Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2019 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 "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
32 : variables for the atoms that lie in a box defined by the positions of four atoms.
33 :
34 : Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three
35 : dimensional space. For example, if we have the coordination numbers for all the atoms in the
36 : system each coordination number can be assumed to lie on the position of the central atom.
37 : Because each base quantity can be assigned to a particular point in space we can calculate functions of the
38 : distribution of base quantities in a particular part of the box by using:
39 :
40 : \f[
41 : \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) }
42 : \f]
43 :
44 : 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$.
45 : The function \f$(s_i)\f$ can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.
46 : Notice that here (at variance with what is done in \ref AROUND) we have transformed from the usual \f$(x_i,y_i,z_i)\f$
47 : position to a position in \f$ (u_i,v_i,z_i)\f$. This is done using a rotation matrix as follows:
48 :
49 : \f[
50 : \left(
51 : \begin{matrix}
52 : u_i \\
53 : v_i \\
54 : w_i
55 : \end{matrix}
56 : \right) = \mathbf{R}
57 : \left(
58 : \begin{matrix}
59 : x_i - x_o \\
60 : y_i - y_o \\
61 : z_i - z_o
62 : \end{matrix}
63 : \right)
64 : \f]
65 :
66 : where \f$\mathbf{R}\f$ is a rotation matrix that is calculated by constructing a set of three orthonormal vectors from the
67 : refererence positions specified by the user. The first of these unit vectors points from the first reference atom to the second.
68 : 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
69 : these first two vectors. \f$(x_o,y_o,z_o)\f$, meanwhile, specifies the position of the first reference atom.
70 :
71 : 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
72 : is equal to:
73 :
74 : \f[
75 : 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
76 : K\left( \frac{u - u_i}{\sigma} \right)K\left( \frac{v - v_i}{\sigma} \right)K\left( \frac{w - w_i}{\sigma} \right)
77 : \f]
78 :
79 : where \f$K\f$ is one of the kernel functions described on \ref histogrambead and \f$\sigma\f$ is a bandwidth parameter.
80 : 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$w\f$
81 : directions. Essentially the vector connecting atom 1 to atom 4 is projected onto the three unit vectors
82 : described above and the resulting projections determine the \f$u'\f$, \f$v'\f$ and \f$w'\f$ parameters in the above expression.
83 :
84 : \par Examples
85 :
86 : The following commands tell plumed to calculate the number of atoms in an ion chanel in a protein.
87 : The extent of the chanel is calculated from the positions of atoms 1, 4, 5 and 11. The final value will be labeled cav.
88 :
89 : \plumedfile
90 : d1: DENSITY SPECIES=20-500
91 : CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 LABEL=cav
92 : \endplumedfile
93 :
94 : The following command tells plumed to calculate the coordination numbers (with other water molecules) for the water
95 : molecules in the protein channel described above. The average coordination number and the number of coordination
96 : numbers more than 4 is then calculated. The values of these two quantities are given the labels cav.mean and cav.morethan
97 :
98 : \plumedfile
99 : d1: COORDINATIONNUMBER SPECIES=20-500
100 : CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 MEAN MORE_THAN={RATIONAL R_0=4} LABEL=cav
101 : \endplumedfile
102 :
103 : */
104 : //+ENDPLUMEDOC
105 :
106 : namespace PLMD {
107 : namespace multicolvar {
108 :
