cclib-svn — Log messages of SVN commits

[cclib-svn] SF.net SVN: cclib: [123] trunk/src/cclib/parser

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

Revision: 123
Author:   baoilleach
Date:     2006-05-17 09:56:45 -0700 (Wed, 17 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=123&view=rev

Log Message:
-----------
Completed parsing of atomcoords...still passes tests, although I haven't checked the output to see if it makes sense.

Modified Paths:
--------------
    trunk/src/cclib/parser/gamessparser.py
    trunk/src/cclib/parser/logfileparser.py
Modified: trunk/src/cclib/parser/gamessparser.py
===================================================================
--- trunk/src/cclib/parser/gamessparser.py	2006-05-17 16:27:40 UTC (rev 122)
+++ trunk/src/cclib/parser/gamessparser.py	2006-05-17 16:56:45 UTC (rev 123)
@@ -73,7 +73,7 @@
             oldstep=0
 
 
-        endofopt = False
+        firststdorient = True # Used to decide whether to wipe the atomcoords clean
             
         for line in inputfile:
             
@@ -136,7 +136,7 @@
                 line = inputfile.next()
                 while line.strip():
                     temp = line.strip().split()
-                    atomcoords.append(map(float,temp[2:4]))
+                    atomcoords.append([convertor(float(x),"au","Ang") for x in temp[2:4]])
                     atomnos.append(self.pt.number[temp[0]]) # Use the element name
                     line = inputfile.next()
                 self.atomnos = Numeric.array(atomnos,"i")
@@ -145,7 +145,22 @@
             if line[1:37]=="COORDINATES OF ALL ATOMS ARE":
                 # This is the standard orientation, which is the only coordinate
                 # information available for all geometry optimisation cycles.
-                pass
+                # The input orientation will be overwritten if this is a geometry optimisation
+                # We assume that a previous Input Orientation has been found and
+                # used to extract the atomnos
+                if firststdorient:
+                    firststdorient = False
+                    # Wipes out the single input coordinate at the start of the file
+                    self.atomcoords = []
+                    
+                line = inputfile.next()
+                hyphens = inputfile.next()
+                atomcoords = []
+                while line.strip():
+                    temp = line.strip().split()
+                    atomcoords.append(map(float,temp[2:4]))
+                    line = inputfile.next()
+                self.atomcoords.append(atomcoords)
             
             if line.find("ITER EX DEM")==1:
 # This is the section with the SCF information                

Modified: trunk/src/cclib/parser/logfileparser.py
===================================================================
--- trunk/src/cclib/parser/logfileparser.py	2006-05-17 16:27:40 UTC (rev 122)
+++ trunk/src/cclib/parser/logfileparser.py	2006-05-17 16:56:45 UTC (rev 123)
@@ -29,7 +29,8 @@
     _convertor = {"eV_to_cm-1": lambda x: x*8065.6,
                   "hartree_to_eV": lambda x: x*27.2114,
                   "nm_to_cm-1": lambda x: 1e7/x,
-                  "cm-1_to_nm": lambda x: 1e7/x}
+                  "cm-1_to_nm": lambda x: 1e7/x,
+                  "au_to_Ang": lambda x: x*0.529177}
 
     return _convertor["%s_to_%s" % (fromunits,tounits)] (value)
 


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[cclib-svn] SF.net SVN: cclib: [122] trunk/src/cclib/parser/gamessparser.py

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

Revision: 122
Author:   baoilleach
Date:     2006-05-17 09:27:40 -0700 (Wed, 17 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=122&view=rev

Log Message:
-----------
Now parses aonames (not normalised to Gaussian though), and started work on parsing atomnos and atomcoords

Modified Paths:
--------------
    trunk/src/cclib/parser/gamessparser.py
Modified: trunk/src/cclib/parser/gamessparser.py
===================================================================
--- trunk/src/cclib/parser/gamessparser.py	2006-05-17 16:22:09 UTC (rev 121)
+++ trunk/src/cclib/parser/gamessparser.py	2006-05-17 16:27:40 UTC (rev 122)
@@ -20,7 +20,7 @@
 import re,time
 import Numeric
 import random # For sometimes running the progress updater
-from logfileparser import Logfile,convertor
+from logfileparser import Logfile,convertor,PeriodicTable
 
 class GAMESS(Logfile):
     """A GAMESS log file."""
@@ -29,6 +29,8 @@
 
         # Call the __init__ method of the superclass
         super(GAMESS, self).__init__(logname="GAMESS",*args)
+
+        self.pt = PeriodicTable()
         
     def __str__(self):
         """Return a string representation of the object."""
@@ -120,6 +122,31 @@
                     self.logger.info("Creating attribute scftargets")
                     self.scftargets = Numeric.array([float(line.strip().split()[-1])])
                 
+            if line[11:50]=="ATOMIC                      COORDINATES":
+                # This is the input orientation, which is the only data available for
+                # SP calcs, but which should be overwritten by the standard orientation
+                # values, which is the only information available for all geoopt cycles.
+                if not hasattr(self,"atomcoords"):
+                    self.logger.info("Creating attribute atomcoords, atomnos")
+                    self.atomcoords = []
+                    self.atomnos = []
+                line = inputfile.next()
+                atomcoords = []
+                atomnos = []
+                line = inputfile.next()
+                while line.strip():
+                    temp = line.strip().split()
+                    atomcoords.append(map(float,temp[2:4]))
+                    atomnos.append(self.pt.number[temp[0]]) # Use the element name
+                    line = inputfile.next()
+                self.atomnos = Numeric.array(atomnos,"i")
+                self.atomcoords.append(atomcoords)
+
+            if line[1:37]=="COORDINATES OF ALL ATOMS ARE":
+                # This is the standard orientation, which is the only coordinate
+                # information available for all geometry optimisation cycles.
+                pass
+            
             if line.find("ITER EX DEM")==1:
 # This is the section with the SCF information                
                 if not hasattr(self,"scfvalues"):
@@ -322,8 +349,9 @@
                 # The first is for PC-GAMESS, the second for GAMESS
                 # Read 1-electron overlap matrix
                 if not hasattr(self,"aooverlaps"):
-                    self.logger.info("Creating attribute aooverlaps")
+                    self.logger.info("Creating attribute aooverlaps, aonames")
                     self.aooverlaps = Numeric.zeros((self.nbasis,self.nbasis), "f")
+                    self.aonames = []
                 else:
                     self.logger.info("Reading additional aooverlaps...")
                 base = 0
@@ -334,10 +362,12 @@
                     for i in range(self.nbasis-base): # Fewer lines each time
                         line = inputfile.next()
                         temp = line.split()
+                        if base==0: # Only do this for the first block
+                            self.aonames.append("%s%s_%s" % (temp[1],temp[2],temp[3]))
                         for j in range(4,len(temp)):
                             self.aooverlaps[base+j-4,i+base] = float(temp[j])
                             self.aooverlaps[i+base,base+j-4] = float(temp[j])
-                    base+=5
+                    base += 5
 
         inputfile.close()
 


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[cclib-svn] SF.net SVN: cclib: [121] trunk/src/cclib/parser/g03parser.py

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

Revision: 121
Author:   baoilleach
Date:     2006-05-17 09:22:09 -0700 (Wed, 17 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=121&view=rev

Log Message:
-----------
Fixed bug when creating the Numeric array for atomnos.

Modified Paths:
--------------
    trunk/src/cclib/parser/g03parser.py
Modified: trunk/src/cclib/parser/g03parser.py
===================================================================
--- trunk/src/cclib/parser/g03parser.py	2006-05-16 18:21:53 UTC (rev 120)
+++ trunk/src/cclib/parser/g03parser.py	2006-05-17 16:22:09 UTC (rev 121)
@@ -121,7 +121,7 @@
                     line = inputfile.next()
                 self.atomcoords.append(atomcoords)
                 if not hasattr(self,"natom"):
-                    self.atomnos = Numeric.array(atomnos,'f')
+                    self.atomnos = Numeric.array(atomnos,'i')
                     self.logger.info("Creating attribute atomnos[]")
                     self.natom = len(self.atomnos)
                     self.logger.info("Creating attribute natom: %d" % self.natom)


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[cclib-svn] SF.net SVN: cclib: [120] trunk/test

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

Revision: 120
Author:   atenderholt
Date:     2006-05-16 11:21:53 -0700 (Tue, 16 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=120&view=rev

Log Message:
-----------
Changed nindep to nmo. Gaussian and GAMESS pass the unittests. SCF stuff is still broken in ADF, and Jaguar is very incomplete.

Modified Paths:
--------------
    trunk/src/cclib/parser/adfparser.py
    trunk/src/cclib/parser/g03parser.py
    trunk/src/cclib/parser/gamessparser.py
    trunk/src/cclib/parser/logfileparser.py
    trunk/test/testSP.py
    trunk/test/testSPun.py
Modified: trunk/src/cclib/parser/adfparser.py
===================================================================
--- trunk/src/cclib/parser/adfparser.py	2006-05-16 17:01:46 UTC (rev 119)
+++ trunk/src/cclib/parser/adfparser.py	2006-05-16 18:21:53 UTC (rev 120)
@@ -472,16 +472,16 @@
 #                     
 #             if line[1:7]=="NBsUse":
 # # Extract the number of linearly-independent basis sets
-#                 nindep = int(line.split('=')[1].split()[0])
-#                 if hasattr(self,"nindep"):
-#                     assert nindep==self.nindep
+#                 nmo = int(line.split('=')[1].split()[0])
+#                 if hasattr(self,"nmo"):
+#                     assert nmo==self.nmo
 #                 else:
-#                     self.nindep = nindep
-#                     self.logger.info("Creating attribute nindep: %d" % self.nindep)
+#                     self.nmo = nmo
+#                     self.logger.info("Creating attribute nmo: %d" % self.nmo)
 # 
 #             if line[7:22]=="basis functions,":
 # # For AM1 calculations, set nbasis by a second method
-# # (nindep may not always be explicitly stated)
+# # (nmo may not always be explicitly stated)
 #                     nbasis = int(line.split()[0])
 #                     if hasattr(self,"nbasis"):
 #                         assert nbasis==self.nbasis
@@ -609,15 +609,15 @@
 #                 if line[5:40]=="Beta Molecular Orbital Coefficients":
 #                     beta = True
 #                     # Need to add an extra dimension to self.mocoeffs
-#                     self.mocoeffs = Numeric.resize(self.mocoeffs,(2,nindep,nbasis))
+#                     self.mocoeffs = Numeric.resize(self.mocoeffs,(2,nmo,nbasis))
 #                 else:
 #                     beta = False
 #                     self.logger.info("Creating attributes aonames[], mocoeffs[][]")
 #                     self.aonames = []
-#                     self.mocoeffs = Numeric.zeros((1,nindep,nbasis),"float")
+#                     self.mocoeffs = Numeric.zeros((1,nmo,nbasis),"float")
 # 
 #                 base = 0
-#                 for base in range(0,nindep,5):
+#                 for base in range(0,nmo,5):
 #                     
 #                     if self.progress:
 #                         step=inputfile.tell()
@@ -656,7 +656,7 @@
         if hasattr(self,"scfenergies"): self.scfenergies = Numeric.array(self.scfenergies,"f")
         if hasattr(self,"scfvalues"): self.scfvalues = [Numeric.array(x,"f") for x in self.scfvalues]
         self.parsed = True
-        if hasattr(self,"moenergies"): self.nindep = len(self.moenergies[0])
+        if hasattr(self,"moenergies"): self.nmo = len(self.moenergies[0])
 
