File size: 3,675 Bytes
10f2621 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 | #ifndef H_TABIPB_PARTICLES_STRUCT_H
#define H_TABIPB_PARTICLES_STRUCT_H
#include <vector>
#include <cstdlib>
#include "timer.h"
#include "molecule.h"
#include "params.h"
struct Timers_Particles;
class Particles
{
private:
const class Molecule& molecule_;
const struct Params& params_;
struct Timers_Particles& timers_;
std::size_t num_;
std::size_t num_faces_;
double surface_area_;
std::vector<std::size_t> face_x_;
std::vector<std::size_t> face_y_;
std::vector<std::size_t> face_z_;
std::vector<double> x_;
std::vector<double> y_;
std::vector<double> z_;
std::vector<double> nx_;
std::vector<double> ny_;
std::vector<double> nz_;
std::vector<double> area_;
std::vector<double> source_term_;
std::vector<double> target_charge_;
std::vector<double> target_charge_dx_;
std::vector<double> target_charge_dy_;
std::vector<double> target_charge_dz_;
std::vector<double> source_charge_;
std::vector<double> source_charge_dx_;
std::vector<double> source_charge_dy_;
std::vector<double> source_charge_dz_;
std::vector<std::size_t> order_;
void generate_particles(Params::Mesh, double, double);
void update_source_term_on_host() const;
public:
Particles(const class Molecule&, const struct Params&, struct Timers_Particles&);
~Particles() = default;
int partition_8(std::size_t, std::size_t, std::array<std::size_t, 16>&);
void reorder();
void unorder(std::vector<double>& potential);
void compute_charges(const double* potential);
const std::array<double, 6> bounds(std::size_t begin, std::size_t end) const;
double compute_solvation_energy(std::vector<double>& potential) const;
void output_VTK(const std::vector<double>& potential) const;
std::size_t num() const { return num_; };
double surface_area() const { return surface_area_; };
const double* x_ptr() const { return x_.data(); };
const double* y_ptr() const { return y_.data(); };
const double* z_ptr() const { return z_.data(); };
const double* nx_ptr() const { return nx_.data(); };
const double* ny_ptr() const { return ny_.data(); };
const double* nz_ptr() const { return nz_.data(); };
const double* area_ptr() const { return area_.data(); };
const double* source_term_ptr() const { return source_term_.data(); };
const double* target_charge_ptr() const { return target_charge_.data(); };
const double* target_charge_dx_ptr() const { return target_charge_dx_.data(); };
const double* target_charge_dy_ptr() const { return target_charge_dy_.data(); };
const double* target_charge_dz_ptr() const { return target_charge_dz_.data(); };
const double* source_charge_ptr() const { return source_charge_.data(); };
const double* source_charge_dx_ptr() const { return source_charge_dx_.data(); };
const double* source_charge_dy_ptr() const { return source_charge_dy_.data(); };
const double* source_charge_dz_ptr() const { return source_charge_dz_.data(); };
void compute_source_term();
void copyin_to_device() const;
void delete_from_device() const;
};
struct Timers_Particles
{
Timer ctor;
Timer compute_source_term;
Timer compute_charges;
Timer compute_solvation_energy;
Timer copyin_to_device;
Timer delete_from_device;
Timer output_VTK;
void print() const;
std::string get_durations() const;
std::string get_headers() const;
Timers_Particles() = default;
~Timers_Particles() = default;
};
#endif /* H_PARTICLE_STRUCT_H */
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