Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2015-2019 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 : #include "GridVessel.h"
23 : #include "vesselbase/ActionWithVessel.h"
24 : #include "tools/Random.h"
25 : #include "tools/Tools.h"
26 :
27 : namespace PLMD {
28 : namespace gridtools {
29 :
30 57 : void GridVessel::registerKeywords( Keywords& keys ) {
31 57 : AveragingVessel::registerKeywords( keys );
32 285 : keys.add("compulsory","TYPE","flat","how the grid points are being generated");
33 228 : keys.add("compulsory","COMPONENTS","the names of the components in the vector");
34 228 : keys.add("compulsory","COORDINATES","the names of the coordinates of the grid");
35 228 : keys.add("compulsory","PBC","is the grid periodic in each direction or not");
36 57 : }
37 :
38 58 : GridVessel::GridVessel( const vesselbase::VesselOptions& da ):
39 : AveragingVessel(da),
40 : bounds_set(false),
41 : npoints(0),
42 : cube_units(1.0),
43 : wasforced(false),
44 232 : noderiv(false)
45 : {
46 116 : std::string geom; parse("TYPE",geom);
47 58 : if( geom=="flat" ) gtype=flat;
48 3 : else if( geom=="fibonacci" ) gtype=fibonacci;
49 0 : else plumed_merror( geom + " is invalid geometry type");
50 174 : std::vector<std::string> compnames; parseVector("COMPONENTS",compnames);
51 174 : std::vector<std::string> coordnames; parseVector("COORDINATES",coordnames);
52 58 : if( gtype==flat ) {
53 55 : dimension=coordnames.size();
54 55 : str_min.resize( dimension); str_max.resize( dimension ); stride.resize( dimension );
55 55 : max.resize( dimension ); dx.resize( dimension ); nbin.resize( dimension ); min.resize( dimension );
56 3 : } else if( gtype==fibonacci ) {
57 3 : if( coordnames.size()!=3 ) error("cannot generate fibonacci grid points on surface of sphere if not 3 input coordinates");
58 3 : dimension=3;
59 : }
60 :
61 116 : unsigned n=0; nper=compnames.size()*( 1 + coordnames.size() );
62 58 : arg_names.resize( coordnames.size() + compnames.size()*( 1 + coordnames.size() ) );
63 322 : for(unsigned i=0; i<coordnames.size(); ++i) { arg_names[n] = coordnames[i]; n++; }
64 174 : for(unsigned i=0; i<compnames.size(); ++i) {
65 116 : arg_names[n]=compnames[i]; n++;
66 644 : for(unsigned j=0; j<coordnames.size(); ++j) { arg_names[n] = "d" + compnames[i] + "_" + coordnames[j]; n++; }
67 : }
68 58 : pbc.resize( dimension );
69 174 : std::vector<std::string> spbc( dimension ); parseVector("PBC",spbc);
70 146 : for(unsigned i=0; i<dimension; ++i) {
71 176 : if( spbc[i]=="F" ) pbc[i]=false;
72 22 : else if( spbc[i]=="T" ) pbc[i]=true;
73 0 : else plumed_error();
74 : }
75 58 : }
76 :
77 19 : void GridVessel::setNoDerivatives() {
78 19 : nper = ( nper/(1+dimension) ); noderiv=true;
79 38 : std::vector<std::string> tnames( dimension ), cnames(nper);
80 41 : for(unsigned i=0; i<dimension; ++i) tnames[i]=arg_names[i];
81 57 : unsigned k=dimension; for(unsigned i=0; i<nper; ++i) { cnames[i]=arg_names[k]; k+=(1+dimension); }
82 19 : arg_names.resize( dimension + nper );
83 44 : for(unsigned i=0; i<dimension; ++i) arg_names[i]=tnames[i];
84 76 : for(unsigned i=0; i<nper; ++i) arg_names[dimension+i]=cnames[i];
85 19 : }
86 :
87 85 : void GridVessel::setBounds( const std::vector<std::string>& smin, const std::vector<std::string>& smax,
88 : const std::vector<unsigned>& binsin, const std::vector<double>& spacing ) {
89 : plumed_dbg_assert( smin.size()==dimension && smax.size()==dimension );
