[cclib-svn] SF.net SVN: cclib: [151] trunk/src/cclib/method

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

Revision: 151
Author:   atenderholt
Date:     2006-05-22 18:28:46 -0700 (Mon, 22 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=151&view=rev

Log Message:
-----------
Added method for mayer's bond orders. I checked it against one known result, and it seems to work.

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

Added Paths:
-----------
    trunk/src/cclib/method/mbo.py
Modified: trunk/src/cclib/method/__init__.py
===================================================================
--- trunk/src/cclib/method/__init__.py	2006-05-23 00:16:35 UTC (rev 150)
+++ trunk/src/cclib/method/__init__.py	2006-05-23 01:28:46 UTC (rev 151)
@@ -2,3 +2,4 @@
 from cspa import CSPA
 from mpa import MPA
 from opa import OPA
+from mbo import MBO

Modified: trunk/src/cclib/method/density.py
===================================================================
--- trunk/src/cclib/method/density.py	2006-05-23 00:16:35 UTC (rev 150)
+++ trunk/src/cclib/method/density.py	2006-05-23 01:28:46 UTC (rev 151)
@@ -20,14 +20,15 @@
 import re,time
 import Numeric
 import random # For sometimes running the progress updater
+import logging
 from calculationmethod import Method
 
 class Density(Method):
     """Calculate the density matrix"""
-    def __init__(self,*args):
+    def __init__(self,parser,progress=None,loglevel=logging.INFO,logname="Log"):
 
         # Call the __init__ method of the superclass
-        super(Density, self).__init__(logname="Density",*args)
+        super(Density, self).__init__(parser, progress,loglevel,logname)
         
     def __str__(self):
         """Return a string representation of the object."""

Added: trunk/src/cclib/method/mbo.py
===================================================================
--- trunk/src/cclib/method/mbo.py	                        (rev 0)
+++ trunk/src/cclib/method/mbo.py	2006-05-23 01:28:46 UTC (rev 151)
@@ -0,0 +1,129 @@
+"""
+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 density import Density
+
+class MBO(Density):
+    """Calculate the density matrix"""
+    def __init__(self,*args):
+
+        # Call the __init__ method of the superclass
+        super(MBO, self).__init__(logname="MBO",*args)
+        
+    def __str__(self):
+        """Return a string representation of the object."""
+        return "Mayer's bond order of" % (self.parser)
+
+    def __repr__(self):
+        """Return a representation of the object."""
+        return 'Mayer\'s bond order("%s")' % (self.parser)
+    
+    def calculate(self,indices=None,fupdate=0.05):
+        """Calculate Mayer's bond orders given the results of a parser"""
+    
+        if not self.parser.parsed:
+            self.parser.parse()
+
+        super(MBO,self).calculate(fupdate)
+
+        #do we have the needed info in the parser?
+        if not ( hasattr(self.parser,"aooverlaps") or hasattr(self.parser,"fooverlaps")):
+            self.logger.error("Missing overlap matrix")
+            return False #let the caller of function know we didn't finish
+
+        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)
+#done building list
+
+        self.logger.info("Creating attribute fragresults: array[3]")
+        size=len(indices)
+        unrestricted=(len(self.parser.mocoeffs)==2)
+
+        #determine number of steps, and whether process involves beta orbitals
+        PS=[]
+        PS.append(Numeric.matrixmultiply(self.density[0],self.parser.aooverlaps))
+        nstep=size**2 #approximately quadratic in size
+        if unrestricted:
+            self.fragresults=Numeric.zeros([2,size,size],"f")
+            PS.append(Numeric.matrixmultiply(self.density[1],self.parser.aooverlaps))
+        else:
+            self.fragresults=Numeric.zeros([1,size,size],"f")
+
+        #intialize progress if available
+        if self.progress:
+            self.progress.initialize(nstep)
+
+        step=0
+        for i in range(len(indices)):
+
+            if self.progress and random.random() < fupdate:
+                self.progress.update(step,"Mayer's Bond Order")
+
+            for j in range(i+1,len(indices)):
+
+                tempsumA=0
+                tempsumB=0
+                
+                for a in indices[i]:
+
+                    for b in indices[j]:
+
+                        tempsumA+=2*PS[0][a][b]*PS[0][b][a]
+                        if unrestricted:
+                            tempsumB+=2*PS[1][a][b]*PS[1][b][a]
+
+                self.fragresults[0][i,j]=tempsumA
+                self.fragresults[0][j,i]=tempsumA
+
+                if unrestricted:
+                    self.fragresults[1][i,j]=tempsumB
+                    self.fragresults[1][j,i]=tempsumB
+
+        if self.progress:
+            self.progress.update(nstep,"Done")
+
+        return True
+
+if __name__=="__main__":
+    import doctest,g03parser
+    doctest.testmod(g03parser,verbose=False)


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


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