forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14366 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
75de12f26a
commit
5f802f86b5
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@ -9,23 +9,20 @@ INC = $(LPKINC) $(TCINC) $(SPGINC)
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LIB = $(LPKLIB) $(TCLIB) $(SPGLIB)
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#
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# cLapack library needed
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LPKINC = -I/opt/clapack/3.2.1/include
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LPKLIB = -L/opt/clapack/3.2.1/lib -lclapack -lblas -lf2c #-lm
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LPKINC = -I/opt/libs/clapack/3.2.1/include
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LPKLIB = -L/opt/libs/clapack/3.2.1/lib -lclapack -lblas -lf2c #-lm
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#
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# Tricubic library needed
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TCINC = -I/opt/tricubic/1.0/include
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TCLIB = -L/opt/tricubic/1.0/lib -ltricubic
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TCINC = -I/opt/libs/tricubic/1.0/include
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TCLIB = -L/opt/libs/tricubic/1.0/lib -ltricubic
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#
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# spglib 0.7.1, used to get the irreducible q-points
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# spglib 1.8.2, used to get the irreducible q-points
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# if UFLAG is not set, spglib won't be used.
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UFLAG = -DUseSPG
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SPGINC = -I/opt/spglib/0.7.1/include
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SPGLIB = -L/opt/spglib/0.7.1/lib -lsymspg
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# if spglib > 0.7.1 is used, please
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# 1) modify file phonon.cpp, instruction can be found by searching 0.7.1
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# 2) uncomment the following two lines
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#SPGINC = -I/opt/spglib/1.1.2/include
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#SPGLIB = -L/opt/spglib/1.1.2/lib -lsymspg
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SPGINC = -I/opt/libs/spglib/1.8.2/include
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SPGLIB = -L/opt/libs/spglib/1.8.2/lib -lsymspg
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# if spglib other than version 1.8.2 is used, please
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# modify file phonon.cpp, instruction can be found by searching 1.8.2
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# Debug flags
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#DEBUG = -g -DDEBUG
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@ -39,7 +36,7 @@ SRC = $(wildcard *.cpp)
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OBJ = $(SRC:.cpp=.o)
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#====================================================================
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all: ${EXE}
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all: ver ${EXE}
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${EXE}: $(OBJ)
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$(LINK) $(OFLAGS) $(OBJ) $(LIB) -o $@
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@ -51,7 +48,7 @@ tar:
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rm -f ${ROOT}.tar; tar -czvf ${ROOT}.tar.gz *.cpp *.h Makefile README
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ver:
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@echo "#define VERSION `svn info|grep '^Revision'|cut -d: -f2`" > version.h
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@echo "#define VERSION `git log|grep '^commit'|wc -l`" > version.h
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#====================================================================
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.f.o:
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@ -1,31 +1,48 @@
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phana = post-processing program for the fix phonon command
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#-------------------------------------------------------------------------------
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phana
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#
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This program reads the binary file created by fix_phonon and helps to
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analyse the phonon related information.
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#-------------------------------------------------------------------------------
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1. Dependencies
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The clapack library is needed to solve the eigen problems,
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which could be downloaded from:
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http://www.netlib.org/clapack/
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The tricubic library is also needed to do tricubic interpolations,
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which could be obtained from:
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http://orca.princeton.edu/francois/software/tricubic/
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or
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http://1drv.ms/1J2WFYk
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The spglib is optionally needed, enabling one to evaluate the
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phonon density of states or vibrational thermal properties
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using only the irreducible q-points in the first Brillouin zone,
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as well as to evaluate the phonon dispersion curvers with the
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automatic mode. Currently, the 1.8.3 version of spglib is used.
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It can be obtained from:
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http://spglib.sourceforge.net/
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2. Compilation
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To compile the code, one needs therefore to install the above
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libraries and set the paths correctly in the Makefile.
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Once this is done, by typing
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make
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will yield the executable "phana".
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This program reads the binary file created by the fix phonon command
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and helps to analyse the phonon related info.
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3. Unit system
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The units of the output frequencies by this code is THz for
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LAMMPS units "real", "si", "metal", and "cgs"; in these cases,
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the frequencies are $\nu$ instead of $\omega$.
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The clapack library is needed to solve the eigen problems, which could
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be downloaded from: http://www.netlib.org/clapack/
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4. Updates
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For updates of phana, please check:
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http://nes.sjtu.edu.cn/english/research/software.htm
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or
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https://github.com/lingtikong/phana.git
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The tricubic library is also needed to to tricubic interpolations,
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which could be obtained from:
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http://orca.princeton.edu/francois/software/tricubic/ or
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http://code.google.com/p/fix-phonon/downloads/list
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The spglib (version 0.7.1) is optionally needed, enabling one to
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evaluate the phonon density of states or vibrational thermal
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properties using only the irreducible q-points in the first Brillouin
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zone.
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To compile the code, one needs therefore to install the above
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libraries and set the paths correctly in the Makefile.
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The units of the output frequencies by this code is THz for LAMMPS
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units "real", "si", "metal", and "cgs"; in these cases, the
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frequencies are $\nu$ instead of $\omega$.
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One is encouraged to visit http://code.google.com/p/fix-phonon/ to
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check out the latest revision on fix-phonon and the post-processing
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code.
