Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2019 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 "MultiColvarBase.h"
23 : #include "AtomValuePack.h"
24 : #include "core/ActionRegister.h"
25 :
26 : #include <string>
27 : #include <cmath>
28 :
29 : using namespace std;
30 :
31 : namespace PLMD {
32 : namespace multicolvar {
33 :
34 : //+PLUMEDOC MCOLVAR XDISTANCES
35 : /*
36 : Calculate the x components of the vectors connecting one or many pairs of atoms.
37 : You can then calculate functions of the distribution of
38 : values such as the minimum, the number less than a certain quantity and so on.
39 :
40 : \par Examples
41 :
42 : The following input tells plumed to calculate the x-component of the vector connecting atom 3 to atom 5 and
43 : the x-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
44 : printed
45 : \plumedfile
46 : XDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
47 : PRINT ARG=d1.min
48 : \endplumedfile
49 : (See also \ref PRINT).
50 :
51 :
52 : The following input tells plumed to calculate the x-component of the vector connecting atom 3 to atom 5 and
53 : the x-component of the vector connecting atom 1 to atom 2. The number of values that are
54 : less than 0.1nm is then printed to a file.
55 : \plumedfile
56 : XDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
57 : PRINT ARG=d1.lt0.1
58 : \endplumedfile
59 : (See also \ref PRINT \ref switchingfunction).
60 :
61 : The following input tells plumed to calculate the x-components of all the distinct vectors that can be created
62 : between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
63 : The average of these quantities is then calculated.
64 : \plumedfile
65 : XDISTANCES GROUP=1-3 AVERAGE LABEL=d1
66 : PRINT ARG=d1.average
67 : \endplumedfile
68 : (See also \ref PRINT)
69 :
70 : The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
71 : In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
72 : more than 0.1 is then printed to a file.
73 : \plumedfile
74 : XDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
75 : PRINT ARG=d1.gt0.1
76 : \endplumedfile
77 : (See also \ref PRINT \ref switchingfunction)
78 : */
79 : //+ENDPLUMEDOC
80 :
81 : //+PLUMEDOC MCOLVAR YDISTANCES
82 : /*
83 : Calculate the y components of the vectors connecting one or many pairs of atoms.
84 : You can then calculate functions of the distribution of
85 : values such as the minimum, the number less than a certain quantity and so on.
86 :
87 : \par Examples
88 :
89 : The following input tells plumed to calculate the y-component of the vector connecting atom 3 to atom 5 and
90 : the y-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
91 : printed
92 : \plumedfile
93 : YDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
94 : PRINT ARG=d1.min
95 : \endplumedfile
96 : (See also \ref PRINT).
97 :
98 :
99 : The following input tells plumed to calculate the y-component of the vector connecting atom 3 to atom 5 and
100 : the y-component of the vector connecting atom 1 to atom 2. The number of values that are
101 : less than 0.1nm is then printed to a file.
102 : \plumedfile
103 : YDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
104 : PRINT ARG=d1.lt0.1
105 : \endplumedfile
106 : (See also \ref PRINT \ref switchingfunction).
107 :
108 : The following input tells plumed to calculate the y-components of all the distinct vectors that can be created
109 : between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
110 : The average of these quantities is then calculated.
111 : \plumedfile
112 : YDISTANCES GROUP=1-3 AVERAGE LABEL=d1
113 : PRINT ARG=d1.average
114 : \endplumedfile
115 : (See also \ref PRINT)
116 :
117 : The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
118 : In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
119 : more than 0.1 is then printed to a file.
120 : \plumedfile
121 : YDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
122 : PRINT ARG=d1.gt0.1
123 : \endplumedfile
124 : (See also \ref PRINT \ref switchingfunction)
125 :
126 : */
127 : //+ENDPLUMEDOC
128 :
129 : //+PLUMEDOC MCOLVAR ZDISTANCES
130 : /*
131 : Calculate the z components of the vectors connecting one or many pairs of atoms.
132 : You can then calculate functions of the distribution of
133 : values such as the minimum, the number less than a certain quantity and so on.
134 :
135 : \par Examples
136 :
137 : The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and
138 : the z-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
139 : printed
140 : \plumedfile
141 : ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
142 : PRINT ARG=d1.min
143 : \endplumedfile
144 : (See also \ref PRINT).
145 :
146 :
147 : The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and
148 : the z-component of the vector connecting atom 1 to atom 2. The number of values that are
149 : less than 0.1nm is then printed to a file.
