Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2015-2018 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_gridtools_GridVessel_h
23 : #define __PLUMED_gridtools_GridVessel_h
24 :
25 : #include <string>
26 : #include <cstring>
27 : #include <vector>
28 : #include "vesselbase/AveragingVessel.h"
29 :
30 : namespace PLMD {
31 : namespace gridtools {
32 :
33 44 : class GridVessel : public vesselbase::AveragingVessel {
34 : friend class ActionWithInputGrid;
35 : friend class DumpGrid;
36 : private:
37 : /// Have the minimum and maximum for the grid been set
38 : bool bounds_set;
39 : /// The number of points in the grid
40 : unsigned npoints;
41 : /// Units for Gaussian Cube file
42 : double cube_units;
43 : /// This flag is used to check if the user has created a valid input
44 : bool foundprint;
45 : /// The minimum and maximum of the grid stored as doubles
46 : std::vector<double> min, max;
47 : /// The numerical distance between adjacent grid points
48 : std::vector<unsigned> stride;
49 : /// The number of bins in each grid direction
50 : std::vector<unsigned> nbin;
51 : /// The grid point that was requested last by getGridPointCoordinates
52 : unsigned currentGridPoint;
53 : protected:
54 : /// Do we have derivatives
55 : bool noderiv;
56 : /// The names of the various columns in the grid file
57 : std::vector<std::string> arg_names;
58 : /// The number of pieces of information we are storing for each
59 : /// point in the grid
60 : unsigned nper;
61 : /// Is this direction periodic
62 : std::vector<bool> pbc;
63 : /// The minimum and maximum in the grid stored as strings
64 : std::vector<std::string> str_min, str_max;
65 : /// The spacing between grid points
66 : std::vector<double> dx;
67 : /// The dimensionality of the grid
68 : unsigned dimension;
69 : /// Which grid points are we actively accumulating
70 : std::vector<bool> active;
71 : /// Convert a point in space the the correspoinding grid point
72 : unsigned getIndex( const std::vector<double>& p ) const ;
73 : public:
74 : /// keywords
75 : static void registerKeywords( Keywords& keys );
76 : /// Constructor
77 : explicit GridVessel( const vesselbase::VesselOptions& );
78 : /// Remove the derivatives
79 : void setNoDerivatives();
80 : /// Set the minimum and maximum of the grid
81 : virtual void setBounds( const std::vector<std::string>& smin, const std::vector<std::string>& smax, const std::vector<unsigned>& nbins, const std::vector<double>& spacing );
82 : /// Get a description of the grid to output to the log
83 : std::string description();
84 : /// Convert an index into indices
85 : void convertIndexToIndices( const unsigned& index, const std::vector<unsigned>& nnbin, std::vector<unsigned>& indices ) const ;
86 : /// Flatten the grid and get the grid index for a point
87 : unsigned getIndex( const std::vector<unsigned>& indices ) const ;
88 : /// Get the indices fof a point
89 : void getIndices( const unsigned& index, std::vector<unsigned>& indices ) const ;
90 : /// Get the indices of a particular point
91 : void getIndices( const std::vector<double>& point, std::vector<unsigned>& indices ) const ;
92 : /// Operations on one of the elements of grid point i
93 : void setGridElement( const unsigned&, const unsigned&, const double& );
94 : /// Add data to an element of the grid
95 : void addToGridElement( const unsigned& ipoint, const unsigned& jelement, const double& value );
96 : /// Operations on one of the elements of grid point specified by vector
97 : double getGridElement( const std::vector<unsigned>&, const unsigned& ) const ;
98 : void setGridElement( const std::vector<unsigned>&, const unsigned&, const double& );
99 : /// Set the size of the buffer equal to nper*npoints
100 : virtual void resize();
101 : /// Get the number of points in the grid
102 : unsigned getNumberOfPoints() const;
103 : /// Get the coordinates for a point in the grid
104 : void getGridPointCoordinates( const unsigned&, std::vector<double>& ) const ;
105 : /// Get the dimensionality of the function
106 : unsigned getDimension() const ;
107 : /// Get the number of components in the vector stored on each grid point
108 : virtual unsigned getNumberOfComponents() const ;
109 : /// Is the grid periodic in the ith direction
110 : bool isPeriodic( const unsigned& i ) const ;
111 : /// Get the number of quantities we have stored at each grid point
112 : unsigned getNumberOfQuantities() const ;
113 : /// Get the number of grid points for each dimension
