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lammps/tools/phonon/phonon.cpp
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phonon.cpp
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#include <vector>
#include "string.h"
#include "phonon.h"
#include "green.h"
#include "timer.h"
#ifdef UseSPG
extern "C"{
#include "spglib.h"
}
#endif
#define MAXLINE 256
#define MIN(a,b) ((a)>(b)?(b):(a))
#define MAX(a,b) ((a)>(b)?(a):(b))
/* ----------------------------------------------------------------------------
* Class Phonon is the main driver to calculate phonon DOS, phonon
* dispersion curve and some other things.
* ---------------------------------------------------------------------------- */
Phonon::Phonon(DynMat *dm)
{
// create memory
memory = new Memory();
// pass the class from main
dynmat = dm;
sysdim = dynmat->sysdim;
ndim = dynmat->fftdim;
dos = NULL;
ldos = NULL;
qpts = NULL;
wt = NULL;
eigs = NULL;
locals = NULL;
#ifdef UseSPG
attyp = NULL;
atpos = NULL;
#endif
// display the menu
char str[MAXLINE];
while ( 1 ){
printf("\n"); for (int i=0; i<37;i++) printf("="); printf(" Menu "); for (int i=0; i<37;i++) printf("="); printf("\n");
printf(" 1. Phonon DOS evaluation;\n");
printf(" 2. Phonon dispersion curves;\n");
printf(" 3. Dynamical matrix at arbitrary q;\n");
printf(" 4. Vibrational frequencies at arbitrary q;\n");
printf(" 5. Dispersion-like curve for dynamical matrix;\n");
printf(" 6. Vibrational thermodynamical properties;\n");
printf(" 7. Local phonon DOS from eigenvectors;\n");
printf(" 8. Local phonon DOS by RSGF method;\n");
printf(" 9. Freqs and eigenvectors at arbitrary q;\n");
printf(" -1. Reset the interpolation method;\n");
printf(" 0. Exit.\n");
// read user choice
int job = 0;
printf("Your choice[0]: ");
if (count_words(fgets(str,MAXLINE,stdin)) > 0) job = atoi(strtok(str," \t\n\r\f"));
printf("\nYour selection: %d\n", job);
for (int i=0; i<80;i++) printf("=");printf("\n\n");
// now to do the job according to user's choice
if (job == 1) pdos();
else if (job == 2) pdisp();
else if (job == 3) dmanyq();
else if (job == 4) vfanyq();
else if (job == 5) DMdisp();
else if (job == 6) therm();
else if (job == 7) ldos_egv();
else if (job == 8) ldos_rsgf();
else if (job == 9) vecanyq();
else if (job ==-1) dynmat->reset_interp_method();
else break;
}
return;
}
/* ----------------------------------------------------------------------------
* Deconstructor to free memory
* ---------------------------------------------------------------------------- */
Phonon::~Phonon()
{
dynmat = NULL;
memory->destroy(wt);
memory->destroy(qpts);
memory->destroy(eigs);
memory->destroy(locals);
memory->destroy(dos);
memory->destroy(ldos);
#ifdef UseSPG
memory->destroy(attyp);
memory->destroy(atpos);
#endif
delete memory;
}
/* ----------------------------------------------------------------------------
* Private method to calculate the phonon DOS
* ---------------------------------------------------------------------------- */
void Phonon::pdos()
{
// get frequencies on a q-mesh
QMesh(); // generate q-points, hopefully irreducible
ComputeAll(); // get all eigen values ==> frequencies
// now to get the frequency range
char str[MAXLINE];
fmin = fmax = eigs[0][0];
for (int iq=0; iq<nq; iq++){
for (int j=0; j<ndim; j++){
fmin = MIN(fmin, eigs[iq][j]);
fmax = MAX(fmax, eigs[iq][j]);
}
}
// Now to ask for the output frequency range
printf("\nThe frequency range of all q-points are: [%g %g]\n", fmin, fmax);
printf("Please input the desired range to get DOS [%g %g]: ", fmin, fmax);
if (count_words(fgets(str,MAXLINE,stdin)) >= 2){
fmin = atof(strtok(str," \t\n\r\f"));
fmax = atof(strtok(NULL," \t\n\r\f"));
}
if (fmin > fmax){double swap = fmin; fmin = fmax; fmax = swap;}
printf("The fequency range for your phonon DOS is [%g %g].\n", fmin, fmax);
ndos = 201;
printf("Please input the number of intervals [%d]: ", ndos);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) ndos = atoi(strtok(str," \t\n\r\f"));
ndos += (ndos+1)%2; ndos = MAX(2,ndos);
df = (fmax-fmin)/double(ndos-1);
rdf = 1./df;
memory->destroy(dos);
dos = memory->create(dos, ndos, "pdos:dos");
for (int i=0; i<ndos; i++) dos[i] = 0.;
// now to calculate the DOS
double offset = fmin-0.5*df;
for (int iq=0; iq<nq; iq++){
if (wt[iq] > 0.){
for (int j=0; j<ndim; j++){
int idx = int((eigs[iq][j]-offset)*rdf);
if (idx>=0 && idx<ndos) dos[idx] += wt[iq];
}
}
}
// smooth dos ?
printf("Would you like to smooth the phonon dos? (y/n)[n]: ");
if (count_words(fgets(str,MAXLINE,stdin)) > 0){
char *flag = strtok(str," \t\n\r\f");
if (strcmp(flag,"y") == 0 || strcmp(flag,"Y") == 0){
smooth(dos, ndos);
}
}
// normalize dos to 1
Normalize();
// output DOS
writeDOS();
return;
}
/* ----------------------------------------------------------------------------
* Private method to write the phonon DOS to file
* ---------------------------------------------------------------------------- */
void Phonon::writeDOS()
{
if (dos == NULL) return;
char str[MAXLINE];
// now to output the phonon DOS
printf("\nPlease input the filename to write DOS [pdos.dat]: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str, "pdos.dat");
char *fname = strtok(str," \t\n\r\f");
printf("The total phonon DOS will be written to file: %s\n", fname);
FILE *fp = fopen(fname, "w");
fprintf(fp,"# frequency DOS\n");
fprintf(fp,"#%s number\n", dynmat->funit);
double freq = fmin;
for (int i=0; i<ndos; i++){
fprintf(fp,"%lg %lg\n", freq, dos[i]);
freq += df;
}
fclose(fp);
// also write the gnuplot script to generate the figure
fp = fopen("pdos.gnuplot", "w");
fprintf(fp,"set term post enha colo 20\nset out %cpdos.eps%c\n\n",char(34),char(34));
fprintf(fp,"set xlabel %cfrequency (THz)%c\n",char(34),char(34));
fprintf(fp,"set ylabel %cPhonon DOS%c\n",char(34),char(34));
fprintf(fp,"unset key\n");
fprintf(fp,"plot %c%s%c u 1:2 w l\n",char(34),fname,char(34));
fclose(fp);
fname = NULL;
return;
}
/* ----------------------------------------------------------------------------
* Private method to write the local DOS to files.
