n2p2 - A neural network potential package
nnp::SymFncBaseExpAng Class Reference

Intermediate class for angular SFs based on cutoffs and exponentials. More...

#include <SymFncBaseExpAng.h>

Inheritance diagram for nnp::SymFncBaseExpAng:
Collaboration diagram for nnp::SymFncBaseExpAng:

Public Member Functions

virtual void setParameters (std::string const &parameterString)
 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 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...
 
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...
 
bool getUseIntegerPow () const
 Get private useIntegerPow member variable. More...
 
std::size_t getE1 () const
 Get private e1 member variable. More...
 
std::size_t getE2 () const
 Get private e2 member variable. More...
 
int getZetaInt () const
 Get private zetaInt member variable. More...
 
double getLambda () const
 Get private lambda member variable. More...
 
double getEta () const
 Get private eta member variable. More...
 
double getZeta () const
 Get private zeta member variable. More...
 
double getRs () const
 Get private rs member variable. 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 &parameterString)=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...
 

Protected Member Functions

 SymFncBaseExpAng (std::size_t type, ElementMap const &)
 Constructor, initializes type. More...
 
- 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...
 

Protected Attributes

bool useIntegerPow
 Whether to use integer version of power function (faster). More...
 
std::size_t e1
 Element index of neighbor atom 1. More...
 
std::size_t e2
 Element index of neighbor atom 2. More...
 
int zetaInt
 Integer version of \(\zeta\). More...
 
double lambda
 Cosine shift factor. More...
 
double eta
 Width \(\eta\) of gaussian. More...
 
double zeta
 Exponent \(\zeta\) of cosine term. More...
 
double rs
 Shift \(r_s\) of gaussian. 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...
 

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
 
- 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...
 
- 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...
 

Detailed Description

Intermediate class for angular SFs based on cutoffs and exponentials.

Definition at line 29 of file SymFncBaseExpAng.h.

Constructor & Destructor Documentation

◆ SymFncBaseExpAng()

SymFncBaseExpAng::SymFncBaseExpAng ( std::size_t  type,
ElementMap const &   
)
protected

Constructor, initializes type.

Definition at line 30 of file SymFncBaseExpAng.cpp.

30 :
32 useIntegerPow(false),
33 e1 (0 ),
34 e2 (0 ),
35 zetaInt (0 ),
36 lambda (0.0 ),
37 eta (0.0 ),
38 zeta (0.0 ),
39 rs (0.0 )
40{
41 minNeighbors = 2;
42 parameters.insert("e1");
43 parameters.insert("e2");
44 parameters.insert("eta");
45 parameters.insert("zeta");
46 parameters.insert("lambda");
47 parameters.insert("rs/rl");
48}
SymFncBaseCutoff(std::size_t type, ElementMap const &)
Constructor, initializes type.
double lambda
Cosine shift factor.
double zeta
Exponent of cosine term.
double eta
Width of gaussian.
std::size_t e1
Element index of neighbor atom 1.
std::size_t e2
Element index of neighbor atom 2.
int zetaInt
Integer version of .
double rs
Shift of gaussian.
bool useIntegerPow
Whether to use integer version of power function (faster).
std::size_t type
Symmetry function type.
Definition: SymFnc.h:268
std::set< std::string > parameters
Set with symmetry function parameter IDs (lookup for printing).
Definition: SymFnc.h:300
ElementMap elementMap
Copy of element map.
Definition: SymFnc.h:270
std::size_t minNeighbors
Minimum number of neighbors required.
Definition: SymFnc.h:278

References nnp::SymFnc::minNeighbors, and nnp::SymFnc::parameters.

Member Function Documentation

◆ setParameters()

void SymFncBaseExpAng::setParameters ( std::string const &  parameterString)
virtual

Set symmetry function parameters.

Parameters
[in]parameterStringString containing angular symmetry function parameters.

Implements nnp::SymFnc.

Definition at line 50 of file SymFncBaseExpAng.cpp.

