diff --git a/arkane/data/gaussian/water.out b/arkane/data/gaussian/water.out new file mode 100644 index 0000000000..a38d7ad8f4 --- /dev/null +++ b/arkane/data/gaussian/water.out @@ -0,0 +1,754 @@ + Entering Gaussian System, Link 0=g09 + Initial command: + /usr/local/g09/l1.exe "/gtmp/jintaowu/scratch/g09/1026695.zeus-master/Gau-3719775.inp" -scrdir="/gtmp/jintaowu/scratch/g09/1026695.zeus-master/" + Entering Link 1 = /usr/local/g09/l1.exe PID= 3719776. + + Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2013, + Gaussian, Inc. All Rights Reserved. + + This is part of the Gaussian(R) 09 program. It is based on + 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 09, Revision D.01, + M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, + M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, + G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, + A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, + M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, + Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., + J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, + K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, + K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, + M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, + V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, + O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, + R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, + P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, + O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, + and D. J. Fox, Gaussian, Inc., Wallingford CT, 2013. + + ****************************************** + Gaussian 09: EM64L-G09RevD.01 24-Apr-2013 + 10-Dec-2023 + ****************************************** + %chk=check.chk + %mem=184320mb + %NProcShared=16 + Will use up to 16 processors via shared memory. + ------------------------------------------------------------ + #P opt SCRF=(smd, Solvent=water) guess=mix uff IOp(2/9=2000) + ------------------------------------------------------------ + 1/14=-1,18=20,19=15,38=1,56=1,64=2/1,3; + 2/9=2000,12=2,17=6,18=5,40=1/2; + 3/5=30,11=9,16=1,25=1,30=1,41=10200000,43=2,70=40032201,71=1,72=1/1; + 4/20=10,22=1,24=3/2; + 7/44=-1/16; + 1/14=-1,18=20,19=15,64=2/3(2); + 2/9=2000/2; + 99//99; + 2/9=2000/2; + 3/5=30,11=9,16=1,25=1,30=1,41=10200000,43=2,70=40032205,71=1,72=1/1; + 4/16=2,20=10,22=1,24=3/2; + 7/44=-1/16; + 1/14=-1,18=20,19=15,64=2/3(-4); + 2/9=2000/2; + 99//99; + Leave Link 1 at Sun Dec 10 04:35:55 2023, MaxMem= 24159191040 cpu: 0.3 + (Enter /usr/local/g09/l101.exe) + ---- + spc1 + ---- + Symbolic Z-matrix: + Charge = 0 Multiplicity = 1 + O -0.00033 0.39781 0. + H -0.7633 -0.19954 0. + H 0.76363 -0.19828 0. + + NAtoms= 3 NQM= 3 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 + IAtWgt= 16 1 1 + AtmWgt= 15.9949146 1.0078250 1.0078250 + NucSpn= 0 1 1 + AtZEff= 0.0000000 0.0000000 0.0000000 + NQMom= 0.0000000 0.0000000 0.0000000 + NMagM= 0.0000000 2.7928460 2.7928460 + AtZNuc= 8.0000000 1.0000000 1.0000000 + Generating MM parameters. + Include all MM classes + + MM sanity checks: + All charges sum to: 0.00000000 + Charges of atoms sum to: 0.00000000 + MMInit generated parameter data with length LenPar= 499. + Leave Link 101 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 4.9 + (Enter /usr/local/g09/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Initialization pass. + ---------------------------- + ! Initial Parameters ! + ! (Angstroms and Degrees) ! + -------------------------- -------------------------- + ! Name Definition Value Derivative Info. ! + -------------------------------------------------------------------------------- + ! R1 R(1,2) 0.969 estimate D2E/DX2 ! + ! R2 R(1,3) 0.969 estimate D2E/DX2 ! + ! A1 A(2,1,3) 103.978 estimate D2E/DX2 ! + -------------------------------------------------------------------------------- + Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 + Number of steps in this run= 20 maximum