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 {
      48           0 :     plumed_error();
      49             :   }
      50             : };
      51             : 
      52             : PLUMED_REGISTER_ACTION(GeometricPath,"GEOMETRIC_PATH")
      53             : 
      54          10 : void GeometricPath::registerKeywords(Keywords& keys) {
      55          10 :   ActionWithVector::registerKeywords(keys);
      56          10 :   PathProjectionCalculator::registerKeywords(keys);
      57          20 :   keys.addInputKeyword("compulsory","PROPERTY","vector","the label of a value that contains the coordinates we are projecting these points onto");
      58          20 :   keys.addOutputComponent("s","default","scalar","the position on the path");
      59          20 :   keys.addOutputComponent("z","default","scalar","the distance from the path");
      60          10 :   keys.needsAction("GEOMETRIC_PATH");
      61          10 :   keys.needsAction("PDB2CONSTANT");
      62          10 : }
      63             : 
      64           4 : GeometricPath::GeometricPath(const ActionOptions&ao):
      65             :   Action(ao),
      66             :   ActionWithVector(ao),
      67           4 :   path_projector(this) {
      68           4 :   plumed_assert( !actionInChain() );
      69             :   // Get the coordinates in the low dimensional space
      70             :   std::vector<std::string> pcoord;
      71           8 :   parseVector("PROPERTY", pcoord );
      72             :   std::vector<Value*> theprop;
      73           4 :   ActionWithArguments::interpretArgumentList( pcoord, plumed.getActionSet(), this, theprop );
      74           4 :   if( theprop.size()!=1 ) {
      75           0 :     error("did not find property to project on");
      76             :   }
      77           4 :   if( theprop[0]->getNumberOfValues()!=getPntrToArgument(0)->getShape()[0] ) {
      78           0 :     error("mismatch between number of frames and property of interest");
      79             :   }
      80           4 :   log.printf("  projecting onto : %s \n", theprop[0]->getName().c_str() );
      81           4 :   std::vector<Value*> args( getArguments() );
      82           4 :   args.push_back( theprop[0] );
      83           4 :   requestArguments( args );
      84             :   // Create the values to store the output
      85           8 :   addComponentWithDerivatives("s");
      86           8 :   componentIsNotPeriodic("s");
      87           8 :   addComponentWithDerivatives("z");
      88           8 :   componentIsNotPeriodic("z");
      89           4 : }
      90             : 
      91        1677 : unsigned GeometricPath::getNumberOfDerivatives() {
      92        1677 :   return getPntrToArgument(0)->getShape()[0]*getPntrToArgument(0)->getShape()[1] + getPntrToArgument(1)->getShape()[0];
      93             : }
      94             : 
      95        1665 : void GeometricPath::calculate() {
      96        1665 :   unsigned k=0, iclose1=0, iclose2=0;
      97             :   double v1v1=0, v3v3=0;
      98        1665 :   unsigned nrows = getPntrToArgument(0)->getShape()[0];
      99        1665 :   unsigned ncols = getPntrToArgument(0)->getShape()[1];
     100       79201 :   for(unsigned i=0; i<nrows; ++i) {
     101             :     double dist = 0;
     102     1814580 :     for(unsigned j=0; j<ncols; ++j) {
     103     1737044 :       double tmp = getPntrToArgument(0)->get(k);
     104     1737044 :       dist += tmp*tmp;
     105     1737044 :       k++;
     106             :     }
     107       77536 :     if( i==0 ) {
     108             :       v1v1 = dist;
     109        1665 :       iclose1 = 0;
     110       75871 :     } else if( dist<v1v1 ) {
     111             :       v3v3=v1v1;
     112             :       v1v1=dist;
     113       30300 :       iclose2=iclose1;
