Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2019 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 :
26 : using namespace std;
27 :
28 :
29 : namespace PLMD {
30 : namespace bias {
31 :
32 : //+PLUMEDOC BIAS BIASVALUE
33 : /*
34 : Takes the value of one variable and use it as a bias
35 :
36 : This is the simplest possible bias: the bias potential is equal to a collective variable.
37 : It is useful to create custom biasing potential, e.g. applying a function (see \ref Function)
38 : to some collective variable then using the value of this function directly as a bias.
39 :
40 : \par Examples
41 :
42 : The following input tells plumed to use the value of the distance between atoms 3 and 5
43 : and the value of the distance between atoms 2 and 4 as biases.
44 : It then tells plumed to print the energy of the restraint
45 : \plumedfile
46 : DISTANCE ATOMS=3,5 LABEL=d1
47 : DISTANCE ATOMS=3,6 LABEL=d2
48 : BIASVALUE ARG=d1,d2 LABEL=b
49 : PRINT ARG=d1,d2,b.d1,b.d2
50 : \endplumedfile
51 :
52 : Another thing one can do is asking one system to follow
53 : a circle in sin/cos according a time dependence
54 :
55 : \plumedfile
56 : t: TIME
57 : # this just print cos and sin of time
58 : cos: MATHEVAL ARG=t VAR=t FUNC=cos(t) PERIODIC=NO
59 : sin: MATHEVAL ARG=t VAR=t FUNC=sin(t) PERIODIC=NO
60 : c1: COM ATOMS=1,2
61 : c2: COM ATOMS=3,4
62 : d: DISTANCE COMPONENTS ATOMS=c1,c2
63 : PRINT ARG=t,cos,sin,d.x,d.y,d.z STRIDE=1 FILE=colvar FMT=%8.4f
64 : # this calculates sine and cosine of a projected component of distance
65 : mycos: MATHEVAL ARG=d.x,d.y VAR=x,y FUNC=x/sqrt(x*x+y*y) PERIODIC=NO
66 : mysin: MATHEVAL ARG=d.x,d.y VAR=x,y FUNC=y/sqrt(x*x+y*y) PERIODIC=NO
67 : # this creates a moving spring so that the system follows a circle-like dynamics
68 : # but it is not a bias, it is a simple value now
69 : vv1: MATHEVAL ARG=mycos,mysin,cos,sin VAR=mc,ms,c,s FUNC=100*((mc-c)^2+(ms-s)^2) PERIODIC=NO
70 : # this takes the value calculated with matheval and uses as a bias
71 : cc: BIASVALUE ARG=vv1
72 : # some printout
73 : PRINT ARG=t,cos,sin,d.x,d.y,d.z,mycos,mysin,cc.bias.vv1 STRIDE=1 FILE=colvar FMT=%8.4f
74 : \endplumedfile
75 :
76 : */
77 : //+ENDPLUMEDOC
78 :
79 38 : class BiasValue : public Bias {
80 : public:
81 : explicit BiasValue(const ActionOptions&);
82 : void calculate();
83 : static void registerKeywords(Keywords& keys);
84 : };
85 :
86 6471 : PLUMED_REGISTER_ACTION(BiasValue,"BIASVALUE")
87 :
88 20 : void BiasValue::registerKeywords(Keywords& keys) {
89 20 : Bias::registerKeywords(keys);
90 40 : keys.use("ARG");
91 : // Should be _bias below
92 80 : keys.addOutputComponent("_bias","default","one or multiple instances of this quantity will be refereceable elsewhere in the input file. "
93 : "these quantities will named with the arguments of the bias followed by "
94 : "the character string _bias. These quantities tell the user how much the bias is "
95 : "due to each of the colvars.");
96 20 : }
97 :
98 19 : BiasValue::BiasValue(const ActionOptions&ao):
99 19 : PLUMED_BIAS_INIT(ao)
100 : {
101 19 : checkRead();
102 : // add one bias for each argument
103 59 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
104 20 : string ss=getPntrToArgument(i)->getName()+"_bias";
105 20 : addComponent(ss); componentIsNotPeriodic(ss);
106 : }
107 19 : }
108 :
109 138 : void BiasValue::calculate() {
110 : double bias=0.0;
111 426 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
112 : double val; val=getArgument(i);
113 144 : getPntrToComponent(i+1)->set(val);
114 144 : setOutputForce(i,-1.);
115 144 : bias+=val;
116 : }
117 : setBias(bias);
118 138 : }
119 :
120 : }
121 4839 : }
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