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 "core/ActionRegister.h"
24 : #include "core/PlumedMain.h"
25 : #include "tools/Communicator.h"
26 :
27 : namespace PLMD {
28 : namespace colvar {
29 :
30 : //+PLUMEDOC COLVAR DIMER
31 : /*
32 : This CV computes the dimer interaction energy for a collection of dimers.
33 :
34 : Each dimer represents an atom, as described in the dimer paper \cite dimer-metad.
35 : A system of N atoms is thus represented with N dimers, each
36 : Dimer being composed of two beads and eventually a virtual site representing its center of mass.
37 :
38 : A typical configuration for a dimerized system has the following ordering of atoms:
39 :
40 : 1 TAG1 X Y Z N atoms representing the first bead of each Dimer
41 :
42 : 2 TAG2 X Y Z
43 :
44 : ...
45 :
46 : N TAGN X Y Z N atoms representing the second bead of each Dimer
47 :
48 : N+1 TAG1 X Y Z
49 :
50 : N+2 TAG2 X Y Z
51 :
52 : ...
53 :
54 : 2N TAGN X Y Z Optional: N atoms representing the center of mass of each Dimer
55 :
56 : 2N+1 TAG1 X Y Z
57 :
58 : 2N+2 TAG2 X Y Z
59 :
60 : ...
61 :
62 : 3N TAGN X Y Z The configuration might go on with un-dimerized atoms (like a solvent)
63 :
64 : 3N+1
65 :
66 : 3N+2
67 :
68 : ...
69 :
70 :
71 : The Dimer interaction energy is defined between atoms x and N+x, for x=1,...,N and is
72 : characterized by two parameters Q and DSIGMA. These are passed as mandatory arguments along with
73 : the temperature of the system.
74 :
75 : \par Examples
76 :
77 : This line tells Plumed to compute the Dimer interaction energy for every dimer in the system.
78 :
79 : \plumedfile
80 : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002
81 : \endplumedfile
82 :
83 : If the simulation doesn't use virtual sites for the dimers centers of mass,
84 : Plumed has to know in order to determine correctly the total number of dimers from
85 : the total number of atoms:
86 : \plumedfile
87 : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002 NOVSITES
88 : \endplumedfile
89 :
90 : The NOVSITES flag is not required if one provides the atom serials of each Dimer. These are
91 : defined through two lists of atoms provided __instead__ of the ALLATOMS keyword.
92 : For example, the Dimer interaction energy of dimers specified by beads (1;23),(5;27),(7;29) is:
93 : \plumedfile
94 : dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002
95 : \endplumedfile
96 :
97 : Note that the ATOMS1,ATOMS2 keywords can support atom groups and
98 : interval notation as defined in \ref GROUP.
99 :
100 :
101 : In a Replica Exchange simulation the keyword DSIGMA can be used in two ways:
102 : if a plumed.n.dat file is provided for each replica, then DSIGMA is passed as a single value,
103 : like in the previous examples, and each replica will read its own DSIGMA value. If
104 : a unique plumed.dat is given, DSIGMA has to be a list containing a value for each replica.
105 : For 4 replicas:
106 : \plumedfile
107 : #SETTINGS NREPLICAS=4
108 : dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002,0.002,0.004,0.01
109 : \endplumedfile
110 :
111 :
112 : \par Usage of the CV
113 :
114 : The dimer interaction is not coded in the driver program and has to be inserted
115 : in the Hamiltonian of the system as a linear RESTRAINT (see \ref RESTRAINT):
116 : \plumedfile
117 : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002
118 : RESTRAINT ARG=dim AT=0 KAPPA=0 SLOPE=1 LABEL=dimforces
119 : \endplumedfile
120 :
121 : In a replica exchange, Metadynamics (see \ref METAD) can be used on the Dimer CV to reduce
122 : the number of replicas. Just keep in mind that METAD SIGMA values should be tuned
123 : in the standard way for each replica according to the value of DSIGMA.
124 : */
125 : //+ENDPLUMEDOC
126 :
127 : class Dimer : public Colvar {
128 : public:
129 : static void registerKeywords( Keywords& keys);
130 : explicit Dimer(const ActionOptions&);
131 : void calculate() override;
132 : protected:
133 : bool trimer,useall;
134 : int myrank, nranks;
135 : double qexp,temperature,beta,dsigma;
136 : std::vector<double> dsigmas;
137 : private:
138 : void consistencyCheck();
139 : std::vector<AtomNumber> usedatoms1;
140 : std::vector<AtomNumber> usedatoms2;
141 :
142 : };
143 :
144 : PLUMED_REGISTER_ACTION(Dimer, "DIMER")
145 :
146 :
147 :
148 10 : void Dimer::registerKeywords( Keywords& keys) {
149 10 : Colvar::registerKeywords(keys);
150 :
151 20 : keys.add("compulsory","DSIGMA","The interaction strength of the dimer bond.");
152 20 : keys.add("compulsory", "Q", "The exponent of the dimer potential.");
153 20 : keys.add("compulsory", "TEMP", "The temperature (in Kelvin) of the simulation.");
154 20 : 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");
155 20 : 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");
156 20 : keys.addFlag("ALLATOMS", false, "Use EVERY atom of the system. Overrides ATOMS keyword.");
157 20 : keys.addFlag("NOVSITES", false, "If present the configuration is without virtual sites at the centroid positions.");
158 10 : keys.setValueDescription("the dimer interaction energy");
159 10 : }
160 :
161 :
162 :
163 6 : Dimer::Dimer(const ActionOptions& ao):
164 6 : PLUMED_COLVAR_INIT(ao) {
165 :
166 12 : log<<" Bibliography "<<plumed.cite("M Nava, F. Palazzesi, C. Perego and M. Parrinello, J. Chem. Theory Comput. 13, 425(2017)")<<"\n";
167 6 : parseVector("DSIGMA",dsigmas);
168 6 : parse("Q",qexp);
169 12 : parse("TEMP",temperature);
170 :
171 :
172 : std::vector<AtomNumber> atoms;
173 6 : parseFlag("ALLATOMS",useall);
174 6 : trimer=true;
175 : bool notrim;
176 6 : parseFlag("NOVSITES",notrim);
177 6 : trimer=!notrim;
178 :
179 : // multi_sim_comm is valid only on rank 0 of each replica
180 6 : nranks=0;
181 6 : myrank=0;
182 6 : if(comm.Get_rank()==0) {
183 4 : nranks=multi_sim_comm.Get_size();
184 4 : myrank=multi_sim_comm.Get_rank();
185 : }
186 6 : comm.Bcast(nranks,0);
187 6 : comm.Bcast(myrank,0);
188 6 : if(dsigmas.size()==1) {
189 2 : dsigma=dsigmas[0];
190 : } else {
191 4 : dsigma=dsigmas[myrank];
192 : }
193 :
194 :
195 :
196 :
197 6 : if(useall) {
198 : // go with every atom in the system but not the virtuals...
199 : int natoms;
200 1 : if(trimer) {
201 1 : natoms= 2*getTotAtoms()/3;
202 : } else {
203 0 : natoms=getTotAtoms()/2;
204 : }
205 :
206 45 : for(unsigned int i=0; i<((unsigned int)natoms); i++) {
207 : AtomNumber ati;
208 : ati.setIndex(i);
209 44 : atoms.push_back(ati);
210 : }
211 : } else { // serials for the first beads of each dimer are given
212 5 : parseAtomList("ATOMS1",usedatoms1);
213 10 : parseAtomList("ATOMS2",usedatoms2);
214 :
215 : int isz1 = usedatoms1.size();
216 :
217 25 : for(unsigned int i=0; i<isz1; i++) {
218 : AtomNumber ati;
219 20 : ati.setIndex(usedatoms1[i].index());
220 20 : atoms.push_back(ati);
221 : }
222 :
223 : int isz2 = usedatoms2.size();
224 25 : for(unsigned int i=0; i<isz2; i++) {
225 : AtomNumber atip2;
226 20 : atip2.setIndex(usedatoms2[i].index());
227 20 : atoms.push_back(atip2);
228 : }
229 :
230 : }
231 6 : consistencyCheck();
232 6 : checkRead();
233 6 : beta = 1./(kBoltzmann*temperature);
234 :
235 6 : addValueWithDerivatives(); // allocate
236 6 : requestAtoms(atoms);
237 6 : setNotPeriodic();
238 6 : }
239 :
240 16 : void Dimer::calculate() {
241 16 : double cv_val=0;
242 16 : Tensor virial;
243 : std::vector<Vector> derivatives;
244 16 : std::vector<Vector> my_pos=getPositions();
245 16 : int atms = my_pos.size();
246 : std::vector<Vector> der_b2;
247 98 : for(int i=0; i<atms/2; i++) {
248 82 : Vector dist;
249 82 : dist = pbcDistance(my_pos[i],my_pos[i+atms/2]);
250 : double distquad=0;
251 328 : for(int j=0; j<3; j++) {
252 246 : distquad += dist[j]*dist[j];
253 : }
254 :
255 82 : double dsigquad = dsigma*dsigma;
256 82 : double fac1 = 1.0 + distquad/(2*qexp*dsigquad);
257 82 : double fac1qm1 = std::pow(fac1,qexp-1);
258 :
259 :
260 82 : cv_val += (fac1*fac1qm1-1.0)/beta;
261 82 : Vector der_val;
262 82 : Vector mder_val;
263 328 : for(int j=0; j<3; j++) {
264 246 : der_val[j] = -fac1qm1*dist[j]/(dsigquad*beta);
265 246 : mder_val[j]=-der_val[j];
266 : }
267 82 : derivatives.push_back(der_val);
268 82 : der_b2.push_back(mder_val);
269 :
270 : // virial part: each dimer contributes -x_{ij}*ds/dx_{ij} (s is the CV)
271 82 : double dfunc = fac1qm1/(beta*dsigquad);
272 82 : Vector dd(dfunc*dist);
273 82 : Tensor vv(dd,dist);
274 82 : virial -= vv;
275 :
276 : }
277 :
278 16 : derivatives.insert(derivatives.end(), der_b2.begin(), der_b2.end());
279 :
280 180 : for(unsigned int i=0; i<derivatives.size(); i++) {
281 164 : setAtomsDerivatives(i,derivatives[i]);
282 : }
283 :
284 16 : setValue(cv_val);
285 16 : setBoxDerivatives(virial);
286 :
287 16 : }
288 :
289 :
290 :
291 : /*****************
292 : There are some conditions that a valid input should satisfy.
293 : These are checked here and PLUMED error handlers are (eventually) called.
294 : ******************/
295 6 : void Dimer::consistencyCheck() {
296 6 : if(!useall && usedatoms1.size()!=usedatoms2.size()) {
297 0 : error("The provided atom lists are of different sizes.");
298 : }
299 :
300 6 : if(qexp<0.5 || qexp>1) {
301 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. :-)");
302 : }
303 :
304 6 : if(dsigma<0) {
305 0 : error("Please use positive sigma values for the Dimer strength constant");
306 : }
307 :
308 6 : if(temperature<0) {
309 0 : error("Please, use a positive value for the temperature...");
310 : }
311 :
312 : // if dsigmas has only one element means that either
313 : // you are using different plumed.x.dat files or a plumed.dat with a single replica
314 6 : if(dsigmas.size()!=nranks && dsigmas.size()!=1) {
315 0 : error("Mismatch between provided sigmas and number of replicas");
316 : }
317 :
318 6 : }
319 :
320 :
321 : }
322 : }
323 :
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