90 234 : plumed_assert( gtype==flat && (spacing.size()==dimension || binsin.size()==dimension) );
91 :
92 85 : npoints=1; bounds_set=true;
93 212 : for(unsigned i=0; i<dimension; ++i) {
94 127 : str_min[i]=smin[i]; str_max[i]=smax[i];
95 127 : Tools::convert( str_min[i], min[i] );
96 127 : Tools::convert( str_max[i], max[i] );
97 160 : if( spacing.size()==dimension && binsin.size()==dimension ) {
98 99 : double range = max[i] - min[i]; unsigned spc = std::floor( range / spacing[i]);
99 : // This check ensures that nbins is set correctly if spacing is set the same as the number of bins
100 33 : if( fabs( binsin[i]*spacing[i]-range )>epsilon ) spc += 1;
101 66 : if( spc>binsin[i] ) nbin[i]=spc; else nbin[i]=binsin[i];
102 188 : } else if( binsin.size()==dimension ) nbin[i]=binsin[i];
103 0 : else if( spacing.size()==dimension ) nbin[i] = std::floor(( max[i] - min[i] ) / spacing[i]) + 1;
104 0 : else plumed_error();
105 381 : dx[i] = ( max[i] - min[i] ) / static_cast<double>( nbin[i] );
106 397 : if( !pbc[i] ) { max[i] +=dx[i]; nbin[i]+=1; }
107 127 : stride[i]=npoints;
108 127 : npoints*=nbin[i];
109 : }
110 85 : resize(); // Always resize after setting new bounds as grid size may have have changed
111 85 : }
112 :
113 3 : void GridVessel::setupFibonacciGrid( const unsigned& np ) {
114 3 : bounds_set=true; root5 = sqrt(5);
115 3 : npoints = np; golden = ( 1 + sqrt(5) ) / 2.0; igolden = golden - 1;
116 3 : fib_increment = 2*pi*igolden; log_golden2 = std::log( golden*golden );
117 3 : fib_offset = 2 / static_cast<double>( npoints );
118 3 : fib_shift = fib_offset/2 - 1;
119 3 : resize();
120 :
121 3 : std::vector<double> icoord( dimension ), jcoord( dimension );
122 : // Find minimum distance between each pair of points
123 3 : std::vector<double> mindists( npoints );
124 347 : for(unsigned i=0; i<npoints; ++i) {
125 688 : getFibonacciCoordinates( i, icoord ); mindists[i] = 0;
126 41080 : for(unsigned j=0; j<npoints; ++j) {
127 40736 : if( i==j ) continue ; // Points are not neighbors to themselves
128 40392 : getFibonacciCoordinates( j, jcoord );
129 : // Calculate the dot product
130 363528 : double dot=0; for(unsigned k=0; k<dimension; ++k) dot += icoord[k]*jcoord[k];
131 80784 : if( dot>mindists[i] ) mindists[i]=dot;
132 : }
133 : }
134 : // And now take minimum of dot products
135 3 : double min=mindists[0];
136 344 : for(unsigned i=1; i<npoints; ++i) {
137 682 : if( mindists[i]<min ) min=mindists[i];
138 : }
139 : double final_cutoff;
140 3 : if( getFibonacciCutoff()<-1 ) final_cutoff=-1;
141 2 : else final_cutoff = cos( acos( getFibonacciCutoff() ) + acos( min ) );
142 :
143 : // And now construct the neighbor list
144 3 : fib_nlist.resize( npoints );
145 347 : for(unsigned i=0; i<npoints; ++i) {
146 344 : getFibonacciCoordinates( i, icoord );
147 41080 : for(unsigned j=0; j<npoints; ++j) {
148 40736 : if( i==j ) continue ; // Points are not neighbors to themselves
149 40392 : getFibonacciCoordinates( j, jcoord );
150 : // Calculate the dot product
151 363528 : double dot=0; for(unsigned k=0; k<dimension; ++k) dot += icoord[k]*jcoord[k];
152 63278 : if( dot>final_cutoff ) { fib_nlist[i].push_back(j); }
153 : }
154 : }
155 3 : }
156 :
157 56 : std::string GridVessel::description() {
158 56 : if( !bounds_set ) return "";
159 :
160 : std::string des;
161 43 : if( gtype==flat ) {
162 : des="grid of "; std::string num;
