cclib-svn — Log messages of SVN commits

[cclib-svn] SF.net SVN: cclib: [7] trunk

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

Revision: 7
Author:   baoilleach
Date:     2006-03-07 01:56:19 -0800 (Tue, 07 Mar 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=7&view=rev

Log Message:
-----------
Rearrangement of file structure.

Modified Paths:
--------------
    trunk/setup.py

Removed Paths:
-------------
    trunk/src/cclib/parser.py
Modified: trunk/setup.py
===================================================================
--- trunk/setup.py	2006-03-07 09:52:22 UTC (rev 6)
+++ trunk/setup.py	2006-03-07 09:56:19 UTC (rev 7)
@@ -5,4 +5,4 @@
       author_email="bao...@us...",
       url="http://cclib.sourceforge.net",
       package_dir = {'cclib':'src/cclib'},
-      packages=['cclib'])
+      packages=['cclib','cclib.parser'])

Deleted: trunk/src/cclib/parser.py
===================================================================
--- trunk/src/cclib/parser.py	2006-03-07 09:52:22 UTC (rev 6)
+++ trunk/src/cclib/parser.py	2006-03-07 09:56:19 UTC (rev 7)
@@ -1,541 +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 math,sys,logging,copy,re,os,time # How many of these are necessary?
-import Numeric
-
-def convertor(value,fromunits,tounits):
-    """Convert from one set of units to another.
-
-    >>> convertor(8,"eV","cm-1")
-    64000
-    """
-    _convertor = {"eV_to_cm-1": lambda x: x*8065.6,
-                  "nm_to_cm-1": lambda x: 1e7/x,
-                  "cm-1_to_nm": lambda x: 1e7/x}
-
-    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"]
-        self.number = {}
-        for i in range(1,len(self.element)):
-            self.number[self.element[i]] = i
-
-class Logfile(object):
-    """Abstract class that contains the methods that act on data
-    parsed from various types of logfile."""
-    def __init__(self,filename):
-        self.filename = filename
-
-    def float(self,number):
-        """Convert a string to a float avoiding the problem with Ds."""
-        number = number.replace("D","E")
-        return float(number)
-
-class G03(Logfile):
-    """A Gaussian 03 log file
-    
-    Attributes:
-     filename -- the name of the log file
-     logger -- a logging object
-     NAtoms -- the number of atoms in the molecule
-     atomicNo[] -- the atomic numbers of the atoms
-
-     scfenergy[] -- the SCF energies
-
-    Class Methods:
-     float(a) -- convert a string to a float
-
-    Methods:
-     parse() -- extract general info from the logfile
-    """
-    SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftarget[]
-    def __init__(self,filename):
-
-        # Call the __init__ method of the superclass
-        super(G03, self).__init__(filename)
-        
-        # Set up the logger...will move this into superclass
-        # through a function call with G03 as a parameter.
-        # Note: all loggers with the same name share the logger.
-        # Here, loggers with different filenames are different
-        self.logger = logging.getLogger('G03.%s' % self.filename)
-        self.logger.setLevel(logging.INFO)
-        handler = logging.StreamHandler(sys.stdout)
-        handler.setFormatter(logging.Formatter("[%(name)s %(levelname)s] %(message)s"))
-        self.logger.addHandler(handler)
-
-    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 parse(self):
-        """Extract general info from the logfile.
-        
-        Creates the following instance attributes:
-         NAtoms, atomicNo[], 
-         scfProgress[], SCF_target_rms, SCF_target_energy, SCF_target_max,
-         geoProgress[], scfenergy[]
-         evalue [[]]
-        """
-        inputfile = open(self.filename,"r")
-        for line in inputfile:
-            
-            if line[1:8]=="NAtoms=":
-# Find the number of atoms
-                NAtoms = int(line.split()[1])
-                if hasattr(self,"NAtoms"):
-                    assert self.NAtoms==NAtoms
-                else:
-                    # I wonder whether this code will ever be executed
-                    self.NAtoms = NAtoms
-                    self.logger.info("Creating attribute NAtoms: %d" % self.NAtoms)                    
-            
-            if not hasattr(self,"atomicNo") and (line.find("Z-Matrix orientation")>=0
-                                                 or line[25:45]=="Standard orientation"
-                                                 or line[26:43]=="Input orientation"):
-# Extract the atomic numbers of the atoms
-                self.logger.info("Creating attribute atomicNo[]")
-                self.atomicNo = []
-                hyphens = inputfile.next()
-                colmNames = inputfile.next(); colmNames = inputfile.next()
-                hyphens = inputfile.next()
-                line = inputfile.next()
-                while line!=hyphens:
-                    self.atomicNo.append(int(line.split()[1]))
-                    line = inputfile.next()
-                NAtoms = len(self.atomicNo)
-                if hasattr(self,"NAtoms"):
-                    assert self.NAtoms==NAtoms
-                else:
-                    self.NAtoms = NAtoms
-                    self.logger.info("Creating attribute NAtoms: %d" % self.NAtoms)
-
-
-# Find the targets for the SCF convergence (QM calcs)
-# We assume that the targets don't change, although it's
-# easy enough to store all of the targets
-            if line[1:44]=='Requested convergence on RMS density matrix':
-                if not hasattr(self,"scftarget"):
-                    self.logger.info("Creating attribute scftarget[]")
-                self.scftarget = [None]*3
-                self.scftarget[G03.SCFRMS] = self.float(line.split('=')[1].split()[0])
-            if line[1:44]=='Requested convergence on MAX density matrix':
-                self.scftarget[G03.SCFMAX] = self.float(line.strip().split('=')[1][:-1])
-            if line[1:44]=='Requested convergence on             energy':
-                self.scftarget[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,"scfvalue"):
-                    self.logger.info("Creating attribute scfvalue[[]]")
-                    self.scfvalue = []
-                newlist = [ [] for x in self.scftarget ]
-                line = inputfile.next()
-                while line.find("SCF Done")==-1:
-                    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)
-                        self.logger.debug(line)
-                    try:
-                        line = inputfile.next()
-                    except StopIteration: # May be interupted by EOF
-                        break
-                self.scfvalue.append(newlist)
-
-            if line[1:4]=='It=':
-# Extract SCF convergence information (AM1 calcs)
-                self.logger.info("Creating attributes scftarget[],scfvalue[[]]")
-                self.scftarget = [1E-7] # This is the target value for the rms
-                self.scfvalue = [[]]
-                line = inputfile.next()
-                while line.find(" Energy")==-1:
-                    self.logger.debug(line)
-                    parts = line.strip().split()
-                    self.scfvalue[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 extract SCF convergence information
-                self.logger.debug(line)
-                self.logger.debug("SCF Done")
-                if hasattr(self,"scfenergy"):
-                    self.scfenergy.append(line.split()[4])
-                else:
-                    self.scfenergy = [line.split()[4]]
-                    self.logger.info("Creating attribute scfenergy[]")
-
-            if line[49:59]=='Converged?':
-# Extract Geometry convergence information
-                if not hasattr(self,"geotarget"):
-                    self.logger.info("Creating attributes geotarget[],geovalue[[]]")
-                    self.geovalue = []
-                    self.geotarget = [None]*4
-                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.geotarget[i] = self.float(parts[3])
-                self.geovalue.append(newlist)
-
-            if line[1:19]=='Orbital symmetries' and not hasattr(self,"orbsym"):
