Revision: 134
Author: atenderholt
Date: 2006-05-19 18:08:57 -0700 (Fri, 19 May 2006)
ViewCVS: http://svn.sourceforge.net/cclib/?rev=134&view=rev
Log Message:
-----------
Made MPA work with new population class
Modified Paths:
--------------
trunk/src/cclib/method/mpa.py
Modified: trunk/src/cclib/method/mpa.py
===================================================================
--- trunk/src/cclib/method/mpa.py 2006-05-19 21:43:32 UTC (rev 133)
+++ trunk/src/cclib/method/mpa.py 2006-05-20 01:08:57 UTC (rev 134)
@@ -20,9 +20,9 @@
import re,time
import Numeric
import random # For sometimes running the progress updater
-from calculationmethod import Method
+from population import Population
-class MPA(Method):
+class MPA(Population):
"""The Mulliken population analysis"""
def __init__(self,*args):
@@ -37,7 +37,7 @@
"""Return a representation of the object."""
return 'MPA("%s")' % (self.parser)
- def calculate(self,fupdate=0.05):
+ def calculate(self,indices=None,fupdate=0.05):
"""Perform a Mulliken population analysis given the results of a parser"""
if not self.parser.parsed:
@@ -95,73 +95,29 @@
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(MPA, 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,mpa
doctest.testmod(mpa,verbose=False)
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