Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2016-2018 The VES code team
3 : (see the PEOPLE-VES file at the root of this folder for a list of names)
4 :
5 : See http://www.ves-code.org for more information.
6 :
7 : This file is part of VES code module.
8 :
9 : The VES code module 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 : The VES code module 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 the VES code module. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #ifndef __PLUMED_ves_CoeffsBase_h
23 : #define __PLUMED_ves_CoeffsBase_h
24 :
25 : #include <vector>
26 : #include <string>
27 :
28 :
29 : namespace PLMD {
30 :
31 : class Action;
32 : class Value;
33 : class IFile;
34 : class OFile;
35 :
36 : namespace ves {
37 :
38 : class BasisFunctions;
39 : class VesBias;
40 :
41 : /// \ingroup TOOLBOX
42 111530 : class CoeffsBase
43 : {
44 : public:
45 : // the type of 1D index
46 : // typedef size_t index_t;
47 : // typedef unsigned int index_t;
48 : private:
49 : std::string label_;
50 : std::string data_label_;
51 : enum CoeffsType {
52 : Generic,
53 : LinearBasisSet,
54 : MultiCoeffs_LinearBasisSet
55 : } coeffs_type_;
56 : //
57 : bool iteration_and_time_active_;
58 : unsigned int iteration_opt;
59 : double time_md;
60 : //
61 : bool active;
62 : //
63 : Action* action_pntr_;
64 : VesBias* vesbias_pntr_;
65 : //
66 : unsigned int ndimensions_;
67 : std::vector<unsigned int> indices_shape_;
68 : size_t ncoeffs_;
69 : std::vector<std::string> coeffs_descriptions_;
70 : std::vector<std::string> dimension_labels_;
71 : //
72 : std::vector<Value*> args_;
73 : std::vector<BasisFunctions*> basisf_;
74 : //
75 : bool multicoeffs_;
76 : std::vector<std::vector<Value*> > multicoeffs_args_;
77 : std::vector<std::vector<BasisFunctions*> >multicoeffs_basisf_;
78 : // Labels for fields in output/input files
79 : const std::string field_type_;
80 : const std::string field_ndimensions_;
81 : const std::string field_ncoeffs_total_;
82 : const std::string field_shape_prefix_;
83 : const std::string field_time_;
84 : const std::string field_iteration_;
85 : //
86 : std::string output_fmt_;
87 : //
88 : void initializeIndices(const std::vector<unsigned int>&, const std::vector<std::string>&);
89 : void reinitializeIndices(const std::vector<unsigned int>&);
90 : public:
91 : explicit CoeffsBase();
92 : //
93 : explicit CoeffsBase(
94 : const std::string&,
95 : const std::vector<std::string>&,
96 : const std::vector<unsigned int>&,
97 : const bool use_iteration_counter=false);
98 : //
99 : explicit CoeffsBase(
100 : const std::string&,
101 : std::vector<Value*>&,
102 : std::vector<BasisFunctions*>&,
103 : const bool use_iteration_counter=false);
104 : //
105 : explicit CoeffsBase(
106 : const std::string&,
107 : std::vector<std::vector<Value*> >&,
108 : std::vector<std::vector<BasisFunctions*> >&,
109 : const bool use_iteration_counter=false,
110 : const std::string& multicoeffs_label="bias"
111 : );
112 : //
113 : ~CoeffsBase();
114 : //
115 : std::string getLabel() const {return label_;}
116 : void setLabel(const std::string&);
117 : std::string getDataLabel() const {return data_label_;};
118 : void setDataLabel(const std::string&);
119 : void setLabels(const std::string&);
120 : void setLabels(const std::string&, const std::string&);
121 : //
122 : CoeffsType getType() const {return coeffs_type_;}
123 : std::string getTypeStr() const;
124 : void setType(const CoeffsType coeffs_type);
125 : void linkVesBias(VesBias*);
126 : void linkAction(Action*);
127 : VesBias* getPntrToVesBias() const {return vesbias_pntr_;}
128 9 : Action* getPntrToAction() const {return action_pntr_;}
129 : bool isGenericCoeffs() const {return coeffs_type_==Generic;}
130 : bool isLinearBasisSetCoeffs() const {return coeffs_type_==LinearBasisSet;}
131 : bool isMultiLinearBasisSetCoeffs() const {return coeffs_type_==MultiCoeffs_LinearBasisSet;}
132 : //
133 : std::vector<unsigned int> shapeOfIndices() const {return indices_shape_;}
134 3977 : unsigned int shapeOfIndices(const unsigned int dim_index) const {return indices_shape_[dim_index];}
135 216674475 : size_t numberOfCoeffs() const {return ncoeffs_;}
136 2844178 : unsigned int numberOfDimensions() const {return ndimensions_;}
137 : //
138 770 : bool isActive() const {return active;}
139 1540 : void activate() {active=true;}
140 180 : void deactivate() {active=false;}
141 : //
142 : size_t getIndex(const std::vector<unsigned int>&) const;
143 : std::vector<unsigned int> getIndices(const size_t) const;
144 : bool indicesExist(const std::vector<unsigned int>&) const;
145 : //
146 : std::string getCoeffDescription(const size_t index) const {return coeffs_descriptions_[index];}