* ---------------------------------------------------------------------------- */
void Phonon::writeLDOS()
{
if (ldos == NULL) return;
printf("The phonon LDOSs will be written to file(s) : pldos_?.dat\n\n");
const double one3 = 1./double(sysdim);
char str[MAXLINE];
for (int ilocal=0; ilocal<nlocal; ilocal++){
sprintf(str,"pldos_%d.dat", locals[ilocal]);
char *fname = strtok(str," \t\n\r\f");
FILE *fp = fopen(fname, "w"); fname = NULL;
fprintf(fp,"#freq xDOS yDOS zDOS total\n");
double freq = fmin;
for (int i=0; i<ndos; i++){
fprintf(fp,"%lg", freq);
double total = 0.;
for (int idim=0; idim<sysdim; idim++) {fprintf(fp," %lg",ldos[ilocal][i][idim]); total += ldos[ilocal][i][idim];}
fprintf(fp," %lg\n", total*one3);
freq += df;
}
fclose(fp);
}
return;
}
/* ----------------------------------------------------------------------------
* Private method to calculate the local phonon DOS via the real space Green's
* function method
* ---------------------------------------------------------------------------- */
void Phonon::ldos_rsgf()
{
char str[MAXLINE];
const double tpi = 8.*atan(1.);
double **Hessian, scale;
scale = dynmat->eml2f*tpi; scale *= scale;
Hessian = memory->create(Hessian, ndim, ndim, "phonon_ldos:Hessian");
double q0[3];
q0[0] = q0[1] = q0[2] = 0.;
dynmat->getDMq(q0);
for (int i=0; i<ndim; i++)
for (int j=0; j<ndim; j++) Hessian[i][j] = dynmat->DM_q[i][j].r*scale;
if (ndim < 300){
double *egvs = new double [ndim];
dynmat->geteigen(egvs, 0);
fmin = fmax = egvs[0];
for (int i=1; i<ndim; i++){fmin = MIN(fmin, egvs[i]); fmax = MAX(fmax, egvs[i]);}
delete []egvs;
} else {
fmin = 0.; fmax = 20.;
}
ndos = 201;
int ik = 0, nit = MAX(ndim*0.1, MIN(ndim,50));
double eps = 12.; // for Cu with 1000+ atoms, 12 is enough; for small system, eps should be large.
while (1) {
int istr, iend, iinc;
// ask for relevant info
printf("\nThere are %d atoms in each unit cell of your lattice.\n", dynmat->nucell);
printf("Please input the index/index range/index range and increment of atom(s)\n");
printf("in the unit cell to evaluate LDOS, q to exit [%d]: ", ik);
int nr = count_words( fgets(str,MAXLINE,stdin) );
if (nr < 1){
istr = iend = ik;
iinc = 1;
} else if (nr == 1) {
char *ptr = strtok(str," \t\n\r\f");
if (strcmp(ptr,"q") == 0) break;
ik = atoi(ptr);
if (ik < 0 || ik >= dynmat->nucell) break;
istr = iend = ik;
iinc = 1;
} else if (nr == 2) {
istr = atoi(strtok(str," \t\n\r\f"));
iend = atoi(strtok(NULL," \t\n\r\f"));
iinc = 1;
if (istr < 0||iend >= dynmat->nucell||istr > iend) break;
} else if (nr >= 3) {
istr = atoi(strtok(str," \t\n\r\f"));
iend = atoi(strtok(NULL," \t\n\r\f"));
iinc = atoi(strtok(NULL," \t\n\r\f"));
if (istr<0 || iend >= dynmat->nucell || istr > iend || iinc<1) break;
}
printf("Please input the frequency range to evaluate LDOS [%g %g]: ", fmin, fmax);
if (count_words(fgets(str,MAXLINE,stdin)) >= 2){
fmin = atof(strtok(str," \t\n\r\f"));
fmax = atof(strtok(NULL," \t\n\r\f"));
}
if (fmax < fmin) break;
printf("The frequency range for your LDOS is [%g %g].\n", fmin, fmax);
printf("Please input the desired number of points in LDOS [%d]: ", ndos);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) ndos = atoi(strtok(str," \t\n\r\f"));
if (ndos < 2) break;
ndos += (ndos+1)%2;
printf("Please input the maximum # of Lanczos iterations [%d]: ", nit);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) nit = atoi(strtok(str," \t\n\r\f"));
if (nit < 1) break;
printf("Please input the value of epsilon for delta-function [%g]: ", eps);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) eps = atof(strtok(str," \t\n\r\f"));
if (eps <= 0.) break;
// prepare array for local pdos
nlocal = 0;
for (ik = istr; ik <= iend; ik += iinc) nlocal++;
memory->destroy(ldos);
ldos = memory->create(ldos,nlocal,ndos,dynmat->sysdim,"ldos_rsgf:ldos");
memory->destroy(locals);
locals = memory->create(locals, nlocal, "ldos_rsgf:locals");
df = (fmax-fmin)/double(ndos-1);
rdf = 1./df;
// to measure the LDOS via real space Green's function method
int ilocal = 0;
for (ik = istr; ik <= iend; ik += iinc){
locals[ilocal] = ik;
// time info
Timer *time = new Timer();
printf("\nNow to compute the LDOS for atom %d by Real Space Greens function method ...\n", ik);
fflush(stdout);
// run real space green's function calculation
Green *green = new Green(dynmat->nucell, dynmat->sysdim, nit, fmin, fmax, ndos, eps, Hessian, ik, ldos[ilocal++]);
delete green;
time->stop(); time->print(); delete time;
}
Normalize();
writeLDOS();
// evaluate the local vibrational thermal properties optionally
local_therm();
}
memory->destroy(Hessian);
return;
}
/*------------------------------------------------------------------------------
* Private method to evaluate the phonon dispersion curves
*----------------------------------------------------------------------------*/
void Phonon::pdisp()
{
// ask the output file name and write the header.
