tblite

This directory contains the Python API of the tblite project.

This interface provides access to the C-API of tblite via the CFFI module. The low-level CFFI interface is available in the tblite.library module and only required for implementing other interfaces. A more pythonic interface is provided in the tblite.interface module which can be used to build more specific interfaces.

from tblite.interface import Calculator
import numpy as np
numbers = np.array([1, 1, 6, 5, 1, 15, 8, 17, 13, 15, 5, 1, 9, 15, 1, 15])
positions = np.array([  # Coordinates in Bohr
    [+2.79274810283778, +3.82998228828316, -2.79287054959216],
    [-1.43447454186833, +0.43418729987882, +5.53854345129809],
    [-3.26268343665218, -2.50644032426151, -1.56631149351046],
    [+2.14548759959147, -0.88798018953965, -2.24592534506187],
    [-4.30233097423181, -3.93631518670031, -0.48930754109119],
    [+0.06107643564880, -3.82467931731366, -2.22333344469482],
    [+0.41168550401858, +0.58105573172764, +5.56854609916143],
    [+4.41363836635653, +3.92515871809283, +2.57961724984000],
    [+1.33707758998700, +1.40194471661647, +1.97530004949523],
    [+3.08342709834868, +1.72520024666801, -4.42666116106828],
    [-3.02346932078505, +0.04438199934191, -0.27636197425010],
    [+1.11508390868455, -0.97617412809198, +6.25462847718180],
    [+0.61938955433011, +2.17903547389232, -6.21279842416963],
    [-2.67491681346835, +3.00175899761859, +1.05038813614845],
    [-4.13181080289514, -2.34226739863660, -3.44356159392859],
    [+2.85007173009739, -2.64884892757600, +0.71010806424206],
])
calc = Calculator("GFN2-xTB", numbers, positions)
res = calc.singlepoint()
print(res.get("energy"))  # Results in atomic units
# => -31.716159156026254

Alternatively, a parametrization mapping can be passed directly to the calculator:

params = {"charge": {"effective": {"average": "arithmetic", "gexp": 2.0}}}
calc = Calculator(params, np.array([1, 1]), np.array([[0.0, 0.0, -0.37], [0.0, 0.0, 0.37]]))
print(calc.singlepoint().get("energy"))

Building the extension module

The Python bindings can be built against an existing installation of tblite or free-standing. The free-standing implementation will select a matching version of the shared library, when building against an existing tblite library the API version of the two parts must match.

Setuptools build

This project support installation with pip as an easy way to build the Python API.

C compiler to build the C-API and compile the extension module (the compiler name should be exported in the CC environment variable)
Python 3.6 or newer
The following Python packages are required additionally
- cffi
- numpy
- pkgconfig (setup only)

Ensure that you can find tblite via

pkg-config --modversion tblite

Adjust the PKG_CONFIG_PATH environment variable to include the correct directories to find the installation if necessary. Alternatively, you can set the TBLITE_PREFIX environment variable to point to the installation of the library.

Make sure to have your C compiler set to the CC environment variable

export CC=gcc

Install the project with pip

pip install .

Using meson

This directory contains a separate meson build file to allow the out-of-tree build of the CFFI extension module. The out-of-tree build requires

C compiler to build the C-API and compile the extension module
meson version 0.57.2 or newer
a build-system backend, i.e. ninja version 1.7 or newer
Python 3.6 or newer with the CFFI package installed

To make a free-standing build you can provide the main repository as subproject to the Python bindings without having to build the shared library first. This can be done for example by symlinking the main repository to the subprojects directory.

mkdir subprojects
ln -s $(realpath ..) subprojects/tblite

Note that this step is not needed if you built against an existing tblite installation.

Setup a build with

meson setup _build -Dpython_version=$(which python3) --prefix=/path/to/install

The Python version can be used to select a different Python version, it defaults to 'python3'. Python 2 is not supported with this project, the Python version key is meant to select between several local Python 3 versions.

Compile the project with

meson compile -C _build

The extension module is now available in _build/tblite/_libtblite.*.so. You can install as usual with

meson install -C _build

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tblite 0.7.0

Building the extension module

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SHA256	`327e8f62e8b89c55a1117d5ab3644132fe6c4947bae70dfd018e189f2238164c`
MD5	`6a643ae043005f37af7542eed62f2c60`
BLAKE2b-256	`9d2c281a98602cb93b72419fe32de54aa3783166bbe5ab34f3996267750a04d5`

Algorithm	Hash digest
SHA256	`0faa6ffc2af5ecc457523fc6190dba25f5608a68646a3840298e1e25d493b594`
MD5	`17005c85db903e7c649e6ecf6783132b`
BLAKE2b-256	`2bac63fb9749dbeb0b419706548e8b2a231a526267502bd68d0bb536cb1e7d52`

Algorithm	Hash digest
SHA256	`81f860a6241ae6f568cd17684ff883a67ec59b1f67bf1cb958d549f81b859c0c`
MD5	`270f3d04bc144d4973a510c6fbcced14`
BLAKE2b-256	`7d347441944a5f6127f0ca9b6238c2fcdfbdd7936d8ee2835b65b5c63f87618b`

Algorithm	Hash digest
SHA256	`9dc8e653f5192805c648b827417614b47f9b9b673f7152a665ac3909e6d4b912`
MD5	`90f18f913be7dbdd106a4cd75f7f9097`
BLAKE2b-256	`e655651abb7aff241acedcc8715abbc5330815493d9355190d0a7e0cfb61dce5`