integrate CMake build procedure for tools/phonon
This commit is contained in:
Axel Kohlmeyer
@ -1,9 +1,20 @@
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#ifdef FFTW3
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#include <map>
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#include "phonopy.h"
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#include "math.h"
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#include "kpath.h"
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#include "fftw3.h"
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#include "global.h"
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#include "dynmat.h"
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#include "input.h"
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#include "memory.h"
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#include <fftw3.h>
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#include <cmath>
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#include <cstdio>
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#include <cstdlib>
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#include <cstring>
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#include <map>
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/* ----------------------------------------------------------------------------
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* Class Phonopy is designed to interface with phonopy.
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@ -14,13 +25,16 @@ Phonopy::Phonopy(DynMat *dynmat)
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memory = new Memory();
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sysdim = dm->sysdim;
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fftdim = dm->fftdim;
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input = dm->input;
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fftdim2 = fftdim * fftdim;
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nucell = dm->nucell;
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nx = ny = nz = 5;
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write(1);
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char str[MAXLINE];
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if (count_words(fgets(str,MAXLINE,stdin)) >= 3){
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if (input == NULL) input = new UserInput(0);
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input->read_stdin(str);
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if (count_words(str) >= 3){
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nx = atoi(strtok(str," \t\n\r\f"));
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ny = atoi(strtok(NULL," \t\n\r\f"));
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nz = atoi(strtok(NULL," \t\n\r\f"));
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@ -36,7 +50,7 @@ Phonopy::Phonopy(DynMat *dynmat)
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memory->create(mass, nucell, "Phonopy:mass");
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for (int i = 0; i < nucell; ++i){
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double m = 1./dm->M_inv_sqrt[i];
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double m = 1.0/dm->M_inv_sqrt[i];
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mass[i] = m * m;
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}
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@ -68,7 +82,7 @@ return;
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void Phonopy::write(int flag)
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{
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if (flag == 1){ // basic information
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for (int ii = 0; ii < 80; ++ii) printf("="); printf("\n");
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puts("================================================================================");
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printf("Now to prepare the input files for phonopy.\n");
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printf("The dimension of your present supercell is : %d x %d x %d.\n", dm->nx, dm->ny, dm->nz);
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printf("The size of the force constant matrix will be: %d x %d.\n", dm->npt*3, dm->npt*3);
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@ -84,19 +98,18 @@ void Phonopy::write(int flag)
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} else if (flag == 4){
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printf("Done!\nThe force constants information is extracted and written to FORCE_CONSTANTS,\n");
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printf("the primitive cell is written to POSCAR.primitive, and the input file for\n");
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printf("phonopy band evaluation is written to band.conf.\n");
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printf("One should be able to obtain the phonon band structure after correcting\n");
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printf("the element names in POSCAR.primitive and band.conf by running\n");
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printf("`phonopy --readfc -c POSCAR.primitive -p band.conf`.\n");
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for (int ii = 0; ii < 80; ++ii) printf("-");
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printf("\n*** Remember to change the element names. ***\n");
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#ifdef UseSPG
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for (int ii = 0; ii < 80; ++ii) printf("-");
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#endif
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printf("phonopy band evaluation is written to band.conf.\n\n");
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printf("One should be able to obtain the phonon band structure after\n");
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printf(" 1) Correcting the `element names` in POSCAR.primitive and band.conf;\n");
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printf(" 2) Running `phonopy --readfc -c POSCAR.primitive -p band.conf`.\n\n");
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printf("Or the phonon density of states after\n");
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printf(" 1) Correcting the `element names` in POSCAR.primitive and mesh.conf;\n");
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printf(" 2) Running `phonopy --readfc -c POSCAR.primitive -p mesh.conf`.\n");
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puts("--------------------------------------------------------------------------------");
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printf("*** Remember to modify the `element names`. ***\n");
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} else if (flag == 5){
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for (int ii = 0; ii < 80; ++ii) printf("="); printf("\n");
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puts("================================================================================");
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}
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return;
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}
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@ -162,7 +175,9 @@ void Phonopy::phonopy()
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memory->destroy(out);
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// in POSCAR, atoms are sorted/aggregated by type, while for LAMMPS there is no such requirment
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int type_id[nucell], num_type[nucell], ntype = 0;
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int *type_id = new int[nucell];
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int *num_type = new int[nucell];
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int ntype = 0;
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for (int i = 0; i < nucell; ++i) num_type[i] = 0;
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for (int i = 0; i < nucell; ++i){
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int ip = ntype;
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@ -221,7 +236,14 @@ void Phonopy::phonopy()
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// write the primitive cell in POSCAR format
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fp = fopen("POSCAR.primitive", "w");
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fprintf(fp, "Fix-phonon unit cell");
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for (int ip = 0; ip < ntype; ++ip) fprintf(fp, ", Elem-%d: %lg", type_id[ip], mass[ip]);
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for (int ip = 0; ip < ntype; ++ip){
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for (int i = 0; i < nucell; ++i){