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Author: Ling-Ti Kong (konglt at sjtu.edu.cn)
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Feb 2013
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5. Bug report
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If any bug found, please drop a line to: konglt(at)sjtu.edu.cn
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#-------------------------------------------------------------------------------
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Author: Ling-Ti Kong, konglt(at)sjtu.edu.cn
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Oct 2015
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@ -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];
|
||||
geteigen(egvs, 0);
|
||||
printf("\nEigenvalues of Phi at gamma before enforcing ASR:\n");
|
||||
for (int i=0; i<fftdim; i++){
|
||||
for (int i = 0; i < fftdim; ++i){
|
||||
printf("%lg ", egvs[i]);
|
||||
if (i%10 == 9) printf("\n");
|
||||
if (i == 99){ printf("...... (%d more skipped)\n", fftdim-100); break;}
|
||||
|
|
@ -355,20 +337,23 @@ void DynMat::EnforceASR()
|
|||
fgets(str,MAXLINE,stdin);
|
||||
char *ptr = strtok(str," \t\n\r\f");
|
||||
if (ptr) nasr = atoi(ptr);
|
||||
if (nasr < 1){return; for (int i=0; i<80; i++) printf("="); printf("\n");}
|
||||
if (nasr < 1){
|
||||
for (int i=0; i<80; i++) printf("="); printf("\n");
|
||||
return;
|
||||
}
|
||||
|
||||
for (int iit=0; iit<nasr; iit++){
|
||||
for (int iit = 0; iit < nasr; ++iit){
|
||||
// simple ASR; the resultant matrix might not be symmetric
|
||||
for (int a=0; a<sysdim; a++)
|
||||
for (int b=0; b<sysdim; b++){
|
||||
for (int k=0; k<nucell; k++){
|
||||
for (int a = 0; a < sysdim; ++a)
|
||||
for (int b = 0; b < sysdim; ++b){
|
||||
for (int k = 0; k < nucell; ++k){
|
||||
double sum = 0.;
|
||||
for (int kp=0; kp<nucell; kp++){
|
||||
for (int kp = 0; kp < nucell; ++kp){
|
||||
int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
|
||||
sum += DM_all[0][idx].r;
|
||||
}
|
||||
sum /= double(nucell);
|
||||
for (int kp=0; kp<nucell; kp++){
|
||||
for (int kp = 0; kp < nucell; ++kp){
|
||||
int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
|
||||
DM_all[0][idx].r -= sum;
|
||||
}
|
||||
|
|
@ -376,11 +361,11 @@ void DynMat::EnforceASR()
|
|||
}
|
||||
|
||||
// symmetrize
|
||||
for (int k=0; k<nucell; k++)
|
||||
for (int kp=k; kp<nucell; kp++){
|
||||
for (int k = 0; k < nucell; ++k)
|
||||
for (int kp = k; kp < nucell; ++kp){
|
||||
double csum = 0.;
|
||||
for (int a=0; a<sysdim; a++)
|
||||
for (int b=0; b<sysdim; b++){
|
||||
for (int a = 0; a < sysdim; ++a)
|
||||
for (int b = 0; b < sysdim; ++b){
|
||||
int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
|
||||
int jdx = (kp*sysdim+b)*fftdim+k*sysdim+a;
|
||||
csum = (DM_all[0][idx].r + DM_all[0][jdx].r )*0.5;
|
||||
|
|
@ -390,16 +375,16 @@ void DynMat::EnforceASR()
|
|||
}
|
||||
|
||||
// symmetric ASR
|
||||
for (int a=0; a<sysdim; a++)
|
||||
for (int b=0; b<sysdim; b++){
|
||||
for (int k=0; k<nucell; k++){
|
||||
for (int a = 0; a < sysdim; ++a)
|
||||
for (int b = 0; b < sysdim; ++b){
|
||||
for (int k = 0; k < nucell; ++k){
|
||||
double sum = 0.;
|
||||
for (int kp=0; kp<nucell; kp++){
|
||||
for (int kp = 0; kp < nucell; ++kp){
|
||||
int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
|
||||
sum += DM_all[0][idx].r;
|
||||
}
|
||||
sum /= double(nucell-k);
|
||||
for (int kp=k; kp<nucell; kp++){
|
||||
for (int kp = k; kp < nucell; ++kp){
|
||||
int idx = (k*sysdim+a)*fftdim+kp*sysdim+b;
|
||||
int jdx = (kp*sysdim+b)*fftdim+k*sysdim+a;
|
||||
DM_all[0][idx].r -= sum;
|
||||
|
|
@ -409,16 +394,17 @@ void DynMat::EnforceASR()
|
|||
}
|
||||
|
||||
// compute and display eigenvalues of Phi at gamma after ASR
|
||||
for (int i=0; i<fftdim; i++)
|
||||
for (int j=0; j<fftdim; j++) DM_q[i][j] = DM_all[0][i*fftdim+j];
|
||||
for (int i = 0; i < fftdim; ++i)
|
||||
for (int j = 0; j < fftdim; ++j) DM_q[i][j] = DM_all[0][i*fftdim+j];
|
||||
geteigen(egvs, 0);
|
||||
printf("Eigenvalues of Phi at gamma after enforcing ASR:\n");
|
||||
for (int i=0; i<fftdim; i++){
|
||||
for (int i = 0; i < fftdim; ++i){
|
||||
printf("%lg ", egvs[i]);
|
||||
if (i%10 == 9) printf("\n");
|
||||
if (i == 99){ printf("...... (%d more skiped)", fftdim-100); break;}
|
||||
}
|
||||
printf("\n"); for (int i=0; i<80; i++) printf("="); printf("\n\n");
|
||||
printf("\n");
|
||||
for (int i = 0; i < 80; ++i) printf("="); printf("\n\n");
|
||||
|
||||
return;
|
||||
}
|
||||
|
|
@ -441,23 +427,23 @@ void DynMat::real2rec()
|
|||
ibasevec[8] = basevec[0]*basevec[4] - basevec[1]*basevec[3];
|
||||
|
||||
double vol = 0.;
|
||||
for (int i=0; i<sysdim; i++) vol += ibasevec[i] * basevec[i];
|
||||
for (int i = 0; i < sysdim; ++i) vol += ibasevec[i] * basevec[i];
|
||||
vol = 8.*atan(1.)/vol;
|
||||
|
||||
for (int i=0; i<9; i++) ibasevec[i] *= vol;
|
||||
for (int i = 0; i < 9; ++i) ibasevec[i] *= vol;
|
||||
|
||||
printf("\n"); for (int i=0; i<80; i++) printf("=");
|
||||
printf("\n"); for (int i = 0; i < 80; ++i) printf("=");
|
||||
printf("\nBasis vectors of the unit cell in real space:");
|
||||
for (int i=0; i<sysdim; i++){
|
||||
for (int i = 0; i < sysdim; ++i){
|
||||
printf("\n A%d: ", i+1);
|
||||
for (int j=0; j<sysdim; j++) printf("%8.4f ", basevec[i*3+j]);
|
||||
for (int j = 0; j < sysdim; ++j) printf("%8.4f ", basevec[i*3+j]);
|
||||
}
|
||||
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;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -56,7 +56,7 @@ private:
|
|||
|
||||
doublecomplex **DM_all;
|
||||
|
||||
void car2dir(int); // to convert basis from cartisian coordinate into factional.
|
||||
void car2dir(); // to convert basis from cartisian coordinate into factional.
