Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2017 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             : #ifndef __PLUMED_volumes_VolumeShortcut_h
      23             : #define __PLUMED_volumes_VolumeShortcut_h
      24             : 
      25             : #include "core/ActionShortcut.h"
      26             : #include "core/ActionRegister.h"
      27             : #include "core/PlumedMain.h"
      28             : #include "core/ActionSet.h"
      29             : #include "core/Group.h"
      30             : 
      31             : namespace PLMD {
      32             : namespace volumes {
      33             : 
      34             : template <const char* v>
      35             : class VolumeShortcut : public ActionShortcut {
      36             : public:
      37             :   static void registerKeywords( Keywords& keys );
      38             :   VolumeShortcut(const ActionOptions&ao);
      39             : };
      40             : 
      41             : template <const char* v>
      42          87 : void VolumeShortcut<v>::registerKeywords( Keywords& keys ) {
      43         174 :   actionRegister().getKeywords( std::string(v) + "_CALC", keys );
      44         174 :   keys.add("hidden","IS_SHORTCUT","hidden keyword to tell if actions are shortcuts so that example generator can provide expansions of shortcuts");
      45         174 :   keys.add("optional","DATA","the label of an action that calculates multicolvars.  Weighted sums based on the location of the colvars calculated by this action will be calcualted");
      46         174 :   keys.add("optional","LESS_THAN","calcualte the number of colvars that are inside the region of interest and that are less than a certain threshold");
      47         174 :   keys.addOutputComponent("lessthan","LESS_THAN","the number of cvs in the region of interest that are less than a certain threshold");
      48         174 :   keys.add("optional","MORE_THAN","calcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold");
      49         174 :   keys.addOutputComponent("morethan","MORE_THAN","the number of cvs in the region of interest that are more than a certain threshold");
      50         174 :   keys.add("optional","BETWEEN","calculate the number of colvars that are inside the region of interest and that have a CV value that is between a particular set of bounds");
      51         174 :   keys.addOutputComponent("between","BETWEEN","the number of cvs in the region of interest that are within a certain range");
      52         174 :   keys.addFlag("SUM",false,"calculate the sum of all the quantities.");
      53         174 :   keys.addOutputComponent("sum","SUM","the sum of all the colvars weighted by the function that determines if we are in the region");
      54         174 :   keys.addFlag("MEAN",false,"calculate the average value of the colvar inside the region of interest");
      55         174 :   keys.addOutputComponent("mean","MEAN","the average values of the colvar in the region of interest");
      56          87 :   keys.addActionNameSuffix("_CALC");
      57          87 :   keys.needsAction("LESS_THAN");
      58          87 :   keys.needsAction("MORE_THAN");
      59          87 :   keys.needsAction("GROUP");
      60          87 :   keys.needsAction("BETWEEN");
      61          87 :   keys.needsAction("SUM");
      62          87 :   keys.needsAction("MEAN");
      63          87 :   keys.needsAction("CUSTOM");
      64          87 : }
      65             : 
      66             : template <const char* v>
      67          59 : VolumeShortcut<v>::VolumeShortcut(const ActionOptions&ao):
      68             :   Action(ao),
      69          59 :   ActionShortcut(ao) {
      70          59 :   std::string voltype(v), mc_lab;
      71          59 :   parse("DATA",mc_lab);
      72             :   bool dosum;
      73         118 :   parseFlag("SUM",dosum);
      74          59 :   if( mc_lab.length()>0 ) {
      75          12 :     Group* mygrp = plumed.getActionSet().template selectWithLabel<Group*>(mc_lab);
      76          12 :     Group* mygrp2 = plumed.getActionSet().template selectWithLabel<Group*>(mc_lab + "_grp");
      77          12 :     if( mygrp || mygrp2 ) {
      78          20 :       readInputLine( getShortcutLabel() + "_grp: GROUP ATOMS=" + mc_lab );
      79             :     }
      80             :     bool domean;
      81          24 :     parseFlag("MEAN",domean);
      82             :     std::string lt_input, mt_input, bt_input;
      83          12 :     parse("LESS_THAN",lt_input);
