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Re: [cclib-users] cclib.method -- Problem solved
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From: Frank <fra...@gm...> - 2012-02-18 22:46:10
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Hi, folks.
I finally nailed it down.
Here is the root problem: cclib (the current released version) cannot parse
the log file of system with natom >= 100.
In the log file for the Eigenvalues/MOs:
518 H 98 S -0.000000 0.000000 -0.000000 -0.000000 -0.000000
519 C 99 S -0.000000 0.000000 -0.000000 -0.000000 -0.000000
520 C 99 S -0.000000 0.000000 -0.000000 -0.000000 -0.000000
521 C 99 X -0.000000 0.000000 -0.000000 -0.000000 -0.000000
522 C 99 Y -0.000000 0.000000 -0.000000 -0.000000 -0.000000
523 C 99 Z -0.000000 0.000000 -0.000000 -0.000000 -0.000000
524 H 0 S -0.000000 0.000000 -0.000000 -0.000000 -0.000000
525 H 1 S -0.000000 0.000000 -0.000000 -0.000000 -0.000000
526 C 2 S -0.000000 0.000000 -0.000000 -0.000000 -0.000000
The number of atoms are recorded as 0, 1, ..., instead of 100/200/...,
101/201/..., which is however problematic in calculating CSPA.
My resolution is: introducing a switch to monitor this change. The
corresponding code, in gamessparser.py is partially copied in the following:
LINE 714:
p = re.compile("(\d+)\s*([A-Z][A-Z]?)\s*(\d+)\s*([A-Z]+)")
oldatom ='0'
i_atom = 0 #couter to translate to 0s to some
hundreds, by C.W.
flag_w = True #Flag to whether
for i in range(self.nbasis):
line = inputfile.next()
# If line is empty, break (ex. for FMO in exam37).
if not line.strip(): break
# Fill atombasis and aonames only first time around
if readatombasis and base == 0:
aonames = []
start = line[:17].strip()
m = p.search(start)
if m:
g = m.groups()
g2 = int(g[2]) #atom index from GAMESS's log
file
if g2 == 0 and flag_w:
#c.w.
i_atom = i_atom + 100 #c.w
flag_w = False
if g2 != 0:
flag_w = True
g2 = g2 + i_atom #c.w.
aoname = "%s%s_%s" % (g[1].capitalize(),
str(g2), g[3]) #c.w.
# aoname = "%s%s_%s" % (g[1].capitalize(), g[2],
g[3])
oldatom = str(g2) #c.w.
atomno = g2 - 1 #c.w.
# oldatom = g[2]
# atomno = int(g[2])-1
orbno = int(g[0])-1
else: # For F orbitals, as shown above
g = [x.strip() for x in line.split()]
g2 = int(g[2]) #atom index from GAMESS's log
file
if g2 == 0 and flag_w:
#c.w.
i_atom = i_atom + 100 #c.w.
flag_w = False #c.w.
if g2 != 0: #c.w.
flag_w = True #c.w.
g2 = g2 + i_atom #c.w.
# aoname = "%s%s_%s" % (g[1].capitalize(),
oldatom, g[2])
aoname = "%s%s_%s" % (g[1].capitalize(),
oldatom, str(g2))
atomno = int(oldatom)-1
orbno = int(g[0])-1
self.atombasis[atomno].append(orbno)
self.aonames.append(aoname)
coeffs = line[15:] # Strip off the crud at the start.
j = 0
while j*11+4 < len(coeffs):
self.mocoeffs[0][base+j, i] = float(coeffs[j *
11:(j + 1) * 11])
j += 1
line = inputfile.next()
Enjoy!
Best.
Frank
On Fri, Jan 13, 2012 at 2:20 AM, Chengju Wang
<fra...@gm...>wrote:
> Hi, Adam and other folks.
