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Elastic properties #16

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f6a0d07
Elastic properies in new module vasprun.elastic
Mellechowicz Jul 30, 2021
46351d5
Short __doc__ string added to each new module
Mellechowicz Jul 30, 2021
51f0b25
Spelling check
Mellechowicz Jul 30, 2021
e6fbb2d
Spelling check
Mellechowicz Jul 30, 2021
0df9e86
setup.py: and update
Mellechowicz Jul 30, 2021
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22 changes: 22 additions & 0 deletions scripts/vasprun
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Expand Up @@ -43,6 +43,22 @@ if __name__ == "__main__":
help="figure' dpi, default: 300", metavar="dpi")
parser.add_option("-S", "--save-bands", dest="saveBands", action='store_true',
help="saving of bands contributing to the plot, default: false", metavar="saveBands")
parser.add_option("-E", "--elastic", dest="runElasticCalculations", action='store_true',
help="run calculations for the elastic properties (requires IBRION >=5), default: false")
parser.add_option("-C", "--elasticsymmetry", dest="symmetry", default="Triclinic",
choices=['Triclinic', 'Monoclinic', 'Orthorhombic',
'Trigonal6', 'Trigonal7', 'Hexagonal',
'Tetragonal6', 'Tetragonal7', 'Cubic'],
help="symmetry group of the supercell, default: Triclinic;\
For calculation of elastic properties only!\
choices: \"Triclinic\", \"Monoclinic\", \"Orthorhombic\",\
\"Trigonal6\", \"Trigonal7\", \"Hexagonal\",\
\"Tetragonal6\", \"Tetragonal7\", and \"Cubic\"")
parser.add_option("-A", "--approximation", dest="approximation", default="voigt",
choices=['voigt','reuss','hill','all'],
help="approximation used for the calculation of the elastic moduli, default: voigt;\
For calculation of elastic properties only!\
choices: \"voigt\", \"reuss\", \"hill\", and \"all\"")

(options, args) = parser.parse_args()
if options.vasprun is None:
Expand Down Expand Up @@ -145,3 +161,9 @@ if __name__ == "__main__":
print("{:25s} {:12.3f} {:12.3f} {:12.3f}".format('DFPT', eps[0,0], eps[0,1], eps[0,2]))
print("{:25s} {:12.3f} {:12.3f} {:12.3f}".format('DFPT', eps[1,0], eps[1,1], eps[1,2]))
print("{:25s} {:12.3f} {:12.3f} {:12.3f}".format('DFPT', eps[2,0], eps[2,1], eps[2,2]))
elif options.runElasticCalculations:
from vasprun.elastic import elastic
solver = elastic.Calculator(options=options,verbosity=0)
solver() # running calculations
solver.print()

2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -17,7 +17,7 @@
long_description = long_description,
long_description_content_type = 'text/markdown',
url="https://github.com/qzhu2017/vasprun",
packages=['vasprun'],
packages=['vasprun','vasprun.elastic'],
scripts=['scripts/vasprun'],
classifiers=[
"Programming Language :: Python :: 3",
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299 changes: 299 additions & 0 deletions vasprun/elastic/CMatrices.py
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@@ -0,0 +1,299 @@
"""
Functions allowing for calculation a 6x6 elastic-constant matrix
for 9 different point-symmetry space groups. Make sure that you use
the proper ordering of the Cij constants!
"""
import numpy as np

class ElasticTensor:
DegreesOfFreedom = {
'Triclinic' : 21,
'Monoclinic' : 13,
'Orthorhombic' : 9,
'Trigonal6' : 6,
'Trigonal7' : 7,
'Hexagonal' : 5,
'Tetragonal6' : 6,
'Tetragonal7' : 7,
'Cubic' : 3,
}
def __init__(self,symmetry=None):
self.CMatrix = {
'Triclinic': ElasticTensor.CMatrixTriclinic,
'Monoclinic': ElasticTensor.CMatrixMonoclinic,
'Orthorhombic': ElasticTensor.CMatrixOrthorhombic,
'Trigonal6': ElasticTensor.CMatrixTrigonal6,
'Trigonal7': ElasticTensor.CMatrixTrigonal7,
'Hexagonal': ElasticTensor.CMatrixHexagonal,
'Tetragonal6': ElasticTensor.CMatrixTetragonal6,
'Tetragonal7': ElasticTensor.CMatrixTetragonal7,
'Cubic': ElasticTensor.CMatrixCubic
}

self.symmetry = None
if isinstance(symmetry,str):
self.symmetry = symmetry

def __call__(self,*args,symmetry=None):
if symmetry is not None:
return self.CMatrix[symmetry](*args)
elif self.symmetry is not None:
return self.CMatrix[self.symmetry](*args)
else:
raise TypeError("You must define symmetry!")

