Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2018 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 "MultiColvar.h"
23 : #include "core/ActionRegister.h"
24 :
25 : #include <string>
26 : #include <cmath>
27 :
28 : using namespace std;
29 :
30 : namespace PLMD {
31 : namespace multicolvar {
32 :
33 : //+PLUMEDOC MCOLVAR XDISTANCES
34 : /*
35 : Calculate the x components of the vectors connecting one or many pairs of atoms.
36 : You can then calculate functions of the distribution of
37 : values such as the minimum, the number less than a certain quantity and so on.
38 :
39 : \par Examples
40 :
41 : The following input tells plumed to calculate the x-component of the vector connecting atom 3 to atom 5 and
42 : the x-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
43 : printed
44 : \verbatim
45 : XDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
46 : PRINT ARG=d1.min
47 : \endverbatim
48 : (See also \ref PRINT).
49 :
50 :
51 : The following input tells plumed to calculate the x-component of the vector connecting atom 3 to atom 5 and
52 : the x-component of the vector connecting atom 1 to atom 2. The number of values that are
53 : less than 0.1nm is then printed to a file.
54 : \verbatim
55 : XDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
56 : PRINT ARG=d1.lt0.1
57 : \endverbatim
58 : (See also \ref PRINT \ref switchingfunction).
59 :
60 : The following input tells plumed to calculate the x-components of all the distinct vectors that can be created
61 : between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
62 : The average of these quantities is then calculated.
63 : \verbatim
64 : XDISTANCES GROUP=1-3 AVERAGE LABEL=d1
65 : PRINT ARG=d1.average
66 : \endverbatim
67 : (See also \ref PRINT)
68 :
69 : The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
70 : In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
71 : more than 0.1 is then printed to a file.
72 : \verbatim
73 : XDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
74 : PRINT ARG=d1.gt0.1
75 : \endverbatim
76 : (See also \ref PRINT \ref switchingfunction)
77 : */
78 : //+ENDPLUMEDOC
79 :
80 : //+PLUMEDOC MCOLVAR YDISTANCES
81 : /*
82 : Calculate the y components of the vectors connecting one or many pairs of atoms.
83 : You can then calculate functions of the distribution of
84 : values such as the minimum, the number less than a certain quantity and so on.
85 :
86 : \par Examples
87 :
88 : The following input tells plumed to calculate the y-component of the vector connecting atom 3 to atom 5 and
89 : the y-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
90 : printed
91 : \verbatim
92 : YDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
93 : PRINT ARG=d1.min
94 : \endverbatim
95 : (See also \ref PRINT).
96 :
97 :
98 : The following input tells plumed to calculate the y-component of the vector connecting atom 3 to atom 5 and
99 : the y-component of the vector connecting atom 1 to atom 2. The number of values that are
100 : less than 0.1nm is then printed to a file.
101 : \verbatim
102 : YDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
103 : PRINT ARG=d1.lt0.1
104 : \endverbatim
105 : (See also \ref PRINT \ref switchingfunction).
106 :
107 : The following input tells plumed to calculate the y-components of all the distinct vectors that can be created
108 : between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
109 : The average of these quantities is then calculated.
110 : \verbatim
111 : YDISTANCES GROUP=1-3 AVERAGE LABEL=d1
112 : PRINT ARG=d1.average
113 : \endverbatim
114 : (See also \ref PRINT)
115 :
116 : The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
117 : In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
118 : more than 0.1 is then printed to a file.
119 : \verbatim
120 : YDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
121 : PRINT ARG=d1.gt0.1
122 : \endverbatim
123 : (See also \ref PRINT \ref switchingfunction)
124 :
125 : */
126 : //+ENDPLUMEDOC
127 :
128 : //+PLUMEDOC MCOLVAR ZDISTANCES
129 : /*
130 : Calculate the z components of the vectors connecting one or many pairs of atoms.
131 : You can then calculate functions of the distribution of
132 : values such as the minimum, the number less than a certain quantity and so on.
133 :
134 : \par Examples
135 :
136 : The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and
137 : the z-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
138 : printed
139 : \verbatim
140 : ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
141 : PRINT ARG=d1.min
142 : \endverbatim
143 : (See also \ref PRINT).
