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Tue, Aug 27, 09:40

dynmat.cpp
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#include "dynmat.h"
#include "math.h"
#include "version.h"
#define MAXLINE 256
// to intialize the class
DynMat::DynMat(int narg, char **arg)
{
attyp = NULL;
memory = NULL;
M_inv_sqrt = NULL;
interpolate = NULL;
DM_q = DM_all = NULL;
binfile = funit = dmfile = NULL;
flag_reset_gamma = flag_skip = 0;
// analyze the command line options
int iarg = 1;
while (narg > iarg){
if (strcmp(arg[iarg], "-s") == 0){
flag_reset_gamma = flag_skip = 1;
} else if (strcmp(arg[iarg], "-r") == 0){
flag_reset_gamma = 1;
} else if (strcmp(arg[iarg], "-h") == 0){
help();
} else {
if (binfile) delete []binfile;
int n = strlen(arg[iarg]) + 1;
binfile = new char[n];
strcpy(binfile, arg[iarg]);
}
iarg++;
}
ShowVersion();
// get the binary file name from user input if not found in command line
char str[MAXLINE];
if (binfile == NULL) {
char *ptr = NULL;
printf("\n");
do {
printf("Please input the binary file name from fix_phonon: ");
fgets(str,MAXLINE,stdin);
ptr = strtok(str, " \n\t\r\f");
} while (ptr == NULL);
int n = strlen(ptr) + 1;
binfile = new char[n];
strcpy(binfile, ptr);
}
// open the binary file
FILE *fp = fopen(binfile, "rb");
if (fp == NULL) {
printf("\nFile %s not found! Programe terminated.\n", binfile);
help();
}
// read header info from the binary file
if ( fread(&sysdim, sizeof(int), 1, fp) != 1) {printf("\nError while reading sysdim from file: %s\n", binfile); fclose(fp); exit(2);}
if ( fread(&nx, sizeof(int), 1, fp) != 1) {printf("\nError while reading nx from file: %s\n", binfile); fclose(fp); exit(2);}
if ( fread(&ny, sizeof(int), 1, fp) != 1) {printf("\nError while reading ny from file: %s\n", binfile); fclose(fp); exit(2);}
if ( fread(&nz, sizeof(int), 1, fp) != 1) {printf("\nError while reading nz from file: %s\n", binfile); fclose(fp); exit(2);}
if ( fread(&nucell, sizeof(int), 1, fp) != 1) {printf("\nError while reading nucell from file: %s\n", binfile); fclose(fp); exit(2);}
if ( fread(&boltz, sizeof(double), 1, fp) != 1) {printf("\nError while reading boltz from file: %s\n", binfile); fclose(fp); exit(2);}
fftdim = sysdim*nucell; fftdim2 = fftdim*fftdim;
npt = nx*ny*nz;
// display info related to the read file
printf("\n"); for (int i=0; i<80; i++) printf("="); printf("\n");
printf("Dynamical matrix is read from file: %s\n", binfile);
printf("The system size in three dimension: %d x %d x %d\n", nx, ny, nz);
printf("Number of atoms per unit cell : %d\n", nucell);
printf("System dimension : %d\n", sysdim);
printf("Boltzmann constant in used units : %g\n", boltz);
for (int i=0; i<80; i++) printf("="); printf("\n");
if (sysdim<1||sysdim>3||nx<1||ny<1||nz<1||nucell<1){
printf("Wrong values read from header of file: %s, please check the binary file!\n", binfile);
fclose(fp); exit(3);
}
funit = new char[4];
strcpy(funit, "THz");
if (boltz == 1.){eml2f = 1.; delete funit; funit=new char[22]; strcpy(funit,"sqrt(epsilon/(m.sigma^2))");}
else if (boltz == 0.0019872067) eml2f = 3.256576161;
else if (boltz == 8.617343e-5) eml2f = 15.63312493;
else if (boltz == 1.3806504e-23) eml2f = 1.;
else if (boltz == 1.3806504e-16) eml2f = 1.591549431e-14;
else {
printf("WARNING: Because of float precision, I cannot get the factor to convert sqrt(E/ML^2)\n");
printf("into THz, instead, I set it to be 1; you should check the unit used by LAMMPS.\n");
eml2f = 1.;
}
// now to allocate memory for DM
memory = new Memory;
DM_all = memory->create(DM_all, npt, fftdim2, "DynMat:DM_all");
DM_q = memory->create(DM_q, fftdim,fftdim,"DynMat:DM_q");
