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 47 : void GridVessel::registerKeywords( Keywords& keys ) {
31 47 : AveragingVessel::registerKeywords( keys );
32 235 : keys.add("compulsory","TYPE","flat","how the grid points are being generated");
33 188 : keys.add("compulsory","COMPONENTS","the names of the components in the vector");
34 188 : keys.add("compulsory","COORDINATES","the names of the coordinates of the grid");
35 188 : keys.add("compulsory","PBC","is the grid periodic in each direction or not");
36 47 : }
37 :
38 47 : GridVessel::GridVessel( const vesselbase::VesselOptions& da ):
39 : AveragingVessel(da),
40 : bounds_set(false),
41 : cube_units(1.0),
42 : noderiv(false),
43 : npoints(0),
44 517 : wasforced(false)
45 : {
46 94 : std::string geom; parse("TYPE",geom);
47 47 : if( geom=="flat" ) gtype=flat;
48 3 : else if( geom=="fibonacci" ) gtype=fibonacci;
49 0 : else plumed_merror( geom + " is invalid geometry type");
50 141 : std::vector<std::string> compnames; parseVector("COMPONENTS",compnames);
51 141 : std::vector<std::string> coordnames; parseVector("COORDINATES",coordnames);
52 47 : if( gtype==flat ) {
53 44 : dimension=coordnames.size();
54 44 : str_min.resize( dimension); str_max.resize( dimension ); stride.resize( dimension );
55 44 : 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 94 : unsigned n=0; nper=compnames.size()*( 1 + coordnames.size() );
62 47 : arg_names.resize( coordnames.size() + compnames.size()*( 1 + coordnames.size() ) );
63 325 : for(unsigned i=0; i<coordnames.size(); ++i) { arg_names[n] = coordnames[i]; n++; }
64 235 : for(unsigned i=0; i<compnames.size(); ++i) {
65 94 : arg_names[n]=compnames[i]; n++;
66 633 : for(unsigned j=0; j<coordnames.size(); ++j) { arg_names[n] = "d" + compnames[i] + "_" + coordnames[j]; n++; }
67 : }
68 47 : pbc.resize( dimension );
69 141 : std::vector<std::string> spbc( dimension ); parseVector("PBC",spbc);
70 201 : for(unsigned i=0; i<dimension; ++i) {
71 154 : if( spbc[i]=="F" ) pbc[i]=false;
72 28 : else if( spbc[i]=="T" ) pbc[i]=true;
73 0 : else plumed_error();
74 : }
75 47 : }
76 :
77 7 : void GridVessel::setNoDerivatives() {
78 7 : nper = ( nper/(1+dimension) ); noderiv=true;
79 14 : std::vector<std::string> tnames( dimension ), cnames(nper);
80 27 : for(unsigned i=0; i<dimension; ++i) tnames[i]=arg_names[i];
81 28 : unsigned k=dimension; for(unsigned i=0; i<nper; ++i) { cnames[i]=arg_names[k]; k+=(1+dimension); }
82 7 : arg_names.resize( dimension + nper );
83 27 : for(unsigned i=0; i<dimension; ++i) arg_names[i]=tnames[i];
84 28 : for(unsigned i=0; i<nper; ++i) arg_names[dimension+i]=cnames[i];
85 7 : }
86 :
87 70 : 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 );
90 193 : plumed_assert( gtype==flat && (spacing.size()==dimension || binsin.size()==dimension) );
91 :
92 70 : npoints=1; bounds_set=true;
93 296 : for(unsigned i=0; i<dimension; ++i) {
94 113 : str_min[i]=smin[i]; str_max[i]=smax[i];
95 113 : Tools::convert( str_min[i], min[i] );
96 113 : Tools::convert( str_max[i], max[i] );
97 143 : if( spacing.size()==dimension && binsin.size()==dimension ) {
98 32 : if( spacing[i]==0 ) nbin[i] = binsin[i];
99 : else {
