GridVessel.cpp

/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Copyright (c) 2015,2016 The plumed team
   (see the PEOPLE file at the root of the distribution for a list of names)

   See http://www.plumed.org for more information.

   This file is part of plumed, version 2.

   plumed is free software: you can redistribute it and/or modify
   it under the terms of the GNU Lesser General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.

   plumed is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU Lesser General Public License for more details.

   You should have received a copy of the GNU Lesser General Public License
   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "GridVessel.h"
#include "vesselbase/ActionWithVessel.h"
#include "tools/Random.h"
#include "tools/Tools.h"

namespace PLMD {
namespace gridtools {

void GridVessel::registerKeywords( Keywords& keys ){
  AveragingVessel::registerKeywords( keys );
  keys.add("compulsory","TYPE","flat","how the grid points are being generated");
  keys.add("compulsory","COMPONENTS","the names of the components in the vector");
  keys.add("compulsory","COORDINATES","the names of the coordinates of the grid");
  keys.add("compulsory","PBC","is the grid periodic in each direction or not");
}

GridVessel::GridVessel( const vesselbase::VesselOptions& da ):
AveragingVessel(da),
bounds_set(false),
cube_units(1.0),
noderiv(false),
npoints(0),
wasforced(false)
{
  std::string geom; parse("TYPE",geom);
  if( geom=="flat" ) gtype=flat;
  else if( geom=="fibonacci" ) gtype=fibonacci;
  else plumed_merror( geom + " is invalid geometry type");
  std::vector<std::string> compnames; parseVector("COMPONENTS",compnames);
  std::vector<std::string> coordnames; parseVector("COORDINATES",coordnames);
  if( gtype==flat ){
      dimension=coordnames.size();
      str_min.resize( dimension);  str_max.resize( dimension ); stride.resize( dimension ); 
      max.resize( dimension ); dx.resize( dimension ); nbin.resize( dimension ); min.resize( dimension ); 
  } else if( gtype==fibonacci ){
      if( coordnames.size()!=3 ) error("cannot generate fibonacci grid points on surface of sphere if not 3 input coordinates");
      dimension=3; 
  }

  unsigned n=0; nper=compnames.size()*( 1 + coordnames.size() );
  arg_names.resize( coordnames.size() + compnames.size()*( 1 + coordnames.size() ) );
  for(unsigned i=0;i<coordnames.size();++i){ arg_names[n] = coordnames[i]; n++; }
  for(unsigned i=0;i<compnames.size();++i){
      arg_names[n]=compnames[i]; n++;
      for(unsigned j=0;j<coordnames.size();++j){ arg_names[n] = "d" + compnames[i] + "_" + coordnames[j]; n++; }
  }
  pbc.resize( dimension );
  std::vector<std::string> spbc( dimension ); parseVector("PBC",spbc);
  for(unsigned i=0;i<dimension;++i){
      if( spbc[i]=="F" ) pbc[i]=false;
      else if( spbc[i]=="T" ) pbc[i]=true;
      else plumed_error();
  }
}

void GridVessel::setNoDerivatives(){
  nper = ( nper/(1+dimension) ); noderiv=true;
  std::vector<std::string> tnames( dimension ), cnames(nper);
  for(unsigned i=0;i<dimension;++i) tnames[i]=arg_names[i];
  unsigned k=dimension; for(unsigned i=0;i<nper;++i){ cnames[i]=arg_names[k]; k+=(1+dimension); }
  arg_names.resize( dimension + nper );
  for(unsigned i=0;i<dimension;++i) arg_names[i]=tnames[i];
  for(unsigned i=0;i<nper;++i) arg_names[dimension+i]=cnames[i];
}

void GridVessel::setBounds( const std::vector<std::string>& smin, const std::vector<std::string>& smax,
                            const std::vector<unsigned>& binsin, const std::vector<double>& spacing ){
  plumed_dbg_assert( smin.size()==dimension && smax.size()==dimension );
  plumed_assert( gtype==flat && (spacing.size()==dimension || binsin.size()==dimension) );

