Line data Source code
1 : // Copyright (C) 2015 Technische Universitaet Muenchen
2 : // This file is part of the Mamico project. For conditions of distribution
3 : // and use, please see the copyright notice in Mamico's main folder, or at
4 : // www5.in.tum.de/mamico
5 : #ifndef _MOLECULARDYNAMICS_COUPLING_COUPLINGCELLPLOTTER_H_
6 : #define _MOLECULARDYNAMICS_COUPLING_COUPLINGCELLPLOTTER_H_
7 :
8 : #include "coupling/KineticEnergyController.h"
9 : #include "coupling/cell-mappings/ComputeMassMapping.h"
10 : #include "coupling/cell-mappings/ComputeMomentumMapping.h"
11 : #include "coupling/cell-mappings/VTKMoleculePlotter.h"
12 : #include "coupling/datastructures/LinkedCellContainer.h"
13 : #include "coupling/interface/MDSolverInterface.h"
14 : #include "tarch/la/Vector.h"
15 : #include <fstream>
16 : #include <sstream>
17 :
18 : namespace coupling {
19 : template <class LinkedCell, unsigned int dim> class CouplingCellPlotter;
20 : }
21 :
22 : /** @brief plots the coupling cell data.
23 : * @author Philipp Neumann
24 : * @tparam LinkedCell the LinkedCell class is given by the implementation of
25 : * linked cells in the molecular dynamics simulation
26 : * @tparam dim refers to the spacial dimension of the simulation, can be 1, 2,
27 : * or 3*/
28 : template <class LinkedCell, unsigned int dim> class coupling::CouplingCellPlotter {
29 : public:
30 : /** @brief a simple constructor
31 : * @param ID the id of the md simulation
32 : * @param filename name for the file
33 : * @param rank mpi rank of the current process
34 : * @param t number of time step to plot
35 : * @param cells coupling cells to plot
36 : * @param mdSolverInterface interface of the md solver */
37 0 : CouplingCellPlotter(unsigned int ID, std::string filename, unsigned int rank, unsigned int t, datastructures::LinkedCellContainer<LinkedCell, dim>& cells,
38 : coupling::interface::MDSolverInterface<LinkedCell, dim>* const mdSolverInterface) {
39 0 : plotMoleculeFile(ID, filename, rank, t, cells, mdSolverInterface);
40 0 : plotCouplingCellFile(ID, filename, rank, t, cells, mdSolverInterface);
41 0 : }
42 :
43 : /** @brief a simple destructor*/
44 0 : ~CouplingCellPlotter() {}
45 :
46 : private:
47 : /** the file will contain the velocity, position, and potentials of the
48 : * molecules
49 : * @brief writes molecule information to VTK file.
50 : * @param ID the id of the md simulation
51 : * @param filename name for the file
52 : * @param rank mpi rank of the current process
53 : * @param t number of time step to plot
54 : * @param cells coupling cells to plot
55 : * @param mdSolverInterface interface of the md solver */
56 0 : void plotMoleculeFile(unsigned int ID, std::string filename, unsigned int rank, unsigned int t,
57 : coupling::datastructures::LinkedCellContainer<LinkedCell, dim>& cells,
58 : coupling::interface::MDSolverInterface<LinkedCell, dim>* const mdSolverInterface) {
59 : // open files
60 0 : std::ofstream moleculeFile;
61 : // store positions and velocities of molecules
62 0 : std::stringstream moleculeVelocities;
63 0 : std::stringstream moleculePositions;
64 0 : std::stringstream moleculePotentials;
65 : // zeros appended in vtk file
66 0 : std::string appendFloatZeros("");
67 : switch (dim) {
68 : case 1:
69 : appendFloatZeros = " 0.0 0.0";
70 : break;
71 : case 2:
72 : appendFloatZeros = " 0.0";
73 : break;
74 : case 3:
75 0 : appendFloatZeros = "";
76 : break;
77 : default:
78 : break;
79 : }
80 0 : Writer4Molecules writer(moleculeVelocities, moleculePositions, moleculePotentials, appendFloatZeros, mdSolverInterface);
81 0 : cells.applyToLocalNonGhostCouplingCellsWithLinkedCells(writer);
82 : // open file and write info
83 0 : open(ID, filename, "Molecules", rank, t, moleculeFile);
84 0 : moleculeFile << "# vtk DataFile Version 2.0" << std::endl;
85 0 : moleculeFile << "Generated by MaMiCo (Philipp Neumann)" << std::endl;
86 0 : moleculeFile << "ASCII" << std::endl;
87 0 : moleculeFile << "DATASET UNSTRUCTURED_GRID" << std::endl;
88 0 : moleculeFile << "POINTS " << writer.getMoleculeCounter() << " float" << std::endl;
89 0 : moleculeFile << moleculePositions.str() << std::endl << std::endl;
90 0 : moleculeFile << "POINT_DATA " << writer.getMoleculeCounter() << std::endl;
91 0 : moleculeFile << "VECTORS velocity float" << std::endl;
92 0 : moleculeFile << moleculeVelocities.str() << std::endl;
93 0 : moleculeFile << "SCALARS potentialEnergy float 1" << std::endl;
94 0 : moleculeFile << "LOOKUP_TABLE DEFAULT" << std::endl;
95 0 : moleculeFile << moleculePotentials.str() << std::endl;
96 0 : moleculePositions.clear();
97 0 : moleculePositions.str("");
98 0 : moleculeVelocities.clear();
99 0 : moleculeVelocities.str("");
100 0 : moleculePotentials.clear();
101 0 : moleculePotentials.str("");
102 0 : moleculeFile.close();
103 0 : }
104 :
105 : /** @brief writes molecule information + coupling cell information to VTK
106 : * file.
107 : * @param ID the id of the md simulation
108 : * @param filename name for the file
109 : * @param rank mpi rank of the current process
110 : * @param t number of time step to plot
111 : * @param cells coupling cells to plot
112 : * @param mdSolverInterface interface of the md solver */
113 0 : void plotCouplingCellFile(unsigned int ID, std::string filename, unsigned int rank, unsigned int t,
114 : coupling::datastructures::LinkedCellContainer<LinkedCell, dim>& cells,
115 : coupling::interface::MDSolverInterface<LinkedCell, dim>* const mdSolverInterface) {
116 : // stringstreams for all cell properties of interest
117 0 : std::stringstream microscopicMasses;
118 0 : microscopicMasses << "SCALARS microscopicMassBuffer float 1" << std::endl;
119 0 : microscopicMasses << "LOOKUP_TABLE DEFAULT" << std::endl;
120 0 : std::stringstream macroscopicMasses;
121 0 : macroscopicMasses << "SCALARS macroscopicMassBuffer float 1" << std::endl;
122 0 : macroscopicMasses << "LOOKUP_TABLE DEFAULT" << std::endl;
123 0 : std::stringstream microscopicMomenta;
124 0 : microscopicMomenta << "VECTORS microscopicMomentumBuffer float" << std::endl;
125 0 : std::stringstream macroscopicMomenta;
126 0 : macroscopicMomenta << "VECTORS macroscopicMomentumBuffer float" << std::endl;
127 0 : std::stringstream meanVelocities;
128 0 : meanVelocities << "VECTORS meanVelocity float" << std::endl;
129 0 : std::stringstream masses;
130 0 : masses << "SCALARS mass float 1" << std::endl;
131 0 : masses << "LOOKUP_TABLE DEFAULT" << std::endl;
132 0 : std::stringstream energies;
133 0 : energies << "SCALARS meanPotentialEnergyBuffer float 1" << std::endl;
134 0 : energies << "LOOKUP_TABLE DEFAULT" << std::endl;
135 0 : std::stringstream temperatures;
136 0 : temperatures << "SCALARS temperature float 1" << std::endl;
137 0 : temperatures << "LOOKUP_TABLE DEFAULT" << std::endl;
138 : // ofstream for file
139 0 : std::ofstream ofCell;
140 : // zeros appended in vtk file
141 0 : std::string appendFloatZeros("");
142 : switch (dim) {
143 : case 1:
144 : appendFloatZeros = " 0.0 0.0";
145 : break;
146 : case 2:
147 : appendFloatZeros = " 0.0";
148 : break;
149 : case 3:
150 0 : appendFloatZeros = "";
151 : break;
152 : default:
153 : break;
154 : }
155 :
156 0 : tarch::la::Vector<3, double> original = I11{{0, 0, 0}}.getCellMidPoint() - 0.5 * IDXS.getCouplingCellSize();
157 :
158 : // open file
159 0 : open(ID, filename, "CouplingCells", rank, t, ofCell);
160 0 : Writer4Cells writer(microscopicMasses, macroscopicMasses, microscopicMomenta, macroscopicMomenta, meanVelocities, masses, energies, temperatures,
161 : appendFloatZeros, mdSolverInterface);
162 0 : cells.applyToAllLocalCouplingCellsWithLinkedCells(writer);
163 0 : ofCell << "# vtk DataFile Version 2.0" << std::endl;
164 0 : ofCell << "generated by MaMiCo (Philipp Neumann)" << std::endl;
165 0 : ofCell << "ASCII" << std::endl << std::endl;
166 0 : ofCell << "DATASET STRUCTURED_POINTS" << std::endl;
167 0 : ofCell << "DIMENSIONS " << I03::numberCellsInDomain << std::endl;
168 0 : ofCell << "ORIGIN ";
169 0 : for (unsigned int d = 0; d < 3; d++) {
170 0 : ofCell << original[d] << " ";
171 : }
172 0 : ofCell << std::endl;
173 0 : ofCell << "SPACING ";
174 0 : for (unsigned int d = 0; d < dim; d++) {
175 0 : ofCell << IDXS.getCouplingCellSize()[d] << " ";
176 : }
177 0 : for (unsigned int d = dim; d < 3; d++) {
178 : ofCell << "1.0 ";
179 : }
180 0 : ofCell << std::endl;
181 0 : ofCell << "POINT_DATA " << I02::linearNumberCellsInDomain << std::endl << std::endl;
182 0 : ofCell << microscopicMasses.str() << std::endl << std::endl;
183 0 : microscopicMasses.clear();
184 0 : microscopicMasses.str("");
185 0 : ofCell << macroscopicMasses.str() << std::endl << std::endl;
186 0 : macroscopicMasses.clear();
187 0 : macroscopicMasses.str("");
188 0 : ofCell << masses.str() << std::endl << std::endl;
189 0 : masses.clear();
190 0 : masses.str("");
191 0 : ofCell << energies.str() << std::endl << std::endl;
192 0 : energies.clear();
193 0 : energies.str("");
194 0 : ofCell << temperatures.str() << std::endl << std::endl;
195 0 : temperatures.clear();
196 0 : temperatures.str("");
197 0 : ofCell << microscopicMomenta.str() << std::endl << std::endl;
198 0 : microscopicMomenta.clear();
199 0 : microscopicMomenta.str("");
200 0 : ofCell << macroscopicMomenta.str() << std::endl << std::endl;
201 0 : macroscopicMomenta.clear();
202 0 : macroscopicMomenta.str("");
203 0 : ofCell << meanVelocities.str() << std::endl << std::endl;
204 0 : meanVelocities.clear();
205 0 : meanVelocities.str("");
206 : // close file
207 0 : ofCell.close();
208 0 : }
209 :
210 : /** @brief opens a file
211 : * @param ID the id of the md simulation
212 : * @param filename name for the file
213 : * @param fileType type of the file (e.g. vtk)
214 : * @param rank mpi rank of the current process
215 : * @param t number of time step to plot
216 : * @param of this is the stream, where it will be written to */
217 0 : void open(unsigned int ID, std::string filename, std::string fileType, unsigned int rank, unsigned int t, std::ofstream& of) {
218 0 : std::stringstream ss;
219 0 : ss << filename << "_" << fileType << "_" << ID << "_" << rank << "_" << t << ".vtk";
220 0 : of.open(ss.str().c_str());
221 0 : if (!of.is_open()) {
222 0 : std::cout << "ERROR coupling::CouplingCellPlotter: Could not open file " << ss.str() << "!" << std::endl;
223 0 : exit(EXIT_FAILURE);
224 : }
225 0 : }
226 :
227 : /** @brief class for writing coupling cell data to stringstreams.
