Example scripts¶
Copy-paste the text blocks below and save them as .py files to try them out.
Ground state volume of bcc bulk iron¶
#!/usr/bin/python
# An example script of how to automatically
# calculate the equilibrium volume and
# bulk modulus of bulk bcc Fe using pyEMTO.
import pyemto
emtopath = "/wrk/hpleva/pyEMTO_examples/fe" # Define a folder for our KGRN and KFCD input and output files.
latpath = "/wrk/hpleva/structures" # 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.
nky = 21) # Number of k-points.
sws = [2.6,2.62,2.64,2.66,2.68,2.70] # A list of Wigner-Seitz radii
# Generate all the necessary input files with this function:
#fe.lattice_constants_batch_generate(sws=sws)
#The newly created batch scripts are then submitted by hand.
# Analyze the results using this function once all the calculations
# have finished:
#fe.lattice_constants_analyze(sws=sws)
# This function combines the features of the previous two:
fe.lattice_constants_batch_calculate(sws=sws)
The output of this script should look like this:
Submitted batch job 1021841
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*****lattice_constants_analyze*****
********************************
lattice_constants_analyze(cubic)
********************************
SWS Energy
2.600000 -2545.605517
2.620000 -2545.606394
2.640000 -2545.606680
2.660000 -2545.606435
2.680000 -2545.605705
2.700000 -2545.604616
5.2.2015 -- 16:21:13
JOBNAM = fe1.00 -- PBE
Using morse function
Chi squared = 2.7459052408e-10
Reduced Chi squared = 1.3729526204e-10
R squared = 0.999907593903
morse parameters:
a = 0.117551
b = -122.663728
c = 32000.491593
lambda = 2.370150
Ground state parameters:
V0 = 2.640005 Bohr^3 (unit cell volume)
= 2.640005 Bohr (WS-radius)
E0 = -2545.606678 Ry
Bmod = 195.204183 GPa
Grun. param. = 3.128604
sws Einp Eout Residual err (% * 10**6)
2.600000 -2545.605517 -2545.605515 0.000002 -0.000870
2.620000 -2545.606394 -2545.606400 -0.000006 0.002524
2.640000 -2545.606680 -2545.606678 0.000002 -0.000950
2.660000 -2545.606435 -2545.606426 0.000009 -0.003632
2.680000 -2545.605705 -2545.605716 -0.000011 0.004368
2.700000 -2545.604616 -2545.604612 0.000004 -0.001440
lattice_constants_analyze(cubic):
sws0 = 2.640005
B0 = 195.204183
E0 = -2545.606678
Elastic constants of bcc bulk iron¶
#!/usr/bin/python
# An example script showing how to automatically calculate
# the elastic constants of bulk bcc Fe using pyEMTO.
import pyemto
emtopath = "/wrk/hpleva/pyEMTO_examples/fe_elastic_constants" # Define a folder for our KGRN and KFCD input and output files.
latpath = "/wrk/hpleva/structures" # 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 elastic constants of Fe.
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) # Mixing parameter.
sws0 = 2.64 # Eq. WS-radius that we computed previously.
B0 = 195 # Eq. bulk modulus.
# Generate all the necessary input files with this function:
#fe.elastic_constants_batch_generate(sws=sws0)
#The newly created batch scripts are then submitted by hand.
# Analyze the results using this function once all the calculations
# have finished:
#fe.elastic_constants_analyze(sws=sws,bmod=B0)
# This function combines the features of the previous two:
fe.elastic_constants_batch_calculate(sws=sws0,bmod=B0)
The output of this script should look like this:
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***cubic_elastic_constants***
fe1.00
c11(GPa) = 299.60
c12(GPa) = 142.70
c44(GPa) = 105.95
c' (GPa) = 78.45
B (GPa) = 195.00
Voigt average:
BV(GPa) = 195.00
GV(GPa) = 94.95
EV(GPa) = 245.07
vV(GPa) = 0.29
Reuss average:
BR(GPa) = 195.00
GR(GPa) = 92.92
ER(GPa) = 240.55
vR(GPa) = 0.29
Hill average:
BH(GPa) = 195.00
GH(GPa) = 93.93
EH(GPa) = 242.81
vH(GPa) = 0.29
Elastic anisotropy:
AVR(GPa) = 0.01
Ground state volume and elastic constants of hcp bulk titanium¶
#!/usr/bin/python
# This script will automatically accomplish:
# 1. Calculate the equilibrium volume and bulk modulus of hcp Ti.
# 2. Calculate the elastic constants of hcp Ti.
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 files are located.
