[cclib-svn] SF.net SVN: cclib: [112] trunk/src/cclib/method

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

Revision: 112
Author:   atenderholt
Date:     2006-05-10 17:52:59 -0700 (Wed, 10 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=112&view=rev

Log Message:
-----------
Started CSPA method, still need atomresults and other possibilities

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

Added Paths:
-----------
    trunk/src/cclib/method/cspa.py
Modified: trunk/src/cclib/method/__init__.py
===================================================================
--- trunk/src/cclib/method/__init__.py	2006-05-10 23:28:49 UTC (rev 111)
+++ trunk/src/cclib/method/__init__.py	2006-05-11 00:52:59 UTC (rev 112)
@@ -1 +1,2 @@
 from density import Density
+from cspa import CSPA

Added: trunk/src/cclib/method/cspa.py
===================================================================
--- trunk/src/cclib/method/cspa.py	                        (rev 0)
+++ trunk/src/cclib/method/cspa.py	2006-05-11 00:52:59 UTC (rev 112)
@@ -0,0 +1,89 @@
+"""
+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 CSPA(Method):
+    """The C-squared population analysis"""
+    def __init__(self,*args):
+
+        # Call the __init__ method of the superclass
+        super(CSPA, self).__init__(logname="Density",*args)
+        
+    def __str__(self):
+        """Return a string representation of the object."""
+        return "Density matrix of" % (self.parser)
+
+    def __repr__(self):
+        """Return a representation of the object."""
+        return 'CSPA("%s")' % (self.parser)
+    
+    def calculate(self,fupdate=0.05):
+        """Perform a C-squared population analysis given the results of a parser"""
+    
+        if not self.parser.parsed:
+            self.parser.parse()
+
+        #do we have the needed info in the parser?
+        if not hasattr(self.parser,"mocoeffs") \
+          and not hasattr(self.parser,"nbasis"):
+            self.logger.error("Missing mocoeffs or nbasis")
+            return False #let the caller of function know we didn't finish
+
+        self.logger.info("Creating attribute aoresults: array[3]")
+        unrestricted=(len(self.parser.mocoeffs)==2)
+        nmocoeffs=len(self.parser.mocoeffs[0])
+        nbasis=self.parser.nbasis
+
+        #determine number of steps, and whether process involves beta orbitals
+        nstep=nmocoeffs
+        if unrestricted:
+            self.aoresults=Numeric.zeros([2,nmocoeffs,nbasis],"f")
+            nstep+=nmocoeffs
+        else:
+            self.aoresults=Numeric.zeros([1,nmocoeffs,nbasis],"f")
+
+        #intialize progress if available
+        if self.progress:
+            self.progress.initialize(nstep)
+
+        step=0
+        for spin in range(len(self.parser.mocoeffs)):
+
+            for i in range(nmocoeffs):
+
+                if self.progress and random.random()<fupdate:
+                    self.progress.update(step,"C^2 Population Analysis")
+
+                submocoeffs=self.parser.mocoeffs[spin][i]
+                scale=Numeric.innerproduct(submocoeffs,submocoeffs)
+                tempcoeffs=Numeric.multiply(submocoeffs,submocoeffs)
+                self.aoresults[spin][i]=Numeric.divide(tempcoeffs,scale)
+
+                step+=1
+
+        if self.progress:
+            self.progress.update(nstep,"Done")
+
+if __name__=="__main__":
+    import doctest,g03parser
+    doctest.testmod(g03parser,verbose=False)


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


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