Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2023 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 : #include <cstddef>
31 :
32 : namespace PLMD {
33 :
34 :
35 : // simple function to enable various weighting
36 :
37 : class WeightBase {
38 : public:
39 : virtual double projectInnerLoop(double &input, double &v)=0;
40 : virtual double projectOuterLoop(double &v)=0;
41 : virtual ~WeightBase() {}
42 : };
43 :
44 3 : class BiasWeight:public WeightBase {
45 : public:
46 : double beta,invbeta;
47 : double shift=0.0;
48 3 : explicit BiasWeight(double v) {beta=v; invbeta=1./beta;}
49 : //double projectInnerLoop(double &input, double &v) override {return input+exp(beta*v);}
50 : //double projectOuterLoop(double &v) override {return -invbeta*std::log(v);}
51 13603 : double projectInnerLoop(double &input, double &v) override {
52 13603 : auto betav=beta*v;
53 13603 : auto x=betav-shift;
54 13603 : if(x>0) {
55 1187 : shift=betav;
56 1187 : return input*std::exp(-x)+1;
57 : } else {
58 12416 : return input+std::exp(x);
59 : }
60 : }
61 187 : double projectOuterLoop(double &v) override {
62 187 : auto res=-invbeta*(std::log(v)+shift);
63 187 : shift=0.0;
64 187 : return res;
65 : }
66 : };
67 :
68 : class ProbWeight:public WeightBase {
69 : public:
70 : double beta,invbeta;
71 : explicit ProbWeight(double v) {beta=v; invbeta=1./beta;}
72 : double projectInnerLoop(double &input, double &v) override {return input+v;}
73 : double projectOuterLoop(double &v) override {return -invbeta*std::log(v);}
74 : };
75 :
76 :
77 :
78 :
79 :
80 :
81 : class Value;
82 : class IFile;
83 : class OFile;
84 : class KernelFunctions;
85 : class Communicator;
86 :
87 : /// \ingroup TOOLBOX
88 : class GridBase
89 : {
90 : public:
91 : // we use a size_t here
92 : // should be 8 bytes on all 64-bit machines
93 : // and more portable than "unsigned long long"
94 : typedef std::size_t index_t;
95 : // to restore old implementation (unsigned) use the following instead:
96 : // typedef unsigned index_t;
97 : /// Maximum dimension (exaggerated value).
98 : /// Can be used to replace local std::vectors with std::arrays (allocated on stack).
99 : static constexpr std::size_t maxdim=64;
100 : protected:
101 : std::string funcname;
102 : std::vector<std::string> argnames;
103 : std::vector<std::string> str_min_, str_max_;
104 : std::vector<double> min_,max_,dx_;
105 : std::vector<unsigned> nbin_;
106 : std::vector<bool> pbc_;
107 : index_t maxsize_;
108 : unsigned dimension_;
109 : bool dospline_, usederiv_;
110 : std::string fmt_; // format for output
111 : /// get "neighbors" for spline
112 : void getSplineNeighbors(const std::vector<unsigned> & indices, std::vector<index_t>& neigh, unsigned& nneigh )const;
113 : // std::vector<index_t> getSplineNeighbors(const std::vector<unsigned> & indices)const;
114 :
115 :
116 : public:
117 : /// this constructor here is Value-aware
118 : GridBase(const std::string& funcl, const std::vector<Value*> & args, const std::vector<std::string> & gmin,
119 : const std::vector<std::string> & gmax, const std::vector<unsigned> & nbin, bool dospline,
120 : bool usederiv);
121 : /// this constructor here is not Value-aware
122 : GridBase(const std::string& funcl, const std::vector<std::string> &names, const std::vector<std::string> & gmin,
123 : const std::vector<std::string> & gmax, const std::vector<unsigned> & nbin, bool dospline,
124 : bool usederiv, const std::vector<bool> &isperiodic, const std::vector<std::string> &pmin,
125 : const std::vector<std::string> &pmax );
126 : /// this is the real initializator
127 : void Init(const std::string & funcl, const std::vector<std::string> &names, const std::vector<std::string> & gmin,
128 : const std::vector<std::string> & gmax, const std::vector<unsigned> & nbin, bool dospline, bool usederiv,
