Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2016-2023 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 "MultiColvarBase.h"
23 : #include "AtomValuePack.h"
24 : #include "core/ActionRegister.h"
25 : #include "tools/KernelFunctions.h"
26 : #include "tools/RootFindingBase.h"
27 : #include "vesselbase/ValueVessel.h"
28 :
29 : //+PLUMEDOC COLVAR DISTANCE_FROM_CONTOUR
30 : /*
31 : Calculate the perpendicular distance from a Willard-Chandler dividing surface.
32 :
33 : Suppose that you have calculated a multicolvar. By doing so you have calculated a
34 : set of colvars, \f$s_i\f$, and each of these colvars has a well defined position in
35 : space \f$(x_i,y_i,z_i)\f$. You can use this information to calculate a phase-field
36 : model of the colvar density using:
37 :
38 : \f[
39 : p(x,y,x) = \sum_{i} s_i K\left[\frac{x-x_i}{\sigma_x},\frac{y-y_i}{\sigma_y},\frac{z-z_i}{\sigma_z} \right]
40 : \f]
41 :
42 : In this expression \f$\sigma_x, \sigma_y\f$ and \f$\sigma_z\f$ are bandwidth parameters and
43 : \f$K\f$ is one of the \ref kernelfunctions. This is what is done within \ref MULTICOLVARDENS
44 :
45 : The Willard-Chandler surface is a surface of constant density in the above phase field \f$p(x,y,z)\f$.
46 : In other words, it is a set of points, \f$(x',y',z')\f$, in your box which have:
47 :
48 : \f[
49 : p(x',y',z') = \rho
50 : \f]
51 :
52 : where \f$\rho\f$ is some target density. This action calculates the distance projected on the \f$x, y\f$ or
53 : \f$z\f$ axis between the position of some test particle and this surface of constant field density.
54 :
55 : \par Examples
56 :
57 : In this example atoms 2-100 are assumed to be concentrated along some part of the \f$z\f$ axis so that you
58 : an interface between a liquid/solid and the vapor. The quantity dc measures the distance between the
59 : surface at which the density of 2-100 atoms is equal to 0.2 and the position of the test particle atom 1.
60 :
61 : \plumedfile
62 : dens: DENSITY SPECIES=2-100
63 : dc: DISTANCE_FROM_CONTOUR DATA=dens ATOM=1 BANDWIDTH=0.5,0.5,0.5 DIR=z CONTOUR=0.2
64 : \endplumedfile
65 :
66 : */
67 : //+ENDPLUMEDOC
68 :
69 : namespace PLMD {
70 : namespace multicolvar {
71 :
72 : class DistanceFromContour : public MultiColvarBase {
73 : private:
74 : unsigned dir;
75 : bool derivTime;
76 : double rcut2;
77 : double contour;
78 : double pbc_param;
79 : std::string kerneltype;
80 : std::vector<std::unique_ptr<Value>> pval;
81 : std::vector<double> bw, pos1, pos2, dirv, dirv2;
82 : std::vector<double> forces;
83 : std::vector<unsigned> perp_dirs;
84 : vesselbase::ValueVessel* myvalue_vessel;
85 : vesselbase::ValueVessel* myderiv_vessel;
86 : RootFindingBase<DistanceFromContour> mymin;
87 : public:
88 : static void registerKeywords( Keywords& keys );
89 : explicit DistanceFromContour( const ActionOptions& );
90 3115 : bool isDensity() const override { return true; }
91 : void calculate() override;
92 : unsigned getNumberOfQuantities() const override;
93 0 : bool isPeriodic() override { return false; }
94 : double compute( const unsigned& tindex, AtomValuePack& myatoms ) const override;
95 : double getDifferenceFromContour( const std::vector<double>& x, std::vector<double>& der );
96 : // We need an apply action as we are using an independent value
97 : void apply() override;
98 : };
99 :
