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Interface with BoltzTraP
Date: 2022/10/30 03:17
Name: Wiwik   <wiwikfis@gmail.com>

Dear Prof. T. Ozaki and Openmx developers,


I want to study calculate the thermoelectric properties of Si using the interface with BoltzTraP.
I have done the SCF calculation using an input &#64257;le fSi_BoltzTraP.datf which is available in the directory fwork.

After the SCF calculation &#64257;nishes normally, I obtain the 14 &#64257;les i.e. fSi_BoltzTraP_rstf, eresult.stdf, fSi_BoltzTraP.bulk.xyzf, 'Si_BoltzTraP.ciff, fSi_BoltzTraP.dat#f, fSi_BoltzTraP.dden.cubef, fSi_BoltzTraP.enef, fSi_BoltzTraP.mdf, fSi_BoltzTraP.md2f, fSi_BoltzTraP.outf, fSi_BoltzTraP.tden.cubef, fSi_BoltzTraP.v0.cubef, fSi_BoltzTraP.vhart.cubef, and fSi_BoltzTraP.xyzf.

Then, I copy MX TRAP.sh which is stored in the directory fsourcef to the directory fwork'. After that, I can perform MX TRAP.sh as follows:
% sh MX_TRAP.sh

Then, the name of the 'out' files in the directory is listed as may be shown below.
-e =========================Output List================================
Si_BoltzTraP.out
-e =================================================================
Please enter the outputfile name; outputfile name = Si_BoltzTraP.out


When I press the enter key, the following message will be displayed:
..
c..
Nospin::kloop kx ky kz:1050/1050
grep: kloop=1050$: No such file or directory
grep: kloop=1050$: No such file or directory
Nospin::kloop kx ky kz:1686/1686
grep: kloop=1050$: No such file or directory
grep: kloop=1686$: No such file or directory
grep: kloop=1686$: No such file or directory
grep: kloop=1686$: No such file or directory
grep: kloop=1051$: No such file or directory
grep: kloop=1687$: No such file or directory
..
c.
cat: Si_BoltzTraP.energy_1: No such file or directory
cat: Si_BoltzTraP.energy_2: No such file or directory
..
...
cat: Si_BoltzTraP.energy_8: No such file or directory
touch: invalid option -- 'e'
Try 'touch --help' for more information.
cat: Si_BoltzTraP.energydammy: No such file or directory
rm: invalid option -- 'e'
Try 'rm --help' for more information.
touch: invalid option -- 'e'
Try 'touch --help' for more information.
sed: -e expression #1, char 1: unknown command: `S'
sed: -e expression #1, char 1: unknown command: `S'
-e .energy file for BoltzTraP has been generated.
touch: invalid option -- 'e'
Try 'touch --help' for more information.
grep: Atoms.UnitVectors.Unit: No such file or directory
MX_TRAP.sh: 2730: [: =: unexpected operator
sed: -e expression #1, char 1: unknown command: `S'
-e .struct file for BoltzTraP has been generated.

touch: invalid option -- 'e'
Try 'touch --help' for more information.
touch: invalid option -- 'e'
Try 'touch --help' for more information.
grep: scf.ElectronicTemperature: No such file or directory
grep: scf.ElectronicTemperature: No such file or directory
grep: ^\s*$: No such file or directory
rm: invalid option -- 'e'
Try 'rm --help' for more information.
-e .intrans file for BoltzTraP has been generated.

-e Conversion has been finished.

-e Directory is -e Si_BoltzTraP
..
c.

After the above message is displayed, I obtain the &#64257;les i.e. -e Si_BoltzTraP.energy, -e Si_BoltzTraP.energy_1, e Si_BoltzTraP.energy_2, e Si_BoltzTraP.energy_3, e Si_BoltzTraP.energy_4, e Si_BoltzTraP.energy_5, e Si_BoltzTraP.energy_6, e Si_BoltzTraP.energy_7, e Si_BoltzTraP.energy_8, e Si_BoltzTraP.intrans, e Si_BoltzTraP.intrans_, and -e Si_BoltzTraP.struct in the directory.

I just did the calculations up to this step. Is my calculation step wrong or incomplete?
Thanks,

Sincerely,
Wiwik
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Page: [1]

Re: Interface with BoltzTraP ( No.1 )
Date: 2022/10/30 06:10
Name: Yung-Ting Lee

Dear Wiwik,

Please try the following command:
$ bash MX_TRAP.sh

Best regards,
YTL
e
Re: Interface with BoltzTraP ( No.2 )
Date: 2022/10/30 12:57
Name: Wiwik  <wiwikfis@gmail.com>

Dear Yung-Ting Lee

Thank you very much for your kind and fast reply.
I appreciate a lot.


