Added qp_json

scripts/qp_exc_energy.py

@@ -42,13 +42,15 @@ import sys, os
 import scipy
 import scipy.stats
 from math import sqrt, gamma, exp
-import json
+import qp_json
 
 
-def read_data(filename,state):
+def read_data(ezfio_filename,state):
   """ Read energies and PT2 from input file """
-  with open(filename,'r') as f:
-      lines = json.load(f)['fci']
+  data = qp_json.load_last(ezfio_filename)
+  for method in data.keys():
+    x = data[method]
+  lines = x
 
   print(f"State: {state}")
 
@@ -138,15 +140,15 @@ def compute(data):
 
     return mu, err, bias, p
 
-filename = sys.argv[1]
-print(filename)
+ezfio_filename = sys.argv[1]
+print(ezfio_filename)
 if len(sys.argv) > 2:
     state = int(sys.argv[2])
 else:
     state = 1
-data = read_data(filename,state)
+data = read_data(ezfio_filename,state)
 mu, err, bias, _ = compute(data)
-print(" %s: %8.3f +/- %5.3f eV\n"%(filename, mu, err))
+print(" %s: %8.3f +/- %5.3f eV\n"%(ezfio_filename, mu, err))
 
 import numpy as np
 A = np.array( [ [ data[-1][1], 1. ],

scripts/utility/qp_json.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+import os
+import json
+
+def fix_json(s):
+   """Properly termitates an incomplete JSON file"""
+
+   s = s.replace(' ','')
+   s = s.replace('\n','')
+   s = s.replace('\t','')
+   s = s.replace(",{}",'')
+   tmp = [ c for c in s if c in "[]{}" ]
+   tmp = "".join(tmp)
+   tmp_old = ""
+   while tmp != tmp_old:
+      tmp_old = tmp
+      tmp = tmp.replace("{}","")
+      tmp = tmp.replace("[]","")
+   while s[-1] in [ ',', '\n', ' ', '\t' ]:
+      s = s[:-1]
+   tmp = [ c for c in tmp ]
+   tmp.reverse()
+   for c in tmp:
+      if c == '[': s += "]"
+      elif c == '{': s += "}"
+   return s
+
+
+def load(filename):
+  """Loads a JSON file after calling the fix_json function."""
+  with open(filename,'r') as f:
+    data = f.read()
+  new_data = fix_json(data)
+  return json.loads(new_data)
+
+
+def load_all(ezfio_filename):
+  """Loads all JSON files of an EZFIO."""
+  d = {}
+  prefix = ezfio_filename+'/json/'
+  for filename in [ x for x in os.listdir(prefix) if x.endswith(".json")]:
+    d[filename] = load(prefix+filename)
+  return d
+
+
+def load_last(ezfio_filename):
+  """Loads last JSON file of an EZFIO."""
+  d = {}
+  prefix = ezfio_filename+'/json/'
+  l = [ x for x in os.listdir(prefix) if x.endswith(".json")]
+  l.sort()
+  filename = l[-1]
+  print(filename)
+  return load(prefix+filename)
+
+
+def fix(ezfio_filename):
+  """Fixes all JSON files in an EZFIO."""
+  d = load_all(ezfio_filename)
+  prefix = ezfio_filename+'/json/'
+  for filename in d.keys():
+        with open(prefix+filename, 'w') as json_file:
+            json.dump(d[filename], json_file)
+
+
+