convert README.rst to README.md

Author: bast

Cargo.toml

@@ -5,7 +5,7 @@ authors = ["Radovan Bast <[email protected]>"]
 description = "Numerical integration grid for molecules."
 license = "MPL-2.0"
 edition = "2018"
-readme = "README.rst"
+readme = "README.md"
 homepage = "https://github.com/dftlibs/numgrid/"
 
 [lib]

README.md

@@ -0,0 +1,332 @@
+[![test status](https://github.com/dftlibs/numgrid/workflows/Test/badge.svg)](https://github.com/dftlibs/numgrid/actions)
+[![license badge](https://img.shields.io/badge/license-%20GPL-blue.svg)](LICENSE)
+[![link to PyPI](https://badge.fury.io/py/numgrid.svg)](https://badge.fury.io/py/numgrid)
+[![link to Zenodo/DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1470276.svg)](https://doi.org/10.5281/zenodo.1470276)
+
+- [Changelog](CHANGES.md)
+- Licensed under [MPL v2.0](LICENSE) (except John
+  Burkardt’s Lebedev code which is redistributed under LGPL v3.0)
+
+
+# Numgrid
+
+Numgrid is a library that produces numerical integration grid for
+molecules based on atom coordinates, atom types, and basis set
+information. This library provides Rust and Python bindings.
+
+
+## Who are the people behind this code?
+
+Authors
+-  Radovan Bast
+
+Contributors
+-  Roberto Di Remigio (OS X testing, streamlined Travis testing, better
+   C++, error handling)
+
+For a list of all the contributions see
+https://github.com/dftlibs/numgrid/contributors.
+
+
+### Acknowledgements
+
+-  Simon Neville (reporting issues)
+-  Jaime Axel Rosal Sandberg (reporting issues)
+
+This tool uses SPHERE_LEBEDEV_RULE, a C library written by John Burkardt which
+computes a Lebedev quadrature rule over the surface of the unit sphere in 3D,
+see also:
+http://people.sc.fsu.edu/~jburkardt/c_src/sphere_lebedev_rule/sphere_lebedev_rule.html
+
+This library uses and acknowledges the
+MolSSI BSE (https://molssi-bse.github.io/basis_set_exchange/),
+which is a rewrite of the Basis Set Exchange
+(https://bse.pnl.gov/bse/portal) and is a collaboration between the Molecular
+Sciences Software Institute (http://www.molssi.org) and the Environmental
+Molecular Sciences Laboratory (https://www.emsl.pnl.gov).
+
+
+### Citation
+
+If you use this tool in a program or publication, please acknowledge its
+author(s)
+```bibtex
+@misc{numgrid,
+  author    = {Bast, Radovan},
+  title     = {Numgrid: Numerical integration grid for molecules},
+  month     = {1},
+  year      = {2021},
+  publisher = {Zenodo},
+  version   = {v2.1.0},
+  doi       = {10.5281/zenodo.1470276},
+  url       = {https://doi.org/10.5281/zenodo.1470276}
+}
+
+@misc{sphere_lebedev_rule,
+  author = {Burkardt, John},
+  title  = {SPHERE_LEBEDEV_RULE: Quadrature Rules for the Unit Sphere},
+  year   = {2010},
+  url    = {https://people.sc.fsu.edu/~jburkardt/c_src/sphere_lebedev_rule/sphere_lebedev_rule.html}
+}
+```
+
+I kindly ask you to also cite the latter since Numgrid is basically a "shell"
+around SPHERE_LEBEDEV_RULE, with added radial integration and molecular
+partitioning.
+
+
+### Would you like to contribute?
+
+Yes please! Please follow [this excellent
+guide](http://www.contribution-guide.org). We do not require any formal
+copyright assignment or contributor license agreement. Any contributions
+intentionally sent upstream are presumed to be offered under terms of the
+Mozilla Public License Version 2.0.
+
+
+## Requirements
+
+- Python (3.8 - 3.12).
+- For the Rust version: A [Rust installation](https://www.rust-lang.org/tools/install).
+
+
+## Installation
+
+
+### Installing via pip
+
+```bash
+python -m pip install numgrid
+```
+
+
+### Building from sources and testing
+
+Building the code:
+```bash
+cargo build --release
+```
+
+Testing the Rust interface:
+```bash
+cargo test --release
+```
+
+Running also the longer tests:
+```bash
+cargo test --release -- --ignored
+```
+
+Testing the Python layer:
+```bash
+pip install -r requirements.txt  # ideally into a virtual environment
+maturin develop
+pytest tests/test.py
+```
+
+
+## API
+
+
+### The API changed
+
+The API changed (sorry!) for easier maintenance and simpler use:
+
+- No initialization or deallocation necessary.
+
+- One-step instead of two steps (since the radial grid generation time is
+  negligible compared to space partitioning, it did not make sense anymore to
+  separate these steps and introduce a state).
+
+- `alpha_min` is given as dictionary which saves an argument and simplifies
+  explaining the API.
+
+- The library now provides Rust and Python bindings. It used to provide C and
+  Fortran bindings. The C/Fortran code lives on the [cpp-version branch](https://github.com/dftlibs/numgrid/tree/cpp-version).  I might bring the
+  C interfaces back into the Rust code if there is sufficient interest/need.
+
+
+### Units
+
+Coordinates are in bohr.
+
+
+### Python example
+
+As an example let us generate a grid for the water molecule:
+```python
+import numgrid
+
+radial_precision = 1.0e-12
+min_num_angular_points = 86
+max_num_angular_points = 302
+
+proton_charges = [8, 1, 1]
+
+center_coordinates_bohr = [(0.0, 0.0, 0.0), (1.43, 0.0, 1.1), (-1.43, 0.0, 1.1)]
+
+# cc-pVDZ basis
+alpha_max = [
+    11720.0,  # O
+    13.01,  # H
+    13.01,  # H
