Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2023 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 UPPER_WALLS
29 : /*
30 : Defines a wall for the value of one or more collective variables,
31 : which limits the region of the phase space accessible during the simulation.
32 :
33 : The restraining potential starts acting on the system when the value of the CV is greater
34 : (in the case of UPPER_WALLS) or lower (in the case of LOWER_WALLS) than a certain limit \f$a_i\f$ (AT)
35 : minus an offset \f$o_i\f$ (OFFSET).
36 : The expression for the bias due to the wall is given by:
37 :
38 : for UPPER_WALLS:
39 : \f$
40 : \sum_i {k_i}((x_i-a_i+o_i)/s_i)^e_i
41 : \f$
42 :
43 : for LOWER_WALLS:
44 : \f$
45 : \sum_i {k_i}|(x_i-a_i-o_i)/s_i|^e_i
46 : \f$
47 :
48 : \f$k_i\f$ (KAPPA) is an energy constant in internal unit of the code, \f$s_i\f$ (EPS) a rescaling factor and
49 : \f$e_i\f$ (EXP) the exponent determining the power law. By default: EXP = 2, EPS = 1.0, OFFSET = 0.
50 :
51 :
52 : \par Examples
53 :
54 : The following input tells plumed to add both a lower and an upper walls on the distance
55 : between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits
56 : are defined at different values. The strength of the walls is the same for the four cases.
57 : It also tells plumed to print the energy of the walls.
58 : \plumedfile
59 : DISTANCE ATOMS=3,5 LABEL=d1
60 : DISTANCE ATOMS=2,4 LABEL=d2
61 : UPPER_WALLS ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=uwall
62 : LOWER_WALLS ARG=d1,d2 AT=0.0,1.0 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=lwall
63 : PRINT ARG=uwall.bias,lwall.bias
64 : \endplumedfile
65 :
66 :
67 : \par Periodic arguments
68 :
69 : If an argument is periodic (e.g. a \ref TORSION), the wall acts on the value of the argument in its periodic domain
70 : and periodic boundary conditions are __not__ applied to the difference \f$x_i-a_i\f$. The value of AT must thus be within the
71 : periodic domain of the argument. This is the case both when the arguments are scalars and when they are vectors.
72 : The following input restrains a torsion within the interval \f$[-2,2]\f$:
73 : \plumedfile
74 : t: TORSION ATOMS=1,2,3,4
75 : uwall: UPPER_WALLS ARG=t AT=2.0 KAPPA=150.0
76 : lwall: LOWER_WALLS ARG=t AT=-2.0 KAPPA=150.0
77 : PRINT ARG=t,uwall.bias,lwall.bias
78 : \endplumedfile
79 :
80 : Notice that the bias is discontinuous at the boundary of the periodic domain (here at \f$\pm\pi\f$). You should thus make sure that
81 : the walls keep the argument far from this boundary, e.g. by using both an upper and a lower wall as in the input above.
82 :
83 : Versions of PLUMED before 2.9.7 applied periodic boundary conditions to the difference \f$x_i-a_i\f$. With that choice, each wall acts on half of the
84 : periodic domain, and the region left free by an upper and a lower wall is smaller than the one between AT values
85 : (see \issue{658}).
86 :
87 : */
88 : //+ENDPLUMEDOC
89 :
90 : //+PLUMEDOC BIAS UPPER_WALLS_SCALAR
91 : /*
92 : Defines a wall for the value of one or more collective variables,
93 : which limits the region of the phase space accessible during the simulation.
