diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..058eef3 --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +*.pyc + +.idea/ diff --git a/DC-MBI-UNIT-ASS.log b/DC-MBI-UNIT-ASS.log deleted file mode 100644 index b31e37f..0000000 --- a/DC-MBI-UNIT-ASS.log +++ /dev/null @@ -1,848 +0,0 @@ - Entering Gaussian System, Link 0=g16 - Input=1-DC-MBI-UNIT-ASS.gjf - Output=1-DC-MBI-UNIT-ASS.log - Initial command: - /opt/ohpc/pub/apps/gaussian/16b01/g16/l1.exe "/scratch/local/Gau-17233.inp" -scrdir="/scratch/local/" - Entering Link 1 = /opt/ohpc/pub/apps/gaussian/16b01/g16/l1.exe PID= 17234. - - Copyright (c) 1988-2017, Gaussian, Inc. All Rights Reserved. - - This is part of the Gaussian(R) 16 program. It is based on - the Gaussian(R) 09 system (copyright 2009, Gaussian, Inc.), - the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.), - the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), - the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), - the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), - the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), - the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), - the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon - University), and the Gaussian 82(TM) system (copyright 1983, - Carnegie Mellon University). Gaussian is a federally registered - trademark of Gaussian, Inc. - - This software contains proprietary and confidential information, - including trade secrets, belonging to Gaussian, Inc. - - This software is provided under written license and may be - used, copied, transmitted, or stored only in accord with that - written license. - - The following legend is applicable only to US Government - contracts under FAR: - - RESTRICTED RIGHTS LEGEND - - Use, reproduction and disclosure by the US Government is - subject to restrictions as set forth in subparagraphs (a) - and (c) of the Commercial Computer Software - Restricted - Rights clause in FAR 52.227-19. - - Gaussian, Inc. - 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 - - - --------------------------------------------------------------- - Warning -- This program may not be used in any manner that - competes with the business of Gaussian, Inc. or will provide - assistance to any competitor of Gaussian, Inc. The licensee - of this program is prohibited from giving any competitor of - Gaussian, Inc. access to this program. By using this program, - the user acknowledges that Gaussian, Inc. is engaged in the - business of creating and licensing software in the field of - computational chemistry and represents and warrants to the - licensee that it is not a competitor of Gaussian, Inc. and that - it will not use this program in any manner prohibited above. - --------------------------------------------------------------- - - - Cite this work as: - Gaussian 16, Revision B.01, - M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, - M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, - G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, - J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, - J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, - F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, - T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, - G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, - J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, - T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, - F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. N. Brothers, K. N. Kudin, - V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand, - K. Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar, - J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, - J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, - J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016. - - ****************************************** - Gaussian 16: ES64L-G16RevB.01 20-Dec-2017 - 16-Nov-2022 - ****************************************** - %mem=42GB - %Nprocs=20 - Will use up to 20 processors via shared memory. - ---------------------------------------------------------- - #p cam-b3lyp/aug-cc-pVDZ POP=CHELPG density=current NoSymm - ---------------------------------------------------------- - 1/30=1,38=1,172=1/1; - 2/12=2,15=1,17=6,18=5,40=1/2; - 3/5=16,7=10,11=2,25=1,30=1,74=-40/1,2,3; - 4//1; - 5/5=2,38=5/2; - 6/7=2,8=2,9=2,10=2,15=8,20=3,22=-1,28=1/1,2; - 99/5=1,9=1/99; - Leave Link 1 at Wed Nov 16 10:43:17 2022, MaxMem= 5637144576 cpu: 1.9 elap: 0.2 - (Enter /opt/ohpc/pub/apps/gaussian/16b01/g16/l101.exe) - ------------------------- - DAST UAEnvolvida passo 15 - ------------------------- - Symbolic Z-matrix: - Charge = 0 Multiplicity = 1 - Cl 0.52951 -1.62665 1.24734 - Cl 0.36293 -1.51156 4.37537 - N 3.70316 2.47026 1.67928 - N 3.58214 2.53111 3.90653 - C 4.1125 3.08953 2.78251 - C 5.073 4.21889 2.80434 - C 2.86041 1.45634 2.12431 - C 2.79065 1.4916 3.51764 - C 2.01966 0.58686 4.23407 - C 1.33268 -0.36792 3.53324 - C 1.40387 -0.4174 2.12743 - C 2.1713 0.49075 1.40373 - H 2.22113 0.45152 0.47623 - H 1.97054 0.6278 5.16261 - H 3.80155 2.76937 4.72069 - H 5.68239 4.10686 3.53844 - H 4.5946 5.04458 2.90832 - H 5.56563 4.23595 1.98082 - - ITRead= 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - MicOpt= -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 - NAtoms= 18 NQM= 18 NQMF= 0 NMMI= 0 NMMIF= 0 - NMic= 0 NMicF= 0. - 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= 35 35 14 14 12 12 12 12 12 12 - AtmWgt= 34.9688527 34.9688527 14.0030740 14.0030740 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 - NucSpn= 3 3 2 2 0 0 0 0 0 0 - AtZEff= -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 - NQMom= -8.1650000 -8.1650000 2.0440000 2.0440000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 - NMagM= 0.8218740 0.8218740 0.4037610 0.4037610 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 - AtZNuc= 17.0000000 17.0000000 7.0000000 7.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 - - Atom 11 12 13 14 15 16 17 18 - IAtWgt= 12 12 1 1 1 1 1 1 - AtmWgt= 12.0000000 12.0000000 1.0078250 1.0078250 1.0078250 1.0078250 1.0078250 1.0078250 - NucSpn= 0 0 1 1 1 1 1 1 - AtZEff= -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 - NMagM= 0.0000000 0.0000000 2.7928460 2.7928460 2.7928460 2.7928460 2.7928460 2.7928460 - AtZNuc= 6.0000000 6.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 - Leave Link 101 at Wed Nov 16 10:43:18 2022, MaxMem= 5637144576 cpu: 1.8 elap: 0.2 - (Enter /opt/ohpc/pub/apps/gaussian/16b01/g16/l202.exe) - Input orientation: - --------------------------------------------------------------------- - Center Atomic Atomic Coordinates (Angstroms) - Number Number Type X Y Z - --------------------------------------------------------------------- - 1 17 0 0.529511 -1.626652 1.247344 - 2 17 0 0.362927 -1.511555 4.375374 - 3 7 0 3.703161 2.470259 1.679277 - 4 7 0 3.582138 2.531106 3.906529 - 5 6 0 4.112504 3.089530 2.782505 - 6 6 0 5.072999 4.218889 2.804341 - 7 6 0 2.860414 1.456338 2.124311 - 8 6 0 2.790648 1.491595 3.517643 - 9 6 0 2.019660 0.586857 4.234066 - 10 6 0 1.332677 -0.367923 3.533240 - 11 6 0 1.403867 -0.417396 2.127431 - 12 6 0 2.171295 0.490754 1.403730 - 13 1 0 2.221128 0.451516 0.476228 - 14 1 0 1.970539 0.627801 5.162607 - 15 1 0 3.801546 2.769374 4.720692 - 16 1 0 5.682386 4.106863 3.538439 - 17 1 0 4.594603 5.044583 2.908321 - 18 1 0 5.565634 4.235948 1.980819 - --------------------------------------------------------------------- - Distance matrix (angstroms): - 1 2 3 4 5 - 1 Cl 0.000000 - 2 Cl 3.134576 0.000000 - 3 N 5.200317 5.854993 0.000000 - 4 N 5.803167 5.189050 2.231367 0.000000 - 5 C 6.118573 6.145449 1.329726 1.362555 0.000000 - 6 C 7.565572 7.582276 2.489966 2.507209 1.482727 - 7 C 3.963207 4.484765 1.391515 2.202797 2.160617 - 8 C 4.471069 3.955811 2.273775 1.363184 2.200256 - 9 C 4.005081 2.677324 3.592816 2.515695 3.570770 - 10 C 2.730347 1.719738 4.136623 3.688331 4.499447 - 11 C 1.732441 2.708134 3.718353 4.074766 4.479327 - 12 C 2.683900 4.013739 2.518130 3.523850 3.524620 - 13 H 2.788363 4.744460 2.778322 4.236037 3.981876 - 14 H 4.742194 2.789444 4.304674 2.792410 4.038937 - 15 H 6.488097 5.501790 3.057671 0.876227 1.988910 - 16 H 8.042041 7.782270 3.170534 2.651328 2.017655 - 17 H 7.986814 7.939916 2.988706 2.887745 2.017543 - 18 H 7.763414 8.113929 2.584065 3.247938 2.017068 - 6 7 8 9 10 - 6 C 0.000000 - 7 C 3.604117 0.000000 - 8 C 3.627128 1.395523 0.000000 - 9 C 4.955668 2.431857 1.387889 0.000000 - 10 C 5.963233 2.765319 2.362992 1.369200 0.000000 - 11 C 5.951124 2.373272 2.738631 2.413635 1.408480 - 12 C 4.927534 1.387975 2.419485 2.836024 2.444467 - 13 H 5.267483 2.033355 3.264402 3.765668 