Update tutorials

Author: AndrewSazonov

docs/docs/tutorials/ed-1.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ab0fa7f5",
+   "id": "62acbe5c",
    "metadata": {
     "tags": [
      "hide-in-docs"
@@ -205,11 +205,11 @@
     "# define aliases and then use them to create a constraint.\n",
     "project.analysis.aliases.create(\n",
     "    label='biso_La',\n",
-    "    param=project.structures['lbco'].atom_sites['La'].b_iso,\n",
+    "    param=project.structures['lbco'].atom_sites['La'].adp_iso,\n",
     ")\n",
     "project.analysis.aliases.create(\n",
     "    label='biso_Ba',\n",
-    "    param=project.structures['lbco'].atom_sites['Ba'].b_iso,\n",
+    "    param=project.structures['lbco'].atom_sites['Ba'].adp_iso,\n",
     ")\n",
     "project.analysis.constraints.create(expression='biso_Ba = biso_La')"
    ]

docs/docs/tutorials/ed-10.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "dc88a9ac",
+   "id": "7340ff71",
    "metadata": {
     "tags": [
      "hide-in-docs"
@@ -105,7 +105,7 @@
     "    fract_y=0.0,\n",
     "    fract_z=0.0,\n",
     "    wyckoff_letter='a',\n",
-    "    b_iso=0.5,\n",
+    "    adp_iso=0.5,\n",
     ")"
    ]
   },
@@ -176,7 +176,7 @@
    "outputs": [],
    "source": [
     "project.structures['ni'].cell.length_a.free = True\n",
-    "project.structures['ni'].atom_sites['Ni'].b_iso.free = True"
+    "project.structures['ni'].atom_sites['Ni'].adp_iso.free = True"
    ]
   },
   {
@@ -207,7 +207,8 @@
    "outputs": [],
    "source": [
     "project.analysis.fit()\n",
-    "project.analysis.display.fit_results()"
+    "project.analysis.display.fit_results()\n",
+    "project.plotter.plot_param_correlations()"
    ]
   },
   {

docs/docs/tutorials/ed-10.py

@@ -83,6 +83,7 @@
 # %%
 project.analysis.fit()
 project.analysis.display.fit_results()
+project.plotter.plot_param_correlations()
 
 # %% [markdown]
 # ## Plot Measured vs Calculated

docs/docs/tutorials/ed-11.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9736040b",
+   "id": "a4f76dce",
    "metadata": {
     "tags": [
      "hide-in-docs"
@@ -134,7 +134,7 @@
     "    fract_y=0,\n",
     "    fract_z=0,\n",
     "    wyckoff_letter='a',\n",
-    "    b_iso=0.5,\n",
+    "    adp_iso=0.5,\n",
     ")"
    ]
   },
@@ -206,7 +206,7 @@
    "outputs": [],
    "source": [
     "project.structures['si'].cell.length_a.free = True\n",
-    "project.structures['si'].atom_sites['Si'].b_iso.free = True\n",
+    "project.structures['si'].atom_sites['Si'].adp_iso.free = True\n",
     "experiment.linked_phases['si'].scale.free = True"
    ]
   },
@@ -239,7 +239,8 @@
    "outputs": [],
    "source": [
     "project.analysis.fit()\n",
-    "project.analysis.display.fit_results()"
+    "project.analysis.display.fit_results()\n",
+    "project.plotter.plot_param_correlations()"
    ]
   },
   {

docs/docs/tutorials/ed-11.py

@@ -96,6 +96,7 @@
 # %%
 project.analysis.fit()
 project.analysis.display.fit_results()
+project.plotter.plot_param_correlations()
 
 # %% [markdown]
 # ## Plot Measured vs Calculated

docs/docs/tutorials/ed-12.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "44960a4c",
+   "id": "dfcbd6ef",
    "metadata": {
     "tags": [
      "hide-in-docs"
@@ -137,7 +137,7 @@
     "    fract_y=0,\n",
     "    fract_z=0,\n",
     "    wyckoff_letter='a',\n",
-    "    b_iso=1.0,\n",
+    "    adp_iso=1.0,\n",
     ")\n",
     "project.structures['nacl'].atom_sites.create(\n",
     "    label='Cl',\n",
@@ -146,7 +146,7 @@
     "    fract_y=0.5,\n",
     "    fract_z=0.5,\n",
     "    wyckoff_letter='b',\n",
-    "    b_iso=1.0,\n",
+    "    adp_iso=1.0,\n",
     ")"
    ]
   },
@@ -256,8 +256,8 @@
    "outputs": [],
    "source": [
     "project.structures['nacl'].cell.length_a.free = True\n",
-    "project.structures['nacl'].atom_sites['Na'].b_iso.free = True\n",
-    "project.structures['nacl'].atom_sites['Cl'].b_iso.free = True"
+    "project.structures['nacl'].atom_sites['Na'].adp_iso.free = True\n",
+    "project.structures['nacl'].atom_sites['Cl'].adp_iso.free = True"
    ]
   },
   {
@@ -288,7 +288,8 @@
    "outputs": [],
    "source": [
     "project.analysis.fit()\n",
-    "project.analysis.display.fit_results()"
+    "project.analysis.display.fit_results()\n",
+    "project.plotter.plot_param_correlations()"
    ]
   },
   {

