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Subject: RE: [NWCHEM] unrecognised pseudopotential
Date: Fri, 21 Jul 2006 13:27:23 -0600
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Thread-Topic: [NWCHEM] unrecognised pseudopotential
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From: "Chang, Christopher" <Christopher_Chang@nrel.gov>
To: =?iso-8859-1?Q?Edoardo_Apr=E0?= <edoardo.apra@pnl.gov>
Cc: <nwchem-users@emsl.pnl.gov>
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Edo,

   Thanks for the reply. The documentation for Cartesian coordinate input states that the default charge value equals the atomic number (= nuclear charge) for that particular atom. I thus assumed that the number of electrons were related to this, and that by decreasing the value by 1, it would be equivalent to specifying a formal sulfur charge of -1 (16 + -1 = +15).
   I still see an inconsistency with the default value = atomic number, and what you've just told me that the value is the number of electrons to remove (from an atomic reference?). If this is so (which I had originally thought, so I could just specify the formal charge on each atom), shouldn't the default values be 0 rather than the atomic number?
   I just tried a simpler high-spin job (all atoms in one geometry) with the AO guess, and specified formal charges on atoms where they are expected, i.e. thiolate and sulfido sulfurs, and irons. Got the same result, and the charge table follows. Should these "charges" be adding up instead to the total number of electrons?

    1 S1                  -1.0000    -1.30390698    -1.30451970     2.64464761
    2 C                    6.0000    -1.44533031    -3.11985871     2.20959586
    3 H                    1.0000    -0.45877040    -3.61510465     2.23944755
    4 H                    1.0000    -2.11129324    -3.61351843     2.94358201
    5 H                    1.0000    -1.86941241    -3.24802891     1.19837339
    6 S1                  -1.0000    -1.64228597     2.42294944    -2.44931567
    7 C                    6.0000    -3.36399158     2.36687622    -1.71466538
    8 H                    1.0000    -3.75269463     1.33386200    -1.69278055
    9 H                    1.0000    -3.36164565     2.75979342    -0.68311073
   10 H                    1.0000    -4.03916378     2.98866106    -2.33384058
   11 S1                  -1.0000     3.24256311     2.82600499     1.45338468
   12 C                    6.0000     2.67529396     4.57307519     1.08925612
   13 H                    1.0000     1.65455558     4.74076468     1.47451052
   14 H                    1.0000     3.36661080     5.28528227     1.57977565
   15 H                    1.0000     2.67452389     4.76805756     0.00282180
   16 S1                  -1.0000     2.70046746    -2.07218513    -2.36734347
   17 C                    6.0000     2.48834975    -3.78404539    -1.64138773
   18 H                    1.0000     2.85215987    -3.81692610    -0.59954672
   19 H                    1.0000     1.42787679    -4.09212806    -1.65067424
   20 H                    1.0000     3.07282727    -4.50468779    -2.24545181
   21 S2                  -2.0000     2.07546160    -0.63336549     1.04949464
   22 S2                  -2.0000    -0.32312399     1.81608075     0.99258610
   23 S2                  -2.0000     1.74587671     1.38657361    -1.68814986
   24 S2                  -2.0000    -0.64308258    -0.95684054    -0.99875320
   25 Fe3                  3.0000     1.75930250     1.45697943     0.47619297
   26 Fe2                  2.0000    -0.07136458    -0.34864186     1.01288881
   27 Fe3                  3.0000    -0.34346985     1.19497210    -1.08736869
   28 Fe2                  2.0000     1.51041367    -0.68186775    -1.04521070



> -----Original Message-----
> From: Edoardo Apr [mailto:edoardo.apra@pnl.gov] 
> Sent: Friday, July 21, 2006 12:18 PM
> To: Chang, Christopher
> Subject: Re: [NWCHEM] unrecognised pseudopotential
> 
> Christopher
> the problem is in the following geometry line
> S1        -1.669763    1.897252    2.813787  charge 15
> 
> This remove 15 electrons (out of 16) for the sulfur atom and, 
> therefore, 
> causes the atomic calculation (used in the starting guess) to crash.