|
||||
void real2rec();
|
||||
void GaussJordan(int, double *);
|
||||
|
||||
|
|
|
|||
|
|
@ -4,8 +4,7 @@
|
|||
#include <math.h>
|
||||
#include "green.h"
|
||||
#include <complex>
|
||||
|
||||
#define MAXLINE 256
|
||||
#include "global.h"
|
||||
|
||||
/*******************************************************************************
|
||||
* The class of Green is designed to evaluate the LDOS via the Green's Function
|
||||
|
|
@ -45,7 +44,7 @@ Green::Green(const int ntm, const int sdim, const int niter, const double min, c
|
|||
H = Hessian; iatom = itm;
|
||||
ldos = lpdos;
|
||||
|
||||
memory = new Memory;
|
||||
memory = new Memory();
|
||||
if (natom < 1 || iatom < 0 || iatom >= natom){
|
||||
printf("\nError: Wrong number of total atoms or wrong index of interested atom!\n");
|
||||
return;
|
||||
|
|
@ -58,9 +57,9 @@ Green::Green(const int ntm, const int sdim, const int niter, const double min, c
|
|||
|
||||
// initialize variables and allocate local memories
|
||||
dw = (wmax - wmin)/double(nw-1);
|
||||
alpha = memory->create(alpha, sysdim,nit, "Green_Green:alpha");
|
||||
beta = memory->create(beta, sysdim,nit+1,"Green_Green:beta");
|
||||
//ldos = memory->create(ldos, nw,sysdim, "Green_Green:ldos");
|
||||
memory->create(alpha, sysdim,nit, "Green_Green:alpha");
|
||||
memory->create(beta, sysdim,nit+1,"Green_Green:beta");
|
||||
//memory->create(ldos, nw,sysdim, "Green_Green:ldos");
|
||||
|
||||
// use Lanczos algorithm to diagonalize the Hessian
|
||||
Lanczos();
|
||||
|
|
@ -100,35 +99,35 @@ void Green::Lanczos()
|
|||
int ipos = iatom*sysdim;
|
||||
|
||||
// Loop over dimension
|
||||
for (int idim=0; idim<sysdim; idim++){
|
||||
for (int idim = 0; idim < sysdim; ++idim){
|
||||
beta[idim][0] = 0.;
|
||||
for (int i=0; i<ndim; i++){vp[i] = v[i] = 0.;}
|
||||
for (int i = 0; i < ndim; ++i) vp[i] = v[i] = 0.;
|
||||
v[ipos+idim] = 1.;
|
||||
|
||||
// Loop on fraction levels
|
||||
for (int i=0; i<nit; i++){
|
||||
for (int i = 0; i < nit; ++i){
|
||||
double sum_a = 0.;
|
||||
for (int j=0; j<ndim; j++){
|
||||
for (int j = 0; j < ndim; ++j){
|
||||
double sumHv = 0.;
|
||||
for (int k=0; k<ndim; k++) sumHv += H[j][k]*v[k];
|
||||
for (int k = 0; k < ndim; ++k) sumHv += H[j][k]*v[k];
|
||||
w[j] = sumHv - beta[idim][i]*vp[j];
|
||||
sum_a += w[j]*v[j];
|
||||
}
|
||||
alpha[idim][i] = sum_a;
|
||||
|
||||
for (int k=0; k<ndim; k++) w[k] -= alpha[idim][i]*v[k];
|
||||
for (int k = 0; k < ndim; ++k) w[k] -= alpha[idim][i]*v[k];
|
||||
|
||||
double gamma = 0.;
|
||||
for (int k=0; k<ndim; k++) gamma += w[k]*v[k];
|
||||
for (int k=0; k<ndim; k++) w[k] -= gamma*v[k];
|
||||
for (int k = 0; k < ndim; ++k) gamma += w[k]*v[k];
|
||||
for (int k = 0; k < ndim; ++k) w[k] -= gamma*v[k];
|
||||
|
||||
double sum_b = 0.;
|
||||
for (int k=0; k<ndim; k++) sum_b += w[k]*w[k];
|
||||
for (int k = 0; k < ndim; ++k) sum_b += w[k]*w[k];
|
||||
beta[idim][i+1] = sqrt(sum_b);
|
||||
|
||||
ptr = vp; vp = v; v = ptr;
|
||||
double tmp = 1./beta[idim][i+1];
|
||||
for (int k=0; k<ndim; k++) v[k] = w[k]*tmp;
|
||||
for (int k = 0; k < ndim; ++k) v[k] = w[k] * tmp;
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -154,10 +153,10 @@ void Green::Recursion()
|
|||
xmax = new double [sysdim];
|
||||
|
||||
int nave = nit/4;
|
||||
for (int idim=0; idim<sysdim; idim++){
|
||||
for (int idim = 0; idim < sysdim; ++idim){
|
||||
alpha_inf[idim] = beta_inf[idim] = 0.;
|
||||
|
||||
for (int i= nit-nave; i<nit; i++){
|
||||
for (int i = nit-nave; i < nit; ++i){
|
||||
alpha_inf[idim] += alpha[idim][i];
|
||||
beta_inf[idim] += beta[idim][i+1];
|
||||
}
|
||||
|
|
@ -173,11 +172,11 @@ void Green::Recursion()
|
|||
double sr, si;
|
||||
|
||||
double w = wmin;
|
||||
for (int i=0; i<nw; i++){
|
||||
for (int i = 0; i < nw; ++i){
|
||||
double a = w*w, ax, bx;
|
||||
Z = std::complex<double>(w*w, epson);
|
||||
|
||||
for (int idim=0; idim<sysdim; idim++){
|
||||
for (int idim = 0; idim < sysdim; ++idim){
|
||||
double two_b = 2.*beta_inf[idim]*beta_inf[idim];
|
||||
double rtwob = 1./two_b;
|
||||
|
||||
|
|
@ -201,7 +200,7 @@ void Green::Recursion()
|
|||
si = epson * rtwob + bx;
|
||||
rec_x = std::complex<double> (sr, si);
|
||||
|
||||
for (int j=0; j<nit; j++){
|
||||
for (int j = 0; j < nit; ++j){
|
||||
rec_x_inv = Z - alpha[idim][nit-j-1] - beta[idim][nit-j]*beta[idim][nit-j]*rec_x;
|
||||
rec_x = 1./rec_x_inv;
|
||||
}
|
||||
|
|
@ -229,13 +228,13 @@ void Green::recursion()
|
|||
|
||||
double w = wmin;
|
||||
|
||||
for (int i=0; i<nw; i++){
|
||||
for (int i = 0; i < nw; ++i){
|
||||
Z = std::complex<double>(w*w, epson);
|
||||
|
||||
for (int idim=0; idim<sysdim; idim++){
|
||||
for (int idim = 0; idim < sysdim; ++idim){
|
||||
rec_x = std::complex<double>(0.,0.);
|
||||
|
||||
for (int j=0; j<nit; j++){
|
||||
for (int j = 0; j < nit; ++j){
|
||||
rec_x_inv = Z - alpha[idim][nit-j-1] - beta[idim][nit-j]*beta[idim][nit-j]*rec_x;
|
||||
rec_x = 1./rec_x_inv;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,9 +1,6 @@
|
|||
#include "interpolate.h"
|
||||
#include "math.h"
|
||||
|
||||
#define MAXLINE 256
|
||||
#define MIN(a,b) ((a)>(b)?(b):(a))
|
||||
#define MAX(a,b) ((a)>(b)?(a):(b))
|
||||
#include "global.h"
|
||||
|
||||
/* ----------------------------------------------------------------------------
|
||||
* Constructor used to get info from caller, and prepare other necessary data
|
||||
|
|
@ -15,7 +12,7 @@ Interpolate::Interpolate(int nx, int ny, int nz, int ndm, doublecomplex **DM)
|
|||
Nz = nz;
|
||||
Npt = Nx*Ny*Nz;
|
||||
ndim = ndm;
|
||||
memory = new Memory;
|
||||
memory = new Memory();
|
||||
|
||||
which = UseGamma = 0;
|
||||
|
||||
|
|
@ -33,13 +30,13 @@ void Interpolate::tricubic_init()
|
|||
{
|
||||
// prepare necessary data for tricubic
|
||||
if (flag_allocated_dfs == 0){
|
||||
Dfdx = memory->create(Dfdx, Npt, ndim, "Interpolate_Interpolate:Dfdx");