docs/docs/tutorials/ed-12.py

@@ -117,6 +117,7 @@
 # %%
 project.analysis.fit()
 project.analysis.display.fit_results()
+project.plotter.plot_param_correlations()
 
 # %% [markdown]
 # ## Plot Measured vs Calculated

docs/docs/tutorials/ed-13.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1ac207fe",
+   "id": "25279ff1",
    "metadata": {
     "tags": [
      "hide-in-docs"
@@ -497,8 +497,7 @@
     "\n",
     "The next set of parameters is needed to define the peak profile used\n",
     "in the fitting process. The peak profile describes the shape of the\n",
-    "diffraction peaks. They include parameters for the broadening and\n",
-    "asymmetry of the peaks.\n",
+    "diffraction peaks.\n",
     "\n",
     "There are several commonly used peak profile functions:\n",
     "- **Gaussian**: Describes peaks with a symmetric bell-shaped curve,\n",
@@ -547,14 +546,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "project_1.experiments['sim_si'].peak_profile_type = 'pseudo-voigt * ikeda-carpenter'\n",
+    "project_1.experiments['sim_si'].peak_profile_type = 'jorgensen'\n",
     "project_1.experiments['sim_si'].peak.broad_gauss_sigma_0 = 69498\n",
     "project_1.experiments['sim_si'].peak.broad_gauss_sigma_1 = -55578\n",
     "project_1.experiments['sim_si'].peak.broad_gauss_sigma_2 = 14560\n",
-    "project_1.experiments['sim_si'].peak.broad_mix_beta_0 = 0.0019\n",
-    "project_1.experiments['sim_si'].peak.broad_mix_beta_1 = 0.0137\n",
-    "project_1.experiments['sim_si'].peak.asym_alpha_0 = -0.0055\n",
-    "project_1.experiments['sim_si'].peak.asym_alpha_1 = 0.0147"
+    "project_1.experiments['sim_si'].peak.exp_decay_beta_0 = 0.0019\n",
+    "project_1.experiments['sim_si'].peak.exp_decay_beta_1 = 0.0137\n",
+    "project_1.experiments['sim_si'].peak.exp_rise_alpha_0 = -0.0055\n",
+    "project_1.experiments['sim_si'].peak.exp_rise_alpha_1 = 0.0147"
    ]
   },
   {
@@ -832,7 +831,7 @@
     "    fract_y=0,\n",
     "    fract_z=0,\n",
     "    wyckoff_letter='a',\n",
-    "    b_iso=0.89,\n",
+    "    adp_iso=0.89,\n",
     ")"
    ]
   },
@@ -955,10 +954,10 @@
     "project_1.experiments['sim_si'].peak.broad_gauss_sigma_0.free = True\n",
     "project_1.experiments['sim_si'].peak.broad_gauss_sigma_1.free = True\n",
     "project_1.experiments['sim_si'].peak.broad_gauss_sigma_2.free = True\n",
-    "project_1.experiments['sim_si'].peak.broad_mix_beta_0.free = True\n",
-    "project_1.experiments['sim_si'].peak.broad_mix_beta_1.free = True\n",
-    "project_1.experiments['sim_si'].peak.asym_alpha_0.free = True\n",
-    "project_1.experiments['sim_si'].peak.asym_alpha_1.free = True"
+    "project_1.experiments['sim_si'].peak.exp_decay_beta_0.free = True\n",
+    "project_1.experiments['sim_si'].peak.exp_decay_beta_1.free = True\n",
+    "project_1.experiments['sim_si'].peak.exp_rise_alpha_0.free = True\n",
+    "project_1.experiments['sim_si'].peak.exp_rise_alpha_1.free = True"
    ]
   },
   {
@@ -1443,14 +1442,14 @@
    "source": [
     "# # Create a reference to the peak profile parameters from the Si\n",
     "sim_si_peak = project_1.experiments['sim_si'].peak\n",
-    "project_2.experiments['sim_lbco'].peak_profile_type = 'pseudo-voigt * ikeda-carpenter'\n",
+    "project_2.experiments['sim_lbco'].peak_profile_type = 'jorgensen'\n",
     "project_2.experiments['sim_lbco'].peak.broad_gauss_sigma_0 = sim_si_peak.broad_gauss_sigma_0.value\n",