> 
> Why did you specify a charge of +15?
> 
> Thanks, Edo
> 
> Chang, Christopher wrote:
> >
> > I am encountering the same "unrecognised pseudopotential  
> 911" problem 
> > outlined in the Archived message pasted at the bottom of 
> this message, 
> > on the Jacquard system at NERSC (NWChem 4.7). Was there any 
> resolution 
> > to this that didn't show up in the Archive? My input deck 
> follows, but 
> > is essentially an LSD single-point DFT calculation on a high-spin 
> > [4Fe4S]2+ cluster built up from fragments. It's not getting 
> past the 
> > first fragment anyway, so I guess it has something to do with the 
> > charge input. I am not using a pseudopotential.
> >
> > Thanks in advance,
> >
> > Chris
> >
> > MY INPUT:
> >
> > START FS4Cys4
> > SCRATCH_DIR ./
> > PERMANENT_DIR /u0/cchang/NWChem
> > MEMORY total 100 mb
> > ECHO
> > PRINT medium "ga stats" "ma stats"
> >
> > title "Calculation of high-spin Cys4[4Fe4S] from fragments"
> >
> > geometry FS4_2+_HS noautoz
> > S1        -1.669763    1.897252    2.813787
> > C         -3.485171    2.042282    2.380213
> > H         -3.979269    1.054837    2.396936
> > H         -3.979770    2.697931    3.122802
> > H         -3.613616    2.479513    1.374641
> > S1         2.058422    2.307128   -2.274398
> > C          2.000174    4.018929   -1.517120
> > H          0.966701    4.406104   -1.490353
> > H          2.392868    4.003438   -0.485594
> > H          2.621304    4.702933   -2.127192
> > S1         2.466338   -2.628290    1.563639
> > C          4.212823   -2.054230    1.207432
> > H          4.379234   -1.038466    1.606153
> > H          4.925731   -2.751124    1.688959
> > H          4.408042   -2.038905    0.121148
> > S1        -2.431647   -2.041571   -2.250755
> > C         -4.143913   -1.841043   -1.522466
> > H         -4.176596   -2.218599   -0.485521
> > H         -4.453234   -0.780900   -1.517839
> > H         -4.863739   -2.418344   -2.134354
> > S2        -0.994307   -1.460001    1.174365
> > S2         1.452344    0.941983    1.149666
> > S2         1.025844   -1.091985   -1.558222
> > S2        -1.320514    1.284939   -0.837930
> > Fe3        1.095792   -1.133870    0.605772
> > Fe2       -0.712087    0.687452    1.166140
> > Fe3        0.831667    0.989032   -0.929985
> > Fe2       -1.043012   -0.867435   -0.912718
> > end
> >
> > geometry Cys+S noautoz
> > S1        -1.669763    1.897252    2.813787  charge 15
> > C         -3.485171    2.042282    2.380213  charge 6
> > H         -3.979269    1.054837    2.396936  charge 1
> > H         -3.979770    2.697931    3.122802  charge 1
> > H         -3.613616    2.479513    1.374641  charge 1
> > S1         2.058422    2.307128   -2.274398  charge 15
> > C          2.000174    4.018929   -1.517120  charge 6
> > H          0.966701    4.406104   -1.490353  charge 1
> > H          2.392868    4.003438   -0.485594  charge 1
> > H          2.621304    4.702933   -2.127192  charge 1
> > S1         2.466338   -2.628290    1.563639  charge 15
> > C          4.212823   -2.054230    1.207432  charge 6
> > H          4.379234   -1.038466    1.606153  charge 1
> > H          4.925731   -2.751124    1.688959  charge 1
> > H          4.408042   -2.038905    0.121148  charge 1
> > S1        -2.431647   -2.041571   -2.250755  charge 15
> > C         -4.143913   -1.841043   -1.522466  charge 6