emtopath = folder+"/ti_hcp" # Folder where the calculation take place.
ti_hcp=pyemto.System(folder=emtopath)
# 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
sws = np.linspace(2.9,3.1,7) # A list of 7 different volumes from 2.9 to 3.1
sws0,ca0,B0,e0,R0,cs0 = ti_hcp.lattice_constants_batch_calculate(sws=sws)
ti_hcp.elastic_constants_batch_calculate(sws=sws0,bmod=B0,ca=ca0,R=R0,cs=cs0)
# If the batch jobs are submitted by hand use these functions.
# To evaluate the results, comment out the _generate functions
# and uncomment the _analyze functions.
ti_hcp.lattice_constants_batch_generate(sws=sws)
#ti_hcp.lattice_constants_analyze(sws=sws)
# Results. These are inputed to the elastic_constants functions.
#sws0 = 3.002260
#ca0 = 1.610122
#B0 = 115.952318
#E0 = -1705.738844
#R0 = 0.019532
#cs0 = 498.360422
#ti_hcp.elastic_constants_batch_generate(sws=sws0,ca=ca0)
#ti_hcp.elastic_constants_analyze(sws=sws0,bmod=B0,ca=ca0,R=R0,cs=cs0)
The output of this script should look like this:
Submitted batch job 1021973
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*****lattice_constants_analyze*****
******************************
lattice_constants_analyze(hcp)
******************************
SWS Energy0 c'a0
2.900000 -1705.733796 1.613939
2.933333 -1705.736608 1.612527
2.966667 -1705.738262 1.611196
3.000000 -1705.738843 1.610175
3.033333 -1705.738424 1.609326
3.066667 -1705.737080 1.608336
3.100000 -1705.734889 1.607505
5.2.2015 -- 18:51:51
JOBNAM = ti1.00 -- P07
Using morse function
Chi squared = 1.16375610448e-11
Reduced Chi squared = 3.87918701493e-12
R squared = 0.999999464309
morse parameters:
a = 0.757678
b = -15.168890
c = 75.921091
lambda = 0.767287
Ground state parameters:
V0 = 3.002260 Bohr^3 (unit cell volume)
= 3.002260 Bohr (WS-radius)
E0 = -1705.738844 Ry
Bmod = 115.952318 GPa
Grun. param. = 1.151798
sws Einp Eout Residual err (% * 10**6)
2.900000 -1705.733796 -1705.733796 0.000000 -0.000275
2.933333 -1705.736608 -1705.736609 -0.000001 0.000498
2.966667 -1705.738262 -1705.738263 -0.000001 0.000376
3.000000 -1705.738843 -1705.738842 0.000001 -0.000810
3.033333 -1705.738424 -1705.738423 0.000001 -0.000680
3.066667 -1705.737080 -1705.737082 -0.000002 0.001450
3.100000 -1705.734889 -1705.734889 0.000001 -0.000558
5.2.2015 -- 18:51:51
JOBNAM = ti1.00 -- P07
Using morse function
Chi squared = 1.06749728331e-10
Reduced Chi squared = 3.5583242777e-11
R squared = 0.999995355882
morse parameters:
a = 0.748045
b = -15.100334
c = 76.203651
lambda = 0.769114
Ground state parameters:
V0 = 3.005849 Bohr^3 (unit cell volume)
= 3.005849 Bohr (WS-radius)
E0 = -1705.736830 Ry
Bmod = 114.888885 GPa
Grun. param. = 1.155920
sws Einp Eout Residual err (% * 10**6)
2.900000 -1705.731449 -1705.731449 -0.000000 0.000021
2.933333 -1705.734368 -1705.734369 -0.000001 0.000770
2.966667 -1705.736134 -1705.736130 0.000004 -0.002260
3.000000 -1705.736814 -1705.736815 -0.000001 0.000665
3.033333 -1705.736497 -1705.736503 -0.000006 0.003550
3.066667 -1705.735275 -1705.735268 0.000007 -0.004035
3.100000 -1705.733178 -1705.733180 -0.000002 0.001288
5.2.2015 -- 18:51:51
JOBNAM = ti1.00 -- P07
Using morse function
Chi squared = 3.64530335255e-11
Reduced Chi squared = 1.21510111752e-11
R squared = 0.999998386204
morse parameters:
a = 0.743238
b = -15.271044
c = 78.441514
lambda = 0.775451
Ground state parameters:
V0 = 3.004114 Bohr^3 (unit cell volume)
= 3.004114 Bohr (WS-radius)
E0 = -1705.737897 Ry
Bmod = 116.104730 GPa
Grun. param. = 1.164771
sws Einp Eout Residual err (% * 10**6)
2.900000 -1705.732644 -1705.732643 0.000001 -0.000875
2.933333 -1705.735527 -1705.735531 -0.000004 0.002534
2.966667 -1705.737255 -1705.737252 0.000003 -0.001704
3.000000 -1705.737891 -1705.737890 0.000001 -0.000729
3.033333 -1705.737524 -1705.737524 -0.000000 0.000183
3.066667 -1705.736229 -1705.736231 -0.000002 0.001216
3.100000 -1705.734082 -1705.734081 0.000001 -0.000625
5.2.2015 -- 18:51:51
JOBNAM = ti1.00 -- P07
Using morse function
Chi squared = 1.18175890217e-11
Reduced Chi squared = 3.93919634056e-12
R squared = 0.999999463488
morse parameters:
a = 0.759517
b = -15.168958
c = 75.737639
lambda = 0.766269
Ground state parameters:
V0 = 3.003084 Bohr^3 (unit cell volume)
= 3.003084 Bohr (WS-radius)
E0 = -1705.738555 Ry
Bmod = 115.894284 GPa
Grun. param. = 1.150586
sws Einp Eout Residual err (% * 10**6)
2.900000 -1705.733423 -1705.733423 -0.000000 0.000259
2.933333 -1705.736267 -1705.736265 0.000002 -0.001035
2.966667 -1705.737944 -1705.737946 -0.000002 0.001386
3.000000 -1705.738551 -1705.738550 0.000001 -0.000391
3.033333 -1705.738157 -1705.738156 0.000001 -0.000679
3.066667 -1705.736836 -1705.736837 -0.000001 0.000606
3.100000 -1705.734664 -1705.734664 0.000000 -0.000147
5.2.2015 -- 18:51:51
JOBNAM = ti1.00 -- P07
Using morse function
Chi squared = 5.45131762039e-12
Reduced Chi squared = 1.81710587346e-12
R squared = 0.999999749818
morse parameters:
a = 0.772765
b = -15.129144
c = 74.049208
lambda = 0.759794
Ground state parameters:
V0 = 3.002465 Bohr^3 (unit cell volume)
= 3.002465 Bohr (WS-radius)
E0 = -1705.738834 Ry
Bmod = 115.954728 GPa
Grun. param. = 1.140627
sws Einp Eout Residual err (% * 10**6)
2.900000 -1705.733769 -1705.733768 0.000001 -0.000320
2.933333 -1705.736585 -1705.736586 -0.000001 0.000827
2.966667 -1705.738247 -1705.738246 0.000001 -0.000325
3.000000 -1705.738832 -1705.738831 0.000001 -0.000454
3.033333 -1705.738419 -1705.738419 0.000000 -0.000175
3.066667 -1705.737081 -1705.737082 -0.000001 0.000791
3.100000 -1705.734892 -1705.734891 0.000001 -0.000345
5.2.2015 -- 18:51:52
JOBNAM = ti1.00 -- P07
Using morse function
Chi squared = 1.19109949001e-11
Reduced Chi squared = 3.97033163337e-12
R squared = 0.999999449336
morse parameters:
a = 0.745414
b = -15.182081
c = 77.304565
lambda = 0.773045
Ground state parameters:
V0 = 3.002133 Bohr^3 (unit cell volume)
= 3.002133 Bohr (WS-radius)
E0 = -1705.738728 Ry
Bmod = 115.798751 GPa
Grun. param. = 1.160392
sws Einp Eout Residual err (% * 10**6)
2.900000 -1705.733697 -1705.733697 0.000000 -0.000064
2.933333 -1705.736504 -1705.736504 0.000000 -0.000199
2.966667 -1705.738150 -1705.738152 -0.000002 0.001152
3.000000 -1705.738728 -1705.738726 0.000002 -0.001245
3.033333 -1705.738305 -1705.738305 0.000000 -0.000241
3.066667 -1705.736961 -1705.736963 -0.000002 0.000983
3.100000 -1705.734771 -1705.734770 0.000001 -0.000387
5.2.2015 -- 18:51:52
JOBNAM = ti1.00 -- P07
Using morse function
Chi squared = 1.38286217253e-11
Reduced Chi squared = 4.60954057509e-12
R squared = 0.999999356009
morse parameters:
a = 0.759904
b = -15.070597
c = 74.720674
lambda = 0.764158
Ground state parameters:
V0 = 3.002206 Bohr^3 (unit cell volume)
= 3.002206 Bohr (WS-radius)
E0 = -1705.738293 Ry
