Rename b_iso to adp_iso and expand adp_type to four values

docs/architecture/architecture.md

@@ -334,8 +334,8 @@ data live in separate collections on `Structure`. Every atom always has
 an entry in both collections; when `adp_type` is isotropic, the aniso
 parameters hold `0.0` and are ignored by calculators.
 
-**Type-neutral names.** `atom_site.adp_iso` replaces the former
-`atom_site.b_iso`. Its physical meaning (B or U) is determined by
+**Type-neutral names.** `atom_site.adp_iso` is the type-neutral
+isotropic ADP parameter. Its physical meaning (B or U) is determined by
 `atom_site.adp_type`. Similarly, `atom_site_aniso.adp_11`…`adp_23` are
 type-neutral tensor components.
 
@@ -868,7 +868,7 @@ project.structures['lbco'].atom_sites.create(
     fract_y=0,
     fract_z=0,
     wyckoff_letter='a',
-    b_iso=0.5,
+    adp_iso=0.5,
     occupancy=0.5,
 )
 

docs/docs/tutorials/ed-1.py

@@ -80,11 +80,11 @@
 # define aliases and then use them to create a constraint.
 project.analysis.aliases.create(
     label='biso_La',
-    param=project.structures['lbco'].atom_sites['La'].b_iso,
+    param=project.structures['lbco'].atom_sites['La'].adp_iso,
 )
 project.analysis.aliases.create(
     label='biso_Ba',
-    param=project.structures['lbco'].atom_sites['Ba'].b_iso,
+    param=project.structures['lbco'].atom_sites['Ba'].adp_iso,
 )
 project.analysis.constraints.create(expression='biso_Ba = biso_La')
 

docs/docs/tutorials/ed-10.py

@@ -37,7 +37,7 @@
     fract_y=0.0,
     fract_z=0.0,
     wyckoff_letter='a',
-    b_iso=0.5,
+    adp_iso=0.5,
 )
 
 # %% [markdown]
@@ -70,7 +70,7 @@
 
 # %%
 project.structures['ni'].cell.length_a.free = True
-project.structures['ni'].atom_sites['Ni'].b_iso.free = True
+project.structures['ni'].atom_sites['Ni'].adp_iso.free = True
 
 # %%
 project.experiments['pdf'].linked_phases['ni'].scale.free = True

docs/docs/tutorials/ed-11.py

@@ -47,7 +47,7 @@
     fract_y=0,
     fract_z=0,
     wyckoff_letter='a',
-    b_iso=0.5,
+    adp_iso=0.5,
 )
 
 # %% [markdown]
@@ -81,7 +81,7 @@
 
 # %%
 project.structures['si'].cell.length_a.free = True
-project.structures['si'].atom_sites['Si'].b_iso.free = True
+project.structures['si'].atom_sites['Si'].adp_iso.free = True
 experiment.linked_phases['si'].scale.free = True
 
 # %%

docs/docs/tutorials/ed-12.py

@@ -50,7 +50,7 @@
     fract_y=0,
     fract_z=0,
     wyckoff_letter='a',
-    b_iso=1.0,
+    adp_iso=1.0,
 )
 project.structures['nacl'].atom_sites.create(
     label='Cl',
@@ -59,7 +59,7 @@
     fract_y=0.5,
     fract_z=0.5,
     wyckoff_letter='b',
-    b_iso=1.0,
+    adp_iso=1.0,
 )
 
 # %% [markdown]
@@ -103,8 +103,8 @@
 
 # %%
 project.structures['nacl'].cell.length_a.free = True
-project.structures['nacl'].atom_sites['Na'].b_iso.free = True
-project.structures['nacl'].atom_sites['Cl'].b_iso.free = True
+project.structures['nacl'].atom_sites['Na'].adp_iso.free = True
+project.structures['nacl'].atom_sites['Cl'].adp_iso.free = True
 
 # %%
 project.experiments['xray_pdf'].linked_phases['nacl'].scale.free = True

docs/docs/tutorials/ed-13.py

@@ -488,7 +488,7 @@
     fract_y=0,
     fract_z=0,
     wyckoff_letter='a',
-    b_iso=0.89,
+    adp_iso=0.89,
 )
 
 # %% [markdown]
@@ -1013,7 +1013,7 @@
     fract_y=0,
     fract_z=0,
     wyckoff_letter='a',
-    b_iso=0.95,
+    adp_iso=0.95,
     occupancy=0.5,
 )
 project_2.structures['lbco'].atom_sites.create(
@@ -1023,7 +1023,7 @@
     fract_y=0,
     fract_z=0,
     wyckoff_letter='a',
-    b_iso=0.95,
+    adp_iso=0.95,
     occupancy=0.5,
 )
 project_2.structures['lbco'].atom_sites.create(
@@ -1033,7 +1033,7 @@
     fract_y=0.5,
     fract_z=0.5,
     wyckoff_letter='b',
-    b_iso=0.80,
+    adp_iso=0.80,
 )
 project_2.structures['lbco'].atom_sites.create(
     label='O',
@@ -1042,7 +1042,7 @@
     fract_y=0.5,
     fract_z=0.5,
     wyckoff_letter='c',
-    b_iso=1.66,
+    adp_iso=1.66,
 )
 
 # %% [markdown]
@@ -1385,7 +1385,7 @@
     fract_y=0,
     fract_z=0,
     wyckoff_letter='a',
-    b_iso=0.89,
+    adp_iso=0.89,
 )
 
 # Assign Structure to Experiment

docs/docs/tutorials/ed-14.py

@@ -34,10 +34,10 @@
 structure = project.structures['tbti']
 
 # %%
-structure.atom_sites['Tb'].b_iso = 0.0
-structure.atom_sites['Ti'].b_iso = 0.0
-structure.atom_sites['O1'].b_iso = 0.0
-structure.atom_sites['O2'].b_iso = 0.0
+structure.atom_sites['Tb'].adp_iso = 0.0
+structure.atom_sites['Ti'].adp_iso = 0.0
+structure.atom_sites['O1'].adp_iso = 0.0
+structure.atom_sites['O2'].adp_iso = 0.0
 
 # %%
 structure.show_as_cif()

docs/docs/tutorials/ed-16.py

@@ -53,7 +53,7 @@
     fract_y=0,
     fract_z=0,
     wyckoff_letter='a',
-    b_iso=0.2,
+    adp_iso=0.2,
 )
 
 # %% [markdown]
@@ -209,7 +209,7 @@
 
 # %%
 structure.cell.length_a.free = True
-structure.atom_sites['Si'].b_iso.free = True
+structure.atom_sites['Si'].adp_iso.free = True
 
 # %% [markdown]
 # Bragg experiment parameters.

docs/docs/tutorials/ed-17.py

@@ -66,7 +66,7 @@
     fract_y=0,
     fract_z=0,
     wyckoff_letter='a',
-    b_iso=0.3,
+    adp_iso=0.3,
 )
 structure.atom_sites.create(
     label='Co2',
@@ -75,7 +75,7 @@
     fract_y=0.25,
     fract_z=0.985,
     wyckoff_letter='c',
-    b_iso=0.3,
+    adp_iso=0.3,
 )
 structure.atom_sites.create(
     label='Si',
@@ -84,7 +84,7 @@
     fract_y=0.25,
     fract_z=0.429,
     wyckoff_letter='c',
-    b_iso=0.34,
+    adp_iso=0.34,
 )
 structure.atom_sites.create(
     label='O1',
@@ -93,7 +93,7 @@
     fract_y=0.25,
     fract_z=0.771,
     wyckoff_letter='c',
-    b_iso=0.63,
+    adp_iso=0.63,
 )
 structure.atom_sites.create(
     label='O2',
@@ -102,7 +102,7 @@
     fract_y=0.25,
     fract_z=0.217,
     wyckoff_letter='c',
-    b_iso=0.59,
+    adp_iso=0.59,
 )
 structure.atom_sites.create(
     label='O3',
@@ -111,7 +111,7 @@
     fract_y=0.032,
     fract_z=0.28,
     wyckoff_letter='d',
-    b_iso=0.83,
+    adp_iso=0.83,
 )
 
 # %% [markdown]
@@ -218,12 +218,12 @@
 structure.atom_sites['O3'].fract_y.free = True
 structure.atom_sites['O3'].fract_z.free = True
 
