nested-fit 5.6.2.dev115__tar.gz → 5.6.4__tar.gz

{nested_fit-5.6.2.dev115 → nested_fit-5.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nested_fit
-Version: 5.6.2.dev115
+Version: 5.6.4
 Summary: The nested_fit package.
 Author: Martino Trassinelli, Lune Maillard, César Godinho
 Project-URL: Homepage, https://github.com/martinit18/nested_fit
@@ -73,10 +73,38 @@ Other jupyter notebook examples can be found in `examples/jupyter_notebooks`.
 > :warning: Windows support is deprecated. Compile at own risk.
 
 ### Using PIP
-For most users if you are running on Linux or MacOS, chances are you can just install directly from pip.
+For most users if you are running on Linux or MacOS, you can just install directly from pip.
 ```sh
 pipx install nested_fit
 ```
+(If you need to install a beta version from the **nightly** branch, use the command `pip install --pre nested_fit`)
+
+The `examples/` directory is bundled with the package. After installation you can
+copy it to a local working area in a couple of ways:
+
+* **directly from the installed site‑packages**
+
+```sh
+pkgdir=$(python -c "import os,nested_fit; print(os.path.join(os.path.dirname(nested_fit.__file__), 'examples'))")
+cp -rp "$pkgdir" ./nested_fit_examples
+```
+
+* **or grab them from GitHub with `curl` alone** – no git required.  Download
+  the repository tarball and extract just the examples directory:
+
+  ```sh
+  curl -L -o nf.tar.gz \
+       https://github.com/martinit18/nested_fit/archive/refs/heads/main.tar.gz
+  mkdir -p nested_fit_examples
+  tar -xzf nf.tar.gz --strip-components=1 nested_fit-main/examples
+  rm nf.tar.gz
+  ```
+
+  the result is a local `nested_fit_examples` tree containing all of the input
+  files and notebooks.
+Either approach gives you a local copy of the input files and notebooks without
+needing to clone the entire repository.
+
 
 ### Installing from source (automatic)
 If you cannot use pip you can install via the following script:
@@ -186,7 +214,7 @@ For this purpose, the python module `nested_py` can be used also for compressed
 Together with this file, also the files `nf_output_points.paramnames` and `nf_output_points.ranges` are created for the use of GetDist and Anesthetic python libraries.
 - `nf_output_cluster_mean_std.dat`: contains the number of clusters, number of point per clusters, and mean and standard deviations for each cluster (if the clustering option is activated).
 - `nf_output_cluster_max.dat`: contains the number of clusters, the maximum value of the likelihood and the corresponding parameter values (if the clustering option is activated).
-- `nf_energy.txt`: contains the volume and energy associated to the discarded and final live points. For a quantum potential, the decomposition of the energy between the avergaed potential and the replicas interaction is also given, as well as the temperature. Only created when exploring potentials.
+- `nf_output_energy.txt`: contains the volume and energy associated to the discarded and final live points. For a quantum potential, the decomposition of the energy between the avergaed potential and the replicas interaction is also given, as well as the temperature. Only created when exploring potentials.
 
 **Details of the input file line by line**
 
@@ -416,8 +444,9 @@ Examples of use of a legacy function can be found in `examples/data_analysis/aaa
 
 ## Present version and history of the past versions
 
-The present version is 5.6.2\
+The present version is 5.6.4\
 New features:
+- New function to visualizing the capacty heat for POTENTIAL calculations
 - Latex input support for compound variable names (i.e. x_{sub})
 - PyPI available development builds
 - PyPI binary distribution for arm64 macOS

{nested_fit-5.6.2.dev115 → nested_fit-5.6.4}/README.md

@@ -48,10 +48,38 @@ Other jupyter notebook examples can be found in `examples/jupyter_notebooks`.
 > :warning: Windows support is deprecated. Compile at own risk.
 
 ### Using PIP
-For most users if you are running on Linux or MacOS, chances are you can just install directly from pip.
+For most users if you are running on Linux or MacOS, you can just install directly from pip.
 ```sh
 pipx install nested_fit
 ```
+(If you need to install a beta version from the **nightly** branch, use the command `pip install --pre nested_fit`)
+
+The `examples/` directory is bundled with the package. After installation you can
+copy it to a local working area in a couple of ways:
+
+* **directly from the installed site‑packages**
+
+```sh
+pkgdir=$(python -c "import os,nested_fit; print(os.path.join(os.path.dirname(nested_fit.__file__), 'examples'))")
+cp -rp "$pkgdir" ./nested_fit_examples
+```
+
+* **or grab them from GitHub with `curl` alone** – no git required.  Download
+  the repository tarball and extract just the examples directory:
+
+  ```sh
+  curl -L -o nf.tar.gz \
+       https://github.com/martinit18/nested_fit/archive/refs/heads/main.tar.gz
+  mkdir -p nested_fit_examples
+  tar -xzf nf.tar.gz --strip-components=1 nested_fit-main/examples
+  rm nf.tar.gz
+  ```
+
+  the result is a local `nested_fit_examples` tree containing all of the input
+  files and notebooks.
+Either approach gives you a local copy of the input files and notebooks without
+needing to clone the entire repository.
+
 