228 : * @author Philipp Neumann*/
229 : class Writer4Cells {
230 : public:
231 : /** @brief a simple constructor
232 : * @param microscopicMasses stream for the microscopic masses
233 : * @param macroscopicMasses stream for the macroscopic masses
234 : * @param microscopicMomenta stream for the microscopic momenta
235 : * @param macroscopicMomenta stream for the macroscopic momenta
236 : * @param meanVelocities stream for the mean velocities
237 : * @param masses stream for the masses
238 : * @param energies stream for the energies
239 : * @param temperatures stream for the temperatures
240 : * @param appendFloatZeros string containing '0' to add in the case of 1d
241 : * or 2d
242 : * @param mdSolverInterface interface of the md solver */
243 0 : Writer4Cells(std::stringstream& microscopicMasses, std::stringstream& macroscopicMasses, std::stringstream& microscopicMomenta,
244 : std::stringstream& macroscopicMomenta, std::stringstream& meanVelocities, std::stringstream& masses, std::stringstream& energies,
245 : std::stringstream& temperatures, const std::string& appendFloatZeros,
246 : coupling::interface::MDSolverInterface<LinkedCell, dim>* const mdSolverInterface)
247 0 : : _microscopicMasses(microscopicMasses), _macroscopicMasses(macroscopicMasses), _microscopicMomenta(microscopicMomenta),
248 0 : _macroscopicMomenta(macroscopicMomenta), _meanVelocities(meanVelocities), _masses(masses), _energies(energies), _temperatures(temperatures),
249 0 : _appendFloatZeros(appendFloatZeros), _computeMassMapping(mdSolverInterface), _computeMomentumMapping(mdSolverInterface),
250 0 : _kineticEnergyController(mdSolverInterface) {}
251 :
252 : /** @brief a simple destructor*/
253 0 : ~Writer4Cells() {}
254 :
255 : /** @brief does everything which is neccessary before the application of the
256 : * writer to the cells */
257 : void beginCellIteration() {}
258 :
259 : /** @brief does everything which is neccessary after the application of the
260 : * writer to the cells */
261 : void endCellIteration() {}
262 :
263 : /** @brief writes the data from the cell to the stringstreams
264 : * @param cell coupling cell
265 : * @param index linearised index of the coupling cell*/
266 0 : void apply(coupling::datastructures::CouplingCellWithLinkedCells<LinkedCell, dim>& cell, const I02& index) {
267 : // compute local quantities from molecules, if this is an inner cell
268 0 : double mass = 0.0;
269 0 : tarch::la::Vector<dim, double> meanVelocity(0.0);
270 0 : double temperature = 0.0;
271 :
272 0 : if (I10::contains(index)) {
273 0 : cell.iterateConstCells(_computeMassMapping);
274 0 : mass = _computeMassMapping.getMass();
275 0 : cell.iterateConstCells(_computeMomentumMapping);
276 0 : meanVelocity = _computeMomentumMapping.getMeanVelocity();
277 0 : temperature = _kineticEnergyController.computeTemperature(cell);
278 : }
279 :
280 : // write data to streams
281 0 : _microscopicMasses << cell.getMicroscopicMass() << std::endl;
282 0 : _macroscopicMasses << cell.getMacroscopicMass() << std::endl;
283 0 : _masses << mass << std::endl;
284 0 : _temperatures << temperature << std::endl;
285 0 : _energies << cell.getPotentialEnergy() << std::endl;
286 0 : for (unsigned int d = 0; d < dim; d++) {
287 0 : _microscopicMomenta << cell.getMicroscopicMomentum()[d] << " ";
288 0 : _macroscopicMomenta << cell.getMacroscopicMomentum()[d] << " ";
289 0 : _meanVelocities << meanVelocity[d] << " ";
290 : }
291 0 : _microscopicMomenta << _appendFloatZeros << std::endl;
292 0 : _macroscopicMomenta << _appendFloatZeros << std::endl;
293 0 : _meanVelocities << _appendFloatZeros << std::endl;
294 0 : }
295 :
296 : private:
297 : /** stream containing the microscopic mass of the cells (buffer to transfer
298 : * mass from macro to md)*/
299 : std::stringstream& _microscopicMasses;
300 : /** stream containing the macroscopic mass of the cells (buffer to transfer
301 : * mass from md to macro)*/
302 : std::stringstream& _macroscopicMasses;
303 : /** stream containing the microscopic momenta of the cells (buffer to
304 : * transfer momenta from macro to md)*/
305 : std::stringstream& _microscopicMomenta;
306 : /** stream containing the macroscopic momenta of the cells (buffer to
307 : * transfer momenta from md to macro )*/
308 : std::stringstream& _macroscopicMomenta;
309 : /** stream containing the mean velocity of the cells*/
310 : std::stringstream& _meanVelocities;
311 : /** stream containing the total mass in the cells*/
312 : std::stringstream& _masses;
313 : /** stream containing the total energy in the cells*/
314 : std::stringstream& _energies;
315 : /** stream containing the mean temperature in the cells*/
316 : std::stringstream& _temperatures;
317 : /** string containing '0' to add in the case of 1d or 2d */
318 : const std::string _appendFloatZeros;
319 : /** instance of the computeMassMapping*/
320 : coupling::cellmappings::ComputeMassMapping<LinkedCell, dim> _computeMassMapping;
321 : /** instance of the computeMomentumMapping*/
322 : coupling::cellmappings::ComputeMomentumMapping<LinkedCell, dim> _computeMomentumMapping;
323 : /** instance of the KineticEnergyController*/
324 : coupling::KineticEnergyController<LinkedCell, dim> _kineticEnergyController;
325 : };
326 :
327 : /** We make use of the traversal callback pattern of CouplingCells.
