = 2*nvalues;
natoms = atom->natoms;
bik_rows = 1;
if (bikflag) bik_rows = natoms;
size_array_rows = bik_rows+ndims_force*natoms+ndims_virial;
size_array_cols = nvalues*atom->ntypes+1;
lastcol = size_array_cols-1;
ndims_peratom = ndims_force;
size_peratom = ndims_peratom*nvalues*atom->ntypes;
nmax = 0;
}
/* ---------------------------------------------------------------------- */
ComputeSnap::~ComputeSnap()
{
memory->destroy(snap);
memory->destroy(snapall);
memory->destroy(snap_peratom);
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
delete snaptr;
if (chemflag) memory->destroy(map);
if (switchinnerflag) {
memory->destroy(sinnerelem);
memory->destroy(dinnerelem);
}
}
/* ---------------------------------------------------------------------- */
void ComputeSnap::init()
{
if (force->pair == nullptr)
error->all(FLERR,"Compute snap requires a pair style be defined");
if (cutmax > force->pair->cutforce)
error->all(FLERR,"Compute snap cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
if (modify->get_compute_by_style("snap").size() > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute snap");
snaptr->init();
// allocate memory for global array
memory->create(snap,size_array_rows,size_array_cols,
"snap:snap");
memory->create(snapall,size_array_rows,size_array_cols,
"snap:snapall");
array = snapall;
// find compute for reference energy
std::string id_pe = std::string("thermo_pe");
int ipe = modify->find_compute(id_pe);
if (ipe == -1)
error->all(FLERR,"compute thermo_pe does not exist.");
c_pe = modify->compute[ipe];
// add compute for reference virial tensor
std::string id_virial = std::string("snap_press");
std::string pcmd = id_virial + " all pressure NULL virial";
modify->add_compute(pcmd);
int ivirial = modify->find_compute(id_virial);
if (ivirial == -1)
error->all(FLERR,"compute snap_press does not exist.");
c_virial = modify->compute[ivirial];
}
/* ---------------------------------------------------------------------- */
void ComputeSnap::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeSnap::compute_array()
{
int ntotal = atom->nlocal + atom->nghost;
invoked_array = update->ntimestep;
// grow snap_peratom array if necessary
if (atom->nmax > nmax) {
memory->destroy(snap_peratom);
nmax = atom->nmax;
memory->create(snap_peratom,nmax,size_peratom,
"snap:snap_peratom");
}
// clear global array
for (int irow = 0; irow < size_array_rows; irow++)
for (int icoeff = 0; icoeff < size_array_cols; icoeff++)
snap[irow][icoeff] = 0.0;
// clear local peratom array
for (int i = 0; i < ntotal; i++)
for (int icoeff = 0; icoeff < size_peratom; icoeff++) {
snap_peratom[i][icoeff] = 0.0;
}
// invoke full neighbor list (will copy or build if necessary)
neighbor->build_one(list);
const int inum = list->inum;
const int* const ilist = list->ilist;
const int* const numneigh = list->numneigh;
int** const firstneigh = list->firstneigh;
int * const type = atom->type;
// compute sna derivatives for each atom in group
// use full neighbor list to count atoms less than cutoff
double** const x = atom->x;
const int* const mask = atom->mask;
for (int ii = 0; ii < inum; ii++) {
int irow = 0;
if (bikflag) irow = atom->tag[ilist[ii] & NEIGHMASK]-1;
const int i = ilist[ii];
if (mask[i] & groupbit) {
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
const int itype = type[i];
int ielem = 0;
if (chemflag)
ielem = map[itype];
const double radi = radelem[itype];
const int* const jlist = firstneigh[i];
const int jnum = numneigh[i];
const int typeoffset_local = ndims_peratom*nvalues*(itype-1);
const int typeoffset_global = nvalues*(itype-1);
// insure rij, inside, and typej are of size jnum
snaptr->grow_rij(jnum);
// rij[][3] = displacements between atom I and those neighbors
// inside = indices of neighbors of I within cutoff
// typej = types of neighbors of I within cutoff
// note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi
int ninside = 0;
for (int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
j &= NEIGHMASK;
const double delx = x[j][0] - xtmp;
const double dely = x[j][1] - ytmp;
const double delz = x[j][2] - ztmp;
const double rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
int jelem = 0;
if (chemflag)
jelem = map[jtype];
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
snaptr->rij[ninside][2] = delz;
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
if (switchinnerflag) {
snaptr->sinnerij[ninside] = 0.5*(sinnerelem[itype]+sinnerelem[jtype]);
snaptr->dinnerij[ninside] = 0.5*(dinnerelem[itype]+dinnerelem[jtype]);
}
if (chemflag) snaptr->element[ninside] = jelem;
ninside++;
}
}
snaptr->compute_ui(ninside, ielem);
snaptr->compute_zi();
snaptr->compute_bi(ielem);
for (int jj = 0; jj < ninside; jj++) {
const int j = snaptr->inside[jj];
snaptr->compute_duidrj(jj);
snaptr->compute_dbidrj();
// Accumulate dBi/dRi, -dBi/dRj
double *snadi = snap_peratom[i]+typeoffset_local;
double *snadj = snap_peratom[j]+typeoffset_local;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
snadi[icoeff] += snaptr->dblist[icoeff][0];
snadi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
snadi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
snadj[icoeff] -= snaptr->dblist[icoeff][0];
snadj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
