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 : The following input tells plumed to calculate the angle around the x direction between the positive y-axis and the vector connecting atom 3 to atom 5 and
31 : the angle around the x direction between the positive y axis and the vector connecting atom 1 to atom 2. The average of these two quantities is then output
32 :
33 : ```plumed
34 : d1: XYTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
35 : PRINT ARG=d1_mean
36 : ```
37 :
38 : Notice that this command is a shortcut. You can thus learn more about how to use PLUMED by examining the expanded version of the input above.
39 :
40 : */
41 : //+ENDPLUMEDOC
42 :
43 : //+PLUMEDOC COLVAR XZTORSIONS
44 : /*
45 : Calculate the torsional angle around the x axis between an arbitrary vector and the positive z direction
46 :
47 : The following input tells plumed to calculate the angle around the x direction between the positive z-axis and the vector connecting atom 3 to atom 5 and
48 : the angle around the x direction between the positive z axis and the vector connecting atom 1 to atom 2. The average of these two quantities is then output
49 :
50 : ```plumed
51 : d1: XZTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
52 : PRINT ARG=d1_mean
53 : ```
54 :
55 : Notice that this command is a shortcut. You can thus learn more about how to use PLUMED by examining the expanded version of the input above.
56 :
57 : */
58 : //+ENDPLUMEDOC
59 :
60 : //+PLUMEDOC COLVAR YXTORSIONS
61 : /*
62 : Calculate the torsional angle around the y axis between an arbitrary vector and the positive x direction
63 :
64 : The following input tells plumed to calculate the angle around the y direction between the positive x-axis and the vector connecting atom 3 to atom 5 and
65 : the angle around the y direction between the positive x axis and the vector connecting atom 1 to atom 2. The average of these two quantities is then output
66 :
67 : ```plumed
68 : d1: YXTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
69 : PRINT ARG=d1_mean
70 : ```
71 :
72 : Notice that this command is a shortcut. You can thus learn more about how to use PLUMED by examining the expanded version of the input above.
73 :
74 : */
75 : //+ENDPLUMEDOC
76 :
77 : //+PLUMEDOC COLVAR YZTORSIONS
78 : /*
79 : Calculate the torsional angle around the y axis between an arbitrary vector and the positive z direction
80 :
81 : The following input tells plumed to calculate the angle around the y direction between the positive z-axis and the vector connecting atom 3 to atom 5 and
82 : the angle around the y direction between the positive z axis and the vector connecting atom 1 to atom 2. The average of these two quantities is then output
83 :
84 : ```plumed
85 : d1: YZTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
86 : PRINT ARG=d1_mean
87 : ```
88 :
89 : Notice that this command is a shortcut. You can thus learn more about how to use PLUMED by examining the expanded version of the input above.
90 :
91 : */
92 : //+ENDPLUMEDOC
93 :
94 : //+PLUMEDOC COLVAR ZXTORSIONS
95 : /*
96 : Calculate the torsional angle around the z axis between an arbitrary vector and the positive x direction
97 :
98 : The following input tells plumed to calculate the angle around the z direction between the positive x-axis and the vector connecting atom 3 to atom 5 and
99 : the angle around the z direction between the positive x axis and the vector connecting atom 1 to atom 2. The average of these two quantities is then output
100 :
101 : ```plumed
102 : d1: ZXTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
103 : PRINT ARG=d1_mean
104 : ```
105 :
106 : Notice that this command is a shortcut. You can thus learn more about how to use PLUMED by examining the expanded version of the input above.
107 :
108 : */
109 : //+ENDPLUMEDOC
110 :
111 : //+PLUMEDOC COLVAR ZYTORSIONS
112 : /*
113 : Calculate the torsional angle around the z axis between an arbitrary vector and the positive y direction
114 :
115 : The following input tells plumed to calculate the angle around the z direction between the positive y-axis and the vector connecting atom 3 to atom 5 and
116 : the angle around the z direction between the positive y-axis and the vector connecting atom 1 to atom 2. The average of these two quantities is then output
117 :
118 : ```plumed
119 : d1: ZYTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
120 : PRINT ARG=d1_mean
121 : ```
122 :
123 : Notice that this command is a shortcut. You can thus learn more about how to use PLUMED by examining the expanded version of the input above.