// read all dynamical matrix info into DM_all
if ( fread(DM_all[0], sizeof(doublecomplex), npt*fftdim2, fp) != size_t(npt*fftdim2)){
printf("\nError while reading the DM from file: %s\n", binfile);
fclose(fp);
exit(1);
}
// now try to read unit cell info from the binary file
flag_latinfo = 0;
basis = memory->create(basis,nucell,sysdim,"DynMat:basis");
attyp = memory->create(attyp,nucell, "DynMat:attyp");
M_inv_sqrt = memory->create(M_inv_sqrt, nucell, "DynMat:M_inv_sqrt");
int flag_mass_read = 0;
if ( fread(&Tmeasure, sizeof(double), 1, fp) == 1) flag_latinfo |= 1;
if ( fread(&basevec[0], sizeof(double), 9, fp) == 9) flag_latinfo |= 2;
if ( fread(basis[0], sizeof(double), fftdim, fp) == fftdim) flag_latinfo |= 4;
if ( fread(&attyp[0], sizeof(int), nucell, fp) == nucell) flag_latinfo |= 8;
if ( fread(&M_inv_sqrt[0], sizeof(double), nucell, fp) == nucell) flag_mass_read = 1;
fclose(fp);
if ((flag_latinfo&15) == 15){
car2dir(flag_mass_read);
real2rec();
flag_latinfo = 1;
} else {
Tmeasure = 0.;
flag_latinfo = 0;
}
// initialize interpolation
interpolate = new Interpolate(nx,ny,nz,fftdim2,DM_all);
if (flag_reset_gamma) interpolate->reset_gamma();
if ( flag_mass_read ){ // M_inv_sqrt info read, the data stored are force constant matrix instead of dynamical matrix.
EnforceASR();
// get the dynamical matrix from force constant matrix: D = 1/M x Phi
for (int idq=0; idq< npt; idq++){
int ndim =0;
for (int idim=0; idim<fftdim; idim++){
for (int jdim=0; jdim<fftdim; jdim++){
double inv_mass = M_inv_sqrt[idim/sysdim]*M_inv_sqrt[jdim/sysdim];
DM_all[idq][ndim].r *= inv_mass;
DM_all[idq][ndim].i *= inv_mass;
ndim++;
}
}
}
}
// ask for the interpolation method
interpolate->set_method();
return;
}
// to destroy the class
DynMat::~DynMat()
{
// destroy all memory allocated
if (funit) delete []funit;
if (dmfile) delete []dmfile;
if (binfile) delete []binfile;
if (interpolate) delete interpolate;
memory->destroy(DM_q);
memory->destroy(attyp);
memory->destroy(basis);
memory->destroy(DM_all);
memory->destroy(M_inv_sqrt);
if (memory) delete memory;
}
/* ----------------------------------------------------------------------------
* method to write DM_q to file, single point
* ---------------------------------------------------------------------------- */
void DynMat::writeDMq(double *q)
{
FILE *fp;
// only ask for file name for the first time
// other calls will append the result to the file.
if (dmfile == NULL){
char str[MAXLINE], *ptr;
printf("\n");
while (1){
printf("Please input the filename to output the DM at selected q: ");
fgets(str,MAXLINE,stdin);
ptr = strtok(str, " \r\t\n\f");
if (ptr) break;
}
int n = strlen(ptr) + 1;
dmfile = new char[n];
strcpy(dmfile, ptr);
fp = fopen(dmfile,"w");
} else {
fp = fopen(dmfile,"a");
}
fprintf(fp,"# q = [%lg %lg %lg]\n", q[0], q[1], q[2]);
for (int i=0; i<fftdim; i++){
for (int j=0; j<fftdim; j++) fprintf(fp,"%lg %lg\t", DM_q[i][j].r, DM_q[i][j].i);
fprintf(fp,"\n");
}
fprintf(fp,"\n");
fclose(fp);
return;
}
/* ----------------------------------------------------------------------------
* method to write DM_q to file, dispersion-like
* ---------------------------------------------------------------------------- */
void DynMat::writeDMq(double *q, const double qr, FILE *fp)
{
fprintf(fp, "%lg %lg %lg %lg ", q[0], q[1], q[2], qr);
for (int i=0; i<fftdim; i++){
for (int j=0; j<fftdim; j++) fprintf(fp,"%lg %lg\t", DM_q[i][j].r, DM_q[i][j].i);
}
fprintf(fp,"\n");
return;
}
/* ----------------------------------------------------------------------------
* method to evaluate the eigenvalues of current q-point;
* return the eigenvalues in egv.
