Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2017-2023 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 "Colvar.h"
23 : #include "ActionRegister.h"
24 : #include "core/PlumedMain.h"
25 :
26 : namespace PLMD {
27 : namespace colvar {
28 :
29 : //+PLUMEDOC COLVAR DIMER
30 : /*
31 : This CV computes the dimer interaction energy for a collection of dimers.
32 :
33 : Each dimer represents an atom, as described in the dimer paper \cite dimer-metad.
34 : A system of N atoms is thus represented with N dimers, each
35 : Dimer being composed of two beads and eventually a virtual site representing its center of mass.
36 :
37 : A typical configuration for a dimerized system has the following ordering of atoms:
38 :
39 : 1 TAG1 X Y Z N atoms representing the first bead of each Dimer
40 :
41 : 2 TAG2 X Y Z
42 :
43 : ...
44 :
45 : N TAGN X Y Z N atoms representing the second bead of each Dimer
46 :
47 : N+1 TAG1 X Y Z
48 :
49 : N+2 TAG2 X Y Z
50 :
51 : ...
52 :
53 : 2N TAGN X Y Z Optional: N atoms representing the center of mass of each Dimer
54 :
55 : 2N+1 TAG1 X Y Z
56 :
57 : 2N+2 TAG2 X Y Z
58 :
59 : ...
60 :
61 : 3N TAGN X Y Z The configuration might go on with un-dimerized atoms (like a solvent)
62 :
63 : 3N+1
64 :
65 : 3N+2
66 :
67 : ...
68 :
69 :
70 : The Dimer interaction energy is defined between atoms x and N+x, for x=1,...,N and is
71 : characterized by two parameters Q and DSIGMA. These are passed as mandatory arguments along with
72 : the temperature of the system.
73 :
74 : \par Examples
75 :
76 : This line tells Plumed to compute the Dimer interaction energy for every dimer in the system.
77 :
78 : \plumedfile
79 : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002
80 : \endplumedfile
81 :
82 : If the simulation doesn't use virtual sites for the dimers centers of mass,
83 : Plumed has to know in order to determine correctly the total number of dimers from
84 : the total number of atoms:
85 : \plumedfile
86 : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002 NOVSITES
87 : \endplumedfile
88 :
89 : The NOVSITES flag is not required if one provides the atom serials of each Dimer. These are
90 : defined through two lists of atoms provided __instead__ of the ALLATOMS keyword.
91 : For example, the Dimer interaction energy of dimers specified by beads (1;23),(5;27),(7;29) is:
92 : \plumedfile
93 : dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002
94 : \endplumedfile
95 :
96 : Note that the ATOMS1,ATOMS2 keywords can support atom groups and
97 : interval notation as defined in \ref GROUP.
98 :
99 :
100 : In a Replica Exchange simulation the keyword DSIGMA can be used in two ways:
101 : if a plumed.n.dat file is provided for each replica, then DSIGMA is passed as a single value,
102 : like in the previous examples, and each replica will read its own DSIGMA value. If
103 : a unique plumed.dat is given, DSIGMA has to be a list containing a value for each replica.
104 : For 4 replicas:
105 : \plumedfile
106 : #SETTINGS NREPLICAS=4
107 : dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002,0.002,0.004,0.01
108 : \endplumedfile
109 :
110 :
111 : \par Usage of the CV
112 :
113 : The dimer interaction is not coded in the driver program and has to be inserted
114 : in the Hamiltonian of the system as a linear RESTRAINT (see \ref RESTRAINT):
115 : \plumedfile
116 : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002
117 : RESTRAINT ARG=dim AT=0 KAPPA=0 SLOPE=1 LABEL=dimforces
118 : \endplumedfile
119 :
120 : In a replica exchange, Metadynamics (see \ref METAD) can be used on the Dimer CV to reduce
121 : the number of replicas. Just keep in mind that METAD SIGMA values should be tuned
122 : in the standard way for each replica according to the value of DSIGMA.
