Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2020 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 "Colvar.h"
23 : #include "ActionRegister.h"
24 : #include "core/PlumedMain.h"
25 :
26 : #include <string>
27 : #include <cmath>
28 :
29 : using namespace std;
30 :
31 : namespace PLMD {
32 : namespace colvar {
33 :
34 : //+PLUMEDOC COLVAR GYRATION
35 : /*
36 : Calculate the radius of gyration, or other properties related to it.
37 :
38 : The different properties can be calculated and selected by the TYPE keyword:
39 : the Radius of Gyration (RADIUS); the Trace of the Gyration Tensor (TRACE);
40 : the Largest Principal Moment of the Gyration Tensor (GTPC_1); the middle Principal Moment of the Gyration Tensor (GTPC_2);
41 : the Smallest Principal Moment of the Gyration Tensor (GTPC_3); the Asphericiry (ASPHERICITY); the Acylindricity (ACYLINDRICITY);
42 : the Relative Shape Anisotropy (KAPPA2); the Smallest Principal Radius Of Gyration (GYRATION_3);
43 : the Middle Principal Radius of Gyration (GYRATION_2); the Largest Principal Radius of Gyration (GYRATION_1).
44 : A derivation of all these different variants can be found in \cite Vymetal:2011gv
45 :
46 : The radius of gyration is calculated using:
47 :
48 : \f[
49 : s_{\rm Gyr}=\Big ( \frac{\sum_i^{n}
50 : m_i \vert {r}_i -{r}_{\rm COM} \vert ^2 }{\sum_i^{n} m_i} \Big)^{1/2}
51 : \f]
52 :
53 : with the position of the center of mass \f${r}_{\rm COM}\f$ given by:
54 :
55 : \f[
56 : {r}_{\rm COM}=\frac{\sum_i^{n} {r}_i\ m_i }{\sum_i^{n} m_i}
57 : \f]
58 :
59 : The radius of gyration usually makes sense when atoms used for the calculation
60 : are all part of the same molecule.
61 : When running with periodic boundary conditions, the atoms should be
62 : in the proper periodic image. This is done automatically since PLUMED 2.2,
63 : by considering the ordered list of atoms and rebuilding the broken entities using a procedure
64 : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that
65 : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES
66 : which actually modifies the coordinates stored in PLUMED.
67 :
68 : In case you want to recover the old behavior you should use the NOPBC flag.
69 : In that case you need to take care that atoms are in the correct
70 : periodic image.
71 :
72 :
73 : \par Examples
74 :
75 : The following input tells plumed to print the radius of gyration of the
76 : chain containing atoms 10 to 20.
77 : \plumedfile
78 : GYRATION TYPE=RADIUS ATOMS=10-20 LABEL=rg
79 : PRINT ARG=rg STRIDE=1 FILE=colvar
80 : \endplumedfile
81 :
82 : */
83 : //+ENDPLUMEDOC
84 :
85 48 : class Gyration : public Colvar {
86 : private:
87 : enum CV_TYPE {RADIUS, TRACE, GTPC_1, GTPC_2, GTPC_3, ASPHERICITY, ACYLINDRICITY, KAPPA2, GYRATION_3, GYRATION_2, GYRATION_1, TOT};
88 : int rg_type;