  npoints=1; bounds_set=true;
  for(unsigned i=0;i<dimension;++i){
      str_min[i]=smin[i]; str_max[i]=smax[i];
      Tools::convert( str_min[i], min[i] );
      Tools::convert( str_max[i], max[i] );
      if( spacing.size()==dimension && binsin.size()==dimension ){
          double range = max[i] - min[i]; unsigned spc = std::floor( range / spacing[i]);
          // This check ensures that nbins is set correctly if spacing is set the same as the number of bins
          if( fabs( binsin[i]*spacing[i]-range )>epsilon ) spc += 1;
          if( spc>binsin[i] ) nbin[i]=spc; else nbin[i]=binsin[i]; 
      } else if( binsin.size()==dimension ) nbin[i]=binsin[i];
      else if( spacing.size()==dimension ) nbin[i] = std::floor(( max[i] - min[i] ) / spacing[i]) + 1; 
      else plumed_error();
      dx[i] = ( max[i] - min[i] ) / static_cast<double>( nbin[i] );
      if( !pbc[i] ){ max[i] +=dx[i]; nbin[i]+=1; }
      stride[i]=npoints;
      npoints*=nbin[i]; 
  }
  resize();  // Always resize after setting new bounds as grid size may have have changed 
} 

void GridVessel::setupFibonacciGrid( const unsigned& np ){
  bounds_set=true;
  npoints = np; fib_increment = pi*( 3 - sqrt(5) );
  fib_offset = 2 / static_cast<double>( npoints ); 
  Random random; fib_rnd = std::floor( npoints*random.RandU01() );
  resize();
}

std::string GridVessel::description(){
  if( !bounds_set ) return "";
 
  std::string des;
  if( gtype==flat ){
      des="grid of "; std::string num;
      for(unsigned i=0;i<dimension-1;++i){
          Tools::convert( nbin[i], num );
          des += num + " X ";
      }
      Tools::convert( nbin[dimension-1], num );
      des += num + " equally spaced points between (";
      for(unsigned i=0;i<dimension-1;++i) des += str_min[i] + ",";
      Tools::convert( nbin[dimension-1], num );
      des += str_min[dimension-1] + ") and (";
      for(unsigned i=0;i<dimension-1;++i) des += str_max[i] + ",";
      des += str_max[dimension-1] + ")";
  } else if( gtype==fibonacci ){
     std::string num; Tools::convert( npoints, num );
     des += "fibonacci grid of " + num + " points on spherical surface"; 
  }
  return des;
}

void GridVessel::resize(){
  plumed_massert( nper>0, "Number of datapoints at each grid point has not been set");
  if( getAction() ) resizeBuffer( getNumberOfBufferPoints()*nper + 1 + 2*getAction()->getNumberOfDerivatives() ); 
  setDataSize( npoints*nper ); forces.resize( npoints );
  if( active.size()!=npoints) active.resize( npoints, true );
}

unsigned GridVessel::getIndex( const std::vector<unsigned>& indices ) const {
  plumed_dbg_assert( gtype==flat && bounds_set && indices.size()==dimension );
  // indices are flattended using a column-major order
  unsigned index=indices[dimension-1];
  for(unsigned i=dimension-1;i>0;--i){
    index=index*nbin[i-1]+indices[i-1];
  } 
  return index;
}

void GridVessel::getIndices( const std::vector<double>& point, std::vector<unsigned>& indices ) const { 
  plumed_dbg_assert( gtype==flat && bounds_set && point.size()==dimension && indices.size()==dimension );
  for(unsigned i=0;i<dimension;++i){
      indices[i]=std::floor( (point[i] - min[i])/dx[i] );
      if( pbc[i] ) indices[i]=indices[i]%nbin[i];
  }
}