94 :
95 : \par Examples
96 :
97 : */
98 : //+ENDPLUMEDOC
99 :
100 : class UWalls : public Bias {
101 : std::vector<double> at;
102 : std::vector<double> kappa;
103 : std::vector<double> exp;
104 : std::vector<double> eps;
105 : std::vector<double> offset;
106 : public:
107 : explicit UWalls(const ActionOptions&);
108 : void calculate() override;
109 : static void registerKeywords(Keywords& keys);
110 : };
111 :
112 : PLUMED_REGISTER_ACTION(UWalls,"UPPER_WALLS_SCALAR")
113 :
114 38 : void UWalls::registerKeywords(Keywords& keys) {
115 38 : Bias::registerKeywords(keys);
116 38 : keys.setDisplayName("UPPER_WALLS");
117 38 : keys.use("ARG");
118 76 : keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log");
119 76 : keys.add("compulsory","AT","the positions of the wall. The a_i in the expression for a wall.");
120 76 : keys.add("compulsory","KAPPA","the force constant for the wall. The k_i in the expression for a wall.");
121 76 : keys.add("compulsory","OFFSET","0.0","the offset for the start of the wall. The o_i in the expression for a wall.");
122 76 : keys.add("compulsory","EXP","2.0","the powers for the walls. The e_i in the expression for a wall.");
123 76 : keys.add("compulsory","EPS","1.0","the values for s_i in the expression for a wall");
124 76 : keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
125 38 : }
126 :
127 17 : UWalls::UWalls(const ActionOptions&ao):
128 : PLUMED_BIAS_INIT(ao),
129 34 : at(getNumberOfArguments(),0),
130 17 : kappa(getNumberOfArguments(),0.0),
131 17 : exp(getNumberOfArguments(),2.0),
132 17 : eps(getNumberOfArguments(),1.0),
133 34 : offset(getNumberOfArguments(),0.0) {
134 : // Note : the sizes of these vectors are checked automatically by parseVector
135 17 : parseVector("OFFSET",offset);
136 17 : parseVector("EPS",eps);
137 17 : parseVector("EXP",exp);
138 17 : parseVector("KAPPA",kappa);
139 17 : parseVector("AT",at);
140 17 : checkRead();
141 :
142 17 : log.printf(" at");
143 36 : for(unsigned i=0; i<at.size(); i++) {
144 19 : log.printf(" %f",at[i]);
145 : }
146 17 : log.printf("\n");
147 17 : log.printf(" with an offset");
148 36 : for(unsigned i=0; i<offset.size(); i++) {
149 19 : log.printf(" %f",offset[i]);
150 : }
151 17 : log.printf("\n");
152 17 : log.printf(" with force constant");
153 36 : for(unsigned i=0; i<kappa.size(); i++) {
154 19 : log.printf(" %f",kappa[i]);
155 : }
156 17 : log.printf("\n");
157 17 : log.printf(" and exponent");
158 36 : for(unsigned i=0; i<exp.size(); i++) {
159 19 : log.printf(" %f",exp[i]);
160 : }
161 17 : log.printf("\n");
162 17 : log.printf(" rescaled");
163 36 : for(unsigned i=0; i<eps.size(); i++) {
164 19 : log.printf(" %f",eps[i]);
165 : }
166 17 : log.printf("\n");
167 :
168 : // The wall acts on the value of the argument in its domain, without periodic images
169 : // (see https://github.com/plumed/plumed2/issues/658).
170 36 : for(unsigned i=0; i<getNumberOfArguments(); i++) {
171 : Value* arg=getPntrToArgument(i);
172 19 : if( arg->isPeriodic() ) {
173 : double min, max;
174 4 : arg->getDomain( min, max );
175 4 : if( at[i]<min || at[i]>max ) {
176 0 : error("the position of the wall (AT) for periodic argument " + arg->getName() + " should be within its periodic domain");
177 : }
178 4 : log.printf(" WARNING: argument %s is periodic. The wall acts on its value in the domain [%f,%f]\n"
179 : " without periodic images, so the bias is discontinuous at the boundary of the domain.\n"
180 : " Make sure that the walls keep the argument far from it (e.g. use both an upper and a lower wall).\n",
181 : arg->getName().c_str(), min, max );
182 : }
183 : }
184 :
185 34 : addComponent("force2");
186 17 : componentIsNotPeriodic("force2");
187 17 : }
188 :
189 14127 : void UWalls::calculate() {
190 : double ene=0.0;
191 : double totf2=0.0;
192 28318 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
193 : double f = 0.0;
194 : // no periodic boundary conditions here, see the documentation and issue #658
195 14191 : const double cv=getArgument(i)-at[i];
196 14191 : const double off=offset[i];
197 14191 : const double epsilon=eps[i];
198 14191 : const double uscale = (cv+off)/epsilon;
199 14191 : if( uscale > 0.) {
200 57 : const double k=kappa[i];
201 57 : const double exponent=exp[i];
202 57 : double power = pow( uscale, exponent );
203 57 : f = -( k / epsilon ) * exponent * power / uscale;
204 57 : ene += k * power;
205 57 : totf2 += f * f;
206 : }
207 14191 : setOutputForce(i,f);
208 : }
209 14127 : setBias(ene);
210 14127 : getPntrToComponent("force2")->set(totf2);
211 14127 : }
212 :
213 : }
214 : }
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