The InChI API used by OpenBabel to generate the InChI *does* need to
have the charge assigned to individual atoms, in spite of the InChI
identifier output not reflecting this.
Rather than modify inchiformat, I've committed an alternative to
OBMol::SetTotalCharge() which does its best to assign a specified total
charge to atoms. This is not very robust in the general case but works
for the simpler charged molecules and Zwitter ions.
So, with your (modified) patch for Gamess output files, the correct
InChI is obtained:
obabel ch3+.out -oinchi
==============================
*** Open Babel Warning in InChI code
ch3+.out :Accepted unusual valence(s): C+1,d(3)
InChI=1S/CH3/h1H3/q+1
1 molecule converted
I guess a version of this patch should be added to other compchem formats.
Chris
On 04/01/2013 18:12, fulvio ciriaco wrote:
> What was then SetTotalCharge thought for?
> Is there any reason why InChI should not use
> GetTotalCharge for designing the charge layer,
> at least when formal charges are not set/perceived?
> Setting sensible formal atomic charges seams to me much
> more work, perhaps needed for describing chemical properties,
> but not for obtaining an identifier.
> Fulvio
>
> From: "Noel O'Boyle" <baoille...@gmail.com>
> Subject: Re: [OpenBabel-Devel] add charge/mult input from gamout
> Date: Thu, 3 Jan 2013 20:46:14 +0000
>
>> InChI can handle charges no problem...
>>
>> $ obabel -:"[CH3+]" -oinchi
>> InChI=1S/CH3/h1H3/q+1
>>
>> You need to set charges on a particular atom. Small molecule file
>> formats don't really support the idea of a global charge without a
>> specified location.
>>
>> - Noel
>>
>> On 3 January 2013 17:50, fulvio ciriaco <oiv...@gmail.com> wrote:
>>> Hallo,
>>> here is the output for ch3+ from gamess, also the relevant
>>> input is attached.
>>> If I perform: ($?% is the prompt)
>>> 0% ~/local/bin/obabel -i gamout ch3+.out -o inchi
>>> InChI=1S/CH3/h1H3
>>> However
>>> import sys
>>> sys.path.insert(0,'/home/fc/local/lib')
>>> import mybabel
>>> mol=mybabel.OBMol()
>>> conv=mybabel.OBConversion()
>>> conv.SetInFormat('gamout')
>>> conv.ReadFile(mol,"ch3+.out")
>>> True
>>>>>> mol.GetTotalCharge()
>>> 1
>>>>>> mol.GetTotalSpinMultiplicity()
>>> 1
>>> What am I getting wrong?
>>> Fulvio
>>>
>>>
>>> From: Chris Morley <c.mor...@gaseq.co.uk>
>>> Subject: Re: [OpenBabel-Devel] add charge/mult input from gamout
>>> Date: Sat, 29 Dec 2012 23:23:29 +0000
>>>
>>>> On 26/12/2012 19:24, fulvio ciriaco wrote:
>>>>> Hallo,
>>>>> in the attached patch to openbabel current I made babel read the gamout
>>>>> input parameters ICHARG and MULT containing total charge
>>>>> and spin multiplicity.
>>>>> I checked that it works from the babel python bindings.
>>>>> However this did not solve my problem, i.e. obtain the right
>>>>> InChI descriptor. InChI appears to be insensitive to global
>>>>> charge setting.
>>>>> Also bonds and aromaticity sensing are not affected by the
>>>>> charge assignment.
>>>>> Anyhow, thanks for the very smart tool
>>>>
>>>> Thank you for the bug report #852. I shall ensure that CML outputs the
>>>> total charge and spin multiplicity if these are not 0 and 1 respectively.
>>>>
>>>> So that I can test the patch to gamessformat could you let me have a
>>>> copy of your gamess output file?
>>>>
>>>> On the InChI difficulty, InChI output *is* sensitive to total charge:
>>>>
>>>> obabel -:[CH3] -:[CH3+] -oinchi
>>>> InChI=1S/CH3/h1H3
>>>> InChI=1S/CH3/h1H3/q+1
>>>> 2 molecules converted
>>>>
>>>> so something else must be wrong.