unsigned GridVessel::getIndex( const std::vector<double>& point ) const {
  plumed_dbg_assert( gtype==flat && bounds_set && point.size()==dimension );
  std::vector<unsigned> indices(dimension); getIndices( point, indices );
  return getIndex( indices );
}

void GridVessel::convertIndexToIndices( const unsigned& index, const std::vector<unsigned>& nnbin, std::vector<unsigned>& indices ) const {
 plumed_dbg_assert( gtype==flat ); unsigned kk=index; indices[0]=index%nnbin[0];
 for(unsigned i=1;i<dimension-1;++i){
    kk=(kk-indices[i-1])/nnbin[i-1];
    indices[i]=kk%nnbin[i];
 } 
 if(dimension>=2){  // I think this is wrong
    indices[dimension-1]=(kk-indices[dimension-2])/nnbin[dimension-2];
 }

}

void GridVessel::getIndices( const unsigned& index, std::vector<unsigned>& indices ) const {
 plumed_dbg_assert( gtype==flat ); convertIndexToIndices( index, nbin, indices );
}

void GridVessel::getGridPointCoordinates( const unsigned& ipoint , std::vector<double>& x ) const {
  plumed_dbg_assert( bounds_set && x.size()==dimension && ipoint<npoints );
  if( gtype==flat ){
      std::vector<unsigned> tindices( dimension ); getIndices( ipoint, tindices ); 
      for(unsigned i=0;i<dimension;++i) x[i] = min[i] + dx[i]*tindices[i];
  } else if( gtype==fibonacci ){
      x[1] = ((ipoint*fib_offset) - 1) + (fib_offset/2);
      double r = sqrt( 1 -x[1]*x[1] );
      double phi = ((ipoint+fib_rnd)%npoints)*fib_increment;
      x[0] = r*cos(phi); x[2] = r*sin(phi);
      double norm=0; 
      for(unsigned j=0;j<3;++j) norm+=x[j]*x[j]; 
      norm = sqrt(norm);
      for(unsigned j=0;j<3;++j) x[j] = x[j] / norm;
  } else {
      plumed_error();
  }
}

void GridVessel::getSplineNeighbors( const unsigned& mybox, unsigned& nneighbors, std::vector<unsigned>& mysneigh ) const {
  plumed_dbg_assert( gtype==flat ); unsigned nneigh=unsigned(pow(2.0,int(dimension)));
  if( mysneigh.size()!=nneigh ) mysneigh.resize(nneigh);

  unsigned inind; nneighbors = 0;
  std::vector<unsigned> tmp_indices( dimension );
  std::vector<unsigned> my_indices( dimension );
  getIndices( mybox, my_indices );
  for(unsigned i=0;i<nneigh;++i){
     unsigned tmp=i; inind=0;
     for(unsigned j=0;j<dimension;++j){
        unsigned i0=tmp%2+my_indices[j]; tmp/=2;
        if(!pbc[j] && i0==nbin[j]) continue;
        if( pbc[j] && i0==nbin[j]) i0=0;
        tmp_indices[inind++]=i0;
     }
     if(inind==dimension ){
        unsigned findex=getIndex( tmp_indices );
        mysneigh[nneighbors++]=findex;
        plumed_massert( active[findex], "inactive grid point required for splines"); 
    }
  }
}

double GridVessel::getGridElement( const unsigned& ipoint, const unsigned& jelement ) const {
  plumed_assert( bounds_set && ipoint<npoints && jelement<nper && active[ipoint] );
  return getDataElement( nper*ipoint + jelement  );
}

void GridVessel::setGridElement( const unsigned& ipoint, const unsigned& jelement, const double& value ){
  plumed_dbg_assert( bounds_set && ipoint<npoints && jelement<nper );
  setDataElement( nper*ipoint + jelement, value );
}

