source: src/Potentials/Specifics/SaturationPotential.hpp@ 5c3ad5

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Last change on this file since 5c3ad5 was 5c3ad5, checked in by Frederik Heber <heber@…>, 12 years ago

Modified SaturationPotential to allow fitting to e.g. HCC as well.

  • i.e. now not only saturated elements are fitted but also "saturated" C-C bonds.
  • Property mode set to 100644
File size: 6.9 KB
RevLine 
[4ffbb7]1/*
2 * SaturationPotential.hpp
3 *
4 * Created on: Oct 11, 2012
5 * Author: heber
6 */
7
8#ifndef SATURATIONPOTENTIAL_HPP_
9#define SATURATIONPOTENTIAL_HPP_
10
11
12// include config.h
13#ifdef HAVE_CONFIG_H
14#include <config.h>
15#endif
16
17#include <boost/function.hpp>
[ed2551]18#include <iosfwd>
[4ffbb7]19#include <limits>
20
21#include "Potentials/EmpiricalPotential.hpp"
[ed2551]22#include "Potentials/SerializablePotential.hpp"
[4ffbb7]23#include "Potentials/Specifics/PairPotential_Angle.hpp"
24#include "Potentials/Specifics/PairPotential_Morse.hpp"
25#include "FunctionApproximation/FunctionModel.hpp"
26
[d52819]27class TrainingData;
28
[4ffbb7]29/** This is a combination of Morse and Angle potentials for saturated elements.
30 *
31 */
[ed2551]32class SaturationPotential :
33 virtual public EmpiricalPotential,
34 virtual public FunctionModel,
35 virtual public SerializablePotential
[4ffbb7]36{
37 //!> grant unit test access to internal parts
38 friend class SaturationPotentialTest;
[ed2551]39 //!> grant operator access to private functions
40 friend std::ostream& operator<<(std::ostream &ost, const SaturationPotential &potential);
41 //!> grant operator access to private functions
42 friend std::istream& operator>>(std::istream &ost, SaturationPotential &potential);
43
[4ffbb7]44 // some repeated typedefs to avoid ambiguities
45 typedef FunctionModel::arguments_t arguments_t;
46 typedef FunctionModel::result_t result_t;
47 typedef FunctionModel::results_t results_t;
48 typedef EmpiricalPotential::derivative_components_t derivative_components_t;
49 typedef FunctionModel::parameters_t parameters_t;
50public:
51 SaturationPotential(
[775dd1a]52 const ParticleTypes_t &_ParticleTypes
[4ffbb7]53 );
54 SaturationPotential(
[ed2551]55 const ParticleTypes_t &_ParticleTypes,
[b3eabc]56 const double _all_energy_offset,
[4ffbb7]57 const double _morse_spring_constant,
58 const double _morse_equilibrium_distance,
59 const double _morse_dissociation_energy,
60 const double _angle_spring_constant,
[775dd1a]61 const double _angle_equilibrium_distance
[4ffbb7]62 );
63 virtual ~SaturationPotential() {}
64
65 /** Setter for parameters as required by FunctionModel interface.
66 *
67 * \param _params given set of parameters
68 */
69 void setParameters(const parameters_t &_params);
70
71 /** Getter for parameters as required by FunctionModel interface.
72 *
73 * \return set of parameters
74 */
75 parameters_t getParameters() const;
76
[d52819]77 /** Sets the parameter randomly within the sensible range of each parameter.
78 *
79 * \param data container with training data for guesstimating range
80 */
81 void setParametersToRandomInitialValues(const TrainingData &data);
82
[4ffbb7]83 /** Getter for the number of parameters of this model function.
84 *
85 * \return number of parameters
86 */
87 size_t getParameterDimension() const
88 { return MAXPARAMS; }
89
90 /** Evaluates the harmonic potential function for the given arguments.
91 *
92 * @param arguments single distance
93 * @return value of the potential function
94 */
95 results_t operator()(const arguments_t &arguments) const;
96
97 /** Evaluates the derivative of the potential function.
98 *
99 * @param arguments single distance
100 * @return vector with derivative with respect to the input degrees of freedom
101 */
102 derivative_components_t derivative(const arguments_t &arguments) const;
103
104 /** Evaluates the derivative of the function with the given \a arguments
105 * with respect to a specific parameter indicated by \a index.
106 *
107 * \param arguments set of arguments as input variables to the function
