Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2023 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 :
25 : namespace PLMD {
26 : namespace bias {
27 :
28 : //+PLUMEDOC BIAS MOVINGRESTRAINT
29 : /*
30 : Add a time-dependent, harmonic restraint on one or more variables.
31 :
32 : This form of bias can be used to performed steered MD \cite Grubmuller3
33 : and Jarzynski sampling \cite jarzynski.
34 :
35 : The harmonic restraint on your system is given by:
36 :
37 : \f[
38 : V(\vec{s},t) = \frac{1}{2} \kappa(t) ( \vec{s} - \vec{s}_0(t) )^2
39 : \f]
40 :
41 : The time dependence of \f$\kappa\f$ and \f$\vec{s}_0\f$ are specified by a list of
42 : STEP, KAPPA and AT keywords. These keywords tell plumed what values \f$\kappa\f$ and \f$\vec{s}_0\f$
43 : should have at the time specified by the corresponding STEP keyword. In between these times
44 : the values of \f$\kappa\f$ and \f$\vec{s}_0\f$ are linearly interpolated.
45 :
46 : Additional material and examples can be also found in the tutorial \ref belfast-5
47 :
48 : \par Examples
49 :
50 : The following input is dragging the distance between atoms 2 and 4
51 : from 1 to 2 in the first 1000 steps, then back in the next 1000 steps.
52 : In the following 500 steps the restraint is progressively switched off.
53 : \plumedfile
54 : DISTANCE ATOMS=2,4 LABEL=d
55 : MOVINGRESTRAINT ...
56 : ARG=d
57 : STEP0=0 AT0=1.0 KAPPA0=100.0
58 : STEP1=1000 AT1=2.0
59 : STEP2=2000 AT2=1.0
60 : STEP3=2500 KAPPA3=0.0
61 : ... MOVINGRESTRAINT
62 : \endplumedfile
63 : The following input is progressively building restraints
64 : distances between atoms 1 and 5 and between atoms 2 and 4
65 : in the first 1000 steps. Afterwards, the restraint is kept
66 : static.
67 : \plumedfile
68 : DISTANCE ATOMS=1,5 LABEL=d1
69 : DISTANCE ATOMS=2,4 LABEL=d2
70 : MOVINGRESTRAINT ...
71 : ARG=d1,d2
72 : STEP0=0 AT0=1.0,1.5 KAPPA0=0.0,0.0
73 : STEP1=1000 AT1=1.0,1.5 KAPPA1=1.0,1.0
74 : ... MOVINGRESTRAINT
75 : \endplumedfile
76 : The following input is progressively bringing atoms 1 and 2
77 : close to each other with an upper wall
78 : \plumedfile
79 : DISTANCE ATOMS=1,2 LABEL=d1
80 : MOVINGRESTRAINT ...
81 : ARG=d1
82 : VERSE=U
83 : STEP0=0 AT0=1.0 KAPPA0=10.0
84 : STEP1=1000 AT1=0.0
85 : ... MOVINGRESTRAINT
86 : \endplumedfile
87 :
88 : By default the Action is issuing some values which are
89 : the work on each degree of freedom, the center of the harmonic potential,
90 : the total bias deposited
91 :
92 : (See also \ref DISTANCE).
93 :
94 : \attention Work is not computed properly when KAPPA is time dependent.
