1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 Copyright (c) 2015-2021 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 "HistogramOnGrid.h"
23 #include "tools/KernelFunctions.h"
24
25 namespace PLMD {
26 namespace gridtools {
27
registerKeywords(Keywords & keys)28 void HistogramOnGrid::registerKeywords( Keywords& keys ) {
29 GridVessel::registerKeywords( keys );
30 keys.add("compulsory","KERNEL","the type of kernel to use");
31 keys.add("compulsory","BANDWIDTH","the bandwidths");
32 keys.add("compulsory","CONCENTRATION","the concentration parameter for Von Mises-Fisher distributions");
33 }
34
HistogramOnGrid(const vesselbase::VesselOptions & da)35 HistogramOnGrid::HistogramOnGrid( const vesselbase::VesselOptions& da ):
36 GridVessel(da),
37 neigh_tot(0),
38 addOneKernelAtATime(false),
39 bandwidths(dimension),
40 discrete(false)
41 {
42 if( getType()=="flat" ) {
43 parse("KERNEL",kerneltype);
44 if( kerneltype=="discrete" || kerneltype=="DISCRETE" ) {
45 discrete=true; setNoDerivatives();
46 } else {
47 parseVector("BANDWIDTH",bandwidths);
48 }
49 } else {
50 parse("CONCENTRATION",von_misses_concentration);
51 von_misses_norm = von_misses_concentration / ( 4*pi*sinh( von_misses_concentration ) );
52 }
53 }
54
getFibonacciCutoff() const55 double HistogramOnGrid::getFibonacciCutoff() const {
56 return std::log( epsilon / von_misses_norm ) / von_misses_concentration;
57 }
58
noDiscreteKernels() const59 bool HistogramOnGrid::noDiscreteKernels() const {
60 return !discrete;
61 }
62
setBounds(const std::vector<std::string> & smin,const std::vector<std::string> & smax,const std::vector<unsigned> & nbins,const std::vector<double> & spacing)63 void HistogramOnGrid::setBounds( const std::vector<std::string>& smin, const std::vector<std::string>& smax,
64 const std::vector<unsigned>& nbins, const std::vector<double>& spacing ) {
65 GridVessel::setBounds( smin, smax, nbins, spacing );
66 if( !discrete ) {
67 std::vector<double> point(dimension,0);
68 KernelFunctions kernel( point, bandwidths, kerneltype, "DIAGONAL", 1.0 ); neigh_tot=1;
69 nneigh=kernel.getSupport( dx ); std::vector<double> support( kernel.getContinuousSupport() );
70 for(unsigned i=0; i<dimension; ++i) {
71 if( pbc[i] && 2*support[i]>getGridExtent(i) ) error("bandwidth is too large for periodic grid");
72 neigh_tot *= (2*nneigh[i]+1);
73 }
74 }
75 }
76
getKernelAndNeighbors(std::vector<double> & point,unsigned & num_neigh,std::vector<unsigned> & neighbors) const77 std::unique_ptr<KernelFunctions> HistogramOnGrid::getKernelAndNeighbors( std::vector<double>& point, unsigned& num_neigh, std::vector<unsigned>& neighbors ) const {
78 if( discrete ) {
79 plumed_assert( getType()=="flat" );
80 num_neigh=1; for(unsigned i=0; i<dimension; ++i) point[i] += 0.5*dx[i];
81 neighbors[0] = getIndex( point ); return NULL;
82 } else if( getType()=="flat" ) {
83 std::unique_ptr<KernelFunctions> kernel(new KernelFunctions( point, bandwidths, kerneltype, "DIAGONAL", 1.0 ));
84 // GB: Now values is destroyed when exiting this function.
85 // I think before there was a leak
86 std::vector<std::unique_ptr<Value>> values=getVectorOfValues();
87 kernel->normalize( Tools::unique2raw(values) ); getNeighbors( kernel->getCenter(), nneigh, num_neigh, neighbors );
88 return kernel;
89 } else if( getType()=="fibonacci" ) {
90 getNeighbors( point, nneigh, num_neigh, neighbors );
91 return NULL;
92 } else {
93 plumed_error();
94 }
95 return NULL;
96 }
97
getVectorOfValues() const98 std::vector<std::unique_ptr<Value>> HistogramOnGrid::getVectorOfValues() const {
99 std::vector<std::unique_ptr<Value>> vv;
100 for(unsigned i=0; i<dimension; ++i) {
101 vv.emplace_back(new Value());
102 if( pbc[i] ) vv[i]->setDomain( str_min[i], str_max[i] );
103 else vv[i]->setNotPeriodic();
104 }
105 return vv;
106 }
107
calculate(const unsigned & current,MultiValue & myvals,std::vector<double> & buffer,std::vector<unsigned> & der_list) const108 void HistogramOnGrid::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
109 if( addOneKernelAtATime ) {
110 plumed_dbg_assert( myvals.getNumberOfValues()==2 && !wasforced );
111 std::vector<double> der( dimension );
112 for(unsigned i=0; i<dimension; ++i) der[i]=myvals.getDerivative( 1, i );
113 accumulate( getAction()->getPositionInCurrentTaskList(current), myvals.get(0), myvals.get(1), der, buffer );
114 } else {
115 plumed_dbg_assert( myvals.getNumberOfValues()==dimension+2 );
116 std::vector<double> point( dimension ); double weight=myvals.get(0)*myvals.get( 1+dimension );
117 for(unsigned i=0; i<dimension; ++i) point[i]=myvals.get( 1+i );
118 // Get the kernel
119 unsigned num_neigh; std::vector<unsigned> neighbors(1);
120 std::vector<double> der( dimension );
121 std::unique_ptr<KernelFunctions> kernel=getKernelAndNeighbors( point, num_neigh, neighbors );
