Luthaf

import gzip
import json
import numpy as np

input_path = "TODO"
output_path = "TODO"


if input_path.endswith(".gz"):
    with gzip.open(input_path) as fd:

Luthaf

import gzip
import json
import numpy as np

input_path = "./app/examples/Zeolites.json.gz"
output_path = "Zeolites.json.gz"


with gzip.open(input_path) as fd:
    data = json.load(fd)

Luthaf

set(CMAKE_SYSTEM_NAME Linux)
set(CMAKE_SYSTEM_PROCESSOR aarch64)

set(CMAKE_CROSSCOMPILING TRUE)

if (CMAKE_TOOLCHAIN_FILE)
endif()

set(CMAKE_C_COMPILER /usr/bin/aarch64-linux-gnu-gcc)
set(CMAKE_CXX_COMPILER /usr/bin/aarch64-linux-gnu-g++)

Luthaf

#include <cstddef>

/// A non-owning memory view in a C++ std::vector<double> like object.
class ExternalBuffer {
public:
    ExternalBuffer(double* data, size_t length):
        data_(data), length_(length) {}

    void* data() {
        return reinterpret_cast<void*>(data_);

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"

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

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

==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

[input]
version = 1.0

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

[[simulations]]

Luthaf

use std::slice;

pub struct Vector3d([f64; 3]);

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