Two points

Find the nearest neighbour of each of two atoms in a 10-unit cubic box.

C

Save as two_points.c:

#include "linkcell.h"
#include <stdio.h>

int main(void) {
  double xyz[] = {0.0, 0.0, 0.0, 1.0, 0.0, 0.0};
  lc_cell box = lc_cell_ortho(10.0, 10.0, 10.0);
  int out[2];
  if (lc_knearest(xyz, 2, &box, 1, NULL, 0.0, out) != 0) {
    fprintf(stderr, "%s\n", lc_last_error());
    return 1;
  }
  printf("0 -> %d\n1 -> %d\n", out[0], out[1]);
  return 0;
}

xyz is packed x y z triples. out has length n * k (here 2). n and k are size_t; the integer literals convert. out[i * k + j] is the j-th neighbour of source i, nearest first. Unused slots are -1.

With an installed prefix:

cc two_points.c $(pkg-config --cflags --libs linkcell) -o two_points
./two_points

Prints:

0 -> 1
1 -> 0

examples/two_points.c is a longer form (cubic and sheared). A Meson or CMake build of the crate runs it as the two_points test.

Periodic image

Replace the coordinates with a pair that wraps:

  double xyz[] = {0.2, 0.0, 0.0, 9.4, 0.0, 0.0};

The printed pairing is still 0 -> 1 and 1 -> 0. The image across the a-face (distance 0.8) is nearer than the raw 9.2 vector.

C++

Same packed n * k contract. Neighbours owns the buffer. Failure throws linkcell::Error.

#include "linkcell.hpp"
#include <iostream>

int main() {
  const linkcell::Cell box = linkcell::Cell::ortho(10.0, 10.0, 10.0);
  const double xyz[] = {0.0, 0.0, 0.0, 1.0, 0.0, 0.0};
  const linkcell::Neighbours nn = linkcell::knearest(xyz, 2, box, 1);
  std::cout << "0 -> " << nn.neighbour(0, 0) << "\n";
  std::cout << "1 -> " << nn.neighbour(1, 0) << "\n";
}

c++ -std=c++17 two_points.cpp $(pkg-config --cflags --libs linkcell) -o two_points_cpp

Next: embed from C or embed from C++. Why the wrap is 0.8, not 9.2: MIC and cells.