> > H         -4.176596   -2.218599   -0.485521  charge 1
> > H         -4.453234   -0.780900   -1.517839  charge 1
> > H         -4.863739   -2.418344   -2.134354  charge 1
> > S2        -0.994307   -1.460001    1.174365  charge 14
> > S2         1.452344    0.941983    1.149666  charge 14
> > S2         1.025844   -1.091985   -1.558222  charge 14
> > S2        -1.320514    1.284939   -0.837930  charge 14
> > Bq3        1.095792   -1.133870    0.605772  charge +3 # Fe1 ferric
> > Bq2       -0.712087    0.687452    1.166140  charge +2 # Fe2 ferrous
> > Bq3        0.831667    0.989032   -0.929985  charge +3 # Fe3 ferric
> > Bq2       -1.043012   -0.867435   -0.912718  charge +2 # Fe4 ferrous
> > end
> >
> > geometry Fe1 noautoz
> > Fe3        1.095792   -1.133870    0.605772  charge 29 # ferric
> > Bq2       -0.712087    0.687452    1.166140  charge +2 # Fe2 ferrous
> > Bq3        0.831667    0.989032   -0.929985  charge +3 # Fe3 ferric
> > Bq2       -1.043012   -0.867435   -0.912718  charge +2 # Fe4 ferrous
> > Bq1       -1.669763    1.897252    2.813787  charge -1 # Cys1 S
> > Bq1        2.058422    2.307128   -2.274398  charge -1 # Cys2 S
> > Bq1        2.466338   -2.628290    1.563639  charge -1 # Cys3 S
> > Bq1       -2.431647   -2.041571   -2.250755  charge -1 # Cys4 S
> > Bq4       -0.994307   -1.460001    1.174365  charge -2 # sulfide 1
> > Bq4        1.452344    0.941983    1.149666  charge -2 # sulfide 2
> > Bq4        1.025844   -1.091985   -1.558222  charge -2 # sulfide 3
> > Bq4       -1.320514    1.284939   -0.837930  charge -2 # sulfide 4
> > end
> >
> > geometry Fe2 noautoz
> > Fe2       -0.712087    0.687452    1.166140  charge 28 # ferrous
> > Bq3        1.095792   -1.133870    0.605772  charge +3 # Fe1 ferric
> > Bq3        0.831667    0.989032   -0.929985  charge +3 # Fe3 ferric
> > Bq2       -1.043012   -0.867435   -0.912718  charge +2 # Fe4 ferrous
> > Bq1       -1.669763    1.897252    2.813787  charge -1 # Cys1 S
> > Bq1        2.058422    2.307128   -2.274398  charge -1 # Cys2 S
> > Bq1        2.466338   -2.628290    1.563639  charge -1 # Cys3 S
> > Bq1       -2.431647   -2.041571   -2.250755  charge -1 # Cys4 S
> > Bq4       -0.994307   -1.460001    1.174365  charge -2 # sulfide 1
> > Bq4        1.452344    0.941983    1.149666  charge -2 # sulfide 2
> > Bq4        1.025844   -1.091985   -1.558222  charge -2 # sulfide 3
> > Bq4       -1.320514    1.284939   -0.837930  charge -2 # sulfide 4
> > end
> >
> > geometry Fe3 noautoz
> > Fe3        0.831667    0.989032   -0.929985  charge 29 # ferric
> > Bq3        1.095792   -1.133870    0.605772  charge +3 # Fe1 ferric
> > Bq2       -0.712087    0.687452    1.166140  charge +2 # Fe2 ferrous
> > Bq2       -1.043012   -0.867435   -0.912718  charge +2 # Fe4 ferrous
> > Bq1       -1.669763    1.897252    2.813787  charge -1 # Cys1 S
> > Bq1        2.058422    2.307128   -2.274398  charge -1 # Cys2 S
> > Bq1        2.466338   -2.628290    1.563639  charge -1 # Cys3 S
> > Bq1       -2.431647   -2.041571   -2.250755  charge -1 # Cys4 S
> > Bq4       -0.994307   -1.460001    1.174365  charge -2 # sulfide 1
> > Bq4        1.452344    0.941983    1.149666  charge -2 # sulfide 2
> > Bq4        1.025844   -1.091985   -1.558222  charge -2 # sulfide 3
> > Bq4       -1.320514    1.284939   -0.837930  charge -2 # sulfide 4
> > end
> >
> > geometry Fe4 noautoz
> > Fe2       -1.043012   -0.867435   -0.912718  charge 28 # ferrous
