Metadata-Version: 2.4
Name: imce
Version: 1.0.0
Summary: A simple framework for molecular Monte Carlo sampling with uncertainty quantification
Author-email: Erik Tsvetaev <erik.tsvetaev@tu-braunschweig.de>, Christoph Jacob <c.jacob@tu-braunschweig.de>
Maintainer-email: Erik Tsvetaev <erik.tsvetaev@tu-braunschweig.de>
License-Expression: LGPL-3.0-or-later
Project-URL: Homepage, https://github.com/erik-tsvetaev/imce
Project-URL: Repository, https://github.com/erik-tsvetaev/imce.git
Project-URL: Issues, https://github.com/erik-tsvetaev/imce/issues
Keywords: simulation,monte carlo,quantum chemistry
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: COPYING
License-File: COPYING.LESSER
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: h5py
Requires-Dist: matplotlib
Requires-Dist: seaborn
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Requires-Dist: attrs>19.2; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: asv; extra == "dev"
Requires-Dist: sphinx; extra == "dev"
Requires-Dist: sphinx_rtd_theme; extra == "dev"
Requires-Dist: k3d; extra == "dev"
Dynamic: license-file

# imce

Small Python based code for ab initio molecular simulations (using Monte Carlo) using modified sampling criteria (derived from computed spectra uncertainty in the molecular structure). See the following publication for further details: [DOI here]

## Installation and Requirements:

Install XTB and STD2 as the required backends (see their respective manuals). On a M2 Macbook, STD2 is compiled with the following flags:

```bash
LDFLAGS="-L/opt/homebrew/opt/openblas/lib" CPPFLAGS="-I/opt/homebrew/opt/openblas/include" FC=gfortran-14 CC=gcc-14 meson setup _build -Dla_backend=openblas --wipe
```

The package can be installed locally with

```bash
pip install .
```

or (with additional packages for development)

```bash
pip install '.[dev]'
```

## Usage: 

The framework can be accessed as a Python module:

```python
#!/usr/bin/env python3

import imce
from imce.utility import xyz_to_if, if_to_xyz

xtb = imce.xtb_std2_itrf(['ENERGY', 'UVVIS'])  

settings = imce.settings(seed = 0, windows = [[1.5, 8.0]], itrf = xtb, unit = 'eV', convolution_factor = 0.25)

mol = xyz_to_if('dfhbi.xyz')

simbox = imce.simbox(settings, '_uq_02_short.hdf5', mol)
simbox.init() 

sim = imce.uqmc(simbox, steps = 250, delta = 0.01875, sc = 0.2, method = 'UVVIS').run()
```

Then script is the run on the TU BS ThC cluster using the following command:

```bash
tcsub -q s -a generic imce_jobfile.py
```

## Contributing:

Contributions require signature of the commit, acknowledging the following statement:

```
Developer Certificate of Origin
Version 1.1

Copyright (C) 2004, 2006 The Linux Foundation and its contributors.

Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.


Developer's Certificate of Origin 1.1

By making a contribution to this project, I certify that:

(a) The contribution was created in whole or in part by me and I
    have the right to submit it under the open source license
    indicated in the file; or

(b) The contribution is based upon previous work that, to the best
    of my knowledge, is covered under an appropriate open source
    license and I have the right under that license to submit that
    work with modifications, whether created in whole or in part
    by me, under the same open source license (unless I am
    permitted to submit under a different license), as indicated
    in the file; or

(c) The contribution was provided directly to me by some other
    person who certified (a), (b) or (c) and I have not modified
    it.

(d) I understand and agree that this project and the contribution
    are public and that a record of the contribution (including all
    personal information I submit with it, including my sign-off) is
    maintained indefinitely and may be redistributed consistent with
    this project or the open source license(s) involved.
```
