cclib-users — Help and support for cclib users

Re: [cclib-users] cclib-users Digest, Vol 34, Issue 1

[Edward H. <hol...@ca...>]

Hi Yishen,

Its only in a very recent patch we have added any support for thermochemistry data. Currently it only supports gaussian and only collects free energy, enthalpy, entropy and temperature, although it would be fairly easy to patch to also collect ZPE if people feel thats important.
If you want to collect thermochem data you will need to checkout a development version from the SVN hosted on source forge.

Yours

Ed Holland

On 14 May 2012, at 13:04, ccl...@li... wrote:

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> Today's Topics:
> 
>   1. [Question] Finding Thermchemistry Data (Yishen Miao)
> 
> From: Yishen Miao <mys...@gm...>
> Subject: [cclib-users] [Question] Finding Thermchemistry Data
> Date: 14 May 2012 08:39:52 GMT+01:00
> To: ccl...@li...
> 
> 
> Hello everyone,
> 
> I am trying to use cclib to parsing logs from Gaussian 09. However, after running mydata = myfile.parse() , I find I am not able to find thermchemistry data like zero-point energy from mydata's attributes. Could you please tell me how to find those data?
> 
> Thanks!
> Yishen Miao
> 
> 
> 
> 
> 
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[cclib-users] [Question] Finding Thermchemistry Data

[Yishen M. <mys...@gm...>]

Hello everyone,

I am trying to use cclib to parsing logs from Gaussian 09. However, after running mydata = myfile.parse() , I find I am not able to find thermchemistry data like zero-point energy from mydata's attributes. Could you please tell me how to find those data?

Thanks!
Yishen Miao

Re: [cclib-users] cclib.method -- Problem solved

[Chengju W. <fra...@gm...>]

Thanks. I am not familiar with SVN. Does it not mean that we will have
the capability in the next released version?

Benefited a lot from cclib. Thanks.

Frank

Sent from my Windows Phone
From: Adam Tenderholt
Sent: 2/25/2012 2:25 PM
To: Frank
Cc: ccl...@li...
Subject: Re: [cclib-users] cclib.method -- Problem solved
Ah, I just realized your code does handle past 199; I didn't see the
part where you reset flag_w to True. I'll add your changes to the SVN
trunk now.

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.
> >
> >
> >
> > ------------------------------------------------------------------------------
> > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> > infrastructure or vast IT resources to deliver seamless, secure access to
> > virtual desktops. With this all-in-one solution, easily deploy virtual
> > desktops for less than the cost of PCs and save 60% on VDI infrastructure
> > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
>
>

Re: [cclib-users] cclib.method -- Problem solved

[Adam T. <ate...@gm...>]

Ah, I just realized your code does handle past 199; I didn't see the part where you reset flag_w to True. I'll add your changes to the SVN trunk now.

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.
> >
> >
> >
> > ------------------------------------------------------------------------------
> > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> > infrastructure or vast IT resources to deliver seamless, secure access to
> > virtual desktops. With this all-in-one solution, easily deploy virtual
> > desktops for less than the cost of PCs and save 60% on VDI infrastructure
> > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> 
> 

Re: [cclib-users] cclib.method -- Problem solved

[Adam T. <ate...@gm...>]

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.
> >
> >
> >
> > ------------------------------------------------------------------------------
> > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> > infrastructure or vast IT resources to deliver seamless, secure access to
> > virtual desktops. With this all-in-one solution, easily deploy virtual
> > desktops for less than the cost of PCs and save 60% on VDI infrastructure
> > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> 
> 

Re: [cclib-users] cclib.method -- Problem solved

[Frank <fra...@gm...>]

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.
>> >
>> >
>> >
>> > ------------------------------------------------------------
>> ------------------
>> > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a
>> complex
>> > infrastructure or vast IT resources to deliver seamless, secure access
>> to
>> > virtual desktops. With this all-in-one solution, easily deploy virtual
>> > desktops for less than the cost of PCs and save 60% on VDI
>> infrastructure
>> > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>> > _______________________________________________
>> > cclib-users mailing list
>> > ccl...@li...
>> > https://lists.sourceforge.net/lists/listinfo/cclib-users
>> >
>>
>
>

Re: [cclib-users] A question about LPA

[Karol M. L. <kar...@gm...>]

Hi,

The differences are just due to me using an ultra-stable isntallation
on this particular computer. I will test with newer version on
another machine (probably tommorrow).

- Karol

On Jan 27 2012, Martin Rahm wrote:
> Hi Karol,
> 
> Interesting. I'm using Python 2.7.1, so different but newer than yours,
> with GCC 4.2.1, if that matters. cclib is 1.01 (the latest), and finally,
> Numpy 1.5.1, which also is newer than yours.
> 
> It's all on a OS X 10.6.8 machine.
> 
> Clearly there are some external differences, however, going back to older
> versions are cumbersome. Does this mean one always have to use older
> packages to be sure, or is there a possibility to make cclib work with the
> new ones?
> 
> Thanks again for your hard work & with best regards,
> Martin
> 
> On Fri, Jan 27, 2012 at 4:51 PM, Karol M. Langner
> <kar...@gm...>wrote:
> 
> > Hi Martin,
> >
> > I've come around to this issue. First of all, in this case I don't get
> > the complex number error your report, and my fragcharges sum up nicely.
> > That is a good thing, because it means the cause is perhaps external
> > to cclib.
> >
> > I'm using Python 2.6 here, but I assume that would not be a problem.
> > My NumPy version is 1.4.1 and I'm using the latest cclib revision from svn.
> > What are your version?
> >
> > - Karol
> >
> > On Jan 12 2012, Martin Rahm wrote:
> > > Hello again,
> > >
> > > I've come across another case of the "complex number" error. This time
> > in a
> > > very small diatomic.
> > >
> > > Running LPA on a M062X/cc-pwCV5Z wave function of ClF, and gets this
> > error:
> > >
> > > [LPA <cclib.parser.data.ccData object at 0x1015ba1d0> INFO] Creating
> > > attribute aoresults: [array[2]]
> > >
> > /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
> > > ComplexWarning: Casting complex values to real discards the imaginary
> > part
> > >   self.aoresults[spin][i] = numpy.multiply(temp1, temp2).astype("d")
> > >
> > > This is quite cumbersome, since there is really no way of breaking
> > symmetry
> > > of a linear molecule (which solved the problem for larger molecules)!
> > >
> > > I've attached my log file, and also my script just in case.
> > >
> > > I hope you have a quick fix :)
> > >
> > > Best regards,
> > > Martin
> >
> > > Archive:  /tmp/ClF-M06-cc-pwCV5Z.log.zip
> > >   Length      Date    Time    Name
> > > ---------  ---------- -----   ----
> > >   8430472  2012-01-11 09:10   ClF-M06-cc-pwCV5Z.log
> > > ---------                     -------
> > >   8430472                     1 file
> >
> >
> > >
> > ------------------------------------------------------------------------------
> > > RSA(R) Conference 2012
> > > Mar 27 - Feb 2
> > > Save $400 by Jan. 27
> > > Register now!
> > > http://p.sf.net/sfu/rsa-sfdev2dev2
> >
> > > _______________________________________________
> > > cclib-users mailing list
> > > ccl...@li...
> > > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> >
> > --
> > written by Karol Langner
> > Sat Jan 28 01:46:35 CET 2012
> >

-- 
written by Karol Langner
Sat Jan 28 03:40:06 CET 2012

Re: [cclib-users] A question about LPA

[Martin R. <mar...@gm...>]

Hi Karol,

Interesting. I'm using Python 2.7.1, so different but newer than yours,
with GCC 4.2.1, if that matters. cclib is 1.01 (the latest), and finally,
Numpy 1.5.1, which also is newer than yours.

It's all on a OS X 10.6.8 machine.

Clearly there are some external differences, however, going back to older
versions are cumbersome. Does this mean one always have to use older
packages to be sure, or is there a possibility to make cclib work with the
new ones?

Thanks again for your hard work & with best regards,
Martin

On Fri, Jan 27, 2012 at 4:51 PM, Karol M. Langner
<kar...@gm...>wrote:

> Hi Martin,
>
> I've come around to this issue. First of all, in this case I don't get
> the complex number error your report, and my fragcharges sum up nicely.
> That is a good thing, because it means the cause is perhaps external
> to cclib.
>
> I'm using Python 2.6 here, but I assume that would not be a problem.
> My NumPy version is 1.4.1 and I'm using the latest cclib revision from svn.
> What are your version?
>
> - Karol
>
> On Jan 12 2012, Martin Rahm wrote:
> > Hello again,
> >
> > I've come across another case of the "complex number" error. This time
> in a
> > very small diatomic.
> >
> > Running LPA on a M062X/cc-pwCV5Z wave function of ClF, and gets this
> error:
> >
> > [LPA <cclib.parser.data.ccData object at 0x1015ba1d0> INFO] Creating
> > attribute aoresults: [array[2]]
> >
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
> > ComplexWarning: Casting complex values to real discards the imaginary
> part
> >   self.aoresults[spin][i] = numpy.multiply(temp1, temp2).astype("d")
> >
> > This is quite cumbersome, since there is really no way of breaking
> symmetry
> > of a linear molecule (which solved the problem for larger molecules)!
> >
> > I've attached my log file, and also my script just in case.
> >
> > I hope you have a quick fix :)
> >
> > Best regards,
> > Martin
>
> > Archive:  /tmp/ClF-M06-cc-pwCV5Z.log.zip
> >   Length      Date    Time    Name
> > ---------  ---------- -----   ----
> >   8430472  2012-01-11 09:10   ClF-M06-cc-pwCV5Z.log
> > ---------                     -------
> >   8430472                     1 file
>
>
> >
> ------------------------------------------------------------------------------
> > RSA(R) Conference 2012
> > Mar 27 - Feb 2
> > Save $400 by Jan. 27
> > Register now!
> > http://p.sf.net/sfu/rsa-sfdev2dev2
>
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>
> --
> written by Karol Langner
> Sat Jan 28 01:46:35 CET 2012
>

Re: [cclib-users] A question about LPA

[Karol M. L. <kar...@gm...>]

Hi Martin,

I've come around to this issue. First of all, in this case I don't get
the complex number error your report, and my fragcharges sum up nicely.
That is a good thing, because it means the cause is perhaps external
to cclib.

