Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2023 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 "core/ActionRegister.h"
23 : #include "core/PlumedMain.h"
24 : #include "core/Atoms.h"
25 : #include "tools/Units.h"
26 : #include "tools/Pbc.h"
27 : #include "ActionVolume.h"
28 :
29 : //+PLUMEDOC VOLUMES CAVITY
30 : /*
31 : This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a box defined by the positions of four atoms.
32 :
33 : Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three
34 : dimensional space. For example, if we have the coordination numbers for all the atoms in the
35 : system each coordination number can be assumed to lie on the position of the central atom.
36 : Because each base quantity can be assigned to a particular point in space we can calculate functions of the
37 : distribution of base quantities in a particular part of the box by using:
38 :
39 : \f[
40 : \overline{s}_{\tau} = \frac{ \sum_i f(s_i) w(u_i,v_i,w_i) }{ \sum_i w(u_i,v_i,w_i) }
41 : \f]
42 :
43 : where the sum is over the collective variables, \f$s_i\f$, each of which can be thought to be at \f$ (u_i,v_i,z_i)\f$.
44 : The function \f$(s_i)\f$ can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.
45 : Notice that here (at variance with what is done in \ref AROUND) we have transformed from the usual \f$(x_i,y_i,z_i)\f$
46 : position to a position in \f$ (u_i,v_i,z_i)\f$. This is done using a rotation matrix as follows:
47 :
48 : \f[
49 : \left(
50 : \begin{matrix}
51 : u_i \\
52 : v_i \\
53 : w_i
54 : \end{matrix}
55 : \right) = \mathbf{R}
56 : \left(
57 : \begin{matrix}
58 : x_i - x_o \\
59 : y_i - y_o \\
60 : z_i - z_o
61 : \end{matrix}
62 : \right)
63 : \f]
64 :
65 : where \f$\mathbf{R}\f$ is a rotation matrix that is calculated by constructing a set of three orthonormal vectors from the
66 : reference positions specified by the user. The first of these unit vectors points from the first reference atom to the second.
67 : The second is then the normal to the plane containing atoms 1,2 and 3 and the the third is the unit vector orthogonal to
68 : these first two vectors. \f$(x_o,y_o,z_o)\f$, meanwhile, specifies the position of the first reference atom.
69 :
70 : In the previous function \f$ w(u_i,v_i,w_i) \f$ measures whether or not the system is in the subregion of interest. It
71 : is equal to:
72 :
73 : \f[
74 : w(u_i,v_i,w_i) = \int_{0}^{u'} \int_{0}^{v'} \int_{0}^{w'} \textrm{d}u\textrm{d}v\textrm{d}w
75 : K\left( \frac{u - u_i}{\sigma} \right)K\left( \frac{v - v_i}{\sigma} \right)K\left( \frac{w - w_i}{\sigma} \right)
76 : \f]
77 :
78 : where \f$K\f$ is one of the kernel functions described on \ref histogrambead and \f$\sigma\f$ is a bandwidth parameter.
79 : The vector connecting atom 1 to atom 4 is used to define the extent of the box in each of the \f$u\f$, \f$v\f$ and \f$w\f$
80 : directions. Essentially the vector connecting atom 1 to atom 4 is projected onto the three unit vectors
81 : described above and the resulting projections determine the \f$u'\f$, \f$v'\f$ and \f$w'\f$ parameters in the above expression.
82 :
83 : \par Examples
84 :
85 : The following commands tell plumed to calculate the number of atoms in an ion channel in a protein.
86 : The extent of the channel is calculated from the positions of atoms 1, 4, 5 and 11. The final value will be labeled cav.
