Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2018 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 "Path.h"
      23             : #include "tools/PDB.h"
      24             : #include "core/ActionRegister.h"
      25             : 
      26             : //+PLUMEDOC COLVAR GPATH
      27             : /*
      28             : Distance along and from a path calculated using geometric formulas
      29             : 
      30             : The Path Collective Variables developed by Branduardi and that are described in the first paper that is cited below allow one
      31             : to compute the progress along a high-dimensional path and the distance from the high-dimensional path.  The method introduced in that
      32             : paper is implemented in the shortcut [PATH](PATH.md). This action provides an implementation of the alternative method for calculating
      33             : the position on and distance from the path that was proposed by Diaz Leines and Ensing in the second paper that is cited below.  In their
      34             : method, the progress along the path $s$ is calculated using:
      35             : 
      36             : $$
      37             : s = i_2 + \textrm{sign}(i_2-i_1) \frac{ \sqrt{( \mathbf{v}_1\cdot\mathbf{v}_2 )^2 - |\mathbf{v}_3|^2(|\mathbf{v}_1|^2 - |\mathbf{v}_2|^2) } }{2|\mathbf{v}_3|^2} - \frac{\mathbf{v}_1\cdot\mathbf{v}_3 - |\mathbf{v}_3|^2}{2|\mathbf{v}_3|^2}
      38             : $$
      39             : 
      40             : where $\mathbf{v}_1$ and $\mathbf{v}_3$ are the vectors connecting the current position to the closest and second closest node of the path,
      41             : respectfully and $i_1$ and $i_2$ are the projections of the closest and second closest frames of the path. $\mathbf{v}_2$, meanwhile, is the
      42             : vector connecting the closest frame to the second closest frame.  The distance from the path, $z$ is calculated using:
      43             : 
      44             : $$
      45             : z = \sqrt{ \left[ |\mathbf{v}_1|^2 - |\mathbf{v}_2| \left( \frac{ \sqrt{( \mathbf{v}_1\cdot\mathbf{v}_2 )^2 - |\mathbf{v}_3|^2(|\mathbf{v}_1|^2 - |\mathbf{v}_2|^2) } }{2|\mathbf{v}_3|^2} - \frac{\mathbf{v}_1\cdot\mathbf{v}_3 - |\mathbf{v}_3|^2}{2|\mathbf{v}_3|^2} \right) \right]^2 }
      46             : $$
      47             : 
      48             : The symbols here are as they were for $s$.
      49             : 
      50             : ## Examples
      51             : 
      52             : The example input below shows how to use this shortcut.
      53             : 
      54             : ```plumed
      55             : #SETTINGS INPUTFILES=regtest/mapping/rt-adapt/mypath.pdb
      56             : d1: DISTANCE ATOMS=1,2 COMPONENTS
      57             : pp: GPATH ...
      58             :    ARG=d1.x,d1.y PROPERTY=path
      59             :    REFERENCE=regtest/mapping/rt-adapt/mypath.pdb
      60             : ...
      61             : PRINT ARG=d1.x,d1.y,pp.* FILE=colvar
      62             : ```
      63             : 
      64             : The curved path here is defined using a series of points in a two dimensional space.  Furthermore, the coordinates that these points should be projected at on the low dimensional path
      65             : (the $i$ values in the equation for $s$ above) are specified in the `path` property of the input pdb file.
      66             : 
      67             : The input below illustrates how to the positions of atoms to define the path:
      68             : 
      69             : ```plumed
      70             : ##SETTINGS INPUTFILES=regtest/trajectories/path_msd/all.pdb
      71             : p1b: GPATH REFERENCE=regtest/trajectories/path_msd/all.pdb
      72             : PRINT ARG=p1b.* FILE=colvar_b STRIDE=1
      73             : ```
      74             : 
      75             : When an input like the one above is used the vectors $\mathbf{v}_1$, $\mathbf{v}_2$ and $\mathbf{v}_3$ from the expression above are computed using an [RMSD](RMSD.md)
      76             : action with the DISPLACEMENT flag enabled.  The instantaneous structure is thus aligned with the reference structures so as to remove motions due to translation of the center
      77             : of mass and rotation of the reference frame.  Furthermore, because we have not used the PROPERTY keyword in this input, the $i$ values in the equation for $s$
      78             : above are set equal to 1, 2, 3...