         
 

Modified: trunk/src/cclib/parser/g03parser.py
===================================================================
--- trunk/src/cclib/parser/g03parser.py	2006-05-16 17:01:46 UTC (rev 119)
+++ trunk/src/cclib/parser/g03parser.py	2006-05-16 18:21:53 UTC (rev 120)
@@ -445,16 +445,16 @@
                     
             if line[1:7]=="NBsUse":
 # Extract the number of linearly-independent basis sets
-                nindep = int(line.split('=')[1].split()[0])
-                if hasattr(self,"nindep"):
-                    assert nindep==self.nindep
+                nmo = int(line.split('=')[1].split()[0])
+                if hasattr(self,"nmo"):
+                    assert nmo==self.nmo
                 else:
-                    self.nindep = nindep
-                    self.logger.info("Creating attribute nindep: %d" % self.nindep)
+                    self.nmo = nmo
+                    self.logger.info("Creating attribute nmo: %d" % self.nmo)
 
             if line[7:22]=="basis functions,":
 # For AM1 calculations, set nbasis by a second method
-# (nindep may not always be explicitly stated)
+# (nmo may not always be explicitly stated)
                     nbasis = int(line.split()[0])
                     if hasattr(self,"nbasis"):
                         assert nbasis==self.nbasis
@@ -497,15 +497,15 @@
                 if line[5:40]=="Beta Molecular Orbital Coefficients":
                     beta = True
                     # Need to add an extra dimension to self.mocoeffs
-                    self.mocoeffs = Numeric.resize(self.mocoeffs,(2,nindep,nbasis))
+                    self.mocoeffs = Numeric.resize(self.mocoeffs,(2,nmo,nbasis))
                 else:
                     beta = False
                     self.logger.info("Creating attributes aonames[], mocoeffs[][]")
                     self.aonames = []
-                    self.mocoeffs = Numeric.zeros((1,nindep,nbasis),"float")
+                    self.mocoeffs = Numeric.zeros((1,nmo,nbasis),"float")
 
                 base = 0
-                for base in range(0,nindep,5):
+                for base in range(0,nmo,5):
                     
                     if self.progress:
                         step=inputfile.tell()

Modified: trunk/src/cclib/parser/gamessparser.py
===================================================================
--- trunk/src/cclib/parser/gamessparser.py	2006-05-16 17:01:46 UTC (rev 119)
+++ trunk/src/cclib/parser/gamessparser.py	2006-05-16 18:21:53 UTC (rev 120)
@@ -236,12 +236,12 @@
                     self.logger.info("Creating attributes moenergies, mosyms")
                 self.moenergies = [[]]
                 self.mosyms = [[]]
-                if not hasattr(self,"nindep"):
-                    self.logger.info("Creating attribute nindep with default value")
-                    self.nindep = self.nbasis
-                self.mocoeffs = Numeric.zeros((1,self.nindep,self.nbasis),"f")
+                if not hasattr(self,"nmo"):
+                    self.logger.info("Creating attribute nmo with default value")
+                    self.nmo = self.nbasis
+                self.mocoeffs = Numeric.zeros((1,self.nmo,self.nbasis),"f")
                 line = inputfile.next()
-                for base in range(0,self.nindep,5):
+                for base in range(0,self.nmo,5):
                     blank = inputfile.next()
                     line = inputfile.next() # Eigenvector no
                     line = inputfile.next()
@@ -273,12 +273,12 @@
 #
 #                      1          2          3          4          5
 
-                    self.mocoeffs.resize((2,self.nindep,self.nbasis))
+                    self.mocoeffs.resize((2,self.nmo,self.nbasis))
                     self.moenergies.append([])
                     self.mosyms.append([])
                     for i in range(5):
                         line = inputfile.next()
-                    for base in range(0,self.nindep,5):
+                    for base in range(0,self.nmo,5):
                         blank = inputfile.next()
                         line = inputfile.next() # Eigenvector no
                         line = inputfile.next()
@@ -315,7 +315,7 @@
             elif line.find("TOTAL NUMBER OF MOS IN VARIATION SPACE")==1:
                 # Note that this line is not always present, so by default
                 # NBsUse is set equal to NBasis (see below).
-                self.logger.info("Creating attribute nindep")
+                self.logger.info("Creating attribute nmo")
                 self.indep = int(line.split()[-1])
                 
             elif line.find("OVERLAP MATRIX")==0 or line.find("OVERLAP MATRIX")==1:
@@ -351,9 +351,9 @@
         if hasattr(self,"scfvalues"):
             self.scfvalues = [Numeric.array(x,"f") for x in self.scfvalues]
         if hasattr(self,"geovalues"): self.geovalues = Numeric.array(self.geovalues,"f")
-        if not hasattr(self,"nindep"):
-            self.logger.info("Creating attribute nindep with default value")
-            self.nindep = self.nbasis
+        if not hasattr(self,"nmo"):
+            self.logger.info("Creating attribute nmo with default value")
+            self.nmo = self.nbasis
 
         self.parsed = True
 

Modified: trunk/src/cclib/parser/logfileparser.py
===================================================================
--- trunk/src/cclib/parser/logfileparser.py	2006-05-16 17:01:46 UTC (rev 119)
+++ trunk/src/cclib/parser/logfileparser.py	2006-05-16 18:21:53 UTC (rev 120)
@@ -72,7 +72,7 @@
         mosyms -- orbital symmetries (list[2])
         natom -- number of atoms (integer)
         nbasis -- number of basis functions (integer)
-        nindep -- number of linearly-independent basis functions (integer)
+        nmo -- number of linearly-independent basis functions (integer)
         scfenergies -- the electronic energy of the molecule (array[1], a.u.)
         scftargets -- targets for convergence of the SCF (array[1])
         scfvalues -- current values for convergence of the SCF (array[2], same units as scftargets)

Modified: trunk/test/testSP.py
===================================================================
--- trunk/test/testSP.py	2006-05-16 17:01:46 UTC (rev 119)
+++ trunk/test/testSP.py	2006-05-16 18:21:53 UTC (rev 120)
@@ -10,8 +10,8 @@
         self.assertEquals(self.data.aooverlaps.shape,(self.data.nbasis,self.data.nbasis))
 
     def testdimmocoeffs(self):
-        """Are the dimensions of mocoeffs equal to 1 x nindep x nbasis?"""
-        self.assertEquals(self.data.mocoeffs.shape,(1,self.data.nindep,self.data.nbasis))
+        """Are the dimensions of mocoeffs equal to 1 x nmo x nbasis?"""
+        self.assertEquals(self.data.mocoeffs.shape,(1,self.data.nmo,self.data.nbasis))
 
 class GaussianSPTest(GenericSPTest):
     def setUp(self):

Modified: trunk/test/testSPun.py
===================================================================
--- trunk/test/testSPun.py	2006-05-16 17:01:46 UTC (rev 119)
+++ trunk/test/testSPun.py	2006-05-16 18:21:53 UTC (rev 120)
@@ -10,8 +10,8 @@
         self.assertEquals(self.data.aooverlaps.shape,(self.data.nbasis,self.data.nbasis))
 
     def testdimmocoeffs(self):
-        """Are the dimensions of mocoeffs equal to 1 x nindep x nbasis?"""
-        self.assertEquals(self.data.mocoeffs.shape,(2,self.data.nindep,self.data.nbasis))
+        """Are the dimensions of mocoeffs equal to 1 x nmo x nbasis?"""
+        self.assertEquals(self.data.mocoeffs.shape,(2,self.data.nmo,self.data.nbasis))
 
     def testhomos(self):
         """What are the homos?"""


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[cclib-svn] SF.net SVN: cclib: [119] trunk/src/cclib/parser/g03parser.py

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

Revision: 119
Author:   baoilleach
Date:     2006-05-16 10:01:46 -0700 (Tue, 16 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=119&view=rev

Log Message:
-----------
Added atomcoords which stores the input orientation at all stages of a geometry optimisation. Needed to add a flag to indicate when the GeoOpt was over to avoid extracting the final geometry twice.

Modified Paths:
--------------
    trunk/src/cclib/parser/g03parser.py
Modified: trunk/src/cclib/parser/g03parser.py
===================================================================
--- trunk/src/cclib/parser/g03parser.py	2006-05-13 21:05:51 UTC (rev 118)
+++ trunk/src/cclib/parser/g03parser.py	2006-05-16 17:01:46 UTC (rev 119)
@@ -64,6 +64,8 @@
             self.progress.initialize(nstep)
             oldstep=0
             
+        optfinished = False # Flag that indicates whether it has reached the end of a geoopt
+        
         for line in inputfile:
             
             if self.progress and random.random()<cupdate:
@@ -89,30 +91,39 @@
                     self.natom = natom
                     self.logger.info("Creating attribute natom: %d" % self.natom)                    
             
-            if not hasattr(self,"atomnos") and (line.find("Z-Matrix orientation")>=0
-                                                 or line[25:45]=="Standard orientation"
-                                                 or line[26:43]=="Input orientation"):
-# Extract the atomic numbers of the atoms
+            if line[1:23]=="Optimization completed":
+                optfinished = True
+            
+            if not optfinished and line[26:43]=="Input orientation":
+# Extract the atomic numbers and coordinates of the atoms
                 if self.progress and random.random()<cupdate:
                     step = inputfile.tell()
                     if step!=oldstep:
                         self.progress.update(step,"Attributes")
                         oldstep=step
                         
-                self.logger.info("Creating attribute atomnos[]")
-                self.atomnos = []
+                if not hasattr(self,"atomcoords"):
+                    self.logger.info("Creating attribute atomcoords[]")
+                    self.atomcoords = []
+                
                 hyphens = inputfile.next()
-                colmNames = inputfile.next(); colmNames = inputfile.next()
+                colmNames = inputfile.next()
+                colmNames = inputfile.next()
                 hyphens = inputfile.next()
+                
+                atomnos = []
+                atomcoords = []
                 line = inputfile.next()
                 while line!=hyphens:
-                    self.atomnos.append(int(line.split()[1]))
+                    broken = line.split()
+                    atomnos.append(int(broken[1]))
+                    atomcoords.append(map(float,broken[3:6]))
                     line = inputfile.next()
-                natom = len(self.atomnos)
-                if hasattr(self,"natom"):
-                    assert self.natom==natom
-                else:
-                    self.natom = natom
+                self.atomcoords.append(atomcoords)
+                if not hasattr(self,"natom"):
+                    self.atomnos = Numeric.array(atomnos,'f')
+                    self.logger.info("Creating attribute atomnos[]")
+                    self.natom = len(self.atomnos)
                     self.logger.info("Creating attribute natom: %d" % self.natom)
 
             if line[1:44]=='Requested convergence on RMS density matrix':
@@ -534,6 +545,7 @@
         if hasattr(self,"geovalues"): self.geovalues = Numeric.array(self.geovalues,"f")
         if hasattr(self,"scfenergies"): self.scfenergies = Numeric.array(self.scfenergies,"f")
         if hasattr(self,"scfvalues"): self.scfvalues = [Numeric.array(x,"f") for x in self.scfvalues]
+        if hasattr(self,"atomcoords"): self.atomcoords = Numeric.array(self.atomcoords,"f")
         self.parsed = True
 
         


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[cclib-svn] SF.net SVN: cclib: [118] trunk/test

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

Revision: 118
Author:   baoilleach
Date:     2006-05-13 14:05:51 -0700 (Sat, 13 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=118&view=rev

Log Message:
-----------
Based on the new dvb_gopt_b.adfout I've corrected the adfparser, but the results are still strange and I'm planning to post a question to the ADF users' forum.