|
||||
Dfdy = memory->create(Dfdy, Npt, ndim, "Interpolate_Interpolate:Dfdy");
|
||||
Dfdz = memory->create(Dfdz, Npt, ndim, "Interpolate_Interpolate:Dfdz");
|
||||
D2fdxdy = memory->create(D2fdxdy, Npt, ndim, "Interpolate_Interpolate:D2fdxdy");
|
||||
D2fdxdz = memory->create(D2fdxdz, Npt, ndim, "Interpolate_Interpolate:D2fdxdz");
|
||||
D2fdydz = memory->create(D2fdydz, Npt, ndim, "Interpolate_Interpolate:D2fdydz");
|
||||
D3fdxdydz = memory->create(D3fdxdydz, Npt, ndim, "Interpolate_Interpolate:D2fdxdydz");
|
||||
memory->create(Dfdx, Npt, ndim, "Interpolate_Interpolate:Dfdx");
|
||||
memory->create(Dfdy, Npt, ndim, "Interpolate_Interpolate:Dfdy");
|
||||
memory->create(Dfdz, Npt, ndim, "Interpolate_Interpolate:Dfdz");
|
||||
memory->create(D2fdxdy, Npt, ndim, "Interpolate_Interpolate:D2fdxdy");
|
||||
memory->create(D2fdxdz, Npt, ndim, "Interpolate_Interpolate:D2fdxdz");
|
||||
memory->create(D2fdydz, Npt, ndim, "Interpolate_Interpolate:D2fdydz");
|
||||
memory->create(D3fdxdydz, Npt, ndim, "Interpolate_Interpolate:D2fdxdydz");
|
||||
|
||||
flag_allocated_dfs = 1;
|
||||
}
|
||||
|
|
@ -47,9 +44,9 @@ void Interpolate::tricubic_init()
|
|||
// get the derivatives
|
||||
int n=0;
|
||||
const double half = 0.5, one4 = 0.25, one8 = 0.125;
|
||||
for (int ii=0; ii<Nx; ii++)
|
||||
for (int jj=0; jj<Ny; jj++)
|
||||
for (int kk=0; kk<Nz; kk++){
|
||||
for (int ii = 0; ii < Nx; ++ii)
|
||||
for (int jj = 0; jj < Ny; ++jj)
|
||||
for (int kk = 0; kk < Nz; ++kk){
|
||||
|
||||
int ip = (ii+1)%Nx, jp = (jj+1)%Ny, kp = (kk+1)%Nz;
|
||||
int im = (ii-1+Nx)%Nx, jm = (jj-1+Ny)%Ny, km = (kk-1+Nz)%Nz;
|
||||
|
|
@ -127,8 +124,8 @@ void Interpolate::tricubic(double *qin, doublecomplex *DMq)
|
|||
{
|
||||
// qin should be in unit of 2*pi/L
|
||||
double q[3];
|
||||
for (int i=0; i<3; i++) q[i] = qin[i];
|
||||
for (int i=0; i<3; i++){
|
||||
for (int i = 0; i < 3; ++i) q[i] = qin[i];
|
||||
for (int i = 0; i < 3; ++i){
|
||||
while (q[i] < 0.) q[i] += 1.;
|
||||
while (q[i] >= 1.) q[i] -= 1.;
|
||||
}
|
||||
|
|
@ -150,8 +147,8 @@ void Interpolate::tricubic(double *qin, doublecomplex *DMq)
|
|||
vidx[7] = (ixp*Ny+iyp)*Nz+izp;
|
||||
for (int i=0; i<8; i++) if (vidx[i] == 0) UseGamma = 1;
|
||||
|
||||
for (int idim=0; idim<ndim; idim++){
|
||||
for (int i=0; i<8; i++){
|
||||
for (int idim = 0; idim < ndim; ++idim){
|
||||
for (int i = 0; i < 8; ++i){
|
||||
f[i] = data[vidx[i]][idim].r;
|
||||
dfdx[i] = Dfdx[vidx[i]][idim].r;
|
||||
dfdy[i] = Dfdy[vidx[i]][idim].r;
|
||||
|
|
@ -164,7 +161,7 @@ void Interpolate::tricubic(double *qin, doublecomplex *DMq)
|
|||
tricubic_get_coeff(&a[0],&f[0],&dfdx[0],&dfdy[0],&dfdz[0],&d2fdxdy[0],&d2fdxdz[0],&d2fdydz[0],&d3fdxdydz[0]);
|
||||
DMq[idim].r = tricubic_eval(&a[0],x,y,z);
|
||||
|
||||
for (int i=0; i<8; i++){
|
||||
for (int i = 0; i < 8; ++i){
|
||||
f[i] = data[vidx[i]][idim].i;
|
||||
dfdx[i] = Dfdx[vidx[i]][idim].i;
|
||||
dfdy[i] = Dfdy[vidx[i]][idim].i;
|
||||
|
|
@ -177,6 +174,8 @@ void Interpolate::tricubic(double *qin, doublecomplex *DMq)
|
|||
tricubic_get_coeff(&a[0],&f[0],&dfdx[0],&dfdy[0],&dfdz[0],&d2fdxdy[0],&d2fdxdz[0],&d2fdydz[0],&d3fdxdydz[0]);
|
||||
DMq[idim].i = tricubic_eval(&a[0],x,y,z);
|
||||
}
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------------
|
||||
|
|
@ -188,8 +187,8 @@ void Interpolate::trilinear(double *qin, doublecomplex *DMq)
|
|||
{
|
||||
// rescale q[i] into [0 1)
|
||||
double q[3];
|
||||
for (int i=0; i<3; i++) q[i] = qin[i];
|
||||
for (int i=0; i<3; i++){
|
||||
for (int i = 0; i < 3; ++i) q[i] = qin[i];
|
||||
for (int i = 0; i < 3; ++i){
|
||||
while (q[i] < 0.) q[i] += 1.;
|
||||
while (q[i] >= 1.) q[i] -= 1.;
|
||||
}
|
||||
|
|
@ -220,7 +219,7 @@ void Interpolate::trilinear(double *qin, doublecomplex *DMq)
|
|||
vidx[5] = ((ix*Ny)+iyp)*Nz + izp;
|
||||
vidx[6] = ((ixp*Ny)+iyp)*Nz + iz;
|
||||
vidx[7] = ((ixp*Ny)+iyp)*Nz + izp;
|
||||
for (int i=0; i<8; i++) if (vidx[i] == 0) UseGamma = 1;
|
||||
for (int i = 0; i < 8; ++i) if (vidx[i] == 0) UseGamma = 1;
|
||||
|
||||
double fac[8];
|
||||
fac[0] = (1.-x)*(1.-y)*(1.-z);
|
||||
|
|
@ -233,10 +232,10 @@ void Interpolate::trilinear(double *qin, doublecomplex *DMq)
|
|||
fac[7] = x*y*z;
|
||||
|
||||
// now to do the interpolation
|
||||
for (int idim=0; idim<ndim; idim++){
|
||||
for (int idim = 0; idim < ndim; ++idim){
|
||||
DMq[idim].r = 0.;
|
||||
DMq[idim].i = 0.;
|
||||
for (int i=0; i<8; i++){
|
||||
for (int i = 0; i < 8; ++i){
|
||||
DMq[idim].r += data[vidx[i]][idim].r*fac[i];
|
||||
DMq[idim].i += data[vidx[i]][idim].i*fac[i];
|
||||
}
|
||||
|
|
@ -268,13 +267,13 @@ void Interpolate::set_method()
|
|||
printf("\n");for(int i=0; i<80; i++) printf("=");
|
||||
printf("\nWhich interpolation method would you like to use?\n");
|
||||
printf(" 1. Tricubic;\n 2. Trilinear;\n");
|
||||
printf("Your choice[1]: ");
|
||||
printf("Your choice [1]: ");
|
||||
fgets(str,MAXLINE,stdin);
|
||||
char *ptr = strtok(str," \t\n\r\f");
|
||||
if (ptr) im = atoi(ptr);
|
||||
|
||||
which =2-im%2;
|
||||
printf("Your selection: %d\n", which);
|
||||
printf("Your selection: %d\n", which);
|
||||
for(int i=0; i<80; i++) printf("="); printf("\n\n");
|
||||
|
||||
if (which == 1) tricubic_init();
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@
|
|||
#include "phonon.h"
|
||||
#include "green.h"
|
||||
#include "timer.h"
|
||||
#include "global.h"
|
||||
|
||||
#ifdef UseSPG
|
||||
extern "C"{
|
||||
|
|
@ -10,10 +11,6 @@ extern "C"{
|
|||
}
|
||||
#endif
|
||||
|
||||
#define MAXLINE 256
|
||||
#define MIN(a,b) ((a)>(b)?(b):(a))
|
||||
#define MAX(a,b) ((a)>(b)?(a):(b))
|
||||
|
||||
/* ----------------------------------------------------------------------------
|
||||
* Class Phonon is the main driver to calculate phonon DOS, phonon
|
||||
* dispersion curve and some other things.
