ScriptInterface::Particles Namespace Reference

Namespaces
namespace	traits

Classes
class	ParticleHandle
class	ParticleList
class	ParticleModifier
	Thin wrapper to read and write particle attributes in batches. More...
class	ParticleSlice
class	Polymer

Functions
void	initialize (Utils::Factory< ObjectHandle > *om)
static void	sanity_checks_rotation (VariantMap const &params)
static uint8_t	bitfield_from_flag (Utils::Vector3i const &flag)
static auto	quat2vector (Utils::Quaternion< double > const &q)
static auto	get_quaternion_safe (std::string const &name, Variant const &value)
static auto	get_gamma_safe (Variant const &value)
auto	error_msg (std::string const &name, std::string const &reason)
auto	get_real_particle (boost::mpi::communicator const &comm, int p_id, ::CellStructure &cell_structure)
void	particle_checks (int p_id, Utils::Vector3d const &pos)
void	local_add_exclusion (int pid1, int pid2, ::CellStructure &cell_structure)
	Locally add an exclusion to a particle.
void	local_remove_exclusion (int pid1, int pid2, ::CellStructure &cell_structure)
	Locally remove an exclusion to a particle.
void	particle_exclusion_sanity_checks (int pid1, int pid2, ::CellStructure &cell_structure, auto const &comm)
static void	auto_exclusions (boost::mpi::communicator const &comm, int const n_bonds_max)
	Use the bond topology to automatically add exclusions between particles that are up to n_bonds_max bonds apart in a chain.
static void	set_particles_bonds (std::vector< int > const &pids, std::vector< std::vector< int > > const &all_bonds_ids, std::vector< std::vector< std::vector< int > > > const &all_bonds_partner_ids, ::CellStructure &cell_structure, ::System::System &system)
static void	set_particles_exclusions (std::vector< int > const &pids, std::vector< std::vector< int > > const &exclusion_lists, boost::mpi::communicator const &comm, ::CellStructure &cell_structure, ::System::System &system)
static void	set_particles_positions (std::vector< int > const &pids, std::vector< Utils::Vector3d > const &positions)
static void	set_particles_types (std::vector< int > const &pids, std::vector< int > const &types, CellStructure &cell_structure, ::System::System &system)
static void	set_particles_charges (std::vector< int > const &pids, std::vector< double > const &charges, CellStructure &cell_structure, ::System::System &system)
template<class Container >
void	set_from_vector_like (std::vector< int > const &pids, std::string const &param_name, Container const &values, Context *context, std::shared_ptr< CellSystem::CellSystem > cell_structure, std::shared_ptr< Interactions::BondedInteractions > bonded_ias)
template<typename T >
auto	get_particles_properties (std::vector< int > const &pids, std::function< T(Particle const &)> const &getter, Context *context, CellStructure const &cell_structure)

Variables
static std::array< std::array< std::string_view, 3 >, 4 > constexpr	contradicting_arguments_quat

Function Documentation

auto_exclusions()

static void ScriptInterface::Particles::auto_exclusions ( boost::mpi::communicator const &  comm, int const  n_bonds_max  )

static

Use the bond topology to automatically add exclusions between particles that are up to n_bonds_max bonds apart in a chain.

Definition at line 58 of file ParticleList.cpp.

References add_exclusion(), Utils::Mpi::gather_buffer(), System::get_system(), and stream.

Referenced by ScriptInterface::Particles::ParticleList::do_call_method().

bitfield_from_flag()

static uint8_t ScriptInterface::Particles::bitfield_from_flag ( Utils::Vector3i const &  flag )

static

Definition at line 103 of file ParticleHandle.cpp.

References stream.

Referenced by ScriptInterface::Particles::ParticleHandle::ParticleHandle().

error_msg()

auto ScriptInterface::Particles::error_msg ( std::string const &  name, std::string const &  reason  )

inline

Definition at line 47 of file ParticleHandle.hpp.

References stream.

