Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2020 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/ActionRegister.h"
      23             : #include "core/ActionShortcut.h"
      24             : #include "core/PlumedMain.h"
      25             : #include "core/ActionSet.h"
      26             : #include "core/ActionWithArguments.h"
      27             : 
      28             : namespace PLMD {
      29             : namespace bias {
      30             : 
      31             : class RestraintShortcut : public ActionShortcut {
      32             : public:
      33             :   static void registerKeywords(Keywords& keys);
      34             :   explicit RestraintShortcut(const ActionOptions&);
      35             : };
      36             : 
      37             : PLUMED_REGISTER_ACTION(RestraintShortcut,"RESTRAINT")
      38             : 
      39         322 : void RestraintShortcut::registerKeywords(Keywords& keys) {
      40         322 :   ActionShortcut::registerKeywords( keys );
      41         644 :   keys.addInputKeyword("numbered","ARG","scalar/vector","the values the harmonic restraint acts upon");
      42         322 :   keys.add("compulsory","SLOPE","0.0","specifies that the restraint is linear and what the values of the force constants on each of the variables are");
      43         322 :   keys.add("compulsory","KAPPA","0.0","specifies that the restraint is harmonic and what the values of the force constants on each of the variables are");
      44         322 :   keys.add("compulsory","AT","the position of the restraint");
      45         322 :   keys.add("hidden","STRIDE","1","the frequency with which the forces due to the bias should be calculated.  This can be used to correctly set up multistep algorithms");
      46         644 :   keys.addOutputComponent("bias","default","scalar","the instantaneous value of the bias potential");
      47         644 :   keys.addOutputComponent("force2","default","scalar/vector","the instantaneous value of the squared force due to this bias potential");
      48         322 :   keys.addActionNameSuffix("_SCALAR");
      49         322 :   keys.needsAction("COMBINE");
      50         322 :   keys.needsAction("SUM");
      51         322 :   keys.needsAction("CUSTOM");
      52         322 :   keys.needsAction("BIASVALUE");
      53         322 : }
      54             : 
      55         291 : RestraintShortcut::RestraintShortcut(const ActionOptions&ao):
      56             :   Action(ao),
      57         291 :   ActionShortcut(ao) {
      58             :   // Read in the args
      59             :   std::vector<std::string> args;
      60         582 :   parseVector("ARG",args);
      61         291 :   if( args.size()==0 ) {
      62           0 :     error("found no input arguments");
      63             :   }
      64             :   std::vector<Value*> vals;
      65         291 :   ActionWithArguments::interpretArgumentList( args, plumed.getActionSet(), this, vals );
      66         288 :   if( vals.size()==0 ) {
      67           0 :     error("found no input arguments");
      68             :   }
      69             : 
      70             :   // Find the rank
      71         288 :   unsigned rank=vals[0]->getRank();
      72         638 :   for(unsigned i=0; i<vals.size(); ++i) {
      73         350 :     if( vals[i]->getRank()>0 && vals[i]->hasDerivatives() ) {
      74           0 :       error("argument should not be function on grid");
      75             :     }
      76         350 :     if( vals[i]->getRank()!=rank ) {
      77           0 :       error("all arguments should have same rank");
      78             :     }
      79             :   }
      80         288 :   if( rank==0 ) {
      81         290 :     std::vector<std::string> slope(args.size());
      82         287 :     parseVector("SLOPE",slope);
      83         287 :     std::string slopestr="";
      84         287 :     if( slope[0]!="0.0" ) {
      85          64 :       slopestr="SLOPE=" + slope[0];
      86         107 :       for(unsigned i=1; i<slope.size(); ++i) {
      87          86 :         slopestr += "," + slope[i];
      88             :       }
      89             :     }
      90         287 :     std::string allargs=args[0];
