n2p2 - A neural network potential package
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Radial symmetry function (type 2) More...
#include <SymFncExpRad.h>
Public Member Functions | |
SymFncExpRad (ElementMap const &elementMap) | |
Constructor, sets type = 2. More... | |
virtual bool | operator== (SymFnc const &rhs) const |
Overload == operator. More... | |
virtual bool | operator< (SymFnc const &rhs) const |
Overload < operator. More... | |
virtual void | setParameters (std::string const ¶meterString) |
Set symmetry function parameters. More... | |
virtual void | changeLengthUnit (double convLength) |
Change length unit. More... | |
virtual std::string | getSettingsLine () const |
Get settings file line from currently set parameters. More... | |
virtual void | calculate (Atom &atom, bool const derivatives) const |
Calculate symmetry function for one atom. More... | |
virtual std::string | parameterLine () const |
Give symmetry function parameters in one line. More... | |
virtual std::vector< std::string > | parameterInfo () const |
Get description with parameter names and values. More... | |
std::size_t | getE1 () const |
Get private e1 member variable. More... | |
double | getEta () const |
Get private eta member variable. More... | |
double | getRs () const |
Get private rs member variable. More... | |
virtual double | calculateRadialPart (double distance) const |
Calculate (partial) symmetry function value for one given distance. More... | |
virtual double | calculateAngularPart (double angle) const |
Calculate (partial) symmetry function value for one given angle. More... | |
virtual bool | checkRelevantElement (std::size_t index) const |
Check whether symmetry function is relevant for given element. More... | |
virtual std::vector< std::string > | getCacheIdentifiers () const |
Get unique cache identifiers. More... | |
Public Member Functions inherited from nnp::SymFncBaseCutoff | |
virtual std::vector< std::string > | parameterInfo () const |
Get description with parameter names and values. More... | |
void | setCutoffFunction (CutoffFunction::CutoffType cutoffType, double cutoffAlpha) |
Set cutoff function type and parameter. More... | |
double | getCutoffAlpha () const |
Get private cutoffAlpha member variable. More... | |
std::string | getSubtype () const |
Get private subtype member variable. More... | |
CutoffFunction::CutoffType | getCutoffType () const |
Get private cutoffType member variable. More... | |
Public Member Functions inherited from nnp::SymFnc | |
virtual | ~SymFnc () |
Virtual destructor. More... | |
virtual bool | operator== (SymFnc const &rhs) const =0 |
Overload == operator. More... | |
virtual bool | operator< (SymFnc const &rhs) const =0 |
Overload < operator. More... | |
bool | operator!= (SymFnc const &rhs) const |
Overload != operator. More... | |
bool | operator> (SymFnc const &rhs) const |
Overload > operator. More... | |
bool | operator<= (SymFnc const &rhs) const |
Overload <= operator. More... | |
bool | operator>= (SymFnc const &rhs) const |
Overload >= operator. More... | |
virtual void | setParameters (std::string const ¶meterString)=0 |
Set parameters. More... | |
virtual void | changeLengthUnit (double convLength)=0 |
Change length unit. More... | |
virtual std::string | getSettingsLine () const =0 |
Get settings file line from currently set parameters. More... | |
virtual void | calculate (Atom &atom, bool const derivatives) const =0 |
Calculate symmetry function for one atom. More... | |
virtual std::string | parameterLine () const =0 |
Give symmetry function parameters in one line. More... | |
virtual std::vector< std::string > | parameterInfo () const |
Get description with parameter names and values. More... | |
void | setScalingType (ScalingType scalingType, std::string statisticsLine, double Smin, double Smax) |
Set symmetry function scaling type. More... | |
double | scale (double value) const |
Apply symmetry function scaling and/or centering. More... | |
double | unscale (double value) const |
Undo symmetry function scaling and/or centering. More... | |
std::size_t | getType () const |
Get private type member variable. More... | |
std::size_t | getIndex () const |