144 :
145 :
146 : The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and
147 : the z-component of the vector connecting atom 1 to atom 2. The number of values that are
148 : less than 0.1nm is then printed to a file.
149 : \verbatim
150 : ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
151 : PRINT ARG=d1.lt0.1
152 : \endverbatim
153 : (See also \ref PRINT \ref switchingfunction).
154 :
155 : The following input tells plumed to calculate the z-components of all the distinct vectors that can be created
156 : between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
157 : The average of these quantities is then calculated.
158 : \verbatim
159 : ZDISTANCES GROUP=1-3 AVERAGE LABEL=d1
160 : PRINT ARG=d1.average
161 : \endverbatim
162 : (See also \ref PRINT)
163 :
164 : The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
165 : In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
166 : more than 0.1 is then printed to a file.
167 : \verbatim
168 : ZDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
169 : PRINT ARG=d1.gt0.1
170 : \endverbatim
171 : (See also \ref PRINT \ref switchingfunction)
172 :
173 : */
174 : //+ENDPLUMEDOC
175 :
176 :
177 0 : class XDistances : public MultiColvar {
178 : private:
179 : unsigned myc;
180 : public:
181 : static void registerKeywords( Keywords& keys );
182 : explicit XDistances(const ActionOptions&);
183 : // active methods:
184 : virtual double compute( const unsigned& tindex, AtomValuePack& myatoms ) const ;
185 : /// Returns the number of coordinates of the field
186 0 : bool isPeriodic() { return false; }
187 : };
188 :
189 2523 : PLUMED_REGISTER_ACTION(XDistances,"XDISTANCES")
190 2523 : PLUMED_REGISTER_ACTION(XDistances,"YDISTANCES")
191 2523 : PLUMED_REGISTER_ACTION(XDistances,"ZDISTANCES")
192 :
193 3 : void XDistances::registerKeywords( Keywords& keys ) {
194 3 : MultiColvar::registerKeywords( keys );
195 3 : keys.use("ATOMS"); keys.use("MAX"); keys.use("ALT_MIN");
196 3 : keys.use("MEAN"); keys.use("MIN"); keys.use("LESS_THAN");
197 3 : keys.use("LOWEST"); keys.use("HIGHEST");
198 3 : keys.use("MORE_THAN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
199 3 : keys.add("atoms-1","GROUP","Calculate the distance between each distinct pair of atoms in the group");
200 : keys.add("atoms-2","GROUPA","Calculate the distances between all the atoms in GROUPA and all "
201 3 : "the atoms in GROUPB. This must be used in conjuction with GROUPB.");
202 : keys.add("atoms-2","GROUPB","Calculate the distances between all the atoms in GROUPA and all the atoms "
203 3 : "in GROUPB. This must be used in conjuction with GROUPA.");
204 3 : }
205 :
206 0 : XDistances::XDistances(const ActionOptions&ao):
207 0 : PLUMED_MULTICOLVAR_INIT(ao)
208 : {
209 0 : if( getName().find("X")!=std::string::npos) myc=0;
210 0 : else if( getName().find("Y")!=std::string::npos) myc=1;
211 0 : else if( getName().find("Z")!=std::string::npos) myc=2;
212 0 : else plumed_error();
213 :
214 : // Read in the atoms
215 0 : std::vector<AtomNumber> all_atoms;
216 0 : readTwoGroups( "GROUP", "GROUPA", "GROUPB", all_atoms );
217 0 : int natoms=2; readAtoms( natoms, all_atoms );
218 : // And check everything has been read in correctly
219 0 : checkRead();
220 0 : }
221 :
222 0 : double XDistances::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
223 0 : Vector distance;
224 0 : distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
225 0 : const double value=distance[myc];
226 :
227 0 : Vector myvec; myvec.zero();
228 : // And finish the calculation
229 0 : myvec[myc]=+1; addAtomDerivatives( 1, 1, myvec, myatoms );
230 0 : myvec[myc]=-1; addAtomDerivatives( 1, 0, myvec, myatoms );
231 0 : myatoms.addBoxDerivatives( 1, Tensor(distance,myvec) );
232 0 : return value;
233 : }
234 :
235 : }
236 2523 : }
237 :
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