>>>>
>>>> Chris
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
>>>> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
>>>> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
>>>> MVPs and experts. SALE $99.99 this month only -- learn more at:
>>>> http://p.sf.net/sfu/learnmore_122912
>>>> _______________________________________________
>>>> OpenBabel-Devel mailing list
>>>> OpenBabel-Devel@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>>>
>>> $contrl icharg=1 $end
>>> $basis gbasis=n31 ngauss=6 $end
>>> $data
>>> test ch3+
>>> C1
>>> C 6.0 -0.0000161805 0.0000000000 -0.3750370006
>>> H 1.0 1.0766201989 -0.0000000000 -0.3348930828
>>> H 1.0 -0.5383020092 0.9330744440 -0.3950349583
>>> H 1.0 -0.5383020092 -0.9330744440 -0.3950349583
>>> $end
>>>
>>> running in /home/scratch//home/fc/Damiana/test/ch3+
>>> ----- GAMESS execution script -----
>>> This job is running on host m4300fc
>>> under operating system Linux at gio 3 gen 2013, 18.42.33, CET
>>> Available scratch disk space at beginning of the job is
>>> Filesystem 1M-blocks Used Available Use% Mounted on
>>> /dev/sda7 64104 37181 23667 62% /home
>>> scratch dir is /home/scratch//home/fc/Damiana/test/ch3+
>>> /home/fc/bin/ddikick.x /home/fc/bin/gamess.00.x
>>> /home/fc/Damiana/test/ch3+.inp -ddi 1 1 m4300fc:cpus=1
>>>
>>> Distributed Data Interface kickoff program.
>>> Initiating 1 compute processes on 1 nodes to run the following command:
>>> /home/fc/bin/gamess.00.x /home/fc/Damiana/test/ch3+.inp
>>>
>>> ******************************************************
>>> * GAMESS VERSION = 1 MAY 2012 (R1) *
>>> * FROM IOWA STATE UNIVERSITY *
>>> * M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, *
>>> * M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, *
>>> * K.A.NGUYEN, S.J.SU, T.L.WINDUS, *
>>> * TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY *
>>> * J.COMPUT.CHEM. 14, 1347-1363(1993) *
>>> **************** 64 BIT LINUX VERSION ****************
>>>
>>> SINCE 1993, STUDENTS AND POSTDOCS WORKING AT IOWA STATE UNIVERSITY
>>> AND ALSO IN THEIR VARIOUS JOBS AFTER LEAVING ISU HAVE MADE IMPORTANT
>>> CONTRIBUTIONS TO THE CODE:
>>> IVANA ADAMOVIC, CHRISTINE AIKENS, YURI ALEXEEV, POOJA ARORA,
>>> ANDREY ASADCHEV, ROB BELL, PRADIPTA BANDYOPADHYAY, JONATHAN BENTZ,
>>> BRETT BODE, GALINA CHABAN, WEI CHEN, CHEOL HO CHOI, PAUL DAY,
>>> ALBERT DEFUSCO, TIM DUDLEY, DMITRI FEDOROV, GRAHAM FLETCHER,
>>> MARK FREITAG, KURT GLAESEMANN, DAN KEMP, GRANT MERRILL,
>>> NORIYUKI MINEZAWA, JONATHAN MULLIN, TAKESHI NAGATA,
>>> SEAN NEDD, HEATHER NETZLOFF, BOSILJKA NJEGIC, RYAN OLSON, MIKE PAK,
>>> JIM SHOEMAKER, LYUDMILA SLIPCHENKO, SAROM SOK, JIE SONG,
>>> TETSUYA TAKETSUGU, SIMON WEBB, SOOHAENG YOO, FEDERICO ZAHARIEV
>>>
>>> ADDITIONAL CODE HAS BEEN PROVIDED BY COLLABORATORS IN OTHER GROUPS:
>>> IOWA STATE UNIVERSITY:
>>> JOE IVANIC, LAIMUTIS BYTAUTAS, KLAUS RUEDENBERG
>>> UNIVERSITY OF TOKYO: KIMIHIKO HIRAO, TAKAHITO NAKAJIMA,
>>> TAKAO TSUNEDA, MUNEAKI KAMIYA, SUSUMU YANAGISAWA,
>>> KIYOSHI YAGI, MAHITO CHIBA, SEIKEN TOKURA, NAOAKI KAWAKAMI
>>> UNIVERSITY OF AARHUS: FRANK JENSEN
>>> UNIVERSITY OF IOWA: VISVALDAS KAIRYS, HUI LI
>>> NATIONAL INST. OF STANDARDS AND TECHNOLOGY: WALT STEVENS, DAVID GARMER
>>> UNIVERSITY OF PISA: BENEDETTA MENNUCCI, JACOPO TOMASI
>>> UNIVERSITY OF MEMPHIS: HENRY KURTZ, PRAKASHAN KORAMBATH
>>> UNIVERSITY OF ALBERTA: TOBY ZENG, MARIUSZ KLOBUKOWSKI
>>> UNIVERSITY OF NEW ENGLAND: MARK SPACKMAN
>>> MIE UNIVERSITY: HIROAKI UMEDA
>>> MICHIGAN STATE UNIVERSITY:
>>> KAROL KOWALSKI, MARTA WLOCH, JEFFREY GOUR, JESSE LUTZ, PIOTR
>>> PIECUCH
>>> UNIVERSITY OF SILESIA: MONIKA MUSIAL, STANISLAW KUCHARSKI
>>> FACULTES UNIVERSITAIRES NOTRE-DAME DE LA PAIX:
>>> OLIVIER QUINET, BENOIT CHAMPAGNE
>>> UNIVERSITY OF CALIFORNIA - SANTA BARBARA: BERNARD KIRTMAN
>>> INSTITUTE FOR MOLECULAR SCIENCE:
>>> KAZUYA ISHIMURA, MICHIO KATOUDA, AND SHIGERU NAGASE
>>> UNIVERSITY OF NOTRE DAME: DAN CHIPMAN
>>> KYUSHU UNIVERSITY:
>>> HARUYUKI NAKANO,
>>> FENG LONG GU, JACEK KORCHOWIEC, MARCIN MAKOWSKI, AND YURIKO AOKI,
>>> HIROTOSHI MORI AND EISAKU MIYOSHI
>>> PENNSYLVANIA STATE UNIVERSITY:
>>> TZVETELIN IORDANOV, CHET SWALINA, JONATHAN SKONE,
>>> SHARON HAMMES-SCHIFFER
>>> WASEDA UNIVERSITY:
>>> MASATO KOBAYASHI, TOMOKO AKAMA, TSUGUKI TOUMA,
>>> TAKESHI YOSHIKAWA, YASUHIRO IKABATA, HIROMI NAKAI
>>> UNIVERSITY OF NEBRASKA:
>>> PEIFENG SU, DEJUN SI, NANDUN THELLAMUREGE, YALI WANG, HUI LI
>>> UNIVERSITY OF ZURICH:
>>> ROBERTO PEVERATI, KIM BALDRIDGE
>>> N. COPERNICUS UNIVERSITY AND JACKSON STATE UNIVERSITY:
>>> MARIA BARYSZ
>>>
>>> EXECUTION OF GAMESS BEGUN Thu Jan 3 18:42:33 2013
>>>
>>> ECHO OF THE FIRST FEW INPUT CARDS -
>>> INPUT CARD> $contrl icharg=1 $end
>>> INPUT CARD> $basis gbasis=n31 ngauss=6 $end
>>> INPUT CARD> $data
>>> INPUT CARD>test ch3+
>>> INPUT CARD> C1
>>> INPUT CARD> C 6.0 -0.0000161805 0.0000000000 -0.3750370006
>>> INPUT CARD> H 1.0 1.0766201989 -0.0000000000 -0.3348930828
>>> INPUT CARD> H 1.0 -0.5383020092 0.9330744440 -0.3950349583
>>> INPUT CARD> H 1.0 -0.5383020092 -0.9330744440 -0.3950349583
>>> INPUT CARD> $end
>>> 1000000 WORDS OF MEMORY AVAILABLE
>>>
>>> BASIS OPTIONS
>>> -------------
>>> GBASIS=N31 IGAUSS= 6 POLAR=NONE
>>> NDFUNC= 0 NFFUNC= 0 DIFFSP= F
>>> NPFUNC= 0 DIFFS= F BASNAM=
>>>
>>>
>>> RUN TITLE
>>> ---------
>>> test ch3+
>>>
>>> THE POINT GROUP OF THE MOLECULE IS C1
>>> THE ORDER OF THE PRINCIPAL AXIS IS 0
>>>
>>> ATOM ATOMIC COORDINATES (BOHR)
>>> CHARGE X Y Z
>>> C 6.0 -0.0000305767 0.0000000000 -0.7087171664
>>> H 1.0 2.0345171688 -0.0000000000 -0.6328561617
>>> H 1.0 -1.0172432960 1.7632550253 -0.7465078268
>>> H 1.0 -1.0172432960 -1.7632550253 -0.7465078268
>>>
>>> INTERNUCLEAR DISTANCES (ANGS.)