char str[MAXLINE];
printf("Please input the filename to output the dispersion data [pdisp.dat]:");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str, "pdisp.dat");
char *ptr = strtok(str," \t\n\r\f");
char *fname = new char[strlen(ptr)+1];
strcpy(fname,ptr);
FILE *fp = fopen(fname, "w");
fprintf(fp,"# q qr freq\n");
fprintf(fp,"# 2pi/L 2pi/L %s\n", dynmat->funit);
// to store the nodes of the dispersion curve
std::vector<double> nodes; nodes.clear();
// now the calculate the dispersion curve
double qstr[3], qend[3], q[3], qinc[3], qr=0., dq;
int nq = MAX(MAX(dynmat->nx,dynmat->ny),dynmat->nz)/2+1;
qend[0] = qend[1] = qend[2] = 0.;
double *egvs = new double [ndim];
while (1){
for (int i=0; i<3; i++) qstr[i] = qend[i];
int quit = 0;
printf("\nPlease input the start q-point in unit of B1->B3, q to exit [%g %g %g]: ", qstr[0], qstr[1], qstr[2]);
int n = count_words(fgets(str,MAXLINE,stdin));
ptr = strtok(str," \t\n\r\f");
if ((n == 1) && (strcmp(ptr,"q") == 0)) break;
else if (n >= 3){
qstr[0] = atof(ptr);
qstr[1] = atof(strtok(NULL," \t\n\r\f"));
qstr[2] = atof(strtok(NULL," \t\n\r\f"));
}
do printf("Please input the end q-point in unit of B1->B3: ");
while (count_words(fgets(str,MAXLINE,stdin)) < 3);
qend[0] = atof(strtok(str," \t\n\r\f"));
qend[1] = atof(strtok(NULL," \t\n\r\f"));
qend[2] = atof(strtok(NULL," \t\n\r\f"));
printf("Please input the # of points along the line [%d]: ", nq);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) nq = atoi(strtok(str," \t\n\r\f"));
nq = MAX(nq,2);
for (int i=0; i<3; i++) qinc[i] = (qend[i]-qstr[i])/double(nq-1);
dq = sqrt(qinc[0]*qinc[0]+qinc[1]*qinc[1]+qinc[2]*qinc[2]);
nodes.push_back(qr);
for (int i=0; i<3; i++) q[i] = qstr[i];
for (int ii=0; ii<nq; ii++){
double wii = 1.;
dynmat->getDMq(q, &wii);
if (wii > 0.){
dynmat->geteigen(egvs, 0);
fprintf(fp,"%lg %lg %lg %lg ", q[0], q[1], q[2], qr);
for (int i=0; i<ndim; i++) fprintf(fp," %lg", egvs[i]);
}
fprintf(fp,"\n");
for (int i=0; i<3; i++) q[i] += qinc[i];
qr += dq;
}
qr -= dq;
}
if (qr > 0.) nodes.push_back(qr);
fclose(fp);
delete []egvs;
// write the gnuplot script which helps to visualize the result
int nnd = nodes.size();
if (nnd > 1){
fp = fopen("pdisp.gnuplot", "w");
fprintf(fp,"set term post enha colo 20\nset out %cpdisp.eps%c\n\n",char(34),char(34));
fprintf(fp,"set xlabel %cq%c\n",char(34),char(34));
fprintf(fp,"set ylabel %cfrequency (THz)%c\n\n",char(34),char(34));
fprintf(fp,"set xrange [0:%lg]\nset yrange [0:*]\n\n", nodes[nnd-1]);
fprintf(fp,"set grid xtics\n");
fprintf(fp,"# {/Symbol G} will give you letter gamma in the label\nset xtics (");
for (int i=0; i<nnd-1; i++) fprintf(fp,"%c%c %lg, ", char(34),char(34),nodes[i]);
fprintf(fp,"%c%c %lg)\n\n",char(34),char(34),nodes[nnd-1]);
fprintf(fp,"unset key\n\n");
fprintf(fp,"plot %c%s%c u 4:5 w l lt 1",char(34),fname,char(34));
for (int i=1; i<ndim; i++) fprintf(fp,",\\\n%c%c u 4:%d w l lt 1",char(34),char(34),i+5);
fclose(fp);
}
delete []fname;
nodes.clear();
return;
}
/* ----------------------------------------------------------------------------
* Private method to write out the dynamical matrix at selected q
* ---------------------------------------------------------------------------- */
void Phonon::dmanyq()
{
char str[MAXLINE];
double q[3];
do printf("Please input the q-point to output the dynamical matrix:");
while (count_words(fgets(str,MAXLINE,stdin)) < 3);
q[0] = atof(strtok(str," \t\n\r\f"));
q[1] = atof(strtok(NULL," \t\n\r\f"));
q[2] = atof(strtok(NULL," \t\n\r\f"));
dynmat->getDMq(q);
dynmat->writeDMq(q);
return;
}
/* ----------------------------------------------------------------------------
* Private method to get the vibrational frequencies at selected q
* ---------------------------------------------------------------------------- */
void Phonon::vfanyq()
{
char str[MAXLINE];
double q[3], egvs[ndim];
while (1){
printf("Please input the q-point to compute the frequencies, q to exit: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 3) break;
q[0] = atof(strtok(str, " \t\n\r\f"));
q[1] = atof(strtok(NULL," \t\n\r\f"));
q[2] = atof(strtok(NULL," \t\n\r\f"));
dynmat->getDMq(q);
dynmat->geteigen(egvs, 0);
printf("q-point: [%lg %lg %lg], ", q[0], q[1], q[2]);
printf("vibrational frequencies at this q-point:\n");
for (int i=0; i<ndim; i++) printf("%lg ", egvs[i]); printf("\n\n");
}
return;
}
/* ----------------------------------------------------------------------------
* Private method to get the vibrational frequencies and eigenvectors at selected q
* ---------------------------------------------------------------------------- */
