Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2015-2023 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 "Bias.h"
23 : #include "core/ActionRegister.h"
24 : #include "tools/Random.h"
25 : #include "core/PlumedMain.h"
26 :
27 : namespace PLMD {
28 : namespace bias {
29 :
30 : //+PLUMEDOC BIAS EXTENDED_LAGRANGIAN
31 : /*
32 : Add extended Lagrangian.
33 :
34 : This action can be used to create fictitious collective variables coupled to the real ones.
35 : Given \f$x_i\f$ the \f$i\f$th argument of this bias potential, potential
36 : and kinetic contributions are added to the energy of the system as
37 : \f[
38 : V=\sum_i \frac{k_i}{2} (x_i-s_i)^2 + \sum_i \frac{\dot{s}_i^2}{2m_i}
39 : \f].
40 :
41 : The resulting potential is thus similar to a \ref RESTRAINT,
42 : but the restraint center moved with time following Hamiltonian
43 : dynamics with mass \f$m_i\f$.
44 :
45 : This bias potential accepts thus vectorial keywords (one element per argument)
46 : to define the coupling constant (KAPPA) and a relaxation time \f$tau\f$ (TAU).
47 : The mass is them computed as \f$m=k(\frac{\tau}{2\pi})^2\f$.
48 :
49 : Notice that this action creates several components.
50 : The ones named XX_fict are the fictitious coordinates. It is possible
51 : to add further forces on them by means of other bias potential,
52 : e.g. to obtain an indirect \ref METAD as in \cite continua .
53 : Also notice that the velocities of the fictitious coordinates
54 : are reported (XX_vfict). However, printed velocities are the ones
55 : at the previous step.
56 :
57 : It is also possible to provide a non-zero friction (one value per component).
58 : This is then used to implement a Langevin thermostat, so as to implement
59 : TAMD/dAFED method \cite Maragliano2006 \cite AbramsJ2008 . Notice that
60 : here a massive Langevin thermostat is used, whereas usually
61 : TAMD employs an overamped Langevin dynamics and dAFED
62 : a Gaussian thermostat.
63 :
64 : \warning
65 : The bias potential is reported in the component bias.
66 : Notice that this bias potential, although formally compatible with
67 : replica exchange framework, probably does not work as expected in that case.
68 : Indeed, since fictitious coordinates are not swapped upon exchange,
69 : acceptace can be expected to be extremely low unless (by chance) two neighboring
70 : replicas have the fictitious variables located properly in space.
71 :
72 : \warning
73 : \ref RESTART is not properly supported by this action. Indeed,
74 : at every start the position of the fictitious variable is reset to the value
75 : of the real variable, and its velocity is set to zero.
76 : This is not expected to introduce big errors, but certainly is
77 : introducing a small inconsistency between a single long run
78 : and many shorter runs.
79 :
80 : \par Examples
81 :
82 : The following input tells plumed to perform a metadynamics
83 : with an extended Lagrangian on two torsional angles.
