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compute_xrd.cpp
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compute_xrd.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 authors: Shawn Coleman & Douglas Spearot (Arkansas)
Updated: 06/17/2015-2
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include "math_const.h"
#include "compute_xrd.h"
#include "compute_xrd_consts.h"
#include "atom.h"
#include "comm.h"
#include "update.h"
#include "domain.h"
#include "group.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
#include <stdio.h>
#include <string.h>
using namespace LAMMPS_NS;
using namespace MathConst;
static const char cite_compute_xrd_c[] =
"compute_xrd command:\n\n"
"@Article{Coleman13,\n"
" author = {S. P. Coleman, D. E. Spearot, L. Capolungo},\n"
" title = {Virtual diffraction analysis of Ni [010] symmetric tilt grain boundaries},\n"
" journal = {Modelling and Simulation in Materials Science and Engineering},\n"
" year = 2013,\n"
" volume = 21,\n"
" pages = {055020}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), ztype(NULL), store_tmp(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_compute_xrd_c);
int ntypes = atom->ntypes;
int natoms = group->count(igroup);
int dimension = domain->dimension;
int *periodicity = domain->periodicity;
int triclinic = domain->triclinic;
me = comm->me;
// Checking errors
if (dimension == 2)
error->all(FLERR,"Compute XRD does not work with 2d structures");
if (narg < 4+ntypes)
error->all(FLERR,"Illegal Compute XRD Command");
if (triclinic == 1)
error->all(FLERR,"Compute XRD does not work with triclinic structures");
array_flag = 1;
extarray = 0;
// Store radiation wavelength
lambda = atof(arg[3]);
if (lambda < 0)
error->all(FLERR,"Compute SAED: Wavelength must be greater than zero");
// Define atom types for atomic scattering factor coefficients
int iarg = 4;
ztype = new int[ntypes];
for (int i = 0; i < ntypes; i++){
ztype[i] = XRDmaxType + 1;
}
for (int i = 0; i < ntypes; i++) {
for(int j = 0; j < XRDmaxType; j++){
if (strcasecmp(arg[iarg],XRDtypeList[j]) == 0) {
ztype[i] = j;
}
}
if ( ztype[i] == XRDmaxType + 1 )
error->all(FLERR,"Compute XRD: Invalid ASF atom type");
iarg++;
}
// Set defaults for optional args
Min2Theta = 1;
Max2Theta = 179;
radflag = 1;
c[0] = 1; c[1] = 1; c[2] = 1;
LP = 1;
manual = false;
echo = false;
// Process optional args
while (iarg < narg) {
if (strcmp(arg[iarg],"2Theta") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal Compute XRD Command");
Min2Theta = atof(arg[iarg+1]) / 2;
Max2Theta = atof(arg[iarg+2]) / 2;
if (Max2Theta > MY_PI ){
Min2Theta = Min2Theta * MY_PI / 180; // converting to radians if necessary
Max2Theta = Max2Theta * MY_PI / 180;
radflag = 0;
}
if (Min2Theta <= 0)
error->all(FLERR,"Minimum 2theta value must be greater than zero");
if (Max2Theta >= MY_PI )
error->all(FLERR,"Maximum 2theta value must be less than 180 degrees");
if (Max2Theta-Min2Theta <= 0)
error->all(FLERR,"Two-theta range must be greater than zero");
iarg += 3;
} else if (strcmp(arg[iarg],"c") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal Compute XRD Command");
c[0] = atof(arg[iarg+1]);
c[1] = atof(arg[iarg+2]);
c[2] = atof(arg[iarg+3]);
if (c[0] < 0 || c[1] < 0 || c[2] < 0)