122
123 if( !kernel && getType()=="flat" ) {
124 plumed_dbg_assert( num_neigh==1 ); der.resize(0);
125 accumulate( neighbors[0], weight, 1.0, der, buffer );
126 } else {
127 double totwforce=0.0;
128 std::vector<double> intforce( 2*dimension, 0.0 );
129 std::vector<std::unique_ptr<Value>> vv( getVectorOfValues() );
130
131 double newval; std::vector<unsigned> tindices( dimension ); std::vector<double> xx( dimension );
132 for(unsigned i=0; i<num_neigh; ++i) {
133 unsigned ineigh=neighbors[i];
134 if( inactive( ineigh ) ) continue ;
135 getGridPointCoordinates( ineigh, tindices, xx );
136 if( kernel ) {
137 for(unsigned j=0; j<dimension; ++j) vv[j]->set(xx[j]);
138 newval = kernel->evaluate( Tools::unique2raw(vv), der, true );
139 } else {
140 // Evalulate dot product
141 double dot=0; for(unsigned j=0; j<dimension; ++j) { dot+=xx[j]*point[j]; der[j]=xx[j]; }
142 // Von misses distribution for concentration parameter
143 newval = von_misses_norm*exp( von_misses_concentration*dot );
144 // And final derivatives
145 for(unsigned j=0; j<dimension; ++j) der[j] *= von_misses_concentration*newval;
146 }
147 accumulate( ineigh, weight, newval, der, buffer );
148 if( wasForced() ) {
149 accumulateForce( ineigh, weight, der, intforce );
150 totwforce += myvals.get( 1+dimension )*newval*forces[ineigh];
151 }
152 }
153 if( wasForced() ) {
154 // Minus sign for kernel here as we are taking derivative with respect to position of center of
155 // kernel NOT derivative wrt to grid point
156 double pref = 1; if( kernel ) pref = -1;
157 unsigned nder = getAction()->getNumberOfDerivatives();
158 unsigned gridbuf = getNumberOfBufferPoints()*getNumberOfQuantities();
159 for(unsigned j=0; j<dimension; ++j) {
160 for(unsigned k=0; k<myvals.getNumberActive(); ++k) {
161 unsigned kder=myvals.getActiveIndex(k);
162 buffer[ bufstart + gridbuf + kder ] += pref*intforce[j]*myvals.getDerivative( j+1, kder );
163 }
164 }
165 // Accumulate the sum of all the weights
166 buffer[ bufstart + gridbuf + nder ] += myvals.get(0);
167 // Add the derivatives of the weights into the force -- this is separate loop as weights of all parts are considered together
168 for(unsigned k=0; k<myvals.getNumberActive(); ++k) {
169 unsigned kder=myvals.getActiveIndex(k);
170 buffer[ bufstart + gridbuf + kder ] += totwforce*myvals.getDerivative( 0, kder );
171 buffer[ bufstart + gridbuf + nder + 1 + kder ] += myvals.getDerivative( 0, kder );
172 }
173 }
174 }
175 }
176 }
177
accumulate(const unsigned & ipoint,const double & weight,const double & dens,const std::vector<double> & der,std::vector<double> & buffer) const178 void HistogramOnGrid::accumulate( const unsigned& ipoint, const double& weight, const double& dens, const std::vector<double>& der, std::vector<double>& buffer ) const {
179 buffer[bufstart+nper*ipoint] += weight*dens;
180 if( der.size()>0 ) for(unsigned j=0; j<dimension; ++j) buffer[bufstart+nper*ipoint + 1 + j] += weight*der[j];
181 }
182
accumulateForce(const unsigned & ipoint,const double & weight,const std::vector<double> & der,std::vector<double> & intforce) const183 void HistogramOnGrid::accumulateForce( const unsigned& ipoint, const double& weight, const std::vector<double>& der, std::vector<double>& intforce ) const {
184 for(unsigned j=0; j<der.size(); ++j) intforce[j] += forces[ipoint]*weight*der[j];
185 }
186
getFinalForces(const std::vector<double> & buffer,std::vector<double> & finalForces)187 void HistogramOnGrid::getFinalForces( const std::vector<double>& buffer, std::vector<double>& finalForces ) {
188 if( finalForces.size()!=getAction()->getNumberOfDerivatives() ) finalForces.resize( getAction()->getNumberOfDerivatives() );
189 // And the final force
190 unsigned nder = getAction()->getNumberOfDerivatives();
191 // Derivatives due to normalization
192 unsigned gridbuf = getNumberOfBufferPoints()*getNumberOfQuantities();
193 for(unsigned i=0; i<finalForces.size(); ++i) finalForces[i] = buffer[ bufstart + gridbuf + i ];
194 // Derivatives due to normalization
195 if( !noAverage() ) {
196 unsigned wderstart = bufstart + gridbuf + nder; double pref=0;
197 for(unsigned ipoint=0; ipoint<getNumberOfPoints(); ++ipoint) {
198 pref += forces[ipoint]*buffer[ bufstart + ipoint*nper ] / buffer[wderstart];
199 }
200 for(unsigned j=0; j<finalForces.size(); ++j) finalForces[j] -= pref*buffer[ wderstart + 1 + j ];
201 }
202 }
203
finish(const std::vector<double> & buffer)204 void HistogramOnGrid::finish( const std::vector<double>& buffer ) {
205 if( addOneKernelAtATime ) {
206 for(unsigned i=0; i<getAction()->getCurrentNumberOfActiveTasks(); ++i) {
207 for(unsigned j=0; j<nper; ++j) addDataElement( nper*getAction()->getActiveTask(i)+j, buffer[bufstart+i*nper+j] );
208 }
209 } else {
210 GridVessel::finish( buffer );
211 }
212 }
213
214 }
215 }
216