Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2018-2023 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/ActionShortcut.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace dimred {
      27             : 
      28             : //+PLUMEDOC DIMRED SKETCH_MAP
      29             : /*
      30             : This can be used to output the data that has been stored in an Analysis object.
      31             : 
      32             : \par Examples
      33             : 
      34             : */
      35             : //+ENDPLUMEDOC
      36             : 
      37             : class SketchMap : public ActionShortcut {
      38             : public:
      39             :   static void registerKeywords( Keywords& keys );
      40             :   explicit SketchMap( const ActionOptions& );
      41             : };
      42             : 
      43       13785 : PLUMED_REGISTER_ACTION(SketchMap,"SKETCH_MAP")
      44             : 
      45           4 : void SketchMap::registerKeywords( Keywords& keys ) {
      46           4 :   ActionShortcut::registerKeywords( keys );
      47           8 :   keys.add("compulsory","NLOW_DIM","the dimension of the low dimensional space in which the projections will be constructed");
      48           8 :   keys.add("compulsory","MATRIX","the matrix of distances between points that you want to reproduce in your sketch-map projection");
      49           8 :   keys.add("compulsory","HIGH_DIM_FUNCTION","the parameters of the switching function in the high dimensional space");
      50           8 :   keys.add("compulsory","LOW_DIM_FUNCTION","the parameters of the switching function in the low dimensional space");
      51           8 :   keys.add("compulsory","ANNEAL_RATE","0.5","the rate at which to do the annealing");
      52           8 :   keys.add("compulsory","ANNEAL_STEPS","10","the number of steps of annealing to do");
      53           8 :   keys.add("compulsory","CGTOL","1E-6","the tolerance for the conjugate gradient minimization");
      54             : // Smap pointwise input
      55           8 :   keys.add("compulsory","NCYCLES","5","the number of cycles of global optimization to attempt");
      56           8 :   keys.add("compulsory","BUFFER","1.1","grid extent for search is (max projection - minimum projection) multiplied by this value");
      57           8 :   keys.add("compulsory","CGRID_SIZE","10","number of points to use in each grid direction");
      58           8 :   keys.add("compulsory","FGRID_SIZE","0","interpolate the grid onto this number of points -- only works in 2D");
      59           4 : }
      60             : 
      61           0 : SketchMap::SketchMap( const ActionOptions& ao ) :
      62             :   Action(ao),
      63           0 :   ActionShortcut(ao) {
      64             :   // Input for MDS
      65           0 :   std::string mds_line = getShortcutLabel() + "_mds: CLASSICAL_MDS";
      66             :   std::string nlow;
      67           0 :   parse("NLOW_DIM",nlow);
      68           0 :   mds_line += " NLOW_DIM=" + nlow;
      69             :   std::string mat;
      70           0 :   parse("MATRIX",mat);
      71           0 :   mds_line += " USE_OUTPUT_DATA_FROM=" + mat;
      72           0 :   readInputLine( mds_line );
      73             :   // Create generic input for all conjgrad cycles
      74             :   std::string cgtol;
      75           0 :   parse("CGTOL",cgtol);
      76             :   std::string ncyc;
      77           0 :   parse("NCYCLES",ncyc);
      78             :   std::string buf;
      79           0 :   parse("BUFFER",buf);
      80             :   std::string cg_grid;
      81           0 :   parse("CGRID_SIZE",cg_grid);
      82             :   std::string fg_grid;
      83           0 :   parse("FGRID_SIZE",fg_grid);
      84           0 :   std::string cg_step_input = " CGTOL=" + cgtol;