51{
52 vector<string> splitLine = split(reduce(parameterString));
53
54 if (type != (size_t)atoi(splitLine.at(1).c_str()))
55 {
56 throw runtime_error("ERROR: Incorrect symmetry function type.\n");
57 }
58
59 ec = elementMap[splitLine.at(0)];
60 e1 = elementMap[splitLine.at(2)];
61 e2 = elementMap[splitLine.at(3)];
62 eta = atof(splitLine.at(4).c_str());
63 lambda = atof(splitLine.at(5).c_str());
64 zeta = atof(splitLine.at(6).c_str());
65 rc = atof(splitLine.at(7).c_str());
66 // Shift parameter is optional.
67 if (splitLine.size() > 8)
68 {
69 rs = atof(splitLine.at(8).c_str());
70 }
71
74
75 if (e1 > e2)
76 {
77 size_t tmp = e1;
78 e1 = e2;
79 e2 = tmp;
80 }
81
82 zetaInt = round(zeta);
83 if (fabs(zeta - zetaInt) <= numeric_limits<double>::min())
84 {
85 useIntegerPow = true;
86 }
87 else
88 {
89 useIntegerPow = false;
90 }
91
92 return;
93}
void setCutoffParameter(double const alpha)
Set parameter for polynomial cutoff function (CT_POLY).
void setCutoffRadius(double const cutoffRadius)
Set cutoff radius.
CutoffFunction fc
Cutoff function used by this symmetry function.
double cutoffAlpha
Cutoff parameter .
double rc
Cutoff radius .
Definition: SymFnc.h:292
std::size_t ec
Element index of center atom.
Definition: SymFnc.h:276
vector< string > split(string const &input, char delimiter)
Split string at each delimiter.
Definition: utility.cpp:33
string reduce(string const &line, string const &whitespace, string const &fill)
Replace multiple whitespaces with fill.
Definition: utility.cpp:60

References nnp::SymFncBaseCutoff::cutoffAlpha, e1, e2, nnp::SymFnc::ec, nnp::SymFnc::elementMap, eta, nnp::SymFncBaseCutoff::fc, lambda, nnp::SymFnc::rc, nnp::reduce(), rs, nnp::CutoffFunction::setCutoffParameter(), nnp::CutoffFunction::setCutoffRadius(), nnp::split(), nnp::SymFnc::type, useIntegerPow, zeta, and zetaInt.

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◆ changeLengthUnit()

void SymFncBaseExpAng::changeLengthUnit ( double  convLength)
virtual

Change length unit.

Parameters
[in]convLengthMultiplicative length unit conversion factor.

Implements nnp::SymFnc.

Definition at line 95 of file SymFncBaseExpAng.cpp.

96{
97 this->convLength = convLength;
99 rc *= convLength;
100 rs *= convLength;
101
104
105 return;
106}
double convLength
Data set normalization length conversion factor.
Definition: SymFnc.h:296

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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◆ getSettingsLine()

string SymFncBaseExpAng::getSettingsLine ( ) const
virtual

Get settings file line from currently set parameters.

Returns
Settings file string ("symfunction_short ...").

Implements nnp::SymFnc.

Definition at line 108 of file SymFncBaseExpAng.cpp.

109{
110 string s = strpr("symfunction_short %2s %2zu %2s %2s %16.8E %16.8E "
111 "%16.8E %16.8E %16.8E\n",
112 elementMap[ec].c_str(),
113 type,
114 elementMap[e1].c_str(),
115 elementMap[e2].c_str(),
117 lambda,
118 zeta,
119 rc / convLength,
120 rs / convLength);
121
122 return s;
123}
string strpr(const char *format,...)
String version of printf function.
Definition: utility.cpp:90

References nnp::SymFnc::convLength, e1, e2, nnp::SymFnc::ec, nnp::SymFnc::elementMap, eta, lambda, nnp::SymFnc::rc, rs, nnp::strpr(), nnp::SymFnc::type, and zeta.

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◆ parameterLine()

string SymFncBaseExpAng::parameterLine ( ) const
virtual

Give symmetry function parameters in one line.

Returns
String containing symmetry function parameter values.

Implements nnp::SymFnc.

Definition at line 125 of file SymFncBaseExpAng.cpp.