>>> ------------------------------
>>>
>>> 1 C 2 H 3 H 4 H
>>>
>>> 1 C 0.0000000 1.0773845 * 1.0773948 * 1.0773948 *
>>> 2 H 1.0773845 * 0.0000000 1.8660704 * 1.8660704 *
>>> 3 H 1.0773948 * 1.8660704 * 0.0000000 1.8661489 *
>>> 4 H 1.0773948 * 1.8660704 * 1.8661489 * 0.0000000
>>>
>>> * ... LESS THAN 3.000
>>>
>>>
>>> ATOMIC BASIS SET
>>> ----------------
>>> THE CONTRACTED PRIMITIVE FUNCTIONS HAVE BEEN UNNORMALIZED
>>> THE CONTRACTED BASIS FUNCTIONS ARE NOW NORMALIZED TO UNITY
>>>
>>> SHELL TYPE PRIMITIVE EXPONENT CONTRACTION COEFFICIENT(S)
>>>
>>> C
>>>
>>> 1 S 1 3047.5248800 0.001834737132
>>> 1 S 2 457.3695180 0.014037322813
>>> 1 S 3 103.9486850 0.068842622264
>>> 1 S 4 29.2101553 0.232184443216
>>> 1 S 5 9.2866630 0.467941348435
>>> 1 S 6 3.1639270 0.362311985337
>>>
>>> 2 L 7 7.8682723 -0.119332419775
>>> 0.068999066591
>>> 2 L 8 1.8812885 -0.160854151696
>>> 0.316423960957
>>> 2 L 9 0.5442493 1.143456437840
>>> 0.744308290898
>>>
>>> 3 L 10 0.1687145 1.000000000000
>>> 1.000000000000
>>>
>>> H
>>>
>>> 4 S 11 18.7311370 0.033494604338
>>> 4 S 12 2.8253944 0.234726953484
>>> 4 S 13 0.6401217 0.813757326146
>>>
>>> 5 S 14 0.1612778 1.000000000000
>>>
>>> H
>>>
>>> 6 S 15 18.7311370 0.033494604338
>>> 6 S 16 2.8253944 0.234726953484
>>> 6 S 17 0.6401217 0.813757326146
>>>
>>> 7 S 18 0.1612778 1.000000000000
>>>
>>> H
>>>
>>> 8 S 19 18.7311370 0.033494604338
>>> 8 S 20 2.8253944 0.234726953484
>>> 8 S 21 0.6401217 0.813757326146
>>>
>>> 9 S 22 0.1612778 1.000000000000
>>>
>>> TOTAL NUMBER OF BASIS SET SHELLS = 9
>>> NUMBER OF CARTESIAN GAUSSIAN BASIS FUNCTIONS = 15
>>> NUMBER OF ELECTRONS = 8
>>> CHARGE OF MOLECULE = 1
>>> SPIN MULTIPLICITY = 1
>>> NUMBER OF OCCUPIED ORBITALS (ALPHA) = 4
>>> NUMBER OF OCCUPIED ORBITALS (BETA ) = 4
>>> TOTAL NUMBER OF ATOMS = 4
>>> THE NUCLEAR REPULSION ENERGY IS 9.6916987169
>>>
>>> $CONTRL OPTIONS
>>> ---------------
>>> SCFTYP=RHF RUNTYP=ENERGY EXETYP=RUN
>>> MPLEVL= 0 CITYP =NONE CCTYP =NONE VBTYP =NONE
>>> DFTTYP=NONE TDDFT =NONE
>>> MULT = 1 ICHARG= 1 NZVAR = 0 COORD =UNIQUE
>>> PP =NONE RELWFN=NONE LOCAL =NONE NUMGRD=
>>> F
>>> ISPHER= -1 NOSYM = 0 MAXIT = 30 UNITS =ANGS
>>> PLTORB= F MOLPLT= F AIMPAC= F FRIEND=
>>> NPRINT= 7 IREST = 0 GEOM =INPUT
>>> NORMF = 0 NORMP = 0 ITOL = 20 ICUT =
>>> 9
>>> INTTYP=BEST GRDTYP=BEST QMTTOL= 1.0E-06
>>>
>>> $SYSTEM OPTIONS
>>> ---------------
>>> REPLICATED MEMORY= 1000000 WORDS (ON EVERY NODE).
>>> DISTRIBUTED MEMDDI= 0 MILLION WORDS IN AGGREGATE,
>>> MEMDDI DISTRIBUTED OVER 1 PROCESSORS IS 0 WORDS/PROCESSOR.
>>> TOTAL MEMORY REQUESTED ON EACH PROCESSOR= 1000000 WORDS.
>>> TIMLIM= 525600.00 MINUTES, OR 365.0 DAYS.