void Phonon::vecanyq()
{
char str[MAXLINE];
double q[3], egvs[ndim];
doublecomplex **eigvec = dynmat->DM_q;
printf("Please input the filename to output the result [eigvec.dat]: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str,"eigvec.dat");
FILE *fp = fopen(strtok(str," \t\n\r\f"), "w");
while (1){
printf("Please input the q-point to compute the frequencies, q to exit: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 3) break;
q[0] = atof(strtok(str, " \t\n\r\f"));
q[1] = atof(strtok(NULL," \t\n\r\f"));
q[2] = atof(strtok(NULL," \t\n\r\f"));
dynmat->getDMq(q);
dynmat->geteigen(egvs, 1);
fprintf(fp,"# q-point: [%lg %lg %lg], sysdim: %d, # of atoms per cell: %d\n",
q[0],q[1],q[2], sysdim, dynmat->nucell);
for (int i=0; i<ndim; i++){
fprintf(fp,"# frequency %d at [%lg %lg %lg]: %lg\n",i+1,q[0],q[1],q[2],egvs[i]);
fprintf(fp,"# atom eigenvector : |e|\n");
for (int j=0; j<dynmat->nucell; j++){
int ipos = j * sysdim;
double sum = 0.;
fprintf(fp,"%d", j+1);
for (int idim=0; idim<sysdim; idim++){
fprintf(fp," %lg %lg", eigvec[i][ipos+idim].r, eigvec[i][ipos+idim].i);
sum += eigvec[i][ipos+idim].r * eigvec[i][ipos+idim].r + eigvec[i][ipos+idim].i * eigvec[i][ipos+idim].i;
}
fprintf(fp," : %lg\n", sqrt(sum));
}
fprintf(fp,"\n");
}
fprintf(fp,"\n");
}
fclose(fp);
eigvec = NULL;
return;
}
/* ----------------------------------------------------------------------------
* Private method to get the dispersion-like data for dynamical matrix
* ---------------------------------------------------------------------------- */
void Phonon::DMdisp()
{
// ask the output file name and write the header.
char str[MAXLINE];
printf("Please input the filename to output the DM data [DMDisp.dat]: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str, "DMDisp.dat");
char *fname = strtok(str," \t\n\r\f");
FILE *fp = fopen(fname, "w"); fname = NULL;
fprintf(fp,"# q qr D\n");
// now the calculate the dispersion-like curve
double qstr[3], qend[3], q[3], qinc[3], qr=0., dq;
int nq = MAX(MAX(dynmat->nx,dynmat->ny),dynmat->nz)/2;
qend[0] = qend[1] = qend[2] = 0.;
while (1){
for (int i=0; i<3; i++) qstr[i] = qend[i];
printf("\nPlease input the start q-point in unit of B1->B3, q to exit [%g %g %g]: ", qstr[0], qstr[1], qstr[2]);
int n = count_words(fgets(str,MAXLINE,stdin));
char *ptr = strtok(str," \t\n\r\f");
if ((n == 1) && (strcmp(ptr,"q") == 0)) break;
else if (n >= 3){
qstr[0] = atof(ptr);
qstr[1] = atof(strtok(NULL," \t\n\r\f"));
qstr[2] = atof(strtok(NULL," \t\n\r\f"));
}
do printf("Please input the end q-point in unit of B1->B3: ");
while (count_words(fgets(str,MAXLINE,stdin)) < 3);
qend[0] = atof(strtok(str," \t\n\r\f"));
qend[1] = atof(strtok(NULL," \t\n\r\f"));
qend[2] = atof(strtok(NULL," \t\n\r\f"));
printf("Please input the # of points along the line [%d]: ", nq);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) nq = atoi(strtok(str," \t\n\r\f"));
nq = MAX(nq,2);
for (int i=0; i<3; i++) qinc[i] = (qend[i]-qstr[i])/double(nq-1);
dq = sqrt(qinc[0]*qinc[0]+qinc[1]*qinc[1]+qinc[2]*qinc[2]);
for (int i=0; i<3; i++) q[i] = qstr[i];
for (int ii=0; ii<nq; ii++){
dynmat->getDMq(q);
dynmat->writeDMq(q, qr, fp);
for (int i=0; i<3; i++) q[i] += qinc[i];
qr += dq;
}
qr -= dq;
}
fclose(fp);
return;
}
/* ----------------------------------------------------------------------------
* Private method to smooth the dos
* ---------------------------------------------------------------------------- */
void Phonon::smooth(double *array, const int npt)
{
if (npt < 4) return;
int nlag = npt/4;
double *tmp, *table;
tmp = memory->create(tmp, npt, "smooth:tmp");
table = memory->create(table, nlag+1, "smooth:table");
double fnorm = -1.;
double sigma = 4., fac = 1./(sigma*sigma);
for (int jj=0; jj<= nlag; jj++){
table[jj] = exp(-double(jj*jj)*fac);
fnorm += table[jj];
}
fnorm = 1./fnorm;
for (int i=0; i<npt; i++){
tmp[i] = 0.;
for (int jj=-nlag; jj<= nlag; jj++){
int j = (i+jj+npt)%npt; // assume periodical data
tmp [i] += array[j]*table[abs(jj)];
}
}
for (int i=0; i<npt; i++) array[i] = tmp[i]*fnorm;
memory->destroy(tmp);
memory->destroy(table);
return;
}
/* ----------------------------------------------------------------------------
* Private method to calculate the thermal properties
* ---------------------------------------------------------------------------- */
void Phonon::therm()
{
// get frequencies on a q-mesh
QMesh();
ComputeAll();
// get the filename to output thermal properties
char str[MAXLINE];
printf("\nPlease input the filename to output thermal properties [therm.dat]:");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str, "therm.dat");