114 : std::vector<unsigned> getNbin() const ;
115 : /// Get the name of the ith component
116 : std::string getComponentName( const unsigned& i ) const ;
117 : /// Get the vector containing the minimum value of the grid in each dimension
118 : std::vector<std::string> getMin() const ;
119 : /// Get the vector containing the maximum value of the grid in each dimension
120 : std::vector<std::string> getMax() const ;
121 : /// Get the number of points needed in the buffer
122 : virtual unsigned getNumberOfBufferPoints() const ;
123 : /// Get the stride (the distance between the grid points of an index)
124 : const std::vector<unsigned>& getStride() const ;
125 : /// Return the volume of one of the grid cells
126 : double getCellVolume() const ;
127 : /// Get the value of the ith grid element
128 : virtual double getGridElement( const unsigned&, const unsigned& ) const ;
129 : /// Get the set of points neighouring a particular location in space
130 : void getNeighbors( const std::vector<double>& pp, const std::vector<unsigned>& nneigh,
131 : unsigned& num_neighbours, std::vector<unsigned>& neighbors ) const ;
132 : /// Get the neighbors for a set of indices of a point
133 : void getNeighbors( const std::vector<unsigned>& indices, const std::vector<unsigned>& nneigh,
134 : unsigned& num_neighbors, std::vector<unsigned>& neighbors ) const ;
135 : /// Get the points neighboring a particular spline point
136 : void getSplineNeighbors( const unsigned& mybox, std::vector<unsigned>& mysneigh ) const ;
137 : /// Get the spacing between grid points
138 : const std::vector<double>& getGridSpacing() const ;
139 : /// Get the extent of the grid in one of the axis
140 : double getGridExtent( const unsigned& i ) const ;
141 : /// Copy data from the action into the grid
142 : virtual void calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const ;
143 : /// This ensures that Gaussian cube fies are in correct units
144 : void setCubeUnits( const double& units );
145 : /// This ensures that Gaussian cube files are in correct units
146 : double getCubeUnits() const ;
147 : /// Return a string containing the input to the grid so we can clone it
148 : std::string getInputString() const ;
149 : /// Does this have derivatives
150 : bool noDerivatives() const ;
151 : /// Get the value and derivatives at a particular location using spline interpolation
152 : double getValueAndDerivatives( const std::vector<double>& x, const unsigned& ind, std::vector<double>& der ) const ;
153 : /// Deactivate all the grid points
154 : void activateThesePoints( const std::vector<bool>& to_activate );
155 : /// Is this point active
156 : bool inactive( const unsigned& ip ) const ;
157 : };
158 :
159 : inline
160 13561 : unsigned GridVessel::getNumberOfQuantities() const {
161 13561 : return nper;
162 : }
163 :
164 : inline
165 108208 : unsigned GridVessel::getNumberOfPoints() const {
166 108208 : return npoints;
167 : }
168 :
169 : inline
170 596 : const std::vector<double>& GridVessel::getGridSpacing() const {
171 596 : return dx;
172 : }
173 :
174 : inline
175 : double GridVessel::getCellVolume() const {
176 : double myvol=1.0; for(unsigned i=0; i<dimension; ++i) myvol *= dx[i];
177 : return myvol;
178 : }
179 :
180 : inline
181 201913 : unsigned GridVessel::getDimension() const {
182 201913 : return dimension;
183 : }
184 :
185 : inline
186 77389 : bool GridVessel::isPeriodic( const unsigned& i ) const {
187 77389 : return pbc[i];
188 : }
189 :
190 : inline
191 24256 : std::string GridVessel::getComponentName( const unsigned& i ) const {
192 24256 : return arg_names[i];
193 : }
194 :
195 : inline
196 16 : unsigned GridVessel::getNumberOfComponents() const {
197 16 : if( noderiv ) return nper;
198 14 : return nper / ( dimension + 1 );
199 : }
200 :
201 : inline
202 45 : double GridVessel::getGridExtent( const unsigned& i ) const {
203 45 : return max[i] - min[i];
204 : }
205 :
206 : inline
207 8750 : bool GridVessel::noDerivatives() const {
208 8750 : return noderiv;
209 : }
210 :
211 : inline
212 15536664 : bool GridVessel::inactive( const unsigned& ip ) const {
213 : plumed_dbg_assert( ip<npoints );
214 15536664 : return !active[ip];
215 : }
216 :
217 : inline
218 16696 : const std::vector<unsigned>& GridVessel::getStride() const {
219 16696 : return stride;
220 : }
221 :
222 : inline
223 93 : unsigned GridVessel::getNumberOfBufferPoints() const {
224 93 : return npoints;
225 : }
226 :
227 : }
228 : }
229 : #endif
|
