git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14366 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -1,8 +1,7 @@
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#include "dynmat.h"
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#include "math.h"
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#include "version.h"
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#define MAXLINE 256
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#include "global.h"
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// to intialize the class
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DynMat::DynMat(int narg, char **arg)
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@ -14,6 +13,8 @@ DynMat::DynMat(int narg, char **arg)
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DM_q = DM_all = NULL;
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binfile = funit = dmfile = NULL;
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attyp = NULL;
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basis = NULL;
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flag_reset_gamma = flag_skip = 0;
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// analyze the command line options
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@ -74,23 +75,23 @@ DynMat::DynMat(int narg, char **arg)
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npt = nx*ny*nz;
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// display info related to the read file
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printf("\n"); for (int i=0; i<80; i++) printf("="); printf("\n");
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printf("\n"); for (int i = 0; i < 80; ++i) printf("="); printf("\n");
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printf("Dynamical matrix is read from file: %s\n", binfile);
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printf("The system size in three dimension: %d x %d x %d\n", nx, ny, nz);
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printf("Number of atoms per unit cell : %d\n", nucell);
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printf("System dimension : %d\n", sysdim);
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printf("Boltzmann constant in used units : %g\n", boltz);
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for (int i=0; i<80; i++) printf("="); printf("\n");
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if (sysdim<1||sysdim>3||nx<1||ny<1||nz<1||nucell<1){
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for (int i = 0; i < 80; ++i) printf("="); printf("\n");
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if (sysdim < 1||sysdim > 3||nx < 1||ny < 1||nz < 1||nucell < 1){
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printf("Wrong values read from header of file: %s, please check the binary file!\n", binfile);
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fclose(fp); exit(3);
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}
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funit = new char[4];
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strcpy(funit, "THz");
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if (boltz == 1.){eml2f = 1.; delete funit; funit=new char[22]; strcpy(funit,"sqrt(epsilon/(m.sigma^2))");}
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else if (boltz == 0.0019872067) eml2f = 3.256576161;
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else if (boltz == 8.617343e-5) eml2f = 15.63312493;
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if (boltz == 1.){eml2f = 1.; delete funit; funit = new char[27]; strcpy(funit,"sqrt(epsilon/(m.sigma^2))");}
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else if (boltz == 0.0019872067) eml2f = 3.256576161;
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else if (boltz == 8.617343e-5) eml2f = 15.63312493;
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else if (boltz == 1.3806504e-23) eml2f = 1.;
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else if (boltz == 1.3806504e-16) eml2f = 1.591549431e-14;
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else {
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@ -100,9 +101,9 @@ DynMat::DynMat(int narg, char **arg)
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}
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// now to allocate memory for DM
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memory = new Memory;
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DM_all = memory->create(DM_all, npt, fftdim2, "DynMat:DM_all");
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DM_q = memory->create(DM_q, fftdim,fftdim,"DynMat:DM_q");
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memory = new Memory();
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memory->create(DM_all, npt, fftdim2, "DynMat:DM_all");
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memory->create(DM_q, fftdim,fftdim,"DynMat:DM_q");
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// read all dynamical matrix info into DM_all
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if ( fread(DM_all[0], sizeof(doublecomplex), npt*fftdim2, fp) != size_t(npt*fftdim2)){
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@ -112,48 +113,36 @@ DynMat::DynMat(int narg, char **arg)
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}
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// now try to read unit cell info from the binary file
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flag_latinfo = 0;
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basis = memory->create(basis,nucell,sysdim,"DynMat:basis");
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attyp = memory->create(attyp,nucell, "DynMat:attyp");
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M_inv_sqrt = memory->create(M_inv_sqrt, nucell, "DynMat:M_inv_sqrt");
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int flag_mass_read = 0;
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memory->create(basis, nucell, sysdim, "DynMat:basis");
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memory->create(attyp, nucell, "DynMat:attyp");
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memory->create(M_inv_sqrt, nucell, "DynMat:M_inv_sqrt");
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if ( fread(&Tmeasure, sizeof(double), 1, fp) == 1) flag_latinfo |= 1;
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if ( fread(&basevec[0], sizeof(double), 9, fp) == 9) flag_latinfo |= 2;
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if ( fread(basis[0], sizeof(double), fftdim, fp) == fftdim) flag_latinfo |= 4;
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if ( fread(&attyp[0], sizeof(int), nucell, fp) == nucell) flag_latinfo |= 8;
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if ( fread(&M_inv_sqrt[0], sizeof(double), nucell, fp) == nucell) flag_mass_read = 1;
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if ( fread(&Tmeasure, sizeof(double), 1, fp) != 1 ){printf("\nError while reading temperature from file: %s\n", binfile); fclose(fp); exit(3);}
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if ( fread(&basevec[0], sizeof(double), 9, fp) != 9 ){printf("\nError while reading lattice info from file: %s\n", binfile); fclose(fp); exit(3);}
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if ( fread(basis[0], sizeof(double), fftdim, fp) != fftdim){printf("\nError while reading basis info from file: %s\n", binfile); fclose(fp); exit(3);}
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if ( fread(&attyp[0], sizeof(int), nucell, fp) != nucell){printf("\nError while reading atom types from file: %s\n", binfile); fclose(fp); exit(3);}
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if ( fread(&M_inv_sqrt[0], sizeof(double), nucell, fp) != nucell){printf("\nError while reading atomic masses from file: %s\n", binfile); fclose(fp); exit(3);}
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fclose(fp);
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if ((flag_latinfo&15) == 15){
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car2dir(flag_mass_read);
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real2rec();
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flag_latinfo = 1;
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} else {
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Tmeasure = 0.;
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flag_latinfo = 0;
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}
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car2dir();
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real2rec();
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// initialize interpolation
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interpolate = new Interpolate(nx,ny,nz,fftdim2,DM_all);
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if (flag_reset_gamma) interpolate->reset_gamma();
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if ( flag_mass_read ){ // M_inv_sqrt info read, the data stored are force constant matrix instead of dynamical matrix.
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// Enforcing Austic Sum Rule
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EnforceASR();
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EnforceASR();
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// get the dynamical matrix from force constant matrix: D = 1/M x Phi
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for (int idq=0; idq< npt; idq++){
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int ndim =0;
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for (int idim=0; idim<fftdim; idim++){
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for (int jdim=0; jdim<fftdim; jdim++){
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double inv_mass = M_inv_sqrt[idim/sysdim]*M_inv_sqrt[jdim/sysdim];
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DM_all[idq][ndim].r *= inv_mass;
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DM_all[idq][ndim].i *= inv_mass;
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ndim++;
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}
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}
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// get the dynamical matrix from force constant matrix: D = 1/M x Phi
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for (int idq = 0; idq < npt; ++idq){
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int ndim =0;
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for (int idim = 0; idim < fftdim; ++idim)
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for (int jdim = 0; jdim < fftdim; ++jdim){
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double inv_mass = M_inv_sqrt[idim/sysdim]*M_inv_sqrt[jdim/sysdim];
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DM_all[idq][ndim].r *= inv_mass;
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DM_all[idq][ndim].i *= inv_mass;
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ndim++;
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}
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}
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@ -191,7 +180,7 @@ void DynMat::writeDMq(double *q)
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if (dmfile == NULL){
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char str[MAXLINE], *ptr;
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printf("\n");
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while (1){
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while ( 1 ){
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printf("Please input the filename to output the DM at selected q: ");
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fgets(str,MAXLINE,stdin);
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ptr = strtok(str, " \r\t\n\f");
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@ -208,8 +197,8 @@ void DynMat::writeDMq(double *q)
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}
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fprintf(fp,"# q = [%lg %lg %lg]\n", q[0], q[1], q[2]);
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for (int i=0; i<fftdim; i++){
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for (int j=0; j<fftdim; j++) fprintf(fp,"%lg %lg\t", DM_q[i][j].r, DM_q[i][j].i);
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for (int i = 0; i < fftdim; ++i){
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for (int j = 0; j < fftdim; ++j) fprintf(fp,"%lg %lg\t", DM_q[i][j].r, DM_q[i][j].i);
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fprintf(fp,"\n");
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}
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fprintf(fp,"\n");
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@ -225,9 +214,9 @@ void DynMat::writeDMq(double *q, const double qr, FILE *fp)
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fprintf(fp, "%lg %lg %lg %lg ", q[0], q[1], q[2], qr);
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for (int i=0; i<fftdim; i++){
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for (int j=0; j<fftdim; j++) fprintf(fp,"%lg %lg\t", DM_q[i][j].r, DM_q[i][j].i);
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}
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for (int i = 0; i < fftdim; ++i)
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for (int j = 0; j < fftdim; ++j) fprintf(fp,"%lg %lg\t", DM_q[i][j].r, DM_q[i][j].i);
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fprintf(fp,"\n");
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return;
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}
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@ -254,14 +243,14 @@ int DynMat::geteigen(double *egv, int flag)
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liwork = 3 + 5*n;
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lda = n;
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work = memory->create(work, lwork, "geteigen:work");
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rwork = memory->create(rwork, lrwork, "geteigen:rwork");
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iwork = memory->create(iwork, liwork, "geteigen:iwork");
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memory->create(work, lwork, "geteigen:work");
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memory->create(rwork, lrwork, "geteigen:rwork");
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memory->create(iwork, liwork, "geteigen:iwork");
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zheevd_(&jobz, &uplo, &n, DM_q[0], &lda, w, work, &lwork, rwork, &lrwork, iwork, &liwork, &info);
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// to get w instead of w^2; and convert w into v (THz hopefully)
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for (int i=0; i<n; i++){
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for (int i = 0; i < n; ++i){
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if (w[i]>= 0.) w[i] = sqrt(w[i]);
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else w[i] = -sqrt(-w[i]);
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@ -298,24 +287,17 @@ return;
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/* ----------------------------------------------------------------------------
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* private method to convert the cartisan coordinate of basis into fractional
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* ---------------------------------------------------------------------------- */
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void DynMat::car2dir(int flag)
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void DynMat::car2dir()
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{
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if (!flag){ // in newer version, this is done in fix-phonon
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for (int i=0; i<3; i++){
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basevec[i] /= double(nx);
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basevec[i+3] /= double(ny);
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basevec[i+6] /= double(nz);
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}
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}
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double mat[9];
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for (int idim=0; idim<9; idim++) mat[idim] = basevec[idim];
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for (int idim = 0; idim < 9; ++idim) mat[idim] = basevec[idim];
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GaussJordan(3, mat);
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for (int i=0; i<nucell; i++){
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for (int i = 0; i < nucell; ++i){
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double x[3];
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x[0] = x[1] = x[2] = 0.;
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for (int idim=0; idim<sysdim; idim++) x[idim] = basis[i][idim];
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for (int idim=0; idim<sysdim; idim++)
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for (int idim = 0; idim < sysdim; idim++) x[idim] = basis[i][idim];
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for (int idim = 0; idim < sysdim; idim++)
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basis[i][idim] = x[0]*mat[idim] + x[1]*mat[3+idim] + x[2]*mat[6+idim];
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}
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@ -330,7 +312,7 @@ void DynMat::EnforceASR()
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char str[MAXLINE];
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int nasr = 20;
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if (nucell <= 1) nasr = 1;
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printf("\n"); for (int i=0; i<80; i++) printf("=");
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printf("\n"); for (int i = 0; i < 80; ++i) printf("=");
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// compute and display eigenvalues of Phi at gamma before ASR
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if (nucell > 100){
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@ -339,11 +321,11 @@ void DynMat::EnforceASR()
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}
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double egvs[fftdim];
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for (int i=0; i<fftdim; i++)
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for (int j=0; j<fftdim; j++) DM_q[i][j] = DM_all[0][i*fftdim+j];
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for (int i = 0; i < fftdim; ++i)
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for (int j = 0; j < fftdim; ++j) DM_q[i][j] = DM_all[0][i*fftdim+j];
