cclib-svn — Log messages of SVN commits

[cclib-svn] SF.net SVN: cclib: [219] trunk/src/cclib/parser/jaguarparser.py

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

Revision: 219
Author:   baoilleach
Date:     2006-06-18 08:24:17 -0700 (Sun, 18 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=219&view=rev

Log Message:
-----------
Implemented pylint recommendations on spacing

Modified Paths:
--------------
    trunk/src/cclib/parser/jaguarparser.py

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

[cclib-svn] SF.net SVN: cclib: [218] trunk/src/cclib/parser

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

Revision: 218
Author:   baoilleach
Date:     2006-06-18 07:55:07 -0700 (Sun, 18 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=218&view=rev

Log Message:
-----------
Setting the svn:keywords property of all of these Python files to 'Rev'

Property Changed:
----------------
    trunk/src/cclib/parser/__init__.py
    trunk/src/cclib/parser/adfparser.py
    trunk/src/cclib/parser/gamessparser.py
    trunk/src/cclib/parser/gaussianparser.py
    trunk/src/cclib/parser/jaguarparser.py
    trunk/src/cclib/parser/logfileparser.py

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

[cclib-svn] SF.net SVN: cclib: [217] trunk/src/cclib/parser/gamessparser.py

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

Revision: 217
Author:   baoilleach
Date:     2006-06-18 07:53:43 -0700 (Sun, 18 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=217&view=rev

Log Message:
-----------
Implemented all pylint recommmendations on spacing

Modified Paths:
--------------
    trunk/src/cclib/parser/gamessparser.py

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

[cclib-svn] SF.net SVN: cclib: [216] trunk/src/cclib/parser/utils.py

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

Revision: 216
Author:   baoilleach
Date:     2006-06-18 07:40:16 -0700 (Sun, 18 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=216&view=rev

Log Message:
-----------
Asking SVN to substitute the revision number in to the __revision__ variable in the source code.

Property Changed:
----------------
    trunk/src/cclib/parser/utils.py

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

[cclib-svn] SF.net SVN: cclib: [215] trunk/src/cclib/parser/utils.py

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

Revision: 215
Author:   baoilleach
Date:     2006-06-18 07:39:09 -0700 (Sun, 18 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=215&view=rev

Log Message:
-----------
Implementing pylint recommendations

Modified Paths:
--------------
    trunk/src/cclib/parser/utils.py

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

[cclib-svn] SF.net SVN: cclib: [214] trunk/src/cclib/parser/adfparser.py

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

Revision: 214
Author:   baoilleach
Date:     2006-06-18 06:10:04 -0700 (Sun, 18 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=214&view=rev

Log Message:
-----------
Finished the pylint recommendations on spacing.

Modified Paths:
--------------
    trunk/src/cclib/parser/adfparser.py

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

[cclib-svn] SF.net SVN: cclib: [213] trunk/src/cclib/parser/adfparser.py

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

Revision: 213
Author:   baoilleach
Date:     2006-06-18 03:43:32 -0700 (Sun, 18 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=213&view=rev

Log Message:
-----------
More pylint style improvements

Modified Paths:
--------------
    trunk/src/cclib/parser/adfparser.py

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

[cclib-svn] SF.net SVN: cclib: [212] trunk/src/cclib/parser/adfparser.py

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

Revision: 212
Author:   baoilleach
Date:     2006-06-16 08:39:09 -0700 (Fri, 16 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=212&view=rev

Log Message:
-----------
Pylint recommended changes.

Modified Paths:
--------------
    trunk/src/cclib/parser/adfparser.py

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

[cclib-svn] SF.net SVN: cclib: [211] trunk/src/cclib

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

Revision: 211
Author:   baoilleach
Date:     2006-06-16 08:26:43 -0700 (Fri, 16 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=211&view=rev

Log Message:
-----------
Tidied up code formatting after looking at output of pylint

Modified Paths:
--------------
    trunk/src/cclib/__init__.py
    trunk/src/cclib/parser/gaussianparser.py

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

[cclib-svn] SF.net SVN: cclib: [210] trunk/src/scripts/ccget

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

Revision: 210
Author:   baoilleach
Date:     2006-06-15 09:01:15 -0700 (Thu, 15 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=210&view=rev

Log Message:
-----------
Doc: Updated usage info.

Modified Paths:
--------------
    trunk/src/scripts/ccget

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

[cclib-svn] SF.net SVN: cclib: [209] trunk/test/regression.py

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

Revision: 209
Author:   baoilleach
Date:     2006-06-15 07:32:47 -0700 (Thu, 15 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=209&view=rev

Log Message:
-----------
Test: Adding regression tests for data files that could not be parsed.