I have tried the following command:
$ bash MX_TRAP.sh


a directory named 'Si BoltzTraP' is created, and 4 files such as 'Si_BoltzTraP.out', 'Si_BoltzTraP.energy', 'Si_BoltzTraP.intrans', 'Si_BoltzTraP.struct' will be stored in the directory.


Then I move to the directory 'Si BoltzTraP', copy compiler 'BoltzTraP' from folder 'src' and paste to the directory 'Si BoltzTraP'

and then I calculate with command as follow
% /home/fismatel1/boltztrap-1.2.5/src/x-trans BoltzTraP

where /home/fismatel1/boltztrap-1.2.5/src is the path of compiler 'BoltzTraP'.


The following message will be displayed:
bash: /home/fismatel1/boltztrap-1.2.5/src/x-trans: No such files or directory


Is my calculation step or command wrong or incomplete?
Thanks for your reply,


Sincerely,
Wiwik
e
Re: Interface with BoltzTraP ( No.3 )
Date: 2022/10/31 02:35
Name: Yung-Ting Lee

Dear Wiwik,

(1) Following the reply, I guess that what you need to do is
(a) go to your "Si BoltzTraP" (after the calculation),
(b) type in "% /home/fismatel1/boltztrap-1.2.5/src/x-trans BoltzTraP" (after the BoltzTrap2 compilation), and then
(c) check outputs.


(2) My simple note is listed below for your reference.

https://drive.google.com/file/d/1gVg3t5woeBBXwLwwFOnRfaVjan52GGCl/view

It includes (a) how to compile the BoltzTrap2, (b) outputs of the Si example in OpenMX, and (c) how to perform BoltzTrap2 to calculate the thermal conductivity of the Si example. The result is the same as the data in the OpenMX official document ( http://www.openmx-square.org/openmx_man3.9/node204.html ).


Best regards,
YTL

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Re: Interface with BoltzTraP ( No.4 )
Date: 2022/10/31 15:51
Name: Wiwik  <wiwikfis@gmail.com>

Dear Yung-Ting Lee


Thank you very much for your kind and fast reply.
I appreciate a lot.


I have tried to compile the BoltzTrap2 and the following message will be displayed:
make: 'BoltzTraP' is up to date


Then, I tried the following command:
% /home/fismatel1/boltztrap-1.2.5/src/x-trans BoltzTraP

the following message will be displayed:
set: Variable name must begin with a letter


Is my calculation step or command wrong or incomplete?
Thanks for your reply,


Sincerely,
Wiwik
e
Re: Interface with BoltzTraP ( No.5 )
Date: 2022/11/01 00:03
Name: Yung-Ting Lee

(1) %cd "Si BoltzTraP"
(2) %/home/fismatel1/boltztrap-1.2.5/src/x-trans BoltzTraP

Best regards,
YTL
e
Re: Interface with BoltzTraP ( No.6 )
Date: 2022/11/02 14:49
Name: Wiwik  <wiwikfis@gmail.com>

Dear Yung-Ting Lee


Thank you very much for your kind and fast reply.
I appreciate a lot.

I have tried the following command:
(1) %cd "Si BoltzTraP"
(2) %/home/fismatel1/boltztrap-1.2.5/src/x-trans BoltzTraP

the following message will be displayed:
set: Variable name must begin with a letter.


Then, I tried the following command:
%./BoltzTraP

the following message will be displayed:
================== BoltzTraP vs 1.2.5 ========================
STOP GTFNAM - Exactly one commandline argument has to be given.


Is the openmx-BoltzTraP calculation supposed to get the Si_BoltzTraP.def file?
because I saw that in the calculation with quantum expresso-BoltzTraP appears the Si_BoltzTraP.def file
so that the calculation in boltztrap is successful.

Thanks for your reply,

Sincerely,
Wiwik
e
Re: Interface with BoltzTraP ( No.7 )
Date: 2022/11/02 16:36
Name: Masanobu Miyata  <m-miyata@jaist.ac.jp>

Dear Wiwik,

This is Miyata. I'm the creator of the BoltzTraP interface program.
I apologize for any inconvenience caused.
I just read the forum a few minutes ago, so I have not been able to pinpoint the cause of the problem. It looks like it is probably not an interface problem, but a problem with the BoltzTraP installation environment.
I will address this issue shortly.
Thank you in advance for your patience.


Dear Yung-Ting Lee,

Thank you very much for your help on my behalf.

Best regards,
Miyata
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Re: Interface with BoltzTraP ( No.8 )
Date: 2022/11/02 17:15
Name: Yung-Ting Lee  <ytl821@gmail.com>

Dear Wiwik,

Problem about "set: Variable name must begin with a letter." may come from csh.
Maybe csh is required.

