Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2020 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed is distributed in the hope that it will be useful,
15 : but WITHOUT ANY WARRANTY; without even the implied warranty of
16 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #ifndef __PLUMED_tools_Grid_h
23 : #define __PLUMED_tools_Grid_h
24 :
25 : #include <vector>
26 : #include <string>
27 : #include <map>
28 : #include <cmath>
29 : #include <memory>
30 :
31 : namespace PLMD {
32 :
33 :
34 : // simple function to enable various weighting
35 :
36 : class WeightBase {
37 : public:
38 : virtual double projectInnerLoop(double &input, double &v)=0;
39 : virtual double projectOuterLoop(double &v)=0;
40 : virtual ~WeightBase() {}
41 : };
42 :
43 0 : class BiasWeight:public WeightBase {
44 : public:
45 : double beta,invbeta;
46 2 : explicit BiasWeight(double v) {beta=v; invbeta=1./beta;}
47 13120 : double projectInnerLoop(double &input, double &v) {return input+exp(beta*v);}
48 164 : double projectOuterLoop(double &v) {return -invbeta*std::log(v);}
49 : };
50 :
51 : class ProbWeight:public WeightBase {
52 : public:
53 : double beta,invbeta;
54 : explicit ProbWeight(double v) {beta=v; invbeta=1./beta;}
55 : double projectInnerLoop(double &input, double &v) {return input+v;}
56 : double projectOuterLoop(double &v) {return -invbeta*std::log(v);}
57 : };
58 :
59 :
60 :
61 :
62 :
63 :
64 : class Value;
65 : class IFile;
66 : class OFile;
67 : class KernelFunctions;
68 : class Communicator;
69 :
70 : /// \ingroup TOOLBOX
71 138 : class Grid
72 : {
73 : public:
74 : // we use a size_t here
75 : // should be 8 bytes on all 64-bit machines
76 : // and more portable than "unsigned long long"
77 : typedef size_t index_t;
78 : // to restore old implementation (unsigned) use the following instead:
79 : // typedef unsigned index_t;
80 : /// Maximum dimension (exaggerated value).
81 : /// Can be used to replace local std::vectors with std::arrays (allocated on stack).
82 : static constexpr size_t maxdim=64;
83 : private:
84 : double contour_location;
85 : std::vector<double> grid_;
86 : std::vector< std::vector<double> > der_;
87 : protected:
88 : std::string funcname;
89 : std::vector<std::string> argnames;
90 : std::vector<std::string> str_min_, str_max_;
91 : std::vector<double> min_,max_,dx_;
92 : std::vector<unsigned> nbin_;
93 : std::vector<bool> pbc_;
94 : index_t maxsize_;
95 : unsigned dimension_;
96 : bool dospline_, usederiv_;
97 : std::string fmt_; // format for output
98 : /// get "neighbors" for spline
99 : void getSplineNeighbors(const std::vector<unsigned> & indices, std::vector<index_t>& neigh, unsigned& nneigh )const;
100 : // std::vector<index_t> getSplineNeighbors(const std::vector<unsigned> & indices)const;
101 :
102 :
103 : public:
104 : /// clear grid
105 : virtual void clear();
106 : /// this constructor here is Value-aware
107 : Grid(const std::string& funcl, const std::vector<Value*> & args, const std::vector<std::string> & gmin,
108 : const std::vector<std::string> & gmax, const std::vector<unsigned> & nbin, bool dospline,
109 : bool usederiv, bool doclear=true);
110 : /// this constructor here is not Value-aware
111 : Grid(const std::string& funcl, const std::vector<std::string> &names, const std::vector<std::string> & gmin,
112 : const std::vector<std::string> & gmax, const std::vector<unsigned> & nbin, bool dospline,
113 : bool usederiv, bool doclear, const std::vector<bool> &isperiodic, const std::vector<std::string> &pmin,
114 : const std::vector<std::string> &pmax );
115 : /// this is the real initializator
116 : void Init(const std::string & funcl, const std::vector<std::string> &names, const std::vector<std::string> & gmin,
117 : const std::vector<std::string> & gmax, const std::vector<unsigned> & nbin, bool dospline, bool usederiv,
118 : bool doclear, const std::vector<bool> &isperiodic, const std::vector<std::string> &pmin, const std::vector<std::string> &pmax);
119 : /// get lower boundary
120 : std::vector<std::string> getMin() const;
121 : /// get upper boundary
122 : std::vector<std::string> getMax() const;
123 : /// get bin size
124 : std::vector<double> getDx() const;
125 : double getDx(index_t j) const ;
