Commit a3a3a5c2 authored by Doak, Peter W's avatar Doak, Peter W
Browse files

Merge branch 'master' of code.ornl.gov:CNMS/CNMS_Computing_Resources

parents e50400e8 67a2be52
### IPythonNotebook template
# Temporary data
.ipynb_checkpoints/
### Python template
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
*.so
# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
*.egg-info/
.installed.cfg
*.egg
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*,cover
.hypothesis/
# Translations
*.mo
*.pot
# Django stuff:
*.log
local_settings.py
# Flask instance folder
instance/
# Scrapy stuff:
.scrapy
# Sphinx documentation
docs/_build/
# PyBuilder
target/
# IPython Notebook
.ipynb_checkpoints
# pyenv
.python-version
# celery beat schedule file
celerybeat-schedule
# dotenv
.env
# virtualenv
venv/
ENV/
# Spyder project settings
.spyderproject
# Rope project settings
.ropeproject
### CMake template
CMakeCache.txt
CMakeFiles
CMakeScripts
Makefile
cmake_install.cmake
install_manifest.txt
### C template
# Object files
*.o
*.ko
*.obj
*.elf
# Precompiled Headers
*.gch
*.pch
# Libraries
*.lib
*.a
*.la
*.lo
# Shared objects (inc. Windows DLLs)
*.dll
*.so.*
*.dylib
# Executables
*.exe
*.out
*.app
*.i*86
*.x86_64
*.hex
# Debug files
*.dSYM/
### C++ template
# Compiled Object files
*.slo
# Fortran module files
*.mod
# Compiled Static libraries
*.lai
*.x
*.pyc
a.out
.idea/
.svn/
.hg/
*.d
*.png
*_0*
*.gz
*.eps
GPATH
GTAGS
GRTAGS
*.s
*.ii
# emacs
*~
\#*\#
.\#*
This source diff could not be displayed because it is too large. You can view the blob instead.
This source diff could not be displayed because it is too large. You can view the blob instead.
#!/bin/bash
#PBS -S /bin/bash
#PBS -m be
#PBS -M youremail@ornl.gov
#PBS -N sample_job
#PBS -M your_email
#PBS -N abinit_t23
#PBS -q batch
#PBS -l nodes=2:ppn=32
#PBS -l nodes=1:ppn=32:hw32
#PBS -l walltime=4:00:00
#PBS -l naccesspolicy=singlejob
#PBS -W group_list=cades-cnms
#PBS -l qos=condo
#PBS -l naccesspolicy=singlejob
export OMP_NUM_THREADS=1
cd $PBS_O_WORKDIR
module load env/cades-cnms
module load abinit/8.0.8
#this can be useful to see from outside shells
cat $PBS_NODEFILE >pbs_nodefile
printenv
cat $PBS_NODEFILE > pbs_nodefile
#VASP runs including significant communication especially for SCALAPACK run
#slower than they should. Refrain from using more than ~1 cpu per atom
#past 64 or 128 cores LSCALAPACK=.FALSE.
module load env/cades-cnms
module load vasp
mpirun -np 2 -x OMP_NUM_THREADS=1 $ABINIT_MPI_FLAGS $ABINIT < in 2>&1 >out
mpirun -v --report-bindings ${VASP_MPI_FLAGS} $VASP 2>&1 >vasp_out
t23.in
t23.out
t23i
t23o
t23
./13al.pspnc
./33as.pspnc
\ No newline at end of file
# CrystallIne AlAs
# first two runs are for calculation of ground state at finite electric field
# the third run performs response calculations of phonon-type perturbation (q=0) and
# electric-field-type perturbation
ndtset 3
# Dataset #1 ground state calculation *************
kptopt1 1
toldfe1 1.0d-10
nband1 4
berryopt1 -1
rfdir1 1 1 1
# Dataset #2 ground state in electric field *******
nband2 4
kptopt2 2
berryopt2 4
toldfe2 1.0d-13
getwfk2 1
efield2 0.6d-3 0.0 0.0
# Dataset #3 Response-function calculation
rfphon3 1
rfatpol3 1 2
rfdir3 1 1 1
nqpt3 1
kptopt3 3
berryopt3 4
toldfe3 1.0d-8
getwfk3 2
nsym3 1
efield3 0.6d-3 0.0 0.0
qpt3 0.0 0.0 0.0
prtwf3 0
rfelfd3 3
#Common input variables
acell 3*10.62
rprim 0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
#Definition of the atom types
ntypat 2
znucl 13 33
natom 2
typat 1 2
xred
0.0 0.0 0.0
0.25 0.25 0.25
nband 4
ixc 1
ecut 2.0
ngkpt 2 2 2
nbdbuf 0
nshiftk 1
shiftk 0.5 0.5 0.5
chksymbreak 0 # For historical reasons: actually, the k point grid should be changed,
nstep 100
diemac 9.0
## After modifying the following section, one might need to regenerate the pickle database with runtests.py -r
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
#%% [files]
#%% files_to_test =
#%% t23.out, tolnlines = 0, tolabs = 2.000e-07, tolrel = 2.000e-07, fld_options = -easy
#%% psp_files = 13al.pspnc, 33as.pspnc
#%% [paral_info]
#%% max_nprocs = 2
#%% [extra_info]
#%% authors = X. Wang
#%% keywords = NC, DFPT, FAILS_IFMPI
#%% description =
#%% AlAs in Zincblende structure.