84 : \plumedfile
85 : phi: TORSION ATOMS=5,7,9,15
86 : psi: TORSION ATOMS=7,9,15,17
87 : ex: EXTENDED_LAGRANGIAN ARG=phi,psi KAPPA=20,20.0 TAU=0.1,0.1
88 : METAD ARG=ex.phi_fict,ex.psi_fict PACE=100 SIGMA=0.35,0.35 HEIGHT=0.1
89 : # monitor the two variables
90 : PRINT STRIDE=10 ARG=phi,psi,ex.phi_fict,ex.psi_fict FILE=COLVAR
91 : \endplumedfile
92 :
93 : The following input tells plumed to perform a TAMD (or dAFED)
94 : calculation on two torsional angles, keeping the two variables
95 : at a fictitious temperature of 3000K with a Langevin thermostat
96 : with friction 10
97 : \plumedfile
98 : phi: TORSION ATOMS=5,7,9,15
99 : psi: TORSION ATOMS=7,9,15,17
100 : ex: EXTENDED_LAGRANGIAN ARG=phi,psi KAPPA=20,20.0 TAU=0.1,0.1 FRICTION=10,10 TEMP=3000
101 : # monitor the two variables
102 : PRINT STRIDE=10 ARG=phi,psi,ex.phi_fict,ex.psi_fict FILE=COLVAR
103 : \endplumedfile
104 :
105 : */
106 : //+ENDPLUMEDOC
107 :
108 : class ExtendedLagrangian : public Bias {
109 : bool firsttime;
110 : std::vector<double> fict;
111 : std::vector<double> vfict;
112 : std::vector<double> vfict_laststep;
113 : std::vector<double> ffict;
114 : std::vector<double> kappa;
115 : std::vector<double> tau;
116 : std::vector<double> friction;
117 : std::vector<Value*> fictValue;
118 : std::vector<Value*> vfictValue;
119 : double kbt;
120 : Random rand;
121 : public:
122 : explicit ExtendedLagrangian(const ActionOptions&);
123 : void calculate() override;
124 : void update() override;
125 : static void registerKeywords(Keywords& keys);
126 : };
127 :
128 : PLUMED_REGISTER_ACTION(ExtendedLagrangian,"EXTENDED_LAGRANGIAN")
129 :
130 4 : void ExtendedLagrangian::registerKeywords(Keywords& keys) {
131 4 : Bias::registerKeywords(keys);
132 4 : keys.add("compulsory","KAPPA","specifies that the restraint is harmonic and what the values of the force constants on each of the variables are");
133 4 : keys.add("compulsory","TAU","specifies that the restraint is harmonic and what the values of the force constants on each of the variables are");
134 4 : keys.add("compulsory","FRICTION","0.0","add a friction to the variable");
135 4 : keys.add("optional","TEMP","the system temperature - needed when FRICTION is present. If not provided will be taken from MD code (if available)");
136 8 : keys.addOutputComponent("_fict","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
137 : "These quantities will named with the arguments of the bias followed by "
138 : "the character string _tilde. It is possible to add forces on these variable.");
139 8 : keys.addOutputComponent("_vfict","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
140 : "These quantities will named with the arguments of the bias followed by "
141 : "the character string _tilde. It is NOT possible to add forces on these variable.");
142 4 : }
143 :
144 2 : ExtendedLagrangian::ExtendedLagrangian(const ActionOptions&ao):
145 : PLUMED_BIAS_INIT(ao),
146 2 : firsttime(true),
147 4 : fict(getNumberOfArguments(),0.0),
148 2 : vfict(getNumberOfArguments(),0.0),
149 2 : vfict_laststep(getNumberOfArguments(),0.0),
150 2 : ffict(getNumberOfArguments(),0.0),
151 2 : kappa(getNumberOfArguments(),0.0),
152 2 : tau(getNumberOfArguments(),0.0),
153 2 : friction(getNumberOfArguments(),0.0),
154 2 : fictValue(getNumberOfArguments(),NULL),
155 2 : vfictValue(getNumberOfArguments(),NULL),
156 4 : kbt(0.0) {
157 2 : parseVector("TAU",tau);
158 2 : parseVector("FRICTION",friction);
159 2 : parseVector("KAPPA",kappa);
160 2 : kbt=getkBT();
161 2 : checkRead();
162 :
163 2 : log.printf(" with harmonic force constant");