100 84 : double range = max[i] - min[i]; nbin[i] = std::round( range / spacing[i]);
101 : // This check ensures that nbins is set correctly if spacing is set the same as the number of bins
102 56 : if( nbin[i]!=binsin[i] ) plumed_merror("mismatch between input spacing and input number of bins");
103 : }
104 166 : } else if( binsin.size()==dimension ) nbin[i]=binsin[i];
105 0 : else if( spacing.size()==dimension ) nbin[i] = std::floor(( max[i] - min[i] ) / spacing[i]) + 1;
106 0 : else plumed_error();
107 452 : dx[i] = ( max[i] - min[i] ) / static_cast<double>( nbin[i] );
108 314 : if( !pbc[i] ) { max[i] +=dx[i]; nbin[i]+=1; }
109 113 : stride[i]=npoints;
110 113 : npoints*=nbin[i];
111 : }
112 70 : resize(); // Always resize after setting new bounds as grid size may have have changed
113 70 : }
114 :
115 3 : void GridVessel::setupFibonacciGrid( const unsigned& np ) {
116 3 : bounds_set=true; root5 = sqrt(5);
117 3 : npoints = np; golden = ( 1 + sqrt(5) ) / 2.0; igolden = golden - 1;
118 3 : fib_increment = 2*pi*igolden; log_golden2 = std::log( golden*golden );
119 3 : fib_offset = 2 / static_cast<double>( npoints );
120 3 : fib_shift = fib_offset/2 - 1;
121 3 : resize();
122 :
123 3 : std::vector<double> icoord( dimension ), jcoord( dimension );
124 : // Find minimum distance between each pair of points
125 3 : std::vector<double> mindists( npoints );
126 347 : for(unsigned i=0; i<npoints; ++i) {
127 688 : getFibonacciCoordinates( i, icoord ); mindists[i] = 0;
128 41080 : for(unsigned j=0; j<npoints; ++j) {
129 40736 : if( i==j ) continue ; // Points are not neighbors to themselves
130 40392 : getFibonacciCoordinates( j, jcoord );
131 : // Calculate the dot product
132 403920 : double dot=0; for(unsigned k=0; k<dimension; ++k) dot += icoord[k]*jcoord[k];
133 80784 : if( dot>mindists[i] ) mindists[i]=dot;
134 : }
135 : }
136 : // And now take minimum of dot products
137 3 : double min=mindists[0];
138 685 : for(unsigned i=1; i<npoints; ++i) {
139 682 : if( mindists[i]<min ) min=mindists[i];
140 : }
141 : double final_cutoff;
142 3 : if( getFibonacciCutoff()<-1 ) final_cutoff=-1;
143 2 : else final_cutoff = cos( acos( getFibonacciCutoff() ) + acos( min ) );
144 :
145 : // And now construct the neighbor list
146 3 : fib_nlist.resize( npoints );
147 347 : for(unsigned i=0; i<npoints; ++i) {
148 344 : getFibonacciCoordinates( i, icoord );
149 41080 : for(unsigned j=0; j<npoints; ++j) {
150 40736 : if( i==j ) continue ; // Points are not neighbors to themselves
151 40392 : getFibonacciCoordinates( j, jcoord );
152 : // Calculate the dot product
153 403920 : double dot=0; for(unsigned k=0; k<dimension; ++k) dot += icoord[k]*jcoord[k];
154 63278 : if( dot>final_cutoff ) { fib_nlist[i].push_back(j); }
155 : }
156 : }
157 3 : }
158 :
159 47 : std::string GridVessel::description() {
160 47 : if( !bounds_set ) return "";
161 :
162 : std::string des;
163 34 : if( gtype==flat ) {
164 : des="grid of "; std::string num;
165 66 : for(unsigned i=0; i<dimension-1; ++i) {
166 34 : Tools::convert( nbin[i], num );
167 34 : des += num + " X ";
168 : }
169 64 : Tools::convert( nbin[dimension-1], num );
170 64 : des += num + " equally spaced points between (";
