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colvarproxy_namd.h
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Mon, Nov 18, 08:49

colvarproxy_namd.h
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#ifndef COLVARPROXY_NAMD_H
#define COLVARPROXY_NAMD_H
#include "Vector.h"
#include "ResizeArray.h"
#include "NamdTypes.h"
#include "SimParameters.h"
#include "Lattice.h"
#include "GlobalMaster.h"
#include "Random.h"
#include "colvarmodule.h"
#include "colvarproxy.h"
/// \brief Communication between colvars and NAMD (implementation of
/// \link colvarproxy \endlink)
class colvarproxy_namd : public colvarproxy, public GlobalMaster {
protected:
/// Pointer to the NAMD simulation input object
SimParameters const *simparams;
/// Pointer to the NAMD boundary conditions object
Lattice const *lattice;
BigReal thermostat_temperature;
/// NAMD-style PRNG object
Random random;
std::string input_prefix_str, output_prefix_str, restart_output_prefix_str;
size_t restart_frequency_s;
size_t previous_NAMD_step;
bool first_timestep;
bool system_force_requested;
std::vector<int> colvars_atoms;
std::vector<size_t> colvars_atoms_ncopies;
std::vector<cvm::rvector> positions;
std::vector<cvm::rvector> total_forces;
std::vector<cvm::rvector> applied_forces;
size_t init_namd_atom (AtomID const &aid);
SubmitReduction *reduction;
public:
friend class cvm::atom;
colvarproxy_namd();
~colvarproxy_namd();
/// \brief Reimplements GlobalMaster member function, to be called
/// at every step
void calculate();
void add_energy (cvm::real energy);
void request_system_force (bool yesno);
void log (std::string const &message);
void fatal_error (std::string const &message);
void exit (std::string const &message);
inline cvm::real unit_angstrom()
{
return 1.0;
}
cvm::real boltzmann()
{
return 0.001987191;
}
cvm::real temperature()
{
return thermostat_temperature;
}
cvm::real dt()
{
return simparams->dt;
}
inline std::string input_prefix()
{
return input_prefix_str;
}
inline std::string restart_output_prefix()
{
return restart_output_prefix_str;
}
inline std::string output_prefix()
{
return output_prefix_str;
}
inline size_t restart_frequency()
{
return restart_frequency_s;
}
cvm::rvector position_distance (cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2);
cvm::real position_dist2 (cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2);
void select_closest_image (cvm::atom_pos &pos,
cvm::atom_pos const &ref_pos);
void load_atoms (char const *filename,
std::vector<cvm::atom> &atoms,
std::string const pdb_field,
double const pdb_field_value = 0.0);
void load_coords (char const *filename,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const pdb_field,
double const pdb_field_value = 0.0);
void backup_file (char const *filename);
cvm::real rand_gaussian (void)
{
return random.gaussian();
}
};
inline cvm::rvector colvarproxy_namd::position_distance (cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
{
Position const p1 (pos1.x, pos1.y, pos1.z);
Position const p2 (pos2.x, pos2.y, pos2.z);
// return p2 - p1
Vector const d = this->lattice->delta (p2, p1);
return cvm::rvector (d.x, d.y, d.z);
}
inline void colvarproxy_namd::select_closest_image (cvm::atom_pos &pos,
cvm::atom_pos const &ref_pos)
{
Position const p (pos.x, pos.y, pos.z);
Position const rp (ref_pos.x, ref_pos.y, ref_pos.z);
ScaledPosition const srp = this->lattice->scale (rp);
Position const np = this->lattice->nearest (p, srp);
pos.x = np.x;
pos.y = np.y;
pos.z = np.z;
}
inline cvm::real colvarproxy_namd::position_dist2 (cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
{
Lattice const *l = this->lattice;
Vector const p1 (pos1.x, pos1.y, pos1.z);
Vector const p2 (pos2.x, pos2.y, pos2.z);
Vector const d = l->delta (p1, p2);
return cvm::real (d.x*d.x + d.y*d.y + d.z*d.z);
}
#endif
// Emacs
// Local Variables:
// mode: C++
// End:

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