Merge branch 'master' of github.com:rasmusthog/nafuma

nafuma/dft/electrons.py

@@ -786,12 +786,10 @@ def prettify_dos_plot(fig, ax, options):
 
 
 
-def plot_coop(plot_data, options):
+def plot_coop(data, options):
     ''' interactions = list with number of interaction (index + 1 of interactions list from read_coop)'''
 
 
-    required_options = ['plot_kind', 'mode', 'up', 'down', 'collapse', 'interactions', 'flip_xy', 'fill', 'colours', 'palettes']
-
     default_options = {
         'plot_kind': 'COOP',
         'mode': 'individual',
@@ -806,17 +804,17 @@ def plot_coop(plot_data, options):
     
     }
 
-    options = update_options(options=options, required_options=required_options, default_options=default_options)
+    options = aux.update_options(options=options, default_options=default_options)
 
 
-    fig, ax = prepare_plot(options=options)
+    fig, ax = btp.prepare_plot(options=options)
 
-    coopcar, coop_interactions = dft.io.read_coop(plot_data=plot_data, options=options)
+    coopcar, coop_interactions = dft.io.read_coop(data=data, options=options)
 
 
 
     if not options['colours']:
-        colour_cycle = generate_colours(palettes=options['palettes'])
+        colour_cycle = btp.generate_colours(palettes=options['palettes'])
 
         colours = []
         for interaction in range(len(coop_interactions)):
@@ -894,6 +892,8 @@ def plot_coop(plot_data, options):
                     to_plot = ['mean_down']
                         
 
+
+            
             # Plot all columns as decided above
             for j, column in enumerate(to_plot):
                 if options['fill']:
@@ -912,9 +912,9 @@ def plot_coop(plot_data, options):
                     else:
                         coopcar.plot(x='Energy', y=column, ax=ax, color=colour)
 
-    prettify_dos_plot(fig=fig, ax=ax, options=options)
+    fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options)
 
-    return coopcar
+    return coopcar, fig, ax
 
 
 

nafuma/dft/io.py

@@ -94,7 +94,8 @@ def read_coop(data={}, options={}):
     required_options = ['collapse']
 
     default_options = {
-        'collapse': False
+        'collapse': False,
+        'adjust': None,
     }
 
 
@@ -128,6 +129,9 @@ def read_coop(data={}, options={}):
 
     coopcar.columns = columns
 
+    if options['adjust']:
+        coopcar['Energy'] = coopcar['Energy'] - options['adjust']
+
 
     if options['collapse']:
         

nafuma/xrd/refinement.py

@@ -926,10 +926,18 @@ def refine(data: dict, options={}):
 
 
 
-def read_results(path):
+def read_results(path, options={}):
+    
+
+    default_options = {
+        'errors': True
+    }
+
+    options = aux.update_options(options=options, default_options=default_options)
 
     results = pd.read_csv(path, delim_whitespace=True, index_col=0, header=None)
 
+    if options['errors']:
         atoms = int((results.shape[1] - 24) / 10)
 
         headers = [
@@ -938,13 +946,25 @@ def read_results(path):
         'a', 'a_err', 'b', 'b_err', 'c', 'c_err', 'alpha', 'alpha_err', 'beta', 'beta_err', 'gamma', 'gamma_err',
         ]
     
+    else:
+        atoms = int((results.shape[1] - 15) / 5)
+
+        headers = [
+            'r_wp', 'r_exp', 'r_p', 'r_p_dash', 'r_exp_dash', 'gof',
+            'vol', 'mass', 'wp',
+            'a', 'b', 'c', 'alpha', 'beta', 'gamma',
+        ]
+
 
     labels = ['x', 'y', 'z', 'occ', 'beq']
     for i in range(atoms):
         for label in labels:
             headers.append(f'atom_{i+1}_{label}')
+            
+            if options['errors']:
                 headers.append(f'atom_{i+1}_{label}_err')
 
+
     results.columns = headers
     
     return results