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 4 : void Dimer::registerKeywords( Keywords& keys) {
149 4 : Colvar::registerKeywords(keys);
150 :
151 8 : keys.add("compulsory","DSIGMA","The interaction strength of the dimer bond.");
152 8 : keys.add("compulsory", "Q", "The exponent of the dimer potential.");
153 8 : keys.add("compulsory", "TEMP", "The temperature (in Kelvin) of the simulation.");
154 8 : 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 8 : 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 8 : keys.addFlag("ALLATOMS", false, "Use EVERY atom of the system. Overrides ATOMS keyword.");
157 8 : keys.addFlag("NOVSITES", false, "If present the configuration is without virtual sites at the centroid positions.");
158 4 : keys.setValueDescription("the dimer interaction energy");
159 4 : }
160 :
161 :
162 :
163 2 : Dimer::Dimer(const ActionOptions& ao):
164 2 : PLUMED_COLVAR_INIT(ao)
165 : {
166 :
167 4 : log<<" Bibliography "<<plumed.cite("M Nava, F. Palazzesi, C. Perego and M. Parrinello, J. Chem. Theory Comput. 13, 425(2017)")<<"\n";
168 2 : parseVector("DSIGMA",dsigmas);
169 2 : parse("Q",qexp);
170 4 : parse("TEMP",temperature);
171 :
172 :
173 : std::vector<AtomNumber> atoms;
174 2 : parseFlag("ALLATOMS",useall);
175 2 : trimer=true;
176 : bool notrim;
177 2 : parseFlag("NOVSITES",notrim);
178 2 : trimer=!notrim;
179 :
180 2 : nranks=multi_sim_comm.Get_size();
181 2 : myrank=multi_sim_comm.Get_rank();
182 2 : if(dsigmas.size()==1)
183 2 : dsigma=dsigmas[0];
184 : else
185 0 : dsigma=dsigmas[myrank];
186 :
187 :
188 :
189 :
190 2 : if(useall)
191 : {
192 : // go with every atom in the system but not the virtuals...
193 : int natoms;
194 1 : if(trimer)
195 1 : natoms= 2*getTotAtoms()/3;
196 : else
197 0 : natoms=getTotAtoms()/2;
198 :
199 45 : for(unsigned int i=0; i<((unsigned int)natoms); i++)
200 : {
201 : AtomNumber ati;
202 : ati.setIndex(i);
203 44 : atoms.push_back(ati);
204 : }
205 : }
206 : else // serials for the first beads of each dimer are given
207 : {
208 1 : parseAtomList("ATOMS1",usedatoms1);
209 2 : parseAtomList("ATOMS2",usedatoms2);
210 :
211 : int isz1 = usedatoms1.size();
212 :
213 5 : for(unsigned int i=0; i<isz1; i++)
214 : {
215 : AtomNumber ati;
216 4 : ati.setIndex(usedatoms1[i].index());
217 4 : atoms.push_back(ati);
218 : }
219 :
220 : int isz2 = usedatoms2.size();
221 5 : for(unsigned int i=0; i<isz2; i++)
222 : {
223 : AtomNumber atip2;
224 4 : atip2.setIndex(usedatoms2[i].index());
225 4 : atoms.push_back(atip2);
226 : }
227 :
228 : }
229 2 : consistencyCheck();
230 2 : checkRead();
231 2 : beta = 1./(kBoltzmann*temperature);
232 :
233 2 : addValueWithDerivatives(); // allocate
234 2 : requestAtoms(atoms);
235 2 : setNotPeriodic();
236 2 : }
237 :
238 4 : void Dimer::calculate()
239 : {
240 4 : double cv_val=0;
241 4 : Tensor virial;
242 : std::vector<Vector> derivatives;
243 4 : std::vector<Vector> my_pos=getPositions();
244 4 : int atms = my_pos.size();
245 : std::vector<Vector> der_b2;
246 38 : for(int i=0; i<atms/2; i++)
247 : {
248 34 : Vector dist;
249 34 : dist = pbcDistance(my_pos[i],my_pos[i+atms/2]);
250 : double distquad=0;
251 136 : for(int j=0; j<3; j++)
252 102 : distquad += dist[j]*dist[j];
253 :
254 34 : double dsigquad = dsigma*dsigma;
255 34 : double fac1 = 1.0 + distquad/(2*qexp*dsigquad);
256 34 : double fac1qm1 = std::pow(fac1,qexp-1);
257 :
258 :
259 34 : cv_val += (fac1*fac1qm1-1.0)/beta;
260 34 : Vector der_val;
261 34 : Vector mder_val;
262 136 : for(int j=0; j<3; j++)
263 : {
264 102 : der_val[j] = -fac1qm1*dist[j]/(dsigquad*beta);
265 102 : mder_val[j]=-der_val[j];
266 : }
267 34 : derivatives.push_back(der_val);
268 34 : der_b2.push_back(mder_val);
269 :
270 : // virial part: each dimer contributes -x_{ij}*ds/dx_{ij} (s is the CV)
271 34 : double dfunc = fac1qm1/(beta*dsigquad);
272 34 : Vector dd(dfunc*dist);
273 34 : Tensor vv(dd,dist);
274 34 : virial -= vv;
275 :
276 : }
277 :
278 4 : derivatives.insert(derivatives.end(), der_b2.begin(), der_b2.end());
279 :
280 72 : for(unsigned int i=0; i<derivatives.size(); i++)
281 68 : setAtomsDerivatives(i,derivatives[i]);
282 :
283 4 : setValue(cv_val);
284 4 : setBoxDerivatives(virial);
285 :
286 4 : }
287 :
288 :
289 :
290 : /*****************
291 : There are some conditions that a valid input should satisfy.
292 : These are checked here and PLUMED error handlers are (eventually) called.
293 : ******************/
294 2 : void Dimer::consistencyCheck()
295 : {
296 2 : if(!useall && usedatoms1.size()!=usedatoms2.size())
297 0 : error("The provided atom lists are of different sizes.");
298 :
299 2 : if(qexp<0.5 || qexp>1)
300 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. :-)");
301 :
302 2 : if(dsigma<0)
303 0 : error("Please use positive sigma values for the Dimer strength constant");
304 :
305 2 : if(temperature<0)
306 0 : error("Please, use a positive value for the temperature...");
307 :
308 : // if dsigmas has only one element means that either
309 : // you are using different plumed.x.dat files or a plumed.dat with a single replica
310 2 : if(dsigmas.size()!=nranks && dsigmas.size()!=1)
311 0 : error("Mismatch between provided sigmas and number of replicas");
312 :
313 2 : }
314 :
315 :
316 : }
317 : }
318 :
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