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From: <bao...@us...> - 2006-03-19 20:11:10
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Revision: 32 Author: baoilleach Date: 2006-03-19 12:10:58 -0800 (Sun, 19 Mar 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=32&view=rev Log Message: ----------- Adding a couple of tests Added Paths: ----------- trunk/test/parseGAMESS.py trunk/test/parseGaussian.py trunk/test/testall.py Added: trunk/test/parseGAMESS.py =================================================================== --- trunk/test/parseGAMESS.py (rev 0) +++ trunk/test/parseGAMESS.py 2006-03-19 20:10:58 UTC (rev 32) @@ -0,0 +1,17 @@ +import os +from cclib.parser import GAMESS + +os.chdir(os.path.join("..","data","GAMESS")) + +for file in ["ex.out","WinGAMESS.log","exam01.out"]: + t = GAMESS(file) + t.parse() + +os.chdir("basicPCGAMESS") + +for file in ["dvb_gopt.out","dvb_sp.out","dvb_ir.out","dvb_raman.out", + "dvb_un_sp.out"]: + t = GAMESS(file) + t.parse() + + Property changes on: trunk/test/parseGAMESS.py ___________________________________________________________________ Name: svn:executable + * Added: trunk/test/parseGaussian.py =================================================================== --- trunk/test/parseGaussian.py (rev 0) +++ trunk/test/parseGaussian.py 2006-03-19 20:10:58 UTC (rev 32) @@ -0,0 +1,13 @@ +import os +from cclib.parser import G03 + +os.chdir(os.path.join("..","data","Gaussian")) + +os.chdir("basicGaussian03") + +for file in ["dvb_gopt.out","dvb_sp.out","dvb_ir.out","dvb_raman.out", + "dvb_un_sp.out"]: + t = G03(file) + t.parse() + + Property changes on: trunk/test/parseGaussian.py ___________________________________________________________________ Name: svn:executable + * Added: trunk/test/testall.py =================================================================== --- trunk/test/testall.py (rev 0) +++ trunk/test/testall.py 2006-03-19 20:10:58 UTC (rev 32) @@ -0,0 +1,27 @@ +import os +from cclib.parser import GAMESS,G03 + +os.chdir(os.path.join("..","data")) + +testfiles = [G03(os.path.join("Gaussian","basicGaussian03","dvb_gopt.out")), + GAMESS(os.path.join("GAMESS","basicPCGAMESS","dvb_gopt_a.out"))] + +for testfile in testfiles: + testfile.logger.setLevel(0) + testfile.parse() + +attribs = ['natom','homos','nbasis'] +for attrib in attribs: + print attrib, + for testfile in testfiles: + print testfile.__getattribute__(attrib), + print + +print "Energy of optimised molecule", +for testfile in testfiles: + print testfile.scfenergies[-1], +print +print "Energy of HOMO", +for testfile in testfiles: + print testfile.moenergies[0,testfile.homos[0]], +print Property changes on: trunk/test/testall.py ___________________________________________________________________ Name: svn:executable + * This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-04-04 16:06:16
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Revision: 55 Author: baoilleach Date: 2006-04-04 09:06:01 -0700 (Tue, 04 Apr 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=55&view=rev Log Message: ----------- Added tests for initial GAMESS-US calculations (on Linux). Modified Paths: -------------- trunk/test/parseGAMESS.py trunk/test/testall.py Modified: trunk/test/parseGAMESS.py =================================================================== --- trunk/test/parseGAMESS.py 2006-04-04 15:28:30 UTC (rev 54) +++ trunk/test/parseGAMESS.py 2006-04-04 16:06:01 UTC (rev 55) @@ -7,11 +7,15 @@ t = GAMESS(file) t.parse() -os.chdir("basicPCGAMESS") for file in ["dvb_gopt_a.out","dvb_gopt_b.out","dvb_sp.out","dvb_ir.out","dvb_raman.out", "dvb_un_sp.out"]: - t = GAMESS(file) + t = GAMESS(os.path.join("basicPCGAMESS",file)) t.parse() +for file in ["dvb_gopt_a.out","dvb_sp.out"]: + t = GAMESS(os.path.join("basicGAMESS-US",file)) + t.parse() + + Modified: trunk/test/testall.py =================================================================== --- trunk/test/testall.py 2006-04-04 15:28:30 UTC (rev 54) +++ trunk/test/testall.py 2006-04-04 16:06:01 UTC (rev 55) @@ -23,8 +23,12 @@ def setUp(self): self.data = getfile(G03,"basicGaussian03","dvb_gopt.out") -class GamessGeoOptTest(GenericGeoOptTest): +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): @@ -46,23 +50,30 @@ """These are not formal tests -- but they should be eyeballed.""" logfiles = [ getfile(G03,"basicGaussian03","dvb_gopt.out"), getfile(GAMESS,"basicPCGAMESS","dvb_gopt_a.out"), + getfile(GAMESS,"basicGAMESS-US","dvb_gopt_a.out"), getfile(ADF,"basicADF2004.01","dvb_gopt.adfout") ] print "\n\nMO energies of optimised dvb" - print " ","".join(["%7s" % x for x in ['Gaussian','GAMESS','ADF']]) - print "HOMO", " ".join(["%+2.4f" % x.moenergies[0,x.homos[0]] for x in logfiles]) - 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]) + print " ","".join(["%8s" % x for x in ['Gaussian','PCGAMESS','GAMESS-US','ADF']]) + print "HOMO", " ".join(["%+2.4f" % x.moenergies[0,x.homos[0]] for x in logfiles]) + 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]) + + for x in logfiles: + print x.mosyms if __name__=="__main__": gaussiantests = unittest.makeSuite(GaussianGeoOptTest) - gamesstests = unittest.makeSuite(GamessGeoOptTest) + pcgamesstests = unittest.makeSuite(PCGamessGeoOptTest) + gamessustests = unittest.makeSuite(GamessUSGeoOptTest) adftests = unittest.makeSuite(ADFGeoOptTest) print "\n*** Testing Gaussian dvb_gopt.out ***" unittest.TextTestRunner(verbosity=2).run(gaussiantests) - print "\n\n*** Testing GAMESS dvb_gopt_a.out ***" - unittest.TextTestRunner(verbosity=2).run(gamesstests) + 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*** Visual tests ***" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-04-07 10:39:18
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Revision: 56 Author: baoilleach Date: 2006-04-07 03:38:57 -0700 (Fri, 07 Apr 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=56&view=rev Log Message: ----------- Added prototype function normalisesym() to Logfile() for standardising the symmetry labels of molecular orbitals (and other symmetry labels too?). This should be overwritten in the subclasses. Added a unittest to testall.py that checks to make sure that the prototype has been overwritten. Modified Paths: -------------- trunk/src/cclib/parser/logfileparser.py trunk/test/testall.py Modified: trunk/src/cclib/parser/logfileparser.py =================================================================== --- trunk/src/cclib/parser/logfileparser.py 2006-04-04 16:06:01 UTC (rev 55) +++ trunk/src/cclib/parser/logfileparser.py 2006-04-07 10:38:57 UTC (rev 56) @@ -103,6 +103,15 @@ handler.setFormatter(logging.Formatter("[%(name)s %(levelname)s] %(message)s")) self.logger.addHandler(handler) + def normalisesym(self,symlabel): + """Standardise the symmetry labels between parsers. + + This method should be overwritten by individual parsers, and should + contain appropriate doctests. If is not overwritten, this is detected + as an error by unit tests. + """ + return "ERROR: This should be overwritten by this subclass" + def float(self,number): """Convert a string to a float avoiding the problem with Ds. Modified: trunk/test/testall.py =================================================================== --- trunk/test/testall.py 2006-04-04 16:06:01 UTC (rev 55) +++ trunk/test/testall.py 2006-04-07 10:38:57 UTC (rev 56) @@ -19,6 +19,10 @@ """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") + class GaussianGeoOptTest(GenericGeoOptTest): def setUp(self): self.data = getfile(G03,"basicGaussian03","dvb_gopt.out") This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-04-15 08:40:40
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Revision: 69 Author: baoilleach Date: 2006-04-15 01:40:26 -0700 (Sat, 15 Apr 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=69&view=rev Log Message: ----------- Adding the bones of a jaguarparser, along with some tests Modified Paths: -------------- trunk/src/cclib/parser/__init__.py trunk/test/testall.py Added Paths: ----------- trunk/src/cclib/parser/jaguarparser.py trunk/test/parseJaguar.py Modified: trunk/src/cclib/parser/__init__.py =================================================================== --- trunk/src/cclib/parser/__init__.py 2006-04-15 04:17:14 UTC (rev 68) +++ trunk/src/cclib/parser/__init__.py 2006-04-15 08:40:26 UTC (rev 69) @@ -1,3 +1,4 @@ from g03parser import G03 from gamessparser import GAMESS from adfparser import ADF +from jaguarparser import Jaguar Added: trunk/src/cclib/parser/jaguarparser.py =================================================================== --- trunk/src/cclib/parser/jaguarparser.py (rev 0) +++ trunk/src/cclib/parser/jaguarparser.py 2006-04-15 08:40:26 UTC (rev 69) @@ -0,0 +1,140 @@ +""" +cclib is a parser for computational chemistry log files. + +See http://cclib.sf.net for more information. + +Copyright (C) 2006 Noel O'Boyle and Adam Tenderholt + + This program is free software; you can redistribute and/or modify it + under the terms of the GNU General Public License as published by the + Free Software Foundation; either version 2, or (at your option) any later + version. + + This program is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY, without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + General Public License for more details. + +Contributions (monetary as well as code :-) are encouraged. +""" +import re,time +import Numeric +import random # For sometimes running the progress updater +from logfileparser import Logfile,convertor + +class Jaguar(Logfile): + """A Jaguar output file""" + + def __init__(self,*args): + + # Call the __init__ method of the superclass + super(Jaguar, self).__init__(logname="Jaguar",*args) + + def __str__(self): + """Return a string representation of the object.""" + return "Jaguar output file %s" % (self.filename) + + def __repr__(self): + """Return a representation of the object.""" + return 'Jaguar("%s")' % (self.filename) + + def parse(self,fupdate=0.05,cupdate=0.002): + """Extract information from the logfile.""" + inputfile = open(self.filename,"r") + + if self.progress: + + inputfile.seek(0,2) #go to end of file + nstep=inputfile.tell() + inputfile.seek(0) + self.progress.initialize(nstep) + oldstep=0 + + for line in inputfile: + + if self.progress and random.random()<cupdate: + + step = inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Unsupported Information") + oldstep = step + + if line[0:4]=="etot": +# Get SCF convergence information + if not hasattr(self,"scfvalues"): + self.scfvalues = [] + self.logger.info("Creating attribute: scfvalues") + while line[0:4]=="etot": + if line[39:47].strip(): + denergy = float(line[39:47]) + else: + denergy = 0 # Should really be greater than target value + # or should we just ignore the values in this line + ddensity = float(line[48:56]) + maxdiiserr = float(line[57:65]) + self.scfvalues.append([denergy,ddensity,maxdiiserr]) + line = inputfile.next() + + if line[1:5]=="SCFE": +# Get the energy of the molecule + if not hasattr(self,"scfenergies"): + self.logger.info("Creating attribute scfenergies") + self.scfenergies = [] + temp = line.strip().split() + self.scfenergies.append(float(temp[temp.index("hartrees")-1])) + + if line[2:28]=="geometry optimization step": +# Get Geometry Opt convergence information + if not hasattr(self,"geovalues"): + self.geovalues = [] + self.geotargets = Numeric.zeros(4,"float") + self.logger.info("Creating attributes: geovalues,geotargets") + blank = inputfile.next() + blank = inputfile.next() + line = inputfile.next() + i = 0 + values = [] + while line!