>>> PARALL= F BALTYP= DLB KDIAG= 0 COREFL= F
>>> MXSEQ2= 300 MXSEQ3= 150
>>>
>>> ----------------
>>> PROPERTIES INPUT
>>> ----------------
>>>
>>> MOMENTS FIELD POTENTIAL DENSITY
>>> IEMOM = 1 IEFLD = 0 IEPOT = 0 IEDEN = 0
>>> WHERE =COMASS WHERE =NUCLEI WHERE =NUCLEI WHERE =NUCLEI
>>> OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH
>>> IEMINT= 0 IEFINT= 0 IEDINT= 0
>>> MORB = 0
>>> EXTRAPOLATION IN EFFECT
>>> SOSCF IN EFFECT
>>> ORBITAL PRINTING OPTION: NPREO= 1 15 2 1
>>>
>>> -------------------------------
>>> INTEGRAL TRANSFORMATION OPTIONS
>>> -------------------------------
>>> NWORD = 0
>>> CUTOFF = 1.0E-09 MPTRAN = 0
>>> DIRTRF = F AOINTS =DUP
>>>
>>> ----------------------
>>> INTEGRAL INPUT OPTIONS
>>> ----------------------
>>> NOPK = 1 NORDER= 0 SCHWRZ= F
>>>
>>> ------------------------------------------
>>> THE POINT GROUP IS C1 , NAXIS= 0, ORDER= 1
>>> ------------------------------------------
>>>
>>> DIMENSIONS OF THE SYMMETRY SUBSPACES ARE
>>> A = 15
>>>
>>> ..... DONE SETTING UP THE RUN .....
>>> STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
>>> TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 0.00%
>>>
>>> ********************
>>> 1 ELECTRON INTEGRALS
>>> ********************
>>> ...... END OF ONE-ELECTRON INTEGRALS ......
>>> STEP CPU TIME = 0.01 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
>>> TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 100.00%
>>>
>>> -------------
>>> GUESS OPTIONS
>>> -------------
>>> GUESS =HUCKEL NORB = 0 NORDER= 0
>>> MIX = F PRTMO = F PUNMO = F
>>> TOLZ = 1.0E-08 TOLE = 1.0E-05
>>> SYMDEN= F PURIFY= F
>>>
>>> INITIAL GUESS ORBITALS GENERATED BY HUCKEL ROUTINE.
>>> HUCKEL GUESS REQUIRES 4657 WORDS.
>>>
>>> SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BOTH SET(S).
>>> 4 ORBITALS ARE OCCUPIED ( 1 CORE ORBITALS).
>>> 2=A 3=A 4=A 5=A 6=A 7=A 8=A
>>> 9=A 10=A 11=A 12=A 13=A 14=A
>>> ...... END OF INITIAL ORBITAL SELECTION ......
>>> STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
>>> TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 100.00%
>>>
>>> ----------------------
>>> AO INTEGRAL TECHNOLOGY
>>> ----------------------
>>> S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY
>>> KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR).
>>> S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY
>>> KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE).
>>> S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5,
>>> ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED
>>> SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER).
>>> S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY
>>> MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY).
>>>
>>> --------------------
>>> 2 ELECTRON INTEGRALS
>>> --------------------
>>>
>>> THE -PK- OPTION IS OFF, THE INTEGRALS ARE NOT IN SUPERMATRIX FORM.
>>> STORING 15000 INTEGRALS/RECORD ON DISK, USING 12 BYTES/INTEGRAL.
>>> TWO ELECTRON INTEGRAL EVALUATION REQUIRES 89401 WORDS OF MEMORY.
>>> II,JST,KST,LST = 1 1 1 1 NREC = 1 INTLOC = 1
>>> II,JST,KST,LST = 2 1 1 1 NREC = 1 INTLOC = 2
>>> II,JST,KST,LST = 3 1 1 1 NREC = 1 INTLOC = 34
>>> II,JST,KST,LST = 4 1 1 1 NREC = 1 INTLOC = 214
>>> II,JST,KST,LST = 5 1 1 1 NREC = 1 INTLOC = 529
>>> II,JST,KST,LST = 6 1 1 1 NREC = 1 INTLOC = 960
>>> II,JST,KST,LST = 7 1 1 1 NREC = 1 INTLOC = 1830
>>> II,JST,KST,LST = 8 1 1 1 NREC = 1 INTLOC = 2935
>>> II,JST,KST,LST = 9 1 1 1 NREC = 1 INTLOC = 4296
>>> TOTAL NUMBER OF NONZERO TWO-ELECTRON INTEGRALS = 5972
>>> 1 INTEGRAL RECORDS WERE STORED ON DISK FILE 8.
