From owner-chemistry@ccl.net Thu Mar 17 08:21:01 2011 From: "Alfred Gil Arranz agil ~ cesca.cat" To: CCL Subject: CCL: IR intensities from VASP Message-Id: <-44149-110317035112-24825-fXocy3MU7TAJ4JU0SmIM6Q[a]server.ccl.net> X-Original-From: Alfred Gil Arranz Content-Transfer-Encoding: 8bit Content-Type: text/html; charset=ISO-8859-15 Date: Thu, 17 Mar 2011 08:51:02 +0100 MIME-Version: 1.0 Sent to CCL by: Alfred Gil Arranz [agil|a|cesca.cat] Dear Ralf,

Sorry for the delay in the answer. I must check where the code would be right now (so many years have passed...). Hope this week I can have a look at my older files.

But answering your mail, yes, essentially the IR intensities are calculated taking into account two topics:

- Intensities are directly related to the square of the derivative of dipole moment with respect to the normal mode.
- The surface selection rule: only normal modes of adsorbed species giving rise to a dynamic dipole moment perpendicular to the surface are seen in IR spectra. Therefore, I only payed attention to the changes of dipole moment in the z direction.

Best regards,

Alfred.


Al 14/03/11 11:22, En/na Ralf Tonner ha escrit:
Dear Alfred,

thank you very much for your answer.
I would indeed be interested in IR intensities of adsorbed molecules in a later stage of my research.
Do I understand correctly, that your program uses the dipolmoment changes in one direction for the intensity calculations?

If it is not too much hassle for you, I would be interested in obtaining the code and give it a go. I have access to VASP4, so I could start with these calculations first to test the program.
I might need Google translate from time to time, but that should be possible :)

Kind regards,
Ralf.

Am 11.03.2011 09:03, schrieb Alfred Gil Arranz agil^^^cesca.cat:
Sent to CCL by: Alfred Gil Arranz [agil!A!cesca.cat] Dear Ralf,

Some years ago, I did a graphical tool to analyze the output of vasp, which
included infrared intensities. The point is that there are two important
limitations. First, it only works for 4.5 version, so a revision of the code is
needed. And second, I was only interested in adsorption of molecules on
surfaces, in the adsorbate vibrational modes perpendicular to surface to be
precise. Therefore, several approximations were applied to obtain the relative
intensities of the modes. You can see how it looks at chapter 10 of my doctoral
thesis (in Spanish, sorry :-( ) (http://www.tesisenxarxa.net/index.html and
search by Author).

To be honest, I need to recover the code to remember the algorithm that
calculates the intensities. So, if that limitations are ok to you, please let me
know and I'll try to find out the information.

Best regards,

Alfred Gil

Al 10/03/11 16:15, En/na Ralf Tonner ralf.tonner%googlemail.com ha escrit:

 Sent to CCL by: Ralf Tonner [ralf.tonner(!)googlemail.com]
 Dear CCL-members,

 in moving from molecular quantum chemistry to surface and solid state problems
 I am investigating vibrational properties of molecular crystals with VASP.
 Now I would like to extract the infrared intensities of the respective modes
 but this is unfortunately not given directly.

 Is anyone out there with experience in extracting IR intensities from VASP
 calculations ?

 Thank you in advance,
 Ralf.


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-- 
......................................................................
       __
      / /           Alfred Gil i Arranz
C E / S / C A       Tčcnic d'Aplicacions
    /_/             Centre de Supercomputació de Catalunya