-# Extracting orbital symmetries
-                self.logger.info("Creating attribute orbsym[[]]")
-                self.orbsym = [[]]
-                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.HOMO = [i-1] # 'HOMO' indexes the HOMO in the arrays
-                        self.logger.info("Creating attribute HOMO[]")
-                    parts = line[17:].split()
-                    for x in parts:
-                        self.orbsym[0].append(x.strip('()'))
-                        i+= 1 
-                    line = inputfile.next()
-                if unres:
-                    line = inputfile.next()
-                    # Repeat with beta orbital information
-                    i = 0
-                    self.orbsym.append([])
-                    while len(line)>18 and line[17]=='(':
-                        if line.find('Virtual')>=0:
-                            self.HOMO.append(i-1) # 'HOMO' indexes the HOMO in the arrays
-                        parts = line[17:].split()
-                        for x in parts:
-                            self.orbsym[1].append(x.strip('()'))
-                            i+= 1
-                        line = inputfile.next()
-
-            if line[1:6]=="Alpha" and line.find("eigenvalues")>=0:
-# Extract the alpha electron eigenvalues
-                self.logger.info("Creating attribute evalue[[]]")
-                self.evalue = [[]]
-                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.evalue[0])-1
-                        if hasattr(self,"HOMO"):
-                            assert HOMO==self.HOMO[0]
-                        else:
-                            self.logger.info("Creating attribute HOMO[]")
-                            self.HOMO = [HOMO]
-                    part = line[28:]
-                    i = 0
-                    while i*10+4<len(part):
-                        x = part[i*10:(i+1)*10]
-                        self.evalue[0].append(self.float(x)*27.2114) # from a.u. (hartrees) to eV
-                        i += 1
-                    line = inputfile.next()            
-                if line.find('Beta')==2:
-                    self.evalue.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.evalue[1])-1
-                        if len(self.HOMO)==2:
-                            # It already has a self.HOMO (with the Alpha value)
-                            # but does it already have a Beta value?
-                            assert HOMO==self.HOMO[1]
-                        else:
-                             self.HOMO.append(HOMO)
-                    part = line[28:]
-                    i = 0
-                    while i*10+4<len(part):
-                        x = part[i*10:(i+1)*10]
-                        self.evalue[1].append(self.float(x)*27.2114) # from a.u. (hartrees) to eV
-                        i += 1
-                    line = inputfile.next()   
-
-            if line[1:14]=="Harmonic freq":
-# Start of the IR/Raman frequency section
-                self.vibsym = []
-                self.ir = []
-                self.vibfreq = []
-                self.logger.info("Creating attribute vibsym[]")
-                self.logger.info("Creating attribute vibfreq[]")
-                self.logger.info("Creating attribute ir[]")                
-                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.vibsym.extend(line.split()) # Adding new symmetry
-                    line = inputfile.next()
-                    self.vibfreq.extend(map(self.float,line[15:].split())) # Adding new frequencies
-                    [inputfile.next() for i in [0,1]] # Skip two lines
-                    line = inputfile.next()
-                    self.ir.extend(map(self.float,line[15:].split())) # Adding IR intensities
-                    line = inputfile.next()
-                    if line.find("Raman")>=0:
-                        if not hasattr(self,"raman"):
-                            self.raman = []
-                            self.logger.info("Creating attribute raman[]")
-                        line = inputfile.next()
-                        self.raman.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
-                    
-            if line[1:14]=="Excited State":
-# Extract the electronic transitions
-                if not hasattr(self,"etenergy"):
-                    self.etenergy = []
-                    self.etwavelen = []
-                    self.etosc = []
-                    self.etsym = []
-                    self.etcis = []
-                    self.logger.info("Creating attributes etenergy[], etwavelen[], etosc[], etsym[], etcis[]")
-                # 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.logger.debug(parts)
-                self.etenergy.append(convertor(self.float(parts[0]),"eV","cm-1"))
-                self.etwavelen.append(self.float(parts[2]))
-                self.etosc.append(self.float(parts[4].split("=")[1]))
-                self.etsym.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.etcis.append(CIScontrib)
-
-
-            if line[1:52]=="<0|r|b> * <b|rxdel|0>  (Au), Rotatory Strengths (R)":
-# Extract circular dichroism data
-                self.rotatory = []
-                self.logger.info("Creating attribute rotatory[]")
-                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.rotatory.append(R)
-                    line = inputfile.next()
-                    temp = line.strip().split()
-                    parts = line.strip().split()                
-
-            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
-                NBsUse = int(line.split('=')[1].split()[0])
-                if hasattr(self,"NBsUse"):
-                    assert NBsUse==self.NBsUse
-                else:
-                    self.NBsUse = NBsUse
-                    self.logger.info("Creating attribute NBsUse: %d" % self.NBsUse)
-
-            if line[7:22]=="basis functions,":
-# For AM1 calculations, set NBasis by a second method
-# (NBsUse 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 overlap[x,y]")
-                import time; oldtime = time.time()
-                self.overlap = Numeric.zeros( (self.NBasis,self.NBasis), "float")
-                # Overlap integrals for basis fn#1 are in overlap[0]
-                base = 0
-                colmNames = inputfile.next()
-                while base<self.NBasis:
-                    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].replace("D","E"))
-                            self.overlap[base+j,i+base] = k
-                            self.overlap[i+base,base+j] = k
-                    base += 5
-                    colmNames = inputfile.next()
-                self.logger.info("Took %f seconds" % (time.time()-oldtime))
-
-            if line[5:35]=="Molecular Orbital Coefficients" or line[5:41]=="Alpha Molecular Orbital Coefficients" or line[5:40]=="Beta Molecular Orbital Coefficients":
-                import time; oldtime = time.time()
-                if line[5:40]=="Beta Molecular Orbital Coefficients":
-                    beta = True
-                    # Need to add an extra dimension to self.mocoeff
-                    self.mocoeff = Numeric.resize(self.mocoeff,(2,NBsUse,NBasis))
-                else:
-                    beta = False
-                    self.logger.info("Creating attributes orbitals[], mocoeff[][]")
-                    self.orbitals = []
-                    self.mocoeff = Numeric.zeros((NBsUse,NBasis),"float")
-
-                base = 0
-                for base in range(0,NBsUse,5):
-                    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.orbitals.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.mocoeff[1,base:base+len(part)/10,i] = temp
-                        else:
-                            self.mocoeff[base:base+len(part)/10,i] = temp
-                self.logger.info("Took %f seconds" % (time.time()-oldtime))
-
-                 
-        inputfile.close()
-
-# 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.NAtoms):
-                    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,parser
-    doctest.testmod(parser,verbose=False)