109 : class VolumeCavity : public ActionVolume {
110 : private:
111 : bool boxout;
112 : OFile boxfile;
113 : double lenunit;
114 : double jacob_det;
115 : double len_bi, len_cross, len_perp, sigma;
116 : Vector origin, bi, cross, perp;
117 : std::vector<Vector> dlbi, dlcross, dlperp;
118 : std::vector<Tensor> dbi, dcross, dperp;
119 : public:
120 : static void registerKeywords( Keywords& keys );
121 : explicit VolumeCavity(const ActionOptions& ao);
122 : ~VolumeCavity();
123 : void setupRegions();
124 : void update();
125 : double calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& refders ) const ;
126 : };
127 :
128 6454 : PLUMED_REGISTER_ACTION(VolumeCavity,"CAVITY")
129 :
130 3 : void VolumeCavity::registerKeywords( Keywords& keys ) {
131 3 : ActionVolume::registerKeywords( keys );
132 12 : keys.add("atoms","ATOMS","the positions of four atoms that define spatial extent of the cavity");
133 9 : keys.addFlag("PRINT_BOX",false,"write out the positions of the corners of the box to an xyz file");
134 12 : keys.add("optional","FILE","the file on which to write out the box coordinates");
135 12 : keys.add("optional","UNITS","( default=nm ) the units in which to write out the corners of the box");
136 3 : }
137 :
138 2 : VolumeCavity::VolumeCavity(const ActionOptions& ao):
139 : Action(ao),
140 : ActionVolume(ao),
141 : boxout(false),
142 : lenunit(1.0),
143 : dlbi(4),
144 : dlcross(4),
145 : dlperp(4),
146 : dbi(3),
147 : dcross(3),
148 2 : dperp(3)
149 : {
150 : std::vector<AtomNumber> atoms;
151 4 : parseAtomList("ATOMS",atoms);
152 2 : if( atoms.size()!=4 ) error("number of atoms should be equal to four");
153 :
154 2 : log.printf(" boundaries for region are calculated based on positions of atoms : ");
155 28 : for(unsigned i=0; i<atoms.size(); ++i) log.printf("%d ",atoms[i].serial() );
156 2 : log.printf("\n");
157 :
158 4 : boxout=false; parseFlag("PRINT_BOX",boxout);
159 2 : if(boxout) {
160 0 : std::string boxfname; parse("FILE",boxfname);
161 0 : if(boxfname.length()==0) error("no name for box file specified");
162 0 : std::string unitname; parse("UNITS",unitname);
163 0 : if ( unitname.length()>0 ) {
164 0 : Units u; u.setLength(unitname);
165 0 : lenunit=plumed.getAtoms().getUnits().getLength()/u.getLength();
166 : } else {
167 : unitname="nm";
168 : }
169 0 : boxfile.link(*this);
170 0 : boxfile.open( boxfname.c_str() );
171 0 : log.printf(" printing box coordinates on file named %s in %s \n",boxfname.c_str(), unitname.c_str() );
172 : }
173 :
174 2 : checkRead();
175 2 : requestAtoms(atoms);
176 : // We have to readd the dependency because requestAtoms removes it
177 2 : addDependency( getPntrToMultiColvar() );
178 2 : }
179 :
180 6 : VolumeCavity::~VolumeCavity() {
181 4 : }
182 :
183 1620 : void VolumeCavity::setupRegions() {
184 : // Make some space for things
185 1620 : Vector d1, d2, d3;
186 :
187 : // Retrieve the sigma value
188 1620 : sigma=getSigma();
189 : // Set the position of the origin
190 1620 : origin=getPosition(0);
191 :
192 : // Get two vectors
193 3240 : d1 = pbcDistance(origin,getPosition(1));
194 1620 : double d1l=d1.modulo();
195 3240 : d2 = pbcDistance(origin,getPosition(2));
196 :
197 : // Find the vector connecting the origin to the top corner of
198 : // the subregion
199 3240 : d3 = pbcDistance(origin,getPosition(3));
200 :
201 : // Create a set of unit vectors
202 1620 : bi = d1 / d1l; len_bi=dotProduct( d3, bi );
203 1620 : cross = crossProduct( d1, d2 ); double crossmod=cross.modulo();
204 1620 : cross = cross / crossmod; len_cross=dotProduct( d3, cross );
205 1620 : perp = crossProduct( cross, bi ); len_perp=dotProduct( d3, perp );
206 :
