Simpatico
v1.10
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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.
#include <LJPair.h>
Public Member Functions | |
LJPair () | |
Default constructor. More... | |
LJPair (const LJPair &other) | |
Copy constructor. More... | |
LJPair & | operator= (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... | |
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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... | |
Begin & | readBegin (std::istream &in, const char *label, bool isRequired=true) |
Add and read a class label and opening bracket. More... | |
End & | readEnd (std::istream &in) |
Add and read the closing bracket. More... | |
Blank & | readBlank (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... | |
Begin & | addBegin (const char *label) |
Add a Begin object representing a class name and bracket. More... | |
End & | addEnd () |
Add a closing bracket. More... | |
Blank & | addBlank () |
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... | |
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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... | |
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virtual | ~Serializable () |
Destructor. More... | |
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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 | |
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typedef BinaryFileOArchive | OArchive |
Type of output archive used by save method. More... | |
typedef BinaryFileIArchive | IArchive |
Type of input archive used by load method. More... | |
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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... | |
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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 ¶m, bool next=true) |
Set this to the parent of a child component. More... | |
void | addComponent (ParamComponent ¶m, 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... | |
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ParamComponent () | |
Constructor. More... | |
ParamComponent (const ParamComponent &other) | |
Copy constructor. More... | |
Simp::LJPair::LJPair | ( | ) |
Default constructor.
Definition at line 24 of file LJPair.cpp.
References Util::ParamComposite::setClassName().
Simp::LJPair::LJPair | ( | const LJPair & | other | ) |
Assignment.
other | LJPair 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.
nAtomType | number of atom types. |
Definition at line 78 of file LJPair.cpp.
References MaxAtomType, nAtomType_, and UTIL_THROW.
Referenced by Tools::PairEnergy::readParameters().
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virtual |
Read epsilon, sigma, and cutoff, and initialize other variables.
in | input 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().
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virtual |
Load internal state from an archive.
ar | input/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.
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virtual |
Save internal state to an archive.
ar | output/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.
i | type of Atom 1 |
j | type of Atom 2 |
epsilon | LJ 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.
i | atom type index (1st atom) |
j | atom type index (2nd atom) |
sigma | LJ 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.
name | parameter name |
i | atom type index 1 |
j | atom type index 2 |
value | new value of parameter |
Definition at line 270 of file LJPair.cpp.
References cutoffSq_, eps48_, epsilon_, ljShift_, sigma_, sigmaSq_, and UTIL_THROW.
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inline |
Returns interaction energy for a single pair of atoms.
rsq | square of distance between atoms |
i | type of atom 1 |
j | type of atom 2 |
Definition at line 237 of file LJPair.h.
References cutoffSq_, epsilon_, ljShift_, and sigmaSq_.
Referenced by Tools::PairEnergy::sample().
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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
rsq | square of distance between atoms |
i | type of atom 1 |
j | type of atom 2 |
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inline |
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.
i | type of Atom 1 |
j | type of Atom 2 |
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.
i | atom type index 1 |
j | atom type index 2 |
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.
name | parameter name |
i | atom type index 1 |
j | atom type index 2 |
Definition at line 304 of file LJPair.cpp.
References cutoff_, epsilon_, sigma_, and UTIL_THROW.
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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().
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protected |
LJ interaction energies.
Definition at line 205 of file LJPair.h.
Referenced by energy(), epsilon(), get(), LJPair(), loadParameters(), operator=(), Simp::WcaPair::readParameters(), readParameters(), save(), Simp::WcaPair::set(), set(), setEpsilon(), and setSigma().
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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().
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protected |
square of sigma[][].
Definition at line 207 of file LJPair.h.
Referenced by energy(), forceOverR(), LJPair(), loadParameters(), operator=(), Simp::WcaPair::readParameters(), readParameters(), save(), Simp::WcaPair::set(), set(), setEpsilon(), and setSigma().
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protected |
LJ cutoff distance.
Definition at line 208 of file LJPair.h.
Referenced by get(), LJPair(), loadParameters(), operator=(), Simp::WcaPair::readParameters(), readParameters(), and save().
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protected |
square of cutoff[][].
Definition at line 209 of file LJPair.h.
Referenced by cutoffSq(), energy(), LJPair(), loadParameters(), operator=(), Simp::WcaPair::readParameters(), readParameters(), save(), Simp::WcaPair::set(), set(), setEpsilon(), and setSigma().
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protected |
shift in LJ potential.
Definition at line 210 of file LJPair.h.
Referenced by energy(), LJPair(), loadParameters(), operator=(), Simp::WcaPair::readParameters(), readParameters(), save(), Simp::WcaPair::set(), set(), setEpsilon(), and setSigma().
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protected |
48*epsilon
Definition at line 211 of file LJPair.h.
Referenced by forceOverR(), LJPair(), loadParameters(), operator=(), Simp::WcaPair::readParameters(), readParameters(), save(), Simp::WcaPair::set(), set(), and setEpsilon().
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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().
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protected |
Total number of atom types.
Definition at line 223 of file LJPair.h.
Referenced by epsilon(), LJPair(), loadParameters(), operator=(), Simp::WcaPair::readParameters(), readParameters(), save(), setEpsilon(), setNAtomType(), setSigma(), and sigma().
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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().