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.add("compulsory","VERSE","B","Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than "
128 : "the restraint or whether it is acting on both sides (B)");
129 6 : keys.add("numbered","STEP","This keyword appears multiple times as STEPx with x=0,1,2,...,n. Each value given represents "
130 : "the MD step at which the restraint parameters take the values KAPPAx and ATx.");
131 12 : keys.reset_style("STEP","compulsory");
132 6 : keys.add("numbered","AT","ATx is equal to the position of the restraint at time STEPx. For intermediate times this parameter "
133 : "is linearly interpolated. If no ATx is specified for STEPx then the values of AT are kept constant "
134 : "during the interval of time between STEP(x-1) and STEPx.");
135 12 : keys.reset_style("AT","compulsory");
136 6 : keys.add("numbered","KAPPA","KAPPAx is equal to the value of the force constants at time STEPx. For intermediate times this "
137 : "parameter is linearly interpolated. If no KAPPAx is specified for STEPx then the values of KAPPAx "
138 : "are kept constant during the interval of time between STEP(x-1) and STEPx.");
139 12 : keys.reset_style("KAPPA","compulsory");
140 12 : keys.addOutputComponent("work","default","scalar","the total work performed changing this restraint");
141 12 : keys.addOutputComponent("force2","default","scalar","the instantaneous value of the squared force due to this bias potential");
142 12 : keys.addOutputComponent("_cntr","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
143 : "these quantities will named with the arguments of the bias followed by "
144 : "the character string _cntr. These quantities give the instantaneous position "
145 : "of the center of the harmonic potential.");
146 12 : keys.addOutputComponent("_work","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
147 : "These quantities will named with the arguments of the bias followed by "
148 : "the character string _work. These quantities tell the user how much work has "
149 : "been done by the potential in dragging the system along the various colvar axis.");
150 12 : keys.addOutputComponent("_kappa","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
151 : "These quantities will named with the arguments of the bias followed by "
152 : "the character string _kappa. These quantities tell the user the time dependent value of kappa.");
153 6 : }
154 :
155 4 : MovingRestraint::MovingRestraint(const ActionOptions&ao):
156 : PLUMED_BIAS_INIT(ao),
157 4 : verse(getNumberOfArguments()),
158 4 : kk(getNumberOfArguments()),
159 4 : aa(getNumberOfArguments()),
160 4 : f(getNumberOfArguments()),
161 8 : dpotdk(getNumberOfArguments()) {
162 4 : parseVector("VERSE",verse);
163 4 : std::vector<long long int> ss(1);
164 4 : ss[0]=-1;
165 4 : std::vector<double> kk( getNumberOfArguments() ), aa( getNumberOfArguments() );
166 10 : for(int i=0;; i++) {
167 : // Read in step
168 28 : if( !parseNumberedVector("STEP",i,ss) ) {
169 : break;
170 : }
171 19 : for(unsigned j=0; j<step.size(); j++) {
172 9 : if(ss[0]<step[j]) {
173 0 : error("in moving restraint step number must always increase");
174 : }
175 : }
176 10 : step.push_back(ss[0]);
177 :
178 : // Try to read kappa
179 20 : if( !parseNumberedVector("KAPPA",i,kk) ) {
180 3 : kk=kappa[i-1];
181 : }
182 10 : kappa.push_back(kk);
183 :
184 : // Now read AT
185 20 : if( !parseNumberedVector("AT",i,aa) ) {
186 1 : aa=at[i-1];
187 : }
188 10 : at.push_back(aa);
189 10 : }
190 4 : checkRead();
191 :
192 14 : for(unsigned i=0; i<step.size(); i++) {
193 10 : log.printf(" step%u %lld\n",i,step[i]);
194 10 : log.printf(" at");
195 22 : for(unsigned j=0; j<at[i].size(); j++) {