 ### Installing from source (automatic)
 If you cannot use pip you can install via the following script:
@@ -161,7 +189,7 @@ For this purpose, the python module `nested_py` can be used also for compressed
 Together with this file, also the files `nf_output_points.paramnames` and `nf_output_points.ranges` are created for the use of GetDist and Anesthetic python libraries.
 - `nf_output_cluster_mean_std.dat`: contains the number of clusters, number of point per clusters, and mean and standard deviations for each cluster (if the clustering option is activated).
 - `nf_output_cluster_max.dat`: contains the number of clusters, the maximum value of the likelihood and the corresponding parameter values (if the clustering option is activated).
-- `nf_energy.txt`: contains the volume and energy associated to the discarded and final live points. For a quantum potential, the decomposition of the energy between the avergaed potential and the replicas interaction is also given, as well as the temperature. Only created when exploring potentials.
+- `nf_output_energy.txt`: contains the volume and energy associated to the discarded and final live points. For a quantum potential, the decomposition of the energy between the avergaed potential and the replicas interaction is also given, as well as the temperature. Only created when exploring potentials.
 
 **Details of the input file line by line**
 
@@ -391,8 +419,9 @@ Examples of use of a legacy function can be found in `examples/data_analysis/aaa
 
 ## Present version and history of the past versions
 
-The present version is 5.6.2\
+The present version is 5.6.4\
 New features:
+- New function to visualizing the capacty heat for POTENTIAL calculations
 - Latex input support for compound variable names (i.e. x_{sub})
 - PyPI available development builds
 - PyPI binary distribution for arm64 macOS

