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 43 : void GridVessel::registerKeywords( Keywords& keys ) {
31 43 : AveragingVessel::registerKeywords( keys );
32 43 : keys.add("compulsory","TYPE","flat","how the grid points are being generated");
33 43 : keys.add("compulsory","COMPONENTS","the names of the components in the vector");
34 43 : keys.add("compulsory","COORDINATES","the names of the coordinates of the grid");
35 43 : keys.add("compulsory","PBC","is the grid periodic in each direction or not");
36 43 : }
37 :
38 43 : 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 43 : wasforced(false)
45 : {
46 43 : std::string geom; parse("TYPE",geom);
47 43 : if( geom=="flat" ) gtype=flat;
48 3 : else if( geom=="fibonacci" ) gtype=fibonacci;
49 0 : else plumed_merror( geom + " is invalid geometry type");
50 86 : std::vector<std::string> compnames; parseVector("COMPONENTS",compnames);
51 86 : std::vector<std::string> coordnames; parseVector("COORDINATES",coordnames);
52 43 : if( gtype==flat ) {
53 40 : dimension=coordnames.size();
54 40 : str_min.resize( dimension); str_max.resize( dimension ); stride.resize( dimension );
55 40 : 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 43 : unsigned n=0; nper=compnames.size()*( 1 + coordnames.size() );
62 43 : arg_names.resize( coordnames.size() + compnames.size()*( 1 + coordnames.size() ) );
63 43 : for(unsigned i=0; i<coordnames.size(); ++i) { arg_names[n] = coordnames[i]; n++; }
64 86 : for(unsigned i=0; i<compnames.size(); ++i) {
65 43 : arg_names[n]=compnames[i]; n++;
66 43 : for(unsigned j=0; j<coordnames.size(); ++j) { arg_names[n] = "d" + compnames[i] + "_" + coordnames[j]; n++; }
67 : }
68 43 : pbc.resize( dimension );
69 86 : std::vector<std::string> spbc( dimension ); parseVector("PBC",spbc);
70 114 : for(unsigned i=0; i<dimension; ++i) {
71 71 : if( spbc[i]=="F" ) pbc[i]=false;
72 22 : else if( spbc[i]=="T" ) pbc[i]=true;
73 0 : else plumed_error();
74 43 : }
75 43 : }
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 7 : for(unsigned i=0; i<dimension; ++i) tnames[i]=arg_names[i];
81 7 : 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 7 : for(unsigned i=0; i<dimension; ++i) arg_names[i]=tnames[i];
84 14 : for(unsigned i=0; i<nper; ++i) arg_names[dimension+i]=cnames[i];
85 7 : }
86 :
87 64 : 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 64 : plumed_assert( gtype==flat && (spacing.size()==dimension || binsin.size()==dimension) );
91 :
92 64 : npoints=1; bounds_set=true;
93 168 : for(unsigned i=0; i<dimension; ++i) {
94 104 : str_min[i]=smin[i]; str_max[i]=smax[i];
95 104 : Tools::convert( str_min[i], min[i] );
96 104 : Tools::convert( str_max[i], max[i] );
97 104 : if( spacing.size()==dimension && binsin.size()==dimension ) {
98 27 : 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 27 : if( fabs( binsin[i]*spacing[i]-range )>epsilon ) spc += 1;
101 27 : if( spc>binsin[i] ) nbin[i]=spc; else nbin[i]=binsin[i];
102 77 : } 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();
105 104 : dx[i] = ( max[i] - min[i] ) / static_cast<double>( nbin[i] );
106 104 : if( !pbc[i] ) { max[i] +=dx[i]; nbin[i]+=1; }
107 104 : stride[i]=npoints;
108 104 : npoints*=nbin[i];
109 : }
110 64 : resize(); // Always resize after setting new bounds as grid size may have have changed
111 64 : }