Added Paths:
-----------
    trunk/test/regression.py

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

[cclib-svn] SF.net SVN: cclib: [208] trunk/data/Gaussian/wildGaussian98

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

Revision: 208
Author:   baoilleach
Date:     2006-06-15 07:31:09 -0700 (Thu, 15 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=208&view=rev

Log Message:
-----------
Data: Added the wrong file

Added Paths:
-----------
    trunk/data/Gaussian/wildGaussian98/oo-LAN.out

Removed Paths:
-------------
    trunk/data/Gaussian/wildGaussian98/oo-lan.dat

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

[cclib-svn] SF.net SVN: cclib: [207] trunk/data/GAMESS

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

Revision: 207
Author:   baoilleach
Date:     2006-06-15 07:20:16 -0700 (Thu, 15 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=207&view=rev

Log Message:
-----------
Data: Example PCGAMESS file from AOMIX examples (available on web). Broke parser: fixed by r184

Added Paths:
-----------
    trunk/data/GAMESS/wildPCGAMESS/
    trunk/data/GAMESS/wildPCGAMESS/gamess.log

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

[cclib-svn] SF.net SVN: cclib: [206] trunk/data/GAMESS

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

Revision: 206
Author:   baoilleach
Date:     2006-06-15 07:16:05 -0700 (Thu, 15 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=206&view=rev

Log Message:
-----------
Data: Supplied by Joe Townsend. Different syntax for scftargets as it's as an earlier version of GAMESS.

Added Paths:
-----------
    trunk/data/GAMESS/wildGAMESS-US/
    trunk/data/GAMESS/wildGAMESS-US/bv6010sup1molecule_4.inp.cml_.log

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

[cclib-svn] SF.net SVN: cclib: [205] trunk/data/Gaussian

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

Revision: 205
Author:   baoilleach
Date:     2006-06-15 07:11:13 -0700 (Thu, 15 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=205&view=rev

Log Message:
-----------
Data: Gaussian98 file from AOMIX examples (available on the web). Broke the parser as there are fewer scftargets in Gaussian98.

Added Paths:
-----------
    trunk/data/Gaussian/wildGaussian98/
    trunk/data/Gaussian/wildGaussian98/oo-lan.dat

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

[cclib-svn] SF.net SVN: cclib: [163] trunk/test

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

Revision: 163
Author:   baoilleach
Date:     2006-05-27 01:24:22 -0700 (Sat, 27 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=163&view=rev

Log Message:
-----------
Sped up the tests 70 times or so, by avoiding re-parsing the file for every test. There's no built-in way to avoid reinitialising using the unittest framework, so you have to figure out a way yourself.

Modified Paths:
--------------
    trunk/test/testGeoOpt.py
    trunk/test/testSP.py
    trunk/test/testSPun.py
Modified: trunk/test/testGeoOpt.py
===================================================================
--- trunk/test/testGeoOpt.py	2006-05-27 07:58:33 UTC (rev 162)
+++ trunk/test/testGeoOpt.py	2006-05-27 08:24:22 UTC (rev 163)
@@ -70,19 +70,19 @@
 
 class GaussianGeoOptTest(GenericGeoOptTest):
     def setUp(self):
-        self.data = getfile(Gaussian,"basicGaussian03","dvb_gopt.out")
+        self.data = data[0]
 
 class GamessUSGeoOptTest(GenericGeoOptTest):
     def setUp(self):
-        self.data = getfile(GAMESS,"basicGAMESS-US","dvb_gopt_a.out")
+        self.data = data[2]
 
 class PCGamessGeoOptTest(GenericGeoOptTest):
     def setUp(self):
-        self.data = getfile(GAMESS,"basicPCGAMESS","dvb_gopt_a.out")
-
+        self.data = data[1]
+        
 class ADFGeoOptTest(GenericGeoOptTest):
     def setUp(self):
-        self.data = getfile(ADF,"basicADF2004.01","dvb_gopt_b.adfout")
+        self.data = data[3]
 
     def testscfvaluedim(self):
         """Do the scf values have the right dimensions? 
@@ -100,12 +100,18 @@
 
 class JaguarGeoOptTest(GenericGeoOptTest):
     def setUp(self):
-        self.data = getfile(Jaguar,"basicJaguar","eg01","dvb_gopt_b.out")
+        self.data = data[4]
+        
 
 names = [ "Gaussian", "PCGamess", "GAMESS", "ADF", "Jaguar" ]
 tests = [ GaussianGeoOptTest, PCGamessGeoOptTest,
           GamessUSGeoOptTest, ADFGeoOptTest,
           JaguarGeoOptTest ]
+data = [ getfile(Gaussian,"basicGaussian03","dvb_gopt.out"),
+         getfile(GAMESS,"basicPCGAMESS","dvb_gopt_a.out"),
+         getfile(GAMESS,"basicGAMESS-US","dvb_gopt_a.out"),
+         getfile(ADF,"basicADF2004.01","dvb_gopt_b.adfout"),
+         getfile(Jaguar,"basicJaguar","eg01","dvb_gopt_b.out") ]
 
 if __name__=="__main__":
     total = errors = failures = 0

Modified: trunk/test/testSP.py
===================================================================
--- trunk/test/testSP.py	2006-05-27 07:58:33 UTC (rev 162)
+++ trunk/test/testSP.py	2006-05-27 08:24:22 UTC (rev 163)
@@ -19,19 +19,19 @@
 
 class GaussianSPTest(GenericSPTest):
     def setUp(self):
-        self.data = getfile(Gaussian,"basicGaussian03","dvb_sp.out")
+        self.data = data[0]
 
