inftools 2026.1__tar.gz

inftools-2026.1/LICENSE

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+MIT License
+
+Copyright (c) 2023 infretis
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

inftools-2026.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: inftools
+Version: 2026.1
+Summary: Useful tools for infRETIS simulations
+License: MIT
+License-File: LICENSE
+Keywords: simulation,retis,molecular-dynamics,path-sampling
+Author: Daniel Zhang
+Author-email: daniel.t.zhang@ntnu.no
+Requires-Python: >=3.10,<3.14
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: typer (>=0.19,<0.20)
+Project-URL: Homepage, https://github.com/infretis/inftools
+Project-URL: Repository, https://github.com/infretis/inftools
+Description-Content-Type: text/markdown
+
+# &infin;tools 🧰
+👷‍♂️ Work in progress python package that provide various &infin;RETIS tools for tasks like setting up simulations and analyzing data. 📈
+
+🤝 Contributions of tools and modifications are welcome – feel free to submit your enhancements! 🚀
+## Installation 
+
+1. Clone the repository
+2. (Optional) Create a virtual environment
+3. Install with:
+   ```bash
+   python -m pip install -e .
+   ```
+## Usage
+```bash
+inft -h
+```
+
+#### `inft center_periodic`
+
+The command `inft center_periodic` can be run to re-center an .xyz trajectory to a certain atom index. For example, to center the first atom `C` at index 0 in the `co2.xyz` frame in [`examples/co2.xyz`](examples/co2.xyz) with cubic box length of 12.4138, the following command can be ran:
+
+```bash
+inft center_periodic -i co2.xyz -o co2_c.xyz -c 12.4138 -idx 0
+```
+
+## Development practice
+
+Current CLI capabilities is powered by the [Typer](https://typer.tiangolo.com/) python library.
+
+### Python files
+
+Any function `function_name` in a python file `*.py` with the following structure
+
+```python3
+from typing import Annotated
+
+def function_name(
+    args1: Annotated[str, typer.Option("-args1", help="var1")],
+    args2: Annotated[int, typer.Option("-args2", help="var2")],
+    ):
+    """
+    Function description
+    """
+```
+
+added to the folders [`inftools/exercises`](inftools/exercises), [`inftools/tistools`](inftools/tistools) and [`inftools/xyz`](inftools/xyz) will automatically be callable via the terminal as
+
+```bash
+inft function_name -args1 var1 -args2 var2
+```
+
+### Individual functions
+
+Individual functions can also be added to the CLI library by including them in [`inftools/bin.py`](inftools/bin.py), as done for the wham function in the [`inftools/analysis`](inftools/analysis) folder:
+
+```python3
+from inftools.analysis.wham import wham
+
+MAPPER["wham"] = wham
+```
+
+### Testing
+
+The CLI functions are tested by utilizing the [pytest](https://docs.pytest.org/en/stable/) python library.
+
+The tests included in the [`inftools/test`](inftools/) folder can be ran by running the following command in the terminal:
+
+```bash
+pytest
+```
+
+We currently do not have a testing policy but please do include tests for the included CLI functions for higher coverage.
+

inftools-2026.1/README.md

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+# ∞tools 🧰
+👷‍♂️ Work in progress python package that provide various ∞RETIS tools for tasks like setting up simulations and analyzing data. 📈
+
+🤝 Contributions of tools and modifications are welcome – feel free to submit your enhancements! 🚀
+## Installation 
+
+1. Clone the repository
+2. (Optional) Create a virtual environment
+3. Install with:
+   ```bash
+   python -m pip install -e .
+   ```
+## Usage
+```bash
+inft -h
+```
+
+#### `inft center_periodic`
+
+The command `inft center_periodic` can be run to re-center an .xyz trajectory to a certain atom index. For example, to center the first atom `C` at index 0 in the `co2.xyz` frame in [`examples/co2.xyz`](examples/co2.xyz) with cubic box length of 12.4138, the following command can be ran:
+
+```bash
+inft center_periodic -i co2.xyz -o co2_c.xyz -c 12.4138 -idx 0
+```
+
+## Development practice
+
+Current CLI capabilities is powered by the [Typer](https://typer.tiangolo.com/) python library.
+
+### Python files
+
+Any function `function_name` in a python file `*.py` with the following structure
+
+```python3
+from typing import Annotated
+
+def function_name(
+    args1: Annotated[str, typer.Option("-args1", help="var1")],
+    args2: Annotated[int, typer.Option("-args2", help="var2")],
+    ):
+    """
+    Function description
+    """
+```
+
+added to the folders [`inftools/exercises`](inftools/exercises), [`inftools/tistools`](inftools/tistools) and [`inftools/xyz`](inftools/xyz) will automatically be callable via the terminal as
+
+```bash
+inft function_name -args1 var1 -args2 var2
+```
+
+### Individual functions
+
+Individual functions can also be added to the CLI library by including them in [`inftools/bin.py`](inftools/bin.py), as done for the wham function in the [`inftools/analysis`](inftools/analysis) folder:
+
+```python3
+from inftools.analysis.wham import wham
+
+MAPPER["wham"] = wham
+```
+
+### Testing
+
+The CLI functions are tested by utilizing the [pytest](https://docs.pytest.org/en/stable/) python library.
+
+The tests included in the [`inftools/test`](inftools/) folder can be ran by running the following command in the terminal:
+
+```bash
+pytest
+```
+
+We currently do not have a testing policy but please do include tests for the included CLI functions for higher coverage.