|
||||
|
|
@ -42,7 +39,10 @@ Phonon::Phonon(DynMat *dm)
|
|||
// 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("\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");
|
||||
|
|
@ -52,14 +52,15 @@ Phonon::Phonon(DynMat *dm)
|
|||
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");
|
||||
printf(" -1. Reset the interpolation method;\n");
|
||||
printf(" 0. Exit.\n");
|
||||
// read user choice
|
||||
int job = 0;
|
||||
printf("Your choice[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");
|
||||
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();
|
||||
|
|
@ -71,6 +72,7 @@ Phonon::Phonon(DynMat *dm)
|
|||
else if (job == 7) ldos_egv();
|
||||
else if (job == 8) ldos_rsgf();
|
||||
else if (job == 9) vecanyq();
|
||||
else if (job ==10) ShowCell();
|
||||
else if (job ==-1) dynmat->reset_interp_method();
|
||||
else break;
|
||||
}
|
||||
|
|
@ -113,11 +115,10 @@ void Phonon::pdos()
|
|||
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]);
|
||||
}
|
||||
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
|
||||
|
|
@ -139,14 +140,14 @@ void Phonon::pdos()
|
|||
df = (fmax-fmin)/double(ndos-1);
|
||||
rdf = 1./df;
|
||||
memory->destroy(dos);
|
||||
dos = memory->create(dos, ndos, "pdos: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++){
|
||||
for (int iq = 0; iq < nq; ++iq){
|
||||
if (wt[iq] > 0.){
|
||||
for (int j=0; j<ndim; j++){
|
||||
for (int j = 0; j < ndim; ++j){
|
||||
int idx = int((eigs[iq][j]-offset)*rdf);
|
||||
if (idx>=0 && idx<ndos) dos[idx] += wt[iq];
|
||||
}
|
||||
|
|
@ -220,17 +221,20 @@ void Phonon::writeLDOS()
|
|||
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++){
|
||||
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++){
|
||||
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];}
|
||||
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;
|
||||
}
|
||||
|
|
@ -250,21 +254,21 @@ void Phonon::ldos_rsgf()
|
|||
const double tpi = 8.*atan(1.);
|
||||
double **Hessian, scale;
|
||||
scale = dynmat->eml2f*tpi; scale *= scale;
|
||||
Hessian = memory->create(Hessian, ndim, ndim, "phonon_ldos:Hessian");
|
||||
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;
|
||||
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]);}
|
||||
for (int i = 1; i < ndim; ++i){fmin = MIN(fmin, egvs[i]); fmax = MAX(fmax, egvs[i]);}
|
||||
delete []egvs;
|
||||
} else {
|
||||
fmin = 0.; fmax = 20.;
|
||||
|
|
@ -284,24 +288,29 @@ void Phonon::ldos_rsgf()
|
|||
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);
|
||||
if (ik < 0 || ik >= dynmat->nucell) break;
|
||||
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;
|
||||
if (istr < 0||iend >= dynmat->nucell||istr > iend) break;
|
||||
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"));
|
||||
if (istr<0 || iend >= dynmat->nucell || istr > iend || iinc<1) break;
|
||||
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);
|
||||
|
|
@ -332,7 +341,7 @@ void Phonon::ldos_rsgf()
|
|||
ldos = memory->create(ldos,nlocal,ndos,dynmat->sysdim,"ldos_rsgf:ldos");
|
||||
|
||||
memory->destroy(locals);
|
||||
locals = memory->create(locals, nlocal, "ldos_rsgf:locals");
|
||||
memory->create(locals, nlocal, "ldos_rsgf:locals");
|
||||
|
||||
df = (fmax-fmin)/double(ndos-1);
|
||||
rdf = 1./df;
|
||||
|
|
@ -366,104 +375,6 @@ void Phonon::ldos_rsgf()
|
|||
return;
|
||||
}
|
||||
|
||||
/*------------------------------------------------------------------------------
|
||||
* Private method to evaluate the phonon dispersion curves
|
||||
*----------------------------------------------------------------------------*/
|
||||
void Phonon::pdisp()
|
||||
{
|
||||
// ask the output file name and write the header.
|
||||
char str[MAXLINE];
|
||||
printf("Please input the filename to output the dispersion data [pdisp.dat]:");
|
||||
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str, "pdisp.dat");
|
||||
char *ptr = strtok(str," \t\n\r\f");
|
||||
char *fname = new char[strlen(ptr)+1];
|
||||
strcpy(fname,ptr);
|
||||
|
||||
FILE *fp = fopen(fname, "w");
|
||||
fprintf(fp,"# q qr freq\n");
|
||||
fprintf(fp,"# 2pi/L 2pi/L %s\n", dynmat->funit);
|
||||
|
||||
// to store the nodes of the dispersion curve
|
||||
std::vector<double> nodes; nodes.clear();
|
||||
|
||||
// now the calculate the dispersion curve
|
||||
double qstr[3], qend[3], q[3], qinc[3], qr=0., dq;
|
||||
int nq = MAX(MAX(dynmat->nx,dynmat->ny),dynmat->nz)/2+1;
|
||||
qend[0] = qend[1] = qend[2] = 0.;
|
||||
|
||||
double *egvs = new double [ndim];
|
||||
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");
|
||||
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]);
|
||||
|
||||
nodes.push_back(qr);
|
||||
for (int i=0; i<3; i++) q[i] = qstr[i];
|
||||
for (int ii=0; ii<nq; ii++){
|
||||
double wii = 1.;
|
||||
dynmat->getDMq(q, &wii);
|
||||
if (wii > 0.){
|
||||
dynmat->geteigen(egvs, 0);
|
||||
fprintf(fp,"%lg %lg %lg %lg ", q[0], q[1], q[2], qr);
|
||||
for (int i=0; i<ndim; i++) fprintf(fp," %lg", egvs[i]);
|
||||
}
|
||||
fprintf(fp,"\n");
|
||||
|
||||
for (int i=0; i<3; i++) q[i] += qinc[i];
|
||||
qr += dq;
|
||||
}
|
||||
qr -= dq;
|
||||
}
|
||||
if (qr > 0.) nodes.push_back(qr);
|
||||
fclose(fp);
|
||||
delete []egvs;
|
||||
|
||||
// write the gnuplot script which helps to visualize the result
|
||||
int nnd = nodes.size();
|
||||
if (nnd > 1){
|
||||
fp = fopen("pdisp.gnuplot", "w");
|
||||
fprintf(fp,"set term post enha colo 20\nset out %cpdisp.eps%c\n\n",char(34),char(34));
|
||||
fprintf(fp,"set xlabel %cq%c\n",char(34),char(34));
|
||||
fprintf(fp,"set ylabel %cfrequency (THz)%c\n\n",char(34),char(34));
|
||||
fprintf(fp,"set xrange [0:%lg]\nset yrange [0:*]\n\n", nodes[nnd-1]);
|
||||
fprintf(fp,"set grid xtics\n");
|
||||