328 : * @brief class for writing molecule data to stringstreams.
329 : * @author Philipp Neumann */
330 0 : class Writer4Molecules {
331 : public:
332 : /** @brief a simple constructor
333 : * @param moleculeVelocities stream for the molecule velocities
334 : * @param moleculePositions stream for the molecule positions
335 : * @param moleculePotentials stream for the molecule potentials
336 : * @param appendFloatZeros string containing '0' to add in the case of 1d
337 : * or 2d
338 : * @param mdSolverInterface interface of the md solver */
339 0 : Writer4Molecules(std::stringstream& moleculeVelocities, std::stringstream& moleculePositions, std::stringstream& moleculePotentials,
340 : const std::string& appendFloatZeros, coupling::interface::MDSolverInterface<LinkedCell, dim>* const mdSolverInterface)
341 0 : : _moleculeVelocities(moleculeVelocities), _moleculePositions(moleculePositions), _moleculePotentials(moleculePotentials),
342 0 : _appendFloatZeros(appendFloatZeros), _mdSolverInterface(mdSolverInterface), _moleculeCounter(0) {}
343 :
344 : /** @brief does everything which is neccessary before the application of the
345 : * writer to the cells */
346 : void beginCellIteration() {}
347 :
348 : /** @brief does everything which is neccessary after the application of the
349 : * writer to the cells */
350 : void endCellIteration() {}
351 :
352 : /** @brief aplication of the vtkMoleculePlotter to the coupling cells*/
353 0 : void apply(coupling::datastructures::CouplingCellWithLinkedCells<LinkedCell, dim>& cell, const I02& index) {
354 0 : coupling::cellmappings::VTKMoleculePlotter<LinkedCell, dim> vtkMoleculePlotter(_moleculeVelocities, _moleculePositions, _moleculePotentials,
355 0 : _appendFloatZeros, _mdSolverInterface);
356 0 : cell.iterateConstCells(vtkMoleculePlotter);
357 0 : _moleculeCounter += vtkMoleculePlotter.getParticleCounter();
358 0 : }
359 :
360 : /** @brief returns the number of molecules
361 : * @returns the number of molecules plotted */
362 0 : unsigned int getMoleculeCounter() const { return _moleculeCounter; }
363 :
364 : private:
365 : /** stringstream for the velocities of the molecules*/
366 : std::stringstream& _moleculeVelocities;
367 : /** stringstream for the positions of the molecules*/
368 : std::stringstream& _moleculePositions;
369 : /** stringstream for the potentials of the molecules*/
370 : std::stringstream& _moleculePotentials;
371 : /** string containing '0' to add in the case of 1d or 2d */
372 : const std::string _appendFloatZeros;
373 : /** interface to the md solver*/
374 : coupling::interface::MDSolverInterface<LinkedCell, dim>* const _mdSolverInterface;
375 : /** counter for the molecules that have been plotted*/
376 : unsigned int _moleculeCounter;
377 : };
378 : };
379 : #endif // _MOLECULARDYNAMICS_COUPLING_COUPLINGCELLPLOTTER_H_
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