207 : // Calculate derivatives of box shape with respect to atoms
208 1620 : double d1l3=d1l*d1l*d1l;
209 3240 : dbi[0](0,0) = ( -(d1[1]*d1[1]+d1[2]*d1[2])/d1l3 ); // dx/dx
210 3240 : dbi[0](0,1) = ( d1[0]*d1[1]/d1l3 ); // dx/dy
211 3240 : dbi[0](0,2) = ( d1[0]*d1[2]/d1l3 ); // dx/dz
212 3240 : dbi[0](1,0) = ( d1[1]*d1[0]/d1l3 ); // dy/dx
213 3240 : dbi[0](1,1) = ( -(d1[0]*d1[0]+d1[2]*d1[2])/d1l3 ); // dy/dy
214 3240 : dbi[0](1,2) = ( d1[1]*d1[2]/d1l3 );
215 3240 : dbi[0](2,0) = ( d1[2]*d1[0]/d1l3 );
216 3240 : dbi[0](2,1) = ( d1[2]*d1[1]/d1l3 );
217 3240 : dbi[0](2,2) = ( -(d1[1]*d1[1]+d1[0]*d1[0])/d1l3 );
218 :
219 3240 : dbi[1](0,0) = ( (d1[1]*d1[1]+d1[2]*d1[2])/d1l3 );
220 3240 : dbi[1](0,1) = ( -d1[0]*d1[1]/d1l3 );
221 3240 : dbi[1](0,2) = ( -d1[0]*d1[2]/d1l3 );
222 3240 : dbi[1](1,0) = ( -d1[1]*d1[0]/d1l3 );
223 3240 : dbi[1](1,1) = ( (d1[0]*d1[0]+d1[2]*d1[2])/d1l3 );
224 3240 : dbi[1](1,2) = ( -d1[1]*d1[2]/d1l3 );
225 3240 : dbi[1](2,0) = ( -d1[2]*d1[0]/d1l3 );
226 3240 : dbi[1](2,1) = ( -d1[2]*d1[1]/d1l3 );
227 3240 : dbi[1](2,2) = ( (d1[1]*d1[1]+d1[0]*d1[0])/d1l3 );
228 1620 : dbi[2].zero();
229 :
230 1620 : Tensor tcderiv; double cmod3=crossmod*crossmod*crossmod; Vector ucross=crossmod*cross;
231 3240 : tcderiv.setCol( 0, crossProduct( d1, Vector(-1.0,0.0,0.0) ) + crossProduct( Vector(-1.0,0.0,0.0), d2 ) );
232 3240 : tcderiv.setCol( 1, crossProduct( d1, Vector(0.0,-1.0,0.0) ) + crossProduct( Vector(0.0,-1.0,0.0), d2 ) );
233 3240 : tcderiv.setCol( 2, crossProduct( d1, Vector(0.0,0.0,-1.0) ) + crossProduct( Vector(0.0,0.0,-1.0), d2 ) );
234 3240 : 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
235 3240 : 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
236 3240 : 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
237 3240 : 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
238 3240 : 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
239 3240 : 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
240 3240 : 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
241 3240 : 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
242 3240 : 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
243 :
244 1620 : tcderiv.setCol( 0, crossProduct( Vector(1.0,0.0,0.0), d2 ) );
245 1620 : tcderiv.setCol( 1, crossProduct( Vector(0.0,1.0,0.0), d2 ) );
246 1620 : tcderiv.setCol( 2, crossProduct( Vector(0.0,0.0,1.0), d2 ) );
247 3240 : 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
248 3240 : 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
249 3240 : 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
250 3240 : 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
251 3240 : 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
252 3240 : 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
253 3240 : 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
254 3240 : 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
255 3240 : 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
256 :
257 1620 : tcderiv.setCol( 0, crossProduct( d1, Vector(1.0,0.0,0.0) ) );
258 1620 : tcderiv.setCol( 1, crossProduct( d1, Vector(0.0,1.0,0.0) ) );
259 1620 : tcderiv.setCol( 2, crossProduct( d1, Vector(0.0,0.0,1.0) ) );
260 3240 : 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
261 3240 : 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
262 3240 : 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
263 3240 : 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
264 3240 : 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
265 3240 : 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
266 3240 : 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
267 3240 : 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
