Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2023 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 "Colvar.h"
23 : #include "ColvarShortcut.h"
24 : #include "core/ActionRegister.h"
25 : #include "MultiColvarTemplate.h"
26 : #include "tools/Pbc.h"
27 :
28 : //+PLUMEDOC MCOLVAR CHARGE
29 : /*
30 : Get the charges of one or multiple atoms
31 :
32 : The following example shows how you can print the charge of atom one:
33 :
34 : ```plumed
35 : q: CHARGE ATOM=1
36 : PRINT ARG=q FILE=colvar
37 : ```
38 :
39 : If you want to output the charges of multiple atoms you would use an input similar to the one below:
40 :
41 : ```plumed
42 : q: CHARGE ATOMS=1-10
43 : PRINT ARG=q FILE=colvar
44 : ```
45 :
46 : This input outputs a 10 dimensional vector that contains the charges of the first 10 atoms.
47 :
48 : */
49 : //+ENDPLUMEDOC
50 :
51 : //+PLUMEDOC MCOLVAR CHARGE_SCALAR
52 : /*
53 : Get the charges of one or multiple atoms
54 :
55 : \par Examples
56 :
57 : */
58 : //+ENDPLUMEDOC
59 :
60 : //+PLUMEDOC MCOLVAR CHARGE_VECTOR
61 : /*
62 : Get the charges of one or multiple atoms
63 :
64 : \par Examples
65 :
66 : */
67 : //+ENDPLUMEDOC
68 :
69 : //+PLUMEDOC MCOLVAR MASS
70 : /*
71 : Get the mass of one or multiple atoms
72 :
73 : The following example shows how you can print the mass of atom one:
74 :
75 : ```plumed
76 : m: MASS ATOM=1
77 : PRINT ARG=m FILE=colvar
78 : ```
79 :
80 : If you want to output the masses of multiple atoms you would use an input similar to the one below:
81 :
82 : ```plumed
83 : m: MASS ATOMS=1-10
84 : PRINT ARG=m FILE=colvar
85 : ```
86 :
87 : This input outputs a 10 dimensional vector that contains the masses of the first 10 atoms.
88 :
89 : */
90 : //+ENDPLUMEDOC
91 :
92 : //+PLUMEDOC MCOLVAR MASS_SCALAR
93 : /*
94 : Get the mass of one or multiple atoms
95 :
96 : \par Examples
97 :
98 : */
99 : //+ENDPLUMEDOC
100 :
101 : //+PLUMEDOC MCOLVAR MASS_VECTOR
102 : /*
103 : Get the mass of one or multiple atoms
104 :
105 : \par Examples
106 :
107 : */
108 : //+ENDPLUMEDOC
109 :
110 : namespace PLMD {
111 : namespace colvar {
112 :
113 : class SelectMassCharge : public Colvar {
114 : public:
115 : static void registerKeywords( Keywords& keys );
116 : explicit SelectMassCharge(const ActionOptions&);
117 : static void parseAtomList( const int& num, std::vector<AtomNumber>& t, ActionAtomistic* aa );
118 : static unsigned getModeAndSetupValues( ActionWithValue* av );
119 : // active methods:
120 : void calculate() override;
121 : static void calculateCV( const unsigned& mode, const std::vector<double>& masses, const std::vector<double>& charges,
122 : const std::vector<Vector>& pos, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
123 : std::vector<Tensor>& virial, const ActionAtomistic* aa );
124 : };
125 :
126 : typedef ColvarShortcut<SelectMassCharge> MQShortcut;
127 : PLUMED_REGISTER_ACTION(MQShortcut,"MASS")
128 : PLUMED_REGISTER_ACTION(MQShortcut,"CHARGE")
129 : PLUMED_REGISTER_ACTION(SelectMassCharge,"MASS_SCALAR")
130 : PLUMED_REGISTER_ACTION(SelectMassCharge,"CHARGE_SCALAR")
131 : typedef MultiColvarTemplate<SelectMassCharge> MQMulti;
132 : PLUMED_REGISTER_ACTION(MQMulti,"MASS_VECTOR")
133 : PLUMED_REGISTER_ACTION(MQMulti,"CHARGE_VECTOR")
