Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2017-2020 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 :
23 :
24 : #include "Colvar.h"
25 : #include "ActionRegister.h"
26 : #include "core/PlumedMain.h"
27 :
28 : #include <string>
29 : #include <cmath>
30 : #include <cassert>
31 : #include <iostream>
32 : #include <vector>
33 :
34 : using namespace std;
35 :
36 : namespace PLMD {
37 : namespace colvar {
38 :
39 : //+PLUMEDOC COLVAR DIMER
40 : /*
41 : This CV computes the dimer interaction energy for a collection of dimers.
42 :
43 : Each dimer represents an atom, as described in the dimer paper \cite dimer-metad.
44 : A system of N atoms is thus represented with N dimers, each
45 : Dimer being composed of two beads and eventually a virtual site representing its center of mass.
46 :
47 : A typical configuration for a dimerized system has the following ordering of atoms:
48 :
49 : 1 TAG1 X Y Z N atoms representing the first bead of each Dimer
50 :
51 : 2 TAG2 X Y Z
52 :
53 : ...
54 :
55 : N TAGN X Y Z N atoms representing the second bead of each Dimer
56 :
57 : N+1 TAG1 X Y Z
58 :
59 : N+2 TAG2 X Y Z
60 :
61 : ...
62 :
63 : 2N TAGN X Y Z Optional: N atoms representing the center of mass of each Dimer
64 :
65 : 2N+1 TAG1 X Y Z
66 :
67 : 2N+2 TAG2 X Y Z
68 :
69 : ...
70 :
71 : 3N TAGN X Y Z The configuration might go on with un-dimerized atoms (like a solvent)
72 :
73 : 3N+1
74 :
75 : 3N+2
76 :
77 : ...
78 :
79 :
80 : The Dimer interaction energy is defined between atoms x and N+x, for x=1,...,N and is
81 : characterized by two parameters Q and DSIGMA. These are passed as mandatory arguments along with
82 : the temperature of the system.
83 :
84 : \par Examples
85 :
86 : This line tells Plumed to compute the Dimer interaction energy for every dimer in the system.
87 :
88 : \plumedfile
89 : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002
90 : \endplumedfile
91 :
92 : If the simulation doesn't use virtual sites for the dimers centers of mass,
93 : Plumed has to know in order to determine correctly the total number of dimers from
94 : the total number of atoms:
95 : \plumedfile
96 : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002 NOVSITES
97 : \endplumedfile
98 :
99 : The NOVSITES flag is not required if one provides the atom serials of each Dimer. These are
100 : defined through two lists of atoms provided __instead__ of the ALLATOMS keyword.
101 : For example, the Dimer interaction energy of dimers specified by beads (1;23),(5;27),(7;29) is:
102 : \plumedfile
103 : dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002
104 : \endplumedfile
105 :
106 : Note that the ATOMS1,ATOMS2 keywords can support atom groups and
107 : interval notation as defined in \ref GROUP.
108 :
109 :
110 : In a Replica Exchange simulation the keyword DSIGMA can be used in two ways:
111 : if a plumed.n.dat file is provided for each replica, then DSIGMA is passed as a single value,
112 : like in the previous examples, and each replica will read its own DSIGMA value. If
113 : a unique plumed.dat is given, DSIGMA has to be a list containing a value for each replica.
114 : For 4 replicas:
115 : \plumedfile
116 : #SETTINGS NREPLICAS=4
117 : dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002,0.002,0.004,0.01
118 : \endplumedfile
119 :
120 :
121 : \par Usage of the CV
122 :
123 : The dimer interaction is not coded in the driver program and has to be inserted
124 : in the Hamiltonian of the system as a linear RESTRAINT (see \ref RESTRAINT):
125 : \plumedfile
126 : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002
127 : RESTRAINT ARG=dim AT=0 KAPPA=0 SLOPE=1 LABEL=dimforces
128 : \endplumedfile
129 :
130 : In a replica exchange, Metadynamics (see \ref METAD) can be used on the Dimer CV to reduce
131 : the number of replicas. Just keep in mind that METAD SIGMA values should be tuned
132 : in the standard way for each replica according to the value of DSIGMA.
133 : */
134 : //+ENDPLUMEDOC
135 :
136 6 : class Dimer : public Colvar {
137 : public:
138 : static void registerKeywords( Keywords& keys);
139 : explicit Dimer(const ActionOptions&);
140 : virtual void calculate();
141 : protected:
142 : bool trimer,useall;
143 : int myrank, nranks;
144 : double qexp,temperature,beta,dsigma;
145 : vector<double> dsigmas;
146 : private:
147 : void consistencyCheck();
148 : vector<AtomNumber> usedatoms1;
149 : vector<AtomNumber> usedatoms2;
150 :
151 : };
152 :
153 7360 : PLUMED_REGISTER_ACTION(Dimer, "DIMER")
154 :
155 :
156 :
157 3 : void Dimer::registerKeywords( Keywords& keys) {
158 3 : Colvar::registerKeywords(keys);
159 :
160 12 : keys.add("compulsory","DSIGMA","The interaction strength of the dimer bond.");
161 12 : keys.add("compulsory", "Q", "The exponent of the dimer potential.");
162 12 : keys.add("compulsory", "TEMP", "The temperature (in Kelvin) of the simulation.");
163 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");
164 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");
165 9 : keys.addFlag("ALLATOMS", false, "Use EVERY atom of the system. Overrides ATOMS keyword.");
166 9 : keys.addFlag("NOVSITES", false, "If present the configuration is without virtual sites at the centroid positions.");
167 :
168 3 : }
169 :
170 :
171 :
172 2 : Dimer::Dimer(const ActionOptions& ao):
173 6 : PLUMED_COLVAR_INIT(ao)
174 : {
175 :
176 6 : log<<" Bibliography "<<plumed.cite("M Nava, F. Palazzesi, C. Perego and M. Parrinello, J. Chem. Theory Comput. 13, 425(2017)")<<"\n";
177 4 : parseVector("DSIGMA",dsigmas);
178 4 : parse("Q",qexp);
179 4 : parse("TEMP",temperature);
180 :
181 :
182 : vector<AtomNumber> atoms;
183 4 : parseFlag("ALLATOMS",useall);
184 2 : trimer=true;
185 : bool notrim;
186 4 : parseFlag("NOVSITES",notrim);
187 2 : trimer=!notrim;
188 :
189 2 : nranks=multi_sim_comm.Get_size();
190 2 : myrank=multi_sim_comm.Get_rank();
191 2 : if(dsigmas.size()==1)
192 2 : dsigma=dsigmas[0];
193 : else
194 0 : dsigma=dsigmas[myrank];
195 :
196 :
197 :
198 :
199 2 : if(useall)
200 : {
201 : // go with every atom in the system but not the virtuals...