I'm using Python 2.6 here, but I assume that would not be a problem.
My NumPy version is 1.4.1 and I'm using the latest cclib revision from svn.
What are your version?

- Karol

On Jan 12 2012, Martin Rahm wrote:
> Hello again,
> 
> I've come across another case of the "complex number" error. This time in a
> very small diatomic.
> 
> Running LPA on a M062X/cc-pwCV5Z wave function of ClF, and gets this error:
> 
> [LPA <cclib.parser.data.ccData object at 0x1015ba1d0> INFO] Creating
> attribute aoresults: [array[2]]
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
> ComplexWarning: Casting complex values to real discards the imaginary part
>   self.aoresults[spin][i] = numpy.multiply(temp1, temp2).astype("d")
> 
> This is quite cumbersome, since there is really no way of breaking symmetry
> of a linear molecule (which solved the problem for larger molecules)!
> 
> I've attached my log file, and also my script just in case.
> 
> I hope you have a quick fix :)
> 
> Best regards,
> Martin

> Archive:  /tmp/ClF-M06-cc-pwCV5Z.log.zip
>   Length      Date    Time    Name
> ---------  ---------- -----   ----
>   8430472  2012-01-11 09:10   ClF-M06-cc-pwCV5Z.log
> ---------                     -------
>   8430472                     1 file


> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Mar 27 - Feb 2
> Save $400 by Jan. 27
> Register now!
> http://p.sf.net/sfu/rsa-sfdev2dev2

> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users


-- 
written by Karol Langner
Sat Jan 28 01:46:35 CET 2012

Re: [cclib-users] A question about LPA

[Adam T. <ate...@gm...>]

Hi Martin,

Thanks for the info and logfile. A fix isn't immediately apparent to
me, so I will (unless Noel or Karol get to it first) have to spend
some time figuring out what is going on. I probably can't get to it
for a few weeks though.

Adam


On Mon, Jan 16, 2012 at 1:00 PM, Martin Rahm <mar...@gm...> wrote:
> Hi Adam,
>
> Unfortunately Int=ultrafine doesn't do anything. Neither does smaller basis
> sets (tried cc-pVTZ and cc-pV5Z). Since the exact same error occurs for Oh
> systems, but goes away upon distortion to C3v, it seems like something else
> is wrong.
>
> Best,
> Martin
>
>
> On Mon, Jan 16, 2012 at 10:43 AM, Adam Tenderholt <ate...@gm...>
> wrote:
>>
>> Hi Martin,
>>
>> Any idea what happens if you use Int=UltraFine? Does this error still
>> appear for the diatomic with smaller basis sets? What about with for
>> cc-pV5Z?
>>
>> Adam
>>
>>
>> On Thu, Jan 12, 2012 at 3:56 PM, Martin Rahm <mar...@gm...>
>> wrote:
>> > Hello again,
>> >
>> > I've come across another case of the "complex number" error. This time
>> > in a
>> > very small diatomic.
>> >
>> > Running LPA on a M062X/cc-pwCV5Z wave function of ClF, and gets this
>> > error:
>> >
>> > [LPA <cclib.parser.data.ccData object at 0x1015ba1d0> INFO] Creating
>> > attribute aoresults: [array[2]]
>> >
>> > /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
>> > ComplexWarning: Casting complex values to real discards the imaginary
>> > part
>> >   self.aoresults[spin][i] = numpy.multiply(temp1, temp2).astype("d")
>> >
>> > This is quite cumbersome, since there is really no way of breaking
>> > symmetry
>> > of a linear molecule (which solved the problem for larger molecules)!
>> >
>> > I've attached my log file, and also my script just in case.
>> >
>> > I hope you have a quick fix :)
>> >
>> > Best regards,
>> > Martin
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > RSA(R) Conference 2012
>> > Mar 27 - Feb 2
>> > Save $400 by Jan. 27
>> > Register now!
>> > http://p.sf.net/sfu/rsa-sfdev2dev2
>> > _______________________________________________
>> > cclib-users mailing list
>> > ccl...@li...
>> > https://lists.sourceforge.net/lists/listinfo/cclib-users
>> >
>
>

Re: [cclib-users] read the log file after HESSIAN calculation by GAMESS

[Karol M. L. <kar...@gm...>]

Hi Chengju,

Thanks for the file and sorry for taking so long. Your file is parsed
correctly as of r951. Enjoy!

It seems GAMESS-US added some extra output to the normal coord. analysis,
including symmetry details which actually caused the problem. Note that
I just added a fix for the parser to not die on this output, but cclib
does not parser the symmetries.

Thanks for your feedback,
Karol

On Dec 17 2011, Chengju Wang wrote:
> Sure, thanks for the prompt response.
> 
> Attached please find the log file I've run into. Since this is a test case
> of water, you are free to do ANYTHING with it.
> 
> 
> Best regards and happy holidays!
> 
> Chengju
> 
> On Sat, Dec 17, 2011 at 2:51 PM, Karol M. Langner
> <kar...@gm...>wrote:
> 
> > Hi Chengju,
> >
> > Could you make the log file available?
> >
> > We need it to test the fix, and we need your consent to redistribute
> > it with our regression suite.
> >
> > If you provide us with the file, there is a good chance the
> > problem will be fixed.
> >
> > Best,
> > Karol
> >
> > On Dec 16 2011, Chengju Wang wrote:
> > > *Hi, everyone.*
> > > *
> > > *
> > > *I'm new to cclib. I just found a 'problem' with cclib. *
> > > *
> > > *
> > > *After run this n_water.inp*
> > >
> > > *!   File created by MacMolPlt 7.4.2*
> > > * $CONTRL SCFTYP=RHF RUNTYP=HESSIAN MAXIT=60 MULT=1 $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 HSSEND=.t. PROJCT=.FALSE. $END*
> > > * $FORCE METHOD=ANALYTIC VIBANL=.TRUE. $END*
> > > * $DATA*
> > > *Test run of H2O*
> > > *CNV 2*
> > > *
> > > *
> > > *O     8.0     0.00000     0.00000     0.00000*
> > > *H     1.0    -0.75800     0.00000     0.54500*
> > > * $END*
> > >
> > > *I tried to open the log file using GaussSum, I got this message"cclib
> > has
> > > problems parsing n_water.log. If you .....".*
> > > *
> > > *
> > > *Then I go to Python to call cclib directly, I got this*
> > > *
> > > *
> > > *>>> from cclib.parser import ccopen*
> > > *>>> p=ccopen("n_water.log")*
> > > *>>> date=p.parse()*
> > > *[GAMESS n_water.log INFO] Creating attribute atomcoords[]*
> > > *[GAMESS n_water.log INFO] Creating attribute atomnos[]*
> > > *[GAMESS n_water.log INFO] Creating attribute gbasis[]*
> > > *[GAMESS n_water.log INFO] Creating attribute nbasis: 19*
> > > *[GAMESS n_water.log INFO] Creating attribute charge: 0*
> > > *[GAMESS n_water.log INFO] Creating attribute mult: 1*
> > > *[GAMESS n_water.log INFO] Creating attribute homos[]*
> > > *[GAMESS n_water.log INFO] Creating attribute natom: 3*
> > > *[GAMESS n_water.log INFO] Creating attribute scftargets[]*
> > > *[GAMESS n_water.log INFO] Creating attribute scfvalues[]*
> > > *[GAMESS n_water.log INFO] Creating attribute scfenergies[]*
> > > *[GAMESS n_water.log INFO] Creating attribute moenergies[]*
> > > *[GAMESS n_water.log INFO] Creating attribute mosyms[]*
> > > *[GAMESS n_water.log INFO] Creating attribute nmo: 19*
> > > *[GAMESS n_water.log INFO] Creating attribute mocoeffs[]*
> > > *[GAMESS n_water.log INFO] Creating attribute atombasis[]*
> > > *[GAMESS n_water.log INFO] Creating attribute aonames[]*
> > > *[GAMESS n_water.log INFO] Creating attribute vibfreqs[]*
> > > *[GAMESS n_water.log INFO] Creating attribute vibirs[]*
> > > *[GAMESS n_water.log INFO] Creating attribute vibdisps[]*
> > > *[GAMESS n_water.log WARNING] This is not a stationary point on the
> > > molecularPES.*
> > > * The vibrational analysis is not valid.*
> > > *Traceback (most recent call last):*
> > > *  File "<stdin>", line 1, in ?*
> > > *  File "/usr/lib/python2.4/site-packages/cclib/parser/logfileparser.py",
> > > line 22*
> > > *1, in parse*
> > > *    self.extract(inputfile, line)*
> > > *  File "/usr/lib/python2.4/site-packages/cclib/parser/gamessparser.py",
> > > line 528*
> > > *, in extract*
> > > *    newfreq.append(float(x))*
> > > *ValueError: invalid literal for float(): MASSES*
> > >
> > > *Thank you for your suggestion to read my log file w/ cclib.*
> > > *
> > > *
> > > *Best and happy holidays!*
> > > *
> > > *
> > > *Frank*
> >
> > >
> > ------------------------------------------------------------------------------
> > > Learn Windows Azure Live!  Tuesday, Dec 13, 2011
> > > Microsoft is holding a special Learn Windows Azure training event for
> > > developers. It will provide a great way to learn Windows Azure and what
> > it
> > > provides. You can attend the event by watching it streamed LIVE online.
> > > Learn more at http://p.sf.net/sfu/ms-windowsazure
> >
> > > _______________________________________________
> > > cclib-users mailing list
> > > ccl...@li...
> > > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> >
> > --
> > written by Karol M. Langner
> > Sat Dec 17 20:48:58 CET 2011
> >