Get private index member variable. More... | |
std::size_t | getLineNumber () const |
Get private lineNumber member variable. More... | |
std::size_t | getEc () const |
Get private ec member variable. More... | |
std::size_t | getMinNeighbors () const |
Get private minNeighbors member variable. More... | |
double | getRc () const |
Get private rc member variable. More... | |
double | getGmin () const |
Get private Gmin member variable. More... | |
double | getGmax () const |
Get private Gmax member variable. More... | |
double | getScalingFactor () const |
Get private scalingFactor member variable. More... | |
double | getConvLength () const |
Get private convLength member variable. More... | |
std::set< std::string > | getParameters () const |
Get private parameters member variable. More... | |
std::vector< std::size_t > | getIndexPerElement () const |
Get private indexPerElement member variable. More... | |
void | setIndex (std::size_t index) |
Set private index member variable. More... | |
void | setIndexPerElement (std::size_t elementIndex, std::size_t index) |
Set private indexPerElement member variable. More... | |
void | setLineNumber (std::size_t lineNumber) |
Set line number. More... | |
std::string | scalingLine () const |
Get string with scaling information. More... | |
virtual double | calculateRadialPart (double distance) const =0 |
Calculate (partial) symmetry function value for one given distance. More... | |
virtual double | calculateAngularPart (double angle) const =0 |
Calculate (partial) symmetry function value for one given angle. More... | |
virtual bool | checkRelevantElement (std::size_t index) const =0 |
Check whether symmetry function is relevant for given element. More... | |
virtual std::vector< std::string > | getCacheIdentifiers () const |
Get unique cache identifiers. More... | |
void | addCacheIndex (std::size_t element, std::size_t cacheIndex, std::string cacheIdentifier) |
Add one cache index for given neighbor element and check identifier. More... | |
std::vector< std::vector< std::size_t > > | getCacheIndices () const |
Getter for cacheIndices. More... | |
Private Attributes | |
std::size_t | e1 |
Element index of neighbor atom. More... | |
double | eta |
Width \(\eta\) of gaussian. More... | |
double | rs |
Shift \(r_s\) of gaussian. More... | |
Additional Inherited Members | |
Public Types inherited from nnp::SymFnc | |
enum | ScalingType { ST_NONE , ST_SCALE , ST_CENTER , ST_SCALECENTER , ST_SCALESIGMA } |
List of available scaling types. More... | |
Protected Types inherited from nnp::SymFnc | |
typedef std::map< std::string, std::pair< std::string, std::string > > | PrintFormat |
typedef std::vector< std::string > | PrintOrder |
Protected Member Functions inherited from nnp::SymFncBaseCutoff | |
SymFncBaseCutoff (std::size_t type, ElementMap const &) | |
Constructor, initializes type. More... | |
Protected Member Functions inherited from nnp::SymFnc | |
SymFnc (std::size_t type, ElementMap const &) | |
Constructor, initializes type. More... | |
std::string | getPrintFormat () const |
Generate format string for symmetry function parameter printing. More... | |
Static Protected Member Functions inherited from nnp::SymFnc | |
static PrintFormat const | initializePrintFormat () |
Initialize static print format map for all possible parameters. More... | |
static PrintOrder const | initializePrintOrder () |
Initialize static print order vector for all possible parameters. More... | |
Protected Attributes inherited from nnp::SymFncBaseCutoff | |
double | cutoffAlpha |
Cutoff parameter \(\alpha\). More... | |
std::string | subtype |
Subtype string (specifies cutoff type). More... | |
CutoffFunction | fc |
Cutoff function used by this symmetry function. More... | |
CutoffFunction::CutoffType | cutoffType |
Cutoff type used by this symmetry function. More... | |
Protected Attributes inherited from nnp::SymFnc | |
std::size_t | type |
Symmetry function type. More... | |
ElementMap | elementMap |
Copy of element map. More... | |
std::size_t | index |
Symmetry function index (per element). More... | |
std::size_t | lineNumber |
Line number. More... | |
std::size_t | ec |
Element index of center atom. More... | |
std::size_t | minNeighbors |