87 :
88 : \plumedfile
89 : d1: DENSITY SPECIES=20-500
90 : CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 LABEL=cav
91 : \endplumedfile
92 :
93 : The following command tells plumed to calculate the coordination numbers (with other water molecules) for the water
94 : molecules in the protein channel described above. The average coordination number and the number of coordination
95 : numbers more than 4 is then calculated. The values of these two quantities are given the labels cav.mean and cav.morethan
96 :
97 : \plumedfile
98 : d1: COORDINATIONNUMBER SPECIES=20-500 R_0=0.1
99 : CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 MEAN MORE_THAN={RATIONAL R_0=4} LABEL=cav
100 : \endplumedfile
101 :
102 : */
103 : //+ENDPLUMEDOC
104 :
105 : namespace PLMD {
106 : namespace multicolvar {
107 :
108 : class VolumeCavity : public ActionVolume {
109 : private:
110 : bool boxout;
111 : OFile boxfile;
112 : double lenunit;
113 : double jacob_det;
114 : double len_bi, len_cross, len_perp, sigma;
115 : Vector origin, bi, cross, perp;
116 : std::vector<Vector> dlbi, dlcross, dlperp;
117 : std::vector<Tensor> dbi, dcross, dperp;
118 : public:
119 : static void registerKeywords( Keywords& keys );
120 : explicit VolumeCavity(const ActionOptions& ao);
121 : ~VolumeCavity();
122 : void setupRegions() override;
123 : void update() override;
124 : double calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const override;
125 : };
126 :
127 13789 : PLUMED_REGISTER_ACTION(VolumeCavity,"CAVITY")
128 :
129 6 : void VolumeCavity::registerKeywords( Keywords& keys ) {
130 6 : ActionVolume::registerKeywords( keys );
131 12 : keys.add("atoms","ATOMS","the positions of four atoms that define spatial extent of the cavity");
132 12 : keys.addFlag("PRINT_BOX",false,"write out the positions of the corners of the box to an xyz file");
133 12 : keys.add("optional","FILE","the file on which to write out the box coordinates");
134 12 : keys.add("optional","UNITS","( default=nm ) the units in which to write out the corners of the box");
135 6 : }
136 :
137 2 : VolumeCavity::VolumeCavity(const ActionOptions& ao):
138 : Action(ao),
139 : ActionVolume(ao),
140 2 : boxout(false),
141 2 : lenunit(1.0),
142 2 : dlbi(4),
143 2 : dlcross(4),
144 2 : dlperp(4),
145 2 : dbi(3),
146 2 : dcross(3),
147 4 : dperp(3) {
148 : std::vector<AtomNumber> atoms;
149 4 : parseAtomList("ATOMS",atoms);
150 2 : if( atoms.size()!=4 ) {
151 0 : error("number of atoms should be equal to four");
152 : }
153 :
154 2 : log.printf(" boundaries for region are calculated based on positions of atoms : ");
155 10 : for(unsigned i=0; i<atoms.size(); ++i) {
156 8 : log.printf("%d ",atoms[i].serial() );
157 : }
158 2 : log.printf("\n");
159 :
160 2 : boxout=false;
161 2 : parseFlag("PRINT_BOX",boxout);
162 2 : if(boxout) {
163 : std::string boxfname;
164 0 : parse("FILE",boxfname);
165 0 : if(boxfname.length()==0) {
166 0 : error("no name for box file specified");
167 : }
168 : std::string unitname;
169 0 : parse("UNITS",unitname);
170 0 : if ( unitname.length()>0 ) {
171 0 : Units u;
172 0 : u.setLength(unitname);
173 0 : lenunit=plumed.getAtoms().getUnits().getLength()/u.getLength();
174 0 : } else {
175 : unitname="nm";
176 : }
177 0 : boxfile.link(*this);
178 0 : boxfile.open( boxfname );
179 0 : log.printf(" printing box coordinates on file named %s in %s \n",boxfname.c_str(), unitname.c_str() );