error->all(FLERR,"Compute XRD: c's must be greater than 0");
iarg += 4;
} else if (strcmp(arg[iarg],"LP") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal Compute XRD Command");
LP = atof(arg[iarg+1]);
if (!(LP == 1 || LP == 0))
error->all(FLERR,"Compute XRD: LP must have value of 0 or 1");
iarg += 2;
} else if (strcmp(arg[iarg],"echo") == 0) {
echo = true;
iarg += 1;
} else if (strcmp(arg[iarg],"manual") == 0) {
manual = true;
iarg += 1;
} else error->all(FLERR,"Illegal Compute XRD Command");
}
Kmax = 2 * sin(Max2Theta) / lambda;
// Calculating spacing between reciprocal lattice points
// Using distance based on periodic repeating distance
if (!manual) {
if (!periodicity[0] && !periodicity[1] && !periodicity[2])
error->all(FLERR,"Compute SAED must have at least one periodic boundary unless manual spacing specified");
double *prd;
double ave_inv = 0.0;
prd = domain->prd;
if (periodicity[0]){
prd_inv[0] = 1 / prd[0];
ave_inv += prd_inv[0];
}
if (periodicity[1]){
prd_inv[1] = 1 / prd[1];
ave_inv += prd_inv[1];
}
if (periodicity[2]){
prd_inv[2] = 1 / prd[2];
ave_inv += prd_inv[2];
}
// Using the average inverse dimensions for non-periodic direction
ave_inv = ave_inv / (periodicity[0] + periodicity[1] + periodicity[2]);
if (!periodicity[0]){
prd_inv[0] = ave_inv;
}
if (!periodicity[1]){
prd_inv[1] = ave_inv;
}
if (!periodicity[2]){
prd_inv[2] = ave_inv;
}
}
// Use manual mapping of reciprocal lattice
if (manual) {
for (int i=0; i<3; i++) {
prd_inv[i] = 1.0;
}
}
// Find reciprocal spacing and integer dimensions
for (int i=0; i<3; i++) {
dK[i] = prd_inv[i]*c[i];
Knmax[i] = ceil(Kmax / dK[i]);
}
// Finding the intersection of the reciprocal space and Ewald sphere
int nRows = 0;
double dinv2= 0.0;
double ang = 0.0;
double K[3];
// Procedure to determine how many rows are needed given the constraints on 2theta
for (int i = -Knmax[0]; i <= Knmax[0]; i++) {
for (int j = -Knmax[1]; j <= Knmax[1]; j++) {
for (int k = -Knmax[2]; k <= Knmax[2]; k++) {
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
if (4 >= dinv2 * lambda * lambda ) {
ang = asin(lambda * sqrt(dinv2) * 0.5);
if ((ang <= Max2Theta) && (ang >= Min2Theta)) {
nRows++;
}
}
}
}
}
size_array_rows = nRows;
size_array_cols = 2;
if (me == 0) {
if (screen && echo) {
fprintf(screen,"-----\nCompute XRD id:%s, # of atoms:%d, # of relp:%d\n",id,natoms,nRows);
fprintf(screen,"Reciprocal point spacing in k1,k2,k3 = %g %g %g\n-----\n",
dK[0], dK[1], dK[2]);
}
}
memory->create(array,size_array_rows,size_array_cols,"xrd:array");
memory->create(store_tmp,3*size_array_rows,"xrd:store_tmp");
}
/* ---------------------------------------------------------------------- */
ComputeXRD::~ComputeXRD()
{
memory->destroy(array);
memory->destroy(store_tmp);
delete ztype;
}
/* ---------------------------------------------------------------------- */
void ComputeXRD::init()
{
int mmax = (2*Knmax[0]+1)*(2*Knmax[1]+1)*(2*Knmax[2]+1);
double K[3];
double dinv2 = 0.0;
double ang = 0.0;
double convf = 360 / MY_PI;
if (radflag ==1){
convf = 1;
}
int n = 0;
for (int m = 0; m < mmax; m++) {
int k = m%(2*Knmax[2]+1);
int j = (m%((2*Knmax[2]+1)*(2*Knmax[1]+1))-k)/(2*Knmax[2]+1);
int i = (m-j*(2*Knmax[2]+1)-k)/((2*Knmax[2]+1)*(2*Knmax[1]+1))-Knmax[0];
j = j-Knmax[1];
