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wanghan-iapcm merged 2 commits into from
Dec 19, 2022
Merged

gaussian: support PBC #397

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4bf1c22
gaussian: support PBC
njzjz Dec 16, 2022
d711a18
fix
njzjz Dec 16, 2022
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6 changes: 6 additions & 0 deletions dpdata/gaussian/gjf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -229,6 +229,12 @@ def make_gaussian_input(
(symbol, frag_index[ii] + 1, *coordinate))
else:
buff.append("%s %f %f %f" % (symbol, *coordinate))
if not sys_data.get('nopbc', False):
# PBC condition
cell = sys_data['cells'][0]
for ii in range(3):
# use TV as atomic symbol, see https://gaussian.com/pbc/
buff.append('TV %f %f %f' % (symbol, *cell[ii]))
if basis_set is not None:
# custom basis set
buff.extend(['', basis_set, ''])
Expand Down
27 changes: 22 additions & 5 deletions dpdata/gaussian/log.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ def to_system_data(file_name, md=False):
coords_t = []
atom_symbols = []
forces_t = []
cells_t = []
nopbc = True

with open(file_name) as fp:
for line in fp:
Expand All @@ -29,6 +31,7 @@ def to_system_data(file_name, md=False):
flag = 5
coords = []
atom_symbols = []
cells = []

if 1 <= flag <= 3 or 5 <= flag <= 9:
flag += 1
Expand All @@ -38,18 +41,31 @@ def to_system_data(file_name, md=False):
forces_t.append(forces)
energy_t.append(energy)
coords_t.append(coords)
if cells:
nopbc = False
cells_t.append(cells)
else:
cells_t.append([[100., 0., 0.], [0., 100., 0.], [0., 0., 100.]])
flag = 0
else:
s = line.split()
forces.append([float(line[23:38]), float(line[38:53]), float(line[53:68])])
if line[14:16] == "-2":
# PBC
pass
else:
forces.append([float(line[23:38]), float(line[38:53]), float(line[53:68])])
elif flag == 10:
# atom_symbols and coords
if line.startswith(" -------"):
flag = 0
else:
s = line.split()
coords.append([float(x) for x in s[3:6]])
atom_symbols.append(symbols[int(s[1])])
if int(s[1]) == -2:
# PBC cells, see https://gaussian.com/pbc/
cells.append([float(x) for x in s[3:6]])
else:
coords.append([float(x) for x in s[3:6]])
atom_symbols.append(symbols[int(s[1])])

assert(coords_t), "cannot find coords"
assert(energy_t), "cannot find energies"
Expand All @@ -62,10 +78,11 @@ def to_system_data(file_name, md=False):
forces_t = forces_t[-1:]
energy_t = energy_t[-1:]
coords_t = coords_t[-1:]
cells_t = cells_t[-1:]
data['forces'] = np.array(forces_t) * force_convert
data['energies'] = np.array(energy_t) * energy_convert
data['coords'] = np.array(coords_t)
data['orig'] = np.array([0, 0, 0])
data['cells'] = np.array([[[100., 0., 0.], [0., 100., 0.], [0., 0., 100.]] for _ in energy_t])
data['nopbc'] = True
data['cells'] = np.array(cells_t)
data['nopbc'] = nopbc
return data
301 changes: 301 additions & 0 deletions tests/gaussian/h2pbc.gaussianlog
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Original file line number Diff line number Diff line change
@@ -0,0 +1,301 @@
Entering Gaussian System, Link 0=g16
Input=h.gjf
Output=h.log
Initial command:
/home/jz748/g16/g16/l1.exe "/home/jz748/tmp/Gau-1950599.inp" -scrdir="/home/jz748/tmp/"
Entering Link 1 = /home/jz748/g16/g16/l1.exe PID= 1950600.

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
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 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
19-Dec-2022
******************************************
--------------------
# force wb97x/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=1,11=2,25=1,30=1,71=1,74=-57/1,2,3;
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;
-
H
-
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
H 0. 0. 0.
H 1. 1. 0.
TV 10. 0. 0.
TV 0. 10. 0.
TV 0. 0. 10.