124 :
125 : */
126 : //+ENDPLUMEDOC
127 :
128 : namespace PLMD {
129 : namespace multicolvar {
130 :
131 : class XYTorsions : public ActionShortcut {
132 : public:
133 : static void registerKeywords(Keywords& keys);
134 : explicit XYTorsions(const ActionOptions&);
135 : };
136 :
137 : PLUMED_REGISTER_ACTION(XYTorsions,"XYTORSIONS")
138 : PLUMED_REGISTER_ACTION(XYTorsions,"XZTORSIONS")
139 : PLUMED_REGISTER_ACTION(XYTorsions,"YXTORSIONS")
140 : PLUMED_REGISTER_ACTION(XYTorsions,"YZTORSIONS")
141 : PLUMED_REGISTER_ACTION(XYTorsions,"ZXTORSIONS")
142 : PLUMED_REGISTER_ACTION(XYTorsions,"ZYTORSIONS")
143 :
144 15 : void XYTorsions::registerKeywords(Keywords& keys) {
145 15 : ActionShortcut::registerKeywords( keys );
146 15 : keys.add("numbered","ATOMS","the pairs of atoms that you would like to calculate the angles for");
147 30 : keys.reset_style("ATOMS","atoms");
148 15 : MultiColvarShortcuts::shortcutKeywords( keys );
149 30 : keys.setValueDescription("vector","the angle between the vector connecting each pair of atoms and the the positive X/Y/Z direction around the X/Y/Z axis");
150 15 : keys.needsAction("FIXEDATOM");
151 15 : keys.needsAction("TORSION");
152 15 : }
153 :
154 1 : XYTorsions::XYTorsions(const ActionOptions& ao):
155 : Action(ao),
156 1 : ActionShortcut(ao) {
157 2 : std::string vdir = getShortcutLabel() + "_vec2," + getShortcutLabel() + "_origin";
158 2 : std::string adir = getShortcutLabel() + "_axis," + getShortcutLabel() + "_origin";
159 : // Create action for position of origin
160 2 : readInputLine( getShortcutLabel() + "_origin: FIXEDATOM AT=0,0,0");
161 1 : if( getName()=="XYTORSIONS" ) {
162 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=1,0,0");
163 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,1,0");
164 : }
165 1 : if( getName()=="XZTORSIONS" ) {
166 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=1,0,0");
167 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,0,1");
168 : }
169 1 : if( getName()=="YXTORSIONS" ) {
170 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,1,0");
171 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=1,0,0");
172 : }
173 1 : if( getName()=="YZTORSIONS" ) {
174 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,1,0");
175 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,0,1");
176 : }
177 1 : if( getName()=="ZXTORSIONS" ) {
178 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,0,1");
179 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=1,0,0");
180 : }
181 1 : if( getName()=="ZYTORSIONS" ) {
182 1 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,0,1");
183 2 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,1,0");
184 : }
185 :
186 : // Now create action to compute all torsions
187 1 : std::string torsions_str = getShortcutLabel() + ": TORSION";
188 1 : for(unsigned i=1;; ++i) {
189 : std::string atstring;
190 6 : parseNumbered("ATOMS",i,atstring);
191 3 : if( atstring.length()==0 ) {
192 : break;
193 : }
194 : std::string num;
195 2 : Tools::convert( i, num );
196 4 : torsions_str += " VECTORA" + num + "=" + atstring + " VECTORB" + num + "=" + vdir + " AXIS" + num + "=" + adir;
197 2 : }
198 1 : readInputLine( torsions_str );
199 : // Add shortcuts to label
200 2 : MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this );
201 1 : }
202 :
203 : }
204 : }
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