89 : bool use_masses;
90 : bool nopbc;
91 : public:
92 : static void registerKeywords(Keywords& keys);
93 : explicit Gyration(const ActionOptions&);
94 : virtual void calculate();
95 : };
96 :
97 7406 : PLUMED_REGISTER_ACTION(Gyration,"GYRATION")
98 :
99 27 : void Gyration::registerKeywords(Keywords& keys) {
100 27 : Colvar::registerKeywords(keys);
101 108 : keys.add("atoms","ATOMS","the group of atoms that you are calculating the Gyration Tensor for");
102 135 : keys.add("compulsory","TYPE","RADIUS","The type of calculation relative to the Gyration Tensor you want to perform");
103 81 : keys.addFlag("MASS_WEIGHTED",false,"set the masses of all the atoms equal to one");
104 27 : }
105 :
106 26 : Gyration::Gyration(const ActionOptions&ao):
107 : PLUMED_COLVAR_INIT(ao),
108 : use_masses(false),
109 28 : nopbc(false)
110 : {
111 : std::vector<AtomNumber> atoms;
112 52 : parseAtomList("ATOMS",atoms);
113 25 : if(atoms.size()==0) error("no atoms specified");
114 50 : parseFlag("MASS_WEIGHTED",use_masses);
115 : std::string Type;
116 50 : parse("TYPE",Type);
117 50 : parseFlag("NOPBC",nopbc);
118 25 : checkRead();
119 :
120 25 : if(Type=="RADIUS") rg_type=RADIUS;
121 21 : else if(Type=="TRACE") rg_type=TRACE;
122 19 : else if(Type=="GTPC_1") rg_type=GTPC_1;
123 17 : else if(Type=="GTPC_2") rg_type=GTPC_2;
124 15 : else if(Type=="GTPC_3") rg_type=GTPC_3;
125 13 : else if(Type=="ASPHERICITY") rg_type=ASPHERICITY;
126 11 : else if(Type=="ACYLINDRICITY") rg_type=ACYLINDRICITY;
127 9 : else if(Type=="KAPPA2") rg_type=KAPPA2;
128 7 : else if(Type=="RGYR_3") rg_type=GYRATION_3;
129 5 : else if(Type=="RGYR_2") rg_type=GYRATION_2;
130 3 : else if(Type=="RGYR_1") rg_type=GYRATION_1;
131 2 : else error("Unknown GYRATION type");
132 :
133 24 : switch(rg_type)
134 : {
135 4 : case RADIUS: log.printf(" GYRATION RADIUS (Rg);"); break;
136 2 : case TRACE: log.printf(" TRACE OF THE GYRATION TENSOR;"); break;
137 2 : case GTPC_1: log.printf(" THE LARGEST PRINCIPAL MOMENT OF THE GYRATION TENSOR (S'_1);"); break;
138 2 : case GTPC_2: log.printf(" THE MIDDLE PRINCIPAL MOMENT OF THE GYRATION TENSOR (S'_2);"); break;
139 2 : case GTPC_3: log.printf(" THE SMALLEST PRINCIPAL MOMENT OF THE GYRATION TENSOR (S'_3);"); break;
140 2 : case ASPHERICITY: log.printf(" THE ASPHERICITY (b');"); break;
141 2 : case ACYLINDRICITY: log.printf(" THE ACYLINDRICITY (c');"); break;
142 2 : case KAPPA2: log.printf(" THE RELATIVE SHAPE ANISOTROPY (kappa^2);"); break;
143 2 : case GYRATION_3: log.printf(" THE SMALLEST PRINCIPAL RADIUS OF GYRATION (r_g3);"); break;
144 2 : case GYRATION_2: log.printf(" THE MIDDLE PRINCIPAL RADIUS OF GYRATION (r_g2);"); break;
145 2 : case GYRATION_1: log.printf(" THE LARGEST PRINCIPAL RADIUS OF GYRATION (r_g1);"); break;
146 : }
