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Grid.cpp
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Grid.cpp
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/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Copyright (c) 2011-2020 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 "Grid.h"
#include "Tools.h"
#include "core/Value.h"
#include "File.h"
#include "Exception.h"
#include "KernelFunctions.h"
#include "RootFindingBase.h"
#include "Communicator.h"
#include <vector>
#include <cmath>
#include <iostream>
#include <sstream>
#include <cstdio>
#include <cfloat>
#include <array>
using namespace std;
namespace PLMD {
constexpr size_t Grid::maxdim;
Grid::Grid(const std::string& funcl, const std::vector<Value*> & args, const vector<std::string> & gmin,
const vector<std::string> & gmax, const vector<unsigned> & nbin, bool dospline, bool usederiv, bool doclear) {
// various checks
plumed_assert(args.size()<=maxdim) << "grid dim cannot exceed "<<maxdim;
plumed_massert(args.size()==gmin.size(),"grid min dimensions in input do not match number of arguments");
plumed_massert(args.size()==nbin.size(),"number of bins on input do not match number of arguments");
plumed_massert(args.size()==gmax.size(),"grid max dimensions in input do not match number of arguments");
unsigned dim=gmax.size();
std::vector<std::string> names;
std::vector<bool> isperiodic;
std::vector<string> pmin,pmax;
names.resize( dim );
isperiodic.resize( dim );
pmin.resize( dim );
pmax.resize( dim );
for(unsigned int i=0; i<dim; ++i) {
names[i]=args[i]->getName();
if( args[i]->isPeriodic() ) {
isperiodic[i]=true;
args[i]->getDomain( pmin[i], pmax[i] );
} else {
isperiodic[i]=false;
pmin[i]="0.";
pmax[i]="0.";
}
}
// this is a value-independent initializator
Init(funcl,names,gmin,gmax,nbin,dospline,usederiv,doclear,isperiodic,pmin,pmax);
}
Grid::Grid(const std::string& funcl, const std::vector<string> &names, const std::vector<std::string> & gmin,
const vector<std::string> & gmax, const std::vector<unsigned> & nbin, bool dospline, bool usederiv, bool doclear, const std::vector<bool> &isperiodic, const std::vector<std::string> &pmin, const std::vector<std::string> &pmax ) {
// this calls the initializator
Init(funcl,names,gmin,gmax,nbin,dospline,usederiv,doclear,isperiodic,pmin,pmax);
}
void Grid::Init(const std::string& funcl, const std::vector<std::string> &names, const vector<std::string> & gmin,
const std::vector<std::string> & gmax, const std::vector<unsigned> & nbin, bool dospline, bool usederiv, bool doclear,
const std::vector<bool> &isperiodic, const std::vector<std::string> &pmin, const std::vector<std::string> &pmax ) {
contour_location=0.0; fmt_="%14.9f";
// various checks
plumed_assert(names.size()<=maxdim) << "grid size cannot exceed "<<maxdim;
plumed_massert(names.size()==gmin.size(),"grid dimensions in input do not match number of arguments");
plumed_massert(names.size()==nbin.size(),"grid dimensions in input do not match number of arguments");
plumed_massert(names.size()==gmax.size(),"grid dimensions in input do not match number of arguments");
dimension_=gmax.size();
str_min_=gmin; str_max_=gmax;
argnames.resize( dimension_ );
min_.resize( dimension_ );
max_.resize( dimension_ );
pbc_.resize( dimension_ );
for(unsigned int i=0; i<dimension_; ++i) {
argnames[i]=names[i];
if( isperiodic[i] ) {
pbc_[i]=true;
str_min_[i]=pmin[i];
str_max_[i]=pmax[i];
} else {
pbc_[i]=false;
}
Tools::convert(str_min_[i],min_[i]);
Tools::convert(str_max_[i],max_[i]);
funcname=funcl;
plumed_massert(max_[i]>min_[i],"maximum in grid must be larger than minimum");
plumed_massert(nbin[i]>0,"number of grid points must be greater than zero");
}
nbin_=nbin;
dospline_=dospline;
usederiv_=usederiv;
if(dospline_) plumed_assert(dospline_==usederiv_);
maxsize_=1;
for(unsigned int i=0; i<dimension_; ++i) {
dx_.push_back( (max_[i]-min_[i])/static_cast<double>( nbin_[i] ) );
if( !pbc_[i] ) { max_[i] += dx_[i]; nbin_[i] += 1; }