Gran Capitą, 2-4 (Edifici Nexus) · 08034 Barcelona
T. 93 205 6464 (ext 201) · F. 93 205 6979 · agil{:}cesca.cat
......................................................................
From owner-chemistry@ccl.net Thu Mar 17 08:56:00 2011 From: "Budzak Simon Simon.Budzak^^umb.sk" To: CCL Subject: CCL:G: VSCF Message-Id: <-44150-110317040323-28803-0U7eBhMF/f0MVjeHCo4eRw]^[server.ccl.net> X-Original-From: Budzak Simon Content-Language: sk-SK Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 17 Mar 2011 09:03:15 +0100 MIME-Version: 1.0 Sent to CCL by: Budzak Simon [Simon.Budzak(~)umb.sk] Dear All, I have a question regarding anharmonicity: In Gamess is available VSCF method and VPT2 as perturbational treatment of coupling between modes. In Gaussian there is some kind of perturbational treatment of anharmonicity. But and this is my question - are the VPT2 results from Gamess and Gaussian 09's results the same? Have both methods performed the same vscf followed by vibrational pt2? I tried to calculate water fundamental frequencies by both approaches and they are close each t other (up to 50 cm-1 difference) but: is this only numerical noise(analytical second derivatives in G09 vs. numerical in Gamess...) or they are different in some sense? Thanks for your time Simon From owner-chemistry@ccl.net Thu Mar 17 11:52:00 2011 From: "Carlos Silva Lopez carlos.silva(~)uvigo.es" To: CCL Subject: CCL: WATOC satellite meeting: SimOC 2011 - Simulations in Organic Chemistry Message-Id: <-44151-110317103656-5861-3N+Rz/PhseLY8N3FOGsKWg*server.ccl.net> X-Original-From: "Carlos Silva Lopez" Date: Thu, 17 Mar 2011 10:36:54 -0400 Sent to CCL by: "Carlos Silva Lopez" [carlos.silva()uvigo.es] Simulations in Organic Chemistry (SimOC 2011) Vigo (Spain) July 15-16th, University of Vigo. Chairs: Armando Navarro and Carlos Silva Website: http://webs.uvigo.es/simoc2011 This WATOC 2011 satellite meeting will gather lectures by 10 invited speakers who have made prominent contributions to the broad field of Computational Chemistry applied to Organic Chemistry challenges. The meeting also seeks to provide an excellent environment to interact with different researchers in the field, to promote technology transfer, and to establish new collaborations among the participants. To facilitate the participation of everyone, from professors to undergraduate students, we are glad to announce that the participation to SimOC 2011 is open to everyone at no cost. Registration is, however, necessary, since the number of participants is limited to 150 persons. Vigo is conveniently located just 90 km (60 miles) south from Santiago de Compostela, where the WATOC conference will be held between July 17-22nd. Hourly trains connect both cities in 90 min trips. Vigo is a medium sized city with vibrant harbour activity, gorgeous marine landscapes and outdoor Celtic remains right at the center of the town. Carlos Silva and Armando Navarro Chairs of Simoc 2011 From owner-chemistry@ccl.net Thu Mar 17 13:07:00 2011 From: "Pilar Constanza Suarez pcs_3+*+hotmail.com" To: CCL Subject: CCL:G: How to generate the band structure from Gaussian PBC calculations Message-Id: <-44152-110317130436-9900-FSqD4SAz9N5P78lY9Rgryg-#-server.ccl.net> X-Original-From: "Pilar Constanza Suarez" Date: Thu, 17 Mar 2011 13:04:34 -0400 Sent to CCL by: "Pilar Constanza Suarez" [pcs_3*hotmail.com] Dear all. I am trying to generate the band structure of neoprene with Gaussian 09. This is my input file: %mem=1GB %nprocsh=2 %chk=neoprene.chk #p pbepbe/6-31**/auto SCF=Tight neoprene, -CH2-CH=C(Cl)-CH2- optimized geometry 0 1 C -1.9267226529 0.4060180273 0.0316702826 H -2.3523143977 0.9206168644 0.9131400756 H -1.8372739404 1.1548899113 -0.770750797 C -0.5737182157 -0.1434584477 0.3762843235 H -0.5015912465 -0.7653394047 1.2791284293 C 0.5790889876 0.0220081655 -0.3005160849 C 1.9237098673 -0.5258773194 0.0966261209 H 1.772234452 -1.2511397907 0.915962512 H 2.3627869487 -1.0792380182 -0.752511583 Cl 0.6209825739 0.9860944599 -1.7876398696 TV 4.8477468928 0.1714181332 0.5112729831 It had a normal termination. But my question is which values Should I take to make the graph? There are a lot of values and I really do not know what to take. I got the logfile I pasted just a part of it: %mem=1GB %nprocsh=2 Will use up to 2 processors via shared memory. %chk=neoprene.chk ------------------------------- #p pbepbe/6-31**/auto SCF=Tight ------------------------------- 1/38=1/1; 2/17=6,18=5,40=1/2; 3/5=1,6=6,7=101,11=2,16=1,25=1,30=1,74=1009,82=28/1,2,3; 4//1; 5/5=2,32=2,38=5/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; Leave Link 1 at Wed Mar 16 11:32:01 2011, MaxMem= 134217728 cpu: 0.2 (Enter /opt/g03-e01/g03/l101.exe) ----------------------------------------------- neoprene, -CH2-CH=C(Cl)-CH2- optimized geometry ----------------------------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C -1.92672 0.40602 0.03167 H -2.35231 0.92062 0.91314 H -1.83727 1.15489 -0.77075 C -0.57372 -0.14346 0.37628 H -0.50159 -0.76534 1.27913 C 0.57909 0.02201 -0.30052 C 1.92371 -0.52588 0.09663 H 1.77223 -1.25114 0.91596 H 2.36279 -1.07924 -0.75251 Cl 0.62098 0.98609 -1.78764 TV 4.84775 0.17142 0.51127 Isotopes and Nuclear Properties: (Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM) in nuclear magnetons) Atom 1 2 3 4 5 6 7 8 9 10 IAtWgt= 12 1 1 12 1 12 12 1 1 35 AtmWgt= 12.0000000 1.0078250 1.0078250 12.0000000 1.0078250 12.0000000 12.0000000 1.0078250 1.0078250 34.9688527 NucSpn= 0 1 1 0 1 0 0 1 1 3 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -8.1650000 NMagM= 0.0000000 2.7928460 2.7928460 0.0000000 2.7928460 0.0000000 0.0000000 2.7928460 2.7928460 0.8218740 Leave Link 101 at Wed Mar 16 11:32:02 2011, MaxMem= 134217728 cpu: 0.1 (Enter /opt/g03-e01/g03/l202.exe) Before rotation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 -1.926723 0.406018 0.031670 2 1 0 -2.352314 0.920617 0.913140 3 1 0 -1.837274 1.154890 -0.770751 4 6 0 -0.573718 -0.143458 0.376284 5 1 0 -0.501591 -0.765339 1.279128 6 6 0 0.579089 0.022008 -0.300516 7 6 0 1.923710 -0.525877 0.096626 8 1 0 1.772234 -1.251140 0.915963 9 1 0 2.362787 -1.079238 -0.752512 10 17 0 0.620983 0.986094 -1.787640 11 -2 0 4.847747 0.171418 0.511273 --------------------------------------------------------------------- Lengths of translation vectors: 4.877646 --------------------------------------------------------------------- Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 -1.903047 0.552788 0.000000 2 1 0 -2.215550 1.419400 0.611764 3 1 0 -1.871938 0.888610 -1.048306 4 6 0 -0.541525 0.096413 0.435067 5 1 0 -0.397059 -0.094771 1.507282 6 6 0 0.539089 -0.124333 -0.338203 7 6 0 1.897841 -0.556678 0.144266 8 1 0 1.807688 -0.859339 1.202817 9 1 0 2.225773 -1.445896 -0.422994 10 17 0 0.458728 0.123807 -2.091692 11 -2 0 4.877646 0.000000 0.000000 --------------------------------------------------------------------- Lengths of translation vectors: 4.877646 --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 C 0.000000 2 H 1.105861 0.000000 3 H 1.101222 