allowed number of steps= 100. + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Leave Link 103 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.1 + (Enter /usr/local/g09/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 10081003 -0.000328 0.397815 0.000000 + 2 1 10011000 -0.763303 -0.199538 0.000000 + 3 1 10011000 0.763632 -0.198277 0.000000 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 + 1 O 0.000000 + 2 H 0.969000 0.000000 + 3 H 0.969000 1.526936 0.000000 + Stoichiometry H2O + Framework group C2V[C2(O),SGV(H2)] + Deg. of freedom 2 + Full point group C2V NOp 4 + Largest Abelian subgroup C2V NOp 4 + Largest concise Abelian subgroup C2 NOp 2 + Standard orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 10081003 0.000000 0.000000 0.119345 + 2 1 10011000 0.000000 0.763468 -0.477378 + 3 1 10011000 0.000000 -0.763468 -0.477378 + --------------------------------------------------------------------- + Rotational constants (GHZ): 792.8710505 430.1505895 278.8617459 + Leave Link 202 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.0 + (Enter /usr/local/g09/l301.exe) + Standard basis: Dummy (5D, 7F) + There are 2 symmetry adapted cartesian basis functions of A1 symmetry. + There are 0 symmetry adapted cartesian basis functions of A2 symmetry. + There are 0 symmetry adapted cartesian basis functions of B1 symmetry. + There are 1 symmetry adapted cartesian basis functions of B2 symmetry. + There are 2 symmetry adapted basis functions of A1 symmetry. + There are 0 symmetry adapted basis functions of A2 symmetry. + There are 0 symmetry adapted basis functions of B1 symmetry. + There are 1 symmetry adapted basis functions of B2 symmetry. + 3 basis functions, 3 primitive gaussians, 3 cartesian basis functions + 2 alpha electrons 2 beta electrons + nuclear repulsion energy 2.5309875879 Hartrees. + IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 + IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 + NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F + Integral buffers will be 131072 words long. + Raffenetti 1 integral format. + Two-electron integral symmetry is turned on. + ------------------------------------------------------------------------------ + Polarizable Continuum Model (PCM) + ================================= + Model : PCM (using non-symmetric T matrix). + Atomic radii : SMD-Coulomb. + Polarization charges : Total charges. + Charge compensation : None. + Solution method : On-the-fly selection. + Cavity type : VdW (van der Waals Surface) (Alpha=1.000). + Cavity algorithm : GePol (No added spheres) + Default sphere list used, NSphG= 3. + Lebedev-Laikov grids with approx. 5.0 points / Ang**2. + Smoothing algorithm: Karplus/York (Gamma=1.0000). + Polarization charges: spherical gaussians, with + point-specific exponents (IZeta= 3). + Self-potential: point-specific (ISelfS= 7). + Self-field : sphere-specific E.n sum rule (ISelfD= 2). + 1st derivatives : Analytical E(r).r(x)/FMM algorithm (CHGder, D1EAlg=3). + Cavity 1st derivative terms included. + Solvent : Water, Eps= 78.355300 Eps(inf)= 1.777849 + ------------------------------------------------------------------------------ + Spheres list: + ISph on Nord Re0 Alpha Xe Ye Ze + 1 O 1 1.5200 1.000 0.000000 0.000000 0.119345 + 2 H 2 1.2000 1.000 0.000000 0.763468 -0.477378 + 3 H 3 1.2000 1.000 0.000000 -0.763468 -0.477378 + ------------------------------------------------------------------------------ + Leave Link 301 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.3 + (Enter /usr/local/g09/l402.exe) + UFF calculation of energy and first derivatives. + Energy per function type: + Direct Coulomb + vdW (small) 0.000000000 + Direct Coulomb (large) 0.000000000 + Direct vdW (large) 253.543839672 + Non-direct Coulomb + vdW (small) 0.000000000 + Non-direct Coulomb (large) 0.000000000 + Non-direct vdW (large) -253.543839672 + Harmonic stretch III 0.000806285 + UFF 3-term bend 0.000008298 + Energy per function class: + Coulomb 0.000000000 + Vanderwaals 0.000000000 + Stretching 0.000806285 + Bending 0.000008298 + GePol: Number of generator spheres = 3 + GePol: Total number of spheres = 3 + GePol: Number of exposed spheres = 3 (100.00%) + GePol: Number of points = 240 + GePol: Average weight of points = 0.15 + GePol: Minimum weight of points = 0.24D-03 + GePol: Maximum weight of points = 0.21991 + GePol: Number of points with low weight = 12 + GePol: Fraction of low-weight points (<1% of avg) = 5.00% + GePol: Cavity surface area = 36.124 Ang**2 + GePol: Cavity volume = 19.244 Ang**3 + GePol: Maximum number of non-zero 1st derivatives = 150 + ------------------------------------------------------------------------------ + Atomic radii for non-electrostatic terms: SMD-CDS. + ------------------------------------------------------------------------------ + PCMMM is using the matrix inversion algorithm. + Iteration 1 A*A^-1 deviation from unit magnitude is 2.66D-15 for 2. + Iteration 1 A*A^-1 deviation from orthogonality is 1.85D-15 for 215 8. + Iteration 1 A^-1*A deviation from unit magnitude is 2.55D-15 for 16. + Iteration 1 A^-1*A deviation from orthogonality is 8.12D-16 for 176 70. + No energy partition over atoms because of zero polarization charges. + SMD-CDS (non-electrostatic) energy (kcal/mol) = 1.46 + (included in total energy below) + Energy= 3.139477018E-03 NIter= 0. + Dipole moment= 0.000000 0.000000 0.000000 + Leave Link 402 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 2.0 + (Enter /usr/local/g09/l716.exe) + Dipole = 0.00000000D+00 0.00000000D+00 0.00000000D+00 + ***** Axes restored to original set ***** + ------------------------------------------------------------------- + Center Atomic Forces (Hartrees/Bohr) + Number Number X Y Z + ------------------------------------------------------------------- + 1 8 -0.000018909 0.022910930 0.000000000 + 2 1 -0.015852348 -0.011468556 0.000000000 + 3 1 0.015871256 -0.011442374 0.000000000 + ------------------------------------------------------------------- + Cartesian Forces: Max 0.022910930 RMS 0.011974790 + Leave Link 716 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.3 + (Enter /usr/local/g09/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + FormGI is forming the generalized inverse of G from B-inverse, IUseBI=4. + Internal Forces: Max 0.019551823 RMS 0.015983270 + Search for a local minimum. + Step number 1 out of a maximum of 20 + All quantities printed in internal units (Hartrees-Bohrs-Radians) + RMS Force = .15983D-01 SwitMx=.10000D-02 MixMth= 1 + Mixed Optimization -- RFO/linear search + Second derivative matrix not updated -- first step. + The second derivative matrix: + R1 R2 A1 + R1 0.53582 + R2 0.00000 0.53582 + A1 0.00000 0.00000 0.16000 + ITU= 0 + Eigenvalues --- 0.16000 0.53582 0.53582 + RFO step: Lambda=-1.43451227D-03 EMin= 1.60000000D-01 + Linear search not attempted -- first point. + Iteration 1 RMS(Cart)= 0.02835335 RMS(Int)= 0.00009563 + Iteration 2 RMS(Cart)= 0.00009062 RMS(Int)= 0.00000001 + Iteration 3 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000000 + ITry= 1 IFail=0 DXMaxC= 3.35D-02 DCOld= 1.00D+10 DXMaxT= 3.00D-01 DXLimC= 3.00D+00 Rises=F + ClnCor: largest displacement from symmetrization is 1.11D-13 for atom 3. + Variable Old X -DE/DX Delta X Delta X Delta X New X + (Linear) (Quad) (Total) + R1 1.83114 0.01955 0.00000 0.03639 0.03639 1.86754 + R2 1.83114 0.01955 0.00000 0.03639 0.03639 1.86754 + A1 1.81476 0.00136 0.00000 0.00842 0.00842 1.82318 + Item Value Threshold Converged? + Maximum Force 0.019552 0.000450 NO + RMS Force 0.015983 0.000300 NO + Maximum Displacement 0.033506 0.001800 NO + RMS Displacement 0.028401 0.001200 NO + Predicted change in Energy=-7.192068D-04 + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Leave Link 103 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.0 + (Enter /usr/local/g09/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 10081003 -0.000333 0.403532 0.000000 + 2 1 10011000 -0.781029 -0.202411 