     114       30300 :       iclose1=i;
     115       45571 :     } else if( i==1 ) {
     116             :       v3v3=dist;
     117         327 :       iclose2=1;
     118       45244 :     } else if( dist<v3v3 ) {
     119             :       v3v3=dist;
     120        1325 :       iclose2=i;
     121             :     }
     122             :   }
     123             :   // And find third closest point
     124        1665 :   int isign = iclose1 - iclose2;
     125             :   if( isign>1 ) {
     126             :     isign=1;
     127             :   } else if( isign<-1 ) {
     128             :     isign=-1;
     129             :   }
     130        1665 :   int iclose3 = iclose1 + isign;
     131        1665 :   unsigned ifrom=iclose1, ito=iclose3;
     132        1665 :   if( iclose3<0 || iclose3>=nrows ) {
     133          31 :     ifrom=iclose2;
     134          31 :     ito=iclose1;
     135             :   }
     136             : 
     137             :   // And calculate projection of vector connecting current point to closest frame on vector connecting nearest two frames
     138             :   std::vector<double> displace;
     139        1665 :   path_projector.getDisplaceVector( ifrom, ito, displace );
     140             :   double v2v2=0, v1v2=0;
     141        1665 :   k=ncols*iclose1;
     142       42661 :   for(unsigned i=0; i<displace.size(); ++i) {
     143       40996 :     v2v2 += displace[i]*displace[i];
     144       40996 :     v1v2 += displace[i]*getPntrToArgument(0)->get(k+i);
     145             :   }
     146             : 
     147             :   // This computes s value
     148        1665 :   double spacing = getPntrToArgument(1)->get(iclose1) - getPntrToArgument(1)->get(iclose2);
     149        1665 :   double root = sqrt( v1v2*v1v2 - v2v2 * ( v1v1 - v3v3) );
     150        1665 :   double dx = 0.5 * ( (root + v1v2) / v2v2 - 1.);
     151        1665 :   double path_s = getPntrToArgument(1)->get(iclose1) + spacing * dx;
     152        1665 :   Value* sp = getPntrToComponent(0);
     153             :   sp->set( path_s );
     154        1665 :   if( !doNotCalculateDerivatives() ) {
     155       23478 :     for(unsigned i=0; i<ncols; ++i) {
     156       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 );
     157       22386 :       sp->addDerivative( ncols*iclose2 + i, 0.5*spacing*getPntrToArgument(0)->get(ncols*iclose2 + i)/root );
     158             :     }
     159             :   }
     160             : 
     161             :   // This computes z value
     162        1665 :   path_projector.getDisplaceVector( iclose2, iclose1, displace );
     163             :   double v4v4=0, proj=0;
     164        1665 :   k=ncols*iclose1;
     165       42661 :   for(unsigned i=0; i<displace.size(); ++i) {
     166       40996 :     v4v4 += displace[i]*displace[i];
     167       40996 :     proj += displace[i]*getPntrToArgument(0)->get(k+i);
     168             :   }
     169        1665 :   double path_z = v1v1 + dx*dx*v4v4 - 2*dx*proj;
     170        1665 :   path_z = sqrt(path_z);
     171        1665 :   Value* zp = getPntrToComponent(1);
     172             :   zp->set( path_z );
     173        1665 :   if( !doNotCalculateDerivatives() ) {
     174       23478 :     for(unsigned i=0; i<ncols; ++i) {
     175       22386 :       zp->addDerivative( ncols*iclose1 + i, (1/path_z)*(getPntrToArgument(0)->get(ncols*iclose1 + i) +
     176       22386 :                          (v4v4*dx-proj)*sp->getDerivative(ncols*iclose1 + i)/spacing -
     177       22386 :                          dx*displace[i]) );
     178       22386 :       zp->addDerivative( ncols*iclose2 + i, (v4v4*dx-proj)*sp->getDerivative(ncols*iclose2 + i)/(path_z*spacing) );
     179             :     }
     180             :   }
     181        1665 : }
     182             : 
     183             : }
     184             : }