maxsize_*=nbin_[i];
}
if(doclear) clear();
}
void Grid::clear() {
grid_.resize(maxsize_);
if(usederiv_) der_.resize(maxsize_);
for(index_t i=0; i<maxsize_; ++i) {
grid_[i]=0.0;
if(usederiv_) {
(der_[i]).resize(dimension_);
for(unsigned int j=0; j<dimension_; ++j) der_[i][j]=0.0;
}
}
}
vector<std::string> Grid::getMin() const {
return str_min_;
}
vector<std::string> Grid::getMax() const {
return str_max_;
}
vector<double> Grid::getDx() const {
return dx_;
}
double Grid::getDx(index_t j) const {
return dx_[j];
}
double Grid::getBinVolume() const {
double vol=1.;
for(unsigned i=0; i<dx_.size(); ++i) vol*=dx_[i];
return vol;
}
vector<bool> Grid::getIsPeriodic() const {
return pbc_;
}
vector<unsigned> Grid::getNbin() const {
return nbin_;
}
vector<string> Grid::getArgNames() const {
return argnames;
}
Grid::index_t Grid::getSize() const {
return maxsize_;
}
unsigned Grid::getDimension() const {
return dimension_;
}
// we are flattening arrays using a column-major order
Grid::index_t Grid::getIndex(const vector<unsigned> & indices) const {
plumed_dbg_assert(indices.size()==dimension_);
for(unsigned int i=0; i<dimension_; i++)
if(indices[i]>=nbin_[i]) {
std::string is;
Tools::convert(i,is);
std::string msg="ERROR: the system is looking for a value outside the grid along the " + is + " ("+getArgNames()[i]+")";
plumed_merror(msg+" index!");
}
index_t index=indices[dimension_-1];
for(unsigned int i=dimension_-1; i>0; --i) {
index=index*nbin_[i-1]+indices[i-1];
}
return index;
}
Grid::index_t Grid::getIndex(const vector<double> & x) const {
plumed_dbg_assert(x.size()==dimension_);
return getIndex(getIndices(x));
}
// we are flattening arrays using a column-major order
vector<unsigned> Grid::getIndices(index_t index) const {
vector<unsigned> indices(dimension_);
index_t kk=index;
indices[0]=(index%nbin_[0]);
for(unsigned int i=1; i<dimension_-1; ++i) {
kk=(kk-indices[i-1])/nbin_[i-1];
indices[i]=(kk%nbin_[i]);
}
if(dimension_>=2) {
indices[dimension_-1]=((kk-indices[dimension_-2])/nbin_[dimension_-2]);
}
return indices;
}
void Grid::getIndices(index_t index, std::vector<unsigned>& indices) const {
if (indices.size()!=dimension_) indices.resize(dimension_);
index_t kk=index;
indices[0]=(index%nbin_[0]);
for(unsigned int i=1; i<dimension_-1; ++i) {
kk=(kk-indices[i-1])/nbin_[i-1];
indices[i]=(kk%nbin_[i]);
}
if(dimension_>=2) {
indices[dimension_-1]=((kk-indices[dimension_-2])/nbin_[dimension_-2]);
}
}
vector<unsigned> Grid::getIndices(const vector<double> & x) const {
plumed_dbg_assert(x.size()==dimension_);
vector<unsigned> indices(dimension_);
for(unsigned int i=0; i<dimension_; ++i) {
indices[i] = unsigned(floor((x[i]-min_[i])/dx_[i]));
}
return indices;
}
void Grid::getIndices(const vector<double> & x, std::vector<unsigned>& indices) const {
plumed_dbg_assert(x.size()==dimension_);
if (indices.size()!=dimension_) indices.resize(dimension_);
for(unsigned int i=0; i<dimension_; ++i) {
indices[i] = unsigned(floor((x[i]-min_[i])/dx_[i]));
}
}
vector<double> Grid::getPoint(const vector<unsigned> & indices) const {
plumed_dbg_assert(indices.size()==dimension_);
vector<double> x(dimension_);
for(unsigned int i=0; i<dimension_; ++i) {
x[i]=min_[i]+(double)(indices[i])*dx_[i];
}
return x;
}
vector<double> Grid::getPoint(index_t index) const {
plumed_dbg_assert(index<maxsize_);
return getPoint(getIndices(index));
}
vector<double> Grid::getPoint(const vector<double> & x) const {
plumed_dbg_assert(x.size()==dimension_);
return getPoint(getIndices(x));
}
void Grid::getPoint(index_t index,std::vector<double> & point) const {
plumed_dbg_assert(index<maxsize_);
getPoint(getIndices(index),point);
}
void Grid::getPoint(const std::vector<unsigned> & indices,std::vector<double> & point) const {
plumed_dbg_assert(indices.size()==dimension_);
plumed_dbg_assert(point.size()==dimension_);
for(unsigned int i=0; i<dimension_; ++i) {
point[i]=min_[i]+(double)(indices[i])*dx_[i];
}
}