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[cclib-svn] SF.net SVN: cclib: [6] trunk/src/cclib/parser

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

Revision: 6
Author:   baoilleach
Date:     2006-03-07 01:52:22 -0800 (Tue, 07 Mar 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=6&view=rev

Log Message:
-----------
Separated G03 from Logfile.

Modified Paths:
--------------
    trunk/src/cclib/parser/G03.py

Added Paths:
-----------
    trunk/src/cclib/parser/Logfile.py
    trunk/src/cclib/parser/__init__.py
Modified: trunk/src/cclib/parser/G03.py
===================================================================
--- trunk/src/cclib/parser/G03.py	2006-03-07 09:49:10 UTC (rev 5)
+++ trunk/src/cclib/parser/G03.py	2006-03-07 09:52:22 UTC (rev 6)
@@ -19,45 +19,8 @@
 """
 import math,sys,logging,copy,re,os,time # How many of these are necessary?
 import Numeric
+from Logfile import Logfile # import the superclass
 
-def convertor(value,fromunits,tounits):
-    """Convert from one set of units to another.
-
-    >>> convertor(8,"eV","cm-1")
-    64000
-    """
-    _convertor = {"eV_to_cm-1": lambda x: x*8065.6,
-                  "nm_to_cm-1": lambda x: 1e7/x,
-                  "cm-1_to_nm": lambda x: 1e7/x}
-
-    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"]
-        self.number = {}
-        for i in range(1,len(self.element)):
-            self.number[self.element[i]] = i
-
-class Logfile(object):
-    """Abstract class that contains the methods that act on data
-    parsed from various types of logfile."""
-    def __init__(self,filename):
-        self.filename = filename
-
-    def float(self,number):
-        """Convert a string to a float avoiding the problem with Ds."""
-        number = number.replace("D","E")
-        return float(number)
-
 class G03(Logfile):
     """A Gaussian 03 log file
     

Copied: trunk/src/cclib/parser/Logfile.py (from rev 5, trunk/src/cclib/parser/G03.py)
===================================================================
--- trunk/src/cclib/parser/Logfile.py	                        (rev 0)
+++ trunk/src/cclib/parser/Logfile.py	2006-03-07 09:52:22 UTC (rev 6)
@@ -0,0 +1,63 @@
+"""
+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 math,sys,logging,copy,re,os,time # How many of these are necessary?
+import Numeric
+
+def convertor(value,fromunits,tounits):
+    """Convert from one set of units to another.
+
+    >>> convertor(8,"eV","cm-1")
+    64000
+    """
+    _convertor = {"eV_to_cm-1": lambda x: x*8065.6,
+                  "nm_to_cm-1": lambda x: 1e7/x,
+                  "cm-1_to_nm": lambda x: 1e7/x}
+
+    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"]
+        self.number = {}
+        for i in range(1,len(self.element)):
+            self.number[self.element[i]] = i
+
+class Logfile(object):
+    """Abstract class that contains the methods that act on data
+    parsed from various types of logfile."""
+    def __init__(self,filename):
+        self.filename = filename
+
+    def float(self,number):
+        """Convert a string to a float avoiding the problem with Ds."""
+        number = number.replace("D","E")
+        return float(number)
+
+if __name__=="__main__":
+    import doctest,parser
+    doctest.testmod(parser,verbose=False)

Added: trunk/src/cclib/parser/__init__.py
===================================================================


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

[cclib-svn] SF.net SVN: cclib: [5] trunk/src/cclib

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

Revision: 5
Author:   baoilleach
Date:     2006-03-07 01:49:10 -0800 (Tue, 07 Mar 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=5&view=rev

Log Message:
-----------
Rearranging the file structure.