1.776412 0.000000 4 C 1.500435 2.140999 2.144288 0.000000 5 H 2.226933 2.530133 3.110198 1.098665 0.000000 6 C 2.556737 3.297512 2.709862 1.346998 2.069556 7 C 3.962131 4.587311 4.209789 2.541968 2.708826 8 H 4.148545 4.661377 4.654302 2.649850 2.353333 9 H 4.606606 5.385721 4.757328 3.282214 3.525728 10 Cl 3.183894 4.017337 2.665629 2.717677 3.705774 11 TV 6.803189 7.259641 6.888067 5.437462 5.486657 6 7 8 9 10 6 C 0.000000 7 C 1.505293 0.000000 8 H 2.127045 1.104655 0.000000 9 H 2.144440 1.104550 1.778232 0.000000 10 Cl 1.772782 2.744743 3.693246 2.893263 0.000000 11 TV 4.353495 3.034789 3.407327 3.049913 4.890537 11 11 TV 0.000000 Unit Cell Distance matrix (angstroms): 1 2 3 4 5 1 C 0.000000 2 H 1.105861 0.000000 3 H 1.101222 1.776412 0.000000 4 C 1.500435 2.140999 2.144288 0.000000 5 H 2.226933 2.530133 3.110198 1.098665 0.000000 6 C 2.550409 2.791543 2.759440 3.881254 4.352252 7 C 1.552783 2.169683 2.176799 2.540926 2.956645 8 H 2.191472 2.504397 3.091623 2.809960 2.796721 9 H 2.175868 3.077503 2.539534 2.751101 3.261241 10 Cl 3.299820 3.720493 2.856692 4.628115 5.401458 6 7 8 9 10 6 C 0.000000 7 C 1.505293 0.000000 8 H 2.127045 1.104655 0.000000 9 H 2.144440 1.104550 1.778232 0.000000 10 Cl 1.772782 2.744743 3.693246 2.893263 0.000000 Symmetry turned off: Cannot cope with ghost atoms or with translation vectors. Stoichiometry C4H5Cl Framework group C1[X(C4H5Cl)] Deg. of freedom 24 Full point group C1 Leave Link 202 at Wed Mar 16 11:32:03 2011, MaxMem= 134217728 cpu: 0.1 (Enter /opt/g03-e01/g03/l301.exe) Standard basis: 6-31G(d,p) (6D, 7F) Integral buffers will be 131072 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned off. 104 basis functions, 199 primitive gaussians, 104 cartesian basis functions 23 alpha electrons 23 beta electrons nuclear repulsion energy 193.2112039567 Hartrees. IExCor=1009 DFT=T Ex=PBE Corr=PBE ExCW=0 ScaHFX= 0.000000 ScaDFX= 1.000000 1.000000 1.000000 1.000000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 NAtoms= 10 NActive= 10 NUniq= 10 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F Standard density basis: Auto (5D, 7F) Shells with S=P=... and L > 2 split apart in FixB. 612 Density fitting functions Leave Link 301 at Wed Mar 16 11:32:04 2011, MaxMem= 134217728 cpu: 0.1 (Enter /opt/g03-e01/g03/l302.exe) FOutLm= 100.00. Periodicity: 1 0 0 Max integer dimensions: 11 0 0 PBC vector 1 X= 9.2174 Y= 0.0000 Z= 0.0000 Recp vector 1 X= 0.1085 Y= 0.0000 Z= 0.0000 Generated k point mesh (from -Pi to Pi): K space mesh: X= 138 Y= 0 Z= 0 A half-cell shift: 1 Using k point mesh (from -Pi to Pi): K space mesh: X= 138 Y= 0 Z= 0 A half-cell shift: 1 CountK=T Total number of k points: 0 CountK=T Total number of k points: 69 NPDir=1 NMtPBC= 15 NCelOv= 15 NCel= 23 NClECP= 15 NCelD= 15 NCelK= 23 NCelE2= 23 NClLst= 7 CellRange= 100.0. One-electron integrals computed using PRISM. NBasis= 104 RedAO= T NBF= 104 NBsUse= 104 1.00D-06 NBFU= 104 NBasis= 104 NBas6D= 104 NTT= 5460 NTT6D= 5460 NDBShl= 92 NDBF= 612 NDBF6D= 713 NNucDB= 0 IDenFi= 4 ISolve= 4 FullAP=F BlkAPC=T NucTyp= 0 TolInv= 1.00D-05 TolIt= 1.00D-10. MaxSav= 6 NSavIt= 613 MaxIt= 1000. Symmetry not used in FoFDir. MinBra= 0 MaxBra= 3 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Precomputing XC quadrature grid using IXCGrd= 2 IRadAn= 0 IRanWt= -1 IRanGd= 0. RepCel: MaxNCR= 15 NClRep= 15 NMtPBC= 15. NRdTot= 675 NPtTot= 86958 NUsed= 92284 NTot= 92316 NSgBfM= 405 407 407 407. Leave Link 302 at Wed Mar 16 11:32:06 2011, MaxMem= 134217728 cpu: 2.2 (Enter /opt/g03-e01/g03/l303.exe) DipDrv: MaxL=1. Leave Link 303 at Wed Mar 16 11:32:07 2011, MaxMem= 134217728 cpu: 0.1 (Enter /opt/g03-e01/g03/l401.exe) Harris functional with IExCor= 1009 diagonalized for initial guess. RepCel: MaxNCR= 15 NClRep= 15 NMtPBC= 15. HarFok: IExCor=1009 AccDes= 0.00D+00 IRadAn= 0 IDoV=1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 Harris En= -1375.37134197213 Leave Link 401 at Wed Mar 16 11:32:12 2011, MaxMem= 134217728 cpu: 7.0 (Enter /opt/g03-e01/g03/l502.exe) Closed shell SCF: Requested convergence on RMS density matrix=1.00D-07 within 128 cycles. Requested convergence on MAX density matrix=1.00D-05. Requested convergence on energy=1.00D-05. No special actions if energy rises. Density fitting will be used, IDenFit=4 NucTyp= 0. Using DIIS extrapolation, IDIIS= 1040. NCelOv= 15 NClRep= 15 NMtPBC= 15 NRecip= 138 NKPnt= 69. Two-electron integral symmetry not used. 92283 words used for storage of precomputed grid. IEnd= 688456 IEndB= 688456 NGot= 134217728 MDV= 133709713 LenX= 133709713 Threshold for overlap eigenvalues 1.000D-06 Ratio Low Low Low Low Low High Min 3.268D-04 7.2D+00 5.6D+00 4.5D+00 4.4D+00 3.4D+00 2.4D-03 Max 3.592D-04 7.3D+00 6.8D+00 5.4D+00 4.9D+00 3.7D+00 2.6D-03 S in ortho basis: MxErrOnDiag= 0.1376D-12 MxErrOfDiag= 0.7609D-13 Cycle 1 Pass 0 IDiag 1: E= (Non-Variational) Sum_Occ: Avg-Min 1.75862D-02 Max-Avg 1.38503D-02 Dif 3.14365D-02 (eV) Alpha HOCO: -8.400585 LUCO: -4.154551 indirect gap: 4.246033 direct gap: 4.246033 (eV) Diagonalized old Fock matrix for initial guess. Cycle 1 Pass 1 IDiag 1: FoFCou: FMM=T IPFlag= 0 FMFlag= 990000 FMFlg1= 4097 NFxFlg= 0 DoJE=T BraDBF=T KetDBF=F FulRan=T. Symmetry not used in FoFCou. FMM levels: 2 Number of levels for PrismC: 1 ItDFit: ISolve= 4 NSavIt= 613 ITol= 0 Tol= 1.00D-09 ItMax= 1000 IStorA=2 Conv0= 2.47D-08 BNorm= 1.78D+03 BPNorm= 4.28D+01 Conv= 1.00D-09 AccInt= 1.00D-12 Generalized Minimum Residual for N= 612 ITol= 0 MaxL= 612 KMP= 612 Iter Natral Err Est Error Estimate ISDGMR: 0 0.7984311D+00 0.7984311D+00 ISDGMR: 1 0.3631159D+00 0.3631159D+00 ISDGMR: 2 0.1422776D+00 0.1422776D+00 ISDGMR: 3 0.4674426D-01 0.4674426D-01 ISDGMR: 4 0.2323826D-01 0.2323826D-01 ISDGMR: 5 0.1072247D-01 0.1072247D-01 ISDGMR: 6 0.6884398D-02 0.6884398D-02 ISDGMR: 7 0.5217462D-02 0.5217462D-02 ISDGMR: 8 0.4081214D-02 0.4081214D-02 ISDGMR: 9 0.3240607D-02 0.3240607D-02 ISDGMR: 10 0.2802294D-02 0.2802294D-02 ISDGMR: 11 0.2295755D-02 0.2295755D-02 ISDGMR: 12 0.2080999D-02 0.2080999D-02 ISDGMR: 13 0.1815559D-02 0.1815559D-02 ISDGMR: 14 0.1621032D-02 0.1621032D-02 ISDGMR: 15 0.1472319D-02 0.1472319D-02 ISDGMR: 16 0.1225542D-02 0.1225542D-02 ISDGMR: 17 0.1051446D-02 0.1051446D-02 ISDGMR: 18 0.9057327D-03 0.9057327D-03 ISDGMR: 19 0.8126676D-03 0.8126676D-03 ISDGMR: 20 0.7195811D-03 0.7195811D-03 ISDGMR: 21 0.6288456D-03 0.6288456D-03 ISDGMR: 22 0.5767315D-03 0.5767315D-03 ISDGMR: 23 0.5422502D-03 0.5422502D-03 ISDGMR: 24 0.5045198D-03 0.5045198D-03 ISDGMR: 25 0.4603230D-03 0.4603230D-03 ISDGMR: 26 0.4362648D-03 0.4362648D-03 ISDGMR: 27 0.3913183D-03 0.3913183D-03 ISDGMR: 28 0.3522117D-03 0.3522117D-03 ISDGMR: 29 0.3277870D-03 0.3277870D-03 ISDGMR: 30 0.3196549D-03 0.3196549D-03 ISDGMR: 31 0.3051560D-03 0.3051560D-03 ISDGMR: 32 0.2796782D-03 0.2796782D-03 ISDGMR: 33 0.2704873D-03 0.2704873D-03 ISDGMR: 34 0.2580055D-03 0.2580055D-03 ISDGMR: 35 0.2327185D-03 0.2327185D-03 ISDGMR: 36 0.2113979D-03 0.2113979D-03 ISDGMR: 37 0.2016239D-03 0.2016239D-03 ISDGMR: 38 0.1953767D-03 0.1953767D-03 ISDGMR: 39 0.1790447D-03 0.1790447D-03 