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

Before rotation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 1 0 0.000000 0.000000 0.000000
2 1 0 1.000000 1.000000 0.000000
3 -2 0 10.000000 0.000000 0.000000
4 -2 0 0.000000 10.000000 0.000000
5 -2 0 0.000000 0.000000 10.000000
---------------------------------------------------------------------
Lengths of translation vectors: 10.000000 10.000000 10.000000
Angles of translation vectors: 90.000000 90.000000 90.000000
---------------------------------------------------------------------
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 1 0 -0.500000 -0.500000 0.000000
2 1 0 0.500000 0.500000 0.000000
3 -2 0 10.000000 0.000000 0.000000
4 -2 0 0.000000 10.000000 0.000000
5 -2 0 0.000000 0.000000 10.000000
---------------------------------------------------------------------
Lengths of translation vectors: 10.000000 10.000000 10.000000
Angles of translation vectors: 90.000000 90.000000 90.000000
---------------------------------------------------------------------
Distance matrix (angstroms):
1 2 3 4 5
1 H 0.000000
2 H 1.414214 0.000000
3 TV 10.511898 9.513149 0.000000
4 TV 10.511898 9.513149 14.142136 0.000000
5 TV 10.024969 10.024969 14.142136 14.142136 0.000000
Unit Cell Distance matrix (angstroms):
1 2
1 H 0.000000
2 H 12.727922 0.000000
Symmetry turned off:
Cannot cope with ghost atoms or with translation vectors.
Stoichiometry H2
Framework group C1[X(H2)]
Deg. of freedom 0
Full point group C1 NOp 1
Standard basis: 6-31G(d) (6D, 7F)
4 basis functions, 8 primitive gaussians, 4 cartesian basis functions
1 alpha electrons 1 beta electrons
nuclear repulsion energy 0.3741847943 Hartrees.
NAtoms= 2 NActive= 2 NUniq= 2 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.
FOutLm= 100.00.
Periodicity: 1 1 1
Max integer dimensions: 6 6 6
PBC vector 1 X= 18.8973 Y= 0.0000 Z= 0.0000
PBC vector 2 X= 0.0000 Y= 18.8973 Z= 0.0000
PBC vector 3 X= 0.0000 Y= 0.0000 Z= 18.8973
Recp vector 1 X= 0.0529 Y= 0.0000 Z= 0.0000
Recp vector 2 X= 0.0000 Y= 0.0529 Z= 0.0000
Recp vector 3 X= 0.0000 Y= 0.0000 Z= 0.0529
Generated k point mesh (from -Pi to Pi):
K space mesh: X= 14 Y= 14 Z= 14
A half-cell shift: 0
Using k point mesh (from -Pi to Pi):
K space mesh: X= 14 Y= 14 Z= 14
A half-cell shift: 0
CountK=T Total number of k points: 0
CountK=T Total number of k points: 1376
One-electron integrals computed using PRISM.
NBasis= 4 RedAO= T EigKep= 2.13D-01 NBF= 4
NBsUse= 4 1.00D-06 EigRej= -1.00D+00 NBFU= 4
RepCel: MaxNCR= 37 NClRep= 37 NMtPBC= 1389.
Harris functional with IExCor= 4538 and IRadAn= 5 diagonalized for initial guess.
RepCel: MaxNCR= 37 NClRep= 37 NMtPBC= 1389.
HarFok: IExCor= 4538 AccDes= 0.00D+00 IRadAn= 5 IDoV= 2 UseB2=F ITyADJ=14
ICtDFT= 3500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000
FoFCou: FMM=T IPFlag= 524288 FMFlag= 990000 FMFlg1= 1001
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.
FMM levels: 3 Number of levels for PrismC: 2
Requested convergence on RMS density matrix=1.00D-07 within 128 cycles.
Requested convergence on MAX density matrix=1.00D-05.
Requested convergence on energy=1.00D-05.
No special actions if energy rises.
Diagonalized old Fock matrix for initial guess.
RepCel: MaxNCR= 37 NClRep= 37 NMtPBC= 1389.
RepCel: MaxNCR= 37 NClRep= 37 NMtPBC= 1389.
RepCel: MaxNCR= 37 NClRep= 37 NMtPBC= 1389.
RepCel: MaxNCR= 37 NClRep= 37 NMtPBC= 1389.
RepCel: MaxNCR= 37 NClRep= 37 NMtPBC= 1389.
RepCel: MaxNCR= 37 NClRep= 37 NMtPBC= 1389.
SCF Done: E(RwB97X) = -1.06463933888 A.U. after 6 cycles
NFock= 6 Conv=0.16D-08 -V/T= 2.3027

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

Population analysis using the SCF density.

