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36 /*! \internal \file
37 * \brief
38 * Implements gmx::analysismodules::Freevolume.
39 *
40 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
41 * \ingroup module_trajectoryanalysis
42 */
43 #include "gmxpre.h"
44
45 #include "freevolume.h"
46
47 #include <string>
48
49 #include "gromacs/analysisdata/analysisdata.h"
50 #include "gromacs/analysisdata/modules/average.h"
51 #include "gromacs/analysisdata/modules/plot.h"
52 #include "gromacs/math/functions.h"
53 #include "gromacs/math/units.h"
54 #include "gromacs/math/vec.h"
55 #include "gromacs/options/basicoptions.h"
56 #include "gromacs/options/filenameoption.h"
57 #include "gromacs/options/ioptionscontainer.h"
58 #include "gromacs/pbcutil/pbc.h"
59 #include "gromacs/random/threefry.h"
60 #include "gromacs/random/uniformrealdistribution.h"
61 #include "gromacs/selection/nbsearch.h"
62 #include "gromacs/selection/selection.h"
63 #include "gromacs/selection/selectionoption.h"
64 #include "gromacs/topology/atomprop.h"
65 #include "gromacs/topology/mtop_util.h"
66 #include "gromacs/topology/topology.h"
67 #include "gromacs/trajectory/trajectoryframe.h"
68 #include "gromacs/trajectoryanalysis/analysissettings.h"
69 #include "gromacs/trajectoryanalysis/topologyinformation.h"
70 #include "gromacs/utility/arrayref.h"
71 #include "gromacs/utility/exceptions.h"
72 #include "gromacs/utility/pleasecite.h"
73
74 namespace gmx
75 {
76
77 namespace analysismodules
78 {
79
80 namespace
81 {
82
83 /*! \brief
84 * Class used to compute free volume in a simulations box.
85 *
86 * Inherits TrajectoryAnalysisModule and all functions from there.
87 * Does not implement any new functionality.
88 *
89 * \ingroup module_trajectoryanalysis
90 */
91 class FreeVolume : public TrajectoryAnalysisModule
92 {
93 public:
94 FreeVolume();
~FreeVolume()95 ~FreeVolume() override {}
96
97 void initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings) override;
98 void initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& top) override;
99 void analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata) override;
100 void finishAnalysis(int nframes) override;
101 void writeOutput() override;
102
103 private:
104 std::string fnFreevol_;
105 Selection sel_;
106 AnalysisData data_;
107 AnalysisDataAverageModulePointer adata_;
108
109 int nmol_;
110 double mtot_;
111 double cutoff_;
112 double probeRadius_;
113 gmx::DefaultRandomEngine rng_;
114 int seed_, ninsert_;
115 AnalysisNeighborhood nb_;
116 //! The van der Waals radius per atom
117 std::vector<double> vdw_radius_;
118
119 // Copy and assign disallowed by base.
120 };
121
122 // Constructor. Here it is important to initialize the pointer to
123 // subclasses that are elements of the main class. Here we have only
124 // one. The type of this depends on what kind of tool you need.
125 // Here we only have simple value/time kind of data.
FreeVolume()126 FreeVolume::FreeVolume() : adata_(new AnalysisDataAverageModule())
127 {
128 // We only compute two numbers per frame
129 data_.setColumnCount(0, 2);
130 // Tell the analysis framework that this component exists
131 registerAnalysisDataset(&data_, "freevolume");
132 nmol_ = 0;
133 mtot_ = 0;
134 cutoff_ = 0;
135 probeRadius_ = 0;
136 seed_ = 0;
137 ninsert_ = 1000;
138 }
139
140
initOptions(IOptionsContainer * options,TrajectoryAnalysisSettings * settings)141 void FreeVolume::initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings)
142 {
143 static const char* const desc[] = {
144 "[THISMODULE] calculates the free volume in a box as",
145 "a function of time. The free volume is",
146 "plotted as a fraction of the total volume.",
147 "The program tries to insert a probe with a given radius,",
148 "into the simulations box and if the distance between the",
149 "probe and any atom is less than the sums of the",
150 "van der Waals radii of both atoms, the position is",
151 "considered to be occupied, i.e. non-free. By using a",
152 "probe radius of 0, the true free volume is computed.",
153 "By using a larger radius, e.g. 0.14 nm, roughly corresponding",
154 "to a water molecule, the free volume for a hypothetical",
155 "particle with that size will be produced.",
156 "Note however, that since atoms are treated as hard-spheres",
157 "these number are very approximate, and typically only",
158 "relative changes are meaningful, for instance by doing a",
159 "series of simulations at different temperature.[PAR]",
160 "The group specified by the selection is considered to",
161 "delineate non-free volume.",
162 "The number of insertions per unit of volume is important",
163 "to get a converged result. About 1000/nm^3 yields an overall",
164 "standard deviation that is determined by the fluctuations in",
165 "the trajectory rather than by the fluctuations due to the",
166 "random numbers.[PAR]",
167 "The results are critically dependent on the van der Waals radii;",
168 "we recommend to use the values due to Bondi (1964).[PAR]",
169 "The Fractional Free Volume (FFV) that some authors like to use",
170 "is given by 1 - 1.3*(1-Free Volume). This value is printed on",
171 "the terminal."
