<filename>pydii/scripts/gen_def_profile.py
#!/usr/bin/env python
"""
PyDIM file for generating defect concentrations
"""

from __future__ import division

#__author__ == '<NAME>'
#__version__ = "0.1"
#__maintainer__ = "<NAME>"
#__email__ = "<EMAIL>"
#__status__ = "Beta"
#__date__ = "9/16/14"

import json
import os
from argparse import ArgumentParser

#import numpy as np
#import scipy
#import matplotlib
#matplotlib.use('ps')
#import matplotlib.pyplot as plt

from monty.serialization import loadfn, dumpfn
from monty.json import MontyEncoder, MontyDecoder
from pydii.dilute_solution_model import \
        solute_site_preference_finder, compute_defect_density, \
        solute_defect_density

def get_def_profile(mpid, T,  file):

    raw_energy_dict = loadfn(file,cls=MontyDecoder)

    e0 = raw_energy_dict[mpid]['e0']
    struct = raw_energy_dict[mpid]['structure']
    vacs = raw_energy_dict[mpid]['vacancies']
    antisites = raw_energy_dict[mpid]['antisites']
    vacs.sort(key=lambda entry: entry['site_index'])
    antisites.sort(key=lambda entry: entry['site_index'])
    for vac_def in vacs:
        if not vac_def:
            print 'All vacancy defect energies not present'
            continue
    for antisite_def in antisites:
        if not antisite_def:
            print 'All antisite defect energies not preset'
            continue

    try:
        def_conc, def_en, mu = compute_defect_density(struct, e0, vacs, antisites, T,
                plot_style='gnuplot')
        return def_conc, def_en, mu
    except:
        raise

def get_solute_def_profile(mpid, solute, solute_conc, T, def_file, sol_file, 
        trial_chem_pot):

    raw_energy_dict = loadfn(def_file,cls=MontyDecoder)
    sol_raw_energy_dict = loadfn(sol_file,cls=MontyDecoder)

    #try:
    e0 = raw_energy_dict[mpid]['e0']
    struct = raw_energy_dict[mpid]['structure']
    vacs = raw_energy_dict[mpid]['vacancies']
    antisites = raw_energy_dict[mpid]['antisites']
    solutes = sol_raw_energy_dict[mpid]['solutes']
    for vac_def in vacs:
        if not vac_def:
            print 'All vacancy defect energies not present'
            continue
    for antisite_def in antisites:
        if not antisite_def:
            print 'All antisite defect energies not preset'
            continue
    for solute_def in solutes:
        if not solute_def:
            print 'All solute defect energies not preset'
            continue

    try:
        def_conc = solute_defect_density(struct, e0, vacs, 
                antisites, solutes, solute_concen=solute_conc, T=T, 
                trial_chem_pot=trial_chem_pot, plot_style="gnuplot")
        return  def_conc
    except:
        raise

def im_vac_antisite_def_profile():
    m_description = 'Command to generate vacancy and antisite defect ' \
                    'concentration for intermetallics from the raw defect energies.' 

    parser = ArgumentParser(description=m_description)

    parser.add_argument("--mpid",
            type=str.lower,
            help="Materials Project id of the intermetallic structure.\n" \
                 "For more info on Materials Project, please refer to " \
                 "www.materialsproject.org")

    parser.add_argument('-T', "--temp", type=float, default=1000,
            help="Temperature in Kelvin")

    parser.add_argument("--file",
            default = None,
            help = "The default file is 'mpid'+'_raw_defect_energy.json'.\n" \
                   "If the file is named differently supply it.")

    #parser.add_argument("--mapi_key",
    #        default = None,
    #        help="Your Materials Project REST API key.\n" \
    #             "For more info, please refer to " \
    #             "www.materialsproject.org/opne")

    args = parser.parse_args()

    if not args.mpid:
        print ('===========\nERROR: mpid is not given.\n===========')
        return
    if not args.file:
        file = args.mpid+'_raw_defect_energy.json'
    else:
        file = args.file


    conc_dat, en_dat, mu_dat = get_def_profile(args.mpid, args.temp,  file)
    if conc_dat:
        fl_nm = args.mpid+'_def_concentration.dat'
        with open(fl_nm,'w') as fp:
            for row in conc_dat:
                print >> fp, row
        fl_nm = args.mpid+'_def_energy.dat'
        with open(fl_nm,'w') as fp:
            for row in en_dat:
                print >> fp, row
        fl_nm = args.mpid+'_chem_pot.dat'
        with open(fl_nm,'w') as fp:
            for row in mu_dat:
                print >> fp, row


def im_sol_sub_def_profile():
    m_description = 'Command to generate solute defect site preference ' \
                    'in an intermetallics from the raw defect energies.' 