Added Paths:
-----------
    trunk/src/cclib/parser/
    trunk/src/cclib/parser/G03.py
Copied: trunk/src/cclib/parser/G03.py (from rev 4, trunk/src/cclib/parser.py)
===================================================================
--- trunk/src/cclib/parser/G03.py	                        (rev 0)
+++ trunk/src/cclib/parser/G03.py	2006-03-07 09:49:10 UTC (rev 5)
@@ -0,0 +1,541 @@
+"""
+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 math,sys,logging,copy,re,os,time # How many of these are necessary?
+import Numeric
+
+def convertor(value,fromunits,tounits):
+    """Convert from one set of units to another.
+
+    >>> convertor(8,"eV","cm-1")
+    64000
+    """
+    _convertor = {"eV_to_cm-1": lambda x: x*8065.6,
+                  "nm_to_cm-1": lambda x: 1e7/x,
+                  "cm-1_to_nm": lambda x: 1e7/x}
+
+    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"]
+        self.number = {}
+        for i in range(1,len(self.element)):
+            self.number[self.element[i]] = i
+
+class Logfile(object):
+    """Abstract class that contains the methods that act on data
+    parsed from various types of logfile."""
+    def __init__(self,filename):
+        self.filename = filename
+
+    def float(self,number):
+        """Convert a string to a float avoiding the problem with Ds."""
+        number = number.replace("D","E")
+        return float(number)
+
+class G03(Logfile):
+    """A Gaussian 03 log file
+    
+    Attributes:
+     filename -- the name of the log file
+     logger -- a logging object
+     NAtoms -- the number of atoms in the molecule
+     atomicNo[] -- the atomic numbers of the atoms
+
+     scfenergy[] -- the SCF energies
+
+    Class Methods:
+     float(a) -- convert a string to a float
+
+    Methods:
+     parse() -- extract general info from the logfile
+    """
+    SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftarget[]
+    def __init__(self,filename):
+
+        # Call the __init__ method of the superclass
+        super(G03, self).__init__(filename)
+        
+        # Set up the logger...will move this into superclass
+        # through a function call with G03 as a parameter.
+        # Note: all loggers with the same name share the logger.
+        # Here, loggers with different filenames are different
+        self.logger = logging.getLogger('G03.%s' % self.filename)
+        self.logger.setLevel(logging.INFO)
+        handler = logging.StreamHandler(sys.stdout)
+        handler.setFormatter(logging.Formatter("[%(name)s %(levelname)s] %(message)s"))
+        self.logger.addHandler(handler)
+
+    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 parse(self):
+        """Extract general info from the logfile.
+        
+        Creates the following instance attributes:
+         NAtoms, atomicNo[], 
+         scfProgress[], SCF_target_rms, SCF_target_energy, SCF_target_max,
+         geoProgress[], scfenergy[]
+         evalue [[]]
+        """
+        inputfile = open(self.filename,"r")
+        for line in inputfile:
+            
+            if line[1:8]=="NAtoms=":
+# Find the number of atoms
+                NAtoms = int(line.split()[1])
+                if hasattr(self,"NAtoms"):
+                    assert self.NAtoms==NAtoms
+                else:
+                    # I wonder whether this code will ever be executed
+                    self.NAtoms = NAtoms
+                    self.logger.info("Creating attribute NAtoms: %d" % self.NAtoms)                    
+            
+            if not hasattr(self,"atomicNo") and (line.find("Z-Matrix orientation")>=0
+                                                 or line[25:45]=="Standard orientation"
+                                                 or line[26:43]=="Input orientation"):
+# Extract the atomic numbers of the atoms
+                self.logger.info("Creating attribute atomicNo[]")
+                self.atomicNo = []
+                hyphens = inputfile.next()
+                colmNames = inputfile.next(); colmNames = inputfile.next()
+                hyphens = inputfile.next()
+                line = inputfile.next()
+                while line!=hyphens:
+                    self.atomicNo.append(int(line.split()[1]))
+                    line = inputfile.next()
+                NAtoms = len(self.atomicNo)
+                if hasattr(self,"NAtoms"):
+                    assert self.NAtoms==NAtoms
+                else:
+                    self.NAtoms = NAtoms
+                    self.logger.info("Creating attribute NAtoms: %d" % self.NAtoms)
+
+
+# Find the targets for the SCF convergence (QM calcs)
+# We assume that the targets don't change, although it's
+# easy enough to store all of the targets
+            if line[1:44]=='Requested convergence on RMS density matrix':
+                if not hasattr(self,"scftarget"):
+                    self.logger.info("Creating attribute scftarget[]")
+                self.scftarget = [None]*3
+                self.scftarget[G03.SCFRMS] = self.float(line.split('=')[1].split()[0])
+            if line[1:44]=='Requested convergence on MAX density matrix':
+                self.scftarget[G03.SCFMAX] = self.float(line.strip().split('=')[1][:-1])
+            if line[1:44]=='Requested convergence on             energy':
+                self.scftarget[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,"scfvalue"):
+                    self.logger.info("Creating attribute scfvalue[[]]")
+                    self.scfvalue = []
+                newlist = [ [] for x in self.scftarget ]
+                line = inputfile.next()
+                while line.find("SCF Done")==-1:
+                    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)
+                        self.logger.debug(line)
+                    try:
+                        line = inputfile.next()
+                    except StopIteration: # May be interupted by EOF
+                        break
+                self.scfvalue.append(newlist)
+
+            if line[1:4]=='It=':
+# Extract SCF convergence information (AM1 calcs)
+                self.logger.info("Creating attributes scftarget[],scfvalue[[]]")
+                self.scftarget = [1E-7] # This is the target value for the rms
+                self.scfvalue = [[]]
+                line = inputfile.next()
+                while line.find(" Energy")==-1:
+                    self.logger.debug(line)
+                    parts = line.strip().split()
+                    self.scfvalue[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 extract SCF convergence information
+                self.logger.debug(line)
+                self.logger.debug("SCF Done")
+                if hasattr(self,"scfenergy"):
+                    self.scfenergy.append(line.split()[4])
+                else:
+                    self.scfenergy = [line.split()[4]]
+                    self.logger.info("Creating attribute scfenergy[]")
+
+            if line[49:59]=='Converged?':
+# Extract Geometry convergence information
+                if not hasattr(self,"geotarget"):
+                    self.logger.info("Creating attributes geotarget[],geovalue[[]]")
+                    self.geovalue = []
+                    self.geotarget = [None]*4
+                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.geotarget[i] = self.float(parts[3])
+                self.geovalue.append(newlist)
+
+            if line[1:19]=='Orbital symmetries' and not hasattr(self,"orbsym"):
+# Extracting orbital symmetries
+                self.logger.info("Creating attribute orbsym[[]]")
+                self.orbsym = [[]]
+                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.HOMO = [i-1] # 'HOMO' indexes the HOMO in the arrays
+                        self.logger.info("Creating attribute HOMO[]")
+                    parts = line[17:].split()
+                    for x in parts:
+                        self.orbsym[0].append(x.strip('()'))
+                        i+= 1 
+                    line = inputfile.next()
+                if unres:
+                    line = inputfile.next()
+                    # Repeat with beta orbital information
+                    i = 0
+                    self.orbsym.append([])
+                    while len(line)>18 and line[17]=='(':
+                        if line.find('Virtual')>=0:
+                            self.HOMO.append(i-1) # 'HOMO' indexes the HOMO in the arrays
+                        parts = line[17:].split()
+                        for x in parts:
+                            self.orbsym[1].append(x.strip('()'))
+                            i+= 1
+                        line = inputfile.next()
+
+            if line[1:6]=="Alpha" and line.find("eigenvalues")>=0:
+# Extract the alpha electron eigenvalues
+                self.logger.info("Creating attribute evalue[[]]")
+                self.evalue = [[]]
+                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.evalue[0])-1
+                        if hasattr(self,"HOMO"):
+                            assert HOMO==self.HOMO[0]
+                        else:
+                            self.logger.info("Creating attribute HOMO[]")
+                            self.HOMO = [HOMO]
+                    part = line[28:]
+                    i = 0
+                    while i*10+4<len(part):
+                        x = part[i*10:(i+1)*10]
+                        self.evalue[0].append(self.float(x)*27.2114) # from a.u. (hartrees) to eV
+                        i += 1
+                    line = inputfile.next()            
+                if line.find('Beta')==2:
+                    self.evalue.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.evalue[1])-1
+                        if len(self.HOMO)==2:
+                            # It already has a self.HOMO (with the Alpha value)
+                            # but does it already have a Beta value?
+                            assert HOMO==self.HOMO[1]
+                        else:
+                             self.HOMO.append(HOMO)
+                    part = line[28:]
+                    i = 0
+                    while i*10+4<len(part):
+                        x = part[i*10:(i+1)*10]
+                        self.evalue[1].append(self.float(x)*27.2114) # from a.u. (hartrees) to eV
+                        i += 1
+                    line = inputfile.next()   
+
+            if line[1:14]=="Harmonic freq":
+# Start of the IR/Raman frequency section
+                self.vibsym = []
+                self.ir = []
+                self.vibfreq = []
+                self.logger.info("Creating attribute vibsym[]")
+                self.logger.info("Creating attribute vibfreq[]")
+                self.logger.info("Creating attribute ir[]")                
+                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.vibsym.extend(line.split()) # Adding new symmetry
+                    line = inputfile.next()
+                    self.vibfreq.extend(map(self.float,line[15:].split())) # Adding new frequencies
+                    [inputfile.next() for i in [0,1]] # Skip two lines
+                    line = inputfile.next()
+                    self.ir.extend(map(self.float,line[15:].split())) # Adding IR intensities
+                    line = inputfile.next()
+                    if line.find("Raman")>=0:
+                        if not hasattr(self,"raman"):
+                            self.raman = []
+                            self.logger.info("Creating attribute raman[]")
+                        line = inputfile.next()
+                        self.raman.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
+                    
+            if line[1:14]=="Excited State":
+# Extract the electronic transitions
+                if not hasattr(self,"etenergy"):
+                    self.etenergy = []
+                    self.etwavelen = []
+                    self.etosc = []
+                    self.etsym = []
+                    self.etcis = []
+                    self.logger.info("Creating attributes etenergy[], etwavelen[], etosc[], etsym[], etcis[]")
+                # 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.logger.debug(parts)
+                self.etenergy.append(convertor(self.float(parts[0]),"eV","cm-1"))
+                self.etwavelen.append(self.float(parts[2]))
+                self.etosc.append(self.float(parts[4].split("=")[1]))
+                self.etsym.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.etcis.append(CIScontrib)
+
+
+            if line[1:52]=="<0|r|b> * <b|rxdel|0>  (Au), Rotatory Strengths (R)":
+# Extract circular dichroism data
+                self.rotatory = []
+                self.logger.info("Creating attribute rotatory[]")
+                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.rotatory.append(R)
+                    line = inputfile.next()
+                    temp = line.strip().split()
+                    parts = line.strip().split()                
+
+            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
+                NBsUse = int(line.split('=')[1].split()[0])
+                if hasattr(self,"NBsUse"):
+                    assert NBsUse==self.NBsUse
+                else:
+                    self.NBsUse = NBsUse
+                    self.logger.info("Creating attribute NBsUse: %d" % self.NBsUse)
+
+            if line[7:22]=="basis functions,":
+# For AM1 calculations, set NBasis by a second method
+# (NBsUse 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 overlap[x,y]")
+                import time; oldtime = time.time()
+                self.overlap = Numeric.zeros( (self.NBasis,self.NBasis), "float")
+                # Overlap integrals for basis fn#1 are in overlap[0]
+                base = 0
+                colmNames = inputfile.next()
+                while base<self.NBasis:
+                    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].replace("D","E"))
+                            self.overlap[base+j,i+base] = k
+                            self.overlap[i+base,base+j] = k
+                    base += 5
+                    colmNames = inputfile.next()
+                self.logger.info("Took %f seconds" % (time.time()-oldtime))
+
+            if line[5:35]=="Molecular Orbital Coefficients" or line[5:41]=="Alpha Molecular Orbital Coefficients" or line[5:40]=="Beta Molecular Orbital Coefficients":
+                import time; oldtime = time.time()
+                if line[5:40]=="Beta Molecular Orbital Coefficients":
+                    beta = True
+                    # Need to add an extra dimension to self.mocoeff
+                    self.mocoeff = Numeric.resize(self.mocoeff,(2,NBsUse,NBasis))
+                else:
+                    beta = False
+                    self.logger.info("Creating attributes orbitals[], mocoeff[][]")
+                    self.orbitals = []
+                    self.mocoeff = Numeric.zeros((NBsUse,NBasis),"float")
+
+                base = 0
+                for base in range(0,NBsUse,5):
+                    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.orbitals.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.mocoeff[1,base:base+len(part)/10,i] = temp
+                        else:
+                            self.mocoeff[base:base+len(part)/10,i] = temp
+                self.logger.info("Took %f seconds" % (time.time()-oldtime))
+
+                 
+        inputfile.close()
+
+# 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.NAtoms):
+                    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,parser
+    doctest.testmod(parser,verbose=False)