95 :
96 : */
97 : //+ENDPLUMEDOC
98 :
99 :
100 : class MovingRestraint : public Bias {
101 : std::vector<std::vector<double> > at;
102 : std::vector<std::vector<double> > kappa;
103 : std::vector<long long int> step;
104 : std::vector<double> oldaa;
105 : std::vector<double> oldk;
106 : std::vector<double> olddpotdk;
107 : std::vector<double> oldf;
108 : std::vector<std::string> verse;
109 : std::vector<double> work;
110 : std::vector<double> kk,aa,f,dpotdk;
111 : double tot_work;
112 : std::vector<Value*> valueCntr;
113 : std::vector<Value*> valueWork;
114 : std::vector<Value*> valueKappa;
115 : Value* valueTotWork=nullptr;
116 : Value* valueForce2=nullptr;
117 : public:
118 : explicit MovingRestraint(const ActionOptions&);
119 : void calculate() override;
120 : static void registerKeywords( Keywords& keys );
121 : };
122 :
123 : PLUMED_REGISTER_ACTION(MovingRestraint,"MOVINGRESTRAINT")
124 :
125 6 : void MovingRestraint::registerKeywords( Keywords& keys ) {
126 6 : Bias::registerKeywords(keys);
127 6 : keys.use("ARG");
128 12 : keys.add("compulsory","VERSE","B","Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than "
129 : "the restraint or whether it is acting on both sides (B)");
130 12 : keys.add("numbered","STEP","This keyword appears multiple times as STEPx with x=0,1,2,...,n. Each value given represents "
131 : "the MD step at which the restraint parameters take the values KAPPAx and ATx.");
132 12 : keys.reset_style("STEP","compulsory");
133 12 : keys.add("numbered","AT","ATx is equal to the position of the restraint at time STEPx. For intermediate times this parameter "
134 : "is linearly interpolated. If no ATx is specified for STEPx then the values of AT are kept constant "
135 : "during the interval of time between STEP(x-1) and STEPx.");
136 12 : keys.reset_style("AT","compulsory");
137 12 : keys.add("numbered","KAPPA","KAPPAx is equal to the value of the force constants at time STEPx. For intermediate times this "
138 : "parameter is linearly interpolated. If no KAPPAx is specified for STEPx then the values of KAPPAx "
139 : "are kept constant during the interval of time between STEP(x-1) and STEPx.");
140 12 : keys.reset_style("KAPPA","compulsory");
141 12 : keys.addOutputComponent("work","default","the total work performed changing this restraint");
142 12 : keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
143 12 : keys.addOutputComponent("_cntr","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
144 : "these quantities will named with the arguments of the bias followed by "
145 : "the character string _cntr. These quantities give the instantaneous position "
146 : "of the center of the harmonic potential.");
147 12 : keys.addOutputComponent("_work","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
148 : "These quantities will named with the arguments of the bias followed by "
149 : "the character string _work. These quantities tell the user how much work has "
150 : "been done by the potential in dragging the system along the various colvar axis.");
151 12 : keys.addOutputComponent("_kappa","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
152 : "These quantities will named with the arguments of the bias followed by "
153 : "the character string _kappa. These quantities tell the user the time dependent value of kappa.");
154 6 : }
155 :
156 4 : MovingRestraint::MovingRestraint(const ActionOptions&ao):
157 : PLUMED_BIAS_INIT(ao),
158 4 : verse(getNumberOfArguments()),
159 4 : kk(getNumberOfArguments()),
160 4 : aa(getNumberOfArguments()),
161 4 : f(getNumberOfArguments()),
162 8 : dpotdk(getNumberOfArguments())
163 : {
164 4 : parseVector("VERSE",verse);
165 4 : std::vector<long long int> ss(1); ss[0]=-1;
166 4 : std::vector<double> kk( getNumberOfArguments() ), aa( getNumberOfArguments() );
167 10 : for(int i=0;; i++) {
168 : // Read in step
169 28 : if( !parseNumberedVector("STEP",i,ss) ) break;
170 19 : for(unsigned j=0; j<step.size(); j++) {
171 9 : if(ss[0]<step[j]) error("in moving restraint step number must always increase");