 class GamessUSSPTest(GenericSPTest):
     def setUp(self):
-        self.data = getfile(GAMESS,"basicGAMESS-US","dvb_sp.out")
+        self.data = data[1]
 
 class PCGamessSPTest(GenericSPTest):
     def setUp(self):
-        self.data = getfile(GAMESS,"basicPCGAMESS","dvb_sp.out")
+        self.data = data[2]
 
 class ADFSPTest(GenericSPTest):
     def setUp(self):
-        self.data = getfile(ADF,"basicADF2004.01","dvb_sp_b.adfout")
+        self.data = data[3]
     
     def testdimaooverlaps(self):
         """Are the dims of the overlap matrix consistent with nbasis?"""
@@ -41,6 +41,10 @@
 names = [ "Gaussian", "PCGamess", "GAMESS", "ADF", "Jaguar" ]
 tests = [ GaussianSPTest, PCGamessSPTest,
           GamessUSSPTest, ADFSPTest ]
+data = [getfile(Gaussian,"basicGaussian03","dvb_sp.out"),
+        getfile(GAMESS,"basicGAMESS-US","dvb_sp.out"),
+        getfile(GAMESS,"basicPCGAMESS","dvb_sp.out"),
+        getfile(ADF,"basicADF2004.01","dvb_sp_b.adfout")]
               
 if __name__=="__main__":
     total = errors = failures = 0

Modified: trunk/test/testSPun.py
===================================================================
--- trunk/test/testSPun.py	2006-05-27 07:58:33 UTC (rev 162)
+++ trunk/test/testSPun.py	2006-05-27 08:24:22 UTC (rev 163)
@@ -22,19 +22,19 @@
 
 class GaussianSPunTest(GenericSPunTest):
     def setUp(self):
-        self.data = getfile(Gaussian,"basicGaussian03","dvb_un_sp.out")
+        self.data = data[0]
 
 class GamessUSSPunTest(GenericSPunTest):
     def setUp(self):
-        self.data = getfile(GAMESS,"basicGAMESS-US","dvb_un_sp.out")
+        self.data = data[1]
 
 class PCGamessSPunTest(GenericSPunTest):
     def setUp(self):
-        self.data = getfile(GAMESS,"basicPCGAMESS","dvb_un_sp.out")
+        self.data = data[2]
 
 class ADFSPunTest(GenericSPunTest):
     def setUp(self):
-        self.data = getfile(ADF,"basicADF2004.01","dvb_un_sp.adfout")
+        self.data = data[3]
 
     def testdimaooverlaps(self):
         """Are the dims of the overlap matrix consistent with nbasis?"""
@@ -45,6 +45,10 @@
 names = [ "Gaussian", "PCGamess", "GAMESS", "ADF" ]
 tests = [ GaussianSPunTest, PCGamessSPunTest,
           GamessUSSPunTest, ADFSPunTest ]
+data = [ getfile(Gaussian,"basicGaussian03","dvb_un_sp.out"),
+         getfile(GAMESS,"basicGAMESS-US","dvb_un_sp.out"),
+         getfile(GAMESS,"basicPCGAMESS","dvb_un_sp.out"),
+         getfile(ADF,"basicADF2004.01","dvb_un_sp.adfout") ]
               
 if __name__=="__main__":
     total = errors = failures = 0


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

[cclib-svn] SF.net SVN: cclib: [162] trunk/test

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

Revision: 162
Author:   baoilleach
Date:     2006-05-27 00:58:33 -0700 (Sat, 27 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=162&view=rev

Log Message:
-----------
Jaguar parser now reads scftargets and values correctly, at least for geometry optimisations. Have also converted scfenergies to eV. The GeoOpt test now looks at dvb_gopt_b, which has all of the virtual orbitals included, instead of dvb_gopt

Modified Paths:
--------------
    trunk/src/cclib/parser/jaguarparser.py
    trunk/test/testGeoOpt.py
Modified: trunk/src/cclib/parser/jaguarparser.py
===================================================================
--- trunk/src/cclib/parser/jaguarparser.py	2006-05-26 18:45:47 UTC (rev 161)
+++ trunk/src/cclib/parser/jaguarparser.py	2006-05-27 07:58:33 UTC (rev 162)
@@ -50,6 +50,8 @@
             inputfile.seek(0)
             self.progress.initialize(nstep)
             oldstep=0
+
+        geoopt = False # Is this a GeoOpt? Needed for SCF targets/values.
             
         for line in inputfile:
             
@@ -64,8 +66,12 @@
 # Get SCF convergence information
                 if not hasattr(self,"scfvalues"):
                     self.scfvalues = []
-                    self.logger.info("Creating attribute: scfvalues")
-                values = []
+                    self.logger.info("Creating attribute: scfvalues,scftargets")
+                    self.scftargets = Numeric.array([5E-5,5E-6],"f")
+                if not geoopt:
+                    values = [[],[]]
+                else:
+                    values = [[]]
                 while line[0:4]=="etot":
                     if line[39:47].strip():
                         denergy = float(line[39:47])
@@ -74,7 +80,11 @@
                                     # or should we just ignore the values in this line
                     ddensity = float(line[48:56])
                     maxdiiserr = float(line[57:65])
-                    values.append([denergy,ddensity,maxdiiserr])
+                    if not geoopt:
+                        values[0].append(denergy)
+                        values[1].append(ddensity)
+                    else:
+                        values[0].append(ddensity)
                     line = inputfile.next()
                 self.scfvalues.append(values)
 