100 10421 : PLUMED_REGISTER_ACTION(DistanceFromContour,"DISTANCE_FROM_CONTOUR")
101 :
102 2 : void DistanceFromContour::registerKeywords( Keywords& keys ) {
103 2 : MultiColvarBase::registerKeywords( keys );
104 4 : keys.addOutputComponent("dist1","default","the distance between the reference atom and the nearest contour");
105 4 : keys.addOutputComponent("dist2","default","the distance between the reference atom and the other contour");
106 4 : keys.addOutputComponent("qdist","default","the differentiable (squared) distance between the two contours (see above)");
107 4 : keys.addOutputComponent("thickness","default","the distance between the two contours on the line from the reference atom");
108 4 : keys.add("compulsory","DATA","The input base multicolvar which is being used to calculate the contour");
109 4 : keys.add("atoms","ATOM","The atom whose perpendicular distance we are calculating from the contour");
110 4 : keys.add("compulsory","BANDWIDTH","the bandwidths for kernel density estimation");
111 4 : keys.add("compulsory","KERNEL","gaussian","the kernel function you are using. More details on the kernels available "
112 : "in plumed plumed can be found in \\ref kernelfunctions.");
113 4 : keys.add("compulsory","DIR","the direction perpendicular to the contour that you are looking for");
114 4 : keys.add("compulsory","CONTOUR","the value we would like for the contour");
115 4 : keys.add("compulsory","TOLERANCE","0.1","this parameter is used to manage periodic boundary conditions. The problem "
116 : "here is that we can be between contours even when we are not within the membrane "
117 : "because of periodic boundary conditions. When we are in the contour, however, we "
118 : "should have it so that the sums of the absolute values of the distances to the two "
119 : "contours is approximately the distance between the two contours. There can be numerical errors in these calculations, however, so "
120 : "we specify a small tolerance here");
121 2 : }
122 :
123 1 : DistanceFromContour::DistanceFromContour( const ActionOptions& ao ):
124 : Action(ao),
125 : MultiColvarBase(ao),
126 1 : derivTime(false),
127 1 : bw(3),
128 1 : pos1(3,0.0),
129 1 : pos2(3,0.0),
130 1 : dirv(3,0.0),
131 1 : dirv2(3,0.0),
132 1 : perp_dirs(2),
133 2 : mymin(this)
134 : {
135 : // Read in the multicolvar/atoms
136 1 : std::vector<AtomNumber> all_atoms; parse("TOLERANCE",pbc_param);
137 1 : bool read2 = parseMultiColvarAtomList("DATA", -1, all_atoms);
138 1 : if( !read2 ) error("missing DATA keyword");
139 1 : bool read1 = parseMultiColvarAtomList("ATOM", -1, all_atoms);
140 1 : if( !read1 ) error("missing ATOM keyword");
141 1 : if( all_atoms.size()!=1 ) error("should only be one atom specified");
142 : // Read in the center of the binding object
143 1 : log.printf(" computing distance of atom %d from contour \n",all_atoms[0].serial() );
144 1 : setupMultiColvarBase( all_atoms ); forces.resize( 3*getNumberOfAtoms() + 9 );
145 1 : if( getNumberOfBaseMultiColvars()!=1 ) error("should only be one input multicolvar");
146 :
147 : // Get the direction
148 2 : std::string ldir; parse("DIR",ldir );
149 1 : if( ldir=="x" ) { dir=0; perp_dirs[0]=1; perp_dirs[1]=2; dirv[0]=1; dirv2[0]=-1; }
150 1 : else if( ldir=="y" ) { dir=1; perp_dirs[0]=0; perp_dirs[1]=2; dirv[1]=1; dirv2[1]=-1; }
151 1 : else if( ldir=="z" ) { dir=2; perp_dirs[0]=0; perp_dirs[1]=1; dirv[2]=1; dirv2[2]=-1; }