Modified Paths:
--------------
    trunk/src/cclib/parser/adfparser.py
    trunk/test/testGeoOpt.py
Modified: trunk/src/cclib/parser/adfparser.py
===================================================================
--- trunk/src/cclib/parser/adfparser.py	2006-05-13 18:48:19 UTC (rev 117)
+++ trunk/src/cclib/parser/adfparser.py	2006-05-13 21:05:51 UTC (rev 118)
@@ -25,6 +25,7 @@
 class ADF(Logfile):
     """An ADF log file"""
     SCFCNV,SCFCNV2 = range(2) #used to index self.scftargets[]
+    maxelem,norm = range(2) # used to index scf.values
     def __init__(self,*args):
 
         # Call the __init__ method of the superclass
@@ -139,9 +140,8 @@
                 for i in range(3): inputfile.next()
 
                 line=inputfile.next()
-                self.scftargets[ADF.SCFCNV]=float(line.split()[2])
-                line=inputfile.next()
-                self.scftargets[ADF.SCFCNV2]=float(line.split()[2])
+                self.scftargets[ADF.maxelem] = float(line.split()[2])
+                self.scftargets[ADF.norm] = self.scftargets[ADF.maxelem]*10
               
             if line[1:11]=="CYCLE    1":
               
@@ -151,29 +151,24 @@
                         self.progress.update(step, "QM Convergence")
                         oldstep=step
               
-                if not hasattr(self,"scfvalues"):
-                    self.logger.info("Creating attribute scfvalues")
-                    self.scfvalues = []
-                
-                newlist = [ [] for x in self.scftargets ]
+                newlist = []
                 line=inputfile.next()
 
                 while line.find("SCF CONVERGED")==-1:
+                    if line[4:12]=="SCF test":
+                        if not hasattr(self,"scfvalues"):
+                            self.logger.info("Creating attribute scfvalues")
+                            self.scfvalues = []
+                                                
+                        info = line.split()
+                        newlist.append([float(info[4]),abs(float(info[6]))])
+                    try:
+                        line=inputfile.next()
+                    except StopIteration: #EOF reached?
+                        break            
 
-                  if line[1:7]=="d-Pmat":
-                      info=line.split()
-                      newlist[ADF.SCFCNV].append(float(info[2]))
-                  
-                      line=inputfile.next()
-                      info=line.split()
-                      newlist[ADF.SCFCNV2].append(float(info[2]))
-
-                  try:
-                      line=inputfile.next()
-                  except StopIteration: #EOF reached?
-                      break
-
-                self.scfvalues.append(newlist)
+                if hasattr(self,"scfvalues"):
+                    self.scfvalues.append(newlist)
               
 #             if line[1:10]=='Cycle   1':
 # # Extract SCF convergence information (QM calcs)

Modified: trunk/test/testGeoOpt.py
===================================================================
--- trunk/test/testGeoOpt.py	2006-05-13 18:48:19 UTC (rev 117)
+++ trunk/test/testGeoOpt.py	2006-05-13 21:05:51 UTC (rev 118)
@@ -55,7 +55,7 @@
 
 class ADFGeoOptTest(GenericGeoOptTest):
     def setUp(self):
-        self.data = getfile(ADF,"basicADF2004.01","dvb_gopt.adfout")
+        self.data = getfile(ADF,"basicADF2004.01","dvb_gopt_b.adfout")
 
     def testscfvaluedim(self):
         """Do the scf values have the right dimensions? 


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[cclib-svn] SF.net SVN: cclib: [117] trunk/src/cclib/parser/adfparser.py

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

Revision: 117
Author:   baoilleach
Date:     2006-05-13 11:48:19 -0700 (Sat, 13 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=117&view=rev

Log Message:
-----------
Changed indentation of 2-spaces to 4-spaces. I think we should standardise on 4.

Modified Paths:
--------------
    trunk/src/cclib/parser/adfparser.py
Modified: trunk/src/cclib/parser/adfparser.py
===================================================================
--- trunk/src/cclib/parser/adfparser.py	2006-05-13 18:45:57 UTC (rev 116)
+++ trunk/src/cclib/parser/adfparser.py	2006-05-13 18:48:19 UTC (rev 117)
@@ -23,8 +23,7 @@
 from logfileparser import Logfile,convertor
 
 class ADF(Logfile):
-    """A Gaussian 98/03 log file"""
-    #SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftargets[]
+    """An ADF log file"""
     SCFCNV,SCFCNV2 = range(2) #used to index self.scftargets[]
     def __init__(self,*args):
 
@@ -132,50 +131,50 @@
             if line[1:22]=="S C F   U P D A T E S":
 # find targets for SCF convergence (QM calcs)
 
-              if not hasattr(self,"scftargets"):
-                self.logger.info("Creating attribute scftargets[]")
-              self.scftargets = Numeric.array([0.0, 0.0],'f')
+                if not hasattr(self,"scftargets"):
+                    self.logger.info("Creating attribute scftargets[]")
+                    self.scftargets = Numeric.array([0.0, 0.0],'f')
+
+                #underline, blank, nr
+                for i in range(3): inputfile.next()
+
+                line=inputfile.next()
+                self.scftargets[ADF.SCFCNV]=float(line.split()[2])
+                line=inputfile.next()
+                self.scftargets[ADF.SCFCNV2]=float(line.split()[2])
               
-              #underline, blank, nr
-              for i in range(3): inputfile.next()
-              
-              line=inputfile.next()
-              self.scftargets[ADF.SCFCNV]=float(line.split()[2])
-              line=inputfile.next()
-              self.scftargets[ADF.SCFCNV2]=float(line.split()[2])
-              
             if line[1:11]=="CYCLE    1":
               
-              if self.progress and random.random() < fupdate:
-                step=inputfile.tell()
-                if step!=oldstep:
-                  self.progress.update(step, "QM Convergence")
-                  oldstep=step
+                if self.progress and random.random() < fupdate:
+                    step=inputfile.tell()
+                    if step!=oldstep:
+                        self.progress.update(step, "QM Convergence")
+                        oldstep=step
               
-              if not hasattr(self,"scfvalues"):
-                self.logger.info("Creating attribute scfvalues")
-                self.scfvalues = []
+                if not hasattr(self,"scfvalues"):
+                    self.logger.info("Creating attribute scfvalues")
+                    self.scfvalues = []
                 
-              newlist = [ [] for x in self.scftargets ]
-              line=inputfile.next()
-              
-              while line.find("SCF CONVERGED")==-1:
-              
-                if line[1:7]=="d-Pmat":
-                  info=line.split()
-                  newlist[ADF.SCFCNV].append(float(info[2]))
+                newlist = [ [] for x in self.scftargets ]
+                line=inputfile.next()
+
+                while line.find("SCF CONVERGED")==-1:
+
+                  if line[1:7]=="d-Pmat":
+                      info=line.split()
+                      newlist[ADF.SCFCNV].append(float(info[2]))
                   
-                  line=inputfile.next()
-                  info=line.split()
-                  newlist[ADF.SCFCNV2].append(float(info[2]))
+                      line=inputfile.next()
+                      info=line.split()
+                      newlist[ADF.SCFCNV2].append(float(info[2]))
+
+                  try:
+                      line=inputfile.next()
+                  except StopIteration: #EOF reached?
+                      break
+
+                self.scfvalues.append(newlist)
               
-                try:
-                  line=inputfile.next()
-                except StopIteration: #EOF reached?
-                  break
-              
-              self.scfvalues.append(newlist)
-              
 #             if line[1:10]=='Cycle   1':
 # # Extract SCF convergence information (QM calcs)
 #                 if self.progress and random.random()<fupdate:


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[cclib-svn] SF.net SVN: cclib: [116] trunk/src/cclib/progress/__init__.py

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

Revision: 116
Author:   baoilleach
Date:     2006-05-13 11:45:57 -0700 (Sat, 13 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=116&view=rev

Log Message:
-----------
Changed so it doesn't import qtprogress if Qt is not installed.

Modified Paths:
--------------
    trunk/src/cclib/progress/__init__.py
Modified: trunk/src/cclib/progress/__init__.py
===================================================================
--- trunk/src/cclib/progress/__init__.py	2006-05-12 23:50:23 UTC (rev 115)
+++ trunk/src/cclib/progress/__init__.py	2006-05-13 18:45:57 UTC (rev 116)
@@ -1,2 +1,7 @@
 from textprogress import TextProgress
-from qtprogress import QtProgress
+try:
+    import qt
+except ImportError:
+    pass # import QtProgress will cause an error
+else:
+    from qtprogress import QtProgress


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[cclib-svn] SF.net SVN: cclib: [115] trunk/src/cclib/parser/adfparser.py

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

Revision: 115
Author:   atenderholt
Date:     2006-05-12 16:50:23 -0700 (Fri, 12 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=115&view=rev

Log Message:
-----------
Made nindep in the ADF parser equal to the length of moenergies[0]

Modified Paths:
--------------
    trunk/src/cclib/parser/adfparser.py
Modified: trunk/src/cclib/parser/adfparser.py
===================================================================
--- trunk/src/cclib/parser/adfparser.py	2006-05-12 09:12:05 UTC (rev 114)
+++ trunk/src/cclib/parser/adfparser.py	2006-05-12 23:50:23 UTC (rev 115)
@@ -662,6 +662,7 @@
         if hasattr(self,"scfenergies"): self.scfenergies = Numeric.array(self.scfenergies,"f")
         if hasattr(self,"scfvalues"): self.scfvalues = [Numeric.array(x,"f") for x in self.scfvalues]
         self.parsed = True
+        if hasattr(self,"moenergies"): self.nindep = len(self.moenergies[0])
 
         
 


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[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
   + *


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[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
   + *


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[cclib-svn] SF.net SVN: cclib: [111] trunk/src/cclib/parser

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

Revision: 111
Author:   atenderholt
Date:     2006-05-10 16:28:49 -0700 (Wed, 10 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=111&view=rev

Log Message:
-----------
Progress info in density method, and some fix to adfparser

Modified Paths:
--------------
    trunk/src/cclib/method/density.py
    trunk/src/cclib/parser/adfparser.py
Modified: trunk/src/cclib/method/density.py
===================================================================
--- trunk/src/cclib/method/density.py	2006-05-10 23:02:55 UTC (rev 110)
+++ trunk/src/cclib/method/density.py	2006-05-10 23:28:49 UTC (rev 111)
@@ -37,7 +37,7 @@
         """Return a representation of the object."""
         return 'Density matrix("%s")' % (self.parser)
     
