ESPResSo
Extensible Simulation Package for Research on Soft Matter Systems
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polymer.cpp File Reference

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/Constraints.hpp"
#include "constraints/ShapeBasedConstraint.hpp"
#include "random.hpp"
#include "system/System.hpp"
#include <utils/Vector.hpp>
#include <utils/math/vec_rotate.hpp>
#include <boost/mpi/collectives/all_reduce.hpp>
#include <cmath>
#include <cstddef>
#include <functional>
#include <memory>
#include <numbers>
#include <optional>
#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 (System::System const &system, Utils::Vector3d const &pos, std::vector< std::vector< Utils::Vector3d > > const &positions, 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
systemparticle system
n_polymershow many polymers to create
beads_per_chainmonomers per chain
bond_lengthlength of the bonds between two monomers
start_positionsstarting positions of each polymers
min_distanceminimum distance between all particles
max_trieshow often a monomer/polymer should be reset if current position collides with a previous particle
use_bond_anglewhether to use the bond_angle argument
bond_angledesired bond-angle to be fixed
respect_constraintswhether to respect constraints
seedseed for RNG

Definition at line 143 of file polymer.cpp.

References System::System::box_geo, is_valid_position(), Random::mt19937(), 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 ( System::System const &  system,
Utils::Vector3d const &  pos,
std::vector< std::vector< Utils::Vector3d > > const &  positions,
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
systemthe system containing the particles
posthe trial position in question
positionsbuffered positions to respect
box_geoBox geometry
min_distancethreshold for the minimum distance between trial position and buffered/existing particles
respect_constraintswhether to respect constraints
Returns
true if valid position, false if not.

Definition at line 86 of file polymer.cpp.

References System::System::cell_structure, comm_cart, System::System::constraints, BoxGeometry::folded_position(), and BoxGeometry::get_mi_vector().

Referenced by draw_polymer_positions().

◆ random_position()

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

Definition at line 55 of file polymer.cpp.

References BoxGeometry::length().

Referenced by draw_polymer_positions().

◆ random_unit_vector()

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

Definition at line 62 of file polymer.cpp.

References Utils::Vector< T, N >::norm().

Referenced by draw_polymer_positions().