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geteigen(egvs, 0);
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printf("\nEigenvalues of Phi at gamma before enforcing ASR:\n");
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for (int i=0; i<fftdim; i++){
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for (int i = 0; i < fftdim; ++i){
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printf("%lg ", egvs[i]);
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if (i%10 == 9) printf("\n");
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if (i == 99){ printf("...... (%d more skipped)\n", fftdim-100); break;}
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@ -355,20 +337,23 @@ void DynMat::EnforceASR()
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fgets(str,MAXLINE,stdin);
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char *ptr = strtok(str," \t\n\r\f");
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if (ptr) nasr = atoi(ptr);
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if (nasr < 1){return; for (int i=0; i<80; i++) printf("="); printf("\n");}
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if (nasr < 1){
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for (int i=0; i<80; i++) printf("="); printf("\n");
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return;
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}
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for (int iit=0; iit<nasr; iit++){
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for (int iit = 0; iit < nasr; ++iit){
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// simple ASR; the resultant matrix might not be symmetric
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for (int a=0; a<sysdim; a++)
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for (int b=0; b<sysdim; b++){
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for (int k=0; k<nucell; k++){
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for (int a = 0; a < sysdim; ++a)
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for (int b = 0; b < sysdim; ++b){
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for (int k = 0; k < nucell; ++k){
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double sum = 0.;
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for (int kp=0; kp<nucell; kp++){
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for (int kp = 0; kp < nucell; ++kp){
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int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
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sum += DM_all[0][idx].r;
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}
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sum /= double(nucell);
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for (int kp=0; kp<nucell; kp++){
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for (int kp = 0; kp < nucell; ++kp){
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int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
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DM_all[0][idx].r -= sum;
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}
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@ -376,11 +361,11 @@ void DynMat::EnforceASR()
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}
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// symmetrize
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for (int k=0; k<nucell; k++)
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for (int kp=k; kp<nucell; kp++){
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for (int k = 0; k < nucell; ++k)
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for (int kp = k; kp < nucell; ++kp){
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double csum = 0.;
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for (int a=0; a<sysdim; a++)
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for (int b=0; b<sysdim; b++){
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for (int a = 0; a < sysdim; ++a)
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for (int b = 0; b < sysdim; ++b){
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int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
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int jdx = (kp*sysdim+b)*fftdim+k*sysdim+a;
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csum = (DM_all[0][idx].r + DM_all[0][jdx].r )*0.5;
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@ -390,16 +375,16 @@ void DynMat::EnforceASR()
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}
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// symmetric ASR
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for (int a=0; a<sysdim; a++)
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for (int b=0; b<sysdim; b++){
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for (int k=0; k<nucell; k++){
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for (int a = 0; a < sysdim; ++a)
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for (int b = 0; b < sysdim; ++b){
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for (int k = 0; k < nucell; ++k){
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double sum = 0.;
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for (int kp=0; kp<nucell; kp++){
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for (int kp = 0; kp < nucell; ++kp){
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int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
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sum += DM_all[0][idx].r;
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}
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sum /= double(nucell-k);
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for (int kp=k; kp<nucell; kp++){
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for (int kp = k; kp < nucell; ++kp){
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int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
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int jdx = (kp*sysdim+b)*fftdim+k*sysdim+a;
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DM_all[0][idx].r -= sum;
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@ -409,16 +394,17 @@ void DynMat::EnforceASR()