* cLapack subroutine zheevd is employed.
* ---------------------------------------------------------------------------- */
int DynMat::geteigen(double *egv, int flag)
{
char jobz, uplo;
integer n, lda, lwork, lrwork, *iwork, liwork, info;
doublecomplex *work;
doublereal *w = &egv[0], *rwork;
n = fftdim;
if (flag) jobz = 'V';
else jobz = 'N';
uplo = 'U';
lwork = (n+2)*n;
lrwork = 1 + (5+n+n)*n;
liwork = 3 + 5*n;
lda = n;
work = memory->create(work, lwork, "geteigen:work");
rwork = memory->create(rwork, lrwork, "geteigen:rwork");
iwork = memory->create(iwork, liwork, "geteigen:iwork");
zheevd_(&jobz, &uplo, &n, DM_q[0], &lda, w, work, &lwork, rwork, &lrwork, iwork, &liwork, &info);
// to get w instead of w^2; and convert w into v (THz hopefully)
for (int i=0; i<n; i++){
if (w[i]>= 0.) w[i] = sqrt(w[i]);
else w[i] = -sqrt(-w[i]);
w[i] *= eml2f;
}
memory->destroy(work);
memory->destroy(rwork);
memory->destroy(iwork);
return info;
}
/* ----------------------------------------------------------------------------
* method to get the Dynamical Matrix at q
* ---------------------------------------------------------------------------- */
void DynMat::getDMq(double *q)
{
interpolate->execute(q, DM_q[0]);
return;
}
/* ----------------------------------------------------------------------------
* method to get the Dynamical Matrix at q
* ---------------------------------------------------------------------------- */
void DynMat::getDMq(double *q, double *wt)
{
interpolate->execute(q, DM_q[0]);
if (flag_skip && interpolate->UseGamma ) wt[0] = 0.;
return;
}
/* ----------------------------------------------------------------------------
* private method to convert the cartisan coordinate of basis into fractional
* ---------------------------------------------------------------------------- */
void DynMat::car2dir(int flag)
{
if (!flag){ // in newer version, this is done in fix-phonon
for (int i=0; i<3; i++){
basevec[i] /= double(nx);
basevec[i+3] /= double(ny);
basevec[i+6] /= double(nz);
}
}
double mat[9];
for (int idim=0; idim<9; idim++) mat[idim] = basevec[idim];
GaussJordan(3, mat);
for (int i=0; i<nucell; i++){
double x[3];
x[0] = x[1] = x[2] = 0.;
for (int idim=0; idim<sysdim; idim++) x[idim] = basis[i][idim];
for (int idim=0; idim<sysdim; idim++)
basis[i][idim] = x[0]*mat[idim] + x[1]*mat[3+idim] + x[2]*mat[6+idim];
}
return;
}
/* ----------------------------------------------------------------------------
* private method to enforce the acoustic sum rule on force constant matrix at G
* ---------------------------------------------------------------------------- */
void DynMat::EnforceASR()
{
char str[MAXLINE];
int nasr = 20;
if (nucell <= 1) nasr = 1;
printf("\n"); for (int i=0; i<80; i++) printf("=");
// compute and display eigenvalues of Phi at gamma before ASR
if (nucell > 100){
printf("\nYour unit cell is rather large, eigenvalue evaluation takes some time...");
fflush(stdout);
}
double egvs[fftdim];
for (int i=0; i<fftdim; i++)
for (int j=0; j<fftdim; j++) DM_q[i][j] = DM_all[0][i*fftdim+j];
geteigen(egvs, 0);
printf("\nEigenvalues of Phi at gamma before enforcing ASR:\n");
for (int i=0; i<fftdim; i++){
printf("%lg ", egvs[i]);
if (i%10 == 9) printf("\n");
if (i == 99){ printf("...... (%d more skipped)\n", fftdim-100); break;}
}
printf("\n\n");
// ask for iterations to enforce ASR
printf("Please input the # of iterations to enforce ASR [%d]: ", nasr);
fgets(str,MAXLINE,stdin);
char *ptr = strtok(str," \t\n\r\f");
if (ptr) nasr = atoi(ptr);