0.000000 + 3 1 10011000 0.781362 -0.201121 0.000000 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 + 1 O 0.000000 + 2 H 0.988258 0.000000 + 3 H 0.988258 1.562392 0.000000 + Stoichiometry H2O + Framework group C2V[C2(O),SGV(H2)] + Deg. of freedom 2 + Full point group C2V NOp 4 + RotChk: IX=0 Diff= 2.10D-16 + Largest Abelian subgroup C2V NOp 4 + Largest concise Abelian subgroup C2 NOp 2 + Standard orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 10081003 0.000000 0.000000 0.121060 + 2 1 10011000 0.000000 0.781196 -0.484239 + 3 1 10011000 0.000000 -0.781196 -0.484239 + --------------------------------------------------------------------- + Rotational constants (GHZ): 770.5625398 410.8488160 267.9716134 + Leave Link 202 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.0 + (Enter /usr/local/g09/l301.exe) + Standard basis: Dummy (5D, 7F) + There are 2 symmetry adapted cartesian basis functions of A1 symmetry. + There are 0 symmetry adapted cartesian basis functions of A2 symmetry. + There are 0 symmetry adapted cartesian basis functions of B1 symmetry. + There are 1 symmetry adapted cartesian basis functions of B2 symmetry. + There are 2 symmetry adapted basis functions of A1 symmetry. + There are 0 symmetry adapted basis functions of A2 symmetry. + There are 0 symmetry adapted basis functions of B1 symmetry. + There are 1 symmetry adapted basis functions of B2 symmetry. + 3 basis functions, 3 primitive gaussians, 3 cartesian basis functions + 2 alpha electrons 2 beta electrons + nuclear repulsion energy 2.4805554745 Hartrees. + IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 + IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 + NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F + Integral buffers will be 131072 words long. + Raffenetti 1 integral format. + Two-electron integral symmetry is turned on. + ------------------------------------------------------------------------------ + Polarizable Continuum Model (PCM) + ================================= + Model : PCM (using non-symmetric T matrix). + Atomic radii : SMD-Coulomb. + Polarization charges : Total charges. + Charge compensation : None. + Solution method : Matrix inversion. + Cavity type : VdW (van der Waals Surface) (Alpha=1.000). + Cavity algorithm : GePol (No added spheres) + Default sphere list used, NSphG= 3. + Lebedev-Laikov grids with approx. 5.0 points / Ang**2. + Smoothing algorithm: Karplus/York (Gamma=1.0000). + Polarization charges: spherical gaussians, with + point-specific exponents (IZeta= 3). + Self-potential: point-specific (ISelfS= 7). + Self-field : sphere-specific E.n sum rule (ISelfD= 2). + 1st derivatives : Analytical E(r).r(x)/FMM algorithm (CHGder, D1EAlg=3). + Cavity 1st derivative terms included. + Solvent : Water, Eps= 78.355300 Eps(inf)= 1.777849 + ------------------------------------------------------------------------------ + Spheres list: + ISph on Nord Re0 Alpha Xe Ye Ze + 1 O 1 1.5200 1.000 0.000000 0.000000 0.121060 + 2 H 2 1.2000 1.000 0.000000 0.781196 -0.484239 + 3 H 3 1.2000 1.000 0.000000 -0.781196 -0.484239 + ------------------------------------------------------------------------------ + Leave Link 301 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.3 + (Enter /usr/local/g09/l402.exe) + UFF calculation of energy and first derivatives. + Energy per function type: + Direct Coulomb + vdW (small) 0.000000000 + Direct Coulomb (large) 0.000000000 + Direct vdW (large) 200.168754316 + Non-direct Coulomb + vdW (small) 0.000000000 + Non-direct Coulomb (large) 0.000000000 + Non-direct vdW (large) -200.168754316 + Harmonic stretch III 0.000007113 + UFF 3-term bend 0.000000072 + Energy per function class: + Coulomb 0.000000000 + Vanderwaals 0.000000000 + Stretching 0.000007113 + Bending 0.000000072 + GePol: Number of generator spheres = 3 + GePol: Total number of spheres = 3 + GePol: Number of exposed spheres = 3 (100.00%) + GePol: Number of points = 240 + GePol: Average weight of points = 0.15 + GePol: Minimum weight of points = 0.12D-03 + GePol: Maximum weight of points = 0.21991 + GePol: Number of points with low weight = 4 + GePol: Fraction of low-weight points (<1% of avg) = 1.67% + GePol: Cavity surface area = 36.385 Ang**2 + GePol: Cavity volume = 19.405 Ang**3 + GePol: Maximum number of non-zero 1st derivatives = 150 + ------------------------------------------------------------------------------ + Atomic radii for non-electrostatic terms: SMD-CDS. + ------------------------------------------------------------------------------ + PCMMM is using the matrix inversion algorithm. + Iteration 1 A*A^-1 deviation from unit magnitude is 2.66D-15 for 48. + Iteration 1 A*A^-1 deviation from orthogonality is 2.20D-15 for 172 82. + Iteration 1 A^-1*A deviation from unit magnitude is 2.55D-15 for 120. + Iteration 1 A^-1*A deviation from orthogonality is 9.41D-16 for 225 197. + No energy partition over atoms because of zero polarization charges. + SMD-CDS (non-electrostatic) energy (kcal/mol) = 1.48 + (included in total energy below) + Energy= 2.372367174E-03 NIter= 0. + Dipole moment= 0.000000 0.000000 0.000000 + Leave Link 402 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.7 + (Enter /usr/local/g09/l716.exe) + Dipole = 0.00000000D+00 0.00000000D+00 0.00000000D+00 + ***** Axes restored to original set ***** + ------------------------------------------------------------------- + Center Atomic Forces (Hartrees/Bohr) + Number Number X Y Z + ------------------------------------------------------------------- + 1 8 -0.000001570 0.001901962 0.000000000 + 2 1 -0.001031320 -0.000951833 0.000000000 + 3 1 0.001032890 -0.000950129 0.000000000 + ------------------------------------------------------------------- + Cartesian Forces: Max 0.001901962 RMS 0.000916313 + Leave Link 716 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.3 + (Enter /usr/local/g09/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Using GEDIIS/GDIIS optimizer. + FormGI is forming the generalized inverse of G from B-inverse, IUseBI=4. + Internal Forces: Max 0.001398323 RMS 0.001148983 + Search for a local minimum. + Step number 2 out of a maximum of 20 + All quantities printed in internal units (Hartrees-Bohrs-Radians) + RMS Force = .11490D-02 SwitMx=.10000D-02 MixMth= 1 + Mixed Optimization -- RFO/linear search + Update second derivatives using D2CorX and points 1 2 + DE= -7.67D-04 DEPred=-7.19D-04 R= 1.07D+00 + TightC=F SS= 1.41D+00 RLast= 5.22D-02 DXNew= 5.0454D-01 1.5645D-01 + Trust test= 1.07D+00 RLast= 5.22D-02 DXMaxT set to 3.00D-01 + The second derivative matrix: + R1 R2 A1 + R1 0.51696 + R2 -0.01886 0.51696 + A1 0.00316 0.00316 0.16061 + ITU= 1 0 + Use linear search instead of GDIIS. + Eigenvalues --- 0.16055 0.49816 0.53582 + RFO step: Lambda=-7.35437790D-07 EMin= 1.60548598D-01 + Quartic linear search produced a step of 0.07488. + Iteration 1 RMS(Cart)= 0.00174200 RMS(Int)= 0.00000137 + Iteration 2 RMS(Cart)= 0.00000153 RMS(Int)= 0.00000000 + Iteration 3 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000000 + ITry= 1 IFail=0 DXMaxC= 1.89D-03 DCOld= 1.00D+10 DXMaxT= 3.00D-01 DXLimC= 3.00D+00 Rises=F + ClnCor: largest displacement from symmetrization is 7.15D-14 for atom 3. + Variable Old X -DE/DX Delta X Delta X Delta X New X + (Linear) (Quad) (Total) + R1 1.86754 0.00140 0.00273 0.00009 0.00282 1.87035 + R2 1.86754 0.00140 0.00273 0.00009 0.00282 1.87035 + A1 1.82318 -0.00022 0.00063 -0.00213 -0.00150 1.82168 + Item Value Threshold Converged? + Maximum Force 0.001398 0.000450 NO + RMS Force 0.001149 0.000300 NO + Maximum Displacement 0.001890 0.001800 NO + RMS Displacement 0.001742 0.001200 NO + Predicted change in Energy=-4.106530D-06 + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Leave Link 103 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.0 + (Enter /usr/local/g09/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 10081003 -0.000334 0.404533 0.000000 + 2 1 10011000 -0.781753 -0.202912 0.000000 + 3 1 10011000 