nested_fit-5.6.4/examples/jupyter_notebooks/LJ17/nf_input.yaml

@@ -0,0 +1,324 @@
+calculation_mode: POTENTIAL
+clustering:
+  enabled: false
+  method: k
+  parameter1: 0.5
+  parameter2: 0.2
+convergence:
+  accuracy: -10
+  method: ENERGY_MAX
+  parameter: 0.01
+datafiles: []
+function:
+  expression: ENERGY_LJ_3D_PBC
+  params:
+    r_0:
+      fixed: true
+      max: 3
+      min: -3
+      npar: 1
+      step: -1
+      value: 0.5
+    x_1:
+      max: 3
+      min: -3
+      npar: 2
+      step: -1
+      value: 0.0
+    x_10:
+      max: 3
+      min: -3
+      npar: 29
+      step: -1
+      value: 0.0
+    x_11:
+      max: 3
+      min: -3
+      npar: 32
+      step: -1
+      value: 0.0
+    x_12:
+      max: 3
+      min: -3
+      npar: 35
+      step: -1
+      value: 0.0
+    x_13:
+      max: 3
+      min: -3
+      npar: 38
+      step: -1
+      value: 0.0
+    x_14:
+      max: 3
+      min: -3
+      npar: 41
+      step: -1
+      value: 0.0
+    x_16:
+      max: 3
+      min: -3
+      npar: 44
+      step: -1
+      value: 0.0
+    x_17:
+      max: 3
+      min: -3
+      npar: 47
+      step: -1
+      value: 0.0
+    x_2:
+      max: 3
+      min: -3
+      npar: 5
+      step: -1
+      value: 0.0
+    x_3:
+      max: 3
+      min: -3
+      npar: 8
+      step: -1
+      value: 0.0
+    x_4:
+      max: 3
+      min: -3
+      npar: 11
+      step: -1
+      value: 0.0
+    x_5:
+      max: 3
+      min: -3
+      npar: 14
+      step: -1
+      value: 0.0
+    x_6:
+      max: 3
+      min: -3
+      npar: 17
+      step: -1
+      value: 0.0
+    x_7:
+      max: 3
+      min: -3
+      npar: 20
+      step: -1
+      value: 0.0
+    x_8:
+      max: 3
+      min: -3
+      npar: 23
+      step: -1
+      value: 0.0
+    x_9:
+      max: 3
+      min: -3
+      npar: 26
+      step: -1
+      value: 0.0
+    y_1:
+      max: 3
+      min: -3
+      npar: 3
+      step: -1
+      value: 0.0
+    y_10:
+      max: 3
+      min: -3
+      npar: 30
+      step: -1
+      value: 0.0
+    y_11:
+      max: 3
+      min: -3
+      npar: 33
+      step: -1
+      value: 0.0
+    y_12:
+      max: 3
+      min: -3
+      npar: 36
+      step: -1
+      value: 0.0
+    y_13:
+      max: 3
+      min: -3
+      npar: 39
+      step: -1
+      value: 0.0
+    y_15:
+      max: 3
+      min: -3
+      npar: 42
+      step: -1
+      value: 0.0
+    y_16:
+      max: 3
+      min: -3
+      npar: 45
+      step: -1
+      value: 0.0
+    y_17:
+      max: 3
+      min: -3
+      npar: 48
+      step: -1
+      value: 0.0
+    y_2:
+      max: 3
+      min: -3
+      npar: 6
+      step: -1
+      value: 0.0
+    y_3:
+      max: 3
+      min: -3
+      npar: 9
+      step: -1
+      value: 0.0
+    y_4:
+      max: 3
+      min: -3
+      npar: 12
+      step: -1
+      value: 0.0
+    y_5:
+      max: 3
+      min: -3
+      npar: 15
+      step: -1
+      value: 0.0
+    y_6:
+      max: 3
+      min: -3
+      npar: 18
+      step: -1
+      value: 0.0
+    y_7:
+      max: 3
+      min: -3
+      npar: 21
+      step: -1
+      value: 0.0
+    y_8:
+      max: 3
+      min: -3
+      npar: 24
+      step: -1
+      value: 0.0
+    y_9:
+      max: 3
+      min: -3
+      npar: 27
+      step: -1
+      value: 0.0
+    z_1:
+      max: 3
+      min: -3
+      npar: 4
+      step: -1
+      value: 0.0
+    z_10:
+      max: 3
+      min: -3
+      npar: 31
+      step: -1
+      value: 0.0
+    z_11:
+      max: 3
+      min: -3
+      npar: 34
+      step: -1
+      value: 0.0
+    z_12:
+      max: 3
+      min: -3
+      npar: 37
+      step: -1
+      value: 0.0
+    z_13:
+      max: 3
+      min: -3
+      npar: 40
+      step: -1
+      value: 0.0
+    z_15:
+      max: 3
+      min: -3
+      npar: 43
+      step: -1
+      value: 0.0
+    z_16:
+      max: 3
+      min: -3
+      npar: 46
+      step: -1
+      value: 0.0
+    z_17:
+      max: 3
+      min: -3
+      npar: 49
+      step: -1
+      value: 0.0
+    z_2:
+      max: 3
+      min: -3
+      npar: 7
+      step: -1
+      value: 0.0
+    z_3:
+      max: 3
+      min: -3
+      npar: 10
+      step: -1
+      value: 0.0
+    z_4:
+      max: 3
+      min: -3
+      npar: 13
+      step: -1
+      value: 0.0
+    z_5:
+      max: 3
+      min: -3
+      npar: 16
+      step: -1
+      value: 0.0
+    z_6:
+      max: 3
+      min: -3
+      npar: 19
+      step: -1
+      value: 0.0
+    z_7:
+      max: 3
+      min: -3
+      npar: 22
+      step: -1
+      value: 0.0
+    z_8:
+      max: 3
+      min: -3
+      npar: 25
+      step: -1
+      value: 0.0
+    z_9:
+      max: 3
+      min: -3
+      npar: 28
+      step: -1
+      value: 0.0
+likelihood: GAUSSIAN
+search:
+  hard_writing: true
+  livepoints: 50000
+  max_steps: 100000
+  max_tries: 1000
+  method: SLICE_SAMPLING
+  num_tries: 1
+  param1: 0.5
+  param2: 3
+  tries_mult: 100
+version: 5.6
+writing:
+  all_parameters: true
+  statistics: true