if (nasr < 1){return; for (int i=0; i<80; i++) printf("="); printf("\n");}
for (int iit=0; iit<nasr; iit++){
// simple ASR; the resultant matrix might not be symmetric
for (int a=0; a<sysdim; a++)
for (int b=0; b<sysdim; b++){
for (int k=0; k<nucell; k++){
double sum = 0.;
for (int kp=0; kp<nucell; kp++){
int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
sum += DM_all[0][idx].r;
}
sum /= double(nucell);
for (int kp=0; kp<nucell; kp++){
int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
DM_all[0][idx].r -= sum;
}
}
}
// symmetrize
for (int k=0; k<nucell; k++)
for (int kp=k; kp<nucell; kp++){
double csum = 0.;
for (int a=0; a<sysdim; a++)
for (int b=0; b<sysdim; b++){
int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
int jdx = (kp*sysdim+b)*fftdim+k*sysdim+a;
csum = (DM_all[0][idx].r + DM_all[0][jdx].r )*0.5;
DM_all[0][idx].r = DM_all[0][jdx].r = csum;
}
}
}
// symmetric ASR
for (int a=0; a<sysdim; a++)
for (int b=0; b<sysdim; b++){
for (int k=0; k<nucell; k++){
double sum = 0.;
for (int kp=0; kp<nucell; kp++){
int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
sum += DM_all[0][idx].r;
}
sum /= double(nucell-k);
for (int kp=k; kp<nucell; kp++){
int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
int jdx = (kp*sysdim+b)*fftdim+k*sysdim+a;
DM_all[0][idx].r -= sum;
DM_all[0][jdx].r = DM_all[0][idx].r;
}
}
}
// compute and display eigenvalues of Phi at gamma after ASR
for (int i=0; i<fftdim; i++)
for (int j=0; j<fftdim; j++) DM_q[i][j] = DM_all[0][i*fftdim+j];
geteigen(egvs, 0);
printf("Eigenvalues of Phi at gamma after enforcing ASR:\n");
for (int i=0; i<fftdim; i++){
printf("%lg ", egvs[i]);
if (i%10 == 9) printf("\n");
if (i == 99){ printf("...... (%d more skiped)", fftdim-100); break;}
}
printf("\n"); for (int i=0; i<80; i++) printf("="); printf("\n\n");
return;
}
/* ----------------------------------------------------------------------------
* private method to get the reciprocal lattice vectors from the real space ones
* ---------------------------------------------------------------------------- */
void DynMat::real2rec()
{
ibasevec[0] = basevec[4]*basevec[8] - basevec[5]*basevec[7];
ibasevec[1] = basevec[5]*basevec[6] - basevec[3]*basevec[8];
ibasevec[2] = basevec[3]*basevec[7] - basevec[4]*basevec[6];
ibasevec[3] = basevec[7]*basevec[2] - basevec[8]*basevec[1];
ibasevec[4] = basevec[8]*basevec[0] - basevec[6]*basevec[2];
ibasevec[5] = basevec[6]*basevec[1] - basevec[7]*basevec[0];
ibasevec[6] = basevec[1]*basevec[5] - basevec[2]*basevec[4];
ibasevec[7] = basevec[2]*basevec[3] - basevec[0]*basevec[5];
ibasevec[8] = basevec[0]*basevec[4] - basevec[1]*basevec[3];
double vol = 0.;
for (int i=0; i<sysdim; i++) vol += ibasevec[i] * basevec[i];
vol = 8.*atan(1.)/vol;
for (int i=0; i<9; i++) ibasevec[i] *= vol;
printf("\n"); for (int i=0; i<80; i++) printf("=");
printf("\nBasis vectors of the unit cell in real space:");
for (int i=0; i<sysdim; i++){
printf("\n A%d: ", i+1);
for (int j=0; j<sysdim; j++) printf("%8.4f ", basevec[i*3+j]);
}
printf("\nBasis vectors of the corresponding reciprocal cell:");
for (int i=0; i<sysdim; i++){
printf("\n B%d: ", i+1);
for (int j=0; j<sysdim; j++) printf("%8.4f ", ibasevec[i*3+j]);
}
printf("\n"); for (int i=0; i<80; i++) printf("="); printf("\n");
return;
}
/* ----------------------------------------------------------------------
* private method, to get the inverse of a double matrix by means of
* Gaussian-Jordan Elimination with full pivoting; square matrix required.
*
* Adapted from the Numerical Recipes in Fortran.