snadj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
}
if (quadraticflag) {
const int quadraticoffset = ncoeff;
snadi += quadraticoffset;
snadj += quadraticoffset;
int ncount = 0;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr->blist[icoeff];
double bix = snaptr->dblist[icoeff][0];
double biy = snaptr->dblist[icoeff][1];
double biz = snaptr->dblist[icoeff][2];
// diagonal elements of quadratic matrix
double dbxtmp = bi*bix;
double dbytmp = bi*biy;
double dbztmp = bi*biz;
snadi[ncount] += dbxtmp;
snadi[ncount+yoffset] += dbytmp;
snadi[ncount+zoffset] += dbztmp;
snadj[ncount] -= dbxtmp;
snadj[ncount+yoffset] -= dbytmp;
snadj[ncount+zoffset] -= dbztmp;
ncount++;
// upper-triangular elements of quadratic matrix
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double dbxtmp = bi*snaptr->dblist[jcoeff][0]
+ bix*snaptr->blist[jcoeff];
double dbytmp = bi*snaptr->dblist[jcoeff][1]
+ biy*snaptr->blist[jcoeff];
double dbztmp = bi*snaptr->dblist[jcoeff][2]
+ biz*snaptr->blist[jcoeff];
snadi[ncount] += dbxtmp;
snadi[ncount+yoffset] += dbytmp;
snadi[ncount+zoffset] += dbztmp;
snadj[ncount] -= dbxtmp;
snadj[ncount+yoffset] -= dbytmp;
snadj[ncount+zoffset] -= dbztmp;
ncount++;
}
}
}
}
// Accumulate Bi
// linear contributions
int k = typeoffset_global;
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
snap[irow][k++] += snaptr->blist[icoeff];
// quadratic contributions
if (quadraticflag) {
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bveci = snaptr->blist[icoeff];
snap[irow][k++] += 0.5*bveci*bveci;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double bvecj = snaptr->blist[jcoeff];
snap[irow][k++] += bveci*bvecj;
}
}
}
}
}
// accumulate bispectrum force contributions to global array
for (int itype = 0; itype < atom->ntypes; itype++) {
const int typeoffset_local = ndims_peratom*nvalues*itype;
const int typeoffset_global = nvalues*itype;
for (int icoeff = 0; icoeff < nvalues; icoeff++) {
for (int i = 0; i < ntotal; i++) {
double *snadi = snap_peratom[i]+typeoffset_local;
int iglobal = atom->tag[i];
int irow = 3*(iglobal-1)+bik_rows;
snap[irow++][icoeff+typeoffset_global] += snadi[icoeff];
snap[irow++][icoeff+typeoffset_global] += snadi[icoeff+yoffset];
snap[irow][icoeff+typeoffset_global] += snadi[icoeff+zoffset];
}
}
}
// accumulate forces to global array
for (int i = 0; i < atom->nlocal; i++) {
int iglobal = atom->tag[i];
int irow = 3*(iglobal-1)+bik_rows;
snap[irow++][lastcol] = atom->f[i][0];
snap[irow++][lastcol] = atom->f[i][1];
snap[irow][lastcol] = atom->f[i][2];
}
// accumulate bispectrum virial contributions to global array
dbdotr_compute();
// sum up over all processes
MPI_Allreduce(&snap[0][0],&snapall[0][0],size_array_rows*size_array_cols,MPI_DOUBLE,MPI_SUM,world);
// assign energy to last column
for (int i = 0; i < bik_rows; i++) snapall[i][lastcol] = 0;
int irow = 0;
double reference_energy = c_pe->compute_scalar();
snapall[irow][lastcol] = reference_energy;
// assign virial stress to last column
// switch to Voigt notation
c_virial->compute_vector();
irow += 3*natoms+bik_rows;
snapall[irow++][lastcol] = c_virial->vector[0];
snapall[irow++][lastcol] = c_virial->vector[1];
snapall[irow++][lastcol] = c_virial->vector[2];
snapall[irow++][lastcol] = c_virial->vector[5];
snapall[irow++][lastcol] = c_virial->vector[4];
snapall[irow][lastcol] = c_virial->vector[3];
}
/* ----------------------------------------------------------------------
compute global virial contributions via summing r_i.dB^j/dr_i over
own & ghost atoms
------------------------------------------------------------------------- */
void ComputeSnap::dbdotr_compute()
{
double **x = atom->x;
int irow0 = bik_rows+ndims_force*natoms;
// sum over bispectrum contributions to forces
// on all particles including ghosts
int nall = atom->nlocal + atom->nghost;
for (int i = 0; i < nall; i++)
for (int itype = 0; itype < atom->ntypes; itype++) {
const int typeoffset_local = ndims_peratom*nvalues*itype;
const int typeoffset_global = nvalues*itype;
double *snadi = snap_peratom[i]+typeoffset_local;
for (int icoeff = 0; icoeff < nvalues; icoeff++) {
double dbdx = snadi[icoeff];
double dbdy = snadi[icoeff+yoffset];
double dbdz = snadi[icoeff+zoffset];
int irow = irow0;
snap[irow++][icoeff+typeoffset_global] += dbdx*x[i][0];
snap[irow++][icoeff+typeoffset_global] += dbdy*x[i][1];
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][2];
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][1];
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][0];
snap[irow][icoeff+typeoffset_global] += dbdy*x[i][0];
}
}
}
/* ----------------------------------------------------------------------
memory usage
------------------------------------------------------------------------- */
double ComputeSnap::memory_usage()
{
double bytes = (double)size_array_rows*size_array_cols *
sizeof(double); // snap
bytes += (double)size_array_rows*size_array_cols *
sizeof(double); // snapall
bytes += (double)nmax*size_peratom * sizeof(double); // snap_peratom
bytes += snaptr->memory_usage(); // SNA object
int n = atom->ntypes+1;
bytes += (double)n*sizeof(int); // map
return bytes;
}
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