This is a work in progress!
pip install git+https://github.com/luthaf/vesinGeneric interface:
from vesin import NeighborList
import numpy as np
positions = [
(0, 0, 0),
(0, 1.3, 1.3),
]
box = 3.2 * np.eye(3)
nl = NeighborList(cutoff=4.2, full_list=True)
i, j, S, d = nl.compute(
points=points,
box=box,
periodic=True,
quantities="ijSd"
)ASE interface:
from vesin import ase_neighbor_list
import ase
atoms = ase.Atoms(...)
i, j, S, d = ase_neighbor_list("ijSd", atoms, cutoff=4.2)git clone git+https://github.com/luthaf/vesin
cd vesin
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$INSTALL_PREFIX ..
cmake --build .
cmake --install .Alternatively, run
./create-single-cpp.pyCopy vesin-single-build.cpp and include/vesin.h in your project, and compile
the code in C++17 or higher mode. In this case, you'll need to define
VESIN_SHARED whenever you include the header to use the code as a shared
library, and additionally define VESIN_EXPORTS when building the shared
library itself. If you are using the code as a static library, you don't have to
do anything.
Compile with -I $INSTALL_PREFIX/include, and link with -L $INSTALL_PREFIX/lib -lvesin.
#include <string.h>
#include <stdio.h>
#include <vesin.h>
int main() {
// data
double points[][3] = {
{0, 0, 0},
{0, 1.3, 1.3},
};
size_t n_points = 2;
double box[3][3] = {
{3.2, 0.0, 0.0},
{0.0, 3.2, 0.0},
{0.0, 0.0, 3.2},
};
bool periodic = true;
// calculation setup
VesinOptions options;
options.cutoff = 4.2;
options.full = true;
options.return_shifts = true;
options.return_distances = true;
options.return_vectors = false;
VesinNeighbors neighbors;
memset(&neighbors, 0, sizeof(VesinNeighbors));
const char* error_message = NULL;
int status = vesin_neighbors(
points, n_points, box, periodic,
VesinCPU, options,
&neighbors,
&error_message,
);
if (status != EXIT_SUCCESS) {
fprintf(stderr, "error: %s\n", error_message);
return 1;
}
// use neighbors as needed
vesin_free(&neighbors);
return 0;
}