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 : \f$
39 : \sum_i {k_i}((x_i-a_i+o_i)/s_i)^e_i
40 : \f$
41 :
42 : \f$k_i\f$ (KAPPA) is an energy constant in internal unit of the code, \f$s_i\f$ (EPS) a rescaling factor and
43 : \f$e_i\f$ (EXP) the exponent determining the power law. By default: EXP = 2, EPS = 1.0, OFFSET = 0.
44 :
45 :
46 : \par Examples
47 :
48 : The following input tells plumed to add both a lower and an upper walls on the distance
49 : between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits
50 : are defined at different values. The strength of the walls is the same for the four cases.
51 : It also tells plumed to print the energy of the walls.
52 : \plumedfile
53 : DISTANCE ATOMS=3,5 LABEL=d1
54 : DISTANCE ATOMS=2,4 LABEL=d2
55 : 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
56 : 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
57 : PRINT ARG=uwall.bias,lwall.bias
58 : \endplumedfile
59 :
60 : */
61 : //+ENDPLUMEDOC
62 :
63 : class UWalls : public Bias {
64 : std::vector<double> at;
65 : std::vector<double> kappa;
66 : std::vector<double> exp;
67 : std::vector<double> eps;
68 : std::vector<double> offset;
69 : public:
70 : explicit UWalls(const ActionOptions&);
71 : void calculate() override;
72 : static void registerKeywords(Keywords& keys);
73 : };
74 :
75 10453 : PLUMED_REGISTER_ACTION(UWalls,"UPPER_WALLS")
76 :
77 18 : void UWalls::registerKeywords(Keywords& keys) {
78 18 : Bias::registerKeywords(keys);
79 18 : keys.use("ARG");
80 36 : keys.add("compulsory","AT","the positions of the wall. The a_i in the expression for a wall.");
81 36 : keys.add("compulsory","KAPPA","the force constant for the wall. The k_i in the expression for a wall.");
82 36 : keys.add("compulsory","OFFSET","0.0","the offset for the start of the wall. The o_i in the expression for a wall.");
83 36 : keys.add("compulsory","EXP","2.0","the powers for the walls. The e_i in the expression for a wall.");
84 36 : keys.add("compulsory","EPS","1.0","the values for s_i in the expression for a wall");
85 36 : keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
86 18 : }
87 :
88 17 : UWalls::UWalls(const ActionOptions&ao):
89 : PLUMED_BIAS_INIT(ao),
90 34 : at(getNumberOfArguments(),0),
91 17 : kappa(getNumberOfArguments(),0.0),
92 17 : exp(getNumberOfArguments(),2.0),
93 17 : eps(getNumberOfArguments(),1.0),
94 34 : offset(getNumberOfArguments(),0.0)
95 : {
96 : // Note : the sizes of these vectors are checked automatically by parseVector
97 17 : parseVector("OFFSET",offset);
98 17 : parseVector("EPS",eps);
99 17 : parseVector("EXP",exp);
100 17 : parseVector("KAPPA",kappa);
101 17 : parseVector("AT",at);
102 17 : checkRead();
103 :
104 17 : log.printf(" at");
105 34 : for(unsigned i=0; i<at.size(); i++) log.printf(" %f",at[i]);
106 17 : log.printf("\n");
107 17 : log.printf(" with an offset");
108 34 : for(unsigned i=0; i<offset.size(); i++) log.printf(" %f",offset[i]);
109 17 : log.printf("\n");
110 17 : log.printf(" with force constant");
111 34 : for(unsigned i=0; i<kappa.size(); i++) log.printf(" %f",kappa[i]);
112 17 : log.printf("\n");
113 17 : log.printf(" and exponent");
114 34 : for(unsigned i=0; i<exp.size(); i++) log.printf(" %f",exp[i]);
115 17 : log.printf("\n");
116 17 : log.printf(" rescaled");
117 34 : for(unsigned i=0; i<eps.size(); i++) log.printf(" %f",eps[i]);
118 17 : log.printf("\n");
119 :
120 34 : addComponent("force2"); componentIsNotPeriodic("force2");
121 17 : }
122 :
123 28015 : void UWalls::calculate() {
124 : double ene=0.0;
125 : double totf2=0.0;
126 56030 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
127 : double f = 0.0;
128 28015 : const double cv=difference(i,at[i],getArgument(i));
129 28015 : const double off=offset[i];
130 28015 : const double epsilon=eps[i];
131 28015 : const double uscale = (cv+off)/epsilon;
132 28015 : if( uscale > 0.) {
133 6 : const double k=kappa[i];
134 6 : const double exponent=exp[i];
135 6 : double power = pow( uscale, exponent );
136 6 : f = -( k / epsilon ) * exponent * power / uscale;
137 6 : ene += k * power;
138 6 : totf2 += f * f;
139 : }
140 : setOutputForce(i,f);
141 : }
142 : setBias(ene);
143 28015 : getPntrToComponent("force2")->set(totf2);
144 28015 : }
145 :
146 : }
147 : }
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