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
>>>
>>>
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>>
>> $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
>>
>> ------------------------------------------------------------------------------
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