-- 
written by Karol Langner
Thu Jan 19 15:50:44 CET 2012

Re: [cclib-users] A question about LPA

[Martin R. <mar...@gm...>]

Hi Adam,

Unfortunately Int=ultrafine doesn't do anything. Neither does smaller basis
sets (tried cc-pVTZ and cc-pV5Z). Since the exact same error occurs for Oh
systems, but goes away upon distortion to C3v, it seems like something else
is wrong.

Best,
Martin

On Mon, Jan 16, 2012 at 10:43 AM, Adam Tenderholt <ate...@gm...>wrote:

> Hi Martin,
>
> Any idea what happens if you use Int=UltraFine? Does this error still
> appear for the diatomic with smaller basis sets? What about with for
> cc-pV5Z?
>
> Adam
>
>
> On Thu, Jan 12, 2012 at 3:56 PM, Martin Rahm <mar...@gm...>
> wrote:
> > Hello again,
> >
> > I've come across another case of the "complex number" error. This time
> in a
> > very small diatomic.
> >
> > Running LPA on a M062X/cc-pwCV5Z wave function of ClF, and gets this
> error:
> >
> > [LPA <cclib.parser.data.ccData object at 0x1015ba1d0> INFO] Creating
> > attribute aoresults: [array[2]]
> >
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
> > ComplexWarning: Casting complex values to real discards the imaginary
> part
> >   self.aoresults[spin][i] = numpy.multiply(temp1, temp2).astype("d")
> >
> > This is quite cumbersome, since there is really no way of breaking
> symmetry
> > of a linear molecule (which solved the problem for larger molecules)!
> >
> > I've attached my log file, and also my script just in case.
> >
> > I hope you have a quick fix :)
> >
> > Best regards,
> > Martin
> >
> >
> ------------------------------------------------------------------------------
> > RSA(R) Conference 2012
> > Mar 27 - Feb 2
> > Save $400 by Jan. 27
> > Register now!
> > http://p.sf.net/sfu/rsa-sfdev2dev2
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
>

Re: [cclib-users] A question about LPA

[Adam T. <ate...@gm...>]

Hi Martin,

Any idea what happens if you use Int=UltraFine? Does this error still
appear for the diatomic with smaller basis sets? What about with for
cc-pV5Z?

Adam


On Thu, Jan 12, 2012 at 3:56 PM, Martin Rahm <mar...@gm...> wrote:
> Hello again,
>
> I've come across another case of the "complex number" error. This time in a
> very small diatomic.
>
> Running LPA on a M062X/cc-pwCV5Z wave function of ClF, and gets this error:
>
> [LPA <cclib.parser.data.ccData object at 0x1015ba1d0> INFO] Creating
> attribute aoresults: [array[2]]
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
> ComplexWarning: Casting complex values to real discards the imaginary part
>   self.aoresults[spin][i] = numpy.multiply(temp1, temp2).astype("d")
>
> This is quite cumbersome, since there is really no way of breaking symmetry
> of a linear molecule (which solved the problem for larger molecules)!
>
> I've attached my log file, and also my script just in case.
>
> I hope you have a quick fix :)
>
> Best regards,
> Martin
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Mar 27 - Feb 2
> Save $400 by Jan. 27
> Register now!
> http://p.sf.net/sfu/rsa-sfdev2dev2
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

Re: [cclib-users] cclib.method

[Chengju W. <fra...@gm...>]