129 : const std::vector<bool> &isperiodic, const std::vector<std::string> &pmin, const std::vector<std::string> &pmax);
130 : /// get lower boundary
131 : std::vector<std::string> getMin() const;
132 : /// get upper boundary
133 : std::vector<std::string> getMax() const;
134 : /// get bin size
135 : std::vector<double> getDx() const;
136 : double getDx(index_t j) const ;
137 : /// get bin volume
138 : double getBinVolume() const;
139 : /// get number of bins
140 : std::vector<unsigned> getNbin() const;
141 : /// get if periodic
142 : std::vector<bool> getIsPeriodic() const;
143 : /// get grid dimension
144 : unsigned getDimension() const;
145 : /// get argument names of this grid
146 : std::vector<std::string> getArgNames() const;
147 : /// get if the grid has derivatives
148 1986398 : bool hasDerivatives() const {return usederiv_;}
149 :
150 : /// methods to handle grid indices
151 : void getIndices(index_t index, std::vector<unsigned>& rindex) const;
152 : void getIndices(const std::vector<double> & x, std::vector<unsigned>& rindex) const;
153 : std::vector<unsigned> getIndices(index_t index) const;
154 : std::vector<unsigned> getIndices(const std::vector<double> & x) const;
155 : index_t getIndex(const std::vector<unsigned> & indices) const;
156 : index_t getIndex(const std::vector<double> & x) const;
157 : std::vector<double> getPoint(index_t index) const;
158 : std::vector<double> getPoint(const std::vector<unsigned> & indices) const;
159 : std::vector<double> getPoint(const std::vector<double> & x) const;
160 : /// faster versions relying on preallocated vectors
161 : void getPoint(index_t index,std::vector<double> & point) const;
162 : void getPoint(const std::vector<unsigned> & indices,std::vector<double> & point) const;
163 : void getPoint(const std::vector<double> & x,std::vector<double> & point) const;
164 :
165 : /// get neighbors
166 : std::vector<index_t> getNeighbors(index_t index,const std::vector<unsigned> & neigh) const;
167 : std::vector<index_t> getNeighbors(const std::vector<unsigned> & indices,const std::vector<unsigned> & neigh) const;
168 : std::vector<index_t> getNeighbors(const std::vector<double> & x,const std::vector<unsigned> & neigh) const;
169 : /// get nearest neighbors (those separated by exactly one lattice unit)
170 : std::vector<index_t> getNearestNeighbors(const index_t index) const;
171 : std::vector<index_t> getNearestNeighbors(const std::vector<unsigned> &indices) const;
172 :
173 : /// write header for grid file
174 : void writeHeader(OFile& file);
175 :
176 : /// read grid from file
177 : static std::unique_ptr<GridBase> create(const std::string&,const std::vector<Value*>&,IFile&,bool,bool,bool);
178 : /// read grid from file and check boundaries are what is expected from input
179 : static std::unique_ptr<GridBase> create(const std::string&,const std::vector<Value*>&, IFile&,
180 : const std::vector<std::string>&,const std::vector<std::string>&,
181 : const std::vector<unsigned>&,bool,bool,bool);
182 : /// get grid size
183 : virtual index_t getSize() const=0;
184 : /// get grid value
185 : virtual double getValue(index_t index) const=0;
186 : double getValue(const std::vector<unsigned> & indices) const;
187 : double getValue(const std::vector<double> & x) const;
188 : /// get grid value and derivatives
189 : virtual double getValueAndDerivatives(index_t index, std::vector<double>& der) const=0;
190 : double getValueAndDerivatives(const std::vector<unsigned> & indices, std::vector<double>& der) const;
191 : double getValueAndDerivatives(const std::vector<double> & x, std::vector<double>& der) const;
192 :
193 : /// set grid value
194 : virtual void setValue(index_t index, double value)=0;
195 : void setValue(const std::vector<unsigned> & indices, double value);
196 : /// set grid value and derivatives