202 : int natoms;
203 1 : if(trimer)
204 1 : natoms= 2*getTotAtoms()/3;
205 : else
206 0 : natoms=getTotAtoms()/2;
207 :
208 89 : for(unsigned int i=0; i<((unsigned int)natoms); i++)
209 : {
210 : AtomNumber ati;
211 : ati.setIndex(i);
212 44 : atoms.push_back(ati);
213 : }
214 : }
215 : else // serials for the first beads of each dimer are given
216 : {
217 2 : parseAtomList("ATOMS1",usedatoms1);
218 2 : parseAtomList("ATOMS2",usedatoms2);
219 :
220 : int isz1 = usedatoms1.size();
221 :
222 9 : for(unsigned int i=0; i<isz1; i++)
223 : {
224 : AtomNumber ati;
225 4 : ati.setIndex(usedatoms1[i].index());
226 4 : atoms.push_back(ati);
227 : }
228 :
229 : int isz2 = usedatoms2.size();
230 9 : for(unsigned int i=0; i<isz2; i++)
231 : {
232 : AtomNumber atip2;
233 4 : atip2.setIndex(usedatoms2[i].index());
234 4 : atoms.push_back(atip2);
235 : }
236 :
237 : }
238 2 : consistencyCheck();
239 2 : checkRead();
240 2 : beta = 1./(kBoltzmann*temperature);
241 :
242 2 : addValueWithDerivatives(); // allocate
243 2 : requestAtoms(atoms);
244 2 : setNotPeriodic();
245 2 : }
246 :
247 4 : void Dimer::calculate()
248 : {
249 4 : double cv_val=0;
250 4 : Tensor virial;
251 : vector<Vector> derivatives;
252 4 : vector<Vector> my_pos=getPositions();
253 4 : int atms = my_pos.size();
254 : vector<Vector> der_b2;
255 72 : for(int i=0; i<atms/2; i++)
256 : {
257 34 : Vector dist;
258 102 : dist = pbcDistance(my_pos[i],my_pos[i+atms/2]);
259 : double distquad=0;
260 238 : for(int j=0; j<3; j++)
261 102 : distquad += dist[j]*dist[j];
262 :
263 34 : double dsigquad = dsigma*dsigma;
264 34 : double fac1 = 1.0 + distquad/(2*qexp*dsigquad);
265 34 : double fac1qm1 = pow(fac1,qexp-1);
266 :
267 :
268 34 : cv_val += (fac1*fac1qm1-1.0)/beta;
269 34 : Vector der_val;
270 34 : Vector mder_val;
271 238 : for(int j=0; j<3; j++)
272 : {
273 102 : der_val[j] = -fac1qm1*dist[j]/(dsigquad*beta);
274 102 : mder_val[j]=-der_val[j];
275 : }
276 34 : derivatives.push_back(der_val);
277 34 : der_b2.push_back(mder_val);
278 :
279 : // virial part: each dimer contributes -x_{ij}*ds/dx_{ij} (s is the CV)
280 34 : double dfunc = fac1qm1/(beta*dsigquad);
281 34 : Vector dd(dfunc*dist);
282 34 : Tensor vv(dd,dist);
283 34 : virial -= vv;
284 :
285 : }
286 :
287 4 : derivatives.insert(derivatives.end(), der_b2.begin(), der_b2.end());
288 :
289 212 : for(unsigned int i=0; i<derivatives.size(); i++)
290 136 : setAtomsDerivatives(i,derivatives[i]);
291 :
292 4 : setValue(cv_val);
293 4 : setBoxDerivatives(virial);
294 :
295 4 : }
296 :
297 :
298 :
299 : /*****************
300 : There are some conditions that a valid input should satisfy.
301 : These are checked here and PLUMED error handlers are (eventually) called.
302 : ******************/
303 2 : void Dimer::consistencyCheck()
304 : {
305 3 : if(!useall && usedatoms1.size()!=usedatoms2.size())
306 0 : error("The provided atom lists are of different sizes.");
307 :
308 2 : if(qexp<0.5 || qexp>1)
309 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. :-)");
310 :
311 2 : if(dsigma<0)
312 0 : error("Please use positive sigma values for the Dimer strength constant");
313 :
314 2 : if(temperature<0)
315 0 : error("Please, use a positive value for the temperature...");
316 :
317 : // if dsigmas has only one element means that either
318 : // you are using different plumed.x.dat files or a plumed.dat with a single replica
319 2 : if(dsigmas.size()!=nranks && dsigmas.size()!=1)
320 0 : error("Mismatch between provided sigmas and number of replicas");
321 :
322 2 : }
323 :
324 :
325 : }
326 5517 : }
327 :
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