0.782086 -0.201621 0.000000 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 + 1 O 0.000000 + 2 H 0.989749 0.000000 + 3 H 0.989749 1.563840 0.000000 + Stoichiometry H2O + Framework group C2V[C2(O),SGV(H2)] + Deg. of freedom 2 + Full point group C2V NOp 4 + RotChk: IX=0 Diff= 7.87D-17 + Largest Abelian subgroup C2V NOp 4 + Largest concise Abelian subgroup C2 NOp 2 + Standard orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 10081003 0.000000 0.000000 0.121360 + 2 1 10011000 0.000000 0.781920 -0.485439 + 3 1 10011000 0.000000 -0.781920 -0.485439 + --------------------------------------------------------------------- + Rotational constants (GHZ): 766.7570740 410.0885774 267.1873897 + Leave Link 202 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.0 + (Enter /usr/local/g09/l301.exe) + Standard basis: Dummy (5D, 7F) + There are 2 symmetry adapted cartesian basis functions of A1 symmetry. + There are 0 symmetry adapted cartesian basis functions of A2 symmetry. + There are 0 symmetry adapted cartesian basis functions of B1 symmetry. + There are 1 symmetry adapted cartesian basis functions of B2 symmetry. + There are 2 symmetry adapted basis functions of A1 symmetry. + There are 0 symmetry adapted basis functions of A2 symmetry. + There are 0 symmetry adapted basis functions of B1 symmetry. + There are 1 symmetry adapted basis functions of B2 symmetry. + 3 basis functions, 3 primitive gaussians, 3 cartesian basis functions + 2 alpha electrons 2 beta electrons + nuclear repulsion energy 2.4770147996 Hartrees. + IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 + IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 + NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F + Integral buffers will be 131072 words long. + Raffenetti 1 integral format. + Two-electron integral symmetry is turned on. + ------------------------------------------------------------------------------ + Polarizable Continuum Model (PCM) + ================================= + Model : PCM (using non-symmetric T matrix). + Atomic radii : SMD-Coulomb. + Polarization charges : Total charges. + Charge compensation : None. + Solution method : Matrix inversion. + Cavity type : VdW (van der Waals Surface) (Alpha=1.000). + Cavity algorithm : GePol (No added spheres) + Default sphere list used, NSphG= 3. + Lebedev-Laikov grids with approx. 5.0 points / Ang**2. + Smoothing algorithm: Karplus/York (Gamma=1.0000). + Polarization charges: spherical gaussians, with + point-specific exponents (IZeta= 3). + Self-potential: point-specific (ISelfS= 7). + Self-field : sphere-specific E.n sum rule (ISelfD= 2). + 1st derivatives : Analytical E(r).r(x)/FMM algorithm (CHGder, D1EAlg=3). + Cavity 1st derivative terms included. + Solvent : Water, Eps= 78.355300 Eps(inf)= 1.777849 + ------------------------------------------------------------------------------ + Spheres list: + ISph on Nord Re0 Alpha Xe Ye Ze + 1 O 1 1.5200 1.000 0.000000 0.000000 0.121360 + 2 H 2 1.2000 1.000 0.000000 0.781920 -0.485439 + 3 H 3 1.2000 1.000 0.000000 -0.781920 -0.485439 + ------------------------------------------------------------------------------ + Leave Link 301 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.3 + (Enter /usr/local/g09/l402.exe) + UFF calculation of energy and first derivatives. + Energy per function type: + Direct Coulomb + vdW (small) 0.000000000 + Direct Coulomb (large) 0.000000000 + Direct vdW (large) 196.576892227 + Non-direct Coulomb + vdW (small) 0.000000000 + Non-direct Coulomb (large) 0.000000000 + Non-direct vdW (large) -196.576892227 + Harmonic stretch III 0.000000455 + UFF 3-term bend 0.000000538 + Energy per function class: + Coulomb 0.000000000 + Vanderwaals 0.000000000 + Stretching 0.000000455 + Bending 0.000000538 + GePol: Number of generator spheres = 3 + GePol: Total number of spheres = 3 + GePol: Number of exposed spheres = 3 (100.00%) + GePol: Number of points = 240 + GePol: Average weight of points = 0.15 + GePol: Minimum weight