k = k-Knmax[2];
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
if (4 >= dinv2 * lambda * lambda ) {
ang = asin(lambda * sqrt(dinv2) * 0.5);
if ((ang <= Max2Theta) && (ang >= Min2Theta)) {
store_tmp[3*n] = k;
store_tmp[3*n+1] = j;
store_tmp[3*n+2] = i;
array[n][0] = ang * convf;
n++;
}
}
}
if (n != size_array_rows)
error->all(FLERR,"Compute XRD compute_array() rows mismatch");
}
/* ---------------------------------------------------------------------- */
void ComputeXRD::compute_array()
{
invoked_array = update->ntimestep;
if (me == 0 && echo) {
if (screen)
fprintf(screen,"-----\nComputing XRD intensities");
}
double t0 = MPI_Wtime();
double *Fvec = new double[2*size_array_rows]; // Strct factor (real & imaginary)
// -- Note: array rows correspond to different RELP
ntypes = atom->ntypes;
int nlocal = atom->nlocal;
int *type = atom->type;
int natoms = group->count(igroup);
int *mask = atom->mask;
nlocalgroup = 0;
for (int ii = 0; ii < nlocal; ii++) {
if (mask[ii] & groupbit) {
nlocalgroup++;
}
}
double *xlocal = new double [3*nlocalgroup];
int *typelocal = new int [nlocalgroup];
nlocalgroup = 0;
for (int ii = 0; ii < nlocal; ii++) {
if (mask[ii] & groupbit) {
xlocal[3*nlocalgroup+0] = atom->x[ii][0];
xlocal[3*nlocalgroup+1] = atom->x[ii][1];
xlocal[3*nlocalgroup+2] = atom->x[ii][2];
typelocal[nlocalgroup]=type[ii];
nlocalgroup++;
}
}
// Setting up OMP
#if defined(_OPENMP)
if (me == 0 && echo) {
if (screen)
fprintf(screen," using %d OMP threads\n",comm->nthreads);
}
#endif
if (me == 0 && echo) {
if (screen) {
fprintf(screen,"\n");
if (LP == 1)
fprintf(screen,"Applying Lorentz-Polarization Factor During XRD Calculation 2\n");
}
}
int m = 0;
double frac = 0.1;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(typelocal,xlocal,Fvec,m,frac,ASFXRD)
#endif
{
double *f = new double[ntypes]; // atomic structure factor by type
int n,typei = 0;
double Fatom1 = 0.0; // structure factor per atom (real)
double Fatom2 = 0.0; // structure factor per atom (imaginary)
double K[3];
double dinv2 = 0.0;
double dinv = 0.0;
double SinTheta_lambda = 0.0;
double SinTheta = 0.0;
double ang = 0.0;
double Cos2Theta = 0.0;
double CosTheta = 0.0;
double inners = 0.0;
double sqrt_lp = 0.0;
if (LP == 1) {
#if defined(_OPENMP)
#pragma omp for
#endif
for (n = 0; n < size_array_rows; n++) {
int k = store_tmp[3*n];
int j = store_tmp[3*n+1];
int i = store_tmp[3*n+2];
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
dinv = sqrt(dinv2);
SinTheta_lambda = 0.5*dinv;
SinTheta = SinTheta_lambda * lambda;
ang = asin( SinTheta );
Cos2Theta = cos( 2 * ang);
CosTheta = cos( ang );
Fatom1 = 0.0;
Fatom2 = 0.0;
// Calculate the atomic structure factor by type
for (int ii = 0; ii < ntypes; ii++){
f[ii] = 0;
for (int C = 0; C < 8 ; C+=2){
f[ii] += ASFXRD[ztype[ii]][C] * exp(-1 * ASFXRD[ztype[ii]][C+1] * SinTheta_lambda * SinTheta_lambda );
}
f[ii] += ASFXRD[ztype[ii]][8];
}
// Evaluate the structure factor equation -- looping over all atoms
for (int ii = 0; ii < nlocalgroup; ii++){
typei=typelocal[ii]-1;
inners = 2 * MY_PI * (K[0] * xlocal[3*ii] + K[1] * xlocal[3*ii+1] +
K[2] * xlocal[3*ii+2]);
Fatom1 += f[typei] * cos(inners);
Fatom2 += f[typei] * sin(inners);
}
sqrt_lp = sqrt( (1 + Cos2Theta * Cos2Theta) /
