[docs]
def get_baker_data():
"""10.1002/jcc.540140910
HF/STO-3G
"""
data = (
("00_water.xyz", 0, 1, -74.96590),
("01_ammonia.xyz", 0, 1, -55.45542),
("02_ethane.xyz", 0, 1, -78.30618),
("03_acetylene.xyz", 0, 1, -75.85625),
("04_allene.xyz", 0, 1, -114.42172),
("05_hydroxysulphane.xyz", 0, 1, -468.12592),
("06_benzene.xyz", 0, 1, -227.89136),
("07_methylamine.xyz", 0, 1, -94.01617),
("08_ethanol.xyz", 0, 1, -152.13267),
("09_acetone.xyz", 0, 1, -189.53603),
("10_disilylether.xyz", 0, 1, -648.58003),
("11_135trisilacyclohexane.xyz", 0, 1, -976.13242),
("12_benzaldehyde.xyz", 0, 1, -339.12084),
("13_13difluorobenzene.xyz", 0, 1, -422.81106),
("14_135trifluorobenzene.xyz", 0, 1, -520.27052),
("15_neopentane.xyz", 0, 1, -194.04677),
("16_furan.xyz", 0, 1, -225.75126),
("17_naphthalene.xyz", 0, 1, -378.68685),
("18_15difluoronaphthalene.xyz", 0, 1, -573.60633),
("19_2hydroxybicyclopentane.xyz", 0, 1, -265.46482),
("20_achtar10.xyz", 0, 1, -356.28265),
("21_acanil01.xyz", 0, 1, -432.03012),
("22_benzidine.xyz", 0, 1, -563.27798),
("23_pterin.xyz", 0, 1, -569.84884),
("24_difuropyrazine.xyz", 0, 1, -556.71910),
("25_mesityloxide.xyz", 0, 1, -304.05919),
("26_histidine.xyz", 0, 1, -538.54910),
("27_dimethylpentane.xyz", 0, 1, -271.20088),
("28_caffeine.xyz", 0, 1, -667.73565),
("29_menthone.xyz", 0, 1, -458.44639),
)
prefix = "lib:baker/"
return prefix, data
[docs]
def get_baker_ts_data():
"""10.1002/(SICI)1096-987X(199605)17:7<888::AID-JCC12>3.0.CO;2-7
HF/3-21G
"""