Minimum number of neighbors required. More... | |
double | Smin |
Minimum for scaling range. More... | |
double | Smax |
Maximum for scaling range. More... | |
double | Gmin |
Minimum unscaled symmetry function value. More... | |
double | Gmax |
Maximum unscaled symmetry function value. More... | |
double | Gmean |
Mean unscaled symmetry function value. More... | |
double | Gsigma |
Sigma of unscaled symmetry function values. More... | |
double | rc |
Cutoff radius \(r_c\). More... | |
double | scalingFactor |
Scaling factor. More... | |
double | convLength |
Data set normalization length conversion factor. More... | |
ScalingType | scalingType |
Symmetry function scaling type used by this symmetry function. More... | |
std::set< std::string > | parameters |
Set with symmetry function parameter IDs (lookup for printing). More... | |
std::vector< std::size_t > | indexPerElement |
Per-element index for derivative memory in Atom::Neighbor::dGdr arrays. More... | |
std::vector< std::vector< std::size_t > > | cacheIndices |
Cache indices for each element. More... | |
Static Protected Attributes inherited from nnp::SymFnc | |
static std::size_t const | sfinfoWidth = 12 |
Width of the SFINFO parameter description field (see parameterInfo()). More... | |
static PrintFormat const | printFormat = initializePrintFormat() |
Map of parameter format strings and empty strings. More... | |
static PrintOrder const | printOrder = initializePrintOrder() |
Vector of parameters in order of printing. More... | |
Radial symmetry function (type 2)
\[ G^2_i = \sum_{j \neq i} \mathrm{e}^{-\eta(r_{ij} - r_\mathrm{s})^2} f_c(r_{ij}) \]
Parameter string:
where
<element-central> ....
element symbol of central atom<element-neighbor> ...
element symbol of neighbor atom<eta> ................
\(\eta\)<rshift> .............
\(r_\mathrm{s}\)<rcutoff> ............
\(r_c\) Definition at line 48 of file SymFncExpRad.h.
SymFncExpRad::SymFncExpRad | ( | ElementMap const & | elementMap | ) |
Constructor, sets type = 2.
Definition at line 29 of file SymFncExpRad.cpp.
References nnp::SymFnc::minNeighbors, and nnp::SymFnc::parameters.
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Overload == operator.
Implements nnp::SymFnc.
Definition at line 41 of file SymFncExpRad.cpp.
References nnp::SymFncBaseCutoff::cutoffAlpha, nnp::SymFncBaseCutoff::cutoffType, e1, nnp::SymFnc::ec, eta, nnp::SymFnc::getEc(), nnp::SymFnc::getType(), nnp::SymFnc::rc, rs, and nnp::SymFnc::type.
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virtual |
Overload < operator.
Implements nnp::SymFnc.
Definition at line 55 of file SymFncExpRad.cpp.
References nnp::SymFncBaseCutoff::cutoffAlpha, nnp::SymFncBaseCutoff::cutoffType, e1, nnp::SymFnc::ec, eta, nnp::SymFnc::getEc(), nnp::SymFnc::getType(), nnp::SymFnc::rc, rs, and nnp::SymFnc::type.
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Set symmetry function parameters.
[in] | parameterString | String containing radial symmetry function parameters. |
Implements nnp::SymFnc.
Definition at line 77 of file SymFncExpRad.cpp.
References nnp::SymFncBaseCutoff::cutoffAlpha, e1, nnp::SymFnc::ec, nnp::SymFnc::elementMap, eta, nnp::SymFncBaseCutoff::fc, nnp::SymFnc::rc, nnp::reduce(), rs, nnp::CutoffFunction::setCutoffParameter(), nnp::CutoffFunction::setCutoffRadius(), nnp::split(), and nnp::SymFnc::type.
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Change length unit.
[in] | convLength | Multiplicative length unit conversion factor. |
Implements nnp::SymFnc.
Definition at line 98 of file SymFncExpRad.cpp.
References nnp::SymFnc::convLength, nnp::SymFncBaseCutoff::cutoffAlpha, eta, nnp::SymFncBaseCutoff::fc, nnp::SymFnc::rc, rs, nnp::CutoffFunction::setCutoffParameter(), and nnp::CutoffFunction::setCutoffRadius().
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Get settings file line from currently set parameters.
Implements nnp::SymFnc.
Definition at line 111 of file SymFncExpRad.cpp.
References nnp::SymFnc::convLength, e1, nnp::SymFnc::ec, nnp::SymFnc::elementMap, eta, nnp::SymFnc::rc, rs, nnp::strpr(), and nnp::SymFnc::type.
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virtual |
Calculate symmetry function for one atom.
