Adding pourbaix dir again - RF

Author: raulf2012

pourbaix_pymatgen/LICENSE

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+MIT License
+
+Copyright (c) 2017 Raul Flores
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pourbaix_pymatgen/README.md

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+# pourbaix_pymatgen
+Pourbaix construction and analysis using Materials Project database

pourbaix_pymatgen/data_exp_form_e.py

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+"""TEMP TEMP - 180317"""
+
+def formation_e_data_dict():
+	"""
+	Dictionary of formation energies for transition metal species.
+
+	All energies are in [eV]
+	"""
+	#start_fold - formation_e_data_dict
+	import ast
+	direct_0 = '/home/flores12/01_ORR-MatStabScreen/01_virenv-pymatgen/01_data/03_formation_e/'
+	List = open(direct_0+'data.py').read().splitlines()
+	# Returns python list of entries_lst from read data file
+	entries_lst = []
+	line_cnt = 1
+	for i in List:
+		# print str(line_cnt)+'	:'+str(i)
+		if not i=="":
+			if i[0]=='#':
+				line_cnt=line_cnt+1
+				continue
+			else:
+				try:
+					entries_lst.append(ast.literal_eval(i))
+				except:
+					print 'data_exp_form_e.formation_e_data_dict - error with line: '+str(line_cnt)
+		line_cnt=line_cnt+1
+	## Turns entry lists into dictionaries
+	cf_k = "chem_formula"	# Chemical formula list key
+	fe_k = "form_e"			# Formation energy key
+	r_k = "reference"		# Literature reference key
+	c_k = "comments"		# Comments key
+
+	entries = []
+	for i in entries_lst:
+		entry_dict = {}
+		entry_dict[cf_k] = i[0]
+		entry_dict[fe_k] = i[1]
+		entry_dict[r_k] = i[2]
+		entry_dict[c_k] = i[3]
+		entries.append(entry_dict)
+
+	chem_form_lst = []
+	for entry in entries:
+		# chem_form = entry[0]
+		chem_form_lst.append(frozenset(entry[cf_k]))
+	unique_entries_lst = list(list(i) for i in list(set(chem_form_lst)))
+
+	dict = {}
+	for i in unique_entries_lst:
+		dict[frozenset(i)]=[]
+		for j in entries:
+			if set(j[cf_k])==set(i):
+				dict[frozenset(i)].append(j)
+	return dict
+
+	#end_fold
+
+def get_entry(chemical_formula_list, data_dict):
+	"""
+
+	Args:
+		chemical_formula_list:
+		data_dict:
+	"""
+	#start_fold - get_entry
+	# print chemical_formula_list
+	key = frozenset(chemical_formula_list)
+
+	try:
+		entry = data_dict[key]
+	except KeyError:
+		entry = None
+		# print 'data_exp_form_e.get_entry - no experimental data available'
+
+	return entry
+
+	#end_fold
+
+# form_e_data = formation_e_data_dict()
+# temp = get_entry(['Pt1','O2'],form_e_data)
+
+def oxygen_stoich(exp_entry):
+	"""
+
+	Args:
+		exp_entry
+	"""
+	#start_fold - oxygen_stoich
+	formula = exp_entry['chem_formula']
+	for i in formula:
+		if i[0]=='O' and i[1].isdigit()==True:
+			num_of_digits = len(i)-1
+			if num_of_digits==1:
+				oxy_num = int(i[1])
+			elif num_of_digits>1:
+				oxy_num = int(i[1:])
+			break
+	return oxy_num
+
+	#end_fold
+
+
+#start_fold - Possible code to take "Pt2O3 and extract out the elements and stoicheometric numbers"
+# import re
+#
+# chem_form_lst = []
+# for entry in entries_lst:
+#
+# 	chem_form = entry[0]
+# 	form_e = entry[1]
+# 	ref = entry[2]
+# 	comments = entry[3]
+#
+# 	chem_form_lst.append(set(chem_form))
+#
+# 	## Separating the element name from the stoicheometric factor
+# 	for element in chem_form:
+# 		elem_stoich = re.match(r"([a-z]+)([0-9]+)", element, re.I).groups()
+# 		elem = elem_stoich[0]
+# 		stoich = elem_stoich[1]
+#end_fold