(lp0
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p962
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p1021
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p1024
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p1038
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p1048
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p1061
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p1062
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p1063
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p1066
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p1072
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p1073
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p1074
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p1075
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p1076
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p1078
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p1080
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p1081
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p1082
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p1083
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p1084
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p1086
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p1087
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p1088
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p1089
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p1091
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p1092
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p1093
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p1096
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p1097
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p1098
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p1099
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p1100
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p1101
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p1102
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p1103
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p1104
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p1105
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p1106
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p1107
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p1108
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p1109
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p1110
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p1111
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p1112
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p1113
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p1114
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p1115
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p1116
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p1117
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p1118
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p1119
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p1120
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p1121
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p1122
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p1123
aS'C91_XY'
p1124
aS'C91_XZ'
p1125
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p1126
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p1127
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p1128
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p1129
aS'H92_X'
p1130
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p1131
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p1132
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p1133
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p1134
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p1135
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p1136
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p1137
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p1138
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p1140
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p1141
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p1142
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p1143
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p1144
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p1145
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p1146
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p1147
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p1148
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p1149
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p1150
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p1151
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p1152
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p1153
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p1154
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p1155
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p1156
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p1157
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p1158
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p1159
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p1160
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p1161
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p1162
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p1163
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p1164
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p1165
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p1166
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p1167
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p1168
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p1169
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p1170
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p1171
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p1172
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p1173
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p1174
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p1175
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p1176
aS'C97_Y'
p1177
aS'C97_Z'
p1178
aS'C97_S'
p1179
aS'C97_X'
p1180
aS'C97_Y'
p1181
aS'C97_Z'
p1182
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p1183
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p1184
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p1185
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p1186
aS'C97_XZ'
p1187
aS'C97_YZ'
p1188
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p1189
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p1190
aS'H98_S'
p1191
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p1192
aS'H98_Y'
p1193
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p1194
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p1195
aS'H99_S'
p1196
aS'H99_S'
p1197
aS'H99_X'
p1198
aS'H99_Y'
p1199
aS'H99_Z'
p1200
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p1201
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p1202
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p1203
aS'C0_Y'
p1204
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p1205
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p1206
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p1207
aS'C0_Y'
p1208
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p1209
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p1210
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p1211
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p1212
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p1213
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p1214
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p1215
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p1216
aS'C0_XY'
p1217
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p1218
aS'C0_YZ'
p1219
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p1220
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p1221
aS'H1_S'
p1222
aS'H1_X'
p1223
aS'H1_Y'
p1224
aS'H1_Z'
p1225
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p1226
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p1227
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p1228
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p1229
aS'H2_Y'
p1230
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p1231
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p1232
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p1233
aS'C3_X'
p1234
aS'C3_Y'
p1235
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p1236
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p1237
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p1238
aS'C3_Y'
p1239
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p1240
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p1241
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p1242
aS'C3_Y'
p1243
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p1244
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p1245
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p1246
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p1247
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p1248
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p1249
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p1250
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p1251
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p1252
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p1253
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p1254
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p1255
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p1256
aS'H5_S'
p1257
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p1258
aS'H5_S'
p1259
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p1260
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p1261
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p1262
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p1263
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p1264
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p1265
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p1266
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p1268
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p1269
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p1270
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p1271
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p1272
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p1273
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p1274
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p1275
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p1276
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p1277
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p1278
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p1279
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p1280
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p1281
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p1282
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p1283
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p1284
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p1285
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p1286
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p1287
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p1288
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p1289
aS'H8_S'
p1290
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p1291
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p1292
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p1293
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p1295
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p1296
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p1297
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p1298
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p1299
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p1300
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p1301
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p1302
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p1303
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p1304
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p1305
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p1306
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p1307
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p1308
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p1309
aS'C9_XY'
p1310
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p1311
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p1312
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p1313
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p1314
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p1315
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p1316
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p1317
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p1318
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p1319
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p1320
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p1321
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p1322
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p1323
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p1324
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p1326
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p1327
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p1328
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p1329
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p1330
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p1331
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p1332
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p1333
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p1335
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p1340
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p1345
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p1348
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p1350
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p1351
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p1371
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p1414
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p1415
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p1416
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p1417
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p1419
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p1420
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p1423
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p1424
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p1425
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p1427
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p1428
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p1429
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p1430
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p1431
aS'C21_YY'
p1432
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p1433
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p1434
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p1435
aS'C21_YZ'
p1436
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p1437
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p1438
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p1439
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p1440
aS'H22_Y'
p1441
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p1442
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p1443
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p1444
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p1445
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p1446
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p1447
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p1448
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p1450
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p1451
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p1452
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p1453
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p1454
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p1455
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p1456
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p1457
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p1458
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p1459
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p1460
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p1461
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p1462
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p1463
aS'C24_ZZ'
p1464
aS'C24_XY'
p1465
aS'C24_XZ'
p1466
aS'C24_YZ'
p1467
aS'H25_S'
p1468
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p2019
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p2021
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p2022
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p2023
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p2025
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p2026
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p2027
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p2028
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p2029
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p2030
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p2032
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p2034
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p2035
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p2066
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p2100
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p2109
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p2110
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p2111
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p2113
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p2114
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p2115
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p2116
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p2163
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p2164
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p2165
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p2167
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p2175
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p2182
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p2183
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p2184
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p2186
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p2187
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p2189
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p2222
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p2288
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p2557
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p2559
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p2560
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p3103
aS'C83_Z'
p3104
aS'C83_XX'
p3105
aS'C83_YY'
p3106
aS'C83_ZZ'
p3107
aS'C83_XY'
p3108
aS'C83_XZ'
p3109
aS'C83_YZ'
p3110
aS'H84_S'
p3111
aS'H84_S'
p3112
aS'H84_S'
p3113
aS'H84_X'
p3114
aS'H84_Y'
p3115
aS'H84_Z'
p3116
aS'H85_S'
p3117
aS'H85_S'
p3118
aS'H85_S'
p3119
aS'H85_X'
p3120
aS'H85_Y'
p3121
aS'H85_Z'
p3122
aS'C86_S'
p3123
aS'C86_S'
p3124
aS'C86_X'
p3125
aS'C86_Y'
p3126
aS'C86_Z'
p3127
aS'C86_S'
p3128
aS'C86_X'
p3129
aS'C86_Y'
p3130
aS'C86_Z'
p3131
aS'C86_S'
p3132
aS'C86_X'
p3133
aS'C86_Y'
p3134
aS'C86_Z'
p3135
aS'C86_XX'
p3136
aS'C86_YY'
p3137
aS'C86_ZZ'
p3138
aS'C86_XY'
p3139
aS'C86_XZ'
p3140
aS'C86_YZ'
p3141
aS'H87_S'
p3142
aS'H87_S'
p3143
aS'H87_S'
p3144
aS'H87_X'
p3145
aS'H87_Y'
p3146
aS'H87_Z'
p3147
aS'H88_S'
p3148
aS'H88_S'
p3149
aS'H88_S'
p3150
aS'H88_X'
p3151
aS'H88_Y'
p3152
aS'H88_Z'
p3153
aS'C89_S'
p3154
aS'C89_S'
p3155
aS'C89_X'
p3156
aS'C89_Y'
p3157
aS'C89_Z'
p3158
aS'C89_S'
p3159
aS'C89_X'
p3160
aS'C89_Y'
p3161
aS'C89_Z'
p3162
aS'C89_S'
p3163
aS'C89_X'
p3164
aS'C89_Y'
p3165
aS'C89_Z'
p3166
aS'C89_XX'
p3167
aS'C89_YY'
p3168
aS'C89_ZZ'
p3169
aS'C89_XY'
p3170
aS'C89_XZ'
p3171
aS'C89_YZ'
p3172
aS'H90_S'
p3173
aS'H90_S'
p3174
aS'H90_S'
p3175
aS'H90_X'
p3176
aS'H90_Y'
p3177
aS'H90_Z'
p3178
aS'H91_S'
p3179
aS'H91_S'
p3180
aS'H91_S'
p3181
aS'H91_X'
p3182
aS'H91_Y'
p3183
aS'H91_Z'
p3184
aS'C92_S'
p3185
aS'C92_S'
p3186
aS'C92_X'
p3187
aS'C92_Y'
p3188
aS'C92_Z'
p3189
aS'C92_S'
p3190
aS'C92_X'
p3191
aS'C92_Y'
p3192
aS'C92_Z'
p3193
aS'C92_S'
p3194
aS'C92_X'
p3195
aS'C92_Y'
p3196
aS'C92_Z'
p3197
aS'C92_XX'
p3198
aS'C92_YY'
p3199
aS'C92_ZZ'
p3200
aS'C92_XY'
p3201
aS'C92_XZ'
p3202
aS'C92_YZ'
p3203
aS'H93_S'
p3204
aS'H93_S'
p3205
aS'H93_S'
p3206
aS'H93_X'
p3207
aS'H93_Y'
p3208
aS'H93_Z'
p3209
aS'H94_S'
p3210
aS'H94_S'
p3211
aS'H94_S'
p3212
aS'H94_X'
p3213
aS'H94_Y'
p3214
aS'H94_Z'
p3215
aS'C95_S'
p3216
aS'C95_S'
p3217
aS'C95_X'
p3218
aS'C95_Y'
p3219
aS'C95_Z'
p3220
aS'C95_S'
p3221
aS'C95_X'
p3222
aS'C95_Y'
p3223
aS'C95_Z'
p3224
aS'C95_S'
p3225
aS'C95_X'
p3226
aS'C95_Y'
p3227
aS'C95_Z'
p3228
aS'C95_XX'
p3229
aS'C95_YY'
p3230
aS'C95_ZZ'
p3231
aS'C95_XY'
p3232
aS'C95_XZ'
p3233
aS'C95_YZ'
p3234
aS'H96_S'
p3235
aS'H96_S'
p3236
aS'H96_S'
p3237
aS'H96_X'
p3238
aS'H96_Y'
p3239
aS'H96_Z'
p3240
aS'H97_S'
p3241
aS'H97_S'
p3242
aS'H97_S'
p3243
aS'H97_X'
p3244
aS'H97_Y'
p3245
aS'H97_Z'
p3246
aS'C98_S'
p3247
aS'C98_S'
p3248
aS'C98_X'
p3249
aS'C98_Y'
p3250
aS'C98_Z'
p3251
aS'C98_S'
p3252
aS'C98_X'
p3253
aS'C98_Y'
p3254
aS'C98_Z'
p3255
aS'C98_S'
p3256
aS'C98_X'
p3257
aS'C98_Y'
p3258
aS'C98_Z'
p3259
aS'C98_XX'
p3260
aS'C98_YY'
p3261
aS'C98_ZZ'
p3262
aS'C98_XY'
p3263
aS'C98_XZ'
p3264
aS'C98_YZ'
p3265
aS'H99_S'
p3266
aS'H99_S'
p3267
aS'H99_S'
p3268
aS'H99_X'
p3269
aS'H99_Y'
p3270
aS'H99_Z'
p3271
aS'H0_S'
p3272
aS'H0_S'
p3273
aS'H0_S'
p3274
aS'H0_X'
p3275
aS'H0_Y'
p3276
aS'H0_Z'
p3277
aS'C1_S'
p3278
aS'C1_S'
p3279
aS'C1_X'
p3280
aS'C1_Y'
p3281
aS'C1_Z'
p3282
aS'C1_S'
p3283
aS'C1_X'
p3284
aS'C1_Y'
p3285
aS'C1_Z'
p3286
aS'C1_S'
p3287
aS'C1_X'
p3288
aS'C1_Y'
p3289
aS'C1_Z'
p3290
aS'C1_XX'
p3291
aS'C1_YY'
p3292
aS'C1_ZZ'
p3293
aS'C1_XY'
p3294
aS'C1_XZ'
p3295
aS'C1_YZ'
p3296
aS'H2_S'
p3297
aS'H2_S'
p3298
aS'H2_S'
p3299
aS'H2_X'
p3300
aS'H2_Y'
p3301
aS'H2_Z'
p3302
aS'H3_S'
p3303
aS'H3_S'
p3304
aS'H3_S'
p3305
aS'H3_X'
p3306
aS'H3_Y'
p3307
aS'H3_Z'
p3308
aS'C4_S'
p3309
aS'C4_S'
p3310
aS'C4_X'
p3311
aS'C4_Y'
p3312
aS'C4_Z'
p3313
aS'C4_S'
p3314
aS'C4_X'
p3315
aS'C4_Y'
p3316
aS'C4_Z'
p3317
aS'C4_S'
p3318
aS'C4_X'
p3319
aS'C4_Y'
p3320
aS'C4_Z'
p3321
aS'C4_XX'
p3322
aS'C4_YY'
p3323
aS'C4_ZZ'
p3324
aS'C4_XY'
p3325
aS'C4_XZ'
p3326
aS'C4_YZ'
p3327
aS'H5_S'
p3328
aS'H5_S'
p3329
aS'H5_S'
p3330
aS'H5_X'
p3331
aS'H5_Y'
p3332
aS'H5_Z'
p3333
aS'H6_S'
p3334
aS'H6_S'
p3335
aS'H6_S'
p3336
aS'H6_X'
p3337
aS'H6_Y'
p3338
aS'H6_Z'
p3339
aS'C7_S'
p3340
aS'C7_S'
p3341
aS'C7_X'
p3342
aS'C7_Y'
p3343
aS'C7_Z'
p3344
aS'C7_S'
p3345
aS'C7_X'
p3346
aS'C7_Y'
p3347
aS'C7_Z'
p3348
aS'C7_S'
p3349
aS'C7_X'
p3350
aS'C7_Y'
p3351
aS'C7_Z'
p3352
aS'C7_XX'
p3353
aS'C7_YY'
p3354
aS'C7_ZZ'
p3355
aS'C7_XY'
p3356
aS'C7_XZ'
p3357
aS'C7_YZ'
p3358
aS'H8_S'
p3359
aS'H8_S'
p3360
aS'H8_S'
p3361
aS'H8_X'
p3362
aS'H8_Y'
p3363
aS'H8_Z'
p3364
aS'H9_S'
p3365
aS'H9_S'
p3366
aS'H9_S'
p3367
aS'H9_X'
p3368
aS'H9_Y'
p3369
aS'H9_Z'
p3370
aS'C10_S'
p3371
aS'C10_S'
p3372
aS'C10_X'
p3373
aS'C10_Y'
p3374
aS'C10_Z'
p3375
aS'C10_S'
p3376
aS'C10_X'
p3377
aS'C10_Y'
p3378
aS'C10_Z'
p3379
aS'C10_S'
p3380
aS'C10_X'
p3381
aS'C10_Y'
p3382
aS'C10_Z'
p3383
aS'C10_XX'
p3384
aS'C10_YY'
p3385
aS'C10_ZZ'
p3386
aS'C10_XY'
p3387
aS'C10_XZ'
p3388
aS'C10_YZ'
p3389
aS'H11_S'
p3390
aS'H11_S'
p3391
aS'H11_S'
p3392
aS'H11_X'
p3393
aS'H11_Y'
p3394
aS'H11_Z'
p3395
aS'H12_S'
p3396
aS'H12_S'
p3397
aS'H12_S'
p3398
aS'H12_X'
p3399
aS'H12_Y'
p3400
aS'H12_Z'
p3401
aS'C13_S'
p3402
aS'C13_S'
p3403
aS'C13_X'
p3404
aS'C13_Y'
p3405
aS'C13_Z'
p3406
aS'C13_S'
p3407
aS'C13_X'
p3408
aS'C13_Y'
p3409
aS'C13_Z'
p3410
aS'C13_S'
p3411
aS'C13_X'
p3412
aS'C13_Y'
p3413
aS'C13_Z'
p3414
aS'C13_XX'
p3415
aS'C13_YY'
p3416
aS'C13_ZZ'
p3417
aS'C13_XY'
p3418
aS'C13_XZ'
p3419
aS'C13_YZ'
p3...
 
