cclib-svn

[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
   + *


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[cclib-svn] SF.net SVN: cclib: [113] trunk/src/cclib/method

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

Revision: 113
Author:   atenderholt
Date:     2006-05-11 16:55:35 -0700 (Thu, 11 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=113&view=rev

Log Message:
-----------
More work on the Mulliken and C-sqared PAs

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

Added Paths:
-----------
    trunk/src/cclib/method/mpa.py
Modified: trunk/src/cclib/method/__init__.py
===================================================================
--- trunk/src/cclib/method/__init__.py	2006-05-11 00:52:59 UTC (rev 112)
+++ trunk/src/cclib/method/__init__.py	2006-05-11 23:55:35 UTC (rev 113)
@@ -1,2 +1,3 @@
 from density import Density
 from cspa import CSPA
+from mpa import MPA

Modified: trunk/src/cclib/method/cspa.py
===================================================================
--- trunk/src/cclib/method/cspa.py	2006-05-11 00:52:59 UTC (rev 112)
+++ trunk/src/cclib/method/cspa.py	2006-05-11 23:55:35 UTC (rev 113)
@@ -31,7 +31,7 @@
         
     def __str__(self):
         """Return a string representation of the object."""
-        return "Density matrix of" % (self.parser)
+        return "CSPA of" % (self.parser)
 
     def __repr__(self):
         """Return a representation of the object."""
@@ -84,6 +84,75 @@
         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
+
+        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]
+            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")
+        
+        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):
+
+        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,g03parser
-    doctest.testmod(g03parser,verbose=False)
+    import doctest,cspa
+    doctest.testmod(cspa,verbose=False)

Added: trunk/src/cclib/method/mpa.py
===================================================================
--- trunk/src/cclib/method/mpa.py	                        (rev 0)
+++ trunk/src/cclib/method/mpa.py	2006-05-11 23:55:35 UTC (rev 113)
@@ -0,0 +1,167 @@
+"""
+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 MPA(Method):
+    """The Mulliken population analysis"""
+    def __init__(self,*args):
+
+        # Call the __init__ method of the superclass
+        super(MPA, self).__init__(logname="MPA",*args)
+        
+    def __str__(self):
+        """Return a string representation of the object."""
+        return "MPA of" % (self.parser)
+
+    def __repr__(self):
+        """Return a representation of the object."""
+        return 'MPA("%s")' % (self.parser)
+    
+    def calculate(self,fupdate=0.05):
+        """Perform a Mulliken 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,"aooverlaps") \
+                    or hasattr(self.parser, "fooverlaps") ) \
+          and not hasattr(self.parser,"nbasis"):
+            self.logger.error("Missing mocoeffs, aooverlaps/fooverlaps or nbasis")
+            return False #let the caller of function know we didn't finish
+
+        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
+        self.logger.info("Creating attribute aoresults: array[3]")
+        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,"Mulliken Population Analysis")
+
+                #X_{ai} = \sum_b c_{ai} c_{bi} S_{ab}
+                #       = c_{ai} \sum_b c_{bi} S_{ab}
+                #       = c_{ai} C(i) \cdot S(a)
+                # X = C(i) * [C(i) \cdot S]
+                # C(i) is 1xn and S is nxn, result of matrix mult is 1xn
+
+                ci = self.parser.mocoeffs[spin][i]
+                if hasattr(self.parser,"aooverlaps"):
+                    temp = Numeric.matrixmultiply(ci,self.parser.aooverlaps)
+                elif hasattr(self.parser,"fooverlaps"):
+                    temp = Numeric.matrixmultiply(ci,self.parser.fooverlaps)
+
+                self.aoresults[spin][i]=Numeric.multiply(ci,temp)
+
+                step+=1
+
+        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
+
+        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]
+            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")
+        
+        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):
+
+        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,mpa
+    doctest.testmod(mpa,verbose=False)


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


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[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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[cclib-svn] SF.net SVN: cclib: [148] trunk/src/cclib/method

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

Revision: 148
Author:   atenderholt
Date:     2006-05-22 15:20:58 -0700 (Mon, 22 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=148&view=rev

Log Message:
-----------
Added overlap population analysis. Still need to do extensive testing.

