update phana tool for USER-PHONON from github (7df8a630) · Commits · 郑智淋 / lammps

tools/phonon/Makefile

+26 −32

Original line number	Diff line number	Diff line
		.SUFFIXES : .o .cpp
		# compiler and flags
		CC = g++ -Wall
		LINK = $(CC)
		CC = g++ -Wno-unused-result
		LINK = $(CC) -static
		CFLAGS = -O3 $(DEBUG) $(UFLAG)
		#

		OFLAGS = -O3 $(DEBUG)
		INC = $(LPKINC) $(TCINC) $(SPGINC)
		LIB = $(LPKLIB) $(TCLIB) $(SPGLIB)
		#
		INC = $(LPKINC) $(TCINC) $(SPGINC) $(FFTINC)
		LIB = $(LPKLIB) $(TCLIB) $(SPGLIB) $(FFTLIB)

		# cLapack library needed
		LPKINC =
		LPKLIB =-llapack
		#
		#
		# spglib 1.8.2, used to get the irreducible q-points
		# if UFLAG is not set, spglib won't be used.
		LPKINC = -I/opt/clapack/3.2.1/include
		LPKLIB = -L/opt/clapack/3.2.1/lib -lclapack -lblas -lf2c -lm

		# Tricubic library needed
		TCINC = -I/opt/tricubic/1.0/include
		TCLIB = -L/opt/tricubic/1.0/lib -ltricubic

		# UFLAG = -DUseSPG
		# SPGINC = -I/opt/libs/spglib/1.8.2/include
		# SPGLIB = -L/opt/libs/spglib/1.8.2/lib -lsymspg
		# spglib, used to get the irreducible q-points
		# if SFLAG is not set, spglib won't be used.
		SFLAG = -DUseSPG
		SPGINC = -I/opt/spglib/1.9.7/include/spglib
		SPGLIB = -L/opt/spglib/1.9.7/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
		# FFTW 3， used to deduce the force constants in real space
		# if FFLAG is not set, fftw won't be used.
		FFLAG = -DFFTW3
		FFTINC = -I/opt/fftw/3.3.7/include
		FFTLIB = -L/opt/fftw/3.3.7/lib -lfftw3

		# Debug flags
		# DEBUG = -g -DDEBUG
		UFLAG = $(SFLAG) $(FFLAG)

		#====================================================================
		ROOT = phana
		# executable name
		@@ -44,7 +51,7 @@ clean:
		rm -f .o ~ *.mod ${EXE}

		tar:
		rm -f ${ROOT}.tar; tar -czvf ${ROOT}.tar.gz .cpp .h Makefile README
		rm -f ${ROOT}.tar.gz; tar -czvf ${ROOT}.tar.gz .cpp .h Makefile README

		ver:
		@echo "#define VERSION `git log\|grep '^commit'\|wc -l`" > version.h
		@@ -58,16 +65,3 @@ 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

+18 −9

Original line number	Diff line number	Diff line
		@@ -5,9 +5,13 @@
		analyse the phonon related information.
		#-------------------------------------------------------------------------------
		1. Dependencies
		The LAPACK library is needed to solve the eigen problems.
		http://www.netlib.org/lapack/
		Intel MKL can be used as well.
		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 now be obtained from:
		https://github.com/nbigaouette/libtricubic/

		The spglib is optionally needed, enabling one to evaluate the
		phonon density of states or vibrational thermal properties
		@@ -17,6 +21,12 @@
		It can be obtained from:
		http://spglib.sourceforge.net/

		FFTW 3 might also be needed if you would like to interface with
		phonopy: necessary input files for phonopy will be prepared so
		that you can make use of the functions provided by phonopy.
		FFTW 3 can be downloaded from:
		http://www.fftw.org

		2. Compilation
		To compile the code, one needs therefore to install the above
		libraries and set the paths correctly in the Makefile.
		@@ -26,17 +36,16 @@

		3. Unit system
		The units of the output frequencies by this code is THz for
		LAMMPS units "real", "si", "metal", and "cgs"; in these cases,
		the frequencies are $\nu$ instead of $\omega$.
		LAMMPS units "real", "si", "metal", "cgs", "micro", "nano";
		in these cases, the frequencies are $\nu$ instead of $\omega$.