ISDGMR: 40 0.1666730D-03 0.1666730D-03 ISDGMR: 41 0.1581366D-03 0.1581366D-03 ISDGMR: 42 0.1434048D-03 0.1434048D-03 ISDGMR: 43 0.1376573D-03 0.1376573D-03 ISDGMR: 44 0.1277225D-03 0.1277225D-03 ISDGMR: 45 0.1127215D-03 0.1127215D-03 ISDGMR: 46 0.1049294D-03 0.1049294D-03 ISDGMR: 47 0.9834115D-04 0.9834115D-04 ISDGMR: 48 0.9147975D-04 0.9147975D-04 ISDGMR: 49 0.8653176D-04 0.8653176D-04 ISDGMR: 50 0.8062031D-04 0.8062031D-04 ISDGMR: 51 0.7657199D-04 0.7657199D-04 ISDGMR: 52 0.7247412D-04 0.7247412D-04 ISDGMR: 53 0.6896934D-04 0.6896934D-04 ISDGMR: 54 0.6672528D-04 0.6672528D-04 ISDGMR: 55 0.6423547D-04 0.6423547D-04 ISDGMR: 56 0.6026025D-04 0.6026025D-04 ISDGMR: 57 0.5706789D-04 0.5706789D-04 ISDGMR: 58 0.5506506D-04 0.5506506D-04 ISDGMR: 59 0.5338671D-04 0.5338671D-04 ISDGMR: 60 0.5123803D-04 0.5123803D-04 ISDGMR: 61 0.4920178D-04 0.4920178D-04 ISDGMR: 62 0.4690389D-04 0.4690389D-04 ISDGMR: 63 0.4513418D-04 0.4513418D-04 ISDGMR: 64 0.4278745D-04 0.4278745D-04 ISDGMR: 65 0.4098438D-04 0.4098438D-04 ISDGMR: 66 0.3844654D-04 0.3844654D-04 ISDGMR: 67 0.3719911D-04 0.3719911D-04 ISDGMR: 68 0.3562897D-04 0.3562897D-04 ISDGMR: 69 0.3446271D-04 0.3446271D-04 ISDGMR: 70 0.3270885D-04 0.3270885D-04 ISDGMR: 71 0.3126366D-04 0.3126366D-04 ISDGMR: 72 0.2861873D-04 0.2861873D-04 ISDGMR: 73 0.2741260D-04 0.2741260D-04 ISDGMR: 74 0.2671555D-04 0.2671555D-04 ISDGMR: 75 0.2609094D-04 0.2609094D-04 ISDGMR: 76 0.2544114D-04 0.2544114D-04 ISDGMR: 77 0.2483977D-04 0.2483977D-04 ISDGMR: 78 0.2419247D-04 0.2419247D-04 ISDGMR: 79 0.2371346D-04 0.2371346D-04 ISDGMR: 80 0.2276107D-04 0.2276107D-04 ISDGMR: 81 0.2206895D-04 0.2206895D-04 ISDGMR: 82 0.2152827D-04 0.2152827D-04 ISDGMR: 83 0.2109500D-04 0.2109500D-04 ISDGMR: 84 0.2057366D-04 0.2057366D-04 ISDGMR: 85 0.1993410D-04 0.1993410D-04 ISDGMR: 86 0.1927526D-04 0.1927526D-04 ISDGMR: 87 0.1883203D-04 0.1883203D-04 ISDGMR: 88 0.1820411D-04 0.1820411D-04 ISDGMR: 89 0.1805689D-04 0.1805689D-04 ISDGMR: 90 0.1781632D-04 0.1781632D-04 ISDGMR: 91 0.1761969D-04 0.1761969D-04 ISDGMR: 92 0.1760639D-04 0.1760639D-04 ISDGMR: 93 0.1751958D-04 0.1751958D-04 ISDGMR: 94 0.1747134D-04 0.1747134D-04 ISDGMR: 95 0.1704121D-04 0.1704121D-04 ISDGMR: 96 0.1684175D-04 0.1684175D-04 ISDGMR: 97 0.1649262D-04 0.1649262D-04 ISDGMR: 98 0.1550588D-04 0.1550588D-04 ISDGMR: 99 0.1513756D-04 0.1513756D-04 ISDGMR: 100 0.1471604D-04 0.1471604D-04 ISDGMR: 101 0.1415108D-04 0.1415108D-04 ISDGMR: 102 0.1358116D-04 0.1358116D-04 ISDGMR: 103 0.1305628D-04 0.1305628D-04 ISDGMR: 104 0.1250219D-04 0.1250219D-04 ISDGMR: 105 0.1187478D-04 0.1187478D-04 ISDGMR: 106 0.1151850D-04 0.1151850D-04 ISDGMR: 107 0.1109323D-04 0.1109323D-04 ISDGMR: 108 0.1088969D-04 0.1088969D-04 ISDGMR: 109 0.1054131D-04 0.1054131D-04 ISDGMR: 110 0.1028353D-04 0.1028353D-04 ISDGMR: 111 0.1000995D-04 0.1000995D-04 ISDGMR: 112 0.9819096D-05 0.9819096D-05 ISDGMR: 113 0.9686104D-05 0.9686104D-05 ISDGMR: 114 0.9064683D-05 0.9064683D-05 ISDGMR: 115 0.8980348D-05 0.8980348D-05 ISDGMR: 116 0.8702404D-05 0.8702404D-05 ISDGMR: 117 0.8573666D-05 0.8573666D-05 ISDGMR: 118 0.8540053D-05 0.8540053D-05 ISDGMR: 119 0.8424420D-05 0.8424420D-05 ISDGMR: 120 0.8208878D-05 0.8208878D-05 ISDGMR: 121 0.7987177D-05 0.7987177D-05 ISDGMR: 122 0.7913476D-05 0.7913476D-05 ISDGMR: 123 0.7747406D-05 0.7747406D-05 ISDGMR: 124 0.7662730D-05 0.7662730D-05 ISDGMR: 125 0.7512482D-05 0.7512482D-05 ISDGMR: 126 0.7387125D-05 0.7387125D-05 ISDGMR: 127 0.7249870D-05 0.7249870D-05 ISDGMR: 128 0.7185254D-05 0.7185254D-05 ISDGMR: 129 0.7108772D-05 0.7108772D-05 ISDGMR: 130 0.6837666D-05 0.6837666D-05 ISDGMR: 131 0.6770271D-05 0.6770271D-05 ISDGMR: 132 0.6709730D-05 0.6709730D-05 ISDGMR: 133 0.6593448D-05 0.6593448D-05 ISDGMR: 134 0.6589724D-05 0.6589724D-05 ISDGMR: 135 0.6533522D-05 0.6533522D-05 ISDGMR: 136 0.6466915D-05 0.6466915D-05 ISDGMR: 137 0.6454432D-05 0.6454432D-05 ISDGMR: 138 0.6245444D-05 0.6245444D-05 ISDGMR: 139 0.6237907D-05 0.6237907D-05 ISDGMR: 140 0.6177439D-05 0.6177439D-05 ISDGMR: 141 0.6132951D-05 0.6132951D-05 ISDGMR: 142 0.6131913D-05 0.6131913D-05 ISDGMR: 143 0.6091878D-05 0.6091878D-05 ISDGMR: 144 0.6040682D-05 0.6040682D-05 ISDGMR: 145 0.5944861D-05 0.5944861D-05 ISDGMR: 146 0.5811133D-05 0.5811133D-05 ISDGMR: 147 0.5657522D-05 0.5657522D-05 ISDGMR: 148 0.5522019D-05 0.5522019D-05 ISDGMR: 149 0.5448494D-05 0.5448494D-05 ISDGMR: 150 0.5317639D-05 0.5317639D-05 ISDGMR: 151 0.5293022D-05 0.5293022D-05 ISDGMR: 152 0.5121655D-05 0.5121655D-05 ISDGMR: 153 0.5098635D-05 0.5098635D-05 ISDGMR: 154 0.4956039D-05 0.4956039D-05 ISDGMR: 155 0.4647273D-05 0.4647273D-05 ISDGMR: 156 0.4606971D-05 0.4606971D-05 ISDGMR: 157 0.4444240D-05 0.4444240D-05 ISDGMR: 158 0.4368526D-05 0.4368526D-05 ISDGMR: 159 0.4351963D-05 0.4351963D-05 ISDGMR: 160 0.4334470D-05 0.4334470D-05 ISDGMR: 161 0.4326016D-05 0.4326016D-05 ISDGMR: 162 0.4321237D-05 0.4321237D-05 ISDGMR: 163 0.4266349D-05 0.4266349D-05 ISDGMR: 164 0.4199657D-05 0.4199657D-05 ISDGMR: 165 0.4127494D-05 0.4127494D-05 ISDGMR: 166 0.4103857D-05 0.4103857D-05 ISDGMR: 167 0.4083828D-05 0.4083828D-05 ISDGMR: 168 0.4014288D-05 0.4014288D-05 ISDGMR: 169 0.3949437D-05 0.3949437D-05 ISDGMR: 170 0.3878889D-05 0.3878889D-05 ISDGMR: 171 0.3804709D-05 0.3804709D-05 ISDGMR: 172 0.3727289D-05 0.3727289D-05 ISDGMR: 173 0.3715015D-05 0.3715015D-05 ISDGMR: 174 0.3661311D-05 0.3661311D-05 ISDGMR: 175 0.3624235D-05 0.3624235D-05 ISDGMR: 176 0.3586721D-05 0.3586721D-05 ISDGMR: 177 0.3586403D-05 0.3586403D-05 ISDGMR: 178 0.3579075D-05 0.3579075D-05 ISDGMR: 179 0.3561823D-05 0.3561823D-05 ISDGMR: 180 0.3535726D-05 0.3535726D-05 ISDGMR: 181 0.3525813D-05 0.3525813D-05 ISDGMR: 182 0.3521068D-05 0.3521068D-05 ISDGMR: 183 0.3519079D-05 0.3519079D-05 ISDGMR: 184 0.3486608D-05 0.3486608D-05 ISDGMR: 185 0.3478764D-05 0.3478764D-05 ISDGMR: 186 0.3431605D-05 0.3431605D-05 ISDGMR: 187 0.3423011D-05 0.3423011D-05 ISDGMR: 188 0.3419386D-05 0.3419386D-05 ISDGMR: 189 0.3412257D-05 0.3412257D-05 ISDGMR: 190 0.3403328D-05 0.3403328D-05 ISDGMR: 191 0.3378446D-05 0.3378446D-05 ISDGMR: 192 0.3372100D-05 0.3372100D-05 ISDGMR: 193 0.3351739D-05 0.3351739D-05 ISDGMR: 194 0.3346721D-05 0.3346721D-05 ISDGMR: 195 0.3338713D-05 0.3338713D-05 ISDGMR: 196 0.3282936D-05 0.3282936D-05 ISDGMR: 197 0.3220691D-05 0.3220691D-05 ISDGMR: 198 0.3207231D-05 0.3207231D-05 ISDGMR: 199 0.3207142D-05 0.3207142D-05 ISDGMR: 200 0.3207142D-05 0.3207142D-05 ISDGMR: 201 0.3191044D-05 0.3191044D-05 ISDGMR: 202 0.3173854D-05 0.3173854D-05 ISDGMR: 203 0.3163989D-05 0.3163989D-05 ISDGMR: 204 0.3106256D-05 0.3106256D-05 ISDGMR: 205 0.3086939D-05 0.3086939D-05 ISDGMR: 206 0.3041493D-05 0.3041493D-05 ISDGMR: 207 0.3024874D-05 0.3024874D-05 ISDGMR: 208 0.2951773D-05 0.2951773D-05 ISDGMR: 209 0.2925210D-05 0.2925210D-05 ISDGMR: 210 0.2911052D-05 0.2911052D-05 ISDGMR: 211 0.2900903D-05 0.2900903D-05 ISDGMR: 212 0.2890113D-05 0.2890113D-05 ISDGMR: 213 0.2886908D-05 0.2886908D-05 ISDGMR: 214 0.2880057D-05 0.2880057D-05 ISDGMR: 215 0.2854508D-05 0.2854508D-05 ISDGMR: 216 0.2840618D-05 0.2840618D-05 ISDGMR: 217 0.2840546D-05 