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[cclib-svn] SF.net SVN: cclib: [4] trunk/MANIFEST

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

Revision: 4
Author:   baoilleach
Date:     2006-03-06 06:36:27 -0800 (Mon, 06 Mar 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=4&view=rev

Log Message:
-----------
Removed reference to utils.py in MANIFEST

Modified Paths:
--------------
    trunk/MANIFEST
Modified: trunk/MANIFEST
===================================================================
--- trunk/MANIFEST	2006-03-06 10:33:31 UTC (rev 3)
+++ trunk/MANIFEST	2006-03-06 14:36:27 UTC (rev 4)
@@ -1,4 +1,3 @@
 setup.py
 src/cclib/__init__.py
 src/cclib/parser.py
-src/cclib/utils.py


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[Cclib-svn] SF.net SVN: cclib: [3] trunk

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

Revision: 3
Author:   baoilleach
Date:     2006-03-06 02:33:31 -0800 (Mon, 06 Mar 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=3&view=rev

Log Message:
-----------
Made necessary fixes to get cclib up and running. It now parses Adam's large test file. 
Removed references to gausssum in setup.py. 
Added call to superclass __init__ method for G03.
Fixed error in Logfile.float.

Modified Paths:
--------------
    trunk/setup.py
    trunk/src/cclib/parser.py
Modified: trunk/setup.py
===================================================================
--- trunk/setup.py	2006-03-05 22:18:59 UTC (rev 2)
+++ trunk/setup.py	2006-03-06 10:33:31 UTC (rev 3)
@@ -1,9 +1,8 @@
 from distutils.core import setup
 setup(name="cclib",
-      version="0.1.2",
+      version="0.1",
       author="Noel O'Boyle",
       author_email="bao...@us...",
-      url="http://gausssum.sf.net",
-      scripts=['src/gausssum/gausssum.py'],
+      url="http://cclib.sourceforge.net",
       package_dir = {'cclib':'src/cclib'},
       packages=['cclib'])

Modified: trunk/src/cclib/parser.py
===================================================================
--- trunk/src/cclib/parser.py	2006-03-05 22:18:59 UTC (rev 2)
+++ trunk/src/cclib/parser.py	2006-03-06 10:33:31 UTC (rev 3)
@@ -53,7 +53,7 @@
     def __init__(self,filename):
         self.filename = filename
 
-    def float(number):
+    def float(self,number):
         """Convert a string to a float avoiding the problem with Ds."""
         number = number.replace("D","E")
         return float(number)
@@ -78,7 +78,11 @@
     SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftarget[]
     def __init__(self,filename):
 
-        # Set up the logger...
+        # Call the __init__ method of the superclass
+        super(G03, self).__init__(filename)
+        
+        # Set up the logger...will move this into superclass
+        # through a function call with G03 as a parameter.
         # Note: all loggers with the same name share the logger.
         # Here, loggers with different filenames are different
         self.logger = logging.getLogger('G03.%s' % self.filename)



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[Cclib-svn] SF.net SVN: cclib: [2] trunk/src/cclib/parser.py

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

Revision: 2
Author:   baoilleach
Date:     2006-03-05 14:18:59 -0800 (Sun, 05 Mar 2006)
ViewCVS:  http://svn.sourceforge.net/cclib/?rev=2&view=rev

Log Message:
-----------
Removed GaussSum code from cclib. Moved G03.float to Logfile.float. Removed ref
rence to non-cclib modules (namely, utils.py and gnupy.py).

Modified Paths:
--------------
    trunk/src/cclib/parser.py
Modified: trunk/src/cclib/parser.py
===================================================================
--- trunk/src/cclib/parser.py	2006-03-04 17:23:22 UTC (rev 1)
+++ trunk/src/cclib/parser.py	2006-03-05 22:18:59 UTC (rev 2)
@@ -1,9 +1,9 @@
 """
-GaussSum is a parser for computational chemistry log files.
+cclib is a parser for computational chemistry log files.
 
-See http://gausssum.sf.net for more information.
+See http://cclib.sf.net for more information.
 
-Copyright (C) 2005 Noel O'Boyle <bao...@gm...>
+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
@@ -17,10 +17,8 @@
 
 Contributions (monetary as well as code :-) are encouraged.
 """
-import math,sys,logging,copy,re,os,time
+import math,sys,logging,copy,re,os,time # How many of these are necessary?
 import Numeric
-from utils import *
-from gnupy import Gnuplot
 
 def convertor(value,fromunits,tounits):
     """Convert from one set of units to another.
@@ -52,474 +50,14 @@
 class Logfile(object):
     """Abstract class that contains the methods that act on data
     parsed from various types of logfile."""
+    def __init__(self,filename):
+        self.filename = filename
 
-    def tidyevalue(self):
-        """Create a namedlist of orbital number, orbital name and evalue."""
+    def float(number):
+        """Convert a string to a float avoiding the problem with Ds."""
+        number = number.replace("D","E")
+        return float(number)
 