171 83 : for(unsigned i=0; i<dimension-1; ++i) des += str_min[i] + ",";
172 64 : Tools::convert( nbin[dimension-1], num );
173 96 : des += str_min[dimension-1] + ") and (";
174 83 : for(unsigned i=0; i<dimension-1; ++i) des += str_max[i] + ",";
175 96 : des += str_max[dimension-1] + ")";
176 2 : } else if( gtype==fibonacci ) {
177 2 : std::string num; Tools::convert( npoints, num );
178 6 : des += "fibonacci grid of " + num + " points on spherical surface";
179 : }
180 : return des;
181 : }
182 :
183 165 : void GridVessel::resize() {
184 165 : plumed_massert( nper>0, "Number of datapoints at each grid point has not been set");
185 330 : resizeBuffer( getNumberOfBufferPoints()*nper + 1 + 2*getAction()->getNumberOfDerivatives() );
186 165 : setDataSize( npoints*nper ); forces.resize( npoints );
187 165 : if( active.size()!=npoints) active.resize( npoints, true );
188 165 : }
189 :
190 21249266 : unsigned GridVessel::getIndex( const std::vector<unsigned>& indices ) const {
191 : plumed_dbg_assert( gtype==flat && bounds_set && indices.size()==dimension );
192 : // indices are flattended using a column-major order
193 42498532 : unsigned index=indices[dimension-1];
194 106193892 : for(unsigned i=dimension-1; i>0; --i) {
195 127416939 : index=index*nbin[i-1]+indices[i-1];
196 : }
197 21249266 : return index;
198 : }
199 :
200 17885 : void GridVessel::getIndices( const std::vector<double>& point, std::vector<unsigned>& indices ) const {
201 : plumed_dbg_assert( gtype==flat && bounds_set && point.size()==dimension && indices.size()==dimension );
202 123575 : for(unsigned i=0; i<dimension; ++i) {
203 264225 : indices[i]=std::floor( (point[i] - min[i])/dx[i] );
204 143897 : if( pbc[i] ) indices[i]=indices[i]%nbin[i];
205 14638 : else if( indices[i]>nbin[i] ) plumed_merror("point is outside grid range");
206 : }
207 17885 : }
208 :
209 8651 : unsigned GridVessel::getIndex( const std::vector<double>& point ) const {
210 : plumed_dbg_assert( gtype==flat && bounds_set && point.size()==dimension );
211 8651 : if( gtype==flat ) {
212 8651 : std::vector<unsigned> indices(dimension); getIndices( point, indices );
213 8651 : return getIndex( indices );
214 0 : } else if( gtype==fibonacci ) {
215 0 : return getFibonacciIndex( point );
216 : } else {
217 0 : plumed_error();
218 : }
219 : }
220 :
221 57 : unsigned GridVessel::getFibonacciIndex( const std::vector<double>& p ) const {
222 : plumed_dbg_assert( gtype==fibonacci );
223 : // Convert input point to coordinates on cylinder
224 114 : int k=2; double phi = atan2( p[2], p[0] ), sinthet2 = 1 - p[1]*p[1];
225 : // Calculate power to raise golden ratio
226 57 : if( sinthet2<epsilon ) { k = 2; }
227 : else {
228 57 : k = std::floor( std::log( npoints*pi*root5*sinthet2 ) / log_golden2 );
229 57 : if( k<2 ) k = 2;
230 : }
231 57 : double Fk = pow( golden, k ) / root5, F0 = std::round(Fk), F1 = std::round(Fk*golden);
232 57 : Matrix<double> B(2,2), invB(2,2); std::vector<double> thisp(3);
233 114 : B(0,0) = 2*pi*((F0+1)*igolden - std::floor((F0+1)*igolden)) - fib_increment;
234 114 : B(0,1) = 2*pi*((F1+1)*igolden - std::floor((F1+1)*igolden)) - fib_increment;
