File size: 1,571 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 | #ifndef H_TABIPB_MOLECULE_STRUCT_H
#define H_TABIPB_MOLECULE_STRUCT_H
#include <vector>
#include <string>
#include <fstream>
#include <cstddef>
#include "timer.h"
#include "params.h"
#ifdef TABIPB_APBS
#include "generic/valist.h"
#endif
struct Timers_Molecule;
class Molecule
{
private:
const struct Params& params_;
struct Timers_Molecule& timers_;
std::size_t num_atoms_;
std::vector<double> coords_;
std::vector<double> charge_;
std::vector<double> radius_;
double coulombic_energy_;
public:
Molecule(struct Params&, struct Timers_Molecule&);
~Molecule() = default;
#ifdef TABIPB_APBS
Molecule(Valist*, struct Params&, struct Timers_Molecule&);
#endif
void build_xyzr_file() const;
std::size_t num_atoms() const { return num_atoms_; };
double coulombic_energy() const { return coulombic_energy_; };
const double* coords_ptr() const { return coords_.data(); };
const double* charge_ptr() const { return charge_.data(); };
const double* radius_ptr() const { return radius_.data(); };
void compute_coulombic_energy();
void copyin_to_device() const;
void delete_from_device() const;
};
struct Timers_Molecule
{
Timer ctor;
Timer compute_coulombic_energy;
Timer build_xyzr_file;
Timer copyin_to_device;
Timer delete_from_device;
void print() const;
std::string get_durations() const;
std::string get_headers() const;
Timers_Molecule() = default;
~Timers_Molecule() = default;
};
#endif /* H_MOLECULE_STRUCT_H */
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