@@ -84,7 +94,7 @@
                     self.logger.info("Creating attribute scfenergies")
                     self.scfenergies = []
                 temp = line.strip().split()
-                self.scfenergies.append(float(temp[temp.index("hartrees")-1]))
+                self.scfenergies.append(utils.convertor(float(temp[temp.index("hartrees")-1]),"hartree","eV"))
 
             if line[2:14]=="new geometry" or line[1:21]=="Symmetrized geometry":
 # Get the atom coordinates
@@ -107,6 +117,14 @@
                 self.atomnos = Numeric.array(atomnos,"i")
                 self.natom = len(atomcoords)
 
+            if not geoopt and line[2:24]=="start of program geopt":
+                geoopt = True
+                if hasattr(self,"scfvalues"):
+                    # Need to keep only the RMS density change info
+                    # if this is a geoopt
+                    self.scfvalues[0] = [self.scfvalues[0][1]]
+                    self.scftargets = self.scftargets[0]
+
             if line[2:28]=="geometry optimization step":
 # Get Geometry Opt convergence information
                 if not hasattr(self,"geovalues"):
@@ -187,8 +205,8 @@
 
         inputfile.close()
 
-##        if hasattr(self,"scfvalues"):
-##            self.scfvalues = Numeric.array(self.scfvalues,"f")
+        if hasattr(self,"scfvalues"):
+            self.scfvalues = [Numeric.array(x,"f") for x in self.scfvalues]
         if hasattr(self,"scfenergies"):
             self.scfenergies = Numeric.array(self.scfenergies,"f")
         if hasattr(self,"atomcoords"):

Modified: trunk/test/testGeoOpt.py
===================================================================
--- trunk/test/testGeoOpt.py	2006-05-26 18:45:47 UTC (rev 161)
+++ trunk/test/testGeoOpt.py	2006-05-27 07:58:33 UTC (rev 162)
@@ -33,7 +33,6 @@
         coords = self.data.atomcoords
         self.assertEquals(len(self.data.geovalues),len(coords),"len(atomcoords) is %d but len(geovalues) is %d" % (len(coords),len(self.data.geovalues)))
         
-    
     def testnatom(self):
         """Is the number of atoms equal to 20?"""
         self.assertEquals(self.data.natom,20)
@@ -101,7 +100,7 @@
 
 class JaguarGeoOptTest(GenericGeoOptTest):
     def setUp(self):
-        self.data = getfile(Jaguar,"basicJaguar","eg01","dvb_gopt.out")
+        self.data = getfile(Jaguar,"basicJaguar","eg01","dvb_gopt_b.out")
 
 names = [ "Gaussian", "PCGamess", "GAMESS", "ADF", "Jaguar" ]
 tests = [ GaussianGeoOptTest, PCGamessGeoOptTest,


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

[cclib-svn] SF.net SVN: cclib: [161] trunk/test

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

Revision: 161
Author:   baoilleach
Date:     2006-05-26 11:45:47 -0700 (Fri, 26 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=161&view=rev

Log Message:
-----------
Added some basic geoopt parsing for Jaguar. Coordinates, atomnos and natom. Corrected 'typo' in testGeoOpt.py

Modified Paths:
--------------
    trunk/src/cclib/parser/jaguarparser.py
    trunk/test/testGeoOpt.py
Modified: trunk/src/cclib/parser/jaguarparser.py
===================================================================
--- trunk/src/cclib/parser/jaguarparser.py	2006-05-26 17:33:53 UTC (rev 160)
+++ trunk/src/cclib/parser/jaguarparser.py	2006-05-26 18:45:47 UTC (rev 161)
@@ -86,25 +86,49 @@
                 temp = line.strip().split()
                 self.scfenergies.append(float(temp[temp.index("hartrees")-1]))
 
+            if line[2:14]=="new geometry" or line[1:21]=="Symmetrized geometry":
+# Get the atom coordinates
+                if not hasattr(self,"atomcoords"):
+                    self.logger.info("Creating attributes: atomcoords, atomnos, natom")
+                    self.atomcoords = []
+                p = re.compile("(\D+)\d+") # One/more letters followed by a number
+                atomcoords = []
+                atomnos = []
+                angstrom = inputfile.next()
+                title = inputfile.next()
+                line = inputfile.next()
+                while line.strip():
+                    temp = line.split()
+                    element = p.findall(temp[0])[0]
+                    atomnos.append(self.table.number[element])
+                    atomcoords.append(map(float,temp[1:]))
+                    line = inputfile.next()
+                self.atomcoords.append(atomcoords)
+                self.atomnos = Numeric.array(atomnos,"i")
+                self.natom = len(atomcoords)
+
             if line[2:28]=="geometry optimization step":
 # Get Geometry Opt convergence information
                 if not hasattr(self,"geovalues"):
                     self.geovalues = []
-                    self.geotargets = Numeric.zeros(4,"float")
-                    self.logger.info("Creating attributes: geovalues,geotargets")
+                    geotargets = Numeric.zeros(4,"f")
+                    i = 0
+                    self.logger.info("Creating attributs: geovalues,geotargets")
                 blank = inputfile.next()
                 blank = inputfile.next()
                 line = inputfile.next()
-                i = 0
                 values = []
                 while line!=blank:
                     if line[41]=="(":
                         # A new geo convergence value
                         values.append(float(line[26:37]))
-                        self.geotargets[i] = float(line[43:54])
-                        i+=1
+                        if not hasattr(self,"geotargets"):
+                            geotargets[i] = float(line[43:54])
+                            i += 1
                     line = inputfile.next()
                 self.geovalues.append(values)
+                if not hasattr(self,"geotargets"):
+                    self.geotargets = geotargets
 