235 171 : B(1,0) = -2*F0/npoints; B(1,1) = -2*F1/npoints; Invert( B, invB );
236 228 : std::vector<double> vv(2), rc(2); vv[0]=-phi; vv[1] = p[1] - fib_shift;
237 285 : mult( invB, vv, rc ); std::vector<int> c(2); c[0]=std::floor(rc[0]); c[1]=std::floor(rc[1]);
238 : unsigned outind; double mindist = 10000000.;
239 513 : for(int s=0; s<4; ++s) {
240 684 : double ttt, costheta = B(1,0)*( c[0] + s%2 ) + B(1,1)*( c[1] + s/2 ) + fib_shift;
241 228 : if( costheta>1 ) ttt=1; else if( costheta<-1 ) ttt=-1; else ttt=costheta;
242 228 : costheta = 2*ttt - costheta;
243 228 : unsigned i = std::floor( 0.5*npoints*(1+costheta) ); getFibonacciCoordinates( i, thisp );
244 2280 : double dist=0; for(unsigned j=0; j<3; ++j) { double tmp=thisp[j]-p[j]; dist += tmp*tmp; }
245 228 : if( dist<mindist ) { outind = i; mindist = dist; }
246 : }
247 57 : return outind;
248 : }
249 :
250 108707058 : void GridVessel::convertIndexToIndices( const unsigned& index, const std::vector<unsigned>& nnbin, std::vector<unsigned>& indices ) const {
251 326121174 : plumed_dbg_assert( gtype==flat ); unsigned kk=index; indices[0]=index%nnbin[0];
252 325666464 : for(unsigned i=1; i<dimension-1; ++i) {
253 325439109 : kk=(kk-indices[i-1])/nnbin[i-1];
254 325439109 : indices[i]=kk%nnbin[i];
255 : }
256 108707058 : if(dimension>=2) { // I think this is wrong
257 434768160 : indices[dimension-1]=(kk-indices[dimension-2])/nnbin[dimension-2];
258 : }
259 108707058 : }
260 :
261 12161812 : void GridVessel::getIndices( const unsigned& index, std::vector<unsigned>& indices ) const {
262 12161812 : plumed_dbg_assert( gtype==flat ); convertIndexToIndices( index, nbin, indices );
263 12161812 : }
264 :
265 107408 : void GridVessel::getGridPointCoordinates( const unsigned& ipoint, std::vector<double>& x ) const {
266 107408 : std::vector<unsigned> tindices( dimension ); getGridPointCoordinates( ipoint, tindices, x );
267 107408 : }
268 :
269 11954882 : void GridVessel::getGridPointCoordinates( const unsigned& ipoint, std::vector<unsigned>& tindices, std::vector<double>& x ) const {
270 : plumed_dbg_assert( bounds_set && x.size()==dimension && tindices.size()==dimension && ipoint<npoints );
271 11954882 : if( gtype==flat ) {
272 11949765 : getFlatGridCoordinates( ipoint, tindices, x );
273 5117 : } else if( gtype==fibonacci ) {
274 5117 : getFibonacciCoordinates( ipoint, x );
275 : } else {
276 0 : plumed_error();
277 : }
278 11954882 : }
279 :
280 11958411 : void GridVessel::getFlatGridCoordinates( const unsigned& ipoint, std::vector<unsigned>& tindices, std::vector<double>& x ) const {
281 11958411 : plumed_dbg_assert( gtype==flat ); getIndices( ipoint, tindices );
282 190731351 : for(unsigned i=0; i<dimension; ++i) x[i] = min[i] + dx[i]*tindices[i];
283 11958411 : }
284 :
285 86817 : void GridVessel::getFibonacciCoordinates( const unsigned& ipoint, std::vector<double>& x ) const {
286 : plumed_dbg_assert( gtype==fibonacci );
287 260451 : x[1] = (ipoint*fib_offset) + fib_shift; double r = sqrt( 1 - x[1]*x[1] );
288 260451 : double phi = ipoint*fib_increment; x[0] = r*cos(phi); x[2] = r*sin(phi);
289 607719 : double norm=0; for(unsigned j=0; j<3; ++j) norm+=x[j]*x[j];