-        if not hasattr(self,"orbitalname"):
-            self.calcorbitalname()
-
-        numbers = range(len(self.evalue[0]),0,-1)
-        orbitalname = copy.deepcopy(self.orbitalname)
-
-        for x in orbitalname:
-            x.reverse()
-        evalue = copy.deepcopy(self.evalue)
-        for y in evalue:
-            y.reverse()
-        
-        if len(self.HOMO)==1:
-            # Restricted
-            colA = Namedlist("Orbital no.",numbers)
-            colB = Namedlist("Name",orbitalname[0])
-            colC = Namedlist("Eigenvalue (eV)",evalue[0])
-            t = colA + colB + colC
-        else:
-            # Unrestricted
-            colA = Namedlist("Orbital no.",numbers)
-            colB = Namedlist("Alpha Name",orbitalname[0])
-            colC = Namedlist("Alpha Eigenvalue (eV?)",evalue[0])
-            colD = Namedlist("Beta Name",orbitalname[1])
-            colE = Namedlist("Beta Eigenvalue (eV?)",evalue[1])
-            t = colA + colB + colC + colD + colE
-
-        return t
-
-    def calcorbitalname(self):
-        """Calculate the name of each orbital in terms of HOMO/LUMO."""
-
-        self.logger.info("Calculating orbitalname [[]]")
-        self.orbitalname = []
-        for homo in self.HOMO:
-            names = []
-            for i in range(0,len(self.evalue[0])): # i runs over orbital indices
-                if i==homo:
-                    name = "HOMO"
-                elif i==homo+1:
-                    name = "LUMO"
-                elif i>homo:
-                    name = "L + %d" % (i-homo-1)
-                else:
-                    name = "H - %d" % (homo-i)
-                names.append(name)
-            self.orbitalname.append(names)
-                
-    
-    def calcscfprogress(self):
-        """Calculate the progress of the self-consistent field convergence.
-
-        Requires:
-         scfvalue
-         scftarget
-        """
-        self.logger.info("Calculating scfprogress [[]]")
-        answer = []
-        for geom in self.scfvalue:
-            thisgeom = []
-            for scfcycle in range(len(geom[0])):
-                progress = 0
-                for i in range(len(self.scftarget)):
-                    target = self.scftarget[i]
-                    value = geom[i][scfcycle]
-                    if value>target:
-                        progress += math.log(value/target)
-                thisgeom.append(progress)
-            answer.append(thisgeom)
-        self.scfprogress = answer
-
-    def tidyscfprogress(self):
-        """Print out the progress of the self-consistent field convergence."""
-
-        df = Namedlist("Step",range(1,len(self.scfprogress[-1])+1))
-        df += Namedlist("Progress",self.scfprogress[-1])
-
-        return df
-
-    def plotscfprogress(self,filename):
-        """Plot the progress of the SCF optimisation."""
-        self.logger.info("Plotting the progress of the SCF convergence")
-
-        g = Gnuplot(filename)        
-
-        g.data( zip(range(1,len(self.scfprogress[-1])+1),self.scfprogress[-1]),"notitle with lines")
-        g.data( zip(range(1,len(self.scfprogress[-1])+1),self.scfprogress[-1]),"notitle with points")
-
-        g.commands( "set xrange [%d:%d]" % (1,len(self.scfprogress[-1])),
-                    "set yrange [0:]",
-                    "set title 'Progress of the SCF convergence'",
-                    "set xlabel 'Step number",
-                    "set ylabel 'Progress'" )
-
-        g.plot()
-        
-
-    def tidygeoprogress(self):
-        """Print out the progress of the geometry optimisation."""
-
-        df = Namedlist("Step",range(1,len(self.geoprogress)+1))
-        df += Namedlist("Progress",self.geoprogress)
-
-        return df
-                   
-    def calcgeoprogress(self):
-        """Calculate the progress of the geometry optimisation.
-
-        Requires:
-         geovalue
-         geotarget
-        """
-        self.logger.info("Calculating geoprogress []")        
-        answer = []
-        for geom in self.geovalue:
-            progress = 0
-            for i in range(len(self.geotarget)):
-                target = self.geotarget[i]
-                value = geom[i]
-                if value>target:
-                    progress += math.log(value/target)
-            answer.append(progress)
-        self.geoprogress = answer
-
-    def plotgeoprogress(self,filename):
-        """Plot the progress of the geometry optimisation."""
-        self.logger.info("Plotting the progress of the geometry optimisation")
-
-        g = Gnuplot(filename)
-
-        g.data( zip(range(1,len(self.geoprogress)+1),self.geoprogress),"notitle with lines")
-        g.data( zip(range(1,len(self.geoprogress)+1),self.geoprogress),"notitle with points")
-
-        g.commands(  "set xrange [%d:%d]" % (1,len(self.geoprogress)),
-                     "set yrange [0:]",
-                     'set title "Progress of the geometry optimisation"',
-                     'set xlabel "Step number"',
-                     'set ylabel "Progress"' )
-                    
-        g.plot()
-
-
-    def tidyirspectrum(self):
-        """Print out the IR spectrum."""
-
-        df = Namedlist("Energy (cm-1)",self.irspectrum.xvalues)
-        df += Namedlist("Intensity",self.irspectrum.spectrum[:,0])
-
-        return df
-
-    def plotirspectrum(self,filename):
-        """Plot the IR spectrum."""
-
-        self.logger.info("Plotting the IR spectrum")
-        
-        start = self.irspectrum.start
-        end = self.irspectrum.end
-
-        g = Gnuplot(filename)
-
-        g.data( zip(self.irspectrum.xvalues,self.irspectrum.spectrum[:,0]),"notitle with lines")
-
-        g.commands( "set xlabel 'Frequency (cm-1)'",
-                    "set ylabel 'IR activity'",
-                    "set xrange [%f:%f] reverse" % (start,end),
-                    "set yrange [*:*] reverse",
-                    "set key bottom",
-                    "set title 'IR spectrum'" )
-        
-        g.plot()
-
-    def tidyramanspectrum(self):
-        """Print out the Raman spectrum."""
-
-        df = Namedlist("Energy (cm-1)",self.ramanspectrum.xvalues)
-        df += Namedlist("Intensity",self.ramanspectrum.spectrum[:,0])
-
-        return df
-
-    def plotramanspectrum(self,filename):
-        """Plot the Raman spectrum."""
-
-        self.logger.info("Plotting the Raman spectrum")
-        
-        start = self.ramanspectrum.start
-        end = self.ramanspectrum.end
-
-        g = Gnuplot(filename)
-
-        g.data( zip(self.ramanspectrum.xvalues,self.ramanspectrum.spectrum[:,0]),"notitle with lines")
-
-        g.commands( "set xlabel 'Frequency (cm-1)'",
-                    "set ylabel 'Raman activity'",
-                    "set title 'Raman spectrum'" )
-        
-        g.plot()
-
-    def tidyuvspectrum(self):
-        """Print out the UV spectrum."""
-
-        df = Namedlist("Energy (cm-1)",self.uvspectrum.xvalues)
-        df += Namedlist("Wavelength (nm)",
-                        [convertor(x,"cm-1","nm") for x in self.uvspectrum.xvalues])
-        df += Namedlist("Oscillator strength", self.uvspectrum.spectrum[:,0])
-
-        return df    
-
-
-    def calcuvspectrum(self):
-        """Convolute the UV spectrum.
-
-        Requires:
-         etenergy
-         etosc
-        """
-        self.logger.info("Calculating uvspectrum 'GaussianSpectrum'")        
-        # UV spectrum is Gaussian in *energy* not *wavelength*
-        start = convertor(self.pref['uvvis.start'],"nm","cm-1")
-        end = convertor(self.pref['uvvis.end'],"nm","cm-1")
-        
-        t = GaussianSpectrum(start,end,self.pref['uvvis.numpoints'],
-                             ( self.etenergy,[[x*2.174e8/self.pref['uvvis.fwhm'] for x in self.etosc]] ),
-                             self.pref['uvvis.fwhm'])
-        self.uvspectrum = t
-
-    def plotuvspectrum(self,filename):
-        """Plot the UV spectrum."""
-
-        self.logger.info("Plotting the UV spectrum")
-        wavelen = [convertor(x,"cm-1","nm") for x in self.uvspectrum.xvalues]
-        start = convertor(self.uvspectrum.start,"cm-1","nm")
-        end = convertor(self.uvspectrum.end,"cm-1","nm")
-
-        g = Gnuplot(filename)
-
-        g.data( zip(wavelen,self.uvspectrum.spectrum[:,0]),"notitle with lines")
-        g.data( zip(self.etwavelen,self.etosc),"notitle axes x1y2 with impulses")
-