fprintf(fp,"# {/Symbol G} will give you letter gamma in the label\nset xtics (");
|
||||
for (int i=0; i<nnd-1; i++) fprintf(fp,"%c%c %lg, ", char(34),char(34),nodes[i]);
|
||||
fprintf(fp,"%c%c %lg)\n\n",char(34),char(34),nodes[nnd-1]);
|
||||
fprintf(fp,"unset key\n\n");
|
||||
fprintf(fp,"plot %c%s%c u 4:5 w l lt 1",char(34),fname,char(34));
|
||||
for (int i=1; i<ndim; i++) fprintf(fp,",\\\n%c%c u 4:%d w l lt 1",char(34),char(34),i+5);
|
||||
fclose(fp);
|
||||
}
|
||||
|
||||
delete []fname;
|
||||
nodes.clear();
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------------
|
||||
* Private method to write out the dynamical matrix at selected q
|
||||
* ---------------------------------------------------------------------------- */
|
||||
|
|
@ -491,7 +402,7 @@ void Phonon::vfanyq()
|
|||
char str[MAXLINE];
|
||||
double q[3], egvs[ndim];
|
||||
|
||||
while (1){
|
||||
while ( 1 ){
|
||||
printf("Please input the q-point to compute the frequencies, q to exit: ");
|
||||
if (count_words(fgets(str,MAXLINE,stdin)) < 3) break;
|
||||
|
||||
|
|
@ -503,7 +414,7 @@ void Phonon::vfanyq()
|
|||
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");
|
||||
for (int i = 0; i < ndim; ++i) printf("%lg ", egvs[i]); printf("\n\n");
|
||||
}
|
||||
|
||||
return;
|
||||
|
|
@ -521,7 +432,7 @@ void Phonon::vecanyq()
|
|||
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str,"eigvec.dat");
|
||||
FILE *fp = fopen(strtok(str," \t\n\r\f"), "w");
|
||||
|
||||
while (1){
|
||||
while ( 1 ){
|
||||
printf("Please input the q-point to compute the frequencies, q to exit: ");
|
||||
if (count_words(fgets(str,MAXLINE,stdin)) < 3) break;
|
||||
|
||||
|
|
@ -533,14 +444,14 @@ void Phonon::vecanyq()
|
|||
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++){
|
||||
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++){
|
||||
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++){
|
||||
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;
|
||||
}
|
||||
|
|
@ -575,9 +486,8 @@ void Phonon::DMdisp()
|
|||
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];
|
||||
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));
|
||||
|
|
@ -602,16 +512,17 @@ void Phonon::DMdisp()
|
|||
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++){
|
||||
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];
|
||||
for (int i = 0; i < 3; ++i) q[i] += qinc[i];
|
||||
qr += dq;
|
||||
}
|
||||
qr -= dq;
|
||||
}
|
||||
fclose(fp);
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
|
|
@ -625,26 +536,26 @@ void Phonon::smooth(double *array, const int npt)
|
|||
int nlag = npt/4;
|
||||
|
||||
double *tmp, *table;
|
||||
tmp = memory->create(tmp, npt, "smooth:tmp");
|
||||
table = memory->create(table, nlag+1, "smooth: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++){
|
||||
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++){
|
||||
for (int i = 0; i < npt; ++i){
|
||||
tmp[i] = 0.;
|
||||
for (int jj=-nlag; jj<= nlag; jj++){
|
||||
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;
|
||||
for (int i = 0; i < npt; ++i) array[i] = tmp[i]*fnorm;
|
||||
|
||||
memory->destroy(tmp);
|
||||
memory->destroy(table);
|
||||
|
|
@ -682,9 +593,9 @@ void Phonon::therm()
|
|||
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++){
|
||||
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++){
|
||||
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.);
|
||||
|
|
@ -709,6 +620,7 @@ void Phonon::therm()
|
|||
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);
|
||||
|
||||
|
|
@ -737,15 +649,15 @@ void Phonon::local_therm()
|
|||
fprintf(fp,"#-------------------------------------------------------------------------------\n");
|
||||
|
||||
double **Uvib, **Svib, **Fvib, **Cvib, **ZPE;
|
||||
Uvib = memory->create(Uvib,nlocal,sysdim,"local_therm:Uvib");
|
||||
Svib = memory->create(Svib,nlocal,sysdim,"local_therm:Svib");
|
||||
Fvib = memory->create(Fvib,nlocal,sysdim,"local_therm:Fvib");
|
||||
Cvib = memory->create(Cvib,nlocal,sysdim,"local_therm:Cvib");
|
||||
ZPE = memory->create(ZPE ,nlocal,sysdim,"local_therm: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){
|
||||
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){
|
||||
|
|
@ -755,11 +667,11 @@ void Phonon::local_therm()
|
|||
// 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.;
|
||||
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++){
|
||||
for (int i = 0; i < ndos; ++i){
|
||||
freq += df;
|
||||
if (freq <= 0.) continue;
|
||||
|
||||
|
|
@ -772,8 +684,8 @@ void Phonon::local_therm()
|
|||
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++){
|
||||
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;
|
||||
|
|
@ -781,8 +693,8 @@ void Phonon::local_therm()
|
|||
ZPE [il][idim] += ldos[il][i][idim]*Ztmp;
|
||||
}
|
||||
}
|
||||
for (int il=0; il<nlocal; il++)
|
||||
for (int idim=0; idim<sysdim; idim++){
|
||||
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;
|
||||
|
|
@ -791,34 +703,34 @@ void Phonon::local_therm()
|
|||
}
|
||||
|
||||
// output result under current temperature
|
||||
for (int il=0; il<nlocal; il++){
|
||||
for (int il = 0; il < nlocal; ++il){
|
||||
fprintf(fp,"%d %g ", locals[il], T);
|
||||
double total = 0.;
|
||||
for (int idim=0; idim<sysdim; idim++){
|
||||
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++){
|
||||
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++){
|
||||
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++){
|
||||
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++){
|
||||
for (int idim = 0; idim < sysdim; ++idim){
|
||||
fprintf(fp,"%g ", ZPE[il][idim]);
|
||||
total += ZPE[il][idim];
|
||||
}
|
||||
|
|
@ -846,7 +758,7 @@ void Phonon::QMesh()
|
|||