      85             :   unsigned nlow_dim;
      86           0 :   Tools::convert( nlow, nlow_dim );
      87           0 :   std::string pw_step_input = cg_step_input + " NCYCLES=" + ncyc + " BUFFER=" + buf;
      88           0 :   pw_step_input += " CGRID_SIZE=" + cg_grid;
      89           0 :   for(unsigned i=1; i<nlow_dim; ++i) {
      90           0 :     pw_step_input += "," + cg_grid;
      91             :   }
      92           0 :   pw_step_input += " FGRID_SIZE=" + fg_grid;
      93           0 :   for(unsigned i=1; i<nlow_dim; ++i) {
      94           0 :     pw_step_input += "," + fg_grid;
      95             :   }
      96             :   // Input for iterative distance matching
      97           0 :   std::string imds_line_cg = getShortcutLabel() + "_smap1_cg: SKETCHMAP_CONJGRAD USE_OUTPUT_DATA_FROM=" + getShortcutLabel() + "_mds";
      98             :   std::string hd_func;
      99           0 :   parse("HIGH_DIM_FUNCTION",hd_func);
     100           0 :   imds_line_cg += " HIGH_DIM_FUNCTION={" + hd_func + "}";
     101             :   std::string ld_func;
     102           0 :   parse("LOW_DIM_FUNCTION",ld_func);
     103           0 :   imds_line_cg += " LOW_DIM_FUNCTION={" + ld_func + "}";
     104           0 :   imds_line_cg += cg_step_input + " MIXPARAM=1.0";
     105           0 :   readInputLine( imds_line_cg );
     106           0 :   std::string imds_line_pw = getShortcutLabel() + "_smap1_pw: SKETCHMAP_POINTWISE USE_OUTPUT_DATA_FROM=" + getShortcutLabel() + "_smap1_cg";
     107           0 :   imds_line_pw += pw_step_input + " MIXPARAM=1.0";
     108           0 :   readInputLine( imds_line_pw );
     109             :   // Now sketch-map
     110             :   unsigned asteps;
     111           0 :   parse("ANNEAL_STEPS",asteps);
     112           0 :   std::string psmap = getShortcutLabel() + "_smap1_pw";
     113           0 :   if( asteps>1 ) {
     114             :     double smear;
     115           0 :     parse("ANNEAL_RATE", smear);
     116           0 :     double old_mix = 1.0;
     117           0 :     double new_mix = old_mix*smear;
     118           0 :     for(unsigned i=0; i<asteps; ++i) {
     119             :       std::string omix;
     120           0 :       Tools::convert( old_mix, omix );
     121             :       std::string nmix;
     122           0 :       Tools::convert( new_mix, nmix );
     123           0 :       imds_line_cg = getShortcutLabel() + "_smap" + nmix + "_cg: SKETCHMAP_CONJGRAD USE_OUTPUT_DATA_FROM=" + getShortcutLabel() + "_smap" + omix + "_pw";
     124           0 :       imds_line_cg += cg_step_input + " MIXPARAM=" + nmix;
     125           0 :       readInputLine( imds_line_cg );
     126           0 :       imds_line_pw = getShortcutLabel() + "_smap" + nmix + "_pw: SKETCHMAP_POINTWISE USE_OUTPUT_DATA_FROM=" + getShortcutLabel() + "_smap" + omix + "_cg";
     127           0 :       imds_line_pw += pw_step_input + " MIXPARAM=" + nmix;
     128           0 :       readInputLine( imds_line_pw );
     129           0 :       old_mix = new_mix;
     130           0 :       new_mix = old_mix*smear;
     131           0 :       psmap = getShortcutLabel() + "_smap" + nmix + "_pw";
     132             :     }
     133             :   }
     134             :   // Final sketch-map with no mixing of distance matching
     135           0 :   imds_line_cg = getShortcutLabel() + "_smap_cg: SKETCHMAP_CONJGRAD USE_OUTPUT_DATA_FROM=" + psmap + cg_step_input;
     136           0 :   readInputLine( imds_line_cg );
     137           0 :   imds_line_pw = getShortcutLabel() + ": SKETCHMAP_POINTWISE USE_OUTPUT_DATA_FROM=" + getShortcutLabel() + "_smap_cg" + pw_step_input;
     138           0 :   readInputLine( imds_line_pw );
     139           0 : }
     140             : 
     141             : }
     142             : }