Simpatico  v1.10
List of all members | Public Member Functions | Protected Attributes | Static Protected Attributes
Simp::LJPair Class Reference

Detailed Description

A cutoff, shifted Lennard-Jones nonbonded pair interaction.

This class defines a Lennard-Jones potential that is cutoff and shifted so that the potential is zero at the cutoff distance.

See also
Parameter file format
Pair Interaction Class Interface
Pair Interactions

Definition at line 33 of file LJPair.h.

#include <LJPair.h>

Inheritance diagram for Simp::LJPair:
Util::ParamComposite Util::ParamComponent Util::Serializable Util::MpiFileIo Simp::WcaPair

Public Member Functions

 LJPair ()
 Default constructor. More...
 
 LJPair (const LJPair &other)
 Copy constructor. More...
 
LJPairoperator= (const LJPair &other)
 Assignment. More...
 
Mutators
void setNAtomType (int nAtomType)
 Set nAtomType value. More...
 
void readParameters (std::istream &in)
 Read epsilon, sigma, and cutoff, and initialize other variables. More...
 
virtual void loadParameters (Serializable::IArchive &ar)
 Load internal state from an archive. More...
 
virtual void save (Serializable::OArchive &ar)
 Save internal state to an archive. More...
 
void setEpsilon (int i, int j, double epsilon)
 Set LJ interaction energy for a specific pair of Atom types. More...
 
void setSigma (int i, int j, double sigma)
 Get LJ range for a specific pair of Atom types. More...
 
void set (std::string name, int i, int j, double value)
 Modify a parameter, identified by a string. More...
 
Accessors
double energy (double rsq, int i, int j) const
 Returns interaction energy for a single pair of atoms. More...
 
double forceOverR (double rsq, int i, int j) const
 Returns ratio of scalar pair interaction force to pair separation. More...
 
double cutoffSq (int i, int j) const
 Get square of cutoff distance for specific type pair. More...
 
double maxPairCutoff () const
 Get maximum of pair cutoff distance, for all atom type pairs. More...
 
double epsilon (int i, int j) const
 Get LJ interaction energy for a specific pair of Atom types. More...
 
double sigma (int i, int j) const
 Get LJ range for a specific pair of Atom types. More...
 
double get (std::string name, int i, int j) const
 Get a parameter value, identified by a string. More...
 
- Public Member Functions inherited from Util::ParamComposite
 ParamComposite ()
 Constructor. More...
 
 ParamComposite (const ParamComposite &other)
 Copy constructor. More...
 
 ParamComposite (int capacity)
 Constructor. More...
 
virtual ~ParamComposite ()
 Virtual destructor. More...
 
void resetParam ()
 Resets ParamComposite to its empty state. More...
 
virtual void readParam (std::istream &in)
 Read the parameter file block. More...
 
virtual void readParamOptional (std::istream &in)
 Read optional parameter file block. More...
 
virtual void writeParam (std::ostream &out)
 Write all parameters to an output stream. More...
 
virtual void load (Serializable::IArchive &ar)
 Load all parameters from an input archive. More...
 
virtual void loadOptional (Serializable::IArchive &ar)
 Load an optional ParamComposite. More...
 
void saveOptional (Serializable::OArchive &ar)
 Saves isActive flag, and then calls save() iff isActive is true. More...
 
void readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
 Add and read a required child ParamComposite. More...
 
void readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
 Add and attempt to read an optional child ParamComposite. More...
 
template<typename Type >
ScalarParam< Type > & read (std::istream &in, const char *label, Type &value)
 Add and read a new required ScalarParam < Type > object. More...
 
template<typename Type >
ScalarParam< Type > & readOptional (std::istream &in, const char *label, Type &value)
 Add and read a new optional ScalarParam < Type > object. More...
 
template<typename Type >
CArrayParam< Type > & readCArray (std::istream &in, const char *label, Type *value, int n)
 Add and read a required C array parameter. More...
 
template<typename Type >
CArrayParam< Type > & readOptionalCArray (std::istream &in, const char *label, Type *value, int n)
 Add and read an optional C array parameter. More...
 
template<typename Type >
DArrayParam< Type > & readDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
 Add and read a required DArray < Type > parameter. More...
 
template<typename Type >
DArrayParam< Type > & readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
 Add and read an optional DArray < Type > parameter. More...
 
