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AndrewSazonovAndrewSazonov
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Refactors atom site addition for clarity and consistency
1 parent 08d0f60 commit 94d270c

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4 files changed

+158
-29
lines changed

4 files changed

+158
-29
lines changed

‎tutorials/cryst-struct_pd-neut-cwl_HS-HRPT.py‎

Lines changed: 46 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -44,11 +44,51 @@
4444
# #### Set Atom Sites
4545

4646
# %%
47-
model.atom_sites.add_from_args('Zn', 'Zn', 0, 0, 0.5, wyckoff_letter='b', b_iso=0.5)
48-
model.atom_sites.add_from_args('Cu', 'Cu', 0.5, 0, 0, wyckoff_letter='e', b_iso=0.5)
49-
model.atom_sites.add_from_args('O', 'O', 0.21, -0.21, 0.06, wyckoff_letter='h', b_iso=0.5)
50-
model.atom_sites.add_from_args('Cl', 'Cl', 0, 0, 0.197, wyckoff_letter='c', b_iso=0.5)
51-
model.atom_sites.add_from_args('H', '2H', 0.13, -0.13, 0.08, wyckoff_letter='h', b_iso=0.5)
47+
model.atom_sites.add_from_args(
48+
label='Zn',
49+
type_symbol='Zn',
50+
fract_x=0,
51+
fract_y=0,
52+
fract_z=0.5,
53+
wyckoff_letter='b',
54+
b_iso=0.5,
55+
)
56+
model.atom_sites.add_from_args(
57+
label='Cu',
58+
type_symbol='Cu',
59+
fract_x=0.5,
60+
fract_y=0,
61+
fract_z=0,
62+
wyckoff_letter='e',
63+
b_iso=0.5,
64+
)
65+
model.atom_sites.add_from_args(
66+
label='O',
67+
type_symbol='O',
68+
fract_x=0.21,
69+
fract_y=-0.21,
70+
fract_z=0.06,
71+
wyckoff_letter='h',
72+
b_iso=0.5,
73+
)
74+
model.atom_sites.add_from_args(
75+
label='Cl',
76+
type_symbol='Cl',
77+
fract_x=0,
78+
fract_y=0,
79+
fract_z=0.197,
80+
wyckoff_letter='c',
81+
b_iso=0.5,
82+
)
83+
model.atom_sites.add_from_args(
84+
label='H',
85+
type_symbol='2H',
86+
fract_x=0.13,
87+
fract_y=-0.13,
88+
fract_z=0.08,
89+
wyckoff_letter='h',
90+
b_iso=0.5,
91+
)
5292

5393
# %% [markdown]
5494
# #### Symmetry constraints
@@ -122,7 +162,7 @@
122162
# #### Set Linked Phases
123163

124164
# %%
125-
expt.linked_phases.add_from_args('hs', scale=0.5)
165+
expt.linked_phases.add_from_args(id='hs', scale=0.5)
126166

127167
# %% [markdown]
128168
# ## Define Project

‎tutorials/cryst-struct_pd-neut-tof_Si-SEPD.py‎

Lines changed: 9 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,14 @@
4242
# #### Set Atom Sites
4343

4444
# %%
45-
model.atom_sites.add_from_args('Si', 'Si', 0.125, 0.125, 0.125, b_iso=0.5)
45+
model.atom_sites.add_from_args(
46+
label='Si',
47+
type_symbol='Si',
48+
fract_x=0.125,
49+
fract_y=0.125,
50+
fract_z=0.125,
51+
b_iso=0.5,
52+
)
4653

4754
# %% [markdown]
4855
# ## Define Experiment
@@ -100,7 +107,7 @@
100107
# #### Set Linked Phases
101108

102109
# %%
103-
expt.linked_phases.add_from_args('si', scale=10.0)
110+
expt.linked_phases.add_from_args(id='si', scale=10.0)
104111

105112
# %% [markdown]
106113
# ## Define Project

‎tutorials/cryst-struct_pd-neut-tof_multidata_NCAF-WISH.py‎

Lines changed: 58 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -45,12 +45,60 @@
4545
# #### Set Atom Sites
4646