#%% Test calculation of the Born effective charge and dielectric constant
#%% tensor at finite electric fields.
#%% The first dataset is for normal ground-state calculation at zero electric field.
#%% The second dataset is for ground-state calculation at finite electric field.
#%% The final datasetis the linear-response calculation at finite electric field.
#%%<END TEST_INFO>
#!/bin/bash
#PBS -S /bin/bash
#PBS -m be
#PBS -M your_email@ornl.gov
#PBS -N NiO110_bulk
#PBS -q batch
#PBS -l nodes=2:ppn=32:hw32
#PBS -l walltime=00:30:00
#PBS -W group_list=cades-cnms
#PBS -l qos=condo
#PBS -l naccesspolicy=singlejob
export OMP_NUM_THREADS=1
cd $PBS_O_WORKDIR
module load env/cades-cnms
module load espresso
printenv
cat $PBS_NODEFILE > pbs_nodefile
mpirun -x OMP_NUM_THREADS=1 $PWSCF_MPI_FLAGS $PWSCF -npool 4 -in in 2>&1 >out
&control
prefix = 'NiO110_bulk',
calculation = 'relax',
restart_mode = 'from_scratch',
forc_conv_thr = 1.0D-4
wf_collect = .true.,
nstep = 2
tstress = .false.,
tprnfor = .false.,
outdir = './',
wfcdir = './',
pseudo_dir = '/software/user_tools/current/cades-cnms/for_nti/QE_pseudo'
disk_io = 'low'
/
&system
ibrav = 0
nat = 16
nbnd = 93
ntyp = 3
nspin = 2
starting_magnetization(1) = 2
starting_magnetization(2) =-2
starting_magnetization(3) = 0
input_dft = 'pbe'
occupations = 'smearing'
smearing = 'gaussian'
degauss = 0.001
lda_plus_u = .TRUE.
lda_plus_u_kind = 0
Hubbard_U(1) = 5.4
Hubbard_U(2) = 5.4
Hubbard_U(3) = 0
U_projection_type = 'pseudo'
ecutwfc = 60.D0
ecutrho = 480.D0
/
&electrons
electron_maxstep = 100
conv_thr = 1.0d-10
mixing_mode = 'plain'
mixing_beta = 0.3
diagonalization = 'david'
/
&ions
ion_dynamics = 'bfgs'
/
CELL_PARAMETERS angstrom
8.408000 0.000000 0.000000
0.000000 5.945354 0.000000
0.000000 0.000000 2.972677
ATOMIC_SPECIES
NiU 1.00 Ni.pbe-n-kjpaw_psl.0.1.UPF
NiD 1.00 Ni.pbe-n-kjpaw_psl.0.1.UPF
O 1.00 O.pbe-n-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS (angstrom)
NiD 0.000000000 2.972676908 0.000000000
O 2.101999997 2.972676908 0.000000000
O 0.000000000 4.459015362 1.486338454
NiD 2.101999997 4.459015362 1.486338454
O 0.000000000 1.486338454 1.486338454
NiU 2.101999997 1.486338454 1.486338454
NiU 0.000000000 0.000000000 0.000000000
O 2.101999997 0.000000000 0.000000000
NiU 4.203999993 2.972676908 0.000000000
O 6.305999989 2.972676908 0.000000000
O 4.203999993 4.459015362 1.486338454
NiU 6.305999989 4.459015362 1.486338454
O 4.203999993 1.486338454 1.486338454
NiD 6.305999989 1.486338454 1.486338454
NiD 4.203999993 0.000000000 0.000000000
O 6.305999989 0.000000000 0.000000000
K_POINTS automatic
2 4 8 0 0 0
......@@ -4,7 +4,7 @@
#PBS -M youremail@ornl.gov
#PBS -N sample_job
#PBS -q batch
#PBS -l nodes=1:ppn=32
#PBS -l nodes=1:ppn=32:hw32
#PBS -l walltime=0:10:00
#PBS -l naccesspolicy=singlejob
#PBS -W group_list=cades-cnms
......