void Grid::getPoint(const std::vector<double> & x,std::vector<double> & point) const {
plumed_dbg_assert(x.size()==dimension_);
getPoint(getIndices(x),point);
}
vector<Grid::index_t> Grid::getNeighbors
(const vector<unsigned> &indices,const vector<unsigned> &nneigh)const {
plumed_dbg_assert(indices.size()==dimension_ && nneigh.size()==dimension_);
vector<index_t> neighbors;
vector<unsigned> small_bin(dimension_);
unsigned small_nbin=1;
for(unsigned j=0; j<dimension_; ++j) {
small_bin[j]=(2*nneigh[j]+1);
small_nbin*=small_bin[j];
}
vector<unsigned> small_indices(dimension_);
vector<unsigned> tmp_indices;
for(unsigned index=0; index<small_nbin; ++index) {
tmp_indices.resize(dimension_);
unsigned kk=index;
small_indices[0]=(index%small_bin[0]);
for(unsigned i=1; i<dimension_-1; ++i) {
kk=(kk-small_indices[i-1])/small_bin[i-1];
small_indices[i]=(kk%small_bin[i]);
}
if(dimension_>=2) {
small_indices[dimension_-1]=((kk-small_indices[dimension_-2])/small_bin[dimension_-2]);
}
unsigned ll=0;
for(unsigned i=0; i<dimension_; ++i) {
int i0=small_indices[i]-nneigh[i]+indices[i];
if(!pbc_[i] && i0<0) continue;
if(!pbc_[i] && i0>=static_cast<int>(nbin_[i])) continue;
if( pbc_[i] && i0<0) i0=nbin_[i]-(-i0)%nbin_[i];
if( pbc_[i] && i0>=static_cast<int>(nbin_[i])) i0%=nbin_[i];
tmp_indices[ll]=static_cast<unsigned>(i0);
ll++;
}
tmp_indices.resize(ll);
if(tmp_indices.size()==dimension_) {neighbors.push_back(getIndex(tmp_indices));}
}
return neighbors;
}
vector<Grid::index_t> Grid::getNeighbors
(const vector<double> & x,const vector<unsigned> & nneigh)const {
plumed_dbg_assert(x.size()==dimension_ && nneigh.size()==dimension_);
return getNeighbors(getIndices(x),nneigh);
}
vector<Grid::index_t> Grid::getNeighbors
(index_t index,const vector<unsigned> & nneigh)const {
plumed_dbg_assert(index<maxsize_ && nneigh.size()==dimension_);
return getNeighbors(getIndices(index),nneigh);
}
void Grid::getSplineNeighbors(const vector<unsigned> & indices, vector<Grid::index_t>& neighbors, unsigned& nneighbors)const {
plumed_dbg_assert(indices.size()==dimension_);
unsigned nneigh=unsigned(pow(2.0,int(dimension_)));
if (neighbors.size()!=nneigh) neighbors.resize(nneigh);
vector<unsigned> nindices(dimension_);
unsigned inind; nneighbors = 0;
for(unsigned int i=0; i<nneigh; ++i) {
unsigned tmp=i; inind=0;
for(unsigned int j=0; j<dimension_; ++j) {
unsigned i0=tmp%2+indices[j];
tmp/=2;
if(!pbc_[j] && i0==nbin_[j]) continue;
if( pbc_[j] && i0==nbin_[j]) i0=0;
nindices[inind++]=i0;
}
if(inind==dimension_) neighbors[nneighbors++]=getIndex(nindices);
}
}
vector<Grid::index_t> Grid::getNearestNeighbors(const index_t index) const {
vector<index_t> nearest_neighs = vector<index_t>();
for (unsigned i = 0; i < dimension_; i++) {
vector<unsigned> neighsneeded = vector<unsigned>(dimension_, 0);
neighsneeded[i] = 1;
vector<index_t> singledim_nearest_neighs = getNeighbors(index, neighsneeded);
for (unsigned j = 0; j < singledim_nearest_neighs.size(); j++) {
index_t neigh = singledim_nearest_neighs[j];
if (neigh != index) {
nearest_neighs.push_back(neigh);
}
}
}
return nearest_neighs;
}
vector<Grid::index_t> Grid::getNearestNeighbors(const vector<unsigned> &indices) const {
plumed_dbg_assert(indices.size() == dimension_);
return getNearestNeighbors(getIndex(indices));
}
void Grid::addKernel( const KernelFunctions& kernel ) {
plumed_dbg_assert( kernel.ndim()==dimension_ );
std::vector<unsigned> nneighb=kernel.getSupport( dx_ );
std::vector<index_t> neighbors=getNeighbors( kernel.getCenter(), nneighb );
std::vector<double> xx( dimension_ );
std::vector<std::unique_ptr<Value>> vv( dimension_ );
std::string str_min, str_max;
for(unsigned i=0; i<dimension_; ++i) {
vv[i].reset(new Value());
if( pbc_[i] ) {
Tools::convert(min_[i],str_min);
Tools::convert(max_[i],str_max);
vv[i]->setDomain( str_min, str_max );
} else {
vv[i]->setNotPeriodic();
}
}
// vv_ptr contains plain pointers obtained from vv.
// this is the simplest way to replace a unique_ptr here.