3.287271 - 14 H 5.299301 3.272552 2.030917 0.930740 2.013249 - 15 H 2.718472 3.057938 2.025330 2.859249 4.165092 - 16 H 0.960626 4.121719 3.899001 5.127368 6.240489 - 17 H 0.959919 4.061722 4.031036 5.315943 6.350268 - 18 H 0.959775 3.881370 4.194502 5.564793 6.443878 - 11 12 13 14 15 - 11 C 0.000000 - 12 C 1.391914 0.000000 - 13 H 2.037006 0.929668 0.000000 - 14 H 3.259731 3.766728 4.696384 0.000000 - 15 H 4.757034 4.341896 5.087795 2.852054 0.000000 - 16 H 6.384793 5.473663 5.892283 5.340375 2.593098 - 17 H 6.373680 5.373414 5.713556 5.610301 3.014997 - 18 H 6.244630 5.087342 5.269861 6.005598 3.573479 - 16 17 18 - 16 H 0.000000 - 17 H 1.568324 0.000000 - 18 H 1.567314 1.567499 0.000000 - Symmetry turned off by external request. - Stoichiometry C8H6Cl2N2 - Framework group C1[X(C8H6Cl2N2)] - Deg. of freedom 48 - Full point group C1 NOp 1 - Rotational constants (GHZ): 1.7084129 0.4124602 0.3328113 - Leave Link 202 at Wed Nov 16 10:43:18 2022, MaxMem= 5637144576 cpu: 1.5 elap: 0.1 - (Enter /opt/ohpc/pub/apps/gaussian/16b01/g16/l301.exe) - Standard basis: Aug-CC-pVDZ (5D, 7F) - Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. - Ernie: 40 primitive shells out of 398 were deleted. - 338 basis functions, 658 primitive gaussians, 362 cartesian basis functions - 51 alpha electrons 51 beta electrons - nuclear repulsion energy 835.4499809625 Hartrees. - IExCor=20419 DFT=T Ex+Corr=CAM-B3LYP ExCW=0 ScaHFX= 1.000000 - ScaDFX= 1.000000 1.000000 1.000000 0.810000 ScalE2= 1.000000 1.000000 - IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 - HFx wShort= 0.000000 wLong= 0.330000 cFull= 0.190000 cShort= 0.000000 cLong= 0.460000 - DFx wShort= 0.000000 wLong= 0.330000 cFull= 0.190000 cShort= 0.000000 cLong= 0.460000 - NAtoms= 18 NActive= 18 NUniq= 18 SFac= 1.00D+00 NAtFMM= 60 NAOKFM=F Big=F - Integral buffers will be 131072 words long. - Raffenetti 2 integral format. - Two-electron integral symmetry is turned off. - Leave Link 301 at Wed Nov 16 10:43:18 2022, MaxMem= 5637144576 cpu: 1.5 elap: 0.2 - (Enter /opt/ohpc/pub/apps/gaussian/16b01/g16/l302.exe) - NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 - NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. - One-electron integrals computed using PRISM. - NBasis= 338 RedAO= T EigKep= 1.82D-06 NBF= 338 - NBsUse= 337 1.00D-06 EigRej= 8.38D-07 NBFU= 337 - Precomputing XC quadrature grid using - IXCGrd= 4 IRadAn= 5 IRanWt= -1 IRanGd= 0 AccXCQ= 0.00D+00. - Generated NRdTot= 0 NPtTot= 0 NUsed= 0 NTot= 32 - NSgBfM= 361 361 361 361 361 MxSgAt= 18 MxSgA2= 18. - Leave Link 302 at Wed Nov 16 10:43:20 2022, MaxMem= 5637144576 cpu: 24.4 elap: 2.3 - (Enter /opt/ohpc/pub/apps/gaussian/16b01/g16/l303.exe) - DipDrv: MaxL=1. - Leave Link 303 at Wed Nov 16 10:43:20 2022, MaxMem= 5637144576 cpu: 2.6 elap: 0.2 - (Enter /opt/ohpc/pub/apps/gaussian/16b01/g16/l401.exe) - ExpMin= 2.97D-02 ExpMax= 1.28D+05 ExpMxC= 1.24D+03 IAcc=3 IRadAn= 5 AccDes= 0.00D+00 - Harris functional with IExCor=20419 and IRadAn= 5 diagonalized for initial guess. - HarFok: IExCor=20419 AccDes= 0.00D+00 IRadAn= 5 IDoV= 1 UseB2=F ITyADJ=14 - ICtDFT= 3500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000 - FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 - NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T - wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0 - NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Symmetry not used in FoFCou. - Harris En= -1308.35056237338 - JPrj=0 DoOrth=F DoCkMO=F. - Leave Link 401 at Wed Nov 16 10:43:23 2022, MaxMem= 5637144576 cpu: 40.1 elap: 2.3 - (Enter /opt/ohpc/pub/apps/gaussian/16b01/g16/l502.exe) - Two-electron integral symmetry not used. - Closed shell SCF: - Using DIIS extrapolation, IDIIS= 1040. - NGot= 5637144576 LenX= 5636872714 LenY= 5636741229 - Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. - Requested convergence on MAX density matrix=1.00D-06. - Requested convergence on energy=1.00D-06. - No special actions if energy rises. - Fock matrices will be formed incrementally for 20 cycles. - - Cycle 1 Pass 1 IDiag 1: - FoFJK: IHMeth= 1 ICntrl= 0 DoSepK=T KAlg= 0 I1Cent= 0 FoldK=F - IRaf= 1 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 IDoP0=0 IntGTp=1. - FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 - NFxFlg= 0 DoJE=T BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Symmetry not used in FoFCou. - E= -1337.73360526009 - DIIS: error= 2.76D-02 at cycle 1 NSaved= 1. - NSaved= 1 IEnMin= 1 EnMin= -1337.73360526009 IErMin= 1 ErrMin= 2.76D-02 - ErrMax= 2.76D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.55D-01 BMatP= 5.55D-01 - IDIUse=3 WtCom= 7.24D-01 WtEn= 2.76D-01 - Coeff-Com: 0.100D+01 - Coeff-En: 0.100D+01 - Coeff: 0.100D+01 - Gap= 0.388 Goal= None Shift= 0.000 - GapD= 0.388 DampG=1.000 DampE=0.500 DampFc=0.5000 IDamp=-1. - Damping current iteration by 5.00D-01 - RMSDP=8.43D-02 MaxDP=6.78D+00 OVMax= 2.28D-01 - - Cycle 2 Pass 1 IDiag 1: - RMSU= 1.51D-02 CP: 8.60D-01 - E= -1337.93790506986 Delta-E= -0.204299809770 Rises=F Damp=T - DIIS: error= 7.69D-03 at cycle 2 NSaved= 2. - NSaved= 2 IEnMin= 2 EnMin= -1337.93790506986 IErMin= 2 ErrMin= 7.69D-03 - ErrMax= 7.69D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.37D-02 BMatP= 5.55D-01 - IDIUse=3 WtCom= 9.23D-01 WtEn= 7.69D-02 - Coeff-Com: -0.162D+00 0.116D+01 - Coeff-En: 0.000D+00 0.100D+01 - Coeff: -0.150D+00 0.115D+01 - Gap= 0.388 Goal= None Shift= 0.000 - RMSDP=3.72D-02 MaxDP=2.98D+00 DE=-2.04D-01 OVMax= 1.48D-01 - - Cycle 3 Pass 1 IDiag 1: - RMSU= 1.13D-02 CP: 7.35D-01 9.54D-01 - E= -1338.12177874285 Delta-E= -0.183873672995 Rises=F Damp=F - DIIS: error= 4.05D-03 at cycle 3 NSaved= 3. - NSaved= 3 IEnMin= 3 EnMin= -1338.12177874285 IErMin= 3 ErrMin= 4.05D-03 - ErrMax= 4.05D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.66D-02 BMatP= 5.37D-02 - IDIUse=3 WtCom= 9.59D-01 WtEn= 4.05D-02 - Coeff-Com: -0.128D+00 0.435D+00 0.694D+00 - Coeff-En: 0.000D+00 0.000D+00 0.100D+01 - Coeff: -0.123D+00 0.417D+00 0.706D+00 - Gap= 0.288 Goal= None Shift= 0.000 - RMSDP=5.34D-03 MaxDP=2.22D-01 DE=-1.84D-01 OVMax= 4.17D-02 - - Cycle 4 Pass 1 IDiag 1: - RMSU= 2.25D-03 CP: 7.24D-01 1.13D+00 7.49D-01 - E= -1338.13580118171 Delta-E= -0.014022438855 Rises=F Damp=F - DIIS: error= 1.68D-03 at cycle 4 NSaved= 4. - NSaved= 4 IEnMin= 4 EnMin= -1338.13580118171 IErMin= 4 ErrMin= 1.68D-03 - ErrMax= 1.68D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.91D-03 BMatP= 1.66D-02 - IDIUse=3 WtCom= 9.83D-01 WtEn= 1.68D-02 - Coeff-Com: -0.416D-01 0.886D-01 0.342D+00 0.611D+00 - Coeff-En: 0.000D+00 0.000D+00 0.746D-01 0.925D+00 - Coeff: -0.409D-01 0.871D-01 0.337D+00 0.616D+00 - Gap= 0.282 Goal= None Shift= 0.000 - RMSDP=1.11D-03 MaxDP=7.58D-02 DE=-1.40D-02 OVMax= 1.60D-02 - - Cycle 5 Pass 1 IDiag 1: - RMSU= 6.66D-04 CP: 7.23D-01 1.11D+00 7.97D-01 7.61D-01 - E= -1338.13846012744 Delta-E= -0.002658945732 Rises=F Damp=F - DIIS: error= 5.08D-04 at cycle 5 NSaved= 5. - NSaved= 5 IEnMin= 5 EnMin= -1338.13846012744 IErMin= 5 ErrMin= 5.08D-04 - ErrMax= 5.08D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.21D-04 BMatP= 2.91D-03 - IDIUse=3 WtCom= 9.95D-01 WtEn= 5.08D-03 - Coeff-Com: -0.115D-01 0.156D-01 0.128D+00 0.314D+00 0.554D+00 - Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.100D+01 - Coeff: -0.114D-01 0.156D-01 0.128D+00 0.312D+00 0.556D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=3.66D-04 MaxDP=1.78D-02 DE=-2.66D-03 OVMax= 4.84D-03 - - Cycle 6 Pass 1 IDiag 1: - RMSU= 2.32D-04 CP: 7.23D-01 1.10D+00 8.08D-01 7.88D-01 7.15D-01 - E= -1338.13867206928 Delta-E= -0.000211941844 Rises=F Damp=F - DIIS: error= 1.59D-04 at cycle 6 NSaved= 6. - NSaved= 6 IEnMin= 6 EnMin= -1338.13867206928 IErMin= 6 ErrMin= 1.59D-04 - ErrMax= 1.59D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.54D-05 BMatP= 2.21D-04 - IDIUse=3 WtCom= 9.98D-01 WtEn= 1.59D-03 - Coeff-Com: 0.165D-02-0.712D-02 0.791D-02 0.495D-01 0.222D+00 0.727D+00 - Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.100D+01 - Coeff: 0.164D-02-0.711D-02 0.790D-02 0.494D-01 0.221D+00 0.727D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=7.38D-05 MaxDP=3.71D-03 DE=-2.12D-04 OVMax= 1.65D-03 - - Cycle 7 Pass 1 IDiag 1: - RMSU= 5.89D-05 CP: 7.23D-01 1.10D+00 8.09D-01 7.92D-01 7.58D-01 - CP: 1.09D+00 - E= -1338.13869139904 Delta-E= -0.000019329762 Rises=F Damp=F - DIIS: error= 6.34D-05 at cycle 7 NSaved= 7. - NSaved= 7 IEnMin= 7 EnMin= -1338.13869139904 IErMin= 7 ErrMin= 6.34D-05 - ErrMax= 6.34D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.10D-06 BMatP= 1.54D-05 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.297D-02-0.606D-02-0.195D-01-0.364D-01-0.673D-02 0.283D+00 - Coeff-Com: 0.783D+00 - Coeff: 0.297D-02-0.606D-02-0.195D-01-0.364D-01-0.673D-02 