[cclib-devel] Parsing GAMESS Force Matrix

[Mark M. <mo...@oc...>]

Hi Karol,

Your fix for exam17 works great! I went ahead and wrote a parsing
routine to parse the Force Constant Matrix of a GAMESS output file. Not
sure if your interested in adding it to your code. It is pasted at the
end of the message.

Mark

Code to put in gamessparser.py:
The below parsing routine creates a numpy matrix and fills it with the
force constant values in the GAMESS output file.
Numpy matrices don't like to be sparse, so I padded the matrix with
blank entries to make it square. 
When those blanks are set to a float in arrayify in data.py an error
occurs. 
The hessian _attrtypes needs to be changed to list to fix the error.


# MJM-----------
        if line.find("CARTESIAN FORCE CONSTANT MATRIX") >= 0:

            self.logger.info("Creating attribute hessian")

            for i in range(1,7):
                line = inputfile.next()

            hessx = []
            hessy =[]
            hessz = []
            while line.find("--") < 0:

index=int(line[0:3])-1                                                 
                if len(hessx) <= index:
                    hessx.insert(index,[])
                    hessy.insert(index,[])
                    hessz.insert(index,[])
                hessx[index].extend([line[20:29].strip(),
line[29:38].strip(),
                    line[38:47].strip(), line[47:56].strip(),
                    line[56:65].strip(),line[65:74].strip()])
                line = inputfile.next()
                hessy[index].extend([line[20:29].strip(),
line[29:38].strip(),
                    line[38:47].strip(), line[47:56].strip(),
                    line[56:65].strip(),line[65:74].strip()])
                line = inputfile.next()
                hessz[index].extend([line[20:29].strip(),
line[29:38].strip(),
                    line[38:47].strip(), line[47:56].strip(),
                    line[56:65].strip(),line[65:74].strip()])
                line = inputfile.next()
                
                if line.isspace():
                    for i in range(1,5):
                        line = inputfile.next()
                        if line.find("--") >= 0:
                            break

            longest=0
            for x in hessx[:]:
                if len(x) > longest:
                    longest=len(x)
            for i in range(0,len(hessx)):
                for j in range(0,longest-len(hessx[i])):
                    hessx[i].append('')
                    hessy[i].append('')
                    hessz[i].append('')

            self.hessian=numpy.vstack((hessx[0],hessy[0],hessz[0]))
            for i in range(1,len(hessx)):
                self.hessian=numpy.vstack([self.hessian,hessx[i],
                    hessy[i],hessz[i]])
    


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