268 3240 : 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
269 :
270 3240 : dperp[0].setCol( 0, ( crossProduct( dcross[0].getCol(0), bi ) + crossProduct( cross, dbi[0].getCol(0) ) ) );
271 3240 : dperp[0].setCol( 1, ( crossProduct( dcross[0].getCol(1), bi ) + crossProduct( cross, dbi[0].getCol(1) ) ) );
272 3240 : dperp[0].setCol( 2, ( crossProduct( dcross[0].getCol(2), bi ) + crossProduct( cross, dbi[0].getCol(2) ) ) );
273 :
274 3240 : dperp[1].setCol( 0, ( crossProduct( dcross[1].getCol(0), bi ) + crossProduct( cross, dbi[1].getCol(0) ) ) );
275 3240 : dperp[1].setCol( 1, ( crossProduct( dcross[1].getCol(1), bi ) + crossProduct( cross, dbi[1].getCol(1) ) ) );
276 3240 : dperp[1].setCol( 2, ( crossProduct( dcross[1].getCol(2), bi ) + crossProduct( cross, dbi[1].getCol(2) ) ) );
277 :
278 1620 : dperp[2].setCol( 0, ( crossProduct( dcross[2].getCol(0), bi ) ) );
279 1620 : dperp[2].setCol( 1, ( crossProduct( dcross[2].getCol(1), bi ) ) );
280 1620 : dperp[2].setCol( 2, ( crossProduct( dcross[2].getCol(2), bi ) ) );
281 :
282 : // Ensure that all lengths are positive
283 1620 : if( len_bi<0 ) {
284 0 : bi=-bi; len_bi=-len_bi;
285 0 : for(unsigned i=0; i<3; ++i) dbi[i]*=-1.0;
286 : }
287 1620 : if( len_cross<0 ) {
288 0 : cross=-cross; len_cross=-len_cross;
289 0 : for(unsigned i=0; i<3; ++i) dcross[i]*=-1.0;
290 : }
291 1620 : if( len_perp<0 ) {
292 0 : perp=-perp; len_perp=-len_perp;
293 0 : for(unsigned i=0; i<3; ++i) dperp[i]*=-1.0;
294 : }
295 1620 : if( len_bi<=0 || len_cross<=0 || len_bi<=0 ) plumed_merror("Invalid box coordinates");
296 :
297 : // Now derivatives of lengths
298 1620 : Tensor dd3( Tensor::identity() );
299 4860 : dlbi[0] = matmul(d3,dbi[0]) - matmul(bi,dd3);
300 1620 : dlbi[1] = matmul(d3,dbi[1]);
301 1620 : dlbi[2] = matmul(d3,dbi[2]);
302 1620 : dlbi[3] = matmul(bi,dd3);
303 :
304 4860 : dlcross[0] = matmul(d3,dcross[0]) - matmul(cross,dd3);
305 1620 : dlcross[1] = matmul(d3,dcross[1]);
306 1620 : dlcross[2] = matmul(d3,dcross[2]);
307 1620 : dlcross[3] = matmul(cross,dd3);
308 :
309 4860 : dlperp[0] = matmul(d3,dperp[0]) - matmul(perp,dd3);
310 1620 : dlperp[1] = matmul(d3,dperp[1]);
311 1620 : dlperp[2] = matmul(d3,dperp[2]);
312 1620 : dlperp[3] = matmul(perp,dd3);
313 :
314 : // Need to calculate the jacobian
315 1620 : Tensor jacob;
316 1620 : jacob(0,0)=bi[0]; jacob(1,0)=bi[1]; jacob(2,0)=bi[2];
317 1620 : jacob(0,1)=cross[0]; jacob(1,1)=cross[1]; jacob(2,1)=cross[2];
318 1620 : jacob(0,2)=perp[0]; jacob(1,2)=perp[1]; jacob(2,2)=perp[2];
319 1620 : jacob_det = fabs( jacob.determinant() );
320 1620 : }
321 :
322 120 : void VolumeCavity::update() {
323 120 : if(boxout) {
324 0 : boxfile.printf("%d\n",8);
325 0 : const Tensor & t(getPbc().getBox());
326 0 : if(getPbc().isOrthorombic()) {
327 0 : boxfile.printf(" %f %f %f\n",lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2));
328 : } else {
329 0 : boxfile.printf(" %f %f %f %f %f %f %f %f %f\n",
330 0 : lenunit*t(0,0),lenunit*t(0,1),lenunit*t(0,2),
331 0 : lenunit*t(1,0),lenunit*t(1,1),lenunit*t(1,2),
332 0 : lenunit*t(2,0),lenunit*t(2,1),lenunit*t(2,2)
333 : );
334 : }
335 0 : boxfile.printf("AR %f %f %f \n",lenunit*origin[0],lenunit*origin[1],lenunit*origin[2]);
336 0 : Vector ut, vt, wt;
337 0 : ut = origin + len_bi*bi;
338 0 : vt = origin + len_cross*cross;
339 0 : wt = origin + len_perp*perp;
340 0 : boxfile.printf("AR %f %f %f \n",lenunit*(ut[0]), lenunit*(ut[1]), lenunit*(ut[2]) );
341 0 : boxfile.printf("AR %f %f %f \n",lenunit*(vt[0]), lenunit*(vt[1]), lenunit*(vt[2]) );
342 0 : boxfile.printf("AR %f %f %f \n",lenunit*(wt[0]), lenunit*(wt[1]), lenunit*(wt[2]) );