180 : }
181 :
182 2 : checkRead();
183 2 : requestAtoms(atoms);
184 : // We have to readd the dependency because requestAtoms removes it
185 2 : addDependency( getPntrToMultiColvar() );
186 2 : }
187 :
188 4 : VolumeCavity::~VolumeCavity() {
189 4 : }
190 :
191 1620 : void VolumeCavity::setupRegions() {
192 : // Make some space for things
193 1620 : Vector d1, d2, d3;
194 :
195 : // Retrieve the sigma value
196 1620 : sigma=getSigma();
197 : // Set the position of the origin
198 1620 : origin=getPosition(0);
199 :
200 : // Get two vectors
201 1620 : d1 = pbcDistance(origin,getPosition(1));
202 1620 : double d1l=d1.modulo();
203 1620 : d2 = pbcDistance(origin,getPosition(2));
204 :
205 : // Find the vector connecting the origin to the top corner of
206 : // the subregion
207 1620 : d3 = pbcDistance(origin,getPosition(3));
208 :
209 : // Create a set of unit vectors
210 1620 : bi = d1 / d1l;
211 1620 : len_bi=dotProduct( d3, bi );
212 1620 : cross = crossProduct( d1, d2 );
213 1620 : double crossmod=cross.modulo();
214 1620 : cross = cross / crossmod;
215 1620 : len_cross=dotProduct( d3, cross );
216 1620 : perp = crossProduct( cross, bi );
217 1620 : len_perp=dotProduct( d3, perp );
218 :
219 : // Calculate derivatives of box shape with respect to atoms
220 1620 : double d1l3=d1l*d1l*d1l;
221 1620 : dbi[0](0,0) = ( -(d1[1]*d1[1]+d1[2]*d1[2])/d1l3 ); // dx/dx
222 1620 : dbi[0](0,1) = ( d1[0]*d1[1]/d1l3 ); // dx/dy
223 1620 : dbi[0](0,2) = ( d1[0]*d1[2]/d1l3 ); // dx/dz
224 1620 : dbi[0](1,0) = ( d1[1]*d1[0]/d1l3 ); // dy/dx
225 1620 : dbi[0](1,1) = ( -(d1[0]*d1[0]+d1[2]*d1[2])/d1l3 ); // dy/dy
226 1620 : dbi[0](1,2) = ( d1[1]*d1[2]/d1l3 );
227 1620 : dbi[0](2,0) = ( d1[2]*d1[0]/d1l3 );
228 1620 : dbi[0](2,1) = ( d1[2]*d1[1]/d1l3 );
229 1620 : dbi[0](2,2) = ( -(d1[1]*d1[1]+d1[0]*d1[0])/d1l3 );
230 :
231 1620 : dbi[1](0,0) = ( (d1[1]*d1[1]+d1[2]*d1[2])/d1l3 );
232 1620 : dbi[1](0,1) = ( -d1[0]*d1[1]/d1l3 );
233 1620 : dbi[1](0,2) = ( -d1[0]*d1[2]/d1l3 );
234 1620 : dbi[1](1,0) = ( -d1[1]*d1[0]/d1l3 );
235 1620 : dbi[1](1,1) = ( (d1[0]*d1[0]+d1[2]*d1[2])/d1l3 );
236 1620 : dbi[1](1,2) = ( -d1[1]*d1[2]/d1l3 );
237 1620 : dbi[1](2,0) = ( -d1[2]*d1[0]/d1l3 );
238 1620 : dbi[1](2,1) = ( -d1[2]*d1[1]/d1l3 );
239 1620 : dbi[1](2,2) = ( (d1[1]*d1[1]+d1[0]*d1[0])/d1l3 );
240 1620 : dbi[2].zero();
241 :
242 1620 : Tensor tcderiv;
243 1620 : double cmod3=crossmod*crossmod*crossmod;
244 1620 : Vector ucross=crossmod*cross;
245 1620 : tcderiv.setCol( 0, crossProduct( d1, Vector(-1.0,0.0,0.0) ) + crossProduct( Vector(-1.0,0.0,0.0), d2 ) );
246 1620 : tcderiv.setCol( 1, crossProduct( d1, Vector(0.0,-1.0,0.0) ) + crossProduct( Vector(0.0,-1.0,0.0), d2 ) );
247 1620 : tcderiv.setCol( 2, crossProduct( d1, Vector(0.0,0.0,-1.0) ) + crossProduct( Vector(0.0,0.0,-1.0), d2 ) );
248 1620 : dcross[0](0,0)=( tcderiv(0,0)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 ); // dx/dx
249 1620 : dcross[0](0,1)=( tcderiv(0,1)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 ); // dx/dy
250 1620 : dcross[0](0,2)=( tcderiv(0,2)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 ); // dx/dz
251 1620 : dcross[0](1,0)=( tcderiv(1,0)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 ); // dy/dx
252 1620 : dcross[0](1,1)=( tcderiv(1,1)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 ); // dy/dy
253 1620 : dcross[0](1,2)=( tcderiv(1,2)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 ); // dy/dz
