Class representing star polymers. More...
#include <StarPolymers.hpp>
Public Types | |
| typedef PositionCoordinate | ForceCoordinate |
| The type to store force coordinates. More... | |
| typedef ImplementationDetails::StarPolymers::ParticleType | ParticleType |
| Holds the enumeration of particle types. More... | |
Public Member Functions | |
| StarPolymers (const Configuration::Setting &settings, const BoundaryCondition::Base *const boundaryCondition) | |
| The constructor. More... | |
| virtual | ~StarPolymers () |
| The destructor. More... | |
| void | performMDTimestep () |
Performs, on the Device, an MD timestep of size getMDTimeStepSize(). More... | |
| std::size_t | getStarCount () const |
| Returns the total number of polymer stars in this instance. More... | |
| std::size_t | getArmCountPerStar () const |
| Returns the number of arms per star. More... | |
| std::size_t | getParticleCountPerArm () const |
| Returns the number of particles per arm. More... | |
| bool | hasMagneticParticles () const |
| Returns whether arms have an additional magnetic particle attached. More... | |
| std::size_t | getParticleCountPerArmIncludingMagneticParticles () const |
| Returns the number of particles per arm, including magnetic particles. More... | |
| std::size_t | getParticleCountPerStar () const |
| Returns the total number of individual particles per star. More... | |
| std::size_t | getParticleCount () const |
| Returns the total number of individual particles in all stars. More... | |
| std::size_t | getNumberOfLogicalEntities () const |
| Returns the number of logical entities in the solute. More... | |
| virtual FP | getParticleMass () const |
| Returns the mass of a particle, which is assumed to be equal for all particles in this instance. More... | |
| void | writeStructureToSnapshot (VTFSnapshotFile *const snapshot) const |
| Writes structure information to the given snapshot file. More... | |
| void | writeStateToSnapshot (VTFSnapshotFile *const snapshot) const |
| Writes the particle positions and velocities to the given snapshot file. More... | |
| void | readStateFromSnapshot (VTFSnapshotFile *const snapshot) |
| Reads the next timestep block from the given snapshot file, and uses it as the current state. More... | |
| bool | snapshotStructureIsCompatible (const VTFSnapshotFile &snapshot) const |
| Returns whether the given snapshot file is compatible with the star polymer architecture, e.g. More... | |
| virtual std::size_t | getParticleCount () const=0 |
| Returns the number of MPC solute particles. More... | |
| virtual std::size_t | getNumberOfLogicalEntities () const=0 |
| Returns the number of logical entities in the solute. More... | |
| void | fetchFromDevice () const |
| Copies the MPC solute particles from the CUDA Device to the Host. More... | |
| const RemotelyStoredVector< const MPCParticlePositionType > | getPosition (const std::size_t particleID) const |
| Returns a MPC solute particle's position vector. More... | |
| const RemotelyStoredVector< const MPCParticleVelocityType > | getVelocity (const std::size_t particleID) const |
| Returns a MPC solute particle's velocity vector. More... | |
| const MPCParticlePositionType * | getDevicePositions () const |
| Returns a const pointer to the MPC solute positions on the Device. More... | |
| MPCParticlePositionType * | getDevicePositions () |
| Returns a pointer to the MPC solute positions on the Device. More... | |
| MPCParticlePositionType * | getHostPositions () |
| Returns a pointer to the MPC solute positions on the Host. More... | |
| const MPCParticleVelocityType * | getDeviceVelocities () const |
| Returns a const pointer to the MPC solute velocities on the Device. More... | |
| MPCParticleVelocityType * | getDeviceVelocities () |
| Returns a pointer to the MPC solute velocities on the Device. More... | |
| MPCParticleVelocityType * | getHostVelocities () |
| Returns a pointer to the MPC solute velocities on the Host. More... | |
| FP | getMDTimeStepSize () const |
| Returns the number of time units advanced per MD step. More... | |
| bool | hasInstrumentation () const |
| Returns whether the solute has instrumentation configured. More... | |
| Instrumentation::Base & | getInstrumentation () const |
| Returns the solute instrumentation. More... | |
| virtual FP | getParticleMass () const=0 |
| Returns the mass of a particle, which is assumed to be equal for all particles in this instance. More... | |
Protected Member Functions | |
| void | pushToDevice () |
| Copies the MPC solute particles from the Host to the CUDA Device. More... | |
Protected Attributes | |
| DeviceMemoryManager | deviceMemoryManager |
| The Device memory manager. More... | |
| FP | mdTimeStepSize |
| The number of time units to advance per MD step. More... | |
| Instrumentation::Base * | instrumentation |
| The solute instrumentation. More... | |
| boost::scoped_array< MPCParticlePositionType > | h_positions |
| Host buffer for particle positions. More... | |
| boost::scoped_array< MPCParticleVelocityType > | h_velocities |
| Host buffer for particle velocities. More... | |
| MPCParticlePositionType * | d_positions |
| Particle positions on the Device. More... | |
| MPCParticleVelocityType * | d_velocities |
| Particle velocities on the Device. More... | |
Detailed Description
template<typename PositionCoordinate = MPCParticlePositionType, typename VelocityCoordinate = MPCParticleVelocityType>
class OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >
Class representing star polymers.
A star polymer consists of one central core particle, attached to which there are a number of linear, homogeneous polymer chains, called "arms". The ends of the arms may be functionalized, by attaching an additional particle that carries a magnetic dipole moment.
The following three interaction potentials (magnetic, FENE, and WCA) are cumulative, i.e. a pair of particles can be subject to interaction due to two or more interactions at the same time.
The functionalized magnetic particles interact with one another via the OpenMPCD::PairPotentials::MagneticDipoleDipoleInteraction_ConstantIdenticalDipoles interaction. The prefactor property of the interaction class is set according to the interactionParameters.magneticPrefactor configuration property. The orientation of the dipoles may be set via the interactionParameters.dipoleOrientation setting, which must be an array of three floating-point values which define an axis. The vector formed by these three values need not be normalized; its magnitude is of no relevance.
Bonded particles – i.e. next neighbors in an arm, the central core particle and the particles attached to it, or the functionalized particles with their direct neighbor in the corresponding arm – interact via the OpenMPCD::PairPotentials::FENE potential. The interaction parameters K, l_0 and R are set to \( K_{\mu\nu} \), \( l_{\mu\nu} \), and \( R_{\mu\nu} \), respectively, which will be described below. The indices \( \mu \) and \( \nu \) denote between which kinds of particles (i.e. core, arm, or magnetic) the interaction effects a force.
Finally, each pair of particles interacts via the OpenMPCD::PairPotentials::WeeksChandlerAndersen_DistanceOffset (WCA) potential. The interaction parameters epsilon, sigma, and d are set to \( \varepsilon_{\mu\nu} \), \( \sigma_{\mu\nu} \), and \( D_{\mu\nu} \), respectively, which will be described below. The indices \( \mu \) and \( \nu \) have the same meaning as with the FENE potential.
In the configuration group interactionParameters, one has to set epsilon_core, epsilon_arm, and epsilon_magnetic, which will be referred to as \( \varepsilon_C \), \( \varepsilon_A \), and \( \varepsilon_M \), respectively. Similarly, the properties sigma_core, sigma_arm, and sigma_magnetic define \( \sigma_C \), \( \sigma_A \), and \( \sigma_M \), and D_core, D_arm, and D_magnetic define \( D_C \), \( D_A \), and \( D_M \). Finally, one also has to set magneticPrefactor in the interactionParameters group. The dipoleOrientation array, if not set, will be assumed to be [0, 0, 1].
From these quantities, the values for \( \varepsilon_{\mu\nu} \), \( \sigma{\mu\nu} \), and \( D_{\mu\nu} \), where each \( \mu \) and \( \nu \) can take on the values \( C \) for core particles, \( A \) for non-functionalized arm particles, and \( M \) for functionalized magnetic particles, can be calculated according to the Lorentz-Berthelot mixing rules:
\[ \varepsilon_{\mu\nu} = \sqrt{ \varepsilon_\mu \varepsilon_\nu } \]
\[ \sigma_{\mu\nu} = \frac{ \sigma_\mu + \sigma_\nu }{ 2 } \]
\[ D_{\mu\nu} = \frac{ D_\mu + D_\nu }{ 2 } \]
Finally, the parameters \( l_{\mu\nu} \), \( R_{\mu\nu} \), and \( K_{\mu\nu} \), are defined via
\[ l_{\mu\nu} = D_{\mu\nu} \]
\[ R_{\mu\nu} = 1.5 \sigma_{\mu\nu} \]
\[ K_{\mu\nu} = 30 \varepsilon_{\mu\nu} \sigma_{\mu\nu}^{-2} \]
In addition to the interactionParmeters settings group, the configuration passed to the constructor is expected to contain the structure group, which contains in starCount the number of stars, in armCountPerStar how many arms each star has, in armParticlesPerArm how many ordinary arm particles there are in each arm, and in hasMagneticParticles whether each arm should be terminated with a magnetic particle (in addition to the ordinary arm particles). Furthermore, particleMass contains the mass each individual particle has.
Furthermore, one must set mdTimeStepSize to the number of MPC time units one should advance per MD time-step, which must be a positive number.
If the configuration contains the value initialState, its value is taken as a path of a VTF snapshot file (see OpenMPCD::VTFSnapshotFile) that specifies the initial configuration of the stars. If the snapshot does not contain velocity information, initial velocities are assumed to be zero.
- Template Parameters
-
PositionCoordinate The type to store position coordinates. VelocityCoordinate The type to store velocity coordinates.
Definition at line 123 of file StarPolymers.hpp.
Member Typedef Documentation
◆ ForceCoordinate
| typedef PositionCoordinate OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::ForceCoordinate |
The type to store force coordinates.
Definition at line 127 of file StarPolymers.hpp.
◆ ParticleType
| typedef ImplementationDetails::StarPolymers::ParticleType OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::ParticleType |
Holds the enumeration of particle types.
Definition at line 130 of file StarPolymers.hpp.
Constructor & Destructor Documentation
◆ StarPolymers()
| OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::StarPolymers | ( | const Configuration::Setting & | settings, |
| const BoundaryCondition::Base *const | boundaryCondition | ||
| ) |
The constructor.
- Exceptions
-
OpenMPCD::InvalidConfigurationException Throws if the configuration is not valid.
- Parameters
-
[in] settings The configuration for this instance. [in] boundaryCondition The boundary conditions that have been configured. Currently, only LeesEdwards boundary conditions are supported.
◆ ~StarPolymers()
|
virtual |
The destructor.
Member Function Documentation
◆ fetchFromDevice()
|
inherited |
◆ getArmCountPerStar()
| std::size_t OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::getArmCountPerStar | ( | ) | const |
Returns the number of arms per star.
◆ getDevicePositions() [1/2]
|
inlineinherited |
Returns a pointer to the MPC solute positions on the Device.
Definition at line 116 of file CUDA/MPCSolute/Base.hpp.
◆ getDevicePositions() [2/2]
|
inlineinherited |
Returns a const pointer to the MPC solute positions on the Device.
Definition at line 108 of file CUDA/MPCSolute/Base.hpp.
◆ getDeviceVelocities() [1/2]
|
inlineinherited |
Returns a pointer to the MPC solute velocities on the Device.
Definition at line 140 of file CUDA/MPCSolute/Base.hpp.
◆ getDeviceVelocities() [2/2]
|
inlineinherited |
Returns a const pointer to the MPC solute velocities on the Device.
Definition at line 132 of file CUDA/MPCSolute/Base.hpp.
◆ getHostPositions()
|
inlineinherited |
Returns a pointer to the MPC solute positions on the Host.
Definition at line 124 of file CUDA/MPCSolute/Base.hpp.
◆ getHostVelocities()
|
inlineinherited |
Returns a pointer to the MPC solute velocities on the Host.
Definition at line 148 of file CUDA/MPCSolute/Base.hpp.
◆ getInstrumentation()
|
inlineinherited |
Returns the solute instrumentation.
- Exceptions
-
OpenMPCD::NULLPointerException If OPENMPCD_DEBUGis defined, throws if!hasInstrumentation().
Definition at line 175 of file CUDA/MPCSolute/Base.hpp.
◆ getMDTimeStepSize()
|
inlineinherited |
Returns the number of time units advanced per MD step.
Definition at line 156 of file CUDA/MPCSolute/Base.hpp.
◆ getNumberOfLogicalEntities() [1/2]
|
inline |
Returns the number of logical entities in the solute.
Definition at line 206 of file StarPolymers.hpp.
◆ getNumberOfLogicalEntities() [2/2]
|
pure virtualinherited |
Returns the number of logical entities in the solute.
◆ getParticleCount() [1/2]
| std::size_t OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::getParticleCount | ( | ) | const |
Returns the total number of individual particles in all stars.
◆ getParticleCount() [2/2]
|
pure virtualinherited |
Returns the number of MPC solute particles.
◆ getParticleCountPerArm()
| std::size_t OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::getParticleCountPerArm | ( | ) | const |
Returns the number of particles per arm.
◆ getParticleCountPerArmIncludingMagneticParticles()
| std::size_t OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::getParticleCountPerArmIncludingMagneticParticles | ( | ) | const |
Returns the number of particles per arm, including magnetic particles.
◆ getParticleCountPerStar()
| std::size_t OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::getParticleCountPerStar | ( | ) | const |
Returns the total number of individual particles per star.
◆ getParticleMass() [1/2]
|
inlinevirtual |
Returns the mass of a particle, which is assumed to be equal for all particles in this instance.
Definition at line 215 of file StarPolymers.hpp.
◆ getParticleMass() [2/2]
|
pure virtualinherited |
Returns the mass of a particle, which is assumed to be equal for all particles in this instance.
◆ getPosition()
|
inherited |
Returns a MPC solute particle's position vector.
- Warning
- This function only returns the position that was current the last time
fetchFromDevicewas called.
- Exceptions
-
OpenMPCD::OutOfBoundsException If OPENMPCD_DEBUGis defined, throws ifparticleID >= getParticleCount().
- Parameters
-
[in] particleID The particle ID.
◆ getStarCount()
|
inline |
Returns the total number of polymer stars in this instance.
Definition at line 168 of file StarPolymers.hpp.
◆ getVelocity()
|
inherited |
Returns a MPC solute particle's velocity vector.
- Warning
- This function only returns the velocity that was current the last time
fetchFromDevicewas called.
- Exceptions
-
OpenMPCD::OutOfBoundsException If OPENMPCD_DEBUGis defined, throws ifparticleID >= getParticleCount().
- Parameters
-
[in] particleID The particle ID.
◆ hasInstrumentation()
|
inlineinherited |
Returns whether the solute has instrumentation configured.
Definition at line 164 of file CUDA/MPCSolute/Base.hpp.
◆ hasMagneticParticles()
| bool OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::hasMagneticParticles | ( | ) | const |
Returns whether arms have an additional magnetic particle attached.
◆ performMDTimestep()
|
virtual |
Performs, on the Device, an MD timestep of size getMDTimeStepSize().
Implements OpenMPCD::CUDA::MPCSolute::Base< MPCParticlePositionType, MPCParticleVelocityType >.
◆ pushToDevice()
|
protectedinherited |
◆ readStateFromSnapshot()
| void OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::readStateFromSnapshot | ( | VTFSnapshotFile *const | snapshot | ) |
Reads the next timestep block from the given snapshot file, and uses it as the current state.
If no velocities are specified, the current ones are kept.
- Exceptions
-
OpenMPCD::NULLPointerException If OPENMPCD_DEBUGis defined, throws ifsnapshot == nullptr.OpenMPCD::InvalidArgumentException Throws if !snapshotStructureIsCompatible().
- Parameters
-
[in,out] snapshot The snapshot file to read from.
◆ snapshotStructureIsCompatible()
| bool OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::snapshotStructureIsCompatible | ( | const VTFSnapshotFile & | snapshot | ) | const |
Returns whether the given snapshot file is compatible with the star polymer architecture, e.g.
whether the number of stars, arms per star, etc. match.
If !snapshot.isInReadMode(), false is returned.
- Parameters
-
[in] snapshot The snapshot to check for compatibility.
◆ writeStateToSnapshot()
| void OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::writeStateToSnapshot | ( | VTFSnapshotFile *const | snapshot | ) | const |
Writes the particle positions and velocities to the given snapshot file.
This function will call fetchFromDevice, and write the current Device data to the given snapshot file.
- Exceptions
-
OpenMPCD::NULLPointerException Throws if snapshot == nullptr.OpenMPCD::InvalidArgumentException Throws if the number of atoms declared in the snapshot does not match the number of particles in this instance. OpenMPCD::InvalidArgumentException Throws if the given snapshot is not in write mode.
- Parameters
-
[in,out] snapshot The snapshot file.
◆ writeStructureToSnapshot()
| void OpenMPCD::CUDA::MPCSolute::StarPolymers< PositionCoordinate, VelocityCoordinate >::writeStructureToSnapshot | ( | VTFSnapshotFile *const | snapshot | ) | const |
Writes structure information to the given snapshot file.
- Exceptions
-
OpenMPCD::NULLPointerException Throws if snapshot == nullptr.OpenMPCD::InvalidArgumentException Throws if the given snapshot is not in write mode, or if the structure block already has been processed.
- Parameters
-
[in,out] snapshot The snapshot file.
Member Data Documentation
◆ d_positions
|
protectedinherited |
Particle positions on the Device.
Definition at line 210 of file CUDA/MPCSolute/Base.hpp.
◆ d_velocities
|
protectedinherited |
Particle velocities on the Device.
Definition at line 211 of file CUDA/MPCSolute/Base.hpp.
◆ deviceMemoryManager
|
protectedinherited |
The Device memory manager.
Definition at line 199 of file CUDA/MPCSolute/Base.hpp.
◆ h_positions
|
mutableprotectedinherited |
Host buffer for particle positions.
Definition at line 205 of file CUDA/MPCSolute/Base.hpp.
◆ h_velocities
|
mutableprotectedinherited |
Host buffer for particle velocities.
Definition at line 207 of file CUDA/MPCSolute/Base.hpp.
◆ instrumentation
|
protectedinherited |
The solute instrumentation.
Definition at line 203 of file CUDA/MPCSolute/Base.hpp.
◆ mdTimeStepSize
|
protectedinherited |
The number of time units to advance per MD step.
Definition at line 201 of file CUDA/MPCSolute/Base.hpp.
The documentation for this class was generated from the following file:
