#include <vector>
#include "string.h"
#include "phonon.h"
#include "green.h"
#include "timer.h"
#include "global.h"

#ifdef UseSPG
extern "C"{
#include "spglib.h"
}
#endif
#ifdef FFTW3
#include "phonopy.h"
#endif

/* ----------------------------------------------------------------------------
 * 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(" 10. Show information related to the unit cell;\n");
#ifdef FFTW3
      printf(" 11. Write input files for working with phonopy;\n");
#endif
      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 ==10) ShowCell();
#ifdef FFTW3
      else if (job == 11){
         Phonopy *ph = new Phonopy(dynmat);
         delete ph;
      }
#endif
      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;

   return;
}

/* ----------------------------------------------------------------------------
 * 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);
   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;
   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);
         ik = MAX(0, MIN(ik, dynmat->nucell-1));
         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;
         istr = MAX(0, MIN(istr, dynmat->nucell-1));
         iend = MAX(0, MIN(iend, dynmat->nucell-1));
  
      } 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"));
         istr = MAX(0, MIN(istr, dynmat->nucell-1));
         iend = MAX(0, MIN(iend, dynmat->nucell-1));
      }
  
      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);
      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 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;
   memory->create(tmp, npt, "smooth:tmp");
   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;
   memory->create(Uvib,nlocal,sysdim,"local_therm:Uvib");
   memory->create(Svib,nlocal,sysdim,"local_therm:Svib");
   memory->create(Fvib,nlocal,sysdim,"local_therm:Fvib");
   memory->create(Cvib,nlocal,sysdim,"local_therm:Cvib");
   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);
      memory->create(wt,   nq, "QMesh:wt");
      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
   } else {
      if (atpos == NULL) memory->create(atpos, dynmat->nucell,3,"QMesh:atpos");
      if (attyp == NULL) memory->create(attyp, dynmat->nucell,  "QMesh:attyp");
  
      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)
      for (int j = 0; j < 3; ++j) latvec[i][j] = 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 < MIN(num_atom, NUMATOM); ++i)
         printf("  %d %d %lg %lg %lg\n", i+1, attyp[i], atpos[i][0], atpos[i][1], atpos[i][2]);
      if (num_atom > NUMATOM) printf("  ... (%d atoms omitted.)\n", num_atom - NUMATOM);
  
      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];
  
      // 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);
  
      memory->create(wt,   nq, "QMesh:wt");
      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);
   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);
 
   memory->create(dos, ndos,"ldos_egv:dos");
   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 show the unit cell info
 * ---------------------------------------------------------------------------- */
void Phonon::ShowCell()
{
   printf("\n");
   for (int i = 0; i < 30; ++i) printf("=");
   printf("   Unit Cell Info   ");
   for (int i = 0; i < 30; ++i) printf("="); printf("\n");
   printf("Number of atoms in the unit cell: %d\n", dynmat->nucell);
   printf("Basis  vectors  of the unit cell:\n");
   printf("  %15.8f  %15.8f  %15.8f\n", dynmat->basevec[0],  dynmat->basevec[1],  dynmat->basevec[2]);
   printf("  %15.8f  %15.8f  %15.8f\n", dynmat->basevec[3],  dynmat->basevec[4],  dynmat->basevec[5]);
   printf("  %15.8f  %15.8f  %15.8f\n", dynmat->basevec[6],  dynmat->basevec[7],  dynmat->basevec[8]);
   printf("Basis  vectors  of the reciprocal:\n");
   printf("  %15.8f  %15.8f  %15.8f\n", dynmat->ibasevec[0],  dynmat->ibasevec[1],  dynmat->ibasevec[2]);
   printf("  %15.8f  %15.8f  %15.8f\n", dynmat->ibasevec[3],  dynmat->ibasevec[4],  dynmat->ibasevec[5]);
   printf("  %15.8f  %15.8f  %15.8f\n", dynmat->ibasevec[6],  dynmat->ibasevec[7],  dynmat->ibasevec[8]);
   printf("Atomic type and fractional coordinates:\n");
   for (int i = 0; i < dynmat->nucell; ++i)
     printf("%4d %12.8f %12.8f %12.8f\n", dynmat->attyp[i], dynmat->basis[i][0], dynmat->basis[i][1], dynmat->basis[i][2]);
   for (int i = 0; i < 80; ++i) printf("=");
   printf("\n");
 
   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);
   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;
   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;
}

/*----------------------------------------------------------------------------*/
