Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2016-2023 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 "MultiColvarBase.h"
23 : #include "AtomValuePack.h"
24 : #include "core/ActionRegister.h"
25 : #include "tools/Torsion.h"
26 : #include "tools/SwitchingFunction.h"
27 :
28 : #include <string>
29 : #include <cmath>
30 :
31 : namespace PLMD {
32 : namespace multicolvar {
33 :
34 : //+PLUMEDOC MCOLVAR XYTORSIONS
35 : /*
36 : Calculate the torsional angle around the x axis from the positive y direction.
37 :
38 : \par Examples
39 :
40 : 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
41 : the angle around the x direction between the positive y axis and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
42 : \plumedfile
43 : d1: XYTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
44 : PRINT ARG=d1.between
45 : \endplumedfile
46 : (See also \ref PRINT).
47 : */
48 : //+ENDPLUMEDOC
49 :
50 : //+PLUMEDOC MCOLVAR XZTORSIONS
51 : /*
52 : Calculate the torsional angle around the x axis from the positive z direction.
53 :
54 : \par Examples
55 :
56 : 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
57 : the angle around the x direction between the positive z direction and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
58 : \plumedfile
59 : d1: XZTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
60 : PRINT ARG=d1.*
61 : \endplumedfile
62 : (See also \ref PRINT).
63 : */
64 : //+ENDPLUMEDOC
65 :
66 : //+PLUMEDOC MCOLVAR YXTORSIONS
67 : /*
68 : Calculate the torsional angle around the y axis from the positive x direction.
69 :
70 : \par Examples
71 :
72 : The following input tells plumed to calculate the angle around the y direction between the positive x-direction and the vector connecting atom 3 to atom 5 and
73 : the angle around the y direction between the positive x axis and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
74 : \plumedfile
75 : d1: YXTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
76 : PRINT ARG=d1.*
77 : \endplumedfile
78 : (See also \ref PRINT).
79 : */
80 : //+ENDPLUMEDOC
81 :
82 : //+PLUMEDOC MCOLVAR YZTORSIONS
83 : /*
84 : Calculate the torsional angle around the y axis from the positive z direction.
85 :
86 : \par Examples
87 :
88 : The following input tells plumed to calculate the angle around the y direction between the positive z-direction and the vector connecting atom 3 to atom 5 and
89 : the angle around the y direction between the positive z direction and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
90 : \plumedfile
91 : d1: YZTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
92 : PRINT ARG=d1.*
93 : \endplumedfile
94 : (See also \ref PRINT).
95 : */
96 : //+ENDPLUMEDOC
97 :
98 : //+PLUMEDOC MCOLVAR ZXTORSIONS
99 : /*
100 : Calculate the torsional angle around the z axis from the positive x direction.
101 :
102 : \par Examples
103 :
104 : The following input tells plumed to calculate the angle around the z direction between the positive x-direction and the vector connecting atom 3 to atom 5 and
105 : the angle around the z direction between the positive x-direction and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
106 : \plumedfile
107 : d1: ZXTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
108 : PRINT ARG=d1.*
109 : \endplumedfile
110 : (See also \ref PRINT).
111 : */
112 : //+ENDPLUMEDOC
113 :
114 : //+PLUMEDOC MCOLVAR ZYTORSIONS
115 : /*
116 : Calculate the torsional angle around the z axis from the positive y direction.
117 :
118 : \par Examples
119 :
120 : 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
121 : the angle around the z direction between the positive y axis and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
122 : \plumedfile
123 : d1: ZYTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
124 : PRINT ARG=d1.*
125 : \endplumedfile
126 : (See also \ref PRINT).