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if (dm->attyp[i] == type_id[ip]){
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fprintf(fp, ", Elem-%d: %lg", type_id[ip], mass[i]);
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break;
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}
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}
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}
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fprintf(fp, "\n1.\n");
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int ndim = 0;
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for (int idim = 0; idim < 3; ++idim){
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@ -240,57 +262,48 @@ void Phonopy::phonopy()
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}
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fclose(fp);
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#ifdef UseSPG
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// Get high symmetry k-path
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QNodes *q = new QNodes();
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kPath *kp = new kPath(dm, q);
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kp->kpath();
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#endif
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// mesh.conf
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fp = fopen("mesh.conf", "w");
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fprintf(fp, "# From Fix-phonon");
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for (int ip = 0; ip < ntype; ++ip){
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for (int i = 0; i < nucell; ++i){
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if (dm->attyp[i] == type_id[ip]){
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fprintf(fp, ", Elem-%d: %lg", type_id[ip], mass[i]);
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break;
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}
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}
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}
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fprintf(fp, "\n\nATOM_NAME = ");
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for (int ip = 0; ip < ntype; ++ip) fprintf(fp, "Elem-%d ", type_id[ip]);
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fprintf(fp, "\nDIM = %d %d %d\n", nx, ny, nz);
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fprintf(fp, "MP = 31 31 31\nFORCE_CONSTANTS = READ\n");
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fprintf(fp, "#FC_SYMMETRY = .TRUE.\n#SYMMETRY_TOLERANCE = 0.01\n");
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fclose(fp);
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// band.conf
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fp = fopen("band.conf", "w");
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fprintf(fp, "# From Fix-phonon");
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for (int ip = 0; ip < ntype; ++ip) fprintf(fp, ", Elem-%d: %lg", type_id[ip], mass[ip]);
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for (int ip = 0; ip < ntype; ++ip){
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for (int i = 0; i < nucell; ++i){
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if (dm->attyp[i] == type_id[ip]){
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fprintf(fp, ", Elem-%d: %lg", type_id[ip], mass[i]);
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break;
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}
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}
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}
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fprintf(fp, "\n\nATOM_NAME = ");
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for (int ip = 0; ip < ntype; ++ip) fprintf(fp, "Elem-%d ", type_id[ip]);
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fprintf(fp, "\nDIM = %d %d %d\nBAND = ", nx, ny, nz);
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#ifdef UseSPG
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int nsect = q->qs.size();
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for (int i = 0; i < nsect; ++i){
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fprintf(fp, " %lg %lg %lg", q->qs[i][0], q->qs[i][1], q->qs[i][2]);
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if (i+1 < nsect){
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double dq = 0.;
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for (int j = 0; j < 3; ++j) dq += (q->qe[i][j] - q->qs[i+1][j]) * (q->qe[i][j] - q->qs[i+1][j]);
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if (dq > ZERO) {
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fprintf(fp, " %lg %lg %lg,", q->qe[i][0], q->qe[i][1], q->qe[i][2]);
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}
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} else if (i+1 == nsect){
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fprintf(fp, " %lg %lg %lg\n", q->qe[i][0], q->qe[i][1], q->qe[i][2]);
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}
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}
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#endif
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fprintf(fp, "\nBAND_POINTS = 21\nBAND_LABELS =");
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#ifdef UseSPG
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for (int i = 0; i < q->ndstr.size(); ++i){
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std::size_t found = q->ndstr[i].find("{/Symbol G}");
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if (found != std::string::npos) q->ndstr[i].replace(found, found+11, "$\\Gamma$");
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found = q->ndstr[i].find("/");
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if (found != std::string::npos) q->ndstr[i].replace(found, found, " ");
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fprintf(fp, " %s", q->ndstr[i].c_str());
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}
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#endif
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fprintf(fp, "\nFORCE_CONSTANTS = READ\nBAND_CONNECTION = .TRUE.\n");
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fprintf(fp, "\nDIM = %d %d %d\nBAND = AUTO\n", nx, ny, nz);
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fprintf(fp, "BAND_POINTS = 21\nFORCE_CONSTANTS = READ\nBAND_CONNECTION = .TRUE.\n");
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fprintf(fp, "#FC_SYMMETRY = .TRUE.\n#SYMMETRY_TOLERANCE = 0.01\n");
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// output info
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write(4);
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#ifdef UseSPG
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kp->show_path();
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delete kp;
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delete q;
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#endif
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write(5);
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return;
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delete[] type_id;
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delete[] num_type;
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return;
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}
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/*------------------------------------------------------------------------------
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@ -304,7 +317,7 @@ int Phonopy::count_words(const char *line)
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strcpy(copy,line);
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char *ptr;
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if (ptr = strchr(copy,'#')) *ptr = '\0';
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if ((ptr = strchr(copy,'#'))) *ptr = '\0';
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if (strtok(copy," \t\n\r\f") == NULL) {
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memory->destroy(copy);
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@ -314,7 +327,7 @@ int Phonopy::count_words(const char *line)
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while (strtok(NULL," \t\n\r\f")) n++;
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memory->destroy(copy);
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return n;
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return n;
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}
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/*----------------------------------------------------------------------------*/
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#endif
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