290 347268 : norm = sqrt(norm); for(unsigned j=0; j<3; ++j) x[j] = x[j] / norm;
291 86817 : }
292 :
293 8646 : void GridVessel::getSplineNeighbors( const unsigned& mybox, std::vector<unsigned>& mysneigh ) const {
294 8646 : plumed_dbg_assert( gtype==flat ); mysneigh.resize( static_cast<unsigned>(pow(2.,dimension)) );
295 :
296 8646 : std::vector<unsigned> tmp_indices( dimension );
297 8646 : std::vector<unsigned> my_indices( dimension );
298 8646 : getIndices( mybox, my_indices );
299 221196 : for(unsigned i=0; i<mysneigh.size(); ++i) {
300 : unsigned tmp=i;
301 474176 : for(unsigned j=0; j<dimension; ++j) {
302 406208 : unsigned i0=tmp%2+my_indices[j]; tmp/=2;
303 230008 : if(!pbc[j] && i0==nbin[j]) getAction()->error("Extrapolating function on grid");
304 379304 : if( pbc[j] && i0==nbin[j]) i0=0;
305 203104 : tmp_indices[j]=i0;
306 : }
307 67968 : mysneigh[i]=getIndex( tmp_indices );
308 135936 : plumed_massert( active[mysneigh[i]], "inactive grid point required for splines");
309 : }
310 8646 : }
311 :
312 314678 : double GridVessel::getGridElement( const unsigned& ipoint, const unsigned& jelement ) const {
313 629356 : plumed_assert( bounds_set && ipoint<npoints && jelement<nper && active[ipoint] );
314 629356 : return getDataElement( nper*ipoint + jelement );
315 : }
316 :
317 0 : void GridVessel::setGridElement( const unsigned& ipoint, const unsigned& jelement, const double& value ) {
318 : plumed_dbg_assert( bounds_set && ipoint<npoints && jelement<nper );
319 0 : setDataElement( nper*ipoint + jelement, value );
320 0 : }
321 :
322 5 : void GridVessel::addToGridElement( const unsigned& ipoint, const unsigned& jelement, const double& value ) {
323 : plumed_dbg_assert( bounds_set && ipoint<npoints && jelement<nper );
324 5 : addDataElement( nper*ipoint + jelement, value );
325 5 : }
326 :
327 12181 : void GridVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
328 : plumed_dbg_assert( myvals.getNumberOfValues()==(nper+1) );
329 138316 : for(unsigned i=0; i<nper; ++i) buffer[bufstart + nper*current + i] += myvals.get(i+1);
330 12181 : }
331 :
332 99 : void GridVessel::finish( const std::vector<double>& buffer ) {
333 99 : if( wasforced ) getFinalForces( buffer, finalForces );
334 79 : else AveragingVessel::finish( buffer );
335 99 : }
336 :
337 0 : double GridVessel::getGridElement( const std::vector<unsigned>& indices, const unsigned& jelement ) const {
338 0 : return getGridElement( getIndex( indices ), jelement );
339 : }
340 :
341 0 : void GridVessel::setGridElement( const std::vector<unsigned>& indices, const unsigned& jelement, const double& value ) {
342 0 : setGridElement( getIndex( indices ), jelement, value );
343 0 : }
344 :
345 176647 : std::vector<std::string> GridVessel::getMin() const {
346 176647 : plumed_dbg_assert( gtype==flat ); return str_min;
347 : }
348 :
349 176680 : std::vector<std::string> GridVessel::getMax() const {
350 176680 : plumed_dbg_assert( gtype==flat ); return str_max;
351 : }
352 :
353 177267 : std::vector<unsigned> GridVessel::getNbin() const {
354 : plumed_dbg_assert( gtype==flat && bounds_set );
355 177267 : std::vector<unsigned> ngrid( dimension );
356 879125 : for(unsigned i=0; i<dimension; ++i) {