-    def calculate(self,fupdate=0.05,cupdate=0.002):
+    def calculate(self,fupdate=0.05):
         """Calculate the density matrix given the results of a parser"""
     
         if not self.parser.parsed:
@@ -45,33 +45,49 @@
 
         #do we have the needed info in the parser?
         if not hasattr(self.parser,"mocoeffs") \
-          and not hasattr(self.parser,"aooverlaps") \
           and not hasattr(self.parser,"nbasis") \
           and not hasattr(self.parser,"homos"):
-            self.logger.error("Missing mocoeffs or aooverlaps")
+            self.logger.error("Missing mocoeffs, nbasis, or homos")
             return False #let the caller of function know we didn't finish
 
         self.logger.info("Creating attribute density: array[3]")
         size=self.parser.nbasis
         unrestricted=(len(self.parser.mocoeffs)==2)
 
+        #determine number of steps, and whether process involves beta orbitals
+        nstep=self.parser.homos[0]+1
         if unrestricted:
             self.density=Numeric.zeros([2,size,size],"f")
+            nstep+=self.parser.homos[1]+1
         else:
             self.density=Numeric.zeros([1,size,size],"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(self.parser.homos[spin]+1):
+
+                if self.progress and random.random()<fupdate:
+                    self.progress.update(step,"Density Matrix")
+
                 col=Numeric.reshape(self.parser.mocoeffs[spin][i],(size,1))
                 colt=Numeric.reshape(col,(1,size))
 
                 tempdensity=Numeric.matrixmultiply(col,colt)
                 self.density[spin]=Numeric.add(self.density[spin],tempdensity)
 
+                step+=1
+
         if not unrestricted: #multiply by two to account for second electron
             self.density[0]=Numeric.add(self.density[0],self.density[0])
 
+        if self.progress:
+            self.progress.update(nstep,"Done")
+
 if __name__=="__main__":
     import doctest,g03parser
     doctest.testmod(g03parser,verbose=False)

Modified: trunk/src/cclib/parser/adfparser.py
===================================================================
--- trunk/src/cclib/parser/adfparser.py	2006-05-10 23:02:55 UTC (rev 110)
+++ trunk/src/cclib/parser/adfparser.py	2006-05-10 23:28:49 UTC (rev 111)
@@ -295,6 +295,7 @@
 
               temp=Numeric.array(self.moenergies,"f")
               self.moenergies=temp
+              self.homos=Numeric.array(self.homos)
 
             if line[1:24]=="List of All Frequencies":
 # Start of the IR/Raman frequency section


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[cclib-svn] SF.net SVN: cclib: [110] trunk/test

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

Revision: 110
Author:   atenderholt
Date:     2006-05-10 16:02:55 -0700 (Wed, 10 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=110&view=rev

Log Message:
-----------
Fixed the aooverlap problem in ADF by replacing it with fooverlaps

Modified Paths:
--------------
    trunk/test/testSP.py
    trunk/test/testSPun.py
Modified: trunk/test/testSP.py
===================================================================
--- trunk/test/testSP.py	2006-05-10 22:55:56 UTC (rev 109)
+++ trunk/test/testSP.py	2006-05-10 23:02:55 UTC (rev 110)
@@ -28,6 +28,11 @@
 class ADFSPTest(GenericSPTest):
     def setUp(self):
         self.data = getfile(ADF,"basicADF2004.01","dvb_sp_b.adfout")
+    
+    def testdimaooverlaps(self):
+        """Are the dims of the overlap matrix consistent with nbasis?"""
+        #ADF uses fooverlaps
+        self.assertEquals(self.data.fooverlaps.shape,(self.data.nbasis,self.data.nbasis))
 
 names = [ "Gaussian", "PCGamess", "GAMESS", "ADF", "Jaguar" ]
 tests = [ GaussianSPTest, PCGamessSPTest,

Modified: trunk/test/testSPun.py
===================================================================
--- trunk/test/testSPun.py	2006-05-10 22:55:56 UTC (rev 109)
+++ trunk/test/testSPun.py	2006-05-10 23:02:55 UTC (rev 110)
@@ -34,6 +34,12 @@
     def setUp(self):
         self.data = getfile(ADF,"basicADF2004.01","dvb_un_sp.adfout")
 
+    def testdimaooverlaps(self):
+        """Are the dims of the overlap matrix consistent with nbasis?"""
+        #ADF uses fooverlaps
+        self.assertEquals(self.data.fooverlaps.shape,(self.data.nbasis,self.data.nbasis))
+
+
 names = [ "Gaussian", "PCGamess", "GAMESS", "ADF" ]
 tests = [ GaussianSPunTest, PCGamessSPunTest,
           GamessUSSPunTest, ADFSPunTest ]


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[cclib-svn] SF.net SVN: cclib: [109] trunk/src/cclib/parser

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

Revision: 109
Author:   atenderholt
Date:     2006-05-10 15:55:56 -0700 (Wed, 10 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=109&view=rev

Log Message:
-----------
Density checks to see if the logfile has been parsed (ie. parser.parsed == True). If not, it parses it.

Modified Paths:
--------------
    trunk/src/cclib/method/density.py
    trunk/src/cclib/parser/adfparser.py
    trunk/src/cclib/parser/g03parser.py
    trunk/src/cclib/parser/gamessparser.py
    trunk/src/cclib/parser/jaguarparser.py
    trunk/src/cclib/parser/logfileparser.py
Modified: trunk/src/cclib/method/density.py
===================================================================
--- trunk/src/cclib/method/density.py	2006-05-10 22:20:20 UTC (rev 108)
+++ trunk/src/cclib/method/density.py	2006-05-10 22:55:56 UTC (rev 109)
@@ -40,8 +40,8 @@
     def calculate(self,fupdate=0.05,cupdate=0.002):
         """Calculate the density matrix given the results of a parser"""
     
-        #if not self.parser.parsed:
-        #    self.parser.parse()
+        if not self.parser.parsed:
+            self.parser.parse()
 
         #do we have the needed info in the parser?
         if not hasattr(self.parser,"mocoeffs") \

Modified: trunk/src/cclib/parser/adfparser.py
===================================================================
--- trunk/src/cclib/parser/adfparser.py	2006-05-10 22:20:20 UTC (rev 108)
+++ trunk/src/cclib/parser/adfparser.py	2006-05-10 22:55:56 UTC (rev 109)
@@ -660,6 +660,7 @@
         if hasattr(self,"geovalues"): self.geovalues = Numeric.array(self.geovalues,"f")
         if hasattr(self,"scfenergies"): self.scfenergies = Numeric.array(self.scfenergies,"f")
         if hasattr(self,"scfvalues"): self.scfvalues = [Numeric.array(x,"f") for x in self.scfvalues]
+        self.parsed = True
 
         
 

Modified: trunk/src/cclib/parser/g03parser.py
===================================================================
--- trunk/src/cclib/parser/g03parser.py	2006-05-10 22:20:20 UTC (rev 108)
+++ trunk/src/cclib/parser/g03parser.py	2006-05-10 22:55:56 UTC (rev 109)
@@ -534,6 +534,7 @@
         if hasattr(self,"geovalues"): self.geovalues = Numeric.array(self.geovalues,"f")
         if hasattr(self,"scfenergies"): self.scfenergies = Numeric.array(self.scfenergies,"f")
         if hasattr(self,"scfvalues"): self.scfvalues = [Numeric.array(x,"f") for x in self.scfvalues]
+        self.parsed = True
 
         
 

Modified: trunk/src/cclib/parser/gamessparser.py
===================================================================
--- trunk/src/cclib/parser/gamessparser.py	2006-05-10 22:20:20 UTC (rev 108)
+++ trunk/src/cclib/parser/gamessparser.py	2006-05-10 22:55:56 UTC (rev 109)
@@ -355,7 +355,9 @@
             self.logger.info("Creating attribute nindep with default value")
             self.nindep = self.nbasis
 
+        self.parsed = True
 
+
         
 if __name__=="__main__":
     import doctest,gamessparser

Modified: trunk/src/cclib/parser/jaguarparser.py
===================================================================
--- trunk/src/cclib/parser/jaguarparser.py	2006-05-10 22:20:20 UTC (rev 108)
+++ trunk/src/cclib/parser/jaguarparser.py	2006-05-10 22:55:56 UTC (rev 109)
@@ -166,6 +166,7 @@
 ##            self.scfvalues = Numeric.array(self.scfvalues,"f")
         if hasattr(self,"scfenergies"):
             self.scfenergies = Numeric.array(self.scfenergies,"f")
+        self.parsed = True
         
 if __name__=="__main__":
     import doctest,g03parser

Modified: trunk/src/cclib/parser/logfileparser.py
===================================================================
--- trunk/src/cclib/parser/logfileparser.py	2006-05-10 22:20:20 UTC (rev 108)
+++ trunk/src/cclib/parser/logfileparser.py	2006-05-10 22:55:56 UTC (rev 109)
@@ -93,6 +93,7 @@
         """
         self.filename = filename
         self.progress = progress
+        self.parsed = False
         self.loglevel = loglevel
         self.logname  = logname
         self.table = PeriodicTable()


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[cclib-svn] SF.net SVN: cclib: [108] trunk/src/cclib/method/density.py

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

Revision: 108
Author:   atenderholt
Date:     2006-05-10 15:20:20 -0700 (Wed, 10 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=108&view=rev

Log Message:
-----------
Hopefully finished up density, more testing is needed.

Modified Paths:
--------------
    trunk/src/cclib/method/density.py
Modified: trunk/src/cclib/method/density.py
===================================================================
--- trunk/src/cclib/method/density.py	2006-05-10 21:58:18 UTC (rev 107)
+++ trunk/src/cclib/method/density.py	2006-05-10 22:20:20 UTC (rev 108)
@@ -40,22 +40,22 @@
     def calculate(self,fupdate=0.05,cupdate=0.002):
         """Calculate the density matrix given the results of a parser"""
     
-        if not self.parser.parsed:
-            self.parser.parse()
+        #if not self.parser.parsed:
+        #    self.parser.parse()
 
         #do we have the needed info in the parser?
-        if not hasattr(self.parser,"mocoeffs") 
-          and not hasattr(self.parser,"aooverlaps") 
-          and not hasattr(self.parser,"nbasis") 
+        if not hasattr(self.parser,"mocoeffs") \
+          and not hasattr(self.parser,"aooverlaps") \
+          and not hasattr(self.parser,"nbasis") \
           and not hasattr(self.parser,"homos"):
             self.logger.error("Missing mocoeffs or aooverlaps")
             return False #let the caller of function know we didn't finish
 
         self.logger.info("Creating attribute density: array[3]")
         size=self.parser.nbasis
-        beta=(len(self.parser.mocoeffs)==2)
+        unrestricted=(len(self.parser.mocoeffs)==2)
 
-        if beta:
+        if unrestricted:
             self.density=Numeric.zeros([2,size,size],"f")
         else:
             self.density=Numeric.zeros([1,size,size],"f")
@@ -66,9 +66,12 @@
                 col=Numeric.reshape(self.parser.mocoeffs[spin][i],(size,1))
                 colt=Numeric.reshape(col,(1,size))
 
-                tempdensity=Numeric.matrixmultipy(col,colt)
-                density[spin]=Numeric.add(density[spin],tempdensity)
+                tempdensity=Numeric.matrixmultiply(col,colt)
+                self.density[spin]=Numeric.add(self.density[spin],tempdensity)
 
+        if not unrestricted: #multiply by two to account for second electron
+            self.density[0]=Numeric.add(self.density[0],self.density[0])
+
 if __name__=="__main__":
     import doctest,g03parser
     doctest.testmod(g03parser,verbose=False)


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[cclib-svn] SF.net SVN: cclib: [107] trunk/src/cclib