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 6 : std::vector<double> icoord( dimension ), jcoord( dimension );
122 : // Find minimum distance between each pair of points
123 6 : std::vector<double> mindists( npoints );
124 347 : for(unsigned i=0; i<npoints; ++i) {
125 344 : 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 40392 : double dot=0; for(unsigned k=0; k<dimension; ++k) dot += icoord[k]*jcoord[k];
131 40392 : 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) {
137 341 : 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 40392 : double dot=0; for(unsigned k=0; k<dimension; ++k) dot += icoord[k]*jcoord[k];
152 40392 : if( dot>final_cutoff ) { fib_nlist[i].push_back(j); }
153 : }
154 3 : }
155 3 : }
156 :
157 43 : std::string GridVessel::description() {
158 43 : if( !bounds_set ) return "";
159 :
160 30 : std::string des;
161 30 : if( gtype==flat ) {
162 28 : des="grid of "; std::string num;
163 43 : for(unsigned i=0; i<dimension-1; ++i) {
164 15 : Tools::convert( nbin[i], num );
165 15 : des += num + " X ";
166 : }
167 28 : Tools::convert( nbin[dimension-1], num );
168 28 : des += num + " equally spaced points between (";
169 28 : for(unsigned i=0; i<dimension-1; ++i) des += str_min[i] + ",";
170 28 : Tools::convert( nbin[dimension-1], num );
171 28 : des += str_min[dimension-1] + ") and (";
172 28 : for(unsigned i=0; i<dimension-1; ++i) des += str_max[i] + ",";
173 28 : des += str_max[dimension-1] + ")";
174 2 : } else if( gtype==fibonacci ) {
175 2 : std::string num; Tools::convert( npoints, num );
176 2 : des += "fibonacci grid of " + num + " points on spherical surface";
177 : }
178 30 : return des;
179 : }
180 :
181 155 : void GridVessel::resize() {
182 155 : plumed_massert( nper>0, "Number of datapoints at each grid point has not been set");
183 155 : resizeBuffer( getNumberOfBufferPoints()*nper + 1 + 2*getAction()->getNumberOfDerivatives() );
184 155 : setDataSize( npoints*nper ); forces.resize( npoints );
185 155 : if( active.size()!=npoints) active.resize( npoints, true );
186 155 : }
187 :
188 21240426 : 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 21240426 : unsigned index=indices[dimension-1];
192 63699056 : for(unsigned i=dimension-1; i>0; --i) {
193 42458019 : index=index*nbin[i-1]+indices[i-1];
194 : }
195 21241037 : return index;
196 : }
197 :
198 17871 : 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 70714 : for(unsigned i=0; i<dimension; ++i) {
201 52829 : indices[i]=std::floor( (point[i] - min[i])/dx[i] );
202 52842 : if( pbc[i] ) indices[i]=indices[i]%nbin[i];
203 7321 : else if( indices[i]>nbin[i] ) plumed_merror("point is outside grid range");
204 : }
205 17885 : }
206 :
207 8650 : unsigned GridVessel::getIndex( const std::vector<double>& point ) const {
208 : plumed_dbg_assert( gtype==flat && bounds_set && point.size()==dimension );
209 8650 : if( gtype==flat ) {
210 8650 : std::vector<unsigned> indices(dimension); getIndices( point, indices );
211 8651 : return getIndex( indices );
212 0 : } else if( gtype==fibonacci ) {
213 0 : return getFibonacciIndex( point );
214 : } else {
215 0 : plumed_error();
216 : }
217 : }
218 :
219 55 : unsigned GridVessel::getFibonacciIndex( const std::vector<double>& p ) const {
220 : plumed_dbg_assert( gtype==fibonacci );
221 : // Convert input point to coordinates on cylinder