char *fname = strtok(str," \t\n\r\f");
FILE *fp = fopen(fname, "a"); fname = NULL;
// header line
fprintf(fp,"#Temp Uvib Svib Fvib ZPE Cvib\n");
fprintf(fp,"# K eV Kb eV eV Kb\n");
// constants J.s J/K J
const double h = 6.62606896e-34, Kb = 1.380658e-23, eV = 1.60217733e-19;
// first temperature
double T = dynmat->Tmeasure;
do {
// constants under the same temperature; assuming angular frequency in THz
double h_o_KbT = h/(Kb*T)*1.e12, KbT_in_eV = Kb*T/eV;
double Uvib = 0., Svib = 0., Fvib = 0., Cvib = 0., ZPE = 0.;
for (int iq=0; iq<nq; iq++){
double Utmp = 0., Stmp = 0., Ftmp = 0., Ztmp = 0., Ctmp = 0.;
for (int i=0; i<ndim; i++){
if (eigs[iq][i] <= 0.) continue;
double x = eigs[iq][i] * h_o_KbT;
double expterm = 1./(exp(x)-1.);
Stmp += x*expterm - log(1.-exp(-x));
Utmp += (0.5+expterm)*x;
Ftmp += log(2.*sinh(0.5*x));
Ctmp += x*x*exp(x)*expterm*expterm;
Ztmp += 0.5*h*eigs[iq][i];
}
Svib += wt[iq]*Stmp;
Uvib += wt[iq]*Utmp;
Fvib += wt[iq]*Ftmp;
Cvib += wt[iq]*Ctmp;
ZPE += wt[iq]*Ztmp;
}
Uvib *= KbT_in_eV;
Fvib *= KbT_in_eV;
ZPE /= eV*1.e-12;
// output result under current temperature
fprintf(fp,"%lg %lg %lg %lg %lg %lg\n", T, Uvib, Svib, Fvib, ZPE, Cvib);
printf("Please input the desired temperature (K), enter to exit: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) break;
T = atof(strtok(str," \t\n\r\f"));
} while (T > 0.);
fclose(fp);
return;
}
/* ----------------------------------------------------------------------------
* Private method to calculate the local thermal properties
* ---------------------------------------------------------------------------- */
void Phonon::local_therm()
{
char str[MAXLINE];
printf("\nWould you like to compute the local thermal properties (y/n)[n]: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) return;
char *ptr = strtok(str," \t\n\r\f");
if (strcmp(ptr,"y") != 0 && strcmp(ptr, "Y") != 0 && strcmp(ptr, "yes") != 0) return;
printf("Please input the filename to output vibrational thermal info [localtherm.dat]: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str, "localtherm.dat");
FILE *fp = fopen(strtok(str," \t\n\r\f"), "w");
fprintf(fp,"# atom Temp U_vib (eV) S_vib (kB) F_vib (eV) C_vib (kB) ZPE (eV)\n");
fprintf(fp,"# ------------ ------------ ----------- ----------- ------------\n");
fprintf(fp,"# Ux Uy Uz Ut Sx Sy Sz St Fx Fy Fz Ft Cx Cy Cz Ct Zx Zy Zz Zt\n");
fprintf(fp,"# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22\n");
fprintf(fp,"#-------------------------------------------------------------------------------\n");
double **Uvib, **Svib, **Fvib, **Cvib, **ZPE;
Uvib = memory->create(Uvib,nlocal,sysdim,"local_therm:Uvib");
Svib = memory->create(Svib,nlocal,sysdim,"local_therm:Svib");
Fvib = memory->create(Fvib,nlocal,sysdim,"local_therm:Fvib");
Cvib = memory->create(Cvib,nlocal,sysdim,"local_therm:Cvib");
ZPE = memory->create(ZPE ,nlocal,sysdim,"local_therm:ZPE");
// constants J.s J/K J
const double h = 6.62606896e-34, Kb = 1.380658e-23, eV = 1.60217733e-19;
double T = dynmat->Tmeasure;
while (1){
printf("\nPlease input the temperature at which to evaluate the local vibrational\n");
printf("thermal properties, non-positive number to exit [%g]: ", T);
if (count_words(fgets(str,MAXLINE,stdin)) > 0){
T = atoi(strtok(str," \t\n\r\f"));
if (T <= 0.) break;
}
// constants under the same temperature; assuming angular frequency in THz
double h_o_KbT = h/(Kb*T)*1.e12, KbT_in_eV = Kb*T/eV;
for (int i=0; i<nlocal; i++)
for (int j=0; j<sysdim; j++) Uvib[i][j] = Svib[i][j] = Fvib[i][j] = Cvib[i][j] = ZPE[i][j] = 0.;
double freq = fmin-df;
for (int i=0; i<ndos; i++){
freq += df;
if (freq <= 0.) continue;
double x = freq * h_o_KbT;
double expterm = 1./(exp(x)-1.);
double Stmp = x*expterm - log(1.-exp(-x));
double Utmp = (0.5+expterm)*x;
double Ftmp = log(2.*sinh(0.5*x));
double Ctmp = x*x*exp(x)*expterm*expterm;
double Ztmp = 0.5*h*freq;
for (int il=0; il<nlocal; il++)
for (int idim=0; idim<sysdim; idim++){
Uvib[il][idim] += ldos[il][i][idim]*Utmp;
Svib[il][idim] += ldos[il][i][idim]*Stmp;
Fvib[il][idim] += ldos[il][i][idim]*Ftmp;
Cvib[il][idim] += ldos[il][i][idim]*Ctmp;
ZPE [il][idim] += ldos[il][i][idim]*Ztmp;
}
}
for (int il=0; il<nlocal; il++)
for (int idim=0; idim<sysdim; idim++){
Uvib[il][idim] *= KbT_in_eV*df;
Svib[il][idim] *= df;
Fvib[il][idim] *= KbT_in_eV*df;
Cvib[il][idim] *= df;
ZPE [il][idim] /= eV*1.e-12*rdf;
}
// output result under current temperature
for (int il=0; il<nlocal; il++){
fprintf(fp,"%d %g ", locals[il], T);
double total = 0.;
for (int idim=0; idim<sysdim; idim++){
fprintf(fp,"%g ", Uvib[il][idim]);