template<typename Type , int N>
FArrayParam< Type, N > & readFArray (std::istream &in, const char *label, FArray< Type, N > &array)
 Add and read a required FArray < Type, N > array parameter. More...
 
template<typename Type , int N>
FArrayParam< Type, N > & readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array)
 Add and read an optional FArray < Type, N > array parameter. More...
 
template<typename Type >
CArray2DParam< Type > & readCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np)
 Add and read a required CArray2DParam < Type > 2D C-array. More...
 
template<typename Type >
CArray2DParam< Type > & readOptionalCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np)
 Add and read an optional CArray2DParam < Type > 2D C-array parameter. More...
 
template<typename Type >
DMatrixParam< Type > & readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
 Add and read a required DMatrix < Type > matrix parameter. More...
 
template<typename Type >
DMatrixParam< Type > & readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
 Add and read an optional DMatrix < Type > matrix parameter. More...
 
template<typename Type >
DSymmMatrixParam< Type > & readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
 Add and read a required symmetrix DMatrix. More...
 
template<typename Type >
DSymmMatrixParam< Type > & readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
 Add and read an optional DMatrix matrix parameter. More...
 
BeginreadBegin (std::istream &in, const char *label, bool isRequired=true)
 Add and read a class label and opening bracket. More...
 
EndreadEnd (std::istream &in)
 Add and read the closing bracket. More...
 
BlankreadBlank (std::istream &in)
 Add and read a new Blank object, representing a blank line. More...
 
void loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
 Add and load a required child ParamComposite. More...
 
void loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
 Add and load an optional child ParamComposite if isActive. More...
 
template<typename Type >
ScalarParam< Type > & loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
 Add and load a new ScalarParam < Type > object. More...
 
template<typename Type >
ScalarParam< Type > & loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
 Add and load new required ScalarParam < Type > object. More...
 
template<typename Type >
CArrayParam< Type > & loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n, bool isRequired)
 Add a C array parameter and load its elements. More...
 
template<typename Type >
CArrayParam< Type > & loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n)
 Add and load a required CArrayParam< Type > array parameter. More...
 
template<typename Type >
DArrayParam< Type > & loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired)
 Add an load a DArray < Type > array parameter. More...
 
template<typename Type >
DArrayParam< Type > & loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n)
 Add and load a required DArray< Type > array parameter. More...
 
template<typename Type , int N>
FArrayParam< Type, N > & loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired)
 Add and load an FArray < Type, N > fixed-size array parameter. More...
 
template<typename Type , int N>
FArrayParam< Type, N > & loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array)
 Add and load a required FArray < Type > array parameter. More...
 
template<typename Type >
CArray2DParam< Type > & loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np, bool isRequired)
 Add and load a CArray2DParam < Type > C 2D array parameter. More...
 
template<typename Type >
CArray2DParam< Type > & loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np)
 Add and load a required < Type > matrix parameter. More...
 
template<typename Type >
DMatrixParam< Type > & loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired)
 Add and load a DMatrixParam < Type > matrix parameter. More...
 
template<typename Type >
DMatrixParam< Type > & loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n)
 Add and load a required DMatrixParam < Type > matrix parameter. More...
 
template<typename Type >
DSymmMatrixParam< Type > & loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired)
 Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More...
 
template<typename Type >
DSymmMatrixParam< Type > & loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n)
 Add and load a required DSymmMatrixParam < Type > matrix parameter. More...
 
void addParamComposite (ParamComposite &child, bool next=true)
 Add a child ParamComposite object to the format array. More...
 
BeginaddBegin (const char *label)
 Add a Begin object representing a class name and bracket. More...
 
EndaddEnd ()
 Add a closing bracket. More...
 
BlankaddBlank ()
 Create and add a new Blank object, representing a blank line. More...
 
std::string className () const
 Get class name string. More...
 
bool isRequired () const
 Is this ParamComposite required in the input file? More...
 
bool isActive () const
 Is this parameter active? More...
 
- Public Member Functions inherited from Util::ParamComponent
virtual ~ParamComponent ()
 Destructor. More...
 
void setIndent (const ParamComponent &parent, bool next=true)
 Set indent level. More...
 
std::string indent () const
 Return indent string for this object (string of spaces). More...
 
template<class Archive >
void serialize (Archive &ar, const unsigned int version)
 Serialize this ParamComponent as a string. More...
 
