Domain Class Reference

This class is used to read in the phasespace and to handle macroscopic values. More...

#include <Domain.h>

Public Member Functions
	Domain (int rank)
	The constructor sets _localRank to rank and initializes all member variables.
void	readXML (XMLfileUnits &xmlconfig)
void	writeCheckpoint (std::string filename, ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, double currentTime, bool useBinaryFormat=false)
	writes a checkpoint file that can be used to continue the simulation More...
void	writeCheckpointHeader (std::string filename, ParticleContainer *particleContainer, const DomainDecompBase *domainDecomp, double currentTime)
	writes a checkpoint file that can be used to continue the simulation More...
void	writeCheckpointHeaderXML (std::string filename, ParticleContainer *particleContainer, const DomainDecompBase *domainDecomp, double currentTime)
void	initParameterStreams (double cutoffRadius, double cutoffRadiusLJ)
	initialize far field correction parameters More...
void	setLocalUpot (double Upot)
	set the potential of the local process
double	getLocalUpot () const
	get the potential of the local process
void	setLocalUpotCompSpecific (double UpotCspec)
	set the fluid and fluid-solid potential of the local process
void	setNumFluidComponents (unsigned nc)
	set the number of fluid phase components (specified in the config-file)
unsigned	getNumFluidComponents ()
	get the numbr of fluid molecules as specified in the config file (*_1R.cfg)
double	getLocalUpotCompSpecific ()
	get the fluid and fluid-solid potential of the local process
void	setLocalVirial (double Virial)
	set the virial of the local process
double	getLocalVirial () const
	get the virial of the local process
double	getGlobalBetaTrans ()
	get thermostat scaling for translations
double	getGlobalBetaTrans (int thermostat)
double	getGlobalBetaRot ()
	get thermostat scaling for rotations
double	getGlobalBetaRot (int thermostat)
double	getGlobalLength (int d) const
	return the length of the domain More...
void	setGlobalLength (int index, double length)
	set the length of the domain More...
double	getGlobalCurrentTemperature ()
	get the global temperature for the whole system (i.e. thermostat ID 0)
double	getCurrentTemperature (int thermostatID)
double	getTargetTemperature (int thermostatID)
void	setGlobalTemperature (double T)
	set the global temperature
void	setTargetTemperature (int thermostatID, double T)
std::vector< double > &	getmixcoeff ()
	get the mixcoeff
double	getepsilonRF () const
	get the epsilonRF
void	setepsilonRF (double erf)
	set the epsilonRF
unsigned long	getglobalNumMolecules () const
	get globalNumMolecules
void	setglobalNumMolecules (unsigned long glnummol)
	set globalNumMolecules
void	updateglobalNumMolecules (ParticleContainer *particleContainer, DomainDecompBase *domainDecomp)
	update globalNumMolecules
CommVar< uint64_t >	getMaxMoleculeID () const
	get local/global max. moleculeID
void	updateMaxMoleculeID (ParticleContainer *particleContainer, DomainDecompBase *domainDecomp)
	update max. moleculeID
double	getGlobalPressure ()
	get the global pressure
double	getAverageGlobalUpot () const
	get the global average potential per particle More...
double	getGlobalUpot () const
double	getAverageGlobalUpotCSpec ()
	by Stefan Becker: return the average global potential of the fluid-fluid and fluid-solid interaction (but NOT solid-solid interaction)
unsigned long	getNumFluidMolecules ()
double	getAverageGlobalVirial () const
	get the global average virial per particle More...
void	setLocalSummv2 (double summv2, int thermostat)
	sets _localSummv2 to the given value
void	setLocalSumIw2 (double sumIw2, int thermostat)
	sets _localSumIw2 to the given value
void	setLocalNrotDOF (int thermostat, unsigned long N, unsigned long rotDOF)
	sets _localThermostatN and _localRotationalDOF for thermostat
double	getglobalRho ()
	get globalRho
void	setglobalRho (double grho)
	set globalRho
unsigned long	getglobalRotDOF ()
	get globalRotDOF
void	setglobalRotDOF (unsigned long grotdof)
	set globalRotDOF
Comp2Param &	getComp2Params ()
	get the parameter streams
void	calculateGlobalValues (DomainDecompBase *domainDecomp, ParticleContainer *particleContainer, bool collectThermostatVelocities, double Tfactor)
	calculate the global macroscopic values More...
void	calculateGlobalValues (DomainDecompBase *domainDecomp, ParticleContainer *particleContainer)
	calls this->calculateGlobalValues with Tfactor = 1 and without velocity collection
void	calculateVelocitySums (ParticleContainer *partCont)
	calculate _localSummv2 and _localSumIw2 More...
void	calculateThermostatDirectedVelocity (ParticleContainer *partCont)
bool	thermostatIsUndirected (int thermostat)
double	getThermostatDirectedVelocity (int thermostat, int d)
	returns the directed velocity associated with a thermostat More...
bool	severalThermostats ()
	returns whether there are several distinct thermostats in the system
int	getThermostat (int cid)
	thermostat to be applied to component cid More...
void	disableComponentwiseThermostat ()
	disables the componentwise thermostat (so that a single thermostat is applied to all DOF)
void	enableComponentwiseThermostat ()
	enables the componentwise thermostat
unsigned	maxThermostat ()
	returns the ID of the "last" thermostat in the system More...
void	setComponentThermostat (int cid, int thermostat)
	associates a component with a thermostat More...
void	enableUndirectedThermostat (int thermostat)
	enables the "undirected" flag for the specified thermostat More...
unsigned long	N ()
void	Nadd (unsigned cid, int N, int localN)
double	getGlobalVolume () const
void	thermostatOff ()
void	thermostatOn ()
bool	NVE ()
bool	thermostatWarning ()
void	evaluateRho (unsigned long localN, DomainDecompBase *comm)
void	submitDU (unsigned cid, double DU, double *r)
void	setLambda (double lambda)
void	setDensityCoefficient (float coeff)
void	setProfiledComponentMass (double m)
void	init_cv (unsigned N, double U, double UU)
void	record_cv ()
double	cv ()
double	getSigma (unsigned cid, unsigned nthSigma)
	methods implemented by Stefan Becker stefa.nosp@m.n.be.nosp@m.cker@.nosp@m.mv.u.nosp@m.ni-kl.nosp@m..de
unsigned	getNumberOfComponents ()
void	setUpotCorr (double upotcorr)
void	setVirialCorr (double virialcorr)
void	SetExplosionHeuristics (bool bVal)

Detailed Description

This class is used to read in the phasespace and to handle macroscopic values.

Author

Martin Bernreuther bernr.nosp@m.euth.nosp@m.er@hl.nosp@m.rs.d.nosp@m.e et al. (2011)

This class is responsible for all macroscopic values. It is important to differentiate between local and global version of those values Macroscopic values are values that aggregate some property of a set of molecules. As this program is designed to run on a parallel computer, there are typically several processes. Each process has an instance of this class, but with a different subset of molecules. Therefore, also the macroscopic values are only representative for the "local" domain of that process.

member variables that represent "local" macroscopic values begin with _local

properties of the global system begin with _global if only the rank 0 process obtains the correct value (e.g., as a sum over corresponding local properties) and with _universal if the global value must be communicated to all processes.

At some points of the simulation, macroscopic values for the whole set of molecules have to be calculated. Those values are stored in member variables beginning with _global.

Member Function Documentation

calculateGlobalValues()

void Domain::calculateGlobalValues	(	DomainDecompBase *	domainDecomp,
		ParticleContainer *	particleContainer,
		bool	collectThermostatVelocities,
		double	Tfactor
	)

calculate the global macroscopic values

Parameters

domainDecomp	domain decomposition
particleContainer	particle Container
collectThermostatVelocities	flag stating whether the directed velocity should be collected for the corresponding thermostats
Tfactor	temporary factor applied to the temperature during equilibration

Essentially, this method calculates all thermophysical values that require communication between the subdomains of the system.

In particular, it determines:

• the potential energy and the virial
• if (collectThermostatVelocities == true), the directed velocity associated with the appropriately marked thermostats
• the kinetic energy and number of DOF associated with each thermostat
• on that basis, the correction factors for translation and rotation, also applying some heuristics in case of an explosion

The heuristics applied in case of an explosion were already commented on, in the appropriate place (Domain.cpp), but apparently it should be repeated here (according to the requirements communicated by TUM): Sometimes an "explosion" occurs, for instance, by inserting a particle at an unfavorable position, or due to imprecise integration of the equations of motion. The thermostat would then remove the kinetic energy from the rest of the system, effectively destroying a simulation run that could be saved by a more intelligent version, which is provided by the present heuristics. It is essential that such an intervention does not occur regularly, therefore it is limited to three times every 3000 time steps. That limit is implemented using the properties _universalSelectiveThermostatCounter, _universalSelectiveThermostatWarning, and _universalSelectiveThermostatError.

calculateThermostatDirectedVelocity()

void Domain::calculateThermostatDirectedVelocity

(

ParticleContainer *

partCont

)

Calculates the LOCAL directed kinetic energy associated with the appropriately marked thermostats

calculateVelocitySums()

void Domain::calculateVelocitySums

(

ParticleContainer *

partCont

)

calculate _localSummv2 and _localSumIw2

The present method calculates the translational and rotational kinetic energies associated with the thermostats of the system, together with the corresponding number of DOF. If a thermostat is marked as applying to the undirected motion only, this is explicitly considered by subtracting the average directed motion corresponding to the thermostat from the motion of each individual particle, for the purpose of aggregating the kinetic energy of the undirected motion.

enableUndirectedThermostat()

void Domain::enableUndirectedThermostat

(

int

thermostat

)

enables the "undirected" flag for the specified thermostat

Parameters

tst	internal ID of the respective thermostat

getAverageGlobalUpot()

double Domain::getAverageGlobalUpot

(

)

const

get the global average potential per particle

Before this method is called, it has to be sure that the global potential has been calculated (method calculateGlobalValues)

getAverageGlobalVirial()

double Domain::getAverageGlobalVirial

(

)

const

get the global average virial per particle

Before this method is called, it has to be sure that the global virial has been calculated (method calculateGlobalValues)

getGlobalLength()

double Domain::getGlobalLength ( int  d ) const

inline

return the length of the domain

Parameters

d	dimension for which the length should be returned

getNumFluidMolecules()

unsigned long Domain::getNumFluidMolecules

(

)

by Stefan Becker: determine and return the totel number of fluid molecules this method assumes all molecules with a component-ID less than _numFluidComponent to be fluid molecules

getThermostat()

int Domain::getThermostat ( int  cid )

inline

thermostat to be applied to component cid

Parameters

cid	ID of the respective component

getThermostatDirectedVelocity()

double Domain::getThermostatDirectedVelocity ( int  thermostat, int  d  )

inline

returns the directed velocity associated with a thermostat

Parameters

th	ID of the thermostat
d	coordinate 0 (v_x), 1 (v_y), or 2 (v_z).

It should be obvious that this method only returns sensible values for thermostats marked as "undirected", because otherwise the directed velocity is not explicitly computed.

initParameterStreams()

void Domain::initParameterStreams	(	double	cutoffRadius,
		double	cutoffRadiusLJ
	)

initialize far field correction parameters

By limiting the calculation to pairs of particles which have less distance than the given cutoff radius, an error is made By calculating approximations for the neglected pairs, the error can be reduced. The way the cutoff correction works is probably explained by all books on molecular simulation, e.g. Allen/Tildesley [1].

The idea is that for radii above the cutoff radius, the radial distribution function is assumed to be exactly one, so that the correction for the internal energy as well as the virial can be obtained immediately from an integral over the pair potential and its derivative, respectively. For quadrupoles, the long-range correction turns out to be zero so that it is not calculated here. Molecules with point charges and a zero net charge interact over long distances according to their dipole moments, which is why effective dipoles are calculated for the far field correction.

If ions appear, so that the net charge of a molecule is distinct from zero, the far field terms become much more complicated, and THAT IS NOT IMPLEMENTED AT PRESENT.

[1] Computer Simulation of Liquids (1989), Clarendon, Oxford.

Parameters

cutoffRadius	cutoff radius for electrostatics
cutoffRadiusLJ	cutoff radius for the LJ potential

initialize parameter streams

This method should only be called, after the component information and all molecule data have been read in

Parameters

cutoffRadius

cutoff radius

maxThermostat()

unsigned Domain::maxThermostat ( )

inline

returns the ID of the "last" thermostat in the system

The idea is that ID -1 refers to DOF without thermostats, while ID 0 refers to the entire system (or to the unique thermostat if the componentwise thermostat is disabled). In case of componentwise thermostats being applied, these have the IDs from 1 to this->maxThermostat().

readXML()

void Domain::readXML

(

XMLfileUnits &

xmlconfig

)

Todo:

reading temperature is performed in the Ensemble, so check and remove

setComponentThermostat()

void Domain::setComponentThermostat ( int  cid, int  thermostat  )

inline

associates a component with a thermostat

Parameters

cid	internal ID of the component
th	internal ID of the thermostat

setGlobalLength()

void Domain::setGlobalLength	(	int	index,
		double	length
	)

set the length of the domain

Parameters

index	dimension for which the length should be set
length	value which should be set

thermostatIsUndirected()

bool Domain::thermostatIsUndirected ( int  thermostat )

inline

A thermostat is referred to as undirected here if it explicitly excludes the kinetic energy associated with the directed motion of the respective components.

writeCheckpoint()

void Domain::writeCheckpoint	(	std::string	filename,
		ParticleContainer *	particleContainer,
		DomainDecompBase *	domainDecomp,
		double	currentTime,
		bool	useBinaryFormat = false
	)

writes a checkpoint file that can be used to continue the simulation

The format of the checkpointfile written by this method is the same as the format of the input file.

Parameters

filename	Name of the checkpointfile (including path)
particleContainer	The molecules that have to be written to the file are stored here
domainDecomp	In the parallel version, the file has to be written by more than one process. Methods to achieve this are available in domainDecomp
currentTime	The current time to be printed.
useBinaryFormat	indicates wheter binary I/O is used or not

writeCheckpointHeader()

void Domain::writeCheckpointHeader	(	std::string	filename,
		ParticleContainer *	particleContainer,
		const DomainDecompBase *	domainDecomp,
		double	currentTime
	)

writes a checkpoint file that can be used to continue the simulation

The format of the checkpointfile written by this method is the same as the format of the input file.

Parameters

filename	Name of the header file (including path). Dependent on the I/O format, this could be the same file as the data file
particleContainer	The molecules that have to be written to the file are stored here
domainDecomp	In the parallel version, the file has to be written by more than one process. Methods to achieve this are available in domainDecomp
currentTime	The current time to be printed.

---

The documentation for this class was generated from the following files:

• src/Domain.h
• src/Domain.cpp