             if line[2:33]=="Orbital energies/symmetry label":
 # Get MO Energies and symmetrys
@@ -167,6 +191,8 @@
 ##            self.scfvalues = Numeric.array(self.scfvalues,"f")
         if hasattr(self,"scfenergies"):
             self.scfenergies = Numeric.array(self.scfenergies,"f")
+        if hasattr(self,"atomcoords"):
+            self.atomcoords = Numeric.array(self.atomcoords,"f")
         self.parsed = True
         
 if __name__=="__main__":

Modified: trunk/test/testGeoOpt.py
===================================================================
--- trunk/test/testGeoOpt.py	2006-05-26 17:33:53 UTC (rev 160)
+++ trunk/test/testGeoOpt.py	2006-05-26 18:45:47 UTC (rev 161)
@@ -15,7 +15,7 @@
     def testatomcoords(self):
         """Are atomcoords consistent with natom and Angstroms?"""
         coords = self.data.atomcoords
-        self.assertEquals(self.data.natom,len(coords[0]),"len(atomcoords[0]) is %d but natom is %d" % (self.data.natom,len(coords[0])))
+        self.assertEquals(self.data.natom,len(coords[0]),"natom  is %d but len(atomcoords[0]) is %d" % (self.data.natom,len(coords[0])))
 
         # Find the minimum distance between two C atoms
         mindist = 999


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

[cclib-svn] SF.net SVN: cclib: [157] trunk/src/cclib/parser/gamessparser.py

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

Revision: 157
Author:   baoilleach
Date:     2006-05-24 12:43:41 -0700 (Wed, 24 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=157&view=rev

Log Message:
-----------
homos parsed correctly for both restricted and unrestricted calculations.

Modified Paths:
--------------
    trunk/src/cclib/parser/gamessparser.py
Modified: trunk/src/cclib/parser/gamessparser.py
===================================================================
--- trunk/src/cclib/parser/gamessparser.py	2006-05-24 19:16:00 UTC (rev 156)
+++ trunk/src/cclib/parser/gamessparser.py	2006-05-24 19:43:41 UTC (rev 157)
@@ -379,9 +379,22 @@
             if line.find("NUMBER OF OCCUPIED ORBITALS")>=0:
                 if not hasattr(self,"homos"):
                     self.logger.info("Creating attribute homos")
-                    temp = line.strip().split('=')
-                    self.homos = Numeric.array([int(temp[-1])-1],"i")
+                homos = [int(line.split()[-1])-1]
+                line = inputfile.next()
+                homos.append(int(line.split()[-1])-1)
+                # Note that we cannot trust this self.homos until we come to
+                # a line that contains the phrase:
+                # "SYMMETRIES FOR INITAL GUESS ORBITALS FOLLOW"
+                # which either is followed by "ALPHA" or "BOTH"
+                # at which point we can say for certain that it is an
+                # un/restricted calculations
+                self.homos = Numeric.array(homos,"i")
 
+            if line.find("SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW")>=0:
+                # Not unrestricted, so lop off the second index
+                if line.find("BOTH SET(S)")>=0:
+                    self.homos = Numeric.resize(self.homos,[1])
+
             if line.find("TOTAL NUMBER OF ATOMS")==1:
                 self.logger.info("Creating attribute natom")
                 self.natom = int(line.split()[-1])


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

[cclib-svn] SF.net SVN: cclib: [156] trunk/test

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

Revision: 156
Author:   baoilleach
Date:     2006-05-24 12:16:00 -0700 (Wed, 24 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=156&view=rev

Log Message:
-----------
The typecode of homos is 'i', which needed to be specified in the tests and in the parsers

Modified Paths:
--------------
    trunk/src/cclib/parser/adfparser.py
    trunk/test/testGeoOpt.py
    trunk/test/testSPun.py
Modified: trunk/src/cclib/parser/adfparser.py
===================================================================
--- trunk/src/cclib/parser/adfparser.py	2006-05-24 18:20:44 UTC (rev 155)
+++ trunk/src/cclib/parser/adfparser.py	2006-05-24 19:16:00 UTC (rev 156)
@@ -285,7 +285,7 @@
 
               temp=Numeric.array(self.moenergies,"f")
               self.moenergies=temp
-              self.homos=Numeric.array(self.homos)
+              self.homos=Numeric.array(self.homos,"i")
 
             if line[1:24]=="List of All Frequencies":
 # Start of the IR/Raman frequency section