123 : */
124 : //+ENDPLUMEDOC
125 :
126 : class Dimer : public Colvar {
127 : public:
128 : static void registerKeywords( Keywords& keys);
129 : explicit Dimer(const ActionOptions&);
130 : void calculate() override;
131 : protected:
132 : bool trimer,useall;
133 : int myrank, nranks;
134 : double qexp,temperature,beta,dsigma;
135 : std::vector<double> dsigmas;
136 : private:
137 : void consistencyCheck();
138 : std::vector<AtomNumber> usedatoms1;
139 : std::vector<AtomNumber> usedatoms2;
140 :
141 : };
142 :
143 13789 : PLUMED_REGISTER_ACTION(Dimer, "DIMER")
144 :
145 :
146 :
147 6 : void Dimer::registerKeywords( Keywords& keys) {
148 6 : Colvar::registerKeywords(keys);
149 :
150 12 : keys.add("compulsory","DSIGMA","The interaction strength of the dimer bond.");
151 12 : keys.add("compulsory", "Q", "The exponent of the dimer potential.");
152 12 : keys.add("compulsory", "TEMP", "The temperature (in Kelvin) of the simulation.");
153 12 : keys.add("atoms", "ATOMS1", "The list of atoms representing the first bead of each Dimer being considered by this CV. Used if ALLATOMS flag is missing");
154 12 : keys.add("atoms", "ATOMS2", "The list of atoms representing the second bead of each Dimer being considered by this CV. Used if ALLATOMS flag is missing");
155 12 : keys.addFlag("ALLATOMS", false, "Use EVERY atom of the system. Overrides ATOMS keyword.");
156 12 : keys.addFlag("NOVSITES", false, "If present the configuration is without virtual sites at the centroid positions.");
157 :
158 6 : }
159 :
160 :
161 :
162 2 : Dimer::Dimer(const ActionOptions& ao):
163 2 : PLUMED_COLVAR_INIT(ao) {
164 :
165 4 : log<<" Bibliography "<<plumed.cite("M Nava, F. Palazzesi, C. Perego and M. Parrinello, J. Chem. Theory Comput. 13, 425(2017)")<<"\n";
166 2 : parseVector("DSIGMA",dsigmas);
167 2 : parse("Q",qexp);
168 4 : parse("TEMP",temperature);
169 :
170 :
171 : std::vector<AtomNumber> atoms;
172 2 : parseFlag("ALLATOMS",useall);
173 2 : trimer=true;
174 : bool notrim;
175 2 : parseFlag("NOVSITES",notrim);
176 2 : trimer=!notrim;
177 :
178 2 : nranks=multi_sim_comm.Get_size();
179 2 : myrank=multi_sim_comm.Get_rank();
180 2 : if(dsigmas.size()==1) {
181 2 : dsigma=dsigmas[0];
182 : } else {
183 0 : dsigma=dsigmas[myrank];
184 : }
185 :
186 :
187 :
188 :
189 2 : if(useall) {
190 : // go with every atom in the system but not the virtuals...