0.283D+00 - Coeff: 0.783D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=6.26D-05 MaxDP=3.76D-03 DE=-1.93D-05 OVMax= 9.18D-04 - - Cycle 8 Pass 1 IDiag 1: - RMSU= 3.38D-05 CP: 7.23D-01 1.10D+00 8.09D-01 7.94D-01 7.90D-01 - CP: 1.13D+00 1.01D+00 - E= -1338.13869497382 Delta-E= -0.000003574779 Rises=F Damp=F - DIIS: error= 1.71D-05 at cycle 8 NSaved= 8. - NSaved= 8 IEnMin= 8 EnMin= -1338.13869497382 IErMin= 8 ErrMin= 1.71D-05 - ErrMax= 1.71D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.98D-07 BMatP= 2.10D-06 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.753D-03-0.120D-02-0.661D-02-0.167D-01-0.197D-01 0.312D-01 - Coeff-Com: 0.268D+00 0.744D+00 - Coeff: 0.753D-03-0.120D-02-0.661D-02-0.167D-01-0.197D-01 0.312D-01 - Coeff: 0.268D+00 0.744D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=2.12D-05 MaxDP=1.82D-03 DE=-3.57D-06 OVMax= 4.44D-04 - - Cycle 9 Pass 1 IDiag 1: - RMSU= 9.20D-06 CP: 7.23D-01 1.10D+00 8.09D-01 7.96D-01 7.90D-01 - CP: 1.14D+00 1.02D+00 8.64D-01 - E= -1338.13869539092 Delta-E= -0.000000417093 Rises=F Damp=F - DIIS: error= 1.02D-05 at cycle 9 NSaved= 9. - NSaved= 9 IEnMin= 9 EnMin= -1338.13869539092 IErMin= 9 ErrMin= 1.02D-05 - ErrMax= 1.02D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.44D-08 BMatP= 1.98D-07 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.359D-03 0.862D-03 0.164D-02 0.996D-03-0.462D-02-0.399D-01 - Coeff-Com: -0.515D-01 0.226D+00 0.867D+00 - Coeff: -0.359D-03 0.862D-03 0.164D-02 0.996D-03-0.462D-02-0.399D-01 - Coeff: -0.515D-01 0.226D+00 0.867D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=7.35D-06 MaxDP=2.91D-04 DE=-4.17D-07 OVMax= 2.47D-04 - - Cycle 10 Pass 1 IDiag 1: - RMSU= 4.30D-06 CP: 7.23D-01 1.10D+00 8.09D-01 7.95D-01 7.94D-01 - CP: 1.14D+00 1.02D+00 9.57D-01 1.17D+00 - E= -1338.13869549752 Delta-E= -0.000000106602 Rises=F Damp=F - DIIS: error= 4.99D-06 at cycle 10 NSaved= 10. - NSaved=10 IEnMin=10 EnMin= -1338.13869549752 IErMin=10 ErrMin= 4.99D-06 - ErrMax= 4.99D-06 0.00D+00 EMaxC= 1.00D-01 BMatC= 7.85D-09 BMatP= 3.44D-08 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.288D-03 0.571D-03 0.188D-02 0.350D-02 0.174D-02-0.222D-01 - Coeff-Com: -0.742D-01-0.475D-01 0.360D+00 0.777D+00 - Coeff: -0.288D-03 0.571D-03 0.188D-02 0.350D-02 0.174D-02-0.222D-01 - Coeff: -0.742D-01-0.475D-01 0.360D+00 0.777D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=2.43D-06 MaxDP=1.46D-04 DE=-1.07D-07 OVMax= 1.42D-04 - - Cycle 11 Pass 1 IDiag 1: - RMSU= 1.66D-06 CP: 7.23D-01 1.10D+00 8.09D-01 7.95D-01 7.94D-01 - CP: 1.14D+00 1.01D+00 9.63D-01 1.26D+00 1.03D+00 - E= -1338.13869551830 Delta-E= -0.000000020782 Rises=F Damp=F - DIIS: error= 1.82D-06 at cycle 11 NSaved= 11. - NSaved=11 IEnMin=11 EnMin= -1338.13869551830 IErMin=11 ErrMin= 1.82D-06 - ErrMax= 1.82D-06 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.56D-09 BMatP= 7.85D-09 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.611D-04 0.102D-03 0.480D-03 0.122D-02 0.121D-02-0.333D-02 - Coeff-Com: -0.250D-01-0.529D-01 0.200D-01 0.352D+00 0.707D+00 - Coeff: -0.611D-04 0.102D-03 0.480D-03 0.122D-02 0.121D-02-0.333D-02 - Coeff: -0.250D-01-0.529D-01 0.200D-01 0.352D+00 0.707D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=1.47D-06 MaxDP=5.90D-05 DE=-2.08D-08 OVMax= 4.30D-05 - - Cycle 12 Pass 1 IDiag 1: - RMSU= 6.53D-07 CP: 7.23D-01 1.10D+00 8.09D-01 7.95D-01 7.95D-01 - CP: 1.14D+00 1.01D+00 9.79D-01 1.29D+00 1.13D+00 - CP: 8.56D-01 - E= -1338.13869552122 Delta-E= -0.000000002922 Rises=F Damp=F - DIIS: error= 5.84D-07 at cycle 12 NSaved= 12. - NSaved=12 IEnMin=12 EnMin= -1338.13869552122 IErMin=12 ErrMin= 5.84D-07 - ErrMax= 5.84D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.04D-10 BMatP= 1.56D-09 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.293D-04-0.656D-04-0.169D-03-0.155D-03 0.156D-03 0.261D-02 - Coeff-Com: 0.233D-02-0.112D-01-0.521D-01 0.144D-01 0.297D+00 0.747D+00 - Coeff: 0.293D-04-0.656D-04-0.169D-03-0.155D-03 0.156D-03 0.261D-02 - Coeff: 0.233D-02-0.112D-01-0.521D-01 0.144D-01 0.297D+00 0.747D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=4.62D-07 MaxDP=2.96D-05 DE=-2.92D-09 OVMax= 1.32D-05 - - Cycle 13 Pass 1 IDiag 1: - RMSU= 2.17D-07 CP: 7.23D-01 1.10D+00 8.09D-01 7.95D-01 7.94D-01 - CP: 1.14D+00 1.01D+00 9.76D-01 1.28D+00 1.13D+00 - CP: 9.73D-01 9.30D-01 - E= -1338.13869552153 Delta-E= -0.000000000303 Rises=F Damp=F - DIIS: error= 1.76D-07 at cycle 13 NSaved= 13. - NSaved=13 IEnMin=13 EnMin= -1338.13869552153 IErMin=13 ErrMin= 1.76D-07 - ErrMax= 1.76D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.30D-11 BMatP= 2.04D-10 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.161D-04-0.330D-04-0.110D-03-0.174D-03-0.404D-04 0.141D-02 - Coeff-Com: 0.357D-02 0.188D-02-0.246D-01-0.413D-01 0.291D-01 0.295D+00 - Coeff-Com: 0.736D+00 - Coeff: 0.161D-04-0.330D-04-0.110D-03-0.174D-03-0.404D-04 0.141D-02 - Coeff: 0.357D-02 0.188D-02-0.246D-01-0.413D-01 0.291D-01 0.295D+00 - Coeff: 0.736D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=1.48D-07 MaxDP=1.11D-05 DE=-3.03D-10 OVMax= 3.35D-06 - - Cycle 14 Pass 1 IDiag 1: - RMSU= 8.56D-08 CP: 7.23D-01 1.10D+00 8.09D-01 7.95D-01 7.94D-01 - CP: 1.14D+00 1.01D+00 9.75D-01 1.28D+00 1.13D+00 - CP: 9.72D-01 9.61D-01 1.19D+00 - E= -1338.13869552160 Delta-E= -0.000000000073 Rises=F Damp=F - DIIS: error= 4.26D-08 at cycle 14 NSaved= 14. - NSaved=14 IEnMin=14 EnMin= -1338.13869552160 IErMin=14 ErrMin= 4.26D-08 - ErrMax= 4.26D-08 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.06D-12 BMatP= 2.30D-11 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.224D-06 0.104D-05-0.458D-05-0.163D-04-0.175D-04 0.700D-04 - Coeff-Com: 0.520D-03 0.183D-02-0.455D-04-0.892D-02-0.205D-01-0.160D-01 - Coeff-Com: 0.136D+00 0.907D+00 - Coeff: -0.224D-06 0.104D-05-0.458D-05-0.163D-04-0.175D-04 0.700D-04 - Coeff: 0.520D-03 0.183D-02-0.455D-04-0.892D-02-0.205D-01-0.160D-01 - Coeff: 0.136D+00 0.907D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=5.74D-08 MaxDP=2.28D-06 DE=-7.32D-11 OVMax= 7.11D-07 - - Cycle 15 Pass 1 IDiag 1: - RMSU= 1.94D-08 CP: 7.23D-01 1.10D+00 8.09D-01 7.95D-01 7.94D-01 - CP: 1.14D+00 1.01D+00 9.75D-01 1.28D+00 1.13D+00 - CP: 9.72D-01 9.64D-01 1.31D+00 1.16D+00 - E= -1338.13869552161 Delta-E= -0.000000000007 Rises=F Damp=F - DIIS: error= 1.38D-08 at cycle 15 NSaved= 15. - NSaved=15 IEnMin=15 EnMin= -1338.13869552161 IErMin=15 ErrMin= 1.38D-08 - ErrMax= 1.38D-08 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.67D-13 BMatP= 1.06D-12 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.911D-06 0.212D-05 0.356D-05 0.217D-05-0.762D-05-0.472D-04 - Coeff-Com: 0.146D-04 0.671D-03 0.114D-02-0.165D-02-0.104D-01-0.246D-01 - Coeff-Com: 0.158D-01 0.368D+00 0.651D+00 - Coeff: -0.911D-06 0.212D-05 0.356D-05 0.217D-05-0.762D-05-0.472D-04 - Coeff: 0.146D-04 0.671D-03 0.114D-02-0.165D-02-0.104D-01-0.246D-01 - Coeff: 0.158D-01 0.368D+00 0.651D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=1.29D-08 MaxDP=7.38D-07 DE=-7.28D-12 OVMax= 1.98D-07 - - Cycle 16 Pass 1 IDiag 1: - RMSU= 6.75D-09 CP: 7.23D-01 1.10D+00 8.09D-01 7.95D-01 7.94D-01 - CP: 1.14D+00 1.01D+00 9.75D-01 1.28D+00 1.13D+00 - CP: 9.73D-01 9.62D-01 1.33D+00 1.16D+00 9.53D-01 - E= -1338.13869552164 Delta-E= -0.000000000034 Rises=F Damp=F - DIIS: error= 3.96D-09 at cycle 16 NSaved= 16. - NSaved=16 IEnMin=16 EnMin= -1338.13869552164 IErMin=16 ErrMin= 3.96D-09 - ErrMax= 3.96D-09 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.45D-14 BMatP= 1.67D-13 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.288D-06 0.586D-06 0.198D-05 0.371D-05-0.822D-06-0.278D-04 - Coeff-Com: -0.818D-04-0.109D-04 0.413D-03 0.824D-03-0.318D-03-0.607D-02 - Coeff-Com: -0.110D-01-0.278D-02 0.198D+00 0.821D+00 - Coeff: -0.288D-06 0.586D-06 0.198D-05 0.371D-05-0.822D-06-0.278D-04 - Coeff: -0.818D-04-0.109D-04 0.413D-03 0.824D-03-0.318D-03-0.607D-02 - Coeff: -0.110D-01-0.278D-02 0.198D+00 0.821D+00 - Gap= 0.283 Goal= None Shift= 0.000 - RMSDP=3.95D-09 MaxDP=2.32D-07 DE=-3.37D-11 OVMax= 7.13D-08 - - SCF Done: E(RCAM-B3LYP) = -1338.13869552 A.U. after 16 cycles - NFock= 16 Conv=0.40D-08 -V/T= 2.0019 - KE= 1.335552096557D+03 PE=-4.830202254705D+03 EE= 1.321061481664D+03 - Leave Link 502 at Wed Nov 16 10:45:01 2022, MaxMem= 5637144576 cpu: 1812.2 elap: 98.3 - (Enter /opt/ohpc/pub/apps/gaussian/16b01/g16/l601.exe) - Copying SCF densities to generalized density rwf, IOpCl= 0 IROHF=0. - - ********************************************************************** - - Population analysis using the SCF Density. - - ********************************************************************** - - Alpha occ. eigenvalues -- -101.62776-101.62288 -14.46638 -14.40015 -10.34827 - Alpha occ. eigenvalues -- -10.33240 -10.33029 -10.31287 -10.29476 -10.27361 - Alpha occ. eigenvalues -- -10.26661 -10.24720 -9.54544 -9.54038 -7.30914 - Alpha occ. eigenvalues -- -7.30409 -7.29927 -7.29881 -7.29424 -7.29378 - Alpha occ. eigenvalues -- -1.13462 -1.00824 -0.98819 -0.94637 -0.93079 - Alpha occ. eigenvalues -- -0.88139 -0.84829 -0.80006 -0.74918 -0.71095 - Alpha occ. eigenvalues -- -0.69188 -0.65003 -0.59483 -0.57671 -0.56713 - Alpha occ. eigenvalues -- -0.55763 -0.53516 -0.52046 -0.51645 -0.49524 - Alpha occ. eigenvalues -- -0.47807 -0.47056 -0.46517 -0.41783 -0.39463 - Alpha occ. eigenvalues -- -0.38815 -0.37620 -0.36888 -0.35330 -0.29664 - Alpha occ. eigenvalues -- -0.28575 - Alpha virt. eigenvalues -- -0.00241 -0.00034 0.01770 0.02707 0.02916 - Alpha virt. eigenvalues -- 0.03771 0.03900 0.04199 0.05572 0.05966 - Alpha virt. eigenvalues -- 0.07141 0.07206 0.07932 0.08164 0.09207 - Alpha virt. eigenvalues -- 0.09357 0.09520 0.10359 0.10735 0.11107 - Alpha virt. eigenvalues -- 0.11154 0.11883 0.12129 0.12989 0.13565 - Alpha virt. eigenvalues -- 0.14021 0.14224 0.15039 0.15180 0.15363 - Alpha virt. eigenvalues -- 0.15708 0.16762 0.17085 0.17468 0.17750 - Alpha virt. eigenvalues -- 0.18896 0.19463 0.19809 0.20400 0.20650 - Alpha virt. eigenvalues -- 0.20746 0.21167 0.21821 0.22197 0.22591 - Alpha virt. eigenvalues -- 0.22871 0.23425 0.23819 0.24391 0.25374 - Alpha virt. eigenvalues -- 0.26333 0.26818 0.26898 0.27340 0.27930 - Alpha virt. eigenvalues -- 0.29362 0.29722 0.29981 0.30208 0.30820 - Alpha virt. eigenvalues -- 0.32217 0.32513 0.33091 0.33473 0.33874 - Alpha virt. eigenvalues -- 0.34342 0.35419 0.36023 0.36512 0.36993 - Alpha virt. eigenvalues -- 0.37718 0.38577 0.38811 0.39275 0.39609 - Alpha virt. eigenvalues -- 0.39971 0.41551 0.41970 0.43059 0.44251 - Alpha virt. eigenvalues -- 0.44598 0.45378 0.45577 0.47200 0.48146 - Alpha virt. eigenvalues -- 0.48604 0.49324 0.50697 0.51298 0.51948 - Alpha virt. eigenvalues -- 0.52371 0.53250 0.53512 0.54384 0.55123 - Alpha virt. eigenvalues -- 0.55558 0.55666 0.55889 0.56571 0.57070 - Alpha virt. eigenvalues -- 0.57802 0.58903 0.59238 0.59651 0.60561 - Alpha virt. eigenvalues -- 0.61680 0.62285 0.63457 0.64149 0.64397 - Alpha virt. eigenvalues -- 0.64567 0.65257 0.65347 0.65712 0.67137 - Alpha virt. eigenvalues -- 0.68141 0.68625 0.69355 0.70102 0.70905 - Alpha virt. eigenvalues -- 0.71213 0.72286 0.73260 0.73758 0.73986 - Alpha virt. eigenvalues -- 0.75906 0.76929 0.77223 0.78008 0.78447 - Alpha virt. eigenvalues -- 0.78810 0.79442 0.80267 0.80874 0.82004 - Alpha virt. eigenvalues -- 0.83777 0.84770 0.85728 0.86115 0.87060 - Alpha virt. eigenvalues -- 0.87566 0.87959 0.89314 0.90893 0.91656 - Alpha virt. eigenvalues -- 0.93708 0.94573 0.95088 0.95592 0.96581 - Alpha virt. eigenvalues -- 0.96865 1.00749 1.01352 1.02668 1.03219 - Alpha virt. eigenvalues -- 1.03452 1.05252 1.06361 1.07065 1.07541 - Alpha virt. eigenvalues -- 1.08381 1.10406 1.11274 1.12010 1.13895 - Alpha virt. eigenvalues -- 1.15583 1.17665 1.20580 1.21700 1.23399 - Alpha virt. eigenvalues -- 1.24158 1.24820 1.25351 1.26367 1.28210 - Alpha virt. eigenvalues -- 1.28400 1.29328 1.30480 1.31873 1.32753 - Alpha virt. eigenvalues -- 1.32805 1.33157 1.33696 1.34152 1.35536 - Alpha virt. eigenvalues -- 1.38535 1.40567 1.41880 1.42806 1.45601 - Alpha virt. eigenvalues -- 1.46892 1.47644 1.48322 1.49588 1.49920 - Alpha virt. eigenvalues -- 1.50704 1.50964 1.53130 1.54420 1.55408 - Alpha virt. eigenvalues -- 1.56417 1.56937 1.57473 1.60097 1.61772 - Alpha virt. eigenvalues -- 1.62801 1.64685 1.68366 1.68694 1.70779 - Alpha virt. eigenvalues -- 1.71313 1.75203 1.76885 1.77496 1.77930 - Alpha virt. eigenvalues -- 1.79239 1.81445 1.83406 1.84244 1.85636 - Alpha virt. eigenvalues -- 1.87213 1.88132 1.88858 1.91410 1.92914 - Alpha virt. eigenvalues -- 1.94856 1.96642 1.97335 1.98626 1.98812 - Alpha virt. eigenvalues -- 2.00317 2.03905 2.04974 2.06776 2.08592 - Alpha virt. eigenvalues -- 2.10709 2.11681 2.13564 2.14203 2.15619 - Alpha virt. eigenvalues -- 2.19045 2.21279 2.22510 2.23146 2.25738 - Alpha virt. eigenvalues -- 2.27039 2.27873 2.29261 2.30579 2.33906 - Alpha virt. eigenvalues -- 2.35356 2.36760 2.39967 2.44113 2.46144 - Alpha virt. eigenvalues -- 2.50509 2.51317 2.56180 2.58103 2.59891 - Alpha virt. eigenvalues -- 2.61141 2.62345 2.67004 2.70992 2.76415 - Alpha virt. eigenvalues -- 2.79793 2.80663 2.83959 2.92373 2.96508 - Alpha virt. eigenvalues -- 2.99466 3.04709 3.08317 3.09275 3.12512 - Alpha virt. eigenvalues -- 3.18326 3.26712 3.28352 3.34398 3.37904 - Alpha virt. eigenvalues -- 3.42633 3.45610 3.53938 3.77775 3.85943 - Alpha virt. eigenvalues -- 4.47811 - Condensed to atoms (all electrons): - 1 2 3 4 5 6 - 1 Cl 17.352138 -0.053132 0.007059 -0.004566 -0.006234 -0.001567 - 2 Cl -0.053132 17.356495 -0.002668 0.009998 -0.007377 -0.000652 - 3 N 0.007059 -0.002668 7.809975 0.058975 -0.280995 -0.039641 - 4 N -0.004566 0.009998 0.058975 7.563748 0.414727 -0.304047 - 5 C -0.006234 -0.007377 -0.280995 0.414727 9.193671 -0.936154 - 6 C -0.001567 -0.000652 -0.039641 -0.304047 -0.936154 6.533084 - 7 C -0.574668 0.305915 -1.295831 -0.349191 -0.041876 0.229866 - 8 C 0.325087 -0.661540 -0.125613 -1.448197 -0.383408 0.136816 - 9 C -0.438748 0.852357 -0.122049 1.691740 -1.416850 -0.371684 - 10 C 0.417747 -0.511245 0.123909 -0.379937 0.234053 0.040213 - 11 C -0.434115 0.457160 -0.197077 0.101391 0.175188 0.077675 - 12 C 0.729930 -0.413396 1.758349 0.140594 -1.129103 -0.604767 - 13 H -0.156270 0.013338 -0.228586 -0.028052 0.245165 0.033644 - 14 H 0.014645 -0.179548 -0.012846 -0.331957 0.282800 0.026370 - 15 H 0.001168 -0.002888 0.006537 -0.429063 -0.498617 -0.035183 - 16 H -0.000015 -0.000143 0.149239 -0.160407 0.328685 -0.410977 - 17 H -0.000054 -0.000106 0.164649 0.115122 -0.184422 -0.110737 - 18 H -0.000291 0.000160 -0.326526 0.058928 0.971775 -0.709900 - 7 8 9 10 11 12 - 1 Cl -0.574668 0.325087 -0.438748 0.417747 -0.434115 0.729930 - 2 Cl 0.305915 -0.661540 0.852357 -0.511245 0.457160 -0.413396 - 3 N -1.295831 -0.125613 -0.122049 0.123909 -0.197077 1.758349 - 4 N -0.349191 -1.448197 1.691740 -0.379937 0.101391 0.140594 - 5 C -0.041876 -0.383408 -1.416850 0.234053 0.175188 -1.129103 - 6 C 0.229866 0.136816 -0.371684 0.040213 0.077675 -0.604767 - 7 C 33.422028 -6.093637 4.286054 -7.399272 7.360157 -27.091466 - 8 C -6.093637 32.259904 -27.991684 8.192848 -7.477652 4.512126 - 9 C 4.286054 -27.991684 65.335038 -18.107160 8.799293 -20.518239 - 10 C -7.399272 8.192848 -18.107160 22.146129 -8.875544 8.853127 - 11 C 7.360157 -7.477652 8.799293 -8.875544 20.689701 -15.602273 - 12 C -27.091466 4.512126 -20.518239 8.853127 -15.602273 60.589553 - 13 H 5.376857 -0.166337 0.634114 -0.828348 2.357289 -9.579742 - 14 H -0.114052 5.535960 -10.331338 2.815829 -0.846597 0.568474 - 15 H -0.182344 0.731366 -0.495750 0.062060 -0.043855 0.092292 - 16 H 0.055674 -0.031639 -0.014148 0.011344 -0.003393 -0.008399 - 17 H 0.092974 0.085742 -0.058115 0.004475 0.002555 -0.022595 - 18 H -0.108216 0.030899 0.058430 -0.013297 0.017787 -0.063388 - 13 14 15 16 17 18 - 1 Cl -0.156270 0.014645 0.001168 -0.000015 -0.000054 -0.000291 - 2 Cl 0.013338 -0.179548 -0.002888 -0.000143 -0.000106 0.000160 - 3 N -0.228586 -0.012846 0.006537 0.149239 0.164649 -0.326526 - 4 N -0.028052 -0.331957 -0.429063 -0.160407 0.115122 0.058928 - 5 C 0.245165 0.282800 -0.498617 0.328685 -0.184422 0.971775 - 6 C 0.033644 0.026370 -0.035183 -0.410977 -0.110737 -0.709900 - 7 C 5.376857 -0.114052 -0.182344 0.055674 0.092974 -0.108216 - 8 C -0.166337 5.535960 0.731366 -0.031639 0.085742 0.030899 - 9 C 0.634114 -10.331338 -0.495750 -0.014148 -0.058115 0.058430 - 10 C -0.828348 2.815829 0.062060 0.011344 0.004475 -0.013297 - 11 C 2.357289 -0.846597 -0.043855 -0.003393 0.002555 0.017787 - 12 C -9.579742 0.568474 0.092292 -0.008399 -0.022595 -0.063388 - 13 H 4.450086 0.047731 -0.006312 0.002472 0.003221 0.005461 - 14 H 0.047731 4.623715 0.058799 0.007183 0.002531 0.001767 - 15 H -0.006312 0.058799 2.280237 -0.021008 0.001801 0.002610 - 16 H 0.002472 0.007183 -0.021008 2.221590 -0.282179 -0.330050 - 17 H 0.003221 0.002531 0.001801 -0.282179 1.920840 -0.331467 - 18 H 0.005461 0.001767 0.002610 -0.330050 -0.331467 2.272343 - Mulliken charges: - 1 - 1 Cl -0.178113 - 2 Cl -0.162727 - 3 N -0.446862 - 4 N 0.280194 - 5 C -0.961027 - 6 C 2.447638 - 7 C -1.878973 - 8 C -1.431042 - 9 C 4.208739 - 10 C -0.786929 - 11 C -0.557689 - 12 C 3.788922 - 13 H -1.175731 - 14 H -1.169465 - 15 H -0.521850 - 16 H -0.513827 - 17 H -0.404234 - 18 H -0.537022 - Sum of Mulliken charges = -0.00000 - Mulliken charges with hydrogens summed into heavy atoms: - 1 - 1 Cl -0.178113 - 2 Cl -0.162727 - 3 N -0.446862 - 4 N -0.241656 - 5 C -0.961027 - 6 C 0.992555 - 7 C -1.878973 - 8 C -1.431042 - 9 C 3.039273 - 10 C -0.786929 - 11 C -0.557689 - 12 C 2.613192 - Electronic spatial extent (au): = 7763.9825 - Charge= -0.0000 electrons - Dipole moment (field-independent basis, Debye): - X= 2.7814 Y= 3.6252 Z= 3.3717 Tot= 5.6787 - Quadrupole moment (field-independent basis, Debye-Ang): - XX= -68.5758 YY= -73.5266 ZZ= -61.4118 - XY= 14.7606 XZ= 21.1909 YZ= 20.1020 - Traceless Quadrupole moment (field-independent basis, Debye-Ang): - XX= -0.7378 YY= -5.6885 ZZ= 6.4263 - XY= 14.7606 XZ= 21.1909 YZ= 20.1020 - Octapole moment (field-independent basis, Debye-Ang**2): - XXX= -468.8761 YYY= -106.0164 ZZZ= -584.3883 XYY= -124.0403 - XXY= 19.3355 XXZ= -140.7134 XZZ= -75.9117 YZZ= 36.2786 - YYZ= -180.4060 XYZ= 79.4989 - Hexadecapole moment (field-independent basis, Debye-Ang**3): - XXXX= -3231.7191 YYYY= -1908.7634 ZZZZ= -4125.3312 XXXY= -698.6380 - XXXZ= -1098.7817 YYYX= -797.2647 YYYZ= -242.0609 ZZZX= -1006.4236 - ZZZY= -55.7408 XXYY= -644.4755 XXZZ= -965.7185 YYZZ= -919.0404 - XXYZ= 192.7856 YYXZ= -244.2360 ZZXY= -10.8434 - N-N= 8.354499809625D+02 E-N=-4.830202254696D+03 KE= 1.335552096557D+03 - No NMR shielding tensors so no spin-rotation constants. - Leave Link 601 at Wed Nov 16 10:45:02 2022, MaxMem= 5637144576 cpu: 11.2 elap: 1.1 - (Enter /opt/ohpc/pub/apps/gaussian/16b01/g16/l602.exe) - FitSet: NAtFit= 18 NAtPot= 18 NAtFrz= 0 MDM= 22 TotChg= 0.00000 - Breneman (CHELPG) radii used. - Generate Potential Derived Charges using the Breneman model, NDens= 1. - Grid spacing= 0.300 Box extension= 2.800 - NStep X,Y,Z= 37 41 36 Total possible points= 54612 - Number of Points to Fit= 11818 - - ********************************************************************** - - Electrostatic Properties Using The SCF Density. - - ********************************************************************** - - Atomic Center 1 is at 0.529511 -1.626652 1.247344 - Atomic Center 2 is at 0.362927 -1.511555 4.375374 - Atomic Center 3 is at 3.703161 2.470259 1.679277 - Atomic Center 4 is at 3.582138 2.531106 3.906529 - Atomic Center 5 is at 4.112504 3.089530 2.782505 - Atomic Center 6 is at 5.072999 4.218889 2.804341 - Atomic Center 7 is at 2.860414 1.456338 2.124311 - Atomic Center 8 is at 2.790648 1.491595 3.517643 - Atomic Center 9 is at 2.019660 0.586857 4.234066 - Atomic Center 10 is at 1.332677 -0.367923 3.533240 - Atomic Center 11 is at 1.403867 -0.417396 2.127431 - Atomic Center 12 is at 2.171295 0.490754 1.403730 - Atomic Center 13 is at 2.221128 0.451516 0.476228 - Atomic Center 14 is at 1.970539 0.627801 5.162607 - Atomic Center 15 is at 3.801546 2.769374 4.720692 - Atomic Center 16 is at 5.682386 4.106863 3.538439 - Atomic Center 17 is at 4.594603 5.044583 2.908321 - Atomic Center 18 is at 5.565634 4.235948 1.980819 - 11818 points will be used for fitting atomic charges - Fitting point charges to electrostatic potential - Charges from ESP fit, RMS= 0.00452 RRMS= 0.21699: - ESP charges: - 1 - 1 Cl -0.122653 - 2 Cl -0.108213 - 3 N -0.692073 - 4 N -0.518559 - 5 C 0.519349 - 6 C -0.094444 - 7 C 0.399280 - 8 C 0.125796 - 9 C -0.215631 - 10 C 0.034945 - 11 C 0.110077 - 12 C -0.290326 - 13 H 0.190237 - 14 H 0.163761 - 15 H 0.364197 - 16 H 0.025465 - 17 H 0.040002 - 18 H 0.068788 - Sum of ESP charges = 0.00000 - ESP charges with hydrogens summed into heavy atoms: - 1 - 1 Cl -0.122653 - 2 Cl -0.108213 - 3 N -0.692073 - 4 N -0.154361 - 5 C 0.519349 - 6 C 0.039811 - 7 C 0.399280 - 8 C 0.125796 - 9 C -0.051870 - 10 C 0.034945 - 11 C 0.110077 - 12 C -0.100089 - Charge= 0.00000 Dipole= 2.8894 3.7629 3.3221 Tot= 5.7917 - ----------------------------------------------------------------- - - Electrostatic Properties (Atomic Units) - - ----------------------------------------------------------------- - Center Electric -------- Electric Field -------- - Potential X Y Z - ----------------------------------------------------------------- - 1 Atom -64.398562 - 2 Atom -64.393669 - 3 Atom -18.383446 - 4 Atom -18.311324 - 5 Atom -14.669547 - 6 Atom -14.778941 - 7 Atom -14.726083 - 8 Atom -14.707371 - 9 Atom -14.753011 - 10 Atom -14.687413 - 11 Atom -14.688957 - 12 Atom -14.760543 - 13 Atom -1.078349 - 14 Atom -1.065572 - 15 Atom -0.965594 - 16 Atom -1.073607 - 17 Atom -1.075287 - 18 Atom -1.081172 - ----------------------------------------------------------------- - Leave Link 602 at Wed Nov 16 10:45:03 2022, MaxMem= 5637144576 cpu: 7.3 elap: 0.7 - (Enter /opt/ohpc/pub/apps/gaussian/16b01/g16/l9999.exe) - 1\1\GINC-N06\SP\RCAM-B3LYP\Aug-CC-pVDZ\C8H6Cl2N2\TERTIUS\16-Nov-2022\0 - \\#p cam-b3lyp/aug-cc-pVDZ POP=CHELPG density=current NoSymm\\DAST UAE - nvolvida passo 15\\0,1\Cl,0,0.529511,-1.626652,1.247344\Cl,0,0.362927, - -1.511555,4.375374\N,0,3.703161,2.470259,1.679277\N,0,3.582138,2.53110 - 6,3.906529\C,0,4.112504,3.08953,2.782505\C,0,5.072999,4.218889,2.80434 - 1\C,0,2.860414,1.456338,2.124311\C,0,2.790648,1.491595,3.517643\C,0,2. - 01966,0.586857,4.234066\C,0,1.332677,-0.367923,3.53324\C,0,1.403867,-0 - .417396,2.127431\C,0,2.171295,0.490754,1.40373\H,0,2.221128,0.451516,0 - .476228\H,0,1.970539,0.627801,5.162607\H,0,3.801546,2.769374,4.720692\ - H,0,5.682386,4.106863,3.538439\H,0,4.594603,5.044583,2.908321\H,0,5.56 - 5634,4.235948,1.980819\\Version=ES64L-G16RevB.01\HF=-1338.1386955\RMSD - =3.953e-09\Dipole=1.094298,1.4262771,1.3265347\Quadrupole=-0.5485058,- - 4.2292934,4.7777992,10.9741706,15.7548816,14.9453149\PG=C01 [X(C8H6Cl2 - N2)]\\@ - - - WE LEARN WISDOM FROM FAILURE MUCH MORE THAN FROM SUCCESS. - WE DISCOVER WHAT WILL DO BY FINDING OUT WHAT WILL NOT DO... - AND HE WHO NEVER MADE A MISTAKE NEVER MADE A DISCOVERY - Job cpu time: 0 days 0 hours 31 minutes 46.5 seconds. - Elapsed time: 0 days 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n_atoms: 18 + comment: "DC-MBI UAEnvolvida" \ No newline at end of file diff --git a/DC-MBI-3x3x3.gjf b/crystal.example.gjf similarity index 97% rename from DC-MBI-3x3x3.gjf rename to crystal.example.gjf index 825cfbf..53fb5e9 100644 --- a/DC-MBI-3x3x3.gjf +++ b/crystal.example.gjf @@ -1,10 +1,10 @@ %mem=42GB %Nprocs=20 -#p cam-b3lyp/aug-cc-pVDZ POP=CHELPG density=current NoSymm CHARGE +#p ${LEVEL} POP=${POP} density=current NoSymm (CHARGE - A partir do segundo) -DC-MBI UAEnvolvida passo 1 +${COMMENTARY} passo 1 -0 1 +${MULT} Cl 0.529511 -1.626652 1.247344 Cl 0.362927 -1.511555 4.375374 N 3.703161 2.470259 1.679277 @@ -24,7 +24,6 @@ H 5.682386 4.106863 3.538439 H 4.594603 5.044583 2.908321 H 5.565634 4.235948 1.980819 - Cl -13.708489 -7.313252 -9.150656 Cl -13.875073 -7.198155 -6.022626 N -10.534839 -3.216341 -8.718723 diff --git a/crystal.xyz b/crystal.xyz new file mode 100644 index 0000000..8ba5bf2 --- /dev/null +++ b/crystal.xyz @@ -0,0 +1,1944 @@ +Cl 0.529511 -1.626652 1.247344 +Cl 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17.276277 +N 24.893862 8.842094 19.503529 +C 24.363496 8.283670 18.379505 +C 23.403001 7.154311 18.401341 +C 25.615586 9.916862 17.721311 +C 25.685352 9.881605 19.114643 +C 26.456340 10.786343 19.831066 +C 27.143323 11.741123 19.130240 +C 27.072133 11.790596 17.724431 +C 26.304705 10.882446 17.000730 +H 26.254872 10.921684 16.073228 +H 26.505461 10.745399 20.759607 +H 24.674454 8.603826 20.317692 +H 22.793614 7.266337 19.135439 +H 23.881397 6.328617 18.505321 +H 22.910366 7.137252 17.577819 \ No newline at end of file diff --git a/crystalpol/__init__.py b/crystalpol/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/crystalpol/__main__.py b/crystalpol/__main__.py new file mode 100644 index 0000000..6df08a0 --- /dev/null +++ b/crystalpol/__main__.py @@ -0,0 +1,62 @@ +from crystalpol.polarization import Polarization +from crystalpol.shared.config import Config + +from yaml.loader import SafeLoader +import yaml + +import setproctitle +import argparse +import os + + +__VERSION = "v0.0.1" +os.nice(+19) +setproctitle.setproctitle("crystalpol-{}".format(__VERSION)) + + +def main(): + """ + Read and store the arguments passed to the program + and set the usage and help messages. + """ + + parser = argparse.ArgumentParser(prog="CrystalPol") + parser.add_argument( + "-v", "--version", action="version", version=f"crystalpol-{__VERSION}" + ) + parser.add_argument( + "-c", "--config", + dest="config", + default="config.yml", + metavar="INFILE", + help="Config file of crystalpol [default = config.yml]" + ) + parser.add_argument( + "-i", "--input", + dest="infile", + default="crystal.xyz", + metavar="INFILE", + help="Input file of crystalpol [default = crystal.xyz]" + ) + parser.add_argument( + "-o", "--output", + dest="outfile", + default="run.log", + metavar="OUTFILE", + help="Output file of crystalpol [default = run.log]" + ) + args = parser.parse_args() + + try: + with open(args.config) as