参照先
quantumespresso:wannier90:srvo3 [雑多な記録]
www2.yukawa.kyoto-u.ac.jp
$ pwd
~/q-e
$ mkdir SrVO3
$ cd SrVO3/
$ touch SrVO3.scf.in
$ cat SrVO3.scf.in
&CONTROL
calculation = 'scf',
wf_collect = .true.,
prefix = 'SrVO3',
verbosity = 'high'
outdir = './tmp/',
pseudo_dir = './pseudo/',
/
&SYSTEM
ibrav = 1
A = 3.8409
nat = 5
ntyp = 3
ecutwfc = 100
occupations = "tetrahedra_opt"
/
&ELECTRONS
conv_thr = 1d-8,
/
ATOMIC_SPECIES
Sr 87.6200 Sr.pbesol-spn-kjpaw_psl.1.0.0.UPF
V 50.9415 V.pbesol-spnl-kjpaw_psl.1.0.0.UPF
O 15.9994 O.pbesol-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS alat
Sr 0.000000000000000 0.000000000000000 0.000000000000000
V 0.500000000000000 0.500000000000000 0.500000000000000
O 0.000000000000000 0.500000000000000 0.500000000000000
O 0.500000000000000 0.000000000000000 0.500000000000000
O 0.500000000000000 0.500000000000000 0.000000000000000
K_POINTS automatic
6 6 6 0 0 0$ touch SrVO3.bands.in
$ cat SrVO3.bands.in
&CONTROL
calculation = 'bands',
prefix = 'SrVO3',
wf_collect = .true.,
verbosity = 'high'
outdir = './tmp/',
pseudo_dir = './pseudo/',
/
&SYSTEM
ibrav = 1
A = 3.8409
nat = 5
ntyp = 3
ecutwfc = 100
occupations = "tetrahedra_opt"
/
&ELECTRONS
conv_thr = 1d-8,
/
ATOMIC_SPECIES
Sr 87.6200 Sr.pbesol-spn-kjpaw_psl.1.0.0.UPF
V 50.9415 V.pbesol-spnl-kjpaw_psl.1.0.0.UPF
O 15.9994 O.pbesol-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS alat
Sr 0.000000000000000 0.000000000000000 0.000000000000000
V 0.500000000000000 0.500000000000000 0.500000000000000
O 0.000000000000000 0.500000000000000 0.500000000000000
O 0.500000000000000 0.000000000000000 0.500000000000000
O 0.500000000000000 0.500000000000000 0.000000000000000
K_POINTS automatic
8 8 8 0 0 0
!K_POINTS crystal_b
!6
! 0.5 0.5 0.0 20
! 0.0 0.0 0.0 20
! 0.5 0.0 0.0 20
! 0.5 0.5 0.0 20
! 0.5 0.5 0.5 20
! 0.0 0.0 0.0 0$ touch bands.in
$ cat bands.in
&bands
prefix = 'SrVO3',
outdir = './tmp/',
filband = 'bands.dat',
/$ mpirun -n 4 ~/q-e/bin/pw.x < SrVO3.scf.in > SrVO3.scf.out
$ mpirun -n 4 ~/q-e/bin/pw.x < SrVO3.bands.in > SrVO3.bands.out
$ mpirun -n 4 ~/q-e/bin/bands.x < bands.in > bands.out
$ sudo apt-get install intel-mkl
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
The following additional packages will be installed:
libllvm14 libmkl-avx libmkl-avx2 libmkl-avx512 libmkl-avx512-mic libmkl-computational-dev libmkl-core libmkl-def
libmkl-dev libmkl-gf-ilp64 libmkl-gf-lp64 libmkl-gnu-thread libmkl-intel-ilp64 libmkl-intel-lp64 libmkl-intel-thread
libmkl-interface-dev libmkl-locale libmkl-mc libmkl-mc3 libmkl-meta-computational libmkl-meta-interface
libmkl-meta-threading libmkl-pgi-thread libmkl-rt libmkl-sequential libmkl-tbb-thread libmkl-threading-dev
libmkl-vml-avx libmkl-vml-avx2 libmkl-vml-avx512 libmkl-vml-avx512-mic libmkl-vml-cmpt libmkl-vml-def libmkl-vml-mc
libmkl-vml-mc2 libmkl-vml-mc3 libomp-14-dev libomp-dev libomp5-14 libtbb2-dev pkg-config
Suggested packages:
intel-mkl-doc libomp-14-doc libtbb2-doc
The following NEW packages will be installed:
intel-mkl libllvm14 libmkl-avx libmkl-avx2 libmkl-avx512 libmkl-avx512-mic libmkl-computational-dev libmkl-core
libmkl-def libmkl-dev libmkl-gf-ilp64 libmkl-gf-lp64 libmkl-gnu-thread libmkl-intel-ilp64 libmkl-intel-lp64
libmkl-intel-thread libmkl-interface-dev libmkl-locale libmkl-mc libmkl-mc3 libmkl-meta-computational
libmkl-meta-interface libmkl-meta-threading libmkl-pgi-thread libmkl-rt libmkl-sequential libmkl-tbb-thread
libmkl-threading-dev libmkl-vml-avx libmkl-vml-avx2 libmkl-vml-avx512 libmkl-vml-avx512-mic libmkl-vml-cmpt
libmkl-vml-def libmkl-vml-mc libmkl-vml-mc2 libmkl-vml-mc3 libomp-14-dev libomp-dev libomp5-14 libtbb2-dev
pkg-config
0 upgraded, 42 newly installed, 0 to remove and 21 not upgraded.
