Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2018 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 "core/ActionShortcut.h"
      24             : 
      25             : //+PLUMEDOC GRIDCALC INTEGRATE_GRID
      26             : /*
      27             : Calculate the numerical integral of the function stored on the grid
      28             : 
      29             : This action takes a function, $f(x)$, that is stored on a grid of points between $a$ and $b$.  It then computes the following definite integral
      30             : numerically:
      31             : 
      32             : $$
      33             : y = \int_a^b f(x) \textrm{d}x
      34             : $$
      35             : 
      36             : The approximate value of this integral would be computed using:
      37             : 
      38             : $$
      39             : y = \frac{b-a}{n} \sum_{i=0}^{n} f\left( a + \frac{i(b-a)}{n} \right)
      40             : $$
      41             : 
      42             : where $n$ is the number of points at which the grid has been computed.
      43             : 
      44             : The following example input demonstrates how this action can be used:
      45             : 
      46             : ```plumed
      47             : c1: COORDINATIONNUMBER SPECIESA=1-10 SPECIESB=1-200 SWITCH={RATIONAL R_0=1.0}
      48             : hu: KDE ARG=c1 GRID_BIN=200 GRID_MIN=0 GRID_MAX=10 BANDWIDTH=0.1
      49             : h: CUSTOM ARG=hu FUNC=x/10 PERIODIC=NO
      50             : iv: INTEGRATE_GRID ARG=h PERIODIC=NO
      51             : ```
      52             : 
      53             : In this case, the [KDE](KDE.md) action is used to compute a histogram that shows the instanenous distribution for 10 coordination numbers. This distribution is
      54             : unormalised so that [CUSTOM](CUSTOM.md) command here is used to normalise the distribution.  The resulting integral that is computed here should thsu be one.
      55             : 
      56             : Notice also that the action can still be used if the function stored on the grid is a function of 2 or more variables.  For example, the following input performs an integral
      57             : that is very similar to the one performed in the previous.  Now, however, the input grid is two dimensional.
      58             : 
      59             : ```plumed
      60             : c1: COORDINATIONNUMBER SPECIESA=1-10 SPECIESB=1-200 SWITCH={RATIONAL R_0=1.0}
      61             : q6: Q6 SPECIESA=1-10 SPECIESB=1-200 SWITCH={RATIONAL R_0=1.0}
      62             : hu: KDE ARG=c1,q6 GRID_BIN=200,200 GRID_MIN=0,-0.5 GRID_MAX=10,2 BANDWIDTH=0.1,0.1
      63             : h: CUSTOM ARG=hu FUNC=x/10 PERIODIC=NO
      64             : iv: INTEGRATE_GRID ARG=h PERIODIC=NO
      65             : ```
      66             : 
      67             : */
      68             : //+ENDPLUMEDOC
      69             : 
      70             : namespace PLMD {
      71             : namespace gridtools {
      72             : 
      73             : class IntegrateGrid : public ActionShortcut {
      74             : public:
      75             :   static void registerKeywords(Keywords&);
      76             :   explicit IntegrateGrid(const ActionOptions&);
      77             : };
      78             : 
      79             : PLUMED_REGISTER_ACTION(IntegrateGrid,"INTEGRATE_GRID")
      80             : 
      81          28 : void IntegrateGrid::registerKeywords(Keywords& keys ) {
      82          28 :   ActionShortcut::registerKeywords( keys );
      83          56 :   keys.addInputKeyword("compulsory","ARG","grid","the label of the function on a grid that is being integrated");
      84          28 :   keys.add("compulsory","PERIODIC","if the value of the output integral has a periodid domain then you use this keyword to specify the periodicity.  If the output integral is not periodic you must state this using PERIODIC=NO");
      85          56 :   keys.setValueDescription("scalar","the numerical integral of the input function over its whole domain");
      86          28 :   keys.needsAction("GET_VOLUME_ELEMENT");
      87          28 :   keys.needsAction("SUM");
      88          28 :   keys.needsAction("CUSTOM");
      89          28 : }
      90             : 
      91          16 : IntegrateGrid::IntegrateGrid(const ActionOptions&ao):
      92             :   Action(ao),
      93          16 :   ActionShortcut(ao) {
      94             :   std::string gridname;
      95          16 :   parse("ARG", gridname);
      96          16 :   readInputLine( getShortcutLabel() + "_volelem: GET_VOLUME_ELEMENT ARG=" + gridname );
      97          48 :   readInputLine( getShortcutLabel() + "_sum: SUM ARG=" + gridname + " PERIODIC=NO" );
      98             :   std::string period;
      99          16 :   parse("PERIODIC", period);
     100          64 :   readInputLine( getShortcutLabel() + ": CUSTOM ARG=" + getShortcutLabel() + "_volelem," + getShortcutLabel() + "_sum FUNC=x*y PERIODIC=" + period );
     101          16 : }
     102             : 
     103             : 
     104             : }
     105             : }