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         435 : void RestraintShortcut::registerKeywords(Keywords& keys) {
      40         435 :   ActionShortcut::registerKeywords( keys );
      41         870 :   keys.addInputKeyword("numbered","ARG","scalar/vector","the values the harmonic restraint acts upon");
      42         435 :   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         435 :   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         435 :   keys.add("compulsory","AT","the position of the restraint");
      45         435 :   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         870 :   keys.addOutputComponent("bias","default","scalar","the instantaneous value of the bias potential");
      47         870 :   keys.addOutputComponent("force2","default","scalar/vector","the instantaneous value of the squared force due to this bias potential");
      48         435 :   keys.addActionNameSuffix("_SCALAR");
      49         435 :   keys.needsAction("COMBINE");
      50         435 :   keys.needsAction("SUM");
      51         435 :   keys.needsAction("CUSTOM");
      52         435 :   keys.needsAction("BIASVALUE");
      53         435 : }
      54             : 
      55         395 : RestraintShortcut::RestraintShortcut(const ActionOptions&ao):
      56             :   Action(ao),
      57         395 :   ActionShortcut(ao) {
      58             :   // Read in the args
      59         395 :   std::vector<std::string> args;
      60         790 :   parseVector("ARG",args);
      61         395 :   if( args.size()==0 ) {
      62           0 :     error("found no input arguments");
      63             :   }
      64         395 :   std::vector<Value*> vals;
      65         395 :   ActionWithArguments::interpretArgumentList( args, plumed.getActionSet(), this, vals );
      66         392 :   if( vals.size()==0 ) {
      67           0 :     error("found no input arguments");
      68             :   }
      69             : 
      70             :   // Find the rank
      71         392 :   unsigned rank=vals[0]->getRank();
      72         904 :   for(unsigned i=0; i<vals.size(); ++i) {
      73         512 :     if( vals[i]->getRank()>0 && vals[i]->hasDerivatives() ) {
      74           0 :       error("argument should not be function on grid");
      75             :     }
      76         512 :     if( vals[i]->getRank()!=rank ) {
      77           0 :       error("all arguments should have same rank");
      78             :     }
      79             :   }
      80         392 :   if( rank==0 ) {
      81         391 :     std::vector<std::string> slope(args.size());
      82         776 :     parseVector("SLOPE",slope);
      83             :     // all the slopes are passed: checking only the first one dropped e.g. SLOPE=0.0,1.0
      84         388 :     std::string slopestr="SLOPE=" + slope[0];
      85         504 :     for(unsigned i=1; i<slope.size(); ++i) {
      86         232 :       slopestr += "," + slope[i];
      87             :     }
      88         388 :     std::string allargs=args[0];
      89         504 :     for(unsigned i=1; i<args.size(); ++i) {
      90         232 :       allargs += "," + args[i];
      91             :     }
      92        1552 :     readInputLine( getShortcutLabel() + ": RESTRAINT_SCALAR ARG=" + allargs + " " + slopestr + " " + convertInputLineToString() );
      93             :     return;
      94         388 :   }
      95             : 
      96             :   std::string stride;
      97           4 :   parse("STRIDE",stride);
      98           4 :   std::vector<std::string> at;
      99           8 :   parseVector("AT",at);
     100           4 :   std::vector<std::string> slope(at.size());
     101           8 :   parseVector("SLOPE",slope);
     102           4 :   std::vector<std::string> kappa(at.size());
     103           8 :   parseVector("KAPPA",kappa);
     104             : 
     105             :   std::string biasargs, forceargs;
     106          12 :   for(unsigned i=0; i<args.size(); ++i) {
     107             :     std::string argn;
     108           8 :     std::size_t dot=args[i].find_first_of(".");
     109           8 :     if(dot!=std::string::npos) {
     110           6 :       argn = args[i].substr(0,dot) + "_" + args[i].substr(dot+1);
     111             :     } else {
     112             :       argn = args[i];
     113             :     }
     114             :     double kap, slo;
     115           8 :     Tools::convert( kappa[i], kap );
     116           8 :     Tools::convert( slope[i], slo );
     117           8 :     if( kap==0 && slo==0 ) {
     118             :       continue;
     119             :     }
     120             :     // distance from AT: COMBINE applies the periodic boundary conditions; for a non periodic argument
     121             :     // the difference is computed directly in the CUSTOM functions, which saves one action
     122           7 :     std::vector<Value*> argvals;
     123           7 :     ActionWithArguments::interpretArgumentList( std::vector<std::string>(1,args[i]), plumed.getActionSet(), this, argvals );
     124             :     bool periodic=false;
     125          14 :     for(const auto & v : argvals) {
     126           7 :       periodic = periodic || v->isPeriodic();
     127             :     }
     128             :     std::string cvarg, cv;
     129           7 :     if( periodic ) {
     130           0 :       readInputLine( getShortcutLabel() + "_cv_" + argn + ": COMBINE PERIODIC=NO ARG=" + args[i] + " PARAMETERS=" + at[i] );
     131           0 :       cvarg = getShortcutLabel() + "_cv_" + argn;
     132             :       cv = "x";
     133             :     } else {
     134             :       cvarg = args[i];
     135          21 :       cv = "(x-(" + at[i] + "))";
     136             :     }
     137           7 :     if( kap!=0 ) {
     138          28 :       readInputLine( getShortcutLabel() + "_harm_" + argn + ": CUSTOM PERIODIC=NO FUNC=0.5*" + kappa[i] + "*" + cv + "^2 ARG=" + cvarg );
     139          21 :       readInputLine( getShortcutLabel() + "_kap_" + argn + ": SUM PERIODIC=NO ARG=" + getShortcutLabel() + "_harm_" + argn );
     140          24 :       biasargs += (biasargs.length()==0 ? "ARG=" : ",") + getShortcutLabel() + "_kap_" + argn;
     141             :     }
     142           7 :     if( slo!=0 ) {
     143           4 :       readInputLine( getShortcutLabel() + "_linear_" + argn + ": CUSTOM PERIODIC=NO FUNC=" + slope[i] + "*" + cv + " ARG=" + cvarg );
     144           3 :       readInputLine( getShortcutLabel() + "_slope_" + argn + ": SUM PERIODIC=NO ARG=" + getShortcutLabel() + "_linear_" + argn );
     145           4 :       biasargs += (biasargs.length()==0 ? "ARG=" : ",") + getShortcutLabel() + "_slope_" + argn;
     146             :     }
     147             :     // squared force (k*x+m)^2, with x the distance from AT
     148          35 :     readInputLine( getShortcutLabel() + "_f2_" + argn + ": CUSTOM PERIODIC=NO FUNC=((" + kappa[i] + ")*" + cv + "+(" + slope[i] + "))^2 ARG=" + cvarg );
     149          24 :     forceargs += (forceargs.length()==0 ? "ARG=" : ",") + getShortcutLabel() + "_f2_" + argn;
     150             :   }
     151           4 :   if( biasargs.length()==0 ) {
     152           0 :     error("all the values of KAPPA and SLOPE are zero");
     153             :   }
     154             :   // This is the bias
     155           4 :   readInputLine( getShortcutLabel() + "_bias: COMBINE PERIODIC=NO " + biasargs );
     156           8 :   readInputLine( getShortcutLabel() + ": BIASVALUE ARG=" + getShortcutLabel() + "_bias STRIDE=" + stride );
     157           8 :   readInputLine( getShortcutLabel() + "_force2: COMBINE PERIODIC=NO " + forceargs );
     158         405 : }
     159             : 
     160             : }
     161             : 
     162             : 
     163             : }