		4. Updates
		For updates of phana, please check:
		http://nes.sjtu.edu.cn/english/research/software.htm
		or
		https://github.com/lingtikong/phana.git

		5. Bug report
		If any bug found, please drop a line to: konglt(at)sjtu.edu.cn

		#-------------------------------------------------------------------------------
		Author: Ling-Ti Kong, konglt(at)sjtu.edu.cn
		Oct 2015
		May 2020

tools/phonon/disp.cpp

+135 −2832

File changed.

Preview size limit exceeded, changes collapsed.

tools/phonon/dynmat.cpp

+568 −473

Original line number	Diff line number	Diff line
		@@ -3,12 +3,10 @@
		#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
		/* ----------------------------------------------------------------------------
		* Class DynMat stores the Dynamic Matrix read from the binary file from
		* fix-phonon and incorporates some operations w.r.t the DM.
		* ---------------------------------------------------------------------------- */
		DynMat::DynMat(int narg, char **arg)
		{
		attyp = NULL;
		@@ -69,42 +67,48 @@ DynMat::DynMat(int narg, char **arg)
		}

		// read header info from the binary file
		if ( fread(&sysdim, sizeof(int), 1, fp) != 1) {printf("\nError while reading sysdim from file: %s\n", binfile); fclose(fp); exit(2);}
		if ( fread(&nx, sizeof(int), 1, fp) != 1) {printf("\nError while reading nx from file: %s\n", binfile); fclose(fp); exit(2);}
		if ( fread(&ny, sizeof(int), 1, fp) != 1) {printf("\nError while reading ny from file: %s\n", binfile); fclose(fp); exit(2);}
		if ( fread(&nz, sizeof(int), 1, fp) != 1) {printf("\nError while reading nz from file: %s\n", binfile); fclose(fp); exit(2);}
		if ( fread(&nucell, sizeof(int), 1, fp) != 1) {printf("\nError while reading nucell from file: %s\n", binfile); fclose(fp); exit(2);}
		if ( fread(&boltz, sizeof(double), 1, fp) != 1) {printf("\nError while reading boltz from file: %s\n", binfile); fclose(fp); exit(2);}

		fftdim = sysdimnucell; fftdim2 = fftdimfftdim;
		if (fread(&sysdim, sizeof(int), 1, fp) != 1){
		printf("\nError while reading sysdim from file: %s\n", binfile);
		fclose(fp);
		exit(2);
		}
		if (fread(&nx, sizeof(int), 1, fp) != 1){
		printf("\nError while reading nx from file: %s\n", binfile);
		fclose(fp);
		exit(2);
		}
		if (fread(&ny, sizeof(int), 1, fp) != 1){
		printf("\nError while reading ny from file: %s\n", binfile);
		fclose(fp);
		exit(2);
		}
		if (fread(&nz, sizeof(int), 1, fp) != 1){
		printf("\nError while reading nz from file: %s\n", binfile);
		fclose(fp);
		exit(2);
		}
		if (fread(&nucell, sizeof(int), 1, fp) != 1){
		printf("\nError while reading nucell from file: %s\n", binfile);
		fclose(fp);
		exit(2);
		}
		if (fread(&boltz, sizeof(double), 1, fp) != 1){
		printf("\nError while reading boltz from file: %s\n", binfile);
		fclose(fp);
		exit(2);
		}

		fftdim = sysdim * nucell;
		fftdim2 = fftdim * fftdim;
		npt = nx * ny * nz;

		// display info related to the read file
		printf("\n"); for (int i = 0; i < 80; ++i) printf("="); printf("\n");
		printf("Dynamical matrix is read from file: %s\n", binfile);
		printf("The system size in three dimension: %d x %d x %d\n", nx, ny, nz);
		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");
		ShowInfo();
		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);
		}

		funit = new char[4];
		strcpy(funit, "THz");
		if (boltz == 1.){eml2f = 1.; delete funit; funit = new char[27]; strcpy(funit,"sqrt(epsilon/(m.sigma^2))");}
		else if (boltz == 0.0019872067) eml2f = 3.256576161;
		else if (boltz == 8.617343e-5) eml2f = 15.63312493;
		else if (boltz == 1.3806504e-23) eml2f = 1.;
		else if (boltz == 1.3806504e-16) eml2f = 1.591549431e-14;
		else {
		printf("WARNING: Because of float precision, I cannot get the factor to convert sqrt(E/ML^2)\n");
		printf("into THz, instead, I set it to be 1; you should check the unit used by LAMMPS.\n");
		eml2f = 1.;
		}
		Define_Conversion_Factor();

		// now to allocate memory for DM
		memory = new Memory();
		@@ -123,11 +127,31 @@ DynMat::DynMat(int narg, char **arg)
		memory->create(attyp, nucell, "DynMat:attyp");
		memory->create(M_inv_sqrt, nucell, "DynMat:M_inv_sqrt");

		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);}
		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);
		}
		fclose(fp);

		car2dir();
		@@ -158,7 +182,10 @@ DynMat::DynMat(int narg, char **arg)
		return;
		}

		// to destroy the class

		/* ----------------------------------------------------------------------------
		* Free the memories used.
		* ---------------------------------------------------------------------------- */
		DynMat::~DynMat()
		{
		// destroy all memory allocated
		@@ -172,7 +199,9 @@ DynMat::~DynMat()
		memory->destroy(basis);
		memory->destroy(DM_all);
		memory->destroy(M_inv_sqrt);
		if (memory) delete memory;
		delete memory;

		return;
		}

		/* ----------------------------------------------------------------------------
		@@ -209,6 +238,7 @@ void DynMat::writeDMq(double *q)
		}
		fprintf(fp,"\n");
		fclose(fp);

		return;
		}

		@@ -217,7 +247,6 @@ return;
		* ---------------------------------------------------------------------------- */
		void DynMat::writeDMq(double q, const double qr, FILE fp)
		{

		fprintf(fp, "%lg %lg %lg %lg ", q[0], q[1], q[2], qr);

		for (int i = 0; i < fftdim; ++i)
		@@ -235,9 +264,9 @@ return;
		int DynMat::geteigen(double *egv, int flag)
		{
		char jobz, uplo;
		long int n, lda, lwork, lrwork, *iwork, liwork, info;
		integer n, lda, lwork, lrwork, *iwork, liwork, info;
		doublecomplex *work;
		double w = &egv[0], rwork;
		doublereal w = &egv[0], rwork;

		n = fftdim;
		if (flag) jobz = 'V';
		@@ -276,6 +305,7 @@ return info;
		void DynMat::getDMq(double *q)
		{
		interpolate->execute(q, DM_q[0]);

		return;
		}

		@@ -344,8 +374,7 @@ 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;
		}

		@@ -408,11 +437,10 @@ void DynMat::EnforceASR()
		for (int i = 0; i < fftdim; ++i){
		printf("%lg ", egvs[i]);
		if (i%10 == 9) printf("\n");
		if (i == 99){ printf("...... (%d more skipped)", fftdim-100); break;}
		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;
		}
		@@ -464,7 +492,7 @@ return;
		* --------------------------------------------------------------------*/
		void DynMat::GaussJordan(int n, double *Mat)
		{
		int i,icol=0,irow=0,j,k,l,ll,idr,idc;
		int i,icol,irow,j,k,l,ll,idr,idc;
		int indxc,indxr,*ipiv;
		double big, nmjk;
		double dum, pivinv;
		@@ -591,7 +619,74 @@ void DynMat::ShowVersion()
		printf(" )___/ ) _ ( /(__)\\ ) ( /(__)\\ \n");
		printf(" (__) (_) (_)(__)(__)(_)\\_)(__)(__)\n");
		printf("\nPHonon ANAlyzer for Fix-Phonon, version 2.%02d, compiled on %s.\n", VERSION, __DATE__);
		printf("Reference: https://doi.org/10.1016/j.cpc.2011.04.019\n");