-        g.commands(  "set xrange [%f:%f]" % (start,end),
-                     "set ytics nomirror",
-                     "set y2tics",
-                     'set title "UV spectrum"',
-                     'set ylabel "Epsilon"',
-                     'set y2label "Oscillator strength"' )
-
-        g.plot()
-    
-
-    def calcirspectrum(self):
-        """Convolute the IR spectrum.
-
-        Requires:
-         vibfreq
-         ir
-        """
-        self.logger.info("Calculating irspectrum 'Spectrum'")                
-        # IR spectrum is Lorentzian in energy
-        start = self.pref['ir.start']
-        end = self.pref['ir.end']
-        
-        t = Spectrum(start,end,self.pref['ir.numpoints'],
-                     [zip(self.vibfreq,self.ir)],
-                     self.pref['ir.fwhm'], lorentzian)
-        self.irspectrum = t
-
-    def calcramanspectrum(self):
-        """Convolute the Raman spectrum.
-
-        Requires:
-         vibfreq
-         raman
-        """
-        self.logger.info("Calculating ramanspectrum 'Spectrum'")                
-        # Raman spectrum is Lorentzian in energy
-        start = self.pref['raman.start']
-        end = self.pref['raman.end']
-        
-        t = Spectrum(start,end,self.pref['raman.numpoints'],
-                     [zip(self.vibfreq,self.raman)],
-                     self.pref['raman.fwhm'], lorentzian)
-        self.ramanspectrum = t
-
-
-    def calcpdos(self):
-        """Calculate the contribution of various groups to each orbital.
-
-        Requires:
-         mocoeff
-         overlap
-
-        Optional:
-         groups (defaults to "allorbitals")
-        """
-        self.logger.info("Calculating pdos")
-        # contrib is a matrix of the contributions of each basis fn to each MO
-        # dot() is matrix multiplication
-        #  * is tensor multiplication(?): corresponding entries are multiplied
-        contrib = self.mocoeff * Numeric.dot(self.mocoeff,self.overlap)
-
-        if not hasattr(self,"groups"):
-            self.groups = Groups(self.orbitals,type="allorbitals")
-
-        groups = self.groups.groups
-        groupnames = groups.keys()
-        data = Numeric.zeros( (self.NBsUse,len(groups)), "float")
-
-        for i,groupname in enumerate(groupnames):
-            for basisfn in groups[groupname]:
-                data[:,i] += contrib[:,basisfn]
-
-        self.pdos = data
-
-    def tidypdos(self):
-        """Create a nice dataframe for the pdos."""
-
-        if not hasattr(self,"orbitalname"):
-            self.calcorbitalname()
-        orbitalname = copy.deepcopy(self.orbitalname)
-        for x in orbitalname:
-            x.reverse()
-        evalue = copy.deepcopy(self.evalue)
-        for y in evalue:
-            y.reverse()
-            
-        groupnames = self.groups.groups.keys()
-        numbers = range(len(self.evalue[0]),0,-1)            
-        colA = Namedlist("Orbital number",numbers)
-
-        if len(self.HOMO)==1:
-            # Restricted
-            colB = Namedlist("Name",orbitalname[0])
-            colC = Namedlist("Eigenvalue (eV)",evalue[0])
-            t = colA + colB + colC
-            for i in range(len(groupnames)):
-                groupdata = list(self.pdos[:,i])
-                groupdata.reverse()
-                t += Namedlist(groupnames[i],groupdata)
-        else:
-            # Unrestricted
-            pass
-
-        return t
-
-    def tidydosspectrum(self):
-        """Print the dos spectrum nicely."""
-
-        df = Namedlist("Energy (eV)",self.dosspectrum[0].xvalues)
-        for i,spectrum in enumerate(self.dosspectrum):
-            name = "DOS"
-            if len(self.HOMO)==2:
-                name = ["Alpha DOS","Beta DOS"] [i]
-            df += Namedlist(name, spectrum.spectrum[:,i])
-
-        return df
-
-    def plotdosspectrum(self,filename):
-        """Plot the DOS spectrum."""
-
-        self.logger.info("Plotting the DOS spectrum")
-        
-        start = self.dosspectrum[0].start
-        end = self.dosspectrum[0].end
-
-        g = Gnuplot(filename)
-
-        g.data( zip(self.dosspectrum[0].xvalues,self.dosspectrum[0].spectrum[:,0]),'title "DOS spectrum"')
-        # HOMO holds the index of the HOMO in evalue
-        realorbs = [ (x,-1) for x in self.evalue[0][:self.HOMO[0]+1] ]
-        virtorbs = [ (x,-1) for x in self.evalue[0][self.HOMO[0]+1:] ]
-        g.data(realorbs,'title "Occupied orbitals" with impulses')
-        g.data(virtorbs,'title "Virtual orbitals" with impulses')
-        
-        g.commands(  "set data style lines",
-                     "set xlabel 'Energy (eV)'",
-                     "set xrange [%f:%f]" % (start,end),
-                     "set yrange [-1:*]",
-                     'set title "Density of states spectrum"' )
-        
-        g.plot()
-   
-
-    def calcdosspectrum(self):
-        """Convolute the density of states spectrum."""
-        self.logger.info("Calculating dosspectrum")
-        self.dosspectrum = []
-
-        for i in range(len(self.HOMO)):
-             t = GaussianSpectrum(self.pref['dos.start'],self.pref['dos.end'],self.pref['dos.numpoints'],
-                                 ( self.evalue[i], [[1]*len(self.evalue[i])]),
-                                 self.pref['dos.fwhm'])
-             self.dosspectrum.append(t)
-
-    def tidypdosspectrum(self):
-        """Make a nice print out of the pdosspectrum."""
-
-        groups = self.groups.groups
-        groupnames = groups.keys()
-
-        df = Namedlist("Energy (eV)",self.pdosspectrum[0].xvalues)
-        for i,spectrum in enumerate(self.pdosspectrum):
-            prefix = ""
-            if len(self.HOMO)==2:
-                prefix = ["Alpha","Beta"] [i]
-            df += Namedlist([prefix+x for x in groupnames], spectrum.spectrum)
-
-        return df
-
-    def plotpdosspectrum(self,filename,stacked=False):
-        """Plot the PDOS spectrum."""
-
-        self.logger.info("Plotting the PDOS spectrum")
-        
-        start = self.pdosspectrum[0].start
-        end = self.pdosspectrum[0].end
-
-        g = Gnuplot(filename)
-
-        tot = Numeric.zeros( len(self.pdosspectrum[0].xvalues),"double" )
-        for i,v in enumerate(self.groups.groups.keys()):
-            g.data( zip(self.pdosspectrum[0].xvalues,tot+self.pdosspectrum[0].spectrum[:,i]),                    'title "%s"' % v)
-            if stacked:
-                tot += self.pdosspectrum[0].spectrum[:,i]
-        
-        # HOMO holds the index of the HOMO in evalue
-        realorbs = [ (x,-1) for x in self.evalue[0][:self.HOMO[0]+1] ]
-        virtorbs = [ (x,-1) for x in self.evalue[0][self.HOMO[0]+1:] ]
-        g.data(realorbs,'title "Occupied orbitals" with impulses')
-        g.data(virtorbs,'title "Virtual orbitals" with impulses')
-        
-        g.commands( "set data style lines",
-                    "set xlabel 'Energy (eV)'",
-                    "set xrange [%f:%f]" % (start,end),
-                    "set yrange [-1:*]",
-                    'set title "Partial density of states spectrum"' )
-        g.plot()
-
-        
-    def calcpdosspectrum(self):
-        """Convolute the partial density of states spectrum."""
-        self.logger.info("Calculating pdosspectrum")
-        
-        self.pdosspectrum = []
-        groups = self.groups.groups
-        groupnames = groups.keys()
-
-        if len(self.HOMO)==1:
-            # Restricted
-            peaks = ( self.evalue[0],[self.pdos[:,x] for x in range(len(groups))] )
-            t = GaussianSpectrum(self.pref['dos.start'],self.pref['dos.end'],self.pref['dos.numpoints'],
-                         peaks,self.pref['dos.fwhm'])
-            self.pdosspectrum.append(t)
-        else:
-            # Unrestricted
-            peaks = ( self.evalue[0],[self.pdos[0][:,x] for x in range(len(groups))] )
-            t = GaussianSpectrum(self.pref['dos.start'],self.pref['dos.end'],self.pref['dos.numpoints'],
-                         peaks,self.pref['dos.fwhm'])
-            self.pdosspectrum.append(t)
-            peaks = ( self.evalue[1],[self.pdos[1][:,x] for x in range(len(groups))] )
-            t = GaussianSpectrum(self.pref['dos.start'],self.pref['dos.end'],self.pref['dos.numpoints'],
-                         peaks,self.pref['dos.fwhm'])
-            self.pdosspectrum.append(t)
-            
-
-        
 class G03(Logfile):
     """A Gaussian 03 log file
     
