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 10423 : PLUMED_REGISTER_ACTION(Dimer, "DIMER")
144 :
145 :
146 :
147 3 : void Dimer::registerKeywords( Keywords& keys) {
148 3 : Colvar::registerKeywords(keys);
149 :
150 6 : keys.add("compulsory","DSIGMA","The interaction strength of the dimer bond.");
151 6 : keys.add("compulsory", "Q", "The exponent of the dimer potential.");
152 6 : keys.add("compulsory", "TEMP", "The temperature (in Kelvin) of the simulation.");
153 6 : 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 6 : 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 6 : keys.addFlag("ALLATOMS", false, "Use EVERY atom of the system. Overrides ATOMS keyword.");
156 6 : keys.addFlag("NOVSITES", false, "If present the configuration is without virtual sites at the centroid positions.");
157 :
158 3 : }
159 :
160 :
161 :
162 2 : Dimer::Dimer(const ActionOptions& ao):
163 2 : PLUMED_COLVAR_INIT(ao)
164 : {
165 :
166 4 : log<<" Bibliography "<<plumed.cite("M Nava, F. Palazzesi, C. Perego and M. Parrinello, J. Chem. Theory Comput. 13, 425(2017)")<<"\n";
167 2 : parseVector("DSIGMA",dsigmas);
168 2 : parse("Q",qexp);
169 4 : parse("TEMP",temperature);
170 :
171 :
172 : std::vector<AtomNumber> atoms;
173 2 : parseFlag("ALLATOMS",useall);
174 2 : trimer=true;
175 : bool notrim;
176 2 : parseFlag("NOVSITES",notrim);
177 2 : trimer=!notrim;
178 :
179 2 : nranks=multi_sim_comm.Get_size();
180 2 : myrank=multi_sim_comm.Get_rank();
181 2 : if(dsigmas.size()==1)
182 2 : dsigma=dsigmas[0];
183 : else
184 0 : dsigma=dsigmas[myrank];
185 :
186 :
187 :
188 :
189 2 : if(useall)
190 : {
191 : // go with every atom in the system but not the virtuals...
192 : int natoms;
193 1 : if(trimer)
194 1 : natoms= 2*getTotAtoms()/3;
195 : else
196 0 : natoms=getTotAtoms()/2;
197 :
198 45 : for(unsigned int i=0; i<((unsigned int)natoms); i++)
199 : {
200 : AtomNumber ati;
201 : ati.setIndex(i);
202 44 : atoms.push_back(ati);
203 : }
204 : }
205 : else // serials for the first beads of each dimer are given
206 : {
207 1 : parseAtomList("ATOMS1",usedatoms1);
208 2 : parseAtomList("ATOMS2",usedatoms2);
209 :
210 : int isz1 = usedatoms1.size();
211 :
212 5 : for(unsigned int i=0; i<isz1; i++)
213 : {
214 : AtomNumber ati;
215 4 : ati.setIndex(usedatoms1[i].index());
216 4 : atoms.push_back(ati);
217 : }
218 :
219 : int isz2 = usedatoms2.size();
220 5 : for(unsigned int i=0; i<isz2; i++)
221 : {
222 : AtomNumber atip2;
223 4 : atip2.setIndex(usedatoms2[i].index());
224 4 : atoms.push_back(atip2);
225 : }
226 :
227 : }
228 2 : consistencyCheck();
229 2 : checkRead();
230 2 : beta = 1./(kBoltzmann*temperature);
231 :
232 2 : addValueWithDerivatives(); // allocate
233 2 : requestAtoms(atoms);
234 2 : setNotPeriodic();
235 2 : }
236 :
237 4 : void Dimer::calculate()
238 : {
239 4 : double cv_val=0;
240 4 : Tensor virial;
241 : std::vector<Vector> derivatives;
242 4 : std::vector<Vector> my_pos=getPositions();
243 4 : int atms = my_pos.size();
244 : std::vector<Vector> der_b2;
245 38 : for(int i=0; i<atms/2; i++)
246 : {
247 34 : Vector dist;
248 34 : dist = pbcDistance(my_pos[i],my_pos[i+atms/2]);
249 : double distquad=0;
250 136 : for(int j=0; j<3; j++)
251 102 : distquad += dist[j]*dist[j];
252 :
253 34 : double dsigquad = dsigma*dsigma;
254 34 : double fac1 = 1.0 + distquad/(2*qexp*dsigquad);
255 34 : double fac1qm1 = std::pow(fac1,qexp-1);
256 :
257 :
258 34 : cv_val += (fac1*fac1qm1-1.0)/beta;
259 34 : Vector der_val;
260 34 : Vector mder_val;
261 136 : for(int j=0; j<3; j++)
262 : {
263 102 : der_val[j] = -fac1qm1*dist[j]/(dsigquad*beta);
264 102 : mder_val[j]=-der_val[j];
265 : }
266 34 : derivatives.push_back(der_val);
267 34 : der_b2.push_back(mder_val);
268 :
269 : // virial part: each dimer contributes -x_{ij}*ds/dx_{ij} (s is the CV)
270 34 : double dfunc = fac1qm1/(beta*dsigquad);
271 34 : Vector dd(dfunc*dist);
272 34 : Tensor vv(dd,dist);
273 34 : virial -= vv;
274 :
275 : }
276 :
277 4 : derivatives.insert(derivatives.end(), der_b2.begin(), der_b2.end());
278 :
279 72 : for(unsigned int i=0; i<derivatives.size(); i++)
280 68 : setAtomsDerivatives(i,derivatives[i]);
281 :
282 4 : setValue(cv_val);
283 4 : setBoxDerivatives(virial);
284 :
285 4 : }
286 :
287 :
288 :
289 : /*****************
290 : There are some conditions that a valid input should satisfy.
291 : These are checked here and PLUMED error handlers are (eventually) called.
292 : ******************/
293 2 : void Dimer::consistencyCheck()
294 : {
295 2 : if(!useall && usedatoms1.size()!=usedatoms2.size())
296 0 : error("The provided atom lists are of different sizes.");
297 :
298 2 : if(qexp<0.5 || qexp>1)
299 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. :-)");
300 :
301 2 : if(dsigma<0)
302 0 : error("Please use positive sigma values for the Dimer strength constant");
303 :
304 2 : if(temperature<0)
305 0 : error("Please, use a positive value for the temperature...");
306 :
307 : // if dsigmas has only one element means that either
308 : // you are using different plumed.x.dat files or a plumed.dat with a single replica
309 2 : if(dsigmas.size()!=nranks && dsigmas.size()!=1)
310 0 : error("Mismatch between provided sigmas and number of replicas");
311 :
312 2 : }
313 :
314 :
315 : }
316 : }
317 :
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