>>> ...... END OF TWO-ELECTRON INTEGRALS .....
>>> STEP CPU TIME = 0.02 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
>>> TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 100.00%
>>>
>>> --------------------------
>>> RHF SCF CALCULATION
>>> --------------------------
>>>
>>> NUCLEAR ENERGY = 9.6916987169
>>> MAXIT = 30 NPUNCH= 2
>>> EXTRAP=T DAMP=F SHIFT=F RSTRCT=F DIIS=F DEM=F SOSCF=T
>>> DENSITY MATRIX CONV= 1.00E-05
>>> SOSCF WILL OPTIMIZE 44 ORBITAL ROTATIONS, SOGTOL= 0.250
>>> MEMORY REQUIRED FOR RHF ITERS= 31961 WORDS.
>>>
>>> ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD
>>> 1 0 0 -39.0502073739 -39.0502073739 0.269398865 0.000000000
>>> ---------------START SECOND ORDER SCF---------------
>>> 2 1 0 -39.2100477533 -0.1598403795 0.080706851 0.028392040
>>> 3 2 0 -39.2158946974 -0.0058469440 0.012991907 0.010025433
>>> 4 3 0 -39.2162025018 -0.0003078045 0.003832488 0.001978276
>>> 5 4 0 -39.2162106445 -0.0000081426 0.000682206 0.000223432
>>> 6 5 0 -39.2162108688 -0.0000002244 0.000033443 0.000020378
>>> 7 6 0 -39.2162108709 -0.0000000021 0.000017628 0.000003777
>>> 8 7 0 -39.2162108710 -0.0000000001 0.000001782 0.000000692
>>> 9 8 0 -39.2162108710 -0.0000000000 0.000000137 0.000000085
>>>
>>> -----------------
>>> DENSITY CONVERGED
>>> -----------------
>>> TIME TO FORM FOCK OPERATORS= 0.0 SECONDS ( 0.0 SEC/ITER)
>>> TIME TO SOLVE SCF EQUATIONS= 0.0 SECONDS ( 0.0 SEC/ITER)
>>>
>>> FINAL RHF ENERGY IS -39.2162108710 AFTER 9 ITERATIONS
>>>
>>> ------------
>>> EIGENVECTORS
>>> ------------
>>>
>>> 1 2 3 4 5
>>> -11.6820 -1.2857 -0.9564 -0.9563 -0.2832
>>> A A A A A
>>> 1 C 1 S 0.996309 -0.204644 0.000000 0.000005 0.000009
>>> 2 C 1 S 0.023480 0.453541 0.000000 -0.000012 -0.000017
>>> 3 C 1 X 0.000000 0.000013 0.000000 0.516841 -0.018707
>>> 4 C 1 Y -0.000000 0.000000 0.517197 -0.000000 0.000000
>>> 5 C 1 Z -0.000000 0.000012 0.000000 0.019248 0.502325
>>> 6 C 1 S -0.012845 0.374583 0.000000 -0.000012 -0.000047
>>> 7 C 1 X -0.000000 0.000005 0.000000 0.220385 -0.023233
>>> 8 C 1 Y -0.000000 -0.000000 0.220543 -0.000000 0.000000
>>> 9 C 1 Z -0.000000 0.000004 0.000000 0.008207 0.623851
>>> 10 H 2 S -0.000132 0.156533 0.000000 0.286684 0.000009
>>> 11 H 2 S 0.002793 0.021746 0.000000 0.121723 0.000011
>>> 12 H 3 S -0.000132 0.156526 0.248274 -0.143344 0.000009
>>> 13 H 3 S 0.002793 0.021747 0.105405 -0.060864 0.000011
>>> 14 H 4 S -0.000132 0.156526 -0.248274 -0.143344 0.000009
>>> 15 H 4 S 0.002793 0.021747 -0.105405 -0.060864 0.000011
>>>
>>> 6 7 8 9 10
>>> -0.0209 0.0364 0.0364 0.4193 0.4194
>>> A A A A A
>>> 1 C 1 S -0.139558 0.000010 -0.000000 -0.000001 0.000000
>>> 2 C 1 S 0.241743 -0.000018 -0.000000 0.000062 0.000000
>>> 3 C 1 X -0.000023 -0.363767 0.000000 -0.780043 -0.000000
>>> 4 C 1 Y -0.000000 0.000000 0.364029 0.000000 -0.780601
>>> 5 C 1 Z 0.000020 -0.013547 0.000000 -0.029050 -0.000000
>>> 6 C 1 S 2.139376 -0.000213 0.000000 -0.000026 -0.000000
>>> 7 C 1 X -0.000067 -1.459896 0.000000 1.838531 0.000000
>>> 8 C 1 Y -0.000000 0.000000 1.460987 -0.000000 1.840056
>>> 9 C 1 Z 0.000082 -0.054368 0.000000 0.068469 0.000000
>>> 10 H 2 S -0.066109 0.116231 -0.000000 -0.450605 -0.000000