// perhaps the interface of kernel.evaluate() should be changed
// in order to accept a std::vector<std::unique_ptr<Value>>
auto vv_ptr=Tools::unique2raw(vv);
std::vector<double> der( dimension_ );
for(unsigned i=0; i<neighbors.size(); ++i) {
index_t ineigh=neighbors[i];
getPoint( ineigh, xx );
for(unsigned j=0; j<dimension_; ++j) vv[j]->set(xx[j]);
double newval = kernel.evaluate( vv_ptr, der, usederiv_ );
if( usederiv_ ) addValueAndDerivatives( ineigh, newval, der );
else addValue( ineigh, newval );
}
}
double Grid::getValue(index_t index) const {
plumed_dbg_assert(index<maxsize_);
return grid_[index];
}
double Grid::getMinValue() const {
double minval;
minval=DBL_MAX;
for(index_t i=0; i<grid_.size(); ++i) {
if(grid_[i]<minval)minval=grid_[i];
}
return minval;
}
double Grid::getMaxValue() const {
double maxval;
maxval=DBL_MIN;
for(index_t i=0; i<grid_.size(); ++i) {
if(grid_[i]>maxval)maxval=grid_[i];
}
return maxval;
}
double Grid::getValue(const vector<unsigned> & indices) const {
return getValue(getIndex(indices));
}
double Grid::getValue(const vector<double> & x) const {
if(!dospline_) {
return getValue(getIndex(x));
} else {
vector<double> der(dimension_);
return getValueAndDerivatives(x,der);
}
}
double Grid::getValueAndDerivatives
(index_t index, vector<double>& der) const {
plumed_dbg_assert(index<maxsize_ && usederiv_ && der.size()==dimension_);
der=der_[index];
return grid_[index];
}
double Grid::getValueAndDerivatives
(const vector<unsigned> & indices, vector<double>& der) const {
return getValueAndDerivatives(getIndex(indices),der);
}
double Grid::getValueAndDerivatives
(const vector<double> & x, vector<double>& der) const {
plumed_dbg_assert(der.size()==dimension_ && usederiv_);
if(dospline_) {
double X,X2,X3,value;
std::array<double,maxdim> fd, C, D;
std::vector<double> dder(dimension_);
// reset
value=0.0;
for(unsigned int i=0; i<dimension_; ++i) der[i]=0.0;
vector<unsigned> indices(dimension_);
getIndices(x, indices);
vector<double> xfloor(dimension_);
getPoint(indices, xfloor);
vector<index_t> neigh; unsigned nneigh; getSplineNeighbors(indices, neigh, nneigh);
// loop over neighbors
vector<unsigned> nindices;
for(unsigned int ipoint=0; ipoint<nneigh; ++ipoint) {
double grid=getValueAndDerivatives(neigh[ipoint],dder);
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 dx=getDx(j);
X=fabs((x[j]-xfloor[j])/dx-(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)*dx;
D[j]=( -6.0*X +6.0*X2) - (x0?-1.0:1.0)*yy*(1.0-4.0*X +3.0*X2)*dx;
D[j]*=(x0?-1.0:1.0)/dx;
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;
} else {
return getValueAndDerivatives(getIndex(x),der);
}
}
void Grid::setValue(index_t index, double value) {
plumed_dbg_assert(index<maxsize_ && !usederiv_);
grid_[index]=value;
}
void Grid::setValue(const vector<unsigned> & indices, double value) {
setValue(getIndex(indices),value);
}
void Grid::setValueAndDerivatives
(index_t index, double value, vector<double>& der) {
plumed_dbg_assert(index<maxsize_ && usederiv_ && der.size()==dimension_);
grid_[index]=value;
der_[index]=der;
}
void Grid::setValueAndDerivatives
(const vector<unsigned> & indices, double value, vector<double>& der) {
setValueAndDerivatives(getIndex(indices),value,der);
}
void Grid::addValue(index_t index, double value) {
plumed_dbg_assert(index<maxsize_ && !usederiv_);
grid_[index]+=value;
}
void Grid::addValue(const vector<unsigned> & indices, double value) {
addValue(getIndex(indices),value);
}
void Grid::addValueAndDerivatives
(index_t index, double value, vector<double>& der) {
plumed_dbg_assert(index<maxsize_ && usederiv_ && der.size()==dimension_);
grid_[index]+=value;
for(unsigned int i=0; i<dimension_; ++i) der_[index][i]+=der[i];
}
void Grid::addValueAndDerivatives
(const vector<unsigned> & indices, double value, vector<double>& der) {
