111 lines
3.4 KiB
Python
111 lines
3.4 KiB
Python
import numpy as np
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from lammps import lammps, LMP_VAR_EQUAL
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# method for rotating elastic constants
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def rotate_cij(cij, r):
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# K_1
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# R_11^2 R_12^2 R_13^2
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# R_21^2 R_22^2 R_23^2
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# R_31^2 R_32^2 R_33^2
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k1 = r*r
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# K_2
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# R_12.R_13 R_13.R_11 R_11.R_12
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# R_22.R_23 R_23.R_21 R_21.R_22
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# R_32.R_33 R_33.R_31 R_31.R_32
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k2 = np.array([
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[r[0][1]*r[0][2], r[0][2]*r[0][0], r[0][0]*r[0][1]],
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[r[1][1]*r[1][2], r[1][2]*r[1][0], r[1][0]*r[1][1]],
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[r[2][1]*r[2][2], r[2][2]*r[2][0], r[2][0]*r[2][1]],
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])
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# K_3
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# R_21.R_31 R_22.R_32 R_23.R_33
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# R_31.R_11 R_32.R_12 R_33.R_13
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# R_11.R_21 R_12.R_22 R_13.R_23
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k3 = np.array([
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[r[1][0]*r[2][0], r[1][1]*r[2][1], r[1][2]*r[2][2]],
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[r[2][0]*r[0][0], r[2][1]*r[0][1], r[2][2]*r[0][2]],
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[r[0][0]*r[1][0], r[0][1]*r[1][1], r[0][2]*r[1][2]],
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])
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# K_4a
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# R_22.R_33 R_23.R_31 R_21.R_32
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# R_32.R_13 R_33.R_11 R_31.R_12
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# R_12.R_23 R_13.R_21 R_11.R_22
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k4a = np.array([
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[r[1][1]*r[2][2], r[1][2]*r[2][0], r[1][0]*r[2][1]],
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[r[2][1]*r[0][2], r[2][2]*r[0][0], r[2][0]*r[0][1]],
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[r[0][1]*r[1][2], r[0][2]*r[1][0], r[0][0]*r[1][1]],
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])
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# K_4b
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# R_23.R_32 R_21.R_33 R_22.R_31
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# R_33.R_12 R_31.R_13 R_32.R_11
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# R_13.R_22 R_11.R_23 R_12.R_21
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k4b = np.array([
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[r[1][2]*r[2][1], r[1][0]*r[2][2], r[1][1]*r[2][0]],
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[r[2][2]*r[0][1], r[2][0]*r[0][2], r[2][1]*r[0][0]],
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[r[0][2]*r[1][1], r[0][0]*r[1][2], r[0][1]*r[1][0]],
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])
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k = np.block([[k1, 2*k2],[k3, k4a+k4b]])
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cijrot = k.dot(cij.dot(k.T))
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return cijrot
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def calculate_cij(cmdargs):
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lmp = lammps(cmdargs=cmdargs)
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lmp.file("in.elastic")
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C11 = lmp.extract_variable("C11",None, LMP_VAR_EQUAL)
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C22 = lmp.extract_variable("C22",None, LMP_VAR_EQUAL)
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C33 = lmp.extract_variable("C33",None, LMP_VAR_EQUAL)
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C44 = lmp.extract_variable("C44",None, LMP_VAR_EQUAL)
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C55 = lmp.extract_variable("C55",None, LMP_VAR_EQUAL)
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C66 = lmp.extract_variable("C66",None, LMP_VAR_EQUAL)
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C12 = lmp.extract_variable("C12",None, LMP_VAR_EQUAL)
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C13 = lmp.extract_variable("C13",None, LMP_VAR_EQUAL)
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C14 = lmp.extract_variable("C14",None, LMP_VAR_EQUAL)
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C15 = lmp.extract_variable("C15",None, LMP_VAR_EQUAL)
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C16 = lmp.extract_variable("C16",None, LMP_VAR_EQUAL)
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C23 = lmp.extract_variable("C23",None, LMP_VAR_EQUAL)
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C24 = lmp.extract_variable("C24",None, LMP_VAR_EQUAL)
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C25 = lmp.extract_variable("C25",None, LMP_VAR_EQUAL)
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C26 = lmp.extract_variable("C26",None, LMP_VAR_EQUAL)
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C34 = lmp.extract_variable("C34",None, LMP_VAR_EQUAL)
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C35 = lmp.extract_variable("C35",None, LMP_VAR_EQUAL)
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C36 = lmp.extract_variable("C36",None, LMP_VAR_EQUAL)
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C45 = lmp.extract_variable("C45",None, LMP_VAR_EQUAL)
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C46 = lmp.extract_variable("C46",None, LMP_VAR_EQUAL)
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C56 = lmp.extract_variable("C56",None, LMP_VAR_EQUAL)
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cij = np.array([
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[C11, C12, C13, C14, C15, C16],
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[ 0, C22, C23, C24, C25, C26],
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[ 0, 0, C33, C34, C35, C36],
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[ 0, 0, 0, C44, C45, C46],
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[ 0, 0, 0, 0, C55, C56],
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[ 0, 0, 0, 0, 0, C66],
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])
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cij = np.triu(cij) + np.tril(cij.T, -1)
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return cij
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def gen_varargs(varlist):
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cmdargs = []
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for key in varlist:
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cmdargs += ["-var",key,str(varlist[key])]
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return cmdargs
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