0.2840546D-05 ISDGMR: 218 0.2837669D-05 0.2837669D-05 ISDGMR: 219 0.2837511D-05 0.2837511D-05 ISDGMR: 220 0.2828242D-05 0.2828242D-05 ISDGMR: 221 0.2827037D-05 0.2827037D-05 ISDGMR: 222 0.2821140D-05 0.2821140D-05 ISDGMR: 223 0.2814035D-05 0.2814035D-05 ISDGMR: 224 0.2756593D-05 0.2756593D-05 ISDGMR: 225 0.2697158D-05 0.2697158D-05 ISDGMR: 226 0.2684835D-05 0.2684835D-05 ISDGMR: 227 0.2674012D-05 0.2674012D-05 ISDGMR: 228 0.2656102D-05 0.2656102D-05 ISDGMR: 229 0.2624812D-05 0.2624812D-05 ISDGMR: 230 0.2614603D-05 0.2614603D-05 ISDGMR: 231 0.2604063D-05 0.2604063D-05 ISDGMR: 232 0.2601746D-05 0.2601746D-05 ISDGMR: 233 0.2584923D-05 0.2584923D-05 ISDGMR: 234 0.2573841D-05 0.2573841D-05 ISDGMR: 235 0.2531452D-05 0.2531452D-05 ISDGMR: 236 0.2488374D-05 0.2488374D-05 ISDGMR: 237 0.2465769D-05 0.2465769D-05 ISDGMR: 238 0.2459202D-05 0.2459202D-05 ISDGMR: 239 0.2445573D-05 0.2445573D-05 ISDGMR: 240 0.2385995D-05 0.2385995D-05 ISDGMR: 241 0.2260789D-05 0.2260789D-05 ISDGMR: 242 0.2231415D-05 0.2231415D-05 ISDGMR: 243 0.2208887D-05 0.2208887D-05 ISDGMR: 244 0.2197264D-05 0.2197264D-05 ISDGMR: 245 0.2163343D-05 0.2163343D-05 ISDGMR: 246 0.2151032D-05 0.2151032D-05 ISDGMR: 247 0.2150496D-05 0.2150496D-05 ISDGMR: 248 0.2150181D-05 0.2150181D-05 ISDGMR: 249 0.2146117D-05 0.2146117D-05 ISDGMR: 250 0.2083660D-05 0.2083660D-05 ISDGMR: 251 0.2078643D-05 0.2078643D-05 ISDGMR: 252 0.2069058D-05 0.2069058D-05 ISDGMR: 253 0.1905516D-05 0.1905516D-05 ISDGMR: 254 0.1878919D-05 0.1878919D-05 ISDGMR: 255 0.1877397D-05 0.1877397D-05 ISDGMR: 256 0.1789905D-05 0.1789905D-05 ISDGMR: 257 0.1763533D-05 0.1763533D-05 ISDGMR: 258 0.1749604D-05 0.1749604D-05 ISDGMR: 259 0.1401802D-05 0.1401802D-05 ISDGMR: 260 0.1180045D-05 0.1180045D-05 ISDGMR: 261 0.1173245D-05 0.1173245D-05 ISDGMR: 262 0.1117134D-05 0.1117134D-05 ISDGMR: 263 0.1108076D-05 0.1108076D-05 ISDGMR: 264 0.1107930D-05 0.1107930D-05 ISDGMR: 265 0.1085808D-05 0.1085808D-05 ISDGMR: 266 0.9477607D-06 0.9477607D-06 ISDGMR: 267 0.9327369D-06 0.9327369D-06 ISDGMR: 268 0.9026026D-06 0.9026026D-06 ISDGMR: 269 0.8823124D-06 0.8823124D-06 ISDGMR: 270 0.8785158D-06 0.8785158D-06 ISDGMR: 271 0.8675959D-06 0.8675959D-06 ISDGMR: 272 0.8122417D-06 0.8122417D-06 ISDGMR: 273 0.8105070D-06 0.8105070D-06 ISDGMR: 274 0.8080044D-06 0.8080044D-06 ISDGMR: 275 0.7846055D-06 0.7846055D-06 ISDGMR: 276 0.7599035D-06 0.7599035D-06 ISDGMR: 277 0.7594105D-06 0.7594105D-06 ISDGMR: 278 0.7577015D-06 0.7577015D-06 ISDGMR: 279 0.7089736D-06 0.7089736D-06 ISDGMR: 280 0.7080571D-06 0.7080571D-06 ISDGMR: 281 0.7080501D-06 0.7080501D-06 ISDGMR: 282 0.6900187D-06 0.6900187D-06 ISDGMR: 283 0.6072936D-06 0.6072936D-06 ISDGMR: 284 0.6056450D-06 0.6056450D-06 ISDGMR: 285 0.6050989D-06 0.6050989D-06 ISDGMR: 286 0.4509354D-06 0.4509354D-06 ISDGMR: 287 0.4103567D-06 0.4103567D-06 ISDGMR: 288 0.4099814D-06 0.4099814D-06 ISDGMR: 289 0.4059383D-06 0.4059383D-06 ISDGMR: 290 0.3109470D-06 0.3109470D-06 ISDGMR: 291 0.3100146D-06 0.3100146D-06 ISDGMR: 292 0.3093370D-06 0.3093370D-06 ISDGMR: 293 0.2748991D-06 0.2748991D-06 ISDGMR: 294 0.2498252D-06 0.2498252D-06 ISDGMR: 295 0.2497517D-06 0.2497517D-06 ISDGMR: 296 0.2474132D-06 0.2474132D-06 ISDGMR: 297 0.2082847D-06 0.2082847D-06 ISDGMR: 298 0.2079177D-06 0.2079177D-06 ISDGMR: 299 0.2076887D-06 0.2076887D-06 ISDGMR: 300 0.1876752D-06 0.1876752D-06 ISDGMR: 301 0.1871244D-06 0.1871244D-06 ISDGMR: 302 0.1870660D-06 0.1870660D-06 ISDGMR: 303 0.1471650D-06 0.1471650D-06 ISDGMR: 304 0.1300835D-06 0.1300835D-06 ISDGMR: 305 0.1300011D-06 0.1300011D-06 ISDGMR: 306 0.1106255D-06 0.1106255D-06 ISDGMR: 307 0.7770591D-07 0.7770591D-07 ISDGMR: 308 0.7768689D-07 0.7768689D-07 ISDGMR: 309 0.7663403D-07 0.7663403D-07 ISDGMR: 310 0.6374703D-07 0.6374703D-07 ISDGMR: 311 0.6369754D-07 0.6369754D-07 ISDGMR: 312 0.6360206D-07 0.6360206D-07 ISDGMR: 313 0.5892703D-07 0.5892703D-07 ISDGMR: 314 0.5863611D-07 0.5863611D-07 ISDGMR: 315 0.5863383D-07 0.5863383D-07 ISDGMR: 316 0.4929762D-07 0.4929762D-07 ISDGMR: 317 0.3654634D-07 0.3654634D-07 ISDGMR: 318 0.3653630D-07 0.3653630D-07 ISDGMR: 319 0.3359894D-07 0.3359894D-07 ISDGMR: 320 0.2571974D-07 0.2571974D-07 ISDGMR: 321 0.2570781D-07 0.2570781D-07 ISDGMR: 322 0.2526839D-07 0.2526839D-07 ISDGMR: 323 0.2042681D-07 0.2042681D-07 ISDGMR: 324 0.2036543D-07 0.2036543D-07 ISDGMR: 325 0.2026108D-07 0.2026108D-07 ISDGMR: 326 0.9208043D-08 0.9208043D-08 ISDGMR: 327 0.8681268D-08 0.8681268D-08 ISDGMR: 328 0.8663921D-08 0.8663921D-08 ISDGMR: 329 0.7734725D-08 0.7734725D-08 ISDGMR: 330 0.2650542D-08 0.2650542D-08 ISDGMR: 331 0.2647163D-08 0.2647163D-08 ISDGMR: 332 0.2647126D-08 0.2647126D-08 ISDGMR: 333 0.2384078D-08 0.2384078D-08 ISDGMR: 334 0.6341035D-09 0.6341035D-09 IErr= 0 Err= 6.34D-10 NSaved= 2 NIter= 334 NITot= 335. PS= 46.000000000000 PSN= 46.000000000000 RNE= 46.000000000000 Err= 0.00D+00 RepCel: MaxNCR= 15 NClRep= 15 NMtPBC= 15. E= -615.086430663364 DIIS: error= 2.80D-02 at cycle 1 NSaved= 1. NSaved= 1 IEnMin= 1 EnMin= -615.086430663364 IErMin= 1 ErrMin= 2.80D-02 ErrMax= 2.80D-02 EMaxC= 1.00D-01 BMatC= 1.15D-01 BMatP= 1.15D-01 IDIUse=3 WtCom= 7.20D-01 WtEn= 2.80D-01 Coeff-Com: 0.100D+01 Coeff-En: 0.100D+01 Coeff: 0.100D+01 Sum_Occ: Avg-Min 5.99816D-02 Max-Avg 3.03287D-02 Dif 9.03104D-02 (eV) Alpha HOCO: -2.393420 LUCO: 1.113761 indirect gap: 3.507181 direct gap: 3.643837 (eV) GapD= 2.000 DampG=2.000 DampE=0.250 DampFc=0.5000 IDamp=-1. Damping current iteration by 5.00D-01 RMSDP=2.64D-03 MaxDP=1.59D-01 OVMax= 0.00D+00 Cycle 2 Pass 1 IDiag 1: .. .. I also tried with this other input file: %mem=1GB %nprocsh=2 %chk=neoprene.chk #p pbepbe/6-31**/auto SCF=Tight PBC=NKPoint=12 IOP(5/103=10) IOP(5/98=1) IOP(5/33=1) neoprene, -CH2-CH=C(Cl)-CH2- optimized geometry 0 1 C -1.9267226529 0.4060180273 0.0316702826 H -2.3523143977 0.9206168644 0.9131400756 H -1.8372739404 1.1548899113 -0.770750797 C -0.5737182157 -0.1434584477 0.3762843235 H -0.5015912465 -0.7653394047 1.2791284293 C 0.5790889876 0.0220081655 -0.3005160849 C 1.9237098673 -0.5258773194 0.0966261209 H 1.772234452 -1.2511397907 0.915962512 H 2.3627869487 -1.0792380182 -0.752511583 Cl 0.6209825739 0.9860944599 -1.7876398696 TV 4.8477468928 0.1714181332 0.5112729831 logfile: ****************************************** Gaussian 03: AM64L-G03RevE.01 11-Sep-2007 16-Mar-2011 ****************************************** %mem=1GB %nprocsh=2 Will use up to 2 processors via shared memory. %chk=neoprene.chk ---------------------------------------------------------------------- #p pbepbe/6-31**/auto SCF=Tight PBC=NKPoint=12 IOP(5/103=10) IOP(5/98= 1) IOP(5/33=1) ---------------------------------------------------------------------- 1/38=1/1; 2/17=6,18=5,40=1/2; 3/5=1,6=6,7=101,11=2,16=1,25=1,30=1,65=24,74=1009,82=28/1,2,3; 4//1; 5/5=2,32=2,33=1,38=5,98=1,103=10/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; Leave Link 1 at Wed Mar 16 12:54:21 2011, MaxMem= 134217728 cpu: 0.2 (Enter /opt/g03-e01/g03/l101.exe) ----------------------------------------------- neoprene, -CH2-CH=C(Cl)-CH2- optimized geometry ----------------------------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C -1.92672 0.40602 0.03167 H -2.35231 0.92062 0.91314 H -1.83727 1.15489 -0.77075 C -0.57372 -0.14346 0.37628 H -0.50159 -0.76534 1.27913 C 0.57909 0.02201 -0.30052 C 1.92371 -0.52588 0.09663 H 1.77223 -1.25114 0.91596 H 2.36279 -1.07924 -0.75251 Cl 0.62098 0.98609 -1.78764 TV 4.84775 0.17142 0.51127 Isotopes and Nuclear Properties: (Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM) in nuclear magnetons) Atom 1 2 3 4 5 6 7 8 9 10 IAtWgt= 12 1 1 12 1 12 12 1 1 35 AtmWgt= 12.0000000 1.0078250 1.0078250 12.0000000 1.0078250 12.0000000 12.0000000 1.0078250 1.0078250 34.9688527 NucSpn= 0 1 1 0 1 0 0 1 1 3 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -8.1650000 NMagM= 0.0000000 2.7928460 2.7928460 0.0000000 2.7928460 0.0000000 0.0000000 2.7928460 2.7928460 0.8218740 Leave Link 101 at Wed Mar 16 12:54:22 2011, MaxMem= 134217728 cpu: 0.1 (Enter /opt/g03-e01/g03/l202.exe) Before rotation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 -1.926723 0.406018 0.031670 2 1 0 -2.352314 0.920617 0.913140 3 1 0 -1.837274 1.154890 -0.770751 4 6 0 -0.573718 -0.143458 0.376284 5 1 0 -0.501591 -0.765339 1.279128 6 6 0 0.579089 0.022008 -0.300516 7 6 0 1.923710 -0.525877 0.096626 8 1 0 1.772234 -1.251140 0.915963 9 1 0 2.362787 -1.079238 -0.752512 10 17 0 0.620983 0.986094 -1.787640 11 -2 0 4.847747 0.171418 0.511273 --------------------------------------------------------------------- Lengths of translation vectors: 4.877646 --------------------------------------------------------------------- Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 -1.903047 0.552788 0.000000 2 1 0 -2.215550 1.419400 0.611764 3 1 0 -1.871938 0.888610 -1.048306 4 6 0 -0.541525 0.096413 0.435067 5 1 0 -0.397059 -0.094771 1.507282 6 6 0 0.539089 -0.124333 -0.338203 7 6 0 1.897841 -0.556678 0.144266 8 1 0 1.807688 -0.859339 1.202817 9 1 0 2.225773 -1.445896 -0.422994 10 17 0 0.458728 0.123807 -2.091692 11 -2 0 4.877646 0.000000 0.000000 --------------------------------------------------------------------- Lengths of translation vectors: 4.877646 --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 C 0.000000 2 H 1.105861 0.000000 3 H 1.101222 1.776412 0.000000 4 C 1.500435 2.140999 2.144288 0.000000 5 H 2.226933 2.530133 3.110198 1.098665 0.000000 6 C 2.556737 3.297512 2.709862 1.346998 2.069556 7 C 3.962131 4.587311 4.209789 2.541968 2.708826 8 H 4.148545 4.661377 4.654302 2.649850 2.353333 9 H 4.606606 5.385721 4.757328 3.282214 3.525728 10 Cl 3.183894 4.017337 2.665629 2.717677 3.705774 11 TV 6.803189 7.259641 6.888067 5.437462 5.486657 6 7 8 9 10 6 C 0.000000 7 C 1.505293 0.000000 8 H 2.127045 1.104655 0.000000 9 H 2.144440 1.104550 1.778232 0.000000 10 Cl 1.772782 2.744743 3.693246 2.893263 0.000000 11 TV 4.353495 3.034789 3.407327 3.049913 4.890537 11 11 TV 0.000000 Unit Cell Distance matrix (angstroms): 1 2 3 4 5 1 C 0.000000 2 H 1.105861 0.000000 3 H 1.101222 1.776412 0.000000 4 C 1.500435 2.140999 2.144288 0.000000 5 H 2.226933 2.530133 3.110198 1.098665 0.000000 6 C 2.550409 2.791543 2.759440 3.881254 4.352252 7 C 1.552783 2.169683 2.176799 2.540926 2.956645 8 H 2.191472 2.504397 3.091623 2.809960 2.796721 9 H 2.175868 3.077503 2.539534 2.751101 3.261241 10 Cl 3.299820 3.720493 2.856692 4.628115 5.401458 6 7 8 9 10 6 C 0.000000 7 C 1.505293 0.000000 8 H 2.127045 1.104655 0.000000 9 H 2.144440 1.104550 1.778232 0.000000 10 Cl 1.772782 2.744743 3.693246 2.893263 0.000000 Symmetry turned off: Cannot cope with ghost atoms or with translation vectors. Stoichiometry C4H5Cl Framework group C1[X(C4H5Cl)] Deg. of freedom 24 Full point group C1 Leave Link 202 at Wed Mar 16 12:54:23 2011, MaxMem= 134217728 cpu: 0.1 (Enter /opt/g03-e01/g03/l301.exe) Standard basis: 6-31G(d,p) (6D, 7F) Integral buffers will be 131072 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned off. 104 basis functions, 199 primitive gaussians, 104 cartesian basis functions 23 alpha electrons 23 beta electrons nuclear repulsion energy 193.2112039567 Hartrees. IExCor=1009 DFT=T Ex=PBE Corr=PBE ExCW=0 ScaHFX= 0.000000 ScaDFX= 1.000000 1.000000 1.000000 1.000000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 NAtoms= 10 NActive= 10 NUniq= 10 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F Standard density basis: Auto (5D, 7F) Shells with S=P=... and L > 2 split apart in FixB. 612 Density fitting functions Leave Link 301 at Wed Mar 16 12:54:24 2011, MaxMem= 134217728 cpu: 0.1 (Enter /opt/g03-e01/g03/l302.exe) FOutLm= 100.00. Periodicity: 1 0 0 Max integer dimensions: 11 0 0 PBC vector 1 X= 9.2174 Y= 0.0000 Z= 0.0000 Recp vector 1 X= 0.1085 Y= 0.0000 Z= 0.0000 Generated k point mesh (from -Pi to Pi): K space mesh: X= 24 Y= 0 Z= 0 A half-cell shift: 1 Using k point mesh (from -Pi to Pi): K space mesh: X= 24 Y= 0 Z= 0 A half-cell shift: 1 CountK=T Total number of k points: 0 CountK=T Total number of k points: 12 NPDir=1 NMtPBC= 15 NCelOv= 15 NCel= 23 NClECP= 15 NCelD= 15 NCelK= 23 NCelE2= 23 NClLst= 7 CellRange= 100.0. One-electron integrals computed using PRISM. NBasis= 104 RedAO= T NBF= 104 NBsUse= 104 1.00D-06 NBFU= 104 NBasis= 104 NBas6D= 104 NTT= 5460 NTT6D= 5460 NDBShl= 92 NDBF= 612 NDBF6D= 713 NNucDB= 0 IDenFi= 4 ISolve= 4 FullAP=F BlkAPC=T NucTyp= 0 TolInv= 1.00D-05 TolIt= 1.00D-10. MaxSav= 6 NSavIt= 613 MaxIt= 1000. Symmetry not used in FoFDir. MinBra= 0 MaxBra= 3 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Precomputing XC quadrature grid using IXCGrd= 2 IRadAn= 0 IRanWt= -1 IRanGd= 0. RepCel: MaxNCR= 15 NClRep= 15 NMtPBC= 15. NRdTot= 675 NPtTot= 86958 NUsed= 92284 NTot= 92316 NSgBfM= 405 407 407 407. Leave Link 302 at Wed Mar 16 12:54:26 2011, MaxMem= 134217728 cpu: 2.1 (Enter /opt/g03-e01/g03/l303.exe) DipDrv: MaxL=1. Leave Link 303 at Wed Mar 16 12:54:27 2011, MaxMem= 134217728 cpu: 0.1 (Enter /opt/g03-e01/g03/l401.exe) Harris functional with IExCor= 1009 diagonalized for initial guess. RepCel: MaxNCR= 15 NClRep= 15 NMtPBC= 15. HarFok: IExCor=1009 AccDes= 0.00D+00 IRadAn= 0 IDoV=1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 Harris En= -1375.37134197213 Leave Link 401 at Wed Mar 16 12:54:32 2011, MaxMem= 134217728 cpu: 6.9 (Enter /opt/g03-e01/g03/l502.exe) A Direct SCF calculation will be performed. Closed shell SCF: Requested convergence on RMS density matrix=1.00D-07 within 128 cycles. Requested convergence on MAX density matrix=1.00D-05. Requested convergence on energy=1.00D-05. No special actions if energy rises. Density fitting will be used, IDenFit=4 NucTyp= 0. Using DIIS extrapolation, IDIIS= 1040. Using k point mesh (from -Pi to Pi): K space mesh: X= 24 Y= 0 Z= 0 A half-cell shift: 1 CountK=F Total number of k points: 12 NCelOv= 15 NClRep= 15 NMtPBC= 15 NRecip= 24 NKPnt= 12. Two-electron integral symmetry not used. ReadGW: IGet=1 IStart= 412256 Next= 504539 LGW= 92283. 