# !!! NOTE !!!
# This script DOES NOT automatically start running
# the batch scripts. It only generates the input files
# and batch scripts which the user runs by themselves
# !!! NOTE !!!
import pyemto
import os
import numpy as np
# It is recommended to always use absolute paths
folder = os.getcwd() # Get current working directory.
latpath = "/wrk/hpleva/structures" # Folder where the structure output files are.
emtopath = folder + "/cocrfemnni_fcc" # Folder where the calculations will be performed.
cocrfemnni = pyemto.System(folder=emtopath)
sws = np.linspace(2.50, 2.70,
11) # 11 different volumes from 2.5 Bohr to 2.7 Bohr
# Set KGRN and KFCD values using a for loop.
# Use write_input_file functions to write input files to disk:
for i in range(len(sws)):
cocrfemnni.bulk(
lat='fcc',
jobname='cocrfemnni',
latpath=latpath,
atoms=['Co', 'Co', 'Cr', 'Cr', 'Fe', 'Fe', 'Mn', 'Mn', 'Ni', 'Ni'],
splts=[-1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0],
sws=sws[i],
#which_mode = 'analyze'
folder = os.getcwd() # Get current working directory.
emtopath = folder + "/ti_hcp" # Folder where the calculation take place.
latpath = emtopath # Folder where the structure files are located.
ncpu = 16
slurm_options = [
'#SBATCH -n {0}'.format(ncpu), '#SBATCH --ntasks-per-node=4',
'##SBATCH --qos=short', 'ulimit -s unlimited',
'module load compiler/intel/16 intel-mkl/16 openmpi/2.0',
'export OMP_NUM_THREADS=${SLURM_NTASKS_PER_NODE}',
'export OMP_STACKSIZE=400m'
]
ti_hcp = pyemto.System(
folder=emtopath, EMTOdir='/home/minds/jianwang/vasptool/EMTO/5.8.1/build')
# Initialize the bulk system using the bulk() function:
ti_hcp.bulk(
lat='hcp',
latpath=latpath,
atoms=['Ti'],
sws=3.0,
amix=0.02,
efmix=0.9,
#expan='M',
sofc='Y',
xc='P07', # Use PBEsol
nky=31, # k-points
nkz=19, # k-points
runtime='24:00:00', # Allow large enough timelimit for SLURM
#!/usr/bin/python
# Test the functionality of the Bmdl, Kstr and Shape classes
import pyemto
import os
import numpy as np
# It is recommended to use absolute paths
folder = os.getcwd()
latpath = folder
emtopath = folder
structure = pyemto.System(folder=emtopath)
# Create BMDL, KSTR and SHAPE files and run them
#deltas = np.linspace(0.0,0.05,6)
structure.lattice.set_values(latpath=latpath,
kappaw=[0.0, -20.0]) # Double Taylor-expansion
#dmaxs = [2.52,2.49,2.455,2.43,2.4,2.4] # Orthorhombic distortion for c/a = 1.603
#dmaxs = [2.51,2.51,2.51,2.49,2.51,2.49] # Monoclinic distortion for c/a = 1.603
#jobnames = ['bcco0','bcco1','bcco2','bcco3','bcco4','bcco5'] # bcc ortho
#jobnames = ['bccm0','bccm1','bccm2','bccm3','bccm4','bccm5'] # bcc mono
#jobnames = ['fcco0','fcco1','fcco2','fcco3','fcco4','fcco5'] # fcc ortho
#jobnames = ['fccm0','fccm1','fccm2','fccm3','fccm4','fccm5'] # fcc mono
if not os.path.lexists(apath):
os.makedirs(apath)
# Construct base jobname
jobname = ""
for i in range(len(nlist)):
if jobname == "":
pass
else:
jobname = jobname + "_"
jobname = jobname + nlist[i].lower() + "%4.2f" % (clist[i])
finalname = jobname + "_final"
# BCC first
alloy = pyemto.System(folder=apath)
initialsws = initial_sws[0] # We need some clever way to get this
alloy.bulk(lat='bcc',
jobname=jobname + "_bcc",
atoms=s,
concs=c,
latpath=latpath,
sws=initialsws,
xc='PBE')
swsrange = np.linspace(initialsws - 0.1, initialsws + 0.1,
7) # A list of 7 different volumes
#alloy.lattice_constants_batch_generate(sws=swsrange)
sws0, B0, e0 = alloy.lattice_constants_analyze(sws=swsrange, prn=False)
sc_res.append([e0, B0, sws0])
alloy.bulk(lat='bcc',
jobname=finalname + "_bcc",
# Copy QNA parameter file to each folder
os.system("cp ./QNA_database.dat {0}".format(apath))
# Construct base jobname
jobname = ""
for i in range(len(nlist)):
if jobname == "":
pass
else:
jobname = jobname + "_"
jobname = jobname + nlist[i].lower() + "%4.2f" % (clist[i])
# BCC first
alloy = pyemto.System(folder=apath, EMTOdir=EMTOdir)
initialsws = initial_sws[0]
alloy.bulk(lat='bcc',
jobname=jobname + "_bcc",
latpath=latpath,
msgl=0,
sws=initialsws,
atoms=s,
concs=c,
splts=split,
afm=afm,
amix=0.02,
efmix=0.9,
expan='M',
sofc='Y',
xc='PBE',
#!/usr/bin/python
# An example script of how to automatically
# calculate the equilibrium volume and
# bulk modulus of bulk bcc Fe using pyEMTO.
import os
import pyemto
emtopath = os.getcwd(
) + "/fe" # Define a folder for our KGRN and KFCD input and output files.
latpath = os.getcwd(
) + "/fe" # Define a folder where the BMDL, KSTR and KFCD input and output files
# will be located.
fe = pyemto.System(
folder=emtopath) # Create a new instance of the pyemto System-class.
# Let's calculate the equilibrium volume and bulk modulus of Fe.
# Initialize the system using the bulk.() function:
fe.bulk(
lat='bcc', # We want to use the bcc structure.
latpath=latpath, # Path to the folder where the structure files are located.
afm='F', # We want to do a ferromagnetic calculation.
atoms=['Fe'], # A list of atoms.
splts=[2.0], # A list of magnetic splittings.
expan='M', # We want to use the double-Taylor expansion.
sofc='Y', # We want to use soft-core approximation.
xc='PBE', # We want to use the PBE functional.
amix=0.05, # Density mixing.