		return;
		}

		/* ----------------------------------------------------------------------------
		* Private method to define the conversion factor from the DM measured to THZ
		* for the phonon frequency and force constants.
		* ---------------------------------------------------------------------------- */
		void DynMat::Define_Conversion_Factor()
		{
		funit = new char[4];
		strcpy(funit, "THz");

		if (fabs(boltz - 1.) <= ZERO){ // LJ Unit
		eml2f = eml2fc = 1.;
		delete funit;
		funit = new char[27];
		strcpy(funit,"sqrt(epsilon/(m.sigma^2))");

		} else if (fabs(boltz - 0.0019872067) <= ZERO){ // real
		eml2f = 3.255487031;
		eml2fc = 0.0433641042418;

		} else if (fabs(boltz*1.e3 - 8.617343e-2) <= ZERO){ // metal
		eml2f = 15.633304237154924;
		eml2fc = 1.;

		} else if (fabs(boltz*1.e20 - 1.3806504e-3) <= ZERO){ // si
		eml2f = 1.591549431e-13;
		eml2fc = 0.06241509074460763;

		} else if (fabs(boltz*1.e13 - 1.3806504e-3) <= ZERO){ // cgs
		eml2f = 1.591549431e-13;
		eml2fc = 6.241509074460763e-05;

		} else if (fabs(boltz*1.e3 - 3.16681534e-3) <= ZERO){ // electron
		eml2f = 154.10792761319672;
		eml2fc = 97.1736242922823;

		} else if (fabs(boltz*1.e5 - 1.3806504e-3) <= ZERO){ // micro
		eml2f = 1.5915494309189532e-07;
		eml2fc = 6.241509074460763e-05;

		} else if (fabs(boltz - 0.013806504) <= ZERO){ // nano
		eml2f = 0.0001591549431;
		eml2fc = 6.241509074460763e-05;

		} else {
		printf("WARNING: Perhaps because of float precision, I cannot get the factor to convert\n");
		printf("sqrt(E/ML^2)/(2*pi) into THz, instead, I set it to 1; you should check the unit\nused by LAMMPS.\n");
		eml2f = eml2fc = 1.;
		}
		return;
		}

		/* ----------------------------------------------------------------------------
		* Private method to output the information read
		* ---------------------------------------------------------------------------- */
		void DynMat::ShowInfo()
		{
		printf("\n"); for (int i = 0; i < 80; ++i) printf("="); printf("\n");
		printf("Dynamical matrix is read from file: %s\n", binfile);
		printf("The system size in three dimension: %d x %d x %d\n", nx, ny, nz);
		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");
		return;
		}
		/* --------------------------------------------------------------------*/

tools/phonon/dynmat.h

+5 −5

Original line number	Diff line number	Diff line
		@@ -7,8 +7,6 @@
		#include "memory.h"
		#include "interpolate.h"

		using namespace std;

		class DynMat {
		public:

		@@ -17,7 +15,7 @@ public:

		int nx, ny, nz, nucell;
		int sysdim, fftdim;
		double eml2f;
		double eml2f, eml2fc;
		char *funit;

		void getDMq(double *);
		@@ -30,7 +28,9 @@ public:
		doublecomplex **DM_q;

		int flag_latinfo;
		int npt, fftdim2;
		double Tmeasure, basevec[9], ibasevec[9];
		double *M_inv_sqrt;
		double **basis;
		int *attyp;

		@@ -40,14 +40,12 @@ private:
		Interpolate *interpolate;

		Memory *memory;
		int npt, fftdim2;

		int nasr;
		void EnforceASR();

		char binfile, dmfile;
		double boltz, q[3];
		double *M_inv_sqrt;

		doublecomplex **DM_all;

		@@ -56,6 +54,8 @@ private:
		void GaussJordan(int, double *);

		void help();
		void ShowInfo();
		void ShowVersion();
		void Define_Conversion_Factor();
		};
		#endif

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