"""
Bulk RMC6F configuration processing
===================================
This modules holds stuff relevant to processing bulk RMC6F configurations.
"""
#
# -*- coding: utf-8 -*-
#
from rmc_tools.rmc6f_stuff import dist_calc_coord
import os
import timeit
import datetime
[docs]class BulkStuff(object):
"""RMC6F bulk configuration processing class.
This class contains methods for processing bulk RMC6F configurations.
"""
def __init__(self):
from random import random
x_temp = random()
y_temp = random()
z_temp = random()
self.centPos = [x_temp, y_temp, z_temp]
self.centPosInt = [2.0 * x - 1.0 for x in self.centPos]
self.shellThickness = 0.0
# Method for generating shells from a random center.
[docs] def bulk_to_shells(self, rmc6f_config):
"""Method for grabbing shells from bulk RMC6F configuration.
Provided bulk RMC6F configuration, this method can extract shells from it. \
Since this program is to deal with bulk configuration, the center does not \
matter that much and therefore it is randomly placed in the bulk configuration.
Arguments:
rmc6f_config {Object} -- Instance of `RMC6FReader` class
Output:
shell_X.rmc6f -- RMC6F configuration for generated shells.
np_shell_gen.log -- Log information about shells generation.
"""
print("\n****************************************************")
print("1->by thickness, 2->by number of atoms")
print("****************************************************")
div_scheme = int(input("Please select a way to divide particle into shells: "))
while div_scheme != 1 and div_scheme != 2:
print("\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
print("!!!!'1' and '2' are only accepted inputs!!!!")
print("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
print("\n****************************************************")
print("1->by thickness, 2->by number of atoms")
print("****************************************************")
div_scheme = int(input("Please select a way to divide particle into shells: "))
if div_scheme == 1:
self.shellThickness = float(input("\nPlease input shell thickness for the analysis: "))
num_shells = int(input("\nPlease input number of shells to configure: "))
start = timeit.default_timer()
print("\nDividing particle to various shells...")
atoms_include = [i * 0 for i in range(rmc6f_config.numAtoms)]
atoms_to_check = [i for i, x in enumerate(atoms_include) if x == 0]
shell_atoms = []
print("\nShells to configure: ", end='', flush=True)
for i in range(num_shells + 1):
print("*", end='', flush=True)
print("\nShells configured: ", end='', flush=True)
for i in range(num_shells):
shell_atoms.append([])
low_lim = i * self.shellThickness
hi_lim = (i + 1) * self.shellThickness
for ii in atoms_to_check:
dist_temp = dist_calc_coord(self.centPosInt, rmc6f_config.atomsCoordInt[ii],
rmc6f_config.vectors)
if low_lim <= dist_temp < hi_lim:
shell_atoms[i].append(ii)
atoms_include[ii] = 1
atoms_to_check = [i for i, x in enumerate(atoms_include) if x == 0]
print(".", end='', flush=True)
shell_atoms.append(atoms_to_check)
num_shells += 1
print(".")
stop = timeit.default_timer()
print("\n\n--------------------------------------------")
print("Particle successfully divided to " + str(num_shells) + " shells.")
print("Time taken:{0:11.3F} s".format(stop - start))
print("--------------------------------------------")
elif div_scheme == 2:
num_shells = int(input("\nPlease input number of shells to configure: "))
print("\n*************************************************")
for i in range(rmc6f_config.numTypeAtom):
print(str(i+1) + "->" + rmc6f_config.atomTypes[i] + " ", end='', flush=True)
print("\n*************************************************")
at_to_focus = int(input("Please input an atom type to focus on: "))
print("\n------------------------------------------")
print("Total number of atoms selected: {0:10d}".
format(rmc6f_config.numAtomEachType[at_to_focus - 1]))
print("------------------------------------------")
min_num_in_shell = int(input("Please input minimum number of " +
rmc6f_config.atomTypes[at_to_focus - 1] + " atoms in shell: "))
start = timeit.default_timer()
print("\nDividing particle to various shells...")