172 : }
173 10 : step.push_back(ss[0]);
174 :
175 : // Try to read kappa
176 20 : if( !parseNumberedVector("KAPPA",i,kk) ) kk=kappa[i-1];
177 10 : kappa.push_back(kk);
178 :
179 : // Now read AT
180 20 : if( !parseNumberedVector("AT",i,aa) ) aa=at[i-1];
181 10 : at.push_back(aa);
182 10 : }
183 4 : checkRead();
184 :
185 14 : for(unsigned i=0; i<step.size(); i++) {
186 10 : log.printf(" step%u %lld\n",i,step[i]);
187 10 : log.printf(" at");
188 22 : for(unsigned j=0; j<at[i].size(); j++) log.printf(" %f",at[i][j]);
189 10 : log.printf("\n");
190 10 : log.printf(" with force constant");
191 22 : for(unsigned j=0; j<kappa[i].size(); j++) log.printf(" %f",kappa[i][j]);
192 10 : log.printf("\n");
193 : };
194 :
195 8 : addComponent("force2"); componentIsNotPeriodic("force2");
196 4 : valueForce2=getPntrToComponent("force2");
197 :
198 : // add the centers of the restraint as additional components that can be retrieved (useful for debug)
199 :
200 : std::string comp;
201 9 : for(unsigned i=0; i< getNumberOfArguments() ; i++) {
202 10 : comp=getPntrToArgument(i)->getName()+"_cntr"; // each spring has its own center
203 10 : addComponent(comp); componentIsNotPeriodic(comp);
204 5 : valueCntr.push_back(getPntrToComponent(comp));
205 10 : comp=getPntrToArgument(i)->getName()+"_work"; // each spring has its own work
206 10 : addComponent(comp); componentIsNotPeriodic(comp);
207 5 : valueWork.push_back(getPntrToComponent(comp));
208 10 : comp=getPntrToArgument(i)->getName()+"_kappa"; // each spring has its own kappa
209 10 : addComponent(comp); componentIsNotPeriodic(comp);
210 5 : valueKappa.push_back(getPntrToComponent(comp));
211 5 : work.push_back(0.); // initialize the work value
212 : }
213 8 : addComponent("work"); componentIsNotPeriodic("work");
214 4 : valueTotWork=getPntrToComponent("work");
215 4 : tot_work=0.0;
216 :
217 4 : log<<" Bibliography ";
218 8 : log<<cite("Grubmuller, Heymann, and Tavan, Science 271, 997 (1996)")<<"\n";
219 :
220 4 : }
221 :
222 :
223 566 : void MovingRestraint::calculate() {
224 : double ene=0.0;
225 : double totf2=0.0;
226 566 : unsigned narg=getNumberOfArguments();
227 566 : long long int now=getStep();
228 566 : if(now<=step[0]) {
229 3 : kk=kappa[0];
230 3 : aa=at[0];
231 3 : oldaa=at[0];
232 3 : oldk=kappa[0];
233 3 : olddpotdk.resize(narg);
234 3 : oldf.resize(narg);
235 563 : } else if(now>=step[step.size()-1]) {
236 47 : kk=kappa[step.size()-1];
237 47 : aa=at[step.size()-1];
238 : } else {
239 : unsigned i=0;
240 521 : for(i=1; i<step.size()-1; i++) if(now<step[i]) break;
241 516 : double c2=(now-step[i-1])/double(step[i]-step[i-1]);
242 516 : double c1=1.0-c2;
243 1040 : for(unsigned j=0; j<narg; j++) kk[j]=(c1*kappa[i-1][j]+c2*kappa[i][j]);
244 1040 : for(unsigned j=0; j<narg; j++) {
245 524 : const double a1=at[i-1][j];
246 524 : const double a2=at[i][j];
247 524 : aa[j]=(c1*a1+c2*(a1+difference(j,a1,a2)));
248 : }
249 : }
250 566 : tot_work=0.0;
251 1142 : for(unsigned i=0; i<narg; ++i) {
252 576 : const double cv=difference(i,aa[i],getArgument(i)); // this gives: getArgument(i) - aa[i]
253 576 : valueCntr[i]->set(aa[i]);
254 576 : const double k=kk[i];
255 576 : f[i]=-k*cv;
256 576 : if(verse[i]=="U" && cv<0) continue;
257 576 : if(verse[i]=="L" && cv>0) continue;
258 1728 : plumed_assert(verse[i]=="U" || verse[i]=="L" || verse[i]=="B");
259 576 : dpotdk[i]=0.5*cv*cv;
260 576 : if(oldaa.size()==aa.size() && oldf.size()==f.size()) work[i]+=0.5*(oldf[i]+f[i])*(aa[i]-oldaa[i]) + 0.5*( dpotdk[i]+olddpotdk[i] )*(kk[i]-oldk[i]);
261 576 : valueWork[i]->set(work[i]);
262 576 : valueKappa[i]->set(kk[i]);
263 576 : tot_work+=work[i];
264 576 : ene+=0.5*k*cv*cv;
265 576 : setOutputForce(i,f[i]);
266 576 : totf2+=f[i]*f[i];
267 : };
268 566 : valueTotWork->set(tot_work);
269 566 : oldf=f;
270 566 : oldaa=aa;
271 566 : oldk=kk;
272 566 : olddpotdk=dpotdk;
273 566 : setBias(ene);
274 566 : valueForce2->set(totf2);
275 566 : }
276 :
277 : }
278 : }
279 :
280 :
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