=blank: + if line[41]=="(": + # A new geo convergence value + values.append(float(line[26:37])) + self.geotargets[i] = float(line[43:54]) + i+=1 + line = inputfile.next() + self.geovalues.append(values) + + if line[2:33]=="Orbital energies/symmetry label": +# Get MO Energies and symmetrys + if not hasattr(self,"moenergies"): + self.logger.info("Creating attributes: moenergies, mosyms") + self.mosyms = [[]] + self.moenergies = [[]] + line = inputfile.next() + while line.strip(): + temp = line.strip().split() + for i in range(0,len(temp),2): + self.moenergies[0].append(float(temp[i])) + self.mosyms[0].append(temp[i+1]) + line = inputfile.next() + self.moenergies = Numeric.array(self.moenergies,"f") + + if line[1:28]=="number of occupied orbitals": + if not hasattr(self,"homos"): + self.logger.info("Creating attribute: homos") + self.homos = Numeric.array([float(line.strip().split()[-1])-1],"i") + + if line[2:27]=="number of basis functions": + if not hasattr(self,"nbasis"): + self.logger.info("Creating attribute: nbasis") + self.nbasis = float(line.strip().split()[-1]) + + inputfile.close() + + if hasattr(self,"scfvalues"): + self.scfvalues = Numeric.array(self.scfvalues,"f") + if hasattr(self,"scfenergies"): + self.scfenergies = Numeric.array(self.scfenergies,"f") + +if __name__=="__main__": + import doctest,g03parser + doctest.testmod(g03parser,verbose=False) Property changes on: trunk/src/cclib/parser/jaguarparser.py ___________________________________________________________________ Name: svn:executable + * Added: trunk/test/parseJaguar.py =================================================================== --- trunk/test/parseJaguar.py (rev 0) +++ trunk/test/parseJaguar.py 2006-04-15 08:40:26 UTC (rev 69) @@ -0,0 +1,14 @@ +import os +from cclib.parser import Jaguar + +os.chdir(os.path.join("..","data","Jaguar","basicJaguar")) + +os.chdir("eg01") + +for file in ["dvb_gopt.out"]: + t = Jaguar(file) + t.parse() + +print t.moenergies[0,:] +print t.homos[0] +print t.moenergies[0,t.homos[0]] Property changes on: trunk/test/parseJaguar.py ___________________________________________________________________ Name: svn:executable + * Modified: trunk/test/testall.py =================================================================== --- trunk/test/testall.py 2006-04-15 04:17:14 UTC (rev 68) +++ trunk/test/testall.py 2006-04-15 08:40:26 UTC (rev 69) @@ -1,5 +1,5 @@ import os, unittest -from cclib.parser import GAMESS,G03,ADF +from cclib.parser import GAMESS,G03,ADF,Jaguar from Numeric import array class GenericGeoOptTest(unittest.TestCase): @@ -12,7 +12,7 @@ self.assertEquals(self.data.natom,20) def testnbasis(self): - """Is the number of basis set function equal to 60?""" + """Is the number of basis set functions equal to 60?""" self.assertEquals(self.data.nbasis,60) def testscfenergy(self): @@ -39,9 +39,13 @@ def setUp(self): self.data = getfile(ADF,"basicADF2004.01","dvb_gopt.adfout") +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']: + if parser.__name__ in ['GAMESS','ADF','Jaguar']: fullpath = ("..","data",parser.__name__) + location elif parser.__name__=="G03": fullpath = ("..","data","Gaussian") + location @@ -55,7 +59,8 @@ logfiles = [ getfile(G03,"basicGaussian03","dvb_gopt.out"), getfile(GAMESS,"basicPCGAMESS","dvb_gopt_a.out"), getfile(GAMESS,"basicGAMESS-US","dvb_gopt_a.out"), - getfile(ADF,"basicADF2004.01","dvb_gopt.adfout") ] + getfile(ADF,"basicADF2004.01","dvb_gopt.adfout"), + getfile(Jaguar,"basicJaguar","eg01","dvb_gopt.out")] print "\n\nMO energies of optimised dvb" print " ","".join(["%8s" % x for x in ['Gaussian','PCGAMESS','GAMESS-US','ADF']]) @@ -72,6 +77,7 @@ 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 ***" @@ -80,5 +86,7 @@ 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) print "\n\n*** Visual tests ***" visualtests() This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-05-10 12:42:15
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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): This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-05-13 21:06:04
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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? This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <ate...@us...> - 2006-05-16 18:21:59
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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?""" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-05-18 08:39:10
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Revision: 124 Author: baoilleach Date: 2006-05-18 01:38:50 -0700 (Thu, 18 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=124&view=rev Log Message: ----------- Renamed G03 object to Gaussian, and changed name of parser from gaussian03 to gaussian. Modified Paths: -------------- trunk/src/cclib/parser/__init__.py trunk/src/cclib/parser/jaguarparser.py trunk/src/cclib/parser/logfileparser.py trunk/test/parseGaussian.py trunk/test/testGeoOpt.py trunk/test/testSP.py trunk/test/testSPun.py trunk/test/testall.py Added Paths: ----------- trunk/src/cclib/parser/gaussianparser.py Removed Paths: ------------- trunk/src/cclib/parser/g03parser.py Modified: trunk/src/cclib/parser/__init__.py =================================================================== --- trunk/src/cclib/parser/__init__.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/src/cclib/parser/__init__.py 2006-05-18 08:38:50 UTC (rev 124) @@ -1,4 +1,4 @@ -from g03parser import G03 +from gaussianparser import Gaussian from gamessparser import GAMESS from adfparser import ADF from jaguarparser import Jaguar Deleted: trunk/src/cclib/parser/g03parser.py =================================================================== --- trunk/src/cclib/parser/g03parser.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/src/cclib/parser/g03parser.py 2006-05-18 08:38:50 UTC (rev 124) @@ -1,581 +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 logfileparser import Logfile,convertor - -class G03(Logfile): - """A Gaussian 98/03 log file""" - SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftargets[] - def __init__(self,*args): - - # Call the __init__ method of the superclass - super(G03, self).__init__(logname="G03",*args) - - def __str__(self): - """Return a string representation of the object.""" - return "Gaussian 03 log file %s" % (self.filename) - - 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") - - if self.progress: - - inputfile.seek(0,2) #go to end of file - nstep=inputfile.tell() - inputfile.seek(0) - 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: - - step = inputfile.tell() - if step!=oldstep: - self.progress.update(step,"Unsupported Information") - oldstep = step - - if line[1:8]=="NAtoms=": -# Find the number of atoms - if self.progress and random.random()<fupdate: - step = inputfile.tell() - if step!=oldstep: - self.progress.update(step,"Attributes") - oldstep=step - - natom = int(line.split()[1]) - if hasattr(self,"natom"): - assert self.natom==natom - else: - # I wonder whether this code will ever be executed - self.natom = natom - self.logger.info("Creating attribute natom: %d" % self.natom) - - 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 - - if not hasattr(self,"atomcoords"): - self.logger.info("Creating attribute atomcoords[]") - self.atomcoords = [] - - hyphens = inputfile.next() - colmNames = inputfile.next() - colmNames = inputfile.next() - hyphens = inputfile.next() - - atomnos = [] - atomcoords = [] - line = inputfile.next() - while line!=hyphens: - broken = line.split() - atomnos.append(int(broken[1])) - atomcoords.append(map(float,broken[3:6])) - line = inputfile.next() - self.atomcoords.append(atomcoords) - if not hasattr(self,"natom"): - 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) - - if line[1:44]=='Requested convergence on RMS density matrix': -# Find the targets for SCF convergence (QM calcs) - if not hasattr(self,"scftargets"): - self.logger.info("Creating attribute scftargets[]") - self.scftargets = Numeric.array([0.0,0.0,0.0],'f') - self.scftargets[G03.SCFRMS] = self.float(line.split('=')[1].split()[0]) - if line[1:44]=='Requested convergence on MAX density matrix': - self.scftargets[G03.SCFMAX] = self.float(line.strip().split('=')[1][:-1]) - if line[1:44]=='Requested convergence on energy': - self.scftargets[G03.SCFENERGY] = self.float(line.strip().split('=')[1][:-1]) - - if line[1:10]=='Cycle 1': -# Extract SCF convergence information (QM calcs) - - 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 Done")==-1: - - if self.progress and random.random()<fupdate: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"QM Convergence") - oldstep=step - - if line.find(' E=')==0: - self.logger.debug(line) - if line.find(" RMSDP")==0: - parts = line.split() - newlist[G03.SCFRMS].append(self.float(parts[0].split('=')[1])) - newlist[G03.SCFMAX].append(self.float(parts[1].split('=')[1])) - energy = 1.0 - if len(parts)>4: - energy = parts[2].split('=')[1] - if energy=="": - energy = self.float(parts[3]) - else: - energy = self.float(energy) - # I moved the following line back a TAB to see the effect - # (it was originally part of the above "if len(parts)") - newlist[G03.SCFENERGY].append(energy) - try: - line = inputfile.next() - except StopIteration: # May be interupted by EOF - break - self.scfvalues.append(newlist) - - if line[1:4]=='It=': -# Extract SCF convergence information (AM1 calcs) - - self.logger.info("Creating attributes scftargets, scfvalues") - self.scftargets = Numeric.array([1E-7],"f") # This is the target value for the rms - self.scfvalues = [[]] - line = inputfile.next() - while line.find(" Energy")==-1: - - if self.progress: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"AM1 Convergence") - oldstep=step - - parts = line.strip().split() - self.scfvalues[0].append(self.float(parts[-1][:-1])) - line = inputfile.next() - - if line[1:9]=='SCF Done': -# Note: this needs to follow the section where 'SCF Done' is used to terminate -# a loop when extracting SCF convergence information - if not hasattr(self,"scfenergies"): - self.logger.info("Creating attribute scfenergies[]") - self.scfenergies = [] - self.scfenergies.append(self.float(line.split()[4])) - - if line[49:59]=='Converged?': -# Extract Geometry convergence information - if not hasattr(self,"geotargets"): - self.logger.info("Creating attributes geotargets[],geovalues[[]]") - self.geovalues = [] - self.geotargets = Numeric.array( [0.0,0.0,0.0,0.0],"f") - newlist = [0]*4 - for i in range(4): - line = inputfile.next() - self.logger.debug(line) - parts = line.split() - try: - value = self.float(parts[2]) - except ValueError: - self.logger.error("Problem parsing the value for geometry optimisation: %s is not a number." % parts[2]) - else: - newlist[i] = value - self.geotargets[i] = self.float(parts[3]) - self.geovalues.append(newlist) - - if line[1:19]=='Orbital symmetries' and not hasattr(self,"mosyms"): -# Extracting orbital symmetries - if self.progress and random.random()<fupdate: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"MO Symmetries") - oldstep=step - - self.logger.info("Creating attribute mosyms[[]]") - self.mosyms = [[]] - line = inputfile.next() - unres = False - if line.find("Alpha Orbitals")==1: - unres = True - line = inputfile.next() - i = 0 - while len(line)>18 and line[17]=='(': - if line.find('Virtual')>=0: - self.homos = Numeric.array([i-1],"i") # 'HOMO' indexes the HOMO in the arrays - self.logger.info("Creating attribute homos[]") - parts = line[17:].split() - for x in parts: - self.mosyms[0].append(self.normalisesym(x.strip('()'))) - i+= 1 - line = inputfile.next() - if unres: - line = inputfile.next() - # Repeat with beta orbital information - i = 0 - self.mosyms.append([]) - while len(line)>18 and