Luthaf

#include "Foo.hpp"
#include <iostream>
using namespace std;


Foo::Foo(int _a, int _b): a(_a), b(_b){
    cout << "C++ side, constructor" << endl;
}

Foo::~Foo(){

Luthaf

pairs:  # Non bonded atoms pairs
  - atoms: [*, *]  # Default value
    type: NullPotential
  - atoms: [He, He]
    type: LennardJones
    sigma: 3.4 A
    epsilon: 0.45 kJ/mol
  - atoms: [He, Ar]
    type: LennardJones
    sigma: 2.8 A

Luthaf

trait Potential {
    fn energy(&self) -> f64;
}

// This is just a marker trait, to know which potentials can be used as pair
// potentials. I also have AnglePotential, GlobalPotential, ...
trait PairPotential: Potential {}

impl Clone for Box<PairPotential> {
    fn clone(&self) -> Box<PairPotential> {

Luthaf

using PyCall

# Change that to whatever packages you need.
const PACKAGES = ["pyyaml"]

# Import pip
try
    @pyimport pip
catch
    # If it is not found, install it

Luthaf

use std::slice;

pub struct Vector3d([f64; 3]);

pub struct Atom {
    pub position: Vector3d,
    pub velocity: Vector3d,
    pub name: String
}

Luthaf

[input]
version = 1.0

[[systems]]
cell = 20  # Cubic cell
positions = "initial.xyz"
velocities = {init = "300 K"}
potentials = "potentials.toml"

[[simulations]]

Luthaf

==24579== Memcheck, a memory error detector
==24579== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==24579== Using Valgrind-3.11.0.SVN and LibVEX; rerun with -h for copyright info
==24579== Command: tests/xyz
==24579==
--24579-- run: /usr/bin/dsymutil "tests/xyz"
==24579== Conditional jump or move depends on uninitialised value(s)
==24579==    at 0x10000BAB1: boost::filesystem::detail::recur_dir_itr_imp::push_directory(boost::system::error_code&) (operations.hpp:1054)
==24579==    by 0x10000B900: boost::filesystem::detail::recur_dir_itr_imp::increment(boost::system::error_code*) (operations.hpp:1085)
==24579==    by 0x1000079E0: ____C_A_T_C_H____T_E_S_T____102() (operations.hpp:1278)

Luthaf

CRYST1  100.000  100.000  100.000  90.00  90.00  90.00 P 1           1
HETATM    1   He RES X   1       4.905  84.135   0.777  1.00  0.00          He
HETATM    2   He RES X   2      88.376  32.438  11.077  1.00  0.00          He
HETATM    3   He RES X   3      84.431   8.811  41.520  1.00  0.00          He
HETATM    4   He RES X   4     101.038  20.851  52.080  1.00  0.00          He
HETATM    5   He RES X   5      97.902   6.895  72.124  1.00  0.00          He
HETATM    6   He RES X   6       6.789  11.264   7.060  1.00  0.00          He
HETATM    7   He RES X   7      88.061   9.591  13.068  1.00  0.00          He
HETATM    8   He RES X   8       1.762   9.043  29.016  1.00  0.00          He
HETATM    9   He RES X   9       6.755  39.358  58.695  1.00  0.00          He

Luthaf

$ cargo benchcmp safe.log unsafe.log --threshold=2
 name                                  safe.log ns/iter  unsafe.log ns/iter  diff ns/iter   diff % 
 cache_move_all_rigid_molecules        1,463,817         1,168,495               -295,322  -20.17% 
 cache_move_all_rigid_molecules_ewald  10,620,984        8,721,128             -1,899,856  -17.89% 
 cache_move_all_rigid_molecules_wolf   8,386,407         10,278,223             1,891,816   22.56% 
 cache_move_particle                   201,875           244,669                   42,794   21.20% 
 cache_move_particle_ewald             528,745           491,710                  -37,035   -7.00% 
 cache_move_particles                  354,655           282,355                  -72,300  -20.39% 
 cache_move_particles_ewald            1,025,460         887,721                 -137,739  -13.43% 
 cache_move_particles_wolf             507,774           553,008                   45,234    8.91% 

Luthaf

diff --git a/Cargo.toml b/Cargo.toml
index 68e2fc36..5389a05e 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -26,6 +26,7 @@ clap = "2"
 
 [dev-dependencies]
 bencher = "0.1"
+lazy_static = "0.2"
 rand = "0.3"