222 55 : int k=2; double phi = atan2( p[2], p[0] ), sinthet2 = 1 - p[1]*p[1];
223 : // Calculate power to raise golden ratio
224 56 : if( sinthet2<epsilon ) { k = 2; }
225 : else {
226 56 : k = std::floor( std::log( npoints*pi*root5*sinthet2 ) / log_golden2 );
227 56 : if( k<2 ) k = 2;
228 : }
229 56 : double Fk = pow( golden, k ) / root5, F0 = std::round(Fk), F1 = std::round(Fk*golden);
230 113 : Matrix<double> B(2,2), invB(2,2); std::vector<double> thisp(3);
231 56 : B(0,0) = 2*pi*((F0+1)*igolden - std::floor((F0+1)*igolden)) - fib_increment;
232 56 : B(0,1) = 2*pi*((F1+1)*igolden - std::floor((F1+1)*igolden)) - fib_increment;
233 56 : B(1,0) = -2*F0/npoints; B(1,1) = -2*F1/npoints; Invert( B, invB );
234 113 : std::vector<double> vv(2), rc(2); vv[0]=-phi; vv[1] = p[1] - fib_shift;
235 114 : mult( invB, vv, rc ); std::vector<int> c(2); c[0]=std::floor(rc[0]); c[1]=std::floor(rc[1]);
236 53 : unsigned outind; double mindist = 10000000.;
237 281 : for(int s=0; s<4; ++s) {
238 224 : double ttt, costheta = B(1,0)*( c[0] + s%2 ) + B(1,1)*( c[1] + s/2 ) + fib_shift;
239 225 : if( costheta>1 ) ttt=1; else if( costheta<-1 ) ttt=-1; else ttt=costheta;
240 225 : costheta = 2*ttt - costheta;
241 225 : unsigned i = std::floor( 0.5*npoints*(1+costheta) ); getFibonacciCoordinates( i, thisp );
242 228 : double dist=0; for(unsigned j=0; j<3; ++j) { double tmp=thisp[j]-p[j]; dist += tmp*tmp; }
243 228 : if( dist<mindist ) { outind = i; mindist = dist; }
244 : }
245 114 : return outind;
246 : }
247 :
248 108593189 : void GridVessel::convertIndexToIndices( const unsigned& index, const std::vector<unsigned>& nnbin, std::vector<unsigned>& indices ) const {
249 108593189 : plumed_dbg_assert( gtype==flat ); unsigned kk=index; indices[0]=index%nnbin[0];
250 216871541 : for(unsigned i=1; i<dimension-1; ++i) {
251 108430262 : kk=(kk-indices[i-1])/nnbin[i-1];
252 108131579 : indices[i]=kk%nnbin[i];
253 : }
254 108441279 : if(dimension>=2) { // I think this is wrong
255 108557734 : indices[dimension-1]=(kk-indices[dimension-2])/nnbin[dimension-2];
256 : }
257 108013279 : }
258 :
259 12147431 : void GridVessel::getIndices( const unsigned& index, std::vector<unsigned>& indices ) const {
260 12147431 : plumed_dbg_assert( gtype==flat ); convertIndexToIndices( index, nbin, indices );
261 12146524 : }
262 :
263 98562 : void GridVessel::getGridPointCoordinates( const unsigned& ipoint, std::vector<double>& x ) const {
264 98562 : std::vector<unsigned> tindices( dimension ); getGridPointCoordinates( ipoint, tindices, x );
265 98568 : }
266 :
267 11945828 : void GridVessel::getGridPointCoordinates( const unsigned& ipoint, std::vector<unsigned>& tindices, std::vector<double>& x ) const {
268 : plumed_dbg_assert( bounds_set && x.size()==dimension && tindices.size()==dimension && ipoint<npoints );
269 11945828 : if( gtype==flat ) {
270 11940717 : getFlatGridCoordinates( ipoint, tindices, x );
271 5111 : } else if( gtype==fibonacci ) {
272 5111 : getFibonacciCoordinates( ipoint, x );
273 : } else {
274 0 : plumed_error();
275 : }
276 11945208 : }
277 :
278 11949346 : void GridVessel::getFlatGridCoordinates( const unsigned& ipoint, std::vector<unsigned>& tindices, std::vector<double>& x ) const {
279 11949346 : plumed_dbg_assert( gtype==flat ); getIndices( ipoint, tindices );
280 11946811 : for(unsigned i=0; i<dimension; ++i) x[i] = min[i] + dx[i]*tindices[i];