172 };
173
174 settings->setHelpText(desc);
175
176 // Add option for optional output file
177 options->addOption(FileNameOption("o")
178 .filetype(eftPlot)
179 .outputFile()
180 .store(&fnFreevol_)
181 .defaultBasename("freevolume")
182 .description("Computed free volume"));
183
184 // Add option for selecting a subset of atoms
185 options->addOption(
186 SelectionOption("select").store(&sel_).defaultSelectionText("all").onlyAtoms().description(
187 "Atoms that are considered as part of the excluded volume"));
188
189 // Add option for the probe radius and initialize it
190 options->addOption(
191 DoubleOption("radius").store(&probeRadius_).description("Radius of the probe to be inserted (nm, 0 yields the true free volume)"));
192
193 // Add option for the random number seed and initialize it to
194 // generate a value automatically
195 options->addOption(IntegerOption("seed").store(&seed_).description(
196 "Seed for random number generator (0 means generate)."));
197
198 // Add option to determine number of insertion trials per frame
199 options->addOption(IntegerOption("ninsert").store(&ninsert_).description(
200 "Number of probe insertions per cubic nm to try for each frame in the trajectory."));
201
202 // Control input settings
203 settings->setFlags(TrajectoryAnalysisSettings::efRequireTop | TrajectoryAnalysisSettings::efNoUserPBC);
204 settings->setPBC(true);
205 }
206
207
initAnalysis(const TrajectoryAnalysisSettings & settings,const TopologyInformation & top)208 void FreeVolume::initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& top)
209 {
210 // Add the module that will contain the averaging and the time series
211 // for our calculation
212 data_.addModule(adata_);
213
214 // Add a module for plotting the data automatically at the end of
215 // the calculation. With this in place you only have to add data
216 // points to the data et.
217 AnalysisDataPlotModulePointer plotm_(new AnalysisDataPlotModule());
218 plotm_->setSettings(settings.plotSettings());
219 plotm_->setFileName(fnFreevol_);
220 plotm_->setTitle("Free Volume");
221 plotm_->setXAxisIsTime();
222 plotm_->setYLabel("Free Volume (%)");
223 plotm_->appendLegend("Free Volume");
224 plotm_->appendLegend("Volume");
225
226 data_.addModule(plotm_);
227
228 // Initiate variable
229 cutoff_ = 0;
230 int nnovdw = 0;
231 AtomProperties aps;
232 auto atoms = top.copyAtoms();
233
234 // Compute total mass
235 mtot_ = 0;
236 for (int i = 0; (i < atoms->nr); i++)
237 {
238 mtot_ += atoms->atom[i].m;
239 }
240
241 // Extracts number of molecules
242 nmol_ = gmx_mtop_num_molecules(*top.mtop());
243
244 // Loop over atoms in the selection using an iterator
245 const int maxnovdw = 10;
246 ArrayRef<const int> atomind = sel_.atomIndices();
247 for (ArrayRef<const int>::iterator ai = atomind.begin(); (ai < atomind.end()); ++ai)
248 {
249 // Dereference the iterator to obtain an atom number
250 int i = *ai;
251 real value;
252
253 // Lookup the Van der Waals radius of this atom
254 int resnr = atoms->atom[i].resind;
255 if (aps.setAtomProperty(epropVDW, *(atoms->resinfo[resnr].name), *(atoms->atomname[i]), &value))
256 {
257 vdw_radius_.push_back(value);
258 if (value > cutoff_)
259 {
260 cutoff_ = value;
261 }
262 }
263 else
264 {
265 nnovdw++;
266 if (nnovdw < maxnovdw)
267 {
268 fprintf(stderr, "Could not determine VDW radius for %s-%s. Set to zero.\n",
269 *(atoms->resinfo[resnr].name), *(atoms->atomname[i]));
270 }
271 vdw_radius_.push_back(0.0);
272 }
273 }
274
275 // Increase cutoff by proberadius to make sure we do not miss
276 // anything
277 cutoff_ += probeRadius_;
278
279 if (nnovdw >= maxnovdw)
280 {
281 fprintf(stderr, "Could not determine VDW radius for %d particles. These were set to zero.\n", nnovdw);
282 }
283
284 if (seed_ == 0)
285 {
286 seed_ = static_cast<int>(gmx::makeRandomSeed());
287 }
288
289 // Print parameters to output. Maybe should make dependent on
290 // verbosity flag?
