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add tests
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Signed-off-by: Jinzhe Zeng <[email protected]>
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Entering Gaussian System, Link 0=g16
Initial command:
/home/jzzeng/soft/g16/l1.exe "/home/jzzeng/test/Gau-15026.inp" -scrdir="/home/jzzeng/test/"
Entering Link 1 = /home/jzzeng/soft/g16/l1.exe PID= 15028.

Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2016,
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
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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 A.03,
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-G16RevA.03 25-Dec-2016
25-Jun-2019
******************************************
%nproc=28
Will use up to 28 processors via shared memory.
--------------------
#force b3lyp/6-31g**
--------------------
1/10=7,30=1,38=1/1,3;
2/12=2,17=6,18=5,40=1/2;
3/5=1,6=6,7=101,11=2,25=1,30=1,71=1,74=-5/1,2,3;
4//1;
5/5=2,38=5/2;
6/7=2,8=2,9=2,10=2,28=1/1;
7/29=1/1,2,3,16;
1/10=7,30=1/3;
99//99;
-------
methane
-------
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
C 1.07422 -0.06034 0.02917
H 2.16642 -0.06034 0.02917
H 0.71015 -0.92887 -0.52401
H 0.71015 0.85299 -0.44641
H 0.71015 -0.10514 1.05793


GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Initialization pass.
Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 EigMax=2.50D+02 EigMin=1.00D-04
Number of steps in this run= 2 maximum allowed number of steps= 2.
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

Distance matrix (angstroms):
1 2 3 4 5
1 C 0.000000
2 H 1.092200 0.000000
3 H 1.092199 1.783557 0.000000
4 H 1.092197 1.783556 1.783549 0.000000
5 H 1.092200 1.783557 1.783554 1.783550 0.000000
Stoichiometry CH4
Framework group C1[X(CH4)]
Deg. of freedom 9
Full point group C1 NOp 1
Largest Abelian subgroup C1 NOp 1
Largest concise Abelian subgroup C1 NOp 1
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 6 0 -0.000001 0.000000 0.000000
2 1 0 -1.092201 0.000000 0.000000
3 1 0 0.364069 -0.813864 -0.630855
4 1 0 0.364069 -0.139406 1.020252
5 1 0 0.364069 0.953270 -0.389397
---------------------------------------------------------------------
Rotational constants (GHZ): 157.6380023 157.6375616 157.6370163
Standard basis: 6-31G(d,p) (6D, 7F)
There are 35 symmetry adapted cartesian basis functions of A symmetry.
There are 35 symmetry adapted basis functions of A symmetry.
35 basis functions, 56 primitive gaussians, 35 cartesian basis functions
5 alpha electrons 5 beta electrons
nuclear repulsion energy 13.4083363407 Hartrees.
NAtoms= 5 NActive= 5 NUniq= 5 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 on.
One-electron integrals computed using PRISM.
NBasis= 35 RedAO= T EigKep= 1.79D-02 NBF= 35
NBsUse= 35 1.00D-06 EigRej= -1.00D+00 NBFU= 35
ExpMin= 1.61D-01 ExpMax= 3.05D+03 ExpMxC= 4.57D+02 IAcc=3 IRadAn= 5 AccDes= 0.00D+00
Harris functional with IExCor= 402 and IRadAn= 5 diagonalized for initial guess.
HarFok: IExCor= 402 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
Petite list used in FoFCou.
Keep R1 ints in memory in canonical form, NReq=24354403.
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.
Integral accuracy reduced to 1.0D-05 until final iterations.
Initial convergence to 1.0D-05 achieved. Increase integral accuracy.
SCF Done: E(RB3LYP) = -40.5240137309 A.U. after 8 cycles
NFock= 8 Conv=0.23D-08 -V/T= 2.0111

**********************************************************************

Population analysis using the SCF density.