92283 words used for storage of precomputed grid. Pruned ( 75, 302) grid will be used in CalDFT. NBasis= 104 NAllTT= 81900 NAllSq= 41616 NWIIB= 0 INEq= 870 LenNEq= 0 IIJ= 1257 ID= 83221 IDD= 124837 IDA= 83221 IDB= 165121 IF= 247021 IFF= 288637 IFA= 247021 IFB= 328921 IScr2= 410821 IV= 504539 IBuf2E= 504539 LenSav= 0 IMin1= 684979 IMin= 684979 IEnd= 684979 IEnd= 684979 IEndB= 684979 NGot= 134217728 MDV= 133713190 LenX= 133713190 Threshold for overlap eigenvalues 1.000D-06 Ratio Low Low Low Low Low High Min 3.268D-04 7.2D+00 5.6D+00 4.5D+00 4.4D+00 3.4D+00 2.4D-03 Max 3.591D-04 7.3D+00 6.8D+00 5.4D+00 4.9D+00 3.7D+00 2.6D-03 S in ortho basis: MxErrOnDiag= 0.5684D-13 MxErrOfDiag= 0.4234D-13 Cycle 1 Pass 0 IDiag 1: One-electron energy= 0.615665102253D+03 1/2 = 0.000000000000 E= (Non-Variational) TrPFA= -349.7190 TrPFB= -349.7190 Sum_Occ: Avg-Min 1.73951D-02 Max-Avg 1.37829D-02 Dif 3.11780D-02 (eV) Alpha HOCO: -8.401474 LUCO: -4.152499 indirect gap: 4.248974 direct gap: 4.248974 (eV) Using LT method, Correction=T Diagonalized old Fock matrix for initial guess. Cycle 1 Pass 1 IDiag 1: One-electron energy= 0.614205230778D+03 FoFCou: FMM=T IPFlag= 0 FMFlag= 990000 FMFlg1= 4097 NFxFlg= 0 DoJE=T BraDBF=T KetDBF=F FulRan=T. Symmetry not used in FoFCou. FoFCou: KetSym=F NOpSet= 1 NOpAb=1 NOp= 1. FoFCou: CnvScl= 1.00D+00 Thresh= 1.00D-12 SetFMM - NonCub=F LevOld=99 Levels= 2 Other 1 4 0 4 0 4 FoFCou: LinMIO=T DoNuc=T BraDBF=T KetDBF=F NIJTC= 10 NIJTAt= 1 NIJTCD= 3 NIJTT= 14 IJTBeg= 11 IJTEnd= 14 IJTBCv= 12 IJTECv= 14 KLTBeg= 1 KLTEnd= 11 KLTBCv= 1 KLTECv= 10 FMM levels: 2 Number of levels for PrismC: 1 Enter FMMEnt: 133629914 words available. LMax= 27 NLevels= 2 RITol=13.0 IWS= 2 MaxRan= 5 NPair= 1797 AllNF=F NoVFMM=F UseUAB=T NPMax= 3 ThrOK=T. The FMM boxes have sides of length 2.30 Bohr. TotXYZ= 44 TotRan= 136 TotP2C= 11 LnExps= 21 LnExp0= 115 Memory required for boxing and indexing= 4202. Level MPran MPxyz BoxLen 2 115 32 2.30 1 19 8 4.61 0 2 1 9.22 21 total multipole expansions above lowest level. Time for boxing and indexing: 0.00 Number of distributions with range 1 boxes: 708 Number of distributions with range 2 boxes: 719 Number of distributions with range 3 boxes: 276 Number of distributions with range 4 boxes: 87 Number of distributions with range 5 boxes: 7 FMM Zone radius: Tv1- 4 Tv2- 0 Tv3- 0 Memory required to store rotation matrices 1244655 words. Total memory used by FMM= 1850826 words, LenMPS= 162289. FMMEnt: IMat= 1 IDist= 0 IPert= 0 IPertA= 0 IFunc=1 UseSc1=F UseSc2=F Fact= 1.00 SavFL=0 UseMPN=F IJTBeg= 11 IJTEnd= 14 KLTBeg= 1 KLTEnd= 11 NIJTC= 10 NTIJTT= 14 Time for computing MP expansions: 0.22 Just for reference - the total charge is: -0.105471187339D-13 Final dipole: 0.2332 0.1132 -0.0558 Dipole moment was cancelled with the help of 0 charges Total CPU time for the infinite part: 0.06 vFMM at finest mesh level: A= 0.630000 R= 3.000000 Lev NCel MPran MPxyz TRran TRxyz Trtot CPU (sec) 2 7 115 32 10544 3306 6275 0.23 1 9 19 8 598 256 362 0.02 ----------------------------------------------------------------------- Everything at coarser mesh levels: 0.02 Total CPU for subroutine GFMM: 0.37 Time for computing local expansions: 0.01 FMM EC= 79.0753777016 EN= 79.0753777016 NCel replicated for PrismC: 7 CoulSu: NPrtUS= 2 ThrOK=T Enter PrismC DoJE=T Cont=T. PrismC was handed 66718519 working-precision words and 1797 shell-pairs Enter PrismC DoJE=T Cont=T. PrismC was handed 66718519 working-precision words and 1797 shell-pairs CoulSu: NPrtUS= 2 ThrOK=T Enter PrismC DoJE=T Cont=F. PrismC was handed 66695316 working-precision words and 1797 shell-pairs Enter PrismC DoJE=T Cont=F. PrismC was handed 66695316 working-precision words and 1797 shell-pairs FoFCou EC= -729.507968116 EN= -729.507968116 ENF= -808.583345818 ENNF= -808.583345818 FoFCou: FMM=T IPFlag= 0 FMFlag= 990000 FMFlg1= 4097 NFxFlg= 0 DoJE=T BraDBF=T KetDBF=T FulRan=T. Symmetry not used in FoFCou. FoFCou: KetSym=T NOpSet= 1 NOpAb=1 NOp= 1. FoFCou: CnvScl= 1.00D+00 Thresh= 1.00D-12 SetFMM - NonCub=F LevOld= 0 Levels= 0 Other 1 1 0 1 0 1 FoFCou: LinMIO=T DoNuc=T BraDBF=T KetDBF=T NIJTC= 0 NIJTAt= 1 NIJTCD= 3 NIJTT= 4 IJTBeg= 1 IJTEnd= 4 IJTBCv= 2 IJTECv= 4 KLTBeg= 1 KLTEnd= 4 KLTBCv= 2 KLTECv= 4 FMM levels: 0 Number of levels for PrismC: 0 Enter FMMEnt: 133682306 words available. LMax= 27 NLevels= 0 RITol=13.0 IWS= 2 MaxRan= 2 NPair= 102 AllNF=F NoVFMM=F UseUAB=T NPMax= 3 ThrOK=T. The FMM boxes have sides of length 9.22 Bohr. TotXYZ= 2 TotRan= 2 TotP2C= 0 LnExps= 0 LnExp0= 2 Memory required for boxing and indexing= 274. Level MPran MPxyz BoxLen 0 2 1 9.22 0 total multipole expansions above lowest level. Time for boxing and indexing: 0.00 Number of distributions with range 1 boxes: 96 Number of distributions with range 2 boxes: 6 FMM Zone radius: Tv1- 4 Tv2- 0 Tv3- 0 Memory required to store rotation matrices 1244655 words. Total memory used by FMM= 1643731 words, LenMPS= 162609. FMMEnt: IMat= 1 IDist= 0 IPert= 0 IPertA= 0 IFunc=1 UseSc1=F UseSc2=F Fact= 1.00 SavFL=0 UseMPN=F IJTBeg= 1 IJTEnd= 4 KLTBeg= 1 KLTEnd= 4 NIJTC= 0 NTIJTT= 4 Time for computing MP expansions: 0.01 Just for reference - the total charge is: -0.100364161426D-12 Final dipole: -24.1694 -5.9644 106.3325 Dipole moment was cancelled with the help of 0 charges Total CPU time for the infinite part: 0.07 ----------------------------------------------------------------------- Everything at coarser mesh levels: 0.00 Total CPU for subroutine GFMM: 0.07 Time for computing local expansions: 0.00 FMM EC= 1.15538525973 EN= 11.8322408848 NCel replicated for PrismC: 9 CoulSu: NPrtUS= 2 ThrOK=T Enter PrismC DoJE=T Cont=T. PrismC was handed 66833030 working-precision words and 102 shell-pairs Enter PrismC DoJE=T Cont=T. PrismC was handed 66833030 working-precision words and 102 shell-pairs CoulSu: NPrtUS= 2 ThrOK=T Enter PrismC DoJE=T Cont=F. PrismC was handed 66832799 working-precision words and 102 shell-pairs Enter PrismC DoJE=T Cont=F. PrismC was handed 66832799 working-precision words and 102 shell-pairs FoFCou EC= -2185.48183367 EN= -1325.24785311 ENF= -2186.63721893 ENNF= -1337.08009399 ItDFit: ISolve= 4 NSavIt= 613 ITol= 0 Tol= 1.00D-09 ItMax= 1000 IStorA=2 Conv0= 2.47D-08 BNorm= 1.78D+03 BPNorm= 4.28D+01 Conv= 1.00D-09 AccInt= 1.00D-12 FoFCou: FMM=T IPFlag= 0 FMFlag= 990000 FMFlg1= 4097 NFxFlg= 0 DoJE=T BraDBF=T KetDBF=T FulRan=T. Symmetry not used in FoFCou. FoFCou: KetSym=T NOpSet= 1 NOpAb=1 NOp= 1. FoFCou: CnvScl= 1.00D+00 Thresh= 1.00D-12 SetFMM - NonCub=F LevOld= 0 Levels= 0 Other 1 1 0 1 0 1 FoFCou: LinMIO=T DoNuc=F BraDBF=T KetDBF=T NIJTC= 0 NIJTAt= 0 NIJTCD= 3 NIJTT= 3 IJTBeg= 1 IJTEnd= 3 IJTBCv= 1 IJTECv= 3 KLTBeg= 1 KLTEnd= 3 KLTBCv= 1 KLTECv= 3 FMM levels: 0 Number of levels for PrismC: 0 Enter FMMEnt: 132874584 words available. LMax= 27 NLevels= 0 RITol=13.0 IWS= 2 MaxRan= 2 NPair= 92 AllNF=F NoVFMM=F UseUAB=T NPMax= 3 ThrOK=T. The FMM boxes have sides of length 9.22 Bohr. TotXYZ= 2 TotRan= 2 TotP2C= 0 LnExps= 0 LnExp0= 2 Memory required for boxing and indexing= 246. Level MPran MPxyz BoxLen 0 2 1 9.22 0 total multipole expansions above lowest level. Time for boxing and indexing: 0.00 Number of distributions with range 1 boxes: 86 Number of distributions with range 2 boxes: 6 FMM Zone