[truncated message content]

Re: [cclib-users] cclib.method

[Adam T. <ate...@gm...>]

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.
>
>
>
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
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> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

[cclib-users] cclib.method

[Chengju W. <fra...@gm...>]

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.*

Re: [cclib-users] read the log file after HESSIAN calculation by GAMESS

[Karol M. L. <kar...@gm...>]

Hi Chengju,

Could you make the log file available?

We need it to test the fix, and we need your consent to redistribute
it with our regression suite.

If you provide us with the file, there is a good chance the
problem will be fixed.

Best,
Karol

On Dec 16 2011, Chengju Wang wrote:
> *Hi, everyone.*
> *
> *
> *I'm new to cclib. I just found a 'problem' with cclib. *
> *
> *
> *After run this n_water.inp*
> 
> *!   File created by MacMolPlt 7.4.2*
> * $CONTRL SCFTYP=RHF RUNTYP=HESSIAN MAXIT=60 MULT=1 $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 HSSEND=.t. PROJCT=.FALSE. $END*
> * $FORCE METHOD=ANALYTIC VIBANL=.TRUE. $END*
> * $DATA*
> *Test run of H2O*
> *CNV 2*
> *
> *
> *O     8.0     0.00000     0.00000     0.00000*
> *H     1.0    -0.75800     0.00000     0.54500*
> * $END*
> 
> *I tried to open the log file using GaussSum, I got this message"cclib has
> problems parsing n_water.log. If you .....".*
> *
> *
> *Then I go to Python to call cclib directly, I got this*
> *
> *
> *>>> from cclib.parser import ccopen*
> *>>> p=ccopen("n_water.log")*
> *>>> date=p.parse()*
> *[GAMESS n_water.log INFO] Creating attribute atomcoords[]*
> *[GAMESS n_water.log INFO] Creating attribute atomnos[]*
> *[GAMESS n_water.log INFO] Creating attribute gbasis[]*
> *[GAMESS n_water.log INFO] Creating attribute nbasis: 19*
> *[GAMESS n_water.log INFO] Creating attribute charge: 0*
> *[GAMESS n_water.log INFO] Creating attribute mult: 1*
> *[GAMESS n_water.log INFO] Creating attribute homos[]*
> *[GAMESS n_water.log INFO] Creating attribute natom: 3*
> *[GAMESS n_water.log INFO] Creating attribute scftargets[]*
> *[GAMESS n_water.log INFO] Creating attribute scfvalues[]*
> *[GAMESS n_water.log INFO] Creating attribute scfenergies[]*
> *[GAMESS n_water.log INFO] Creating attribute moenergies[]*
> *[GAMESS n_water.log INFO] Creating attribute mosyms[]*
> *[GAMESS n_water.log INFO] Creating attribute nmo: 19*
> *[GAMESS n_water.log INFO] Creating attribute mocoeffs[]*
> *[GAMESS n_water.log INFO] Creating attribute atombasis[]*
> *[GAMESS n_water.log INFO] Creating attribute aonames[]*
> *[GAMESS n_water.log INFO] Creating attribute vibfreqs[]*
> *[GAMESS n_water.log INFO] Creating attribute vibirs[]*
> *[GAMESS n_water.log INFO] Creating attribute vibdisps[]*
> *[GAMESS n_water.log WARNING] This is not a stationary point on the
> molecularPES.*
> * The vibrational analysis is not valid.*
> *Traceback (most recent call last):*
> *  File "<stdin>", line 1, in ?*
> *  File "/usr/lib/python2.4/site-packages/cclib/parser/logfileparser.py",
> line 22*
> *1, in parse*
> *    self.extract(inputfile, line)*
> *  File "/usr/lib/python2.4/site-packages/cclib/parser/gamessparser.py",
> line 528*
> *, in extract*
> *    newfreq.append(float(x))*
> *ValueError: invalid literal for float(): MASSES*
> 
> *Thank you for your suggestion to read my log file w/ cclib.*
> *
> *
> *Best and happy holidays!*
> *
> *
> *Frank*

> ------------------------------------------------------------------------------
> Learn Windows Azure Live!  Tuesday, Dec 13, 2011
> Microsoft is holding a special Learn Windows Azure training event for 
> developers. It will provide a great way to learn Windows Azure and what it 
> provides. You can attend the event by watching it streamed LIVE online.  
> Learn more at http://p.sf.net/sfu/ms-windowsazure

> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users


-- 
written by Karol M. Langner
Sat Dec 17 20:48:58 CET 2011

[cclib-users] read the log file after HESSIAN calculation by GAMESS

[Chengju W. <fra...@gm...>]

*Hi, everyone.*
*
*
*I'm new to cclib. I just found a 'problem' with cclib. *
*
*
*After run this n_water.inp*

*!   File created by MacMolPlt 7.4.2*
* $CONTRL SCFTYP=RHF RUNTYP=HESSIAN MAXIT=60 MULT=1 $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 HSSEND=.t. PROJCT=.FALSE. $END*
* $FORCE METHOD=ANALYTIC VIBANL=.TRUE. $END*
* $DATA*
*Test run of H2O*
*CNV 2*
*
*
*O     8.0     0.00000     0.00000     0.00000*
*H     1.0    -0.75800     0.00000     0.54500*
* $END*

*I tried to open the log file using GaussSum, I got this message"cclib has
problems parsing n_water.log. If you .....".*
*
*
*Then I go to Python to call cclib directly, I got this*
*
*
*>>> from cclib.parser import ccopen*
*>>> p=ccopen("n_water.log")*
*>>> date=p.parse()*
*[GAMESS n_water.log INFO] Creating attribute atomcoords[]*
*[GAMESS n_water.log INFO] Creating attribute atomnos[]*
*[GAMESS n_water.log INFO] Creating attribute gbasis[]*
*[GAMESS n_water.log INFO] Creating attribute nbasis: 19*
*[GAMESS n_water.log INFO] Creating attribute charge: 0*
*[GAMESS n_water.log INFO] Creating attribute mult: 1*
*[GAMESS n_water.log INFO] Creating attribute homos[]*
*[GAMESS n_water.log INFO] Creating attribute natom: 3*
*[GAMESS n_water.log INFO] Creating attribute scftargets[]*
*[GAMESS n_water.log INFO] Creating attribute scfvalues[]*
*[GAMESS n_water.log INFO] Creating attribute scfenergies[]*
*[GAMESS n_water.log INFO] Creating attribute moenergies[]*
*[GAMESS n_water.log INFO] Creating attribute mosyms[]*
*[GAMESS n_water.log INFO] Creating attribute nmo: 19*
*[GAMESS n_water.log INFO] Creating attribute mocoeffs[]*
*[GAMESS n_water.log INFO] Creating attribute atombasis[]*
*[GAMESS n_water.log INFO] Creating attribute aonames[]*
*[GAMESS n_water.log INFO] Creating attribute vibfreqs[]*
*[GAMESS n_water.log INFO] Creating attribute vibirs[]*
*[GAMESS n_water.log INFO] Creating attribute vibdisps[]*
*[GAMESS n_water.log WARNING] This is not a stationary point on the
molecularPES.*
* The vibrational analysis is not valid.*
*Traceback (most recent call last):*
*  File "<stdin>", line 1, in ?*
*  File "/usr/lib/python2.4/site-packages/cclib/parser/logfileparser.py",
line 22*
*1, in parse*
*    self.extract(inputfile, line)*
*  File "/usr/lib/python2.4/site-packages/cclib/parser/gamessparser.py",
line 528*
*, in extract*
*    newfreq.append(float(x))*
*ValueError: invalid literal for float(): MASSES*

*Thank you for your suggestion to read my log file w/ cclib.*
*
*
*Best and happy holidays!*
*
*
*Frank*

Re: [cclib-users] A question about LPA

[Martin R. <mar...@gm...>]

Hi Adam,

No, as long as the symmetry is not Oh or Td, there is no warning.