nested_fit-5.6.4/examples/jupyter_notebooks/LJ3/nf_input.yaml

@@ -0,0 +1,93 @@
+calculation_mode: POTENTIAL
+clustering:
+  enabled: false
+  method: k
+  parameter1: 0.5
+  parameter2: 0.2
+convergence:
+  accuracy: -10
+  method: ENERGY_MAX
+  parameter: 0.01
+data:
+  xmax: 650
+  xmin: 250
+datafiles: []
+function:
+  expression: ENERGY_LJ_3D_PBC
+  params:
+    r_0:
+      fixed: true
+      max: 3
+      min: -3
+      npar: 1
+      step: -1
+      value: 0.5
+    x_1:
+      max: 3
+      min: -3
+      npar: 2
+      step: -1
+      value: 0.0
+    x_2:
+      max: 3
+      min: -3
+      npar: 5
+      step: -1
+      value: 0.0
+    x_3:
+      max: 3
+      min: -3
+      npar: 8
+      step: -1
+      value: 0.0
+    y_1:
+      max: 3
+      min: -3
+      npar: 3
+      step: -1
+      value: 0.0
+    y_2:
+      max: 3
+      min: -3
+      npar: 6
+      step: -1
+      value: 0.0
+    y_3:
+      max: 3
+      min: -3
+      npar: 9
+      step: -1
+      value: 0.0
+    z_1:
+      max: 3
+      min: -3
+      npar: 4
+      step: -1
+      value: 0.0
+    z_2:
+      max: 3
+      min: -3
+      npar: 7
+      step: -1
+      value: 0.0
+    z_3:
+      max: 3
+      min: -3
+      npar: 10
+      step: -1
+      value: 0.0
+likelihood: GAUSSIAN
+search:
+  hard_writing: true
+  livepoints: 1000
+  max_steps: 100000
+  max_tries: 1000
+  method: SLICE_SAMPLING
+  num_tries: 1
+  param1: 0.5
+  param2: 3
+  tries_mult: 100
+version: 5.6
+writing:
+  all_parameters: true
+  statistics: true

nested_fit-5.6.4/examples/jupyter_notebooks/LJ7/nf_input.yaml

@@ -0,0 +1,162 @@
+calculation_mode: POTENTIAL
+clustering:
+  enabled: false
+  method: k
+  parameter1: 0.5
+  parameter2: 0.2
+convergence:
+  accuracy: -10
+  method: ENERGY_MAX
+  parameter: 0.01
+datafiles: []
+function:
+  expression: ENERGY_LJ_3D_PBC
+  params:
+    r_0:
+      fixed: true
+      max: 3
+      min: -3
+      npar: 1
+      step: -1
+      value: 0.5
+    x_1:
+      max: 3
+      min: -3
+      npar: 2
+      step: -1
+      value: 0.0
+    x_2:
+      max: 3
+      min: -3
+      npar: 5
+      step: -1
+      value: 0.0
+    x_3:
+      max: 3
+      min: -3
+      npar: 8
+      step: -1
+      value: 0.0
+    x_4:
+      max: 3
+      min: -3
+      npar: 11
+      step: -1
+      value: 0.0
+    x_5:
+      max: 3
+      min: -3
+      npar: 14
+      step: -1
+      value: 0.0
+    x_6:
+      max: 3
+      min: -3
+      npar: 17
+      step: -1
+      value: 0.0
+    x_7:
+      max: 3
+      min: -3
+      npar: 20
+      step: -1
+      value: 0.0
+    y_1:
+      max: 3
+      min: -3
+      npar: 3
+      step: -1
+      value: 0.0
+    y_2:
+      max: 3
+      min: -3
+      npar: 6
+      step: -1
+      value: 0.0
+    y_3:
+      max: 3
+      min: -3
+      npar: 9
+      step: -1
+      value: 0.0
+    y_4:
+      max: 3
+      min: -3
+      npar: 12
+      step: -1
+      value: 0.0
+    y_5:
+      max: 3
+      min: -3
+      npar: 15
+      step: -1
+      value: 0.0
+    y_6:
+      max: 3
+      min: -3
+      npar: 18
+      step: -1
+      value: 0.0
+    y_7:
+      max: 3
+      min: -3
+      npar: 21
+      step: -1
+      value: 0.0
+    z_1:
+      max: 3
+      min: -3
+      npar: 4
+      step: -1
+      value: 0.0
+    z_2:
+      max: 3
+      min: -3
+      npar: 7
+      step: -1
+      value: 0.0
+    z_3:
+      max: 3
+      min: -3
+      npar: 10
+      step: -1
+      value: 0.0
+    z_4:
+      max: 3
+      min: -3
+      npar: 13
+      step: -1
+      value: 0.0
+    z_5:
+      max: 3
+      min: -3
+      npar: 16
+      step: -1
+      value: 0.0
+    z_6:
+      max: 3
+      min: -3
+      npar: 19
+      step: -1
+      value: 0.0
+    z_7:
+      max: 3
+      min: -3
+      npar: 22
+      step: -1
+      value: 0.0
+likelihood: GAUSSIAN
+search:
+  hard_writing: true
+  livepoints: 1000
+  max_steps: 100000
+  max_tries: 1000
+  method: SLICE_SAMPLING
+  num_tries: 1
+  param1: 0.5
+  param2: 3
+  tries_mult: 100
+version: 5.6
+writing:
+  all_parameters: true
+  statistics: true