134 :
135 84 : void SelectMassCharge::registerKeywords( Keywords& keys ) {
136 84 : Colvar::registerKeywords( keys );
137 84 : keys.add("atoms","ATOM","the atom number");
138 84 : keys.add("atoms","ATOMS","the atom numbers that you would like to store the masses and charges of");
139 84 : keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log");
140 84 : std::string acname = keys.getDisplayName();
141 84 : std::size_t und = acname.find("_SCALAR");
142 84 : if( und==std::string::npos ) {
143 80 : und = acname.find("_VECTOR");
144 : }
145 84 : keys.setDisplayName( acname.substr(0,und) );
146 168 : keys.setValueDescription("scalar/vector","the " + keys.getDisplayName() + " of the atom");
147 84 : }
148 :
149 0 : SelectMassCharge::SelectMassCharge(const ActionOptions&ao):
150 0 : PLUMED_COLVAR_INIT(ao) {
151 : std::vector<AtomNumber> atoms;
152 0 : parseAtomList(-1,atoms,this);
153 0 : unsigned mode=getModeAndSetupValues(this);
154 0 : requestAtoms(atoms);
155 0 : }
156 :
157 0 : void SelectMassCharge::parseAtomList( const int& num, std::vector<AtomNumber>& t, ActionAtomistic* aa ) {
158 0 : aa->parseAtomList("ATOM",num,t);
159 0 : if( t.size()==1 ) {
160 0 : aa->log.printf(" for atom %d\n",t[0].serial());
161 0 : } else if( num<0 || t.size()!=0 ) {
162 0 : aa->error("Number of specified atoms should be 1");
163 : }
164 0 : }
165 :
166 18 : unsigned SelectMassCharge::getModeAndSetupValues( ActionWithValue* av ) {
167 18 : av->addValueWithDerivatives();
168 18 : av->setNotPeriodic();
169 : bool constant=true;
170 18 : ActionAtomistic* aa=dynamic_cast<ActionAtomistic*>( av );
171 18 : plumed_assert( aa );
172 5162 : for(unsigned i=0; i<aa->getNumberOfAtoms(); ++i) {
173 5144 : std::pair<std::size_t,std::size_t> p = aa->getValueIndices( aa->getAbsoluteIndex(i) );
174 5144 : if( av->getName().find("MASS")!=std::string::npos && !aa->masv[p.first]->isConstant() ) {
175 : constant=false;
176 : }
177 5144 : if( av->getName().find("CHARGE")!=std::string::npos && !aa->chargev[p.first]->isConstant() ) {
178 : constant=false;
179 : }
180 : }
181 18 : if( !constant ) {
182 0 : av->error("cannot deal with non-constant " + av->getName() + " values");
183 : }
184 18 : (av->copyOutput(0))->setConstant();
185 18 : return 0;
186 : }
187 :
188 : // calculator
189 0 : void SelectMassCharge::calculate() {
190 0 : std::vector<double> masses(1), charges(1), vals(1);
191 : std::vector<Vector> pos;
192 : std::vector<std::vector<Vector> > derivs;
193 : std::vector<Tensor> virial;
194 0 : calculateCV( 0, masses, charges, pos, vals, derivs, virial, this );
195 0 : setValue( vals[0] );
196 0 : }
197 :
198 5144 : void SelectMassCharge::calculateCV( const unsigned& mode, const std::vector<double>& masses, const std::vector<double>& charges,
199 : const std::vector<Vector>& pos, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
200 : std::vector<Tensor>& virial, const ActionAtomistic* aa ) {
201 5144 : if( aa->getName().find("MASSES")!=std::string::npos ) {
202 0 : vals[0]=masses[0];
203 5144 : } else if( aa->chargesWereSet ) {
204 5144 : vals[0]=charges[0];
205 : }
206 5144 : }
207 :
208 : }
209 : }
210 :
211 :
212 :
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