147 60 : if(rg_type>TRACE) log<<" Bibliography "<<plumed.cite("Jirí Vymetal and Jirí Vondrasek, J. Phys. Chem. A 115, 11455 (2011)");
148 24 : log<<"\n";
149 :
150 24 : log.printf(" atoms involved : ");
151 444 : for(unsigned i=0; i<atoms.size(); ++i) {
152 132 : if(i%25==0) log<<"\n";
153 264 : log.printf("%d ",atoms[i].serial());
154 : }
155 24 : log.printf("\n");
156 :
157 24 : if(nopbc) {
158 4 : log<<" PBC will be ignored\n";
159 : } else {
160 20 : log<<" broken molecules will be rebuilt assuming atoms are in the proper order\n";
161 : }
162 :
163 24 : addValueWithDerivatives(); setNotPeriodic();
164 24 : requestAtoms(atoms);
165 24 : }
166 :
167 1188 : void Gyration::calculate() {
168 :
169 1188 : if(!nopbc) makeWhole();
170 :
171 1188 : Vector com;
172 : double totmass = 0.;
173 1188 : if( use_masses ) {
174 0 : for(unsigned i=0; i<getNumberOfAtoms(); i++) {
175 0 : totmass+=getMass(i);
176 0 : com+=getMass(i)*getPosition(i);
177 : }
178 : } else {
179 1188 : totmass = static_cast<double>(getNumberOfAtoms());
180 19404 : for(unsigned i=0; i<getNumberOfAtoms(); i++) {
181 18216 : com+=getPosition(i);
182 : }
183 : }
184 1188 : com /= totmass;
185 :
186 1188 : double rgyr=0.;
187 1188 : vector<Vector> derivatives( getNumberOfAtoms() );
188 1188 : Tensor virial;
189 :
190 1188 : if(rg_type==RADIUS||rg_type==TRACE) {
191 788 : if( use_masses ) {
192 0 : for(unsigned i=0; i<getNumberOfAtoms(); i++) {
193 0 : const Vector diff = delta( com, getPosition(i) );
194 0 : rgyr += getMass(i)*diff.modulo2();
195 0 : derivatives[i] = diff*getMass(i);
196 0 : virial -= Tensor(getPosition(i),derivatives[i]);
197 : }
198 : } else {
199 15004 : for(unsigned i=0; i<getNumberOfAtoms(); i++) {
200 14216 : const Vector diff = delta( com, getPosition(i) );
201 7108 : rgyr += diff.modulo2();
202 14216 : derivatives[i] = diff;
203 7108 : virial -= Tensor(getPosition(i),derivatives[i]);
204 : }
205 : }
206 : double fact;
207 788 : if(rg_type==RADIUS) {
208 658 : rgyr = sqrt(rgyr/totmass);
209 658 : fact = 1./(rgyr*totmass);
210 : } else {
211 130 : rgyr = 2.*rgyr;
212 : fact = 4;
213 : }
214 788 : setValue(rgyr);
215 22112 : for(unsigned i=0; i<getNumberOfAtoms(); i++) setAtomsDerivatives(i,fact*derivatives[i]);
216 1576 : setBoxDerivatives(fact*virial);
217 : return;
218 : }
219 :
220 :
221 400 : Tensor3d gyr_tens;
222 : //calculate gyration tensor
223 400 : if( use_masses ) {
224 0 : for(unsigned i=0; i<getNumberOfAtoms(); i++) {
225 0 : const Vector diff=delta( com, getPosition(i) );
226 0 : gyr_tens[0][0]+=getMass(i)*diff[0]*diff[0];
227 0 : gyr_tens[1][1]+=getMass(i)*diff[1]*diff[1];
228 0 : gyr_tens[2][2]+=getMass(i)*diff[2]*diff[2];
229 0 : gyr_tens[0][1]+=getMass(i)*diff[0]*diff[1];
230 0 : gyr_tens[0][2]+=getMass(i)*diff[0]*diff[2];
231 0 : gyr_tens[1][2]+=getMass(i)*diff[1]*diff[2];
232 : }
233 : } else {