line[17]=='(': - if line.find('Virtual')>=0: - self.homos.resize([2]) # Extend the array to two elements - self.homos[1] = i-1 # 'HOMO' indexes the HOMO in the arrays - parts = line[17:].split() - for x in parts: - self.mosyms[1].append(self.normalisesym(x.strip('()'))) - i+= 1 - line = inputfile.next() - - if line[1:6]=="Alpha" and line.find("eigenvalues")>=0: -# Extract the alpha electron eigenvalues - if self.progress and random.random()<fupdate: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"Eigenvalues") - oldstep=step - - self.logger.info("Creating attribute moenergies[[]]") - self.moenergies = [[]] - HOMO = -2 - while line.find('Alpha')==1: - if line.split()[1]=="virt." and HOMO==-2: - # If there aren't any symmetries, - # this is a good way to find the HOMO - HOMO = len(self.moenergies[0])-1 - if hasattr(self,"homos"): - assert HOMO==self.homos[0] - else: - self.logger.info("Creating attribute homos[]") - self.homos = Numeric.array([HOMO],"i") - part = line[28:] - i = 0 - while i*10+4<len(part): - x = part[i*10:(i+1)*10] - self.moenergies[0].append(convertor(self.float(x),"hartree","eV")) - i += 1 - line = inputfile.next() - if line.find('Beta')==2: - self.moenergies.append([]) - HOMO = -2 - while line.find('Beta')==2: - if line.split()[1]=="virt." and HOMO==-2: - # If there aren't any symmetries, - # this is a good way to find the HOMO - HOMO = len(self.moenergies[1])-1 - if len(self.homos)==2: - # It already has a self.homos (with the Alpha value) - # but does it already have a Beta value? - assert HOMO==self.homos[1] - else: - self.homos.resize([2]) - self.homos[1] = HOMO - part = line[28:] - i = 0 - while i*10+4<len(part): - x = part[i*10:(i+1)*10] - self.moenergies[1].append(convertor(self.float(x),"hartree","eV")) - i += 1 - line = inputfile.next() - self.moenergies = Numeric.array(self.moenergies,"f") - - if line[1:14]=="Harmonic freq": -# Start of the IR/Raman frequency section - if self.progress and random.random()<fupdate: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"Frequency Information") - oldstep=step - - self.vibsyms = [] - self.vibirs = [] - self.vibfreqs = [] - self.logger.info("Creating attribute vibsyms[]") - self.logger.info("Creating attribute vibfreqs[]") - self.logger.info("Creating attribute vibirs[]") - line = inputfile.next() - while len(line[:15].split())>0: - # Get past the three/four line title of the columns - line = inputfile.next() - line = inputfile.next() # The line with symmetries - while len(line[:15].split())==0: - self.logger.debug(line) - self.vibsyms.extend(line.split()) # Adding new symmetry - line = inputfile.next() - self.vibfreqs.extend(map(self.float,line[15:].split())) # Adding new frequencies - [inputfile.next() for i in [0,1]] # Skip two lines - line = inputfile.next() - self.vibirs.extend(map(self.float,line[15:].split())) # Adding IR intensities - line = inputfile.next() - if line.find("Raman")>=0: - if not hasattr(self,"vibramans"): - self.vibramans = [] - self.logger.info("Creating attribute vibramans[]") - line = inputfile.next() - self.vibramans.extend(map(self.float,line[15:].split())) # Adding Raman intensities - line = inputfile.next() - while len(line[:15].split())>0: - line = inputfile.next() - line = inputfile.next() # Should be the line with symmetries - self.vibfreqs = Numeric.array(self.vibfreqs,"f") - self.vibirs = Numeric.array(self.vibirs,"f") - if hasattr(self,"vibramans"): self.vibramans = Numeric.array(self.vibramans,"f") - - if line[1:14]=="Excited State": -# Extract the electronic transitions - if not hasattr(self,"etenergy"): - self.etenergies = [] - self.etoscs = [] - self.etsyms = [] - self.etsecs = [] - self.logger.info("Creating attributes etenergies[], etoscs[], etsyms[], etsecs[]") - # Need to deal with lines like: - # (restricted calc) - # Excited State 1: Singlet-BU 5.3351 eV 232.39 nm f=0.1695 - # (unrestricted calc) (first excited state is 2!) - # Excited State 2: ?Spin -A 0.1222 eV 10148.75 nm f=0.0000 - parts = line[36:].split() - self.etenergies.append(convertor(self.float(parts[0]),"eV","cm-1")) - self.etoscs.append(self.float(parts[4].split("=")[1])) - self.etsyms.append(line[21:36].split()) - - line = inputfile.next() - - p = re.compile("(\d+)") - CIScontrib = [] - while line.find(" ->")>=0: # This is a contribution to the transition - parts = line.split("->") - self.logger.debug(parts) - # Has to deal with lines like: - # 32 -> 38 0.04990 - # 35A -> 45A 0.01921 - frommoindex = 0 # For restricted or alpha unrestricted - fromMO = parts[0].strip() - if fromMO[-1]=="B": - frommoindex = 1 # For beta unrestricted - fromMO = int(p.match(fromMO).group()) # extract the number - - t = parts[1].split() - tomoindex = 0 - toMO = t[0] - if toMO[-1]=="B": - tomoindex = 1 - toMO = int(p.match(toMO).group()) - - percent = self.float(t[1]) - sqr = percent**2*2 # The fractional contribution of this CI - if percent<0: - sqr = -sqr - CIScontrib.append([(fromMO,frommoindex),(toMO,tomoindex),sqr]) - line = inputfile.next() - self.etsecs.append(CIScontrib) - self.etenergies = Numeric.array(self.etenergies,"f") - self.etoscs = Numeric.array(self.etoscs,"f") - - if line[1:52]=="<0|r|b> * <b|rxdel|0> (Au), Rotatory Strengths (R)": -# Extract circular dichroism data - self.etrotats = [] - self.logger.info("Creating attribute etrotats[]") - inputfile.next() - inputfile.next() - line = inputfile.next() - parts = line.strip().split() - while len(parts)==5: - try: - R = self.float(parts[-1]) - except ValueError: - # nan or -nan if there is no first excited state - # (for unrestricted calculations) - pass - else: - self.etrotats.append(R) - line = inputfile.next() - temp = line.strip().split() - parts = line.strip().split() - self.etrotats = Numeric.array(self.etrotats,"f") - - if line[1:7]=="NBasis" or line[4:10]=="NBasis": -# Extract the number of basis sets - nbasis = int(line.split('=')[1].split()[0]) - # Has to deal with lines like: - # NBasis = 434 NAE= 97 NBE= 97 NFC= 34 NFV= 0 - # NBasis = 148 MinDer = 0 MaxDer = 0 - # Although the former is in every file, it doesn't occur before - # the overlap matrix is printed - if hasattr(self,"nbasis"): - assert nbasis==self.nbasis - else: - self.nbasis= nbasis - self.logger.info("Creating attribute nbasis: %d" % self.nbasis) - - if line[1:7]=="NBsUse": -# Extract the number of linearly-independent basis sets - nmo = int(line.split('=')[1].split()[0]) - if hasattr(self,"nmo"): - assert nmo==self.nmo - else: - 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 -# (nmo may not always be explicitly stated) - nbasis = int(line.split()[0]) - if hasattr(self,"nbasis"): - assert nbasis==self.nbasis - else: - self.nbasis = nbasis - self.logger.info("Creating attribute nbasis: %d" % self.nbasis) - - if line[1:4]=="***" and (line[5:12]=="Overlap" - or line[8:15]=="Overlap"): -# Extract the molecular orbital overlap matrix - # Has to deal with lines such as: - # *** Overlap *** - # ****** Overlap ****** - self.logger.info("Creating attribute aooverlaps[x,y]") - self.aooverlaps = Numeric.zeros( (self.nbasis,self.nbasis), "float") - # Overlap integrals for basis fn#1 are in aooverlaps[0] - base = 0 - colmNames = inputfile.next() - while base<self.nbasis: - - if self.progress and random.random()<fupdate: - step=inputfile.tell() - if step!=oldstep: - self.progress.update(step,"Overlap") - oldstep=step - - for i in range(self.nbasis-base): # Fewer lines this time - line = inputfile.next() - parts = line.split() - for j in range(len(parts)-1): # Some lines are longer than others - k = float(parts[j+1].replace("D","E")) - self.aooverlaps[base+j,i+base] = k - self.aooverlaps[i+base,base+j] = k - base += 5 - colmNames = inputfile.next() - self.aooverlaps = Numeric.array(self.aooverlaps,"f") - - - if line[5:35]=="Molecular Orbital Coefficients" or line[5:41]=="Alpha Molecular Orbital Coefficients" or line[5:40]=="Beta Molecular Orbital Coefficients": - 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,nmo,nbasis)) - else: - beta = False - self.logger.info("Creating attributes aonames[], mocoeffs[][]") - self.aonames = [] - self.mocoeffs = Numeric.zeros((1,nmo,nbasis),"float") - - base = 0 - for base in range(0,nmo,5): - - if self.progress: - step=inputfile.tell() - if step!=oldstep and random.random() < fupdate: - self.progress.update(step,"Coefficients") - oldstep=step - - colmNames = inputfile.next() - symmetries = inputfile.next() - eigenvalues = inputfile.next() - for i in range(nbasis): - - - line = inputfile.next() - if base==0 and not beta: # Just do this the first time 'round - # Changed below from :12 to :11 to deal with Elmar Neumann's example - parts = line[:11].split() - if len(parts)>1: # New atom - atomname = "%s%s" % (parts[2],parts[1]) - orbital = line[11:20].strip() - self.aonames.append("%s_%s" % (atomname,orbital)) - - part = line[21:].replace("D","E").rstrip() - temp = [] - for j in range(0,len(part),10): - temp.append(float(part[j:j+10])) - if beta: - self.mocoeffs[1,base:base+len(part)/10,i] = temp - else: - self.mocoeffs[0,base:base+len(part)/10,i] = temp - - inputfile.close() - - if self.progress: - self.progress.update(nstep,"Done") - - 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 - - - -# Note to self: Needs to be added to the main parser - def extractTrajectory(self): - """Extract trajectory information from a Gaussian logfile.""" - inputfile = open(self.filename,"r") - self.traj = [] - self.trajSummary = [] - for line in inputfile: - if line.find(" Cartesian coordinates:")==0: - coords = [] - for i in range(self.natom): - line = inputfile.next() - parts = line.strip().split() - # Conversion from a.u. to Angstrom - coords.append([ self.float(x)*0.5292 for x in [parts[3],parts[5],parts[7]] ]) - self.traj.append(coords) - if line==" Trajectory summary\n": - # self.trajSummaryHeader = inputfile.next().strip().split() - header = inputfile.next() - line = inputfile.next() - while line.find("Max Error")==-1: - parts = line.strip().split(" ") - self.trajSummary.append(parts) - line = inputfile.next() - inputfile.close() - assert len(self.traj)==len(self.trajSummary) - -if __name__=="__main__": - import doctest,g03parser - doctest.testmod(g03parser,verbose=False) Copied: trunk/src/cclib/parser/gaussianparser.py (from rev 123, trunk/src/cclib/parser/g03parser.py) =================================================================== --- trunk/src/cclib/parser/gaussianparser.py (rev 0) +++ trunk/src/cclib/parser/gaussianparser.py 2006-05-18 08:38:50 UTC (rev 124) @@ -0,0 +1,581 @@ +""" +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 logfileparser import Logfile,convertor + +class Gaussian(Logfile): + """A Gaussian 98/03 log file""" + SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftargets[] + def __init__(self,*args): + + # Call the __init__ method of the superclass + super(Gaussian, self).__init__(logname="Gaussian",*args) + + def __str__(self): + """Return a string representation of the object.""" + return "Gaussian log file %s" % (self.filename) + + def __repr__(self): + """Return a representation of the object.""" + return 'Gaussian("%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 = Gaussian("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") + + if self.progress: + + inputfile.seek(0,2) #go to end of file + nstep=inputfile.tell() + inputfile.seek(0) + 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: + + step = inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Unsupported Information") + oldstep = step + + if line[1:8]=="NAtoms=": +# Find the number of atoms + if self.progress and random.random()<fupdate: + step = inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Attributes") + oldstep=step + + natom = int(line.split()[1]) + if hasattr(self,"natom"): + assert self.natom==natom + else: + # I wonder whether this code will ever be executed + self.natom = natom + self.logger.info("Creating attribute natom: %d" % self.natom) + + 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 + + if not hasattr(self,"atomcoords"): + self.logger.info("Creating attribute atomcoords[]") + self.atomcoords = [] + + hyphens = inputfile.next() + colmNames = inputfile.next() + colmNames = inputfile.next() + hyphens = inputfile.next() + + atomnos = [] + atomcoords = [] + line = inputfile.next() + while line!