152 0 : else error(ldir + " is not a valid direction use x, y or z");
153 :
154 : // Read in details of phase field construction
155 3 : parseVector("BANDWIDTH",bw); parse("KERNEL",kerneltype); parse("CONTOUR",contour);
156 1 : log.printf(" searching for contour in %s direction at %f in phase field for multicolvar %s \n",ldir.c_str(), contour, mybasemulticolvars[0]->getLabel().c_str() );
157 1 : log.printf(" constructing phase field using %s kernels with bandwidth (%f, %f, %f) \n",kerneltype.c_str(), bw[0], bw[1], bw[2] );
158 :
159 : // Now create a task list
160 2 : for(unsigned i=0; i<mybasemulticolvars[0]->getFullNumberOfTasks(); ++i) addTaskToList(i);
161 : // And a cutoff
162 1 : std::vector<double> pp( bw.size(),0 );
163 2 : KernelFunctions kernel( pp, bw, kerneltype, "DIAGONAL", 1.0 );
164 1 : double rcut = kernel.getCutoff( bw[0] );
165 3 : for(unsigned j=1; j<bw.size(); ++j) {
166 2 : if( kernel.getCutoff(bw[j])>rcut ) rcut=kernel.getCutoff(bw[j]);
167 : }
168 1 : rcut2=rcut*rcut;
169 : // Create the values
170 2 : addComponent("thickness"); componentIsNotPeriodic("thickness");
171 2 : addComponent("dist1"); componentIsNotPeriodic("dist1");
172 2 : addComponent("dist2"); componentIsNotPeriodic("dist2");
173 3 : addComponentWithDerivatives("qdist"); componentIsNotPeriodic("qdist");
174 : // Create sum vessels
175 1 : std::string fake_input; std::string deriv_input="COMPONENT=2";
176 1 : if( mybasemulticolvars[0]->isDensity() ) {
177 3 : addVessel( "SUM", fake_input, -1 ); addVessel( "SUM", deriv_input, -1 );
178 : } else {
179 0 : addVessel( "MEAN", fake_input, -1 ); addVessel( "MEAN", deriv_input, -1 );
180 : }
181 : // And convert to a value vessel so we can get the final value
182 1 : myvalue_vessel = dynamic_cast<vesselbase::ValueVessel*>( getPntrToVessel(0) );
183 1 : myderiv_vessel = dynamic_cast<vesselbase::ValueVessel*>( getPntrToVessel(1) );
184 1 : plumed_assert( myvalue_vessel && myderiv_vessel ); resizeFunctions();
185 :
186 : // Create the vector of values that holds the position
187 4 : for(unsigned i=0; i<3; ++i) pval.emplace_back( Tools::make_unique<Value>() );
188 2 : }
189 :
190 6230 : unsigned DistanceFromContour::getNumberOfQuantities() const {
191 6230 : return 3;
192 : }
193 :
194 137 : void DistanceFromContour::calculate() {
195 : // Check box is orthorhombic
196 137 : if( !getPbc().isOrthorombic() ) error("cell box must be orthorhombic");
197 :
198 : // The nanoparticle is at the origin of our coordinate system
199 137 : pos1[0]=pos1[1]=pos1[2]=0.0; pos2[0]=pos2[1]=pos2[2]=0.0;
200 :
201 : // Set bracket as center of mass of membrane in active region
202 137 : deactivateAllTasks();
203 137 : Vector myvec = getSeparation( getPosition(getNumberOfAtoms()-1), getPosition(0) ); pos2[dir]=myvec[dir];
204 137 : taskFlags[0]=1; double mindist = myvec.modulo2();
205 137 : for(unsigned j=1; j<getNumberOfAtoms()-1; ++j) {
206 0 : Vector distance=getSeparation( getPosition(getNumberOfAtoms()-1), getPosition(j) );
207 : double d2;
208 0 : if( (d2=distance[perp_dirs[0]]*distance[perp_dirs[0]])<rcut2 &&
209 0 : (d2+=distance[perp_dirs[1]]*distance[perp_dirs[1]])<rcut2 ) {
210 0 : d2+=distance[dir]*distance[dir];
211 0 : if( d2<mindist && std::fabs(distance[dir])>epsilon ) { pos2[dir]=distance[dir]; mindist = d2; }
212 0 : taskFlags[j]=1;
