diff --git a/kmcos/__init__.py b/kmcos/__init__.py
index 6af6c90d4c92a91b0e35bbbf311aea79a9e7867b..74c6d7f465745c1908f491e5990ac1f444854040 100644
--- a/kmcos/__init__.py
+++ b/kmcos/__init__.py
@@ -50,7 +50,7 @@ from __future__ import print_function
-__version__ = "0.0.67"
+__version__ = "0.0.69"
VERSION = __version__
def evaluate_param_expression(param, parameters={}):
diff --git a/kmcos/run/__init__.py b/kmcos/run/__init__.py
index ebab9f265f5723e5d7ed0185737720f1b8b10e41..c1cf0396b0015bc58534f423da6dce4bb9ca3983 100644
--- a/kmcos/run/__init__.py
+++ b/kmcos/run/__init__.py
@@ -832,7 +832,9 @@ class KMC_Model(Process):
def peek(self, *args, **kwargs):
- """Visualize the current configuration of the model using ASE ag."""
+ """Creates a static image of the model
+
+ """
tag = kwargs.pop('tag', None)
ase = import_ase()
@@ -842,7 +844,9 @@ class KMC_Model(Process):
return self.peek()
def view(self, scaleA = None):
- """Start current model in live view mode."""
+ """Start current model in live view mode.
+
+ """
from kmcos import view
view.main(self, scaleA = scaleA)
@@ -1365,43 +1369,92 @@ class KMC_Model(Process):
else:
return res
- def get_coords(self):
- """
- Config is expected to be a nested array that contains the species's coordinates
+ def get_species_coords(self, filename_csv="", export_csv=True):
+ """Gets each species and their respective coordinates and returns a 3d list that separates the coordinates of each species and returns a dictionary of the species's name
+ EX: [[['CO', [0, 11]],
+ ['CO', [0, 13]],
+ ['CO', [1, 2]],
+ ['CO', [1, 4]],
+ ['empty', [0, 0]],
+ ['empty', [0, 1]],
+ ['empty', [0, 2]],
+ ['empty', [0, 3]]],
+ {'CO': 'carbon', 'empty': ''})
+
+ 'filename' sets the name of the csv file that will be exported if 'export_csv' is true
+ 'export_csv' determines whether the functions exports the species coordinates as a csv file
+
+ 'config' in the function is a nested 4d array that contains the species's coordinates
EX: [[[[0]], [[1]], [[1]], [[0]]]]
- Species is exptected to be a dictionary that contains the names of the species
- EX: {"CO" : "carbon"}
+ 'species' in the function is a dictionary that contains the names of the species
+ EX: {'CO': 'carbon', 'empty': ''}
+
"""
+ if filename_csv == "" and export_csv==True:
+ filename_csv = "species_coords.csv"
+
+ filename_csv.replace(".csv", "") + ".csv"
+
config = self._get_configuration().tolist()
species = self.species_tags
- coords = []
- for i in range(len(config)):
- for j in range(len(config[0])):
- coords.append([i,j])
- return coords, species
-
+ species_list = list(species)
+ coords_list = []
+ species_coords = self.get_species_coordinates(config, species)
+
+ #Note: taking a list of a dictionary turns the keys into a list
+ for species_index in range(len(species_coords)): #loop across each species
+ for coordinate_pair in species_coords[species_index]: #loop across each sublist in the species
+ coords_list.append([species_list[species_index], coordinate_pair]) #appends the coordinates for each respesctive species into coords
+
+ if export_csv==True: #creates the csv file and exports coords_list into two columns
+ import csv
+ with open(filename_csv, 'w') as file:
+ writer = csv.writer(file)
+ writer.writerow(['Species', 'Coordinates'])
+ writer.writerows(coords_list)
+ file.close()
+
+ return coords_list #to do: need to sort and export as a dataframe with the species name, x, and y values of the coordiantes in their own column
+ #put the module "ColumnSort" in the directory and call later for sorting
+
@staticmethod
def get_species_coordinates(config, species):
- """
- Gets the species coordinates from a 4d list and appends it into a 2d array that's then returned
+ """Gets the species coordinates from config and appends it into a 3d array, where each sub array lists the coordinates for a single species
+ EX: [[[0, 11],
+ [0, 13],
+ [1, 2],
+ [1, 4],
+ [19, 10]],
+ [[0, 0],
+ [0, 1],
+ [0, 2],
+ [0, 3],
+ [0, 4]]]
+
+ 'config' is expected to be a nested 4d array that contains the species's coordinates
+ EX: [[[[0]], [[1]], [[1]], [[0]]]]
+ 'species' is exptected to be a dictionary that contains the names of the species
+ EX: {'CO': 'carbon', 'empty': ''}
+
"""
species_coords = []
- for k in range(len(species)):
+ for k in range(len(species)): #The loop appends coordinates for each respective species in the order they appear in 'species' to species_coords
species_coords.append([])
for i in range(len(config)):
for j in range(len(config[0])):
if (config[i][j][0][0] == k):
- species_coords[k].append([i,j])
+ species_coords[k].append([i,j])
return species_coords
- @staticmethod
+ @staticmethod
def create_configuration_plot(coords, species, plot_settings={}, showFigure=True, directory=''):
- """
- coords is expected to be the results from get_species_coordinates(config, species)
+ """Returns the spatial view of the kmc_model and make a graph named 'plottedConfiguration.png,' unless specified by 'figure_name' in plot_settings
+
+ 'coords' is expected to be the results from get_species_coordinates(config, species)
Ex:
- species is expected to be the results from get_coords(), which is a dictionary that contains the names of the species
+ 'species' is expected to be the results from get_coords(), which is a dictionary that contains the names of the species
Ex: {"CO" : "carbon"}
- plot_settings is a dictionary that allows for the plot to change given the arguements
+ 'plot_settings' is a dictionary that allows for the plot to change given the arguements
EX:
"y_label": "test",
"x_label": "test",
@@ -1411,7 +1464,7 @@ class KMC_Model(Process):
"figure_name": "Plot",
"dpi": 220,
"speciesName": False
- create_configuration_plot will return the spatial view of the kmc_model and make a graph named 'plottedConfiguration.png,' unless specified by 'figure_name' in plot_settings
+
"""
import matplotlib.pyplot as plt
exportFigure = True #This variable should be moved to an argument or something in plot_settings.
@@ -1495,10 +1548,13 @@ class KMC_Model(Process):
return
def plot_configuration(self, filename = '', resolution = 150, scale = 20, representation = 'spatial', plot_settings = {}):
- """
- representation is an optional argument for spatial and atomic view
- resolution and scale are strictly for the atomic view
- resolution changes the plot's
+ """Either calls create_configuration_plot to create the spatial representation of the model, or calls export_picture to create the atomic representation of the model
+
+ 'representation' is an optional argument for spatial and atomic view
+ 'scale' increases the size of each species in the structure (currently not working as desired)
+ 'resolution' changes the dpi of the images (currently not working as desired)
+ Note: 'resolution' and 'scale' are strictly for the atomic view
+
You should specify as 'atomic' to see the atomic view. Leaving representation empty returns spatial view by default.
plot_settings is a dictionary that allows for the plot to change given the arguements
@@ -1511,7 +1567,7 @@ class KMC_Model(Process):
"figure_name": "Plot",
"dpi": 220,
"speciesName": False
- plot_configuration either calls create_configuration_plot to create the spatial representation of the model, or calls export_picture to create the atomic representation of the model
+
"""
if representation == 'atomic':
if 'show_unit_cell' in plot_settings: