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lammps/src/USER-PHONON/third_order.cpp

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//
// Created by charlie sievers on 7/5/18.
//
#include "third_order.h"
#include "angle.h"
#include "atom.h"
#include "bond.h"
#include "comm.h"
#include "dihedral.h"
#include "domain.h"
#include "error.h"
#include "finish.h"
#include "force.h"
#include "group.h"
#include "improper.h"
#include "kspace.h"
#include "math_special.h"
#include "memory.h"
#include "neighbor.h"
#include "pair.h"
#include "timer.h"
#include "update.h"
#include <cstring>
#include <algorithm>
using namespace LAMMPS_NS;
using namespace MathSpecial;
enum{REGULAR,BALLISTICO};
/* ---------------------------------------------------------------------- */
ThirdOrder::ThirdOrder(LAMMPS *lmp) : Pointers(lmp), fp(nullptr)
{
external_force_clear = 1;
}
/* ---------------------------------------------------------------------- */
ThirdOrder::~ThirdOrder()
{
if (fp && me == 0) fclose(fp);
fp = nullptr;
memory->destroy(groupmap);
}
/* ----------------------------------------------------------------------
setup without output or one-time post-init setup
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void ThirdOrder::setup()
{
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
domain->image_check();
domain->box_too_small_check();
neighbor->build(1);
// compute all forces
external_force_clear = 0;
eflag=0;
vflag=0;
update_force();
if (gcount == atom->natoms)
for (bigint i=0; i<atom->natoms; i++)
groupmap[i] = i;
else
create_groupmap();
}
/* ---------------------------------------------------------------------- */
void ThirdOrder::command(int narg, char **arg)
{
MPI_Comm_rank(world,&me);
if (domain->box_exist == 0)
error->all(FLERR,"third_order command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal third_order command");
lmp->init();
// orthogonal vs triclinic simulation box
triclinic = domain->triclinic;
if (force->pair && force->pair->compute_flag) pair_compute_flag = 1;
else pair_compute_flag = 0;
if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1;
else kspace_compute_flag = 0;
// group and style
igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find dynamical matrix group ID");
groupbit = group->bitmask[igroup];
gcount = group->count(igroup);
dynlen = (gcount)*3;
memory->create(groupmap,atom->natoms,"total_group_map:totalgm");
update->setupflag = 1;
int style = -1;
if (strcmp(arg[1],"regular") == 0) style = REGULAR;
else if (strcmp(arg[1],"eskm") == 0) style = BALLISTICO;
else error->all(FLERR,"Illegal Dynamical Matrix command");
// set option defaults
binaryflag = 0;
scaleflag = 0;
compressed = 0;
file_flag = 0;
file_opened = 0;
conversion = 1;
// read options from end of input line
if (style == REGULAR) options(narg-3,&arg[3]); //COME BACK
else if (style == BALLISTICO) options(narg-3,&arg[3]); //COME BACK
else if (comm->me == 0 && screen) fprintf(screen,"Illegal Dynamical Matrix command\n");
del = utils::numeric(FLERR, arg[2],false,lmp);
if (atom->map_style == Atom::MAP_NONE)
error->all(FLERR,"third_order command requires an atom map, see atom_modify");
// move atoms by 3-vector or specified variable(s)
if (style == REGULAR) {
setup();
timer->init();
timer->barrier_start();
calculateMatrix();
timer->barrier_stop();
}
if (style == BALLISTICO) {
setup();
convert_units(update->unit_style);
conversion = conv_energy/conv_distance/conv_distance;
timer->init();
timer->barrier_start();
calculateMatrix();
timer->barrier_stop();
}
Finish finish(lmp);
finish.end(1);
}