addValueAndDerivatives(getIndex(indices),value,der);
}
void Grid::scaleAllValuesAndDerivatives( const double& scalef ) {
if(usederiv_) {
for(index_t i=0; i<grid_.size(); ++i) {
grid_[i]*=scalef;
for(unsigned j=0; j<dimension_; ++j) der_[i][j]*=scalef;
}
} else {
for(index_t i=0; i<grid_.size(); ++i) grid_[i]*=scalef;
}
}
void Grid::logAllValuesAndDerivatives( const double& scalef ) {
if(usederiv_) {
for(index_t i=0; i<grid_.size(); ++i) {
grid_[i] = scalef*log(grid_[i]);
for(unsigned j=0; j<dimension_; ++j) der_[i][j] = scalef/der_[i][j];
}
} else {
for(index_t i=0; i<grid_.size(); ++i) grid_[i] = scalef*log(grid_[i]);
}
}
void Grid::setMinToZero() {
double min=grid_[0];
for(index_t i=1; i<grid_.size(); ++i) if(grid_[i]<min) min=grid_[i];
for(index_t i=0; i<grid_.size(); ++i) grid_[i] -= min;
}
void Grid::applyFunctionAllValuesAndDerivatives( double (*func)(double val), double (*funcder)(double valder) ) {
if(usederiv_) {
for(index_t i=0; i<grid_.size(); ++i) {
grid_[i]=func(grid_[i]);
for(unsigned j=0; j<dimension_; ++j) der_[i][j]=funcder(der_[i][j]);
}
} else {
for(index_t i=0; i<grid_.size(); ++i) grid_[i]=func(grid_[i]);
}
}
void Grid::writeHeader(OFile& ofile) {
for(unsigned i=0; i<dimension_; ++i) {
ofile.addConstantField("min_" + argnames[i]);
ofile.addConstantField("max_" + argnames[i]);
ofile.addConstantField("nbins_" + argnames[i]);
ofile.addConstantField("periodic_" + argnames[i]);
}
}
void Grid::writeToFile(OFile& ofile) {
vector<double> xx(dimension_);
vector<double> der(dimension_);
double f;
writeHeader(ofile);
for(index_t i=0; i<getSize(); ++i) {
xx=getPoint(i);
if(usederiv_) {f=getValueAndDerivatives(i,der);}
else {f=getValue(i);}
if(i>0 && dimension_>1 && getIndices(i)[dimension_-2]==0) ofile.printf("\n");
for(unsigned j=0; j<dimension_; ++j) {
ofile.printField("min_" + argnames[j], str_min_[j] );
ofile.printField("max_" + argnames[j], str_max_[j] );
ofile.printField("nbins_" + argnames[j], static_cast<int>(nbin_[j]) );
if( pbc_[j] ) ofile.printField("periodic_" + argnames[j], "true" );
else ofile.printField("periodic_" + argnames[j], "false" );
}
for(unsigned j=0; j<dimension_; ++j) { ofile.fmtField(" "+fmt_); ofile.printField(argnames[j],xx[j]); }
ofile.fmtField(" "+fmt_); ofile.printField(funcname,f);
if(usederiv_) for(unsigned j=0; j<dimension_; ++j) { ofile.fmtField(" "+fmt_); ofile.printField("der_" + argnames[j],der[j]); }
ofile.printField();
}
}
void Grid::writeCubeFile(OFile& ofile, const double& lunit) {
plumed_assert( dimension_==3 );
ofile.printf("PLUMED CUBE FILE\n");
ofile.printf("OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n");
// Number of atoms followed by position of origin (origin set so that center of grid is in center of cell)
ofile.printf("%d %f %f %f\n",1,-0.5*lunit*(max_[0]-min_[0]),-0.5*lunit*(max_[1]-min_[1]),-0.5*lunit*(max_[2]-min_[2]));
ofile.printf("%u %f %f %f\n",nbin_[0],lunit*dx_[0],0.0,0.0); // Number of bins in each direction followed by
ofile.printf("%u %f %f %f\n",nbin_[1],0.0,lunit*dx_[1],0.0); // shape of voxel
ofile.printf("%u %f %f %f\n",nbin_[2],0.0,0.0,lunit*dx_[2]);
ofile.printf("%d %f %f %f\n",1,0.0,0.0,0.0); // Fake atom otherwise VMD doesn't work
std::vector<unsigned> pp(3);
for(pp[0]=0; pp[0]<nbin_[0]; ++pp[0]) {
for(pp[1]=0; pp[1]<nbin_[1]; ++pp[1]) {
for(pp[2]=0; pp[2]<nbin_[2]; ++pp[2]) {
ofile.printf("%f ",getValue(pp) );
if(pp[2]%6==5) ofile.printf("\n");
}
ofile.printf("\n");
}
}
}
std::unique_ptr<Grid> Grid::create(const std::string& funcl, const std::vector<Value*> & args, IFile& ifile,
const vector<std::string> & gmin,const vector<std::string> & gmax,
const vector<unsigned> & nbin,bool dosparse, bool dospline, bool doder) {
std::unique_ptr<Grid> grid=Grid::create(funcl,args,ifile,dosparse,dospline,doder);
std::vector<unsigned> cbin( grid->getNbin() );