print("\nShells to configure: ", end='', flush=True)
for i in range(num_shells):
print("*", end='', flush=True)
atoms_include = [i * 0 for i in range(rmc6f_config.numAtoms)]
atoms_to_check = [i for i, x in enumerate(atoms_include) if x == 0]
low_lim = 0
hi_lim = 0
low_lim_out = []
hi_lim_out = []
check_step = 0.5
shell_atoms = []
shell_processed = 0
print("\nShells configured: ", end='', flush=True)
while shell_processed < num_shells:
shell_atoms.append([])
natoms_focus = 0
while natoms_focus < min_num_in_shell:
hi_lim += check_step
list_temp = []
burst = False
for ii in atoms_to_check:
dist_temp = dist_calc_coord(self.centPosInt, rmc6f_config.atomsCoordInt[ii],
rmc6f_config.vectors)
if low_lim <= dist_temp < hi_lim:
list_temp.append(ii)
space_left = min_num_in_shell - natoms_focus
to_eat = 0
for item in list_temp:
if rmc6f_config.atomsEle[item] == rmc6f_config.atomTypes[at_to_focus - 1]:
to_eat += 1
if space_left < int(0.1 * float(min_num_in_shell)) and \
to_eat > int(0.15 * float(min_num_in_shell)):
burst = True
if not burst:
shell_atoms[shell_processed].extend(list_temp)
for item in list_temp:
atoms_include[item] = 1
if rmc6f_config.atomsEle[item] == rmc6f_config.atomTypes[at_to_focus - 1]:
natoms_focus += 1
else:
hi_lim -= check_step
break
atoms_to_check = [i for i, x in enumerate(atoms_include) if x == 0]
low_lim_out.append(low_lim)
hi_lim_out.append(hi_lim)
shell_processed += 1
low_lim = hi_lim
print(".", end='', flush=True)
for i in range(num_shells):
shell_atoms[i].sort()
stop = timeit.default_timer()
print("\n--------------------------------------------")
print("Particle successfully divided to " + str(num_shells) + " shells.")
print("Time taken:{0:11.3F} s".format(stop - start))
print("--------------------------------------------")
dir_exist = True
i = 1
while dir_exist:
dir_check = rmc6f_config.fileName.split(".")[0] + "_np_shells_" + str(i)
if not os.path.exists(dir_check):
dir_exist = False
dir_use = dir_check
i += 1
os.mkdir(dir_use)
for i in range(num_shells):
atoms_ele = []
atoms_line = []
line_num = 0
for item in shell_atoms[i]:
line_num += 1
atoms_ele.append(rmc6f_config.atomsEle[item])
line_temp = rmc6f_config.atomsLine[item]
line_new = str(line_num) + " " + " ".join(line_temp.split()[1:]) + "\n"
atoms_line.append(line_new)
atoms_ele_uniq = sorted(set(atoms_ele), key=atoms_ele.index)
num_each_type = []
for j in range(len(atoms_ele_uniq)):
num_each_type.append(str(atoms_ele.count(atoms_ele_uniq[j])))
num_rho_new = rmc6f_config.initNumRho * \
float(len(shell_atoms[i])) / \
float(rmc6f_config.numAtoms)
header = rmc6f_config.header.copy()
for j in range(len(header)):
if "Number of atoms:" in header[j]:
header[j] = "Number of atoms: " + str(len(shell_atoms[i])) + "\n"
if "Atom types present:" in header[j]:
header[j] = "Atom types present: " + " ".join(atoms_ele_uniq) + "\n"
if "Number of types of atoms:" in header[j]:
header[j] = "Number of types of atoms: " + str(len(atoms_ele_uniq)) + "\n"
if "Number of each atom type:" in header[j]:
header[j] = "Number of each atom type: " + " ".join(num_each_type) + "\n"
if "Number density (Ang^-3):" in header[j]:
header[j] = "Number density (Ang^-3):" + " {0:.6f}".format(num_rho_new) + "\n"
file_out = open(os.path.join(dir_use, "shell_" + str(i)) + ".rmc6f", "w")
for item in header:
file_out.write(item)
for item in atoms_line:
file_out.write(item)
file_out.close()
now = datetime.datetime.now()
log_file = open(os.path.join(dir_use, "np_shell_gen.log"), "w")
log_file.write("==================================\n")
log_file.write("Log file for np_to_shells routine.\n")
log_file.write("==================================\n")
log_file.write("Time stamp: " + str(now)[:19] + "\n")
if div_scheme == 1:
log_file.write("================================================\n")
log_file.write("Particle divided into shells by equal thickness.\n")
log_file.write("Shell thickness used: {0:10.1F}\n".format(self.shellThickness))
log_file.write("Number of shells generated: {0:10d}\n".format(num_shells))
log_file.write("================================================")
else:
log_file.write("================================================================\n")
log_file.write("Particle divided into shells by equal (roughly) number of atoms.\n")
log_file.write("Atom type focused: {0:2s}\n".format(rmc6f_config.atomTypes[at_to_focus - 1]))
log_file.write("Minimum number of {0:2s} atom in each shell: {1:10d}\n".
format(rmc6f_config.atomTypes[at_to_focus - 1], min_num_in_shell))
log_file.write("Number of shells generated: {0:10d}\n".format(num_shells))
log_file.write("================================================================\n")
log_file.write("Lower and upper limit of each shell:\n")
log_file.write("================================================================\n")
log_file.write("{0:>10s}{1:>10s}\n".format("R_min", "R_max"))
for i in range(num_shells):
log_file.write("{0:10.2F}{1:10.2F}\n".format(low_lim_out[i], hi_lim_out[i]))
log_file.write("================================================================")
log_file.close()
print("\n--------------------------------------------")
print("RMC6F configs of shells output to directory:")
print("--------------------------------------------")
print(dir_use)
print("--------------------------------------------")