Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.
       3             : 
       4             : See http://www.maze-code.github.io for more information.
       5             : 
       6             : This file is part of maze.
       7             : 
       8             : maze is free software: you can redistribute it and/or modify it under the
       9             : terms of the GNU Lesser General Public License as published by the Free
      10             : Software Foundation, either version 3 of the License, or (at your option)
      11             : any later version.
      12             : 
      13             : maze is distributed in the hope that it will be useful, but WITHOUT ANY
      14             : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
      15             : FOR A PARTICULAR PURPOSE.
      16             : 
      17             : See the 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 maze. If not, see <https://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : 
      23             : /**
      24             :  * @file Steered_MD.cpp
      25             :  *
      26             :  * @author J. Rydzewski (jr@fizyka.umk.pl)
      27             :  */
      28             : 
      29             : #include "core/ActionRegister.h"
      30             : #include "Optimizer.h"
      31             : 
      32             : namespace PLMD {
      33             : namespace maze {
      34             : 
      35             : //+PLUMEDOC MAZE_OPTIMIZER MAZE_STEERED_MD
      36             : /*
      37             : 
      38             : Performs a linear unbinding along a predefined biasing direction that
      39             : needs to be provided using the PULLING keyword.
      40             : 
      41             : ## Examples
      42             : 
      43             : Every optimizer implemented in the maze module needs a loss function as
      44             : an argument, and it should be passed using the [MAZE_LOSS](MAZE_LOSS.md) keyword.
      45             : 
      46             : ```plumed
      47             : l: MAZE_LOSS PARAMS=1,1,1
      48             : 
      49             : MAZE_STEERED_MD ...
      50             :   LABEL=smd
      51             : 
      52             :   LOSS=l
      53             :   PULLING=0.3,0.3,0.3
      54             :   OPTIMIZER_STRIDE=200
      55             : 
      56             :   LIGAND=2635-2646
      57             :   PROTEIN=1-2634
      58             : ... MAZE_STEERED_MD
      59             : ```
      60             : 
      61             : As shown above, each optimizer should be provided with the LIGAND and
      62             : the PROTEIN keywords.
      63             : 
      64             : */
      65             : //+ENDPLUMEDOC
      66             : 
      67             : /**
      68             :  * @class Steered_MD Steered_MD.cpp "maze/Steered_MD.cpp"
      69             :  * @brief Performs steered MD simulation.
      70             :  */
      71             : class Steered_MD: public Optimizer {
      72             : public:
      73             :   /**
      74             :    * PLMD constructor.
      75             :    *
      76             :    * @param[in] ao PLMD::ActionOptions&
      77             :    */
      78             :   explicit Steered_MD(const ActionOptions& ao);
      79             : 
      80             :   /**
      81             :    * Registers PLMD keywords.
      82             :    *
      83             :    * @param[in] keys PLMD keywords
      84             :    */
      85             :   static void registerKeywords(Keywords&);
      86             : 
      87             :   /**
      88             :    * Each class deriving from Optimizer needs to override this function.
      89             :    */
      90             :   void optimize() override;
      91             : 
      92             : private:
      93             :   //! Total distance traveled by the ligand.
      94             :   double total_dist_;
      95             : 
      96             :   //! Ligand center of mass.
      97             :   Vector com_;
      98             : 
      99             :   //! Constant direction of biasing.
     100             :   Vector pulling_;
     101             : 
     102             :   //! PLMD::Value of total distance.
     103             :   Value* value_total_dist_;
     104             : };
     105             : 
     106             : // Register MAZE_STEERED_MD.
     107             : PLUMED_REGISTER_ACTION(Steered_MD, "MAZE_STEERED_MD")
     108             : 
     109           5 : void Steered_MD::registerKeywords(Keywords& keys) {
     110           5 :   Optimizer::registerKeywords(keys);
     111             : 
     112          10 :   keys.remove("N_ITER");
     113             : 
     114           5 :   keys.add(
     115             :     "compulsory",
     116             :     "PULLING",
     117             :     "Constant biasing direction."
     118             :   );
     119             : 
     120          10 :   keys.addOutputComponent(
     121             :     "tdist",
     122             :     "default",
     123             :     "scalar",
     124             :     "Total distance traveled by biased atoms."
     125             :   );
     126           5 : }
     127             : 
     128           1 : Steered_MD::Steered_MD(const ActionOptions& ao)
     129             :   : PLUMED_OPT_INIT(ao),
     130           1 :     total_dist_(0.0) {
     131           1 :   log.printf("maze> Steered MD.\n");
     132             : 
     133           1 :   if (keywords.exists("PULLING")) {
     134           1 :     std::vector<double> v;
     135           1 :     parseVector("PULLING", v);
     136           1 :     pulling_ = tls::vector2Vector(v);
     137             : 
     138           1 :     log.printf("maze> PULLING read.\n");
     139             :   }
     140             : 
     141           2 :   set_label("STEERED_MD");
     142             :   set_opt(pulling_);
     143             :   set_opt_value(0.0);
     144             : 
     145             :   start_step_stride();
     146             : 
     147           1 :   checkRead();
     148             : 
     149           1 :   com_ = center_of_mass();
     150             : 
     151           2 :   addComponent("tdist");
     152           1 :   componentIsNotPeriodic("tdist");
     153           1 :   value_total_dist_ = getPntrToComponent("tdist");
     154           1 : }
     155             : 
     156           2 : void Steered_MD::optimize() {
     157           2 :   Vector c = center_of_mass();
     158           2 :   Vector d;
     159             : 
     160           2 :   if (pbc_) {
     161           2 :     d = pbcDistance(c, com_);
     162             :   } else {
     163           0 :     d = delta(c, com_);
     164             :   }
     165             : 
     166           2 :   double dist = d.modulo();
     167           2 :   total_dist_ += dist;
     168             : 
     169             :   set_opt(pulling_);
     170           2 :   set_opt_value(score());
     171           2 :   com_ = c;
     172             : 
     173           2 :   value_total_dist_->set(total_dist_);
     174           2 : }
     175             : 
     176             : } // namespace maze
     177             : } // namespace PLMD