=hyphens: + broken = line.split() + atomnos.append(int(broken[1])) + atomcoords.append(map(float,broken[3:6])) + line = inputfile.next() + self.atomcoords.append(atomcoords) + if not hasattr(self,"natom"): + 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) + + if line[1:44]=='Requested convergence on RMS density matrix': +# Find the targets for SCF convergence (QM calcs) + if not hasattr(self,"scftargets"): + self.logger.info("Creating attribute scftargets[]") + self.scftargets = Numeric.array([0.0,0.0,0.0],'f') + self.scftargets[Gaussian.SCFRMS] = self.float(line.split('=')[1].split()[0]) + if line[1:44]=='Requested convergence on MAX density matrix': + self.scftargets[Gaussian.SCFMAX] = self.float(line.strip().split('=')[1][:-1]) + if line[1:44]=='Requested convergence on energy': + self.scftargets[Gaussian.SCFENERGY] = self.float(line.strip().split('=')[1][:-1]) + + if line[1:10]=='Cycle 1': +# Extract SCF convergence information (QM calcs) + + 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 Done")==-1: + + if self.progress and random.random()<fupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"QM Convergence") + oldstep=step + + if line.find(' E=')==0: + self.logger.debug(line) + if line.find(" RMSDP")==0: + parts = line.split() + newlist[Gaussian.SCFRMS].append(self.float(parts[0].split('=')[1])) + newlist[Gaussian.SCFMAX].append(self.float(parts[1].split('=')[1])) + energy = 1.0 + if len(parts)>4: + energy = parts[2].split('=')[1] + if energy=="": + energy = self.float(parts[3]) + else: + energy = self.float(energy) + # I moved the following line back a TAB to see the effect + # (it was originally part of the above "if len(parts)") + newlist[Gaussian.SCFENERGY].append(energy) + try: + line = inputfile.next() + except StopIteration: # May be interupted by EOF + break + self.scfvalues.append(newlist) + + if line[1:4]=='It=': +# Extract SCF convergence information (AM1 calcs) + + self.logger.info("Creating attributes scftargets, scfvalues") + self.scftargets = Numeric.array([1E-7],"f") # This is the target value for the rms + self.scfvalues = [[]] + line = inputfile.next() + while line.find(" Energy")==-1: + + if self.progress: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"AM1 Convergence") + oldstep=step + + parts = line.strip().split() + self.scfvalues[0].append(self.float(parts[-1][:-1])) + line = inputfile.next() + + if line[1:9]=='SCF Done': +# Note: this needs to follow the section where 'SCF Done' is used to terminate +# a loop when extracting SCF convergence information + if not hasattr(self,"scfenergies"): + self.logger.info("Creating attribute scfenergies[]") + self.scfenergies = [] + self.scfenergies.append(self.float(line.split()[4])) + + if line[49:59]=='Converged?': +# Extract Geometry convergence information + if not hasattr(self,"geotargets"): + self.logger.info("Creating attributes geotargets[],geovalues[[]]") + self.geovalues = [] + self.geotargets = Numeric.array( [0.0,0.0,0.0,0.0],"f") + newlist = [0]*4 + for i in range(4): + line = inputfile.next() + self.logger.debug(line) + parts = line.split() + try: + value = self.float(parts[2]) + except ValueError: + self.logger.error("Problem parsing the value for geometry optimisation: %s is not a number." % parts[2]) + else: + newlist[i] = value + self.geotargets[i] = self.float(parts[3]) + self.geovalues.append(newlist) + + if line[1:19]=='Orbital symmetries' and not hasattr(self,"mosyms"): +# Extracting orbital symmetries + if self.progress and random.random()<fupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"MO Symmetries") + oldstep=step + + self.logger.info("Creating attribute mosyms[[]]") + self.mosyms = [[]] + line = inputfile.next() + unres = False + if line.find("Alpha Orbitals")==1: + unres = True + line = inputfile.next() + i = 0 + while len(line)>18 and line[17]=='(': + if line.find('Virtual')>=0: + self.homos = Numeric.array([i-1],"i") # 'HOMO' indexes the HOMO in the arrays + self.logger.info("Creating attribute homos[]") + parts = line[17:].split() + for x in parts: + self.mosyms[0].append(self.normalisesym(x.strip('()'))) + i+= 1 + line = inputfile.next() + if unres: + line = inputfile.next() + # Repeat with beta orbital information + i = 0 + self.mosyms.append([]) + while len(line)>18 and line[17]=='(': + if line.find('Virtual')>=0: + self.homos.resize([2]) # Extend the array to two elements + self.homos[1] = i-1 # 'HOMO' indexes the HOMO in the arrays + parts = line[17:].split() + for x in parts: + self.mosyms[1].append(self.normalisesym(x.strip('()'))) + i+= 1 + line = inputfile.next() + + if line[1:6]=="Alpha" and line.find("eigenvalues")>=0: +# Extract the alpha electron eigenvalues + if self.progress and random.random()<fupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Eigenvalues") + oldstep=step + + self.logger.info("Creating attribute moenergies[[]]") + self.moenergies = [[]] + HOMO = -2 + while line.find('Alpha')==1: + if line.split()[1]=="virt." and HOMO==-2: + # If there aren't any symmetries, + # this is a good way to find the HOMO + HOMO = len(self.moenergies[0])-1 + if hasattr(self,"homos"): + assert HOMO==self.homos[0] + else: + self.logger.info("Creating attribute homos[]") + self.homos = Numeric.array([HOMO],"i") + part = line[28:] + i = 0 + while i*10+4<len(part): + x = part[i*10:(i+1)*10] + self.moenergies[0].append(convertor(self.float(x),"hartree","eV")) + i += 1 + line = inputfile.next() + if line.find('Beta')==2: + self.moenergies.append([]) + HOMO = -2 + while line.find('Beta')==2: + if line.split()[1]=="virt." and HOMO==-2: + # If there aren't any symmetries, + # this is a good way to find the HOMO + HOMO = len(self.moenergies[1])-1 + if len(self.homos)==2: + # It already has a self.homos (with the Alpha value) + # but does it already have a Beta value? + assert HOMO==self.homos[1] + else: + self.homos.resize([2]) + self.homos[1] = HOMO + part = line[28:] + i = 0 + while i*10+4<len(part): + x = part[i*10:(i+1)*10] + self.moenergies[1].append(convertor(self.float(x),"hartree","eV")) + i += 1 + line = inputfile.next() + self.moenergies = Numeric.array(self.moenergies,"f") + + if line[1:14]=="Harmonic freq": +# Start of the IR/Raman frequency section + if self.progress and random.random()<fupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Frequency Information") + oldstep=step + + self.vibsyms = [] + self.vibirs = [] + self.vibfreqs = [] + self.logger.info("Creating attribute vibsyms[]") + self.logger.info("Creating attribute vibfreqs[]") + self.logger.info("Creating attribute vibirs[]") + line = inputfile.next() + while len(line[:15].split())>0: + # Get past the three/four line title of the columns + line = inputfile.next() + line = inputfile.next() # The line with symmetries + while len(line[:15].split())==0: + self.logger.debug(line) + self.vibsyms.extend(line.split()) # Adding new symmetry + line = inputfile.next() + self.vibfreqs.extend(map(self.float,line[15:].split())) # Adding new frequencies + [inputfile.next() for i in [0,1]] # Skip two lines + line = inputfile.next() + self.vibirs.extend(map(self.float,line[15:].split())) # Adding IR intensities + line = inputfile.next() + if line.find("Raman")>=0: + if not hasattr(self,"vibramans"): + self.vibramans = [] + self.logger.info("Creating attribute vibramans[]") + line = inputfile.next() + self.vibramans.extend(map(self.float,line[15:].split())) # Adding Raman intensities + line = inputfile.next() + while len(line[:15].split())>0: + line = inputfile.next() + line = inputfile.next() # Should be the line with symmetries + self.vibfreqs = Numeric.array(self.vibfreqs,"f") + self.vibirs = Numeric.array(self.vibirs,"f") + if hasattr(self,"vibramans"): self.vibramans = Numeric.array(self.vibramans,"f") + + if line[1:14]=="Excited State": +# Extract the electronic transitions + if not hasattr(self,"etenergy"): + self.etenergies = [] + self.etoscs = [] + self.etsyms = [] + self.etsecs = [] + self.logger.info("Creating attributes etenergies[], etoscs[], etsyms[], etsecs[]") + # Need to deal with lines like: + # (restricted calc) + # Excited State 1: Singlet-BU 5.3351 eV 232.39 nm f=0.1695 + # (unrestricted calc) (first excited state is 2!) + # Excited State 2: ?Spin -A 0.1222 eV 10148.75 nm f=0.0000 + parts = line[36:].split() + self.etenergies.append(convertor(self.float(parts[0]),"eV","cm-1")) + self.etoscs.append(self.float(parts[4].split("=")[1])) + self.etsyms.append(line[21:36].split()) + + line = inputfile.next() + + p = re.compile("(\d+)") + CIScontrib = [] + while line.find(" ->")>=0: # This is a contribution to the transition + parts = line.split("->") + self.logger.debug(parts) + # Has to deal with lines like: + # 32 -> 38 0.04990 + # 35A -> 45A 0.01921 + frommoindex = 0 # For restricted or alpha unrestricted + fromMO = parts[0].strip() + if fromMO[-1]=="B": + frommoindex = 1 # For beta unrestricted + fromMO = int(p.match(fromMO).group()) # extract the number + + t = parts[1].split() + tomoindex = 0 + toMO = t[0] + if toMO[-1]=="B": + tomoindex = 1 + toMO = int(p.match(toMO).group()) + + percent = self.float(t[1]) + sqr = percent**2*2 # The fractional contribution of this CI + if percent<0: + sqr = -sqr + CIScontrib.append([(fromMO,frommoindex),(toMO,tomoindex),sqr]) + line = inputfile.next() + self.etsecs.append(CIScontrib) + self.etenergies = Numeric.array(self.etenergies,"f") + self.etoscs = Numeric.array(self.etoscs,"f") + + if line[1:52]=="<0|r|b> * <b|rxdel|0> (Au), Rotatory Strengths (R)": +# Extract circular dichroism data + self.etrotats = [] + self.logger.info("Creating attribute etrotats[]") + inputfile.next() + inputfile.next() + line = inputfile.next() + parts = line.strip().split() + while len(parts)==5: + try: + R = self.float(parts[-1]) + except ValueError: + # nan or -nan if there is no first excited state + # (for unrestricted calculations) + pass + else: + self.etrotats.append(R) + line = inputfile.next() + temp = line.strip().split() + parts = line.strip().split() + self.etrotats = Numeric.array(self.etrotats,"f") + + if line[1:7]=="NBasis" or line[4:10]=="NBasis": +# Extract the number of basis sets + nbasis = int(line.split('=')[1].split()[0]) + # Has to deal with lines like: + # NBasis = 434 NAE= 97 NBE= 97 NFC= 34 NFV= 0 + # NBasis = 148 MinDer = 0 MaxDer = 0 + # Although the former is in every file, it doesn't occur before + # the overlap matrix is printed + if hasattr(self,"nbasis"): + assert nbasis==self.nbasis + else: + self.nbasis= nbasis + self.logger.info("Creating attribute nbasis: %d" % self.nbasis) + + if line[1:7]=="NBsUse": +# Extract the number of linearly-independent basis sets + nmo = int(line.split('=')[1].split()[0]) + if hasattr(self,"nmo"): + assert nmo==self.nmo + else: + 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 +# (nmo may not always be explicitly stated) + nbasis = int(line.split()[0]) + if hasattr(self,"nbasis"): + assert nbasis==self.nbasis + else: + self.nbasis = nbasis + self.logger.info("Creating attribute nbasis: %d" % self.nbasis) + + if line[1:4]=="***" and (line[5:12]=="Overlap" + or line[8:15]=="Overlap"): +# Extract the molecular orbital overlap matrix + # Has to deal with lines such as: + # *** Overlap *** + # ****** Overlap ****** + self.logger.info("Creating attribute aooverlaps[x,y]") + self.aooverlaps = Numeric.zeros( (self.nbasis,self.nbasis), "float") + # Overlap integrals for basis fn#1 are in aooverlaps[0] + base = 0 + colmNames = inputfile.next() + while base<self.nbasis: + + if self.progress and random.random()<fupdate: + step=inputfile.tell() + if step!