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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