163 56 : for(unsigned i=0; i<dimension-1; ++i) {
164 30 : Tools::convert( nbin[i], num );
165 30 : des += num + " X ";
166 : }
167 82 : Tools::convert( nbin[dimension-1], num );
168 82 : des += num + " equally spaced points between (";
169 71 : for(unsigned i=0; i<dimension-1; ++i) des += str_min[i] + ",";
170 82 : Tools::convert( nbin[dimension-1], num );
171 123 : des += str_min[dimension-1] + ") and (";
172 71 : for(unsigned i=0; i<dimension-1; ++i) des += str_max[i] + ",";
173 123 : des += str_max[dimension-1] + ")";
174 2 : } else if( gtype==fibonacci ) {
175 2 : std::string num; Tools::convert( npoints, num );
176 6 : des += "fibonacci grid of " + num + " points on spherical surface";
177 : }
178 : return des;
179 : }
180 :
181 190 : void GridVessel::resize() {
182 190 : plumed_massert( nper>0, "Number of datapoints at each grid point has not been set");
183 377 : if( getAction() ) resizeBuffer( getNumberOfBufferPoints()*nper + 1 + 2*getAction()->getNumberOfDerivatives() );
184 190 : setDataSize( npoints*nper ); forces.resize( npoints );
185 190 : if( active.size()!=npoints) active.resize( npoints, true );
186 190 : }
187 :
188 24327913 : unsigned GridVessel::getIndex( const std::vector<unsigned>& indices ) const {
189 : plumed_dbg_assert( gtype==flat && bounds_set && indices.size()==dimension );
190 : // indices are flattended using a column-major order
191 48655826 : unsigned index=indices[dimension-1];
192 94202109 : for(unsigned i=dimension-1; i>0; --i) {
193 136638849 : index=index*nbin[i-1]+indices[i-1];
194 : }
195 24327913 : return index;
196 : }
197 :
198 1060340 : void GridVessel::getIndices( const std::vector<double>& point, std::vector<unsigned>& indices ) const {
199 : plumed_dbg_assert( gtype==flat && bounds_set && point.size()==dimension && indices.size()==dimension );
200 3196033 : for(unsigned i=0; i<dimension; ++i) {
201 8542616 : indices[i]=std::floor( (point[i] - min[i])/dx[i] );
202 2226634 : if( pbc[i] ) indices[i]=indices[i]%nbin[i];
203 4180328 : else if( indices[i]>nbin[i] ) {
204 0 : std::string pp, num; Tools::convert( point[0], pp );
205 0 : for(unsigned j=1; j<point.size(); ++j) { Tools::convert( point[j], num ); pp += ", " + num; }
206 0 : plumed_merror("point (" + pp + ") is outside grid range");
207 : }
208 : }
209 1060379 : }
210 :
211 530952 : unsigned GridVessel::getIndex( const std::vector<double>& point ) const {
212 : plumed_dbg_assert( gtype==flat && bounds_set && point.size()==dimension );
213 530952 : if( gtype==flat ) {
214 530952 : std::vector<unsigned> indices(dimension); getIndices( point, indices );
215 530954 : return getIndex( indices );
216 0 : } else if( gtype==fibonacci ) {
217 0 : return getFibonacciIndex( point );
218 : } else {
219 0 : plumed_error();
220 : }
221 : }
222 :
223 55 : unsigned GridVessel::getFibonacciIndex( const std::vector<double>& p ) const {
224 : plumed_dbg_assert( gtype==fibonacci );
225 : // Convert input point to coordinates on cylinder
226 110 : int k=2; double phi = atan2( p[2], p[0] ), sinthet2 = 1 - p[1]*p[1];
227 : // Calculate power to raise golden ratio
228 55 : if( sinthet2<epsilon ) { k = 2; }
229 : else {
230 57 : k = std::floor( std::log( npoints*pi*root5*sinthet2 ) / log_golden2 );
231 57 : if( k<2 ) k = 2;
232 : }
233 55 : double Fk = pow( golden, k ) / root5, F0 = std::round(Fk), F1 = std::round(Fk*golden);
234 55 : Matrix<double> B(2,2), invB(2,2); std::vector<double> thisp(3);