of points = 0.12D-03 + GePol: Maximum weight of points = 0.21991 + GePol: Number of points with low weight = 4 + GePol: Fraction of low-weight points (<1% of avg) = 1.67% + GePol: Cavity surface area = 36.410 Ang**2 + GePol: Cavity volume = 19.419 Ang**3 + GePol: Maximum number of non-zero 1st derivatives = 148 + ------------------------------------------------------------------------------ + Atomic radii for non-electrostatic terms: SMD-CDS. + ------------------------------------------------------------------------------ + PCMMM is using the matrix inversion algorithm. + Iteration 1 A*A^-1 deviation from unit magnitude is 2.78D-15 for 101. + Iteration 1 A*A^-1 deviation from orthogonality is 2.56D-15 for 172 82. + Iteration 1 A^-1*A deviation from unit magnitude is 2.89D-15 for 189. + Iteration 1 A^-1*A deviation from orthogonality is 1.09D-15 for 227 199. + No energy partition over atoms because of zero polarization charges. + SMD-CDS (non-electrostatic) energy (kcal/mol) = 1.49 + (included in total energy below) + Energy= 2.368327194E-03 NIter= 0. + Dipole moment= 0.000000 0.000000 0.000000 + Leave Link 402 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.7 + (Enter /usr/local/g09/l716.exe) + Dipole = 0.00000000D+00 0.00000000D+00 0.00000000D+00 + ***** Axes restored to original set ***** + ------------------------------------------------------------------- + Center Atomic Forces (Hartrees/Bohr) + Number Number X Y Z + ------------------------------------------------------------------- + 1 8 0.000000051 -0.000061804 0.000000000 + 2 1 -0.000014244 0.000030890 0.000000000 + 3 1 0.000014193 0.000030914 0.000000000 + ------------------------------------------------------------------- + Cartesian Forces: Max 0.000061804 RMS 0.000026106 + Leave Link 716 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.3 + (Enter /usr/local/g09/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Using GEDIIS/GDIIS optimizer. + FormGI is forming the generalized inverse of G from B-inverse, IUseBI=4. + Internal Forces: Max 0.000061966 RMS 0.000036326 + Search for a local minimum. + Step number 3 out of a maximum of 20 + All quantities printed in internal units (Hartrees-Bohrs-Radians) + RMS Force = .36326D-04 SwitMx=.10000D-02 MixMth= 2 + Mixed Optimization -- En-DIIS/RFO-DIIS + Update second derivatives using D2CorX and points 1 2 3 + DE= -4.04D-06 DEPred=-4.11D-06 R= 9.84D-01 + TightC=F SS= 1.41D+00 RLast= 4.26D-03 DXNew= 5.0454D-01 1.2776D-02 + Trust test= 9.84D-01 RLast= 4.26D-03 DXMaxT set to 3.00D-01 + The second derivative matrix: + R1 R2 A1 + R1 0.51552 + R2 -0.02030 0.51552 + A1 -0.00696 -0.00696 0.16397 + ITU= 1 1 0 + Use linear search instead of GDIIS. + Eigenvalues --- 0.16367 0.49552 0.53582 + RFO step: Lambda=-2.12931425D-08 EMin= 1.63673301D-01 + Quartic linear search produced a step of -0.01634. + Iteration 1 RMS(Cart)= 0.00021654 RMS(Int)= 0.00000003 + Iteration 2 RMS(Cart)= 0.00000002 RMS(Int)= 0.00000000 + ITry= 1 IFail=0 DXMaxC= 2.08D-04 DCOld= 1.00D+10 DXMaxT= 3.00D-01 DXLimC= 3.00D+00 Rises=F + ClnCor: largest displacement from symmetrization is 1.69D-13 for atom 3. + Variable Old X -DE/DX Delta X Delta X Delta X New X + (Linear) (Quad) (Total) + R1 1.87035 -0.00001 -0.00005 0.00004 -0.00001 1.87034 + R2 1.87035 -0.00001 -0.00005 0.00004 -0.00001 1.87034 + A1 1.82168 0.00006 0.00002 0.00035 0.00038 1.82205 + Item Value Threshold Converged? + Maximum Force 0.000062 0.000450 YES + RMS Force 0.000036 0.000300 YES + Maximum Displacement 0.000208 0.001800 YES + RMS Displacement 0.000217 0.001200 YES + Predicted change in Energy=-1.176120D-08 + Optimization completed. + -- Stationary point found. + ---------------------------- + ! Optimized Parameters ! + ! (Angstroms and Degrees) ! + -------------------------- -------------------------- + ! Name Definition Value Derivative Info. ! + -------------------------------------------------------------------------------- + ! R1 R(1,2) 0.9897 -DE/DX = 0.0 ! + ! R2 R(1,3) 