Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016,2017 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 "core/ActionWithVector.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "core/ActionSet.h"
      25             : #include "PathProjectionCalculator.h"
      26             : 
      27             : //+PLUMEDOC COLVAR GEOMETRIC_PATH
      28             : /*
      29             : Distance along and from a path calculated using geometric formulas
      30             : 
      31             : \par Examples
      32             : 
      33             : */
      34             : //+ENDPLUMEDOC
      35             : 
      36             : namespace PLMD {
      37             : namespace mapping {
      38             : 
      39             : class GeometricPath : public ActionWithVector {
      40             : private:
      41             :   PathProjectionCalculator path_projector;
      42             : public:
      43             :   static void registerKeywords(Keywords& keys);
      44             :   explicit GeometricPath(const ActionOptions&);
      45             :   unsigned getNumberOfDerivatives() override ;
      46             :   void calculate() override ;
      47           0 :   void performTask( const unsigned& current, MultiValue& myvals ) const override { plumed_error(); }
      48             : };
      49             : 
      50             : PLUMED_REGISTER_ACTION(GeometricPath,"GEOMETRIC_PATH")
      51             : 
      52          10 : void GeometricPath::registerKeywords(Keywords& keys) {
      53          10 :   ActionWithVector::registerKeywords(keys); keys.use("ARG");
      54          10 :   PathProjectionCalculator::registerKeywords(keys);
      55          20 :   keys.add("compulsory","PROPERTY","the coordinates we are projecting these points onto");
      56          20 :   keys.addOutputComponent("s","default","the position on the path");
      57          20 :   keys.addOutputComponent("z","default","the distance from the path");
      58          20 :   keys.needsAction("GEOMETRIC_PATH"); keys.needsAction("PDB2CONSTANT");
      59          10 : }
      60             : 
      61           4 : GeometricPath::GeometricPath(const ActionOptions&ao):
      62             :   Action(ao),
      63             :   ActionWithVector(ao),
      64           4 :   path_projector(this)
      65             : {
      66           4 :   plumed_assert( !actionInChain() );
      67             :   // Get the coordinates in the low dimensional space
      68           8 :   std::vector<std::string> pcoord; parseVector("PROPERTY", pcoord ); std::vector<Value*> theprop;
      69           4 :   ActionWithArguments::interpretArgumentList( pcoord, plumed.getActionSet(), this, theprop );
      70           4 :   if( theprop.size()!=1 ) error("did not find property to project on");
      71           4 :   if( theprop[0]->getNumberOfValues()!=getPntrToArgument(0)->getShape()[0] ) error("mismatch between number of frames and property of interest");
      72           4 :   log.printf("  projecting onto : %s \n", theprop[0]->getName().c_str() );
      73           4 :   std::vector<Value*> args( getArguments() ); args.push_back( theprop[0] ); requestArguments( args );
      74             :   // Create the values to store the output
      75          12 :   addComponentWithDerivatives("s"); componentIsNotPeriodic("s");
      76          12 :   addComponentWithDerivatives("z"); componentIsNotPeriodic("z");
      77           4 : }
      78             : 
      79        1677 : unsigned GeometricPath::getNumberOfDerivatives() {
      80        1677 :   return getPntrToArgument(0)->getShape()[0]*getPntrToArgument(0)->getShape()[1] + getPntrToArgument(1)->getShape()[0];
      81             : }
      82             : 
      83        1665 : void GeometricPath::calculate() {
      84        1665 :   unsigned k=0, iclose1=0, iclose2=0; double v1v1=0, v3v3=0;