/* ----------------------------------------------------------------------
parse optional parameters
------------------------------------------------------------------------- */
void ThirdOrder::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal third_order command");
int iarg = 0;
const char *filename = "third_order.dat";
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR, "Illegal third_order command");
filename = arg[iarg + 1];
file_flag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"binary") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal third_order command");
if (strcmp(arg[iarg+1],"gzip") == 0) {
compressed = 1;
} else if (strcmp(arg[iarg+1],"yes") == 0) {
binaryflag = 1;
}
iarg += 2;
} else error->all(FLERR,"Illegal third_order command");
}
if (file_flag == 1 and me == 0) {
openfile(filename);
}
}
/* ----------------------------------------------------------------------
generic opening of a file
ASCII or binary or gzipped
some derived classes override this function
------------------------------------------------------------------------- */
void ThirdOrder::openfile(const char* filename)
{
// if file already opened, return
if (file_opened) return;
if (compressed) {
#ifdef LAMMPS_GZIP
char gzip[128];
sprintf(gzip,"gzip -6 > %s",filename);
#ifdef _WIN32
fp = _popen(gzip,"wb");
#else
fp = popen(gzip,"w");
#endif
#else
error->one(FLERR,"Cannot open gzipped file");
#endif
} else if (binaryflag) {
fp = fopen(filename,"wb");
} else {
fp = fopen(filename,"w");
}
if (fp == nullptr) error->one(FLERR,"Cannot open dump file");
file_opened = 1;
}
/* ----------------------------------------------------------------------
create dynamical matrix
------------------------------------------------------------------------- */
void ThirdOrder::calculateMatrix()
{
int local_idx; // local index
int local_jdx; // second local index
int local_kdx; // third local index
int nlocal = atom->nlocal;
bigint natoms = atom->natoms;
bigint *gm = groupmap;
double **f = atom->f;
double *dynmat = new double[3*dynlen];
double *fdynmat = new double[3*dynlen];
memset(&dynmat[0],0,dynlen*sizeof(double));
memset(&fdynmat[0],0,dynlen*sizeof(double));
if (comm->me == 0 && screen) {
fprintf(screen,"Calculating Third Order ...\n");
fprintf(screen," Total # of atoms = " BIGINT_FORMAT "\n", natoms);
fprintf(screen," Atoms in group = " BIGINT_FORMAT "\n", gcount);
fprintf(screen," Total third order elements = "
BIGINT_FORMAT "\n", (dynlen*dynlen*dynlen) );
}
update->nsteps = 0;
int prog = 0;
for (bigint i=1; i<=natoms; i++){
local_idx = atom->map(i);
for (int alpha=0; alpha<3; alpha++){
for (bigint j=1; j<=natoms; j++){
local_jdx = atom->map(j);
for (int beta=0; beta<3; beta++){
displace_atom(local_idx, alpha, 1);
displace_atom(local_jdx, beta, 1);
update_force();
for (bigint k=1; k<=natoms; k++){
local_kdx = atom->map(k);
for (int gamma=0; gamma<3; gamma++){
if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
&& local_kdx < nlocal) {
dynmat[gm[k-1]*3+gamma] += f[local_kdx][gamma];
}
}
}
displace_atom(local_jdx, beta, -2);
update_force();
for (bigint k=1; k<=natoms; k++){
local_kdx = atom->map(k);
for (int gamma=0; gamma<3; gamma++){
if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
&& local_kdx < nlocal) {
dynmat[gm[k-1]*3+gamma] -= f[local_kdx][gamma];
}
}
}
displace_atom(local_jdx, beta, 1);
displace_atom(local_idx,alpha,-2);
displace_atom(local_jdx, beta, 1);
update_force();
for (bigint k=1; k<=natoms; k++){
local_kdx = atom->map(k);
for (int gamma=0; gamma<3; gamma++){
if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
&& local_kdx < nlocal) {
