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1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 : Copyright (c) 2015-2023 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/ActionShortcut.h" 23 : #include "core/ActionRegister.h" 24 : #include "MultiColvarShortcuts.h" 25 : 26 : #include <string> 27 : #include <cmath> 28 : 29 : //+PLUMEDOC MCOLVAR INPLANEDISTANCES 30 : /* 31 : Calculate the distance between a pair of atoms in the plane 32 : 33 : \par Examples 34 : 35 : */ 36 : //+ENDPLUMEDOC 37 : 38 : namespace PLMD { 39 : namespace multicolvar { 40 : 41 : class InPlaneDistances : public ActionShortcut { 42 : public: 43 : explicit InPlaneDistances(const ActionOptions&); 44 : static void registerKeywords( Keywords& keys ); 45 : }; 46 : 47 : PLUMED_REGISTER_ACTION(InPlaneDistances,"INPLANEDISTANCES") 48 : 49 3 : void InPlaneDistances::registerKeywords( Keywords& keys ) { 50 3 : ActionShortcut::registerKeywords( keys ); 51 6 : keys.add("atoms","GROUP","calculate distance for each distinct set of three atoms in the group"); 52 6 : keys.add("atoms","VECTORSTART","The first atom position that is used to define the normal to the plane of interest"); 53 6 : keys.add("atoms","VECTOREND","The second atom position that is used to defin the normal to the plane of interest"); 54 3 : MultiColvarShortcuts::shortcutKeywords( keys ); 55 6 : keys.needsAction("DISTANCE"); keys.needsAction("ANGLE"); 56 3 : } 57 : 58 1 : InPlaneDistances::InPlaneDistances(const ActionOptions&ao): 59 : Action(ao), 60 1 : ActionShortcut(ao) 61 : { 62 2 : std::vector<std::string> str_atomsA; parseVector("VECTORSTART",str_atomsA); Tools::interpretRanges( str_atomsA ); 63 2 : std::vector<std::string> str_atomsB; parseVector("VECTOREND",str_atomsB); Tools::interpretRanges( str_atomsB ); 64 2 : std::vector<std::string> str_atomsC; parseVector("GROUP",str_atomsC); Tools::interpretRanges( str_atomsC ); 65 1 : unsigned n=1; std::string dinput= getShortcutLabel() + "_dis: DISTANCE", ainput = getShortcutLabel() + "_ang: ANGLE"; 66 2 : for(unsigned i=0; i<str_atomsA.size(); ++i ) { 67 2 : for(unsigned j=0; j<str_atomsB.size(); ++j ) { 68 9 : for(unsigned k=0; k<str_atomsC.size(); ++k) { 69 8 : std::string str_n; Tools::convert( n, str_n ); n++; 70 16 : dinput += " ATOMS" + str_n + "=" + str_atomsA[j] + "," + str_atomsC[k]; 71 16 : ainput += " ATOMS" + str_n + "=" + str_atomsB[j] + "," + str_atomsA[i] + "," + str_atomsC[k]; 72 : } 73 : } 74 : } 75 1 : readInputLine( dinput ); readInputLine( ainput ); 76 2 : readInputLine( getShortcutLabel() + ": CUSTOM PERIODIC=NO FUNC=x*sin(y) ARG=" + getShortcutLabel() + "_dis," + getShortcutLabel() + "_ang"); 77 2 : MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this ); 78 1 : } 79 : 80 : } 81 : }