      85        1665 :   unsigned nrows = getPntrToArgument(0)->getShape()[0];
      86        1665 :   unsigned ncols = getPntrToArgument(0)->getShape()[1];
      87       79201 :   for(unsigned i=0; i<nrows; ++i) {
      88             :     double dist = 0;
      89     1814580 :     for(unsigned j=0; j<ncols; ++j) {
      90     1737044 :       double tmp = getPntrToArgument(0)->get(k);
      91     1737044 :       dist += tmp*tmp; k++;
      92             :     }
      93       77536 :     if( i==0 ) { v1v1 = dist; iclose1 = 0; }
      94       75871 :     else if( dist<v1v1 ) { v3v3=v1v1; v1v1=dist; iclose2=iclose1; iclose1=i; }
      95       45571 :     else if( i==1 ) { v3v3=dist; iclose2=1; }
      96       45244 :     else if( dist<v3v3 ) { v3v3=dist; iclose2=i; }
      97             :   }
      98             :   // And find third closest point
      99        1665 :   int isign = iclose1 - iclose2;
     100             :   if( isign>1 ) isign=1; else if( isign<-1 ) isign=-1;
     101        1665 :   int iclose3 = iclose1 + isign;
     102        1665 :   unsigned ifrom=iclose1, ito=iclose3; if( iclose3<0 || iclose3>=nrows ) { ifrom=iclose2; ito=iclose1; }
     103             : 
     104             :   // And calculate projection of vector connecting current point to closest frame on vector connecting nearest two frames
     105        1665 :   std::vector<double> displace; path_projector.getDisplaceVector( ifrom, ito, displace );
     106        1665 :   double v2v2=0, v1v2=0; k=ncols*iclose1;
     107       42661 :   for(unsigned i=0; i<displace.size(); ++i) { v2v2 += displace[i]*displace[i]; v1v2 += displace[i]*getPntrToArgument(0)->get(k+i); }
     108             : 
     109             :   // This computes s value
     110        1665 :   double spacing = getPntrToArgument(1)->get(iclose1) - getPntrToArgument(1)->get(iclose2);
     111        1665 :   double root = sqrt( v1v2*v1v2 - v2v2 * ( v1v1 - v3v3) );
     112        1665 :   double dx = 0.5 * ( (root + v1v2) / v2v2 - 1.);
     113        1665 :   double path_s = getPntrToArgument(1)->get(iclose1) + spacing * dx;
     114        1665 :   Value* sp = getPntrToComponent(0); sp->set( path_s );
     115        1665 :   if( !doNotCalculateDerivatives() ) {
     116       23478 :     for(unsigned i=0; i<ncols; ++i) {
     117       22386 :       sp->addDerivative( ncols*iclose1 + i, 0.5*spacing*(v1v2*displace[i]/v2v2 - getPntrToArgument(0)->get(ncols*iclose1 + i))/root + 0.5*spacing*displace[i]/v2v2 );
     118       22386 :       sp->addDerivative( ncols*iclose2 + i, 0.5*spacing*getPntrToArgument(0)->get(ncols*iclose2 + i)/root );
     119             :     }
     120             :   }
     121             : 
     122             :   // This computes z value
     123        1665 :   path_projector.getDisplaceVector( iclose2, iclose1, displace ); double v4v4=0, proj=0; k=ncols*iclose1;
     124       42661 :   for(unsigned i=0; i<displace.size(); ++i) { v4v4 += displace[i]*displace[i]; proj += displace[i]*getPntrToArgument(0)->get(k+i); }
     125        1665 :   double path_z = v1v1 + dx*dx*v4v4 - 2*dx*proj; path_z = sqrt(path_z);
     126        1665 :   Value* zp = getPntrToComponent(1); zp->set( path_z );
     127        1665 :   if( !doNotCalculateDerivatives() ) {
     128       23478 :     for(unsigned i=0; i<ncols; ++i) {
     129       22386 :       zp->addDerivative( ncols*iclose1 + i, (1/path_z)*(getPntrToArgument(0)->get(ncols*iclose1 + i) +
     130       22386 :                          (v4v4*dx-proj)*sp->getDerivative(ncols*iclose1 + i)/spacing -
     131       22386 :                          dx*displace[i]) );
     132       22386 :       zp->addDerivative( ncols*iclose2 + i, (v4v4*dx-proj)*sp->getDerivative(ncols*iclose2 + i)/(path_z*spacing) );
     133             :     }
     134             :   }
     135        1665 : }
     136             : 
     137             : }
     138             : }