data = (
("01_hcn.xyz", 0, 1, -92.24604),
("02_hcch.xyz", 0, 1, -76.29343),
("03_h2co.xyz", 0, 1, -113.05003),
("04_ch3o.xyz", 0, 2, -113.69365),
("05_cyclopropyl.xyz", 0, 2, -115.72100),
("06_bicyclobutane.xyz", 0, 1, -153.90494),
("07_bicyclobutane.xyz", 0, 1, -153.89754),
("08_formyloxyethyl.xyz", 0, 2, -264.64757),
("09_parentdieslalder.xyz", 0, 1, -231.60321),
# 10 and 11 don't have any imaginary frequencies at the given
# geometry, so they may be skipped. Until now (jan. 2021) I've
# never seen anybody mention, how they treated these cases ...
# It's not discussed in the 2002 Bakken paper and also not
# in the 1998 Besalu/Bofill paper. And of course not in the
# original 1996 Baker paper ... any advice on these two cases
# is greatly appreciated.
("10_tetrazine.xyz", 0, 1, -292.81026),
("11_trans_butadiene.xyz", 0, 1, -154.05046),
("12_ethane_h2_abstraction.xyz", 0, 1, -78.54323),
("13_hf_abstraction.xyz", 0, 1, -176.98453),
("14_vinyl_alcohol.xyz", 0, 1, -151.91310),
# 15 does not have an imaginary mode in cartesian coordinates
("15_hocl.xyz", 0, 1, -569.897524),
("16_h2po4_anion.xyz", -1, 1, -637.92388),
("17_claisen.xyz", 0, 1, -267.23859),
("18_silyene_insertion.xyz", 0, 1, -367.20778),
("19_hnccs.xyz", 0, 1, -525.43040),
# The energy given in the paper (-168.24752 au) is the correct one
# if one forms the central (0,1) bond (0-based indexing). If this
# bond is missing, as it is if we autogenerate with bond-factor=1.3
# then a TS with -168.241392 will be found.
# For now we will use the original value from the paper.
("20_hconh3_cation.xyz", 1, 1, -168.24752),
("21_acrolein_rot.xyz", 0, 1, -189.67574),
# The published energy -242.25529 corresponds to a planar TS. Without
# symmetry restrictions the planar TS relaxes to -242.25695785.
# As our algorithms obtain the unconstrained TS, we will use the
# updated energy.
# ("22_hconhoh.xyz", 0, 1, -242.25529),
("22_hconhoh.xyz", 0, 1, -242.256958),
("23_hcn_h2.xyz", 0, 1, -93.31114),
("24_h2cnh.xyz", 0, 1, -93.33296),
("25_hcnh2.xyz", 0, 1, -93.28172),
)
prefix = "lib:baker_ts/"
return prefix, data
[docs]
def get_s22_data():
"""
https://doi.org/10.1039/B600027D
"""
data = (
("00_adenine_thymine_wc.xyz", 0, 1, None),
("01_adenine_thymine_stack.xyz", 0, 1, None),
("02_ammonia_dimer.xyz", 0, 1, None),
("03_water_dimer.xyz", 0, 1, None),
("04_methane_dimer.xyz", 0, 1, None),
("05_ethene_dimer.xyz", 0, 1, None),
("06_ethene_ethine.xyz", 0, 1, None),
("07_formic_acid_dimer.xyz", 0, 1, None),
("08_formamide_dimer.xyz", 0, 1, None),
("09_benzene_water.xyz", 0, 1, None),
("10_benzene_ammonia.xyz", 0, 1, None),
("11_benzene_methane.xyz", 0, 1, None),
("12_benzene_dimer_c2v.xyz", 0, 1, None),
("13_benzene_dimer_c2h.xyz", 0, 1, None),
("14_indole_benzene_t-shape.xyz", 0, 1, None),
("15_indole_benzene_stack.xyz", 0, 1, None),
("16_pyrazine_dimer.xyz", 0, 1, None),
("17_2-pyridoxine_2-aminopyridine.xyz", 0, 1, None),
("18_phenol_dimer.xyz", 0, 1, None),
("19_uracil_dimer_stack.xyz", 0, 1, None),
("20_uracil_dimer_hb.xyz", 0, 1, None),
("21_benzene_hcn.xyz", 0, 1, None),
)
prefix = "lib:s22/"
return prefix, data
[docs]
def get_zimmerman_data():
"""
https://dx.doi.org/10.1021/ct400319w
"""
size = 105
prefix = "lib:zimmerman/"
data = list()
for i in range(size):
fn = f"case_{i:03d}.trj"
data.append((fn, 0, 1, None))
data = tuple(data)
return prefix, data
[docs]
def get_zimmerman_xtb_data():
"""
Reoptimization of
https://dx.doi.org/10.1021/ct400319w
at the gfn2-xtb level of theory.
Includes set 1 (first 72 entries), minus (0-based) ids
7, 8, 13, 14, 15, 34, 39
"""
size = 65
prefix = "lib:zimmerman_xtb/"
data = list()
for i in range(size):
fn = f"{i:02d}_zm_xtb.trj"
data.append((fn, 0, 1, None))
data = tuple(data)
return prefix, data
[docs]
def get_birkholz_rx_data():
"""
https://doi.org/10.1002/jcc.23910
"""
data = (
("00_c2no2.trj", 0, 1, None),
("01_c5ht.trj", 0, 1, None),
("02_hcn.trj", 0, 1, None),
("03_cope.trj", 0, 1, None),
("04_cpht.trj", 0, 1, None),
("05_cycbut.trj", 0, 1, None),
("06_dacp2.trj", 0, 1, None),
("07_dacp_eth.trj", 0, 1, None),
("08_dfcp.trj", 0, 1, None),
("09_ene.trj", 0, 1, None),
("10_grignard.trj", 0, 1, None),
("11_h2co.trj", 0, 1, None),
("12_hf_eth.trj", 0, 1, None),
("13_hydro.trj", 0, 1, None),
("14_meoh.trj", 0, 1, None),
("15_oxirane.trj", -1, 1, None),
("16_oxycope.trj", 0, 1, None),
("17_silane.trj", 0, 1, None),
("18_sn2.trj", -1, 1, None),
("19_sulfolene.trj", 0, 1, None),
)
prefix = "lib:birkholz_rx/"
return prefix, data
[docs]
def get_xtb_rx_data():
data = (
("00_c2no2.trj", 0, 1, None),
("01_c5ht.trj", 0, 1, None),
("02_hcn.trj", 0, 1, None),
("03_cope.trj", 0, 1, None),
("04_cpht.trj", 0, 1, None),
("05_cycbut.trj", 0, 1, None),
("06_dacp2.trj", 0, 1, None),
("07_dacp_eth.trj", 0, 1, None),
("08_ene.trj", 0, 1, None),
("09_grignard.trj", 0, 1, None),
("10_h2co.trj", 0, 1, None),
("11_hf_eth.trj", 0, 1, None),
("12_hydro.trj", 0, 1, None),
("13_meoh.trj", 0, 1, None),
("14_oxirane.trj", -1, 1, None),
("15_oxycope.trj", 0, 1, None),
("16_silane.trj", 0, 1, None),
("17_sulfolene.trj", 0, 1, None),
("18_mobh35_14.trj", 0, 1, None),
("19_mobh35_30.trj", 0, 1, None),
)
prefix = "lib:xtb_rx/"
return prefix, data
[docs]
def get_precon_pos_rot_data():
"""
https://doi.org/10.1002/jcc.23910
"""
data = (
("00_c2no2.trj", 0, 1, None),
("06_dacp2.trj", 0, 1, None),
("07_dacp_eth.trj", 0, 1, None),
("08_dfcp.trj", 0, 1, None),
("09_ene.trj", 0, 1, None),
("11_h2co.trj", 0, 1, None),
("12_hf_eth.trj", 0, 1, None),
("14_meoh.trj", 0, 1, None),
("18_sn2.trj", -1, 1, None),
("19_sulfolene.trj", 0, 1, None),
)
prefix = "lib:birkholz_rx/"
return prefix, data