for i in range(np.size(spin_list)):
spin_dict[magnetic_ions[i]] = spin_list[i]
print "project name: " + project_name
#
#read the CIF file to extract a complete unit cell containing the chosen magnetic ions
#
[atoms, fract_coords] = SMMcalc_lib.CIF_to_cell(file_name = CIF_file, select_atoms = magnetic_ions)
#
#make sub-variables that only contain cluster atoms and fract_coords
#
[cluster_atoms, cluster_fract_coords] = \
SMMcalc_lib.cluster_array_maker(cluster_indices = cluster_indices, atoms = atoms, fract_coords = fract_coords)
#
#store the atoms and fract_coords files in a temporary file so they can be acessed by other processes
#
SMMcalc_lib.tmp_write(cluster_atoms, cluster_fract_coords, 'TEMP.txt')
#
#from the cluster_atoms, generate cluster_spins
#
cluster_spins = np.zeros(np.shape(cluster_atoms))
for i in range(np.size(cluster_atoms)):
cluster_spins[i] = spin_dict[cluster_atoms[i]]
spin_dict = {}
for i in range(np.size(spin_list)):
spin_dict[magnetic_ions[i]] = spin_list[i]
print "project name: " + project_name
#
#read the CIF file to extract a complete unit cell containing the chosen magnetic ions
#
[atoms, fract_coords] = SMMcalc_lib.CIF_to_cell(file_name = CIF_file, select_atoms = magnetic_ions)
#
#store the atoms and fract_coords files in a temporary file so they can be acessed by other processes
#
SMMcalc_lib.tmp_write(atoms, fract_coords, 'TEMP.txt')
#
#start another process to render the unit cell in real space
#
if display_plots == 1:
subprocess.Popen("SMMcalc_display.py", shell=True)
#
#choose the atoms to be in the cluster
#
cluster_indices = SMMcalc_lib.cluster_chooser()
#
#make sub-variables that only contain cluster atoms and fract_coords
#
import os #operating system
import re #regular expressions
import numpy as np #numeric python
from enthought.mayavi import mlab
import SMMcalc_lib
f = open(r"SMMcalcINPUT.txt", "r").read().splitlines()
file_name = f[1]
#convert file_name to acceptable format
file_name = "file://" + file_name
file_name = os.path.normpath(file_name)
#read contents of TEMP file
[atoms, fract_coords] = SMMcalc_lib.tmp_read('TEMP.txt')
#read contents of CIF file
cf = CifFile.ReadCif(file_name)
sample_name = cf.dictionary.keys()[0]
#unit cell in meters (converted from Angstroms)
a = float(re.sub('\)','',re.sub('\(','',cf[sample_name]['_cell_length_a']))) * 1e-10
b = float(re.sub('\)','',re.sub('\(','',cf[sample_name]['_cell_length_b']))) * 1e-10
c = float(re.sub('\)','',re.sub('\(','',cf[sample_name]['_cell_length_c']))) * 1e-10
#angles in degrees
alpha = float(re.sub('\)','',re.sub('\(','',cf[sample_name]['_cell_angle_alpha'])))
beta = float(re.sub('\)','',re.sub('\(','',cf[sample_name]['_cell_angle_beta'])))
gamma = float(re.sub('\)','',re.sub('\(','',cf[sample_name]['_cell_angle_gamma'])))