      79             : 
      80             : */
      81             : //+ENDPLUMEDOC
      82             : 
      83             : namespace PLMD {
      84             : namespace mapping {
      85             : 
      86             : class GeometricPathShortcut : public ActionShortcut {
      87             : public:
      88             :   static void registerKeywords(Keywords& keys);
      89             :   explicit GeometricPathShortcut(const ActionOptions&);
      90             : };
      91             : 
      92             : PLUMED_REGISTER_ACTION(GeometricPathShortcut,"GPATH")
      93             : 
      94          17 : void GeometricPathShortcut::registerKeywords( Keywords& keys ) {
      95          17 :   ActionShortcut::registerKeywords( keys );
      96          17 :   Path::registerInputFileKeywords( keys );
      97          17 :   keys.add("optional","PROPERTY","read in path coordinates by finding option with this label in remark of pdb frames");
      98          34 :   keys.addOutputComponent("s","default","scalar","the position on the path");
      99          34 :   keys.addOutputComponent("z","default","scalar","the distance from the path");
     100          17 :   keys.needsAction("DISPLACEMENT");
     101          17 :   keys.needsAction("GEOMETRIC_PATH");
     102          17 :   keys.needsAction("PDB2CONSTANT");
     103          17 :   keys.needsAction("CONSTANT");
     104          17 :   keys.addDOI("10.1063/1.2432340");
     105          17 :   keys.addDOI("10.1103/PhysRevLett.109.020601");
     106          17 : }
     107             : 
     108           5 : GeometricPathShortcut::GeometricPathShortcut( const ActionOptions& ao ):
     109             :   Action(ao),
     110           5 :   ActionShortcut(ao) {
     111             :   std::string mtype, reference_data;
     112           5 :   std::vector<std::string> argnames;
     113           5 :   parseVector("ARG",argnames);
     114          10 :   parse("TYPE", mtype);
     115             :   // Create list of reference configurations that PLUMED will use
     116             :   std::string reference;
     117          10 :   parse("REFERENCE",reference);
     118           5 :   FILE* fp=std::fopen(reference.c_str(),"r");
     119           5 :   PDB mypdb;
     120           5 :   if(!fp) {
     121           0 :     error("could not open reference file " + reference );
     122             :   }
     123           5 :   bool do_read=mypdb.readFromFilepointer(fp,false,0.1);
     124           5 :   if( !do_read ) {
     125           0 :     error("missing file " + reference );
     126             :   }
     127           5 :   Path::readInputFrames( reference, mtype, argnames, true, this, reference_data );
     128             :   // Now get coordinates on spath
     129           5 :   std::vector<std::string> pnames;
     130           5 :   parseVector("PROPERTY",pnames);
     131           5 :   Path::readPropertyInformation( pnames, getShortcutLabel(), reference, this );
     132             :   // Create action that computes the geometric path variablesa
     133           5 :   std::string propstr = getShortcutLabel() + "_ind";
     134           5 :   if( pnames.size()>0 ) {
     135           0 :     propstr = pnames[0] + "_ref";
     136             :   }
     137           5 :   if( argnames.size()>0 ) {
     138           5 :     readInputLine( getShortcutLabel() + ": GEOMETRIC_PATH ARG=" + getShortcutLabel() + "_data " + " PROPERTY=" + propstr + " REFERENCE=" + reference_data + " METRIC={DIFFERENCE}");
     139             :   } else {
     140             :     std::string num, align_str, displace_str;
     141           4 :     Tools::convert( mypdb.getOccupancy()[0], align_str );
     142           4 :     Tools::convert( mypdb.getBeta()[0], displace_str );
     143          52 :     for(unsigned j=1; j<mypdb.getAtomNumbers().size(); ++j ) {
     144          48 :       Tools::convert( mypdb.getOccupancy()[j], num );
     145          48 :       align_str += "," + num;
     146          48 :       Tools::convert( mypdb.getBeta()[0], num );
     147          48 :       displace_str += "," + num;
     148             :     }
     149          12 :     std::string metric = "RMSD DISPLACEMENT TYPE=" + mtype + " ALIGN=" + align_str + " DISPLACE=" + displace_str;
     150          24 :     readInputLine( getShortcutLabel() + ": GEOMETRIC_PATH ARG=" + getShortcutLabel() + "_data.disp " + " PROPERTY=" +  propstr + " REFERENCE=" + reference_data + " METRIC={" + metric + "} METRIC_COMPONENT=disp");
     151             :   }
     152         111 : }
     153             : 
     154             : 
     155             : }
     156             : }
     157             : 
     158             :