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 "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 : //+ENDPLUMEDOC
68 :
69 : class UWalls : public Bias {
70 : std::vector<double> at;
71 : std::vector<double> kappa;
72 : std::vector<double> exp;
73 : std::vector<double> eps;
74 : std::vector<double> offset;
75 : public:
76 : explicit UWalls(const ActionOptions&);
77 : void calculate() override;
78 : static void registerKeywords(Keywords& keys);
79 : };
80 :
81 13827 : PLUMED_REGISTER_ACTION(UWalls,"UPPER_WALLS")
82 :
83 25 : void UWalls::registerKeywords(Keywords& keys) {
84 25 : Bias::registerKeywords(keys);
85 25 : keys.use("ARG");
86 50 : keys.add("compulsory","AT","the positions of the wall. The a_i in the expression for a wall.");
87 50 : keys.add("compulsory","KAPPA","the force constant for the wall. The k_i in the expression for a wall.");
88 50 : keys.add("compulsory","OFFSET","0.0","the offset for the start of the wall. The o_i in the expression for a wall.");
89 50 : keys.add("compulsory","EXP","2.0","the powers for the walls. The e_i in the expression for a wall.");
90 50 : keys.add("compulsory","EPS","1.0","the values for s_i in the expression for a wall");
91 50 : keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
92 25 : }
93 :
94 21 : UWalls::UWalls(const ActionOptions&ao):
95 : PLUMED_BIAS_INIT(ao),
96 42 : at(getNumberOfArguments(),0),
97 21 : kappa(getNumberOfArguments(),0.0),
98 21 : exp(getNumberOfArguments(),2.0),
99 21 : eps(getNumberOfArguments(),1.0),
100 42 : offset(getNumberOfArguments(),0.0) {
101 : // Note : the sizes of these vectors are checked automatically by parseVector
102 21 : parseVector("OFFSET",offset);
103 21 : parseVector("EPS",eps);
104 21 : parseVector("EXP",exp);
105 21 : parseVector("KAPPA",kappa);
106 21 : parseVector("AT",at);
107 21 : checkRead();
108 :
109 21 : log.printf(" at");
110 42 : for(unsigned i=0; i<at.size(); i++) {
111 21 : log.printf(" %f",at[i]);
112 : }
113 21 : log.printf("\n");
114 21 : log.printf(" with an offset");
115 42 : for(unsigned i=0; i<offset.size(); i++) {
116 21 : log.printf(" %f",offset[i]);
117 : }
118 21 : log.printf("\n");
119 21 : log.printf(" with force constant");
120 42 : for(unsigned i=0; i<kappa.size(); i++) {
121 21 : log.printf(" %f",kappa[i]);
122 : }
123 21 : log.printf("\n");
124 21 : log.printf(" and exponent");
125 42 : for(unsigned i=0; i<exp.size(); i++) {
126 21 : log.printf(" %f",exp[i]);
127 : }
128 21 : log.printf("\n");
129 21 : log.printf(" rescaled");
130 42 : for(unsigned i=0; i<eps.size(); i++) {
131 21 : log.printf(" %f",eps[i]);
132 : }
133 21 : log.printf("\n");
134 :
135 21 : addComponent("force2");
136 21 : componentIsNotPeriodic("force2");
137 21 : }
138 :
139 28059 : void UWalls::calculate() {
140 : double ene=0.0;
141 : double totf2=0.0;
142 56118 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
143 : double f = 0.0;
144 28059 : const double cv=difference(i,at[i],getArgument(i));
145 28059 : const double off=offset[i];
146 28059 : const double epsilon=eps[i];
147 28059 : const double uscale = (cv+off)/epsilon;
148 28059 : if( uscale > 0.) {
149 26 : const double k=kappa[i];
150 26 : const double exponent=exp[i];
151 26 : double power = pow( uscale, exponent );
152 26 : f = -( k / epsilon ) * exponent * power / uscale;
153 26 : ene += k * power;
154 26 : totf2 += f * f;
155 : }
156 : setOutputForce(i,f);
157 : }
158 : setBias(ene);
159 28059 : getPntrToComponent("force2")->set(totf2);
160 28059 : }
161 :
162 : }
163 : }
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