126{
127 return strpr(getPrintFormat().c_str(),
128 index + 1,
129 elementMap[ec].c_str(),
130 type,
131 subtype.c_str(),
132 elementMap[e1].c_str(),
133 elementMap[e2].c_str(),
135 rs / convLength,
136 rc / convLength,
137 lambda,
138 zeta,
140 lineNumber + 1);
141}
std::string subtype
Subtype string (specifies cutoff type).
std::size_t index
Symmetry function index (per element).
Definition: SymFnc.h:272
std::size_t lineNumber
Line number.
Definition: SymFnc.h:274
std::string getPrintFormat() const
Generate format string for symmetry function parameter printing.
Definition: SymFnc.cpp:285

References nnp::SymFnc::convLength, nnp::SymFncBaseCutoff::cutoffAlpha, e1, e2, nnp::SymFnc::ec, nnp::SymFnc::elementMap, eta, nnp::SymFnc::getPrintFormat(), nnp::SymFnc::index, lambda, nnp::SymFnc::lineNumber, nnp::SymFnc::rc, rs, nnp::strpr(), nnp::SymFncBaseCutoff::subtype, nnp::SymFnc::type, and zeta.

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◆ parameterInfo()

vector< string > SymFncBaseExpAng::parameterInfo ( ) const
virtual

Get description with parameter names and values.

Returns
Vector of parameter description strings.

Reimplemented from nnp::SymFncBaseCutoff.

Definition at line 143 of file SymFncBaseExpAng.cpp.

144{
145 vector<string> v = SymFncBaseCutoff::parameterInfo();
146 string s;
147 size_t w = sfinfoWidth;
148
149 s = "e1";
150 v.push_back(strpr((pad(s, w) + "%s" ).c_str(), elementMap[e1].c_str()));
151 s = "e2";
152 v.push_back(strpr((pad(s, w) + "%s" ).c_str(), elementMap[e2].c_str()));
153 s = "eta";
154 v.push_back(strpr((pad(s, w) + "%14.8E").c_str(),
156 s = "lambda";
157 v.push_back(strpr((pad(s, w) + "%14.8E").c_str(), lambda));
158 s = "zeta";
159 v.push_back(strpr((pad(s, w) + "%14.8E").c_str(), zeta));
160 s = "rs";
161 v.push_back(strpr((pad(s, w) + "%14.8E").c_str(), rs / convLength));
162
163 return v;
164}
virtual std::vector< std::string > parameterInfo() const
Get description with parameter names and values.
static std::size_t const sfinfoWidth
Width of the SFINFO parameter description field (see parameterInfo()).
Definition: SymFnc.h:309
string pad(string const &input, size_t num, char fill, bool right)
Definition: utility.cpp:79

References nnp::SymFnc::convLength, e1, e2, nnp::SymFnc::elementMap, eta, lambda, nnp::pad(), nnp::SymFncBaseCutoff::parameterInfo(), rs, nnp::SymFnc::sfinfoWidth, nnp::strpr(), and zeta.

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◆ calculateRadialPart()

double SymFncBaseExpAng::calculateRadialPart ( double  distance) const
virtual

Calculate (partial) symmetry function value for one given distance.

Parameters
[in]distanceDistance between two atoms.
Returns
\(\left(e^{-\eta r^2} f_c(r)\right)\)

Implements nnp::SymFnc.

Definition at line 166 of file SymFncBaseExpAng.cpp.

167{
168 double const& r = distance * convLength;
169 double const p = exp(-eta * (r - rs) * (r - rs)) * fc.f(r);
170
171 return p;
172}
double f(double r) const
Cutoff function .
size_t p
Definition: nnp-cutoff.cpp:33

References nnp::SymFnc::convLength, eta, nnp::CutoffFunction::f(), nnp::SymFncBaseCutoff::fc, p, and rs.

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◆ calculateAngularPart()

double SymFncBaseExpAng::calculateAngularPart ( double  angle) const
virtual

Calculate (partial) symmetry function value for one given angle.

Parameters
[in]angleAngle between triplet of atoms (in radians).
Returns
\(1\)

Implements nnp::SymFnc.

Definition at line 174 of file SymFncBaseExpAng.cpp.

175{
176 return 2.0 * pow((1.0 + lambda * cos(angle)) / 2.0, zeta);
177}

References lambda, and zeta.

◆ checkRelevantElement()

bool SymFncBaseExpAng::checkRelevantElement ( std::size_t  index) const
virtual

Check whether symmetry function is relevant for given element.

Parameters
[in]indexIndex of given element.
Returns
True if symmetry function is sensitive to given element, false otherwise.

Implements nnp::SymFnc.

