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 : __As you can see if you expand the inputs below, you can achieve what this shortcut action does by using [TORSION](TORSION.md) together with [CUSTOM](CUSTOM.md),
31 : [BETWEEN](BETWEEN.md), [LESS_THAN](LESS_THAN.md), [SUM](SUM.md) and [MEAN](MEAN.md). We strongly encourage you to use these actions instead as using them will provide
32 : you with a clearer understanding of the equations you are using.__
33 :
34 : 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
35 : 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
36 :
37 : ```plumed
38 : d1: XYTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
39 : PRINT ARG=d1_mean
40 : ```
41 :
42 : 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.
43 :
44 : */
45 : //+ENDPLUMEDOC
46 :
47 : //+PLUMEDOC COLVAR XZTORSIONS
48 : /*
49 : Calculate the torsional angle around the x axis between an arbitrary vector and the positive z direction
50 :
51 : __As you can see if you expand the inputs below, you can achieve what this shortcut action does by using [TORSION](TORSION.md) together with [CUSTOM](CUSTOM.md),
52 : [BETWEEN](BETWEEN.md), [LESS_THAN](LESS_THAN.md), [SUM](SUM.md) and [MEAN](MEAN.md). We strongly encourage you to use these actions instead as using them will provide
53 : you with a clearer understanding of the equations you are using.__
54 :
55 : 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
56 : 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
57 :
58 : ```plumed
59 : d1: XZTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
60 : PRINT ARG=d1_mean
61 : ```
62 :
63 : 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.
64 :
65 : */
66 : //+ENDPLUMEDOC
67 :
68 : //+PLUMEDOC COLVAR YXTORSIONS
69 : /*
70 : Calculate the torsional angle around the y axis between an arbitrary vector and the positive x direction
71 :
72 : __As you can see if you expand the inputs below, you can achieve what this shortcut action does by using [TORSION](TORSION.md) together with [CUSTOM](CUSTOM.md),
73 : [BETWEEN](BETWEEN.md), [LESS_THAN](LESS_THAN.md), [SUM](SUM.md) and [MEAN](MEAN.md). We strongly encourage you to use these actions instead as using them will provide
74 : you with a clearer understanding of the equations you are using.__
75 :
76 : 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
77 : 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
78 :
79 : ```plumed
80 : d1: YXTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
81 : PRINT ARG=d1_mean
82 : ```
83 :
84 : 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.
85 :
86 : */
87 : //+ENDPLUMEDOC
88 :
89 : //+PLUMEDOC COLVAR YZTORSIONS
90 : /*
91 : Calculate the torsional angle around the y axis between an arbitrary vector and the positive z direction
92 :
93 : __As you can see if you expand the inputs below, you can achieve what this shortcut action does by using [TORSION](TORSION.md) together with [CUSTOM](CUSTOM.md),
94 : [BETWEEN](BETWEEN.md), [LESS_THAN](LESS_THAN.md), [SUM](SUM.md) and [MEAN](MEAN.md). We strongly encourage you to use these actions instead as using them will provide
95 : you with a clearer understanding of the equations you are using.__
96 :
97 : 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
98 : 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
99 :
100 : ```plumed
101 : d1: YZTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
102 : PRINT ARG=d1_mean
103 : ```
104 :
105 : 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.
106 :
107 : */
108 : //+ENDPLUMEDOC
109 :
110 : //+PLUMEDOC COLVAR ZXTORSIONS
111 : /*
112 : Calculate the torsional angle around the z axis between an arbitrary vector and the positive x direction
113 :
114 : __As you can see if you expand the inputs below, you can achieve what this shortcut action does by using [TORSION](TORSION.md) together with [CUSTOM](CUSTOM.md),
115 : [BETWEEN](BETWEEN.md), [LESS_THAN](LESS_THAN.md), [SUM](SUM.md) and [MEAN](MEAN.md). We strongly encourage you to use these actions instead as using them will provide
116 : you with a clearer understanding of the equations you are using.__
117 :
118 : 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
119 : 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
120 :
121 : ```plumed
122 : d1: ZXTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
123 : PRINT ARG=d1_mean
124 : ```
125 :
126 : 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.