254 1620 : dcross[0](2,0)=( tcderiv(2,0)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 ); // dz/dx
255 1620 : dcross[0](2,1)=( tcderiv(2,1)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 ); // dz/dy
256 1620 : dcross[0](2,2)=( tcderiv(2,2)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 ); // dz/dz
257 :
258 1620 : tcderiv.setCol( 0, crossProduct( Vector(1.0,0.0,0.0), d2 ) );
259 1620 : tcderiv.setCol( 1, crossProduct( Vector(0.0,1.0,0.0), d2 ) );
260 1620 : tcderiv.setCol( 2, crossProduct( Vector(0.0,0.0,1.0), d2 ) );
261 1620 : dcross[1](0,0)=( tcderiv(0,0)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 ); // dx/dx
262 1620 : dcross[1](0,1)=( tcderiv(0,1)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 ); // dx/dy
263 1620 : dcross[1](0,2)=( tcderiv(0,2)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 ); // dx/dz
264 1620 : dcross[1](1,0)=( tcderiv(1,0)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 ); // dy/dx
265 1620 : dcross[1](1,1)=( tcderiv(1,1)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 ); // dy/dy
266 1620 : dcross[1](1,2)=( tcderiv(1,2)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 ); // dy/dz
267 1620 : dcross[1](2,0)=( tcderiv(2,0)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 ); // dz/dx
268 1620 : dcross[1](2,1)=( tcderiv(2,1)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 ); // dz/dy
269 1620 : dcross[1](2,2)=( tcderiv(2,2)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 ); // dz/dz
270 :
271 1620 : tcderiv.setCol( 0, crossProduct( d1, Vector(1.0,0.0,0.0) ) );
272 1620 : tcderiv.setCol( 1, crossProduct( d1, Vector(0.0,1.0,0.0) ) );
273 1620 : tcderiv.setCol( 2, crossProduct( d1, Vector(0.0,0.0,1.0) ) );
274 1620 : dcross[2](0,0)=( tcderiv(0,0)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 ); // dx/dx
275 1620 : dcross[2](0,1)=( tcderiv(0,1)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 ); // dx/dy
276 1620 : dcross[2](0,2)=( tcderiv(0,2)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 ); // dx/dz
277 1620 : dcross[2](1,0)=( tcderiv(1,0)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 ); // dy/dx
278 1620 : dcross[2](1,1)=( tcderiv(1,1)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 ); // dy/dy
279 1620 : dcross[2](1,2)=( tcderiv(1,2)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 ); // dy/dz
280 1620 : dcross[2](2,0)=( tcderiv(2,0)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 ); // dz/dx
281 1620 : dcross[2](2,1)=( tcderiv(2,1)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 ); // dz/dy
282 1620 : dcross[2](2,2)=( tcderiv(2,2)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 ); // dz/dz
283 :
284 1620 : dperp[0].setCol( 0, ( crossProduct( dcross[0].getCol(0), bi ) + crossProduct( cross, dbi[0].getCol(0) ) ) );
285 1620 : dperp[0].setCol( 1, ( crossProduct( dcross[0].getCol(1), bi ) + crossProduct( cross, dbi[0].getCol(1) ) ) );
286 1620 : dperp[0].setCol( 2, ( crossProduct( dcross[0].getCol(2), bi ) + crossProduct( cross, dbi[0].getCol(2) ) ) );
287 :
288 1620 : dperp[1].setCol( 0, ( crossProduct( dcross[1].getCol(0), bi ) + crossProduct( cross, dbi[1].getCol(0) ) ) );
289 1620 : dperp[1].setCol( 1, ( crossProduct( dcross[1].getCol(1), bi ) + crossProduct( cross, dbi[1].getCol(1) ) ) );
290 1620 : dperp[1].setCol( 2, ( crossProduct( dcross[1].getCol(2), bi ) + crossProduct( cross, dbi[1].getCol(2) ) ) );
