Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2023 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             : //+PLUMEDOC COLVAR XANGLES
      27             : /*
      28             : Calculate the angle between an arbitrary vector and the positive x direction
      29             : 
      30             : __As you can see if you expand the inputs below, you can achieve what this shortcut action does by using [DISTANCE](DISTANCE.md) together with [CUSTOM](CUSTOM.md),
      31             : [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
      32             : you with a clearer understanding of the equations you are using.__
      33             : 
      34             : The following input tells plumed to calculate the angles between the x-axis and the vector connecting atom 3 to atom 5 and between the x-axis
      35             : and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output
      36             : 
      37             : ```plumed
      38             : d1: XANGLES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
      39             : PRINT ARG=d1.min FILE=colvar
      40             : ```
      41             : 
      42             : Notice that this command is a shortcut. You can thus learn more about how to use PLUMED by examining the expanded version of the input above.
      43             : 
      44             : */
      45             : //+ENDPLUMEDOC
      46             : 
      47             : //+PLUMEDOC COLVAR YANGLES
      48             : /*
      49             : Calculate the angle between an arbitrary vector and the positive y direction
      50             : 
      51             : __As you can see if you expand the inputs below, you can achieve what this shortcut action does by using [DISTANCE](DISTANCE.md) together with [CUSTOM](CUSTOM.md),
      52             : [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
      53             : you with a clearer understanding of the equations you are using.__
      54             : 
      55             : The following input tells plumed to calculate the angles between the y-axis and the vector connecting atom 3 to atom 5 and between the y-axis
      56             : and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output
      57             : 
      58             : ```plumed
      59             : d1: YANGLES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
      60             : PRINT ARG=d1.min FILE=colvar
      61             : ```
      62             : 
      63             : Notice that this command is a shortcut. You can thus learn more about how to use PLUMED by examining the expanded version of the input above.
      64             : 
      65             : */
      66             : //+ENDPLUMEDOC
      67             : 
      68             : //+PLUMEDOC COLVAR ZANGLES
      69             : /*
      70             : Calculate the angle between an arbitrary vector and the positive z direction
      71             : 
      72             : __As you can see if you expand the inputs below, you can achieve what this shortcut action does by using [DISTANCE](DISTANCE.md) together with [CUSTOM](CUSTOM.md),
      73             : [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
      74             : you with a clearer understanding of the equations you are using.__
      75             : 
      76             : The following input tells plumed to calculate the angles between the z-axis and the vector connecting atom 3 to atom 5 and between the z-axis
      77             : and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output
      78             : 
      79             : ```plumed
      80             : d1: ZANGLES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
      81             : PRINT ARG=d1.min FILE=colvar
      82             : ```
      83             : 
      84             : Notice that this command is a shortcut. You can thus learn more about how to use PLUMED by examining the expanded version of the input above.
      85             : 
      86             : */
      87             : //+ENDPLUMEDOC
      88             : 
      89             : 
      90             : namespace PLMD {
      91             : namespace multicolvar {
      92             : 
      93             : class XAngle : public ActionShortcut {
      94             : public:
      95             :   static void registerKeywords(Keywords& keys);
      96             :   explicit XAngle(const ActionOptions&);
      97             : };
      98             : 
      99             : PLUMED_REGISTER_ACTION(XAngle,"XANGLES")
     100             : PLUMED_REGISTER_ACTION(XAngle,"YANGLES")
     101             : PLUMED_REGISTER_ACTION(XAngle,"ZANGLES")
     102             : 
     103           9 : void XAngle::registerKeywords(Keywords& keys) {
     104           9 :   ActionShortcut::registerKeywords( keys );
     105           9 :   keys.add("numbered","ATOMS","the pairs of atoms that you would like to calculate the angles for");
     106          18 :   keys.reset_style("ATOMS","atoms");
     107           9 :   MultiColvarShortcuts::shortcutKeywords( keys );
     108           9 :   keys.needsAction("DISTANCE");
     109           9 :   keys.needsAction("COMBINE");
     110           9 :   keys.needsAction("CUSTOM");
     111           9 :   keys.setDeprecated("DISTANCE");
     112           9 : }
     113             : 
     114           1 : XAngle::XAngle(const ActionOptions& ao):
     115             :   Action(ao),
     116           1 :   ActionShortcut(ao) {
     117             :   // Create distances
     118           1 :   std::string dline = getShortcutLabel() + "_dists: DISTANCE COMPONENTS";
     119           1 :   for(unsigned i=1;; ++i) {
     120             :     std::string atstring;
     121           6 :     parseNumbered("ATOMS",i,atstring);
     122           3 :     if( atstring.length()==0 ) {
     123             :       break;
     124             :     }
     125             :     std::string num;
     126           2 :     Tools::convert( i, num );
     127           4 :     dline += " ATOMS" + num + "=" + atstring;
     128           2 :   }
     129           1 :   readInputLine( dline );
     130             :   // Normalize the vectors
     131           2 :   readInputLine( getShortcutLabel() + "_norm2: COMBINE ARG=" + getShortcutLabel() + "_dists.x" + "," + getShortcutLabel() + "_dists.y," + getShortcutLabel() + "_dists.z POWERS=2,2,2 PERIODIC=NO");
     132           2 :   readInputLine( getShortcutLabel() + "_norm: CUSTOM ARG=" + getShortcutLabel() + "_norm2 FUNC=sqrt(x) PERIODIC=NO");
     133           2 :   readInputLine( getShortcutLabel() + "_norm_x: CUSTOM ARG=" + getShortcutLabel() + "_dists.x," + getShortcutLabel() + "_norm FUNC=x/y PERIODIC=NO");
     134           2 :   readInputLine( getShortcutLabel() + "_norm_y: CUSTOM ARG=" + getShortcutLabel() + "_dists.y," + getShortcutLabel() + "_norm FUNC=x/y PERIODIC=NO");
     135           2 :   readInputLine( getShortcutLabel() + "_norm_z: CUSTOM ARG=" + getShortcutLabel() + "_dists.z," + getShortcutLabel() + "_norm FUNC=x/y PERIODIC=NO");
     136             :   // Now compute the angles with matheval
     137           1 :   if( getName()=="XANGLES" ) {
     138           2 :     readInputLine( getShortcutLabel() + "_ang: CUSTOM FUNC=acos(x) PERIODIC=NO ARG=" + getShortcutLabel() + "_norm_x");
     139             :   }
     140           1 :   if( getName()=="YANGLES" ) {
     141           0 :     readInputLine( getShortcutLabel() + "_ang: CUSTOM FUNC=acos(x) PERIODIC=NO ARG=" + getShortcutLabel() + "_norm_y");
     142             :   }
     143           1 :   if( getName()=="ZANGLES" ) {
     144           0 :     readInputLine( getShortcutLabel() + "_ang: CUSTOM FUNC=acos(x) PERIODIC=NO ARG=" + getShortcutLabel() + "_norm_z");
     145             :   }
     146             :   // Add shortcuts to label
     147           2 :   MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel() + "_ang", "", this );
     148           1 : }
     149             : 
     150             : }
     151             : }