281 11948513 : }
282 :
283 86805 : void GridVessel::getFibonacciCoordinates( const unsigned& ipoint, std::vector<double>& x ) const {
284 : plumed_dbg_assert( gtype==fibonacci );
285 86805 : x[1] = (ipoint*fib_offset) + fib_shift; double r = sqrt( 1 - x[1]*x[1] );
286 86812 : double phi = ipoint*fib_increment; x[0] = r*cos(phi); x[2] = r*sin(phi);
287 86775 : double norm=0; for(unsigned j=0; j<3; ++j) norm+=x[j]*x[j];
288 86804 : norm = sqrt(norm); for(unsigned j=0; j<3; ++j) x[j] = x[j] / norm;
289 86805 : }
290 :
291 8644 : void GridVessel::getSplineNeighbors( const unsigned& mybox, std::vector<unsigned>& mysneigh ) const {
292 8644 : plumed_dbg_assert( gtype==flat ); mysneigh.resize( static_cast<unsigned>(pow(2.,dimension)) );
293 :
294 8646 : std::vector<unsigned> tmp_indices( dimension );
295 17292 : std::vector<unsigned> my_indices( dimension );
296 8646 : getIndices( mybox, my_indices );
297 76612 : for(unsigned i=0; i<mysneigh.size(); ++i) {
298 67959 : unsigned tmp=i;
299 270925 : for(unsigned j=0; j<dimension; ++j) {
300 202963 : unsigned i0=tmp%2+my_indices[j]; tmp/=2;
301 203015 : if(!pbc[j] && i0==nbin[j]) getAction()->error("Extrapolating function on grid");
302 202973 : if( pbc[j] && i0==nbin[j]) i0=0;
303 203029 : tmp_indices[j]=i0;
304 : }
305 67962 : mysneigh[i]=getIndex( tmp_indices );
306 67954 : plumed_massert( active[mysneigh[i]], "inactive grid point required for splines");
307 8646 : }
308 8646 : }
309 :
310 295157 : double GridVessel::getGridElement( const unsigned& ipoint, const unsigned& jelement ) const {
311 295157 : plumed_assert( bounds_set && ipoint<npoints && jelement<nper && active[ipoint] );
312 295137 : return getDataElement( nper*ipoint + jelement );
313 : }
314 :
315 0 : void GridVessel::setGridElement( const unsigned& ipoint, const unsigned& jelement, const double& value ) {
316 : plumed_dbg_assert( bounds_set && ipoint<npoints && jelement<nper );
317 0 : setDataElement( nper*ipoint + jelement, value );
318 0 : }
319 :
320 5 : void GridVessel::addToGridElement( const unsigned& ipoint, const unsigned& jelement, const double& value ) {
321 : plumed_dbg_assert( bounds_set && ipoint<npoints && jelement<nper );
322 5 : addDataElement( nper*ipoint + jelement, value );
323 5 : }
324 :
325 9536 : void GridVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
326 : plumed_dbg_assert( myvals.getNumberOfValues()==(nper+1) );
327 9536 : for(unsigned i=0; i<nper; ++i) buffer[bufstart + nper*current + i] += myvals.get(i+1);
328 9578 : }
329 :
330 97 : void GridVessel::finish( const std::vector<double>& buffer ) {
331 97 : if( wasforced ) getFinalForces( buffer, finalForces );
332 77 : else AveragingVessel::finish( buffer );
333 97 : }
334 :
335 0 : double GridVessel::getGridElement( const std::vector<unsigned>& indices, const unsigned& jelement ) const {
336 0 : return getGridElement( getIndex( indices ), jelement );
337 : }
338 :
339 0 : void GridVessel::setGridElement( const std::vector<unsigned>& indices, const unsigned& jelement, const double& value ) {
340 0 : setGridElement( getIndex( indices ), jelement, value );
341 0 : }
342 :
343 166443 : std::vector<std::string> GridVessel::getMin() const {
344 166443 : plumed_dbg_assert( gtype==flat ); return str_min;
345 : }
346 :
