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7 changes: 6 additions & 1 deletion docs/dev/package-structure/full.md
Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,11 @@
│ │ │ ├── 📄 lmfit_leastsq.py
│ │ │ │ └── 🏷️ class LmfitLeastsqMinimizer
│ │ │ └── 📄 lsq_base.py
│ │ │ └── 🏷️ class LeastSquaresMinimizerBase
│ │ │ ├── 🏷️ class LeastSquaresMinimizerBase
│ │ │ ├── 🏷️ class ObjectiveParameterToleranceMinimizerBase
│ │ │ ├── 🏷️ class GradientToleranceMinimizerBase
│ │ │ ├── 🏷️ class PopulationToleranceMinimizerBase
│ │ │ └── 🏷️ class TrustRegionToleranceMinimizerBase
│ │ ├── 📁 sequential_fit
│ │ │ ├── 📄 __init__.py
│ │ │ ├── 📄 default.py
Expand Down Expand Up @@ -744,6 +748,7 @@
│ │ └── 🏷️ class FigureEmbedMode
│ ├── 📄 logging.py
│ │ ├── 🏷️ class IconifiedRichHandler
│ │ ├── 🏷️ class NotebookAwareConsole
│ │ ├── 🏷️ class ConsoleManager
│ │ ├── 🏷️ class LoggerConfig
│ │ ├── 🏷️ class ExceptionHookManager
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66 changes: 38 additions & 28 deletions docs/docs/tutorials/bayesian-dream-lbco-hrpt.ipynb
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Expand Up @@ -467,7 +467,7 @@
"metadata": {},
"outputs": [],
"source": [
"project.analysis.fit()"
"project.analysis.minimizer.chi_square_change_tolerance = 1e-2"
]
},
{
Expand All @@ -476,13 +476,23 @@
"id": "37",
"metadata": {},
"outputs": [],
"source": [
"project.analysis.fit()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "38",
"metadata": {},
"outputs": [],
"source": [
"project.display.fit.results()"
]
},
{
"cell_type": "markdown",
"id": "38",
"id": "39",
"metadata": {},
"source": [
"The correlation plot shows how strongly the fitted parameters move\n",
Expand All @@ -494,7 +504,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "39",
"id": "40",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -504,7 +514,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "40",
"id": "41",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -513,7 +523,7 @@
},
{
"cell_type": "markdown",
"id": "41",
"id": "42",
"metadata": {},
"source": [
"## 🎲 Prepare Sampling\n",
Expand All @@ -535,7 +545,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "42",
"id": "43",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -544,7 +554,7 @@
},
{
"cell_type": "markdown",
"id": "43",
"id": "44",
"metadata": {},
"source": [
"Set fit bounds for all free parameters using the default multiplier of\n",
Expand All @@ -556,7 +566,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "44",
"id": "45",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -566,7 +576,7 @@
},
{
"cell_type": "markdown",
"id": "45",
"id": "46",
"metadata": {},
"source": [
"Displaying the free parameters again is a convenient way to confirm\n",
Expand All @@ -577,7 +587,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "46",
"id": "47",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -586,7 +596,7 @@
},
{
"cell_type": "markdown",
"id": "47",
"id": "48",
"metadata": {},
"source": [
"## 🎲 Run Sampling\n",
Expand All @@ -612,7 +622,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "48",
"id": "49",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -622,7 +632,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "49",
"id": "50",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -632,7 +642,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "50",
"id": "51",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -644,7 +654,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "51",
"id": "52",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -653,7 +663,7 @@
},
{
"cell_type": "markdown",
"id": "52",
"id": "53",
"metadata": {},
"source": [
"## 📊 Inspect Results\n",
Expand All @@ -666,7 +676,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "53",
"id": "54",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -675,7 +685,7 @@
},
{
"cell_type": "markdown",
"id": "54",
"id": "55",
"metadata": {},
"source": [
"The correlation and posterior-pair plots are complementary:\n",
Expand All @@ -692,7 +702,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "55",
"id": "56",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -702,7 +712,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "56",
"id": "57",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -711,7 +721,7 @@
},
{
"cell_type": "markdown",
"id": "57",
"id": "58",
"metadata": {},
"source": [
"The one-dimensional posterior distributions below make it easier to\n",
Expand All @@ -722,7 +732,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "58",
"id": "59",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -731,7 +741,7 @@
},
{
"cell_type": "markdown",
"id": "59",
"id": "60",
"metadata": {},
"source": [
"Finally, the posterior predictive plot propagates the sampled parameter\n",
Expand All @@ -743,7 +753,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "60",
"id": "61",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -752,7 +762,7 @@
},
{
"cell_type": "markdown",
"id": "61",
"id": "62",
"metadata": {},
"source": [
"A final zoomed measured-vs-calculated plot is useful for checking how\n",
Expand All @@ -763,7 +773,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "62",
"id": "63",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -772,7 +782,7 @@
},
{
"cell_type": "markdown",
"id": "63",
"id": "64",
"metadata": {},
"source": [
"## 💾 Save Project\n",
Expand All @@ -783,7 +793,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "64",
"id": "65",
"metadata": {},
"outputs": [],
"source": [
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3 changes: 3 additions & 0 deletions docs/docs/tutorials/bayesian-dream-lbco-hrpt.py
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Expand Up @@ -222,6 +222,9 @@
# %%
project.analysis.minimizer.type = 'bumps (lm)'

# %%
project.analysis.minimizer.chi_square_change_tolerance = 1e-2

# %%
project.analysis.fit()

Expand Down
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