Definition at line 179 of file SymFncBaseExpAng.cpp.

180{
181 if (index == e1 || index == e2) return true;
182 else return false;
183}

References e1, e2, and nnp::SymFnc::index.

◆ getCacheIdentifiers()

vector< string > SymFncBaseExpAng::getCacheIdentifiers ( ) const
virtual

Get unique cache identifiers.

Returns
Vector of string identifying the type of cache this symmetry function requires.

Reimplemented from nnp::SymFnc.

Definition at line 186 of file SymFncBaseExpAng.cpp.

187{
188 vector<string> v;
189 string s("");
190
191 s += subtype;
192 s += " ";
193 s += strpr("alpha = %16.8E", cutoffAlpha);
194 s += " ";
195 s += strpr("rc = %16.8E", rc / convLength);
196
197 v.push_back(strpr("%zu f ", e1) + s);
198 v.push_back(strpr("%zu df ", e1) + s);
199 if (e1 != e2) v.push_back(strpr("%zu f ", e2) + s);
200 if (e1 != e2) v.push_back(strpr("%zu df ", e2) + s);
201
202 return v;
203}

References nnp::SymFnc::convLength, nnp::SymFncBaseCutoff::cutoffAlpha, e1, e2, nnp::SymFnc::rc, nnp::strpr(), and nnp::SymFncBaseCutoff::subtype.

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◆ getUseIntegerPow()

bool nnp::SymFncBaseExpAng::getUseIntegerPow ( ) const
inline

Get private useIntegerPow member variable.

Definition at line 139 of file SymFncBaseExpAng.h.

139{ return useIntegerPow; }

References useIntegerPow.

◆ getE1()

std::size_t nnp::SymFncBaseExpAng::getE1 ( ) const
inline

Get private e1 member variable.

Definition at line 140 of file SymFncBaseExpAng.h.

140{ return e1; }

References e1.

Referenced by nnp::SymGrpExpAngn::addMember(), and nnp::SymGrpExpAngw::addMember().

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◆ getE2()

std::size_t nnp::SymFncBaseExpAng::getE2 ( ) const
inline

Get private e2 member variable.

Definition at line 141 of file SymFncBaseExpAng.h.

141{ return e2; }

References e2.

Referenced by nnp::SymGrpExpAngn::addMember(), and nnp::SymGrpExpAngw::addMember().

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◆ getZetaInt()

int nnp::SymFncBaseExpAng::getZetaInt ( ) const
inline

Get private zetaInt member variable.

Definition at line 142 of file SymFncBaseExpAng.h.

142{ return zetaInt; }

References zetaInt.

◆ getLambda()

double nnp::SymFncBaseExpAng::getLambda ( ) const
inline

Get private lambda member variable.

Definition at line 143 of file SymFncBaseExpAng.h.

143{ return lambda; }

References lambda.

◆ getEta()

double nnp::SymFncBaseExpAng::getEta ( ) const
inline

Get private eta member variable.

Definition at line 144 of file SymFncBaseExpAng.h.

144{ return eta; }

References eta.

◆ getZeta()

double nnp::SymFncBaseExpAng::getZeta ( ) const
inline

Get private zeta member variable.

Definition at line 145 of file SymFncBaseExpAng.h.

145{ return zeta; }

References zeta.

◆ getRs()

double nnp::SymFncBaseExpAng::getRs ( ) const
inline

Get private rs member variable.

Definition at line 146 of file SymFncBaseExpAng.h.

146{ return rs; }

References rs.

Member Data Documentation

◆ useIntegerPow

bool nnp::SymFncBaseExpAng::useIntegerPow
protected

Whether to use integer version of power function (faster).

Definition at line 114 of file SymFncBaseExpAng.h.

Referenced by nnp::SymFncExpAngn::calculate(), nnp::SymFncExpAngw::calculate(), getUseIntegerPow(), and setParameters().

◆ e1

◆ e2

◆ zetaInt

int nnp::SymFncBaseExpAng::zetaInt
protected

Integer version of \(\zeta\).

Definition at line 120 of file SymFncBaseExpAng.h.

Referenced by nnp::SymFncExpAngn::calculate(), nnp::SymFncExpAngw::calculate(), getZetaInt(), and setParameters().

◆ lambda

◆ eta

◆ zeta

◆ rs


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