Modified: trunk/test/testGeoOpt.py
===================================================================
--- trunk/test/testGeoOpt.py	2006-05-24 18:20:44 UTC (rev 155)
+++ trunk/test/testGeoOpt.py	2006-05-24 19:16:00 UTC (rev 156)
@@ -1,16 +1,16 @@
 import os
 import math
+import Numeric
 import unittest
 import bettertest
 
-from Numeric import array
 from testall import getfile
 from cclib.parser import ADF, GAMESS, Gaussian, Jaguar
 
 class GenericGeoOptTest(bettertest.TestCase):
     def testhomos(self):
         """Is the index of the homo equal to 34?"""
-        self.assertArrayEquals(self.data.homos,array([34]),"%s != array([34])" % self.data.homos)
+        self.assertArrayEquals(self.data.homos,Numeric.array([34],"i"),"%s != array([34],'i')" % Numeric.array_repr(self.data.homos))
 
     def testatomcoords(self):
         """Are atomcoords consistent with natom and Angstroms?"""
@@ -62,7 +62,7 @@
     def testscfvaluetype(self):
         """Do the scf values have the right type?"""
         self.assertEquals(type(self.data.scfvalues),type([]))
-        self.assertEquals(type(self.data.scfvalues[0]),type(array([])))
+        self.assertEquals(type(self.data.scfvalues[0]),type(Numeric.array([])))
 
     def testscfvaluedim(self):
         """Do the scf values have the right dimensions?"""

Modified: trunk/test/testSPun.py
===================================================================
--- trunk/test/testSPun.py	2006-05-24 18:20:44 UTC (rev 155)
+++ trunk/test/testSPun.py	2006-05-24 19:16:00 UTC (rev 156)
@@ -1,9 +1,12 @@
-import os, unittest
-from Numeric import array
+import os
+import unittest
+import bettertest
+import Numeric
+
 from testall import getfile
 from cclib.parser import ADF, GAMESS, Gaussian, Jaguar
 
-class GenericSPunTest(unittest.TestCase):
+class GenericSPunTest(bettertest.TestCase):
     """Restricted single point calculations with MO coeffs and overlap info."""
     def testdimaooverlaps(self):
         """Are the dims of the overlap matrix consistent with nbasis?"""
@@ -14,9 +17,8 @@
         self.assertEquals(self.data.mocoeffs.shape,(2,self.data.nmo,self.data.nbasis))
 
     def testhomos(self):
-        """What are the homos?"""
-        self.assertEquals(type(self.data.homos),type(array([])))
-        self.assertEquals(self.data.homos,array([34,33],"i"))
+        """Are the homos correct?"""
+        self.assertArrayEquals(self.data.homos,Numeric.array([34,33],"i"),"%s != array([34,33],'i')" % Numeric.array_repr(self.data.homos))
 
 class GaussianSPunTest(GenericSPunTest):
     def setUp(self):


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

[cclib-svn] SF.net SVN: cclib: [155] trunk/test

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

Revision: 155
Author:   baoilleach
Date:     2006-05-24 11:20:44 -0700 (Wed, 24 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=155&view=rev

Log Message:
-----------
Oops. Thanks to Adam for pointing out an error in the unittests. Apparently all tests of equality between a Numeric array and pretty much anything else return True. Looking at the web, this is a so-called beginner's mistake. In any case, I've created a special assertArrayEquals() which should be used to compare arrays instead of assertEquals. Now there are failures are over the shop...it was nicer with our heads under the sand :-)

Modified Paths:
--------------
    trunk/test/testGeoOpt.py

Added Paths:
-----------
    trunk/test/bettertest.py
Added: trunk/test/bettertest.py
===================================================================
--- trunk/test/bettertest.py	                        (rev 0)
+++ trunk/test/bettertest.py	2006-05-24 18:20:44 UTC (rev 155)
@@ -0,0 +1,25 @@
+import Numeric
+import unittest
+
+class TestCase(unittest.TestCase):
+    """Create a class with extra 'asserts' for testing numerical data.
+
+    It is not possible to test equality of Numeric arrays using assertEquals().
+    Instead use assertArrayEquals() defined below.
+    (For the original solution see:
+    http://mail.python.org/pipermail/python-list/2005-November/311235.html)
+
+    Also, for testing near equality of floats use assertInside.
+    (Taken from Python Cookbook 2nd Ed. Recipe 8.11)
+    """
+    def assertInside(self,first,second,error,msg=None):
+        """Fail if the second number isn't within a certain error of the first."""
+        if not (second-error) < first < (second+error):
+            raise self.failureException, (msg or '%r != %r (+-%r)' % (first,second,error))
+
+    def assertArrayEquals(self,first,second,msg=None):
+        """Fails unless two Numeric arrays are identical."""
+        if not (first.shape==second.shape and
+                first.typecode()==second.typecode() and
+                Numeric.alltrue(first==second)):
+            raise self.failureException, (msg or 'These two arrays are not identical')


