[cclib-svn] SF.net SVN: cclib: [69] trunk/test

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

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()


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