From ebb6f4d49a0288755ac7319a8757cba628d6c03a Mon Sep 17 00:00:00 2001
From: dvt <danevantol51247@gmail.com>
Date: Thu, 11 Apr 2024 16:10:59 -0500
Subject: [PATCH] Add files via upload

Fixed read_adf11.py to have more robust pathing and a bit better optimization
---
 colradpy/read_adf11.py | 209 ++++++++++++++++++++---------------------
 1 file changed, 103 insertions(+), 106 deletions(-)

diff --git a/colradpy/read_adf11.py b/colradpy/read_adf11.py
index 97c870b..68964ff 100644
--- a/colradpy/read_adf11.py
+++ b/colradpy/read_adf11.py
@@ -1,106 +1,103 @@
-import numpy as np
-import re
-
-
-def read_adf11(fil):
-    """ Reads data formatted in adf11 format. This format is generally used for GCR coefficients.
-        The data is stored in arrays of log_10.
-        Creates a dictionary to hold the data
-        Args:
-          :param fil: The file path to the input file
-      :type fil: string
-    """
-    
-    f = open(fil)
-    adf11 = {}
-    adf11['input_file'] = {}
-
-    #reading the first line
-    tmp = re.findall('(\d+)',f.readline())
-    adf11['input_file']['nuc_charge'] = int(tmp[0])
-    adf11['input_file']['num_dens'] = int(tmp[1])
-    adf11['input_file']['num_temp'] = int(tmp[2])
-    adf11['input_file']['charge_min'] = int(tmp[3])
-    adf11['input_file']['charge_max'] = int(tmp[4])
-
-    f.readline() #reading '-------------'
-    if( 'r' in re.split('_',re.split('/',fil)[-1])[0]):
-        
-        adf11['input_file']['metas'] = np.array(list(   #metastables
-                       map(int,re.findall('(\d+)',f.readline()))))
-        f.readline() #reading '---------------'
-    else:
-        adf11['input_file']['metas'] = np.ones(adf11['input_file']['charge_max']+1,dtype='int')
-
-    #read in the density grid
-    adf11['input_file']['dens_grid'] = np.array([])
-    while adf11['input_file']['dens_grid'].size <adf11['input_file']['num_dens']:
-        adf11['input_file']['dens_grid'] = np.append(adf11['input_file']['dens_grid'],np.array(list(map(float,re.findall('(.\d*\.\d+)',f.readline())))))
-    #read in the temperature grid
-    adf11['input_file']['temp_grid'] = np.array([])
-    while adf11['input_file']['temp_grid'].size <adf11['input_file']['num_temp']:
-        adf11['input_file']['temp_grid'] = np.append(adf11['input_file']['temp_grid'],np.array(list(map(float,re.findall('(.\d*\.\d+)',f.readline())))))
-
-    #setting up the GCR stages
-    if(adf11['input_file']['nuc_charge'] == len(adf11['input_file']['metas'])-1):
-        num_stages = adf11['input_file']['nuc_charge']
-    else:
-        num_stages = len(adf11['input_file']['metas'])
-    for i in range(0,num_stages):
-        adf11['input_file'][str(i)] = {}
-        if( 'scd' in fil or 'acd' in fil):
-            adf11['input_file'][str(i)] = np.zeros((adf11['input_file']['metas'][i],
-                                                     adf11['input_file']['metas'][i+1],
-                                             len(adf11['input_file']['temp_grid']),
-                                             len(adf11['input_file']['dens_grid'])))
-        if( 'qcd' in fil ):
-            adf11['input_file'][str(i)] = np.zeros((adf11['input_file']['metas'][i],
-                                                     adf11['input_file']['metas'][i],
-                                             len(adf11['input_file']['temp_grid']),
-                                             len(adf11['input_file']['dens_grid'])))
-        if('xcd' in fil):
-            adf11['input_file'][str(i)] = np.zeros((adf11['input_file']['metas'][i+1],
-                                                     adf11['input_file']['metas'][i+1],
-                                             len(adf11['input_file']['temp_grid']),
-                                             len(adf11['input_file']['dens_grid'])))
-        if('plt' in fil):
-            adf11['input_file'][str(i)] = np.zeros((adf11['input_file']['metas'][i],
-                                                     adf11['input_file']['metas'][i],
-                                             len(adf11['input_file']['temp_grid']),
-                                             len(adf11['input_file']['dens_grid'])))
-        if('prb' in fil):
-            adf11['input_file'][str(i)] = np.zeros((adf11['input_file']['metas'][i],
-                                                     adf11['input_file']['metas'][i],
-                                             len(adf11['input_file']['temp_grid']),
-                                             len(adf11['input_file']['dens_grid'])))
-            
-    #Reading the GCR value portion
-    gcr_line = f.readline()
-    ii = 0
-    
-    while len(gcr_line.strip()) != 0 and 'C-' not in gcr_line:
-        #look for the stage identifying line
-        if('----------' in gcr_line):
-            dens_count = 0
-            temp_count = 0
-            stage_id = np.array(list(map(int,re.findall('(\d+ )',gcr_line))))
-            if('scd' in fil or 'acd' in fil):
-                if(len(stage_id) >1):
-                    tmp = stage_id[0]
-                    stage_id[0] = stage_id[1]
-                    stage_id[1] = tmp
-                else:#this accounts for unresolved files that don't follow the convection of resolved files
-                    tmp = stage_id[0]
-                    stage_id = np.array([1,1,tmp])
-
-            ii = ii+1
-        else:
-            gcr_vals = np.array(list(map(float,re.findall(r'((?:-\d+|\d).\d+)',gcr_line))))#Si gcr has positive vals maybe other do to?
