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37 * Implements nblib integrator
39 * \author Victor Holanda <victor.holanda@cscs.ch>
40 * \author Joe Jordan <ejjordan@kth.se>
41 * \author Prashanth Kanduri <kanduri@cscs.ch>
42 * \author Sebastian Keller <keller@cscs.ch>
43 * \author Artem Zhmurov <zhmurov@gmail.com>
45 #include "nblib/integrator.h"
46 #include "gromacs/pbcutil/pbc.h"
47 #include "gromacs/utility/arrayref.h"
48 #include "nblib/topology.h"
53 LeapFrog::LeapFrog(const Topology& topology, const Box& box) : box_(box)
55 inverseMasses_.resize(topology.numParticles());
56 for (int i = 0; i < topology.numParticles(); i++)
58 int typeIndex = topology.getParticleTypeIdOfAllParticles()[i];
59 inverseMasses_[i] = 1.0 / topology.getParticleTypes()[typeIndex].mass();
63 LeapFrog::LeapFrog(gmx::ArrayRef<const real> inverseMasses, const Box& box) :
64 inverseMasses_(inverseMasses.begin(), inverseMasses.end()), box_(box)
68 void LeapFrog::integrate(const real dt, gmx::ArrayRef<Vec3> x, gmx::ArrayRef<Vec3> v, gmx::ArrayRef<const Vec3> f)
70 for (size_t i = 0; i < x.size(); i++)
72 for (int dim = 0; dim < dimSize; dim++)
74 v[i][dim] += f[i][dim] * dt * inverseMasses_[i];
75 x[i][dim] += v[i][dim] * dt;