/usr/share/psi4/samples/pywrap-molecule/test.in 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 | #! Check that C++ Molecule class and qcdb molecule class
#! are reading molecule input strings identically
from psi4.driver import qcdb
mol1 = """
0 3
X
X 1 1.000000
C 2 CQ 1 90.000000
C 3 CQ 2 60.000000 1 90.000000
C 4 CQ 2 60.000000 1 90.000000
C 5 CQ 2 60.000000 1 90.000000
C 6 CQ 2 60.000000 1 90.000000
C 7 CQ 2 60.000000 1 90.000000
X 3 1.000000 2 90.000000 1 0.000000
H 3 CH1 9 90.000000 2 180.000000
H 4 CH1 3 120.000000 2 180.000000
H 5 CH1 4 120.000000 2 180.000000
H 6 CH1 5 120.000000 2 180.000000
H 7 CH1 6 120.000000 2 180.000000
H 8 CH1 7 120.000000 2 180.000000
--
0 1
C 2 R 3 90.000000 9 0.000000
H 16 CH2 2 0.000000 3 0.000000
H 16 CH2 2 HCH 3 0.000000
H 16 CH2 17 HCH 18 120.000000
H 16 CH2 17 HCH 18 240.000000
HCH = 109.4712090000
CH1 = 1.0952100000
CQ = 1.4057310000
R = 6.0000000000
CH2 = 1.0995030000
"""
mol2 = """
N -1.527107413251 0.745960643462 0.766603000356
C -0.075844098953 0.811790225041 0.711418672248
C 0.503195220163 -0.247849447550 -0.215671574613
O -0.351261319421 -0.748978309671 -1.089590304723
O 1.639498336738 -0.571249748886 -0.174705953194
H -1.207655674855 -0.365913941094 -0.918035522052
--
C 2 rCC 3 aCCC 1 dCCCN
H 7 rCH1 2 aHCC1 3 dHCCC1
H 7 rCH2 2 aHCC2 3 dHCCC2
H 7 rCH3 2 aHCC3 3 dHCCC3
H 0.221781602033 1.772570540211 0.286988509018
H -1.833601608592 0.108401996052 1.481873213172
H -1.925572581453 1.640882152784 0.986471814808
aCCC = 108.0
rCC = 1.4
dCCCN = 120
rCH1 = 1.08
rCH2 = 1.08
rCH3 = 1.08
aHCC1 = 109.0
aHCC2 = 109.0
aHCC3 = 109.0
dHCCC1 = 0.0
dHCCC2 = 120.0
dHCCC3 = 240.0
no_com
no_reorient
"""
mol3 = """
0 1
H 0.35854975 -0.09945835 0.00000000
F 1.28985881 -0.09945835 0.00000000
--
0 2
O -1.44698611 0.06135708 0.00000000
H -1.70882231 1.00055573 0.00000000
no_com
no_reorient
"""
def test_qcdb(): #TEST
print_out("%s\n" % ans[0]) #TEST
print_out(origfrag.create_psi4_string_from_molecule()) #TEST
gorig = origfrag.geometry() #TEST
frag = qcdb.Molecule(origfrag.create_psi4_string_from_molecule()) #TEST
frag.update_geometry() #TEST
gnew = frag.geometry() #TEST
compare_values(ans[1], frag.nuclear_repulsion_energy(), 6, "QCDB %s: NRE" % ans[0]) #TEST
compare_integers(ans[2], frag.molecular_charge(), "QCDB %s: charge" % ans[0]) #TEST
compare_integers(ans[3], frag.multiplicity(), "QCDB %s: multiplicity" % ans[0]) #TEST
qcdb.compare_matrices(gorig, gnew, 5, "QCDB %s: string recreates geometry" % ans[0]) #TEST
def test_libmints(): #TEST
print_out("%s\n" % ans[0]) #TEST
print_out(origfrag.create_psi4_string_from_molecule()) #TEST
gorig = origfrag.geometry() #TEST
frag = geometry(origfrag.create_psi4_string_from_molecule()) #TEST
frag.update_geometry() #TEST
gnew = frag.geometry() #TEST
compare_values(ans[1], frag.nuclear_repulsion_energy(), 6, "Libmints %s: NRE" % ans[0]) #TEST
compare_integers(ans[2], frag.molecular_charge(), "Libmints %s: charge" % ans[0]) #TEST
compare_integers(ans[3], frag.multiplicity(), "Libmints %s: multiplicity" % ans[0]) #TEST
compare_matrices(gorig, gnew, 5, "Libmints %s: string recreates geometry" % ans[0]) #TEST
mol = qcdb.Molecule(mol1)
mol.update_geometry()
ans = ["Mol1 Dimer", 250.994551922, 0, 3]
origfrag = mol
test_qcdb()
ans = ["Mol1 MonoA CP", 201.838536064, 0, 3]
origfrag = mol.extract_fragments(1,2)
test_qcdb()
ans = ["Mol1 MonoB UNCP", 13.3192671807, 0, 1]
origfrag = mol.extract_fragments(2)
test_qcdb()
mol = qcdb.Molecule(mol2)
mol.update_geometry()
ans = ["Mol2 Dimer", 256.652780316, 0, 1]
origfrag = mol
test_qcdb()
ans = ["Mol2 MonoA CP", 144.483917787, 0, 1]
origfrag = mol.extract_fragments(1,2)
test_qcdb()
ans = ["Mol2 MonoB UNCP", 16.209317711, 0, 1]
origfrag = mol.extract_fragments(2)
test_qcdb()
mol = qcdb.Molecule(mol3)
mol.update_geometry()
ans = ["Mol3 Dimer", 27.4057052589, 0, 2]
origfrag = mol
test_qcdb()
ans = ["Mol3 MonoA CP", 5.11387151899, 0, 1]
origfrag = mol.extract_fragments(1,2)
test_qcdb()
ans = ["Mol3 MonoB UNCP", 4.34190449534, 0, 2]
origfrag = mol.extract_fragments(2)
test_qcdb()
#mol = geometry(mol1)
#mol.update_geometry()
#ans = ["Mol1 Dimer", 250.994551922, 0, 3]
#origfrag = mol
#test_libmints()
#ans = ["Mol1 MonoA CP", 201.838536064, 0, 3]
#origfrag = mol.extract_subsets(1,2)
#test_libmints()
#ans = ["Mol1 MonoB UNCP", 13.3192671807, 0, 1]
#origfrag = mol.extract_subsets(2)
#test_libmints()
#mol = geometry(mol2)
#mol.update_geometry()
#ans = ["Mol2 Dimer", 256.652780316, 0, 1]
#origfrag = mol
#test_libmints()
#ans = ["Mol2 MonoA CP", 144.483917787, 0, 1]
#origfrag = mol.extract_subsets(1,2)
#test_libmints()
#ans = ["Mol2 MonoB UNCP", 16.209317711, 0, 1]
#origfrag = mol.extract_subsets(2)
#test_libmints()
mol = geometry(mol3)
mol.update_geometry()
ans = ["Mol3 Dimer", 27.4057052589, 0, 2]
origfrag = mol
test_libmints() #TEST
ans = ["Mol3 MonoA CP", 5.11387151899, 0, 1]
origfrag = mol.extract_subsets(1,2)
test_libmints() #TEST
ans = ["Mol3 MonoB UNCP", 4.34190449534, 0, 2]
origfrag = mol.extract_subsets(2)
test_libmints() #TEST
|