196 12 : log.printf(" %f",at[i][j]);
197 : }
198 10 : log.printf("\n");
199 10 : log.printf(" with force constant");
200 22 : for(unsigned j=0; j<kappa[i].size(); j++) {
201 12 : log.printf(" %f",kappa[i][j]);
202 : }
203 10 : log.printf("\n");
204 : };
205 :
206 8 : addComponent("force2");
207 4 : componentIsNotPeriodic("force2");
208 4 : valueForce2=getPntrToComponent("force2");
209 :
210 : // add the centers of the restraint as additional components that can be retrieved (useful for debug)
211 :
212 : std::string comp;
213 9 : for(unsigned i=0; i< getNumberOfArguments() ; i++) {
214 10 : comp=getPntrToArgument(i)->getName()+"_cntr"; // each spring has its own center
215 5 : addComponent(comp);
216 5 : componentIsNotPeriodic(comp);
217 5 : valueCntr.push_back(getPntrToComponent(comp));
218 10 : comp=getPntrToArgument(i)->getName()+"_work"; // each spring has its own work
219 5 : addComponent(comp);
220 5 : componentIsNotPeriodic(comp);
221 5 : valueWork.push_back(getPntrToComponent(comp));
222 10 : comp=getPntrToArgument(i)->getName()+"_kappa"; // each spring has its own kappa
223 5 : addComponent(comp);
224 5 : componentIsNotPeriodic(comp);
225 5 : valueKappa.push_back(getPntrToComponent(comp));
226 5 : work.push_back(0.); // initialize the work value
227 : }
228 8 : addComponent("work");
229 4 : componentIsNotPeriodic("work");
230 4 : valueTotWork=getPntrToComponent("work");
231 4 : tot_work=0.0;
232 :
233 4 : log<<" Bibliography ";
234 8 : log<<cite("Grubmuller, Heymann, and Tavan, Science 271, 997 (1996)")<<"\n";
235 :
236 4 : }
237 :
238 :
239 566 : void MovingRestraint::calculate() {
240 : double ene=0.0;
241 : double totf2=0.0;
242 566 : unsigned narg=getNumberOfArguments();
243 566 : long long int now=getStep();
244 566 : if(now<=step[0]) {
245 3 : kk=kappa[0];
246 3 : aa=at[0];
247 3 : oldaa=at[0];
248 3 : oldk=kappa[0];
249 3 : olddpotdk.resize(narg);
250 3 : oldf.resize(narg);
251 563 : } else if(now>=step[step.size()-1]) {
252 47 : kk=kappa[step.size()-1];
253 47 : aa=at[step.size()-1];
254 : } else {
255 : unsigned i=0;
256 521 : for(i=1; i<step.size()-1; i++)
257 10 : if(now<step[i]) {
258 : break;
259 : }
260 516 : double c2=(now-step[i-1])/double(step[i]-step[i-1]);
261 516 : double c1=1.0-c2;
262 1040 : for(unsigned j=0; j<narg; j++) {
263 524 : kk[j]=(c1*kappa[i-1][j]+c2*kappa[i][j]);
264 : }
265 1040 : for(unsigned j=0; j<narg; j++) {
266 524 : const double a1=at[i-1][j];
267 524 : const double a2=at[i][j];
268 524 : aa[j]=(c1*a1+c2*(a1+difference(j,a1,a2)));
269 : }
270 : }
271 566 : tot_work=0.0;
272 1142 : for(unsigned i=0; i<narg; ++i) {
273 576 : const double cv=difference(i,aa[i],getArgument(i)); // this gives: getArgument(i) - aa[i]
274 576 : valueCntr[i]->set(aa[i]);
275 576 : const double k=kk[i];
276 576 : f[i]=-k*cv;
277 576 : if(verse[i]=="U" && cv<0) {
278 0 : continue;
279 : }
280 576 : if(verse[i]=="L" && cv>0) {
281 0 : continue;
282 : }
283 1728 : plumed_assert(verse[i]=="U" || verse[i]=="L" || verse[i]=="B");
284 576 : dpotdk[i]=0.5*cv*cv;
285 576 : if(oldaa.size()==aa.size() && oldf.size()==f.size()) {
286 575 : work[i]+=0.5*(oldf[i]+f[i])*(aa[i]-oldaa[i]) + 0.5*( dpotdk[i]+olddpotdk[i] )*(kk[i]-oldk[i]);
287 : }
288 576 : valueWork[i]->set(work[i]);
289 576 : valueKappa[i]->set(kk[i]);
290 576 : tot_work+=work[i];
291 576 : ene+=0.5*k*cv*cv;
292 576 : setOutputForce(i,f[i]);
293 576 : totf2+=f[i]*f[i];
294 : };
295 566 : valueTotWork->set(tot_work);
296 566 : oldf=f;
297 566 : oldaa=aa;
298 566 : oldk=kk;
299 566 : olddpotdk=dpotdk;
300 566 : setBias(ene);
301 566 : valueForce2->set(totf2);
302 566 : }
303 :
304 : }
305 : }
306 :
307 :
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