+]
+alpha_min = [
+    {0: 0.3023, 1: 0.2753, 2: 1.185},  # O
+    {0: 0.122, 1: 0.727},  # H
+    {0: 0.122, 1: 0.727},  # H
+]
+
+for center_index in range(len(center_coordinates_bohr)):
+    # atom grid using explicit basis set parameters
+    coordinates, weights = numgrid.atom_grid(
+        alpha_min[center_index],
+        alpha_max[center_index],
+        radial_precision,
+        min_num_angular_points,
+        max_num_angular_points,
+        proton_charges,
+        center_index,
+        center_coordinates_bohr,
+        hardness=3,
+    )
+
+    # atom grid using basis set name
+    # this takes a second or two for the REST API request
+    coordinates, weights = numgrid.atom_grid_bse(
+        "cc-pVDZ",
+        radial_precision,
+        min_num_angular_points,
+        max_num_angular_points,
+        proton_charges,
+        center_index,
+        center_coordinates_bohr,
+        hardness=3,
+    )
+
+# radial grid (LMG) using explicit basis set parameters
+radii, weights = numgrid.radial_grid_lmg(
+    alpha_min={0: 0.3023, 1: 0.2753, 2: 1.185},
+    alpha_max=11720.0,
+    radial_precision=1.0e-12,
+    proton_charge=8,
+)
+
+# radial grid (LMG) using basis set name
+radii, weights = numgrid.radial_grid_lmg_bse(
+    basis_set="cc-pVDZ",
+    radial_precision=1.0e-12,
+    proton_charge=8,
+)
+
+# radial grid with 100 points using Krack-Koster approach
+radii, weights = numgrid.radial_grid_kk(num_points=100)
+
+# angular grid with 14 points
+coordinates, weights = numgrid.angular_grid(num_points=14)
+```
+
+
+### Notes and recommendations
+
+- The smaller the `radial_precision`, the better grid.
+
+- For `min_num_angular_points` and `max_num_angular_points`, see “Angular
+  grid” below.
+
+- `alpha_max` is the steepest basis set exponent.
+
+- `alpha_min` is a dictionary and holds the smallest exponents for each
+  angular momentum (order does not matter).
+
+- Using `center_index` we tell the code which of the atom centers is the one
+  we have computed the grid for.
+
+- `num_angular_grid_points` has to be one of the many supported Lebedev grids
+  (see table on the bottom of this page).
+
+
+### Rust interface
+
+Needs to be documented better but the library exposes functions with the same
+name as the Python interface and probably the best example on how it can be
+used are the [integration
+tests](https://github.com/dftlibs/numgrid/blob/main/tests/integration_test.rs).
+
+
+### Saving grid in NumPy format
+
+The current API makes is relatively easy to export the computed grid in NumPy format.
+
+In this example we save the angular grid coordinates and weights to two separate files
+in NumPy format:
+```python
+import numgrid
+import numpy as np
+
+coordinates, weights = numgrid.angular_grid(14)
+
+np.save("angular_grid_coordinates.npy", coordinates)
+np.save("angular_grid_weights.npy", weights)
+```
+
+
+## Parallelization
+
+The Becke partitioning step is parallelized using
+[Rayon](https://github.com/rayon-rs/rayon).  In other words, this step should
+be able to use all available cores on the computer or computing node.  Since
+grids are currently generated atom by atom, it is also possible to parallelize
+"outside" by the caller.
+
+
+## Space partitioning
+
+The molecular integration grid is generated from atom-centered grids by scaling
+the grid weights according to the Becke partitioning scheme, [JCP 88, 2547
+(1988)](http://dx.doi.org/10.1063/1.454033). The default Becke hardness is 3.
+
+
+## Radial grid
+
+Two choices are available:
+- Lindh-Malmqvist-Gagliardi (https://dx.doi.org/10.1007/s002140100263)
+- Krack-Köster (https://doi.org/10.1063/1.475719)
+
+Advantage of LMG scheme: The range of the radial grid is basis set dependent.
+The precision can be tuned with one single radial precision parameter. The
+smaller the radial precision, the better quality grid you obtain.  The basis
+set (more precisely the Gaussian primitives/exponents) are used to generate the
+atomic radial grid range. This means that a more diffuse basis set generates a
+more diffuse radial grid.
+
+Advantage of the KK scheme: parameter-free.
+
+
+## Angular grid
+
+The angular grid is generated according to Lebedev and Laikov [A
+quadrature formula for the sphere of the 131st algebraic order of
+accuracy, Russian Academy of Sciences Doklady Mathematics, Volume 59,
+Number 3, 1999, pages 477-481].
+
+The angular grid is pruned. The pruning is a primitive linear
+interpolation between the minimum number and the maximum number of
+angular points per radial shell. The maximum number is reached at 0.2
+times the Bragg radius of the center.
+
+The higher the values for minimum and maximum number of angular points,
+the better.
+
+For the minimum and maximum number of angular points the code will use
+the following table and select the closest number with at least the
+desired precision:
+```
+{6,    14,   26,   38,   50,   74,   86,   110,  146,
+ 170,  194,  230,  266,  302,  350,  434,  590,  770,
+ 974,  1202, 1454, 1730, 2030, 2354, 2702, 3074, 3470,
+ 3890, 4334, 4802, 5294, 5810}
+```
+
+Taking the same number for the minimum and maximum number of angular
+points switches off pruning.