-structure.atom_sites['Co1'].b_iso.free = True
-structure.atom_sites['Co2'].b_iso.free = True
-structure.atom_sites['Si'].b_iso.free = True
-structure.atom_sites['O1'].b_iso.free = True
-structure.atom_sites['O2'].b_iso.free = True
-structure.atom_sites['O3'].b_iso.free = True
+structure.atom_sites['Co1'].adp_iso.free = True
+structure.atom_sites['Co2'].adp_iso.free = True
+structure.atom_sites['Si'].adp_iso.free = True
+structure.atom_sites['O1'].adp_iso.free = True
+structure.atom_sites['O2'].adp_iso.free = True
+structure.atom_sites['O3'].adp_iso.free = True
 
 # %%
 expt.linked_phases['cosio'].scale.free = True
@@ -246,11 +246,11 @@
 # %%
 project.analysis.aliases.create(
     label='biso_Co1',
-    param=structure.atom_sites['Co1'].b_iso,
+    param=structure.atom_sites['Co1'].adp_iso,
 )
 project.analysis.aliases.create(
     label='biso_Co2',
-    param=structure.atom_sites['Co2'].b_iso,
+    param=structure.atom_sites['Co2'].adp_iso,
 )
 
 # %% [markdown]
@@ -353,11 +353,11 @@ def extract_diffrn(file_path):
 # Plot isotropic displacement parameters vs. temperature.
 
 # %%
-project.plotter.plot_param_series(structure.atom_sites['Co1'].b_iso, versus=temperature)
-project.plotter.plot_param_series(structure.atom_sites['Si'].b_iso, versus=temperature)
-project.plotter.plot_param_series(structure.atom_sites['O1'].b_iso, versus=temperature)
-project.plotter.plot_param_series(structure.atom_sites['O2'].b_iso, versus=temperature)
-project.plotter.plot_param_series(structure.atom_sites['O3'].b_iso, versus=temperature)
+project.plotter.plot_param_series(structure.atom_sites['Co1'].adp_iso, versus=temperature)
+project.plotter.plot_param_series(structure.atom_sites['Si'].adp_iso, versus=temperature)
+project.plotter.plot_param_series(structure.atom_sites['O1'].adp_iso, versus=temperature)
+project.plotter.plot_param_series(structure.atom_sites['O2'].adp_iso, versus=temperature)
+project.plotter.plot_param_series(structure.atom_sites['O3'].adp_iso, versus=temperature)
 
 # %% [markdown]
 # Plot selected fractional coordinates vs. temperature.

docs/docs/tutorials/ed-2.py

@@ -56,7 +56,7 @@
     fract_y=0,
     fract_z=0,
     wyckoff_letter='a',
-    b_iso=0.5,
+    adp_iso=0.5,
     occupancy=0.5,
 )
 structure.atom_sites.create(
@@ -66,7 +66,7 @@
     fract_y=0,
     fract_z=0,
     wyckoff_letter='a',
-    b_iso=0.5,
+    adp_iso=0.5,
     occupancy=0.5,
 )
 structure.atom_sites.create(
@@ -76,7 +76,7 @@
     fract_y=0.5,
     fract_z=0.5,
     wyckoff_letter='b',
-    b_iso=0.5,
+    adp_iso=0.5,
 )
 structure.atom_sites.create(
     label='O',
@@ -85,7 +85,7 @@
     fract_y=0.5,
     fract_z=0.5,
     wyckoff_letter='c',
-    b_iso=0.5,
+    adp_iso=0.5,
 )
 
 # %% [markdown]
@@ -136,10 +136,10 @@
 # %%
 structure.cell.length_a.free = True
 
-structure.atom_sites['La'].b_iso.free = True
-structure.atom_sites['Ba'].b_iso.free = True
-structure.atom_sites['Co'].b_iso.free = True
-structure.atom_sites['O'].b_iso.free = True
+structure.atom_sites['La'].adp_iso.free = True
+structure.atom_sites['Ba'].adp_iso.free = True
+structure.atom_sites['Co'].adp_iso.free = True
+structure.atom_sites['O'].adp_iso.free = True
 
 # %%
 experiment.instrument.calib_twotheta_offset.free = True