This file contains everything needed to create a start-up configuration of (possibly charged) polymer chains with counterions and salt molecules, assigning velocities to the particles and cross-linking the polymers if necessary. More...

#include "polymer.hpp"
#include "BoxGeometry.hpp"
#include "cell_system/CellStructure.hpp"
#include "communication.hpp"
#include "constraints.hpp"
#include "constraints/Constraints.hpp"
#include "constraints/ShapeBasedConstraint.hpp"
#include "random.hpp"
#include "system/System.hpp"
#include <utils/Vector.hpp>
#include <utils/constants.hpp>
#include <utils/math/vec_rotate.hpp>
#include <boost/mpi/collectives/all_reduce.hpp>
#include <boost/optional.hpp>
#include <cmath>
#include <cstddef>
#include <functional>
#include <memory>
#include <stdexcept>
#include <vector>

Include dependency graph for polymer.cpp:

Go to the source code of this file.

Functions
template<class RNG >
static Utils::Vector3d	random_position (BoxGeometry const &box_geo, RNG &rng)

template<class RNG >
static Utils::Vector3d	random_unit_vector (RNG &rng)

static bool	is_valid_position (Utils::Vector3d const &pos, std::vector< std::vector< Utils::Vector3d > > const &positions, CellStructure const &cell_structure, BoxGeometry const &box_geo, double const min_distance, int const respect_constraints)
	Determines whether a given position `pos` is valid, i.e., it doesn't collide with existing or buffered particles, nor with existing constraints (if `respect_constraints`).

std::vector< std::vector< Utils::Vector3d > >	draw_polymer_positions (System::System const &system, int const n_polymers, int const beads_per_chain, double const bond_length, std::vector< Utils::Vector3d > const &start_positions, double const min_distance, int const max_tries, int const use_bond_angle, double const bond_angle, int const respect_constraints, int const seed)
	Determines valid polymer positions and returns them.

Detailed Description

This file contains everything needed to create a start-up configuration of (possibly charged) polymer chains with counterions and salt molecules, assigning velocities to the particles and cross-linking the polymers if necessary.

The corresponding header file is polymer.hpp.

Definition in file polymer.cpp.

Function Documentation

◆ draw_polymer_positions()

std::vector< std::vector< Utils::Vector3d > > draw_polymer_positions	(	System::System const &	system,
		int	n_polymers,
		int	beads_per_chain,
		double	bond_length,
		std::vector< Utils::Vector3d > const &	start_positions,
		double	min_distance,
		int	max_tries,
		int	use_bond_angle,
		double	bond_angle,
		int	respect_constraints,
		int	seed
	)

Determines valid polymer positions and returns them.

Parameters

system	particle system
n_polymers	how many polymers to create
beads_per_chain	monomers per chain
bond_length	length of the bonds between two monomers
start_positions	starting positions of each polymers
min_distance	minimum distance between all particles
max_tries	how often a monomer/polymer should be reset if current position collides with a previous particle
use_bond_angle	whether to use the `bond_angle` argument
bond_angle	desired bond-angle to be fixed
respect_constraints	whether to respect constraints
seed	seed for RNG

Definition at line 145 of file polymer.cpp.

References System::System::box_geo, System::System::cell_structure, is_valid_position(), Random::mt19937(), pos, random_position(), random_unit_vector(), Utils::vec_rotate(), and vector_product().

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

◆ is_valid_position()

static bool is_valid_position	(	Utils::Vector3d const &	pos,
		std::vector< std::vector< Utils::Vector3d > > const &	positions,
		CellStructure const &	cell_structure,
		BoxGeometry const &	box_geo,
		double const	min_distance,
		int const	respect_constraints
	)

static

Determines whether a given position pos is valid, i.e., it doesn't collide with existing or buffered particles, nor with existing constraints (if respect_constraints).

Parameters

pos	the trial position in question
positions	buffered positions to respect
cell_structure	existing particles to respect
box_geo	Box geometry
min_distance	threshold for the minimum distance between trial position and buffered/existing particles
respect_constraints	whether to respect constraints