235 57 : B(0,0) = 2*pi*((F0+1)*igolden - std::floor((F0+1)*igolden)) - fib_increment;
236 57 : B(0,1) = 2*pi*((F1+1)*igolden - std::floor((F1+1)*igolden)) - fib_increment;
237 114 : B(1,0) = -2*F0/npoints; B(1,1) = -2*F1/npoints; Invert( B, invB );
238 171 : std::vector<double> vv(2), rc(2); vv[0]=-phi; vv[1] = p[1] - fib_shift;
239 167 : mult( invB, vv, rc ); std::vector<int> c(2); c[0]=std::floor(rc[0]); c[1]=std::floor(rc[1]);
240 : unsigned outind; double mindist = 10000000.;
241 282 : for(int s=0; s<4; ++s) {
242 675 : double ttt, costheta = B(1,0)*( c[0] + s%2 ) + B(1,1)*( c[1] + s/2 ) + fib_shift;
243 225 : if( costheta>1 ) ttt=1; else if( costheta<-1 ) ttt=-1; else ttt=costheta;
244 225 : costheta = 2*ttt - costheta;
245 225 : unsigned i = std::floor( 0.5*npoints*(1+costheta) ); getFibonacciCoordinates( i, thisp );
246 2046 : double dist=0; for(unsigned j=0; j<3; ++j) { double tmp=thisp[j]-p[j]; dist += tmp*tmp; }
247 227 : if( dist<mindist ) { outind = i; mindist = dist; }
248 : }
249 57 : return outind;
250 : }
251 :
252 111784483 : void GridVessel::convertIndexToIndices( const unsigned& index, const std::vector<unsigned>& nnbin, std::vector<unsigned>& indices ) const {
253 223568966 : plumed_dbg_assert( gtype==flat ); unsigned kk=index; indices[0]=index%nnbin[0];
254 220035646 : for(unsigned i=1; i<dimension-1; ++i) {
255 324753489 : kk=(kk-indices[i-1])/nnbin[i-1];
256 216502326 : indices[i]=kk%nnbin[i];
257 : }
258 111784483 : if(dimension>=2) { // I think this is wrong
259 448733336 : indices[dimension-1]=(kk-indices[dimension-2])/nnbin[dimension-2];
260 : }
261 111784483 : }
262 :
263 15771998 : void GridVessel::getIndices( const unsigned& index, std::vector<unsigned>& indices ) const {
264 15771998 : plumed_dbg_assert( gtype==flat ); convertIndexToIndices( index, nbin, indices );
265 15773046 : }
266 :
267 643341 : void GridVessel::getGridPointCoordinates( const unsigned& ipoint, std::vector<double>& x ) const {
268 643341 : std::vector<unsigned> tindices( dimension ); getGridPointCoordinates( ipoint, tindices, x );
269 643342 : }
270 :
271 12489825 : void GridVessel::getGridPointCoordinates( const unsigned& ipoint, std::vector<unsigned>& tindices, std::vector<double>& x ) const {
272 : plumed_dbg_assert( bounds_set && x.size()==dimension && tindices.size()==dimension && ipoint<npoints );
273 12489825 : if( gtype==flat ) {
274 12484711 : getFlatGridCoordinates( ipoint, tindices, x );
275 5114 : } else if( gtype==fibonacci ) {
276 5114 : getFibonacciCoordinates( ipoint, x );
277 : } else {
278 0 : plumed_error();
279 : }
280 12490870 : }
281 :
282 13013526 : void GridVessel::getFlatGridCoordinates( const unsigned& ipoint, std::vector<unsigned>& tindices, std::vector<double>& x ) const {
283 13013526 : plumed_dbg_assert( gtype==flat ); getIndices( ipoint, tindices );
284 126614802 : for(unsigned i=0; i<dimension; ++i) x[i] = min[i] + dx[i]*tindices[i];
285 13014603 : }
286 :
287 86814 : void GridVessel::getFibonacciCoordinates( const unsigned& ipoint, std::vector<double>& x ) const {
288 : plumed_dbg_assert( gtype==fibonacci );
289 173628 : x[1] = (ipoint*fib_offset) + fib_shift; double r = sqrt( 1 - x[1]*x[1] );
290 260442 : double phi = ipoint*fib_increment; x[0] = r*cos(phi); x[2] = r*sin(phi);
291 347237 : double norm=0; for(unsigned j=0; j<3; ++j) norm+=x[j]*x[j];
292 347240 : norm = sqrt(norm); for(unsigned j=0; j<3; ++j) x[j] = x[j] / norm;