213 : }
214 : }
215 137 : lockContributors(); derivTime=false;
216 : // pos1 position of the nanoparticle, in the first time
217 : // pos2 is the position of the closer atom in the membrane with respect the nanoparticle
218 : // fa = distance between pos1 and the contour
219 : // fb = distance between pos2 and the contour
220 137 : std::vector<double> faked(3);
221 137 : double fa = getDifferenceFromContour( pos1, faked );
222 137 : double fb = getDifferenceFromContour( pos2, faked );
223 137 : if( fa*fb>0 ) {
224 0 : unsigned maxtries = std::floor( ( getBox()(dir,dir) ) / bw[dir] );
225 0 : for(unsigned i=0; i<maxtries; ++i) {
226 0 : double sign=(pos2[dir]>0)? -1 : +1; // If the nanoparticle is inside the membrane push it out
227 0 : pos1[dir] += sign*bw[dir]; fa = getDifferenceFromContour( pos1, faked );
228 0 : if( fa*fb<0 ) break;
229 : // if fa*fb is less than zero the new pos 1 is outside the contour
230 : }
231 : }
232 : // Set direction for contour search
233 137 : dirv[dir] = pos2[dir] - pos1[dir];
234 : // Bracket for second root starts in center of membrane
235 137 : double fc = getDifferenceFromContour( pos2, faked );
236 137 : if( fc*fb>0 ) {
237 : // first time is true, because fc=fb
238 : // push pos2 from its initial position inside the membrane towards the second contourn
239 137 : unsigned maxtries = std::floor( ( getBox()(dir,dir) ) / bw[dir] );
240 230 : for(unsigned i=0; i<maxtries; ++i) {
241 230 : double sign=(dirv[dir]>0)? +1 : -1;
242 230 : pos2[dir] += sign*bw[dir]; fc = getDifferenceFromContour( pos2, faked );
243 230 : if( fc*fb<0 ) break;
244 : }
245 137 : dirv2[dir] = ( pos1[dir] + dirv[dir] ) - pos2[dir];
246 : }
247 :
248 : // Now do a search for the two contours
249 137 : mymin.lsearch( dirv, pos1, &DistanceFromContour::getDifferenceFromContour );
250 : // Save the first value
251 137 : Vector root1; root1.zero(); root1[dir] = pval[dir]->get();
252 137 : mymin.lsearch( dirv2, pos2, &DistanceFromContour::getDifferenceFromContour );
253 : // Calculate the separation between the two roots using PBC
254 137 : Vector root2; root2.zero(); root2[dir]=pval[dir]->get();
255 137 : Vector sep = getSeparation( root1, root2 ); double spacing = std::fabs( sep[dir] ); plumed_assert( spacing>epsilon );
256 137 : getPntrToComponent("thickness")->set( spacing );
257 :
258 : // Make sure the sign is right
259 137 : double predir=(root1[dir]*root2[dir]<0)? -1 : 1;
260 : // This deals with periodic boundary conditions - if we are inside the membrane the sum of the absolute
261 : // distances from the contours should add up to the spacing. When this is not the case we must be outside
262 : // the contour
263 : // if( predir==-1 && (std::fabs(root1[dir])+std::fabs(root2[dir]))>(spacing+pbc_param) ) predir=1;
264 : // Set the final value to root that is closest to the "origin" = position of atom
265 137 : if( std::fabs(root1[dir])<std::fabs(root2[dir]) ) {
266 137 : getPntrToComponent("dist1")->set( predir*std::fabs(root1[dir]) );
267 274 : getPntrToComponent("dist2")->set( std::fabs(root2[dir]) );
268 : } else {
269 0 : getPntrToComponent("dist1")->set( predir*std::fabs(root2[dir]) );
270 0 : getPntrToComponent("dist2")->set( std::fabs(root1[dir]) );
271 : }
272 137 : getPntrToComponent("qdist")->set( root2[dir]*root1[dir] );
273 :
274 : // Now calculate the derivatives
