def CalculateElasticConstant(straintype):
"""Calculate the elastic constant corresponding to straintype
using ab-initio energy calculation (VASP).
For a C11 deformation, one can use the deformation tensor:
[[1 0 0]
[0 0 0]
[0 0 0]]
For a C11-C12 deformation, one can use the deformation tensor:
[[1 0 0]
[0 -1 0]
[0 0 0]]
( 8 symmetry operators)
or:
[[1 0 0]
[0 1 0]
[0 0 -2]]
(16 symmetry operators)
For a C44 deformation, one can use the deformation tensor:
[[0 0 0]
[0 0 1]
[0 1 0]]
(4 symmetry operators)
or:
[[0 1 1]
[1 0 1]
[1 1 0]]
(12 symmetry operators)
All these tensors are now listed in the module CubicStandardStrainTensors.
"""
# load a structure from existing POSCAR file:
struct = Structure("POSCAR")
cellvolume = struct.getCellVolume()
# define a sequence of strain amplitudes:
strains=scipy.arange(-0.020, 0.022, 0.002).round(5)
# For a C11 deformation, one can use the deformation tensor:
# [[1 0 0]
# [0 0 0]
# [0 0 0]]
#
# For a C11-C12 deformation, one can use the deformation tensor:
# [[1 0 0]
# [0 -1 0]
# [0 0 0]]
# ( 8 symmetry operators)
# or:
# [[1 0 0]
# [0 1 0]
# [0 0 -2]]
# (16 symmetry operators)
#
# For a C44 deformation, one can use the deformation tensor:
# [[0 0 0]
# [0 0 1]
# [0 1 0]]
# (4 symmetry operators)
# or:
# [[0 1 1]
# [1 0 1]
# [1 1 0]]
# (12 symmetry operators)
# all these tensors are now listed in the module CubicStandardStrainTensors
import CubicStandardStrainTensors as cubic
# straintype = 'C44_2'
tens = cubic.__dict__[straintype]
# tens = cubic.__dict__['C44_2']
# tensor = p4mat.Matrix([[1.0, 0.0, 0.0],[0.0, 0.0, 0.0],[0.0, 0.0, 0.0]])
tensor = p4mat.Matrix( tens.tolist() )
# cmd='rsh -. n00 mpirun -np 8 vasp'
cmd = 'mr vasp'
# Generate the strained POSCAR files
GenStrainPoscar(struct, tensor, strains, straintype)
# Execute the VASP command on the sequence of POSCAR files
CalcStrains(strains, straintype, cmd)
print "Finished calculating strains."
# Collect the energies from the output vasprun.xml files.
runs=[]
energies=[]
forces=[]
for x in strains:
runs.append(XMLSystemPM('vasprun_'+straintype+'_'+repr(x)+'.xml'))
energies.append(runs[-1].FREE_ENERGY)
pass
for i in range(len(runs)):
print runs[i].FINAL_STRUCTURE.getCellVolume()
# for i in range(len(runs)):
# forces.append(runs[i].FORCES_SEQUENCE)
pass
evec=np.array(energies)
data=scipy.zeros((len(evec),2), dtype='f')
# We build the data to outfile to file, which is used later for fitting
# the strains are saved to file in Angstroems, not fractional coordinates
# if the structure read from the POSCAR file is "direct", we need to apply scaling:
# if struct.isDirect():
# scaling = struct.scaling[0]
# data[:,0] = strains * scaling
# else the strains are already in units of length (assumed Angstroems):
# elif struct.isCartesian():
# data[:,0] = strains
data[:,0] = strains
data[:,1] = evec
datafile=open(straintype+"_data.dat", 'w')
scipy.io.write_array(datafile, data)
datafile.close()
elastConst = FitCubicStrain(straintype+"_data.dat", straintype, cellvolume)
print straintype, ": ", elastConst
print straintype, " (GPa) : ", elastConst*160.22
print "Finished all."
pass # End of CalculateElasticConstant
if len(x) != len(y): return False
res = True
for (xi, yi) in zip(x, y):
res = res & isNearlyZero(xi - yi, eps)
# this could be made more efficient'
# since they are unequal as soon as a pair of components are not equal
return res
# name of distortion
name = "X3-_sym1"
# load a structure from existing POSCAR file:
struct = Structure("POSCAR_X3-")
print "Loaded POSCAR."
cellvolume = struct.getCellVolume()
print "Cell volume: ", cellvolume
# backup the original structure
#struct.write("POSCAR_X3-_ref", newformat=0)
# open output file:
outfile = open('frozen_phonon_' + name + '.dat', 'w')
# load the symmetry vector
try:
symfile = open("symmetryvector.in", 'r')
except:
IOError, "symmetryvector.in file not found"
# Load the symmetry vector (here for 2x2x2 BCC supercell):
"""check wether two vectors (hashable containers of numbers) are equal."""
if len(x) != len(y): return False
res = True
for (xi, yi) in zip(x,y):
res = res & isNearlyZero(xi-yi, eps)
# this could be made more efficient'
# since they are unequal as soon as a pair of components are not equal
return res
# name of distortion
name = "X3-_sym1"
# load a structure from existing POSCAR file:
struct = Structure("POSCAR_X3-")
print "Loaded POSCAR."
cellvolume = struct.getCellVolume()
print "Cell volume: ", cellvolume
# backup the original structure
#struct.write("POSCAR_X3-_ref", newformat=0)
# open output file:
outfile = open('frozen_phonon_'+name+'.dat', 'w')
# load the symmetry vector
try:
symfile = open("symmetryvector.in", 'r')
except: IOError, "symmetryvector.in file not found"
# Load the symmetry vector (here for 2x2x2 BCC supercell):