@@ -540,11 +78,6 @@
     SCFRMS,SCFMAX,SCFENERGY = range(3) # Used to index self.scftarget[]
     def __init__(self,filename):
 
-        self.filename = filename
-
-        # Set up the preferences (with the default values)
-        self.pref = Preferences()
-        
         # Set up the logger...
         # Note: all loggers with the same name share the logger.
         # Here, loggers with different filenames are different
@@ -612,11 +145,11 @@
                 if not hasattr(self,"scftarget"):
                     self.logger.info("Creating attribute scftarget[]")
                 self.scftarget = [None]*3
-                self.scftarget[G03.SCFRMS] = G03.float(line.split('=')[1].split()[0])
+                self.scftarget[G03.SCFRMS] = self.float(line.split('=')[1].split()[0])
             if line[1:44]=='Requested convergence on MAX density matrix':
-                self.scftarget[G03.SCFMAX] = G03.float(line.strip().split('=')[1][:-1])
+                self.scftarget[G03.SCFMAX] = self.float(line.strip().split('=')[1][:-1])
             if line[1:44]=='Requested convergence on             energy':
-                self.scftarget[G03.SCFENERGY] = G03.float(line.strip().split('=')[1][:-1])
+                self.scftarget[G03.SCFENERGY] = self.float(line.strip().split('=')[1][:-1])
 
             if line[1:10]=='Cycle   1':
 # Extract SCF convergence information (QM calcs)
@@ -630,15 +163,15 @@
                         self.logger.debug(line)
                     if line.find(" RMSDP")==0:
                         parts = line.split()
-                        newlist[G03.SCFRMS].append(G03.float(parts[0].split('=')[1]))
-                        newlist[G03.SCFMAX].append(G03.float(parts[1].split('=')[1]))
+                        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 = G03.float(parts[3])
+                                energy = self.float(parts[3])
                             else:
-                                energy = G03.float(energy)
+                                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)
@@ -658,7 +191,7 @@
                 while line.find(" Energy")==-1:
                     self.logger.debug(line)
                     parts = line.strip().split()
-                    self.scfvalue[0].append(G03.float(parts[-1][:-1]))
+                    self.scfvalue[0].append(self.float(parts[-1][:-1]))
                     line = inputfile.next()
 
             if line[1:9]=='SCF Done':
@@ -684,12 +217,12 @@
                     self.logger.debug(line)
                     parts = line.split()
                     try:
-                        value = G03.float(parts[2])
+                        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.geotarget[i] = G03.float(parts[3])
+                    self.geotarget[i] = self.float(parts[3])
                 self.geovalue.append(newlist)
 
             if line[1:19]=='Orbital symmetries' and not hasattr(self,"orbsym"):
@@ -744,7 +277,7 @@
                     i = 0
                     while i*10+4<len(part):
                         x = part[i*10:(i+1)*10]
-                        self.evalue[0].append(G03.float(x)*27.2114) # from a.u. (hartrees) to eV
+                        self.evalue[0].append(self.float(x)*27.2114) # from a.u. (hartrees) to eV
                         i += 1
                     line = inputfile.next()            
                 if line.find('Beta')==2:
@@ -765,7 +298,7 @@
                     i = 0
                     while i*10+4<len(part):
                         x = part[i*10:(i+1)*10]
-                        self.evalue[1].append(G03.float(x)*27.2114) # from a.u. (hartrees) to eV
+                        self.evalue[1].append(self.float(x)*27.2114) # from a.u. (hartrees) to eV
                         i += 1
                     line = inputfile.next()   
 
@@ -786,17 +319,17 @@
                     self.logger.debug(line)
                     self.vibsym.extend(line.split()) # Adding new symmetry
                     line = inputfile.next()
-                    self.vibfreq.extend(map(G03.float,line[15:].split())) # Adding new frequencies
+                    self.vibfreq.extend(map(self.float,line[15:].split())) # Adding new frequencies
                     [inputfile.next() for i in [0,1]] # Skip two lines
                     line = inputfile.next()
-                    self.ir.extend(map(G03.float,line[15:].split())) # Adding IR intensities
+                    self.ir.extend(map(self.float,line[15:].split())) # Adding IR intensities
                     line = inputfile.next()
                     if line.find("Raman")>=0:
                         if not hasattr(self,"raman"):
                             self.raman = []
                             self.logger.info("Creating attribute raman[]")
                         line = inputfile.next()
-                        self.raman.extend(map(G03.float,line[15:].split())) # Adding Raman intensities
+                        self.raman.extend(map(self.float,line[15:].split())) # Adding Raman intensities
                     line = inputfile.next()
                     while len(line[:15].split())>0:
                         line = inputfile.next()
@@ -818,9 +351,9 @@
                 # Excited State   2:   ?Spin  -A      0.1222 eV 10148.75 nm  f=0.0000
                 parts = line[36:].split()
                 self.logger.debug(parts)
-                self.etenergy.append(convertor(G03.float(parts[0]),"eV","cm-1"))
-                self.etwavelen.append(G03.float(parts[2]))
-                self.etosc.append(G03.float(parts[4].split("=")[1]))
+                self.etenergy.append(convertor(self.float(parts[0]),"eV","cm-1"))
+                self.etwavelen.append(self.float(parts[2]))
+                self.etosc.append(self.float(parts[4].split("=")[1]))
                 self.etsym.append(line[21:36].split())
                 
                 line = inputfile.next()
@@ -846,7 +379,7 @@
                         tomoindex = 1
                     toMO = int(p.match(toMO).group())
 
-                    percent = G03.float(t[1])
+                    percent = self.float(t[1])
                     sqr = percent**2*2 # The fractional contribution of this CI
                     if percent<0:
                         sqr = -sqr
@@ -865,7 +398,7 @@
                 parts = line.strip().split()
                 while len(parts)==5:
                     try:
-                        R = G03.float(parts[-1])
+                        R = self.float(parts[-1])
                     except ValueError:
                         # nan or -nan if there is no first excited state
                         # (for unrestricted calculations)
@@ -973,18 +506,7 @@
                  
         inputfile.close()
 
-        
-#    @staticmethod
-    def float(number):
-        """Convert a string to a float."""
-        try:
-            ans = float(number)
-        except ValueError:
-            number = "E".join(number.split("D"))
-            ans = float(number)
-        return ans
-    float = staticmethod(float)
-    
+# 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")
@@ -997,7 +519,7 @@
                     line = inputfile.next()
                     parts = line.strip().split()
                     # Conversion from a.u. to Angstrom
-                    coords.append([ G03.float(x)*0.5292 for x in [parts[3],parts[5],parts[7]] ])
+                    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()
@@ -1010,33 +532,6 @@
         inputfile.close()
         assert len(self.traj)==len(self.trajSummary)
         
-    def writeTrajectory(self,outputfilename):
-        """Write trajectory information to a quasi-PDB file."""
-        outputfile = open(outputfilename,"w")
-        pt = PeriodicTable()
-        for i in range(len(self.traj)):
-            for j in range(self.NAtoms):
-                line = "HETATM %4d %2s   UNK            % .3f  % .3f  % .3f  0.00  0.00          %2s\n" % (j+1,pt.element[self.atomicNo[j]],self.traj[i][j][0],self.traj[i][j][1],self.traj[i][j][2],pt.element[self.atomicNo[j]])
-                outputfile.write(line)
-            if hasattr(self,"connect"):
-                for k,v in self.connect[i].iteritems():
-                    line = "CONECT %4d" % (k+1)
-                    for value in v:
-                        line += " %4d" % (value+1)
-                    outputfile.write(line+"\n")
-                    
-            outputfile.write("END\n")
-        outputfile.close()
-
-    def writeTrajectorySummary(self,outputfilename):
-        """Write trajectory summary information to TSF."""
-        outputfile = open(outputfilename,"w")
-        header = "\t".join(["Time (fs)","Kinetic (au)","Potent (au)","Delta E (au)","Delta A (h-bar)"])
-        outputfile.write(header+"\n")
-        for x in self.trajSummary:
-            outputfile.write("\t".join(x)+"\n")
-        outputfile.close()
-
 if __name__=="__main__":
     import doctest,parser
     doctest.testmod(parser,verbose=False)



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