4747
# %%
48-
model.atom_sites.add_from_args('Ca', 'Ca', 0.4663, 0.0, 0.25, wyckoff_letter='b', b_iso=0.92)
49-
model.atom_sites.add_from_args('Al', 'Al', 0.2521, 0.2521, 0.2521, wyckoff_letter='a', b_iso=0.73)
50-
model.atom_sites.add_from_args('Na', 'Na', 0.0851, 0.0851, 0.0851, wyckoff_letter='a', b_iso=2.08)
51-
model.atom_sites.add_from_args('F1', 'F', 0.1377, 0.3054, 0.1195, wyckoff_letter='c', b_iso=0.90)
52-
model.atom_sites.add_from_args('F2', 'F', 0.3625, 0.3633, 0.1867, wyckoff_letter='c', b_iso=1.37)
53-
model.atom_sites.add_from_args('F3', 'F', 0.4612, 0.4612, 0.4612, wyckoff_letter='a', b_iso=0.88)
48+
model.atom_sites.add_from_args(
49+
label='Ca',
50+
type_symbol='Ca',
51+
fract_x=0.4663,
52+
fract_y=0.0,
53+
fract_z=0.25,
54+
wyckoff_letter='b',
55+
b_iso=0.92,
56+
)
57+
model.atom_sites.add_from_args(
58+
label='Al',
59+
type_symbol='Al',
60+
fract_x=0.2521,
61+
fract_y=0.2521,
62+
fract_z=0.2521,
63+
wyckoff_letter='a',
64+
b_iso=0.73,
65+
)
66+
model.atom_sites.add_from_args(
67+
label='Na',
68+
type_symbol='Na',
69+
fract_x=0.0851,
70+
fract_y=0.0851,
71+
fract_z=0.0851,
72+
wyckoff_letter='a',
73+
b_iso=2.08,
74+
)
75+
model.atom_sites.add_from_args(
76+
label='F1',
77+
type_symbol='F',
78+
fract_x=0.1377,
79+
fract_y=0.3054,
80+
fract_z=0.1195,
81+
wyckoff_letter='c',
82+
b_iso=0.90,
83+
)
84+
model.atom_sites.add_from_args(
85+
label='F2',
86+
type_symbol='F',
87+
fract_x=0.3625,
88+
fract_y=0.3633,
89+
fract_z=0.1867,
90+
wyckoff_letter='c',
91+
b_iso=1.37,
92+
)
93+
model.atom_sites.add_from_args(
94+
label='F3',
95+
type_symbol='F',
96+
fract_x=0.4612,
97+
fract_y=0.4612,
98+
fract_z=0.4612,
99+
wyckoff_letter='a',
100+
b_iso=0.88,
101+
)
54102

55103
# %% [markdown]
56104
# ## Define Experiment
@@ -160,7 +208,7 @@
160208
(91958, 268),
161209
(102712, 262),
162210
]:
163-
expt56.background.add_from_args(x, y)
211+
expt56.background.add_from_args(x=x, y=y)
164212

165213
# %%
166214
expt47.background_type = 'line-segment'
@@ -193,16 +241,16 @@
193241
(92770, 255),
194242
(101524, 260),
195243
]:
196-
expt47.background.add_from_args(x, y)
244+
expt47.background.add_from_args(x=x, y=y)
197245

198246
# %% [markdown]
199247
# #### Set Linked Phases
200248

201249
# %%
202-
expt56.linked_phases.add_from_args('ncaf', scale=1.0)
250+
expt56.linked_phases.add_from_args(id='ncaf', scale=1.0)
203251

204252
# %%
205-
expt47.linked_phases.add_from_args('ncaf', scale=2.0)
253+
expt47.linked_phases.add_from_args(id='ncaf', scale=2.0)
206254

207255
# %% [markdown]
208256
# #### Set Excluded Regions

‎tutorials/cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.py‎

Lines changed: 45 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -42,10 +42,44 @@
4242
# #### Set Atom Sites
4343

4444
# %%
45-
model_1.atom_sites.add_from_args('La', 'La', 0, 0, 0, wyckoff_letter='a', b_iso=0.2, occupancy=0.5)
46-
model_1.atom_sites.add_from_args('Ba', 'Ba', 0, 0, 0, wyckoff_letter='a', b_iso=0.2, occupancy=0.5)
47-
model_1.atom_sites.add_from_args('Co', 'Co', 0.5, 0.5, 0.5, wyckoff_letter='b', b_iso=0.2567)
48-
model_1.atom_sites.add_from_args('O', 'O', 0, 0.5, 0.5, wyckoff_letter='c', b_iso=1.4041)
45+
model_1.atom_sites.add_from_args(
46+
label='La',
47+
type_symbol='La',
48+
fract_x=0,
49+
fract_y=0,
50+
fract_z=0,
51+
wyckoff_letter='a',
52+
b_iso=0.2,
53+
occupancy=0.5,
54+
)
55+
model_1.atom_sites.add_from_args(
56+
label='Ba',
57+
type_symbol='Ba',
58+
fract_x=0,
59+
fract_y=0,
60+
fract_z=0,
61+
wyckoff_letter='a',
62+
b_iso=0.2,
63+
occupancy=0.5,
64+
)
65+
model_1.atom_sites.add_from_args(
66+
label='Co',
67+
type_symbol='Co',
68+
fract_x=0.5,
69+
fract_y=0.5,
70+
fract_z=0.5,
71+
wyckoff_letter='b',
72+
b_iso=0.2567,
73+
)
74+
model_1.atom_sites.add_from_args(
75+
label='O',
76+
type_symbol='O',
77+
fract_x=0,
78+
fract_y=0.5,
79+
fract_z=0.5,
80+
wyckoff_letter='c',
81+
b_iso=1.4041,
82+
)
4983

5084
# %% [markdown]
5185
# ### Create Sample Model 2: Si
@@ -71,11 +105,11 @@
71105

72106
# %%
73107
model_2.atom_sites.add_from_args(
74-
'Si',
75-
'Si',
76-
0.0,
77-
0.0,
78-
0.0,
108+
label='Si',
109+
type_symbol='Si',
110+
fract_x=0.0,
111+
fract_y=0.0,
112+
fract_z=0.0,
79113
wyckoff_letter='a',
80114
b_iso=0.0,
81115
)
@@ -157,8 +191,8 @@
157191
# #### Set Linked Phases
158192

159193
# %%
160-
experiment.linked_phases.add_from_args('lbco', scale=4.0)
161-
experiment.linked_phases.add_from_args('si', scale=0.2)
194+
experiment.linked_phases.add_from_args(id='lbco', scale=4.0)
195+
experiment.linked_phases.add_from_args(id='si', scale=0.2)
162196

163197
# %% [markdown]
164198
# ## Define Project

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