Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2023 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 : namespace PLMD {
30 : namespace multicolvar {
31 :
32 : //+PLUMEDOC COLVAR ANGLES
33 : /*
34 : Calculate an angle.
35 :
36 : This command can be used to compute the angle between three atoms. Alternatively
37 : if four atoms appear in the atom
38 : specification it calculates the angle between
39 : two vectors identified by two pairs of atoms.
40 :
41 : If _three_ atoms are given, the angle is defined as:
42 : \f[
43 : \theta=\arccos\left(\frac{ {\bf r}_{21}\cdot {\bf r}_{23}}{
44 : |{\bf r}_{21}| |{\bf r}_{23}|}\right)
45 : \f]
46 : Here \f$ {\bf r}_{ij}\f$ is the distance vector among the
47 : i-th and the j-th listed atom.
48 :
49 : If _four_ atoms are given, the angle is defined as:
50 : \f[
51 : \theta=\arccos\left(\frac{ {\bf r}_{21}\cdot {\bf r}_{34}}{
52 : |{\bf r}_{21}| |{\bf r}_{34}|}\right)
53 : \f]
54 :
55 : Notice that angles defined in this way are non-periodic variables and
56 : their value is limited by definition between 0 and \f$\pi\f$.
57 :
58 : The vectors \f$ {\bf r}_{ij}\f$ are by default evaluated taking
59 : periodic boundary conditions into account.
60 : This behavior can be changed with the NOPBC flag.
61 :
62 : \par Examples
63 :
64 : This command tells plumed to calculate the angle between the vector connecting atom 1 to atom 2 and
65 : the vector connecting atom 2 to atom 3 and to print it on file COLVAR1. At the same time,
66 : the angle between vector connecting atom 1 to atom 2 and the vector connecting atom 3 to atom 4 is printed
67 : on file COLVAR2.
68 : \plumedfile
69 :
70 : a: ANGLE ATOMS=1,2,3
71 : # equivalently one could state:
72 : # a: ANGLE ATOMS=1,2,2,3
73 :
74 : b: ANGLE ATOMS=1,2,3,4
75 :
76 : PRINT ARG=a FILE=COLVAR1
77 : PRINT ARG=b FILE=COLVAR2
78 : \endplumedfile
79 :
80 : This final example instructs plumed to calculate all the angles in the first coordination
81 : spheres of the atoms. The bins for a normalized histogram of the distribution is then output
82 :
83 : \plumedfile
84 : ANGLES GROUP=1-38 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=pi NBINS=20} SWITCH={GAUSSIAN R_0=1.0} LABEL=a1
85 : PRINT ARG=a1.* FILE=colvar
86 : \endplumedfile
87 :
88 :
89 : */
90 : //+ENDPLUMEDOC
91 :
92 : class Angles : public ActionShortcut {
93 : public:
94 : explicit Angles(const ActionOptions&);
95 : static void registerKeywords( Keywords& keys );
96 : };
97 :
98 : PLUMED_REGISTER_ACTION(Angles,"ANGLES")
99 :
100 4 : void Angles::registerKeywords( Keywords& keys ) {
101 4 : ActionShortcut::registerKeywords( keys );
102 8 : keys.add("atoms-1","GROUP","Calculate angles for each distinct set of three atoms in the group");
103 8 : keys.add("atoms-2","GROUPA","A group of central atoms about which angles should be calculated");
104 8 : keys.add("atoms-2","GROUPB","When used in conjunction with GROUPA this keyword instructs plumed "
105 : "to calculate all distinct angles involving one atom from GROUPA "
106 : "and two atoms from GROUPB. The atom from GROUPA is the central atom.");
107 8 : keys.add("atoms-3","GROUPC","This must be used in conjunction with GROUPA and GROUPB. All angles "
108 : "involving one atom from GROUPA, one atom from GROUPB and one atom from "
109 : "GROUPC are calculated. The GROUPA atoms are assumed to be the central "