293 86814 : }
294 :
295 528841 : void GridVessel::getSplineNeighbors( const unsigned& mybox, unsigned& nneighbors, std::vector<unsigned>& mysneigh ) const {
296 528841 : plumed_dbg_assert( gtype==flat ); unsigned nneigh=unsigned(pow(2.0,int(dimension)));
297 528841 : if( mysneigh.size()!=nneigh ) mysneigh.resize(nneigh);
298 :
299 528844 : unsigned inind; nneighbors = 0;
300 528844 : std::vector<unsigned> tmp_indices( dimension );
301 528844 : std::vector<unsigned> my_indices( dimension );
302 528842 : getIndices( mybox, my_indices );
303 2148735 : for(unsigned i=0; i<nneigh; ++i) {
304 : unsigned tmp=i; inind=0;
305 4363227 : for(unsigned j=0; j<dimension; ++j) {
306 8726454 : unsigned i0=tmp%2+my_indices[j]; tmp/=2;
307 8551690 : if(!pbc[j] && i0==nbin[j]) continue;
308 4498449 : if( pbc[j] && i0==nbin[j]) i0=0;
309 8645992 : tmp_indices[inind++]=i0;
310 : }
311 2148574 : if(inind==dimension ) {
312 2107968 : unsigned findex=getIndex( tmp_indices );
313 4216258 : mysneigh[nneighbors++]=findex;
314 4216258 : plumed_massert( active[findex], "inactive grid point required for splines");
315 : }
316 : }
317 528843 : }
318 :
319 6415984 : double GridVessel::getGridElement( const unsigned& ipoint, const unsigned& jelement ) const {
320 12831302 : plumed_assert( bounds_set && ipoint<npoints && jelement<nper && active[ipoint] );
321 12831968 : return getDataElement( nper*ipoint + jelement );
322 : }
323 :
324 72600 : void GridVessel::setGridElement( const unsigned& ipoint, const unsigned& jelement, const double& value ) {
325 : plumed_dbg_assert( bounds_set && ipoint<npoints && jelement<nper );
326 72600 : setDataElement( nper*ipoint + jelement, value );
327 72600 : }
328 :
329 24200 : void GridVessel::setValueAndDerivatives( const unsigned& ipoint, const unsigned& jelement, const double& value, const std::vector<double>& der ) {
330 : plumed_dbg_assert( !noderiv && jelement<getNumberOfComponents() && der.size()==nbin.size() );
331 145200 : setGridElement( ipoint, jelement, value ); for(unsigned i=0; i<der.size(); ++i) setGridElement( ipoint, jelement+1+i, der[i] );
332 24200 : }
333 :
334 5 : void GridVessel::addToGridElement( const unsigned& ipoint, const unsigned& jelement, const double& value ) {
335 : plumed_dbg_assert( bounds_set && ipoint<npoints && jelement<nper );
336 5 : addDataElement( nper*ipoint + jelement, value );
337 5 : }
338 :
339 9883 : void GridVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
340 : plumed_dbg_assert( myvals.getNumberOfValues()==(nper+1) );
341 79133 : for(unsigned i=0; i<nper; ++i) buffer[bufstart + nper*current + i] += myvals.get(i+1);
342 9883 : }
343 :
344 110 : void GridVessel::finish( const std::vector<double>& buffer ) {
345 110 : if( wasforced ) getFinalForces( buffer, finalForces );
346 90 : else AveragingVessel::finish( buffer );
347 110 : }
348 :
349 0 : double GridVessel::getGridElement( const std::vector<unsigned>& indices, const unsigned& jelement ) const {
350 0 : return getGridElement( getIndex( indices ), jelement );
351 : }
352 :
353 0 : void GridVessel::setGridElement( const std::vector<unsigned>& indices, const unsigned& jelement, const double& value ) {
354 0 : setGridElement( getIndex( indices ), jelement, value );
355 0 : }
356 :
357 166607 : std::vector<std::string> GridVessel::getMin() const {
358 166607 : plumed_dbg_assert( gtype==flat ); return str_min;