file: + data = yaml.load(file, Loader=SafeLoader) + config = Config(**data.get('crystal_pol')) + except IOError: + raise RuntimeError('Invalid or Missing Config File.') + + pol = Polarization(args.infile, args.outfile, config) + pol.run() + + +if __name__ == "__main__": + main() diff --git a/crystalpol/gaussian.py b/crystalpol/gaussian.py new file mode 100644 index 0000000..2380627 --- /dev/null +++ b/crystalpol/gaussian.py @@ -0,0 +1,114 @@ +from crystalpol.shared.utils.ptable import atom_symbol +from crystalpol.shared.system.crystal import Crystal +from crystalpol.shared.config import Config + +from pathlib import Path, PosixPath +from typing import TextIO +import subprocess +import textwrap +import shutil +import os + + +class Gaussian: + __slots__ = ('qmprog', 'config', 'keywords') + + def __init__(self, config: Config) -> None: + self.qmprog = "g16" + self.config = config + + self.check_keyword() + + def check_keyword(self): + if self.config.pop not in ["chelpg", "mk", "nbo"]: + self.config.pop = "chelpg" + + def run(self, cycle: int, crystal: Crystal) -> None: + + file = Path("simfiles", f"crystal-{str(cycle).zfill(2)}.gjf") + + self.make_gaussian_input(cycle, file, crystal) + + if shutil.which("bash") is not None: + exit_status = subprocess.call( + [ + "bash", + "-c", + "exec -a {}-step{} {} {}".format( + self.qmprog, cycle, self.qmprog, file.name + ), + ] + ) + else: + exit_status = subprocess.call([self.qmprog, file.name]) + + if exit_status != 0: + raise RuntimeError("Gaussian process did not exit properly") + + return self.read_charges_from_gaussian_output() + + def create_simulation_dir(self): + if not os.path.exists(self.config.simulation_dir): + os.makedirs(self.config.simulation_dir) + else: + raise RuntimeError( + f"Simulation directory '{self.config.simulation_dir}' already exists. " + f"Please remove it before proceeding." + ) + + def make_gaussian_input(self, cycle: int, file: PosixPath, crystal: Crystal) -> str: + + with open(file, 'w+') as fh: + + fh.write(f"%Mem={self.config.mem}MB\n") + + fh.write(f"%Nprocs={self.config.n_procs}\n") + + kwords_line = f"#P {self.config.level} " \ + f"Pop = {self.config.pop} " \ + f"Density = Current " \ + f"NoSymm " + + if cycle > 1: + kwords_line += f"charge" + + fh.write(textwrap.fill(kwords_line, 90)) + fh.write("\n") + + fh.write(f"\n{self.config.comment} - Cycle number {cycle}\n") + fh.write("\n") + fh.write(f"{self.config.mult[0]}, {self.config.mult[1]}\n") + + for atom in crystal[0][0]: + symbol = atom_symbol[atom.na] + fh.write( + f"{symbol:<2s} " + f"{atom.rx:>10.5f} " + f"{atom.ry:>10.5f} " + f"{atom.rz:>10.5f}\n" + ) + + if cycle > 1: + self.make_gaussian_charges(fh, crystal) + + fh.seek(0) + return fh.read() + + def make_gaussian_charges(self, fh: TextIO, crystal: Crystal) -> None: + + fh.write("\n") + + for index_cell, cell in enumerate(crystal): + for index_mol, molecule in enumerate(cell): + if (index_cell == 0 and index_mol != 0) or (index_cell != 0): + for atom in molecule: + symbol = atom_symbol[atom.na] + fh.write( + f"{symbol:<2s} " + f"{atom.rx:>10.5f} " + f"{atom.ry:>10.5f} " + f"{atom.rz:>10.5f}\n" + ) + + def read_charges_from_gaussian_output(self) -> None: + pass \ No newline at end of file diff --git a/crystalpol/polarization.py b/crystalpol/polarization.py new file mode 100644 index 0000000..04564dc --- /dev/null +++ b/crystalpol/polarization.py @@ -0,0 +1,74 @@ +import os + +from crystalpol.shared.system.molecule import Molecule +from crystalpol.shared.system.crystal import Crystal +from crystalpol.shared.system.atom import Atom +from crystalpol.shared.config import Config +from crystalpol.gaussian import Gaussian + +from typing import List + + +class Polarization: + __slots__ = ('geom_file', 'outfile', 'config', 'gaussian', 'crystal') + + def __init__(self, geom_file: str, outfile: str, config: Config) -> None: + self.crystal = None + + self.geom_file = geom_file + self.outfile = outfile + self.config = config + + self.gaussian = Gaussian(config) + + def run(self): + + self.read_crystal() + + self.gaussian.run(1, self.crystal) + + def read_crystal(self) -> None: + with open(self.geom_file, 'r') as geom_file: + lines = geom_file.readlines() + + molecules = self._get_molecules_from_lines(lines) + structure = self._get_crystal_structure(molecules[0]) + + self.crystal = Crystal([structure]) + for molecule in molecules: + self.crystal.add_cell([molecule]) + + def _get_molecules_from_lines(self, lines: List[str]) -> List[Molecule]: + if (len(lines) % self.config.n_atoms) == 0: + molecules: List[Molecule] = [] + + for index, molecule in enumerate(split(lines, self.config.n_atoms)): + mol = Molecule(f"Molecule-{index}") + for atom_line in molecule: + symbol, rx, ry, rz = tuple(atom_line.split()) + mol.add_atom( + Atom( + rx, ry, rz, + symbol=symbol.ljust(2), + ) + ) + molecules.append(mol) + + return molecules + + else: + raise RuntimeError( + "Invalid Geom File, the number of atoms doesn't match the number of lines." + ) + + @staticmethod + def _get_crystal_structure(molecule: Molecule) -> List[str]: + structure: List[str] = [] + for atom in molecule: + structure.append(atom.symbol) + return structure + + +def split(array: List, partitions: int): + for i in range(0, len(array), partitions): + yield array[i: i + partitions] diff --git a/crystalpol/shared/__init__.py b/crystalpol/shared/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/crystalpol/shared/config/__init__.py b/crystalpol/shared/config/__init__.py new file mode 100644 index 0000000..cca5d9b --- /dev/null +++ b/crystalpol/shared/config/__init__.py @@ -0,0 +1 @@ +from .config import Config diff --git a/crystalpol/shared/config/config.py b/crystalpol/shared/config/config.py new file mode 100644 index 0000000..781b923 --- /dev/null +++ b/crystalpol/shared/config/config.py @@ -0,0 +1,42 @@ +from dataclasses import dataclass, field, fields + + +@dataclass +class Config: + + mem: int + level: str + n_atoms: int + + n_procs: int = 1 + pop: str = "chelpg" + comment: str = "crystalpol" + simulation_dir = "simfiles" + mult: list = \ + field(default_factory=lambda: [0, 1]) + + def __post_init__(self): + for field in fields(self): + value = getattr(self, field.name) + if not isinstance(value, field.type): + raise ValueError( + f'Expected {field.name} to be {field.type}, ' + f'got {repr(value)}' + ) + + if self.mem is None or self.mem <= 0: + raise ValueError( + f'Invalid value for mem: {self.mem},' + f'Memory must be a integer greater than 0.' + ) + + if self.level is None: + raise ValueError( + f'Invalid value for level. Level must not be none.' + ) + + if self.n_atoms is None or self.n_atoms <= 0: + raise ValueError( + f'Invalid value for n_atoms: {self.mem},' + f'Number of Atoms must be a integer greater than 0.' + ) diff --git a/crystalpol/shared/system/__init__.py b/crystalpol/shared/system/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/crystalpol/shared/system/atom.py b/crystalpol/shared/system/atom.py new file mode 100644 index 0000000..1276fc1 --- /dev/null +++ b/crystalpol/shared/system/atom.py @@ -0,0 +1,46 @@ +from crystalpol.shared.utils.ptable import atom_mass, atom_symbol + + +class Atom: + """ + Atom class declaration. This class is used throughout the DicePlayer program to represent atoms. + Attributes: + na (int): Atomic number of the represented atom. + symbol (str): Atomic symbol of the represented atom. + rx (float): x cartesian coordinates of the represented atom. + ry (float): y cartesian coordinates of the represented atom. + rz (float): z cartesian coordinates of the represented atom. + """ + + def __init__( + self, + rx: float, + ry: float, + rz: float, + na: int = None, + symbol: str = None, + + ) -> None: + """ + The constructor function __init__ is used to create new instances of the Atom class. + Args: + na (int): Atomic number of the represented atom. + symbol (str): Atomic symbol of the represented atom. + rx (float): x cartesian coordinates of the represented atom. + ry (float): y cartesian coordinates of the represented atom. + rz (float): z cartesian coordinates of the represented atom. + """ + + if na is not None: + self.na = na + self.symbol = atom_symbol[self.na] + + if symbol is not None and symbol in atom_symbol: + self.symbol = symbol + self.na = atom_symbol.index(self.symbol) + + self.rx = rx + self.ry = ry + self.rz = rz + self.chg = None + self.mass = atom_mass[self.na] diff --git a/crystalpol/shared/system/crystal.py b/crystalpol/shared/system/crystal.py new file mode 100644 index 0000000..32c0c5f --- /dev/null +++ b/crystalpol/shared/system/crystal.py @@ -0,0 +1,43 @@ +from crystalpol.shared.system.molecule import Molecule + +from typing import List + + +class Crystal: + """ + This class represents a crystal, it will be organized in a list structure. + Each element is a unitary cell in the crystal. And this unitary cell will have + Molecules in it. + """ + + def __init__(self, structure: List[List[str]]): + self.structure = structure + + self.cells = [] + + def __iter__(self): + for cell in self.cells: + yield cell + + def __len__(self): + return len(self.cells) + + def __getitem__(self, index): + return self.cells[index] + + def add_cell(self, cell: List[Molecule]) -> None: + valid = self._is_valid_cell(cell) + if not valid: + raise ValueError( + "This cell does not obey the declared format for this Crystal." + ) + else: + self.cells.append(cell) + + def _is_valid_cell(self, cell: List[Molecule]) -> bool: + if len(cell) == len(self.structure): + for i, molecule in enumerate(cell): + if len(molecule.atoms) == len(self.structure[i]) \ + and all(atom.symbol == self.structure[i][j] for j, atom in enumerate(molecule.atoms)): + return True + return False diff --git a/crystalpol/shared/system/molecule.py b/crystalpol/shared/system/molecule.py new file mode 100644 index 0000000..bc499ce --- /dev/null +++ b/crystalpol/shared/system/molecule.py @@ -0,0 +1,88 @@ +from crystalpol.shared.system.atom import Atom +from crystalpol.shared.utils.ptable import atom_symbol + +from typing import Final, List, TextIO +import math + + +""" Constants of unit conversion """ +BOHR2ANG: Final[float] = 0.52917721092 +ANG2BOHR: Final[float] = 1 / BOHR2ANG + + +class Molecule: + """ + Molecule class declaration. This class is used throughout the DicePlayer program to represent molecules. + + Atributes: + molname (str): The name of the represented molecule + atom (List[Atom]): List of atoms of the represented molecule + position (NDArray[Any, Any]): The position relative to the internal atoms of the represented molecule + energy (NDArray[Any, Any]): The energy of the represented molecule + gradient (NDArray[Any, Any]): The first derivative of the energy relative to the position + hessian (NDArray[Any, Any]): The second derivative of the energy relative to the position + total_mass (int): The total mass of the molecule + com (NDArray[Any, Any]): The center of mass of the molecule + """ + + __slots__ = ( + 'mol_name', + 'atoms', + 'position', + 'energy', + 'gradient', + 'hessian', + 'total_mass', + 'com' + ) + + def __init__(self, mol_name: str) -> None: + """ + The constructor function __init__ is used to create new instances of the Molecule class. + + Args: + mol_name (str): Molecule name + """ + self.mol_name: str = mol_name + + self.atoms: List[Atom] = [] + + def __iter__(self): + for atom in self.atoms: + yield atom + + def add_atom(self, a: Atom) -> None: + """ + Adds Atom instance to the molecule. + + Args: + a (Atom): Atom instance to be added to atom list. + """ + + self.atoms.append(a) + + def update_charges(self, charges: List[float]) -> None: + + if len(charges) != len(self.atoms): + raise ValueError( + f"The number of charges ({len(charges)}) does not match the number of atoms ({len(self.atoms)})" + ) + + for i, atom in enumerate(self.atoms): + atom.chg = charges[i] + + def print_mol_info(self, fh: TextIO) -> None: + """ + Prints the Molecule information into a Output File + + Args: + fh (TextIO): Output File + """ + + fh.write("-"*80) + fh.write(f"Molecule Name: {self.mol_name}\n") + + fh.write("\n") + + for atom in self.atoms: + fh.write(f"{atom_symbol[atom.na]} r: [{atom.rx}, {atom.ry}, {atom.rz}] charge: {atom.chg}") diff --git a/crystalpol/shared/utils/__init__.py b/crystalpol/shared/utils/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/crystalpol/shared/utils/ptable.py b/crystalpol/shared/utils/ptable.py new file mode 100644 index 0000000..b0f47cd --- /dev/null +++ b/crystalpol/shared/utils/ptable.py @@ -0,0 +1,34 @@ +# Tuple of atom symbols +atom_symbol = ("00", + + "H ", "He", + "Li", "Be", "B ", "C ", "N ", "O ", "F ", "Ne", + "Na", "Mg", "Al", "Si", "P ", "S ", "Cl", "Ar", + "K ", "Ca", "Sc", "Ti", "V ", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", + "Kr", + "Rb", "Sr", "Y ", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I ", + "Xe", + "Cs", "Ba", + "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", + "Hf", "Ta", "W ", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Ti", "Pb", "Bi", "Po", "At", "Rn", + "Fr", "Ra", + "Ac", "Th", "Pa", "U ", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr") + +# Tuple of atom masses +atom_mass = (0.0, + + 1.0079, 4.0026, + 6.9410, 9.0122, 10.811, 12.011, 14.007, 15.999, 18.998, 20.180, + 22.990, 24.305, 26.982, 28.086, 30.974, 32.065, 35.453, 39.948, + 39.098, 40.078, 44.956, 47.867, 50.942, 51.996, 54.938, 55.845, 58.933, 58.693, 63.546, 65.409, 69.723, + 72.640, 74.922, 78.960, 79.904, 83.798, + 85.468, 87.620, 88.906, 91.224, 92.906, 95.940, 98.000, 101.07, 102.91, 106.42, 107.87, 112.41, 114.82, + 118.71, 121.76, 127.60, 126.90, 131.29, + 132.91, 137.33, + 138.91, 140.12, 140.91, 144.24, 145.00, 150.36, 151.96, 157.25, 158.93, 162.50, 164.93, 167.26, 168.93, + 173.04, 174.97, + 178.49, 180.95, 183.84, 186.21, 190.23, 192.22, 195.08, 196.97, 200.59, 204.38, 207.20, 208.98, 209.00, + 210.00, 222.00, + 223.00, 226.00, + 227.00, 232.04, 231.04, 238.03, 237.00, 244.00, 243.00, 247.00, 247.00, 251.00, 252.00, 257.00, 258.00, + 259.00, 262.00) diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/shared/__init__.py b/tests/shared/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/shared/config/__init__.py b/tests/shared/config/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/shared/config/test_config.py b/tests/shared/config/test_config.py new file mode 100644 index 0000000..4d081bc --- /dev/null +++ b/tests/shared/config/test_config.py @@ -0,0 +1,21 @@ +from crystalpol.shared.config import Config + +import unittest + + +class TestConfig(unittest.TestCase): + def test_class_instantiation(self): + config = Config( + mem=1, + level="b3lyp/aug-cc-pVDZ", + n_atoms=10 + ) + self.assertIsInstance(config, Config) + + def test_config_raises_exception(self): + with self.assertRaises(ValueError): + Config( + mem="1", + level="b3lyp/aug-cc-pVDZ", + n_atoms=10 + ) diff --git a/tests/shared/system/__init__.py b/tests/shared/system/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/shared/system/test_atom.py b/tests/shared/system/test_atom.py new file mode 100644 index 0000000..daec990 --- /dev/null +++ b/tests/shared/system/test_atom.py @@ -0,0 +1,19 @@ +from crystalpol.shared.system.atom import Atom + +import unittest + + +class TestAtom(unittest.TestCase): + def test_atom_instantiation(self): + atom = Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + + self.assertIsInstance(atom, Atom) + + +if __name__ == '__main__': + unittest.main() diff --git a/tests/shared/system/test_crystal.py b/tests/shared/system/test_crystal.py new file mode 100644 index 0000000..cdc7668 --- /dev/null +++ b/tests/shared/system/test_crystal.py @@ -0,0 +1,102 @@ +import unittest + +from crystalpol.shared.system.atom import Atom +from crystalpol.shared.system.crystal import Crystal +from crystalpol.shared.system.molecule import Molecule + + +class TestCrystal(unittest.TestCase): + def test_class_instantiation(self): + # Note that this is not a valid crystal + crystal_structure = [ + ['H'] + ] + + crystal = Crystal(crystal_structure) + + self.assertIsInstance(crystal, Crystal) + + def test_is_valid_cell(self): + crystal_structure = [ + ['H '] + ] + + crystal = Crystal(crystal_structure) + + molecule = Molecule("TESTE") + molecule.add_atom( + Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + ) + + self.assertTrue(crystal._is_valid_cell([molecule])) + + molecule.add_atom( + Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + ) + + self.assertFalse(crystal._is_valid_cell([molecule])) + + def test_add_cell(self): + # Note that this is not a valid crystal + crystal_structure = [ + ['H '] + ] + + crystal = Crystal(crystal_structure) + + molecule = Molecule("TESTE") + molecule.add_atom( + Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + ) + + crystal.add_cell([molecule]) + + self.assertIsInstance(crystal, Crystal) + + def test_add_cell_raises_exception(self): + # Note that this is not a valid crystal + crystal_structure = [ + ['H '] + ] + + crystal = Crystal(crystal_structure) + + molecule = Molecule("TESTE") + molecule.add_atom( + Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + ) + molecule.add_atom( + Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + ) + + with self.assertRaises(ValueError): + crystal.add_cell([molecule]) + + +if __name__ == '__main__': + unittest.main() diff --git a/tests/shared/system/test_molecule.py