110 : "atoms");
111 8 : keys.add("optional","SWITCH","the switching function specifies that only those bonds that have a length that is less than a certain threshold are considered");
112 4 : MultiColvarShortcuts::shortcutKeywords( keys );
113 4 : keys.needsAction("ANGLE");
114 4 : keys.needsAction("COORD_ANGLES");
115 4 : }
116 :
117 1 : Angles::Angles(const ActionOptions&ao):
118 : Action(ao),
119 1 : ActionShortcut(ao) {
120 : std::string swit;
121 2 : parse("SWITCH",swit);
122 1 : if( swit.length()>0 ) {
123 : std::string cat, grp;
124 0 : parse("GROUPA",cat);
125 0 : parse("GROUPB",grp);
126 0 : if( cat.length()==0 || grp.length()==0 ) {
127 0 : error("must use GROUPA/GROUPB when using SWITCH");
128 : }
129 0 : readInputLine( getShortcutLabel() + ": COORD_ANGLES SWITCH={" + swit + "} CATOMS=" + cat + " GROUP=" + grp + " " + convertInputLineToString() );
130 : return;
131 : }
132 : std::vector<std::string> group;
133 2 : parseVector("GROUP",group);
134 : std::vector<std::string> groupa;
135 2 : parseVector("GROUPA",groupa);
136 : std::vector<std::string> groupb;
137 2 : parseVector("GROUPB",groupb);
138 : std::vector<std::string> groupc;
139 2 : parseVector("GROUPC",groupc);
140 1 : if( group.size()>0 ) {
141 0 : if( groupa.size()>0 || groupb.size()>0 || groupc.size()>0 ) {
142 0 : error("should only be GROUP keyword in input not GROUPA/GROUPB/GROUPC");
143 : }
144 0 : Tools::interpretRanges( group );
145 0 : std::string ainput = getShortcutLabel() + ": ANGLE";
146 0 : unsigned n=1;
147 : // Not sure if this triple sum makes any sense
148 0 : for(unsigned i=2; i<group.size(); ++i ) {
149 0 : for(unsigned j=1; j<i; ++j ) {
150 0 : for(unsigned k=0; k<j; ++k) {
151 : std::string str_n;
152 0 : Tools::convert( n, str_n );
153 0 : ainput += " ATOMS" + str_n + "=" + group[i] + "," + group[j] + "," + group[k];
154 0 : n++;
155 : }
156 : }
157 : }
158 0 : readInputLine( ainput );
159 1 : } else if( groupc.size()>0 ) {
160 0 : Tools::interpretRanges( groupa );
161 0 : Tools::interpretRanges( groupb );
162 0 : Tools::interpretRanges( groupc );
163 0 : unsigned n=1;
164 0 : std::string ainput = getShortcutLabel() + ": ANGLE";
165 0 : for(unsigned i=0; i<groupa.size(); ++i ) {
166 0 : for(unsigned j=0; j<groupb.size(); ++j ) {
167 0 : for(unsigned k=0; k<groupc.size(); ++k) {
168 : std::string str_n;
169 0 : Tools::convert( n, str_n );
170 0 : ainput += " ATOMS" + str_n + "=" + groupb[j] + "," + groupa[i] + "," + groupc[k];
171 0 : n++;
172 : }
173 : }
174 : }
175 0 : readInputLine( ainput );
176 1 : } else if( groupa.size()>0 ) {
177 1 : Tools::interpretRanges( groupa );
178 1 : Tools::interpretRanges( groupb );
179 1 : unsigned n=1;
180 : std::string ainput;
181 1 : ainput = getShortcutLabel() + ": ANGLE";
182 2 : for(unsigned i=0; i<groupa.size(); ++i ) {
183 9 : for(unsigned j=1; j<groupb.size(); ++j ) {
184 44 : for(unsigned k=0; k<j; ++k) {
185 : std::string str_n;
186 36 : Tools::convert( n, str_n );
187 72 : ainput += " ATOMS" + str_n + "=" + groupb[j] + "," + groupa[i] + "," + groupb[k];
188 36 : n++;
189 : }
190 : }
191 : }
192 1 : readInputLine( ainput );
193 : }
194 1 : MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this );
195 1 : }
196 :
197 : }
198 : }
199 :
200 :
201 :
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