radius: Tv1- 4 Tv2- 0 Tv3- 0 Memory required to store rotation matrices 1244655 words. Total memory used by FMM= 1643541 words, LenMPS= 161614. FMMEnt: IMat= 1 IDist= 0 IPert= 0 IPertA= 0 IFunc=1 UseSc1=F UseSc2=F Fact= 1.00 SavFL=0 UseMPN=F IJTBeg= 1 IJTEnd= 3 KLTBeg= 1 KLTEnd= 3 NIJTC= 0 NTIJTT= 3 Time for computing MP expansions: 0.01 Just for reference - the total charge is: 0.632827124036D-14 Final dipole: 3.0680 1.5962 -24.6378 Dipole moment was cancelled with the help of 0 charges Total CPU time for the infinite part: 0.07 ----------------------------------------------------------------------- Everything at coarser mesh levels: 0.00 Total CPU for subroutine GFMM: 0.07 Time for computing local expansions: 0.00 FMM EC= 0.583191450685E-01 NCel replicated for PrismC: 9 CoulSu: NPrtUS= 2 ThrOK=T Enter PrismC DoJE=T Cont=T. PrismC was handed 66429671 working-precision words and 92 shell-pairs Enter PrismC DoJE=T Cont=T. PrismC was handed 66429671 working-precision words and 92 shell-pairs CoulSu: NPrtUS= 2 ThrOK=T Enter PrismC DoJE=T Cont=F. PrismC was handed 66429517 working-precision words and 92 shell-pairs Enter PrismC DoJE=T Cont=F. PrismC was handed 66429517 working-precision words and 92 shell-pairs FoFCou EC= 17.3588080538 ENF= 17.3004889088 Generalized Minimum Residual for N= 612 ITol= 0 MaxL= 612 KMP= 612 Iter Natral Err Est Error Estimate ISDGMR: 0 0.7984311D+00 0.7984311D+00 FoFCou: FMM=T IPFlag= 0 FMFlag= 990000 FMFlg1= 4097 NFxFlg= 0 DoJE=T BraDBF=T KetDBF=T FulRan=T. Symmetry not used in FoFCou. FoFCou: KetSym=T NOpSet= 1 NOpAb=1 NOp= 1. FoFCou: CnvScl= 1.00D+00 Thresh= 1.00D-12 SetFMM - NonCub=F LevOld= 0 Levels= 0 Other 1 1 0 1 0 1 FoFCou: LinMIO=T DoNuc=F BraDBF=T KetDBF=T NIJTC= 0 NIJTAt= 0 NIJTCD= 3 NIJTT= 3 IJTBeg= 1 IJTEnd= 3 IJTBCv= 1 IJTECv= 3 KLTBeg= 1 KLTEnd= 3 KLTBCv= 1 KLTECv= 3 FMM levels: 0 Number of levels for PrismC: 0 Enter FMMEnt: 132874584 words available. LMax= 27 NLevels= 0 RITol=13.0 IWS= 2 MaxRan= 2 NPair= 92 AllNF=F NoVFMM=F UseUAB=T NPMax= 3 ThrOK=T. The FMM boxes have sides of length 9.22 Bohr. TotXYZ= 2 TotRan= 2 TotP2C= 0 LnExps= 0 LnExp0= 2 Memory required for boxing and indexing= 246. Level MPran MPxyz BoxLen 0 2 1 9.22 0 total multipole expansions above lowest level. Time for boxing and indexing: 0.00 Number of distributions with range 1 boxes: 86 Number of distributions with range 2 boxes: 6 FMM Zone radius: Tv1- 4 Tv2- 0 Tv3- 0 Memory required to store rotation matrices 1244655 words. Total memory used by FMM= 1643541 words, LenMPS= 161614. FMMEnt: IMat= 1 IDist= 0 IPert= 0 IPertA= 0 IFunc=1 UseSc1=F UseSc2=F Fact= 1.00 SavFL=0 UseMPN=F IJTBeg= 1 IJTEnd= 3 KLTBeg= 1 KLTEnd= 3 NIJTC= 0 NTIJTT= 3 Time for computing MP expansions: 0.01 Just for reference - the total charge is: -0.224820162487D-14 Final dipole: 0.6673 0.5748 -11.2406 Dipole moment was cancelled with the help of 0 charges Total CPU time for the infinite part: 0.07 ----------------------------------------------------------------------- Everything at coarser mesh levels: 0.00 Total CPU for subroutine GFMM: 0.07 Time for computing local expansions: 0.00 FMM EC= 0.128705508802E-01 NCel replicated for PrismC: 9 CoulSu: NPrtUS= 2 ThrOK=T Enter PrismC DoJE=T Cont=T. PrismC was handed 66429671 working-precision words and 92 shell-pairs Enter PrismC DoJE=T Cont=T. PrismC was handed 66429671 working-precision words and 92 shell-pairs CoulSu: NPrtUS= 2 ThrOK=T Enter PrismC DoJE=T Cont=F. PrismC was handed 66429517 working-precision words and 92 shell-pairs Enter PrismC DoJE=T Cont=F. PrismC was handed 66429517 working-precision words and 92 shell-pairs FoFCou EC= 1.91251253648 ENF= 1.89964198560 ISDGMR: 1 0.3631159D+00 0.3631159D+00 FoFCou: FMM=T IPFlag= 0 FMFlag= 990000 FMFlg1= 4097 NFxFlg= 0 DoJE=T BraDBF=T KetDBF=T FulRan=T. Symmetry not used in FoFCou. FoFCou: KetSym=T NOpSet= 1 NOpAb=1 NOp= 1. FoFCou: CnvScl= 1.00D+00 Thresh= 1.00D-12 SetFMM - NonCub=F LevOld= 0 Levels= 0 Other 1 1 0 1 0 1 FoFCou: LinMIO=T DoNuc=F BraDBF=T KetDBF=T NIJTC= 0 NIJTAt= 0 NIJTCD= 3 NIJTT= 3 IJTBeg= 1 IJTEnd= 3 IJTBCv= 1 IJTECv= 3 KLTBeg= 1 KLTEnd= 3 KLTBCv= 1 KLTECv= 3 FMM levels: 0 Number of levels for PrismC: 0 Enter FMMEnt: 132874584 words available. LMax= 27 NLevels= 0 RITol=13.0 IWS= 2 MaxRan= 2 NPair= 92 AllNF=F NoVFMM=F UseUAB=T NPMax= 3 ThrOK=T. The FMM boxes have sides of length 9.22 Bohr. TotXYZ= 2 TotRan= 2 TotP2C= 0 LnExps= 0 LnExp0= 2 Memory required for boxing and indexing= 246. Level MPran MPxyz BoxLen 0 2 1 9.22 0 total multipole expansions above lowest level. Time for boxing and indexing: 0.00 Number of distributions with range 1 boxes: 86 Number of distributions with range 2 boxes: 6 FMM Zone radius: Tv1- 4 Tv2- 0 Tv3- 0 Memory required to store rotation matrices 1244655 words. Total memory used by FMM= 1643541 words, LenMPS= 161614. FMMEnt: IMat= 1 IDist= 0 IPert= 0 IPertA= 0 IFunc=1 UseSc1=F UseSc2=F Fact= 1.00 SavFL=0 UseMPN=F IJTBeg= 1 IJTEnd= 3 KLTBeg= 1 KLTEnd= 3 NIJTC= 0 NTIJTT= 3 Time for computing MP expansions: 0.02 Just for reference - the total charge is: -0.333066907388D-14 Final dipole: 0.2259 1.0110 -25.4511 Dipole moment was cancelled with the help of 0 charges Total CPU time for the infinite part: 0.06 ----------------------------------------------------------------------- .. .. Thanks in advance. Pilar. pcs_3|-|hotmail.com From owner-chemistry@ccl.net Thu Mar 17 17:22:00 2011 From: "Arnout RD Voet arnout.voet*fys.kuleuven.be" To: CCL Subject: CCL: protein ligand scoring function / energy Message-Id: <-44153-110317154531-13322-rzrP7fV738CrcikYzZXUPg~~server.ccl.net> X-Original-From: "Arnout RD Voet" Date: Thu, 17 Mar 2011 15:45:29 -0400 Sent to CCL by: "Arnout RD Voet" [arnout.voet : fys.kuleuven.be] Dear CCL members, I am looking for a free/open source command line based tool that can be easily used to produce scoring/energy/affinity values for a series of pdb's each with a different protein and a different ligand) any suggestions are appreciated kind regards Arnout Voet From owner-chemistry@ccl.net Thu Mar 17 20:02:00 2011 From: "Dario Fernando Coral ferchocoralg16(a)gmail.com" To: CCL Subject: CCL: lower energies for transition states Message-Id: <-44154-110317195921-2789-a+zYzsxYFqFaonewi6+Hmg]=[server.ccl.net> X-Original-From: "Dario Fernando Coral" Date: Thu, 17 Mar 2011 19:59:16 -0400 Sent to CCL by: "Dario Fernando Coral" [ferchocoralg16%gmail.com] Greetings Modeling Azepines fragmentations, I have found that the relative energies of some transition states are found to be lower than the corresponding reagent. The modeling of the reactions I've been doing with the B3LYP 6-31G(d)method. Analyzing the output files I noticed that the electronic energy of these transition states is higher than the reactants, the problem occurs when the electron energy is added with the zero point vibrational energy (ZPVE). Maybe some of you know the solution to this problem. Sorry for my very bad english and thanks in advance. Dario Fernando Coral Obando Chemistry Student Universidad de Nario Pasto - Colombia