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 "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 : double tot_work;
111 : public:
112 : explicit MovingRestraint(const ActionOptions&);
113 : void calculate() override;
114 : static void registerKeywords( Keywords& keys );
115 : };
116 :
117 13793 : PLUMED_REGISTER_ACTION(MovingRestraint,"MOVINGRESTRAINT")
118 :
119 8 : void MovingRestraint::registerKeywords( Keywords& keys ) {
120 8 : Bias::registerKeywords(keys);
121 8 : keys.use("ARG");
122 16 : keys.add("compulsory","VERSE","B","Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than "
123 : "the restraint or whether it is acting on both sides (B)");
124 16 : keys.add("numbered","STEP","This keyword appears multiple times as STEP\\f$x\\f$ with x=0,1,2,...,n. Each value given represents "
125 : "the MD step at which the restraint parameters take the values KAPPA\\f$x\\f$ and AT\\f$x\\f$.");
126 16 : keys.reset_style("STEP","compulsory");
127 16 : keys.add("numbered","AT","AT\\f$x\\f$ is equal to the position of the restraint at time STEP\\f$x\\f$. For intermediate times this parameter "
128 : "is linearly interpolated. If no AT\\f$x\\f$ is specified for STEP\\f$x\\f$ then the values of AT are kept constant "
129 : "during the interval of time between STEP\\f$x-1\\f$ and STEP\\f$x\\f$.");
130 16 : keys.reset_style("AT","compulsory");
131 16 : keys.add("numbered","KAPPA","KAPPA\\f$x\\f$ is equal to the value of the force constants at time STEP\\f$x\\f$. For intermediate times this "
132 : "parameter is linearly interpolated. If no KAPPA\\f$x\\f$ is specified for STEP\\f$x\\f$ then the values of KAPPA\\f$x\\f$ "
133 : "are kept constant during the interval of time between STEP\\f$x-1\\f$ and STEP\\f$x\\f$.");
134 16 : keys.reset_style("KAPPA","compulsory");
135 16 : keys.addOutputComponent("work","default","the total work performed changing this restraint");
136 16 : keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
137 16 : keys.addOutputComponent("_cntr","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
138 : "these quantities will named with the arguments of the bias followed by "
139 : "the character string _cntr. These quantities give the instantaneous position "
140 : "of the center of the harmonic potential.");
141 16 : keys.addOutputComponent("_work","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
142 : "These quantities will named with the arguments of the bias followed by "
143 : "the character string _work. These quantities tell the user how much work has "
144 : "been done by the potential in dragging the system along the various colvar axis.");
145 16 : keys.addOutputComponent("_kappa","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
146 : "These quantities will named with the arguments of the bias followed by "
147 : "the character string _kappa. These quantities tell the user the time dependent value of kappa.");
148 8 : }
149 :
150 4 : MovingRestraint::MovingRestraint(const ActionOptions&ao):
151 : PLUMED_BIAS_INIT(ao),
152 4 : verse(getNumberOfArguments()) {
153 4 : parseVector("VERSE",verse);
154 4 : std::vector<long long int> ss(1);
155 4 : ss[0]=-1;
156 4 : std::vector<double> kk( getNumberOfArguments() ), aa( getNumberOfArguments() );
157 10 : for(int i=0;; i++) {
158 : // Read in step
159 28 : if( !parseNumberedVector("STEP",i,ss) ) {
160 : break;
161 : }
162 19 : for(unsigned j=0; j<step.size(); j++) {
163 9 : if(ss[0]<step[j]) {
164 0 : error("in moving restraint step number must always increase");
165 : }
166 : }
167 10 : step.push_back(ss[0]);
168 :
169 : // Try to read kappa
170 20 : if( !parseNumberedVector("KAPPA",i,kk) ) {
171 3 : kk=kappa[i-1];
172 : }
173 10 : kappa.push_back(kk);
174 :
175 : // Now read AT
176 20 : if( !parseNumberedVector("AT",i,aa) ) {
177 1 : aa=at[i-1];
178 : }
179 10 : at.push_back(aa);
180 10 : }