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}
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// compute and display eigenvalues of Phi at gamma after ASR
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for (int i=0; i<fftdim; i++)
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for (int j=0; j<fftdim; j++) DM_q[i][j] = DM_all[0][i*fftdim+j];
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for (int i = 0; i < fftdim; ++i)
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for (int j = 0; j < fftdim; ++j) DM_q[i][j] = DM_all[0][i*fftdim+j];
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geteigen(egvs, 0);
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printf("Eigenvalues of Phi at gamma after enforcing ASR:\n");
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for (int i=0; i<fftdim; i++){
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for (int i = 0; i < fftdim; ++i){
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printf("%lg ", egvs[i]);
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if (i%10 == 9) printf("\n");
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if (i == 99){ printf("...... (%d more skiped)", fftdim-100); break;}
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}
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printf("\n"); for (int i=0; i<80; i++) printf("="); printf("\n\n");
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printf("\n");
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for (int i = 0; i < 80; ++i) printf("="); printf("\n\n");
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return;
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}
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@ -441,23 +427,23 @@ void DynMat::real2rec()
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ibasevec[8] = basevec[0]*basevec[4] - basevec[1]*basevec[3];
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double vol = 0.;
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for (int i=0; i<sysdim; i++) vol += ibasevec[i] * basevec[i];
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for (int i = 0; i < sysdim; ++i) vol += ibasevec[i] * basevec[i];
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vol = 8.*atan(1.)/vol;
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for (int i=0; i<9; i++) ibasevec[i] *= vol;
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for (int i = 0; i < 9; ++i) ibasevec[i] *= vol;
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printf("\n"); for (int i=0; i<80; i++) printf("=");
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printf("\n"); for (int i = 0; i < 80; ++i) printf("=");
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printf("\nBasis vectors of the unit cell in real space:");
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for (int i=0; i<sysdim; i++){
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for (int i = 0; i < sysdim; ++i){
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printf("\n A%d: ", i+1);
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for (int j=0; j<sysdim; j++) printf("%8.4f ", basevec[i*3+j]);
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for (int j = 0; j < sysdim; ++j) printf("%8.4f ", basevec[i*3+j]);
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}
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printf("\nBasis vectors of the corresponding reciprocal cell:");
|
||||
for (int i=0; i<sysdim; i++){
|
||||
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]);
|
||||
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");
|
||||
printf("\n"); for (int i = 0; i < 80; ++i) printf("="); printf("\n");
|
||||
|
||||
return;
|
||||
}
|
||||
@ -479,21 +465,21 @@ void DynMat::GaussJordan(int n, double *Mat)
|
||||
indxr = new int[n];
|
||||
ipiv = new int[n];
|
||||
|
||||
for (i=0; i<n; i++) ipiv[i] = 0;
|
||||
for (i=0; i<n; i++){
|
||||
for (i = 0; i < n; ++i) ipiv[i] = 0;
|
||||
for (i = 0; i < n; ++i){
|
||||
big = 0.;
|
||||
for (j=0; j<n; j++){
|
||||
for (j = 0; j < n; ++j){
|
||||
if (ipiv[j] != 1){
|
||||
for (k=0; k<n; k++){
|
||||
for (k = 0; k < n; ++k){
|
||||
if (ipiv[k] == 0){
|
||||
idr = j*n+k;
|
||||
idr = j * n + k;
|
||||
nmjk = abs(Mat[idr]);
|
||||
if (nmjk >= big){
|
||||
big = nmjk;
|
||||
irow = j;
|
||||
icol = k;
|
||||
}
|
||||
}else if (ipiv[k]>1){
|
||||
} else if (ipiv[k] > 1){
|
||||
printf("DynMat: Singular matrix in double GaussJordan!\n"); exit(1);
|
||||
}
|
||||
}
|
||||
@ -501,7 +487,7 @@ void DynMat::GaussJordan(int n, double *Mat)
|
||||
}
|
||||
ipiv[icol] += 1;
|
||||
if (irow != icol){
|
||||
for (l=0; l<n; l++){
|
||||
for (l = 0; l < n; ++l){
|
||||
idr = irow*n+l;
|
||||
idc = icol*n+l;
|
||||
dum = Mat[idr];
|
||||
@ -511,7 +497,7 @@ void DynMat::GaussJordan(int n, double *Mat)
|
||||
}
|
||||
indxr[i] = irow;
|
||||
indxc[i] = icol;
|
||||
idr = icol*n+icol;
|
||||
idr = icol * n + icol;
|
||||
if (Mat[idr] == 0.){
|
||||
printf("DynMat: Singular matrix in double GaussJordan!");
|
||||
exit(1);
|
||||
@ -520,24 +506,24 @@ void DynMat::GaussJordan(int n, double *Mat)
|
||||
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++){
|
||||
for (l = 0; l < n; ++l) Mat[idr+l] *= pivinv;
|
||||
for (ll = 0; ll < n; ++ll){
|
||||
if (ll != icol){
|
||||
idc = ll*n+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 = 0; l < n; ++l) Mat[idc+l] -= Mat[idr+l]*dum;
|
||||
}
|
||||
}
|
||||
}
|
||||
for (l=n-1; l>=0; l--){
|
||||
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;
|
||||
for (k = 0; k < n; ++k){
|
||||
idr = k * n + rl;
|
||||
idc = k * n + cl;
|
||||
dum = Mat[idr];
|
||||
Mat[idr] = Mat[idc];
|
||||
Mat[idc] = dum;
|
||||
@ -547,6 +533,7 @@ void DynMat::GaussJordan(int n, double *Mat)
|
||||
delete []indxr;
|
||||
delete []indxc;
|
||||
delete []ipiv;
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
@ -595,7 +582,7 @@ void DynMat::ShowVersion()
|
||||
printf(" ( _ \\( )_( ) /__\\ ( \\( ) /__\\ \n");
|
||||
printf(" )___/ ) _ ( /(__)\\ ) ( /(__)\\ \n");
|
||||
printf(" (__) (_) (_)(__)(__)(_)\\_)(__)(__)\n");
|
||||
printf("\nPHonon ANAlyzer for Fix-Phonon, version 2.%d, compiled on %s.\n", VERSION, __DATE__);
|
||||
printf("\nPHonon ANAlyzer for Fix-Phonon, version 2.%02d, compiled on %s.\n", VERSION, __DATE__);
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user