108 * \param index derivative of which parameter
109 * \return result vector containing the derivative with respect to the given
110 * input
111 */
112 results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
113
[6efcae]114 /** Return the token name of this specific potential.
[67cd3a]115 *
[6efcae]116 * \return token name of the potential
[67cd3a]117 */
[ed2551]118 const std::string& getToken() const
119 { return potential_token; }
120
121 /** Returns a vector of parameter names.
122 *
123 * This is required from the specific implementation
124 *
125 * \return vector of strings containing parameter names
126 */
127 const ParameterNames_t& getParameterNames() const
128 { return ParameterNames; }
[67cd3a]129
[3d2559]130 /** Print parameters for both Morse and Angle potential.
131 *
132 * We override default parameter printing of SeralizablePotential
133 * to print both parameters
134 *
135 * @param ost stream to print to
136 */
137 virtual void stream_to(std::ostream &ost) const;
138
139 /** Parse parameters for both Morse and Angle potential.
140 *
141 * We override default parameter parsing of SeralizablePotential
142 * to parse both parameters
143 *
144 * @param ist stream to parse from
145 */
146 virtual void stream_from(std::istream &ist);
147
[4ffbb7]148 /** States whether lower and upper boundaries should be used to constraint
149 * the parameter search for this function model.
150 *
151 * \return true - constraints should be used, false - else
152 */
153 bool isBoxConstraint() const {
154 return true;
155 }
156
157 /** Returns a vector which are the lower boundaries for each parameter_t
158 * of this FunctionModel.
159 *
160 * \return vector of parameter_t resembling lowest allowed values
161 */
162 parameters_t getLowerBoxConstraints() const {
163 parameters_t lowerbounds(getParameterDimension(), -std::numeric_limits<double>::max());
164 lowerbounds[morse_equilibrium_distance] = 0.;
165 lowerbounds[angle_equilibrium_distance] = -1.;
166 return lowerbounds;
167 }
168
169 /** Returns a vector which are the upper boundaries for each parameter_t
170 * of this FunctionModel.
171 *
172 * \return vector of parameter_t resembling highest allowed values
173 */
174 parameters_t getUpperBoxConstraints() const {
175 parameters_t upperbounds(getParameterDimension(), std::numeric_limits<double>::max());
176 upperbounds[angle_equilibrium_distance] = 1.;
177 return upperbounds;
178 }
179
[7b019a]180 /** Returns a bound function to be used with TrainingData, extracting distances
181 * from a Fragment.
182 *
183 * \return bound function extracting distances from a fragment
184 */
[da2d5c]185 FunctionModel::extractor_t getFragmentSpecificExtractor() const;
[7b019a]186
[4ffbb7]187 enum parameter_enum_t {
[2ba2ed]188 all_energy_offset,
[4ffbb7]189 morse_spring_constant,
190 morse_equilibrium_distance,
191 morse_dissociation_energy,
192 angle_spring_constant,
193 angle_equilibrium_distance,
194 MAXPARAMS
195 };
196
[93e908]197private:
198 /** Adds last bond partner one more time to get types for angle potential.
199 *
200 * @param _ParticleTypes types from a pair potential
201 * @return types for a symmetric triple potential
202 */
203 static const ParticleTypes_t symmetrizeTypes(const ParticleTypes_t &_ParticleTypes);
204
[5c3ad5]205 /** Adds saturation type bond partner.
206 *
207 * @param _ParticleTypes types from a pair potential
208 * @return types for a saturation type-enhanced triple potential
209 */
210 static const ParticleTypes_t addSaturationType(const ParticleTypes_t &_ParticleTypes);
211
[4ffbb7]212private:
213 PairPotential_Morse morse;
214 PairPotential_Angle angle;
215 double energy_offset;
216
[ed2551]217 //!> static definitions of the parameter name for this potential
218 static const ParameterNames_t ParameterNames;
219
220 //!> static token of this potential type
221 static const std::string potential_token;
[4ffbb7]222};
223
[ed2551]224
[4ffbb7]225#endif /* SATURATIONPOTENTIAL_HPP_ */
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