>
> Attached please find the requested file, which was given by
> "
> >>> f=open("aonames.txt",'w')
> >>> import pickle
> >>> pickle.dump(ps.aonames,f)
> >>> f.close()
> "
> following the previous email.
>
> By tail this file, one will get
> " tail aonames.txt
> p3711
> aS'H40_S'
> p3712
> aS'H40_X'
> p3713
> aS'H40_Y'
> p3714
> aS'H40_Z'
> p3715
> a."
>
> This file is incomplete. I think this is problem but I don't how to solve
> it. :P
>
> thanks for your attention.
>
> Best.
>
> Chengju
>
>
> On Wed, Jan 4, 2012 at 3:24 PM, Adam Tenderholt <ate...@gm...>wrote:
>
>> Hi Chengju,
>>
>> Sorry for the late reply. Your error is a bit odd, and I'm not sure
>> where the code is failing. Can you send us the aonames parsed by
>> cclib? If that's not available, send fonames.
>>
>> Cheers,
>>
>> Adam
>>
>>
>> On Thu, Dec 29, 2011 at 9:30 PM, Chengju Wang
>> <fra...@gm...> wrote:
>> > Dear all.
>> >
>> > I hope someone here can help me to analysis my GAMESS log file. Thank
>> you.
>> >
>> > I tried to use cclib to extract the pdos, but have met with
>> the following
>> > problem.
>> >
>> > >>> from cclib.parser import GAMESS
>> > >>> from cclib.method import CSPA
>> > >>> s=GAMESS("test.log")
>> > >>> ps=s.parse()
>> > [GAMESS test.log INFO] Creating attribute atomcoords[]
>> > [GAMESS test.log INFO] Creating attribute atomnos[]
>> > [GAMESS test.log INFO] Creating attribute gbasis[]
>> > [GAMESS test.log INFO] Creating attribute nbasis: 2343
>> > [GAMESS test.log INFO] Creating attribute charge: 0
>> > [GAMESS test.log INFO] Creating attribute mult: 1
>> > [GAMESS test.log INFO] Creating attribute homos[]
>> > [GAMESS test.log INFO] Creating attribute natom: 340
>> > [GAMESS test.log INFO] Creating attribute aooverlaps[]
>> > [GAMESS test.log INFO] Creating attribute scftargets[]
>> > [GAMESS test.log INFO] Creating attribute scfvalues[]
>> > [GAMESS test.log INFO] Creating attribute scfenergies[]
>> > [GAMESS test.log INFO] Creating attribute moenergies[]
>> > [GAMESS test.log INFO] Creating attribute mosyms[]
>> > [GAMESS test.log INFO] Creating attribute nmo: 2343
>> > [GAMESS test.log INFO] Creating attribute mocoeffs[]
>> > [GAMESS test.log INFO] Creating attribute atombasis[]
>> > [GAMESS test.log INFO] Creating attribute aonames[]
>> > [GAMESS test.log INFO] Creating attribute coreelectrons[]
>> > >>> m=CSPA(ps)
>> > >>>>>> len(m.fragresults[0])
>> > 2343
>> > >>> len(m.fragresults[0][0])
>> > 204
>> >
>> > Why is it not 340 here?
>> >
>> >
>> > Sorry, the log file is too big to be attached.
>> >
>> >
>> > My input key words:
>> >
>> > $CONTRL SCFTYP=RHF RUNTYP=ENERGY MAXIT=60 MULT=1 $END
>> > $CONTRL MOLPLT=.TRUE. PLTORB=.TRUE. NPRINT=3 $END
>> > $SYSTEM TIMLIM=525600 MWORDS=9000 $END
>> > $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END
>> > $SCF DIRSCF=.TRUE. $END
>> > $STATPT OPTTOL=0.0001 NSTEP=2000 $END
>> > $DATA
>> >
>> > There is no such problem found for my testing runs on smaller systems
>> > (~100), i.e.: len(m.fragresults[0][0] always equals to natom.
>> >
>> >
>> >
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>>
>
>
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