std::vector<std::string> cmin( grid->getMin() ), cmax( grid->getMax() );
for(unsigned i=0; i<args.size(); ++i) {
plumed_massert( cmin[i]==gmin[i], "mismatched grid min" );
plumed_massert( cmax[i]==gmax[i], "mismatched grid max" );
if( args[i]->isPeriodic() ) {
plumed_massert( cbin[i]==nbin[i], "mismatched grid nbins" );
} else {
plumed_massert( (cbin[i]-1)==nbin[i], "mismatched grid nbins");
}
}
return grid;
}
std::unique_ptr<Grid> Grid::create(const std::string& funcl, const std::vector<Value*> & args, IFile& ifile, bool dosparse, bool dospline, bool doder)
{
std::unique_ptr<Grid> grid;
unsigned nvar=args.size(); bool hasder=false; std::string pstring;
std::vector<int> gbin1(nvar); std::vector<unsigned> gbin(nvar);
std::vector<std::string> labels(nvar),gmin(nvar),gmax(nvar);
std::vector<std::string> fieldnames; ifile.scanFieldList( fieldnames );
// Retrieve names for fields
for(unsigned i=0; i<args.size(); ++i) labels[i]=args[i]->getName();
// And read the stuff from the header
plumed_massert( ifile.FieldExist( funcl ), "no column labelled " + funcl + " in in grid input");
for(unsigned i=0; i<args.size(); ++i) {
ifile.scanField( "min_" + labels[i], gmin[i]);
ifile.scanField( "max_" + labels[i], gmax[i]);
ifile.scanField( "periodic_" + labels[i], pstring );
ifile.scanField( "nbins_" + labels[i], gbin1[i]);
plumed_assert( gbin1[i]>0 );
if( args[i]->isPeriodic() ) {
plumed_massert( pstring=="true", "input value is periodic but grid is not");
std::string pmin, pmax;
args[i]->getDomain( pmin, pmax ); gbin[i]=gbin1[i];
if( pmin!=gmin[i] || pmax!=gmax[i] ) plumed_merror("mismatch between grid boundaries and periods of values");
} else {
gbin[i]=gbin1[i]-1; // Note header in grid file indicates one more bin that there should be when data is not periodic
plumed_massert( pstring=="false", "input value is not periodic but grid is");
}
hasder=ifile.FieldExist( "der_" + args[i]->getName() );
if( doder && !hasder ) plumed_merror("missing derivatives from grid file");
for(unsigned j=0; j<fieldnames.size(); ++j) {
for(unsigned k=i+1; k<args.size(); ++k) {
if( fieldnames[j]==labels[k] ) plumed_merror("arguments in input are not in same order as in grid file");
}
if( fieldnames[j]==labels[i] ) break;
}
}
if(!dosparse) {grid.reset(new Grid(funcl,args,gmin,gmax,gbin,dospline,doder));}
else {grid.reset(new SparseGrid(funcl,args,gmin,gmax,gbin,dospline,doder));}
vector<double> xx(nvar),dder(nvar);
vector<double> dx=grid->getDx();
double f,x;
while( ifile.scanField(funcl,f) ) {
for(unsigned i=0; i<nvar; ++i) {
ifile.scanField(labels[i],x); xx[i]=x+dx[i]/2.0;
ifile.scanField( "min_" + labels[i], gmin[i]);
ifile.scanField( "max_" + labels[i], gmax[i]);
ifile.scanField( "nbins_" + labels[i], gbin1[i]);
ifile.scanField( "periodic_" + labels[i], pstring );
}
if(hasder) { for(unsigned i=0; i<nvar; ++i) { ifile.scanField( "der_" + args[i]->getName(), dder[i] ); } }
index_t index=grid->getIndex(xx);
if(doder) {grid->setValueAndDerivatives(index,f,dder);}
else {grid->setValue(index,f);}
ifile.scanField();
}
return grid;
}
// Sparse version of grid with map
void SparseGrid::clear() {
map_.clear();
}
Grid::index_t SparseGrid::getSize() const {
return map_.size();
}
Grid::index_t SparseGrid::getMaxSize() const {
return maxsize_;
}
double Grid::getDifferenceFromContour( const std::vector<double>& x, std::vector<double>& der ) const {
return getValueAndDerivatives( x, der ) - contour_location;
}
void Grid::findSetOfPointsOnContour(const double& target, const std::vector<bool>& nosearch,
unsigned& npoints, std::vector<std::vector<double> >& points ) {
// Set contour location for function
contour_location=target;
// Resize points to maximum possible value
points.resize( dimension_*maxsize_ );
// Two points for search
std::vector<unsigned> ind(dimension_);
std::vector<double> direction( dimension_, 0 );
// Run over whole grid
