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 "DistanceFromContourBase.h"
23 : #include "core/ActionRegister.h"
24 :
25 : //+PLUMEDOC COLVAR DISTANCE_FROM_CONTOUR
26 : /*
27 : Calculate the perpendicular distance from a Willard-Chandler dividing surface.
28 :
29 : Suppose that you have calculated a multicolvar. By doing so you have calculated a
30 : set of colvars, \f$s_i\f$, and each of these colvars has a well defined position in
31 : space \f$(x_i,y_i,z_i)\f$. You can use this information to calculate a phase-field
32 : model of the colvar density using:
33 :
34 : \f[
35 : 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]
36 : \f]
37 :
38 : In this expression \f$\sigma_x, \sigma_y\f$ and \f$\sigma_z\f$ are bandwidth parameters and
39 : \f$K\f$ is one of the \ref kernelfunctions. This is what is done within \ref MULTICOLVARDENS
40 :
41 : The Willard-Chandler surface is a surface of constant density in the above phase field \f$p(x,y,z)\f$.
42 : In other words, it is a set of points, \f$(x',y',z')\f$, in your box which have:
43 :
44 : \f[
45 : p(x',y',z') = \rho
46 : \f]
47 :
48 : where \f$\rho\f$ is some target density. This action calculates the distance projected on the \f$x, y\f$ or
49 : \f$z\f$ axis between the position of some test particle and this surface of constant field density.
50 :
51 : \par Examples
52 :
53 : In this example atoms 2-100 are assumed to be concentrated along some part of the \f$z\f$ axis so that you
54 : an interface between a liquid/solid and the vapor. The quantity dc measures the distance between the
55 : surface at which the density of 2-100 atoms is equal to 0.2 and the position of the test particle atom 1.
56 :
57 : \plumedfile
58 : dens: DENSITY SPECIES=2-100
59 : dc: DISTANCE_FROM_CONTOUR DATA=dens ATOM=1 BANDWIDTH=0.5,0.5,0.5 DIR=z CONTOUR=0.2
60 : \endplumedfile
61 :
62 : */
63 : //+ENDPLUMEDOC
64 :
65 : namespace PLMD {
66 : namespace contour {
67 :
68 : class DistanceFromContour : public DistanceFromContourBase {
69 : private:
70 : unsigned dir;
71 : double pbc_param;
72 : std::vector<double> pos1, pos2, dirv, dirv2;
73 : std::vector<unsigned> perp_dirs;
74 : std::vector<Vector> atom_deriv;
75 : public:
76 : static void registerKeywords( Keywords& keys );
77 : explicit DistanceFromContour( const ActionOptions& );
78 : void calculate() override;
79 : void evaluateDerivatives( const Vector& root1, const double& root2 );
80 : };
81 :
82 : PLUMED_REGISTER_ACTION(DistanceFromContour,"DISTANCE_FROM_CONTOUR")
83 :
84 3 : void DistanceFromContour::registerKeywords( Keywords& keys ) {
85 3 : DistanceFromContourBase::registerKeywords( keys );
86 6 : keys.addOutputComponent("dist1","default","scalar","the distance between the reference atom and the nearest contour");
87 6 : keys.addOutputComponent("dist2","default","scalar","the distance between the reference atom and the other contour");
88 6 : keys.addOutputComponent("qdist","default","scalar","the differentiable (squared) distance between the two contours (see above)");
89 6 : keys.addOutputComponent("thickness","default","scalar","the distance between the two contours on the line from the reference atom");
90 6 : keys.add("compulsory","DIR","the direction perpendicular to the contour that you are looking for");
91 6 : keys.add("compulsory","TOLERANCE","0.1","this parameter is used to manage periodic boundary conditions. The problem "
92 : "here is that we can be between contours even when we are not within the membrane "
93 : "because of periodic boundary conditions. When we are in the contour, however, we "
94 : "should have it so that the sums of the absolute values of the distances to the two "
95 : "contours is approximately the distance between the two contours. There can be numerical errors in these calculations, however, so "
96 : "we specify a small tolerance here");
97 3 : }
98 :
99 1 : DistanceFromContour::DistanceFromContour( const ActionOptions& ao ):
100 : Action(ao),
101 : DistanceFromContourBase(ao),
102 2 : pos1(3,0.0),
103 1 : pos2(3,0.0),
104 1 : dirv(3,0.0),
105 1 : dirv2(3,0.0),
106 1 : perp_dirs(2),
107 2 : atom_deriv(active_list.size())
108 : {
109 : // Get the direction
110 2 : std::string ldir; parse("DIR",ldir );
111 1 : if( ldir=="x" ) { dir=0; perp_dirs[0]=1; perp_dirs[1]=2; dirv[0]=1; dirv2[0]=-1; }
112 1 : else if( ldir=="y" ) { dir=1; perp_dirs[0]=0; perp_dirs[1]=2; dirv[1]=1; dirv2[1]=-1; }
113 1 : else if( ldir=="z" ) { dir=2; perp_dirs[0]=0; perp_dirs[1]=1; dirv[2]=1; dirv2[2]=-1; }
114 0 : else error(ldir + " is not a valid direction use x, y or z");
115 :
116 : // Read in the tolerance for the pbc parameter
117 2 : parse("TOLERANCE",pbc_param);
118 :
119 : std::vector<unsigned> shape;
120 : // Create the values
121 2 : addComponent("thickness", shape ); componentIsNotPeriodic("thickness");
122 2 : addComponent("dist1", shape ); componentIsNotPeriodic("dist1");
123 2 : addComponent("dist2", shape ); componentIsNotPeriodic("dist2");
124 3 : addComponentWithDerivatives("qdist", shape ); componentIsNotPeriodic("qdist");
125 1 : }
126 :
127 137 : void DistanceFromContour::calculate() {
128 : // Check box is orthorhombic
129 137 : if( !getPbc().isOrthorombic() ) error("cell box must be orthorhombic");
130 :
131 : // The nanoparticle is at the origin of our coordinate system
132 137 : pos1[0]=pos1[1]=pos1[2]=0.0; pos2[0]=pos2[1]=pos2[2]=0.0;
133 :
134 : // Set bracket as center of mass of membrane in active region
135 137 : Vector myvec = pbcDistance( getPosition(getNumberOfAtoms()-1), getPosition(0) ); pos2[dir]=myvec[dir];
136 137 : nactive=1; active_list[0]=0; double d2, mindist = myvec.modulo2();
137 137 : for(unsigned j=1; j<getNumberOfAtoms()-1; ++j) {
138 0 : Vector distance=pbcDistance( getPosition(getNumberOfAtoms()-1), getPosition(j) );
139 0 : if( (d2=distance[perp_dirs[0]]*distance[perp_dirs[0]])<rcut2 &&
140 0 : (d2+=distance[perp_dirs[1]]*distance[perp_dirs[1]])<rcut2 ) {
141 0 : d2+=distance[dir]*distance[dir];
142 0 : if( d2<mindist && fabs(distance[dir])>epsilon ) { pos2[dir]=distance[dir]; mindist = d2; }
143 0 : active_list[nactive]=j; nactive++;
144 : }
145 : }
146 : // pos1 position of the nanoparticle, in the first time
147 : // pos2 is the position of the closer atom in the membrane with respect the nanoparticle
148 : // fa = distance between pos1 and the contour
149 : // fb = distance between pos2 and the contour
150 137 : std::vector<double> faked(3);
151 137 : double fa = getDifferenceFromContour( pos1, faked );
152 137 : double fb = getDifferenceFromContour( pos2, faked );
153 137 : if( fa*fb>0 ) {
154 0 : unsigned maxtries = std::floor( ( getBox()(dir,dir) ) / bw[dir] );
155 0 : for(unsigned i=0; i<maxtries; ++i) {
156 0 : double sign=(pos2[dir]>0)? -1 : +1; // If the nanoparticle is inside the membrane push it out
157 0 : pos1[dir] += sign*bw[dir]; fa = getDifferenceFromContour( pos1, faked );
158 0 : if( fa*fb<0 ) break;
159 : // if fa*fb is less than zero the new pos 1 is outside the contour
160 : }
161 : }
162 : // Set direction for contour search
163 137 : dirv[dir] = pos2[dir] - pos1[dir];
164 : // Bracket for second root starts in center of membrane
165 137 : double fc = getDifferenceFromContour( pos2, faked );
166 137 : if( fc*fb>0 ) {
167 : // first time is true, because fc=fb
168 : // push pos2 from its initial position inside the membrane towards the second contourn
169 137 : unsigned maxtries = std::floor( ( getBox()(dir,dir) ) / bw[dir] );
170 230 : for(unsigned i=0; i<maxtries; ++i) {
171 230 : double sign=(dirv[dir]>0)? +1 : -1;