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

Revision: 107
Author:   atenderholt
Date:     2006-05-10 14:58:18 -0700 (Wed, 10 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=107&view=rev

Log Message:
-----------
Trying again

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

Removed Paths:
-------------
    trunk/src/cclib/method/calculationmethod.py
    trunk/src/cclib/method/density.py
    trunk/src/cclib/methods/
Copied: trunk/src/cclib/method (from rev 105, trunk/src/cclib/methods)

Copied: trunk/src/cclib/method/__init__.py (from rev 106, trunk/src/cclib/methods/__init__.py)
===================================================================
--- trunk/src/cclib/method/__init__.py	                        (rev 0)
+++ trunk/src/cclib/method/__init__.py	2006-05-10 21:58:18 UTC (rev 107)
@@ -0,0 +1 @@
+from density import Density

Deleted: trunk/src/cclib/method/calculationmethod.py
===================================================================
--- trunk/src/cclib/methods/calculationmethod.py	2006-05-10 19:29:45 UTC (rev 105)
+++ trunk/src/cclib/method/calculationmethod.py	2006-05-10 21:58:18 UTC (rev 107)
@@ -1,52 +0,0 @@
-"""
-cclib is a parser for computational chemistry log files.
-
-See http://cclib.sf.net for more information.
-
-Copyright (C) 2006 Noel O'Boyle and Adam Tenderholt
-
- This program is free software; you can redistribute and/or modify it
- under the terms of the GNU General Public License as published by the
- Free Software Foundation; either version 2, or (at your option) any later
- version.
-
- This program is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- General Public License for more details.
-
-Contributions (monetary as well as code :-) are encouraged.
-"""
-import logging, sys
-import Numeric
-
-class Method(object):
-    """Abstract class for logfile objects.
-
-    Subclasses:
-        Density
-    
-    Attributes:
-    """
-    def __init__(self,parser,progress=None,
-                 loglevel=logging.INFO,logname="Log"):
-        """Initialise the Logfile object.
-
-        Typically called by subclasses in their own __init__ methods.
-        """
-        self.parser = parser
-        self.progress = progress
-        self.loglevel = loglevel
-        self.logname  = logname
-
-        # Set up the logger
-        self.logger = logging.getLogger('%s %s' % (self.logname,self.parser))
-        self.logger.setLevel(self.loglevel)
-        handler = logging.StreamHandler(sys.stdout)
-        handler.setFormatter(logging.Formatter("[%(name)s %(levelname)s] %(message)s"))
-        self.logger.addHandler(handler)
-
-
-if __name__=="__main__":
-    import doctest,calculationmethod
-    doctest.testmod(calculationmethod,verbose=False)

Copied: trunk/src/cclib/method/calculationmethod.py (from rev 106, trunk/src/cclib/methods/calculationmethod.py)
===================================================================
--- trunk/src/cclib/method/calculationmethod.py	                        (rev 0)
+++ trunk/src/cclib/method/calculationmethod.py	2006-05-10 21:58:18 UTC (rev 107)
@@ -0,0 +1,52 @@
+"""
+cclib is a parser for computational chemistry log files.
+
+See http://cclib.sf.net for more information.
+
+Copyright (C) 2006 Noel O'Boyle and Adam Tenderholt
+
+ This program is free software; you can redistribute and/or modify it
+ under the terms of the GNU General Public License as published by the
+ Free Software Foundation; either version 2, or (at your option) any later
+ version.
+
+ This program is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ General Public License for more details.
+
+Contributions (monetary as well as code :-) are encouraged.
+"""
+import logging, sys
+import Numeric
+
+class Method(object):
+    """Abstract class for logfile objects.
+
+    Subclasses:
+        Density
+    
+    Attributes:
+    """
+    def __init__(self,parser,progress=None,
+                 loglevel=logging.INFO,logname="Log"):
+        """Initialise the Logfile object.
+
+        Typically called by subclasses in their own __init__ methods.
+        """
+        self.parser = parser
+        self.progress = progress
+        self.loglevel = loglevel
+        self.logname  = logname
+
+        # Set up the logger
+        self.logger = logging.getLogger('%s %s' % (self.logname,self.parser))
+        self.logger.setLevel(self.loglevel)
+        handler = logging.StreamHandler(sys.stdout)
+        handler.setFormatter(logging.Formatter("[%(name)s %(levelname)s] %(message)s"))
+        self.logger.addHandler(handler)
+
+
+if __name__=="__main__":
+    import doctest,calculationmethod
+    doctest.testmod(calculationmethod,verbose=False)

Deleted: trunk/src/cclib/method/density.py
===================================================================
--- trunk/src/cclib/methods/density.py	2006-05-10 19:29:45 UTC (rev 105)
+++ trunk/src/cclib/method/density.py	2006-05-10 21:58:18 UTC (rev 107)
@@ -1,72 +0,0 @@
-"""
-cclib is a parser for computational chemistry log files.
-
-See http://cclib.sf.net for more information.
-
-Copyright (C) 2006 Noel O'Boyle and Adam Tenderholt
-
- This program is free software; you can redistribute and/or modify it
- under the terms of the GNU General Public License as published by the
- Free Software Foundation; either version 2, or (at your option) any later
- version.
-
- This program is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- General Public License for more details.
-
-Contributions (monetary as well as code :-) are encouraged.
-"""
-import re,time
-import Numeric
-import random # For sometimes running the progress updater
-from calculationmethod import Method
-
-class Density(Method):
-    """Calculate the density matrix"""
-    def __init__(self,*args):
-
-        # Call the __init__ method of the superclass
-        super(Density, self).__init__(logname="Density",*args)
-        
-    def __str__(self):
-        """Return a string representation of the object."""
-        return "Density matrix of" % (self.parser)
-
-    def __repr__(self):
-        """Return a representation of the object."""
-        return 'Density matrix("%s")' % (self.parser)
-    
-    def calculate(self,fupdate=0.05,cupdate=0.002):
-        """Calculate the density matrix given the results of a parser"""
-    
-        if not self.parser.parsed:
-            self.parser.parse()
-
-        #do we have the needed info in the parser?
-        if not hasattr(self.parser,"mocoeffs") 
-          and not hasattr(self.parser,"aooverlaps") 
-          and not hasattr(self.parser,"nbasis") 
-          and not hasattr(self.parser,"homos"):
-            self.logger.error("Missing mocoeffs or aooverlaps")
-            return False #let the caller of function know we didn't finish
-
-        self.logger.info("Creating attribute density: array[3]")
-        size=self.parser.nbasis
-        beta=(len(self.parser.mocoeffs)==2)
-
-        if beta:
-            self.density=Numeric.zeros([2,size,size],"f")
-        else:
-            self.density=Numeric.zeros([1,size,size],"f")
-
-        for i in range(self.parser.homos[0]+1):
-            col=Numeric.reshape(self.parser.mocoeffs[0][i],(size,1))
-            colt=Numeric.reshape(col,(1,size))
-
-            tempdensity=Numeric.matrixmultipy(col,colt)
-            density[0]=Numeric.add(density[0],tempdensity)
-
-if __name__=="__main__":
-    import doctest,g03parser
-    doctest.testmod(g03parser,verbose=False)

Copied: trunk/src/cclib/method/density.py (from rev 106, trunk/src/cclib/methods/density.py)
===================================================================
--- trunk/src/cclib/method/density.py	                        (rev 0)
+++ trunk/src/cclib/method/density.py	2006-05-10 21:58:18 UTC (rev 107)
@@ -0,0 +1,74 @@
+"""
+cclib is a parser for computational chemistry log files.
+
+See http://cclib.sf.net for more information.
+
+Copyright (C) 2006 Noel O'Boyle and Adam Tenderholt
+
+ This program is free software; you can redistribute and/or modify it
+ under the terms of the GNU General Public License as published by the
+ Free Software Foundation; either version 2, or (at your option) any later
+ version.
+
+ This program is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ General Public License for more details.
+
+Contributions (monetary as well as code :-) are encouraged.
+"""
+import re,time
+import Numeric
+import random # For sometimes running the progress updater
+from calculationmethod import Method
+
+class Density(Method):
+    """Calculate the density matrix"""
+    def __init__(self,*args):
+
+        # Call the __init__ method of the superclass
+        super(Density, self).__init__(logname="Density",*args)
+        
+    def __str__(self):
+        """Return a string representation of the object."""
+        return "Density matrix of" % (self.parser)
+
+    def __repr__(self):
+        """Return a representation of the object."""
+        return 'Density matrix("%s")' % (self.parser)
+    
+    def calculate(self,fupdate=0.05,cupdate=0.002):
+        """Calculate the density matrix given the results of a parser"""
+    
+        if not self.parser.parsed:
+            self.parser.parse()
+
+        #do we have the needed info in the parser?
+        if not hasattr(self.parser,"mocoeffs") 
+          and not hasattr(self.parser,"aooverlaps") 
+          and not hasattr(self.parser,"nbasis") 
+          and not hasattr(self.parser,"homos"):
+            self.logger.error("Missing mocoeffs or aooverlaps")
+            return False #let the caller of function know we didn't finish
+
+        self.logger.info("Creating attribute density: array[3]")
+        size=self.parser.nbasis
+        beta=(len(self.parser.mocoeffs)==2)
+
+        if beta:
+            self.density=Numeric.zeros([2,size,size],"f")
+        else:
+            self.density=Numeric.zeros([1,size,size],"f")
+
+        for spin in range(len(self.parser.mocoeffs)):
+
+            for i in range(self.parser.homos[spin]+1):
+                col=Numeric.reshape(self.parser.mocoeffs[spin][i],(size,1))
+                colt=Numeric.reshape(col,(1,size))
+
+                tempdensity=Numeric.matrixmultipy(col,colt)
+                density[spin]=Numeric.add(density[spin],tempdensity)
+
+if __name__=="__main__":
+    import doctest,g03parser
+    doctest.testmod(g03parser,verbose=False)


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[cclib-svn] SF.net SVN: cclib: [106] trunk

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

Revision: 106
Author:   atenderholt
Date:     2006-05-10 14:56:50 -0700 (Wed, 10 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=106&view=rev

Log Message:
-----------
Added __init__.pys and some work on density, still need to rename methods to method, but don't want to --force svn.

