From b502a622cc4a280610d567d298e872e3818ab6fa Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 7 Nov 2018 15:29:32 +0100
Subject: [PATCH] Fixed Gamess with symmetry

---
 resultsFile/Modules/gamessFile.py | 55 ++++++++++++++++++-------------
 1 file changed, 33 insertions(+), 22 deletions(-)

diff --git a/resultsFile/Modules/gamessFile.py b/resultsFile/Modules/gamessFile.py
index 74ed09f..6681802 100755
--- a/resultsFile/Modules/gamessFile.py
+++ b/resultsFile/Modules/gamessFile.py
@@ -599,15 +599,19 @@ class gamessFile(resultsFile):
         except IndexError:
            return None
         end = self._pos
-        pos += 4
+        pos += 2
         basis_read = []
+        basis_read_dict = {}
+        atom_label = None
         atom = []
         while pos < end:
            line = self.text[pos].split()
            bf = []
            if len(line) == 1:
              basis_read.append(atom)
+             basis_read_dict[atom_label] = atom
              atom = []
+             atom_label = line[0]
            while len(line) > 1:
               index = int(line[0])
               sym = line[1]
@@ -625,20 +629,29 @@ class gamessFile(resultsFile):
            pos += 1
 
         basis_read.append(atom)
+        basis_read_dict[atom_label] = atom
+
+#        new_basis_read = []
+#        ib = 1
+#        for iatom in range(len(basis_read)):
+#          atom = basis_read[iatom]
+#          for (i, s, b) in atom:
+#            new_basis_read += [ [ib, s, b] ]
+#            ib += 1
+#          if iatom+1 < len(basis_read):
+#            while ib < basis_read[iatom+1][0][0]:
+#                for (i, s, b) in atom:
+#                    new_basis_read += [ [ib, s, b] ]
+#                    ib += 1
+#          
+#        basis_read = new_basis_read
 
         new_basis_read = []
-        ib = 1
         for iatom in range(len(basis_read)):
           atom = basis_read[iatom]
-          for (i, s, b) in atom:
-            new_basis_read += [ [ib, s, b] ]
-            ib += 1
-          if iatom+1 < len(basis_read):
-            while ib < basis_read[iatom+1][0][0]:
-                for (i, s, b) in atom:
-                    new_basis_read += [ [ib, s, b] ]
-                    ib += 1
-          
+          for a in atom:
+            new_basis_read += [ a ]
+
         basis_read = new_basis_read
 
         Nmax = basis_read[len(basis_read)-1][0]
@@ -646,18 +659,15 @@ class gamessFile(resultsFile):
         for b in basis_read:
            basis[b[0]-1] = [b[1],b[2]]
 
+        # If symmetry is used, rebuild the basis taking the infos of the atoms
+        if None in basis:
+          basis_aux = []
+          for atom in self.geometry:
+            basis_aux += basis_read_dict[atom._name]
 
-        NotNone = 0
-        ReadNone = False
-        for i in range(len(basis)-1,-1,-1):
-           if basis[i] == None:
-              ReadNone = True
-              basis[i] = list(basis[i+NotNone])
-           else:
-              if ReadNone:
-                 NotNone = 0
-                 ReadNone = False
-              NotNone += 1
+        for i,b in enumerate(basis):
+          if b is None:
+            basis[i] = [ basis_aux[i][1], basis_aux[i][2] ]
 
         k=0
         while k<len(basis):
@@ -697,6 +707,7 @@ class gamessFile(resultsFile):
               basis[k][0] = i
            k+=1
 
+
         for a,i in enumerate(self.atom_to_ao_range):
            for j in range(i[0]-1,i[1]):
               basis[j].append(a)