=oldstep: + self.progress.update(step,"Overlap") + oldstep=step + + for i in range(self.nbasis-base): # Fewer lines this time + line = inputfile.next() + parts = line.split() + for j in range(len(parts)-1): # Some lines are longer than others + k = float(parts[j+1].replace("D","E")) + self.aooverlaps[base+j,i+base] = k + self.aooverlaps[i+base,base+j] = k + base += 5 + colmNames = inputfile.next() + self.aooverlaps = Numeric.array(self.aooverlaps,"f") + + + if line[5:35]=="Molecular Orbital Coefficients" or line[5:41]=="Alpha Molecular Orbital Coefficients" or line[5:40]=="Beta Molecular Orbital Coefficients": + 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,nmo,nbasis)) + else: + beta = False + self.logger.info("Creating attributes aonames[], mocoeffs[][]") + self.aonames = [] + self.mocoeffs = Numeric.zeros((1,nmo,nbasis),"float") + + base = 0 + for base in range(0,nmo,5): + + if self.progress: + step=inputfile.tell() + if step!=oldstep and random.random() < fupdate: + self.progress.update(step,"Coefficients") + oldstep=step + + colmNames = inputfile.next() + symmetries = inputfile.next() + eigenvalues = inputfile.next() + for i in range(nbasis): + + + line = inputfile.next() + if base==0 and not beta: # Just do this the first time 'round + # Changed below from :12 to :11 to deal with Elmar Neumann's example + parts = line[:11].split() + if len(parts)>1: # New atom + atomname = "%s%s" % (parts[2],parts[1]) + orbital = line[11:20].strip() + self.aonames.append("%s_%s" % (atomname,orbital)) + + part = line[21:].replace("D","E").rstrip() + temp = [] + for j in range(0,len(part),10): + temp.append(float(part[j:j+10])) + if beta: + self.mocoeffs[1,base:base+len(part)/10,i] = temp + else: + self.mocoeffs[0,base:base+len(part)/10,i] = temp + + inputfile.close() + + if self.progress: + self.progress.update(nstep,"Done") + + 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 + + + +# Note to self: Needs to be added to the main parser + def extractTrajectory(self): + """Extract trajectory information from a Gaussian logfile.""" + inputfile = open(self.filename,"r") + self.traj = [] + self.trajSummary = [] + for line in inputfile: + if line.find(" Cartesian coordinates:")==0: + coords = [] + for i in range(self.natom): + line = inputfile.next() + parts = line.strip().split() + # Conversion from a.u. to Angstrom + coords.append([ self.float(x)*0.5292 for x in [parts[3],parts[5],parts[7]] ]) + self.traj.append(coords) + if line==" Trajectory summary\n": + # self.trajSummaryHeader = inputfile.next().strip().split() + header = inputfile.next() + line = inputfile.next() + while line.find("Max Error")==-1: + parts = line.strip().split(" ") + self.trajSummary.append(parts) + line = inputfile.next() + inputfile.close() + assert len(self.traj)==len(self.trajSummary) + +if __name__=="__main__": + import doctest,gaussianparser + doctest.testmod(gaussianparser,verbose=False) Modified: trunk/src/cclib/parser/jaguarparser.py =================================================================== --- trunk/src/cclib/parser/jaguarparser.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/src/cclib/parser/jaguarparser.py 2006-05-18 08:38:50 UTC (rev 124) @@ -169,5 +169,5 @@ self.parsed = True if __name__=="__main__": - import doctest,g03parser - doctest.testmod(g03parser,verbose=False) + import doctest,jaguarparser + doctest.testmod(jaguarparser,verbose=False) Modified: trunk/src/cclib/parser/logfileparser.py =================================================================== --- trunk/src/cclib/parser/logfileparser.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/src/cclib/parser/logfileparser.py 2006-05-18 08:38:50 UTC (rev 124) @@ -54,7 +54,7 @@ """Abstract class for logfile objects. Subclasses: - G03 + ADF, GAMESS, Gaussian, Jaguar Attributes: aonames -- "Ru_3p" (list) Modified: trunk/test/parseGaussian.py =================================================================== --- trunk/test/parseGaussian.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/test/parseGaussian.py 2006-05-18 08:38:50 UTC (rev 124) @@ -1,5 +1,5 @@ import os -from cclib.parser import G03 +from cclib.parser import Gaussian os.chdir(os.path.join("..","data","Gaussian")) @@ -7,7 +7,7 @@ for file in ["dvb_gopt.out","dvb_sp.out","dvb_ir.out","dvb_raman.out", "dvb_un_sp.out"]: - t = G03(file) + t = Gaussian(file) t.parse() Modified: trunk/test/testGeoOpt.py =================================================================== --- trunk/test/testGeoOpt.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/test/testGeoOpt.py 2006-05-18 08:38:50 UTC (rev 124) @@ -1,5 +1,5 @@ import os, unittest -from cclib.parser import GAMESS,G03,ADF,Jaguar +from cclib.parser import GAMESS,Gaussian,ADF,Jaguar from Numeric import array from testall import getfile @@ -43,7 +43,7 @@ class GaussianGeoOptTest(GenericGeoOptTest): def setUp(self): - self.data = getfile(G03,"basicGaussian03","dvb_gopt.out") + self.data = getfile(Gaussian,"basicGaussian03","dvb_gopt.out") class GamessUSGeoOptTest(GenericGeoOptTest): def setUp(self): Modified: trunk/test/testSP.py =================================================================== --- trunk/test/testSP.py 2006-05-17 16:56:45 UTC (rev 123) +++ trunk/test/testSP.py 2006-05-18 08:38:50 UTC (rev 124) @@ -1,5 +1,5 @@ import os, unittest -from cclib.parser import GAMESS,G03,ADF,Jaguar +from cclib.parser import GAMESS,Gaussian,ADF,Jaguar from Numeric import array from testall import getfile @@ -15,7 +15,7 @@ class GaussianSPTest(GenericSPTest): def setUp(self): - self.data = getfile(G03,"basicGaussian03","dvb_sp.out") + self.data = getfile(Gaussian,"basicGaussian03","dvb_sp.out") class GamessUSSPTest(GenericSPTest): def setUp(self): Modified: trunk/test/testSPun.py ===================... [truncated message content] |
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From: <bao...@us...> - 2006-05-21 14:40:51
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Revision: 135 Author: baoilleach Date: 2006-05-21 07:40:37 -0700 (Sun, 21 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=135&view=rev Log Message: ----------- I've put the magic back into __init__.py. There was no circular import problem this time. Some of the rearrangements I made first time 'round must have had an effect. Modified Paths: -------------- trunk/src/cclib/parser/__init__.py trunk/test/testGeoOpt.py trunk/test/testSP.py trunk/test/testSPun.py trunk/test/testall.py Modified: trunk/src/cclib/parser/__init__.py =================================================================== --- trunk/src/cclib/parser/__init__.py 2006-05-20 01:08:57 UTC (rev 134) +++ trunk/src/cclib/parser/__init__.py 2006-05-21 14:40:37 UTC (rev 135) @@ -0,0 +1,4 @@ +from gaussianparser import Gaussian +from gamessparser import GAMESS +from adfparser import ADF +from jaguarparser import Jaguar Modified: trunk/test/testGeoOpt.py =================================================================== --- trunk/test/testGeoOpt.py 2006-05-20 01:08:57 UTC (rev 134) +++ trunk/test/testGeoOpt.py 2006-05-21 14:40:37 UTC (rev 135) @@ -1,12 +1,8 @@ import os, unittest from Numeric import array from testall import getfile -from cclib.parser.adfparser import ADF -from cclib.parser.gamessparser import GAMESS -from cclib.parser.gaussianparser import Gaussian -from cclib.parser.jaguarparser import Jaguar +from cclib.parser import ADF, GAMESS, Gaussian, Jaguar - class GenericGeoOptTest(unittest.TestCase): def testhomos(self): """Is the index of the homo equal to 34?""" Modified: trunk/test/testSP.py =================================================================== --- trunk/test/testSP.py 2006-05-20 01:08:57 UTC (rev 134) +++ trunk/test/testSP.py 2006-05-21 14:40:37 UTC (rev 135) @@ -1,10 +1,7 @@ import os, unittest from Numeric import array from testall import getfile -from cclib.parser.adfparser import ADF -from cclib.parser.gamessparser import GAMESS -from cclib.parser.gaussianparser import Gaussian -from cclib.parser.jaguarparser import Jaguar +from cclib.parser import ADF, GAMESS, Gaussian, Jaguar class GenericSPTest(unittest.TestCase): """Restricted single point calculations with MO coeffs and overlap info.""" Modified: trunk/test/testSPun.py =================================================================== --- trunk/test/testSPun.py 2006-05-20 01:08:57 UTC (rev 134) +++ trunk/test/testSPun.py 2006-05-21 14:40:37 UTC (rev 135) @@ -1,10 +1,7 @@ import os, unittest from Numeric import array from testall import getfile -from cclib.parser.adfparser import ADF -from cclib.parser.gamessparser import GAMESS -from cclib.parser.gaussianparser import Gaussian -from cclib.parser.jaguarparser import Jaguar +from cclib.parser import ADF, GAMESS, Gaussian, Jaguar class GenericSPunTest(unittest.TestCase): """Restricted single point calculations with MO coeffs and overlap info.""" Modified: trunk/test/testall.py =================================================================== --- trunk/test/testall.py 2006-05-20 01:08:57 UTC (rev 134) +++ trunk/test/testall.py 2006-05-21 14:40:37 UTC (rev 135) @@ -1,9 +1,6 @@ import unittest import os -from cclib.parser.adfparser import ADF -from cclib.parser.gamessparser import GAMESS -from cclib.parser.gaussianparser import Gaussian -from cclib.parser.jaguarparser import Jaguar +from cclib.parser import ADF, GAMESS, Gaussian, Jaguar def getfile(parser,*location): """Returns a parsed logfile.""" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-05-23 08:46:52
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Revision: 152 Author: baoilleach Date: 2006-05-23 01:46:44 -0700 (Tue, 23 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=152&view=rev Log Message: ----------- Converted scfenergies from a.u. to eV for GAMESS and Gaussian, and updated tests. Modified Paths: -------------- trunk/src/cclib/parser/gamessparser.py trunk/src/cclib/parser/gaussianparser.py trunk/test/testGeoOpt.py Modified: trunk/src/cclib/parser/gamessparser.py =================================================================== --- trunk/src/cclib/parser/gamessparser.py 2006-05-23 01:28:46 UTC (rev 151) +++ trunk/src/cclib/parser/gamessparser.py 2006-05-23 08:46:44 UTC (rev 152) @@ -140,7 +140,7 @@ # FINAL ENERGY IS -379.7594673378 AFTER 9 ITERATIONS # ...so take the number after the "IS" temp = line.split() - self.scfenergies.append(float(temp[temp.index("IS")+1])) + self.scfenergies.append(utils.convertor(float(temp[temp.index("IS")+1]),"hartree","eV")) if line.find("MAXIMUM GRADIENT")>0: if not hasattr(self,"geovalues"): Modified: trunk/src/cclib/parser/gaussianparser.py =================================================================== --- trunk/src/cclib/parser/gaussianparser.py 2006-05-23 01:28:46 UTC (rev 151) +++ trunk/src/cclib/parser/gaussianparser.py 2006-05-23 08:46:44 UTC (rev 152) @@ -201,7 +201,7 @@ if not hasattr(self,"scfenergies"): self.logger.info("Creating attribute scfenergies[]") self.scfenergies = [] - self.scfenergies.append(self.float(line.split()[4])) + self.scfenergies.append(utils.convertor(self.float(line.split()[4]),"hartree","eV")) if line[49:59]=='Converged?': # Extract Geometry convergence information Modified: trunk/test/testGeoOpt.py =================================================================== --- trunk/test/testGeoOpt.py 2006-05-23 01:28:46 UTC (rev 151) +++ trunk/test/testGeoOpt.py 2006-05-23 08:46:44 UTC (rev 152) @@ -42,8 +42,8 @@ self.assertEquals(self.data.nbasis,60) def testscfenergy(self): - """Is the SCF energy within 3eV(?) of -382.3?""" - self.assert_(self.data.scfenergies[-1]+382.3<3) + """Is the SCF energy within 40eV of -10365""" + self.assert_(abs(self.data.scfenergies[-1]-(-10365))<40,"Final scf energy: %f not -10365+-40eV" % self.data.scfenergies[-1]) def testnormalisesym(self): """Did this subclasses overwrite normalisesym?""" @@ -91,6 +91,10 @@ """Are atomcoords consistent with geovalues?""" coords = self.data.atomcoords self.assertEquals(len(self.data.geovalues),len(coords)-1,"len(atomcoords)-1 is %d but len(geovalues) is %d" % (len(coords)-1,len(self.data.geovalues))) + + def testscfenergy(self): + """Is the SCF energy within 1eV of -140eV""" + self.assert_(abs(self.data.scfenergies[-1]-(-140))<1,"Final scf energy: %f not -140+-1eV" % self.data.scfenergies[-1]) class JaguarGeoOptTest(GenericGeoOptTest): def setUp(self): This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-05-24 19:16:12