275 137 : if( !doNotCalculateDerivatives() ) {
276 137 : Value* ival=myvalue_vessel->getFinalValue(); ival->clearDerivatives();
277 548 : std::vector<double> root1v(3); for(unsigned i=0; i<3; ++i) root1v[i]=root1[i];
278 137 : derivTime=true; std::vector<double> der(3); getDifferenceFromContour( root1v, der ); double prefactor;
279 137 : if( mybasemulticolvars[0]->isDensity() ) prefactor = root2[dir] / myderiv_vessel->getOutputValue();
280 0 : else plumed_error();
281 137 : Value* val=getPntrToComponent("qdist");
282 2192 : for(unsigned i=0; i<val->getNumberOfDerivatives(); ++i) val->setDerivative( i, -prefactor*ival->getDerivative(i) );
283 : ival->clearDerivatives();
284 548 : std::vector<double> root2v(3); for(unsigned i=0; i<3; ++i) root2v[i]=root2[i];
285 137 : getDifferenceFromContour( root2v, der );
286 137 : if( mybasemulticolvars[0]->isDensity() ) prefactor = root1[dir] / myderiv_vessel->getOutputValue();
287 0 : else plumed_error();
288 2192 : for(unsigned i=0; i<val->getNumberOfDerivatives(); ++i) val->addDerivative( i, -prefactor*ival->getDerivative(i) );
289 : }
290 137 : }
291 :
292 3115 : double DistanceFromContour::getDifferenceFromContour( const std::vector<double>& x, std::vector<double>& der ) {
293 : std::string min, max;
294 12460 : for(unsigned j=0; j<3; ++j) {
295 9345 : Tools::convert( -0.5*getBox()(j,j), min );
296 9345 : Tools::convert( +0.5*getBox()(j,j), max );
297 9345 : pval[j]->setDomain( min, max ); pval[j]->set( x[j] );
298 : }
299 3115 : runAllTasks();
300 6230 : return myvalue_vessel->getOutputValue() - contour;
301 : }
302 :
303 3115 : double DistanceFromContour::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
304 3115 : Vector distance = getSeparation( getPosition(getNumberOfAtoms()-1), myatoms.getPosition(0) );
305 12460 : std::vector<double> pp(3), der(3,0); for(unsigned j=0; j<3; ++j) pp[j] = distance[j];
306 :
307 : // convert the pointer once
308 3115 : auto pval_ptr=Tools::unique2raw(pval);
309 :
310 : // Now create the kernel and evaluate
311 3115 : KernelFunctions kernel( pp, bw, kerneltype, "DIAGONAL", 1.0 );
312 3115 : kernel.normalize( pval_ptr ); double newval = kernel.evaluate( pval_ptr, der, true );
313 :
314 3115 : if( mybasemulticolvars[0]->isDensity() ) {
315 3115 : if( !doNotCalculateDerivatives() && derivTime ) {
316 : MultiValue& myvals=myatoms.getUnderlyingMultiValue();
317 274 : Vector vder; unsigned basen=myvals.getNumberOfDerivatives() - 12;
318 1096 : for(unsigned i=0; i<3; ++i) {
319 822 : vder[i]=der[i]; myvals.addDerivative( 1, basen+i, vder[i] );
320 : }
321 274 : myatoms.setValue( 2, der[dir] );
322 274 : addAtomDerivatives( 1, 0, -vder, myatoms );
323 274 : myatoms.addBoxDerivatives( 1, Tensor(vder,distance) );
324 : }
325 3115 : myatoms.setValue( 0, 1.0 ); return newval;
326 : }
327 :
328 : // This does the stuff for averaging
329 : myatoms.setValue( 0, newval );
330 :
331 : // This gets the average if we are using a phase field
332 0 : std::vector<double> cvals( mybasemulticolvars[0]->getNumberOfQuantities() );
333 0 : mybasedata[0]->retrieveValueWithIndex( tindex, false, cvals );
334 0 : return newval*cvals[0]*cvals[1];
335 3115 : }
336 :
337 137 : void DistanceFromContour::apply() {
338 274 : if( getPntrToComponent("qdist")->applyForce( forces ) ) setForcesOnAtoms( forces );
339 137 : }
340 :
341 : }
342 : }
|
