Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2023 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/ActionRegister.h"
      23             : #include "GridPrintingBase.h"
      24             : #include "tools/OFile.h"
      25             : 
      26             : //+PLUMEDOC GRIDANALYSIS DUMPCUBE
      27             : /*
      28             : Output a three dimensional grid using the Gaussian cube file format.
      29             : 
      30             : Suppose you have calculated the value of a function on a three dimensional grid.
      31             : This function might be a \ref HISTOGRAM or it might be a free energy energy surface
      32             : that was calculated from this histogram by using \ref CONVERT_TO_FES.  Alternatively,
      33             : your function might be a phase-field that was calculated using \ref MULTICOLVARDENS.
      34             : Whatever the function is, however, you obviously cannot show it using a typical contour
      35             : plotting program such as gnuplot as you have three input variables.
      36             : 
      37             : Tools like VMD have nice features for plotting these types of three dimensional functions
      38             : but typically you are required to use a Gaussian cube file format to input the data.  This
      39             : action thus allows you to output a function evaluated on a grid to a Gaussian cube file format.
      40             : 
      41             : \par Examples
      42             : 
      43             : The input below can be used to post process a trajectory.  A histogram as a function of the distance
      44             : between atoms 1 and 2, the distance between atom 1 and 3 and the angle between the vector connecting atoms 1 and
      45             : 2 and 1 and 3 is computed using kernel density estimation.  Once all the data contained in the trajectory has been read in and
      46             : all the kernels have been added the resulting histogram is output to a file called histoA1.cube.  This file has the
      47             : Gaussian cube file format.  The histogram can thus be visualized using tools such as VMD.
      48             : 
      49             : \plumedfile
      50             : x1: DISTANCE ATOMS=1,2
      51             : x2: DISTANCE ATOMS=1,3
      52             : x3: ANGLE ATOMS=1,2,3
      53             : 
      54             : hA1: HISTOGRAM ARG=x1,x2,x3 GRID_MIN=0.0,0.0,0.0 GRID_MAX=3.0,3.0,3.0 GRID_BIN=10,10,10 BANDWIDTH=1.0,1.0,1.0
      55             : DUMPCUBE GRID=hA1 FILE=histoA1.cube
      56             : \endplumedfile
      57             : 
      58             : */
      59             : //+ENDPLUMEDOC
      60             : 
      61             : namespace PLMD {
      62             : namespace gridtools {
      63             : 
      64             : class DumpCube : public GridPrintingBase {
      65             : private:
      66             :   unsigned mycomp;
      67             : public:
      68             :   static void registerKeywords( Keywords& keys );
      69             :   explicit DumpCube(const ActionOptions&ao);
      70             :   void printGrid( OFile& ofile ) const override;
      71             : };
      72             : 
      73       10431 : PLUMED_REGISTER_ACTION(DumpCube,"DUMPCUBE")
      74             : 
      75           7 : void DumpCube::registerKeywords( Keywords& keys ) {
      76           7 :   GridPrintingBase::registerKeywords( keys );
      77          14 :   keys.add("optional","COMPONENT","if your input is a vector field use this to specify the component of the input vector field for which you wish to output");
      78           7 : }
      79             : 
      80           6 : DumpCube::DumpCube(const ActionOptions&ao):
      81             :   Action(ao),
      82           6 :   GridPrintingBase(ao)
      83             : {
      84           6 :   fmt = fmt + " ";
      85          12 :   if( ingrid->getType()!="flat" ) error("cannot dump grid of type " + ingrid->getType() + " using DUMPCUBE");
      86           6 :   if( ingrid->getDimension()!=3 ) error("cannot print cube file if grid does not contain three dimensional data");
      87             : 
      88           6 :   if( ingrid->getNumberOfComponents()==1 ) {
      89           6 :     mycomp=0;
      90             :   } else {
      91           0 :     int tcomp=-1; parse("COMPONENT",tcomp);
      92           0 :     if( tcomp<0 ) error("component of vector field was not specified - use COMPONENT keyword");
      93           0 :     mycomp=tcomp*(1+ingrid->getDimension()); if( ingrid->noDerivatives() ) mycomp=tcomp;
      94           0 :     log.printf("  using %dth component of grid \n",tcomp );
      95             :   }
      96             : 
      97           6 :   checkRead();
      98           6 : }
      99             : 
     100           8 : void DumpCube::printGrid( OFile& ofile ) const {
     101           8 :   double lunit = ingrid->getCubeUnits();
     102             : 
     103           8 :   ofile.printf("PLUMED CUBE FILE\n");
     104           8 :   ofile.printf("OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n");
     105             :   // Number of atoms followed by position of origin (origin set so that center of grid is in center of cell)
     106          16 :   std::string ostr = "%d " + fmt + fmt + fmt + "\n";
     107           8 :   ofile.printf(ostr.c_str(),1,-0.5*lunit*ingrid->getGridExtent(0),-0.5*lunit*ingrid->getGridExtent(1),-0.5*lunit*ingrid->getGridExtent(2));
     108           8 :   ofile.printf(ostr.c_str(),ingrid->getNbin()[0],lunit*ingrid->getGridSpacing()[0],0.0,0.0);  // Number of bins in each direction followed by
     109           8 :   ofile.printf(ostr.c_str(),ingrid->getNbin()[1],0.0,lunit*ingrid->getGridSpacing()[1],0.0);  // shape of voxel
     110          16 :   ofile.printf(ostr.c_str(),ingrid->getNbin()[2],0.0,0.0,lunit*ingrid->getGridSpacing()[2]);
     111           8 :   ofile.printf(ostr.c_str(),1,0.0,0.0,0.0); // Fake atom otherwise VMD doesn't work
     112           8 :   std::vector<unsigned> pp(3); std::vector<unsigned> nbin( ingrid->getNbin() );
     113         112 :   for(pp[0]=0; pp[0]<nbin[0]; ++pp[0]) {
     114        1800 :     for(pp[1]=0; pp[1]<nbin[1]; ++pp[1]) {
     115       40184 :       for(pp[2]=0; pp[2]<nbin[2]; ++pp[2]) {
     116       38488 :         ofile.printf(fmt.c_str(), ingrid->getGridElement( ingrid->getIndex(pp), mycomp ) );
     117       38488 :         if(pp[2]%6==5) ofile.printf("\n");
     118             :       }
     119        1696 :       ofile.printf("\n");
     120             :     }
     121             :   }
     122           8 : }
     123             : 
     124             : }
     125             : }