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 (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;
|
||||
|
|
@ -855,10 +767,10 @@ void Phonon::QMesh()
|
|||
// 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]: ");
|
||||
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);
|
||||
method = 2 - method%2;
|
||||
printf("Your selection: %d\n", method);
|
||||
#endif
|
||||
|
||||
memory->destroy(wt);
|
||||
|
|
@ -869,149 +781,52 @@ void Phonon::QMesh()
|
|||
#endif
|
||||
nq = nx*ny*nz;
|
||||
double w = 1./double(nq);
|
||||
wt = memory->create(wt, nq, "QMesh:wt");
|
||||
qpts = memory->create(qpts, nq, 3, "QMesh:qpts");
|
||||
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++){
|
||||
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
|
||||
}
|
||||
if ((method == 2) && (atpos == NULL)){
|
||||
atpos = memory->create(atpos, dynmat->nucell,3,"QMesh:atpos");
|
||||
attyp = memory->create(attyp, dynmat->nucell, "QMesh:attyp");
|
||||
} else {
|
||||
if (atpos == NULL) memory->create(atpos, dynmat->nucell,3,"QMesh:atpos");
|
||||
if (attyp == NULL) memory->create(attyp, dynmat->nucell, "QMesh:attyp");
|
||||
|
||||
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++) latvec[i][i] = 1.;
|
||||
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.;
|
||||
|
||||
int flag_lat_info_read = dynmat->flag_latinfo;
|
||||
// get atomic type info
|
||||
for (int i = 0; i < num_atom; ++i) attyp[i] = dynmat->attyp[i];
|
||||
|
||||
if ( flag_lat_info_read ){ // get unit cell info from binary file; done by dynmat
|
||||
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++) latvec[i][i] = 1.;
|
||||
// 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 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];
|
||||
// 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<num_atom; i++) printf(" %d %d %lg %lg %lg\n", i+1, attyp[i], atpos[i][0], atpos[i][1], atpos[i][2]);
|
||||
printf("\nIs the above info correct? (y/n)[y]: ");
|
||||
fgets(str,MAXLINE,stdin);
|
||||
char *ptr = strtok(str," \t\n\r\f");
|
||||
if ( (ptr) && ( (strcmp(ptr,"y") != 0) && (strcmp(ptr,"Y") != 0)) ) flag_lat_info_read = 0;
|
||||
}
|
||||
// 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);
|
||||
|
||||
if (flag_lat_info_read == 0) { // get unit cell info from file or user input
|
||||
int latsrc = 1;
|
||||
printf("\nPlease select the way to provide the unit cell info:\n");
|
||||
printf(" 1. By file;\n 2. Read in.\nYour choice [1]: ");
|
||||
if (count_words(fgets(str,MAXLINE,stdin)) > 0) latsrc = atoi(strtok(str," \t\n\r\f"));
|
||||
latsrc = 2-latsrc%2;
|
||||
/*----------------------------------------------------------------
|
||||
* Ask for lattice info from the user; the format of the file is:
|
||||
* A1_x A1_y A1_z
|
||||
* A2_x A2_y A2_z
|
||||
* A3_x A3_y A3_z
|
||||
* natom
|
||||
* Type_1 sx_1 sy_1 sz_1
|
||||
* ...
|
||||
* Type_n sx_n sy_n sz_n
|
||||
*----------------------------------------------------------------*/
|
||||
if (latsrc == 1){ // to read unit cell info from file; get file name first
|
||||
do printf("Please input the file name containing the unit cell info: ");
|
||||
while (count_words(fgets(str,MAXLINE,stdin)) < 1);
|
||||
char *fname = strtok(str," \t\n\r\f");
|
||||
FILE *fp = fopen(fname,"r"); fname = NULL;
|
||||
|
||||
if (fp == NULL) latsrc = 2;
|
||||
else {
|
||||
for (int i=0; i<3; i++){ // read unit cell vector info; # of atoms per unit cell
|
||||
if (count_words(fgets(str,MAXLINE,fp)) < 3){
|
||||
latsrc = 2;
|
||||
break;
|
||||
}
|
||||
latvec[0][i] = atof(strtok(str, " \t\n\r\f"));
|
||||
latvec[1][i] = atof(strtok(NULL," \t\n\r\f"));
|
||||
latvec[2][i] = atof(strtok(NULL," \t\n\r\f"));
|
||||
}
|
||||
if (count_words(fgets(str,MAXLINE,fp)) < 1) latsrc = 2;
|
||||
else {
|
||||
num_atom = atoi(strtok(str," \t\n\r\f"));
|
||||
if (num_atom > dynmat->nucell){
|
||||
printf("\nError: # of atoms read from file (%d) is bigger than that given by the dynamical matrix (%d)!\n", num_atom, dynmat->nucell);
|
||||
return;
|
||||
}
|
||||
|
||||
for (int i=0; i<num_atom; i++){ // read atomic type and fractional positions
|
||||
if (count_words(fgets(str,MAXLINE,fp)) < 4){
|
||||
latsrc = 2;
|
||||
break;
|
||||
|
||||
} else {
|
||||
attyp[i] = atoi(strtok(str," \t\n\r\f"));
|
||||
|
||||
atpos[i][0] = atof(strtok(NULL," \t\n\r\f"));
|
||||
atpos[i][1] = atof(strtok(NULL," \t\n\r\f"));
|
||||
atpos[i][2] = atof(strtok(NULL," \t\n\r\f"));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
fclose(fp);
|
||||
}
|
||||
if (latsrc == 2){
|
||||
for (int i=0; i<3; i++){
|
||||
do printf("Please input the vector A%d: ", i+1);
|
||||
while (count_words(fgets(str,MAXLINE,stdin)) < 3);
|
||||
latvec[0][i] = atof(strtok(str," \t\n\r\f"));
|
||||
latvec[1][i] = atof(strtok(NULL," \t\n\r\f"));
|
||||
latvec[2][i] = atof(strtok(NULL," \t\n\r\f"));
|
||||
}
|
||||
|
||||
do printf("please input the number of atoms per unit cell: ");
|
||||
while (count_words(fgets(str,MAXLINE,stdin)) < 1);
|
||||
num_atom = atoi(strtok(str," \t\n\r\f"));
|
||||
if (num_atom > dynmat->nucell){
|
||||
printf("\nError: # of atoms input (%d) is bigger than that given by the dynamical matrix (%d)!\n", num_atom, dynmat->nucell);
|
||||
return;
|
||||
}
|
||||
|
||||
for (int i=0; i<num_atom; i++){
|
||||
do printf("Please input the type, and fractional coordinate of atom No.%d: ", i+1);
|
||||
while (count_words(fgets(str,MAXLINE,stdin)) < 4);
|
||||
attyp[i] = atoi(strtok(str," \t\n\r\f"));
|
||||
|
||||
atpos[i][0] = atof(strtok(NULL," \t\n\r\f"));
|
||||
atpos[i][1] = atof(strtok(NULL," \t\n\r\f"));
|
||||
atpos[i][2] = atof(strtok(NULL," \t\n\r\f"));
|
||||
}
|
||||
}
|
||||
} // end of read from file or input
|
||||
} // end of if (method == 2 && ...