357 1355528 : if( !pbc[i] ) ngrid[i]=nbin[i] - 1;
358 24094 : else ngrid[i]=nbin[i];
359 : }
360 177267 : return ngrid;
361 : }
362 :
363 21470 : void GridVessel::getNeighbors( const std::vector<double>& pp, const std::vector<unsigned>& nneigh,
364 : unsigned& num_neighbors, std::vector<unsigned>& neighbors ) const {
365 : plumed_dbg_assert( bounds_set );
366 :
367 21470 : if( gtype == flat ) {
368 : plumed_dbg_assert( nneigh.size()==dimension );
369 21413 : std::vector<unsigned> indices( dimension );
370 340408 : for(unsigned i=0; i<dimension; ++i) indices[i] = std::floor( (pp[i]-min[i])/dx[i] );
371 21413 : getNeighbors( indices, nneigh, num_neighbors, neighbors );
372 57 : } else if( gtype == fibonacci ) {
373 57 : unsigned find = getFibonacciIndex( pp );
374 114 : num_neighbors = 1 + fib_nlist[find].size();
375 57 : if( neighbors.size()<num_neighbors ) neighbors.resize( num_neighbors );
376 14262 : neighbors[0]=find; for(unsigned i=0; i<fib_nlist[find].size(); ++i) neighbors[1+i] = fib_nlist[find][i];
377 : } else {
378 0 : plumed_error();
379 : }
380 21470 : }
381 :
382 40834 : void GridVessel::getNeighbors( const std::vector<unsigned>& indices, const std::vector<unsigned>& nneigh,
383 : unsigned& num_neighbors, std::vector<unsigned>& neighbors ) const {
384 : plumed_dbg_assert( gtype==flat && bounds_set && nneigh.size()==dimension );
385 :
386 40834 : unsigned num_neigh=1; std::vector<unsigned> small_bin( dimension );
387 284958 : for(unsigned i=0; i<dimension; ++i) {
388 366186 : small_bin[i]=(2*nneigh[i]+1);
389 122062 : num_neigh *=small_bin[i];
390 : }
391 40834 : if( neighbors.size()!=num_neigh ) neighbors.resize( num_neigh );
392 :
393 40834 : num_neighbors=0;
394 40834 : std::vector<unsigned> s_indices(dimension), t_indices(dimension);
395 96586080 : for(unsigned index=0; index<num_neigh; ++index) {
396 : bool found=true;
397 96545246 : convertIndexToIndices( index, small_bin, s_indices );
398 675766530 : for(unsigned i=0; i<dimension; ++i) {
399 1158442568 : int i0=s_indices[i]-nneigh[i]+indices[i];
400 289610642 : if(!pbc[i] && i0<0) found=false;
401 382200910 : if(!pbc[i] && i0>=nbin[i]) found=false;
402 304666132 : if( pbc[i] && i0<0) i0=nbin[i]-(-i0)%nbin[i];
403 486631016 : if( pbc[i] && i0>=nbin[i]) i0%=nbin[i];
404 289610642 : t_indices[i]=static_cast<unsigned>(i0);
405 : }
406 96545246 : if( found ) {
407 42184778 : neighbors[num_neighbors]=getIndex( t_indices );
408 21092389 : num_neighbors++;
409 : }
410 : }
411 40834 : }
412 :
413 11 : void GridVessel::setCubeUnits( const double& units ) {
414 11 : plumed_dbg_assert( gtype==flat ); cube_units=units;
415 11 : }
416 :
417 8 : double GridVessel::getCubeUnits() const {
418 8 : plumed_dbg_assert( gtype==flat ); return cube_units;
419 : }
420 :
421 9 : std::string GridVessel::getInputString() const {
422 9 : std::string mstring="COORDINATES="+arg_names[0];
423 24 : for(unsigned i=1; i<dimension; ++i) mstring+="," + arg_names[i];
424 9 : if( gtype==flat ) {
425 : mstring += " TYPE=flat PBC=";
426 9 : if( pbc[0] ) mstring +="T";
427 : else mstring +="F";
428 19 : for(unsigned i=1; i<dimension; ++i) {
429 10 : if( pbc[i] ) mstring +=",T";
430 : else mstring +=",F";