147 : std::string getCoeffDescription(const std::vector<unsigned int>&) const;
148 2181 : std::vector<std::string> getAllCoeffsDescriptions() const {return coeffs_descriptions_;}
149 : void setCoeffDescription(const size_t, const std::string&);
150 : void setCoeffDescription(const std::vector<unsigned int>&, const std::string&);
151 : void setAllCoeffsDescriptions(const std::string& description_prefix="C");
152 : void setAllCoeffsDescriptions(const std::vector<std::string>&);
153 : //
154 : std::string getDimensionLabel(const unsigned int) const;
155 : std::vector<std::string> getAllDimensionLabels() const {return dimension_labels_;}
156 : void setDimensionLabel(const unsigned int, const std::string&);
157 : void setAllDimensionLabels(const std::string&);
158 : void setAllDimensionLabels(const std::vector<std::string>&);
159 : void writeCoeffsInfoToFile(OFile&) const;
160 : void writeTimeInfoToFile(OFile&, const double) const;
161 : void getCoeffsInfoFromFile(IFile&, const bool ignore_coeffs_info=false);
162 : void checkCoeffsInfo(const std::string&, const std::string&, const unsigned int, const size_t, const std::vector<unsigned int>&);
163 : //
164 308 : void turnOnIterationCounter() {iteration_and_time_active_=true;}
165 : void turnOffIterationCounter() {iteration_and_time_active_=false;}
166 3237 : bool isIterationCounterActive() const {return iteration_and_time_active_;}
167 : void setIterationCounter(const unsigned int);
168 : void setTime(const double);
169 : void setIterationCounterAndTime(const unsigned int, const double);
170 153 : unsigned int getIterationCounter() const {return iteration_opt;}
171 : double getTimeValue() const {return time_md;}
172 : //
173 407 : void setOutputFmt(const std::string& ss) { output_fmt_=ss; }
174 : void resetOutputFmt() {output_fmt_="%30.16e";}
175 : std::string getOutputFmt() const {return output_fmt_;}
176 : //
177 : protected:
178 : void setupBasisFunctionsInfo();
179 : void resizeIndices(const std::vector<unsigned int>&);
180 : void resizeIndices(std::vector<BasisFunctions*>&);
181 : bool sameShape(const CoeffsBase&) const;
182 : //
183 : void writeIterationCounterAndTimeToFile(OFile&) const;
184 : bool getIterationCounterAndTimeFromFile(IFile&);
185 : //
186 :
187 : };
188 :
189 : inline
190 : void CoeffsBase::setIterationCounter(const unsigned int iteration_opt_in) {
191 : iteration_opt=iteration_opt_in;
192 : }
193 :
194 : inline
195 : void CoeffsBase::setTime(const double time_md_in) {
196 : time_md=time_md_in;
197 : }
198 :
199 : inline
200 : void CoeffsBase::setIterationCounterAndTime(const unsigned int iteration_opt_in, const double time_md_in) {
201 4804 : iteration_opt=iteration_opt_in;
202 4804 : time_md=time_md_in;
203 : }
204 :
205 : inline
206 : std::string CoeffsBase::getCoeffDescription(const std::vector<unsigned int>& indices) const {
207 : return getCoeffDescription(getIndex(indices));
208 : }
209 :
210 : inline
211 : std::string CoeffsBase::getDimensionLabel(const unsigned int dim_index) const {
212 : // plumed_massert(dim_index<numberOfDimensions(),"Trying to get the label of a dimension outside the number of dimensions");
213 7996 : return dimension_labels_[dim_index];
214 : }
215 :
216 :
217 : // we are flattening arrays using a column-major order
218 : inline
219 : size_t CoeffsBase::getIndex(const std::vector<unsigned int>& indices) const {
220 : // plumed_dbg_assert(indices.size()==ndimensions_);
221 : // for(unsigned int i=0; i<ndimensions_; i++){
222 : // if(indices[i]>=indices_shape_[i]){
223 : // std::string is;
224 : // Tools::convert(i,is);
225 : // std::string msg="ERROR: the system is looking for a value outside the indices along the " + is + "dimension!";
226 : // plumed_merror(msg);
227 : // }
228 : // }
229 21652 : size_t index=indices[ndimensions_-1];
230 13326 : for(unsigned int i=ndimensions_-1; i>0; --i) {
231 7500 : index=index*indices_shape_[i-1]+indices[i-1];
232 : }
233 : return index;
234 : }
235 :
236 : // we are flattening arrays using a column-major order
237 : inline
238 212102589 : std::vector<unsigned int> CoeffsBase::getIndices(const size_t index) const {
239 212102589 : std::vector<unsigned int> indices(ndimensions_);
240 : size_t kk=index;
241 424205178 : indices[0]=(index%indices_shape_[0]);
242 212102589 : for(unsigned int i=1; i<ndimensions_-1; ++i) {
243 0 : kk=(kk-indices[i-1])/indices_shape_[i-1];
244 0 : indices[i]=(kk%indices_shape_[i]);
245 : }
246 212102589 : if(ndimensions_>=2) {
247 845308524 : indices[ndimensions_-1]=((kk-indices[ndimensions_-2])/indices_shape_[ndimensions_-2]);
248 : }
249 212102589 : return indices;
250 : }
251 :
252 :
253 :
254 :
255 : }
256 : }
257 :
258 : #endif
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