dpd.cpp File Reference

Implementation of dpd.hpp. More...

#include <config/config.hpp>
#include "dpd.hpp"
#include "BoxGeometry.hpp"
#include "cell_system/CellStructure.hpp"
#include "cells.hpp"
#include "nonbonded_interactions/nonbonded_interaction_data.hpp"
#include "random.hpp"
#include "system/System.hpp"
#include "thermostat.hpp"
#include <utils/Vector.hpp>
#include <utils/math/sqr.hpp>
#include <utils/math/tensor_product.hpp>
#include <utils/matrix.hpp>
#include <boost/mpi/collectives/reduce.hpp>
#include <algorithm>
#include <cmath>
#include <cstdint>
#include <functional>

Include dependency graph for dpd.cpp:

Go to the source code of this file.

Functions
static Utils::Vector3d	dpd_noise (DPDThermostat const &dpd, int pid1, int pid2)
	Return a random uniform 3D vector with the Philox thermostat.
Utils::Vector3d	dpd_pair_force (Utils::Vector3d const &p1_position, Utils::Vector3d const &p1_velocity, int const &p1_id, Utils::Vector3d const &p2_position, Utils::Vector3d const &p2_velocity, int const &p2_id, DPDThermostat const &dpd, BoxGeometry const &box_geo, IA_parameters const &ia_params, Utils::Vector3d const &d, double dist, double dist2)
static auto	dpd_viscous_stress_local (System::System &system)
Utils::Vector9d	dpd_pressure_local (System::System &system)
	Local contribution to the pressure tensor.
Utils::Vector9d	dpd_stress (System::System &system, boost::mpi::communicator const &comm)
	Viscous stress tensor of the DPD interaction.

Detailed Description

Implementation of dpd.hpp.

Definition in file dpd.cpp.

Function Documentation

dpd_noise()

static Utils::Vector3d dpd_noise ( DPDThermostat const &  dpd, int  pid1, int  pid2  )

static

Return a random uniform 3D vector with the Philox thermostat.

Random numbers depend on

1. dpd_rng_counter (initialized by seed) which is increased on integration
2. Salt (decorrelates different counters)
3. Two particle IDs (order-independent, decorrelates particles, gets rid of seed-per-node)

Definition at line 57 of file dpd.cpp.

References BaseThermostat::rng_counter(), and BaseThermostat::rng_seed().

Referenced by dpd_pair_force().

dpd_pair_force()

Utils::Vector3d dpd_pair_force	(	Utils::Vector3d const &	p1_position,
		Utils::Vector3d const &	p1_velocity,
		int const &	p1_id,
		Utils::Vector3d const &	p2_position,
		Utils::Vector3d const &	p2_velocity,
		int const &	p2_id,
		DPDThermostat const &	dpd,
		BoxGeometry const &	box_geo,
		IA_parameters const &	ia_params,
		Utils::Vector3d const &	d,
		double	dist,
		double	dist2
	)

Definition at line 79 of file dpd.cpp.

References DPDParameters::cutoff, IA_parameters::dpd, dpd_noise(), dpd_pair_force(), P, DPDParameters::pref, DPD_Parameters::radial, DPD_Parameters::trans, and BoxGeometry::velocity_difference().

Referenced by add_non_bonded_pair_force_with_p(), dpd_pair_force(), dpd_viscous_stress_local(), Constraints::ShapeBasedConstraint::force(), and ForcesKernel::operator()().

dpd_pressure_local()

Utils::Vector9d dpd_pressure_local

(

System::System &

system

)

Local contribution to the pressure tensor.

Needs to be rescaled by the box volume.

Definition at line 139 of file dpd.cpp.

References dpd_viscous_stress_local(), and Utils::flatten().

Referenced by System::System::calculate_pressure().

dpd_stress()

Utils::Vector9d dpd_stress	(	System::System &	system,
		boost::mpi::communicator const &	comm
	)

Viscous stress tensor of the DPD interaction.

This calculates the total viscous stress contribution of the DPD interaction. It contains only the dissipative contributions of the interaction without noise. It's calculated as the sum over all pair virials as

\[ \sigma^{\nu\mu} = V^{-1}\sum_i \sum_{j < i} r_{i,j}^{\nu} (- \gamma_{i,j} v_{i,j})^{\mu} \]

where \(\gamma_{i,j}\) is the (in general tensor valued) DPD friction coefficient for particles i and j, \(v_{i,j}\), \(r_{i,j}\) are their relative velocity and distance and \(V\) is the box volume.

Returns

Stress tensor contribution.

Definition at line 159 of file dpd.cpp.

References System::System::box_geo, dpd_viscous_stress_local(), and Utils::flatten().

Referenced by ScriptInterface::Analysis::Analysis::do_call_method(), and Observables::DPDStress::operator()().

dpd_viscous_stress_local()

static auto dpd_viscous_stress_local ( System::System &  system )

static

Definition at line 108 of file dpd.cpp.

References System::System::box_geo, System::System::cell_structure, Distance::dist2, dpd_pair_force(), System::System::nonbonded_ias, System::System::on_observable_calc(), P, Particle::pos(), Particle::type(), Particle::v(), and Distance::vec21.

Referenced by dpd_pressure_local(), and dpd_stress().