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

Added Paths:
-----------
    trunk/src/cclib/methods/__init__.py
Modified: trunk/setup.py
===================================================================
--- trunk/setup.py	2006-05-10 19:29:45 UTC (rev 105)
+++ trunk/setup.py	2006-05-10 21:56:50 UTC (rev 106)
@@ -5,4 +5,4 @@
       author_email="bao...@us...",
       url="http://cclib.sourceforge.net",
       package_dir = {'cclib':'src/cclib'},
-      packages=['cclib','cclib.parser','cclib.progress'])
+      packages=['cclib','cclib.parser','cclib.progress','cclib.method'])

Modified: trunk/src/cclib/__init__.py
===================================================================
--- trunk/src/cclib/__init__.py	2006-05-10 19:29:45 UTC (rev 105)
+++ trunk/src/cclib/__init__.py	2006-05-10 21:56:50 UTC (rev 106)
@@ -1,2 +1,3 @@
 import parser
 import progress
+import method

Added: trunk/src/cclib/methods/__init__.py
===================================================================
--- trunk/src/cclib/methods/__init__.py	                        (rev 0)
+++ trunk/src/cclib/methods/__init__.py	2006-05-10 21:56:50 UTC (rev 106)
@@ -0,0 +1 @@
+from density import Density

Modified: trunk/src/cclib/methods/density.py
===================================================================
--- trunk/src/cclib/methods/density.py	2006-05-10 19:29:45 UTC (rev 105)
+++ trunk/src/cclib/methods/density.py	2006-05-10 21:56:50 UTC (rev 106)
@@ -60,13 +60,15 @@
         else:
             self.density=Numeric.zeros([1,size,size],"f")
 
-        for i in range(self.parser.homos[0]+1):
-            col=Numeric.reshape(self.parser.mocoeffs[0][i],(size,1))
-            colt=Numeric.reshape(col,(1,size))
+        for spin in range(len(self.parser.mocoeffs)):
 
-            tempdensity=Numeric.matrixmultipy(col,colt)
-            density[0]=Numeric.add(density[0],tempdensity)
+            for i in range(self.parser.homos[spin]+1):
+                col=Numeric.reshape(self.parser.mocoeffs[spin][i],(size,1))
+                colt=Numeric.reshape(col,(1,size))
 
+                tempdensity=Numeric.matrixmultipy(col,colt)
+                density[spin]=Numeric.add(density[spin],tempdensity)
+
 if __name__=="__main__":
     import doctest,g03parser
     doctest.testmod(g03parser,verbose=False)


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

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

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

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

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

Added Paths:
-----------
    trunk/src/cclib/methods/
    trunk/src/cclib/methods/calculationmethod.py
    trunk/src/cclib/methods/density.py
Added: trunk/src/cclib/methods/calculationmethod.py
===================================================================
--- trunk/src/cclib/methods/calculationmethod.py	                        (rev 0)
+++ trunk/src/cclib/methods/calculationmethod.py	2006-05-10 19:29:45 UTC (rev 105)
@@ -0,0 +1,52 @@
+"""
+cclib is a parser for computational chemistry log files.
+
+See http://cclib.sf.net for more information.
+
+Copyright (C) 2006 Noel O'Boyle and Adam Tenderholt
+
+ This program is free software; you can redistribute and/or modify it
+ under the terms of the GNU General Public License as published by the
+ Free Software Foundation; either version 2, or (at your option) any later
+ version.
+
+ This program is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ General Public License for more details.
+
+Contributions (monetary as well as code :-) are encouraged.
+"""
+import logging, sys
+import Numeric
+
+class Method(object):
+    """Abstract class for logfile objects.
+
+    Subclasses:
+        Density
+    
+    Attributes:
+    """
+    def __init__(self,parser,progress=None,
+                 loglevel=logging.INFO,logname="Log"):
+        """Initialise the Logfile object.
+
+        Typically called by subclasses in their own __init__ methods.
+        """
+        self.parser = parser
+        self.progress = progress
+        self.loglevel = loglevel
+        self.logname  = logname
+
+        # Set up the logger
+        self.logger = logging.getLogger('%s %s' % (self.logname,self.parser))
+        self.logger.setLevel(self.loglevel)
+        handler = logging.StreamHandler(sys.stdout)
+        handler.setFormatter(logging.Formatter("[%(name)s %(levelname)s] %(message)s"))
+        self.logger.addHandler(handler)
+
+
+if __name__=="__main__":
+    import doctest,calculationmethod
+    doctest.testmod(calculationmethod,verbose=False)


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

Added: trunk/src/cclib/methods/density.py
===================================================================
--- trunk/src/cclib/methods/density.py	                        (rev 0)
+++ trunk/src/cclib/methods/density.py	2006-05-10 19:29:45 UTC (rev 105)
@@ -0,0 +1,72 @@
+"""
+cclib is a parser for computational chemistry log files.
+
+See http://cclib.sf.net for more information.
+
+Copyright (C) 2006 Noel O'Boyle and Adam Tenderholt
+
+ This program is free software; you can redistribute and/or modify it
+ under the terms of the GNU General Public License as published by the
+ Free Software Foundation; either version 2, or (at your option) any later
+ version.
+
+ This program is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ General Public License for more details.
+
+Contributions (monetary as well as code :-) are encouraged.
+"""
+import re,time
+import Numeric
+import random # For sometimes running the progress updater
+from calculationmethod import Method
+
+class Density(Method):
+    """Calculate the density matrix"""
+    def __init__(self,*args):
+
+        # Call the __init__ method of the superclass
+        super(Density, self).__init__(logname="Density",*args)
+        
+    def __str__(self):
+        """Return a string representation of the object."""
+        return "Density matrix of" % (self.parser)
+
+    def __repr__(self):
+        """Return a representation of the object."""
+        return 'Density matrix("%s")' % (self.parser)
+    
+    def calculate(self,fupdate=0.05,cupdate=0.002):
+        """Calculate the density matrix given the results of a parser"""
+    
+        if not self.parser.parsed:
+            self.parser.parse()
+
+        #do we have the needed info in the parser?
+        if not hasattr(self.parser,"mocoeffs") 
+          and not hasattr(self.parser,"aooverlaps") 
+          and not hasattr(self.parser,"nbasis") 
+          and not hasattr(self.parser,"homos"):
+            self.logger.error("Missing mocoeffs or aooverlaps")
+            return False #let the caller of function know we didn't finish
+
+        self.logger.info("Creating attribute density: array[3]")
+        size=self.parser.nbasis
+        beta=(len(self.parser.mocoeffs)==2)
+
+        if beta:
+            self.density=Numeric.zeros([2,size,size],"f")
+        else:
+            self.density=Numeric.zeros([1,size,size],"f")
+
+        for i in range(self.parser.homos[0]+1):
+            col=Numeric.reshape(self.parser.mocoeffs[0][i],(size,1))
+            colt=Numeric.reshape(col,(1,size))
+
+            tempdensity=Numeric.matrixmultipy(col,colt)
+            density[0]=Numeric.add(density[0],tempdensity)
+
+if __name__=="__main__":
+    import doctest,g03parser
+    doctest.testmod(g03parser,verbose=False)


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


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[cclib-svn] SF.net SVN: cclib: [104] trunk/test

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

Revision: 104
Author:   baoilleach
Date:     2006-05-10 05:42:07 -0700 (Wed, 10 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=104&view=rev

Log Message:
-----------
Adding some tests for the unrestricted single point calculations. Note that ADF appears to have the wrong type for homos (should be a Numeric array, but is a list).

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

Added Paths:
-----------
    trunk/test/testSPun.py
Copied: trunk/test/testSPun.py (from rev 103, trunk/test/testSP.py)
===================================================================
--- trunk/test/testSPun.py	                        (rev 0)
+++ trunk/test/testSPun.py	2006-05-10 12:42:07 UTC (rev 104)
@@ -0,0 +1,53 @@
+import os, unittest
+from cclib.parser import GAMESS,G03,ADF,Jaguar
+from Numeric import array
+from testall import getfile
+
+class GenericSPunTest(unittest.TestCase):
+    """Restricted single point calculations with MO coeffs and overlap info."""
+    def testdimaooverlaps(self):
+        """Are the dims of the overlap matrix consistent with nbasis?"""
+        self.assertEquals(self.data.aooverlaps.shape,(self.data.nbasis,self.data.nbasis))
+
+    def testdimmocoeffs(self):
+        """Are the dimensions of mocoeffs equal to 1 x nindep x nbasis?"""
+        self.assertEquals(self.data.mocoeffs.shape,(2,self.data.nindep,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"))
+
+class GaussianSPunTest(GenericSPunTest):
+    def setUp(self):
+        self.data = getfile(G03,"basicGaussian03","dvb_un_sp.out")
+
+class GamessUSSPunTest(GenericSPunTest):
+    def setUp(self):
+        self.data = getfile(GAMESS,"basicGAMESS-US","dvb_un_sp.out")
+
+class PCGamessSPunTest(GenericSPunTest):
+    def setUp(self):
+        self.data = getfile(GAMESS,"basicPCGAMESS","dvb_un_sp.out")
+
+class ADFSPunTest(GenericSPunTest):
+    def setUp(self):
+        self.data = getfile(ADF,"basicADF2004.01","dvb_un_sp.adfout")
+
+names = [ "Gaussian", "PCGamess", "GAMESS", "ADF" ]
+tests = [ GaussianSPunTest, PCGamessSPunTest,
+          GamessUSSPunTest, ADFSPunTest ]
+              
+if __name__=="__main__":
+    total = errors = failures = 0
+
+    for name,test in zip(names,tests):
+        print "\n**** Testing %s SPun ****" % name
+        myunittest = unittest.makeSuite(test)
+        a = unittest.TextTestRunner(verbosity=2).run(myunittest)
+        total += a.testsRun
+        errors += len(a.errors)
+        failures += len(a.failures)
+
+    print "\n\n********* SUMMARY OF SPun **************"
+    print "TOTAL: %d\tPASSED: %d\tFAILED: %d\tERRORS: %d" % (total,total-(errors+failures),failures,errors)

Modified: trunk/test/testall.py
===================================================================
--- trunk/test/testall.py	2006-05-10 09:23:55 UTC (rev 103)
+++ trunk/test/testall.py	2006-05-10 12:42:07 UTC (rev 104)
@@ -41,7 +41,7 @@
 
 if __name__=="__main__":
     total = errors = failures = 0
-    for module in [ "testGeoOpt", "testSP" ]:
+    for module in [ "testGeoOpt", "testSP", "testSPun" ]:
         names = importName(module, "names") # i.e. from testGeoOpt import names
         tests = importName(module, "tests") # i.e. from testGeoOpt import tests
         for name,test in zip(names,tests):


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[cclib-svn] SF.net SVN: cclib: [103] trunk/test

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

Revision: 103
Author:   baoilleach
Date:     2006-05-10 02:23:55 -0700 (Wed, 10 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=103&view=rev

Log Message:
-----------
Separated out different tests into different tests files. Running testall.py will still run all of the tests, but it's also possible to just run tests for single-point calcs (testSP.py) or geoopt calcs (GeoOpt.py). Needs to be tidied up a bit more as there is some duplicated code in __main__.