Referenced by ScriptInterface::Particles::ParticleHandle::do_construct(), get_quaternion_safe(), ScriptInterface::Particles::ParticleHandle::ParticleHandle(), and set_particles_types().

get_gamma_safe()

static auto ScriptInterface::Particles::get_gamma_safe ( Variant const &  value )

static

Definition at line 130 of file ParticleHandle.cpp.

References Utils::Vector< T, N >::broadcast(), and stream.

Referenced by ScriptInterface::Particles::ParticleHandle::ParticleHandle().

get_particles_properties()

template<typename T >

auto ScriptInterface::Particles::get_particles_properties ( std::vector< int > const &  pids, std::function< T(Particle const &)> const &  getter, Context *  context, CellStructure const &  cell_structure  )

inline

Definition at line 82 of file ParticleSlice.hpp.

References Utils::Mpi::gather_buffer(), ScriptInterface::Context::get_comm(), CellStructure::get_local_particle(), ScriptInterface::Context::is_head_node(), and stream.

get_quaternion_safe()

static auto ScriptInterface::Particles::get_quaternion_safe ( std::string const &  name, Variant const &  value  )

static

Definition at line 120 of file ParticleHandle.cpp.

References error_msg(), and stream.

Referenced by ScriptInterface::Particles::ParticleHandle::ParticleHandle().

get_real_particle()

auto ScriptInterface::Particles::get_real_particle ( boost::mpi::communicator const &  comm, int  p_id, ::CellStructure &  cell_structure  )

inline

Definition at line 53 of file ParticleHandle.hpp.

References CellStructure::get_local_particle(), and stream.

Referenced by particle_exclusion_sanity_checks().

initialize()

void ScriptInterface::Particles::initialize

(

Utils::Factory< ObjectHandle > *

om

)

Definition at line 30 of file particle_data/initialize.cpp.

References stream.

Referenced by ScriptInterface::initialize().

local_add_exclusion()

void ScriptInterface::Particles::local_add_exclusion ( int  pid1, int  pid2, ::CellStructure &  cell_structure  )

inline

Locally add an exclusion to a particle.

Parameters

pid1	the identity of the first exclusion partner
pid2	the identity of the second exclusion partner
cell_structure	the cell structure

Definition at line 90 of file ParticleHandle.hpp.

References add_exclusion(), CellStructure::get_local_particle(), and stream.

Referenced by ScriptInterface::Particles::ParticleHandle::do_call_method(), and set_particles_exclusions().

local_remove_exclusion()

void ScriptInterface::Particles::local_remove_exclusion ( int  pid1, int  pid2, ::CellStructure &  cell_structure  )

inline

Locally remove an exclusion to a particle.

Parameters

pid1	the identity of the first exclusion partner
pid2	the identity of the second exclusion partner
cell_structure	the cell structure

Definition at line 106 of file ParticleHandle.hpp.

References delete_exclusion(), CellStructure::get_local_particle(), and stream.

Referenced by ScriptInterface::Particles::ParticleHandle::do_call_method(), and set_particles_exclusions().

particle_checks()

void ScriptInterface::Particles::particle_checks ( int  p_id, Utils::Vector3d const &  pos  )

inline

Definition at line 71 of file ParticleHandle.hpp.

References stream.

Referenced by ScriptInterface::Particles::ParticleHandle::do_construct(), ScriptInterface::Particles::ParticleHandle::ParticleHandle(), and set_particles_positions().

particle_exclusion_sanity_checks()

void ScriptInterface::Particles::particle_exclusion_sanity_checks ( int  pid1, int  pid2, ::CellStructure &  cell_structure, auto const &  comm  )

inline

Definition at line 116 of file ParticleHandle.hpp.

References get_real_particle(), and stream.

Referenced by ScriptInterface::Particles::ParticleHandle::do_call_method(), and set_particles_exclusions().

quat2vector()

static auto ScriptInterface::Particles::quat2vector ( Utils::Quaternion< double > const &  q )

static

Definition at line 116 of file ParticleHandle.cpp.

Referenced by ScriptInterface::Particles::ParticleHandle::do_call_method(), and ScriptInterface::Particles::ParticleHandle::ParticleHandle().

sanity_checks_rotation()

static void ScriptInterface::Particles::sanity_checks_rotation ( VariantMap const &  params )

static

Definition at line 85 of file ParticleHandle.cpp.