127 :
128 : */
129 : //+ENDPLUMEDOC
130 :
131 : //+PLUMEDOC COLVAR ZYTORSIONS
132 : /*
133 : Calculate the torsional angle around the z axis between an arbitrary vector and the positive y direction
134 :
135 : __As you can see if you expand the inputs below, you can achieve what this shortcut action does by using [TORSION](TORSION.md) together with [CUSTOM](CUSTOM.md),
136 : [BETWEEN](BETWEEN.md), [LESS_THAN](LESS_THAN.md), [SUM](SUM.md) and [MEAN](MEAN.md). We strongly encourage you to use these actions instead as using them will provide
137 : you with a clearer understanding of the equations you are using.__
138 :
139 : 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
140 : 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
141 :
142 : ```plumed
143 : d1: ZYTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
144 : PRINT ARG=d1_mean
145 : ```
146 :
147 : 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.
148 :
149 : */
150 : //+ENDPLUMEDOC
151 :
152 : namespace PLMD {
153 : namespace multicolvar {
154 :
155 : class XYTorsions : public ActionShortcut {
156 : public:
157 : static void registerKeywords(Keywords& keys);
158 : explicit XYTorsions(const ActionOptions&);
159 : };
160 :
161 : PLUMED_REGISTER_ACTION(XYTorsions,"XYTORSIONS")
162 : PLUMED_REGISTER_ACTION(XYTorsions,"XZTORSIONS")
163 : PLUMED_REGISTER_ACTION(XYTorsions,"YXTORSIONS")
164 : PLUMED_REGISTER_ACTION(XYTorsions,"YZTORSIONS")
165 : PLUMED_REGISTER_ACTION(XYTorsions,"ZXTORSIONS")
166 : PLUMED_REGISTER_ACTION(XYTorsions,"ZYTORSIONS")
167 :
168 15 : void XYTorsions::registerKeywords(Keywords& keys) {
169 15 : ActionShortcut::registerKeywords( keys );
170 15 : keys.add("numbered","ATOMS","the pairs of atoms that you would like to calculate the angles for");
171 30 : keys.reset_style("ATOMS","atoms");
172 15 : MultiColvarShortcuts::shortcutKeywords( keys );
173 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");
174 15 : keys.needsAction("FIXEDATOM");
175 15 : keys.needsAction("TORSION");
176 15 : keys.setDeprecated("TORSION");
177 15 : }
178 :
179 1 : XYTorsions::XYTorsions(const ActionOptions& ao):
180 : Action(ao),
181 1 : ActionShortcut(ao) {
182 2 : std::string vdir = getShortcutLabel() + "_vec2," + getShortcutLabel() + "_origin";
183 2 : std::string adir = getShortcutLabel() + "_axis," + getShortcutLabel() + "_origin";
184 : // Create action for position of origin
185 2 : readInputLine( getShortcutLabel() + "_origin: FIXEDATOM AT=0,0,0");
186 1 : if( getName()=="XYTORSIONS" ) {
187 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=1,0,0");
188 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,1,0");
189 : }
190 1 : if( getName()=="XZTORSIONS" ) {
191 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=1,0,0");
192 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,0,1");
193 : }
194 1 : if( getName()=="YXTORSIONS" ) {
195 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,1,0");
196 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=1,0,0");
197 : }
198 1 : if( getName()=="YZTORSIONS" ) {
199 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,1,0");
200 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,0,1");
201 : }
202 1 : if( getName()=="ZXTORSIONS" ) {
203 0 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,0,1");
204 0 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=1,0,0");
205 : }
206 1 : if( getName()=="ZYTORSIONS" ) {
207 1 : readInputLine( getShortcutLabel() + "_axis: FIXEDATOM AT=0,0,1");
208 2 : readInputLine( getShortcutLabel() + "_vec2: FIXEDATOM AT=0,1,0");
209 : }
210 :
211 : // Now create action to compute all torsions
212 1 : std::string torsions_str = getShortcutLabel() + ": TORSION";
213 1 : for(unsigned i=1;; ++i) {
214 : std::string atstring;
215 6 : parseNumbered("ATOMS",i,atstring);
216 3 : if( atstring.length()==0 ) {
217 : break;
218 : }
219 : std::string num;
220 2 : Tools::convert( i, num );
221 4 : torsions_str += " VECTORA" + num + "=" + atstring + " VECTORB" + num + "=" + vdir + " AXIS" + num + "=" + adir;
222 2 : }
223 1 : readInputLine( torsions_str );
224 : // Add shortcuts to label
225 2 : MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this );
226 1 : }
227 :
228 : }
229 : }
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