197 : virtual void setValueAndDerivatives(index_t index, double value, std::vector<double>& der)=0;
198 : void setValueAndDerivatives(const std::vector<unsigned> & indices, double value, std::vector<double>& der);
199 : /// add to grid value
200 : virtual void addValue(index_t index, double value)=0;
201 : void addValue(const std::vector<unsigned> & indices, double value);
202 : /// add to grid value and derivatives
203 : virtual void addValueAndDerivatives(index_t index, double value, std::vector<double>& der)=0;
204 : void addValueAndDerivatives(const std::vector<unsigned> & indices, double value, std::vector<double>& der);
205 : /// add a kernel function to the grid
206 : void addKernel( const KernelFunctions& kernel );
207 :
208 : /// get minimum value
209 : virtual double getMinValue() const = 0;
210 : /// get maximum value
211 : virtual double getMaxValue() const = 0;
212 :
213 : /// dump grid on file
214 : virtual void writeToFile(OFile&)=0;
215 : /// dump grid to gaussian cube file
216 : void writeCubeFile(OFile&, const double& lunit);
217 :
218 2994 : virtual ~GridBase() {}
219 :
220 : /// set output format
221 197 : void setOutputFmt(const std::string & ss) {fmt_=ss;}
222 : /// reset output format to the default %14.9f format
223 : void resetToDefaultOutputFmt() {fmt_="%14.9f";}
224 : ///
225 : /// Find the maximum over paths of the minimum value of the gridded function along the paths
226 : /// for all paths of neighboring grid lattice points from a source point to a sink point.
227 : double findMaximalPathMinimum(const std::vector<double> &source, const std::vector<double> &sink);
228 : };
229 :
230 : class Grid : public GridBase
231 : {
232 : std::vector<double> grid_;
233 : std::vector<double> der_;
234 : double contour_location=0.0;
235 : public:
236 1314 : Grid(const std::string& funcl, const std::vector<Value*> & args, const std::vector<std::string> & gmin,
237 : const std::vector<std::string> & gmax,
238 1314 : const std::vector<unsigned> & nbin, bool dospline, bool usederiv):
239 1314 : GridBase(funcl,args,gmin,gmax,nbin,dospline,usederiv)
240 : {
241 1314 : grid_.assign(maxsize_,0.0);
242 1314 : if(usederiv_) der_.assign(maxsize_*dimension_,0.0);
243 1314 : }
244 : /// this constructor here is not Value-aware
245 128 : Grid(const std::string& funcl, const std::vector<std::string> &names, const std::vector<std::string> & gmin,
246 : const std::vector<std::string> & gmax, const std::vector<unsigned> & nbin, bool dospline,
247 : bool usederiv, const std::vector<bool> &isperiodic, const std::vector<std::string> &pmin,
248 128 : const std::vector<std::string> &pmax ):
249 128 : GridBase(funcl,names,gmin,gmax,nbin,dospline,usederiv,isperiodic,pmin,pmax)
250 : {
251 128 : grid_.assign(maxsize_,0.0);
252 128 : if(usederiv_) der_.assign(maxsize_*dimension_,0.0);
253 128 : }
254 : index_t getSize() const override;
255 : /// this is to access to Grid:: version of these methods (allowing overloading of virtual methods)
256 : using GridBase::getValue;
257 : using GridBase::getValueAndDerivatives;
258 : using GridBase::setValue;
259 : using GridBase::setValueAndDerivatives;
260 : using GridBase::addValue;
261 : using GridBase::addValueAndDerivatives;
262 : /// get grid value
263 : double getValue(index_t index) const override;
264 : /// get grid value and derivatives
265 : double getValueAndDerivatives(index_t index, std::vector<double>& der) const override;
266 :
267 : /// set grid value
268 : void setValue(index_t index, double value) override;
269 : /// set grid value and derivatives
270 : void setValueAndDerivatives(index_t index, double value, std::vector<double>& der) override;
271 : /// add to grid value
272 : void addValue(index_t index, double value) override;
273 : /// add to grid value and derivatives