npoints=0; RootFindingBase<Grid> mymin( this );
for(unsigned i=0; i<maxsize_; ++i) {
for(unsigned j=0; j<dimension_; ++j) ind[j]=getIndices(i)[j];
// Get the value of a point on the grid
double val1=getValue(i) - target;
// Now search for contour in each direction
bool edge=false;
for(unsigned j=0; j<dimension_; ++j) {
if( nosearch[j] ) continue ;
// Make sure we don't search at the edge of the grid
if( !pbc_[j] && (ind[j]+1)==nbin_[j] ) continue;
else if( (ind[j]+1)==nbin_[j] ) { edge=true; ind[j]=0; }
else ind[j]+=1;
double val2=getValue(ind) - target;
if( val1*val2<0 ) {
// Use initial point location as first guess for search
points[npoints].resize(dimension_); for(unsigned k=0; k<dimension_; ++k) points[npoints][k]=getPoint(i)[k];
// Setup direction vector
direction[j]=0.999999999*dx_[j];
// And do proper search for contour point
mymin.linesearch( direction, points[npoints], &Grid::getDifferenceFromContour );
direction[j]=0.0; npoints++;
}
if( pbc_[j] && edge ) { edge=false; ind[j]=nbin_[j]-1; }
else ind[j]-=1;
}
}
}
double SparseGrid::getValue(index_t index)const {
plumed_assert(index<maxsize_);
double value=0.0;
const auto it=map_.find(index);
if(it!=map_.end()) value=it->second;
return value;
}
double SparseGrid::getValueAndDerivatives
(index_t index, vector<double>& der)const {
plumed_assert(index<maxsize_ && usederiv_ && der.size()==dimension_);
double value=0.0;
for(unsigned int i=0; i<dimension_; ++i) der[i]=0.0;
const auto it=map_.find(index);
if(it!=map_.end()) value=it->second;
const auto itder=der_.find(index);
if(itder!=der_.end()) der=itder->second;
return value;
}
void SparseGrid::setValue(index_t index, double value) {
plumed_assert(index<maxsize_ && !usederiv_);
map_[index]=value;
}
void SparseGrid::setValueAndDerivatives
(index_t index, double value, vector<double>& der) {
plumed_assert(index<maxsize_ && usederiv_ && der.size()==dimension_);
map_[index]=value;
der_[index]=der;
}
void SparseGrid::addValue(index_t index, double value) {
plumed_assert(index<maxsize_ && !usederiv_);
map_[index]+=value;
}
void SparseGrid::addValueAndDerivatives
(index_t index, double value, vector<double>& der) {
plumed_assert(index<maxsize_ && usederiv_ && der.size()==dimension_);
map_[index]+=value;
der_[index].resize(dimension_);
for(unsigned int i=0; i<dimension_; ++i) der_[index][i]+=der[i];
}
void SparseGrid::writeToFile(OFile& ofile) {
vector<double> xx(dimension_);
vector<double> der(dimension_);
double f;
writeHeader(ofile);
ofile.fmtField(" "+fmt_);
for(const auto & it : map_) {
index_t i=it.first;
xx=getPoint(i);
if(usederiv_) {f=getValueAndDerivatives(i,der);}
else {f=getValue(i);}
if(i>0 && dimension_>1 && getIndices(i)[dimension_-2]==0) ofile.printf("\n");
for(unsigned j=0; j<dimension_; ++j) {
ofile.printField("min_" + argnames[j], str_min_[j] );
ofile.printField("max_" + argnames[j], str_max_[j] );
ofile.printField("nbins_" + argnames[j], static_cast<int>(nbin_[j]) );
if( pbc_[j] ) ofile.printField("periodic_" + argnames[j], "true" );
else ofile.printField("periodic_" + argnames[j], "false" );
}
for(unsigned j=0; j<dimension_; ++j) ofile.printField(argnames[j],xx[j]);
ofile.printField(funcname, f);
if(usederiv_) { for(unsigned j=0; j<dimension_; ++j) ofile.printField("der_" + argnames[j],der[j]); }
ofile.printField();
}
}
double SparseGrid::getMinValue() const {
double minval;
minval=0.0;
for(auto const & i : map_) {
if(i.second<minval) minval=i.second;
}
return minval;
}
double SparseGrid::getMaxValue() const {
double maxval;
maxval=0.0;
for(auto const & i : map_) {
if(i.second>maxval) maxval=i.second;
}
return maxval;
}
void Grid::projectOnLowDimension(double &val, std::vector<int> &vHigh, WeightBase * ptr2obj ) {
unsigned i=0;
for(i=0; i<vHigh.size(); i++) {
if(vHigh[i]<0) { // this bin needs to be integrated out
// parallelize here???
