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integrate CMake build procedure for tools/phonon

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This commit is contained in:
Axel Kohlmeyer
2023-04-29 02:59:04 -04:00
parent 41a0196874
commit 478058119b
34 changed files with 1260 additions and 591 deletions
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72
tools/phonon/dynmat.cpp
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@ -1,7 +1,16 @@
#include "dynmat.h"
#include "math.h"
#include "version.h"
#include "global.h"
#include "input.h"
#include "interpolate.h"
#include "memory.h"
#include "version.h"
#include "zheevd.h"
#include <cmath>
#include <cstdlib>
#include <cstring>
/* ----------------------------------------------------------------------------
* Class DynMat stores the Dynamic Matrix read from the binary file from
@ -9,6 +18,7 @@
* ---------------------------------------------------------------------------- */
DynMat::DynMat(int narg, char **arg)
{
input = NULL;
attyp = NULL;
memory = NULL;
M_inv_sqrt = NULL;
@ -19,6 +29,8 @@ DynMat::DynMat(int narg, char **arg)
attyp = NULL;
basis = NULL;
flag_reset_gamma = flag_skip = 0;
symprec = -1.;
int flag_save = 0;
// analyze the command line options
int iarg = 1;
@ -29,9 +41,16 @@ DynMat::DynMat(int narg, char **arg)
} else if (strcmp(arg[iarg], "-r") == 0){
flag_reset_gamma = 1;
} else if (strcmp(arg[iarg], "-p") == 0){
if (++iarg >= narg) help();
else symprec = fabs(atof(arg[iarg]));
} else if (strcmp(arg[iarg], "-h") == 0){
help();
} else if (strcmp(arg[iarg], "-save") == 0){
flag_save = 1;
} else {
if (binfile) delete []binfile;
int n = strlen(arg[iarg]) + 1;
@ -43,6 +62,8 @@ DynMat::DynMat(int narg, char **arg)
}
ShowVersion();
input = new UserInput(flag_save);
// get the binary file name from user input if not found in command line
char str[MAXLINE];
if (binfile == NULL) {
@ -50,7 +71,7 @@ DynMat::DynMat(int narg, char **arg)
printf("\n");
do {
printf("Please input the binary file name from fix_phonon: ");
fgets(str,MAXLINE,stdin);
input->read_stdin(str);
ptr = strtok(str, " \n\t\r\f");
} while (ptr == NULL);
@ -137,17 +158,17 @@ DynMat::DynMat(int narg, char **arg)
fclose(fp);
exit(3);
}
if (fread(basis[0], sizeof(double), fftdim, fp) != fftdim){
if (fread(basis[0], sizeof(double), fftdim, fp) != (size_t)fftdim){
printf("\nError while reading basis info from file: %s\n", binfile);
fclose(fp);
exit(3);
}
if (fread(&attyp[0], sizeof(int), nucell, fp) != nucell){
if (fread(&attyp[0], sizeof(int), nucell, fp) != (size_t)nucell){
printf("\nError while reading atom types from file: %s\n", binfile);
fclose(fp);
exit(3);
}
if (fread(&M_inv_sqrt[0], sizeof(double), nucell, fp) != nucell){
if (fread(&M_inv_sqrt[0], sizeof(double), nucell, fp) != (size_t)nucell){
printf("\nError while reading atomic masses from file: %s\n", binfile);
fclose(fp);
exit(3);
@ -159,6 +180,7 @@ DynMat::DynMat(int narg, char **arg)
// initialize interpolation
interpolate = new Interpolate(nx,ny,nz,fftdim2,DM_all);
interpolate->input = input;
if (flag_reset_gamma) interpolate->reset_gamma();
// Enforcing Austic Sum Rule
@ -217,7 +239,7 @@ void DynMat::writeDMq(double *q)
printf("\n");
while ( 1 ){
printf("Please input the filename to output the DM at selected q: ");
fgets(str,MAXLINE,stdin);
input->read_stdin(str);
ptr = strtok(str, " \r\t\n\f");
if (ptr) break;
}
@ -264,9 +286,9 @@ void DynMat::writeDMq(double *q, const double qr, FILE *fp)
int DynMat::geteigen(double *egv, int flag)
{
char jobz, uplo;
integer n, lda, lwork, lrwork, *iwork, liwork, info;
int n, lda, lwork, lrwork, *iwork, liwork, info;
doublecomplex *work;
doublereal *w = &egv[0], *rwork;
double *w = &egv[0], *rwork;
n = fftdim;
if (flag) jobz = 'V';
@ -348,7 +370,7 @@ void DynMat::EnforceASR()
char str[MAXLINE];
int nasr = 20;
if (nucell <= 1) nasr = 1;
printf("\n"); for (int i = 0; i < 80; ++i) printf("=");
printf("\n================================================================================");
// compute and display eigenvalues of Phi at gamma before ASR
if (nucell > 100){
@ -356,7 +378,7 @@ void DynMat::EnforceASR()
fflush(stdout);
}
double egvs[fftdim];
double *egvs = new double[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);
@ -370,11 +392,11 @@ void DynMat::EnforceASR()
// ask for iterations to enforce ASR
printf("Please input the # of iterations to enforce ASR [%d]: ", nasr);
fgets(str,MAXLINE,stdin);
input->read_stdin(str);
char *ptr = strtok(str," \t\n\r\f");
if (ptr) nasr = atoi(ptr);
if (nasr < 1){
for (int i=0; i<80; i++) printf("="); printf("\n");
puts("================================================================================");
return;
}
@ -439,9 +461,8 @@ void DynMat::EnforceASR()
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");
delete[] egvs;
puts("\n================================================================================\n");
return;
}
@ -468,7 +489,7 @@ void DynMat::real2rec()
for (int i = 0; i < 9; ++i) ibasevec[i] *= vol;
printf("\n"); for (int i = 0; i < 80; ++i) printf("=");
printf("\n================================================================================");
printf("\nBasis vectors of the unit cell in real space:");
for (int i = 0; i < sysdim; ++i){
printf("\n A%d: ", i+1);
@ -479,8 +500,7 @@ void DynMat::real2rec()
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");
puts("\n================================================================================");
return;
}
@ -500,16 +520,17 @@ void DynMat::GaussJordan(int n, double *Mat)
indxc = new int[n];
indxr = new int[n];
ipiv = new int[n];
irow = icol = -1;
for (i = 0; i < n; ++i) ipiv[i] = 0;
for (i = 0; i < n; ++i){
big = 0.;
big = 0.0;
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]);
nmjk = fabs(Mat[idr]);
if (nmjk >= big){
big = nmjk;
irow = j;
@ -602,6 +623,9 @@ void DynMat::help()
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(" -p prec To define the precision for symmetry identification with spglib.\n");
printf(" By default, 1.e-3.\n\n");
printf(" -save To record user input in `script.inp`, facilitating scripting.\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");
@ -680,13 +704,13 @@ void DynMat::Define_Conversion_Factor()
* ---------------------------------------------------------------------------- */
void DynMat::ShowInfo()
{
printf("\n"); for (int i = 0; i < 80; ++i) printf("="); printf("\n");
puts("\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");
puts("================================================================================");
return;
}
/* --------------------------------------------------------------------*/