From c2477bfd9956ce0c913708862646185318d1a343 Mon Sep 17 00:00:00 2001
From: rasmusthog <code@rasmusthog.me>
Date: Wed, 12 Oct 2022 21:07:22 +0200
Subject: [PATCH 1/2] Update COOP-plotting function

---
 nafuma/dft/electrons.py | 18 +++++++++---------
 nafuma/dft/io.py        |  6 +++++-
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/nafuma/dft/electrons.py b/nafuma/dft/electrons.py
index 8ea1064..1fd3092 100644
--- a/nafuma/dft/electrons.py
+++ b/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
 
 
 
diff --git a/nafuma/dft/io.py b/nafuma/dft/io.py
index e09de45..23d7d41 100644
--- a/nafuma/dft/io.py
+++ b/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']:
         

From 33012c60354c48cc34b5c03c54e866dfd1f20584 Mon Sep 17 00:00:00 2001
From: rasmusthog <code@rasmusthog.me>
Date: Wed, 12 Oct 2022 21:07:44 +0200
Subject: [PATCH 2/2] Allow user to skip read-in of error columns

---
 nafuma/xrd/refinement.py | 30 +++++++++++++++++++++++++-----
 1 file changed, 25 insertions(+), 5 deletions(-)

diff --git a/nafuma/xrd/refinement.py b/nafuma/xrd/refinement.py
index 71b2da9..75ecee2 100644
--- a/nafuma/xrd/refinement.py
+++ b/nafuma/xrd/refinement.py
@@ -926,24 +926,44 @@ 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)
 
-    atoms = int((results.shape[1] - 24) / 10)
+    if options['errors']:
+        atoms = int((results.shape[1] - 24) / 10)
 
-    headers = [
+        headers = [
         'r_wp', 'r_exp', 'r_p', 'r_p_dash', 'r_exp_dash', 'gof',
         'vol', 'vol_err', 'mass', 'mass_err', 'wp', 'wp_err',
         '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}')
-            headers.append(f'atom_{i+1}_{label}_err')
+            
+            if options['errors']:
+                headers.append(f'atom_{i+1}_{label}_err')
+
 
     results.columns = headers