[in,out] | atom | Atom for which the symmetry function is caluclated. |
[in] | derivatives | If also symmetry function derivatives will be calculated and saved. |
Implements nnp::SymFnc.
Definition at line 124 of file SymFncExpRad.cpp.
References nnp::Atom::Neighbor::cache, nnp::SymFnc::cacheIndices, nnp::Atom::Neighbor::d, nnp::Atom::Neighbor::dGdr, nnp::Atom::dGdr, nnp::Atom::Neighbor::dr, e1, nnp::Atom::Neighbor::element, eta, nnp::SymFncBaseCutoff::fc, nnp::CutoffFunction::fdf(), nnp::Atom::G, nnp::Atom::getStoredMinNumNeighbors(), nnp::SymFnc::index, nnp::SymFnc::indexPerElement, nnp::Atom::neighbors, nnp::SymFnc::rc, rs, nnp::SymFnc::scale(), and nnp::SymFnc::scalingFactor.
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Give symmetry function parameters in one line.
Implements nnp::SymFnc.
Definition at line 186 of file SymFncExpRad.cpp.
References nnp::SymFnc::convLength, nnp::SymFncBaseCutoff::cutoffAlpha, e1, nnp::SymFnc::ec, nnp::SymFnc::elementMap, eta, nnp::SymFnc::getPrintFormat(), nnp::SymFnc::index, nnp::SymFnc::lineNumber, nnp::SymFnc::rc, rs, nnp::strpr(), nnp::SymFncBaseCutoff::subtype, and nnp::SymFnc::type.
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virtual |
Get description with parameter names and values.
Reimplemented from nnp::SymFncBaseCutoff.
Definition at line 201 of file SymFncExpRad.cpp.
References nnp::SymFnc::convLength, e1, nnp::SymFnc::elementMap, eta, nnp::pad(), nnp::SymFncBaseCutoff::parameterInfo(), rs, nnp::SymFnc::sfinfoWidth, and nnp::strpr().
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inline |
Get private e1 member variable.
Definition at line 145 of file SymFncExpRad.h.
References e1.
Referenced by nnp::SymGrpExpRad::addMember().
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inline |
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inline |
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virtual |
Calculate (partial) symmetry function value for one given distance.
[in] | distance | Distance between two atoms. |
Implements nnp::SymFnc.
Definition at line 218 of file SymFncExpRad.cpp.
References nnp::SymFnc::convLength, eta, nnp::CutoffFunction::f(), nnp::SymFncBaseCutoff::fc, and rs.
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virtual |
Calculate (partial) symmetry function value for one given angle.
[in] | angle | Angle between triplet of atoms (in radians). |
Implements nnp::SymFnc.
Definition at line 225 of file SymFncExpRad.cpp.
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virtual |
Check whether symmetry function is relevant for given element.
[in] | index | Index of given element. |
Implements nnp::SymFnc.
Definition at line 230 of file SymFncExpRad.cpp.
References e1, and nnp::SymFnc::index.
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Get unique cache identifiers.
Reimplemented from nnp::SymFnc.
Definition at line 237 of file SymFncExpRad.cpp.
References nnp::SymFnc::convLength, nnp::SymFncBaseCutoff::cutoffAlpha, e1, nnp::SymFnc::rc, nnp::strpr(), and nnp::SymFncBaseCutoff::subtype.
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private |
Element index of neighbor atom.
Definition at line 134 of file SymFncExpRad.h.
Referenced by calculate(), checkRelevantElement(), getCacheIdentifiers(), getE1(), getSettingsLine(), operator<(), operator==(), parameterInfo(), parameterLine(), and setParameters().
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Width \(\eta\) of gaussian.
Definition at line 136 of file SymFncExpRad.h.
Referenced by calculate(), calculateRadialPart(), changeLengthUnit(), getEta(), getSettingsLine(), operator<(), operator==(), parameterInfo(), parameterLine(), and setParameters().
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private |
Shift \(r_s\) of gaussian.
Definition at line 138 of file SymFncExpRad.h.
Referenced by calculate(), calculateRadialPart(), changeLengthUnit(), getRs(), getSettingsLine(), operator<(), operator==(), parameterInfo(), parameterLine(), and setParameters().