     "project_2.experiments['sim_lbco'].peak.broad_gauss_sigma_1 = sim_si_peak.broad_gauss_sigma_1.value\n",
     "project_2.experiments['sim_lbco'].peak.broad_gauss_sigma_2 = sim_si_peak.broad_gauss_sigma_2.value\n",
-    "project_2.experiments['sim_lbco'].peak.broad_mix_beta_0 = sim_si_peak.broad_mix_beta_0.value\n",
-    "project_2.experiments['sim_lbco'].peak.broad_mix_beta_1 = sim_si_peak.broad_mix_beta_1.value\n",
-    "project_2.experiments['sim_lbco'].peak.asym_alpha_0 = sim_si_peak.asym_alpha_0.value\n",
-    "project_2.experiments['sim_lbco'].peak.asym_alpha_1 = sim_si_peak.asym_alpha_1.value"
+    "project_2.experiments['sim_lbco'].peak.exp_decay_beta_0 = sim_si_peak.exp_decay_beta_0.value\n",
+    "project_2.experiments['sim_lbco'].peak.exp_decay_beta_1 = sim_si_peak.exp_decay_beta_1.value\n",
+    "project_2.experiments['sim_lbco'].peak.exp_rise_alpha_0 = sim_si_peak.exp_rise_alpha_0.value\n",
+    "project_2.experiments['sim_lbco'].peak.exp_rise_alpha_1 = sim_si_peak.exp_rise_alpha_1.value"
    ]
   },
   {
@@ -1775,7 +1774,7 @@
     "    fract_y=0,\n",
     "    fract_z=0,\n",
     "    wyckoff_letter='a',\n",
-    "    b_iso=0.95,\n",
+    "    adp_iso=0.95,\n",
     "    occupancy=0.5,\n",
     ")\n",
     "project_2.structures['lbco'].atom_sites.create(\n",
@@ -1785,7 +1784,7 @@
     "    fract_y=0,\n",
     "    fract_z=0,\n",
     "    wyckoff_letter='a',\n",
-    "    b_iso=0.95,\n",
+    "    adp_iso=0.95,\n",
     "    occupancy=0.5,\n",
     ")\n",
     "project_2.structures['lbco'].atom_sites.create(\n",
@@ -1795,7 +1794,7 @@
     "    fract_y=0.5,\n",
     "    fract_z=0.5,\n",
     "    wyckoff_letter='b',\n",
-    "    b_iso=0.80,\n",
+    "    adp_iso=0.80,\n",
     ")\n",
     "project_2.structures['lbco'].atom_sites.create(\n",
     "    label='O',\n",
@@ -1804,7 +1803,7 @@
     "    fract_y=0.5,\n",
     "    fract_z=0.5,\n",
     "    wyckoff_letter='c',\n",
-    "    b_iso=1.66,\n",
+    "    adp_iso=1.66,\n",
     ")"
    ]
   },
@@ -2224,10 +2223,10 @@
     "project_2.experiments['sim_lbco'].peak.broad_gauss_sigma_0.free = True\n",
     "project_2.experiments['sim_lbco'].peak.broad_gauss_sigma_1.free = True\n",
     "project_2.experiments['sim_lbco'].peak.broad_gauss_sigma_2.free = True\n",
-    "project_2.experiments['sim_lbco'].peak.broad_mix_beta_0.free = True\n",
-    "project_2.experiments['sim_lbco'].peak.broad_mix_beta_1.free = True\n",
-    "project_2.experiments['sim_lbco'].peak.asym_alpha_0.free = True\n",
-    "project_2.experiments['sim_lbco'].peak.asym_alpha_1.free = True\n",
+    "project_2.experiments['sim_lbco'].peak.exp_decay_beta_0.free = True\n",
+    "project_2.experiments['sim_lbco'].peak.exp_decay_beta_1.free = True\n",
+    "project_2.experiments['sim_lbco'].peak.exp_rise_alpha_0.free = True\n",
+    "project_2.experiments['sim_lbco'].peak.exp_rise_alpha_1.free = True\n",
     "\n",
     "project_2.analysis.fit()\n",
     "project_2.analysis.display.fit_results()\n",
@@ -2469,7 +2468,7 @@
     "    fract_y=0,\n",
     "    fract_z=0,\n",
     "    wyckoff_letter='a',\n",
-    "    b_iso=0.89,\n",
+    "    adp_iso=0.89,\n",
     ")\n",
     "\n",
     "# Assign Structure to Experiment\n",
@@ -2647,7 +2646,7 @@
  ],
  "metadata": {
   "jupytext": {
-   "cell_metadata_filter": "tags,title,-all",
+   "cell_metadata_filter": "title,tags,-all",
    "main_language": "python",
    "notebook_metadata_filter": "-all"
   }