total += Uvib[il][idim];
}
fprintf(fp,"%g ", total); total = 0.;
for (int idim=0; idim<sysdim; idim++){
fprintf(fp,"%g ", Svib[il][idim]);
total += Svib[il][idim];
}
fprintf(fp,"%g ", total); total = 0.;
for (int idim=0; idim<sysdim; idim++){
fprintf(fp,"%g ", Fvib[il][idim]);
total += Fvib[il][idim];
}
fprintf(fp,"%g ", total); total = 0.;
for (int idim=0; idim<sysdim; idim++){
fprintf(fp,"%g ", Cvib[il][idim]);
total += Cvib[il][idim];
}
fprintf(fp,"%g ", total); total = 0.;
for (int idim=0; idim<sysdim; idim++){
fprintf(fp,"%g ", ZPE[il][idim]);
total += ZPE[il][idim];
}
fprintf(fp,"%g\n", total);
}
}
fclose(fp);
return;
}
/* ----------------------------------------------------------------------------
* Private method to generate the q-points from a uniform q-mesh
* ---------------------------------------------------------------------------- */
void Phonon::QMesh()
{
// ask for mesh info
char str[MAXLINE];
int nx = dynmat->nx, ny = dynmat->ny, nz = dynmat->nz;
printf("\nThe q-mesh size from the read dynamical matrix is: %d x %d x %d\n", nx, ny, nz);
printf("A denser mesh can be interpolated, but NOTE a too dense mesh can cause segmentation fault.\n");
printf("Please input your desired q-mesh size [%d %d %d]: ", nx, ny, nz);
if (count_words(fgets(str,MAXLINE,stdin)) >= 3){
nx = atoi(strtok(str," \t\n\r\f"));
ny = atoi(strtok(NULL," \t\n\r\f"));
nz = atoi(strtok(NULL," \t\n\r\f"));
}
if (nx<1||ny<1||nz<1) return;
if (dynmat->nx == 1) nx = 1;
if (dynmat->ny == 1) ny = 1;
if (dynmat->nz == 1) nz = 1;
#ifdef UseSPG
// ask method to generate q-points
int method = 2;
printf("Please select your method to generate the q-points:\n");
printf(" 1. uniform;\n 2. Monkhost-Pack mesh;\nYour choice[2]: ");
if (count_words(fgets(str,MAXLINE,stdin)) > 0) method = atoi(strtok(str," \t\n\r\f"));
method = 2-method%2;
printf("Your selection: %d\n", method);
#endif
memory->destroy(wt);
memory->destroy(qpts);
#ifdef UseSPG
if (method == 1){
#endif
nq = nx*ny*nz;
double w = 1./double(nq);
wt = memory->create(wt, nq, "QMesh:wt");
qpts = memory->create(qpts, nq, 3, "QMesh:qpts");
int iq = 0;
for (int i=0; i<nx; i++)
for (int j=0; j<ny; j++)
for (int k=0; k<nz; k++){
qpts[iq][0] = double(i)/double(nx);
qpts[iq][1] = double(j)/double(ny);
qpts[iq][2] = double(k)/double(nz);
wt[iq++] = w;
}
#ifdef UseSPG
}
if ((method == 2) && (atpos == NULL)){
atpos = memory->create(atpos, dynmat->nucell,3,"QMesh:atpos");
attyp = memory->create(attyp, dynmat->nucell, "QMesh:attyp");
for (int i=0; i<dynmat->nucell; i++)
for (int idim=0; idim<3; idim++) atpos[i][idim] = 0.;
for (int i=0; i<3; i++) latvec[i][i] = 1.;
int flag_lat_info_read = dynmat->flag_latinfo;
if ( flag_lat_info_read ){ // get unit cell info from binary file; done by dynmat
num_atom = dynmat->nucell;
// set default, in case system dimension under study is not 3.
for (int i=0; i<dynmat->nucell; i++)
for (int idim=0; idim<3; idim++) atpos[i][idim] = 0.;
for (int i=0; i<3; i++) latvec[i][i] = 1.;
// get atomic type info
for (int i=0; i<num_atom; i++) attyp[i] = dynmat->attyp[i];
// get unit cell vector info
int ndim = 0;
for (int idim=0; idim<3; idim++)
for (int jdim=0; jdim<3; jdim++) latvec[jdim][idim] = dynmat->basevec[ndim++];
// get atom position in unit cell; fractional
for (int i=0; i<num_atom; i++)
for (int idim=0; idim<sysdim; idim++) atpos[i][idim] = dynmat->basis[i][idim];
// display the unit cell info read
printf("\n");for (int ii=0; ii<80; ii++) printf("="); printf("\n");
printf("The basis vectors of the unit cell:\n");
for (int idim=0; idim<3; idim++) printf(" A%d = %lg %lg %lg\n", idim+1, latvec[0][idim], latvec[1][idim], latvec[2][idim]);
printf("Atom(s) in the unit cell:\n");
printf(" No. type sx sy sz\n");
for (int i=0; i<num_atom; i++) printf(" %d %d %lg %lg %lg\n", i+1, attyp[i], atpos[i][0], atpos[i][1], atpos[i][2]);
printf("\nIs the above info correct? (y/n)[y]: ");
fgets(str,MAXLINE,stdin);
char *ptr = strtok(str," \t\n\r\f");
if ( (ptr) && ( (strcmp(ptr,"y") != 0) && (strcmp(ptr,"Y") != 0)) ) flag_lat_info_read = 0;
}
if (flag_lat_info_read == 0) { // get unit cell info from file or user input
int latsrc = 1;
printf("\nPlease select the way to provide the unit cell info:\n");
printf(" 1. By file;\n 2. Read in.\nYour choice [1]: ");
if (count_words(fgets(str,MAXLINE,stdin)) > 0) latsrc = atoi(strtok(str," \t\n\r\f"));
latsrc = 2-latsrc%2;
/*----------------------------------------------------------------
* Ask for lattice info from the user; the format of the file is:
* A1_x A1_y A1_z
* A2_x A2_y A2_z
* A3_x A3_y A3_z
* natom
* Type_1 sx_1 sy_1 sz_1
* ...