      91         349 :     for(unsigned i=1; i<args.size(); ++i) {
      92         124 :       allargs += "," + args[i];
      93             :     }
      94         574 :     readInputLine( getShortcutLabel() + ": RESTRAINT_SCALAR ARG=" + allargs + " " + slopestr + " " + convertInputLineToString() );
      95             :     return;
      96         287 :   }
      97             : 
      98             :   std::string stride;
      99           2 :   parse("STRIDE",stride);
     100             :   std::vector<std::string> at;
     101           2 :   parseVector("AT",at);
     102           1 :   std::vector<std::string> slope(at.size());
     103           2 :   parseVector("SLOPE",slope);
     104           1 :   std::vector<std::string> kappa(at.size());
     105           2 :   parseVector("KAPPA",kappa);
     106             : 
     107             :   std::string biasargs, forceargs;
     108             :   bool non_constant_force=false;
     109           2 :   for(unsigned i=0; i<args.size(); ++i) {
     110             :     std::string argn;
     111           1 :     std::size_t dot=args[i].find_first_of(".");
     112           1 :     if(dot!=std::string::npos) {
     113           0 :       argn = args[i].substr(0,dot) + "_" + args[i].substr(dot+1);
     114             :     } else {
     115             :       argn = args[i];
     116             :     }
     117           2 :     readInputLine( getShortcutLabel() + "_cv_" + argn + ": COMBINE PERIODIC=NO ARG=" + args[i] + " PARAMETERS=" + at[i] );
     118             :     double kap;
     119           1 :     Tools::convert(  kappa[i], kap );
     120           1 :     if( fabs(kap)>0 ) {
     121             :       non_constant_force = true;
     122           2 :       readInputLine( getShortcutLabel() + "_harm_" + argn + ": CUSTOM PERIODIC=NO FUNC=0.5*" + kappa[i] + "*x^2 ARG=" + getShortcutLabel() + "_cv_" + argn );
     123           2 :       readInputLine( getShortcutLabel() + "_kap_" + argn + ": SUM PERIODIC=NO ARG=" + getShortcutLabel() + "_harm_" + argn );
     124           2 :       readInputLine( getShortcutLabel() + "_f2_" + argn + ": CUSTOM PERIODIC=NO FUNC=" + kappa[i] + "*2*x+" + slope[i] + "*" + slope[i] + " ARG=" + getShortcutLabel() + "_harm_" + argn );
     125           1 :       if( i==0 ) {
     126           2 :         biasargs = "ARG=" + getShortcutLabel() + "_kap_" + argn;
     127             :       } else {
     128           0 :         biasargs += "," + getShortcutLabel() + "_kap_" + argn;
     129             :       }
     130           1 :       if( i==0 ) {
     131           2 :         forceargs = "ARG=" + getShortcutLabel() + "_f2_" + argn;
     132             :       } else {
     133           0 :         forceargs += "," + getShortcutLabel() + "_f2_" + argn;
     134             :       }
     135             :     }
     136             :     double slo;
     137           1 :     Tools::convert( slope[i], slo );
     138           1 :     if( fabs(slo)>0 ) {
     139           0 :       readInputLine( getShortcutLabel() + "_linear_" + argn + ": CUSTOM PERIODIC=NO FUNC=" + slope[i] + "*x ARG=" + getShortcutLabel() + "_cv_" + argn );
     140           0 :       readInputLine( getShortcutLabel() + "_slope_" + argn + ": SUM PERIODIC=NO ARG=" + getShortcutLabel() + "_linear_" + argn );
     141           0 :       if( biasargs.length()==0 ) {
     142           0 :         biasargs = "ARG=" + getShortcutLabel() + "_slope_" + argn;
     143             :       } else {
     144           0 :         biasargs += "," + getShortcutLabel() + "_slope_" + argn;
     145             :       }
     146             :     }
     147             :   }
     148             :   // This is the bias
     149           2 :   readInputLine( getShortcutLabel() + "_bias: COMBINE PERIODIC=NO " + biasargs );
     150           2 :   readInputLine( getShortcutLabel() + ": BIASVALUE ARG=" + getShortcutLabel() + "_bias STRIDE=" + stride );
     151           1 :   if( non_constant_force ) {
     152           2 :     readInputLine( getShortcutLabel() + "_force2: COMBINE PERIODIC=NO " + forceargs );
     153             :   }
     154         298 : }
     155             : 
     156             : }
     157             : 
     158             : 
     159             : }