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Re: [cclib-users] cclib.method -- Problem solved
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From: Adam T. <ate...@gm...> - 2012-02-25 21:17:51
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Hi Frank,
Thanks for hunting down this problem and letting us know about it. Since your code will only handle up to 199 atoms, I'll modify it a bit to make it more flexible. Unfortunately, without a proper test file, I have no way of ensuring it works.
Thanks again,
Adam
On Feb 18, 2012, at 2:46 PM, Frank wrote:
> 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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