> > Bq3        1.095792   -1.133870    0.605772  charge +3 # Fe1 ferric
> > Bq2       -0.712087    0.687452    1.166140  charge +2 # Fe2 ferrous
> > Bq3        0.831667    0.989032   -0.929985  charge +3 # Fe3 ferric
> > Bq1       -1.669763    1.897252    2.813787  charge -1 # Cys1 S
> > Bq1        2.058422    2.307128   -2.274398  charge -1 # Cys2 S
> > Bq1        2.466338   -2.628290    1.563639  charge -1 # Cys3 S
> > Bq1       -2.431647   -2.041571   -2.250755  charge -1 # Cys4 S
> > Bq4       -0.994307   -1.460001    1.174365  charge -2 # sulfide 1
> > Bq4        1.452344    0.941983    1.149666  charge -2 # sulfide 2
> > Bq4        1.025844   -1.091985   -1.558222  charge -2 # sulfide 3
> > Bq4       -1.320514    1.284939   -0.837930  charge -2 # sulfide 4
> > end
> >
> > basis "ao basis"
> >    Fe2 library 6-31g*
> >    Fe3 library 6-31g*
> >    S1 library 6-31+g*
> >    S2 library 6-31+g*
> >    C library 6-31+g*
> >    H library 6-31+g*
> > end
> >
> > basis "cd basis"
> >    Fe2 library "Ahlrichs Coulomb Fitting"
> >    Fe3 library "Ahlrichs Coulomb Fitting"
> >    S1 library "Ahlrichs Coulomb Fitting"
> >    S2 library "Ahlrichs Coulomb Fitting"
> >    C library "Ahlrichs Coulomb Fitting"
> >    H library "Ahlrichs Coulomb Fitting"
> > end
> >
> >
> > charge -2.0
> >
> > set geometry Cys+S
> > dft; mult 1; xc slater vwn_5; iterations 50; convergence 
> density 1e-8;
> >      vectors atomic output Cys+S.mo; end
> > task dft
> >
> > set geometry Fe1
> > dft; mult 6; xc slater vwn_5; iterations 100; convergence 
> density 1e-8;
> >      vectors atomic output Fe1.mo; end
> > task dft
> >
> > set geometry Fe2
> > dft; mult 5; xc slater vwn_5; iterations 300; convergence density 
> > 1e-8; smear;
> >      vectors atomic output Fe2.mo; end
> > task dft
> >
> > set geometry Fe3
> > dft; mult 6; xc slater vwn_5; iterations 100; convergence 
> density 1e-8;
> >      vectors input Fe1.mo output Fe3.mo; end
> > task dft
> >
> > set geometry Fe4
> > dft; mult 5; xc slater vwn_5; iterations 300; convergence density 
> > 1e-8; smear;
> >      vectors input Fe2.mo output Fe4.mo; end
> > task dft
> >
> > # High-spin calculation
> > set geometry FS4_2+_HS
> > dft; mult 19; xc slater vwn_5; iterations 300; convergence density 
> > 1e-8; smear;
> >      vectors input fragment Cys+S.mo Fe1.mo Fe2.mo Fe3.mo Fe4.mo \
> >      output FS4_2+_HS.movecs; end
> >      mulliken; print "final vectors" "mulliken"; end
> > task dft
> >
> >
> > ARCHIVED MESSAGE:
> >
> > Date: Tue, 12 Oct 2004 19:39:53 -0700
> > From: Edoardo Apra` <edoardo.apra@pnl.gov>
> > Subject: Re: SCF / DFT Charged Sistems with Ion
> > In-reply-to: <200410122250.26182.fjornada@terra.com.br>
> > To: Felipe Jornada <fjornada@terra.com.br>
> > Cc: nwchem-users@emsl.pnl.gov
> > Message-id: <416C9579.7040405@pnl.gov>
> > Organization: PNNL
> > MIME-version: 1.0
> > Content-type: text/plain; charset=ISO-8859-1; format=flowed
> > X-Accept-Language: en-us, en
> > User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.3) 
> > Gecko/20041003
> > References: <200410122250.26182.fjornada@terra.com.br>
> > Content-Transfer-Encoding: 8bit
> > X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by 
> > odyssey.emsl.pnl.gov id i9D2di5J007000
> > Sender: owner-nwchem-users@emsl.pnl.gov
> > Precedence: bulk
> >
> > Felipe
> > could you send the complete input?
