/usr/share/psi4/samples/pywrap-db3/input.dat is in psi4-data 1:1.1-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 | #! Test that Python Molecule class processes geometry like psi4 Molecule class.
ref_geom = psi4.Matrix(16,3)
ref_geom.set(
[[ 0.710500000000, -0.794637665924, -1.230622098778],
[ 1.421000000000, -0.794637665924, 0.000000000000],
[ 0.710500000000, -0.794637665924, 1.230622098778],
[ -0.710500000000, -0.794637665924, 1.230622098778],
[ 1.254500000000, -0.794637665924, -2.172857738095],
[ -1.254500000000, -0.794637665924, 2.172857738095],
[ -0.710500000000, -0.794637665924, -1.230622098778],
[ -1.421000000000, -0.794637665924, 0.000000000000],
[ 2.509000000000, -0.794637665924, 0.000000000000],
[ 1.254500000000, -0.794637665924, 2.172857738095],
[ -1.254500000000, -0.794637665924, -2.172857738095],
[ -2.509000000000, -0.794637665924, 0.000000000000],
[ 0.000000000000, 3.205362334076, 0.000000000000],
[ 0.494974746831, 3.555362334076, -0.857321409974],
[ 0.494974746831, 3.555362334076, 0.857321409974],
[ -0.989949493661, 3.555362334076, 0.000000000000]])
set basis 6-31G*
banner('PSI4 Molecule Parsing')
molecule dimer {
1 1
# This part is just a normal Cartesian geometry specification for benzene
C 0.710500000000 -0.794637665924 -1.230622098778
C 1.421000000000 -0.794637665924 0.000000000000
C 0.710500000000 -0.794637665924 1.230622098778
C -0.710500000000 -0.794637665924 1.230622098778
H 1.254500000000 -0.794637665924 -2.172857738095
H -1.254500000000 -0.794637665924 2.172857738095
C -0.710500000000 -0.794637665924 -1.230622098778
C -1.421000000000 -0.794637665924 0.000000000000
H 2.509000000000 -0.794637665924 0.000000000000
H 1.254500000000 -0.794637665924 2.172857738095
H -1.254500000000 -0.794637665924 -2.172857738095
H -2.509000000000 -0.794637665924 0.000000000000
# And the hydronium part is specified using a zmatrix, referencing the benzene coordinates
X 1 CC 3 30 2 A2
O 13 R 1 90 2 90
H 14 OH 13 TDA 1 0
H 14 OH 15 TDA 13 A1
H 14 OH 15 TDA 13 -A1
CC = 1.421
CH = 1.088
A1 = 120.0
A2 = 180.0
OH = 1.05
R = 4.0
units angstrom
}
dimer.update_geometry()
dimer.print_out()
geom_now = dimer.geometry()
geom_now.scale(psi_bohr2angstroms)
banner('QCDB Molecule Parsing')
YYY = qcdb.Molecule("""
1 1
# This part is just a normal Cartesian geometry specification for benzene
C 0.710500000000 -0.794637665924 -1.230622098778
C 1.421000000000 -0.794637665924 0.000000000000
C 0.710500000000 -0.794637665924 1.230622098778
C -0.710500000000 -0.794637665924 1.230622098778
H 1.254500000000 -0.794637665924 -2.172857738095
H -1.254500000000 -0.794637665924 2.172857738095
C -0.710500000000 -0.794637665924 -1.230622098778
C -1.421000000000 -0.794637665924 0.000000000000
H 2.509000000000 -0.794637665924 0.000000000000
H 1.254500000000 -0.794637665924 2.172857738095
H -1.254500000000 -0.794637665924 -2.172857738095
H -2.509000000000 -0.794637665924 0.000000000000
# And the hydronium part is specified using a zmatrix, referencing the benzene coordinates
X 1 CC 3 30 2 A2
O 13 R 1 90 2 90
H 14 OH 13 TDA 1 0
H 14 OH 15 TDA 13 A1
H 14 OH 15 TDA 13 -A1
CC = 1.421
CH = 1.088
A1 = 120.0
A2 = 180.0
OH = 1.05
R = 4.0
units angstrom
""")
YYY.update_geometry()
#geom_now = psi4.Matrix(16,3)
geom_now.set(YYY.geometry())
geom_now.scale(psi_bohr2angstroms)
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