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

Added Paths:
-----------
    trunk/test/testGeoOpt.py
    trunk/test/testSP.py
Copied: trunk/test/testGeoOpt.py (from rev 101, trunk/test/testall.py)
===================================================================
--- trunk/test/testGeoOpt.py	                        (rev 0)
+++ trunk/test/testGeoOpt.py	2006-05-10 09:23:55 UTC (rev 103)
@@ -0,0 +1,85 @@
+import os, unittest
+from cclib.parser import GAMESS,G03,ADF,Jaguar
+from Numeric import array
+from testall import getfile
+
+class GenericGeoOptTest(unittest.TestCase):
+    def testhomos(self):
+        """Is the index of the homo equal to 34?"""
+        self.assertEquals(self.data.homos,array([34]))
+
+    def testnatom(self):
+        """Is the number of atoms equal to 20?"""
+        self.assertEquals(self.data.natom,20)
+
+    def testnbasis(self):
+        """Is the number of basis set functions equal to 60?"""
+        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)
+
+    def testnormalisesym(self):
+        """Did this subclasses overwrite normalisesym?"""
+        self.assertNotEquals(self.data.normalisesym("A"),"ERROR: This should be overwritten by this subclass")
+
+    def testlengthmoenergies(self):
+        """Is the number of evalues equal to 60?"""
+        self.assertEquals(60,len(self.data.moenergies[0]))
+
+    def testsymlabels(self):
+        """Are all the symmetry labels either Ag/u or Bg/u?"""
+        sumwronglabels = sum([x not in ['Ag','Bu','Au','Bg'] for x in self.data.mosyms[0]])
+        self.assertEquals(sumwronglabels,0)
+
+    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([]))
+
+    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))
+
+class GaussianGeoOptTest(GenericGeoOptTest):
+    def setUp(self):
+        self.data = getfile(G03,"basicGaussian03","dvb_gopt.out")
+
+class GamessUSGeoOptTest(GenericGeoOptTest):
+    def setUp(self):
+        self.data = getfile(GAMESS,"basicGAMESS-US","dvb_gopt_a.out")
+
+class PCGamessGeoOptTest(GenericGeoOptTest):
+    def setUp(self):
+        self.data = getfile(GAMESS,"basicPCGAMESS","dvb_gopt_a.out")
+
+class ADFGeoOptTest(GenericGeoOptTest):
+    def setUp(self):
+        self.data = getfile(ADF,"basicADF2004.01","dvb_gopt.adfout")
+
+    def testscfvaluedim(self):
+        """Do the scf values have the right dimensions? 
+           ADF calculations one more SCF cycle after the geometry is converged"""
+        self.assert_(len(self.data.scfvalues)==len(self.data.geovalues)+1 and len(self.data.scfvalues[0])==len(self.data.scftargets))
+
+class JaguarGeoOptTest(GenericGeoOptTest):
+    def setUp(self):
+        self.data = getfile(Jaguar,"basicJaguar","eg01","dvb_gopt.out")
+
+names = [ "Gaussian", "PCGamess", "GAMESS", "ADF", "Jaguar" ]
+tests = [ GaussianGeoOptTest, PCGamessGeoOptTest,
+          GamessUSGeoOptTest, ADFGeoOptTest,
+          JaguarGeoOptTest ]
+
+if __name__=="__main__":
+    total = errors = failures = 0
+    for name,test in zip(names,tests):
+        print "\n**** Testing %s Geo Opt ****" % name
+        myunittest = unittest.makeSuite(test)
+        a = unittest.TextTestRunner(verbosity=2).run(myunittest)
+        total += a.testsRun
+        errors += len(a.errors)
+        failures += len(a.failures)
+    
+    print "\n\n********* SUMMARY OF Geo Opt **************"
+    print "TOTAL: %d\tPASSED: %d\tFAILED: %d\tERRORS: %d" % (total,total-(errors+failures),failures,errors)

Copied: trunk/test/testSP.py (from rev 101, trunk/test/testall.py)
===================================================================
--- trunk/test/testSP.py	                        (rev 0)
+++ trunk/test/testSP.py	2006-05-10 09:23:55 UTC (rev 103)
@@ -0,0 +1,48 @@
+import os, unittest
+from cclib.parser import GAMESS,G03,ADF,Jaguar
+from Numeric import array
+from testall import getfile
+
+class GenericSPTest(unittest.TestCase):
+    """Restricted single point calculations with MO coeffs and overlap info."""
+    def testdimaooverlaps(self):
+        """Are the dims of the overlap matrix consistent with nbasis?"""
+        self.assertEquals(self.data.aooverlaps.shape,(self.data.nbasis,self.data.nbasis))
+
+    def testdimmocoeffs(self):
+        """Are the dimensions of mocoeffs equal to 1 x nindep x nbasis?"""
+        self.assertEquals(self.data.mocoeffs.shape,(1,self.data.nindep,self.data.nbasis))
+
+class GaussianSPTest(GenericSPTest):
+    def setUp(self):
+        self.data = getfile(G03,"basicGaussian03","dvb_sp.out")
+
+class GamessUSSPTest(GenericSPTest):
+    def setUp(self):
+        self.data = getfile(GAMESS,"basicGAMESS-US","dvb_sp.out")
+
+class PCGamessSPTest(GenericSPTest):
+    def setUp(self):
+        self.data = getfile(GAMESS,"basicPCGAMESS","dvb_sp.out")
+
+class ADFSPTest(GenericSPTest):
+    def setUp(self):
+        self.data = getfile(ADF,"basicADF2004.01","dvb_sp_b.adfout")
+
+names = [ "Gaussian", "PCGamess", "GAMESS", "ADF", "Jaguar" ]
+tests = [ GaussianSPTest, PCGamessSPTest,
+          GamessUSSPTest, ADFSPTest ]
+              
+if __name__=="__main__":
+    total = errors = failures = 0
+
+    for name,test in zip(names,tests):
+        print "\n**** Testing %s SP ****" % name
+        myunittest = unittest.makeSuite(test)
+        a = unittest.TextTestRunner(verbosity=2).run(myunittest)
+        total += a.testsRun
+        errors += len(a.errors)
+        failures += len(a.failures)
+
+    print "\n\n********* SUMMARY OF SP **************"
+    print "TOTAL: %d\tPASSED: %d\tFAILED: %d\tERRORS: %d" % (total,total-(errors+failures),failures,errors)

Modified: trunk/test/testall.py
===================================================================
--- trunk/test/testall.py	2006-05-10 01:51:02 UTC (rev 102)
+++ trunk/test/testall.py	2006-05-10 09:23:55 UTC (rev 103)
@@ -1,96 +1,7 @@
-import os, unittest
-from cclib.parser import GAMESS,G03,ADF,Jaguar
-from Numeric import array
+import unittest
+import os
+from cclib.parser import G03,GAMESS,ADF,Jaguar
 
-class GenericSPTest(unittest.TestCase):
-    """Restricted single point calculations with MO coeffs and overlap info."""
-    def testdimaooverlaps(self):
-        """Are the dims of the overlap matrix consistent with nbasis?"""
-        self.assertEquals(self.data.aooverlaps.shape,(self.data.nbasis,self.data.nbasis))
-
-    def testdimmocoeffs(self):
-        """Are the dimensions of mocoeffs equal to 1 x nindep x nbasis?"""
-        self.assertEquals(self.data.mocoeffs.shape,(1,self.data.nindep,self.data.nbasis))
-
-class GaussianSPTest(GenericSPTest):
-    def setUp(self):
-        self.data = getfile(G03,"basicGaussian03","dvb_sp.out")
-
-class GamessUSSPTest(GenericSPTest):
-    def setUp(self):
-        self.data = getfile(GAMESS,"basicGAMESS-US","dvb_sp.out")
-
-class PCGamessSPTest(GenericSPTest):
-    def setUp(self):
-        self.data = getfile(GAMESS,"basicPCGAMESS","dvb_sp.out")
-
-class ADFSPTest(GenericSPTest):
-    def setUp(self):
-        self.data = getfile(ADF,"basicADF2004.01","dvb_sp_b.adfout")
-
-class GenericGeoOptTest(unittest.TestCase):
-    def testhomos(self):
-        """Is the index of the homo equal to 34?"""
-        self.assertEquals(self.data.homos,array([34]))
-
-    def testnatom(self):
-        """Is the number of atoms equal to 20?"""
-        self.assertEquals(self.data.natom,20)
-
-    def testnbasis(self):
-        """Is the number of basis set functions equal to 60?"""
-        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)
-
-    def testnormalisesym(self):
-        """Did this subclasses overwrite normalisesym?"""
-        self.assertNotEquals(self.data.normalisesym("A"),"ERROR: This should be overwritten by this subclass")
-
-    def testlengthmoenergies(self):
-        """Is the number of evalues equal to 60?"""
-        self.assertEquals(60,len(self.data.moenergies[0]))
-
-    def testsymlabels(self):
-        """Are all the symmetry labels either Ag/u or Bg/u?"""
-        sumwronglabels = sum([x not in ['Ag','Bu','Au','Bg'] for x in self.data.mosyms[0]])
-        self.assertEquals(sumwronglabels,0)
-
-    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([]))
-
-    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))
-
-class GaussianGeoOptTest(GenericGeoOptTest):
-    def setUp(self):
-        self.data = getfile(G03,"basicGaussian03","dvb_gopt.out")
-
-class GamessUSGeoOptTest(GenericGeoOptTest):
-    def setUp(self):
-        self.data = getfile(GAMESS,"basicGAMESS-US","dvb_gopt_a.out")
-
-class PCGamessGeoOptTest(GenericGeoOptTest):
-    def setUp(self):
-        self.data = getfile(GAMESS,"basicPCGAMESS","dvb_gopt_a.out")
-
-class ADFGeoOptTest(GenericGeoOptTest):
-    def setUp(self):
-        self.data = getfile(ADF,"basicADF2004.01","dvb_gopt.adfout")
-
-    def testscfvaluedim(self):
-        """Do the scf values have the right dimensions? 
-           ADF calculations one more SCF cycle after the geometry is converged"""
-        self.assert_(len(self.data.scfvalues)==len(self.data.geovalues)+1 and len(self.data.scfvalues[0])==len(self.data.scftargets))
-
-class JaguarGeoOptTest(GenericGeoOptTest):
-    def setUp(self):
-        self.data = getfile(Jaguar,"basicJaguar","eg01","dvb_gopt.out")
-
 def getfile(parser,*location):
     """Returns a parsed logfile."""
     if parser.__name__ in ['GAMESS','ADF','Jaguar']:
@@ -116,32 +27,31 @@
     print "LUMO", "  ".join(["%+2.4f" % x.moenergies[0,x.homos[0]+1] for x in logfiles])
     print "H-L  ", "  ".join(["%2.4f" % (x.moenergies[0,x.homos[0]+1]-x.moenergies[0,x.homos[0]],) for x in logfiles])
 
+def importName(modulename, name):
+    """Import from a module whose name is determined at run-time.
+
+    Taken from Python Cookbook 2nd ed O'Reilly Recipe 16.3
+    """
+    try:
+        module = __import__(modulename, globals(), locals(), [name])
+    except ImportError:
+        return None
+    return getattr(module, name)
     
-    
+
 if __name__=="__main__":
-    names = [ "Gaussian", "PCGamess", "GAMESS", "ADF", "Jaguar" ]
-    tests = [ GaussianGeoOptTest, PCGamessGeoOptTest,
-              GamessUSGeoOptTest, ADFGeoOptTest,
-              JaguarGeoOptTest ]
     total = errors = failures = 0
-    for name,test in zip(names,tests):
-        print "\n**** Testing %s Geo Opt ****" % name
-        myunittest = unittest.makeSuite(test)
-        a = unittest.TextTestRunner(verbosity=2).run(myunittest)
-        total += a.testsRun
-        errors += len(a.errors)
-        failures += len(a.failures)
+    for module in [ "testGeoOpt", "testSP" ]:
+        names = importName(module, "names") # i.e. from testGeoOpt import names
+        tests = importName(module, "tests") # i.e. from testGeoOpt import tests
+        for name,test in zip(names,tests):
+            print "\n**** Testing %s (%s) ****" % (name, module)
+            myunittest = unittest.makeSuite(test)
+            a = unittest.TextTestRunner(verbosity=2).run(myunittest)
+            total += a.testsRun
+            errors += len(a.errors)
+            failures += len(a.failures)
 