164 6 : for(unsigned i=0; i<kappa.size(); i++) {
165 4 : log.printf(" %f",kappa[i]);
166 : }
167 2 : log.printf("\n");
168 :
169 2 : log.printf(" with relaxation time");
170 6 : for(unsigned i=0; i<tau.size(); i++) {
171 4 : log.printf(" %f",tau[i]);
172 : }
173 2 : log.printf("\n");
174 :
175 : bool hasFriction=false;
176 6 : for(unsigned i=0; i<getNumberOfArguments(); ++i)
177 4 : if(friction[i]>0.0) {
178 : hasFriction=true;
179 : }
180 :
181 2 : if(hasFriction) {
182 2 : log.printf(" with friction");
183 6 : for(unsigned i=0; i<friction.size(); i++) {
184 4 : log.printf(" %f",friction[i]);
185 : }
186 2 : log.printf("\n");
187 : }
188 :
189 2 : log.printf(" and kbt");
190 2 : log.printf(" %f",kbt);
191 2 : log.printf("\n");
192 :
193 6 : for(unsigned i=0; i<getNumberOfArguments(); i++) {
194 4 : std::string comp=getPntrToArgument(i)->getName()+"_fict";
195 8 : addComponentWithDerivatives(comp);
196 4 : if(getPntrToArgument(i)->isPeriodic()) {
197 : std::string a,b;
198 4 : getPntrToArgument(i)->getDomain(a,b);
199 4 : componentIsPeriodic(comp,a,b);
200 : } else {
201 0 : componentIsNotPeriodic(comp);
202 : }
203 4 : fictValue[i]=getPntrToComponent(comp);
204 8 : comp=getPntrToArgument(i)->getName()+"_vfict";
205 4 : addComponent(comp);
206 4 : componentIsNotPeriodic(comp);
207 4 : vfictValue[i]=getPntrToComponent(comp);
208 : }
209 :
210 4 : log<<" Bibliography "<<plumed.cite("Iannuzzi, Laio, and Parrinello, Phys. Rev. Lett. 90, 238302 (2003)");
211 2 : if(hasFriction) {
212 4 : log<<plumed.cite("Maragliano and Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006)");
213 4 : log<<plumed.cite("Abrams and Tuckerman, J. Phys. Chem. B 112, 15742 (2008)");
214 : }
215 2 : log<<"\n";
216 2 : }
217 :
218 :
219 24 : void ExtendedLagrangian::calculate() {
220 :
221 24 : if(firsttime) {
222 6 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
223 4 : fict[i]=getArgument(i);
224 : }
225 2 : firsttime=false;
226 : }
227 : double ene=0.0;
228 72 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
229 48 : const double cv=difference(i,fict[i],getArgument(i));
230 48 : const double k=kappa[i];
231 48 : const double f=-k*cv;
232 48 : ene+=0.5*k*cv*cv;
233 48 : setOutputForce(i,f);
234 48 : ffict[i]=-f;
235 : };
236 24 : setBias(ene);
237 72 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
238 48 : fict[i]=fictValue[i]->bringBackInPbc(fict[i]);
239 48 : fictValue[i]->set(fict[i]);
240 48 : vfictValue[i]->set(vfict_laststep[i]);
241 : }
242 24 : }
243 :
244 24 : void ExtendedLagrangian::update() {
245 24 : double dt=getTimeStep()*getStride();
246 72 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
247 48 : double mass=kappa[i]*tau[i]*tau[i]/(4*pi*pi); // should be k/omega**2
248 48 : double c1=std::exp(-0.5*friction[i]*dt);
249 48 : double c2=std::sqrt(kbt*(1.0-c1*c1)/mass);
250 : // consider additional forces on the fictitious particle
251 : // (e.g. MetaD stuff)
252 48 : ffict[i]+=fictValue[i]->getForce();
253 :
254 : // update velocity (half step)
255 48 : vfict[i]+=ffict[i]*0.5*dt/mass;
256 : // thermostat (half step)
257 48 : vfict[i]=c1*vfict[i]+c2*rand.Gaussian();
258 : // save full step velocity to be dumped at next step
259 48 : vfict_laststep[i]=vfict[i];
260 : // thermostat (half step)
261 48 : vfict[i]=c1*vfict[i]+c2*rand.Gaussian();
262 : // update velocity (half step)
263 48 : vfict[i]+=ffict[i]*0.5*dt/mass;
264 : // update position (full step)
265 48 : fict[i]+=vfict[i]*dt;
266 : }
267 24 : }
268 :
269 : }
270 :
271 : }
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