1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 Copyright (c) 2011-2021 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
24
25 namespace PLMD {
26 namespace bias {
27
Bias(const ActionOptions & ao)28 Bias::Bias(const ActionOptions&ao):
29 Action(ao),
30 ActionPilot(ao),
31 ActionWithValue(ao),
32 ActionWithArguments(ao),
33 outputForces(getNumberOfArguments(),0.0)
34 {
35 addComponentWithDerivatives("bias");
36 componentIsNotPeriodic("bias");
37 valueBias=getPntrToComponent("bias");
38
39 if(getStride()>1) {
40 log<<" multiple time step "<<getStride()<<" ";
41 log<<cite("Ferrarotti, Bottaro, Perez-Villa, and Bussi, J. Chem. Theory Comput. 11, 139 (2015)")<<"\n";
42 }
43 for(unsigned i=0; i<getNumberOfArguments(); ++i) {
44 (getPntrToArgument(i)->getPntrToAction())->turnOnDerivatives();
45 }
46
47 turnOnDerivatives();
48 }
49
registerKeywords(Keywords & keys)50 void Bias::registerKeywords( Keywords& keys ) {
51 Action::registerKeywords(keys);
52 ActionPilot::registerKeywords(keys);
53 ActionWithValue::registerKeywords(keys);
54 ActionWithArguments::registerKeywords(keys);
55 keys.add("hidden","STRIDE","the frequency with which the forces due to the bias should be calculated. This can be used to correctly set up multistep algorithms");
56 componentsAreNotOptional(keys);
57 keys.addOutputComponent("bias","default","the instantaneous value of the bias potential");
58 }
59
apply()60 void Bias::apply() {
61 const unsigned noa=getNumberOfArguments();
62 const unsigned ncp=getNumberOfComponents();
63
64 if(onStep()) {
65 double gstr = static_cast<double>(getStride());
66 for(unsigned i=0; i<noa; ++i) {
67 getPntrToArgument(i)->addForce(gstr*outputForces[i]);
68 }
69 }
70
71 // additional forces on the bias component
72 std::vector<double> f(noa,0.0);
73 std::vector<double> forces(noa);
74
75 bool at_least_one_forced=false;
76 for(unsigned i=0; i<ncp; ++i) {
77 if(getPntrToComponent(i)->applyForce(forces)) {
78 at_least_one_forced=true;
79 for(unsigned j=0; j<noa; j++) f[j]+=forces[j];
80 }
81 }
82
83 if(at_least_one_forced && !onStep()) error("you are biasing a bias with an inconsistent STRIDE");
84
85 if(at_least_one_forced) for(unsigned i=0; i<noa; ++i) {
86 getPntrToArgument(i)->addForce(f[i]);
87 }
88
89 }
90
91 }
92 }
93
94
95