source: src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp@ 1e565c

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Last change on this file since 1e565c was fdd23a, checked in by Frederik Heber <heber@…>, 12 years ago

EmpiricalPotential now inherits/combines FunctionModel, SerializablePotential.

  • Property mode set to 100644
File size: 9.1 KB
Line 
1/*
2 * ManyBodyPotential_Tersoff.hpp
3 *
4 * Created on: Sep 26, 2012
5 * Author: heber
6 */
7
8#ifndef MANYBODYPOTENTIAL_TERSOFF_HPP_
9#define MANYBODYPOTENTIAL_TERSOFF_HPP_
10
11// include config.h
12#ifdef HAVE_CONFIG_H
13#include <config.h>
14#endif
15
16#include <boost/function.hpp>
17#include <cmath>
18#include <limits>
19
20#include "Potentials/EmpiricalPotential.hpp"
21
22class TrainingData;
23
24/** This class is the implementation of the Tersoff potential function.
25 *
26 * \note The arguments_t argument list is here in the following order:
27 * -# first \f$ r_{ij} \f$,
28 * -# then all \f$ r_{ik} \f$ that are within the cutoff, i.e. \f$ r_{ik} < R + D\f$
29 *
30 */
31class ManyBodyPotential_Tersoff :
32 public EmpiricalPotential
33{
34 //!> grant unit test access to internal parts
35 friend class ManyBodyPotential_TersoffTest;
36 // some repeated typedefs to avoid ambiguities
37 typedef FunctionModel::arguments_t arguments_t;
38 typedef FunctionModel::result_t result_t;
39 typedef FunctionModel::results_t results_t;
40 typedef EmpiricalPotential::derivative_components_t derivative_components_t;
41 typedef FunctionModel::parameters_t parameters_t;
42public:
43 /** Constructor for class ManyBodyPotential_Tersoff.
44 *
45 * \param _ParticleTypes particle types for this potential
46 */
47 ManyBodyPotential_Tersoff(
48 const ParticleTypes_t &_ParticleTypes
49 );
50
51 /** Constructor for class ManyBodyPotential_Tersoff.
52 *
53 * @param _R offset for cutoff
54 * @param _S halfwidth for cutoff relative to \a _R
55 * @param A
56 * @param B
57 * @param lambda
58 * @param mu
59 * @param lambda3
60 * @param alpha
61 * @param beta
62 * @param chi
63 * @param omega
64 * @param n
65 * @param c
66 * @param d
67 * @param h
68 * @param offset
69 * @param _triplefunction function that returns a list of triples (i.e. the
70 * two remaining distances) to a given pair of points (contained as
71 * indices within the argument)
72 */
73 ManyBodyPotential_Tersoff(
74 const ParticleTypes_t &_ParticleTypes,
75 const double &_R,
76 const double &_S,
77 const double &_A,
78 const double &_B,
79 const double &_lambda,
80 const double &_mu,
81 const double &_lambda3,
82 const double &_alpha,
83 const double &_beta,
84 const double &_chi,
85 const double &_omega,
86 const double &_n,
87 const double &_c,
88 const double &_d,
89 const double &_h,
90 const double &_offset);
91
92 /** Destructor of class ManyBodyPotential_Tersoff.
93 *
94 */
95 virtual ~ManyBodyPotential_Tersoff() {}
96
97 /** Evaluates the Tersoff potential for the given arguments.
98 *
99 * @param arguments single distance
100 * @return value of the potential function
101 */
102 results_t operator()(const arguments_t &arguments) const;
103
104 /** Evaluates the derivative of the Tersoff potential with respect to the
105 * input variables.
106 *
107 * @param arguments single distance
108 * @return vector with components of the derivative
109 */
110 derivative_components_t derivative(const arguments_t &arguments) const;
111
112 /** Evaluates the derivative of the function with the given \a arguments
113 * with respect to a specific parameter indicated by \a index.
114 *
115 * \param arguments set of arguments as input variables to the function
116 * \param index derivative of which parameter
117 * \return result vector containing the derivative with respect to the given
118 * input
119 */
120 results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
121
122 /** Return the token name of this specific potential.
123 *
124 * \return token name of the potential
125 */
126 const std::string& getToken() const
127 { return potential_token; }
128
129 /** Returns a vector of parameter names.
130 *
131 * This is required from the specific implementation
132 *
133 * \return vector of strings containing parameter names
134 */
135 const ParameterNames_t& getParameterNames() const
136 { return ParameterNames; }
137
138 /** States whether lower and upper boundaries should be used to constraint
139 * the parameter search for this function model.
140 *
141 * \return true - constraints should be used, false - else
142 */
143 bool isBoxConstraint() const {
144 return true;
145 }
146
147 /** Returns a vector which are the lower boundaries for each parameter_t
148 * of this FunctionModel.
149 *
150 * \return vector of parameter_t resembling lowest allowed values
151 */
152 parameters_t getLowerBoxConstraints() const {
153 parameters_t lowerbound(getParameterDimension(), -std::numeric_limits<double>::max());
154// lowerbound[R] = 0.;
155// lowerbound[S] = 0.;
156// lowerbound[lambda3] = 0.;
