Merge pull request #110 from mhangaard/cathub_update

change default colormap and misc

Author: Martin Hangaard Hansen

catmap/__init__.py

@@ -1,26 +1,28 @@
-#Standard dependencies
+# Standard dependencies
 import os
 import sys
 import inspect
 import time
 try:
     import cPickle as pickle
-except:
+except (ImportError, ModuleNotFoundError):
     import _pickle as pickle
 
 import re
 from copy import copy
 from string import Template
 
-#Non-standard dependencies
+# Non-standard dependencies
 import numpy as np
 try:
     from scipy.interpolate import InterpolatedUnivariateSpline as spline
 except ImportError:
-    def spline_wrapper(x_data, y_data, k=3):  # input kwarg k is intentionally ignored
+    # input kwarg k is intentionally ignored.
+    def spline_wrapper(x_data, y_data, k=3):
         # behaves like scipy.interpolate.InterpolatedUnivariateSpline for k=1
         def spline_func(x):
-            return np.interp(x, map(float,x_data), map(float,y_data))  # loss of precision here
+            # loss of precision here
+            return np.interp(x, map(float,x_data), map(float,y_data))
         return spline_func
     spline = spline_wrapper
 

catmap/analyze/analysis_base.py

@@ -111,38 +111,38 @@ class MapPlot:
     :param aspect: 
     :type aspect:
 
-    :param subplots_adjust_kwargs: Dictionary of keyword arguments for adjusting matplotlib subplots
+    :param subplots_adjust_kwargs: Dictionary of keyword arguments for
+        adjusting matplotlib subplots
     :type subplots_adjust_kwargs: dict
 
     .. todo:: Some missing descriptions
     """
     def __init__(self):
-        defaults = dict(
-                resolution_enhancement = 1,
-                min = None,
-                max = None,
-                n_ticks = 8,
-                plot_function = None,
-                colorbar = True,
-                colormap = plt.cm.jet,
-                axis_label_decimals = 2,
-                log_scale = False,
-                descriptor_labels = ['X_descriptor','Y_descriptor'],
-                default_descriptor_pt_args = {'marker':'o'},
-                default_descriptor_label_args = {},
-                descriptor_pt_args = {},
-                descriptor_label_args = {},
-                include_descriptors = False,
-                plot_size = 4,
-                aspect = None,
-                subplots_adjust_kwargs = {'hspace':0.35,'wspace':0.35,
-                    'bottom':0.15}
-                )
+        defaults = dict(resolution_enhancement=1,
+                        min=None,
+                        max=None,
+                        n_ticks=8,
+                        plot_function=None,
+                        colorbar=True,
+                        colormap=plt.cm.YlGnBu_r,
+                        axis_label_decimals=2,
+                        log_scale=False,
+                        descriptor_labels=['X_descriptor', 'Y_descriptor'],
+                        default_descriptor_pt_args={'marker': 'o'},
+                        default_descriptor_label_args={},
+                        descriptor_pt_args={},
+                        descriptor_label_args={},
+                        include_descriptors=False,
+                        plot_size=4,
+                        aspect=None,
+                        subplots_adjust_kwargs={'hspace': 0.35,
+                                                'wspace': 0.35,
+                                                'bottom': 0.15})
 
         for key in defaults:
             val = defaults[key]
-            if not hasattr(self,key):
-                setattr(self,key,val)
+            if not hasattr(self, key):
+                setattr(self, key, val)
             elif getattr(self,key) is None:
                 setattr(self,key,val)
 

catmap/analyze/matrix_map.py

@@ -1,6 +1,7 @@
 from .analysis_base import *
 from .vector_map import *
 
+
 class MatrixMap(VectorMap):
     """
     .. todo:: __doc__

catmap/analyze/scaling.py

@@ -1,26 +1,27 @@
-from .analysis_base import *
+from .analysis_base import ScalingPlot, ReactionModelWrapper
 
-class ScalingAnalysis(ScalingPlot,ReactionModelWrapper):
+
+class ScalingAnalysis(ScalingPlot, ReactionModelWrapper):
     """
     .. todo:: __doc__
     """
-    def __init__(self,reaction_model):
+    def __init__(self, reaction_model):
         self._rxm = reaction_model
         self.scaling_mode = 'linear'
-        ScalingPlot.__init__(self,self.descriptor_names,
-                self.descriptor_dict,self.surface_names,
-                self.parameter_dict,
-                self.plotter_scaling_function,
-                self.plotter_x_axis_function)
+        ScalingPlot.__init__(self, self.descriptor_names,
+                             self.descriptor_dict, self.surface_names,
+                             self.parameter_dict,
+                             self.plotter_scaling_function,
+                             self.plotter_x_axis_function)
 
-    def plotter_scaling_function(self,descriptors,**kwargs):
+    def plotter_scaling_function(self, descriptors, **kwargs):
         """
         .. todo:: __doc__
         """
         descriptors = list(descriptors)
-        return self.scaler.get_electronic_energies(descriptors,**kwargs)
+        return self.scaler.get_electronic_energies(descriptors, **kwargs)
 
-    def plotter_x_axis_function(self,descriptors,**kwargs):
+    def plotter_x_axis_function(self, descriptors, **kwargs):
         """
         .. todo:: __doc__
         """
@@ -32,24 +33,24 @@ def plotter_x_axis_function(self,descriptors,**kwargs):
                 self.coefficient_matrix = C
             else:
                 C = self.coefficient_matrix
-            for ads,c in zip(
-                    self.adsorbate_names+self.transition_state_names,C):
+            for ads, c in zip(
+                    self.adsorbate_names+self.transition_state_names, C):
                 x_dict[ads] = sum(
-                        [c[i]*a for i,a in enumerate(descriptors)]) + c[-1]
+                        [c[i]*a for i, a in enumerate(descriptors)]) + c[-1]
                 lab = ''
-                for i,a in enumerate(self.descriptor_names):
-                    c_print =  round(c[i],self.descriptor_decimal_precision)
+                for i, a in enumerate(self.descriptor_names):
+                    c_print = round(c[i], self.descriptor_decimal_precision)
                     if c_print != 0:
                         lab += str(c_print)+'*$E_{'+str(a)+'}$+'
-                const = round(c[-1],self.descriptor_decimal_precision)
+                const = round(c[-1], self.descriptor_decimal_precision)
                 if const > 0:
                     lab += '+' + str(const)
                 elif const < 0:
                     lab += '-' + str(-const)
-                lab = lab.replace('++','+')
-                lab = lab.replace('+-','-')
+                lab = lab.replace('++', '+')
+                lab = lab.replace('+-', '-')
                 labels[ads] = lab
-            return x_dict,labels
+            return x_dict, labels
 
     def get_error(self):
         """
@@ -58,4 +59,3 @@ def get_error(self):
         if not self.scaling_error:
             self.plot(save=False)
         return self.scaling_error
-

catmap/analyze/vector_map.py

@@ -1,6 +1,7 @@
 from .analysis_base import *
 from string import Template
 
+
 class VectorMap(MapPlot, ReactionModelWrapper):
     """
     .. todo:: __doc__