>>> 11 H 2 S -1.091731 1.925413 -0.000000 -0.594626 -0.000000
>>> 12 H 3 S -0.066135 -0.058124 -0.100643 0.225339 -0.390253
>>> 13 H 3 S -1.091901 -0.962535 -1.667423 0.297264 -0.515152
>>> 14 H 4 S -0.066135 -0.058124 0.100643 0.225338 0.390253
>>> 15 H 4 S -1.091901 -0.962534 1.667423 0.297264 0.515152
>>>
>>> 11 12 13 14 15
>>> 0.4632 0.6123 0.8787 0.8980 0.8980
>>> A A A A A
>>> 1 C 1 S 0.000005 -0.065351 0.048648 -0.000025 0.000000
>>> 2 C 1 S -0.000024 -1.161971 -1.739776 0.000752 0.000000
>>> 3 C 1 X -0.041240 -0.000062 0.000361 0.839690 -0.000000
>>> 4 C 1 Y -0.000000 0.000000 0.000000 0.000000 0.840267
>>> 5 C 1 Z 1.107369 0.000027 -0.000037 0.031271 -0.000000
>>> 6 C 1 S -0.000018 2.490020 3.302086 -0.001409 -0.000000
>>> 7 C 1 X 0.038871 0.000252 -0.000414 -1.018321 0.000000
>>> 8 C 1 Y -0.000000 0.000000 -0.000000 -0.000000 -1.018974
>>> 9 C 1 Z -1.043747 0.000060 0.000068 -0.037924 0.000000
>>> 10 H 2 S 0.000020 -0.585529 0.499594 -1.016606 0.000000
>>> 11 H 2 S 0.000005 -0.268375 -1.141323 1.540929 -0.000000
>>> 12 H 3 S 0.000020 -0.585535 0.500289 0.507925 -0.880202
>>> 13 H 3 S 0.000005 -0.268094 -1.142355 -0.769704 1.333989
>>> 14 H 4 S 0.000020 -0.585535 0.500289 0.507925 0.880202
>>> 15 H 4 S 0.000005 -0.268094 -1.142355 -0.769704 -1.333989
>>> ...... END OF RHF CALCULATION ......
>>> STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
>>> TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 75.00%
>>>
>>> ----------------------------------------------------------------
>>> PROPERTY VALUES FOR THE RHF SELF-CONSISTENT FIELD WAVEFUNCTION
>>> ----------------------------------------------------------------
>>>
>>> -----------------
>>> ENERGY COMPONENTS
>>> -----------------
>>>
>>> WAVEFUNCTION NORMALIZATION = 1.0000000000
>>>
>>> ONE ELECTRON ENERGY = -68.0552053924
>>> TWO ELECTRON ENERGY = 19.1472958045
>>> NUCLEAR REPULSION ENERGY = 9.6916987169
>>> ------------------
>>> TOTAL ENERGY = -39.2162108710
>>>
>>> ELECTRON-ELECTRON POTENTIAL ENERGY = 19.1472958045
>>> NUCLEUS-ELECTRON POTENTIAL ENERGY = -107.3312399388
>>> NUCLEUS-NUCLEUS POTENTIAL ENERGY = 9.6916987169
>>> ------------------
>>> TOTAL POTENTIAL ENERGY = -78.4922454175
>>> TOTAL KINETIC ENERGY = 39.2760345465
>>> VIRIAL RATIO (V/T) = 1.9984768402
>>>
>>> ---------------------------------------
>>> MULLIKEN AND LOWDIN POPULATION ANALYSES
>>> ---------------------------------------
>>>
>>> ATOMIC MULLIKEN POPULATION IN EACH MOLECULAR ORBITAL
>>>
>>> 1 2 3 4
>>>
>>> 2.000000 2.000000 2.000000 2.000000
>>>
>>> 1 1.998352 1.498423 1.254907 1.254896
>>> 2 0.000549 0.167201 0.000000 0.496730
>>> 3 0.000549 0.167188 0.372546 0.124187
>>> 4 0.000549 0.167188 0.372547 0.124187
>>>
>>> ----- POPULATIONS IN EACH AO -----
>>> MULLIKEN LOWDIN
>>> 1 C 1 S 1.99803 1.99223
>>> 2 C 1 S 0.80628 0.67994
>>> 3 C 1 X 0.88182 0.78918
>>> 4 C 1 Y 0.88304 0.79027
>>> 5 C 1 Z 0.00122 0.00109
>>> 6 C 1 S 0.69247 0.50950
>>> 7 C 1 X 0.37134 0.45829
>>> 8 C 1 Y 0.37186 0.45892
>>> 9 C 1 Z 0.00052 0.00064
>>> 10 H 2 S 0.51544 0.47416
>>> 11 H 2 S 0.14905 0.29916
>>> 12 H 3 S 0.51543 0.47415
>>> 13 H 3 S 0.14904 0.29916
>>> 14 H 4 S 0.51543 0.47415
>>> 15 H 4 S 0.14904 0.29916
>>>
>>> ----- MULLIKEN ATOMIC OVERLAP POPULATIONS -----
>>> (OFF-DIAGONAL ELEMENTS NEED TO BE MULTIPLIED BY 2)
>>>
>>> 1 2 3 4
>>>
>>> 1 4.9711504
>>> 2 0.3451433 0.3448240
>>> 3 0.3451421 -0.0127433 0.3448099
>>> 4 0.3451421 -0.0127433 -0.0127379 0.3448099
>>>
>>> TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS
>>> ATOM MULL.POP. CHARGE LOW.POP. CHARGE
>>> 1 C 6.006578 -0.006578 5.680067 0.319933
>>> 2 H 0.664481 0.335519 0.773317 0.226683
>>> 3 H 0.664471 0.335529 0.773308 0.226692
>>> 4 H 0.664471 0.335529 0.773308 0.226692
>>>
>>> -------------------------------
>>> BOND ORDER AND VALENCE ANALYSIS BOND ORDER THRESHOLD=0.050
>>> -------------------------------
>>>
>>> BOND BOND
>>> BOND
>>> ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER ATOM PAIR DIST
>>> ORDER
>>> 1 2 1.077 0.875 1 3 1.077 0.875 1 4 1.077
>>> 0.875
>>>
>>> TOTAL BONDED FREE
>>> ATOM VALENCE VALENCE VALENCE
>>> 1 C 2.624 2.624 -0.000
>>> 2 H 0.867 0.867 0.000
>>> 3 H 0.867 0.867 -0.000
>>> 4 H 0.867 0.867 0.000
>>>
>>> ---------------------
>>> ELECTROSTATIC MOMENTS
>>> ---------------------
>>>
>>> POINT 1 X Y Z (BOHR) CHARGE
>>> -0.000022 0.000000 -0.708698 1.00 (A.U.)
>>> DX DY DZ /D/ (DEBYE)
>>> 0.000035 -0.000000 0.000043 0.000055
>>> ...... END OF PROPERTY EVALUATION ......
>>> STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
>>> TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 75.00%
>>> 580000 WORDS OF DYNAMIC MEMORY USED
>>> EXECUTION OF GAMESS TERMINATED NORMALLY Thu Jan 3 18:42:33 2013
>>> DDI: 263624 bytes (0.3 MB / 0 MWords) used by master data server.
>>>
>>> ----------------------------------------
>>> CPU timing information for all processes
>>> ========================================
>>> 0: 0.24 + 0.20 = 0.44
>>> ----------------------------------------
>>> ddikick.x: exited gracefully.
>>> gio 3 gen 2013, 18.42.36, CET
>>>
>>> ------------------------------------------------------------------------------
>>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
>>> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
>>> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
>>> MVPs and experts. ON SALE this month only -- learn more at:
>>> http://p.sf.net/sfu/learnmore_122712
>>> _______________________________________________
>>> OpenBabel-Devel mailing list
>>> OpenBabel-Devel@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>>>
>
> ------------------------------------------------------------------------------
> Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and
> much more. Get web development skills now with LearnDevNow -
> 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts.
> SALE $99.99 this month only -- learn more at:
> http://p.sf.net/sfu/learnmore_122812
> _______________________________________________
> OpenBabel-Devel mailing list
> OpenBabel-Devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>
------------------------------------------------------------------------------
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
MVPs and experts. SALE $99.99 this month only -- learn more at:
http://p.sf.net/sfu/learnmore_122912
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