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Setting up libmkl-meta-threading:amd64 (2020.4.304-2ubuntu3) ...
Setting up libmkl-rt:amd64 (2020.4.304-2ubuntu3) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/libmkl_rt.so to provide /usr/lib/x86_64-linux-gnu/libblas64.so.3 (libblas64.so.3-x86_64-linux-gnu) in auto mode
update-alternatives: using /usr/lib/x86_64-linux-gnu/libmkl_rt.so to provide /usr/lib/x86_64-linux-gnu/liblapack64.so.3 (liblapack64.so.3-x86_64-linux-gnu) in auto mode
Setting MKL as default BLAS/LAPACK implementation as requested.
update-alternatives: using /usr/lib/x86_64-linux-gnu/libmkl_rt.so to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in manual mode
update-alternatives: using /usr/lib/x86_64-linux-gnu/libmkl_rt.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in manual mode
Setting up libmkl-threading-dev:amd64 (2020.4.304-2ubuntu3) ...
Setting up libmkl-interface-dev:amd64 (2020.4.304-2ubuntu3) ...
Setting up libmkl-dev:amd64 (2020.4.304-2ubuntu3) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/libmkl_rt.so to provide /usr/lib/x86_64-linux-gnu/libblas64.so (libblas64.so-x86_64-linux-gnu) in auto mode
update-alternatives: using /usr/lib/x86_64-linux-gnu/libmkl_rt.so to provide /usr/lib/x86_64-linux-gnu/liblapack64.so (liblapack64.so-x86_64-linux-gnu) in auto mode
Setting MKL as default BLAS/LAPACK implementation as requested.
update-alternatives: using /usr/lib/x86_64-linux-gnu/libmkl_rt.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in manual mode
update-alternatives: using /usr/lib/x86_64-linux-gnu/libmkl_rt.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in manual mode
Setting up intel-mkl:amd64 (2020.4.304-2ubuntu3) ...
Processing triggers for man-db (2.10.2-1) ...
Processing triggers for libc-bin (2.35-0ubuntu3.8) ...$ source /opt/intel/oneapi/setvars.sh
:: initializing oneAPI environment ...
-bash: BASH_VERSION = 5.1.16(1)-release
args: Using "$@" for setvars.sh arguments:
:: advisor -- latest
:: ccl -- latest
:: compiler -- latest
:: dal -- latest
:: debugger -- latest
:: dev-utilities -- latest
:: dnnl -- latest
:: dpcpp-ct -- latest
:: dpl -- latest
:: ipp -- latest
:: ippcp -- latest
:: mkl -- latest
:: mpi -- latest
:: tbb -- latest
:: vtune -- latest
:: oneAPI environment initialized ::
$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/mkl/lib/intel64
$ mpirun -n 4 ~/q-e/bin/pw.x < SrVO3.scf.in > SrVO3.scf.out
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Abort(1) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
Abort(1) on node 3 (rank 3 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
$ cat SrVO3.scf.out
Program PWSCF v.7.3.1 starts on 25Jul2024 at 15:15:29
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Parallel version (MPI), running on 4 processors
MPI processes distributed on 1 nodes
6143 MiB available memory on the printing compute node when the environment starts
Waiting for input...