172 230 : pos2[dir] += sign*bw[dir]; fc = getDifferenceFromContour( pos2, faked );
173 230 : if( fc*fb<0 ) break;
174 : }
175 137 : dirv2[dir] = ( pos1[dir] + dirv[dir] ) - pos2[dir];
176 : }
177 :
178 : // Now do a search for the two contours
179 137 : findContour( dirv, pos1 );
180 : // Save the first value
181 137 : Vector root1; root1.zero(); root1[dir] = pval[dir];
182 137 : findContour( dirv2, pos2 );
183 : // Calculate the separation between the two roots using PBC
184 137 : Vector root2; root2.zero(); root2[dir] = pval[dir];
185 137 : Vector sep = pbcDistance( root1, root2 ); double spacing = fabs( sep[dir] ); plumed_assert( spacing>epsilon );
186 137 : getPntrToComponent("thickness")->set( spacing );
187 :
188 : // Make sure the sign is right
189 137 : double predir=(root1[dir]*root2[dir]<0)? -1 : 1;
190 : // This deals with periodic boundary conditions - if we are inside the membrane the sum of the absolute
191 : // distances from the contours should add up to the spacing. When this is not the case we must be outside
192 : // the contour
193 : // if( predir==-1 && (fabs(root1[dir])+fabs(root2[dir]))>(spacing+pbc_param) ) predir=1;
194 : // Set the final value to root that is closest to the "origin" = position of atom
195 137 : if( fabs(root1[dir])<fabs(root2[dir]) ) {
196 137 : getPntrToComponent("dist1")->set( predir*fabs(root1[dir]) );
197 274 : getPntrToComponent("dist2")->set( fabs(root2[dir]) );
198 : } else {
199 0 : getPntrToComponent("dist1")->set( predir*fabs(root2[dir]) );
200 0 : getPntrToComponent("dist2")->set( fabs(root1[dir]) );
201 : }
202 137 : getPntrToComponent("qdist")->set( root2[dir]*root1[dir] );
203 :
204 : // Now calculate the derivatives
205 137 : if( !doNotCalculateDerivatives() ) {
206 137 : evaluateDerivatives( root1, root2[dir] ); evaluateDerivatives( root2, root1[dir] );
207 : }
208 137 : }
209 :
210 274 : void DistanceFromContour::evaluateDerivatives( const Vector& root1, const double& root2 ) {
211 274 : if( getNumberOfArguments()>0 ) plumed_merror("derivatives for phase field distance from contour have not been implemented yet");
212 :
213 274 : Vector origind; origind.zero(); Tensor vir; vir.zero();
214 274 : double sumd = 0; std::vector<double> pp(3), ddd(3,0);
215 548 : for(unsigned i=0; i<nactive; ++i) {
216 274 : double newval = evaluateKernel( getPosition(active_list[i]), root1, ddd );
217 274 : Vector distance = pbcDistance( getPosition(getNumberOfAtoms()-1), getPosition(active_list[i]) );
218 :
219 274 : if( getNumberOfArguments()==1 ) {
220 : } else {
221 274 : sumd += ddd[dir];
222 1096 : for(unsigned j=0; j<3; ++j) atom_deriv[i][j] = -ddd[j];
223 274 : origind += -atom_deriv[i]; vir -= Tensor(atom_deriv[i],distance);
224 : }
225 : }
226 :
227 : // Add derivatives to atoms involved
228 274 : Value* val=getPntrToComponent("qdist"); double prefactor = root2 / sumd;
229 548 : for(unsigned i=0; i<nactive; ++i) {
230 274 : val->addDerivative( 3*active_list[i] + 0, -prefactor*atom_deriv[i][0] );
231 274 : val->addDerivative( 3*active_list[i] + 1, -prefactor*atom_deriv[i][1] );
232 274 : val->addDerivative( 3*active_list[i] + 2, -prefactor*atom_deriv[i][2] );
233 : }
234 :
235 : // Add derivatives to atoms at origin
236 274 : unsigned nbase = 3*(getNumberOfAtoms()-1);
237 274 : val->addDerivative( nbase, -prefactor*origind[0] ); nbase++;
238 274 : val->addDerivative( nbase, -prefactor*origind[1] ); nbase++;
239 274 : val->addDerivative( nbase, -prefactor*origind[2] ); nbase++;
240 :
241 : // Add derivatives to virial
242 3562 : for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) { val->addDerivative( nbase, -prefactor*vir(i,j) ); nbase++; }
243 274 : }
244 :
245 : }
246 : }
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