- Public Member Functions inherited from Util::Serializable
virtual ~Serializable ()
 Destructor. More...
 
- Public Member Functions inherited from Util::MpiFileIo
 MpiFileIo ()
 Constructor. More...
 
 MpiFileIo (const MpiFileIo &other)
 Copy constructor. More...
 
bool isIoProcessor () const
 Can this processor do file I/O ? More...
 
void setIoCommunicator (MPI::Intracomm &communicator)
 Set the communicator. More...
 
void clearCommunicator ()
 Clear (nullify) the communicator. More...
 
bool hasIoCommunicator () const
 Does this object have an associated MPI communicator? More...
 
MPI::Intracomm & ioCommunicator () const
 Get the MPI communicator by reference. More...
 

Protected Attributes

double epsilon_ [MaxAtomType][MaxAtomType]
 LJ interaction energies. More...
 
double sigma_ [MaxAtomType][MaxAtomType]
 LJ range parameters. More...
 
double sigmaSq_ [MaxAtomType][MaxAtomType]
 square of sigma[][]. More...
 
double cutoff_ [MaxAtomType][MaxAtomType]
 LJ cutoff distance. More...
 
double cutoffSq_ [MaxAtomType][MaxAtomType]
 square of cutoff[][]. More...
 
double ljShift_ [MaxAtomType][MaxAtomType]
 shift in LJ potential. More...
 
double eps48_ [MaxAtomType][MaxAtomType]
 48*epsilon More...
 
double maxPairCutoff_
 Maximum pair potential cutoff radius, for all monomer type pairs. More...
 
int nAtomType_
 Total number of atom types. More...
 
bool isInitialized_
 Was this object initialized by calling (read|load)Parameters ? More...
 

Static Protected Attributes

static const int MaxAtomType = 4
 Maximum allowed value for nAtomType (# of atom types) More...
 

Additional Inherited Members

- Public Types inherited from Util::Serializable
typedef BinaryFileOArchive OArchive
 Type of output archive used by save method. More...
 
typedef BinaryFileIArchive IArchive
 Type of input archive used by load method. More...
 
- Static Public Member Functions inherited from Util::ParamComponent
static void initStatic ()
 Initialize static echo member to false. More...
 
static void setEcho (bool echo=true)
 Enable or disable echoing for all subclasses of ParamComponent. More...
 
static bool echo ()
 Get echo parameter. More...
 
- Protected Member Functions inherited from Util::ParamComposite
void setClassName (const char *className)
 Set class name string. More...
 
void setIsRequired (bool isRequired)
 Set or unset the isActive flag. More...
 
void setIsActive (bool isActive)
 Set or unset the isActive flag. More...
 
void setParent (ParamComponent &param, bool next=true)
 Set this to the parent of a child component. More...
 
void addComponent (ParamComponent &param, bool isLeaf=true)
 Add a new ParamComponent object to the format array. More...
 
template<typename Type >
ScalarParam< Type > & add (std::istream &in, const char *label, Type &value, bool isRequired=true)
 Add a new required ScalarParam < Type > object. More...
 
template<typename Type >
CArrayParam< Type > & addCArray (std::istream &in, const char *label, Type *value, int n, bool isRequired=true)
 Add (but do not read) a required C array parameter. More...
 
template<typename Type >
DArrayParam< Type > & addDArray (std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true)
 Add (but do not read) a DArray < Type > parameter. More...
 
template<typename Type , int N>
FArrayParam< Type, N > & addFArray (std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true)
 Add (but do not read) a FArray < Type, N > array parameter. More...
 
template<typename Type >
CArray2DParam< Type > & addCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np, bool isRequired=true)
 Add (but do not read) a CArray2DParam < Type > 2D C-array. More...
 
template<typename Type >
DMatrixParam< Type > & addDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired=true)
 Add and read a required DMatrix < Type > matrix parameter. More...
 
- Protected Member Functions inherited from Util::ParamComponent
 ParamComponent ()
 Constructor. More...
 
 ParamComponent (const ParamComponent &other)
 Copy constructor. More...
 

Constructor & Destructor Documentation

Simp::LJPair::LJPair ( )

Default constructor.

Definition at line 24 of file LJPair.cpp.

References Util::ParamComposite::setClassName().

