Compute Bicrystallographic properties

In this code, we compute and save the bicrystallography properties for each \(\Sigma\)-miorientation. These properties include: 1. sig_mats: The \(\Sigma\)-miorientation in the primitive \(p\) reference frame. For example, we use the variable T_p1top2_p1 2. csl_mats: The CSL lattice basis vectors in the primitive \(p\) reference frame. For example, we use the variable l_csl_p denoting \(\Lambda_{csl}^p\) 3. dsc_mats: The DSC lattice basis vectors in the primitive \(p\) reference frame. For example, we use the variable l_dsc_p denoting \(\Lambda_{dsc}^p\) 4. bxt_symm_props: The symmetry aspects of the \(\Sigma\)-miorientation + bxt_symm_grp: The point-group symmetry of the bicrystal. This is the symmetry for the Boundary-plane orientations. + symm_grp_ax: The axes of the symmetry point-group.

import byxtal.lattice as gbl
import byxtal.csl_utility_functions as cuf
import byxtal.find_csl_dsc as fcd
import numpy as np
import byxtal.tools as gbt
import byxtal.misorient_fz as mfz
import byxtal.disorient_symm_props as dsp

1. l1: The lattice object.

2. l_p_po: \(\Lambda_p^{po}\)

l1 = gbl.Lattice('Al')
sig_type = 'common'
l_p_po = l1.l_p_po

### For cubic only odd Sigma numbers exist!
n1 = 1
n2 = 10
sig_nums = 2*np.arange(n1,n2)+1

num_sigs = 0
sig_mats = {}
csl_mats = {}
dsc_mats = {}
bxt_symm_props = {}

for sig_num in sig_nums:
    s1 = cuf.csl_rotations(sig_num, sig_type, l1)
    for ct1 in range(np.shape(s1['N'])[0]):
        symm_grp_props = {}
        sig_id = str(sig_num)+'_'+str(ct1+1)
        print(sig_id)
        #### Store the sigma-misorientation (in 'p' reference frame)
        T_p1top2_p1 = s1['N'][ct1]/s1['D'][ct1]
        sig_mats[sig_id] = T_p1top2_p1

#         l_csl_p, l_dsc_p = fcd.find_csl_dsc(l_p_po, T_p1top2_p1, 1e-6, False)
        l_csl_p = fcd.find_csl_dsc(l_p_po, T_p1top2_p1, 1e-6, False)
        csl_mats[sig_id] = l_csl_p
#         dsc_mats[sig_id] = l_dsc_p;

        #### Generate boundary-planpe orientations
        l_p_po = l1.l_p_po
        l_po_p = np.linalg.inv(l_p_po)
        T_p1top2_po1 = np.dot(l_p_po, np.dot(T_p1top2_p1, l_po_p))

        ## Find the corresponding disorientation
        quat1 = gbt.mat2quat(T_p1top2_po1)
        # print(quat1)
        dis_quat1 = mfz.misorient_fz(quat1, l1.cryst_ptgrp)
        # print(dis_quat1)
        x_g, y_g, z_g, bxt_symm_grp = dsp.disorient_symm_props(dis_quat1, l1.cryst_ptgrp)
        symm_grp_ax = (np.vstack((x_g, y_g, z_g))).transpose()
        symm_grp_props['symm_grp_ax'] = symm_grp_ax
        symm_grp_props['bxt_symm_grp'] = bxt_symm_grp
        bxt_symm_props[sig_id] = symm_grp_props
        num_sigs = num_sigs + 1
        print(num_sigs)

import pickle as pkl;
pkl_name = l1.elem_type+'_byxtal_props.pkl'
csl_props = {}
csl_props['sig_mats'] = sig_mats
csl_props['csl_mats'] = csl_mats
csl_props['dsc_mats'] = dsc_mats
csl_props['csl_symm_props'] = bxt_symm_props

jar = open(pkl_name, 'wb')
pkl.dump(csl_props, jar)
jar.close()

3_1

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-2-0ea1f0f89914> in <module>
     25
     26 #         l_csl_p, l_dsc_p = fcd.find_csl_dsc(l_p_po, T_p1top2_p1, 1e-6, False)
---> 27         l_csl_p = fcd.find_csl_dsc(l_p_po, T_p1top2_p1, 1e-6, False)
     28         csl_mats[sig_id] = l_csl_p
     29 #         dsc_mats[sig_id] = l_dsc_p;

~/Leila_sndhard/codes/byxtal/byxtal/byxtal/find_csl_dsc.py in find_csl_dsc(l_p_po, T_p1top2_p1, tol1, print_check)
    102     ########################################################################
    103     # l_csl_p = csl_finder(T_p1top2_p1, Sigma, l_p_po, tol1)
--> 104     l_csl_p = csl_finder(T_p1top2_p1, l_p_po, tol1)
    105     check_val1 = check_csl(l_csl_p, l_p_po, T_p1top2_p1, Sigma, print_check)
    106     ########################################################################

~/Leila_sndhard/codes/byxtal/byxtal/byxtal/find_csl_dsc.py in csl_finder(T_p1top2_p1, l_p_po, tol1)
    165     inp_args['mat'] = TI_p1top2_p1
    166     inp_args['sig_num'] = Sigma
--> 167     l_csl1_p = rpl.call_sage_math(exec_str, inp_args)
    168
    169     l_csl_csl1 = rpl.reduce_po_lat(l_csl1_p, l_p_po, tol1)

~/Leila_sndhard/codes/byxtal/byxtal/byxtal/reduce_po_lat.py in call_sage_math(exec_str, inp_args)
     36     for i1 in range(Sz[0]):
     37         for j1 in range(Sz[1]):
---> 38             M_out[i1, j1] = int(str_out[ct1])
     39             ct1 = ct1 + 1
     40

IndexError: list index out of range

csl_props