126 : /// get bin volume
127 : double getBinVolume() const;
128 : /// get number of bins
129 : std::vector<unsigned> getNbin() const;
130 : /// get if periodic
131 : std::vector<bool> getIsPeriodic() const;
132 : /// get grid dimension
133 : unsigned getDimension() const;
134 : /// get argument names of this grid
135 : std::vector<std::string> getArgNames() const;
136 : /// get if the grid has derivatives
137 1898210 : bool hasDerivatives() const {return usederiv_;}
138 :
139 : /// methods to handle grid indices
140 : void getIndices(index_t index, std::vector<unsigned>& rindex) const;
141 : void getIndices(const std::vector<double> & x, std::vector<unsigned>& rindex) const;
142 : std::vector<unsigned> getIndices(index_t index) const;
143 : std::vector<unsigned> getIndices(const std::vector<double> & x) const;
144 : index_t getIndex(const std::vector<unsigned> & indices) const;
145 : index_t getIndex(const std::vector<double> & x) const;
146 : std::vector<double> getPoint(index_t index) const;
147 : std::vector<double> getPoint(const std::vector<unsigned> & indices) const;
148 : std::vector<double> getPoint(const std::vector<double> & x) const;
149 : /// faster versions relying on preallocated vectors
150 : void getPoint(index_t index,std::vector<double> & point) const;
151 : void getPoint(const std::vector<unsigned> & indices,std::vector<double> & point) const;
152 : void getPoint(const std::vector<double> & x,std::vector<double> & point) const;
153 :
154 : /// get neighbors
155 : std::vector<index_t> getNeighbors(index_t index,const std::vector<unsigned> & neigh) const;
156 : std::vector<index_t> getNeighbors(const std::vector<unsigned> & indices,const std::vector<unsigned> & neigh) const;
157 : std::vector<index_t> getNeighbors(const std::vector<double> & x,const std::vector<unsigned> & neigh) const;
158 : /// get nearest neighbors (those separated by exactly one lattice unit)
159 : std::vector<index_t> getNearestNeighbors(const index_t index) const;
160 : std::vector<index_t> getNearestNeighbors(const std::vector<unsigned> &indices) const;
161 :
162 : /// write header for grid file
163 : void writeHeader(OFile& file);
164 :
165 : /// read grid from file
166 : static std::unique_ptr<Grid> create(const std::string&,const std::vector<Value*>&,IFile&,bool,bool,bool);
167 : /// read grid from file and check boundaries are what is expected from input
168 : static std::unique_ptr<Grid> create(const std::string&,const std::vector<Value*>&, IFile&,
169 : const std::vector<std::string>&,const std::vector<std::string>&,
170 : const std::vector<unsigned>&,bool,bool,bool);
171 : /// get grid size
172 : virtual index_t getSize() const;
173 : /// get grid value
174 : virtual double getValue(index_t index) const;
175 : virtual double getValue(const std::vector<unsigned> & indices) const;
176 : virtual double getValue(const std::vector<double> & x) const;
177 : /// get minimum value
178 : virtual double getMinValue() const;
179 : /// get maximum value
180 : virtual double getMaxValue() const;
181 : /// get grid value and derivatives
182 : virtual double getValueAndDerivatives(index_t index, std::vector<double>& der) const ;
183 : virtual double getValueAndDerivatives(const std::vector<unsigned> & indices, std::vector<double>& der) const;
184 : virtual double getValueAndDerivatives(const std::vector<double> & x, std::vector<double>& der) const;
185 : /// Get the difference from the contour
186 : double getDifferenceFromContour(const std::vector<double> & x, std::vector<double>& der) const ;
187 : /// Find a set of points on a contour in the function
188 : void findSetOfPointsOnContour(const double& target, const std::vector<bool>& nosearch, unsigned& npoints, std::vector<std::vector<double> >& points );
189 :
190 : /// set grid value
191 : virtual void setValue(index_t index, double value);
192 : virtual void setValue(const std::vector<unsigned> & indices, double value);
193 : /// set grid value and derivatives
194 : virtual void setValueAndDerivatives(index_t index, double value, std::vector<double>& der);
195 : virtual void setValueAndDerivatives(const std::vector<unsigned> & indices, double value, std::vector<double>& der);