Bmod = 115.348605 GPa
Grun. param. = 1.147079
sws Einp Eout Residual err (% * 10**6)
2.900000 -1705.733279 -1705.733278 0.000001 -0.000462
2.933333 -1705.736071 -1705.736073 -0.000002 0.001462
2.966667 -1705.737719 -1705.737717 0.000002 -0.001374
3.000000 -1705.738290 -1705.738290 -0.000000 0.000238
3.033333 -1705.737873 -1705.737873 0.000000 -0.000175
3.066667 -1705.736536 -1705.736537 -0.000001 0.000590
3.100000 -1705.734353 -1705.734353 0.000000 -0.000280
5.2.2015 -- 18:51:52
JOBNAM = ti1.00 -- P07
Using morse function
Chi squared = 2.17769833254e-11
Reduced Chi squared = 7.25899444181e-12
R squared = 0.99999898819
morse parameters:
a = 0.831171
b = -14.866360
c = 66.474685
lambda = 0.729592
Ground state parameters:
V0 = 3.002865 Bohr^3 (unit cell volume)
= 3.002865 Bohr (WS-radius)
E0 = -1705.737540 Ry
Bmod = 114.985899 GPa
Grun. param. = 1.095434
sws Einp Eout Residual err (% * 10**6)
2.900000 -1705.732490 -1705.732491 -0.000001 0.000576
2.933333 -1705.735292 -1705.735289 0.000003 -0.001807
2.966667 -1705.736942 -1705.736944 -0.000002 0.001443
3.000000 -1705.737535 -1705.737536 -0.000001 0.000646
3.033333 -1705.737140 -1705.737138 0.000002 -0.001159
3.066667 -1705.735820 -1705.735820 -0.000000 0.000187
3.100000 -1705.733649 -1705.733649 -0.000000 0.000114
hcp_lattice_constants_analyze(hcp):
sws0 = 3.002260
c/a0 = 1.610122
B0 = 115.952318
E0 = -1705.738844
R = 0.019532
cs = 498.360422
Ground state volume of fcc CoCrFeMnNi high-entropy alloy using DLM¶
#!/usr/bin/python
# Calculate the equilibrium volume and bulk modulus of
# fcc CoCrFeMnNi high-entropy alloy using DLM.
# !!! 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],
amix=0.02,
efmix=0.9,
expan='M',
sofc='Y',
afm='M', # Fixed-spin DLM calculation.
iex=7, # We want to use self-consistent GGA (PBE).
nz2=16,
tole=1.0E-8,
ncpa=10,
nky=21,
tfermi=5000,
dx=0.015, # Dirac equation parameters
dirac_np=1001, # Dirac equation parameters
nes=50, # Dirac equation parameters
dirac_niter=500) # Dirac equation parameters
cocrfemnni.emto.kgrn.write_input_file(folder=emtopath)
cocrfemnni.emto.kfcd.write_input_file(folder=emtopath)
cocrfemnni.emto.batch.write_input_file(folder=emtopath)
The output of this script should look like this:
25.3.2015 -- 14:57:04
JOBNAM = quick_fit -- N/A
Using morse function
Chi squared = 4.62250902489e-09
Reduced Chi squared = 6.60358432126e-10
R squared = 0.999931991714
morse parameters:
a = 0.139363
b = -66.030179
c = 7819.057118
lambda = 2.099339
Ground state parameters:
V0 = 2.604323 Bohr^3 (unit cell volume)
= 2.604323 Bohr (WS-radius)
E0 = -2558.658938 Ry
Bmod = 184.105793 GPa
Grun. param. = 2.733677
sws Einp Eout Residual err (% * 10**6)
2.500000 -2558.650560 -2558.650581 -0.000021 0.008282
2.520000 -2558.653736 -2558.653710 0.000026 -0.010160
2.540000 -2558.656041 -2558.656024 0.000017 -0.006580
2.560000 -2558.657623 -2558.657612 0.000011 -0.004134
2.580000 -2558.658526 -2558.658555 -0.000029 0.011502
2.600000 -2558.658899 -2558.658926 -0.000027 0.010718
2.620000 -2558.658785 -2558.658792 -0.000007 0.002689
2.640000 -2558.658229 -2558.658212 0.000017 -0.006616
2.660000 -2558.657266 -2558.657242 0.000024 -0.009530
2.680000 -2558.655941 -2558.655930 0.000011 -0.004314
2.700000 -2558.654301 -2558.654322 -0.000021 0.008142
WS-radius vs. energy curve of fcc CoCrFeMnNi.
WS-radius vs. magnetic moments of fcc CoCrFeMnNi.