Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2018 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 : //+PLUMEDOC COLVAR XYTORSIONS
27 : /*
28 : Calculate the torsional angle around the x axis between an arbitrary vector and the positive y direction
29 :
30 : \par Examples
31 :
32 : */
33 : //+ENDPLUMEDOC
34 :
35 : //+PLUMEDOC COLVAR XZTORSIONS
36 : /*
37 : Calculate the torsional angle around the x axis between an arbitrary vector and the positive z direction
38 :
39 : \par Examples
40 :
41 : */
42 : //+ENDPLUMEDOC
43 :
44 : //+PLUMEDOC COLVAR YXTORSIONS
45 : /*
46 : Calculate the torsional angle around the y axis between an arbitrary vector and the positive x direction
47 :
48 : \par Examples
49 :
50 : */
51 : //+ENDPLUMEDOC
52 :
53 : //+PLUMEDOC COLVAR YZTORSIONS
54 : /*
55 : Calculate the torsional angle around the y axis between an arbitrary vector and the positive z direction
56 :
57 : \par Examples
58 :
59 : */
60 : //+ENDPLUMEDOC
61 :
62 : //+PLUMEDOC COLVAR ZXTORSIONS
63 : /*
64 : Calculate the torsional angle around the z axis between an arbitrary vector and the positive x direction
65 :
66 : \par Examples
67 :
68 : */
69 : //+ENDPLUMEDOC
70 :
71 : //+PLUMEDOC COLVAR ZYTORSIONS
72 : /*
73 : Calculate the torsional angle around the z axis between an arbitrary vector and the positive y direction
74 :
75 : \par Examples
76 :
77 : */
78 : //+ENDPLUMEDOC
79 :
80 : namespace PLMD {
81 : namespace multicolvar {
82 :
83 : class XYTorsions : public ActionShortcut {
84 : public:
85 : static void registerKeywords(Keywords& keys);
86 : explicit XYTorsions(const ActionOptions&);
87 : };
88 :
89 : PLUMED_REGISTER_ACTION(XYTorsions,"XYTORSIONS")
90 : PLUMED_REGISTER_ACTION(XYTorsions,"XZTORSIONS")
91 : PLUMED_REGISTER_ACTION(XYTorsions,"YXTORSIONS")
92 : PLUMED_REGISTER_ACTION(XYTorsions,"YZTORSIONS")
93 : PLUMED_REGISTER_ACTION(XYTorsions,"ZXTORSIONS")
94 : PLUMED_REGISTER_ACTION(XYTorsions,"ZYTORSIONS")
95 :
96 15 : void XYTorsions::registerKeywords(Keywords& keys) {
97 15 : ActionShortcut::registerKeywords( keys );
98 30 : keys.add("numbered","ATOMS","the pairs of atoms that you would like to calculate the angles for");
99 30 : keys.reset_style("ATOMS","atoms"); MultiColvarShortcuts::shortcutKeywords( keys );
100 30 : keys.needsAction("FIXEDATOM"); keys.needsAction("TORSION");
101 15 : }
102 :
103 1 : XYTorsions::XYTorsions(const ActionOptions& ao):
104 : Action(ao),
105 1 : ActionShortcut(ao)
106 : {
107 2 : std::string vdir = getShortcutLabel() + "_vec2," + getShortcutLabel() + "_origin";
108 2 : std::string adir = getShortcutLabel() + "_axis," + getShortcutLabel() + "_origin";
109 : // Create action for position of origin
110 2 : readInputLine( getShortcutLabel() + "_origin: FIXEDATOM AT=0,0,0");
111 1 : if( getName()=="XYTORSIONS" ) {
112 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=1,0,0");
113 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,1,0");
114 : }
115 1 : if( getName()=="XZTORSIONS" ) {
116 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=1,0,0");
117 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,0,1");
118 : }
119 1 : if( getName()=="YXTORSIONS" ) {
120 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,1,0");
121 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=1,0,0");
122 : }
123 1 : if( getName()=="YZTORSIONS" ) {
124 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,1,0");
125 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,0,1");
126 : }
127 1 : if( getName()=="ZXTORSIONS" ) {
128 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,0,1");
129 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=1,0,0");
130 : }
131 1 : if( getName()=="ZYTORSIONS" ) {
132 1 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,0,1");
133 2 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,1,0");
134 : }
135 :
136 : // Now create action to compute all torsions
137 1 : std::string torsions_str = getShortcutLabel() + ": TORSION";
138 1 : for(unsigned i=1;; ++i) {
139 6 : std::string atstring; parseNumbered("ATOMS",i,atstring);
140 3 : if( atstring.length()==0 ) break;
141 2 : std::string num; Tools::convert( i, num );
142 4 : torsions_str += " VECTORA" + num + "=" + atstring + " VECTORB" + num + "=" + vdir + " AXIS" + num + "=" + adir;
143 2 : }
144 1 : readInputLine( torsions_str );
145 : // Add shortcuts to label
146 2 : MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this );
147 1 : }
148 :
149 : }
150 : }
|