Property changes on: trunk/test/bettertest.py
___________________________________________________________________
Name: svn:executable
   + *

Modified: trunk/test/testGeoOpt.py
===================================================================
--- trunk/test/testGeoOpt.py	2006-05-24 01:53:21 UTC (rev 154)
+++ trunk/test/testGeoOpt.py	2006-05-24 18:20:44 UTC (rev 155)
@@ -1,15 +1,16 @@
 import os
 import math
 import unittest
+import bettertest
 
 from Numeric import array
 from testall import getfile
 from cclib.parser import ADF, GAMESS, Gaussian, Jaguar
 
-class GenericGeoOptTest(unittest.TestCase):
+class GenericGeoOptTest(bettertest.TestCase):
     def testhomos(self):
         """Is the index of the homo equal to 34?"""
-        self.assertEquals(self.data.homos,array([34]))
+        self.assertArrayEquals(self.data.homos,array([34]),"%s != array([34])" % self.data.homos)
 
     def testatomcoords(self):
         """Are atomcoords consistent with natom and Angstroms?"""
@@ -43,7 +44,7 @@
 
     def testscfenergy(self):
         """Is the SCF energy within 40eV of -10365"""
-        self.assert_(abs(self.data.scfenergies[-1]-(-10365))<40,"Final scf energy: %f not -10365+-40eV" % self.data.scfenergies[-1])
+        self.assertInside(self.data.scfenergies[-1],-10365,40,"Final scf energy: %f not -10365+-40eV" % self.data.scfenergies[-1])
 
     def testnormalisesym(self):
         """Did this subclasses overwrite normalisesym?"""
@@ -60,11 +61,13 @@
 
     def testscfvaluetype(self):
         """Do the scf values have the right type?"""
-        self.assert_(type(self.data.scfvalues[0])==type(array([])) and type(self.data.scfvalues)==type([]))
+        self.assertEquals(type(self.data.scfvalues),type([]))
+        self.assertEquals(type(self.data.scfvalues[0]),type(array([])))
 
     def testscfvaluedim(self):
         """Do the scf values have the right dimensions?"""
-        self.assert_(len(self.data.scfvalues)==len(self.data.geovalues) and len(self.data.scfvalues[0])==len(self.data.scftargets))
+        self.assertEquals(len(self.data.scfvalues),len(self.data.geovalues))
+        self.assertEquals(len(self.data.scfvalues[0]),len(self.data.scftargets))        
 
 class GaussianGeoOptTest(GenericGeoOptTest):
     def setUp(self):
@@ -94,7 +97,7 @@
     
     def testscfenergy(self):
         """Is the SCF energy within 1eV of -140eV"""
-        self.assert_(abs(self.data.scfenergies[-1]-(-140))<1,"Final scf energy: %f not -140+-1eV" % self.data.scfenergies[-1])
+        self.assertInside(self.data.scfenergies[-1],-140,1,"Final scf energy: %f not -140+-1eV" % self.data.scfenergies[-1])
 
 class JaguarGeoOptTest(GenericGeoOptTest):
     def setUp(self):


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

[cclib-svn] SF.net SVN: cclib: [154] trunk/src/cclib/method/population.py

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

Revision: 154
Author:   atenderholt
Date:     2006-05-23 18:53:21 -0700 (Tue, 23 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=154&view=rev

Log Message:
-----------
Fixed a minor problem in population

Modified Paths:
--------------
    trunk/src/cclib/method/population.py
Modified: trunk/src/cclib/method/population.py
===================================================================
--- trunk/src/cclib/method/population.py	2006-05-23 12:23:19 UTC (rev 153)
+++ trunk/src/cclib/method/population.py	2006-05-24 01:53:21 UTC (rev 154)
@@ -68,7 +68,7 @@
 #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"):
+            elif hasattr(self.parser,"fonames"):
                 names=self.parser.fonames
 
             atoms=[]


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

[cclib-svn] SF.net SVN: cclib: [153] trunk/src

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

Revision: 153
Author:   baoilleach
Date:     2006-05-23 05:23:19 -0700 (Tue, 23 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=153&view=rev

Log Message:
-----------
Added a script to demonstrate the capabilities of cclib...currently not installed by setup.py.