Reading input from standard input
Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 40000
Max angular momentum in pseudopotentials (lmaxx) = 4
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine readpp (1):
file ./pseudo/Sr.pbesol-spn-kjpaw_psl.1.0.0.UPF not found
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
$ cd ../pseudo/
$ wget https://pseudopotentials.quantum-espresso.org/upf_files/Sr.pbesol-spn-kjpaw_psl.1.0.0.UPF
--2024-07-25 15:18:56-- https://pseudopotentials.quantum-espresso.org/upf_files/Sr.pbesol-spn-kjpaw_psl.1.0.0.UPF
Resolving pseudopotentials.quantum-espresso.org (pseudopotentials.quantum-espresso.org)... 51.77.118.191
Connecting to pseudopotentials.quantum-espresso.org (pseudopotentials.quantum-espresso.org)|51.77.118.191|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1956161 (1.9M)
Saving to: 'Sr.pbesol-spn-kjpaw_psl.1.0.0.UPF'
Sr.pbesol-spn-kjpa 100%[================>] 1.87M 367KB/s in 5.4s
2024-07-25 15:19:03 (352 KB/s) - 'Sr.pbesol-spn-kjpaw_psl.1.0.0.UPF' saved [1956161/1956161]
$ wget https://www.quantum-espresso.org/upf_files/V.pbesol-spnl-kjpaw_psl.1.0.0.UPF
--2024-07-25 15:33:39-- https://www.quantum-espresso.org/upf_files/V.pbesol-spnl-kjpaw_psl.1.0.0.UPF
Resolving www.quantum-espresso.org (www.quantum-espresso.org)... 51.77.118.191
Connecting to www.quantum-espresso.org (www.quantum-espresso.org)|51.77.118.191|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: / [following]
--2024-07-25 15:33:42-- https://www.quantum-espresso.org/
Reusing existing connection to www.quantum-espresso.org:443.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/html]
Saving to: 'V.pbesol-spnl-kjpaw_psl.1.0.0.UPF'
V.pbesol-spnl-kjpa [ <=> ] 208.69K 184KB/s in 1.1s
2024-07-25 15:33:44 (184 KB/s) - 'V.pbesol-spnl-kjpaw_psl.1.0.0.UPF' saved [213701]
$ wget https://pseudopotentials.quantum-espresso.org/upf_files/V.pbesol-spnl-kjpaw_psl.1.0.0.UPF
--2024-07-25 15:45:23-- https://pseudopotentials.quantum-espresso.org/upf_files/V.pbesol-spnl-kjpaw_psl.1.0.0.UPF
Resolving pseudopotentials.quantum-espresso.org (pseudopotentials.quantum-espresso.org)... 51.77.118.191
Connecting to pseudopotentials.quantum-espresso.org (pseudopotentials.quantum-espresso.org)|51.77.118.191|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1802374 (1.7M)
Saving to: 'V.pbesol-spnl-kjpaw_psl.1.0.0.UPF.1'
V.pbesol-spnl-kjpa 100%[================>] 1.72M 210KB/s in 8.9s
2024-07-25 15:45:33 (198 KB/s) - 'V.pbesol-spnl-kjpaw_psl.1.0.0.UPF.1' saved [1802374/1802374]
$ wget https://pseudopotentials.quantum-espresso.org/upf_files/O.pbesol-n-kjpaw_psl.1.0.0.UPF
--2024-07-25 15:53:17-- https://pseudopotentials.quantum-espresso.org/upf_files/O.pbesol-n-kjpaw_psl.1.0.0.UPF
Resolving pseudopotentials.quantum-espresso.org (pseudopotentials.quantum-espresso.org)... 51.77.118.191
Connecting to pseudopotentials.quantum-espresso.org (pseudopotentials.quantum-espresso.org)|51.77.118.191|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 875308 (855K)
Saving to: 'O.pbesol-n-kjpaw_psl.1.0.0.UPF'
O.pbesol-n-kjpaw_p 100%[================>] 854.79K 271KB/s in 3.2s
2024-07-25 15:53:21 (271 KB/s) - 'O.pbesol-n-kjpaw_psl.1.0.0.UPF' saved [875308/875308]
$ cd ../SrVO3/$ mpirun -n 4 ~/q-e/bin/pw.x < SrVO3.scf.in > SrVO3.scf.out
$ ls -CF
SrVO3.bands.in SrVO3.scf.in SrVO3.scf.out bands.in tmp/
$ tail SrVO3.scf.out
PAW_symme : 0.03s CPU 0.03s WALL ( 59 calls)
PWSCF : 47.61s CPU 50.26s WALL
This run was terminated on: 15:54:31 25Jul2024
=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
$ mpirun -n 4 ~/q-e/bin/pw.x < SrVO3.bands.in > SrVO3.bands.out
$ tail SrVO3.bands.out
PAW_pot : 0.31s CPU 0.36s WALL ( 1 calls)
PWSCF : 24.36s CPU 25.87s WALL
This run was terminated on: 15:59:57 25Jul2024
=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
$ mpirun -n 4 ~/q-e/bin/bands.x < bands.in > bands.out
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
$ tail bands.out
**************************************************************************
BANDS : 5.25s CPU 5.68s WALL
This run was terminated on: 16: 1: 8 25Jul2024
=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
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