359 : }
360 :
361 166640 : std::vector<std::string> GridVessel::getMax() const {
362 166640 : plumed_dbg_assert( gtype==flat ); return str_max;
363 : }
364 :
365 167225 : std::vector<unsigned> GridVessel::getNbin() const {
366 : plumed_dbg_assert( gtype==flat && bounds_set );
367 167225 : std::vector<unsigned> ngrid( dimension );
368 498114 : for(unsigned i=0; i<dimension; ++i) {
369 988773 : if( !pbc[i] ) ngrid[i]=nbin[i] - 1;
370 3888 : else ngrid[i]=nbin[i];
371 : }
372 167227 : return ngrid;
373 : }
374 :
375 21422 : void GridVessel::getNeighbors( const std::vector<double>& pp, const std::vector<unsigned>& nneigh,
376 : unsigned& num_neighbors, std::vector<unsigned>& neighbors ) const {
377 : plumed_dbg_assert( bounds_set );
378 :
379 21422 : if( gtype == flat ) {
380 : plumed_dbg_assert( nneigh.size()==dimension );
381 21367 : std::vector<unsigned> indices( dimension );
382 212567 : for(unsigned i=0; i<dimension; ++i) indices[i] = std::floor( (pp[i]-min[i])/dx[i] );
383 21371 : getNeighbors( indices, nneigh, num_neighbors, neighbors );
384 55 : } else if( gtype == fibonacci ) {
385 55 : unsigned find = getFibonacciIndex( pp );
386 112 : num_neighbors = 1 + fib_nlist[find].size();
387 56 : if( neighbors.size()<num_neighbors ) neighbors.resize( num_neighbors );
388 9126 : neighbors[0]=find; for(unsigned i=0; i<fib_nlist[find].size(); ++i) neighbors[1+i] = fib_nlist[find][i];
389 : } else {
390 0 : plumed_error();
391 : }
392 21432 : }
393 :
394 40787 : void GridVessel::getNeighbors( const std::vector<unsigned>& indices, const std::vector<unsigned>& nneigh,
395 : unsigned& num_neighbors, std::vector<unsigned>& neighbors ) const {
396 : plumed_dbg_assert( gtype==flat && bounds_set && nneigh.size()==dimension );
397 :
398 40787 : unsigned num_neigh=1; std::vector<unsigned> small_bin( dimension );
399 162796 : for(unsigned i=0; i<dimension; ++i) {
400 244000 : small_bin[i]=(2*nneigh[i]+1);
401 122000 : num_neigh *=small_bin[i];
402 : }
403 40796 : if( neighbors.size()!=num_neigh ) neighbors.resize( num_neigh );
404 :
405 40794 : num_neighbors=0;
406 40794 : std::vector<unsigned> s_indices(dimension), t_indices(dimension);
407 96573715 : for(unsigned index=0; index<num_neigh; ++index) {
408 : bool found=true;
409 96532920 : convertIndexToIndices( index, small_bin, s_indices );
410 289338469 : for(unsigned i=0; i<dimension; ++i) {
411 1157353876 : int i0=s_indices[i]-nneigh[i]+indices[i];
412 289338469 : if(!pbc[i] && i0<0) found=false;
413 381924522 : if(!pbc[i] && i0>=nbin[i]) found=false;
414 304391474 : if( pbc[i] && i0<0) i0=nbin[i]-(-i0)%nbin[i];
415 502021018 : if( pbc[i] && i0>=nbin[i]) i0%=nbin[i];
416 289338469 : t_indices[i]=static_cast<unsigned>(i0);
417 : }
418 96533057 : if( found ) {
419 42176736 : neighbors[num_neighbors]=getIndex( t_indices );
420 21088386 : num_neighbors++;
421 : }
422 : }
423 40787 : }
424 :
425 11 : void GridVessel::setCubeUnits( const double& units ) {
426 11 : plumed_dbg_assert( gtype==flat ); cube_units=units;
427 11 : }
428 :
429 8 : double GridVessel::getCubeUnits() const {
430 8 : plumed_dbg_assert( gtype==flat ); return cube_units;
431 : }
432 :
433 13 : std::string GridVessel::getInputString() const {
434 13 : std::string mstring="COORDINATES="+arg_names[0];
435 21 : for(unsigned i=1; i<dimension; ++i) mstring+="," + arg_names[i];
436 13 : if( gtype==flat ) {
437 : mstring += " TYPE=flat PBC=";