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

Added Paths:
-----------
    trunk/src/cclib/method/opa.py
Modified: trunk/src/cclib/method/__init__.py
===================================================================
--- trunk/src/cclib/method/__init__.py	2006-05-22 15:32:53 UTC (rev 147)
+++ trunk/src/cclib/method/__init__.py	2006-05-22 22:20:58 UTC (rev 148)
@@ -1,3 +1,4 @@
 from density import Density
 from cspa import CSPA
 from mpa import MPA
+from opa import OPA

Added: trunk/src/cclib/method/opa.py
===================================================================
--- trunk/src/cclib/method/opa.py	                        (rev 0)
+++ trunk/src/cclib/method/opa.py	2006-05-22 22:20:58 UTC (rev 148)
@@ -0,0 +1,140 @@
+"""
+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 OPA(Method):
+    """The overlap population analysis"""
+    def __init__(self,*args):
+
+        # Call the __init__ method of the superclass
+        super(OPA, self).__init__(logname="OPA",*args)
+        
+    def __str__(self):
+        """Return a string representation of the object."""
+        return "OPA of" % (self.parser)
+
+    def __repr__(self):
+        """Return a representation of the object."""
+        return 'OPA("%s")' % (self.parser)
+    
+    def calculate(self,indices=None,fupdate=0.05):
+        """Perform an overlap 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,"aooverlaps") \
+                    or hasattr(self.parser, "fooverlaps") ) \
+          and not hasattr(self.parser,"nbasis"):
+            self.logger.error("Missing mocoeffs, aooverlaps/fooverlaps or nbasis")
+            return False #let the caller of function know we didn't finish
+
+        unrestricted=(len(self.parser.mocoeffs)==2)
+        nmocoeffs=len(self.parser.mocoeffs[0])
+        nbasis=self.parser.nbasis
+
+        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)
+
+        #determine number of steps, and whether process involves beta orbitals
+        nstep=nmocoeffs
+        nfrag=len(indices) #nfrag
+        self.logger.info("Creating attribute aoresults: array[3]")
+        if unrestricted:
+            self.results=Numeric.ones([2,nmocoeffs,nfrag,nfrag],"f")
+            nstep+=nmocoeffs
+        else:
+            self.results=Numeric.ones([1,nmocoeffs,nfrag,nfrag],"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,"Mulliken Population Analysis")
+
+                # OP_{AB,i} = \sum_{a in A} \sum_{b in B} 2 c_{ai} c_{bi} S_{ab}
+                #       = \sum_{a in A} c_{ai} \sum_{b in B} c_{bi} S_{ab}
+                #       = \sum_{a in A} c_{ai} \sub_{b in B} C_{Bi}
+                #          where C_{Bi} = C(i) times S(a)
+
+                ci = self.parser.mocoeffs[spin][i]
+
+                if hasattr(self.parser,"aooverlaps"):
+                    temp = Numeric.multiply(ci,self.parser.aooverlaps)
+                elif hasattr(self.parser,"fooverlaps"):
+                    temp = Numeric.multiply(ci,self.parser.fooverlaps)
+
+                for A in range(len(indices)-1):
+
+                    for B in range(A+1,len(indices)):
+
+                        tempb=0
+                        for b in indices[B]:
+                            tempb+=temp[:,b]
+
+                        tempresult=0
+                        for a in indices[A]:
+                            tempresult+=ci[a]*tempb[a]
+
+                        self.results[spin][i][A][B]=2*tempresult
+                        self.results[spin][i][B][A]=2*tempresult
+
+                step+=1
+
+        if self.progress:
+            self.progress.update(nstep,"Done")
+
+        return True
+
+if __name__=="__main__":
+    import doctest,opa
+    doctest.testmod(opa,verbose=False)


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


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[cclib-svn] SF.net SVN: cclib: [149] trunk/src/cclib/method

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

Revision: 149
Author:   atenderholt
Date:     2006-05-22 16:32:17 -0700 (Mon, 22 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=149&view=rev

Log Message:
-----------
Minor OPA changes, and a fix to textprogress.

OPA is correct, although it is horribly slow. Need to fix.

