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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 Random_Acceleration_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_RANDOM_ACCELERATION_MD 36 : /* 37 : 38 : Performs random acceleration MD within the protein matrix. 39 : 40 : \par Examples 41 : 42 : Every optimizer implemented in the maze module needs a loss function as 43 : an argument, and it should be passed using the \ref MAZE_LOSS keyword. 44 : 45 : \plumedfile 46 : MAZE_RANDOM_ACCELERATION_MD ... 47 : LABEL=rw 48 : 49 : OPTIMIZER_STRIDE=_ 50 : LOSS=l 51 : RMIN=_ 52 : 53 : LIGAND=2635-2646 54 : PROTEIN=1-2634 55 : ... MAZE_RANDOM_ACCELERATION_MD 56 : \endplumedfile 57 : 58 : As shown above, each optimizer should be provided with the LIGAND and 59 : the PROTEIN keywords. 60 : 61 : */ 62 : //+ENDPLUMEDOC 63 : 64 : /** 65 : * @class Random_Acceleration_MD Random_Acceleration_MD.cpp 66 : * "maze/Random_Acceleration_MD.cpp" 67 : * 68 : * @brief Perform RAMD simulation. 69 : */ 70 : class Random_Acceleration_MD: public Optimizer { 71 : public: 72 : /** 73 : * PLMD constructor. 74 : * 75 : * @param[in] ao PLMD::ActionOptions& 76 : */ 77 : explicit Random_Acceleration_MD(const ActionOptions&); 78 : 79 : /** 80 : * Registers PLMD keywords. 81 : * 82 : * @param[in] keys PLMD keywords 83 : */ 84 : static void registerKeywords(Keywords&); 85 : 86 : /** 87 : * Each class deriving from Optimizer needs to override this function. 88 : */ 89 : void optimize() override; 90 : 91 : private: 92 : //! Threshold distance that the ligand needs to pass. 93 : double r_min_; 94 : 95 : //! Total distance. 96 : double total_dist_; 97 : 98 : //! Distance. 99 : double dist_; 100 : 101 : //! Ligand center of mass. 102 : Vector com_; 103 : 104 : //! PLMD value for distance. 105 : Value* value_dist_; 106 : 107 : //! PLMD value for total distance. 108 : Value* value_total_dist_; 109 : }; 110 : 111 : // Register MAZE_RANDOM_ACCELERATION_MD. 112 : PLUMED_REGISTER_ACTION(Random_Acceleration_MD, "MAZE_RANDOM_ACCELERATION_MD") 113 : 114 3 : void Random_Acceleration_MD::registerKeywords(Keywords& keys) { 115 3 : Optimizer::registerKeywords(keys); 116 : 117 3 : keys.remove("N_ITER"); 118 : 119 6 : keys.add( 120 : "compulsory", 121 : "R_MIN", 122 : "Minimal distance traveled before sampling a new direction of biasing." 123 : ); 124 : 125 6 : keys.addOutputComponent( 126 : "dist", 127 : "default", 128 : "Distance traveled in one sampling interval." 129 : ); 130 : 131 6 : keys.addOutputComponent( 132 : "tdist", 133 : "default", 134 : "Total distance traveled by biased atoms." 135 : ); 136 3 : } 137 : 138 1 : Random_Acceleration_MD::Random_Acceleration_MD(const ActionOptions& ao) 139 : : PLUMED_OPT_INIT(ao), 140 1 : total_dist_(0.0), 141 1 : dist_(0.0) { 142 1 : log.printf("maze> Random accelerated molecular dynamics.\n"); 143 : 144 2 : if(keywords.exists("R_MIN")) { 145 1 : parse("R_MIN", r_min_); 146 : 147 1 : plumed_massert( 148 : r_min_ > 0, 149 : "maze> R_MIN should be explicitly specified and positive.\n" 150 : ); 151 : 152 1 : log.printf( 153 : "maze> R_MIN read: %f [A].\n", 154 : r_min_ 155 : ); 156 : } 157 : 158 1 : set_label("RANDOM_ACCELERATION_MD"); 159 1 : set_opt(rnd::next_plmd_vector()); 160 : set_opt_value(0.0); 161 : 162 : start_step_stride(); 163 : 164 1 : checkRead(); 165 : 166 1 : com_ = center_of_mass(); 167 : 168 2 : addComponent("dist"); 169 1 : componentIsNotPeriodic("dist"); 170 1 : value_dist_ = getPntrToComponent("dist"); 171 : 172 2 : addComponent("tdist"); 173 1 : componentIsNotPeriodic("tdist"); 174 1 : value_total_dist_ = getPntrToComponent("tdist"); 175 1 : } 176 : 177 2 : void Random_Acceleration_MD::optimize() { 178 2 : Vector c = center_of_mass(); 179 2 : Vector d; 180 : 181 2 : if (pbc_) { 182 2 : d = pbcDistance(c, com_); 183 : } 184 : else { 185 0 : d = delta(c, com_); 186 : } 187 : 188 2 : dist_ = d.modulo(); 189 2 : total_dist_ += dist_; 190 : 191 2 : if(dist_ < r_min_) { 192 0 : set_opt(rnd::next_plmd_vector()); 193 : } 194 : 195 2 : set_opt_value(score()); 196 2 : com_ = c; 197 : 198 2 : value_dist_->set(dist_); 199 2 : value_total_dist_->set(total_dist_); 200 2 : } 201 : 202 : } // namespace maze 203 : } // namespace PLMD