Simp::LJPair::LJPair ( const LJPair other)

Copy constructor.

Parameters
otherLJPair to be copied

Definition at line 33 of file LJPair.cpp.

References cutoff_, cutoffSq_, eps48_, epsilon_, ljShift_, nAtomType_, sigma_, and sigmaSq_.

Member Function Documentation

LJPair & Simp::LJPair::operator= ( const LJPair other)

Assignment.

Parameters
otherLJPair to be assigned.

Definition at line 55 of file LJPair.cpp.

References cutoff_, cutoffSq_, eps48_, epsilon_, isInitialized_, ljShift_, maxPairCutoff_, nAtomType_, sigma_, and sigmaSq_.

void Simp::LJPair::setNAtomType ( int  nAtomType)

Set nAtomType value.

Parameters
nAtomTypenumber of atom types.

Definition at line 78 of file LJPair.cpp.

References MaxAtomType, nAtomType_, and UTIL_THROW.

Referenced by Tools::PairEnergy::readParameters().

void Simp::LJPair::readParameters ( std::istream &  in)
virtual

Read epsilon, sigma, and cutoff, and initialize other variables.

Precondition
nAtomType must have been set, by calling setNAtomType().
Parameters
ininput parameter stream

Reimplemented from Util::ParamComposite.

Reimplemented in Simp::WcaPair.

Definition at line 159 of file LJPair.cpp.

References cutoff_, cutoffSq_, eps48_, epsilon_, isInitialized_, ljShift_, MaxAtomType, maxPairCutoff_, nAtomType_, sigma_, sigmaSq_, and UTIL_THROW.

Referenced by Tools::PairEnergy::readParameters().

void Simp::LJPair::loadParameters ( Serializable::IArchive ar)
virtual

Load internal state from an archive.

Parameters
arinput/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 196 of file LJPair.cpp.

References cutoff_, cutoffSq_, eps48_, epsilon_, isInitialized_, ljShift_, MaxAtomType, maxPairCutoff_, nAtomType_, sigma_, sigmaSq_, and UTIL_THROW.

void Simp::LJPair::save ( Serializable::OArchive ar)
virtual

Save internal state to an archive.

Parameters
aroutput/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 229 of file LJPair.cpp.

References cutoff_, cutoffSq_, eps48_, epsilon_, ljShift_, MaxAtomType, maxPairCutoff_, nAtomType_, Util::BinaryFileOArchive::pack(), sigma_, and sigmaSq_.

void Simp::LJPair::setEpsilon ( int  i,
int  j,
double  epsilon 
)

Set LJ interaction energy for a specific pair of Atom types.

Parameters
itype of Atom 1
jtype of Atom 2
epsilonLJ energy parameter

Definition at line 92 of file LJPair.cpp.

References cutoffSq_, eps48_, epsilon(), epsilon_, isInitialized_, ljShift_, nAtomType_, sigmaSq_, and UTIL_THROW.

void Simp::LJPair::setSigma ( int  i,
int  j,
double  sigma 
)

Get LJ range for a specific pair of Atom types.

Parameters
iatom type index (1st atom)
jatom type index (2nd atom)
sigmaLJ range parameter

Definition at line 125 of file LJPair.cpp.

References cutoffSq_, epsilon_, isInitialized_, ljShift_, nAtomType_, sigma(), sigma_, sigmaSq_, and UTIL_THROW.

void Simp::LJPair::set ( std::string  name,
int  i,
int  j,
double  value 
)

Modify a parameter, identified by a string.

Parameters
nameparameter name
iatom type index 1
jatom type index 2
valuenew value of parameter

Definition at line 270 of file LJPair.cpp.

References cutoffSq_, eps48_, epsilon_, ljShift_, sigma_, sigmaSq_, and UTIL_THROW.

double Simp::LJPair::energy ( double  rsq,
int  i,
int  j 
) const
inline

Returns interaction energy for a single pair of atoms.

Parameters
rsqsquare of distance between atoms
itype of atom 1
jtype of atom 2
Returns
pair interaction energy

Definition at line 237 of file LJPair.h.

References cutoffSq_, epsilon_, ljShift_, and sigmaSq_.

Referenced by Tools::PairEnergy::sample().

double Simp::LJPair::forceOverR ( double  rsq,
int  i,
int  j 
) const
inline

Returns ratio of scalar pair interaction force to pair separation.