343 0 : boxfile.printf("AR %f %f %f \n",lenunit*(vt[0]+len_bi*bi[0]),
344 0 : lenunit*(vt[1]+len_bi*bi[1]),
345 0 : lenunit*(vt[2]+len_bi*bi[2]) );
346 0 : boxfile.printf("AR %f %f %f \n",lenunit*(ut[0]+len_perp*perp[0]),
347 0 : lenunit*(ut[1]+len_perp*perp[1]),
348 0 : lenunit*(ut[2]+len_perp*perp[2]) );
349 0 : boxfile.printf("AR %f %f %f \n",lenunit*(vt[0]+len_perp*perp[0]),
350 0 : lenunit*(vt[1]+len_perp*perp[1]),
351 0 : lenunit*(vt[2]+len_perp*perp[2]) );
352 0 : boxfile.printf("AR %f %f %f \n",lenunit*(vt[0]+len_perp*perp[0]+len_bi*bi[0]),
353 0 : lenunit*(vt[1]+len_perp*perp[1]+len_bi*bi[1]),
354 0 : lenunit*(vt[2]+len_perp*perp[2]+len_bi*bi[2]) );
355 : }
356 120 : }
357 :
358 1620 : double VolumeCavity::calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& rderiv ) const {
359 : // Setup the histogram bead
360 4860 : HistogramBead bead; bead.isNotPeriodic(); bead.setKernelType( getKernelType() );
361 :
362 : // Calculate distance of atom from origin of new coordinate frame
363 1620 : Vector datom=pbcDistance( origin, cpos );
364 : double ucontr, uder, vcontr, vder, wcontr, wder;
365 :
366 : // Calculate contribution from integral along bi
367 1620 : bead.set( 0, len_bi, sigma );
368 1620 : double upos=dotProduct( datom, bi );
369 1620 : ucontr=bead.calculate( upos, uder );
370 1620 : double udlen=bead.uboundDerivative( upos );
371 1620 : double uder2 = bead.lboundDerivative( upos ) - udlen;
372 :
373 : // Calculate contribution from integral along cross
374 1620 : bead.set( 0, len_cross, sigma );
375 1620 : double vpos=dotProduct( datom, cross );
376 1620 : vcontr=bead.calculate( vpos, vder );
377 1620 : double vdlen=bead.uboundDerivative( vpos );
378 1620 : double vder2 = bead.lboundDerivative( vpos ) - vdlen;
379 :
380 : // Calculate contribution from integral along perp
381 1620 : bead.set( 0, len_perp, sigma );
382 1620 : double wpos=dotProduct( datom, perp );
383 1620 : wcontr=bead.calculate( wpos, wder );
384 1620 : double wdlen=bead.uboundDerivative( wpos );
385 1620 : double wder2 = bead.lboundDerivative( wpos ) - wdlen;
386 :
387 1620 : Vector dfd; dfd[0]=uder*vcontr*wcontr; dfd[1]=ucontr*vder*wcontr; dfd[2]=ucontr*vcontr*wder;
388 1620 : derivatives[0] = (dfd[0]*bi[0]+dfd[1]*cross[0]+dfd[2]*perp[0]);
389 1620 : derivatives[1] = (dfd[0]*bi[1]+dfd[1]*cross[1]+dfd[2]*perp[1]);
390 1620 : derivatives[2] = (dfd[0]*bi[2]+dfd[1]*cross[2]+dfd[2]*perp[2]);
391 1620 : double tot = ucontr*vcontr*wcontr*jacob_det;
392 :
393 : // Add reference atom derivatives
394 1620 : dfd[0]=uder2*vcontr*wcontr; dfd[1]=ucontr*vder2*wcontr; dfd[2]=ucontr*vcontr*wder2;
395 1620 : Vector dfld; dfld[0]=udlen*vcontr*wcontr; dfld[1]=ucontr*vdlen*wcontr; dfld[2]=ucontr*vcontr*wdlen;
396 8100 : rderiv[0] = dfd[0]*matmul(datom,dbi[0]) + dfd[1]*matmul(datom,dcross[0]) + dfd[2]*matmul(datom,dperp[0]) +
397 9720 : dfld[0]*dlbi[0] + dfld[1]*dlcross[0] + dfld[2]*dlperp[0] - derivatives;
398 8100 : rderiv[1] = dfd[0]*matmul(datom,dbi[1]) + dfd[1]*matmul(datom,dcross[1]) + dfd[2]*matmul(datom,dperp[1]) +
399 9720 : dfld[0]*dlbi[1] + dfld[1]*dlcross[1] + dfld[2]*dlperp[1];
400 8100 : rderiv[2] = dfd[0]*matmul(datom,dbi[2]) + dfd[1]*matmul(datom,dcross[2]) + dfd[2]*matmul(datom,dperp[2]) +
401 9720 : dfld[0]*dlbi[2] + dfld[1]*dlcross[2] + dfld[2]*dlperp[2];
402 6480 : rderiv[3] = dfld[0]*dlbi[3] + dfld[1]*dlcross[3] + dfld[2]*dlperp[3];
403 :
404 1620 : vir.zero(); vir-=Tensor( cpos,derivatives );
405 14580 : for(unsigned i=0; i<4; ++i) {
406 12960 : vir -= Tensor( getPosition(i), rderiv[i] );
407 : }
408 :
409 1620 : return tot;
410 : }
411 :
412 : }
413 4839 : }
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