Best,
Martin

On Tue, Nov 15, 2011 at 12:22 PM, Adam Tenderholt <ate...@gm...>wrote:

> Hi Martin,
>
> Thanks for the info. It's a bit odd that slight distortions return the
> value to 70.00. Out of curiosity, do you still get the complex warning
> at the LPA step for these calculations?
>
> Adam
>
>
> On Tue, Nov 15, 2011 at 11:50 AM, Martin Rahm <mar...@gm...>
> wrote:
> > Hi Adam, and everyone,
> > I just figured out a way around the problem. First, the same thing
> happens
> > for single points, and it remains if one runs with "nosymm", or if the
> > nuclear coordinate input is switched between cartesian/z-mat. However,
> these
> > latter changes do seem to affect the total number of electrons and the
> > orbital populations slightly different.
> > The solution I found was to perturb the Oh symmetry very slightly (into
> > C3v), then the electron count becomes 70.000, and all ligands are treated
> > equally. The same goes for Td systems, which have to be disturbed into
> D2d.
> > In other words it seems like the code has problems with "spherically"
> > symmetric wave functions.
> > Best,
> > Martin
> >
> >
> > On Tue, Nov 15, 2011 at 10:19 AM, Adam Tenderholt <ate...@gm...
> >
> > wrote:
> >>
> >> Hi Martin and others,
> >>
> >> Sorry for the delayed response....
> >>
> >> The complex warning suggests there's a complex value being discarded
> >> that may be important. Does anyone know if we should be taking the
> >> norm instead of simply discarding the imaginary part?
> >>
> >> Also, does it matter that this is an Opt Freq calc? Does Gaussian
> >> print the one-electron overlap matrix (aooverlaps) at the final
> >> geometry? (I usually don't combine Opt and Freq calcs, so I don't
> >> know, but the file looks like the final overlap matrix isn't at the
> >> converged geometry.) If not, perhaps the problem is from using the
> >> overlap matrix at the first structure and the orbital coefficients at
> >> the final structure.
> >>
> >> Take care,
> >>
> >> Adam
> >>
> >> On Sat, Nov 5, 2011 at 1:20 PM, Martin Rahm <mar...@gm...>
> wrote:
> >> > Hi Karol,
> >> > I realized that I had used cartesian coordinates in the original input
> >> > file.
> >> > When I used a z-matrix instead (and defined S as atom 0) the LPA
> warning
> >> > was
> >> > still the same, but the total number of electrons turned out to be
> 70.22
> >> > (instead of 70.3).
> >> > I should also mention that the LPA-charge of all F ligands are
> slightly
> >> > different, even though they are symmetrically identical.
> >> > Best,
> >> > Martin
> >> > On Sat, Nov 5, 2011 at 1:34 AM, Karol M. Langner
> >> > <kar...@gm...>
> >> > wrote:
> >> >>
> >> >> Hi Martin,
> >> >>
> >> >> Can you provide the output file for that Gaussian job?
> >> >>
> >> >> Best,
> >> >> Karol
> >> >>
> >> >> On Nov 04 2011, Martin Rahm wrote:
> >> >> > Dear List,
> >> >> >
> >> >> > I'm running a trial Löwdin population analysis (LPA) on SF6, from a
> >> >> >  B3LYP/cc-pVTZ calculation. Something is awry, the total number of
> >> >> > electrons gets overestimated by 0.3 (70.3), and there is a "complex
> >> >> > warning" when running the LPA.
> >> >> >
> >> >> > LPA is supposed to be rotationally invariant if one use "pure"
> >> >> > spherical
> >> >> > harmonics in the basis set, e.g. 5 d functions instead of 6. (which
> >> >> > cc-pVTZ
> >> >> > does). Anyone have any clue to this behavior?
> >> >> >
> >> >> > Best regards,
> >> >> > Martin
> >> >> >
> >> >> > Gaussian Input: ---------
> >> >> > # opt freq b3lyp/cc-pvtz pop=(nboread,full) iop(3/33=1,3/36=-1)
> >> >> >
> >> >> > Title Card Required
> >> >> >
> >> >> > 0 1
> >> >> >  F                  0.00000000    0.00000000    1.57972200
> >> >> >  F                  0.00000000    1.57972200    0.00000000
> >> >> >  F                  0.00000000    0.00000000   -1.57972200
> >> >> >  F                  0.00000000   -1.57972200    0.00000000
> >> >> >  F                  1.57972200    0.00000000    0.00000000
> >> >> >  F                 -1.57972200    0.00000000    0.00000000
> >> >> >  S                  0.00000000    0.00000000    0.00000000
> >> >> >
> >> >> > Python script: --------
> >> >> > from numpy import *
> >> >> > from cclib.parser import ccopen
> >> >> > from cclib.method import LPA
> >> >> > parser = ccopen("test.log")
> >> >> > data = parser.parse()
> >> >> > method = LPA(data)
> >> >> > method.calculate()
> >> >> >
> >> >> >
> >> >> >
> savetxt("LPA-big.csv",transpose(2*method.aoresults[0][:data.homos[0]+1]))
> >> >> >
> >> >> > Script output: --------
> >> >> > ...
> >> >> > [Gaussian test.log INFO] Creating attribute coreelectrons[]
> >> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO]
> Creating
> >> >> > attribute aoresults: [array[2]]
> >> >> >
> >> >> >
> >> >> >
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
> >> >> > ComplexWarning: Casting complex values to real discards the
> imaginary
> >> >> > part
> >> >> >   self.aoresults[spin][i] = numpy.multiply(temp1,
> temp2).astype("d")
> >> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Saving
> >> >> > partitioned results in fragresults: [array[2]]
> >> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO]
> Creating
> >> >> > fragcharges: array[1]
> >> >>
> >> >> >
> >> >> >
> >> >> >
> ------------------------------------------------------------------------------
> >> >> > RSA(R) Conference 2012
> >> >> > Save $700 by Nov 18
> >> >> > Register now
> >> >> > http://p.sf.net/sfu/rsa-sfdev2dev1
> >> >>
> >> >> > _______________________________________________
> >> >> > cclib-users mailing list
> >> >> > ccl...@li...
> >> >> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >> >>
> >> >>
> >> >> --
> >> >> written by Karol Langner
> >> >> Sat Nov  5 09:34:29 CET 2011
> >> >
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------------
> >> > RSA(R) Conference 2012
> >> > Save $700 by Nov 18
> >> > Register now
> >> > http://p.sf.net/sfu/rsa-sfdev2dev1
> >> > _______________________________________________
> >> > cclib-users mailing list
> >> > ccl...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >> >
> >> >
> >
> >
>

Re: [cclib-users] A question about LPA

[Adam T. <ate...@gm...>]

Hi Martin,

Thanks for the info. It's a bit odd that slight distortions return the
value to 70.00. Out of curiosity, do you still get the complex warning
at the LPA step for these calculations?

