Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2017 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 "MultiColvarShortcuts.h"
      23             : #include "core/ActionShortcut.h"
      24             : #include "core/ActionRegister.h"
      25             : #include "tools/Pbc.h"
      26             : 
      27             : #include <string>
      28             : #include <cmath>
      29             : 
      30             : //+PLUMEDOC MCOLVAR PLANES
      31             : /*
      32             : Calculate the components of the normal to the plane containing three atoms
      33             : 
      34             : \par Examples
      35             : 
      36             : */
      37             : //+ENDPLUMEDOC
      38             : 
      39             : namespace PLMD {
      40             : namespace multicolvar {
      41             : 
      42             : class PlaneShortcut : public ActionShortcut {
      43             : private:
      44             :   void createVectorNormInput( const std::string& ilab, const std::string& olab, const std::string& vlab );
      45             : public:
      46             :   static void registerKeywords( Keywords& keys );
      47             :   PlaneShortcut(const ActionOptions&);
      48             : };
      49             : 
      50             : PLUMED_REGISTER_ACTION(PlaneShortcut,"PLANES")
      51             : 
      52           3 : void PlaneShortcut::registerKeywords( Keywords& keys ) {
      53           3 :   ActionShortcut::registerKeywords( keys );
      54           3 :   MultiColvarShortcuts::shortcutKeywords( keys );
      55           6 :   keys.add("numbered","ATOMS","the sets of atoms that you would like to calculate the planes for");
      56           6 :   keys.add("numbered","LOCATION","the location at which the CV is assumed to be in space");
      57           6 :   keys.reset_style("LOCATION","atoms");
      58           6 :   keys.addFlag("VMEAN",false,"calculate the norm of the mean vector.");
      59           6 :   keys.addOutputComponent("_vmean","VMEAN","the norm of the mean vector");
      60           6 :   keys.addFlag("VSUM",false,"calculate the norm of the sum of all the vectors");
      61           6 :   keys.addOutputComponent("_vsum","VSUM","the norm of the mean vector");
      62           3 :   keys.needsAction("CENTER");
      63           3 :   keys.needsAction("GROUP");
      64           3 :   keys.needsAction("PLANE");
      65           3 :   keys.needsAction("MEAN");
      66           3 :   keys.needsAction("SUM");
      67           3 :   keys.needsAction("COMBINE");
      68           3 :   keys.needsAction("CUSTOM");
      69           3 : }
      70             : 
      71           1 : PlaneShortcut::PlaneShortcut(const ActionOptions&ao):
      72             :   Action(ao),
      73           1 :   ActionShortcut(ao) {
      74             :   bool vmean, vsum;
      75           1 :   parseFlag("VMEAN",vmean);
      76           2 :   parseFlag("VSUM",vsum);
      77             :   std::string dline;
      78           1 :   std::string grpstr = getShortcutLabel() + "_grp: GROUP ATOMS=";
      79           1 :   for(unsigned i=1;; ++i) {
      80             :     std::string atstring;
      81          18 :     parseNumbered("ATOMS",i,atstring);
      82           9 :     if( atstring.length()==0 ) {
      83             :       break;
      84             :     }
      85             :     std::string locstr;
      86          16 :     parseNumbered("LOCATION",i,locstr);
      87           8 :     if( locstr.length()==0 ) {
      88             :       std::string num;
      89           8 :       Tools::convert( i, num );
      90          16 :       readInputLine( getShortcutLabel() + "_vatom" + num + ": CENTER ATOMS=" + atstring );
      91           8 :       if( i==1 ) {
      92           2 :         grpstr += getShortcutLabel() + "_vatom" + num;
      93             :       } else {
      94          14 :         grpstr += "," + getShortcutLabel() + "_vatom" + num;
      95             :       }
      96             :     } else {
      97           0 :       if( i==1 ) {
      98             :         grpstr += locstr;
      99             :       } else {
     100           0 :         grpstr += "," + locstr;
     101             :       }
     102             :     }
     103             :     std::string num;
     104           8 :     Tools::convert( i, num );
     105          16 :     dline += " ATOMS" + num + "=" + atstring;
     106           8 :   }
     107           1 :   readInputLine( grpstr );
     108           2 :   readInputLine( getShortcutLabel() + ": PLANE " + dline + " " + convertInputLineToString() );
     109           1 :   if( vmean ) {
     110           2 :     readInputLine( getShortcutLabel() + "_xs: MEAN ARG=" + getShortcutLabel() + ".x PERIODIC=NO");
     111           2 :     readInputLine( getShortcutLabel() + "_ys: MEAN ARG=" + getShortcutLabel() + ".y PERIODIC=NO");
     112           2 :     readInputLine( getShortcutLabel() + "_zs: MEAN ARG=" + getShortcutLabel() + ".z PERIODIC=NO");
     113             :     // Now calculate the total length of the vector
     114           2 :     createVectorNormInput( getShortcutLabel(), getShortcutLabel() + "_vmean", "s" );
     115             :   }
     116           1 :   if( vsum ) {
     117           0 :     readInputLine( getShortcutLabel() + "_xz: SUM ARG=" + getShortcutLabel() + ".x PERIODIC=NO");
     118           0 :     readInputLine( getShortcutLabel() + "_yz: SUM ARG=" + getShortcutLabel() + ".y PERIODIC=NO");
     119           0 :     readInputLine( getShortcutLabel() + "_zz: SUM ARG=" + getShortcutLabel() + ".z PERIODIC=NO");
     120             :     // Now calculate the total length of the vector
     121           0 :     createVectorNormInput( getShortcutLabel(), getShortcutLabel() + "_vsum", "z" );
     122             :   }
     123           1 : }
     124             : 
     125           1 : void PlaneShortcut::createVectorNormInput( const std::string& ilab, const std::string& olab, const std::string& vlab ) {
     126           2 :   readInputLine( olab + "2: COMBINE ARG=" + ilab + "_x" + vlab + "," + ilab + "_y" + vlab + "," + ilab + "_z" + vlab + " POWERS=2,2,2 PERIODIC=NO");
     127           2 :   readInputLine( olab + ": CUSTOM ARG=" + olab + "2 FUNC=sqrt(x) PERIODIC=NO");
     128           1 : }
     129             : 
     130             : }
     131             : }
     132             : 
     133             : 
     134             :