for(unsigned j=0; j<(getNbin())[i]; j++) {
vHigh[i]=int(j);
projectOnLowDimension(val,vHigh,ptr2obj); // recursive function: this is the core of the mechanism
vHigh[i]=-1;
}
return; //
}
}
// when there are no more bin to dig in then retrieve the value
if(i==vHigh.size()) {
//std::cerr<<"POINT: ";
//for(unsigned j=0;j<vHigh.size();j++){
// std::cerr<<vHigh[j]<<" ";
//}
std::vector<unsigned> vv(vHigh.size());
for(unsigned j=0; j<vHigh.size(); j++)vv[j]=unsigned(vHigh[j]);
//
// this is the real assignment !!!!! (hack this to have bias or other stuff)
//
// this case: produce fes
//val+=exp(beta*getValue(vv)) ;
double myv=getValue(vv);
val=ptr2obj->projectInnerLoop(val,myv) ;
// to be added: bias (same as before without negative sign)
//std::cerr<<" VAL: "<<val <<endl;
}
}
Grid Grid::project(const std::vector<std::string> & proj, WeightBase *ptr2obj ) {
// find extrema only for the projection
vector<string> smallMin,smallMax;
vector<unsigned> smallBin;
vector<unsigned> dimMapping;
vector<bool> smallIsPeriodic;
vector<string> smallName;
// check if the two key methods are there
WeightBase* pp = dynamic_cast<WeightBase*>(ptr2obj);
if (!pp)plumed_merror("This WeightBase is not complete: you need a projectInnerLoop and projectOuterLoop ");
for(unsigned j=0; j<proj.size(); j++) {
for(unsigned i=0; i<getArgNames().size(); i++) {
if(proj[j]==getArgNames()[i]) {
unsigned offset;
// note that at sizetime the non periodic dimension get a bin more
if(getIsPeriodic()[i]) {offset=0;} else {offset=1;}
smallMax.push_back(getMax()[i]);
smallMin.push_back(getMin()[i]);
smallBin.push_back(getNbin()[i]-offset);
smallIsPeriodic.push_back(getIsPeriodic()[i]);
dimMapping.push_back(i);
smallName.push_back(getArgNames()[i]);
break;
}
}
}
Grid smallgrid("projection",smallName,smallMin,smallMax,smallBin,false,false,true,smallIsPeriodic,smallMin,smallMax);
// check that the two grids are commensurate
for(unsigned i=0; i<dimMapping.size(); i++) {
plumed_massert( (smallgrid.getMax())[i] == (getMax())[dimMapping[i]], "the two input grids are not compatible in max" );
plumed_massert( (smallgrid.getMin())[i] == (getMin())[dimMapping[i]], "the two input grids are not compatible in min" );
plumed_massert( (smallgrid.getNbin())[i]== (getNbin())[dimMapping[i]], "the two input grids are not compatible in bin" );
}
vector<unsigned> toBeIntegrated;
for(unsigned i=0; i<getArgNames().size(); i++) {
bool doappend=true;
for(unsigned j=0; j<dimMapping.size(); j++) {
if(dimMapping[j]==i) {doappend=false; break;}
}
if(doappend)toBeIntegrated.push_back(i);
}
//for(unsigned i=0;i<dimMapping.size();i++ ){
// cerr<<"Dimension to preserve "<<dimMapping[i]<<endl;
//}
//for(unsigned i=0;i<toBeIntegrated.size();i++ ){
// cerr<<"Dimension to integrate "<<toBeIntegrated[i]<<endl;
//}
// loop over all the points in the Grid, find the corresponding fixed index, rotate over all the other ones
for(unsigned i=0; i<smallgrid.getSize(); i++) {
std::vector<unsigned> v;
v=smallgrid.getIndices(i);
std::vector<int> vHigh((getArgNames()).size(),-1);
for(unsigned j=0; j<dimMapping.size(); j++)vHigh[dimMapping[j]]=int(v[j]);
// the vector vhigh now contains at the beginning the index of the low dimension and -1 for the values that need to be integrated
double initval=0.;
projectOnLowDimension(initval,vHigh, ptr2obj);
smallgrid.setValue(i,initval);
}
// reset to zero just for biasing (this option can be evtl enabled in a future...)
//double vmin;vmin=-smallgrid.getMinValue()+1;
for(unsigned i=0; i<smallgrid.getSize(); i++) {
// //if(dynamic_cast<BiasWeight*>(ptr2obj)){
// // smallgrid.addValue(i,vmin);// go to 1
// //}
double vv=smallgrid.getValue(i);
smallgrid.setValue(i,ptr2obj->projectOuterLoop(vv));
// //if(dynamic_cast<BiasWeight*>(ptr2obj)){
// // smallgrid.addValue(i,-vmin);// bring back to the value
// //}
}
return smallgrid;
}
double Grid::integrate( std::vector<unsigned>& npoints ) {
plumed_dbg_assert( npoints.size()==dimension_ ); plumed_assert( dospline_ );
unsigned ntotgrid=1; double box_vol=1.0;
std::vector<double> ispacing( npoints.size() );
for(unsigned j=0; j<dimension_; ++j) {
if( !pbc_[j] ) {
ispacing[j] = ( max_[j] - dx_[j] - min_[j] ) / static_cast<double>( npoints[j] );
npoints[j]+=1;
} else {
ispacing[j] = ( max_[j] - min_[j] ) / static_cast<double>( npoints[j] );