inftools-2026.1/inftools/analysis/Free_energy.py

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+import os
+import numpy as np
+
+def extract(trajfile, xcol, ycol=None):
+    # Read and process the file
+    traj = np.loadtxt(trajfile)
+    data = traj[1:-1, xcol] # remove first and last frames
+    if ycol is not None:
+        data = np.vstack((data, traj[1:-1, ycol]))
+    return data
+
+
+def update_histogram(data, factor, histogram, Minx, Miny, dx, dy):
+    if Miny is not None and dy is not None:
+        x = data[0]
+        y = data[1]
+
+        ix = ((x - Minx) / dx).astype(int)
+        iy = ((y - Miny) / dy).astype(int)
+
+        np.add.at(histogram, (ix, iy), factor)
+
+    else:
+        x = data if data.ndim == 1 else data[:,0] # make sure x is one dimensional
+        ix = ((x - Minx) / dx).astype(int)
+        np.add.at(histogram, ix, factor)
+
+    return histogram
+
+
+def calculate_free_energy(trajlabels, WFtot, Trajdir, outfolder, histo_stuff):
+    print("We are now going to perform the Landau Free Energy calculations")
+    Nbinsx, Nbinsy = histo_stuff["nbx"], histo_stuff["nby"]
+    Maxx, Minx = histo_stuff["maxx"], histo_stuff["minx"]
+    Maxy, Miny = histo_stuff["maxy"], histo_stuff["miny"]
+    xcol, ycol = histo_stuff["xcol"], histo_stuff["ycol"]
+
+    if any(var is None for var in [Nbinsy, Maxy, Miny, ycol]):
+        none_vars = [name for name, var in zip(["nby", "maxy", "miny", "ycol"], [Nbinsy, Maxy, Miny, ycol]) if var is None]
+        assert all(var is None for var in [Nbinsy, Maxy, Miny, ycol]), \
+            f"The following variables are None and should be set: {', '.join(none_vars)}"
+    if Nbinsy is not None:
+        histogram = np.zeros((Nbinsx, Nbinsy))
+        dy = (Maxy - Miny) / Nbinsy
+        yval = [Miny + 0.5 * dy + i * dy for i in range(Nbinsy)]
+    else:
+        histogram = np.zeros(Nbinsx)
+        dy = None
+        yval = None
+    dx = (Maxx - Minx) / Nbinsx
+    xval = [Minx + 0.5 * dx + i * dx for i in range(Nbinsx)]
+
+    h5file = histo_stuff.get("h5")
+    if h5file is not None and os.path.exists(h5file):
+        import h5py
+        with h5py.File(h5file, "r") as h5f:
+            for label, factor in zip(trajlabels, WFtot):
+                data = h5f[f"{label}/order.txt"]
+                if ycol is not None:
+                    data = data[1:-1,[xcol,ycol]].T
+                else:
+                    data = data[1:-1, xcol]
+                histogram = update_histogram(data, factor, histogram, Minx, Miny, dx, dy)
+    else:
+        for label, factor in zip(trajlabels, WFtot):
+            trajfile = Trajdir + "/" + str(label) + "/order.txt"
+            data = extract(trajfile, xcol, ycol)
+            histogram = update_histogram(data, factor, histogram, Minx, Miny, dx, dy)
+
+    # normalize such that the highest value equals 1
+    max_value = np.max(histogram)
+    histogram /= max_value
+
+    np.savetxt(os.path.join(outfolder, "histo_xval.txt"), xval)
+    if not yval is None:
+        np.savetxt(os.path.join(outfolder, "histo_yval.txt"), yval)
+    np.savetxt(os.path.join(outfolder, "histo_probability.txt"), histogram)
+
+    histogram = -np.log(histogram)  # get Landau free energy in kBT units
+    np.savetxt(os.path.join(outfolder, "histo_free_energy.txt"), histogram)