[cclib-svn] SF.net SVN: cclib: [105] trunk/src/cclib

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

Revision: 105
Author:   atenderholt
Date:     2006-05-10 12:29:45 -0700 (Wed, 10 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=105&view=rev

Log Message:
-----------
Working on adding calculation methods to cclib.

Yeah, yeah, it probably doesn't run yet but it shouldn't break anything.

Added Paths:
-----------
    trunk/src/cclib/methods/
    trunk/src/cclib/methods/calculationmethod.py
    trunk/src/cclib/methods/density.py
Added: trunk/src/cclib/methods/calculationmethod.py
===================================================================
--- trunk/src/cclib/methods/calculationmethod.py	                        (rev 0)
+++ trunk/src/cclib/methods/calculationmethod.py	2006-05-10 19:29:45 UTC (rev 105)
@@ -0,0 +1,52 @@
+"""
+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 logging, sys
+import Numeric
+
+class Method(object):
+    """Abstract class for logfile objects.
+
+    Subclasses:
+        Density
+    
+    Attributes:
+    """
+    def __init__(self,parser,progress=None,
+                 loglevel=logging.INFO,logname="Log"):
+        """Initialise the Logfile object.
+
+        Typically called by subclasses in their own __init__ methods.
+        """
+        self.parser = parser
+        self.progress = progress
+        self.loglevel = loglevel
+        self.logname  = logname
+
+        # Set up the logger
+        self.logger = logging.getLogger('%s %s' % (self.logname,self.parser))
+        self.logger.setLevel(self.loglevel)
+        handler = logging.StreamHandler(sys.stdout)
+        handler.setFormatter(logging.Formatter("[%(name)s %(levelname)s] %(message)s"))
+        self.logger.addHandler(handler)
+
+
+if __name__=="__main__":
+    import doctest,calculationmethod
+    doctest.testmod(calculationmethod,verbose=False)


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

Added: trunk/src/cclib/methods/density.py
===================================================================
--- trunk/src/cclib/methods/density.py	                        (rev 0)
+++ trunk/src/cclib/methods/density.py	2006-05-10 19:29:45 UTC (rev 105)
@@ -0,0 +1,72 @@
+"""
+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 Density(Method):
+    """Calculate the density matrix"""
+    def __init__(self,*args):
+
+        # Call the __init__ method of the superclass
+        super(Density, 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 'Density matrix("%s")' % (self.parser)
+    
+    def calculate(self,fupdate=0.05,cupdate=0.002):
+        """Calculate the density matrix 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,"aooverlaps") 
+          and not hasattr(self.parser,"nbasis") 
+          and not hasattr(self.parser,"homos"):
+            self.logger.error("Missing mocoeffs or aooverlaps")
+            return False #let the caller of function know we didn't finish
+
+        self.logger.info("Creating attribute density: array[3]")
+        size=self.parser.nbasis
+        beta=(len(self.parser.mocoeffs)==2)
+
+        if beta:
+            self.density=Numeric.zeros([2,size,size],"f")
+        else:
+            self.density=Numeric.zeros([1,size,size],"f")
+
+        for i in range(self.parser.homos[0]+1):
+            col=Numeric.reshape(self.parser.mocoeffs[0][i],(size,1))
+            colt=Numeric.reshape(col,(1,size))
+
+            tempdensity=Numeric.matrixmultipy(col,colt)
+            density[0]=Numeric.add(density[0],tempdensity)
+
+if __name__=="__main__":
+    import doctest,g03parser
+    doctest.testmod(g03parser,verbose=False)


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


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