Adam


On Tue, Nov 15, 2011 at 11:50 AM, Martin Rahm <mar...@gm...> wrote:
> Hi Adam, and everyone,
> I just figured out a way around the problem. First, the same thing happens
> for single points, and it remains if one runs with "nosymm", or if the
> nuclear coordinate input is switched between cartesian/z-mat. However, these
> latter changes do seem to affect the total number of electrons and the
> orbital populations slightly different.
> The solution I found was to perturb the Oh symmetry very slightly (into
> C3v), then the electron count becomes 70.000, and all ligands are treated
> equally. The same goes for Td systems, which have to be disturbed into D2d.
> In other words it seems like the code has problems with "spherically"
> symmetric wave functions.
> Best,
> Martin
>
>
> On Tue, Nov 15, 2011 at 10:19 AM, Adam Tenderholt <ate...@gm...>
> wrote:
>>
>> Hi Martin and others,
>>
>> Sorry for the delayed response....
>>
>> The complex warning suggests there's a complex value being discarded
>> that may be important. Does anyone know if we should be taking the
>> norm instead of simply discarding the imaginary part?
>>
>> Also, does it matter that this is an Opt Freq calc? Does Gaussian
>> print the one-electron overlap matrix (aooverlaps) at the final
>> geometry? (I usually don't combine Opt and Freq calcs, so I don't
>> know, but the file looks like the final overlap matrix isn't at the
>> converged geometry.) If not, perhaps the problem is from using the
>> overlap matrix at the first structure and the orbital coefficients at
>> the final structure.
>>
>> Take care,
>>
>> Adam
>>
>> On Sat, Nov 5, 2011 at 1:20 PM, Martin Rahm <mar...@gm...> wrote:
>> > Hi Karol,
>> > I realized that I had used cartesian coordinates in the original input
>> > file.
>> > When I used a z-matrix instead (and defined S as atom 0) the LPA warning
>> > was
>> > still the same, but the total number of electrons turned out to be 70.22
>> > (instead of 70.3).
>> > I should also mention that the LPA-charge of all F ligands are slightly
>> > different, even though they are symmetrically identical.
>> > Best,
>> > Martin
>> > On Sat, Nov 5, 2011 at 1:34 AM, Karol M. Langner
>> > <kar...@gm...>
>> > wrote:
>> >>
>> >> Hi Martin,
>> >>
>> >> Can you provide the output file for that Gaussian job?
>> >>
>> >> Best,
>> >> Karol
>> >>
>> >> On Nov 04 2011, Martin Rahm wrote:
>> >> > Dear List,
>> >> >
>> >> > I'm running a trial Löwdin population analysis (LPA) on SF6, from a
>> >> >  B3LYP/cc-pVTZ calculation. Something is awry, the total number of
>> >> > electrons gets overestimated by 0.3 (70.3), and there is a "complex
>> >> > warning" when running the LPA.
>> >> >
>> >> > LPA is supposed to be rotationally invariant if one use "pure"
>> >> > spherical
>> >> > harmonics in the basis set, e.g. 5 d functions instead of 6. (which
>> >> > cc-pVTZ
>> >> > does). Anyone have any clue to this behavior?
>> >> >
>> >> > Best regards,
>> >> > Martin
>> >> >
>> >> > Gaussian Input: ---------
>> >> > # opt freq b3lyp/cc-pvtz pop=(nboread,full) iop(3/33=1,3/36=-1)
>> >> >
>> >> > Title Card Required
>> >> >
>> >> > 0 1
>> >> >  F                  0.00000000    0.00000000    1.57972200
>> >> >  F                  0.00000000    1.57972200    0.00000000
>> >> >  F                  0.00000000    0.00000000   -1.57972200
>> >> >  F                  0.00000000   -1.57972200    0.00000000
>> >> >  F                  1.57972200    0.00000000    0.00000000
>> >> >  F                 -1.57972200    0.00000000    0.00000000
>> >> >  S                  0.00000000    0.00000000    0.00000000
>> >> >
>> >> > Python script: --------
>> >> > from numpy import *
>> >> > from cclib.parser import ccopen
>> >> > from cclib.method import LPA
>> >> > parser = ccopen("test.log")
>> >> > data = parser.parse()
>> >> > method = LPA(data)
>> >> > method.calculate()
>> >> >
>> >> >
>> >> > savetxt("LPA-big.csv",transpose(2*method.aoresults[0][:data.homos[0]+1]))
>> >> >
>> >> > Script output: --------
>> >> > ...
>> >> > [Gaussian test.log INFO] Creating attribute coreelectrons[]
>> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Creating
>> >> > attribute aoresults: [array[2]]
>> >> >
>> >> >
>> >> > /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
>> >> > ComplexWarning: Casting complex values to real discards the imaginary
>> >> > part
>> >> >   self.aoresults[spin][i] = numpy.multiply(temp1, temp2).astype("d")
>> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Saving
>> >> > partitioned results in fragresults: [array[2]]
>> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Creating
>> >> > fragcharges: array[1]
>> >>
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > RSA(R) Conference 2012
>> >> > Save $700 by Nov 18
>> >> > Register now
>> >> > http://p.sf.net/sfu/rsa-sfdev2dev1
>> >>
>> >> > _______________________________________________
>> >> > cclib-users mailing list
>> >> > ccl...@li...
>> >> > https://lists.sourceforge.net/lists/listinfo/cclib-users
>> >>
>> >>
>> >> --
>> >> written by Karol Langner
>> >> Sat Nov  5 09:34:29 CET 2011
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > RSA(R) Conference 2012
>> > Save $700 by Nov 18
>> > Register now
>> > http://p.sf.net/sfu/rsa-sfdev2dev1
>> > _______________________________________________
>> > cclib-users mailing list
>> > ccl...@li...
>> > https://lists.sourceforge.net/lists/listinfo/cclib-users
>> >
>> >
>
>

Re: [cclib-users] A question about LPA

[Martin R. <mar...@gm...>]

Hi Adam, and everyone,

I just figured out a way around the problem. First, the same thing happens
for single points, and it remains if one runs with "nosymm", or if the
nuclear coordinate input is switched between cartesian/z-mat. However,
these latter changes do seem to affect the total number of electrons and
the orbital populations slightly different.

The solution I found was to perturb the Oh symmetry very slightly (into
C3v), then the electron count becomes 70.000, and all ligands are treated
equally. The same goes for Td systems, which have to be disturbed into D2d.
In other words it seems like the code has problems with "spherically"
symmetric wave functions.

Best,
Martin



On Tue, Nov 15, 2011 at 10:19 AM, Adam Tenderholt <ate...@gm...>wrote:

> Hi Martin and others,
>
> Sorry for the delayed response....
>
> The complex warning suggests there's a complex value being discarded
> that may be important. Does anyone know if we should be taking the
> norm instead of simply discarding the imaginary part?
>
> Also, does it matter that this is an Opt Freq calc? Does Gaussian
> print the one-electron overlap matrix (aooverlaps) at the final
> geometry? (I usually don't combine Opt and Freq calcs, so I don't
> know, but the file looks like the final overlap matrix isn't at the
> converged geometry.) If not, perhaps the problem is from using the
> overlap matrix at the first structure and the orbital coefficients at
> the final structure.
>
> Take care,
>
> Adam
>
> On Sat, Nov 5, 2011 at 1:20 PM, Martin Rahm <mar...@gm...> wrote:
> > Hi Karol,
> > I realized that I had used cartesian coordinates in the original input
> file.
> > When I used a z-matrix instead (and defined S as atom 0) the LPA warning
> was
> > still the same, but the total number of electrons turned out to be 70.22
> > (instead of 70.3).
> > I should also mention that the LPA-charge of all F ligands are slightly
> > different, even though they are symmetrically identical.
> > Best,
> > Martin
> > On Sat, Nov 5, 2011 at 1:34 AM, Karol M. Langner <
> kar...@gm...>
> > wrote:
> >>
> >> Hi Martin,
> >>
> >> Can you provide the output file for that Gaussian job?
> >>
> >> Best,
> >> Karol
> >>
> >> On Nov 04 2011, Martin Rahm wrote:
> >> > Dear List,
> >> >
> >> > I'm running a trial Löwdin population analysis (LPA) on SF6, from a
> >> >  B3LYP/cc-pVTZ calculation. Something is awry, the total number of
> >> > electrons gets overestimated by 0.3 (70.3), and there is a "complex
> >> > warning" when running the LPA.
> >> >
> >> > LPA is supposed to be rotationally invariant if one use "pure"
> spherical
> >> > harmonics in the basis set, e.g. 5 d functions instead of 6. (which
> >> > cc-pVTZ
> >> > does). Anyone have any clue to this behavior?
> >> >
> >> > Best regards,
> >> > Martin
> >> >
> >> > Gaussian Input: ---------
> >> > # opt freq b3lyp/cc-pvtz pop=(nboread,full) iop(3/33=1,3/36=-1)
> >> >
> >> > Title Card Required
> >> >
> >> > 0 1
> >> >  F                  0.00000000    0.00000000    1.57972200
> >> >  F                  0.00000000    1.57972200    0.00000000
> >> >  F                  0.00000000    0.00000000   -1.57972200
> >> >  F                  0.00000000   -1.57972200    0.00000000
> >> >  F                  1.57972200    0.00000000    0.00000000
> >> >  F                 -1.57972200    0.00000000    0.00000000
> >> >  S                  0.00000000    0.00000000    0.00000000
> >> >
> >> > Python script: --------
> >> > from numpy import *
> >> > from cclib.parser import ccopen
> >> > from cclib.method import LPA
> >> > parser = ccopen("test.log")
> >> > data = parser.parse()
> >> > method = LPA(data)
> >> > method.calculate()
> >> >
> >> >
> savetxt("LPA-big.csv",transpose(2*method.aoresults[0][:data.homos[0]+1]))
> >> >
> >> > Script output: --------
> >> > ...
> >> > [Gaussian test.log INFO] Creating attribute coreelectrons[]
> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Creating
> >> > attribute aoresults: [array[2]]
> >> >
> >> >
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
> >> > ComplexWarning: Casting complex values to real discards the imaginary
> >> > part
> >> >   self.aoresults[spin][i] = numpy.multiply(temp1, temp2).astype("d")
> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Saving
> >> > partitioned results in fragresults: [array[2]]
> >> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Creating
> >> > fragcharges: array[1]
> >>
> >> >
> >> >
> ------------------------------------------------------------------------------
> >> > RSA(R) Conference 2012
> >> > Save $700 by Nov 18
> >> > Register now
> >> > http://p.sf.net/sfu/rsa-sfdev2dev1
> >>
> >> > _______________________________________________
> >> > cclib-users mailing list
> >> > ccl...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >>
> >>
> >> --
> >> written by Karol Langner
> >> Sat Nov  5 09:34:29 CET 2011
> >
> >
> >
> ------------------------------------------------------------------------------
> > RSA(R) Conference 2012
> > Save $700 by Nov 18
> > Register now
> > http://p.sf.net/sfu/rsa-sfdev2dev1
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> >
>

Re: [cclib-users] A question about LPA

[Adam T. <ate...@gm...>]

Hi Martin and others,

Sorry for the delayed response....