pourbaix_pymatgen/element_list.py

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+from pymatgen.core.periodic_table import Element	# Call elements by atomic #
+class ElementList(object):
+	"""
+	Class for creating element lists and ranges
+	By default the first list created is in order of atomic number
+	Args:
+	    N/A
+	"""
+	#start_fold - ElementList
+	def __init__(self, atom_num_lst=[[]]):
+		self.atom_num_lst = atom_num_lst
+		if not atom_num_lst==[[]]:
+			self.list = self.mk_lst_atnum()
+		self.trans_met = self.mk_lst_trans_met()
+
+	def mk_lst_atnum(self):
+		"""
+		Makes list of elements from the atom_num_lst input
+		"""
+		elem_rnge=[]
+		for i in self.atom_num_lst:
+			el_strt=i[0]
+			el_end=i[1]
+			rnge_sect=range(el_strt,el_end+1)
+			elem_rnge.extend(rnge_sect)
+		elements=[]
+		for i in elem_rnge:
+			element=Element.from_Z(i)	# Indice -> pymatgen element object
+			elements.append(element)
+		return elements
+		print elements
+
+	def mk_lst_trans_met(self):
+		"""
+		Produces list of transition metals in order of atomic number
+		"""
+		elem_rnge_I = [[21,30],[39,44],[46,48],[74,76],[78,80]]
+		elem_rnge=[]
+		for i in elem_rnge_I:
+			el_strt=i[0]
+			el_end=i[1]
+			rnge_sect=range(el_strt,el_end+1)
+			elem_rnge.extend(rnge_sect)
+		elements=[]
+		for i in elem_rnge:
+			element=Element.from_Z(i)	# Indice -> pymatgen element object
+			elements.append(element)
+		return elements
+
+	#end_fold
+
+class ElemList_mod(object):
+	"""
+	"""
+	#start_fold - ElemList_mod
+	def __init__(self,elem_lst):
+		self.elem_lst = elem_lst
+	@property
+	def sort(self,srt_type='group_num'):
+		"""
+		Sorts element entries
+		Args:
+		    srt_type
+			DEFAULT: group_num, sorts by group number with lowest group number first, and
+			lowest period first
+		"""
+		if srt_type == 'group_num':
+			elem_lst = self.elem_lst
+			elem_lst_sorted = elem_lst[:]		# Maintains the original unaffected
+			elem_lst_sorted.sort(key=lambda x: x.group)
+			return elem_lst_sorted
+
+		#start_fold - d-band filling
+		if srt_type == 'd-band': #COMBAK
+			tmp = 7
+
+
+
+
+		#end_fold
+
+	def remove(self,element):
+		"""
+		Removes element from element list
+		Args:
+			List of element objects
+			If only 1 element just 1 element number or chemical symbol
+			name "or" atomic number of the element to be removed
+		"""
+		elem_lst_0 = self.elem_lst
+		if type(element)==type([]):
+			for elem in element:
+				if type(elem)==type('string'):
+					# Find the occurance of input 'elem' in the list and returns it
+					elem_0 = next((x for x in elem_lst_0 if x.name == elem), None)
+					elem_lst_0 = [x for x in elem_lst_0 if not x.name == elem]
+				elif type(elem)==type(2):
+					elem_0 = next((x for x in elem_lst_0 if x.number == elem), None)
+					elem_lst_0 = [x for x in elem_lst_0 if not x.number == elem]
+			return elem_lst_0
+		if type(element)==type('string'):
+			# Find the occurance of input 'elem' in the list and returns it
+			elem_0 = next((x for x in self.elem_lst if x.name == element), None)
+			elem_lst_new = [x for x in self.elem_lst if not x.name == element]
+			return elem_lst_new
+
+		elif type(element)==type(2):
+			elem_0 = next((x for x in self.elem_lst if x.number == element), None)
+			elem_lst_new = [x for x in self.elem_lst if not x.number == element]
+			return elem_lst_new
+	#end_fold
+
+def elem_str_mke(elem_lst):
+	"""
+
+	Args:
+		elem_lst:
+	"""
+	#start_fold - elem_str_mke
+	elem_str=[]
+	for i in elem_lst:
+		elem_str.append(i.symbol)
+	return elem_str
+
+	#end_fold