dynmat[gm[k-1]*3+gamma] -= f[local_kdx][gamma];
}
}
}
displace_atom(local_jdx, beta, -2);
update_force();
for (bigint k=1; k<=natoms; k++){
local_kdx = atom->map(k);
for (int gamma=0; gamma<3; gamma++){
if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
&& local_kdx < nlocal) {
dynmat[gm[k-1]*3+gamma] += f[local_kdx][gamma];
dynmat[gm[k-1]*3+gamma] /= (4 * del * del);
}
}
}
displace_atom(local_jdx, beta, 1);
displace_atom(local_idx, alpha, 1);
MPI_Reduce(dynmat,fdynmat,3*dynlen,MPI_DOUBLE,MPI_SUM,0,world);
if (me == 0){
writeMatrix(fdynmat, gm[i-1], alpha, gm[j-1], beta);
}
memset(&dynmat[0],0,dynlen*sizeof(double));
}
}
}
if (comm->me == 0 && screen) {
int p = 10 * gm[i-1] / gcount;
if (p > prog) {
prog = p;
fprintf(screen," %d%%",p*10);
fflush(screen);
}
}
}
delete [] dynmat;
delete [] fdynmat;
if (screen && me ==0 )
fprintf(screen,"Finished Calculating Third Order Tensor\n");
}
/* ----------------------------------------------------------------------
write dynamical matrix
------------------------------------------------------------------------- */
void ThirdOrder::writeMatrix(double *dynmat, bigint i, int a, bigint j, int b)
{
if (me != 0)
return;
double norm;
if (!binaryflag && fp) {
clearerr(fp);
for (int k = 0; k < gcount; k++){
norm = square(dynmat[k*3])+
square(dynmat[k*3+1])+
square(dynmat[k*3+2]);
if (norm > 1.0e-16)
fprintf(fp,
BIGINT_FORMAT " %d " BIGINT_FORMAT " %d " BIGINT_FORMAT
" %7.8f %7.8f %7.8f\n",
i+1, a + 1, j+1, b + 1, groupmap[k]+1,
dynmat[k*3] * conversion,
dynmat[k*3+1] * conversion,
dynmat[k*3+2] * conversion);
}
} else if (binaryflag && fp){
clearerr(fp);
fwrite(&dynmat[0], sizeof(double), dynlen, fp);
}
if (ferror(fp)) error->one(FLERR,"Error writing to file");
}
/* ----------------------------------------------------------------------
Displace atoms
---------------------------------------------------------------------- */
void ThirdOrder::displace_atom(int local_idx, int direction, int magnitude)
{
if (local_idx < 0) return;
double **x = atom->x;
int *sametag = atom->sametag;
int j = local_idx;
x[local_idx][direction] += del*magnitude;
while (sametag[j] >= 0){
j = sametag[j];
x[j][direction] += del*magnitude;
}
}
/* ----------------------------------------------------------------------
evaluate potential energy and forces
may migrate atoms due to reneighboring
return new energy, which should include nextra_global dof
return negative gradient stored in atom->f
return negative gradient for nextra_global dof in fextra
------------------------------------------------------------------------- */
void ThirdOrder::update_force()
{
force_clear();
if (pair_compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (kspace_compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
}
if (force->newton) {
comm->reverse_comm();
timer->stamp(Timer::COMM);
}
++ update->nsteps;
}
/* ----------------------------------------------------------------------
clear force on own & ghost atoms
clear other arrays as needed
------------------------------------------------------------------------- */
void ThirdOrder::force_clear()
{
if (external_force_clear) return;
// clear global force array
// if either newton flag is set, also include ghosts
size_t nbytes = sizeof(double) * atom->nlocal;
if (force->newton) nbytes += sizeof(double) * atom->nghost;
if (nbytes) {
memset(&atom->f[0][0],0,3*nbytes);
}
}
/* ---------------------------------------------------------------------- */
void ThirdOrder::convert_units(const char *style)
{
// physical constants from:
// https://physics.nist.gov/cuu/Constants/Table/allascii.txt