      84          12 :     parse("MORE_THAN",mt_input);
      85          24 :     parse("BETWEEN",bt_input);
      86             :     std::string atomsd;
      87          24 :     parse("ATOMS",atomsd);
      88          12 :     if( atomsd.length()==0 ) {
      89             :       atomsd=mc_lab;
      90             :     }
      91             :     // Create the apprpriate volume object
      92          24 :     readInputLine( getShortcutLabel() + ": " + voltype + "_CALC " + convertInputLineToString() + " ATOMS=" + atomsd );
      93             :     // Now create input for sums
      94          12 :     if( dosum || domean ) {
      95          24 :       readInputLine( getShortcutLabel() + "_prod: CUSTOM ARG=" + mc_lab + "," + getShortcutLabel() + " FUNC=x*y PERIODIC=NO");
      96          12 :       std::string tlab = getShortcutLabel() + "_numer";
      97          12 :       if( dosum ) {
      98           0 :         tlab = getShortcutLabel() + "_sum:";
      99             :       }
     100          24 :       readInputLine( tlab + ": SUM ARG=" + getShortcutLabel() + "_prod PERIODIC=NO");
     101             :     }
     102          12 :     if( domean ) {
     103             :       // Calculate denominator
     104          24 :       readInputLine( getShortcutLabel() + "_norm: SUM ARG=" + getShortcutLabel() + " PERIODIC=NO");
     105             :       // And calculate final quantity which is mean of these two actions
     106          12 :       std::string arg1_lab = getShortcutLabel() + "_numer";
     107          12 :       if( dosum ) {
     108           0 :         arg1_lab = getShortcutLabel()  + "_sum";
     109             :       }
     110          24 :       readInputLine( getShortcutLabel() + "_mean: CUSTOM ARG=" + arg1_lab + "," + getShortcutLabel() + "_norm FUNC=x/y PERIODIC=NO");
     111             :     }
     112          12 :     if( lt_input.length()>0 ) {
     113             :       // Calculate number less than
     114          14 :       readInputLine( mc_lab + "_" + getShortcutLabel() + "_lt: LESS_THAN ARG=" + mc_lab + " SWITCH={" + lt_input +"}");
     115             :       // And the matheval bit
     116          14 :       readInputLine( getShortcutLabel() + "_lt: CUSTOM ARG=" + mc_lab + "_" + getShortcutLabel() + "_lt," + getShortcutLabel() + " FUNC=x*y PERIODIC=NO");
     117             :       // And the final sum
     118          14 :       readInputLine( getShortcutLabel() + "_lessthan: SUM ARG=" + getShortcutLabel() + "_lt PERIODIC=NO");
     119             :     }
     120          12 :     if( mt_input.length()>0 ) {
     121             :       // Calculate number less than
     122           0 :       readInputLine( mc_lab + "_" + getShortcutLabel() + "_mt: MORE_THAN ARG=" + mc_lab + " SWITCH={" + mt_input  + "}");
     123             :       // And the matheval bit
     124           0 :       readInputLine( getShortcutLabel() + "_mt: CUSTOM ARG=" + mc_lab + "_" + getShortcutLabel() + "_mt," + getShortcutLabel() + " FUNC=x*y PERIODIC=NO");
     125             :       // And the final sum
     126           0 :       readInputLine( getShortcutLabel() + "_morethan: SUM ARG=" + getShortcutLabel() + "_mt PERIODIC=NO");
     127             :     }
     128          12 :     if( bt_input.length()>0 ) {
     129             :       // Calculate number less than
     130           0 :       readInputLine( mc_lab + "_" + getShortcutLabel() + "_bt: BETWEEN ARG=" + mc_lab + " SWITCH={" + bt_input +"}");
     131             :       // And the matheval bit
     132           0 :       readInputLine( getShortcutLabel() + "_bt: CUSTOM ARG=" + mc_lab + "_" + getShortcutLabel() + "_bt," + getShortcutLabel() + " FUNC=x*y PERIODIC=NO");
     133             :       // And the final sum
     134           0 :       readInputLine( getShortcutLabel() + "_between: SUM ARG=" + getShortcutLabel() + "_bt PERIODIC=NO");
     135             :     }
     136          47 :   } else if( dosum ) {
     137          20 :     readInputLine( getShortcutLabel() + "_vols: " + voltype + "_CALC " + convertInputLineToString() );
     138          20 :     readInputLine( getShortcutLabel() + ": SUM ARG=" + getShortcutLabel() + "_vols PERIODIC=NO");
     139             :   } else {
     140          74 :     readInputLine( getShortcutLabel() + ": " + voltype + "_CALC " + convertInputLineToString() );
     141             :   }
     142          59 : }
     143             : 
     144             : }
     145             : }
     146             : #endif