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
or-pbs-c72.ornl.gov
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
to continue trajectories of 500hex*
mkdir file_test
. ./convert_ot2nt.sh
qsub run.sh
#!/bin/bash
for file in 500hex*bmc
do
python ./ot2nt.py $file cont_${file}
done
import re
import sys
with open(sys.argv[1],'r') as fin:
with open(sys.argv[2],'w') as fout:
for i in range(5):
fout.write(fin.readline())
fout.write("\"temperature: \"273.15\n")
fin.readline()
fin.readline()
fout.write(fin.readline())
line = fin.readline()
# while True:
# match = re.search("Tick",line)
# if match is not None:
# fout.write(line)
# break
# line = fin.readline()
while len(line) > 0:
match = re.search("^\s*$",line)
if match is None:
match = re.search("(\d+\s+[-\.\dEe]+\s+[-\.\dEe]+\s+[-\.\dEe]+)",line)
if match is None:
fout.write(line)
else:
fout.write("{} false false\n".format(match.group(1)))
line = fin.readline()
#!/bin/bash
#PBS -S /bin/bash
#PBS -m be
#PBS -M doakpw@ornl.gov
#PBS -N netlogo_test
#PBS -q batch
#PBS -l nodes=1:ppn=32:hw32
#PBS -l walltime=48:00:00
#PBS -l naccesspolicy=singlejob
#PBS -W group_list=cades-cnms
#PBS -l qos=condo
export OMP_NUM_THREADS=1
cd $PBS_O_WORKDIR
#this can be useful to see from outside shells
cat $PBS_NODEFILE >pbs_nodefile
module load env/cades-cnms
. $SOFTWARECNMS/spack/share/spack/setup-env.sh
spack load jdk
module load NetLogo/5.3.1
#each of these () surrounded commands launches in a subshell
(java -Xms8g -Xmx16g -Dfile.encoding=UTF-8 -Dnetlogo.extensions.dir=$NETLOGOROOT/app/extensions -classpath $NETLOGOROOT/app/NetLogo.jar org.nlogo.headless.Main --model ./BMC_SelfAssembler.nlogo --experiment experiment1 2>&1 >out1) &
(java -Xms8g -Xmx16g -Dfile.encoding=UTF-8 -Dnetlogo.extensions.dir=$NETLOGOROOT/app/extensions -classpath $NETLOGOROOT/app/NetLogo.jar org.nlogo.headless.Main --model ./BMC_SelfAssembler.nlogo --experiment experiment2 2>&1 >out2) &
(java -Xms8g -Xmx16g -Dfile.encoding=UTF-8 -Dnetlogo.extensions.dir=$NETLOGOROOT/app/extensions -classpath $NETLOGOROOT/app/NetLogo.jar org.nlogo.headless.Main --model ./BMC_SelfAssembler.nlogo --experiment experiment3 3>&1 >out3) &
(java -Xms8g -Xmx16g -Dfile.encoding=UTF-8 -Dnetlogo.extensions.dir=$NETLOGOROOT/app/extensions -classpath $NETLOGOROOT/app/NetLogo.jar org.nlogo.headless.Main --model ./BMC_SelfAssembler.nlogo --experiment experiment4 4>&1 >out4) &
(java -Xms8g -Xmx16g -Dfile.encoding=UTF-8 -Dnetlogo.extensions.dir=$NETLOGOROOT/app/extensions -classpath $NETLOGOROOT/app/NetLogo.jar org.nlogo.headless.Main --model ./BMC_SelfAssembler.nlogo --experiment experiment5 5>&1 >out5) &
# (java -Xms64g -Xmx128g -Dfile.encoding=UTF-8 -Dnetlogo.extensions.dir=$NETLOGOROOT/app/extensions -classpath $NETLOGOROOT/app/NetLogo.jar org.nlogo.headless.Main --model /software/user_tools/current/cades-cnms/epd_work/NetlogoBMCPackage/behavior-test.nlogo --experiment experiment2 2>&1 >out2) &
#wait for all subshells to complete
wait
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment