def __init__(self, m):
test_case.__init__(self, m)
self.xray_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(17.0216, 8.4362, 10.2248, 90, 102.79, 90),
space_group_symbol='hall: -C 2yc'),
scatterers=flex.xray_scatterer((
xray.scatterer( #0
label='S1',
site=(0.525736, 0.737492, 0.619814),
u=(0.000084, 0.000243, 0.000191, 0.000021, 0.000026,
-0.000035)),
xray.scatterer( #1
label='C1',
site=(0.500000, 0.868009, 0.750000),
u=(0.000061, 0.000181, 0.000164, 0.000000, 0.000025,
0.000000)),
xray.scatterer( #2
label='C2',
site=(0.533017, 0.552825, 0.710913),
u=(0.000161, 0.000241, 0.000348, 0.000041, 0.000039,
-0.000020)),
xray.scatterer( #3
label='H2A',
site=(0.525986, 0.462184, 0.647894),
u=0.041420),
xray.scatterer( #4
label='H2B',
site=(0.586473, 0.543642, 0.772877),
u=0.038360),
xray.scatterer( #5
label='C3',
site=(0.425914, 0.971290, 0.682589),
u=(0.000058, 0.000199, 0.000164, -0.000003, 0.000017,
-0.000007)),
xray.scatterer( #6
label='H3',
site=(0.441258, 1.029902, 0.606966),
u=0.023950),
xray.scatterer( #7
label='C4',
site=(0.349971, 0.874741, 0.622481),
u=(0.000064, 0.000236, 0.000219, -0.000015, 0.000011,
-0.000014)),
xray.scatterer( #8
label='H4B',
site=(0.362228, 0.799281, 0.555566),
u=0.026970),
xray.scatterer( #9
label='H4A',
site=(0.333906, 0.812566, 0.694426),
u=0.025070),
xray.scatterer( #10
label='C5',
site=(0.279832, 0.981636, 0.555089),
u=(0.000064, 0.000307, 0.000222, -0.000007, 0.000003,
-0.000021)),
xray.scatterer( #11
label='H5B',
site=(0.294150, 1.037327, 0.478372),
u=0.026970),
xray.scatterer( #12
label='H5A',
site=(0.231706, 0.915594, 0.519984),
u=0.034720),
xray.scatterer( #13
label='C6',
site=(0.259978, 1.103478, 0.653453),
u=(0.000061, 0.000335, 0.000246, 0.000016, 0.000021,
-0.000001)),
xray.scatterer( #14
label='H6B',
site=(0.216403, 1.174193, 0.606307),
u=0.037560),
xray.scatterer( #15
label='H6A',
site=(0.240791, 1.048477, 0.726038),
u=0.024860),
xray.scatterer( #16
label='C7',
site=(0.334517, 1.201490, 0.713404),
u=(0.000071, 0.000265, 0.000251, 0.000019, 0.000019,
-0.000029)),
xray.scatterer( #17
label='H7B',
site=(0.349843, 1.265431, 0.641770),
u=0.031500),
xray.scatterer( #18
label='H7A',
site=(0.321733, 1.275376, 0.780996),
u=0.030620),
xray.scatterer( #19
label='C8',
site=(0.405687, 1.096392, 0.779637),
u=(0.000064, 0.000247, 0.000187, 0.000009, 0.000015,
-0.000033)),
xray.scatterer( #20
label='H8A',
site=(0.392638, 1.042204, 0.858057),
u=0.026000),
xray.scatterer( #21
label='H8B',
site=(0.453574, 1.163891, 0.812432),
u=0.027360))))
self.t_celsius = -153
self.shall_refine_thermal_displacements = True
self.constraints = [
_.secondary_xh2_sites(pivot=2, constrained_site_indices=(3, 4)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=2,
u_iso_scatterer_idx=3,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=2,
u_iso_scatterer_idx=4,
multiplier=1.5),
_.tertiary_xh_site(pivot=5, constrained_site_indices=(6, )),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=5,
u_iso_scatterer_idx=6,
multiplier=1.5),
_.secondary_xh2_sites(pivot=7, constrained_site_indices=(8, 9)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=7,
u_iso_scatterer_idx=8,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=7,
u_iso_scatterer_idx=9,
multiplier=1.5),
_.secondary_xh2_sites(pivot=10, constrained_site_indices=(11, 12)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=10,
u_iso_scatterer_idx=11,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=10,
u_iso_scatterer_idx=12,
multiplier=1.5),
_.secondary_xh2_sites(pivot=13, constrained_site_indices=(14, 15)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=13,
u_iso_scatterer_idx=14,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=13,
u_iso_scatterer_idx=15,
multiplier=1.5),
_.secondary_xh2_sites(pivot=16, constrained_site_indices=(17, 18)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=16,
u_iso_scatterer_idx=17,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=16,
u_iso_scatterer_idx=18,
multiplier=1.5),
_.secondary_xh2_sites(pivot=19, constrained_site_indices=(20, 21)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=19,
u_iso_scatterer_idx=20,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=19,
u_iso_scatterer_idx=21,
multiplier=1.5),
]
self.expected_reparametrisation_for_hydrogen_named = {
"H2A": (core.secondary_xh2_sites, 'C2'),
"H2B": (core.secondary_xh2_sites, 'C2'),
"H3": (core.tertiary_xh_site, 'C3'),
"H4A": (core.secondary_xh2_sites, 'C4'),
"H4B": (core.secondary_xh2_sites, 'C4'),
"H5A": (core.secondary_xh2_sites, 'C5'),
"H5B": (core.secondary_xh2_sites, 'C5'),
"H6A": (core.secondary_xh2_sites, 'C6'),
"H6B": (core.secondary_xh2_sites, 'C6'),
"H7A": (core.secondary_xh2_sites, 'C7'),
"H7B": (core.secondary_xh2_sites, 'C7'),
"H8A": (core.secondary_xh2_sites, 'C8'),
"H8B": (core.secondary_xh2_sites, 'C8'),
}
self.site_refinement_tolerance = 0.01
self.u_star_refinement_tolerance = 5e-7
def __init__(self, m):
test_case.__init__(self, m)
self.xray_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(17.0216, 8.4362, 10.2248, 90, 102.79, 90),
space_group_symbol='hall: -C 2yc'),
scatterers=flex.xray_scatterer((
xray.scatterer( #0
label='S1',
site=(0.525736, 0.737492, 0.619814),
u=(0.000084, 0.000243, 0.000191,
0.000021, 0.000026, -0.000035)),
xray.scatterer( #1
label='C1',
site=(0.500000, 0.868009, 0.750000),
u=(0.000061, 0.000181, 0.000164,
0.000000, 0.000025, 0.000000)),
xray.scatterer( #2
label='C2',
site=(0.533017, 0.552825, 0.710913),
u=(0.000161, 0.000241, 0.000348,
0.000041, 0.000039, -0.000020)),
xray.scatterer( #3
label='H2A',
site=(0.525986, 0.462184, 0.647894),
u=0.041420),
xray.scatterer( #4
label='H2B',
site=(0.586473, 0.543642, 0.772877),
u=0.038360),
xray.scatterer( #5
label='C3',
site=(0.425914, 0.971290, 0.682589),
u=(0.000058, 0.000199, 0.000164,
-0.000003, 0.000017, -0.000007)),
xray.scatterer( #6
label='H3',
site=(0.441258, 1.029902, 0.606966),
u=0.023950),
xray.scatterer( #7
label='C4',
site=(0.349971, 0.874741, 0.622481),
u=(0.000064, 0.000236, 0.000219,
-0.000015, 0.000011, -0.000014)),
xray.scatterer( #8
label='H4B',
site=(0.362228, 0.799281, 0.555566),
u=0.026970),
xray.scatterer( #9
label='H4A',
site=(0.333906, 0.812566, 0.694426),
u=0.025070),
xray.scatterer( #10
label='C5',
site=(0.279832, 0.981636, 0.555089),
u=(0.000064, 0.000307, 0.000222,
-0.000007, 0.000003, -0.000021)),
xray.scatterer( #11
label='H5B',
site=(0.294150, 1.037327, 0.478372),
u=0.026970),
xray.scatterer( #12
label='H5A',
site=(0.231706, 0.915594, 0.519984),
u=0.034720),
xray.scatterer( #13
label='C6',
site=(0.259978, 1.103478, 0.653453),
u=(0.000061, 0.000335, 0.000246,
0.000016, 0.000021, -0.000001)),
xray.scatterer( #14
label='H6B',
site=(0.216403, 1.174193, 0.606307),
u=0.037560),
xray.scatterer( #15
label='H6A',
site=(0.240791, 1.048477, 0.726038),
u=0.024860),
xray.scatterer( #16
label='C7',
site=(0.334517, 1.201490, 0.713404),
u=(0.000071, 0.000265, 0.000251,
0.000019, 0.000019, -0.000029)),
xray.scatterer( #17
label='H7B',
site=(0.349843, 1.265431, 0.641770),
u=0.031500),
xray.scatterer( #18
label='H7A',
site=(0.321733, 1.275376, 0.780996),
u=0.030620),
xray.scatterer( #19
label='C8',
site=(0.405687, 1.096392, 0.779637),
u=(0.000064, 0.000247, 0.000187,
0.000009, 0.000015, -0.000033)),
xray.scatterer( #20
label='H8A',
site=(0.392638, 1.042204, 0.858057),
u=0.026000),
xray.scatterer( #21
label='H8B',
site=(0.453574, 1.163891, 0.812432),
u=0.027360)
)))
self.t_celsius = -153
self.shall_refine_thermal_displacements = True
self.constraints = [
_.secondary_xh2_sites(
pivot=2,
constrained_site_indices=(3,4)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=2,
u_iso_scatterer_idx=3,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=2,
u_iso_scatterer_idx=4,
multiplier=1.5),
_.tertiary_xh_site(
pivot=5,
constrained_site_indices=(6,)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=5,
u_iso_scatterer_idx=6,
multiplier=1.5),
_.secondary_xh2_sites(
pivot=7,
constrained_site_indices=(8, 9)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=7,
u_iso_scatterer_idx=8,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=7,
u_iso_scatterer_idx=9,
multiplier=1.5),
_.secondary_xh2_sites(
pivot=10,
constrained_site_indices=(11, 12)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=10,
u_iso_scatterer_idx=11,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=10,
u_iso_scatterer_idx=12,
multiplier=1.5),
_.secondary_xh2_sites(
pivot=13,
constrained_site_indices=(14, 15)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=13,
u_iso_scatterer_idx=14,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=13,
u_iso_scatterer_idx=15,
multiplier=1.5),
_.secondary_xh2_sites(
pivot=16,
constrained_site_indices=(17, 18)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=16,
u_iso_scatterer_idx=17,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=16,
u_iso_scatterer_idx=18,
multiplier=1.5),
_.secondary_xh2_sites(
pivot=19,
constrained_site_indices=(20, 21)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=19,
u_iso_scatterer_idx=20,
multiplier=1.5),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=19,
u_iso_scatterer_idx=21,
multiplier=1.5),
]
self.expected_reparametrisation_for_hydrogen_named = {
"H2A": (core.secondary_xh2_sites, 'C2'),
"H2B": (core.secondary_xh2_sites, 'C2'),
"H3" : (core.tertiary_xh_site , 'C3'),
"H4A": (core.secondary_xh2_sites, 'C4'),
"H4B": (core.secondary_xh2_sites, 'C4'),
"H5A": (core.secondary_xh2_sites, 'C5'),
"H5B": (core.secondary_xh2_sites, 'C5'),
"H6A": (core.secondary_xh2_sites, 'C6'),
"H6B": (core.secondary_xh2_sites, 'C6'),
"H7A": (core.secondary_xh2_sites, 'C7'),
"H7B": (core.secondary_xh2_sites, 'C7'),
"H8A": (core.secondary_xh2_sites, 'C8'),
"H8B": (core.secondary_xh2_sites, 'C8'),
}
self.site_refinement_tolerance = 0.01
self.u_star_refinement_tolerance = 5e-7
def __init__(self, m):
test_case.__init__(self, m)
self.xray_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(3.753, 14.54, 15.868, 90, 92.58, 90),
space_group_symbol='hall: -P 2ybc (x-z,y,z)'),
scatterers=flex.xray_scatterer((
xray.scatterer( #0
label='O1',
site=(0.299733, 0.262703, 0.397094),
u=(0.003622, 0.000123, 0.000108, 0.000154, -0.000304,
-0.000017)),
xray.scatterer( #1
label='O2',
site=(0.606432, 0.145132, 0.437285),
u=(0.004117, 0.000149, 0.000118, 0.000405, -0.000117,
-0.000042)),
xray.scatterer( #2
label='N1',
site=(0.481175, 0.221358, 0.451529),
u=(0.001750, 0.000091, 0.000090, 0.000016, -0.000027,
-0.000000)),
xray.scatterer( #3
label='N2',
site=(0.669716, 0.393801, 0.763893),
u=(0.002874, 0.000122, 0.000071, 0.000168, -0.000071,
-0.000000)),
xray.scatterer( #4
label='H1N',
site=(0.777763, 0.365311, 0.806784),
u=0.042273),
xray.scatterer( #5
label='H2N',
site=(0.589373, 0.450143, 0.770096),
u=0.042273),
xray.scatterer( #6
label='C1',
site=(0.542801, 0.263225, 0.532794),
u=(0.001423, 0.000084, 0.000076, -0.000009, 0.000000,
-0.000003)),
xray.scatterer( #7
label='C2',
site=(0.718203, 0.216166, 0.600719),
u=(0.001241, 0.000081, 0.000088, -0.000011, 0.000023,
0.000009)),
xray.scatterer( #8
label='C3',
site=(0.754550, 0.260840, 0.677732),
u=(0.001553, 0.000097, 0.000079, 0.000044, -0.000014,
0.000019)),
xray.scatterer( #9
label='H3',
site=(0.868083, 0.229804, 0.724284),
u=0.031215),
xray.scatterer( #10
label='C4',
site=(0.627437, 0.351296, 0.688971),
u=(0.001601, 0.000093, 0.000075, 0.000015, 0.000027,
0.000004)),
xray.scatterer( #11
label='C5',
site=(0.454744, 0.396843, 0.619275),
u=(0.001302, 0.000082, 0.000083, -0.000002, -0.000011,
0.000007)),
xray.scatterer( #12
label='C6',
site=(0.414545, 0.352153, 0.542558),
u=(0.001310, 0.000086, 0.000080, 0.000014, -0.000038,
0.000012)),
xray.scatterer( #13
label='H6',
site=(0.298067, 0.382503, 0.496003),
u=0.028457),
xray.scatterer( #14
label='C7',
site=(0.870740, 0.125780, 0.594964),
u=(0.001485, 0.000100, 0.000087, 0.000015, 0.000006,
0.000009)),
xray.scatterer( #15
label='C8',
site=(1.017756, 0.053520, 0.594148),
u=(0.002161, 0.000095, 0.000112, 0.000070, 0.000030,
0.000015)),
xray.scatterer( #16
label='H8',
site=(1.135411, -0.004309, 0.593494),
u=0.039284),
xray.scatterer( #17
label='C9',
site=(0.317957, 0.487839, 0.631013),
u=(0.001562, 0.000101, 0.000080, 0.000008, -0.000022,
0.000009)),
xray.scatterer( #18
label='C10',
site=(0.204108, 0.561746, 0.646136),
u=(0.001931, 0.000100, 0.000123, 0.000052, -0.000025,
-0.000002)),
xray.scatterer( #19
label='H10',
site=(0.112835, 0.620998, 0.658260),
u=0.039775))))
self.t_celsius = -153
self.shall_refine_thermal_displacements = True
k = 1.5 # that is the multiplier used to refine the structure with ShelXL
self.constraints = [
_.terminal_planar_xh2_sites(pivot=3,
constrained_site_indices=(4, 5)),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=3,
u_iso_scatterer_idx=4,
multiplier=k),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=3,
u_iso_scatterer_idx=5,
multiplier=k),
_.terminal_linear_ch_site(pivot=15,
constrained_site_indices=(16, )),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=15,
u_iso_scatterer_idx=16,
multiplier=k),
_.terminal_linear_ch_site(pivot=18,
constrained_site_indices=(19, )),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=18,
u_iso_scatterer_idx=19,
multiplier=k),
_.secondary_planar_xh_site(pivot=12,
constrained_site_indices=(13, )),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=12,
u_iso_scatterer_idx=13,
multiplier=k),
_.secondary_planar_xh_site(pivot=8,
constrained_site_indices=(9, )),
_.u_iso_proportional_to_pivot_u_eq(u_eq_scatterer_idx=8,
u_iso_scatterer_idx=9,
multiplier=k),
]
self.expected_reparametrisation_for_hydrogen_named = {
'H1N': (core.terminal_planar_xh2_sites, 'N2'),
'H2N': (core.terminal_planar_xh2_sites, 'N2'),
'H10': (core.terminal_linear_ch_site, 'C10'),
'H6': (core.secondary_planar_xh_site, 'C6'),
'H3': (core.secondary_planar_xh_site, 'C3'),
'H8': (core.terminal_linear_ch_site, 'C8'),
}
self.site_refinement_tolerance = 1e-2
self.u_star_refinement_tolerance = 1e-5
def __init__(self, m):
test_case.__init__(self, m)
self.xray_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(3.753, 14.54, 15.868, 90, 92.58, 90),
space_group_symbol='hall: -P 2ybc (x-z,y,z)'),
scatterers=flex.xray_scatterer((
xray.scatterer( #0
label='O1',
site=(0.299733, 0.262703, 0.397094),
u=(0.003622, 0.000123, 0.000108,
0.000154, -0.000304, -0.000017)),
xray.scatterer( #1
label='O2',
site=(0.606432, 0.145132, 0.437285),
u=(0.004117, 0.000149, 0.000118,
0.000405, -0.000117, -0.000042)),
xray.scatterer( #2
label='N1',
site=(0.481175, 0.221358, 0.451529),
u=(0.001750, 0.000091, 0.000090,
0.000016, -0.000027, -0.000000)),
xray.scatterer( #3
label='N2',
site=(0.669716, 0.393801, 0.763893),
u=(0.002874, 0.000122, 0.000071,
0.000168, -0.000071, -0.000000)),
xray.scatterer( #4
label='H1N',
site=(0.777763, 0.365311, 0.806784),
u=0.042273),
xray.scatterer( #5
label='H2N',
site=(0.589373, 0.450143, 0.770096),
u=0.042273),
xray.scatterer( #6
label='C1',
site=(0.542801, 0.263225, 0.532794),
u=(0.001423, 0.000084, 0.000076,
-0.000009, 0.000000, -0.000003)),
xray.scatterer( #7
label='C2',
site=(0.718203, 0.216166, 0.600719),
u=(0.001241, 0.000081, 0.000088,
-0.000011, 0.000023, 0.000009)),
xray.scatterer( #8
label='C3',
site=(0.754550, 0.260840, 0.677732),
u=(0.001553, 0.000097, 0.000079,
0.000044, -0.000014, 0.000019)),
xray.scatterer( #9
label='H3',
site=(0.868083, 0.229804, 0.724284),
u=0.031215),
xray.scatterer( #10
label='C4',
site=(0.627437, 0.351296, 0.688971),
u=(0.001601, 0.000093, 0.000075,
0.000015, 0.000027, 0.000004)),
xray.scatterer( #11
label='C5',
site=(0.454744, 0.396843, 0.619275),
u=(0.001302, 0.000082, 0.000083,
-0.000002, -0.000011, 0.000007)),
xray.scatterer( #12
label='C6',
site=(0.414545, 0.352153, 0.542558),
u=(0.001310, 0.000086, 0.000080,
0.000014, -0.000038, 0.000012)),
xray.scatterer( #13
label='H6',
site=(0.298067, 0.382503, 0.496003),
u=0.028457),
xray.scatterer( #14
label='C7',
site=(0.870740, 0.125780, 0.594964),
u=(0.001485, 0.000100, 0.000087,
0.000015, 0.000006, 0.000009)),
xray.scatterer( #15
label='C8',
site=(1.017756, 0.053520, 0.594148),
u=(0.002161, 0.000095, 0.000112,
0.000070, 0.000030, 0.000015)),
xray.scatterer( #16
label='H8',
site=(1.135411, -0.004309, 0.593494),
u=0.039284),
xray.scatterer( #17
label='C9',
site=(0.317957, 0.487839, 0.631013),
u=(0.001562, 0.000101, 0.000080,
0.000008, -0.000022, 0.000009)),
xray.scatterer( #18
label='C10',
site=(0.204108, 0.561746, 0.646136),
u=(0.001931, 0.000100, 0.000123,
0.000052, -0.000025, -0.000002)),
xray.scatterer( #19
label='H10',
site=(0.112835, 0.620998, 0.658260),
u=0.039775)
)))
self.t_celsius = -153
self.shall_refine_thermal_displacements = True
k=1.5 # that is the multiplier used to refine the structure with ShelXL
self.constraints = [
_.terminal_planar_xh2_sites(
pivot=3,
constrained_site_indices=(4, 5)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=3,
u_iso_scatterer_idx=4,
multiplier=k),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=3,
u_iso_scatterer_idx=5,
multiplier=k),
_.terminal_linear_ch_site(
pivot=15,
constrained_site_indices=(16,)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=15,
u_iso_scatterer_idx=16,
multiplier=k),
_.terminal_linear_ch_site(
pivot=18,
constrained_site_indices=(19,)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=18,
u_iso_scatterer_idx=19,
multiplier=k),
_.secondary_planar_xh_site(
pivot=12,
constrained_site_indices=(13,)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=12,
u_iso_scatterer_idx=13,
multiplier=k),
_.secondary_planar_xh_site(
pivot=8,
constrained_site_indices=(9,)),
_.u_iso_proportional_to_pivot_u_eq(
u_eq_scatterer_idx=8,
u_iso_scatterer_idx=9,
multiplier=k),
]
self.expected_reparametrisation_for_hydrogen_named = {
'H1N': (core.terminal_planar_xh2_sites, 'N2'),
'H2N': (core.terminal_planar_xh2_sites, 'N2'),
'H10': (core.terminal_linear_ch_site, 'C10'),
'H6' : (core.secondary_planar_xh_site, 'C6'),
'H3' : (core.secondary_planar_xh_site, 'C3'),
'H8': (core.terminal_linear_ch_site, 'C8'),
}
self.site_refinement_tolerance = 1e-2
self.u_star_refinement_tolerance = 1e-5