Added Paths:
-----------
    trunk/src/scripts/
    trunk/src/scripts/ccget.py
Added: trunk/src/scripts/ccget.py
===================================================================
--- trunk/src/scripts/ccget.py	                        (rev 0)
+++ trunk/src/scripts/ccget.py	2006-05-23 12:23:19 UTC (rev 153)
@@ -0,0 +1,58 @@
+import sys
+import getopt
+import logging
+
+from cclib.parser import guesstype
+
+def moreusage():
+    """More detailed usage information"""
+    print """Usage:  python ccget.py <attribute> [<attribute>] <compchemlogfile>
+where <attribute> is one of the available attributes parsed by cclib
+from <compchemlogfile>.
+For a list of attributes parsed from the file, type:
+     python ccget.py --list     [or -l]"""
+
+def usage():
+    """Display usage information"""
+    print """Usage:  python ccget.py <attribute> [<attribute>] <compchemlogfile>
+Try     python ccget.py --help    for more information"""
+
+
+def main():
+    try:
+        opts, args = getopt.getopt(sys.argv[1:], "hl", ["help","list"])
+    except getopt.GetoptError:
+        # print help information and exit:
+        usage()
+        sys.exit(2)
+    showattr = False
+    for o, a in opts:
+        if o in ("-h", "--help"):
+            moreusage()
+            sys.exit()
+        if o in ("-l", "--list"):
+            showattr = True
+    if (not showattr and len(args)<2) or (showattr and len(args)!=1): # Need at least one attribute and the filename
+        usage()
+        sys.exit()
+
+    log = guesstype(args[-1])
+    log.logger.setLevel(logging.ERROR)
+    log.parse()
+    if showattr:
+        print "cclib can parse the following attributes from %s:" % args[-1]
+        for x in ['aonames','aooveralps','atomcoords','atomnos',
+                  'etenergies','etoscs','etrotats','etsecs','etsyms',
+                  'fonames','fooverlaps','geotargets','geovalues',
+                  'homos','mocoeffs','moenergies','mosyms','natom','nbasis',
+                  'nmo','scfenergies','scftargets','scfvalues',
+                  'vibfreqs','vibirs','vibramans','vibsyms']:
+            if hasattr(log,x):
+                print "  %s" % x
+    else:
+        for arg in args[:-1]:
+            print getattr(log,arg)
+    return log 
+
+if __name__ == "__main__":
+    t = main()


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

[cclib-svn] SF.net SVN: cclib: [152] trunk/test

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

Revision: 152
Author:   baoilleach
Date:     2006-05-23 01:46:44 -0700 (Tue, 23 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=152&view=rev

Log Message:
-----------
Converted scfenergies from a.u. to eV for GAMESS and Gaussian, and updated tests.

Modified Paths:
--------------
    trunk/src/cclib/parser/gamessparser.py
    trunk/src/cclib/parser/gaussianparser.py
    trunk/test/testGeoOpt.py
Modified: trunk/src/cclib/parser/gamessparser.py
===================================================================
--- trunk/src/cclib/parser/gamessparser.py	2006-05-23 01:28:46 UTC (rev 151)
+++ trunk/src/cclib/parser/gamessparser.py	2006-05-23 08:46:44 UTC (rev 152)
@@ -140,7 +140,7 @@
 #  FINAL ENERGY IS     -379.7594673378 AFTER   9 ITERATIONS
 # ...so take the number after the "IS"
                 temp = line.split()
-                self.scfenergies.append(float(temp[temp.index("IS")+1]))
+                self.scfenergies.append(utils.convertor(float(temp[temp.index("IS")+1]),"hartree","eV"))
 
             if line.find("MAXIMUM GRADIENT")>0:
                 if not hasattr(self,"geovalues"):

Modified: trunk/src/cclib/parser/gaussianparser.py
===================================================================
--- trunk/src/cclib/parser/gaussianparser.py	2006-05-23 01:28:46 UTC (rev 151)
+++ trunk/src/cclib/parser/gaussianparser.py	2006-05-23 08:46:44 UTC (rev 152)
@@ -201,7 +201,7 @@
                 if not hasattr(self,"scfenergies"):
                     self.logger.info("Creating attribute scfenergies[]")
                     self.scfenergies = []
-                self.scfenergies.append(self.float(line.split()[4]))
+                self.scfenergies.append(utils.convertor(self.float(line.split()[4]),"hartree","eV"))
 
             if line[49:59]=='Converged?':
 # Extract Geometry convergence information

Modified: trunk/test/testGeoOpt.py
===================================================================
--- trunk/test/testGeoOpt.py	2006-05-23 01:28:46 UTC (rev 151)
+++ trunk/test/testGeoOpt.py	2006-05-23 08:46:44 UTC (rev 152)
@@ -42,8 +42,8 @@
         self.assertEquals(self.data.nbasis,60)
 
     def testscfenergy(self):
-        """Is the SCF energy within 3eV(?) of -382.3?"""
-        self.assert_(self.data.scfenergies[-1]+382.3<3)
+        """Is the SCF energy within 40eV of -10365"""
+        self.assert_(abs(self.data.scfenergies[-1]-(-10365))<40,"Final scf energy: %f not -10365+-40eV" % self.data.scfenergies[-1])
 
     def testnormalisesym(self):
         """Did this subclasses overwrite normalisesym?"""
@@ -91,6 +91,10 @@
         """Are atomcoords consistent with geovalues?"""
         coords = self.data.atomcoords
         self.assertEquals(len(self.data.geovalues),len(coords)-1,"len(atomcoords)-1 is %d but len(geovalues) is %d" % (len(coords)-1,len(self.data.geovalues)))
+    
+    def testscfenergy(self):
+        """Is the SCF energy within 1eV of -140eV"""
+        self.assert_(abs(self.data.scfenergies[-1]-(-140))<1,"Final scf energy: %f not -140+-1eV" % self.data.scfenergies[-1])
 
 class JaguarGeoOptTest(GenericGeoOptTest):
     def setUp(self):


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

[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
   + *


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