Multiply this quantity by the components of the separation vector to obtain the force vector. A positive value for the return value represents a repulsive force between a pair of atoms.

Precondition: The distance squared rsq must be less than cutoffSq. If rsq > cutoffSq, the return value is undefined (i.e., invalid). Usage: Test for rsq < cutoffSq before calling this function

if (rsq < interaction.cutoffSq(i, j)) {
f = forceOverR(rsq, i, j);
.....
}
Parameters
rsqsquare of distance between atoms
itype of atom 1
jtype of atom 2
Returns
force divided by distance

Definition at line 255 of file LJPair.h.

References eps48_, and sigmaSq_.

double Simp::LJPair::cutoffSq ( int  i,
int  j 
) const
inline

Get square of cutoff distance for specific type pair.

Parameters
itype of atom 1
jtype of atom 2
Returns
cutoffSq_[i][j]

Definition at line 267 of file LJPair.h.

References cutoffSq_.

double Simp::LJPair::maxPairCutoff ( ) const

Get maximum of pair cutoff distance, for all atom type pairs.

Definition at line 244 of file LJPair.cpp.

References maxPairCutoff_.

Referenced by Tools::PairEnergy::readParameters().

double Simp::LJPair::epsilon ( int  i,
int  j 
) const

Get LJ interaction energy for a specific pair of Atom types.

Parameters
itype of Atom 1
jtype of Atom 2
Returns
epsilon_[i][j]

Definition at line 250 of file LJPair.cpp.

References epsilon_, and nAtomType_.

Referenced by setEpsilon().

double Simp::LJPair::sigma ( int  i,
int  j 
) const

Get LJ range for a specific pair of Atom types.

Parameters
iatom type index 1
jatom type index 2
Returns
sigma_[i][j]

Definition at line 260 of file LJPair.cpp.

References nAtomType_, and sigma_.

Referenced by setSigma().

double Simp::LJPair::get ( std::string  name,
int  i,
int  j 
) const

Get a parameter value, identified by a string.

Parameters
nameparameter name
iatom type index 1
jatom type index 2

Definition at line 304 of file LJPair.cpp.

References cutoff_, epsilon_, sigma_, and UTIL_THROW.

Member Data Documentation

const int Simp::LJPair::MaxAtomType = 4
staticprotected

Maximum allowed value for nAtomType (# of atom types)

Definition at line 202 of file LJPair.h.

Referenced by loadParameters(), Simp::WcaPair::readParameters(), readParameters(), save(), and setNAtomType().

double Simp::LJPair::epsilon_[MaxAtomType][MaxAtomType]
protected
double Simp::LJPair::sigma_[MaxAtomType][MaxAtomType]
protected

LJ range parameters.

Definition at line 206 of file LJPair.h.

Referenced by get(), LJPair(), loadParameters(), operator=(), Simp::WcaPair::readParameters(), readParameters(), save(), set(), setSigma(), and sigma().

double Simp::LJPair::sigmaSq_[MaxAtomType][MaxAtomType]
protected
double Simp::LJPair::cutoff_[MaxAtomType][MaxAtomType]
protected

LJ cutoff distance.

Definition at line 208 of file LJPair.h.

Referenced by get(), LJPair(), loadParameters(), operator=(), Simp::WcaPair::readParameters(), readParameters(), and save().

double Simp::LJPair::cutoffSq_[MaxAtomType][MaxAtomType]
protected
double Simp::LJPair::ljShift_[MaxAtomType][MaxAtomType]
protected
double Simp::LJPair::eps48_[MaxAtomType][MaxAtomType]
protected
double Simp::LJPair::maxPairCutoff_
protected

Maximum pair potential cutoff radius, for all monomer type pairs.

Used in construction of a cell list or Verlet pair list.

Definition at line 218 of file LJPair.h.

Referenced by loadParameters(), maxPairCutoff(), operator=(), Simp::WcaPair::readParameters(), readParameters(), and save().

int Simp::LJPair::nAtomType_
protected
bool Simp::LJPair::isInitialized_
protected

Was this object initialized by calling (read|load)Parameters ?

Definition at line 228 of file LJPair.h.

Referenced by loadParameters(), operator=(), Simp::WcaPair::readParameters(), readParameters(), setEpsilon(), and setSigma().


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