274 : void addValueAndDerivatives(index_t index, double value, std::vector<double>& der) override;
275 :
276 : /// get minimum value
277 : double getMinValue() const override;
278 : /// get maximum value
279 : double getMaxValue() const override;
280 : /// Scale all grid values and derivatives by a constant factor
281 : void scaleAllValuesAndDerivatives( const double& scalef );
282 : /// Takes the scalef times the logarithm of all grid values and derivatives
283 : void logAllValuesAndDerivatives( const double& scalef );
284 : /// dump grid on file
285 : void writeToFile(OFile&) override;
286 :
287 : /// Set the minimum value of the grid to zero and translates accordingly
288 : void setMinToZero();
289 : /// apply function: takes pointer to function that accepts a double and apply
290 : void applyFunctionAllValuesAndDerivatives( double (*func)(double val), double (*funcder)(double valder) );
291 : /// Get the difference from the contour
292 : double getDifferenceFromContour(const std::vector<double> & x, std::vector<double>& der) const ;
293 : /// Find a set of points on a contour in the function
294 : void findSetOfPointsOnContour(const double& target, const std::vector<bool>& nosearch, unsigned& npoints, std::vector<std::vector<double> >& points );
295 : /// Since this method returns a concrete Grid, it should be here and not in GridBase - GB
296 : /// project a high dimensional grid onto a low dimensional one: this should be changed at some time
297 : /// to enable many types of weighting
298 : Grid project( const std::vector<std::string> & proj, WeightBase *ptr2obj );
299 : void projectOnLowDimension(double &val, std::vector<int> &varHigh, WeightBase* ptr2obj );
300 : void mpiSumValuesAndDerivatives( Communicator& comm );
301 : /// Integrate the function calculated on the grid
302 : double integrate( std::vector<unsigned>& npoints );
303 : void clear();
304 : };
305 :
306 :
307 : class SparseGrid : public GridBase
308 : {
309 :
310 : std::map<index_t,double> map_;
311 : std::map< index_t,std::vector<double> > der_;
312 :
313 : public:
314 6 : SparseGrid(const std::string& funcl, const std::vector<Value*> & args, const std::vector<std::string> & gmin,
315 : const std::vector<std::string> & gmax,
316 6 : const std::vector<unsigned> & nbin, bool dospline, bool usederiv):
317 6 : GridBase(funcl,args,gmin,gmax,nbin,dospline,usederiv) {}
318 :
319 : index_t getSize() const override;
320 : index_t getMaxSize() const;
321 :
322 : /// this is to access to Grid:: version of these methods (allowing overloading of virtual methods)
323 : using GridBase::getValue;
324 : using GridBase::getValueAndDerivatives;
325 : using GridBase::setValue;
326 : using GridBase::setValueAndDerivatives;
327 : using GridBase::addValue;
328 : using GridBase::addValueAndDerivatives;
329 :
330 : /// get grid value
331 : double getValue(index_t index) const override;
332 : /// get grid value and derivatives
333 : double getValueAndDerivatives(index_t index, std::vector<double>& der) const override;
334 :
335 : /// set grid value
336 : void setValue(index_t index, double value) override;
337 : /// set grid value and derivatives
338 : void setValueAndDerivatives(index_t index, double value, std::vector<double>& der) override;
339 : /// add to grid value
340 : void addValue(index_t index, double value) override;
341 : /// add to grid value and derivatives
342 : void addValueAndDerivatives(index_t index, double value, std::vector<double>& der) override;
343 :
344 : /// get minimum value
345 : double getMinValue() const override;
346 : /// get maximum value
347 : double getMaxValue() const override;
348 : /// dump grid on file
349 : void writeToFile(OFile&) override;
350 :
351 18 : virtual ~SparseGrid() {}
352 : };
353 : }
354 :
355 : #endif
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