The complex warning suggests there's a complex value being discarded
that may be important. Does anyone know if we should be taking the
norm instead of simply discarding the imaginary part?

Also, does it matter that this is an Opt Freq calc? Does Gaussian
print the one-electron overlap matrix (aooverlaps) at the final
geometry? (I usually don't combine Opt and Freq calcs, so I don't
know, but the file looks like the final overlap matrix isn't at the
converged geometry.) If not, perhaps the problem is from using the
overlap matrix at the first structure and the orbital coefficients at
the final structure.

Take care,

Adam

On Sat, Nov 5, 2011 at 1:20 PM, Martin Rahm <mar...@gm...> wrote:
> Hi Karol,
> I realized that I had used cartesian coordinates in the original input file.
> When I used a z-matrix instead (and defined S as atom 0) the LPA warning was
> still the same, but the total number of electrons turned out to be 70.22
> (instead of 70.3).
> I should also mention that the LPA-charge of all F ligands are slightly
> different, even though they are symmetrically identical.
> Best,
> Martin
> On Sat, Nov 5, 2011 at 1:34 AM, Karol M. Langner <kar...@gm...>
> wrote:
>>
>> Hi Martin,
>>
>> Can you provide the output file for that Gaussian job?
>>
>> Best,
>> Karol
>>
>> On Nov 04 2011, Martin Rahm wrote:
>> > Dear List,
>> >
>> > I'm running a trial Löwdin population analysis (LPA) on SF6, from a
>> >  B3LYP/cc-pVTZ calculation. Something is awry, the total number of
>> > electrons gets overestimated by 0.3 (70.3), and there is a "complex
>> > warning" when running the LPA.
>> >
>> > LPA is supposed to be rotationally invariant if one use "pure" spherical
>> > harmonics in the basis set, e.g. 5 d functions instead of 6. (which
>> > cc-pVTZ
>> > does). Anyone have any clue to this behavior?
>> >
>> > Best regards,
>> > Martin
>> >
>> > Gaussian Input: ---------
>> > # opt freq b3lyp/cc-pvtz pop=(nboread,full) iop(3/33=1,3/36=-1)
>> >
>> > Title Card Required
>> >
>> > 0 1
>> >  F                  0.00000000    0.00000000    1.57972200
>> >  F                  0.00000000    1.57972200    0.00000000
>> >  F                  0.00000000    0.00000000   -1.57972200
>> >  F                  0.00000000   -1.57972200    0.00000000
>> >  F                  1.57972200    0.00000000    0.00000000
>> >  F                 -1.57972200    0.00000000    0.00000000
>> >  S                  0.00000000    0.00000000    0.00000000
>> >
>> > Python script: --------
>> > from numpy import *
>> > from cclib.parser import ccopen
>> > from cclib.method import LPA
>> > parser = ccopen("test.log")
>> > data = parser.parse()
>> > method = LPA(data)
>> > method.calculate()
>> >
>> > savetxt("LPA-big.csv",transpose(2*method.aoresults[0][:data.homos[0]+1]))
>> >
>> > Script output: --------
>> > ...
>> > [Gaussian test.log INFO] Creating attribute coreelectrons[]
>> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Creating
>> > attribute aoresults: [array[2]]
>> >
>> > /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
>> > ComplexWarning: Casting complex values to real discards the imaginary
>> > part
>> >   self.aoresults[spin][i] = numpy.multiply(temp1, temp2).astype("d")
>> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Saving
>> > partitioned results in fragresults: [array[2]]
>> > [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Creating
>> > fragcharges: array[1]
>>
>> >
>> > ------------------------------------------------------------------------------
>> > RSA(R) Conference 2012
>> > Save $700 by Nov 18
>> > Register now
>> > http://p.sf.net/sfu/rsa-sfdev2dev1
>>
>> > _______________________________________________
>> > cclib-users mailing list
>> > ccl...@li...
>> > https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>> --
>> written by Karol Langner
>> Sat Nov  5 09:34:29 CET 2011
>
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

Re: [cclib-users] A question about LPA

[Karol M. L. <kar...@gm...>]

Hi Martin,

Can you provide the output file for that Gaussian job?

Best,
Karol

On Nov 04 2011, Martin Rahm wrote:
> Dear List,
> 
> I'm running a trial Löwdin population analysis (LPA) on SF6, from a
>  B3LYP/cc-pVTZ calculation. Something is awry, the total number of
> electrons gets overestimated by 0.3 (70.3), and there is a "complex
> warning" when running the LPA.
> 
> LPA is supposed to be rotationally invariant if one use "pure" spherical
> harmonics in the basis set, e.g. 5 d functions instead of 6. (which cc-pVTZ
> does). Anyone have any clue to this behavior?
> 
> Best regards,
> Martin
> 
> Gaussian Input: ---------
> # opt freq b3lyp/cc-pvtz pop=(nboread,full) iop(3/33=1,3/36=-1)
> 
> Title Card Required
> 
> 0 1
>  F                  0.00000000    0.00000000    1.57972200
>  F                  0.00000000    1.57972200    0.00000000
>  F                  0.00000000    0.00000000   -1.57972200
>  F                  0.00000000   -1.57972200    0.00000000
>  F                  1.57972200    0.00000000    0.00000000
>  F                 -1.57972200    0.00000000    0.00000000
>  S                  0.00000000    0.00000000    0.00000000
> 
> Python script: --------
> from numpy import *
> from cclib.parser import ccopen
> from cclib.method import LPA
> parser = ccopen("test.log")
> data = parser.parse()
> method = LPA(data)
> method.calculate()
> savetxt("LPA-big.csv",transpose(2*method.aoresults[0][:data.homos[0]+1]))
> 
> Script output: --------
> ...
> [Gaussian test.log INFO] Creating attribute coreelectrons[]
> [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Creating
> attribute aoresults: [array[2]]
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
> ComplexWarning: Casting complex values to real discards the imaginary part
>   self.aoresults[spin][i] = numpy.multiply(temp1, temp2).astype("d")
> [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Saving
> partitioned results in fragresults: [array[2]]
> [LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Creating
> fragcharges: array[1]

> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1

> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users


-- 
written by Karol Langner
Sat Nov  5 09:34:29 CET 2011

[cclib-users] A question about LPA

[Martin R. <mar...@gm...>]

Dear List,

I'm running a trial Löwdin population analysis (LPA) on SF6, from a
 B3LYP/cc-pVTZ calculation. Something is awry, the total number of
electrons gets overestimated by 0.3 (70.3), and there is a "complex
warning" when running the LPA.

LPA is supposed to be rotationally invariant if one use "pure" spherical
harmonics in the basis set, e.g. 5 d functions instead of 6. (which cc-pVTZ
does). Anyone have any clue to this behavior?

Best regards,
Martin

Gaussian Input: ---------
# opt freq b3lyp/cc-pvtz pop=(nboread,full) iop(3/33=1,3/36=-1)

Title Card Required

0 1
 F                  0.00000000    0.00000000    1.57972200
 F                  0.00000000    1.57972200    0.00000000
 F                  0.00000000    0.00000000   -1.57972200
 F                  0.00000000   -1.57972200    0.00000000
 F                  1.57972200    0.00000000    0.00000000
 F                 -1.57972200    0.00000000    0.00000000
 S                  0.00000000    0.00000000    0.00000000

Python script: --------
from numpy import *
from cclib.parser import ccopen
from cclib.method import LPA
parser = ccopen("test.log")
data = parser.parse()
method = LPA(data)
method.calculate()
savetxt("LPA-big.csv",transpose(2*method.aoresults[0][:data.homos[0]+1]))

Script output: --------
...
[Gaussian test.log INFO] Creating attribute coreelectrons[]
[LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Creating
attribute aoresults: [array[2]]
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cclib/method/lpa.py:99:
ComplexWarning: Casting complex values to real discards the imaginary part
  self.aoresults[spin][i] = numpy.multiply(temp1, temp2).astype("d")
[LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Saving
partitioned results in fragresults: [array[2]]
[LPA <cclib.parser.data.ccData object at 0x1015ba150> INFO] Creating
fragcharges: array[1]

Re: [cclib-users] Fwd: How to do Population analysis

[Karol M. L. <kar...@gm...>]

Wiki is now updated on that particular page.

'- Karol

On Oct 25 2011, Noel O'Boyle wrote:
> ---------- Forwarded message ----------
> From: Adam Tenderholt <ate...@gm...>
> Date: 25 October 2011 06:31
> Subject: Fwd: [cclib-users] How to do Population analysis
> To: Noel O'Boyle <bao...@gm...>, "Karol M. Langner"
> <kar...@gm...>
> 
> I replied, cc'ing the cclib-users list, but it got rejected.
> 
> The wiki probably hasn't been updated since Karol's refactoring. I
> think Martin's problem is missing data = parser.parse() and passing
> the data object to the MPA constructor.
> 
> Take care,
> 
> Adam
> 
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-- 
written by Karol M. Langner
Fri Oct 28 15:09:06 CEST 2011