347 166476 : std::vector<std::string> GridVessel::getMax() const {
348 166476 : plumed_dbg_assert( gtype==flat ); return str_max;
349 : }
350 :
351 167061 : std::vector<unsigned> GridVessel::getNbin() const {
352 : plumed_dbg_assert( gtype==flat && bounds_set );
353 167061 : std::vector<unsigned> ngrid( dimension );
354 497786 : for(unsigned i=0; i<dimension; ++i) {
355 330723 : if( !pbc[i] ) ngrid[i]=nbin[i] - 1;
356 3888 : else ngrid[i]=nbin[i];
357 : }
358 167063 : return ngrid;
359 : }
360 :
361 21415 : void GridVessel::getNeighbors( const std::vector<double>& pp, const std::vector<unsigned>& nneigh,
362 : unsigned& num_neighbors, std::vector<unsigned>& neighbors ) const {
363 : plumed_dbg_assert( bounds_set );
364 :
365 21415 : if( gtype == flat ) {
366 : plumed_dbg_assert( nneigh.size()==dimension );
367 21361 : std::vector<unsigned> indices( dimension );
368 21387 : for(unsigned i=0; i<dimension; ++i) indices[i] = std::floor( (pp[i]-min[i])/dx[i] );
369 21369 : getNeighbors( indices, nneigh, num_neighbors, neighbors );
370 54 : } else if( gtype == fibonacci ) {
371 54 : unsigned find = getFibonacciIndex( pp );
372 56 : num_neighbors = 1 + fib_nlist[find].size();
373 57 : if( neighbors.size()<num_neighbors ) neighbors.resize( num_neighbors );
374 56 : neighbors[0]=find; for(unsigned i=0; i<fib_nlist[find].size(); ++i) neighbors[1+i] = fib_nlist[find][i];
375 : } else {
376 0 : plumed_error();
377 : }
378 21428 : }
379 :
380 40784 : void GridVessel::getNeighbors( const std::vector<unsigned>& indices, const std::vector<unsigned>& nneigh,
381 : unsigned& num_neighbors, std::vector<unsigned>& neighbors ) const {
382 : plumed_dbg_assert( gtype==flat && bounds_set && nneigh.size()==dimension );
383 :
384 40784 : unsigned num_neigh=1; std::vector<unsigned> small_bin( dimension );
385 162773 : for(unsigned i=0; i<dimension; ++i) {
386 121979 : small_bin[i]=(2*nneigh[i]+1);
387 121985 : num_neigh *=small_bin[i];
388 : }
389 40794 : if( neighbors.size()!=num_neigh ) neighbors.resize( num_neigh );
390 :
391 40790 : num_neighbors=0;
392 81583 : std::vector<unsigned> s_indices(dimension), t_indices(dimension);
393 96530856 : for(unsigned index=0; index<num_neigh; ++index) {
394 96490063 : bool found=true;
395 96490063 : convertIndexToIndices( index, small_bin, s_indices );
396 385160918 : for(unsigned i=0; i<dimension; ++i) {
397 288714028 : int i0=s_indices[i]-nneigh[i]+indices[i];
398 289365148 : if(!pbc[i] && i0<0) found=false;
399 289365167 : if(!pbc[i] && i0>=nbin[i]) found=false;
400 289196995 : if( pbc[i] && i0<0) i0=nbin[i]-(-i0)%nbin[i];
401 288973654 : if( pbc[i] && i0>=nbin[i]) i0%=nbin[i];
402 288953906 : t_indices[i]=static_cast<unsigned>(i0);
403 : }
404 96446890 : if( found ) {
405 21083567 : neighbors[num_neighbors]=getIndex( t_indices );
406 21084883 : num_neighbors++;
407 : }
408 40793 : }
409 40793 : }
410 :
411 11 : void GridVessel::setCubeUnits( const double& units ) {
412 11 : plumed_dbg_assert( gtype==flat ); cube_units=units;
413 11 : }
414 :
415 8 : double GridVessel::getCubeUnits() const {
416 8 : plumed_dbg_assert( gtype==flat ); return cube_units;
417 : }
418 :
419 7 : std::string GridVessel::getInputString() const {
420 7 : std::string mstring="COORDINATES="+arg_names[0];
421 7 : for(unsigned i=1; i<dimension; ++i) mstring+="," + arg_names[i];
422 7 : if( gtype==flat ) {
