Added shortcut to generate input to do anneal fitting of sketch-map

src/core/ActionShortcut.cpp

@@ -48,8 +48,10 @@ void ActionShortcut::readInputLine( const std::string& input ) {
   if( update_until!=std::numeric_limits<double>::max() ) {
       std::string util; Tools::convert( update_until, util ); f_input += " UPDATE_UNTIL=" + util;
   }
-  if( restart ) f_input += " RESTART=YES";
-  if( !restart ) f_input += " RESTART=NO";
+  if( keywords.exists("RESTART") ) {
+      if( restart ) f_input += " RESTART=YES";
+      if( !restart ) f_input += " RESTART=NO";
+  }
   plumed.readInputLine( f_input );
 }
 

src/dimred/SketchMap.cpp

+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2012 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed-code.org for more information.
+
+   This file is part of plumed, version 2.0.
+
+   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 "core/ActionShortcut.h"
+#include "core/ActionRegister.h"
+
+namespace PLMD {
+namespace analysis {
+
+//+PLUMEDOC ANALYSIS SKETCH_MAP
+/*
+This can be used to output the data that has been stored in an Analysis object.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+class SketchMap : public ActionShortcut {
+public:
+  static void registerKeywords( Keywords& keys );
+  SketchMap( const ActionOptions& );
+};
+
+PLUMED_REGISTER_ACTION(SketchMap,"SKETCH_MAP")
+
+void SketchMap::registerKeywords( Keywords& keys ) {
+  ActionShortcut::registerKeywords( keys ); 
+  keys.add("compulsory","NLOW_DIM","the dimension of the low dimensional space in which the projections will be constructed");
+  keys.add("compulsory","MATRIX","the matrix of distances between points that you want to reproduce in your sketch-map projection");
+  keys.add("compulsory","HIGH_DIM_FUNCTION","the parameters of the switching function in the high dimensional space");
+  keys.add("compulsory","LOW_DIM_FUNCTION","the parameters of the switching function in the low dimensional space");
+  keys.add("compulsory","ANNEAL_RATE","0.5","the rate at which to do the annealing");
+  keys.add("compulsory","ANNEAL_STEPS","10","the number of steps of annealing to do");
+  keys.add("compulsory","CGTOL","1E-6","the tolerance for the conjugate gradient minimisation");
+// Smap pointwise input 
+  keys.add("compulsory","NCYCLES","5","the number of cycles of global optimisation to attempt");
+  keys.add("compulsory","BUFFER","1.1","grid extent for search is (max projection - minimum projection) multiplied by this value");
+  keys.add("compulsory","CGRID_SIZE","10","number of points to use in each grid direction");
+  keys.add("compulsory","FGRID_SIZE","0","interpolate the grid onto this number of points -- only works in 2D");
+}
+
+SketchMap::SketchMap( const ActionOptions& ao ) :
+Action(ao),
+ActionShortcut(ao)
+{
+  // Input for MDS
+  std::string mds_line = getShortcutLabel() + "_mds: CLASSICAL_MDS";
+  std::string nlow; parse("NLOW_DIM",nlow); mds_line += " NLOW_DIM=" + nlow; 
+  std::string mat; parse("MATRIX",mat); mds_line += " USE_OUTPUT_DATA_FROM=" + mat;
+  readInputLine( mds_line ); 
+  // Create generic input for all conjgrad cycles
+  std::string cgtol; parse("CGTOL",cgtol); std::string ncyc; parse("NCYCLES",ncyc); std::string buf; parse("BUFFER",buf);
+  std::string cg_grid; parse("CGRID_SIZE",cg_grid); std::string fg_grid; parse("FGRID_SIZE",fg_grid);
+  std::string cg_step_input = " CGTOL=" + cgtol; unsigned nlow_dim; Tools::convert( nlow, nlow_dim );
+  std::string pw_step_input = cg_step_input + " NCYCLES=" + ncyc + " BUFFER=" + buf; 
+  pw_step_input += " CGRID_SIZE=" + cg_grid; for(unsigned i=1;i<nlow_dim;++i) pw_step_input += "," + cg_grid;
+  pw_step_input += " FGRID_SIZE=" + fg_grid; for(unsigned i=1;i<nlow_dim;++i) pw_step_input += "," + fg_grid;
+  // Input for iterative distance matching
+  std::string imds_line_cg = getShortcutLabel() + "_smap1_cg: SKETCHMAP_CONJGRAD USE_OUTPUT_DATA_FROM=" + getShortcutLabel() + "_mds";
+  std::string hd_func; parse("HIGH_DIM_FUNCTION",hd_func); imds_line_cg += " HIGH_DIM_FUNCTION={" + hd_func + "}"; 
+  std::string ld_func; parse("LOW_DIM_FUNCTION",ld_func); imds_line_cg += " LOW_DIM_FUNCTION={" + ld_func + "}";
+  imds_line_cg += cg_step_input + " MIXPARAM=1.0"; readInputLine( imds_line_cg );
+  std::string imds_line_pw = getShortcutLabel() + "_smap1_pw: SKETCHMAP_POINTWISE USE_OUTPUT_DATA_FROM=" + getShortcutLabel() + "_smap1_cg";
+  imds_line_pw += pw_step_input + " MIXPARAM=1.0"; readInputLine( imds_line_pw );
+  // Now sketch-map
+  unsigned asteps; parse("ANNEAL_STEPS",asteps); std::string psmap = getShortcutLabel() + "_smap1.0_pw";
+  if( asteps>1 ) {
+      double smear; parse("ANNEAL_RATE", smear); double old_mix = 1.0; double new_mix = old_mix*smear;
+      for(unsigned i=0;i<asteps;++i) {
+          std::string omix; Tools::convert( old_mix, omix ); std::string nmix; Tools::convert( new_mix, nmix );
+          imds_line_cg = getShortcutLabel() + "_smap" + nmix + "_cg: SKETCHMAP_CONJGRAD USE_OUTPUT_DATA_FROM=" + getShortcutLabel() + "_smap" + omix + "_pw"; 
+          imds_line_cg += cg_step_input + " MIXPARAM=" + nmix; readInputLine( imds_line_cg );
+          imds_line_pw = getShortcutLabel() + "_smap" + nmix + "_pw: SKETCHMAP_POINTWISE USE_OUTPUT_DATA_FROM=" + getShortcutLabel() + "_smap" + omix + "_cg";
+          imds_line_pw += pw_step_input + " MIXPARAM=" + nmix; readInputLine( imds_line_pw ); 
+          old_mix = new_mix; new_mix = old_mix*smear; psmap = getShortcutLabel() + "_smap" + nmix + "_pw";
+      }
+  }
+  // Final sketch-map with no mixing of distance matching
+  imds_line_cg = getShortcutLabel() + "_smap_cg: SKETCHMAP_CONJGRAD USE_OUTPUT_DATA_FROM=" + psmap + cg_step_input;  
+  readInputLine( imds_line_cg );
+  imds_line_pw = getShortcutLabel() + ": SKETCHMAP_POINTWISE USE_OUTPUT_DATA_FROM=" + getShortcutLabel() + "_smap_cg" + pw_step_input; 
+  readInputLine( imds_line_pw ); 
+}
+
+}
+}