[cclib-svn] SF.net SVN: cclib: [145] trunk/test

[<bao...@us...>]

Revision: 145
Author:   baoilleach
Date:     2006-05-22 08:10:43 -0700 (Mon, 22 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=145&view=rev

Log Message:
-----------
Finished looking at atomcoords. It turns out that for some bizarre reason ADF has an extra geometry in it compared to geovalues. I have verified using alignment RMS (Biopython) that each geometry is in fact unique, and not just a rotation/translation.

Modified Paths:
--------------
    trunk/src/cclib/parser/gamessparser.py
    trunk/test/testGeoOpt.py
Modified: trunk/src/cclib/parser/gamessparser.py
===================================================================
--- trunk/src/cclib/parser/gamessparser.py	2006-05-22 13:09:51 UTC (rev 144)
+++ trunk/src/cclib/parser/gamessparser.py	2006-05-22 15:10:43 UTC (rev 145)
@@ -105,6 +105,7 @@
 
 
         firststdorient = True # Used to decide whether to wipe the atomcoords clean
+        geooptfinished = False # Used to avoid extracting the final geometry twice
             
         for line in inputfile:
             
@@ -173,7 +174,11 @@
                 self.atomnos = Numeric.array(atomnos,"i")
                 self.atomcoords.append(atomcoords)
 
-            if line[1:29]=="COORDINATES OF ALL ATOMS ARE":
+            if line[12:40]=="EQUILIBRIUM GEOMETRY LOCATED":
+                # Prevent extraction of the final geometry twice
+                geooptfinished = True
+            
+            if line[1:29]=="COORDINATES OF ALL ATOMS ARE" and not geooptfinished:
                 # This is the standard orientation, which is the only coordinate
                 # information available for all geometry optimisation cycles.
                 # The input orientation will be overwritten if this is a geometry optimisation

Modified: trunk/test/testGeoOpt.py
===================================================================
--- trunk/test/testGeoOpt.py	2006-05-22 13:09:51 UTC (rev 144)
+++ trunk/test/testGeoOpt.py	2006-05-22 15:10:43 UTC (rev 145)
@@ -12,10 +12,10 @@
         self.assertEquals(self.data.homos,array([34]))
 
     def testatomcoords(self):
-        """Are atomcoords consistent with natom, Angstroms and geovalues?"""
+        """Are atomcoords consistent with natom and Angstroms?"""
         coords = self.data.atomcoords
         self.assertEquals(self.data.natom,len(coords[0]),"len(atomcoords[0]) is %d but natom is %d" % (self.data.natom,len(coords[0])))
-        self.assertEquals(len(self.data.geovalues),len(coords)-1,"len(atomcoords)-1 is %d but len(geovalues) is %d" % (len(coords)-1,len(self.data.geovalues)))
+
         # Find the minimum distance between two C atoms
         mindist = 999
         for i in range(self.data.natom-1):
@@ -26,6 +26,12 @@
                         dist = math.sqrt(sum((coords[-1][i]-coords[-1][j])**2))
                         mindist = min(mindist,dist)
         self.assert_(abs(mindist-1.34)<0.03,"Mindist is %f (not 1.34)" % mindist)
+
+    def testatomcoords_more(self):
+        """Are atomcoords consistent with geovalues?"""
+        coords = self.data.atomcoords
+        self.assertEquals(len(self.data.geovalues),len(coords),"len(atomcoords) is %d but len(geovalues) is %d" % (len(coords),len(self.data.geovalues)))
+        
     
     def testnatom(self):
         """Is the number of atoms equal to 20?"""
@@ -81,6 +87,11 @@
            ADF calculations one more SCF cycle after the geometry is converged"""
         self.assert_(len(self.data.scfvalues)==len(self.data.geovalues)+1 and len(self.data.scfvalues[0])==len(self.data.scftargets))
 
+    def testatomcoords_more(self):
+        """Are atomcoords consistent with geovalues?"""
+        coords = self.data.atomcoords
+        self.assertEquals(len(self.data.geovalues),len(coords)-1,"len(atomcoords)-1 is %d but len(geovalues) is %d" % (len(coords)-1,len(self.data.geovalues)))
+
 class JaguarGeoOptTest(GenericGeoOptTest):
     def setUp(self):
         self.data = getfile(Jaguar,"basicJaguar","eg01","dvb_gopt.out")


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