423 7 : mstring += " TYPE=flat PBC=";
424 7 : if( pbc[0] ) mstring +="T";
425 5 : else mstring +="F";
426 11 : for(unsigned i=1; i<dimension; ++i) {
427 4 : if( pbc[i] ) mstring +=",T";
428 4 : else mstring +=",F";
429 : }
430 0 : } else if( gtype==fibonacci ) {
431 0 : mstring += " TYPE=fibonacci";
432 : }
433 7 : return mstring;
434 : }
435 :
436 8643 : double GridVessel::getValueAndDerivatives( const std::vector<double>& x, const unsigned& ind, std::vector<double>& der ) const {
437 : plumed_dbg_assert( gtype==flat && der.size()==dimension && !noderiv && ind<getNumberOfComponents() );
438 :
439 8643 : double X,X2,X3,value=0; der.assign(der.size(),0.0);
440 8645 : std::vector<double> fd(dimension);
441 17292 : std::vector<double> C(dimension);
442 17291 : std::vector<double> D(dimension);
443 17291 : std::vector<double> dder(dimension);
444 :
445 17292 : std::vector<unsigned> nindices(dimension);
446 17292 : std::vector<unsigned> indices(dimension); getIndices( x, indices );
447 17291 : std::vector<unsigned> neigh; getSplineNeighbors( getIndex(indices), neigh );
448 17291 : std::vector<double> xfloor(dimension); getFlatGridCoordinates( getIndex(x), nindices, xfloor );
449 :
450 : // loop over neighbors
451 76606 : for(unsigned int ipoint=0; ipoint<neigh.size(); ++ipoint) {
452 67949 : double grid=getGridElement(neigh[ipoint], ind*(1+dimension) );
453 67994 : for(unsigned j=0; j<dimension; ++j) dder[j] = getGridElement( neigh[ipoint], ind*(1+dimension) + 1 + j );
454 :
455 67959 : getIndices( neigh[ipoint], nindices );
456 67873 : double ff=1.0;
457 :
458 270889 : for(unsigned j=0; j<dimension; ++j) {
459 202875 : int x0=1;
460 202875 : if(nindices[j]==indices[j]) x0=0;
461 203043 : double ddx=dx[j];
462 202965 : X=fabs((x[j]-xfloor[j])/ddx-(double)x0);
463 202755 : X2=X*X;
464 202755 : X3=X2*X;
465 : double yy;
466 202755 : if(fabs(grid)<0.0000001) yy=0.0;
467 188938 : else yy=-dder[j]/grid;
468 203024 : C[j]=(1.0-3.0*X2+2.0*X3) - (x0?-1.0:1.0)*yy*(X-2.0*X2+X3)*ddx;
469 203079 : D[j]=( -6.0*X +6.0*X2) - (x0?-1.0:1.0)*yy*(1.0-4.0*X +3.0*X2)*ddx;
470 203054 : D[j]*=(x0?-1.0:1.0)/ddx;
471 203046 : ff*=C[j];
472 : }
473 271028 : for(unsigned j=0; j<dimension; ++j) {
474 203038 : fd[j]=D[j];
475 203024 : for(unsigned i=0; i<dimension; ++i) if(i!=j) fd[j]*=C[i];
476 : }
477 67990 : value+=grid*ff;
478 67990 : for(unsigned j=0; j<dimension; ++j) der[j]+=grid*fd[j];
479 : }
480 17291 : return value;
481 : }
482 :
483 3 : void GridVessel::activateThesePoints( const std::vector<bool>& to_activate ) {
484 : plumed_dbg_assert( to_activate.size()==npoints );
485 3 : for(unsigned i=0; i<npoints; ++i) active[i]=to_activate[i];
486 3 : }
487 :
488 20 : void GridVessel::setForce( const std::vector<double>& inforces ) {
489 : plumed_dbg_assert( inforces.size()==npoints );
490 20 : wasforced=true; for(unsigned i=0; i<npoints; ++i) forces[i]=inforces[i];
491 20 : }
492 :
493 11868312 : bool GridVessel::wasForced() const {
494 11868312 : return wasforced;
495 : }
496 :
497 20 : bool GridVessel::applyForce( std::vector<double>& fforces ) {
498 : plumed_dbg_assert( fforces.size()==finalForces.size() );
499 20 : if( !wasforced ) return false;
500 20 : for(unsigned i=0; i<finalForces.size(); ++i) fforces[i]=finalForces[i];
501 20 : wasforced=false; return true;
502 : }
503 :
504 : }
505 4821 : }
506 :
|