291 :
292 1620 : dperp[2].setCol( 0, ( crossProduct( dcross[2].getCol(0), bi ) ) );
293 1620 : dperp[2].setCol( 1, ( crossProduct( dcross[2].getCol(1), bi ) ) );
294 1620 : dperp[2].setCol( 2, ( crossProduct( dcross[2].getCol(2), bi ) ) );
295 :
296 : // Ensure that all lengths are positive
297 1620 : if( len_bi<0 ) {
298 0 : bi=-bi;
299 0 : len_bi=-len_bi;
300 0 : for(unsigned i=0; i<3; ++i) {
301 0 : dbi[i]*=-1.0;
302 : }
303 : }
304 1620 : if( len_cross<0 ) {
305 0 : cross=-cross;
306 0 : len_cross=-len_cross;
307 0 : for(unsigned i=0; i<3; ++i) {
308 0 : dcross[i]*=-1.0;
309 : }
310 : }
311 1620 : if( len_perp<0 ) {
312 0 : perp=-perp;
313 0 : len_perp=-len_perp;
314 0 : for(unsigned i=0; i<3; ++i) {
315 0 : dperp[i]*=-1.0;
316 : }
317 : }
318 1620 : if( len_bi<=0 || len_cross<=0 || len_perp<=0 ) {
319 0 : plumed_merror("Invalid box coordinates");
320 : }
321 :
322 : // Now derivatives of lengths
323 1620 : Tensor dd3( Tensor::identity() );
324 1620 : dlbi[0] = matmul(d3,dbi[0]) - matmul(bi,dd3);
325 1620 : dlbi[1] = matmul(d3,dbi[1]);
326 1620 : dlbi[2] = matmul(d3,dbi[2]);
327 1620 : dlbi[3] = matmul(bi,dd3);
328 :
329 1620 : dlcross[0] = matmul(d3,dcross[0]) - matmul(cross,dd3);
330 1620 : dlcross[1] = matmul(d3,dcross[1]);
331 1620 : dlcross[2] = matmul(d3,dcross[2]);
332 1620 : dlcross[3] = matmul(cross,dd3);
333 :
334 1620 : dlperp[0] = matmul(d3,dperp[0]) - matmul(perp,dd3);
335 1620 : dlperp[1] = matmul(d3,dperp[1]);
336 1620 : dlperp[2] = matmul(d3,dperp[2]);
337 1620 : dlperp[3] = matmul(perp,dd3);
338 :
339 : // Need to calculate the jacobian
340 1620 : Tensor jacob;
341 1620 : jacob(0,0)=bi[0];
342 1620 : jacob(1,0)=bi[1];
343 1620 : jacob(2,0)=bi[2];
344 1620 : jacob(0,1)=cross[0];
345 1620 : jacob(1,1)=cross[1];
346 1620 : jacob(2,1)=cross[2];
347 1620 : jacob(0,2)=perp[0];
348 1620 : jacob(1,2)=perp[1];
349 1620 : jacob(2,2)=perp[2];
350 1620 : jacob_det = std::fabs( jacob.determinant() );
351 1620 : }
352 :
353 120 : void VolumeCavity::update() {
354 120 : if(boxout) {
355 0 : boxfile.printf("%d\n",8);
356 0 : const Tensor & t(getPbc().getBox());
357 0 : if(getPbc().isOrthorombic()) {
358 0 : boxfile.printf(" %f %f %f\n",lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2));
359 : } else {
360 0 : boxfile.printf(" %f %f %f %f %f %f %f %f %f\n",
361 0 : lenunit*t(0,0),lenunit*t(0,1),lenunit*t(0,2),
362 0 : lenunit*t(1,0),lenunit*t(1,1),lenunit*t(1,2),
363 0 : lenunit*t(2,0),lenunit*t(2,1),lenunit*t(2,2)
364 : );
365 : }
366 0 : boxfile.printf("AR %f %f %f \n",lenunit*origin[0],lenunit*origin[1],lenunit*origin[2]);
367 0 : Vector ut, vt, wt;
368 0 : ut = origin + len_bi*bi;
369 0 : vt = origin + len_cross*cross;
370 0 : wt = origin + len_perp*perp;
371 0 : boxfile.printf("AR %f %f %f \n",lenunit*(ut[0]), lenunit*(ut[1]), lenunit*(ut[2]) );
372 0 : boxfile.printf("AR %f %f %f \n",lenunit*(vt[0]), lenunit*(vt[1]), lenunit*(vt[2]) );
373 0 : boxfile.printf("AR %f %f %f \n",lenunit*(wt[0]), lenunit*(wt[1]), lenunit*(wt[2]) );
374 0 : boxfile.printf("AR %f %f %f \n",lenunit*(vt[0]+len_bi*bi[0]),
375 0 : lenunit*(vt[1]+len_bi*bi[1]),
376 0 : lenunit*(vt[2]+len_bi*bi[2]) );
377 0 : boxfile.printf("AR %f %f %f \n",lenunit*(ut[0]+len_perp*perp[0]),
378 0 : lenunit*(ut[1]+len_perp*perp[1]),
379 0 : lenunit*(ut[2]+len_perp*perp[2]) );
380 0 : boxfile.printf("AR %f %f %f \n",lenunit*(vt[0]+len_perp*perp[0]),