150 : \plumedfile
151 : ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
152 : PRINT ARG=d1.lt0.1
153 : \endplumedfile
154 : (See also \ref PRINT \ref switchingfunction).
155 :
156 : The following input tells plumed to calculate the z-components of all the distinct vectors that can be created
157 : between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
158 : The average of these quantities is then calculated.
159 : \plumedfile
160 : ZDISTANCES GROUP=1-3 AVERAGE LABEL=d1
161 : PRINT ARG=d1.average
162 : \endplumedfile
163 : (See also \ref PRINT)
164 :
165 : The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
166 : In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
167 : more than 0.1 is then printed to a file.
168 : \plumedfile
169 : ZDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
170 : PRINT ARG=d1.gt0.1
171 : \endplumedfile
172 : (See also \ref PRINT \ref switchingfunction)
173 :
174 : */
175 : //+ENDPLUMEDOC
176 :
177 :
178 0 : class XDistances : public MultiColvarBase {
179 : private:
180 : unsigned myc;
181 : public:
182 : static void registerKeywords( Keywords& keys );
183 : explicit XDistances(const ActionOptions&);
184 : // active methods:
185 : virtual double compute( const unsigned& tindex, AtomValuePack& myatoms ) const ;
186 : /// Returns the number of coordinates of the field
187 0 : bool isPeriodic() { return false; }
188 : };
189 :
190 6452 : PLUMED_REGISTER_ACTION(XDistances,"XDISTANCES")
191 6452 : PLUMED_REGISTER_ACTION(XDistances,"YDISTANCES")
192 6452 : PLUMED_REGISTER_ACTION(XDistances,"ZDISTANCES")
193 :
194 3 : void XDistances::registerKeywords( Keywords& keys ) {
195 3 : MultiColvarBase::registerKeywords( keys );
196 9 : keys.use("MAX"); keys.use("ALT_MIN");
197 12 : keys.use("MEAN"); keys.use("MIN"); keys.use("LESS_THAN");
198 9 : keys.use("LOWEST"); keys.use("HIGHEST");
199 15 : keys.use("MORE_THAN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
200 12 : keys.add("numbered","ATOMS","the atoms involved in each of the distances you wish to calculate. "
201 : "Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one distance will be "
202 : "calculated for each ATOM keyword you specify (all ATOM keywords should "
203 : "specify the indices of two atoms). The eventual number of quantities calculated by this "
204 : "action will depend on what functions of the distribution you choose to calculate.");
205 9 : keys.reset_style("ATOMS","atoms");
206 12 : keys.add("atoms-1","GROUP","Calculate the distance between each distinct pair of atoms in the group");
207 12 : keys.add("atoms-2","GROUPA","Calculate the distances between all the atoms in GROUPA and all "
208 : "the atoms in GROUPB. This must be used in conjuction with GROUPB.");
209 12 : keys.add("atoms-2","GROUPB","Calculate the distances between all the atoms in GROUPA and all the atoms "
210 : "in GROUPB. This must be used in conjuction with GROUPA.");
211 3 : }
212 :
213 0 : XDistances::XDistances(const ActionOptions&ao):
214 : Action(ao),
215 0 : MultiColvarBase(ao)
216 : {
217 0 : if( getName().find("X")!=std::string::npos) myc=0;
218 0 : else if( getName().find("Y")!=std::string::npos) myc=1;
219 0 : else if( getName().find("Z")!=std::string::npos) myc=2;
220 0 : else plumed_error();
221 :
222 : // Read in the atoms
223 : std::vector<AtomNumber> all_atoms;
224 0 : readTwoGroups( "GROUP", "GROUPA", "GROUPB", all_atoms );
225 0 : if( atom_lab.size()==0 ) readAtomsLikeKeyword( "ATOMS", 2, all_atoms );
226 0 : setupMultiColvarBase( all_atoms );
227 : // And check everything has been read in correctly
228 0 : checkRead();
229 0 : }
230 :
231 0 : double XDistances::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
232 0 : Vector distance;
233 0 : distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
234 0 : const double value=distance[myc];
235 :
236 0 : Vector myvec; myvec.zero();
237 : // And finish the calculation
238 0 : myvec[myc]=+1; addAtomDerivatives( 1, 1, myvec, myatoms );
239 0 : myvec[myc]=-1; addAtomDerivatives( 1, 0, myvec, myatoms );
240 0 : myatoms.addBoxDerivatives( 1, Tensor(distance,myvec) );
241 0 : return value;
242 : }
243 :
244 : }
245 4839 : }
246 :
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