@staticmethod
def CMatrixTriclinic(C11,C12,C13,C14,C15,C16,
C22,C23,C24,C25,C26,
C33,C34,C35,C36,
C44,C45,C46,
C55,C56,
C66):
"""
Triclinic cell - 21 constants
Order:
C11,C12,C13,C14,C15,C16,
C22,C23,C24,C25,C26,
C33,C34,C35,C36,
C44,C45,C46,
C55,C56,
C66
returns an array: [
[ C11, C12, C13, C14, C15, C16 ],
[ C12, C22, C23, C24, C25, C26 ],
[ C13, C23, C33, C34, C35, C36 ],
[ C14, C24, C34, C44, C45, C46 ],
[ C15, C25, C35, C45, C55, C56 ],
[ C16, C26, C36, C46, C56, C66 ],
]
"""
return np.array([
[ C11, C12, C13, C14, C15, C16 ],
[ C12, C22, C23, C24, C25, C26 ],
[ C13, C23, C33, C34, C35, C36 ],
[ C14, C24, C34, C44, C45, C46 ],
[ C15, C25, C35, C45, C55, C56 ],
[ C16, C26, C36, C46, C56, C66 ],
])

@staticmethod
def CMatrixMonoclinic(C11,C12,C13, C15,
C22,C23, C25,
C33, C35,
C44, C46,
C55,
C66):
"""
Monoclinic cell - 13 constants
Order:
C11,C12,C13,C15,
C22,C23,C25,
C33,C35,
C44,C46,
C55,
C66
returns an array: [
[ C11, C12, C13, 0.0, C15, 0.0 ],
[ C12, C22, C23, 0.0, C25, 0.0 ],
[ C13, C23, C33, 0.0, C35, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, C46 ],
[ C15, C25, C35, 0.0, C55, 0.0 ],
[ 0.0, 0.0, 0.0, C46, 0.0, C66 ],
]
"""
return np.array([
[ C11, C12, C13, 0.0, C15, 0.0 ],
[ C12, C22, C23, 0.0, C25, 0.0 ],
[ C13, C23, C33, 0.0, C35, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, C46 ],
[ C15, C25, C35, 0.0, C55, 0.0 ],
[ 0.0, 0.0, 0.0, C46, 0.0, C66 ],
])

@staticmethod
def CMatrixOrthorhombic(C11,C12,C13,
C22,C23,
C33,C44,C55,C66):
"""
Orthorhombic cell - 9 constants
Order:
C11,C12,C13,
C22,C23,
C33,C44,C55,C66
returns an array: [
[ C11, C12, C13, 0.0, 0.0, 0.0 ],
[ C12, C22, C23, 0.0, 0.0, 0.0 ],
[ C13, C23, C33, 0.0, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C55, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, 0.0, C66 ],
]
"""
return np.array([
[ C11, C12, C13, 0.0, 0.0, 0.0 ],
[ C12, C22, C23, 0.0, 0.0, 0.0 ],
[ C13, C23, C33, 0.0, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C55, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, 0.0, C66 ],
])

@staticmethod
def CMatrixTrigonal7(C11,C12,C13,C14,C15,
C33,C44):
"""
Trigonal cell - 7 constants
Order
C11,C12,C13,C14,C15,
C33,C44
returns an array: [
[ C11, C12, C13, C14, C15, 0.0 ],
[ C12, C11, C13,-C14,-C15, 0.0 ],
[ C13, C13, C33, 0.0, 0.0, 0.0 ],
[ C14,-C14, 0.0, C44, 0.0,-C15 ],
[ C15,-C15, 0.0, 0.0, C44, C14 ],
[ 0.0, 0.0, 0.0,-C15, C14, C66 ],
]
where C66 = 0.5*(C11-C12)
"""
C66 = 0.5*(C11-C12)
return np.array([
[ C11, C12, C13, C14, C15, 0.0 ],
[ C12, C11, C13,-C14,-C15, 0.0 ],
[ C13, C13, C33, 0.0, 0.0, 0.0 ],
[ C14,-C14, 0.0, C44, 0.0,-C15 ],
[ C15,-C15, 0.0, 0.0, C44, C14 ],
[ 0.0, 0.0, 0.0,-C15, C14, C66 ],
])