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Revision: 156 Author: baoilleach Date: 2006-05-24 12:16:00 -0700 (Wed, 24 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=156&view=rev Log Message: ----------- The typecode of homos is 'i', which needed to be specified in the tests and in the parsers Modified Paths: -------------- trunk/src/cclib/parser/adfparser.py trunk/test/testGeoOpt.py trunk/test/testSPun.py Modified: trunk/src/cclib/parser/adfparser.py =================================================================== --- trunk/src/cclib/parser/adfparser.py 2006-05-24 18:20:44 UTC (rev 155) +++ trunk/src/cclib/parser/adfparser.py 2006-05-24 19:16:00 UTC (rev 156) @@ -285,7 +285,7 @@ temp=Numeric.array(self.moenergies,"f") self.moenergies=temp - self.homos=Numeric.array(self.homos) + self.homos=Numeric.array(self.homos,"i") if line[1:24]=="List of All Frequencies": # Start of the IR/Raman frequency section Modified: trunk/test/testGeoOpt.py =================================================================== --- trunk/test/testGeoOpt.py 2006-05-24 18:20:44 UTC (rev 155) +++ trunk/test/testGeoOpt.py 2006-05-24 19:16:00 UTC (rev 156) @@ -1,16 +1,16 @@ import os import math +import Numeric import unittest import bettertest -from Numeric import array from testall import getfile from cclib.parser import ADF, GAMESS, Gaussian, Jaguar class GenericGeoOptTest(bettertest.TestCase): def testhomos(self): """Is the index of the homo equal to 34?""" - self.assertArrayEquals(self.data.homos,array([34]),"%s != array([34])" % self.data.homos) + self.assertArrayEquals(self.data.homos,Numeric.array([34],"i"),"%s != array([34],'i')" % Numeric.array_repr(self.data.homos)) def testatomcoords(self): """Are atomcoords consistent with natom and Angstroms?""" @@ -62,7 +62,7 @@ def testscfvaluetype(self): """Do the scf values have the right type?""" self.assertEquals(type(self.data.scfvalues),type([])) - self.assertEquals(type(self.data.scfvalues[0]),type(array([]))) + self.assertEquals(type(self.data.scfvalues[0]),type(Numeric.array([]))) def testscfvaluedim(self): """Do the scf values have the right dimensions?""" Modified: trunk/test/testSPun.py =================================================================== --- trunk/test/testSPun.py 2006-05-24 18:20:44 UTC (rev 155) +++ trunk/test/testSPun.py 2006-05-24 19:16:00 UTC (rev 156) @@ -1,9 +1,12 @@ -import os, unittest -from Numeric import array +import os +import unittest +import bettertest +import Numeric + from testall import getfile from cclib.parser import ADF, GAMESS, Gaussian, Jaguar -class GenericSPunTest(unittest.TestCase): +class GenericSPunTest(bettertest.TestCase): """Restricted single point calculations with MO coeffs and overlap info.""" def testdimaooverlaps(self): """Are the dims of the overlap matrix consistent with nbasis?""" @@ -14,9 +17,8 @@ self.assertEquals(self.data.mocoeffs.shape,(2,self.data.nmo,self.data.nbasis)) def testhomos(self): - """What are the homos?""" - self.assertEquals(type(self.data.homos),type(array([]))) - self.assertEquals(self.data.homos,array([34,33],"i")) + """Are the homos correct?""" + self.assertArrayEquals(self.data.homos,Numeric.array([34,33],"i"),"%s != array([34,33],'i')" % Numeric.array_repr(self.data.homos)) class GaussianSPunTest(GenericSPunTest): def setUp(self): This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-05-27 07:58:43
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Revision: 162 Author: baoilleach Date: 2006-05-27 00:58:33 -0700 (Sat, 27 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=162&view=rev Log Message: ----------- Jaguar parser now reads scftargets and values correctly, at least for geometry optimisations. Have also converted scfenergies to eV. The GeoOpt test now looks at dvb_gopt_b, which has all of the virtual orbitals included, instead of dvb_gopt Modified Paths: -------------- trunk/src/cclib/parser/jaguarparser.py trunk/test/testGeoOpt.py Modified: trunk/src/cclib/parser/jaguarparser.py =================================================================== --- trunk/src/cclib/parser/jaguarparser.py 2006-05-26 18:45:47 UTC (rev 161) +++ trunk/src/cclib/parser/jaguarparser.py 2006-05-27 07:58:33 UTC (rev 162) @@ -50,6 +50,8 @@ inputfile.seek(0) self.progress.initialize(nstep) oldstep=0 + + geoopt = False # Is this a GeoOpt? Needed for SCF targets/values. for line in inputfile: @@ -64,8 +66,12 @@ # Get SCF convergence information if not hasattr(self,"scfvalues"): self.scfvalues = [] - self.logger.info("Creating attribute: scfvalues") - values = [] + self.logger.info("Creating attribute: scfvalues,scftargets") + self.scftargets = Numeric.array([5E-5,5E-6],"f") + if not geoopt: + values = [[],[]] + else: + values = [[]] while line[0:4]=="etot": if line[39:47].strip(): denergy = float(line[39:47]) @@ -74,7 +80,11 @@ # or should we just ignore the values in this line ddensity = float(line[48:56]) maxdiiserr = float(line[57:65]) - values.append([denergy,ddensity,maxdiiserr]) + if not geoopt: + values[0].append(denergy) + values[1].append(ddensity) + else: + values[0].append(ddensity) line = inputfile.next() self.scfvalues.append(values) @@ -84,7 +94,7 @@ self.logger.info("Creating attribute scfenergies") self.scfenergies = [] temp = line.strip().split() - self.scfenergies.append(float(temp[temp.index("hartrees")-1])) + self.scfenergies.append(utils.convertor(float(temp[temp.index("hartrees")-1]),"hartree","eV")) if line[2:14]=="new geometry" or line[1:21]=="Symmetrized geometry": # Get the atom coordinates @@ -107,6 +117,14 @@ self.atomnos = Numeric.array(atomnos,"i") self.natom = len(atomcoords) + if not geoopt and line[2:24]=="start of program geopt": + geoopt = True + if hasattr(self,"scfvalues"): + # Need to keep only the RMS density change info + # if this is a geoopt + self.scfvalues[0] = [self.scfvalues[0][1]] + self.scftargets = self.scftargets[0] + if line[2:28]=="geometry optimization step": # Get Geometry Opt convergence information if not hasattr(self,"geovalues"): @@ -187,8 +205,8 @@ inputfile.close() -## if hasattr(self,"scfvalues"): -## self.scfvalues = Numeric.array(self.scfvalues,"f") + if hasattr(self,"scfvalues"): + self.scfvalues = [Numeric.array(x,"f") for x in self.scfvalues] if hasattr(self,"scfenergies"): self.scfenergies = Numeric.array(self.scfenergies,"f") if hasattr(self,"atomcoords"): Modified: trunk/test/testGeoOpt.py =================================================================== --- trunk/test/testGeoOpt.py 2006-05-26 18:45:47 UTC (rev 161) +++ trunk/test/testGeoOpt.py 2006-05-27 07:58:33 UTC (rev 162) @@ -33,7 +33,6 @@ coords = self.data.atomcoords self.assertEquals(len(self.data.geovalues),len(coords),"len(atomcoords) is %d but len(geovalues) is %d" % (len(coords),len(self.data.geovalues))) - def testnatom(self): """Is the number of atoms equal to 20?""" self.assertEquals(self.data.natom,20) @@ -101,7 +100,7 @@ class JaguarGeoOptTest(GenericGeoOptTest): def setUp(self): - self.data = getfile(Jaguar,"basicJaguar","eg01","dvb_gopt.out") + self.data = getfile(Jaguar,"basicJaguar","eg01","dvb_gopt_b.out") names = [ "Gaussian", "PCGamess", "GAMESS", "ADF", "Jaguar" ] tests = [ GaussianGeoOptTest, PCGamessGeoOptTest, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-07-23 17:48:50
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Revision: 263 Author: baoilleach Date: 2006-07-23 10:48:40 -0700 (Sun, 23 Jul 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=263&view=rev Log Message: ----------- GAMESSUK: Fixed problem parsing unrestricted calculations. The test now tests GAMESS UK SP unres calcs too. Modified Paths: -------------- trunk/src/cclib/parser/gamessukparser.py trunk/test/testSPun.py This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-09-09 15:47:46
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Revision: 331
http://svn.sourceforge.net/cclib/?rev=331&view=rev
Author: baoilleach
Date: 2006-09-09 08:47:37 -0700 (Sat, 09 Sep 2006)
Log Message:
-----------
Renaming testccopen.py to regression.py as it is the new regression test suite.
Added Paths:
-----------
trunk/test/regression.py
Removed Paths:
-------------
trunk/test/testccopen.py
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <bao...@us...> - 2006-11-27 08:08:38
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Revision: 426
http://svn.sourceforge.net/cclib/?rev=426&view=rev
Author: baoilleach
Date: 2006-11-27 00:08:37 -0800 (Mon, 27 Nov 2006)
Log Message:
-----------
New tests: Added test suite for vibrations. Only one test added so far.
Modified Paths:
--------------
trunk/test/testall.py
Added Paths:
-----------
trunk/test/testvib.py
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <la...@us...> - 2007-03-14 21:27:31
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Revision: 577
http://svn.sourceforge.net/cclib/?rev=577&view=rev
Author: langner
Date: 2007-03-14 14:27:29 -0700 (Wed, 14 Mar 2007)
Log Message:
-----------
Added testCC: tests for Coupled-Cluster calculations.
Modified Paths:
--------------
trunk/test/testCI.py
Added Paths:
-----------
trunk/test/testCC.py
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <la...@us...> - 2007-09-03 23:09:25
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Revision: 747
http://cclib.svn.sourceforge.net/cclib/?rev=747&view=rev
Author: langner
Date: 2007-09-03 16:09:21 -0700 (Mon, 03 Sep 2007)
Log Message:
-----------
The number of tests skipped (when PASS is in the docstring) is now monitored by setting a 'skipped' attribute in bettertest.TestCase.run() and using it in the summary of testall(). Also, merged testmodule() and testall() in testall.py (as suggested by Noel).
Modified Paths:
--------------
trunk/test/bettertest.py
trunk/test/testBasis.py
trunk/test/testCC.py
trunk/test/testCI.py
trunk/test/testCore.py
trunk/test/testGeoOpt.py
trunk/test/testMP.py
trunk/test/testSP.py
trunk/test/testSPun.py
trunk/test/testTD.py
trunk/test/testall.py
trunk/test/testvib.py
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From: <la...@us...> - 2007-09-05 21:12:02
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Revision: 749
http://cclib.svn.sourceforge.net/cclib/?rev=749&view=rev
Author: langner
Date: 2007-09-05 14:11:59 -0700 (Wed, 05 Sep 2007)
Log Message:
-----------
Moved some common tests from GeoOpt to SP, and vice versa. Added PASS or modified relevant failing test methods - a few for ADF remain. Added Jaguar6.0 to GeoOpt test.