( CosTheta * SinTheta * SinTheta) );
Fvec[2*n] = Fatom1 * sqrt_lp;
Fvec[2*n+1] = Fatom2 * sqrt_lp;
// reporting progress of calculation
if ( echo ) {
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if ( m == round(frac * size_array_rows) ) {
if (me == 0 && screen) fprintf(screen," %0.0f%% -",frac*100);
frac += 0.1;
}
m++;
}
}
} // End of pragma omp for region
} else {
#if defined(_OPENMP)
#pragma omp for
#endif
for (n = 0; n < size_array_rows; n++) {
int k = store_tmp[3*n];
int j = store_tmp[3*n+1];
int i = store_tmp[3*n+2];
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
dinv = sqrt(dinv2);
SinTheta_lambda = 0.5*dinv;
Fatom1 = 0.0;
Fatom2 = 0.0;
// Calculate the atomic structure factor by type
for (int ii = 0; ii < ntypes; ii++){
f[ii] = 0;
for (int C = 0; C < 8 ; C+=2){
f[ii] += ASFXRD[ztype[ii]][C] * exp(-1 * ASFXRD[ztype[ii]][C+1] * SinTheta_lambda * SinTheta_lambda );
}
f[ii] += ASFXRD[ztype[ii]][8];
}
// Evaluate the structure factor equation -- looping over all atoms
for (int ii = 0; ii < nlocalgroup; ii++){
typei=typelocal[ii]-1;
inners = 2 * MY_PI * (K[0] * xlocal[3*ii] + K[1] * xlocal[3*ii+1] +
K[2] * xlocal[3*ii+2]);
Fatom1 += f[typei] * cos(inners);
Fatom2 += f[typei] * sin(inners);
}
Fvec[2*n] = Fatom1;
Fvec[2*n+1] = Fatom2;
// reporting progress of calculation
if ( echo ) {
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if ( m == round(frac * size_array_rows) ) {
if (me == 0 && screen) fprintf(screen," %0.0f%% -",frac*100 );
frac += 0.1;
}
m++;
}
}
} // End of pragma omp for region
} // End of if LP=1 check
delete [] f;
} // End of pragma omp parallel region
double *scratch = new double[2*size_array_rows];
// Sum intensity for each ang-hkl combination across processors
MPI_Allreduce(Fvec,scratch,2*size_array_rows,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < size_array_rows; i++) {
array[i][1] = (scratch[2*i] * scratch[2*i] + scratch[2*i+1] * scratch[2*i+1]) / natoms;
}
double t2 = MPI_Wtime();
// compute memory usage per processor
double bytes = size_array_rows * size_array_cols * sizeof(double); //array
bytes += 4.0 * size_array_rows * sizeof(double); //Fvec1 & 2, scratch1 & 2
bytes += ntypes * sizeof(double); // f
bytes += 3.0 * nlocalgroup * sizeof(double); // xlocal
bytes += nlocalgroup * sizeof(int); // typelocal
bytes += 3.0 * size_array_rows * sizeof(int); // store_temp
if (me == 0 && echo) {
if (screen)
fprintf(screen," 100%% \nTime ellapsed during compute_xrd = %0.2f sec using %0.2f Mbytes/processor\n-----\n", t2-t0, bytes/1024.0/1024.0);
}
delete [] scratch;
delete [] Fvec;
delete [] xlocal;
delete [] typelocal;
}
/* ----------------------------------------------------------------------
memory usage of arrays
------------------------------------------------------------------------- */
double ComputeXRD::memory_usage()
{
double bytes = size_array_rows * size_array_cols * sizeof(double); //array
bytes += 4.0 * size_array_rows * sizeof(double); //Fvec1 & 2, scratch1 & 2
bytes += 3.0 * nlocalgroup * sizeof(double); // xlocal
bytes += nlocalgroup * sizeof(int); // typelocal
bytes += ntypes * sizeof(double); // f
bytes += 3.0 * size_array_rows * sizeof(int); // store_temp
return bytes;
}

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