191 : int natoms;
192 1 : if(trimer) {
193 1 : natoms= 2*getTotAtoms()/3;
194 : } else {
195 0 : natoms=getTotAtoms()/2;
196 : }
197 :
198 45 : for(unsigned int i=0; i<((unsigned int)natoms); i++) {
199 : AtomNumber ati;
200 : ati.setIndex(i);
201 44 : atoms.push_back(ati);
202 : }
203 : } else { // serials for the first beads of each dimer are given
204 1 : parseAtomList("ATOMS1",usedatoms1);
205 2 : parseAtomList("ATOMS2",usedatoms2);
206 :
207 : int isz1 = usedatoms1.size();
208 :
209 5 : for(unsigned int i=0; i<isz1; i++) {
210 : AtomNumber ati;
211 4 : ati.setIndex(usedatoms1[i].index());
212 4 : atoms.push_back(ati);
213 : }
214 :
215 : int isz2 = usedatoms2.size();
216 5 : for(unsigned int i=0; i<isz2; i++) {
217 : AtomNumber atip2;
218 4 : atip2.setIndex(usedatoms2[i].index());
219 4 : atoms.push_back(atip2);
220 : }
221 :
222 : }
223 2 : consistencyCheck();
224 2 : checkRead();
225 2 : beta = 1./(kBoltzmann*temperature);
226 :
227 2 : addValueWithDerivatives(); // allocate
228 2 : requestAtoms(atoms);
229 2 : setNotPeriodic();
230 2 : }
231 :
232 4 : void Dimer::calculate() {
233 4 : double cv_val=0;
234 4 : Tensor virial;
235 : std::vector<Vector> derivatives;
236 4 : std::vector<Vector> my_pos=getPositions();
237 4 : int atms = my_pos.size();
238 : std::vector<Vector> der_b2;
239 38 : for(int i=0; i<atms/2; i++) {
240 34 : Vector dist;
241 34 : dist = pbcDistance(my_pos[i],my_pos[i+atms/2]);
242 : double distquad=0;
243 136 : for(int j=0; j<3; j++) {
244 102 : distquad += dist[j]*dist[j];
245 : }
246 :
247 34 : double dsigquad = dsigma*dsigma;
248 34 : double fac1 = 1.0 + distquad/(2*qexp*dsigquad);
249 34 : double fac1qm1 = std::pow(fac1,qexp-1);
250 :
251 :
252 34 : cv_val += (fac1*fac1qm1-1.0)/beta;
253 34 : Vector der_val;
254 34 : Vector mder_val;
255 136 : for(int j=0; j<3; j++) {
256 102 : der_val[j] = -fac1qm1*dist[j]/(dsigquad*beta);
257 102 : mder_val[j]=-der_val[j];
258 : }
259 34 : derivatives.push_back(der_val);
260 34 : der_b2.push_back(mder_val);
261 :
262 : // virial part: each dimer contributes -x_{ij}*ds/dx_{ij} (s is the CV)
263 34 : double dfunc = fac1qm1/(beta*dsigquad);
264 34 : Vector dd(dfunc*dist);
265 34 : Tensor vv(dd,dist);
266 34 : virial -= vv;
267 :
268 : }
269 :
270 4 : derivatives.insert(derivatives.end(), der_b2.begin(), der_b2.end());
271 :
272 72 : for(unsigned int i=0; i<derivatives.size(); i++) {
273 68 : setAtomsDerivatives(i,derivatives[i]);
274 : }
275 :
276 4 : setValue(cv_val);
277 4 : setBoxDerivatives(virial);
278 :
279 4 : }
280 :
281 :
282 :
283 : /*****************
284 : There are some conditions that a valid input should satisfy.
285 : These are checked here and PLUMED error handlers are (eventually) called.
286 : ******************/
287 2 : void Dimer::consistencyCheck() {
288 2 : if(!useall && usedatoms1.size()!=usedatoms2.size()) {
289 0 : error("The provided atom lists are of different sizes.");
290 : }
291 :
292 2 : if(qexp<0.5 || qexp>1) {
293 0 : warning("Dimer CV is meant to be used with q-exponents between 0.5 and 1. We are not responsible for any black hole. :-)");
294 : }
295 :
296 2 : if(dsigma<0) {
297 0 : error("Please use positive sigma values for the Dimer strength constant");
298 : }
299 :
300 2 : if(temperature<0) {
301 0 : error("Please, use a positive value for the temperature...");
302 : }
303 :
304 : // if dsigmas has only one element means that either
305 : // you are using different plumed.x.dat files or a plumed.dat with a single replica
306 2 : if(dsigmas.size()!=nranks && dsigmas.size()!=1) {
307 0 : error("Mismatch between provided sigmas and number of replicas");
308 : }
309 :
310 2 : }
311 :
312 :
313 : }
314 : }
315 :
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