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35 /*! \internal \file
36 * \brief
37 * Implements nblib SimulationState
38 *
39 * \author Berk Hess <hess@kth.se>
40 * \author Victor Holanda <victor.holanda@cscs.ch>
41 * \author Joe Jordan <ejjordan@kth.se>
42 * \author Prashanth Kanduri <kanduri@cscs.ch>
43 * \author Sebastian Keller <keller@cscs.ch>
44 * \author Artem Zhmurov <zhmurov@gmail.com>
45 */
46 #include <vector>
47
48 #include "gromacs/pbcutil/pbc.h"
49 #include "nblib/exception.h"
50 #include "nblib/simulationstate.h"
51 #include "nblib/simulationstateimpl.h"
52 #include "nblib/util/setup.h"
53
54 namespace nblib
55 {
56
SimulationState(const std::vector<Vec3> & coordinates,const std::vector<Vec3> & velocities,const std::vector<Vec3> & forces,Box box,Topology topology)57 SimulationState::SimulationState(const std::vector<Vec3>& coordinates,
58 const std::vector<Vec3>& velocities,
59 const std::vector<Vec3>& forces,
60 Box box,
61 Topology topology) :
62 simulationStatePtr_(std::make_shared<Impl>(coordinates, velocities, forces, box, topology))
63 {
64 }
65
Impl(const std::vector<Vec3> & coordinates,const std::vector<Vec3> & velocities,const std::vector<Vec3> & forces,const Box & box,Topology topology)66 SimulationState::Impl::Impl(const std::vector<Vec3>& coordinates,
67 const std::vector<Vec3>& velocities,
68 const std::vector<Vec3>& forces,
69 const Box& box,
70 Topology topology) :
71 box_(box),
72 topology_(std::move(topology))
73 {
74 auto numParticles = topology_.numParticles();
75
76 if (int(coordinates.size()) != numParticles)
77 {
78 throw InputException("Coordinates array size mismatch");
79 }
80
81 if (int(velocities.size()) != numParticles)
82 {
83 throw InputException("Velocities array size mismatch");
84 }
85
86 if (int(forces.size()) != numParticles)
87 {
88 throw InputException("Force buffer array size mismatch");
89 }
90
91 if (!isRealValued(coordinates))
92 {
93 throw InputException("Input coordinates has at least one NaN");
94 }
95 coordinates_ = coordinates;
96 if (!isRealValued(velocities))
97 {
98 throw InputException("Input velocities has at least one NaN");
99 }
100
101 velocities_ = velocities;
102
103 forces_ = forces;
104
105 // Ensure that the coordinates are in a box following PBC
106 put_atoms_in_box(PbcType::Xyz, box.legacyMatrix(), coordinates_);
107 }
108
topology() const109 const Topology& SimulationState::Impl::topology() const
110 {
111 return topology_;
112 }
113
box() const114 Box SimulationState::Impl::box() const
115 {
116 return box_;
117 }
118
coordinates()119 std::vector<Vec3>& SimulationState::Impl::coordinates()
120 {
121 return coordinates_;
122 }
123
velocities()124 std::vector<Vec3>& SimulationState::Impl::velocities()
125 {
126 return velocities_;
127 }
128
forces()129 std::vector<Vec3>& SimulationState::Impl::forces()
130 {
131 return forces_;
132 }
133
topology() const134 const Topology& SimulationState::topology() const
135 {
136 return simulationStatePtr_->topology();
137 }
138
box() const139 Box SimulationState::box() const
140 {
141 return simulationStatePtr_->box();
142 }
143
coordinates()144 std::vector<Vec3>& SimulationState::coordinates()
145 {
146 return simulationStatePtr_->coordinates();
147 }
148
coordinates() const149 const std::vector<Vec3>& SimulationState::coordinates() const
150 {
151 return simulationStatePtr_->coordinates();
152 }
153
velocities()154 std::vector<Vec3>& SimulationState::velocities()
155 {
156 return simulationStatePtr_->velocities();
157 }
158
forces()159 std::vector<Vec3>& SimulationState::forces()
160 {
161 return simulationStatePtr_->forces();
162 }
163
164 } // namespace nblib
165