0.9897 -DE/DX = 0.0 ! + ! A1 A(2,1,3) 104.3744 -DE/DX = 0.0001 ! + -------------------------------------------------------------------------------- + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Largest change from initial coordinates is atom 2 0.020 Angstoms. + Leave Link 103 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.0 + (Enter /usr/local/g09/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 10081003 -0.000334 0.404533 0.000000 + 2 1 10011000 -0.781753 -0.202912 0.000000 + 3 1 10011000 0.782086 -0.201621 0.000000 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 + 1 O 0.000000 + 2 H 0.989749 0.000000 + 3 H 0.989749 1.563840 0.000000 + Stoichiometry H2O + Framework group C2V[C2(O),SGV(H2)] + Deg. of freedom 2 + Full point group C2V NOp 4 + RotChk: IX=0 Diff= 3.94D-17 + Largest Abelian subgroup C2V NOp 4 + Largest concise Abelian subgroup C2 NOp 2 + Standard orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 10081003 0.000000 0.000000 0.121360 + 2 1 10011000 0.000000 0.781920 -0.485439 + 3 1 10011000 0.000000 -0.781920 -0.485439 + --------------------------------------------------------------------- + Rotational constants (GHZ): 766.7570740 410.0885774 267.1873897 + Leave Link 202 at Sun Dec 10 04:35:56 2023, MaxMem= 24159191040 cpu: 0.0 + (Enter /usr/local/g09/l9999.exe) + + Test job not archived. + 1\1\GINC-N131\FOpt\RUFF\ZDO\H2O1\JINTAOWU\10-Dec-2023\0\\#P opt SCRF=( + smd, Solvent=water) guess=mix uff IOp(2/9=2000)\\spc1\\0,1\O,-0.000333 + 8653,0.404532511,0.\H,-0.7817525641,-0.2029115842,0.\H,0.7820864374,-0 + .2016209197,0.\\Version=EM64L-G09RevD.01\HF=0.0023683\RMSD=0.000e+00\R + MSF=2.611e-05\Dipole=0.,0.,0.\PG=C02V [C2(O1),SGV(H2)]\\@ + + + WE THE UNWILLING + LED BY THE UNQUALIFIED + HAVE BEEN DOING THE UNBELIEVABLE SO LONG WITH SO LITTLE + THAT WE NOW ATTEMPT THE IMPOSSIBLE WITH NOTHING. + + -- ANONYMOUS + Job cpu time: 0 days 0 hours 0 minutes 11.1 seconds. + File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1 + Normal termination of Gaussian 09 at Sun Dec 10 04:35:56 2023. diff --git a/arkane/ess/gaussian.py b/arkane/ess/gaussian.py index df432631bf..2e84d6f231 100644 --- a/arkane/ess/gaussian.py +++ b/arkane/ess/gaussian.py @@ -365,6 +365,17 @@ def load_energy(self, zpe_scale_factor=1.): start = line.find('\\ZeroPoint=') + 11 end = line.find('\\', start) scaled_zpe = float(line[start:end]) * constants.E_h * constants.Na * zpe_scale_factor + + elif 'HF=' in line: + line = line.strip() + f.readline().strip() + start = line.find('HF=') + 3 + end = line.find('\\', start) + try: + if e_elect is None: + e_elect = float(line[start:end]) * constants.E_h * constants.Na + elect_energy_source = 'HF' + except ValueError: + pass # Read the next line in the file line = f.readline() diff --git a/test/arkane/ess/arkaneGaussianTest.py b/test/arkane/ess/arkaneGaussianTest.py index 9db14e3c98..60c3aecc80 100644 --- a/test/arkane/ess/arkaneGaussianTest.py +++ b/test/arkane/ess/arkaneGaussianTest.py @@ -121,6 +121,7 @@ def test_gaussian_energies(self): log_g4 = GaussianLog(os.path.join(self.data_path, "g4_85_methanol.out")) log_g4mp2 = GaussianLog(os.path.join(self.data_path, "g4mp2_85_methanol.out")) log_rocbsqb3 = GaussianLog(os.path.join(self.data_path, "rocbs-qb3_85_methanol.out")) + log_uff = GaussianLog(os.path.join(self.data_path, "water.out")) assert abs(log_doublehybrid.load_energy() / constants.Na / constants.E_h - -0.40217794572194e02) < 1e-6 assert abs(log_mp2.load_energy() / constants.Na / constants.E_h - -0.37504683723025e02) < 1e-6 @@ -131,6 +132,7 @@ def test_gaussian_energies(self): assert abs(log_g4.load_energy() / constants.Na / constants.E_h - -115.698896) < 1e-6 assert abs(log_g4mp2.load_energy() / constants.Na / constants.E_h - -115.617241) < 1e-6 assert abs(log_rocbsqb3.load_energy() / constants.Na / constants.E_h - -115.590540) < 1e-6 + assert abs(log_uff.load_energy() / constants.Na / constants.E_h - 0.0023683) < 1e-6 def test_load_oxygen_from_gaussian_log(self): """