void GridVessel::setValueAndDerivatives( const unsigned& ipoint, const unsigned& jelement, const double& value, const std::vector<double>& der ){
  plumed_dbg_assert( !noderiv && jelement<getNumberOfComponents() && der.size()==nbin.size() );
  setGridElement( ipoint, jelement, value ); for(unsigned i=0;i<der.size();++i) setGridElement( ipoint, jelement+1+i, der[i] ); 
}

void GridVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
  plumed_dbg_assert( myvals.getNumberOfValues()==(nper+1) );
  for(unsigned i=0;i<nper;++i) buffer[bufstart + nper*current + i] += myvals.get(i+1);
}

void GridVessel::finish( const std::vector<double>& buffer ){
  if( wasforced ) getFinalForces( buffer, finalForces );
  else AveragingVessel::finish( buffer );
}

double GridVessel::getGridElement( const std::vector<unsigned>& indices, const unsigned& jelement ) const {
  return getGridElement( getIndex( indices ), jelement );
}

void GridVessel::setGridElement( const std::vector<unsigned>& indices, const unsigned& jelement, const double& value ){
  setGridElement( getIndex( indices ), jelement, value );
}

std::vector<std::string> GridVessel::getMin() const {
  plumed_dbg_assert( gtype==flat ); return str_min;
}
  
std::vector<std::string> GridVessel::getMax() const {
  plumed_dbg_assert( gtype==flat ); return str_max;
}

std::vector<unsigned> GridVessel::getNbin() const {
  plumed_dbg_assert( gtype==flat && bounds_set );
  std::vector<unsigned> ngrid( dimension );
  for(unsigned i=0;i<dimension;++i){
      if( !pbc[i] ) ngrid[i]=nbin[i] - 1;
      else ngrid[i]=nbin[i];
  }
  return ngrid;
}

void GridVessel::getNeighbors( const std::vector<double>& pp, const std::vector<unsigned>& nneigh,
                               unsigned& num_neighbors, std::vector<unsigned>& neighbors ) const {
  plumed_dbg_assert( gtype==flat && bounds_set && nneigh.size()==dimension );

  std::vector<unsigned> indices( dimension );
  for(unsigned i=0;i<dimension;++i) indices[i] = std::floor( (pp[i]-min[i])/dx[i] );
  getNeighbors( indices, nneigh, num_neighbors, neighbors );
}

void GridVessel::getNeighbors( const std::vector<unsigned>& indices, const std::vector<unsigned>& nneigh, 
                               unsigned& num_neighbors, std::vector<unsigned>& neighbors ) const {
  plumed_dbg_assert( gtype==flat && bounds_set && nneigh.size()==dimension );

  unsigned num_neigh=1; std::vector<unsigned> small_bin( dimension );
  for(unsigned i=0;i<dimension;++i){
     small_bin[i]=(2*nneigh[i]+1);
     num_neigh *=small_bin[i];
  }
  if( neighbors.size()!=num_neigh ) neighbors.resize( num_neigh ); 

  num_neighbors=0;
  std::vector<unsigned> s_indices(dimension), t_indices(dimension);
  for(unsigned index=0;index<num_neigh;++index){
      bool found=true;
      convertIndexToIndices( index, small_bin, s_indices );
      for(unsigned i=0;i<dimension;++i){
          int i0=s_indices[i]-nneigh[i]+indices[i];
          if(!pbc[i] && i0<0)        found=false;
          if(!pbc[i] && i0>=nbin[i]) found=false;
          if( pbc[i] && i0<0)        i0=nbin[i]-(-i0)%nbin[i];
          if( pbc[i] && i0>=nbin[i]) i0%=nbin[i];
          t_indices[i]=static_cast<unsigned>(i0);
      }
      if( found ){
          neighbors[num_neighbors]=getIndex( t_indices );
          num_neighbors++;
      }
  }
}

void GridVessel::setCubeUnits( const double& units ){
  plumed_dbg_assert( gtype==flat ); cube_units=units;
}

double GridVessel::getCubeUnits() const {
  plumed_dbg_assert( gtype==flat ); return cube_units;
}