For Ubuntu-20.04 OS to install csh:
sudo apt-get install csh


Dear Miyata san,

Thanks for your help.

Best regards,
YTL
e
Re: Interface with BoltzTraP ( No.9 )
Date: 2022/11/02 19:05
Name: Masanobu Miyata  <m-miyata@jaist.ac.jp>

Dear Wiwik,

Hi.

I would like to check if BoltzTraP has been successfully installed.

In the Makefile in /home/fismatel1/boltztrap-1.2.5/src, did you specified the lapack library?

For example
LIBS = -L/home/fismatel1/lapack-*. *. * -llapack -lrefblas
(lapack-*. *. * depends on the version of Lapack)


Also, when you refer to the BoltzTraP library as follows, is the library correctly specified?

cd /home/fismatel1/boltztrap-1.2.5/src
ldd BoltzTraP

Best regards,
Miyata
e
Re: Interface with BoltzTraP ( No.10 )
Date: 2022/11/04 13:35
Name: Wiwik  <wiwikfis@gmail.com>

Dear Miyata and Yung-Ting Lee


Thank you very much for your kind and fast reply.
I appreciate a lot.

In the Makefile in /home/fismatel1/boltztrap-1.2.5/src, I just specified that FC and LIBS as follows:
FC = gfortran
LIBS = -llapack -lblas


The make file in /home/fismatel1/boltztrap-1.2.5/src as may be shown below:

SHELL = /bin/sh

# gfortran
FC = gfortran
#FC = gfortran-mp-4.5

FOPT = -g -march=native -funroll-loops -O3 -ffast-math -fgcse-lm -fgcse-sm -ffast-math -ftree-vectorize -fexternal-blas
#FOPT += -g -p -pg -Wall -fbounds-check -finit-integer=-666 -finit-real=nan
#LDFLAGS =
LIBS = -llapack -lblas

# ifort
#FC = ifort
#FOPT = -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML

#LDFLAGS = -L/opt/intel/mkl/10.0.1.014/lib/32/ -Vaxlib -static-libcxa -pthread
#LIBS = -lmkl_lapack -lmkl_ia32 -lguide
# ifort bis: other mkl options
#LDFLAGS = $(FOPT) -L/opt/intel/mkl/10.0.1.014/lib/32 -pthread -i-static
#LIBS = -lmkl_lapack -lmkl -lguide
#LDFLAGS = $(FOPT) -L/cluster/intel/Compiler/11.1/046/mkl/lib/em64t -pthread -i-static
#LIBS = -lmkl_lapack -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lguide

# generic
LINKER = $(FC)
LFLAGS = -g #-pg
FGEN =
DESTDIR = .

EXECNAME = BoltzTraP

###############################################################################

FFLAGS = $(FGEN) $(FOPT)
EXEC = $(DESTDIR)/$(EXECNAME)

#..............................................................................
#
# Object files common to both REAL and COMPLEX type subroutines
#
OBJS = gmlib2.o reallocate.o \
m_bandstructure.o m_input.o m_fermimod.o \
m_interfaces.o \
latgen2.o generic_field.o gtfnam.o gen_lattpoints.o \
BoltzTraP.o crystal_band.o wien_band.o phon_band.o generic_band.o pw_interface.o \
add_inv.o bandana.o stern1.o kdelta.o fite4.o sortag.o gplbands.o \
dos.o ifflim.o setfft.o c3fft.o boseintegrals.o fermiintegrals.o bands.o kcomp.o \
bz.o fermisurface.o setfft2.o write_dx_fs.o write_dx_bz.o write_cube_fs.o \
dos_histogram.o dos_tetra.o noculc.o dosvv.o readvv.o \
phonondrag.o
#OBJS = \
# reallocate.o defs.o modules.o broad.o add_inv.o \
# c3fft.o gtfnam.o ifflim.o mknam.o read_energy.o \
# transport.o stern.o kdelta.o gen_lattpoints.o fite4.o setfft.o \
# starfkt2.o dos.o

$(EXEC): $(OBJS)
$(LINKER) $(LFLAGS) -o $(EXEC) $(OBJS) $(LDFLAGS) $(LIBS) $(LFLAGS)


clean:
rm -f *.o *.mod *.pc *.pcl *~

.SUFFIXES: .F90 .o
.F90.o:
$(FC) $(FFLAGS) -c $<



Is my make file wrong or incomplete? is there anything to change?


Thanks for your reply,

Sincerely,
Wiwik
e
Re: Interface with BoltzTraP ( No.11 )
Date: 2022/11/04 15:53
Name: Masanobu Miyata  <m-miyata@jaist.ac.jp>

Dear Wiwik,

Hi.

It seems to me that the lapack library is not specified.