234 4400 : for(unsigned i=0; i<getNumberOfAtoms(); i++) {
235 4000 : const Vector diff=delta( com, getPosition(i) );
236 2000 : gyr_tens[0][0]+=diff[0]*diff[0];
237 2000 : gyr_tens[1][1]+=diff[1]*diff[1];
238 2000 : gyr_tens[2][2]+=diff[2]*diff[2];
239 2000 : gyr_tens[0][1]+=diff[0]*diff[1];
240 2000 : gyr_tens[0][2]+=diff[0]*diff[2];
241 2000 : gyr_tens[1][2]+=diff[1]*diff[2];
242 : }
243 : }
244 :
245 : // first make the matrix symmetric
246 400 : gyr_tens[1][0] = gyr_tens[0][1];
247 400 : gyr_tens[2][0] = gyr_tens[0][2];
248 400 : gyr_tens[2][1] = gyr_tens[1][2];
249 400 : Tensor3d ttransf,transf;
250 400 : Vector princ_comp,prefactor;
251 : //diagonalize gyration tensor
252 400 : diagMatSym(gyr_tens, princ_comp, ttransf);
253 400 : transf=transpose(ttransf);
254 : //sort eigenvalues and eigenvectors
255 400 : if (princ_comp[0]<princ_comp[1]) {
256 400 : double tmp=princ_comp[0]; princ_comp[0]=princ_comp[1]; princ_comp[1]=tmp;
257 1600 : for (unsigned i=0; i<3; i++) {tmp=transf[i][0]; transf[i][0]=transf[i][1]; transf[i][1]=tmp;}
258 : }
259 400 : if (princ_comp[1]<princ_comp[2]) {
260 400 : double tmp=princ_comp[1]; princ_comp[1]=princ_comp[2]; princ_comp[2]=tmp;
261 1600 : for (unsigned i=0; i<3; i++) {tmp=transf[i][1]; transf[i][1]=transf[i][2]; transf[i][2]=tmp;}
262 : }
263 400 : if (princ_comp[0]<princ_comp[1]) {
264 400 : double tmp=princ_comp[0]; princ_comp[0]=princ_comp[1]; princ_comp[1]=tmp;
265 1600 : for (unsigned i=0; i<3; i++) {tmp=transf[i][0]; transf[i][0]=transf[i][1]; transf[i][1]=tmp;}
266 : }
267 : //calculate determinant of transformation matrix
268 : double det = determinant(transf);
269 : // trasformation matrix for rotation must have positive determinant, otherwise multiply one column by (-1)
270 400 : if(det<0) {
271 1600 : for(unsigned j=0; j<3; j++) transf[j][2]=-transf[j][2];
272 400 : det = -det;
273 : }
274 400 : if(fabs(det-1.)>0.0001) error("Plumed Error: Cannot diagonalize gyration tensor\n");
275 400 : switch(rg_type) {
276 135 : case GTPC_1:
277 : case GTPC_2:
278 : case GTPC_3:
279 : {
280 135 : int pc_index = rg_type-2; //index of principal component
281 135 : rgyr=sqrt(princ_comp[pc_index]/totmass);
282 135 : double rm = rgyr*totmass;
283 135 : if(rm>1e-6) prefactor[pc_index]=1.0/rm; //some parts of derivate
284 : break;
285 : }
286 0 : case GYRATION_3: //the smallest principal radius of gyration
287 : {
288 0 : rgyr=sqrt((princ_comp[1]+princ_comp[2])/totmass);
289 0 : double rm = rgyr*totmass;
290 0 : if (rm>1e-6) {
291 0 : prefactor[1]=1.0/rm;
292 0 : prefactor[2]=1.0/rm;
293 : }
294 : break;
295 : }
296 130 : case GYRATION_2: //the midle principal radius of gyration
297 : {
298 130 : rgyr=sqrt((princ_comp[0]+princ_comp[2])/totmass);
299 130 : double rm = rgyr*totmass;
300 130 : if (rm>1e-6) {
301 130 : prefactor[0]=1.0/rm;