431 : }
432 0 : } else if( gtype==fibonacci ) {
433 : mstring += " TYPE=fibonacci";
434 : }
435 9 : return mstring;
436 : }
437 :
438 8646 : double GridVessel::getValueAndDerivatives( const std::vector<double>& x, const unsigned& ind, std::vector<double>& der ) const {
439 : plumed_dbg_assert( gtype==flat && der.size()==dimension && !noderiv && ind<getNumberOfComponents() );
440 :
441 17292 : double X,X2,X3,value=0; der.assign(der.size(),0.0);
442 8646 : std::vector<double> fd(dimension);
443 8646 : std::vector<double> C(dimension);
444 8646 : std::vector<double> D(dimension);
445 8646 : std::vector<double> dder(dimension);
446 :
447 8646 : std::vector<unsigned> nindices(dimension);
448 8646 : std::vector<unsigned> indices(dimension); getIndices( x, indices );
449 8646 : std::vector<unsigned> neigh; getSplineNeighbors( getIndex(indices), neigh );
450 8646 : std::vector<double> xfloor(dimension); getFlatGridCoordinates( getIndex(x), nindices, xfloor );
451 :
452 : // loop over neighbors
453 221196 : for(unsigned int ipoint=0; ipoint<neigh.size(); ++ipoint) {
454 135936 : double grid=getGridElement(neigh[ipoint], ind*(1+dimension) );
455 677280 : for(unsigned j=0; j<dimension; ++j) dder[j] = getGridElement( neigh[ipoint], ind*(1+dimension) + 1 + j );
456 :
457 67968 : getIndices( neigh[ipoint], nindices );
458 : double ff=1.0;
459 :
460 474176 : for(unsigned j=0; j<dimension; ++j) {
461 : int x0=1;
462 609312 : if(nindices[j]==indices[j]) x0=0;
463 203104 : double ddx=dx[j];
464 406208 : X=fabs((x[j]-xfloor[j])/ddx-(double)x0);
465 203104 : X2=X*X;
466 203104 : X3=X2*X;
467 : double yy;
468 203104 : if(fabs(grid)<0.0000001) yy=0.0;
469 189257 : else yy=-dder[j]/grid;
470 406208 : C[j]=(1.0-3.0*X2+2.0*X3) - (x0?-1.0:1.0)*yy*(X-2.0*X2+X3)*ddx;
471 406208 : D[j]=( -6.0*X +6.0*X2) - (x0?-1.0:1.0)*yy*(1.0-4.0*X +3.0*X2)*ddx;
472 203104 : D[j]*=(x0?-1.0:1.0)/ddx;
473 203104 : ff*=C[j];
474 : }
475 474176 : for(unsigned j=0; j<dimension; ++j) {
476 406208 : fd[j]=D[j];
477 1622432 : for(unsigned i=0; i<dimension; ++i) if(i!=j) fd[j]*=C[i];
478 : }
479 67968 : value+=grid*ff;
480 677280 : for(unsigned j=0; j<dimension; ++j) der[j]+=grid*fd[j];
481 : }
482 8646 : return value;
483 : }
484 :
485 3 : void GridVessel::activateThesePoints( const std::vector<bool>& to_activate ) {
486 : plumed_dbg_assert( to_activate.size()==npoints );
487 59979 : for(unsigned i=0; i<npoints; ++i) active[i]=to_activate[i];
488 3 : }
489 :
490 20 : void GridVessel::setForce( const std::vector<double>& inforces ) {
491 : plumed_dbg_assert( inforces.size()==npoints );
492 5725 : wasforced=true; for(unsigned i=0; i<npoints; ++i) forces[i]=inforces[i];
493 20 : }
494 :
495 11869004 : bool GridVessel::wasForced() const {
496 11869004 : return wasforced;
497 : }
498 :
499 20 : bool GridVessel::applyForce( std::vector<double>& fforces ) {
500 : plumed_dbg_assert( fforces.size()==finalForces.size() );
501 20 : if( !wasforced ) return false;
502 11425 : for(unsigned i=0; i<finalForces.size(); ++i) fforces[i]=finalForces[i];
503 20 : wasforced=false; return true;
504 : }
505 :
506 : }
507 4839 : }
508 :
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