Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2018 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 "ContourFindingBase.h"
      23             : #include "vesselbase/StoreDataVessel.h"
      24             : #include "core/PlumedMain.h"
      25             : #include "core/Atoms.h"
      26             : 
      27             : namespace PLMD {
      28             : namespace gridtools {
      29             : 
      30           6 : void ContourFindingBase::registerKeywords( Keywords& keys ) {
      31           6 :   ActionWithInputGrid::registerKeywords( keys );
      32           6 :   keys.add("compulsory","CONTOUR","the value we would like to draw the contour at in the space");
      33           6 :   keys.add("compulsory","FILE","file on which to output coordinates");
      34           6 :   keys.add("compulsory","UNITS","PLUMED","the units in which to print out the coordinates. PLUMED means internal PLUMED units");
      35           6 :   keys.add("optional", "PRECISION","The number of digits in trajectory file");
      36           6 :   keys.remove("KERNEL"); keys.remove("BANDWIDTH");
      37           6 : }
      38             : 
      39           3 : ContourFindingBase::ContourFindingBase(const ActionOptions&ao):
      40             :   Action(ao),
      41             :   ActionWithInputGrid(ao),
      42             :   mymin(this),
      43           3 :   mydata(NULL)
      44             : {
      45           3 :   if( ingrid->noDerivatives() ) error("cannot find contours if input grid has no derivatives");
      46           3 :   parse("CONTOUR",contour);
      47           3 :   log.printf("  calculating dividing surface along which function equals %f \n", contour);
      48             : 
      49           3 :   if( keywords.exists("FILE") ) {
      50           2 :     std::string file; parse("FILE",file);
      51           2 :     if(file.length()==0 && keywords.style("FILE","compulsory") ) error("name out output file was not specified");
      52           2 :     else if( file.length()>0 ) {
      53           2 :       std::string type=Tools::extension(file);
      54           2 :       log<<"  file name "<<file<<"\n";
      55           2 :       if(type!="xyz") error("can only print xyz file type with contour finding");
      56             : 
      57           2 :       fmt_xyz="%f";
      58           4 :       std::string precision; parse("PRECISION",precision);
      59           2 :       if(precision.length()>0) {
      60           2 :         int p; Tools::convert(precision,p);
      61           2 :         log<<"  with precision "<<p<<"\n";
      62           4 :         std::string a,b;
      63           2 :         Tools::convert(p+5,a);
      64           2 :         Tools::convert(p,b);
      65           4 :         fmt_xyz="%"+a+"."+b+"f";
      66             :       }
      67             : 
      68           4 :       std::string unitname; parse("UNITS",unitname);
      69           2 :       if(unitname!="PLUMED") {
      70           1 :         Units myunit; myunit.setLength(unitname);
      71           1 :         lenunit=plumed.getAtoms().getUnits().getLength()/myunit.getLength();
      72             :       }
      73           1 :       else lenunit=1.0;
      74             : 
      75           2 :       of.link(*this); of.open(file);
      76             : 
      77             :       // Now create a store data vessel to hold the points
      78           4 :       mydata=buildDataStashes( NULL );
      79           2 :     }
      80             :   }
      81           3 : }
      82             : 
      83           4 : void ContourFindingBase::finishAveraging() {
      84             :   // And this looks after the output
      85           4 :   if( mydata ) {
      86           2 :     std::vector<double> point( 1 + ingrid->getDimension() );
      87           2 :     of.printf("%u\n",mydata->getNumberOfStoredValues());
      88           2 :     of.printf("Points found on isocontour\n");
      89         656 :     for(unsigned i=0; i<mydata->getNumberOfStoredValues(); ++i) {
      90         654 :       mydata->retrieveSequentialValue( i, false, point ); of.printf("X");
      91         654 :       for(unsigned j=0; j<ingrid->getDimension(); ++j) of.printf( (" " + fmt_xyz).c_str(), lenunit*point[1+j] );
      92         654 :       of.printf("\n");
      93           2 :     }
      94             :   }
      95           4 : }
      96             : 
      97             : }
      98        2523 : }