b/tests/shared/system/test_molecule.py new file mode 100644 index 0000000..b2ede5c --- /dev/null +++ b/tests/shared/system/test_molecule.py @@ -0,0 +1,87 @@ +from crystalpol.shared.system.molecule import Molecule +from crystalpol.shared.system.atom import Atom + +import io + +import unittest + + +class TestMolecule(unittest.TestCase): + def test_class_instantiation(self): + molecule = Molecule("TEST") + + self.assertEqual(molecule.mol_name, "TEST") + self.assertIsInstance(molecule, Molecule) + + def test_add_atom(self): + molecule = Molecule("TEST") + + atom = Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + + molecule.add_atom(atom) + + self.assertEqual(len(molecule.atoms), 1) + self.assertEqual(molecule.atoms[0], atom) + + def test_update_charges(self): + molecule = Molecule("TEST") + + atom = Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + + molecule.add_atom(atom) + + molecule.update_charges([1]) + + self.assertEqual(molecule.atoms[-1].chg, 1) + + def test_update_charges_raises_exception(self): + molecule = Molecule("TEST") + + atom = Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + + molecule.add_atom(atom) + + with self.assertRaises(ValueError): + molecule.update_charges([1, 1]) + + def test_print_mol_info(self): + molecule = Molecule("TEST") + + atom = Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + + molecule.add_atom(atom) + + with io.StringIO() as file: + molecule.print_mol_info(file) + + file.seek(0) + info_string = file.read() + + self.assertIsNotNone(info_string) + self.assertTrue(len(info_string) > 0) + self.assertTrue("Molecule Name: TEST" in info_string) + self.assertTrue("H r: [0, 0, 0] charge: None" in info_string) + + +if __name__ == '__main__': + unittest.main() diff --git a/tests/shared/test_gaussian.py b/tests/shared/test_gaussian.py new file mode 100644 index 0000000..c18fd07 --- /dev/null +++ b/tests/shared/test_gaussian.py @@ -0,0 +1,199 @@ +from crystalpol.shared.system.molecule import Molecule +from crystalpol.shared.system.crystal import Crystal +from crystalpol.shared.system.atom import Atom +from crystalpol.shared.config import Config +from crystalpol.gaussian import Gaussian + +from io import StringIO + +from unittest import mock, TestCase +import unittest + + +class TestGaussian(TestCase): + + def test_class_instantiation(self): + gaussian = Gaussian( + Config( + mem=1, + level="b3lyp/aug-cc-pVDZ", + n_atoms=10 + ) + ) + + self.assertIsInstance(gaussian, Gaussian) + + def test_check_keyword(self): + gaussian = Gaussian( + Config( + mem=1, + level="b3lyp/aug-cc-pVDZ", + n_atoms=10, + pop="lorota" + ) + ) + + self.assertEqual(gaussian.config.pop, "chelpg") + + @mock.patch('crystalpol.gaussian.os') + def test_create_simulation_dir(self, os_mock): + os_mock.path.exists.return_value = False + + gaussian = Gaussian( + Config( + mem=1, + level="b3lyp/aug-cc-pVDZ", + n_atoms=10 + ) + ) + gaussian.create_simulation_dir() + + self.assertTrue(os_mock.makedirs.called) + + @mock.patch('crystalpol.gaussian.os') + def test_create_simulation_dir_raises_exception(self, os_mock): + os_mock.path.exists.return_value = True + gaussian = Gaussian( + Config( + mem=1, + level="b3lyp/aug-cc-pVDZ", + n_atoms=10 + ) + ) + + with self.assertRaises(RuntimeError): + gaussian.create_simulation_dir() + + @mock.patch('crystalpol.gaussian.open') + def test_make_gaussian_input_cycle_1(self, open_mock): + + open_mock.return_value = StringIO() + + crystal = self.create_crystal() + + gaussian = Gaussian( + Config( + mem=1, + level="b3lyp/aug-cc-pVDZ", + n_atoms=10 + ) + ) + gaussian_input = gaussian.make_gaussian_input(1, crystal) + expected_output = """\ +%Mem=1MB +%Nprocs=1 +#P b3lyp/aug-cc-pVDZ Pop = chelpg Density = Current NoSymm + +crystalpol - Cycle number 1 + +0, 1 +H 0.00000 0.00000 0.00000 +""" + self.assertEqual(gaussian_input, expected_output) + + @mock.patch('crystalpol.gaussian.open') + def test_make_gaussian_input_cycle_2(self, open_mock): + + open_mock.return_value = StringIO() + + crystal = self.create_crystal() + + gaussian = Gaussian( + Config( + mem=1, + level="b3lyp/aug-cc-pVDZ", + n_atoms=10 + ) + ) + gaussian_input = gaussian.make_gaussian_input(2, "test", crystal) + expected_output = """\ +%Mem=1MB +%Nprocs=1 +#P b3lyp/aug-cc-pVDZ Pop = chelpg Density = Current NoSymm charge + +crystalpol - Cycle number 2 + +0, 1 +H 0.00000 0.00000 0.00000 + +H 0.00000 0.00000 0.00000 +""" + self.assertEqual(gaussian_input, expected_output) + + def test_make_gaussian_charges(self): + + file = StringIO() + crystal = self.create_crystal() + + gaussian = Gaussian( + Config( + mem=1, + level="b3lyp/aug-cc-pVDZ", + n_atoms=10 + ) + ) + gaussian.make_gaussian_charges(file, crystal) + file.seek(0) + + charges_string = file.read() + expected_charges = '\nH 0.00000 0.00000 0.00000\n' + + self.assertEqual(charges_string, expected_charges) + + @mock.patch('crystalpol.gaussian.subprocess.call', autospec=True, return_value=0) + @mock.patch('crystalpol.gaussian.Gaussian.make_gaussian_input') + def test_run(self, subprocess_call_mock, make_gaussian_input_mock): + + gaussian = Gaussian( + Config( + mem=1, + level="b3lyp/aug-cc-pVDZ", + n_atoms=10 + ) + ) + gaussian.run(1, self.create_crystal()) + + self.assertTrue(subprocess_call_mock.called) + + @mock.patch('crystalpol.gaussian.subprocess.call', autospec=True, return_value=1) + @mock.patch('crystalpol.gaussian.Gaussian.make_gaussian_input') + def test_run_raises_exception(self, subprocess_call_mock, make_gaussian_input_mock): + + gaussian = Gaussian( + Config( + mem=1, + level="b3lyp/aug-cc-pVDZ", + n_atoms=10 + ) + ) + + with self.assertRaises(RuntimeError): + gaussian.run(1, self.create_crystal()) + + @staticmethod + def create_crystal(): + + crystal_structure = [ + ['H '] + ] + + crystal = Crystal(crystal_structure) + + molecule = Molecule("TESTE") + molecule.add_atom( + Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + ) + + crystal.add_cell([molecule]) + crystal.add_cell([molecule]) + + return crystal + + +if __name__ == '__main__': + unittest.main() diff --git a/tests/test_polarization.py b/tests/test_polarization.py new file mode 100644 index 0000000..f67476f --- /dev/null +++ b/tests/test_polarization.py @@ -0,0 +1,101 @@ +from crystalpol.polarization import Polarization +from crystalpol.shared.config import Config +from crystalpol.shared.system.atom import Atom +from crystalpol.shared.system.molecule import Molecule + +from unittest import TestCase, mock +import unittest + + +GEOM_DATA = """\ + Cl 0.529511 -1.626652 1.247344 + N 3.703161 2.470259 1.679277 + Cl 0.362927 -1.511555 4.375374 + N 3.582138 2.531106 3.906529 +""" + + +class TestPolarization(TestCase): + + def setUp(self): + self.config = Config( + mem=42, + n_atoms=2, + level="b3lyp/aug-cc-pVDZ" + ) + + def test_class_instantiation(self): + pol = Polarization("geom_file", "outfile", self.config) + + self.assertIsInstance(pol, Polarization) + + def test_get_molecules_from_lines(self): + pol = Polarization("geom_file", "outfile", self.config) + + lines = [ + "Cl 0.529511 -1.626652 1.247344", + "N 3.703161 2.470259 1.679277", + "Cl 0.362927 -1.511555 4.375374", + "N 3.582138 2.531106 3.906529", + ] + + molecules = pol._get_molecules_from_lines(lines) + + self.assertIsNotNone(molecules) + self.assertTrue(any(atom.symbol == "Cl" for atom in molecules[0])) + self.assertTrue(any(atom.symbol == "N " for atom in molecules[1])) + + def test_get_molecules_from_lines_raises_exception(self): + pol = Polarization("geom_file", "outfile", self.config) + + lines = [ + "Cl 0.529511 -1.626652 1.247344", + "N 3.703161 2.470259 1.679277", + "Cl 0.362927 -1.511555 4.375374", + "N 3.582138 2.531106 3.906529", + "N 3.582138 2.531106 3.906529", + ] + + with self.assertRaises(RuntimeError): + pol._get_molecules_from_lines(lines) + + def test_get_crystal_structure(self): + pol = Polarization("geom_file", "outfile", self.config) + + molecule = Molecule("TEST") + molecule.add_atom( + Atom( + na=1, + rx=0, + ry=0, + rz=0, + ) + ) + + structure = pol._get_crystal_structure(molecule) + self.assertEqual(structure, ['H ']) + + @mock.patch('builtins.open', mock.mock_open(read_data=GEOM_DATA)) + def test_read_crystal(self): + pol = Polarization("geom_file", "outfile", self.config) + + pol.read_crystal() + + self.assertIsNotNone(pol.crystal) + self.assertEqual(len(pol.crystal), 2) + self.assertEqual(len(pol.crystal[0]), 1) + + + @mock.patch('builtins.open', mock.mock_open(read_data=GEOM_DATA)) + def test_run(self): + pol = Polarization("geom_file", "outfile", self.config) + + pol.run() + + self.assertIsNotNone(pol.crystal) + self.assertEqual(len(pol.crystal), 2) + self.assertEqual(len(pol.crystal[0]), 1) + + +if __name__ == '__main__': + unittest.main()