Modified Paths:
--------------
    trunk/src/cclib/method/opa.py
    trunk/src/cclib/progress/textprogress.py
Modified: trunk/src/cclib/method/opa.py
===================================================================
--- trunk/src/cclib/method/opa.py	2006-05-22 22:20:58 UTC (rev 148)
+++ trunk/src/cclib/method/opa.py	2006-05-22 23:32:17 UTC (rev 149)
@@ -99,7 +99,7 @@
             for i in range(nmocoeffs):
 
                 if self.progress and random.random()<fupdate:
-                    self.progress.update(step,"Mulliken Population Analysis")
+                    self.progress.update(step,"Overlap Population Analysis")
 
                 # OP_{AB,i} = \sum_{a in A} \sum_{b in B} 2 c_{ai} c_{bi} S_{ab}
                 #       = \sum_{a in A} c_{ai} \sum_{b in B} c_{bi} S_{ab}

Modified: trunk/src/cclib/progress/textprogress.py
===================================================================
--- trunk/src/cclib/progress/textprogress.py	2006-05-22 22:20:58 UTC (rev 148)
+++ trunk/src/cclib/progress/textprogress.py	2006-05-22 23:32:17 UTC (rev 149)
@@ -30,7 +30,7 @@
             str+="] %3i"%(self.progress)+"%"
             
             if text:
-                str+="    Parsing "+text
+                str+="    "+text
 
             sys.stdout.write("\r"+70*" ")
             sys.stdout.flush()


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[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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[cclib-svn] SF.net SVN: cclib: [226] trunk/src/cclib/method

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

Revision: 226
Author:   baoilleach
Date:     2006-06-20 13:58:31 -0700 (Tue, 20 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=226&view=rev

Log Message:
-----------
Pylint spacing recommendations

Modified Paths:
--------------
    trunk/src/cclib/method/calculationmethod.py
    trunk/src/cclib/method/cspa.py
    trunk/src/cclib/method/mpa.py
    trunk/src/cclib/method/opa.py
    trunk/src/cclib/method/population.py

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[cclib-svn] SF.net SVN: cclib: [227] trunk/src/cclib/method

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

Revision: 227
Author:   baoilleach
Date:     2006-06-21 03:03:48 -0700 (Wed, 21 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=227&view=rev

Log Message:
-----------
Implementing pylint recommendations and setting the Rev keyword

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

Property Changed:
----------------
    trunk/src/cclib/method/__init__.py
    trunk/src/cclib/method/calculationmethod.py
    trunk/src/cclib/method/cspa.py
    trunk/src/cclib/method/density.py
    trunk/src/cclib/method/mbo.py
    trunk/src/cclib/method/mpa.py
    trunk/src/cclib/method/opa.py
    trunk/src/cclib/method/population.py

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[cclib-svn] SF.net SVN: cclib: [450] trunk/src/cclib/method

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

Revision: 450
          http://svn.sourceforge.net/cclib/?rev=450&view=rev
Author:   atenderholt
Date:     2006-12-19 16:07:32 -0800 (Tue, 19 Dec 2006)

Log Message:
-----------
Methods: Begin work on CDA method by creating class to convert from basis built on atomic orbitals to basis built from fragment molecular orbitals

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

Added Paths:
-----------
    trunk/src/cclib/method/fragments.py


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[cclib-svn] SF.net SVN: cclib: [453] trunk/src/cclib/method

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

Revision: 453
          http://svn.sourceforge.net/cclib/?rev=453&view=rev
Author:   atenderholt
Date:     2006-12-22 21:58:31 -0800 (Fri, 22 Dec 2006)

Log Message:
-----------
FragmentAnalysis: convert aooverlaps into new molecular basis, resulting in the fooverlaps attribute; also has to update MPA to typecase a double into a float

Modified Paths:
--------------
    trunk/src/cclib/method/fragments.py
    trunk/src/cclib/method/mpa.py


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[cclib-svn] SF.net SVN: cclib: [596] trunk/src/cclib/method

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

Revision: 596
          http://svn.sourceforge.net/cclib/?rev=596&view=rev
Author:   atenderholt
Date:     2007-03-26 11:52:59 -0700 (Mon, 26 Mar 2007)

Log Message:
-----------
Change the MPA method to work with parsers that have different number of alpha and beta mocoeffs

Modified Paths:
--------------
    trunk/src/cclib/method/mpa.py
    trunk/src/cclib/method/population.py


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[cclib-svn] SF.net SVN: cclib: [630] trunk/src/cclib/method

[<la...@us...>]

Revision: 630
          http://svn.sourceforge.net/cclib/?rev=630&view=rev
Author:   langner
Date:     2007-05-19 15:41:53 -0700 (Sat, 19 May 2007)

Log Message:
-----------
Committing code for LPA (Lowdin Population Analysis) - was not added to svn repository in previous commit.

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

Added Paths:
-----------
    trunk/src/cclib/method/lpa.py


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