* Type_n sx_n sy_n sz_n
*----------------------------------------------------------------*/
if (latsrc == 1){ // to read unit cell info from file; get file name first
do printf("Please input the file name containing the unit cell info: ");
while (count_words(fgets(str,MAXLINE,stdin)) < 1);
char *fname = strtok(str," \t\n\r\f");
FILE *fp = fopen(fname,"r"); fname = NULL;
if (fp == NULL) latsrc = 2;
else {
for (int i=0; i<3; i++){ // read unit cell vector info; # of atoms per unit cell
if (count_words(fgets(str,MAXLINE,fp)) < 3){
latsrc = 2;
break;
}
latvec[0][i] = atof(strtok(str, " \t\n\r\f"));
latvec[1][i] = atof(strtok(NULL," \t\n\r\f"));
latvec[2][i] = atof(strtok(NULL," \t\n\r\f"));
}
if (count_words(fgets(str,MAXLINE,fp)) < 1) latsrc = 2;
else {
num_atom = atoi(strtok(str," \t\n\r\f"));
if (num_atom > dynmat->nucell){
printf("\nError: # of atoms read from file (%d) is bigger than that given by the dynamical matrix (%d)!\n", num_atom, dynmat->nucell);
return;
}
for (int i=0; i<num_atom; i++){ // read atomic type and fractional positions
if (count_words(fgets(str,MAXLINE,fp)) < 4){
latsrc = 2;
break;
} else {
attyp[i] = atoi(strtok(str," \t\n\r\f"));
atpos[i][0] = atof(strtok(NULL," \t\n\r\f"));
atpos[i][1] = atof(strtok(NULL," \t\n\r\f"));
atpos[i][2] = atof(strtok(NULL," \t\n\r\f"));
}
}
}
}
fclose(fp);
}
if (latsrc == 2){
for (int i=0; i<3; i++){
do printf("Please input the vector A%d: ", i+1);
while (count_words(fgets(str,MAXLINE,stdin)) < 3);
latvec[0][i] = atof(strtok(str," \t\n\r\f"));
latvec[1][i] = atof(strtok(NULL," \t\n\r\f"));
latvec[2][i] = atof(strtok(NULL," \t\n\r\f"));
}
do printf("please input the number of atoms per unit cell: ");
while (count_words(fgets(str,MAXLINE,stdin)) < 1);
num_atom = atoi(strtok(str," \t\n\r\f"));
if (num_atom > dynmat->nucell){
printf("\nError: # of atoms input (%d) is bigger than that given by the dynamical matrix (%d)!\n", num_atom, dynmat->nucell);
return;
}
for (int i=0; i<num_atom; i++){
do printf("Please input the type, and fractional coordinate of atom No.%d: ", i+1);
while (count_words(fgets(str,MAXLINE,stdin)) < 4);
attyp[i] = atoi(strtok(str," \t\n\r\f"));
atpos[i][0] = atof(strtok(NULL," \t\n\r\f"));
atpos[i][1] = atof(strtok(NULL," \t\n\r\f"));
atpos[i][2] = atof(strtok(NULL," \t\n\r\f"));
}
}
} // end of read from file or input
} // end of if (method == 2 && ...
if (method == 2){
int mesh[3], shift[3], is_time_reversal = 0;
mesh[0] = nx; mesh[1] = ny; mesh[2] = nz;
shift[0] = shift[1] = shift[2] = 0;
int num_grid = mesh[0]*mesh[1]*mesh[2];
int grid_point[num_grid][3], map[num_grid];
double symprec = 1.e-4, pos[num_atom][3];
for (int i=0; i<num_atom; i++)
for (int j=0; j<3; j++) pos[i][j] = atpos[i][j];
//spg_show_symmetry(latvec, pos, attyp, num_atom, symprec);
// if spglib 0.7.1 is used
nq = spg_get_ir_reciprocal_mesh(grid_point, map, num_grid, mesh, shift, is_time_reversal, latvec, pos, attyp, num_atom, symprec);
// if spglib >= 1.0.3 is used
//nq = spg_get_ir_reciprocal_mesh(grid_point, map, mesh, shift, is_time_reversal, latvec, pos, attyp, num_atom, symprec);
wt = memory->create(wt, nq, "QMesh:wt");
qpts = memory->create(qpts, nq,3,"QMesh:qpts");
int *iq2idx = new int[num_grid];
int numq = 0;
for (int i=0; i<num_grid; i++){
int iq = map[i];
if (iq == i) iq2idx[iq] = numq++;
}
for (int iq=0; iq<nq; iq++) wt[iq] = 0.;
numq = 0;
for (int i=0; i<num_grid; i++){
int iq = map[i];
if (iq == i){
qpts[numq][0] = double(grid_point[i][0])/double(mesh[0]);
qpts[numq][1] = double(grid_point[i][1])/double(mesh[1]);
qpts[numq][2] = double(grid_point[i][2])/double(mesh[2]);
numq++;
}
wt[iq2idx[iq]] += 1.;
}
delete []iq2idx;
double wsum = 0.;
for (int iq=0; iq<nq; iq++) wsum += wt[iq];
for (int iq=0; iq<nq; iq++) wt[iq] /= wsum;
}
#endif
printf("Your new q-mesh size would be: %d x %d x %d => %d points\n", nx,ny,nz,nq);
return;
}
/* ----------------------------------------------------------------------------
* Private method to calculate the local phonon DOS and total phonon DOS based
* on the eigenvectors
* ---------------------------------------------------------------------------- */
void Phonon::ldos_egv()
{
// get local position info
char str[MAXLINE], *ptr;
printf("\nThe # of atoms per cell is: %d, please input the atom IDs to compute\n", dynmat->nucell);
printf("local PDOS, IDs begin with 0: ");
int nmax = count_words(fgets(str,MAXLINE,stdin));
if (nmax < 1) return;
memory->destroy(locals);
locals = memory->create(locals, nmax, "ldos_egv:locals");
nlocal = 0;
ptr = strtok(str," \t\n\r\f");
while (ptr != NULL){
int id = atoi(ptr);
if (id >= 0 && id < dynmat->nucell) locals[nlocal++] = id;
ptr = strtok(NULL," \t\n\r\f");
}
if (nlocal < 1) return;