181 4 : checkRead();
182 :
183 14 : for(unsigned i=0; i<step.size(); i++) {
184 10 : log.printf(" step%u %lld\n",i,step[i]);
185 10 : log.printf(" at");
186 22 : for(unsigned j=0; j<at[i].size(); j++) {
187 12 : log.printf(" %f",at[i][j]);
188 : }
189 10 : log.printf("\n");
190 10 : log.printf(" with force constant");
191 22 : for(unsigned j=0; j<kappa[i].size(); j++) {
192 12 : log.printf(" %f",kappa[i][j]);
193 : }
194 10 : log.printf("\n");
195 : };
196 :
197 4 : addComponent("force2");
198 8 : componentIsNotPeriodic("force2");
199 :
200 : // add the centers of the restraint as additional components that can be retrieved (useful for debug)
201 :
202 : std::string comp;
203 9 : for(unsigned i=0; i< getNumberOfArguments() ; i++) {
204 5 : comp=getPntrToArgument(i)->getName()+"_cntr"; // each spring has its own center
205 5 : addComponent(comp);
206 5 : componentIsNotPeriodic(comp);
207 5 : comp=getPntrToArgument(i)->getName()+"_work"; // each spring has its own work
208 5 : addComponent(comp);
209 5 : componentIsNotPeriodic(comp);
210 5 : comp=getPntrToArgument(i)->getName()+"_kappa"; // each spring has its own kappa
211 5 : addComponent(comp);
212 5 : componentIsNotPeriodic(comp);
213 5 : work.push_back(0.); // initialize the work value
214 : }
215 4 : addComponent("work");
216 4 : componentIsNotPeriodic("work");
217 4 : tot_work=0.0;
218 :
219 4 : log<<" Bibliography ";
220 8 : log<<cite("Grubmuller, Heymann, and Tavan, Science 271, 997 (1996)")<<"\n";
221 :
222 4 : }
223 :
224 :
225 566 : void MovingRestraint::calculate() {
226 : double ene=0.0;
227 : double totf2=0.0;
228 566 : unsigned narg=getNumberOfArguments();
229 566 : long long int now=getStep();
230 566 : std::vector<double> kk(narg),aa(narg),f(narg),dpotdk(narg);
231 566 : if(now<=step[0]) {
232 3 : kk=kappa[0];
233 3 : aa=at[0];
234 3 : oldaa=at[0];
235 3 : oldk=kappa[0];
236 3 : olddpotdk.resize(narg);
237 3 : oldf.resize(narg);
238 563 : } else if(now>=step[step.size()-1]) {
239 47 : kk=kappa[step.size()-1];
240 47 : aa=at[step.size()-1];
241 : } else {
242 : unsigned i=0;
243 521 : for(i=1; i<step.size()-1; i++)
244 10 : if(now<step[i]) {
245 : break;
246 : }
247 516 : double c2=(now-step[i-1])/double(step[i]-step[i-1]);
248 516 : double c1=1.0-c2;
249 1040 : for(unsigned j=0; j<narg; j++) {
250 524 : kk[j]=(c1*kappa[i-1][j]+c2*kappa[i][j]);
251 : }
252 1040 : for(unsigned j=0; j<narg; j++) {
253 524 : const double a1=at[i-1][j];
254 524 : const double a2=at[i][j];
255 524 : aa[j]=(c1*a1+c2*(a1+difference(j,a1,a2)));
256 : }
257 : }
258 566 : tot_work=0.0;
259 1142 : for(unsigned i=0; i<narg; ++i) {
260 576 : const double cv=difference(i,aa[i],getArgument(i)); // this gives: getArgument(i) - aa[i]
261 1152 : getPntrToComponent(getPntrToArgument(i)->getName()+"_cntr")->set(aa[i]);
262 576 : const double k=kk[i];
263 576 : f[i]=-k*cv;
264 576 : if(verse[i]=="U" && cv<0) {
265 0 : continue;
266 : }
267 576 : if(verse[i]=="L" && cv>0) {
268 0 : continue;
269 : }
270 1728 : plumed_assert(verse[i]=="U" || verse[i]=="L" || verse[i]=="B");
271 576 : dpotdk[i]=0.5*cv*cv;
272 576 : if(oldaa.size()==aa.size() && oldf.size()==f.size()) {
273 575 : work[i]+=0.5*(oldf[i]+f[i])*(aa[i]-oldaa[i]) + 0.5*( dpotdk[i]+olddpotdk[i] )*(kk[i]-oldk[i]);
274 : }
275 1152 : getPntrToComponent(getPntrToArgument(i)->getName()+"_work")->set(work[i]);
276 1152 : getPntrToComponent(getPntrToArgument(i)->getName()+"_kappa")->set(kk[i]);
277 576 : tot_work+=work[i];
278 576 : ene+=0.5*k*cv*cv;
279 576 : setOutputForce(i,f[i]);
280 576 : totf2+=f[i]*f[i];
281 : };
282 566 : getPntrToComponent("work")->set(tot_work);
283 566 : oldf=f;
284 566 : oldaa=aa;
285 566 : oldk=kk;
286 566 : olddpotdk=dpotdk;
287 : setBias(ene);
288 1132 : getPntrToComponent("force2")->set(totf2);
289 566 : }
290 :
291 : }
292 : }
293 :
294 :
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