* --------------------------------------------------------------------*/
void DynMat::GaussJordan(int n, double *Mat)
{
int i,icol,irow,j,k,l,ll,idr,idc;
int *indxc,*indxr,*ipiv;
double big, nmjk;
double dum, pivinv;
indxc = new int[n];
indxr = new int[n];
ipiv = new int[n];
for (i=0; i<n; i++) ipiv[i] = 0;
for (i=0; i<n; i++){
big = 0.;
for (j=0; j<n; j++){
if (ipiv[j] != 1){
for (k=0; k<n; k++){
if (ipiv[k] == 0){
idr = j*n+k;
nmjk = abs(Mat[idr]);
if (nmjk >= big){
big = nmjk;
irow = j;
icol = k;
}
}else if (ipiv[k]>1){
printf("DynMat: Singular matrix in double GaussJordan!\n"); exit(1);
}
}
}
}
ipiv[icol] += 1;
if (irow != icol){
for (l=0; l<n; l++){
idr = irow*n+l;
idc = icol*n+l;
dum = Mat[idr];
Mat[idr] = Mat[idc];
Mat[idc] = dum;
}
}
indxr[i] = irow;
indxc[i] = icol;
idr = icol*n+icol;
if (Mat[idr] == 0.){
printf("DynMat: Singular matrix in double GaussJordan!");
exit(1);
}
pivinv = 1./ Mat[idr];
Mat[idr] = 1.;
idr = icol*n;
for (l=0; l<n; l++) Mat[idr+l] *= pivinv;
for (ll=0; ll<n; ll++){
if (ll != icol){
idc = ll*n+icol;
dum = Mat[idc];
Mat[idc] = 0.;
idc -= icol;
for (l=0; l<n; l++) Mat[idc+l] -= Mat[idr+l]*dum;
}
}
}
for (l=n-1; l>=0; l--){
int rl = indxr[l];
int cl = indxc[l];
if (rl != cl){
for (k=0; k<n; k++){
idr = k*n+rl;
idc = k*n+cl;
dum = Mat[idr];
Mat[idr] = Mat[idc];
Mat[idc] = dum;
}
}
}
delete []indxr;
delete []indxc;
delete []ipiv;
return;
}
/* ----------------------------------------------------------------------------
* Public method to reset the interpolation method
* ---------------------------------------------------------------------------- */
void DynMat::reset_interp_method()
{
interpolate->set_method();
return;
}
/* ----------------------------------------------------------------------------
* Private method to display help info
* ---------------------------------------------------------------------------- */
void DynMat::help()
{
ShowVersion();
printf("\nUsage:\n phana [options] [file]\n\n");
printf("Available options:\n");
printf(" -r To reset the dynamical matrix at the gamma point by a 4th order\n");
printf(" polynomial interpolation along the [100] direction; this might be\n");
printf(" useful for systems with charges. As for charged system, the dynamical\n");
printf(" matrix at Gamma is far from accurate because of the long range nature\n");
printf(" of Coulombic interaction. By reset it by interpolation, will partially\n");
printf(" elliminate the unwanted behavior, but the result is still inaccurate.\n");
printf(" By default, this is not set; and not expected for uncharged systems.\n\n");
printf(" -s This will reset the dynamical matrix at the gamma point, too, but it\n");
printf(" will also inform the code to skip all q-points that is in the vicinity\n");
printf(" of the gamma point when evaluating phonon DOS and/or phonon dispersion.\n\n");
printf(" By default, this is not set; and not expected for uncharged systems.\n\n");
printf(" -h To print out this help info.\n\n");
printf(" file To define the filename that carries the binary dynamical matrice generated\n");
printf(" by fix-phonon. If not provided, the code will ask for it.\n");
printf("\n\n");
exit(0);
}
/* ----------------------------------------------------------------------------
* Private method to display the version info
* ---------------------------------------------------------------------------- */
void DynMat::ShowVersion()
{
printf(" ____ _ _ __ _ _ __ \n");
printf(" ( _ \\( )_( ) /__\\ ( \\( ) /__\\ \n");
printf(" )___/ ) _ ( /(__)\\ ) ( /(__)\\ \n");
printf(" (__) (_) (_)(__)(__)(_)\\_)(__)(__)\n");
printf("\nPHonon ANAlyzer for Fix-Phonon, version 2.%d, compiled on %s.\n", VERSION, __DATE__);
return;
}
/* --------------------------------------------------------------------*/

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