Class AmberFD

Class Documentation

class AmberFD

AmberFD is an umbrella function thatcombines FlucDens force and DispersionPauli force settings into one accessable class. This class does not calculate forces itslf, but is instead used create and access the fluctuating density and dispersion-pauli system and set it’s options.

To use this class, first create an AmberFD object with the number of particles to be added to the system. The, add each particle to the system by calling add_particle(), passing in a ParticleInfo object. Once all particles have been added, create the fluctuating density force and dispersion-pauli force by calling create_fluc_dens_force() and create_disp_pauli_force(), respectively. Each of these forces will then be generated, and a pointer to each force can be obtained by calling get_fluc_dens_force() or get_disp_pauli_force().

Once the forces have been generated, adding new particles will have no effect on the system. Calling create_XXX_force() will simply return a pointer to the already created forces. If periodic boundary conditions are desired, then call set_use_PBC() after all particles have been added.

Public Functions

AmberFD()

Construct a new AmberFD force

AmberFD(const int n_sites)

Construct a new AmberFD force with the number of particles already known. This can help speed up the system creation for very large numbers of particles. More particles can be added than n_sites, but the memory will not be preallocated.

Parameters

n_sites – the estimated number of particles to create a system for

~AmberFD()
int add_particle(int index, ParticleInfo parameters)

Add a new particle to the system with the properties specified in it’s ParticleInfo

Parameters

  • index –

  • parameters –

Returns

index of the particle added

void add_fragment(const vec_i frag_idx)

Set the indicies that define a fragment within the entire molecular system.

Parameters

frag_idx –

inline int get_num_particles()

Get the number of particles in the system

Returns

int

std::vector<vec_d> get_forces()

Return the forces exerted on each particle. This will only have an effect if calc_energy_forces has been called forst with the updated positions. Else, this will return the forces most recently computed.

Returns

std::vector<vec_d>

Energies calc_energy_forces(const vec_d &positions)

Compute the energy and forces on the AmberFD system at the current positions.

Parameters

positions – 1-D array of positions (in a.u.)

Returns

Energies object

std::shared_ptr<FlucDens> get_fluc_dens_force(bool create_if_null = false)

Get a pointer to the FlucDens force object being used

Parameters

create_if_null – create the force if it hasn’t been created yet.

Returns

std::shared_ptr<FlucDens>

std::shared_ptr<DispersionPauli> get_disp_pauli_force(bool create_if_null = false)

Get a pointer to the DispersionPauli force object being used.

Parameters

create_if_null – create the force if it hasn’t been created yet.

Returns

std::shared_ptr<DispersionPauli>

std::shared_ptr<FlucDens> create_fluc_dens_force()

Create a FlucDens force object. Adding particles to the system After creating this force will have no effect.

Returns

std::shared_ptr<FlucDens> a pointer to the created force

std::shared_ptr<DispersionPauli> create_disp_pauli_force()

Create a DispersionPauli force object. Adding particles to the system After creating this force will have no effect.

Returns

std::shared_ptr<DispersionPauli> a pointer to the created force

std::map<int, int> get_index_mapping()

Get the a mapping from the OpenMM particle index to the AmberFD particle index.

Returns

std::map<int, int>

Energies calc_one_pair(const vec_d &positions, int i, int j)

Calculate the interaction between a single pair of particles. Since Polarization is a many-body force, it will not be calculated here.

Parameters

  • positions – The full array of positions of the system that would normally be passed to calc_energy_forces()

  • i – The index of the first particle

  • j – The index of the second particle

Returns

Energies The energies of the pair

DeltaR getDeltaR(const vec_d &positions, int i, int j)

Get the distance object between two pairs of particles.

Parameters

  • positions – The full array of positions of the system that would normally be passed to calc_energy_forces()

  • i – The index of the first particle

  • j – The index of the second particle

Returns

DeltaR

void set_use_PBC(const bool is_periodic)

Turn on or off the use of periodic boundary conditions.

Parameters

is_periodic –

void set_use_PBC(const bool is_periodic, const double x, const double y, const double z)

Turn on or off the use of periodic boundary conditions.

Parameters

  • is_periodic –

  • x – The x-direction box length

  • y – The y-direction box length

  • z – The z-direction box length

bool get_use_PBC()

Determine of the periodic doundary contitions are used or not.

Returns

true

Returns

false

void dump_to_file(std::string file_loc)

Serialize force FlucDens and DisperionPauli forces to a file.

Parameters

file_loc – String of the file location to write data to.

void load_from_file(std::string file_loc)

Load in serialized data previously created with dump_to_file()

Parameters

file_loc – String of the file location to load.

void set_threads(int n_threads)

Set the number of threads to be used in force computations vis OpenMP. If set less than or equal to one, then a serial calculation will take place.

Parameters

n_threads – Number of threads to use

double get_parallel_time()

Get the cumulative wall time used to compute forces and energies so far.

Returns

Wall time in second