[cclib-svn] SF.net SVN: cclib: [130] trunk/src/cclib/method

[<ate...@us...>]

Revision: 130
Author:   atenderholt
Date:     2006-05-19 10:29:54 -0700 (Fri, 19 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=130&view=rev

Log Message:
-----------
Reworked cspa to use base population class, haven't tested because my cclib parser installation seems to be broken. Committing since it's not a high-profile change.

Modified Paths:
--------------
    trunk/src/cclib/method/cspa.py

Added Paths:
-----------
    trunk/src/cclib/method/population.py
Modified: trunk/src/cclib/method/cspa.py
===================================================================
--- trunk/src/cclib/method/cspa.py	2006-05-19 16:37:32 UTC (rev 129)
+++ trunk/src/cclib/method/cspa.py	2006-05-19 17:29:54 UTC (rev 130)
@@ -20,14 +20,14 @@
 import re,time
 import Numeric
 import random # For sometimes running the progress updater
-from calculationmethod import Method
+from population import Population
 
-class CSPA(Method):
+class CSPA(Population):
     """The C-squared population analysis"""
     def __init__(self,*args):
 
         # Call the __init__ method of the superclass
-        super(CSPA, self).__init__(logname="Density",*args)
+        super(CSPA, self).__init__(logname="CSPA",*args)
         
     def __str__(self):
         """Return a string representation of the object."""
@@ -37,7 +37,7 @@
         """Return a representation of the object."""
         return 'CSPA("%s")' % (self.parser)
     
-    def calculate(self,fupdate=0.05):
+    def calculate(self,indices=None,fupdate=0.05):
         """Perform a C-squared population analysis given the results of a parser"""
     
         if not self.parser.parsed:
@@ -84,75 +84,29 @@
         if self.progress:
             self.progress.update(nstep,"Done")
 
-#build list of groups of orbitals in each atom for atomresults
-        if hasattr(self.parser,"aonames"):
-            names=self.parser.aonames
-        elif hasattr(self.parser,"foonames"):
-            names=self.parser.fonames
+        retval=super(CSPA, self).partition(indices)
 
-        atoms=[]
-        indices=[]
+        if not retval:
+            self.logger.error("Error in partitioning results")
+            return False
 
-        name=names[0].split('_')[0]
-        atoms.append(name)
-        indices.append([0])
-
-        for i in range(1,len(names)):
-            name=names[i].split('_')[0]
-            if name==atoms[-1]:
-                indices[-1].append(i)
-            else:
-                atoms.append(name)
-                indices.append([i])
-
-        self.logger.info("Creating atomresults: array[3]")
-        self.atomresults=self.partition(indices)
-
 #create array for mulliken charges
-        self.logger.info("Creating atomcharges: array[1]")
-        size=len(self.atomresults[0][0])
-        self.atomcharges=Numeric.zeros([size],"f")
+        self.logger.info("Creating fragcharges: array[1]")
+        size=len(self.fragresults[0][0])
+        self.fragcharges=Numeric.zeros([size],"f")
         
-        for spin in range(len(self.atomresults)):
+        for spin in range(len(self.fragresults)):
 
             for i in range(self.parser.homos[spin]+1):
 
-                temp=Numeric.reshape(self.atomresults[spin][i],(size,))
-                self.atomcharges=Numeric.add(self.atomcharges,temp)
+                temp=Numeric.reshape(self.fragresults[spin][i],(size,))
+                self.fragcharges=Numeric.add(self.fragcharges,temp)
         
         if not unrestricted:
-            self.atomcharges=Numeric.multiply(self.atomcharges,2)
+            self.fragcharges=Numeric.multiply(self.fragcharges,2)
 
-
         return True
 
-    def partition(self,indices):
-
-        if not hasattr(self,"aoresults"):
-            self.calculate()
-
-        natoms=len(indices)
-        nmocoeffs=len(self.aoresults[0])
-        
-#build results Numeric array[3]
-        if len(self.aoresults)==2:
-            results=Numeric.zeros([2,nmocoeffs,natoms],"f")
-        else:
-            results=Numeric.zeros([1,nmocoeffs,natoms],"f")
-        
-#for each spin, splice Numeric array at ao index, and add to correct result row
-        for spin in range(len(results)):
-
-            for i in range(natoms): #number of groups
-
-                for j in range(len(indices[i])): #for each group
-                
-                    temp=self.aoresults[spin,:,indices[i][j]]
-                    results[spin,:,i]=Numeric.add(results[spin,:,i],temp)
-
-        return results
-
-
 if __name__=="__main__":
     import doctest,cspa
     doctest.testmod(cspa,verbose=False)