Modified Paths:
--------------
trunk/test/testGeoOpt.py
trunk/test/testSP.py
trunk/test/testdata
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From: <ate...@us...> - 2006-05-01 21:04:00
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Revision: 96 Author: atenderholt Date: 2006-05-01 14:03:55 -0700 (Mon, 01 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=96&view=rev Log Message: ----------- SVN targets in the ADF parser Fixed the ADF unittest because ADF does one more scf cycle after the geometry is converged Modified Paths: -------------- trunk/src/cclib/parser/adfparser.py trunk/test/testall.py Modified: trunk/src/cclib/parser/adfparser.py =================================================================== --- trunk/src/cclib/parser/adfparser.py 2006-04-26 01:43:39 UTC (rev 95) +++ trunk/src/cclib/parser/adfparser.py 2006-05-01 21:03:55 UTC (rev 96) @@ -24,7 +24,8 @@ class ADF(Logfile): """A Gaussian 98/03 log file""" - SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftargets[] + #SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftargets[] + SCFCNV,SCFCNV2 = range(2) #used to index self.scftargets[] def __init__(self,*args): # Call the __init__ method of the superclass @@ -128,17 +129,53 @@ self.natom=len(self.atomnos) self.logger.info("Creating attribute natom: %d" % self.natom) -# if line[1:44]=='Requested convergence on RMS density matrix': -# # Find the targets for SCF convergence (QM calcs) -# if not hasattr(self,"scftargets"): -# self.logger.info("Creating attribute scftargets[]") -# self.scftargets = Numeric.array([0.0,0.0,0.0],'f') -# self.scftargets[G03.SCFRMS] = self.float(line.split('=')[1].split()[0]) -# if line[1:44]=='Requested convergence on MAX density matrix': -# self.scftargets[G03.SCFMAX] = self.float(line.strip().split('=')[1][:-1]) -# if line[1:44]=='Requested convergence on energy': -# self.scftargets[G03.SCFENERGY] = self.float(line.strip().split('=')[1][:-1]) -# + 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') + + #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 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])) + + 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 line[1:10]=='Cycle 1': # # Extract SCF convergence information (QM calcs) # if self.progress and random.random()<fupdate: Modified: trunk/test/testall.py =================================================================== --- trunk/test/testall.py 2006-04-26 01:43:39 UTC (rev 95) +++ trunk/test/testall.py 2006-05-01 21:03:55 UTC (rev 96) @@ -56,6 +56,11 @@ 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") This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-05-10 09:24:17
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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) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <ate...@us...> - 2006-05-10 23:02:59
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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 ] This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-05-18 10:30:49
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Revision: 125 Author: baoilleach Date: 2006-05-18 03:30:34 -0700 (Thu, 18 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=125&view=rev Log Message: ----------- Created a function to guess the filetype of a logfile and return an instance or None. Unfortunately, I ran into several non-trivial problems which required me (as far as I could figure out) to reorganise the import statements in cclib. At first I put guesstype() as a method of Logfile. Then I realised it was better as a function in logfileparser.py. Then I realised that due to some restrictions in circular import statements (or something) I needed to stop using 'from x import y' type imports and change to 'import x; use x.y' type statements. In the end the tests are back working and I've moved parser helper utilities into utils.py. What a drag though! I still don't know what exactly was the problem. Unfortunately, I've had to remove the magic from __init__.py so that 'from cclib.parser import ADF' no longer works. We should consider removing the suffix 'parser' from the filenames in the cclib.parser directory, as it does not add anything. Modified Paths: -------------- trunk/src/cclib/parser/__init__.py trunk/src/cclib/parser/adfparser.py trunk/src/cclib/parser/gamessparser.py trunk/src/cclib/parser/gaussianparser.py trunk/src/cclib/parser/jaguarparser.py trunk/src/cclib/parser/logfileparser.py trunk/test/testGeoOpt.py trunk/test/testSP.py trunk/test/testSPun.py trunk/test/testall.py Added Paths: ----------- trunk/src/cclib/parser/utils.py Modified: trunk/src/cclib/parser/__init__.py =================================================================== --- trunk/src/cclib/parser/__init__.py 2006-05-18 08:38:50 UTC (rev 124) +++ trunk/src/cclib/parser/__init__.py 2006-05-18 10:30:34 UTC (rev 125) @@ -1,4 +0,0 @@ -from gaussianparser import Gaussian -from gamessparser import GAMESS -from adfparser import ADF -from jaguarparser import Jaguar Modified: trunk/src/cclib/parser/adfparser.py =================================================================== --- trunk/src/cclib/parser/adfparser.py 2006-05-18 08:38:50 UTC (rev 124) +++ trunk/src/cclib/parser/adfparser.py 2006-05-18 10:30:34 UTC (rev 125) @@ -20,9 +20,10 @@ import re,time import Numeric import random # For sometimes running the progress updater -from logfileparser import Logfile,convertor +import utils +import logfileparser -class ADF(Logfile): +class ADF(logfileparser.Logfile): """An ADF log file""" SCFCNV,SCFCNV2 = range(2) #used to index self.scftargets[] maxelem,norm = range(2) # used to index scf.values @@ -220,7 +221,7 @@ blank = inputfile.next() line = inputfile.next() temp = inputfile.next().strip().split() - self.scfenergies.append(convertor(float(temp[-1]),"hartree","eV")) + self.scfenergies.append(utils.convertor(float(temp[-1]),"hartree","eV")) for i in range(6): line = inputfile.next() values = [] @@ -251,7 +252,7 @@ info=line.split() if len(info)==5: #this is restricted self.mosyms[0].append(self.normalisesym(info[0])) - self.moenergies[0].append(convertor(float(info[3]),'hartree','eV')) + self.moenergies[0].append(utils.convertor(float(info[3]),'hartree','eV')) if info[2]=='0.00' and not hasattr(self,'homos'): self.logger.info("Creating attribute homos[]") self.homos=[len(self.moenergies[0])-2] @@ -262,13 +263,13 @@ self.mosyms.append([]) if info[2]=='A': self.mosyms[0].append(self.normalisesym(info[0])) - self.moenergies[0].append(convertor(float(info[4]),'hartree','eV')) + self.moenergies[0].append(utils.convertor(float(info[4]),'hartree','eV')) if info[3]=='0.00' and homoa==None: homoa=len(self.moenergies[0])-2 if info[2]=='B': self.mosyms[1].append(self.normalisesym(info[0])) - self.moenergies[1].append(convertor(float(info[4]),'hartree','eV')) + self.moenergies[1].append(utils.convertor(float(info[4]),'hartree','eV')) if info[3]=='0.00' and homob==None: homob=len(self.moenergies[1])-2 Modified: trunk/src/cclib/parser/gamessparser.py =================================================================== --- trunk/src/cclib/parser/gamessparser.py 2006-05-18 08:38:50 UTC (rev 124) +++ trunk/src/cclib/parser/gamessparser.py 2006-05-18 10:30:34 UTC (rev 125) @@ -20,9 +20,10 @@ import re,time import Numeric import random # For sometimes running the progress updater -from logfileparser import Logfile,convertor,PeriodicTable +import utils +import logfileparser -class GAMESS(Logfile): +class GAMESS(logfileparser.Logfile): """A GAMESS log file.""" SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftargets[] def __init__(self,*args): @@ -30,8 +31,6 @@ # 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.""" return "GAMESS log file %s" % (self.filename) @@ -136,8 +135,8 @@ line = inputfile.next() while line.strip(): temp = line.strip().split() - atomcoords.append([convertor(float(x),"au","Ang") for x in temp[2:4]]) - atomnos.append(self.pt.number[temp[0]]) # Use the element name + atomcoords.append([utils.convertor(float(x),"au","Ang") for x in temp[2:4]]) + atomnos.append(self.table.number[temp[0]]) # Use the element name line = inputfile.next() self.atomnos = Numeric.array(atomnos,"i") self.atomcoords.append(atomcoords) @@ -287,7 +286,7 @@ blank = inputfile.next() line = inputfile.next() # Eigenvector no line = inputfile.next() - self.moenergies[0].extend([convertor(float(x),"hartree","eV") for x in line.split()]) + self.moenergies[0].extend([utils.convertor(float(x),"hartree","eV") for x in line.split()]) line = inputfile.next() self.mosyms[0].extend(map(self.normalisesym,line.split())) for i in range(self.nbasis): @@ -324,7 +323,7 @@ blank = inputfile.next() line = inputfile.next() # Eigenvector no line = inputfile.next() - self.moenergies[1].extend([convertor(float(x),"hartree","eV") for x in line.split()]) + self.moenergies[1].extend([utils.convertor(float(x),"hartree","eV") for x in line.split()]) line = inputfile.next() self.mosyms[1].extend(map(self.normalisesym,line.split())) for i in range(self.nbasis): Modified: trunk/src/cclib/parser/gaussianparser.py =================================================================== --- trunk/src/cclib/parser/gaussianparser.py 2006-05-18 08:38:50 UTC (rev 124) +++ trunk/src/cclib/parser/gaussianparser.py 2006-05-18 10:30:34 UTC (rev 125) @@ -20,9 +20,10 @@ import re,time import Numeric import random # For sometimes running the progress updater -from logfileparser import Logfile,convertor +import utils +import logfileparser -class Gaussian(Logfile): +class Gaussian(logfileparser.Logfile): """A Gaussian 98/03 log file""" SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftargets[] def __init__(self,*args): @@ -287,7 +288,7 @@ i = 0 while i*10+4<len(part): x = part[i*10:(i+1)*10] - self.moenergies[0].append(convertor(self.float(x),"hartree","eV")) + self.moenergies[0].append(utils.convertor(self.float(x),"hartree","eV")) i += 1 line = inputfile.next() if line.find('Beta')==2: @@ -309,7 +310,7 @@ i = 0 while i*10+4<len(part): x = part[i*10:(i+1)*10] - self.moenergies[1].append(convertor(self.float(x),"hartree","eV")) + self.moenergies[1].append(utils.convertor(self.float(x),"hartree","eV")) i += 1 line = inputfile.next() self.moenergies = Numeric.array(self.moenergies,"f") @@ -370,7 +371,7 @@ # (unrestricted calc) (first excited state is 2!) # Excited State 2: ?Spin -A 0.1222 eV 10148.75 nm f=0.0000 parts = line[36:].split() - self.etenergies.append(convertor(self.float(parts[0]),"eV","cm-1")) + self.etenergies.append(utils.convertor(self.float(parts[0]),"eV","cm-1")) self.etoscs.append(self.float(parts[4].split("=")[1])) self.etsyms.append(line[21:36].split()) Modified: trunk/src/cclib/parser/jaguarparser.py =================================================================== --- trunk/src/cclib/parser/jaguarparser.py 2006-05-18 08:38:50 UTC (rev 124) +++ trunk/src/cclib/parser/jaguarparser.py 2006-05-18 10:30:34 UTC (rev 125) @@ -20,9 +20,10 @@ import re,time import Numeric import random # For sometimes running the progress updater -from logfileparser import Logfile,convertor +import utils +import logfileparser -class Jaguar(Logfile): +class Jaguar(logfileparser.Logfile): """A Jaguar output file""" def __init__(self,*args): @@ -115,7 +116,7 @@ while line.strip(): temp = line.strip().split() for i in range(0,len(temp),2): - self.moenergies[0].append(convertor(float(temp[i]),"hartree","eV")) + self.moenergies[0].append(utils.convertor(float(temp[i]),"hartree","eV")) self.mosyms[0].append(temp[i+1]) line = inputfile.next() self.moenergies = Numeric.array(self.moenergies,"f") Modified: trunk/src/cclib/parser/logfileparser.py =================================================================== --- trunk/src/cclib/parser/logfileparser.py 2006-05-18 