From owner-nwchem-users@emsl.pnl.gov Fri Jul 21 12:27:26 2006 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.6/8.13.6) with ESMTP id k6LJRQEm023629 for ; Fri, 21 Jul 2006 12:27:26 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.6/8.13.6/Submit) id k6LJRQBO023628 for nwchem-users-outgoing-0915; Fri, 21 Jul 2006 12:27:26 -0700 (PDT) X-Ironport-SG: OK_Domains X-Ironport-SBRS: 3.5 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AQAAACbHwESKRAEBCQ4q X-IronPort-AV: i="4.07,169,1151910000"; d="scan'208"; a="2148361:sNHT39837350" X-MimeOLE: Produced By Microsoft Exchange V6.0.6603.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: [NWCHEM] unrecognised pseudopotential Date: Fri, 21 Jul 2006 13:27:23 -0600 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [NWCHEM] unrecognised pseudopotential Thread-Index: Acas8fHjg6EgnKFKQpqN6waR+IuAxgABqepw From: "Chang, Christopher" To: =?iso-8859-1?Q?Edoardo_Apr=E0?= Cc: X-OriginalArrivalTime: 21 Jul 2006 19:28:36.0015 (UTC) FILETIME=[DC57D3F0:01C6ACFB] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by odyssey.emsl.pnl.gov id k6LJRPmT023625 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk 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 Aprà [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` > > Subject: Re: SCF / DFT Charged Sistems with Ion > > In-reply-to: <200410122250.26182.fjornada@terra.com.br> > > To: Felipe Jornada > > 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 Aprà - 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 Aprà - PNNL - P.O. Box 999, MS K8-91 - Richland, WA 99352 > Fax +1-509-376-0420 > >