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

Condensed to atoms (all electrons):
1 2
1 H 0.713229 0.286771
2 H 0.286771 0.713229
Mulliken charges:
1
1 H 0.000000
2 H -0.000000
Sum of Mulliken charges = -0.00000
Mulliken charges with hydrogens summed into heavy atoms:
1
Calling FoFJK, ICntrl= 2127 FMM=T ISym2X=0 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0.
RepCel: MaxNCR= 37 NClRep= 37 NMtPBC= 1389.
-------------------------------------------------------------------
Center Atomic Forces (Hartrees/Bohr)
Number Number X Y Z
-------------------------------------------------------------------
1 1 0.066019420 0.066019420 0.000000000
2 1 -0.066019420 -0.066019420 -0.000000000
-2 -0.000000162 -0.000000016 0.000000000
-2 -0.000000016 -0.000000162 -0.000000000
-2 0.000000000 0.000000000 0.000000123
-------------------------------------------------------------------
Cartesian Forces: Max 0.066019420 RMS 0.034092282
-----------------------------------------------------------------------------------------------
Internal Coordinate Forces (Hartree/Bohr or radian)
Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J
-----------------------------------------------------------------------------------------------
1 H 0.066019( 1) 0.066019( 6) 0.000000( 11)
2 H -0.066019( 2) -0.066019( 7) -0.000000( 12)
TV -0.000000( 3) -0.000000( 8) 0.000000( 13)
TV -0.000000( 4) -0.000000( 9) -0.000000( 14)
TV 0.000000( 5) 0.000000( 10) 0.000000( 15)
-----------------------------------------------------------------------------------------------
Internal Forces: Max 0.066019420 RMS 0.034092282

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.
ITU= 0
Angle between quadratic step and forces= 0.00 degrees.
Linear search not attempted -- first point.
Variable Old X -DE/DX Delta X Delta X Delta X New X
(Linear) (Quad) (Total)
X1 -0.94486 0.06602 0.00000 0.06602 0.06602 -0.87884
Y1 -0.94486 0.06602 0.00000 0.06602 0.06602 -0.87884
Z1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
X2 0.94486 -0.06602 0.00000 -0.06602 -0.06602 0.87884
Y2 0.94486 -0.06602 0.00000 -0.06602 -0.06602 0.87884
Z2 0.00000 -0.00000 0.00000 -0.00000 -0.00000 -0.00000
X3 18.89726 -0.00000 0.00000 -0.00000 -0.00000 18.89726
Y3 0.00000 -0.00000 0.00000 -0.00000 -0.00000 -0.00000
Z3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
X4 0.00000 -0.00000 0.00000 -0.00000 -0.00000 -0.00000
Y4 18.89726 -0.00000 0.00000 -0.00000 -0.00000 18.89726
Z4 0.00000 -0.00000 0.00000 -0.00000 -0.00000 -0.00000
X5 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
Y5 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
Z5 18.89726 0.00000 0.00000 0.00000 0.00000 18.89726
Item Value Threshold Converged?
Maximum Force 0.066019 0.000450 NO
RMS Force 0.034092 0.000300 NO
Maximum Displacement 0.066019 0.001800 NO
RMS Displacement 0.034092 0.001200 NO
Predicted change in Energy=-8.717128D-03
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

1\1\GINC-LOCALHOST\Force\RwB97X\6-31G(d)\H2\JZ748\19-Dec-2022\0\\# for
ce wb97x/6-31g*\\H\\0,1\H,-0.5,-0.5,0.\H,0.5,0.5,0.\TV,10.,0.,0.\TV,0.
,10.,0.\TV,0.,0.,10.\\Version=ES64L-G16RevA.03\HF=-1.0646393\RMSD=1.63
1e-09\RMSF=3.409e-02\PG=C01 [X(H2)]\\@


ABOVE ALL I AM AN OPTIMIST FOR NUMBER THEORY,
AND I HOLD THE HOPE THAT WE MAY NOT BE FAR FROM
A TIME WHEN IRREFUTABLE ARITHMETIC WILL CELEBRATE
ITS TRIUMPHS IN PHYSICS AND CHEMISTRY.
-- HERMANN MINKOWSKI, 1905
Job cpu time: 0 days 0 hours 0 minutes 2.4 seconds.
Elapsed time: 0 days 0 hours 0 minutes 2.3 seconds.
File lengths (MBytes): RWF= 16 Int= 0 D2E= 0 Chk= 2 Scr= 1
Normal termination of Gaussian 16 at Mon Dec 19 01:52:07 2022.
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