08:38:50 UTC (rev 124) +++ trunk/src/cclib/parser/logfileparser.py 2006-05-18 10:30:34 UTC (rev 125) @@ -19,37 +19,8 @@ """ import logging, sys import Numeric +import utils -def convertor(value,fromunits,tounits): - """Convert from one set of units to another. - - >>> print "%.1f" % convertor(8,"eV","cm-1") - 64524.8 - """ - _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, - "au_to_Ang": lambda x: x*0.529177} - - return _convertor["%s_to_%s" % (fromunits,tounits)] (value) - -class PeriodicTable(object): - """Allows conversion between element name and atomic no. - - >>> t = PeriodicTable() - >>> t.element[6] - 'C' - >>> t.number['C'] - 6 - """ - def __init__(self): - self.element = [None,"H","He","Li","Be","B","C","N","O","F","Ne","Na","Mg","Al","Si","P","S","Cl","Ar","K","Ca","Sc","Ti","V","Cr","Mn","Fe" - "Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr","Rb","Sr","Y","Zr","Nb","Mo"] - self.number = {} - for i in range(1,len(self.element)): - self.number[self.element[i]] = i - class Logfile(object): """Abstract class for logfile objects. @@ -97,7 +68,7 @@ self.parsed = False self.loglevel = loglevel self.logname = logname - self.table = PeriodicTable() + self.table = utils.PeriodicTable() # Set up the logger self.logger = logging.getLogger('%s %s' % (self.logname,self.filename)) Added: trunk/src/cclib/parser/utils.py =================================================================== --- trunk/src/cclib/parser/utils.py (rev 0) +++ trunk/src/cclib/parser/utils.py 2006-05-18 10:30:34 UTC (rev 125) @@ -0,0 +1,81 @@ +""" +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 adfparser +import gamessparser +import gaussianparser +import jaguarparser + +def guesstype(filename): + """Guess the identity of a particular log file and return an instance of that. + + Notes: uses the first 20 lines of a log file to guess its identity + + Returns: one of ADF, GAMESS, Gaussian, Jaguar, or None (if it cannot figure it out). + """ + filetype = None + inputfile = open(filename,"r") + for i,line in enumerate(inputfile): + if i>20: break # not elegant, but less buggy than a while loop testing for EOF + if line.find("Amsterdam Density Functional")>=0: + filetype = adfparser.ADF + elif line.find("GAMESS")>=0: + filetype = gamessparser.GAMESS + elif line.find("Gaussian")>=0: + filetype = gaussianparser.Gaussian + elif line.find("Jaguar")>=0: + filetype = jaguarparser.Jaguar + inputfile.close() # Need to close before creating an instance + if filetype: + filetype = apply(filetype,[filename]) # Create an instance of the chosen class + return filetype + +def convertor(value,fromunits,tounits): + """Convert from one set of units to another. + + >>> print "%.1f" % convertor(8,"eV","cm-1") + 64524.8 + """ + _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, + "au_to_Ang": lambda x: x*0.529177} + + return _convertor["%s_to_%s" % (fromunits,tounits)] (value) + +class PeriodicTable(object): + """Allows conversion between element name and atomic no. + + >>> t = PeriodicTable() + >>> t.element[6] + 'C' + >>> t.number['C'] + 6 + """ + def __init__(self): + self.element = [None,"H","He","Li","Be","B","C","N","O","F","Ne","Na","Mg","Al","Si","P","S","Cl","Ar","K","Ca","Sc","Ti","V","Cr","Mn","Fe" + "Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr","Rb","Sr","Y","Zr","Nb","Mo"] + self.number = {} + for i in range(1,len(self.element)): + self.number[self.element[i]] = i + +if __name__=="__main__": + import doctest,utils + doctest.testmod(utils,verbose=False) Property changes on: trunk/src/cclib/parser/utils.py ___________________________________________________________________ Name: svn:executable + * Modified: trunk/test/testGeoOpt.py =================================================================== --- trunk/test/testGeoOpt.py 2006-05-18 08:38:50 UTC (rev 124) +++ trunk/test/testGeoOpt.py 2006-05-18 10:30:34 UTC (rev 125) @@ -1,8 +1,12 @@ import os, unittest -from cclib.parser import GAMESS,Gaussian,ADF,Jaguar from Numeric import array from testall import getfile +from cclib.parser.adfparser import ADF +from cclib.parser.gamessparser import GAMESS +from cclib.parser.gaussianparser import Gaussian +from cclib.parser.jaguarparser import Jaguar + class GenericGeoOptTest(unittest.TestCase): def testhomos(self): """Is the index of the homo equal to 34?""" Modified: trunk/test/testSP.py =================================================================== --- trunk/test/testSP.py 2006-05-18 08:38:50 UTC (rev 124) +++ trunk/test/testSP.py 2006-05-18 10:30:34 UTC (rev 125) @@ -1,7 +1,10 @@ import os, unittest -from cclib.parser import GAMESS,Gaussian,ADF,Jaguar from Numeric import array from testall import getfile +from cclib.parser.adfparser import ADF +from cclib.parser.gamessparser import GAMESS +from cclib.parser.gaussianparser import Gaussian +from cclib.parser.jaguarparser import Jaguar class GenericSPTest(unittest.TestCase): """Restricted single point calculations with MO coeffs and overlap info.""" Modified: trunk/test/testSPun.py =================================================================== --- trunk/test/testSPun.py 2006-05-18 08:38:50 UTC (rev 124) +++ trunk/test/testSPun.py 2006-05-18 10:30:34 UTC (rev 125) @@ -1,7 +1,10 @@ import os, unittest -from cclib.parser import GAMESS,Gaussian,ADF,Jaguar from Numeric import array from testall import getfile +from cclib.parser.adfparser import ADF +from cclib.parser.gamessparser import GAMESS +from cclib.parser.gaussianparser import Gaussian +from cclib.parser.jaguarparser import Jaguar class GenericSPunTest(unittest.TestCase): """Restricted single point calculations with MO coeffs and overlap info.""" Modified: trunk/test/testall.py =================================================================== --- trunk/test/testall.py 2006-05-18 08:38:50 UTC (rev 124) +++ trunk/test/testall.py 2006-05-18 10:30:34 UTC (rev 125) @@ -1,6 +1,9 @@ import unittest import os -from cclib.parser import Gaussian,GAMESS,ADF,Jaguar +from cclib.parser.adfparser import ADF +from cclib.parser.gamessparser import GAMESS +from cclib.parser.gaussianparser import Gaussian +from cclib.parser.jaguarparser import Jaguar def getfile(parser,*location): """Returns a parsed logfile.""" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-05-21 14:49:29
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Revision: 136 Author: baoilleach Date: 2006-05-21 07:49:18 -0700 (Sun, 21 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=136&view=rev Log Message: ----------- Added guesstype() import to __init__.py to allow use of 'from cclib.parser import guesstype'. An example test is also included Modified Paths: -------------- trunk/src/cclib/parser/__init__.py Added Paths: ----------- trunk/test/testauto.py Modified: trunk/src/cclib/parser/__init__.py =================================================================== --- trunk/src/cclib/parser/__init__.py 2006-05-21 14:40:37 UTC (rev 135) +++ trunk/src/cclib/parser/__init__.py 2006-05-21 14:49:18 UTC (rev 136) @@ -1,3 +1,10 @@ +# These import statements are added for the convenience of users... + +# Rather than having to type: +# from cclib.parser.gaussianparser import Gaussian +# they can use: +# from cclib.parser import Gaussian + from gaussianparser import Gaussian from gamessparser import GAMESS from adfparser import ADF @@ -2 +9,6 @@ from jaguarparser import Jaguar + +# This allow users to type: +# from cclib.parser import guesstype + +from utils import guesstype Added: trunk/test/testauto.py =================================================================== --- trunk/test/testauto.py (rev 0) +++ trunk/test/testauto.py 2006-05-21 14:49:18 UTC (rev 136) @@ -0,0 +1,9 @@ +import os +from cclib.parser import guesstype + +os.chdir(os.path.join("..","data","Gaussian")) + +os.chdir("basicGaussian03") + +for filename in ["dvb_gopt.out"]: + print guesstype(filename) Property changes on: trunk/test/testauto.py ___________________________________________________________________ Name: svn:executable + * This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-05-22 13:06:58
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Revision: 143 Author: baoilleach Date: 2006-05-22 06:06:52 -0700 (Mon, 22 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=143&view=rev Log Message: ----------- Added test for atomcoords in SP calcs, and bug fixed gamessparser which was only extracting x and y, and furthermore was making a list, not an array Modified Paths: -------------- trunk/src/cclib/parser/gamessparser.py trunk/test/testSP.py Modified: trunk/src/cclib/parser/gamessparser.py =================================================================== --- trunk/src/cclib/parser/gamessparser.py 2006-05-22 10:43:56 UTC (rev 142) +++ trunk/src/cclib/parser/gamessparser.py 2006-05-22 13:06:52 UTC (rev 143) @@ -167,7 +167,7 @@ line = inputfile.next() while line.strip(): temp = line.strip().split() - atomcoords.append([utils.convertor(float(x),"au","Ang") for x in temp[2:4]]) + atomcoords.append([utils.convertor(float(x),"au","Ang") for x in temp[2:5]]) atomnos.append(self.table.number[temp[0]]) # Use the element name line = inputfile.next() self.atomnos = Numeric.array(atomnos,"i") @@ -191,7 +191,7 @@ line = inputfile.next() while line.strip(): temp = line.strip().split() - atomcoords.append(map(float,temp[2:4])) + atomcoords.append(map(float,temp[2:5])) line = inputfile.next() self.atomcoords.append(atomcoords) @@ -438,6 +438,8 @@ 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 hasattr(self,"atomcoords"): + self.atomcoords = Numeric.array(self.atomcoords,"f") if not hasattr(self,"nmo"): self.logger.info("Creating attribute nmo with default value") self.nmo = self.nbasis Modified: trunk/test/testSP.py =================================================================== --- trunk/test/testSP.py 2006-05-22 10:43:56 UTC (rev 142) +++ trunk/test/testSP.py 2006-05-22 13:06:52 UTC (rev 143) @@ -9,6 +9,10 @@ """Are the dims of the overlap matrix consistent with nbasis?""" self.assertEquals(self.data.aooverlaps.shape,(self.data.nbasis,self.data.nbasis)) + def testatomcoords(self): + """Are the dimensions of atomcoords 1 x natom x 3?""" + self.assertEquals(self.data.atomcoords.shape,(1,self.data.natom,3)) + def testdimmocoeffs(self): """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)) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <bao...@us...> - 2006-05-22 13:09:56
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Revision: 144 Author: baoilleach Date: 2006-05-22 06:09:51 -0700 (Mon, 22 May 2006) ViewCVS: http://svn.sourceforge.net/cclib/?rev=144&view=rev Log Message: ----------- Relaxed the atomcoords Angstrom test so that PCGAMESS will pass Modified Paths: -------------- trunk/test/parseADF.py trunk/test/testGeoOpt.py Modified: trunk/test/parseADF.py =================================================================== --- trunk/test/parseADF.py 2006-05-22 13:06:52 UTC (rev 143) +++ trunk/test/parseADF.py 2006-05-22 13:09:51 UTC (rev 144) @@ -8,5 +8,4 @@ for file in ["dvb_gopt.adfout"]: t = ADF(file) t.parse() - - + print len(t.atomcoords) Modified: trunk/test/testGeoOpt.py =================================================================== --- trunk/test/testGeoOpt.py 2006-05-22 13:06:52 UTC (rev 143) +++ trunk/test/testGeoOpt.py 2006-05-22 13:09:51 UTC (rev 144) @@ -25,7 +25,7 @@ # Find the distance in the final iteration dist = math.sqrt(sum((coords[-1][i]-coords[-1][j])**2)) mindist = min(mindist,dist) - self.assert_(abs(mindist-1.34)<0.02,"Mindist is %f (not 1.34)" % mindist) + self.assert_(abs(mindist-1.34)<0.03,"Mindist is %f (not 1.34)" % mindist) def testnatom(self): """Is the number of atoms equal to 20?""" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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