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 "ActionWithVirtualAtom.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "tools/Vector.h"
      25             : #include "tools/Exception.h"
      26             : 
      27             : namespace PLMD {
      28             : namespace vatom {
      29             : 
      30             : //+PLUMEDOC VATOM FIXEDATOM
      31             : /*
      32             : Add a virtual atom in a fixed position.
      33             : 
      34             : This action creates [a virtual atom](specifying_atoms.md) at a fixed position.  The example input below illustrates
      35             : how this idea can be used to compute the angle between the vector connecting atoms 15 and 20 and the z axis and how this
      36             : quantity can then be restrained so that the angle stays close to zero.
      37             : 
      38             : ```plumed
      39             : a: FIXEDATOM AT=0,0,0
      40             : b: FIXEDATOM AT=0,0,1
      41             : an: ANGLE ATOMS=a,b,15,20
      42             : RESTRAINT ARG=an AT=0.0 KAPPA=100.0
      43             : ```
      44             : 
      45             : By default PLUMED assumes that any coordinates specified using the AT keyword specified are the cartesian coordinates of the fixed atom.
      46             : However, if you use the SCALED_COMPONENTS flag as shown below:
      47             : 
      48             : ```plumed
      49             : a: FIXEDATOM AT=0.25,0.25,0.25 SCALED_COMPONENTS
      50             : DUMPATOMS ATOMS=a FILE=vatom.xyz
      51             : ```
      52             : 
      53             : the coordinates specified using the AT keyword are interpreted as scaled coordinates. The positions output to the `vatom.xyz` file
      54             : in the input above is thus obtained by multiplying the input vector by the cell vectors on every step.  The position of the atom `a`
      55             : thus changes as the box size changes.
      56             : 
      57             : It is also possible to assign a predefined charge or mass to the atom by using the `SET_MASS` and `SET_CHARGE` keywords.
      58             : 
      59             : !!! caution ""
      60             : 
      61             :     This action, like [POSITION](POSITION.md) is not invariant for translation of the system so adding a force on it can cause trouble.
      62             : 
      63             : The problem is that the vector connecting any atom and a virtual atom created using the FIXEDATOM atoms command is not invariant to translation.
      64             : However, if, as has been done in the following example input, one first aligns atoms to a reference using [FIT_TO_TEMPLATE](FIT_TO_TEMPLATE.md),
      65             : then it is safe to add further fixed atoms without breaking translational invariance.
      66             : 
      67             : ```plumed
      68             : #SETTINGS INPUTFILES=regtest/basic/rt63/align.pdb
      69             : FIT_TO_TEMPLATE STRIDE=1 REFERENCE=regtest/basic/rt63/align.pdb TYPE=SIMPLE
      70             : a: FIXEDATOM AT=10,20,30
      71             : d: DISTANCE ATOMS=a,20
      72             : PRINT ARG=d FILE=colvar
      73             : ```
      74             : 
      75             : */
      76             : //+ENDPLUMEDOC
      77             : 
      78             : 
      79             : class FixedAtom:
      80             :   public ActionWithVirtualAtom {
      81             :   Vector coord;
      82             :   std::vector<Tensor> deriv;
      83             :   double mass,charge;
      84             :   bool scaled_components;
      85             :   bool warnedNoBox=false;
      86             : public:
      87             :   explicit FixedAtom(const ActionOptions&ao);
      88             :   void calculate() override;
      89             :   static void registerKeywords( Keywords& keys );
      90             : };
      91             : 
      92             : PLUMED_REGISTER_ACTION(FixedAtom,"FIXEDATOM")
      93             : 
      94          49 : void FixedAtom::registerKeywords(Keywords& keys) {
      95          49 :   ActionWithVirtualAtom::registerKeywords(keys);
      96          49 :   keys.add("compulsory","AT","coordinates of the virtual atom");
      97          49 :   keys.add("compulsory","SET_MASS","1","mass of the virtual atom");
      98          49 :   keys.add("compulsory","SET_CHARGE","0","charge of the virtual atom");
      99          49 :   keys.addFlag("SCALED_COMPONENTS",false,"use scaled components");
     100          98 :   keys.reset_style("ATOMS","hidden");
     101          49 : }
     102             : 
     103          42 : FixedAtom::FixedAtom(const ActionOptions&ao):
     104             :   Action(ao),
     105          42 :   ActionWithVirtualAtom(ao) {
     106          42 :   std::vector<AtomNumber> atoms;
     107          84 :   parseAtomList("ATOMS",atoms);
     108          42 :   if(atoms.size()!=0) {
     109           0 :     error("ATOMS should be empty");
     110             :   }
     111             : 
     112          42 :   parseFlag("SCALED_COMPONENTS",scaled_components);
     113             : 
     114          42 :   std::vector<double> at;
     115          84 :   parseVector("AT",at);
     116          42 :   if(at.size()!=3) {
     117           0 :     error("AT should be a list of three real numbers");
     118             :   }
     119             : 
     120          42 :   parse("SET_MASS",mass);
     121          84 :   parse("SET_CHARGE",charge);
     122             : 
     123          42 :   coord[0]=at[0];
     124          42 :   coord[1]=at[1];
     125          42 :   coord[2]=at[2];
     126             : 
     127          42 :   checkRead();
     128          42 :   log<<"  AT position "<<coord[0]<<" "<<coord[1]<<" "<<coord[2]<<"\n";
     129          42 :   if(scaled_components) {
     130           1 :     log<<"  position is in scaled components\n";
     131             :   }
     132          42 : }
     133             : 
     134         792 : void FixedAtom::calculate() {
     135         792 :   deriv.resize(getNumberOfAtoms());
     136         792 :   if(scaled_components) {
     137             :     // without a cell the scaled components cannot be converted: the atom ends up in the origin
     138           5 :     if(!getPbc().isSet() && !warnedNoBox) {
     139           1 :       warning("SCALED_COMPONENTS was used but the cell is not set: the position of the atom is set to the origin");
     140           1 :       warnedNoBox=true;
     141             :     }
     142           5 :     setPosition(getPbc().scaledToReal(coord));
     143             :   } else {
     144         787 :     setPosition(coord);
     145             :   }
     146         792 :   setMass(mass);
     147         792 :   setCharge(charge);
     148         792 :   setAtomsDerivatives(deriv);
     149             : // Virial contribution
     150         792 :   if(!scaled_components) {
     151         787 :     setBoxDerivativesNoPbc();
     152             :   }
     153             : // notice that with scaled components there is no additional virial contribution
     154         792 : }
     155             : 
     156             : }
     157             : }