381 0 : lenunit*(vt[1]+len_perp*perp[1]),
382 0 : lenunit*(vt[2]+len_perp*perp[2]) );
383 0 : boxfile.printf("AR %f %f %f \n",lenunit*(vt[0]+len_perp*perp[0]+len_bi*bi[0]),
384 0 : lenunit*(vt[1]+len_perp*perp[1]+len_bi*bi[1]),
385 0 : lenunit*(vt[2]+len_perp*perp[2]+len_bi*bi[2]) );
386 : }
387 120 : }
388 :
389 1620 : double VolumeCavity::calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& rderiv ) const {
390 : // Setup the histogram bead
391 1620 : HistogramBead bead;
392 : bead.isNotPeriodic();
393 1620 : bead.setKernelType( getKernelType() );
394 :
395 : // Calculate distance of atom from origin of new coordinate frame
396 1620 : Vector datom=pbcDistance( origin, cpos );
397 : double ucontr, uder, vcontr, vder, wcontr, wder;
398 :
399 : // Calculate contribution from integral along bi
400 1620 : bead.set( 0, len_bi, sigma );
401 1620 : double upos=dotProduct( datom, bi );
402 1620 : ucontr=bead.calculate( upos, uder );
403 1620 : double udlen=bead.uboundDerivative( upos );
404 1620 : double uder2 = bead.lboundDerivative( upos ) - udlen;
405 :
406 : // Calculate contribution from integral along cross
407 1620 : bead.set( 0, len_cross, sigma );
408 1620 : double vpos=dotProduct( datom, cross );
409 1620 : vcontr=bead.calculate( vpos, vder );
410 1620 : double vdlen=bead.uboundDerivative( vpos );
411 1620 : double vder2 = bead.lboundDerivative( vpos ) - vdlen;
412 :
413 : // Calculate contribution from integral along perp
414 1620 : bead.set( 0, len_perp, sigma );
415 1620 : double wpos=dotProduct( datom, perp );
416 1620 : wcontr=bead.calculate( wpos, wder );
417 1620 : double wdlen=bead.uboundDerivative( wpos );
418 1620 : double wder2 = bead.lboundDerivative( wpos ) - wdlen;
419 :
420 1620 : Vector dfd;
421 1620 : dfd[0]=uder*vcontr*wcontr;
422 1620 : dfd[1]=ucontr*vder*wcontr;
423 1620 : dfd[2]=ucontr*vcontr*wder;
424 1620 : derivatives[0] = (dfd[0]*bi[0]+dfd[1]*cross[0]+dfd[2]*perp[0]);
425 1620 : derivatives[1] = (dfd[0]*bi[1]+dfd[1]*cross[1]+dfd[2]*perp[1]);
426 1620 : derivatives[2] = (dfd[0]*bi[2]+dfd[1]*cross[2]+dfd[2]*perp[2]);
427 1620 : double tot = ucontr*vcontr*wcontr*jacob_det;
428 :
429 : // Add reference atom derivatives
430 1620 : dfd[0]=uder2*vcontr*wcontr;
431 1620 : dfd[1]=ucontr*vder2*wcontr;
432 1620 : dfd[2]=ucontr*vcontr*wder2;
433 1620 : Vector dfld;
434 1620 : dfld[0]=udlen*vcontr*wcontr;
435 1620 : dfld[1]=ucontr*vdlen*wcontr;
436 1620 : dfld[2]=ucontr*vcontr*wdlen;
437 1620 : rderiv[0] = dfd[0]*matmul(datom,dbi[0]) + dfd[1]*matmul(datom,dcross[0]) + dfd[2]*matmul(datom,dperp[0]) +
438 3240 : dfld[0]*dlbi[0] + dfld[1]*dlcross[0] + dfld[2]*dlperp[0] - derivatives;
439 1620 : rderiv[1] = dfd[0]*matmul(datom,dbi[1]) + dfd[1]*matmul(datom,dcross[1]) + dfd[2]*matmul(datom,dperp[1]) +
440 3240 : dfld[0]*dlbi[1] + dfld[1]*dlcross[1] + dfld[2]*dlperp[1];
441 1620 : rderiv[2] = dfd[0]*matmul(datom,dbi[2]) + dfd[1]*matmul(datom,dcross[2]) + dfd[2]*matmul(datom,dperp[2]) +
442 3240 : dfld[0]*dlbi[2] + dfld[1]*dlcross[2] + dfld[2]*dlperp[2];
443 1620 : rderiv[3] = dfld[0]*dlbi[3] + dfld[1]*dlcross[3] + dfld[2]*dlperp[3];
444 :
445 1620 : vir.zero();
446 1620 : vir-=Tensor( cpos,derivatives );
447 8100 : for(unsigned i=0; i<4; ++i) {
448 6480 : vir -= Tensor( getPosition(i), rderiv[i] );
449 : }
450 :
451 1620 : return tot;
452 : }
453 :
454 : }
455 : }
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