printf("Local PDOS for atom(s):");
for (int i=0; i<nlocal; i++) printf(" %d", locals[i]);
printf(" will be computed.\n");
fmin = 0.; fmax = 10.;
printf("Please input the freqency (nv, THz) range to compute PDOS [%g %g]: ", fmin, fmax);
if (count_words(fgets(str,MAXLINE,stdin)) >= 2) {
fmin = atof(strtok(str," \t\n\r\f"));
fmax = atof(strtok(NULL," \t\n\r\f"));
}
if (fmax < 0. || fmax < fmin) return;
ndos = 201;
printf("Please input your desired # of points in PDOS [%d]: ", ndos);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) ndos = atoi(strtok(str," \t\n\r\f"));
if (ndos < 2) return;
ndos += (ndos+1)%2;
df = (fmax-fmin)/double(ndos-1);
rdf = 1./df;
// get the q-points
QMesh();
// allocate memory for DOS and LDOS
memory->destroy(dos);
memory->destroy(ldos);
dos = memory->create(dos, ndos,"ldos_egv:dos");
ldos = memory->create(ldos,nlocal,ndos,sysdim,"ldos_egv:ldos");
for (int i=0; i<ndos; i++) dos[i] = 0.;
for (int ilocal=0; ilocal<nlocal; ilocal++)
for (int i=0; i<ndos; i++)
for (int idim=0; idim<sysdim; idim++) ldos[ilocal][i][idim] = 0.;
int nprint;
if (nq > 10) nprint = nq/10;
else nprint = 1;
Timer *time = new Timer();
// memory and pointer for eigenvalues and eigenvectors
double egval[ndim], offset=fmin-0.5*df;
doublecomplex **egvec = dynmat->DM_q;
printf("\nNow to compute the phonons and DOSs "); fflush(stdout);
for (int iq=0; iq<nq; iq++){
if ((iq+1)%nprint == 0) {printf("."); fflush(stdout);}
dynmat->getDMq(qpts[iq], &wt[iq]);
if (wt[iq] <= 0.) continue;
dynmat->geteigen(&egval[0], 1);
for (int idim=0; idim<ndim; idim++){
int hit = int((egval[idim] - offset)*rdf);
if (hit >= 0 && hit <ndos){
dos[hit] += wt[iq];
for (int ilocal=0; ilocal<nlocal; ilocal++){
int ipos = locals[ilocal]*sysdim;
for (int jdim=0; jdim<sysdim; jdim++){
double dr = egvec[idim][ipos+jdim].r, di = egvec[idim][ipos+jdim].i;
double norm = dr * dr + di * di;
ldos[ilocal][hit][jdim] += wt[iq] * norm;
}
}
}
}
}
egvec = NULL;
printf("Done!\nNow to normalize the DOSs ..."); fflush(stdout);
// normalize the measure DOS and LDOS
Normalize();
printf("Done! ");
time->stop(); time->print(); delete time;
// to write the DOSes
writeDOS();
writeLDOS();
// evaluate the local vibrational thermal properties optionally
local_therm();
return;
}
/* ----------------------------------------------------------------------------
* Private method to normalize the DOS and/or Local DOS.
* Simpson's rule is used for the integration.
* ---------------------------------------------------------------------------- */
void Phonon::Normalize()
{
double odd, even, sum;
if (dos){
odd = even = 0.;
for (int i=1; i<ndos-1; i +=2) odd += dos[i];
for (int i=2; i<ndos-1; i +=2) even += dos[i];
sum = dos[0] + dos[ndos-1];
sum += 4.*odd + 2.*even;
sum = 3.*rdf/sum;
for (int i=0; i<ndos; i++) dos[i] *= sum;
}
if (ldos){
for (int ilocal=0; ilocal<nlocal; ilocal++)
for (int idim=0; idim<sysdim; idim++){
odd = even = 0.;
for (int i=1; i<ndos-1; i +=2) odd += ldos[ilocal][i][idim];
for (int i=2; i<ndos-1; i +=2) even += ldos[ilocal][i][idim];
sum = ldos[ilocal][0][idim] + ldos[ilocal][ndos-1][idim];
sum += 4.*odd + 2.*even;
sum = 3.*rdf/sum;
for (int i=0; i<ndos; i++) ldos[ilocal][i][idim] *= sum;
}
}
return;
}
/* ----------------------------------------------------------------------------
* Private method to calculate vibrational frequencies for all q-points
* ---------------------------------------------------------------------------- */
void Phonon::ComputeAll()
{
int nprint;
if (nq > 10) nprint = nq/10;
else nprint = 1;
Timer *time = new Timer();
printf("\nNow to compute the phonons "); fflush(stdout);
// now to calculate the frequencies at all q-points
memory->destroy(eigs);
eigs = memory->create(eigs, nq,ndim,"QMesh_eigs");
for (int iq=0; iq<nq; iq++){
if ((iq+1)%nprint == 0) {printf("."); fflush(stdout);}
dynmat->getDMq(qpts[iq], &wt[iq]);
if (wt[iq] > 0.) dynmat->geteigen(eigs[iq], 0);
}
printf("Done!\n");
time->stop(); time->print(); delete time;
return;
}
/*------------------------------------------------------------------------------
* Method to count # of words in a string, without destroying the string
*----------------------------------------------------------------------------*/
int Phonon::count_words(const char *line)
{
int n = strlen(line) + 1;
char *copy;
copy = memory->create(copy, n, "count_words:copy");
strcpy(copy,line);
char *ptr;
if (ptr = strchr(copy,'#')) *ptr = '\0';
if (strtok(copy," \t\n\r\f") == NULL) {
memory->destroy(copy);
return 0;
}
n = 1;
while (strtok(NULL," \t\n\r\f")) n++;
memory->destroy(copy);
return n;
}
/*----------------------------------------------------------------------------*/
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