@staticmethod
def CMatrixTrigonal6(C11,C12,C13,C14,
C33,C44):
"""
Trigonal cell - 6 constants
Order
C11,C12,C13,C14,
C33,C44
returns an array: [
[ C11, C12, C13, C14, 0.0, 0.0 ],
[ C12, C11, C13,-C14, 0.0, 0.0 ],
[ C13, C13, C33, 0.0, 0.0, 0.0 ],
[ C14,-C14, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C44, C14 ],
[ 0.0, 0.0, 0.0, 0.0, C14, C66 ],
]
where C66 = 0.5*(C11-C12)
"""
C66 = 0.5*(C11-C12)
return np.array([
[ C11, C12, C13, C14, 0.0, 0.0 ],
[ C12, C11, C13,-C14, 0.0, 0.0 ],
[ C13, C13, C33, 0.0, 0.0, 0.0 ],
[ C14,-C14, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C44, C14 ],
[ 0.0, 0.0, 0.0, 0.0, C14, C66 ],
])

@staticmethod
def CMatrixHexagonal(C11,C12,C13,
C33,C44):
"""
Hexagonal cell - 5 constants
Order:
C11,C12,C13,
C33,C44
returns an array: [
[ C11, C12, C13, 0.0, 0.0, 0.0 ],
[ C12, C11, C13, 0.0, 0.0, 0.0 ],
[ C13, C13, C33, 0.0, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C44, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, 0.0, C66 ],
]
where C66 = 0.5*(C11-C12)
"""
C66 = 0.5*(C11-C12)
return np.array([
[ C11, C12, C13, 0.0, 0.0, 0.0 ],
[ C12, C11, C13, 0.0, 0.0, 0.0 ],
[ C13, C13, C33, 0.0, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C44, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, 0.0, C66 ],
])

@staticmethod
def CMatrixTetragonal7(C11,C12,C13, C16,
C33,C44,C66):
"""
Tetragonal cell - 7 constants
Order:
C11,C12,C13, C16,
C33,C44,C66
returns an array: [
[ C11, C12, C13, 0.0, 0.0, C16 ],
[ C12, C11, C13, 0.0, 0.0,-C16 ],
[ C13, C13, C33, 0.0, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C44, 0.0 ],
[ C16,-C16, 0.0, 0.0, 0.0, C66 ],
]
"""
return np.array([
[ C11, C12, C13, 0.0, 0.0, C16 ],
[ C12, C11, C13, 0.0, 0.0,-C16 ],
[ C13, C13, C33, 0.0, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C44, 0.0 ],
[ C16,-C16, 0.0, 0.0, 0.0, C66 ],
])

@staticmethod
def CMatrixTetragonal6(C11,C12,C13,
C33,C44,C66):
"""
Tetragonal cell - 6 constants
Order:
C11,C12,C13,
C33,C44,C66
returns an array: [
[ C11, C12, C13, 0.0, 0.0, 0.0 ],
[ C12, C11, C13, 0.0, 0.0, 0.0 ],
[ C13, C13, C33, 0.0, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C44, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, 0.0, C66 ],
]
"""
return np.array([
[ C11, C12, C13, 0.0, 0.0, 0.0 ],
[ C12, C11, C13, 0.0, 0.0, 0.0 ],
[ C13, C13, C33, 0.0, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C44, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, 0.0, C66 ],
])

@staticmethod
def CMatrixCubic(C11,C12,C44):
"""
Cubic cell - 3 constants
Order:
C11,C12,C44
returns an array: [
[ C11, C12, C12, 0.0, 0.0, 0.0 ],
[ C12, C11, C12, 0.0, 0.0, 0.0 ],
[ C12, C12, C11, 0.0, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C44, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, 0.0, C44 ],
]
"""
return np.array([
[ C11, C12, C12, 0.0, 0.0, 0.0 ],
[ C12, C11, C12, 0.0, 0.0, 0.0 ],
[ C12, C12, C11, 0.0, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, C44, 0.0, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, C44, 0.0 ],
[ 0.0, 0.0, 0.0, 0.0, 0.0, C44 ],
])
16 changes: 16 additions & 0 deletions vasprun/elastic/__init__.py
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"""
Submodule for calculation of the elastic properties
from the stress--strain relation based on VASP's ```vasprun.xml``` file.

Module CMatrix contains a class ```ElasticTensor```
with all 9 different symmetry-based constrains 6x6 elastic tensors.

Module ```elastic``` contains two classes:
(i) ```Calculation``` containing the scipy-based engine
fitting the elastic tensor C to the stress-strain relation.
(ii) ```Properites``` with the methods deriving the elastic properties
from the elastic tensor (within different approximations)

Module ```readdata``` contains a class ```XMLParser``` extracting
both stress and strain from the ```vasprun.xml```
"""
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