|
||||
|
||||
if (method == 2){
|
||||
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;
|
||||
|
|
@ -1019,29 +834,28 @@ void Phonon::QMesh()
|
|||
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];
|
||||
for (int i = 0; i < num_atom; ++i)
|
||||
for (int j = 0; j < 3; ++j) pos[i][j] = atpos[i][j];
|
||||
|
||||
//spg_show_symmetry(latvec, pos, attyp, num_atom, symprec);
|
||||
|
||||
// if spglib 0.7.1 is used
|
||||
nq = spg_get_ir_reciprocal_mesh(grid_point, map, num_grid, mesh, shift, is_time_reversal, latvec, pos, attyp, num_atom, symprec);
|
||||
// nq = spg_get_ir_reciprocal_mesh(grid_point, map, num_grid, mesh, shift, is_time_reversal, latvec, pos, attyp, num_atom, symprec);
|
||||
|
||||
// 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);
|
||||
nq = spg_get_ir_reciprocal_mesh(grid_point, map, mesh, shift, is_time_reversal, latvec, pos, attyp, num_atom, symprec);
|
||||
|
||||
wt = memory->create(wt, nq, "QMesh:wt");
|
||||
qpts = memory->create(qpts, nq,3,"QMesh:qpts");
|
||||
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++){
|
||||
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.;
|
||||
for (int iq = 0; iq < nq; ++iq) wt[iq] = 0.;
|
||||
numq = 0;
|
||||
for (int i=0; i<num_grid; i++){
|
||||
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]);
|
||||
|
|
@ -1054,8 +868,8 @@ void Phonon::QMesh()
|
|||
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;
|
||||
for (int iq = 0; iq < nq; ++iq) wsum += wt[iq];
|
||||
for (int iq = 0; iq < nq; ++iq) wt[iq] /= wsum;
|
||||
|
||||
}
|
||||
#endif
|
||||
|
|
@ -1078,7 +892,7 @@ void Phonon::ldos_egv()
|
|||
if (nmax < 1) return;
|
||||
|
||||
memory->destroy(locals);
|
||||
locals = memory->create(locals, nmax, "ldos_egv:locals");
|
||||
memory->create(locals, nmax, "ldos_egv:locals");
|
||||
|
||||
nlocal = 0;
|
||||
ptr = strtok(str," \t\n\r\f");
|
||||
|
|
@ -1091,7 +905,7 @@ void Phonon::ldos_egv()
|
|||
if (nlocal < 1) return;
|
||||
|
||||
printf("Local PDOS for atom(s):");
|
||||
for (int i=0; i<nlocal; i++) printf(" %d", locals[i]);
|
||||
for (int i = 0; i < nlocal; ++i) printf(" %d", locals[i]);
|
||||
printf(" will be computed.\n");
|
||||
|
||||
fmin = 0.; fmax = 10.;
|
||||
|
|
@ -1118,14 +932,14 @@ void Phonon::ldos_egv()
|
|||
memory->destroy(dos);
|
||||
memory->destroy(ldos);
|
||||
|
||||
dos = memory->create(dos, ndos,"ldos_egv:dos");
|
||||
ldos = memory->create(ldos,nlocal,ndos,sysdim,"ldos_egv: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 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.;
|
||||
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;
|
||||
|
|
@ -1137,7 +951,7 @@ void Phonon::ldos_egv()
|
|||
doublecomplex **egvec = dynmat->DM_q;
|
||||
|
||||
printf("\nNow to compute the phonons and DOSs "); fflush(stdout);
|
||||
for (int iq=0; iq<nq; iq++){
|
||||
for (int iq = 0; iq < nq; ++iq){
|
||||
if ((iq+1)%nprint == 0) {printf("."); fflush(stdout);}
|
||||
|
||||
dynmat->getDMq(qpts[iq], &wt[iq]);
|
||||
|
|
@ -1145,14 +959,14 @@ void Phonon::ldos_egv()
|
|||
|
||||
dynmat->geteigen(&egval[0], 1);
|
||||
|
||||
for (int idim=0; idim<ndim; idim++){
|
||||
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++){
|
||||
for (int ilocal = 0; ilocal < nlocal; ++ilocal){
|
||||
int ipos = locals[ilocal]*sysdim;
|
||||
for (int jdim=0; jdim<sysdim; jdim++){
|
||||
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;
|
||||
|
|
@ -1179,6 +993,33 @@ void Phonon::ldos_egv()
|
|||
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.
|
||||
|
|
@ -1188,24 +1029,24 @@ 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];
|
||||
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;
|
||||
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++){
|
||||
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];
|
||||
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;
|
||||
for (int i = 0; i < ndos; ++i) ldos[ilocal][i][idim] *= sum;
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -1225,9 +1066,9 @@ void Phonon::ComputeAll()
|
|||
printf("\nNow to compute the phonons "); fflush(stdout);
|
||||
// now to calculate the frequencies at all q-points
|
||||
memory->destroy(eigs);
|
||||
eigs = memory->create(eigs, nq,ndim,"QMesh_eigs");
|
||||
memory->create(eigs, nq,ndim,"QMesh_eigs");
|
||||
|
||||
for (int iq=0; iq<nq; iq++){
|
||||
for (int iq = 0; iq < nq; ++iq){
|
||||
if ((iq+1)%nprint == 0) {printf("."); fflush(stdout);}
|
||||
|
||||
dynmat->getDMq(qpts[iq], &wt[iq]);
|
||||
|
|
@ -1246,7 +1087,7 @@ int Phonon::count_words(const char *line)
|
|||
{
|
||||
int n = strlen(line) + 1;
|
||||
char *copy;
|
||||
copy = memory->create(copy, n, "count_words:copy");
|
||||
memory->create(copy, n, "count_words:copy");
|
||||
strcpy(copy,line);
|
||||
|
||||
char *ptr;
|
||||
|
|
|
|||
|
|
@ -43,6 +43,8 @@ private:
|
|||
void DMdisp();
|
||||
void vecanyq();
|
||||
|
||||
void ShowCell();
|
||||
|
||||
void smooth(double *, const int);
|
||||
void writeDOS();
|
||||
void writeLDOS();
|
||||
|
|
|
|||
|
|
@ -1,5 +1,7 @@
|
|||
#include "timer.h"
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
* Initialization of time
|
||||
* -------------------------------------------------------------------------- */
|
||||
Timer::Timer()
|
||||
{
|
||||
flag = 0;
|
||||
|
|
@ -7,6 +9,9 @@ Timer::Timer()
|
|||
return;
|
||||
}
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
* public function, start the timer
|
||||
* -------------------------------------------------------------------------- */
|
||||
void Timer::start()
|
||||
{
|
||||
t1 = clock();
|
||||
|
|
@ -15,6 +20,9 @@ void Timer::start()
|
|||
return;
|
||||
}
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
* public function, stop the timer
|
||||
* -------------------------------------------------------------------------- */
|
||||
void Timer::stop()
|
||||
{
|
||||
if ( flag&1 ) {
|
||||
|
|
@ -24,6 +32,9 @@ void Timer::stop()
|
|||
return;
|
||||
}
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
* public function, print the total time used after timer stops
|
||||
* -------------------------------------------------------------------------- */
|
||||
void Timer::print()
|
||||
{
|
||||
if ( (flag&3) != 3) return;
|
||||
|
|
@ -34,6 +45,9 @@ void Timer::print()
|
|||
return;
|
||||
}
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
* public function, return the total time used up to now, in seconds
|
||||
* -------------------------------------------------------------------------- */
|
||||
double Timer::elapse()
|
||||
{
|
||||
if ( (flag&3) != 3) return 0.;
|
||||
|
|
|
|||
|
|
@ -1 +1 @@
|
|||
#define VERSION 75
|
||||
#define VERSION 7
|
||||
|
|
|
|||
Loading…
Reference in New Issue