-    tests = [ GaussianSPTest, PCGamessSPTest,
-              GamessUSSPTest, ADFSPTest ]
-    for name,test in zip(names,tests):
-        print "\n**** Testing %s SP ****" % name
-        myunittest = unittest.makeSuite(test)
-        a = unittest.TextTestRunner(verbosity=2).run(myunittest)
-        total += a.testsRun
-        errors += len(a.errors)
-        failures += len(a.failures)
-
     print "\n\n********* SUMMARY OF EVERYTHING **************"
     print "TOTAL: %d\tPASSED: %d\tFAILED: %d\tERRORS: %d" % (total,total-(errors+failures),failures,errors)
 


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[cclib-svn] SF.net SVN: cclib: [102] trunk/src/cclib/progress

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

Revision: 102
Author:   atenderholt
Date:     2006-05-09 18:51:02 -0700 (Tue, 09 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=102&view=rev

Log Message:
-----------
QtProgress class :o)

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

Added Paths:
-----------
    trunk/src/cclib/progress/qtprogress.py
Modified: trunk/src/cclib/progress/__init__.py
===================================================================
--- trunk/src/cclib/progress/__init__.py	2006-05-09 16:10:39 UTC (rev 101)
+++ trunk/src/cclib/progress/__init__.py	2006-05-10 01:51:02 UTC (rev 102)
@@ -1 +1,2 @@
 from textprogress import TextProgress
+from qtprogress import QtProgress

Added: trunk/src/cclib/progress/qtprogress.py
===================================================================
--- trunk/src/cclib/progress/qtprogress.py	                        (rev 0)
+++ trunk/src/cclib/progress/qtprogress.py	2006-05-10 01:51:02 UTC (rev 102)
@@ -0,0 +1,35 @@
+import sys
+import thread
+from qt import QProgressDialog,QString
+
+class QtProgress(QProgressDialog):
+    
+    def __init__(self,parent):
+        
+        QProgressDialog.__init__(self,parent,"progress",True)
+        
+        self.nstep=0
+        self.text=None
+        self.oldprogress=0
+        self.progress=0
+        self.calls=0
+        
+        self.setCaption("Progress...")
+        
+    def initialize(self,nstep,text=None):
+        
+        self.nstep=nstep
+        self.text=text
+        self.setTotalSteps(nstep)
+        if text:
+          self.setLabelText(text)
+        self.setProgress(1)
+        #sys.stdout.write("\n")
+        
+    def update(self,step,text=None):
+
+        self.setLabelText(text)
+        self.setProgress(step)    
+            
+        return
+


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[cclib-svn] SF.net SVN: cclib: [101] trunk/test/testall.py

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

Revision: 101
Author:   baoilleach
Date:     2006-05-09 09:10:39 -0700 (Tue, 09 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=101&view=rev

Log Message:
-----------
Adding some tests for the dimensions of aooverlaps and mocoeffs in restricted single point energy calculations -- what's the story with ADF though?

Modified Paths:
--------------
    trunk/test/testall.py
Modified: trunk/test/testall.py
===================================================================
--- trunk/test/testall.py	2006-05-09 01:11:45 UTC (rev 100)
+++ trunk/test/testall.py	2006-05-09 16:10:39 UTC (rev 101)
@@ -2,6 +2,32 @@
 from cclib.parser import GAMESS,G03,ADF,Jaguar
 from Numeric import array
 
+class GenericSPTest(unittest.TestCase):
+    """Restricted single point calculations with MO coeffs and overlap info."""
+    def testdimaooverlaps(self):
+        """Are the dims of the overlap matrix consistent with nbasis?"""
+        self.assertEquals(self.data.aooverlaps.shape,(self.data.nbasis,self.data.nbasis))
+
+    def testdimmocoeffs(self):
+        """Are the dimensions of mocoeffs equal to 1 x nindep x nbasis?"""
+        self.assertEquals(self.data.mocoeffs.shape,(1,self.data.nindep,self.data.nbasis))
+
+class GaussianSPTest(GenericSPTest):
+    def setUp(self):
+        self.data = getfile(G03,"basicGaussian03","dvb_sp.out")
+
+class GamessUSSPTest(GenericSPTest):
+    def setUp(self):
+        self.data = getfile(GAMESS,"basicGAMESS-US","dvb_sp.out")
+
+class PCGamessSPTest(GenericSPTest):
+    def setUp(self):
+        self.data = getfile(GAMESS,"basicPCGAMESS","dvb_sp.out")
+
+class ADFSPTest(GenericSPTest):
+    def setUp(self):
+        self.data = getfile(ADF,"basicADF2004.01","dvb_sp_b.adfout")
+
 class GenericGeoOptTest(unittest.TestCase):
     def testhomos(self):
         """Is the index of the homo equal to 34?"""
@@ -106,6 +132,16 @@
         errors += len(a.errors)
         failures += len(a.failures)
 
+    tests = [ GaussianSPTest, PCGamessSPTest,
+              GamessUSSPTest, ADFSPTest ]
+    for name,test in zip(names,tests):
+        print "\n**** Testing %s SP ****" % name
+        myunittest = unittest.makeSuite(test)
+        a = unittest.TextTestRunner(verbosity=2).run(myunittest)
+        total += a.testsRun
+        errors += len(a.errors)
+        failures += len(a.failures)
+
     print "\n\n********* SUMMARY OF EVERYTHING **************"
     print "TOTAL: %d\tPASSED: %d\tFAILED: %d\tERRORS: %d" % (total,total-(errors+failures),failures,errors)
 


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[cclib-svn] SF.net SVN: cclib: [100] trunk/src/cclib/parser/g03parser.py

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

Revision: 100
Author:   atenderholt
Date:     2006-05-08 18:11:45 -0700 (Mon, 08 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=100&view=rev

Log Message:
-----------
Fixed an off-by-one error in the gaussian parser's aooverlap section. It was parsing the AO numbers, but should be fixed now.

Modified Paths:
--------------
    trunk/src/cclib/parser/g03parser.py
Modified: trunk/src/cclib/parser/g03parser.py
===================================================================
--- trunk/src/cclib/parser/g03parser.py	2006-05-08 21:06:30 UTC (rev 99)
+++ trunk/src/cclib/parser/g03parser.py	2006-05-09 01:11:45 UTC (rev 100)
@@ -474,7 +474,7 @@
                         line = inputfile.next()
                         parts = line.split()
                         for j in range(len(parts)-1): # Some lines are longer than others
-                            k = float(parts[j].replace("D","E"))
+                            k = float(parts[j+1].replace("D","E"))
                             self.aooverlaps[base+j,i+base] = k
                             self.aooverlaps[i+base,base+j] = k
                     base += 5


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[cclib-svn] SF.net SVN: cclib: [98] trunk/test/testall.py

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

Revision: 98
Author:   baoilleach
Date:     2006-05-03 02:14:12 -0700 (Wed, 03 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=98&view=rev

Log Message:
-----------
Tided up the main section, in preparation for adding tests for single point unrestricted.

Modified Paths:
--------------
    trunk/test/testall.py
Modified: trunk/test/testall.py
===================================================================
--- trunk/test/testall.py	2006-05-03 08:44:14 UTC (rev 97)
+++ trunk/test/testall.py	2006-05-03 09:14:12 UTC (rev 98)
@@ -93,20 +93,21 @@
     
     
 if __name__=="__main__":
-    gaussiantests = unittest.makeSuite(GaussianGeoOptTest)
-    pcgamesstests = unittest.makeSuite(PCGamessGeoOptTest)
-    gamessustests = unittest.makeSuite(GamessUSGeoOptTest)
-    adftests = unittest.makeSuite(ADFGeoOptTest)
-    jaguartests = unittest.makeSuite(JaguarGeoOptTest)
-    print "\n*** Testing Gaussian dvb_gopt.out ***"
-    unittest.TextTestRunner(verbosity=2).run(gaussiantests)
-    print "\n\n*** Testing PCGAMESS dvb_gopt_a.out ***"    
-    unittest.TextTestRunner(verbosity=2).run(pcgamesstests)
-    print "\n\n*** Testing GAMESS-US dvb_gopt_a.out ***"    
-    unittest.TextTestRunner(verbosity=2).run(gamessustests)
-    print "\n\n*** Testing ADF dvb_gopt.adfout ***"
-    unittest.TextTestRunner(verbosity=2).run(adftests)
-    print "\n\n*** Testing Jaguar dvb_gopt.out ***"
-    unittest.TextTestRunner(verbosity=2).run(jaguartests)
+    names = [ "Gaussian", "PCGamess", "GAMESS", "ADF", "Jaguar" ]
+    tests = [ GaussianGeoOptTest, PCGamessGeoOptTest,
+              GamessUSGeoOptTest, ADFGeoOptTest,
+              JaguarGeoOptTest ]
+    total = errors = failures = 0
+    for name,test in zip(names,tests):
+        print "\n**** Testing %s Geo Opt ****" % name
+        myunittest = unittest.makeSuite(test)
+        a = unittest.TextTestRunner(verbosity=2).run(myunittest)
+        total += a.testsRun
+        errors += len(a.errors)
+        failures += len(a.failures)
+
+    print "\n\n********* SUMMARY OF EVERYTHING **************"
+    print "TOTAL: %d\tPASSED: %d\tFAILED: %d\tERRORS: %d" % (total,total-(errors+failures),failures,errors)
+
     print "\n\n*** Visual tests ***"
     visualtests()


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[cclib-svn] SF.net SVN: cclib: [97] trunk/src/cclib/parser/g03parser.py

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

Revision: 97
Author:   baoilleach
Date:     2006-05-03 01:44:14 -0700 (Wed, 03 May 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=97&view=rev

Log Message:
-----------
Normalising the symmetries from Gaussian

Modified Paths:
--------------
    trunk/src/cclib/parser/g03parser.py
Modified: trunk/src/cclib/parser/g03parser.py
===================================================================
--- trunk/src/cclib/parser/g03parser.py	2006-05-01 21:03:55 UTC (rev 96)
+++ trunk/src/cclib/parser/g03parser.py	2006-05-03 08:44:14 UTC (rev 97)
@@ -37,7 +37,21 @@
     def __repr__(self):
         """Return a representation of the object."""
         return 'G03("%s")' % (self.filename)
+    
+    def normalisesym(self,label):
+        """Use standard symmetry labels instead of Gaussian labels.
 
+        To normalise:
+        (1) replace any G or U by their lowercase equivalent
+
+        >>> sym = G03("dummyfile").normalisesym
+        >>> labels = ['A1','AG','A1G']
+        >>> map(sym,labels)
+        ['A1', 'Ag', 'A1g']
+        """
+        ans = label.replace("U","u").replace("G","g") 
+        return ans
+
     def parse(self,fupdate=0.05,cupdate=0.002):
         """Extract information from the logfile."""
         inputfile = open(self.filename,"r")
@@ -219,7 +233,7 @@
                         self.logger.info("Creating attribute homos[]")
                     parts = line[17:].split()
                     for x in parts:
-                        self.mosyms[0].append(x.strip('()'))
+                        self.mosyms[0].append(self.normalisesym(x.strip('()')))
                         i+= 1 
                     line = inputfile.next()
                 if unres:
@@ -233,7 +247,7 @@
                             self.homos[1] = i-1 # 'HOMO' indexes the HOMO in the arrays
                         parts = line[17:].split()
                         for x in parts:
-                            self.mosyms[1].append(x.strip('()'))
+                            self.mosyms[1].append(self.normalisesym(x.strip('()')))
                             i+= 1
                         line = inputfile.next()
 


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