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

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

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

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

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

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


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