References contradicting_arguments_quat, and stream.

Referenced by ScriptInterface::Particles::ParticleHandle::do_call_method(), and ScriptInterface::Particles::ParticleHandle::do_construct().

set_from_vector_like()

template<class Container >

void ScriptInterface::Particles::set_from_vector_like	(	std::vector< int > const &	pids,
		std::string const &	param_name,
		Container const &	values,
		Context *	context,
		std::shared_ptr< CellSystem::CellSystem >	cell_structure,
		std::shared_ptr< Interactions::BondedInteractions >	bonded_ias
	)

Definition at line 58 of file ParticleSlice.hpp.

References ScriptInterface::Context::make_shared(), and stream.

Referenced by ScriptInterface::Particles::ParticleSlice::do_call_method().

set_particles_bonds()

static void ScriptInterface::Particles::set_particles_bonds ( std::vector< int > const &  pids, std::vector< std::vector< int > > const &  all_bonds_ids, std::vector< std::vector< std::vector< int > > > const &  all_bonds_partner_ids, ::CellStructure &  cell_structure, ::System::System &  system  )

static

Definition at line 49 of file ParticleSlice.cpp.

References add_bond(), Particle::bonds(), CellStructure::get_local_particle(), and stream.

Referenced by ScriptInterface::Particles::ParticleSlice::do_call_method().

set_particles_charges()

static void ScriptInterface::Particles::set_particles_charges ( std::vector< int > const &  pids, std::vector< double > const &  charges, CellStructure &  cell_structure, ::System::System &  system  )

static

Definition at line 134 of file ParticleSlice.cpp.

References CellStructure::get_local_particle(), Particle::q(), and stream.

Referenced by ScriptInterface::Particles::ParticleSlice::do_call_method().

set_particles_exclusions()

static void ScriptInterface::Particles::set_particles_exclusions ( std::vector< int > const &  pids, std::vector< std::vector< int > > const &  exclusion_lists, boost::mpi::communicator const &  comm, ::CellStructure &  cell_structure, ::System::System &  system  )

static

Definition at line 75 of file ParticleSlice.cpp.

References CellStructure::get_local_particle(), local_add_exclusion(), local_remove_exclusion(), particle_exclusion_sanity_checks(), and stream.

Referenced by ScriptInterface::Particles::ParticleSlice::do_call_method().

set_particles_positions()

static void ScriptInterface::Particles::set_particles_positions ( std::vector< int > const &  pids, std::vector< Utils::Vector3d > const &  positions  )

static

Definition at line 105 of file ParticleSlice.cpp.

References particle_checks(), set_particle_pos(), and stream.

Referenced by ScriptInterface::Particles::ParticleSlice::do_call_method().

set_particles_types()

static void ScriptInterface::Particles::set_particles_types ( std::vector< int > const &  pids, std::vector< int > const &  types, CellStructure &  cell_structure, ::System::System &  system  )

static

Definition at line 115 of file ParticleSlice.cpp.

References error_msg(), CellStructure::get_local_particle(), and stream.

Referenced by ScriptInterface::Particles::ParticleSlice::do_call_method().

Variable Documentation

contradicting_arguments_quat

std::array<std::array<std::string_view, 3>, 4> constexpr ScriptInterface::Particles::contradicting_arguments_quat

staticconstexpr

Initial value:

{{
    {{"dip", "dipm",
      "Setting 'dip' is sufficient as it defines the scalar dipole moment."}},
    {{"quat", "director",
      "Setting 'quat' is sufficient as it defines the director."}},
    {{"dip", "quat",
      "Setting 'dip' would overwrite 'quat'. Set 'quat' and 'dipm' instead."}},
    {{"dip", "director",
      "Setting 'dip' would overwrite 'director'. Set 'director' and "
      "'dipm' instead."}},
}}

Definition at line 73 of file ParticleHandle.cpp.

Referenced by sanity_checks_rotation().