    parser = ArgumentParser(description=m_description)

    parser.add_argument("--mpid",
            type=str.lower,
            help="Materials Project id of the intermetallic structure.\n" \
                 "For more info on Materials Project, please refer to " \
                 "www.materialsproject.org")

    parser.add_argument("--solute", help="Solute Element")

    parser.add_argument("--sol_conc", type=float, default=1.0,
            help="Solute Concentration in %. Default is 1%")

    parser.add_argument("-T", "--temp", type=float, default=1000.0,
            help="Temperature in Kelvin")
    parser.add_argument("--trail_mu_file",  default=None,
            help="Trial chemcal potential in dict format stored in file")

    args = parser.parse_args()

    if not args.mpid:
        print ('===========\nERROR: mpid is not given.\n===========')
        return
    if not args.solute:
        print ('===========\nERROR: Solute atom is not given.\n===========')
        return
    def_file = args.mpid+'_raw_defect_energy.json'
    sol_file = args.mpid+'_solute-'+args.solute+'_raw_defect_energy.json'
    sol_conc = args.sol_conc/100.0 # Convert from percentage
    if not os.path.exists(def_file):
        print ('===========\nERROR: Defect file not found.\n===========')
        return
    if not os.path.exists(sol_file):
        print ('===========\nERROR: Solute file not found.\n===========')
        return
    if args.trail_mu_file:
        trail_chem_pot = loadfn(args.trial_mu_file,cls=MontyDecoder)
    else:
        trail_chem_pot = None

    pt_def_conc = get_solute_def_profile(
            args.mpid, args.solute, sol_conc, args.temp, def_file, 
            sol_file, trial_chem_pot=trail_chem_pot)

    if pt_def_conc:
        fl_nm = args.mpid+'_solute-'+args.solute+'_def_concentration.dat'
        with open(fl_nm,'w') as fp:
            for row in pt_def_conc:
                print >> fp, row


if __name__ == '__main__':
    im_vac_antisite_def_profile()
    #im_sol_sub_def_profile()


<filename>pydii/scripts/gen_def_profile.py
#!/usr/bin/env python
"""
PyDIM file for generating defect concentrations
"""

from __future__ import division

#__author__ == '<NAME>'
#__version__ = "0.1"
#__maintainer__ = "<NAME>"
#__email__ = "<EMAIL>"
#__status__ = "Beta"
#__date__ = "9/16/14"

import json
import os
from argparse import ArgumentParser

#import numpy as np
#import scipy
#import matplotlib
#matplotlib.use('ps')
#import matplotlib.pyplot as plt

from monty.serialization import loadfn, dumpfn
from monty.json import MontyEncoder, MontyDecoder
from pydii.dilute_solution_model import \
        solute_site_preference_finder, compute_defect_density, \
        solute_defect_density

def get_def_profile(mpid, T,  file):

    raw_energy_dict = loadfn(file,cls=MontyDecoder)

    e0 = raw_energy_dict[mpid]['e0']
    struct = raw_energy_dict[mpid]['structure']
    vacs = raw_energy_dict[mpid]['vacancies']
    antisites = raw_energy_dict[mpid]['antisites']
    vacs.sort(key=lambda entry: entry['site_index'])
    antisites.sort(key=lambda entry: entry['site_index'])
    for vac_def in vacs:
        if not vac_def:
            print 'All vacancy defect energies not present'
            continue
    for antisite_def in antisites:
        if not antisite_def:
            print 'All antisite defect energies not preset'
            continue

    try:
        def_conc, def_en, mu = compute_defect_density(struct, e0, vacs, antisites, T,
                plot_style='gnuplot')
        return def_conc, def_en, mu
    except:
        raise

def get_solute_def_profile(mpid, solute, solute_conc, T, def_file, sol_file, 
        trial_chem_pot):

    raw_energy_dict = loadfn(def_file,cls=MontyDecoder)
    sol_raw_energy_dict = loadfn(sol_file,cls=MontyDecoder)

    #try:
    e0 = raw_energy_dict[mpid]['e0']
    struct = raw_energy_dict[mpid]['structure']
    vacs = raw_energy_dict[mpid]['vacancies']
    antisites = raw_energy_dict[mpid]['antisites']
    solutes = sol_raw_energy_dict[mpid]['solutes']
    for vac_def in vacs:
        if not vac_def:
            print 'All vacancy defect energies not present'
            continue
    for antisite_def in antisites:
        if not antisite_def:
            print 'All antisite defect energies not preset'
            continue
    for solute_def in solutes:
        if not solute_def:
            print 'All solute defect energies not preset'
            continue

    try:
        def_conc = solute_defect_density(struct, e0, vacs, 
                antisites, solutes, solute_concen=solute_conc, T=T, 
                trial_chem_pot=trial_chem_pot, plot_style="gnuplot")
        return  def_conc
    except:
        raise

def im_vac_antisite_def_profile():
    m_description = 'Command to generate vacancy and antisite defect ' \
                    'concentration for intermetallics from the raw defect energies.' 