196 : /// add to grid value
197 : virtual void addValue(index_t index, double value);
198 : virtual void addValue(const std::vector<unsigned> & indices, double value);
199 : /// add to grid value and derivatives
200 : virtual void addValueAndDerivatives(index_t index, double value, std::vector<double>& der);
201 : virtual void addValueAndDerivatives(const std::vector<unsigned> & indices, double value, std::vector<double>& der);
202 : /// Scale all grid values and derivatives by a constant factor
203 : virtual void scaleAllValuesAndDerivatives( const double& scalef );
204 : /// Takes the scalef times the logarithm of all grid values and derivatives
205 : virtual void logAllValuesAndDerivatives( const double& scalef );
206 : /// Set the minimum value of the grid to zero and translates accordingly
207 : virtual void setMinToZero();
208 : /// apply function: takes pointer to function that accepts a double and apply
209 : virtual void applyFunctionAllValuesAndDerivatives( double (*func)(double val), double (*funcder)(double valder) );
210 : /// add a kernel function to the grid
211 : void addKernel( const KernelFunctions& kernel );
212 :
213 : /// dump grid on file
214 : virtual void writeToFile(OFile&);
215 : /// dump grid to gaussian cube file
216 : void writeCubeFile(OFile&, const double& lunit);
217 :
218 5962 : virtual ~Grid() {}
219 :
220 : /// project a high dimensional grid onto a low dimensional one: this should be changed at some time
221 : /// to enable many types of weighting
222 : Grid project( const std::vector<std::string> & proj, WeightBase *ptr2obj );
223 : void projectOnLowDimension(double &val, std::vector<int> &varHigh, WeightBase* ptr2obj );
224 : /// set output format
225 143 : void setOutputFmt(const std::string & ss) {fmt_=ss;}
226 : /// reset output format to the default %14.9f format
227 : void resetToDefaultOutputFmt() {fmt_="%14.9f";}
228 : /// Integrate the function calculated on the grid
229 : double integrate( std::vector<unsigned>& npoints );
230 : ///
231 : void mpiSumValuesAndDerivatives( Communicator& comm );
232 : /// Find the maximum over paths of the minimum value of the gridded function along the paths
233 : /// for all paths of neighboring grid lattice points from a source point to a sink point.
234 : virtual double findMaximalPathMinimum(const std::vector<double> &source, const std::vector<double> &sink);
235 : };
236 :
237 :
238 : class SparseGrid : public Grid
239 : {
240 :
241 : std::map<index_t,double> map_;
242 : std::map< index_t,std::vector<double> > der_;
243 :
244 : protected:
245 : void clear();
246 :
247 : public:
248 : SparseGrid(const std::string& funcl, const std::vector<Value*> & args, const std::vector<std::string> & gmin,
249 : const std::vector<std::string> & gmax,
250 12 : const std::vector<unsigned> & nbin, bool dospline, bool usederiv):
251 12 : Grid(funcl,args,gmin,gmax,nbin,dospline,usederiv,false) {}
252 :
253 : index_t getSize() const;
254 : index_t getMaxSize() const;
255 :
256 : /// this is to access to Grid:: version of these methods (allowing overloading of virtual methods)
257 : using Grid::getValue;
258 : using Grid::getValueAndDerivatives;
259 : using Grid::setValue;
260 : using Grid::setValueAndDerivatives;
261 : using Grid::addValue;
262 : using Grid::addValueAndDerivatives;
263 :
264 : /// get grid value
265 : double getValue(index_t index) const;
266 : /// get grid value and derivatives
267 : double getValueAndDerivatives(index_t index, std::vector<double>& der) const;
268 :
269 : /// set grid value
270 : void setValue(index_t index, double value);
271 : /// set grid value and derivatives
272 : void setValueAndDerivatives(index_t index, double value, std::vector<double>& der);
273 : /// add to grid value
274 : void addValue(index_t index, double value);
275 : /// add to grid value and derivatives
276 : void addValueAndDerivatives(index_t index, double value, std::vector<double>& der);
277 :
278 : /// dump grid on file
279 : void writeToFile(OFile&);
280 :
281 36 : virtual ~SparseGrid() {}
282 :
283 : virtual double getMaxValue() const;
284 : virtual double getMinValue() const;
285 :
286 : };
287 : }
288 :
289 : #endif
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