> > You probable have an "ecp" section that did not appear in 
> the message
> > you just sent.
> > Edo
> >
> > Felipe Jornada wrote:
> >
> > > Dear NwChem users, 
> > >  
> > > I'm having problems to converge the DFT energy on a 
> system consisted 
> > > of a cation (Li +1) near a carbon cluster. If I don't set 
> the charge
> > > of each 
> > > atom, I get the following error: 
> > >  
> > > >*** The number of electrons   1 in the ECP does not 
> > > >accord with a known set of completely filled shells !!! 
> > > >
> > > 
> > 
> --------------------------------------------------------------
> ---------- 
> > > > unrecognised pseudopotential      911 
> > > 
> > 
> >-------------------------------------------------------------
> ----------- 
> > >  
> > > When I set the ionic charge with: 
> > >  
> > > " 
> > > set atomscf:z        1 
> > > set atomscf:tags_z Li 
> > > "
> > >  
> > > I get an incorrect charge distribution with Mulliken 
> analisys. The Li
> > > atom 
> > > gets 9 electron, which is absurd. In both cases, I am using these 
> > > directives: 
> > >  
> > > "
> > > charge 1 
> > >  
> > > basis 
> > >  C library sto-3g 
> > >  Li library sto-3g 
> > > end 
> > >  
> > > dft 
> > > odft 
> > > xc b3lyp 
> > > mult 1 
> > > mulliken 
> > > end 
> > > "
> > >  
> > > Also, when I set "vectors input hcore", things get a 
> little better.
> > > Instead 
> > > of the former 9 electrons the Li gets only 0.12 of them. However 
> > this is 
> > > still not the 2 electrons that I set with "set atom_scf:z" 
> > >  
> > > I have tried the "charge" keyword inside the geometry directive, 
> > > but it also doesn't work. I am also aware of the fragment 
> > approximation, 
> > > as described in nwchem's SCF documentation, but I would 
> rather find a 
> > > simpler solution, because this method would be very 
> time-consuming for
> > > me.  
> > >  
> > > Is there anything I can do to solve this problem? 
> > >  
> > > Thanks for your attention, 
> > >  
> > > Felipe Jornada 
> > > fjornada@if.ufrgs.br
> > >
> >
> > --
> > Edoardo Apr - PNNL - Battelle Blvd - Richland, WA 99352, MS K8-91
> > Tel +1-509-376-1280 Fax +1-509-376-0420
> >  
> >
> > Christopher H. Chang, Ph.D.
> > Research Associate
> > National Renewable Energy Laboratory
> > 1617 Cole Blvd., Mail Stop 1608
> > Golden, CO  80401
> > Phone (303) 275-3751
> > Fax (303) 275-4007
> >
> 
> -- 
> Edoardo Apr - PNNL - P.O. Box 999, MS K8-91 - Richland, WA 99352
> Fax +1-509-376-0420
>  
>