438 13 : if( pbc[0] ) mstring +="T";
439 : else mstring +="F";
440 4 : for(unsigned i=1; i<dimension; ++i) {
441 8 : if( pbc[i] ) mstring +=",T";
442 : else mstring +=",F";
443 : }
444 0 : } else if( gtype==fibonacci ) {
445 : mstring += " TYPE=fibonacci";
446 : }
447 13 : return mstring;
448 : }
449 :
450 528839 : double GridVessel::getValueAndDerivatives( const std::vector<double>& x, const unsigned& ind, std::vector<double>& der ) const {
451 : plumed_dbg_assert( gtype==flat && der.size()==dimension && !noderiv && ind<getNumberOfComponents() );
452 :
453 1057676 : double X,X2,X3,value=0; der.assign(der.size(),0.0);
454 528837 : std::vector<double> fd(dimension);
455 528844 : std::vector<double> C(dimension);
456 528844 : std::vector<double> D(dimension);
457 528844 : std::vector<double> dder(dimension);
458 :
459 528844 : std::vector<unsigned> nindices(dimension); unsigned n_neigh;
460 528843 : std::vector<unsigned> indices(dimension); getIndices( x, indices );
461 528841 : std::vector<unsigned> neigh; getSplineNeighbors( getIndex(indices), n_neigh, neigh );
462 528843 : std::vector<double> xfloor(dimension); getFlatGridCoordinates( getIndex(x), nindices, xfloor );
463 :
464 : // loop over neighbors
465 2636937 : for(unsigned int ipoint=0; ipoint<n_neigh; ++ipoint) {
466 4216186 : double grid=getGridElement(neigh[ipoint], ind*(1+dimension) );
467 10674993 : for(unsigned j=0; j<dimension; ++j) dder[j] = getGridElement( neigh[ipoint], ind*(1+dimension) + 1 + j );
468 :
469 2108125 : getIndices( neigh[ipoint], nindices );
470 : double ff=1.0;
471 :
472 4283266 : for(unsigned j=0; j<dimension; ++j) {
473 : int x0=1;
474 12849798 : if(nindices[j]==indices[j]) x0=0;
475 4283266 : double ddx=dx[j];
476 8566532 : X=fabs((x[j]-xfloor[j])/ddx-(double)x0);
477 4283266 : X2=X*X;
478 4283266 : X3=X2*X;
479 : double yy;
480 4283266 : if(fabs(grid)<0.0000001) yy=0.0;
481 4269437 : else yy=-dder[j]/grid;
482 4283266 : C[j]=(1.0-3.0*X2+2.0*X3) - (x0?-1.0:1.0)*yy*(X-2.0*X2+X3)*ddx;
483 4283266 : D[j]=( -6.0*X +6.0*X2) - (x0?-1.0:1.0)*yy*(1.0-4.0*X +3.0*X2)*ddx;
484 4283266 : D[j]*=(x0?-1.0:1.0)/ddx;
485 4283266 : ff*=C[j];
486 : }
487 4283417 : for(unsigned j=0; j<dimension; ++j) {
488 8566834 : fd[j]=D[j];
489 13254701 : for(unsigned i=0; i<dimension; ++i) if(i!=j) fd[j]*=C[i];
490 : }
491 2108144 : value+=grid*ff;
492 10675008 : for(unsigned j=0; j<dimension; ++j) der[j]+=grid*fd[j];
493 : }
494 528844 : return value;
495 : }
496 :
497 3 : void GridVessel::activateThesePoints( const std::vector<bool>& to_activate ) {
498 : plumed_dbg_assert( to_activate.size()==npoints );
499 29991 : for(unsigned i=0; i<npoints; ++i) active[i]=to_activate[i];
500 3 : }
501 :
502 20 : void GridVessel::setForce( const std::vector<double>& inforces ) {
503 : plumed_dbg_assert( inforces.size()==npoints );
504 5725 : wasforced=true; for(unsigned i=0; i<npoints; ++i) forces[i]=inforces[i];
505 20 : }
506 :
507 11868333 : bool GridVessel::wasForced() const {
508 11868333 : return wasforced;
509 : }
510 :
511 20 : bool GridVessel::applyForce( std::vector<double>& fforces ) {
512 : plumed_dbg_assert( fforces.size()==finalForces.size() );
513 20 : if( !wasforced ) return false;
514 7610 : for(unsigned i=0; i<finalForces.size(); ++i) fforces[i]=finalForces[i];
515 20 : wasforced=false; return true;
516 : }
517 :
518 : }
519 5874 : }
520 :
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