// using thermochemical calorie = 4.184 J
if (strcmp(style,"lj") == 0) {
error->all(FLERR,"Conversion Not Set");
//conversion = 1; // lj -> 10 J/mol
} else if (strcmp(style,"real") == 0) {
conv_energy = 418.4; // kcal/mol -> 10 J/mol
conv_mass = 1; // g/mol -> g/mol
conv_distance = 1; // angstrom -> angstrom
} else if (strcmp(style,"metal") == 0) {
conv_energy = 9648.5; // eV -> 10 J/mol
conv_mass = 1; // g/mol -> g/mol
conv_distance = 1; // angstrom -> angstrom
} else if (strcmp(style,"si") == 0) {
if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float");
conv_energy = 6.022E22; // J -> 10 J/mol
conv_mass = 6.022E26; // kg -> g/mol
conv_distance = 1E-10; // meter -> angstrom
} else if (strcmp(style,"cgs") == 0) {
if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float");
conv_energy = 6.022E12; // Erg -> 10 J/mol
conv_mass = 6.022E23; // g -> g/mol
conv_distance = 1E-7; // centimeter -> angstrom
} else if (strcmp(style,"electron") == 0) {
conv_energy = 262550; // Hartree -> 10 J/mol
conv_mass = 1; // amu -> g/mol
conv_distance = 0.529177249; // bohr -> angstrom
} else if (strcmp(style,"micro") == 0) {
if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion");
conv_energy = 6.022E10; // picogram-micrometer^2/microsecond^2 -> 10 J/mol
conv_mass = 6.022E11; // pg -> g/mol
conv_distance = 1E-4; // micrometer -> angstrom
} else if (strcmp(style,"nano") == 0) {
if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion");
conv_energy = 6.022E4; // attogram-nanometer^2/nanosecond^2 -> 10 J/mol
conv_mass = 6.022E5; // ag -> g/mol
conv_distance = 0.1; // angstrom -> angstrom
} else error->all(FLERR,"Units Type Conversion Not Found");
}
/* ---------------------------------------------------------------------- */
void ThirdOrder::create_groupmap()
{
//Create a group map which maps atom order onto group
// groupmap[global atom index-1] = output column/row
int local_idx; // local index
int gid = 0; //group index
int nlocal = atom->nlocal;
int *mask = atom->mask;
bigint natoms = atom->natoms;
int *recv = new int[comm->nprocs];
int *displs = new int[comm->nprocs];
bigint *temp_groupmap = new bigint[natoms];
//find number of local atoms in the group (final_gid)
for (bigint i=1; i<=natoms; i++){
local_idx = atom->map(i);
if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit)
gid += 1; // gid at the end of loop is final_Gid
}
//create an array of length final_gid
bigint *sub_groupmap = new bigint[gid];
gid = 0;
//create a map between global atom id and group atom id for each proc
for (bigint i=1; i<=natoms; i++){
local_idx = atom->map(i);
if ((local_idx >= 0) && (local_idx < nlocal)
&& (mask[local_idx] & groupbit)){
sub_groupmap[gid] = i;
gid += 1;
}
}
//populate arrays for Allgatherv
for (int i=0; i<comm->nprocs; i++){
recv[i] = 0;
}
recv[comm->me] = gid;
MPI_Allreduce(recv,displs,comm->nprocs,MPI_INT,MPI_SUM,world);
for (int i=0; i<comm->nprocs; i++){
recv[i]=displs[i];
if (i>0) displs[i] = displs[i-1]+recv[i-1];
else displs[i] = 0;
}
//combine subgroup maps into total temporary groupmap
MPI_Allgatherv(sub_groupmap,gid,MPI_LMP_BIGINT,
temp_groupmap,recv,displs,MPI_LMP_BIGINT,world);
std::sort(temp_groupmap,temp_groupmap+gcount);
//populate member groupmap based on temp groupmap
bigint j = 0;
for (bigint i=1; i<=natoms; i++){
// flag groupmap contents that are in temp_groupmap
if (j < gcount && i == temp_groupmap[j])
groupmap[i-1] = j++;
else
groupmap[i-1] = -1;
}
//free that memory!
delete[] recv;
delete[] displs;
delete[] sub_groupmap;
delete[] temp_groupmap;
}
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