Commit 0dd7ba26 authored by Steve Plimpton's avatar Steve Plimpton Committed by GitHub
Browse files

Merge pull request #672 from akohlmey/phana-w-tricubic 

Streamline compilation of "phana" tool for fix phonon
parents 7a90eef5 4c71beb0

tools/phonon/Makefile

+23 −11
Original line number Diff line number Diff line 
.SUFFIXES : .o .cpp

# compiler and flags

CC     = g++ -Wno-unused-result

LINK   = $(CC) -static

CC     = g++ -Wall

LINK   = $(CC)

CFLAGS = -O3 $(DEBUG) $(UFLAG)

#

OFLAGS = -O3 $(DEBUG)
@@ -9,18 +9,17 @@ INC = $(LPKINC) $(TCINC) $(SPGINC) 
LIB    = $(LPKLIB) $(TCLIB) $(SPGLIB)

#

# cLapack library needed

LPKINC = -I/opt/libs/clapack/3.2.1/include

LPKLIB = -L/opt/libs/clapack/3.2.1/lib -lclapack -lblas -lf2c #-lm

LPKINC = 

LPKLIB =-llapack

#

# Tricubic library needed

TCINC = -I/opt/libs/tricubic/1.0/include

TCLIB = -L/opt/libs/tricubic/1.0/lib -ltricubic

#

# spglib 1.8.2, used to get the irreducible q-points

# if UFLAG is not set, spglib won't be used.

UFLAG  = -DUseSPG

SPGINC = -I/opt/libs/spglib/1.8.2/include

SPGLIB = -L/opt/libs/spglib/1.8.2/lib -lsymspg



# UFLAG  = -DUseSPG

# SPGINC = -I/opt/libs/spglib/1.8.2/include

# SPGLIB = -L/opt/libs/spglib/1.8.2/lib -lsymspg



# if spglib other than version 1.8.2 is used, please 

# modify file phonon.cpp, instruction can be found by searching 1.8.2
@@ -36,7 +35,7 @@ SRC = $(wildcard *.cpp) 
OBJ = $(SRC:.cpp=.o)



#====================================================================

all:  ver ${EXE}

all:  ${EXE}



${EXE}: $(OBJ)

	$(LINK) $(OFLAGS) $(OBJ) $(LIB) -o $@
@@ -59,3 +58,16 @@ ver: 
	$(CC) $(CFLAGS) -c $<

.cpp.o:

	$(CC) $(CFLAGS) $(INC) -c $<



#====================================================================

# dependencies

disp.o: disp.cpp phonon.h dynmat.h memory.h interpolate.h green.h timer.h \

 global.h

dynmat.o: dynmat.cpp dynmat.h memory.h interpolate.h version.h global.h

green.o: green.cpp green.h memory.h global.h

interpolate.o: interpolate.cpp interpolate.h memory.h global.h

main.o: main.cpp dynmat.h memory.h interpolate.h phonon.h

memory.o: memory.cpp memory.h

phonon.o: phonon.cpp phonon.h dynmat.h memory.h interpolate.h green.h \

 timer.h global.h

timer.o: timer.cpp timer.h

tools/phonon/README

+3 −9
Original line number Diff line number Diff line
@@ -5,15 +5,9 @@ 
   analyse the phonon related information.

#-------------------------------------------------------------------------------

1. Dependencies

   The clapack library is needed to solve the eigen problems,

   which could be downloaded from:

   http://www.netlib.org/clapack/

   

   The tricubic library is also needed to do tricubic interpolations,

   which could be obtained from:

      http://orca.princeton.edu/francois/software/tricubic/

   or

      http://1drv.ms/1J2WFYk

   The LAPACK library is needed to solve the eigen problems.

   http://www.netlib.org/lapack/

   Intel MKL can be used as well.

   

   The spglib is optionally needed, enabling one to evaluate the

   phonon density of states or vibrational thermal properties

tools/phonon/disp.cpp

+4 −3
Original line number Diff line number Diff line
@@ -18,7 +18,8 @@ void Phonon::pdisp() 
{

  // ask the output file name and write the header.

  char str[MAXLINE];

  for (int ii = 0; ii < 80; ++ii) printf("="); printf("\n");

  for (int ii = 0; ii < 80; ++ii) printf("=");

  printf("\n");

#ifdef UseSPG

  // ask method to generate q-lines

  int method = 2;
@@ -53,7 +54,6 @@ void Phonon::pdisp() 
    while (1){

      for (int i = 0; i < 3; ++i) qstr[i] = qend[i];

  

      int quit = 0;