    parser = ArgumentParser(description=m_description)

    parser.add_argument("--mpid",
            type=str.lower,
            help="Materials Project id of the intermetallic structure.\n" \
                 "For more info on Materials Project, please refer to " \
                 "www.materialsproject.org")

    parser.add_argument('-T', "--temp", type=float, default=1000,
            help="Temperature in Kelvin")

    parser.add_argument("--file",
            default = None,
            help = "The default file is 'mpid'+'_raw_defect_energy.json'.\n" \
                   "If the file is named differently supply it.")

    #parser.add_argument("--mapi_key",
    #        default = None,
    #        help="Your Materials Project REST API key.\n" \
    #             "For more info, please refer to " \
    #             "www.materialsproject.org/opne")

    args = parser.parse_args()

    if not args.mpid:
        print ('===========\nERROR: mpid is not given.\n===========')
        return
    if not args.file:
        file = args.mpid+'_raw_defect_energy.json'
    else:
        file = args.file


    conc_dat, en_dat, mu_dat = get_def_profile(args.mpid, args.temp,  file)
    if conc_dat:
        fl_nm = args.mpid+'_def_concentration.dat'
        with open(fl_nm,'w') as fp:
            for row in conc_dat:
                print >> fp, row
        fl_nm = args.mpid+'_def_energy.dat'
        with open(fl_nm,'w') as fp:
            for row in en_dat:
                print >> fp, row
        fl_nm = args.mpid+'_chem_pot.dat'
        with open(fl_nm,'w') as fp:
            for row in mu_dat:
                print >> fp, row


def im_sol_sub_def_profile():
    m_description = 'Command to generate solute defect site preference ' \
                    'in an intermetallics from the raw defect energies.' 

    parser = ArgumentParser(description=m_description)

    parser.add_argument("--mpid",
            type=str.lower,
            help="Materials Project id of the intermetallic structure.\n" \
                 "For more info on Materials Project, please refer to " \
                 "www.materialsproject.org")

    parser.add_argument("--solute", help="Solute Element")

    parser.add_argument("--sol_conc", type=float, default=1.0,
            help="Solute Concentration in %. Default is 1%")

    parser.add_argument("-T", "--temp", type=float, default=1000.0,
            help="Temperature in Kelvin")
    parser.add_argument("--trail_mu_file",  default=None,
            help="Trial chemcal potential in dict format stored in file")

    args = parser.parse_args()

    if not args.mpid:
        print ('===========\nERROR: mpid is not given.\n===========')
        return
    if not args.solute:
        print ('===========\nERROR: Solute atom is not given.\n===========')
        return
    def_file = args.mpid+'_raw_defect_energy.json'
    sol_file = args.mpid+'_solute-'+args.solute+'_raw_defect_energy.json'
    sol_conc = args.sol_conc/100.0 # Convert from percentage
    if not os.path.exists(def_file):
        print ('===========\nERROR: Defect file not found.\n===========')
        return
    if not os.path.exists(sol_file):
        print ('===========\nERROR: Solute file not found.\n===========')
        return
    if args.trail_mu_file:
        trail_chem_pot = loadfn(args.trial_mu_file,cls=MontyDecoder)
    else:
        trail_chem_pot = None

    pt_def_conc = get_solute_def_profile(
            args.mpid, args.solute, sol_conc, args.temp, def_file, 
            sol_file, trial_chem_pot=trail_chem_pot)

    if pt_def_conc:
        fl_nm = args.mpid+'_solute-'+args.solute+'_def_concentration.dat'
        with open(fl_nm,'w') as fp:
            for row in pt_def_conc:
                print >> fp, row


if __name__ == '__main__':
    im_vac_antisite_def_profile()
    #im_sol_sub_def_profile()


#!/usr/bin/env python PyDIM file for generating defect concentrations #__author__ == '<NAME>' #__version__ = "0.1" #__maintainer__ = "<NAME>" #__email__ = "<EMAIL>" #__status__ = "Beta" #__date__ = "9/16/14" #import numpy as np #import scipy #import matplotlib #matplotlib.use('ps') #import matplotlib.pyplot as plt #try: #parser.add_argument("--mapi_key", #        default = None, #        help="Your Materials Project REST API key.\n" \ #             "For more info, please refer to " \ #             "www.materialsproject.org/opne") # Convert from percentage #im_sol_sub_def_profile()