Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2017 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             : #include "core/ActionWithArguments.h"
      25             : #include "core/PlumedMain.h"
      26             : #include "core/ActionSet.h"
      27             : 
      28             : //+PLUMEDOC PRINTANALYSIS SELECT_COMPONENTS
      29             : /*
      30             : Create a new value to hold a subset of the components that are in a vector or matrix
      31             : 
      32             : Output a scalar or vector that contains a subset of the elements in the input vector or matrix.
      33             : In the example below the value `s` is a scalar that contains the distance between atoms 3 and 4.
      34             : 
      35             : ```plumed
      36             : d: DISTANCE ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 ATOMS4=7,8
      37             : s: SELECT_COMPONENTS ARG=d COMPONENTS=2
      38             : ```
      39             : 
      40             : In this example the output z is a 2 dimensional vector containing the distances between atoms 3 and 4
      41             : and 7 and 8.
      42             : 
      43             : ```plumed
      44             : d: DISTANCE ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 ATOMS4=7,8
      45             : s: SELECT_COMPONENTS ARG=d COMPONENTS=2,4
      46             : ```
      47             : 
      48             : Lastly, in this example we calculate a matrix of distances.  The scalar `s` that is output from the
      49             : SELECT_COMPONENTS action contains the distance between atoms 1 and 3 and 3 and 4.
      50             : 
      51             : ```plumed
      52             : d: DISTANCE_MATRIX GROUP=1-5
      53             : s: SELECT_COMPONENTS ARG=d COMPONENTS=1.3,3.4
      54             : ```
      55             : 
      56             : */
      57             : //+ENDPLUMEDOC
      58             : 
      59             : namespace PLMD {
      60             : namespace valtools {
      61             : 
      62             : class SelectComponents : public ActionShortcut {
      63             : public:
      64             :   static void registerKeywords( Keywords& keys );
      65             : /// Constructor
      66             :   explicit SelectComponents(const ActionOptions&);
      67             : };
      68             : 
      69             : PLUMED_REGISTER_ACTION(SelectComponents,"SELECT_COMPONENTS")
      70             : 
      71          88 : void SelectComponents::registerKeywords( Keywords& keys ) {
      72          88 :   ActionShortcut::registerKeywords( keys );
      73         176 :   keys.addInputKeyword("compulsory","ARG","vector/matrix","the value from which we are selecting components");
      74          88 :   keys.add("compulsory","COMPONENTS","the components in the input value that you woul like to build a new vector from");
      75          88 :   keys.needsAction("FLATTEN");
      76          88 :   keys.needsAction("CONSTANT");
      77          88 :   keys.needsAction("SELECT_WITH_MASK");
      78         176 :   keys.setValueDescription("scalar/vector","a vector containing the selected components (a scalar if only one component is selected)");
      79          88 : }
      80             : 
      81          67 : SelectComponents::SelectComponents(const ActionOptions& ao):
      82             :   Action(ao),
      83          67 :   ActionShortcut(ao) {
      84          67 :   std::vector<std::string> argn;
      85          67 :   parseVector("ARG",argn);
      86          67 :   std::vector<Value*> theargs;
      87          67 :   ActionWithArguments::interpretArgumentList( argn, plumed.getActionSet(), this, theargs );
      88          67 :   if( theargs.size()!=1 ) {
      89           0 :     error("should only be one argument input to this action");
      90             :   }
      91             :   // Create an array that will eventually hold the mask
      92          70 :   std::vector<double> mask( theargs[0]->getNumberOfValues(), 1 );
      93          67 :   std::vector<std::string> elements;
      94         134 :   parseVector("COMPONENTS",elements);
      95          67 :   if( theargs[0]->getRank()==1 ) {
      96         282 :     for(unsigned i=0; i<elements.size(); ++i) {
      97             :       unsigned sel;
      98         225 :       if( !Tools::convertNoexcept( elements[i], sel ) || sel<1 || sel>mask.size() ) {
      99           6 :         error("component " + elements[i] + " is not between 1 and the number of elements of " + theargs[0]->getName() );
     100             :       }
     101         223 :       mask[sel-1]=0;
     102             :     }
     103           8 :   } else if( theargs[0]->getRank()==2 ) {
     104          28 :     for(unsigned i=0; i<elements.size(); ++i) {
     105          21 :       std::size_t dot = elements[i].find_first_of(".");
     106          21 :       if( dot==std::string::npos ) {
     107           0 :         error("found no dot in specification of required matrix element");
     108             :       }
     109          21 :       std::string istr=elements[i].substr(0,dot), jstr=elements[i].substr(dot+1);
     110             :       unsigned ival, jval;
     111          42 :       if( !Tools::convertNoexcept( istr, ival ) || !Tools::convertNoexcept( jstr, jval ) || ival<1 || jval<1
     112          42 :           || ival>theargs[0]->getShape()[0] || jval>theargs[0]->getShape()[1] ) {
     113           3 :         error("element " + elements[i] + " is not in the matrix " + theargs[0]->getName() );
     114             :       }
     115          20 :       mask[(ival-1)*theargs[0]->getShape()[1] + jval - 1] = 0;
     116             :     }
     117          14 :     readInputLine( getShortcutLabel() + "_flat: FLATTEN ARG=" + theargs[0]->getName() );
     118             :   } else {
     119           0 :     error("input to this argument should be a vector/matrix");
     120             :   }
     121             :   // Now create the mask action
     122             :   std::string mask_str;
     123          64 :   Tools::convert( mask[0], mask_str );
     124          64 :   unsigned check_mask=mask[0];
     125        1570 :   for(unsigned i=1; i<mask.size(); ++i) {
     126             :     std::string num;
     127        1506 :     Tools::convert( mask[i], num );
     128        1506 :     mask_str += "," + num;
     129        1506 :     check_mask +=mask[i];
     130             :   }
     131          64 :   if( mask.size()-check_mask!=elements.size() ) {
     132           0 :     error("found repeated indexes in COMPONENTS");
     133             :   }
     134         128 :   readInputLine( getShortcutLabel() + "_mask: CONSTANT VALUES=" + mask_str );
     135             :   // And finally create the selector
     136          64 :   if( theargs[0]->getRank()==1 ) {
     137         228 :     readInputLine( getShortcutLabel() + ": SELECT_WITH_MASK ARG=" + theargs[0]->getName() + " MASK=" + getShortcutLabel() + "_mask");
     138           7 :   } else if( theargs[0]->getRank()==2 ) {
     139          28 :     readInputLine( getShortcutLabel() + ": SELECT_WITH_MASK ARG=" + getShortcutLabel() + "_flat MASK=" + getShortcutLabel() + "_mask");
     140             :   }
     141        1646 : }
     142             : 
     143             : }
     144             : }