1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 Copyright (c) 2016-2021 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 "core/ActionRegister.h"
23 #include "ReweightBase.h"
24
25 //+PLUMEDOC REWEIGHTING REWEIGHT_METAD
26 /*
27 Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system.
28
29 This command allows you to use the reweighting algorithm discussed in \cite PratyushReweighting when constructing a histogram
30 of the configurations visited during a metadynamics simulation.
31
32 \par Examples
33
34 In the following example there is a metadynamics bias acting on the distance between atoms 1 and 2. Clearly, this
35 bias will have an effect on the region of phase space that will be sampled when an MD simulation is
36 run using this variable. Consequently, when the histogram as a function of the angle, \f$a\f$, is accumulated,
37 we use reweighting into order to discount the effect of the bias from our final histogram. We do not use
38 \ref REWEIGHT_BIAS here, however, as the bias changes with time. We thus use the reweighting algorithm for
39 metadynamics instead. Notice also that we have to specify how often we would like to calculate the c(t) reweighting
40 factor and the grid over which we calculate c(t) in the input to the METAD command.
41
42 \plumedfile
43 a: ANGLE ATOMS=1,2,3
44 x: DISTANCE ATOMS=1,2
45 METAD ARG=x PACE=100 SIGMA=0.1 HEIGHT=1.5 BIASFACTOR=5 GRID_MIN=0 GRID_MAX=10 GRID_BIN=100 CALC_RCT RCT_USTRIDE=50
46
47 bias: REWEIGHT_METAD TEMP=300
48
49 HISTOGRAM ...
50 ARG=a
51 GRID_MIN=0.0
52 GRID_MAX=pi
53 GRID_BIN=100
54 BANDWIDTH=0.1
55 LOGWEIGHTS=bias
56 LABEL=hB
57 ... HISTOGRAM
58
59 DUMPGRID GRID=hB FILE=histoB STRIDE=1 FMT=%8.4f
60 \endplumedfile
61
62 */
63 //+ENDPLUMEDOC
64
65 namespace PLMD {
66 namespace bias {
67
68 class ReweightMetad : public ReweightBase {
69 public:
70 static void registerKeywords(Keywords&);
71 explicit ReweightMetad(const ActionOptions&ao);
72 double getLogWeight() override;
73 };
74
75 PLUMED_REGISTER_ACTION(ReweightMetad,"REWEIGHT_METAD")
76
registerKeywords(Keywords & keys)77 void ReweightMetad::registerKeywords(Keywords& keys ) {
78 ReweightBase::registerKeywords( keys ); keys.remove("ARG");
79 keys.add("compulsory","ARG","*.rbias","the biases that must be taken into account when reweighting");
80 }
81
ReweightMetad(const ActionOptions & ao)82 ReweightMetad::ReweightMetad(const ActionOptions&ao):
83 Action(ao),
84 ReweightBase(ao)
85 {
86 }
87
getLogWeight()88 double ReweightMetad::getLogWeight() {
89 // Retrieve the bias
90 double bias=0.0; for(unsigned i=0; i<getNumberOfArguments(); ++i) bias+=getArgument(i);
91 return bias / simtemp;
92 }
93
94 }
95 }
96