In my explanation, I will use the following notation for commands and their results.
>command name
Result



(0) Put the boltztrap-1.2.5 folder and the installed lapack folder in the same directory. I installed and use lapack-3.10.0. (https://netlib.org/lapack/lapack-3.10.0.html) For the purpose of this explanation, I assume that you install in the home directory.


>pwd
/home
>ls -c -d */
lapack-3.10.0/ boltztrap-1.2.5/


(1) After installing Lapack, rewrite the contents of "boltztrap-1.2.5/src/Makefile" as follows

>cd boltztrap-1.2.5/src
Open the Makefile with an editor and rewrite it as follows


LIBS = -llapack -lblas

LIBS = -L/home/lapack-3.10.0 -llapack -lblas

(2) Clean up the src folder.
>pwd
/home/boltztrap-1.2.5/src

>make clean
rm -f *.o *.mod *.pc *.pcl *~

If there are old versions of BoltzTraP files, delete them.
>rm BoltzTraP

(3) When ready, run the following in the src directory.

>pwd
/home/boltztrap-1.2.5/src

>make
gfortran -g -march=native -funroll-loops -O3 -ffast-math -fgcse-lm -fgcse-sm -ffast-math -ftree-vectorize -fexternal-blas -c gmlib2.F90
gfortran -g -march=native -funroll-loops -O3 -ffast-math -fgcse-lm -fgcse-sm -ffast-math -ftree-vectorize -fexternal-blas -c reallocate.F90
gfortran -g -march=native -funroll-loops -O3 -ffast-math -fgcse-lm -fgcse-sm -ffast-math -ftree-vectorize -fexternal-blas -c m_bandstructure.F90
EEEE
gfortran -g -o . /BoltzTraP gmlib2.o reallocate.o m_bandstructure.o m_input.o m_fermimod.o m_interfaces.o latgen2.o generic_field.o gtfnam.o gen_lattpoints.o BoltzTraP.o crystal_band.o wien_band.o phon_band.o generic_band.o pw_interface.o add_inv.o bandana.o stern1.o kdelta.o fite4.o sortag.o gplbands.o dos.o ifflim.o setfft.o c3fft.o boseintegrals.o fermiintegrals.o bands.o kcomp.o bz.o fermisurface.o setfft2.o write_dx_fs.o write_dx_bz.o write_cube_fs.o dos_histogram.o dos_tetra.o noculc.o dosvv.o readvv.o phonondrag.o -L/home/lapack-3.10.0 -llapack -lblas -g

(4) After installation, a file named BoltzTraP will be generated in the src folder.

(5) Copy Si_BoltzTraP.out and MX_TRAP.sh to the BoltzTraP tests directory.
>cp Si_BoltzTraP.out /home/boltztrap-1.2.5/tests

>cp MX_TRAP.sh /home/boltztrap-1.2.5/tests


(6)Execute MX_TRAP.sh.

>pwd
/home/boltztrap-1.2.5/tests

>bash MX_TRAP.sh
Please enter the outputfile name ; Outputfile name = Si_BoltzTraP.out
Si_BoltzTraPrm: cannot remove 'Si_BoltzTraP.energy': No such file or directory
SpinPolarization is colliner
Please wait. Generating .energy file ...
rm: cannot remove 'Si_BoltzTraP.energy': No such file or directory
Nospin::kloop kx ky kz:421/630
Nospin::kloop kx ky kz:211/420
Nospin::kloop kx ky kz:841/1050
EEEEE
.energy file for BoltzTraP has been generated.

.struct file for BoltzTraP has been generated.

.intrans file for BoltzTraP has been generated.

Conversion has been finished.

Directory is Si_BoltzTraP

(7) Move to the directory and execute BoltzTraP.

>cd /home/boltztrap-1.2.5/tests/Si_BoltzTraP

>ls
Si_BoltzTraP.energy Si_BoltzTraP.intrans Si_BoltzTraP.out Si_BoltzTraP.struct

>/home/boltztrap-1.2.5/src/x_trans BoltzTraP
================ BoltzTraP vs 1.2.5 =============
34.9u 0.9s 1:23.82 42.8% 0+0k 8128+11712io 18pf+0w


Please try them.

@



e
Re: Interface with BoltzTraP ( No.12 )
Date: 2022/11/11 15:22
Name: Wiwik  <wiwikfis@gmail.com>

Dear Miyata,


Thank you very much for your kind, systematic and fast reply.
I really appreciate.

I have successfully calculated the thermoelectric properties of Si using the interface with BoltzTraP.
So I have obtained graphs of seebeck coefficient vs chemical potential and sigma vs chemical potential.


Once again, Thanks for your reply.



Sincerely,
Wiwik

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