std::string GridVessel::getInputString() const {
  std::string mstring="COORDINATES="+arg_names[0];
  for(unsigned i=1;i<dimension;++i) mstring+="," + arg_names[i];
  if( gtype==flat ){
      mstring += " TYPE=flat PBC=";
      if( pbc[0] ) mstring +="T";
      else mstring +="F";
      for(unsigned i=1;i<dimension;++i){
         if( pbc[i] ) mstring +=",T";
         else mstring +=",F";
      }
  } else if( gtype==fibonacci ){
      mstring += " TYPE=fibonacci";
  }
  return mstring;
}

double GridVessel::getValueAndDerivatives( const std::vector<double>& x, const unsigned& ind, std::vector<double>& der ) const {
  plumed_dbg_assert( gtype==flat && der.size()==dimension && !noderiv && ind<getNumberOfComponents() );

  double X,X2,X3,value=0; der.assign(der.size(),0.0);
  std::vector<double> fd(dimension);
  std::vector<double> C(dimension);
  std::vector<double> D(dimension);
  std::vector<double> dder(dimension);

  std::vector<unsigned> nindices(dimension); unsigned n_neigh;
  std::vector<unsigned> indices(dimension); getIndices( x, indices );
  std::vector<unsigned> neigh; getSplineNeighbors( getIndex(indices), n_neigh, neigh );
  std::vector<double> xfloor(dimension); getGridPointCoordinates( getIndex(x), xfloor );

// loop over neighbors
  for(unsigned int ipoint=0;ipoint<n_neigh;++ipoint){
     double grid=getGridElement(neigh[ipoint], ind*(1+dimension) );          
     for(unsigned j=0;j<dimension;++j) dder[j] = getGridElement( neigh[ipoint], ind*(1+dimension) + 1 + j );
 
     getIndices( neigh[ipoint], nindices );
     double ff=1.0;

     for(unsigned j=0;j<dimension;++j){
         int x0=1;
         if(nindices[j]==indices[j]) x0=0;
         double ddx=dx[j];
         X=fabs((x[j]-xfloor[j])/ddx-(double)x0);
         X2=X*X;
         X3=X2*X;
         double yy;
         if(fabs(grid)<0.0000001) yy=0.0;
          else yy=-dder[j]/grid;
         C[j]=(1.0-3.0*X2+2.0*X3) - (x0?-1.0:1.0)*yy*(X-2.0*X2+X3)*ddx;
         D[j]=( -6.0*X +6.0*X2) - (x0?-1.0:1.0)*yy*(1.0-4.0*X +3.0*X2)*ddx;
         D[j]*=(x0?-1.0:1.0)/ddx;
         ff*=C[j];
      }
      for(unsigned j=0;j<dimension;++j){
         fd[j]=D[j];
         for(unsigned i=0;i<dimension;++i) if(i!=j) fd[j]*=C[i];
      }
      value+=grid*ff;
      for(unsigned j=0;j<dimension;++j) der[j]+=grid*fd[j];
  }
  return value;
}

void GridVessel::activateThesePoints( const std::vector<bool>& to_activate ){
  plumed_dbg_assert( to_activate.size()==npoints );
  for(unsigned i=0;i<npoints;++i) active[i]=to_activate[i];
}

void GridVessel::setForce( const std::vector<double>& inforces ){
  plumed_dbg_assert( inforces.size()==npoints );
  wasforced=true; for(unsigned i=0;i<npoints;++i) forces[i]=inforces[i];
}

bool GridVessel::wasForced() const {
  return wasforced;
}

bool GridVessel::applyForce( std::vector<double>& fforces ){
  plumed_dbg_assert( fforces.size()==finalForces.size() ); 
  if( !wasforced ) return false;
  for(unsigned i=0;i<finalForces.size();++i) fforces[i]=finalForces[i]; 
  wasforced=false; return true;
}

}
}