302 130 : prefactor[2]=1.0/rm;
303 : }
304 : break;
305 : }
306 0 : case GYRATION_1: //the largest principal radius of gyration
307 : {
308 0 : rgyr=sqrt((princ_comp[0]+princ_comp[1])/totmass);
309 0 : double rm = rgyr*totmass;
310 0 : if (rm>1e-6) {
311 0 : prefactor[0]=1.0/rm;
312 0 : prefactor[1]=1.0/rm;
313 : }
314 : break;
315 : }
316 5 : case ASPHERICITY:
317 : {
318 5 : rgyr=sqrt((princ_comp[0]-0.5*(princ_comp[1]+princ_comp[2]))/totmass);
319 5 : double rm = rgyr*totmass;
320 5 : if (rm>1e-6) {
321 5 : prefactor[0]= 1.0/rm;
322 5 : prefactor[1]=-0.5/rm;
323 5 : prefactor[2]=-0.5/rm;
324 : }
325 : break;
326 : }
327 0 : case ACYLINDRICITY:
328 : {
329 0 : rgyr=sqrt((princ_comp[1]-princ_comp[2])/totmass);
330 0 : double rm = rgyr*totmass;
331 0 : if (rm>1e-6) { //avoid division by zero
332 0 : prefactor[1]= 1.0/rm;
333 0 : prefactor[2]=-1.0/rm;
334 : }
335 : break;
336 : }
337 130 : case KAPPA2: // relative shape anisotropy
338 : {
339 130 : double trace = princ_comp[0]+princ_comp[1]+princ_comp[2];
340 130 : double tmp=princ_comp[0]*princ_comp[1]+ princ_comp[1]*princ_comp[2]+ princ_comp[0]*princ_comp[2];
341 130 : rgyr=1.0-3*(tmp/(trace*trace));
342 130 : if (rgyr>1e-6) {
343 130 : prefactor[0]= -3*((princ_comp[1]+princ_comp[2])-2*tmp/trace)/(trace*trace) *2;
344 130 : prefactor[1]= -3*((princ_comp[0]+princ_comp[2])-2*tmp/trace)/(trace*trace) *2;
345 130 : prefactor[2]= -3*((princ_comp[0]+princ_comp[1])-2*tmp/trace)/(trace*trace) *2;
346 : }
347 : break;
348 : }
349 : }
350 :
351 400 : if(use_masses) {
352 0 : for(unsigned i=0; i<getNumberOfAtoms(); i++) {
353 0 : Vector tX;
354 0 : const Vector diff=delta( com,getPosition(i) );
355 : //project atomic postional vectors to diagonalized frame
356 0 : for(unsigned j=0; j<3; j++) tX[j]=transf[0][j]*diff[0]+transf[1][j]*diff[1]+transf[2][j]*diff[2];
357 0 : for(unsigned j=0; j<3; j++) derivatives[i][j]=getMass(i)*(prefactor[0]*transf[j][0]*tX[0]+
358 0 : prefactor[1]*transf[j][1]*tX[1]+
359 0 : prefactor[2]*transf[j][2]*tX[2]);
360 0 : setAtomsDerivatives(i,derivatives[i]);
361 : }
362 : } else {
363 4400 : for(unsigned i=0; i<getNumberOfAtoms(); i++) {
364 2000 : Vector tX;
365 4000 : const Vector diff=delta( com,getPosition(i) );
366 : //project atomic postional vectors to diagonalized frame
367 8000 : for(unsigned j=0; j<3; j++) tX[j]=transf[0][j]*diff[0]+transf[1][j]*diff[1]+transf[2][j]*diff[2];
368 38000 : for(unsigned j=0; j<3; j++) derivatives[i][j]=prefactor[0]*transf[j][0]*tX[0]+
369 18000 : prefactor[1]*transf[j][1]*tX[1]+
370 12000 : prefactor[2]*transf[j][2]*tX[2];
371 2000 : setAtomsDerivatives(i,derivatives[i]);
372 : }
373 : }
374 :
375 400 : setValue(rgyr);
376 400 : setBoxDerivativesNoPbc();
377 : }
378 :
379 : }
380 5517 : }
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