-            adf11['input_file'][str(stage_id[2]-1)][stage_id[0]-1,stage_id[1]-1,
-                                           temp_count,dens_count:dens_count+len(gcr_vals)] = gcr_vals
-            dens_count = dens_count + len(gcr_vals)
-            if(dens_count == len(adf11['input_file']['dens_grid'])):
-                temp_count = temp_count + 1
-                dens_count = 0
-        gcr_line = f.readline()
-    return adf11
+import numpy as np
+import re
+from pathlib import Path
+
+
+def read_adf11(fil):
+    """ Reads data formatted in adf11 format. This format is generally used for GCR coefficients.
+        The data is stored in arrays of log_10.
+        Creates a dictionary to hold the data
+        Args:
+          :param fil: The file path to the input file
+      :type fil: string
+    """
+    
+    path = Path(fil)
+    f = path.open()
+    adf11 = {}
+    adf11['input_file'] = {}
+    
+    is_ascd = 'acd' in path.name or 'scd' in path.name
+    is_qcd = 'qcd' in path.name
+    is_xcd = 'xcd' in path.name
+    is_plt = 'plt' in path.name
+    is_prb = 'prb' in path.name
+
+    #reading the first line
+    tmp = re.findall('(\d+)',f.readline())
+    adf11['input_file']['nuc_charge'] = int(tmp[0])
+    adf11['input_file']['num_dens'] = int(tmp[1])
+    adf11['input_file']['num_temp'] = int(tmp[2])
+    adf11['input_file']['charge_min'] = int(tmp[3])
+    adf11['input_file']['charge_max'] = int(tmp[4])
+
+    f.readline() #reading '-------------'
+    if( 'r' in path.name):
+        
+        adf11['input_file']['metas'] = np.array(list(   #metastables
+                       map(int,re.findall('(\d+)',f.readline()))))
+        f.readline() #reading '---------------'
+    else:
+        adf11['input_file']['metas'] = np.ones(adf11['input_file']['charge_max']+1,dtype='int')
+
+    #read in the density grid
+    adf11['input_file']['dens_grid'] = np.array([])
+    while adf11['input_file']['dens_grid'].size <adf11['input_file']['num_dens']:
+        adf11['input_file']['dens_grid'] = np.append(adf11['input_file']['dens_grid'],np.array(list(map(float,re.findall('(.\d*\.\d+)',f.readline())))))
+    #read in the temperature grid
+    adf11['input_file']['temp_grid'] = np.array([])
+    while adf11['input_file']['temp_grid'].size <adf11['input_file']['num_temp']:
+        adf11['input_file']['temp_grid'] = np.append(adf11['input_file']['temp_grid'],np.array(list(map(float,re.findall('(.\d*\.\d+)',f.readline())))))
+
+    #setting up the GCR stages
+    if(adf11['input_file']['nuc_charge'] == len(adf11['input_file']['metas'])-1):
+        num_stages = adf11['input_file']['nuc_charge']
+    else:
+        num_stages = len(adf11['input_file']['metas'])
+        
+        
+    for i in range(0,num_stages):
+        size_1 = size_2 = i
+        if is_ascd:
+            size_2 += 1
+        elif is_xcd:
+            size_1 += 1
+            size_2 += 1
+        
+        adf11['input_file'][str(i)] = np.zeros((
+            adf11['input_file']['metas'][size_1],
+            adf11['input_file']['metas'][size_2],
+            len(adf11['input_file']['temp_grid']),
+            len(adf11['input_file']['dens_grid'])
+        ))
+            
+    #Reading the GCR value portion
+    gcr_line = f.readline()
+    ii = 0
+    
+    while len(gcr_line.strip()) != 0 and 'C-' not in gcr_line:
+        #look for the stage identifying line
+        if('----------' in gcr_line):
+            dens_count = 0
+            temp_count = 0
+            stage_id = np.array(list(map(int,re.findall('(\d+ )',gcr_line))))
+            if is_ascd:
+                if(len(stage_id) >1):
+                    tmp = stage_id[0]
+                    stage_id[0] = stage_id[1]
+                    stage_id[1] = tmp
+                else:#this accounts for unresolved files that don't follow the convection of resolved files
+                    tmp = stage_id[0]
+                    stage_id = np.array([1,1,tmp])
+
+            ii = ii+1
+        else:
+            gcr_vals = np.array(list(map(float,re.findall(r'((?:-\d+|\d).\d+)',gcr_line))))#Si gcr has positive vals maybe other do to?
+            adf11['input_file'][str(stage_id[2]-1)][stage_id[0]-1,stage_id[1]-1,
+                                           temp_count,dens_count:dens_count+len(gcr_vals)] = gcr_vals
+            dens_count = dens_count + len(gcr_vals)
+            if(dens_count == len(adf11['input_file']['dens_grid'])):
+                temp_count = temp_count + 1
+                dens_count = 0
+        gcr_line = f.readline()
+    return adf11