Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2023 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 "core/ActionShortcut.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "MultiColvarShortcuts.h"
      25             : 
      26             : #include <string>
      27             : #include <cmath>
      28             : 
      29             : //+PLUMEDOC MCOLVAR INPLANEDISTANCES
      30             : /*
      31             : Calculate distances in the plane perpendicular to an axis
      32             : 
      33             : __As you can see if you expand the inputs below, you can achieve what this shortcut action does by using [DISTANCE](DISTANCE.md) and [ANGLE](ANGLE.md) together with [CUSTOM](CUSTOM.md),
      34             : [BETWEEN](BETWEEN.md), [LESS_THAN](LESS_THAN.md), [SUM](SUM.md) and [MEAN](MEAN.md).  We strongly encourage you to use these actions instead as using them will provide
      35             : you with a clearer understanding of the equations you are using.__
      36             : 
      37             : Each quantity calculated in this CV uses the positions of two atoms, this indices of which are specified using the VECTORSTART and VECTOREND keywords, to specify the
      38             : orientation of a vector, $\mathbf{n}$.  The perpendicular distance between this vector and the position of some third atom is then computed using:
      39             : 
      40             : $$
      41             :  x_j = |\mathbf{r}_{j}| \sin (\theta_j)
      42             : $$
      43             : 
      44             : where $\mathbf{r}_j$ is the distance between one of the two atoms that define the vector $\mathbf{n}$ and a third atom (atom $j$) and where $\theta_j$
      45             : is the angle between the vector \f$\mathbf{n}\f$ and the vector $\mathbf{r}_{j}$.  The $x_j$ values for each of the atoms specified using the GROUP keyword are calculated.
      46             : Keywords such as MORE_THAN and LESS_THAN can then be used to calculate the number of these quantities that are more or less than a given cutoff.
      47             : 
      48             : The following input can be used to calculate the number of atoms that have indices greater than 3 and less than 101 that
      49             : are within a cylinder with a radius of 0.3 nm that has its long axis aligned with the vector connecting atoms 1 and 2.
      50             : 
      51             : ```plumed
      52             : d1: INPLANEDISTANCES VECTORSTART=1 VECTOREND=2 GROUP=3-100 LESS_THAN={RATIONAL D_0=0.2 R_0=0.1}
      53             : PRINT ARG=d1.lessthan FILE=colvar
      54             : ```
      55             : 
      56             : Notice that the INPLANEDISTANCES is a shortcut. The syntax that is described in the expanded version of the input above provides much more flexibility for designing new CVs.
      57             : 
      58             : */
      59             : //+ENDPLUMEDOC
      60             : 
      61             : namespace PLMD {
      62             : namespace multicolvar {
      63             : 
      64             : class InPlaneDistances : public ActionShortcut {
      65             : public:
      66             :   explicit InPlaneDistances(const ActionOptions&);
      67             :   static void registerKeywords( Keywords& keys );
      68             : };
      69             : 
      70             : PLUMED_REGISTER_ACTION(InPlaneDistances,"INPLANEDISTANCES")
      71             : 
      72           3 : void InPlaneDistances::registerKeywords( Keywords& keys ) {
      73           3 :   ActionShortcut::registerKeywords( keys );
      74           3 :   keys.add("atoms","GROUP","calculate distance for each distinct set of three atoms in the group");
      75           3 :   keys.add("atoms","VECTORSTART","The first atom position that is used to define the normal to the plane of interest");
      76           3 :   keys.add("atoms","VECTOREND","The second atom position that is used to defin the normal to the plane of interest");
      77           6 :   keys.setValueDescription("vector","the INPLANEDISTANCE between each of the atoms specified using the GROUP keyword and atom A in the plane perpendicular to the vector connecting the atoms specified using VECTORSTART and VECTOREND");
      78           3 :   MultiColvarShortcuts::shortcutKeywords( keys );
      79           3 :   keys.needsAction("DISTANCE");
      80           3 :   keys.needsAction("ANGLE");
      81           3 :   keys.setDeprecated("DISTANCE");
      82           3 : }
      83             : 
      84           1 : InPlaneDistances::InPlaneDistances(const ActionOptions&ao):
      85             :   Action(ao),
      86           1 :   ActionShortcut(ao) {
      87             :   std::vector<std::string> str_atomsA;
      88           1 :   parseVector("VECTORSTART",str_atomsA);
      89           1 :   Tools::interpretRanges( str_atomsA );
      90             :   std::vector<std::string> str_atomsB;
      91           1 :   parseVector("VECTOREND",str_atomsB);
      92           1 :   Tools::interpretRanges( str_atomsB );
      93             :   std::vector<std::string> str_atomsC;
      94           1 :   parseVector("GROUP",str_atomsC);
      95           1 :   Tools::interpretRanges( str_atomsC );
      96           1 :   unsigned n=1;
      97           1 :   std::string dinput= getShortcutLabel() + "_dis: DISTANCE", ainput = getShortcutLabel() + "_ang: ANGLE";
      98           2 :   for(unsigned i=0; i<str_atomsA.size(); ++i ) {
      99           2 :     for(unsigned j=0; j<str_atomsB.size(); ++j ) {
     100           9 :       for(unsigned k=0; k<str_atomsC.size(); ++k) {
     101             :         std::string str_n;
     102           8 :         Tools::convert( n, str_n );
     103           8 :         n++;
     104          16 :         dinput += " ATOMS" + str_n + "=" + str_atomsA[j] + "," + str_atomsC[k];
     105          16 :         ainput += " ATOMS" + str_n + "=" + str_atomsB[j] + "," + str_atomsA[i] + "," + str_atomsC[k];
     106             :       }
     107             :     }
     108             :   }
     109           1 :   readInputLine( dinput );
     110           1 :   readInputLine( ainput );
     111           2 :   readInputLine( getShortcutLabel() + ": CUSTOM PERIODIC=NO FUNC=x*sin(y) ARG=" + getShortcutLabel() + "_dis," + getShortcutLabel() + "_ang");
     112           2 :   MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this );
     113           1 : }
     114             : 
     115             : }
     116             : }