291 printf("cutoff = %g nm\n", cutoff_);
292 printf("probe_radius = %g nm\n", probeRadius_);
293 printf("seed = %d\n", seed_);
294 printf("ninsert = %d probes per nm^3\n", ninsert_);
295
296 // Initiate the random number generator
297 rng_.seed(seed_);
298
299 // Initiate the neighborsearching code
300 nb_.setCutoff(cutoff_);
301 }
302
analyzeFrame(int frnr,const t_trxframe & fr,t_pbc * pbc,TrajectoryAnalysisModuleData * pdata)303 void FreeVolume::analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata)
304 {
305 AnalysisDataHandle dh = pdata->dataHandle(data_);
306 const Selection& sel = TrajectoryAnalysisModuleData::parallelSelection(sel_);
307 gmx::UniformRealDistribution<real> dist;
308
309 GMX_RELEASE_ASSERT(nullptr != pbc, "You have no periodic boundary conditions");
310
311 // Analysis framework magic
312 dh.startFrame(frnr, fr.time);
313
314 // Compute volume and number of insertions to perform
315 real V = det(fr.box);
316 int Ninsert = static_cast<int>(ninsert_ * V);
317
318 // Use neighborsearching tools!
319 AnalysisNeighborhoodSearch nbsearch = nb_.initSearch(pbc, sel);
320
321 // Then loop over insertions
322 int NinsTot = 0;
323 for (int i = 0; (i < Ninsert); i++)
324 {
325 rvec rand, ins, dx;
326
327 for (int m = 0; (m < DIM); m++)
328 {
329 // Generate random number between 0 and 1
330 rand[m] = dist(rng_);
331 }
332 // Generate random 3D position within the box
333 mvmul(fr.box, rand, ins);
334
335 // Find the first reference position within the cutoff.
336 bool bOverlap = false;
337 AnalysisNeighborhoodPair pair;
338 AnalysisNeighborhoodPairSearch pairSearch = nbsearch.startPairSearch(ins);
339 while (!bOverlap && pairSearch.findNextPair(&pair))
340 {
341 int jp = pair.refIndex();
342 // Compute distance vector to first atom in the neighborlist
343 pbc_dx(pbc, ins, sel.position(jp).x(), dx);
344
345 // See whether the distance is smaller than allowed
346 bOverlap = (norm(dx) < probeRadius_ + vdw_radius_[sel.position(jp).refId()]);
347 }
348
349 if (!bOverlap)
350 {
351 // We found some free volume!
352 NinsTot++;
353 }
354 }
355 // Compute total free volume for this frame
356 double frac = 0;
357 if (Ninsert > 0)
358 {
359 frac = (100.0 * NinsTot) / Ninsert;
360 }
361 // Add the free volume fraction to the data set in column 0
362 dh.setPoint(0, frac);
363 // Add the total volume to the data set in column 1
364 dh.setPoint(1, V);
365
366 // Magic
367 dh.finishFrame();
368 }
369
370
finishAnalysis(int)371 void FreeVolume::finishAnalysis(int /* nframes */)
372 {
373 please_cite(stdout, "Bondi1964a");
374 please_cite(stdout, "Lourenco2013a");
375 }
376
writeOutput()377 void FreeVolume::writeOutput()
378 {
379 // Final results come from statistics module in analysis framework
380 double FVaver = adata_->average(0, 0);
381 double FVerror = adata_->standardDeviation(0, 0);
382 printf("Free volume %.2f +/- %.2f %%\n", FVaver, FVerror);
383
384 double Vaver = adata_->average(0, 1);
385 double Verror = adata_->standardDeviation(0, 1);
386 printf("Total volume %.2f +/- %.2f nm^3\n", Vaver, Verror);
387
388 printf("Number of molecules %d total mass %.2f Dalton\n", nmol_, mtot_);
389 double RhoAver = mtot_ / (Vaver * 1e-24 * AVOGADRO);
390 double RhoError = gmx::square(RhoAver / Vaver) * Verror;
391 printf("Average molar mass: %.2f Dalton\n", mtot_ / nmol_);
392
393 double VmAver = Vaver / nmol_;
394 double VmError = Verror / nmol_;
395 printf("Density rho: %.2f +/- %.2f nm^3\n", RhoAver, RhoError);
396 printf("Molecular volume Vm assuming homogeneity: %.4f +/- %.4f nm^3\n", VmAver, VmError);
397
398 double VvdWaver = (1 - FVaver / 100) * VmAver;
399 double VvdWerror = 0;
400 printf("Molecular van der Waals volume assuming homogeneity: %.4f +/- %.4f nm^3\n", VvdWaver, VvdWerror);
401
402 double FFVaver = 1 - 1.3 * ((100 - FVaver) / 100);
403 double FFVerror = (FVerror / FVaver) * FFVaver;
404 printf("Fractional free volume %.3f +/- %.3f\n", FFVaver, FFVerror);
405 }
406
407 } // namespace
408
409 const char FreeVolumeInfo::name[] = "freevolume";
410 const char FreeVolumeInfo::shortDescription[] = "Calculate free volume";
411
create()412 TrajectoryAnalysisModulePointer FreeVolumeInfo::create()
413 {
414 return TrajectoryAnalysisModulePointer(new FreeVolume);
415 }
416
417 } // namespace analysismodules
418
419 } // namespace gmx
420