127 : */
128 : //+ENDPLUMEDOC
129 :
130 :
131 :
132 :
133 : class XYTorsion : public MultiColvarBase {
134 : private:
135 : bool use_sf;
136 : unsigned myc1, myc2;
137 : SwitchingFunction sf1;
138 : public:
139 : static void registerKeywords( Keywords& keys );
140 : explicit XYTorsion(const ActionOptions&);
141 : // active methods:
142 : double compute( const unsigned& tindex, AtomValuePack& myatoms ) const override;
143 : double calculateWeight( const unsigned& taskCode, const double& weight, AtomValuePack& ) const override;
144 : /// Returns the number of coordinates of the field
145 3 : bool isPeriodic() override { return true; }
146 1 : void retrieveDomain( std::string& min, std::string& max) override { min="-pi"; max="pi"; }
147 : };
148 :
149 10419 : PLUMED_REGISTER_ACTION(XYTorsion,"XYTORSIONS")
150 10419 : PLUMED_REGISTER_ACTION(XYTorsion,"XZTORSIONS")
151 10419 : PLUMED_REGISTER_ACTION(XYTorsion,"YXTORSIONS")
152 10419 : PLUMED_REGISTER_ACTION(XYTorsion,"YZTORSIONS")
153 10423 : PLUMED_REGISTER_ACTION(XYTorsion,"ZXTORSIONS")
154 10421 : PLUMED_REGISTER_ACTION(XYTorsion,"ZYTORSIONS")
155 :
156 9 : void XYTorsion::registerKeywords( Keywords& keys ) {
157 9 : MultiColvarBase::registerKeywords( keys );
158 18 : keys.use("MAX"); keys.use("ALT_MIN");
159 18 : keys.use("MEAN"); keys.use("MIN");
160 18 : keys.use("LOWEST"); keys.use("HIGHEST");
161 27 : keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
162 18 : keys.add("numbered","ATOMS","the atoms involved in each of the torsion angles you wish to calculate. "
163 : "Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one torsion will be "
164 : "calculated for each ATOM keyword you specify (all ATOM keywords should "
165 : "specify the indices of two atoms). The eventual number of quantities calculated by this "
166 : "action will depend on what functions of the distribution you choose to calculate.");
167 18 : keys.reset_style("ATOMS","atoms");
168 18 : keys.add("atoms-1","GROUP","Calculate the distance between each distinct pair of atoms in the group");
169 18 : keys.add("atoms-2","GROUPA","Calculate the distances between all the atoms in GROUPA and all "
170 : "the atoms in GROUPB. This must be used in conjunction with GROUPB.");
171 18 : keys.add("atoms-2","GROUPB","Calculate the distances between all the atoms in GROUPA and all the atoms "
172 : "in GROUPB. This must be used in conjunction with GROUPA.");
173 18 : keys.add("optional","SWITCH","A switching function that ensures that only angles are only computed when atoms are within "
174 : "are within a certain fixed cutoff. The following provides information on the \\ref switchingfunction that are available.");
175 9 : }
176 :
177 3 : XYTorsion::XYTorsion(const ActionOptions&ao):
178 : Action(ao),
179 : MultiColvarBase(ao),
180 3 : use_sf(false)
181 : {
182 3 : if( getName().find("XY")!=std::string::npos) { myc1=0; myc2=1; }
183 3 : else if( getName().find("XZ")!=std::string::npos) { myc1=0; myc2=2; }
184 3 : else if( getName().find("YX")!=std::string::npos) { myc1=1; myc2=0; }
185 3 : else if( getName().find("YZ")!=std::string::npos) { myc1=1; myc2=2; }
186 3 : else if( getName().find("ZX")!=std::string::npos) { myc1=2; myc2=0; }
187 1 : else if( getName().find("ZY")!=std::string::npos) { myc1=2; myc2=1; }
188 0 : else plumed_error();
189 :
190 : // Read in switching function
191 6 : std::string sfinput, errors; parse("SWITCH",sfinput);
192 3 : if( sfinput.length()>0 ) {
193 2 : use_sf=true; weightHasDerivatives=true;
194 2 : sf1.set(sfinput,errors);
195 2 : if( errors.length()!=0 ) error("problem reading SWITCH keyword : " + errors );
196 2 : log.printf(" only calculating angles for atoms separated by less than %s\n", sf1.description().c_str() );
197 2 : setLinkCellCutoff( sf1.get_dmax() );
198 : }
199 :
200 : // Read in the atoms
201 : std::vector<AtomNumber> all_atoms;
202 6 : readTwoGroups( "GROUP", "GROUPA", "GROUPB", all_atoms );
203 4 : if( atom_lab.size()==0 ) readAtomsLikeKeyword( "ATOMS", 2, all_atoms );
204 3 : setupMultiColvarBase( all_atoms );
205 : // And check everything has been read in correctly
206 3 : checkRead();
207 3 : }
208 :
209 110 : double XYTorsion::calculateWeight( const unsigned& taskCode, const double& weight, AtomValuePack& myatoms ) const {
210 110 : if(!use_sf) return 1.0;
211 :
212 100 : Vector distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
213 100 : double dw, w = sf1.calculateSqr( distance.modulo2(), dw );
214 100 : addAtomDerivatives( 0, 0, (-dw)*distance, myatoms );
215 100 : addAtomDerivatives( 0, 1, (+dw)*distance, myatoms );
216 100 : myatoms.addBoxDerivatives( 0, (-dw)*Tensor(distance,distance) );
217 100 : return w;
218 : }
219 :
220 50 : double XYTorsion::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
221 50 : Vector dd0, dd1, dd2, axis, rot, distance;
222 50 : axis.zero(); rot.zero(); rot[myc1]=1; axis[myc2]=1;
223 50 : distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
224 50 : PLMD::Torsion t; double torsion=t.compute( distance, rot, axis, dd0, dd1, dd2 );
225 :
226 50 : addAtomDerivatives( 1, 0, -dd0, myatoms );
227 50 : addAtomDerivatives( 1, 1, dd0, myatoms );
228 50 : myatoms.addBoxDerivatives( 1, -extProduct(distance,dd0) );
229 50 : return torsion;
230 : }
231 :
232 : }
233 : }
234 :
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