157// lowerbound[alpha] = 0.;
158 lowerbound[beta] = std::numeric_limits<double>::min();
159 lowerbound[n] = std::numeric_limits<double>::min();
160 lowerbound[c] = std::numeric_limits<double>::min();
161 lowerbound[d] = std::numeric_limits<double>::min();
162 return lowerbound;
163 }
164
165 /** Returns a vector which are the upper boundaries for each parameter_t
166 * of this FunctionModel.
167 *
168 * \return vector of parameter_t resembling highest allowed values
169 */
170 parameters_t getUpperBoxConstraints() const {
171 return parameters_t(getParameterDimension(), std::numeric_limits<double>::max());
172 }
173
174 /** Returns a bound function to be used with TrainingData, extracting distances
175 * from a Fragment.
176 *
177 * \return bound function extracting distances from a fragment
178 */
179 FunctionModel::extractor_t getFragmentSpecificExtractor() const;
180
181 /** Sets the magic triple function that we use for getting angle distances.
182 *
183 * @param _triplefunction function that returns a list of triples (i.e. the
184 * two remaining distances) to a given pair of points (contained as
185 * indices within the argument)
186 */
187 void setTriplefunction(triplefunction_t &_triplefunction)
188 { triplefunction = _triplefunction; }
189
190private:
191 /** Prohibit private default constructor.
192 *
193 * We essentially need the triplefunction, hence without this function cannot
194 * be.
195 */
196 ManyBodyPotential_Tersoff();
197
198private:
199 /** This function represents the cutoff \f$ f_C \f$.
200 *
201 * @param distance variable of the function
202 * @return a value in [0,1].
203 */
204 result_t function_cutoff(
205 const double &distance
206 ) const;
207 /** This function has the exponential feature from the Morse potential.
208 *
209 * @param prefactor prefactor parameter to exp function
210 * @param lambda scale parameter of exp function's argument
211 * @param distance variable of the function
212 * @return
213 */
214 result_t function_smoother(
215 const double &prefactor,
216 const double &lambda,
217 const double &distance
218 ) const;
219
220 /** This function represents \f$ (1 + \alpha^n \eta^n)^{-1/2n} \f$.
221 *
222 * @param alpha prefactor to eta function
223 * @param r_ij distance argument
224 * @param eta result value of eta or zeta
225 * @return \f$ (1 + \alpha^n \eta^n)^{-1/2n} \f$
226 */
227 result_t function_prefactor(
228 const double &alpha,
229 const double &eta
230 ) const;
231
232 result_t
233 function_eta(
234 const argument_t &r_ij
235 ) const;
236
237 result_t
238 function_zeta(
239 const argument_t &r_ij
240 ) const;
241
242 result_t
243 function_theta(
244 const double &r_ij,
245 const double &r_ik,
246 const double &r_jk
247 ) const;
248
249 result_t
250 function_angle(
251 const double &r_ij,
252 const double &r_ik,
253 const double &r_jk
254 ) const;
255
256private:
257 result_t
258 function_derivative_c(
259 const argument_t &r_ij
260 ) const;
261
262 result_t
263 function_derivative_d(
264 const argument_t &r_ij
265 ) const;
266
267 result_t
268 function_derivative_h(
269 const argument_t &r_ij
270 ) const;
271
272public:
273 enum parameter_enum_t {
274 A,
275 B,
276 lambda,
277 mu,
278 beta,
279 n,
280 c,
281 d,
282 h,
283 offset,
284// R,
285// S,
286// lambda3,
287// alpha,
288// chi,
289// omega,
290 MAXPARAMS
291 };
292
293private:
294 //!> parameter vector with parameters as in enum parameter_enum_t
295 parameters_t params;
296
297public:
298 // some internal parameters which are fixed
299 const double R;
300 const double S;
301 const double lambda3;
302 const double alpha;
303 const double chi;
304 const double omega;
305
306public:
307 /** Setter for parameters as required by FunctionModel interface.
308 *
309 * \param _params given set of parameters
310 */
311 void setParameters(const parameters_t &_params);
312
313 /** Getter for parameters as required by FunctionModel interface.
314 *
315 * \return set of parameters
316 */
317 parameters_t getParameters() const
318 {
319 return params;
320 }
321
322 /** Sets the parameter randomly within the sensible range of each parameter.
323 *
324 * \param data container with training data for guesstimating range
325 */
326 void setParametersToRandomInitialValues(const TrainingData &data);
327
328 /** Getter for the number of parameters of this model function.
329 *
330 * \return number of parameters
331 */
332 size_t getParameterDimension() const
333 {
334 return MAXPARAMS;
335 }
336
337private:
338 //!> bound function that obtains the triples for the internal coordinationb summation.
339 boost::function< std::vector< arguments_t >(const argument_t &, const double)> triplefunction;
340
341 //!> static definitions of the parameter name for this potential
342 static const ParameterNames_t ParameterNames;
343
344 //!> static token of this potential type
345 static const std::string potential_token;
346};
347
348
349#endif /* MANYBODYPOTENTIAL_TERSOFF_HPP_ */
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