**********************************************************************

Orbital symmetries:
Occupied (A) (A) (A) (A) (A)
Virtual (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
(A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
(A) (A) (A) (A) (A) (A)
The electronic state is 1-A.
Alpha occ. eigenvalues -- -10.16717 -0.69034 -0.38827 -0.38827 -0.38827
Alpha virt. eigenvalues -- 0.11818 0.17670 0.17670 0.17670 0.52921
Alpha virt. eigenvalues -- 0.52921 0.52921 0.87424 0.87424 0.87424
Alpha virt. eigenvalues -- 0.92208 1.10023 1.36345 1.36345 2.04806
Alpha virt. eigenvalues -- 2.04806 2.04806 2.05141 2.05142 2.05142
Alpha virt. eigenvalues -- 2.62952 2.62953 2.62953 2.91074 2.91074
Alpha virt. eigenvalues -- 3.11458 3.41994 3.41994 3.41994 4.42248
Condensed to atoms (all electrons):
1 2 3 4 5
1 C 4.899051 0.392830 0.392830 0.392830 0.392830
2 H 0.392830 0.573073 -0.027832 -0.027832 -0.027832
3 H 0.392830 -0.027832 0.573075 -0.027833 -0.027832
4 H 0.392830 -0.027832 -0.027833 0.573074 -0.027833
5 H 0.392830 -0.027832 -0.027832 -0.027833 0.573075
Mulliken charges:
1
1 C -0.470371
2 H 0.117593
3 H 0.117593
4 H 0.117593
5 H 0.117593
Sum of Mulliken charges = 0.00000
Mulliken charges with hydrogens summed into heavy atoms:
1
1 C 0.000000
Electronic spatial extent (au): <R**2>= 35.4329
Charge= 0.0000 electrons
Dipole moment (field-independent basis, Debye):
X= 0.0000 Y= -0.0000 Z= 0.0000 Tot= 0.0000
Quadrupole moment (field-independent basis, Debye-Ang):
XX= -8.2465 YY= -8.2465 ZZ= -8.2465
XY= -0.0000 XZ= 0.0000 YZ= 0.0000
Traceless Quadrupole moment (field-independent basis, Debye-Ang):
XX= 0.0000 YY= -0.0000 ZZ= -0.0000
XY= -0.0000 XZ= 0.0000 YZ= 0.0000
Octapole moment (field-independent basis, Debye-Ang**2):
XXX= -0.7604 YYY= 0.2130 ZZZ= 0.4937 XYY= 0.3802
XXY= -0.0000 XXZ= 0.0000 XZZ= 0.3802 YZZ= -0.2130
YYZ= -0.4937 XYZ= 0.0000
Hexadecapole moment (field-independent basis, Debye-Ang**3):
XXXX= -14.9429 YYYY= -15.1704 ZZZZ= -15.1704 XXXY= -0.0000
XXXZ= 0.0000 YYYX= 0.1275 YYYZ= 0.0000 ZZZX= 0.2954
ZZZY= -0.0000 XXYY= -5.2843 XXZZ= -5.2843 YYZZ= -5.0568
XXYZ= 0.0000 YYXZ= -0.2954 ZZXY= -0.1275
N-N= 1.340833634068D+01 E-N=-1.198747475070D+02 KE= 4.007727827872D+01
Calling FoFJK, ICntrl= 2127 FMM=F ISym2X=0 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0.
***** Axes restored to original set *****
-------------------------------------------------------------------
Center Atomic Forces (Hartrees/Bohr)
Number Number X Y Z
-------------------------------------------------------------------
1 6 -0.000000623 -0.000000654 0.000000794
2 1 -0.000215948 -0.000000016 -0.000000010
3 1 0.000072325 0.000170842 0.000109258
4 1 0.000071925 -0.000178640 0.000093176
5 1 0.000072322 0.000008469 -0.000203220
-------------------------------------------------------------------
Cartesian Forces: Max 0.000215948 RMS 0.000111163

GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Search for a local minimum.
Step number 1 out of a maximum of 2
All quantities printed in internal units (Hartrees-Bohrs-Radians)
Second derivative matrix not updated -- first step.
The second derivative matrix:
X1 Y1 Z1 X2 Y2
X1 0.66422
Y1 -0.00000 0.66422
Z1 0.00000 -0.00000 0.66422
X2 -0.34560 -0.00000 0.00000 0.34560
Y2 -0.00000 -0.07628 -0.00000 0.00000 0.05678
Z2 0.00000 -0.00000 -0.07628 -0.00000 0.00000
X3 -0.10621 -0.07139 -0.04547 -0.00000 -0.02998
Y3 -0.07139 -0.24659 -0.10847 0.00000 0.00907
Z3 -0.04547 -0.10847 -0.14537 0.00000 0.00550
X4 -0.10621 0.07507 -0.03909 -0.00000 0.03153
Y4 0.07507 -0.26461 0.09806 -0.00000 0.00998
Z4 -0.03909 0.09806 -0.12735 0.00000 -0.00497
X5 -0.10621 -0.00368 0.08456 0.00000 -0.00155
Y5 -0.00368 -0.07674 0.01040 -0.00000 0.00046
Z5 0.08456 0.01041 -0.31522 0.00000 -0.00053
Z2 X3 Y3 Z3 X4
Z2 0.05678
X3 -0.01910 0.08887
Y3 0.00550 0.07656 0.23942
Z3 0.00394 0.04876 0.11633 0.13087
X4 -0.01642 0.00867 -0.01076 0.01119 0.08887
Y4 -0.00497 0.00975 -0.01251 0.01323 -0.08051
Z4 0.00302 0.01208 -0.01579 0.01685 0.04192
X5 0.03551 0.00867 0.00559 -0.01448 0.00867
Y5 -0.00053 0.01507 0.01062 -0.02659 -0.01533
Z5 0.01255 0.00372 0.00244 -0.00628 0.00240
Y4 Z4 X5 Y5 Z5
Y4 0.25875
Z4 -0.10517 0.11154
X5 -0.00431 -0.01491 0.08887
Y5 0.00840 0.02787 0.00395 0.05726
Z5 -0.00116 -0.00406 -0.09068 -0.01116 0.31302
ITU= 0
Eigenvalues --- 0.11268 0.11268 0.13515 0.13515 0.13515
Eigenvalues --- 0.34560 0.81139 0.81139 0.81140
Angle between quadratic step and forces= 0.37 degrees.
Linear search not attempted -- first point.
B after Tr= -0.000001 0.000000 -0.000000
Rot= 1.000000 0.000000 -0.000000 -0.000000 Ang= 0.00 deg.
Variable Old X -DE/DX Delta X Delta X Delta X New X
(Linear) (Quad) (Total)
X1 2.02998 -0.00000 0.00000 -0.00000 -0.00000 2.02998
Y1 -0.11403 -0.00000 0.00000 0.00000 0.00000 -0.11403
Z1 0.05512 0.00000 0.00000 -0.00000 -0.00000 0.05512
X2 4.09394 -0.00022 0.00000 -0.00063 -0.00063 4.09331
Y2 -0.11403 -0.00000 0.00000 -0.00000 -0.00000 -0.11403
Z2 0.05512 -0.00000 0.00000 0.00000 -0.00000 0.05512
X3 1.34199 0.00007 0.00000 0.00021 0.00021 1.34220
Y3 -1.75531 0.00017 0.00000 0.00049 0.00049 -1.75482
Z3 -0.99024 0.00011 0.00000 0.00032 0.00032 -0.98992
X4 1.34199 0.00007 0.00000 0.00021 0.00021 1.34220
Y4 1.61192 -0.00018 0.00000 -0.00051 -0.00051 1.61140
Z4 -0.84359 0.00009 0.00000 0.00027 0.00027 -0.84332
X5 1.34199 0.00007 0.00000 0.00021 0.00021 1.34220
Y5 -0.19869 0.00001 0.00000 0.00002 0.00002 -0.19866
Z5 1.99920 -0.00020 0.00000 -0.00059 -0.00059 1.99861
Item Value Threshold Converged?
Maximum Force 0.000216 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.000628 0.001800 YES
RMS Displacement 0.000322 0.001200 YES
Predicted change in Energy=-2.681743D-07
Optimization completed.
-- Stationary point found.
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

1\1\GINC-LOCALHOST\Force\RB3LYP\6-31G(d,p)\C1H4\JZZENG\25-Jun-2019\0\\
#force b3lyp/6-31g**\\methane\\0,1\C,1.07422,-0.06034,0.02917\H,2.1664
2,-0.06034,0.02917\H,0.71015,-0.92887,-0.52401\H,0.71015,0.85299,-0.44
641\H,0.71015,-0.10514,1.05793\\Version=ES64L-G16RevA.03\State=1-A\HF=
-40.5240137\RMSD=2.291e-09\RMSF=1.112e-04\Dipole=-0.0000018,0.0000007,
-0.0000007\Quadrupole=0.0000105,-0.0000083,-0.0000022,-0.000001,0.0000
01,0.0000025\PG=C01 [X(C1H4)]\\@


SEE YOU NOW,
YOUR BAIT OF FALSEHOOD TAKES THIS CARP OF TRUTH.
AND THUS DO WE OF WISDOM AND OF REACH...
BY INDIRECTIONS FIND DIRECTIONS OUT. -- HAMLET, II, 1
Job cpu time: 0 days 0 hours 1 minutes 11.1 seconds.
Elapsed time: 0 days 0 hours 0 minutes 3.2 seconds.
File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1
Normal termination of Gaussian 16 at Tue Jun 25 00:14:07 2019.
8 changes: 8 additions & 0 deletions tests/test_gaussian_log.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -102,6 +102,14 @@ def test_cells(self):
def test_nopbc(self):
self.assertEqual(self.system.nopbc, False)

class TestGaussianNoInputOrientation(unittest.TestCase):
"""Raise Error when there is no input orientation."""

def test_no_input_orientation(self):
with self.assertRaises(RuntimeError):
self.system = dpdata.LabeledSystem(
"gaussian/no_input_orient.gaussianlog", fmt="gaussian/log"
)

if __name__ == "__main__":
unittest.main()

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