Added: trunk/src/cclib/method/population.py
===================================================================
--- trunk/src/cclib/method/population.py	                        (rev 0)
+++ trunk/src/cclib/method/population.py	2006-05-19 17:29:54 UTC (rev 130)
@@ -0,0 +1,114 @@
+"""
+cclib is a parser for computational chemistry log files.
+
+See http://cclib.sf.net for more information.
+
+Copyright (C) 2006 Noel O'Boyle and Adam Tenderholt
+
+ This program is free software; you can redistribute and/or modify it
+ under the terms of the GNU General Public License as published by the
+ Free Software Foundation; either version 2, or (at your option) any later
+ version.
+
+ This program is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ General Public License for more details.
+
+Contributions (monetary as well as code :-) are encouraged.
+"""
+import re,time
+import Numeric
+import random # For sometimes running the progress updater
+from calculationmethod import Method
+
+class Population(Method):
+    """A base class for all population-type methods"""
+    def __init__(self,*args):
+
+        # Call the __init__ method of the superclass
+        super(Population, self).__init__(logname="Population",*args)
+        self.fragresults=None
+        
+    def __str__(self):
+        """Return a string representation of the object."""
+        return "Population"
+
+    def __repr__(self):
+        """Return a representation of the object."""
+        return "Population"
+    
+
+#create array for mulliken charges
+        self.logger.info("Creating atomcharges: array[1]")
+        size=len(self.atomresults[0][0])
+        self.atomcharges=Numeric.zeros([size],"f")
+        
+        for spin in range(len(self.atomresults)):
+
+            for i in range(self.parser.homos[spin]+1):
+
+                temp=Numeric.reshape(self.atomresults[spin][i],(size,))
+                self.atomcharges=Numeric.add(self.atomcharges,temp)
+        
+        if not unrestricted:
+            self.atomcharges=Numeric.multiply(self.atomcharges,2)
+
+        return True
+
+    def partition(self,indices=None):
+
+        if not hasattr(self,"aoresults"):
+            self.calculate()
+
+        if not indices:
+#build list of groups of orbitals in each atom for atomresults
+            if hasattr(self.parser,"aonames"):
+                names=self.parser.aonames
+            elif hasattr(self.parser,"foonames"):
+                names=self.parser.fonames
+
+            atoms=[]
+            indices=[]
+
+            name=names[0].split('_')[0]
+            atoms.append(name)
+            indices.append([0])
+
+            for i in range(1,len(names)):
+                name=names[i].split('_')[0]
+                try:
+                    index=atoms.index(name)
+                except ValueError: #not found in atom list
+                    atoms.append(name)
+                    indices.append([i])
+                else:
+                    indices[index].append(i)
+
+        natoms=len(indices)
+        nmocoeffs=len(self.aoresults[0])
+        
+#build results Numeric array[3]
+        if len(self.aoresults)==2:
+            results=Numeric.zeros([2,nmocoeffs,natoms],"f")
+        else:
+            results=Numeric.zeros([1,nmocoeffs,natoms],"f")
+        
+#for each spin, splice Numeric array at ao index, and add to correct result row
+        for spin in range(len(results)):
+
+            for i in range(natoms): #number of groups
+
+                for j in range(len(indices[i])): #for each group
+                
+                    temp=self.aoresults[spin,:,indices[i][j]]
+                    results[spin,:,i]=Numeric.add(results[spin,:,i],temp)
+
+        self.logger.info("Saving partitioned results in fragresults: array[3]")
+        self.fragresults=results
+
+        return True
+
+if __name__=="__main__":
+    import doctest,mpa
+    doctest.testmod(mpa,verbose=False)


Property changes on: trunk/src/cclib/method/population.py
___________________________________________________________________
Name: svn:executable
   + *


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