      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));

      ptr = strtok(str, " \t\n\r\f");
@@ -2844,7 +2844,8 @@ void Phonon::pdisp() 
    printf("\nPhonon dispersion data are written to: %s, you can visualize the results\n", fname);

    printf("by invoking: `gnuplot pdisp.gnuplot; gv pdisp.eps`\n");

  }

  for (int ii = 0; ii < 80; ++ii) printf("="); printf("\n");

  for (int ii = 0; ii < 80; ++ii) printf("=");

  printf("\n");



  delete []fname;

  nodes.clear();

tools/phonon/dynmat.cpp

+19 −11
Original line number Diff line number Diff line
@@ -3,6 +3,11 @@ 
#include "version.h"

#include "global.h"



extern "C" void zheevd_(char *, char *, long int *, doublecomplex *,

                       long int *, double *, doublecomplex *,

                       long int *, double *, long int *, long int *,

                       long int *, long int *);



// to initialize the class

DynMat::DynMat(int narg, char **arg)

{
@@ -81,7 +86,8 @@ DynMat::DynMat(int narg, char **arg) 
  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");

  for (int i = 0; i < 80; ++i) printf("=");

  printf("\n");

  if (sysdim < 1||sysdim > 3||nx < 1||ny < 1||nz < 1||nucell < 1){

    printf("Wrong values read from header of file: %s, please check the binary file!\n", binfile);

    fclose(fp); exit(3);
@@ -117,11 +123,11 @@ DynMat::DynMat(int narg, char **arg) 
  memory->create(attyp, nucell,         "DynMat:attyp");

  memory->create(M_inv_sqrt, nucell,    "DynMat:M_inv_sqrt");

  

  if ( fread(&Tmeasure,      sizeof(double), 1,      fp) != 1     ){printf("\nError while reading temperature from file: %s\n",   binfile); fclose(fp); exit(3);}

  if ( fread(&basevec[0],    sizeof(double), 9,      fp) != 9     ){printf("\nError while reading lattice info from file: %s\n",  binfile); fclose(fp); exit(3);}

  if ( fread(basis[0],       sizeof(double), fftdim, fp) != 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){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){printf("\nError while reading atomic masses from file: %s\n", binfile); fclose(fp); exit(3);}

  if ( (int) fread(&Tmeasure,      sizeof(double), 1,      fp) != 1     ){printf("\nError while reading temperature from file: %s\n",   binfile); fclose(fp); exit(3);}

  if ( (int) fread(&basevec[0],    sizeof(double), 9,      fp) != 9     ){printf("\nError while reading lattice info from file: %s\n",  binfile); fclose(fp); exit(3);}

  if ( (int) fread(basis[0],       sizeof(double), fftdim, fp) != fftdim){printf("\nError while reading basis info from file: %s\n",    binfile); fclose(fp); exit(3);}

  if ( (int) fread(&attyp[0],      sizeof(int),    nucell, fp) != nucell){printf("\nError while reading atom types from file: %s\n",    binfile); fclose(fp); exit(3);}

  if ( (int) 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);}

  fclose(fp);



  car2dir();
@@ -229,9 +235,9 @@ return; 
int DynMat::geteigen(double *egv, int flag)

{

  char jobz, uplo;

  integer n, lda, lwork, lrwork, *iwork, liwork, info;

  long 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';
@@ -338,7 +344,8 @@ void DynMat::EnforceASR() 
  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");

    for (int i=0; i<80; i++) printf("=");

    printf("\n");

    return;

  }
@@ -404,7 +411,8 @@ void DynMat::EnforceASR() 
    if (i == 99){ printf("...... (%d more skiped)", fftdim-100); break;}

  }

  printf("\n");

  for (int i = 0; i < 80; ++i) printf("="); printf("\n\n");

  for (int i = 0; i < 80; ++i) printf("=");

  printf("\n\n");



return;

}
@@ -456,7 +464,7 @@ return; 
 * --------------------------------------------------------------------*/

void DynMat::GaussJordan(int n, double *Mat)

{

  int i,icol,irow,j,k,l,ll,idr,idc;

  int i,icol=0,irow=0,j,k,l,ll,idr,idc;

  int *indxc,*indxr,*ipiv;

  double big, nmjk;

  double dum, pivinv;

tools/phonon/dynmat.h

+0 −5
Original line number Diff line number Diff line
@@ -7,11 +7,6 @@ 
#include "memory.h"

#include "interpolate.h"



extern "C"{

#include "f2c.h"

#include "clapack.h"

}



using namespace std;



class DynMat {

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