Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2023 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/ActionSetup.h"
23 : #include "core/ActionRegister.h"
24 : #include "core/PlumedMain.h"
25 : #include "core/Atoms.h"
26 : #include "tools/Exception.h"
27 :
28 : namespace PLMD {
29 : namespace setup {
30 :
31 : //+PLUMEDOC GENERIC UNITS
32 : /*
33 : This command sets the internal units for the code.
34 :
35 : A new unit can be set by either
36 : specifying a conversion factor from the plumed default unit or by using a string
37 : corresponding to one of the defined units given below. This directive MUST
38 : appear at the BEGINNING of the plumed.dat file. The same units must be used
39 : throughout the plumed.dat file.
40 :
41 : Notice that all input/output will then be made using the specified units.
42 : That is: all the input parameters, all the output files, etc. The only
43 : exceptions are file formats for which there is a specific convention concerning
44 : the units. For example, trajectories written in .gro format (with \ref DUMPATOMS)
45 : are going to be always in nm.
46 :
47 : The following strings can be used to specify units. Note that the strings are
48 : case sensitive.
49 : - LENGTH: nm (default), A (for Angstrom), um (for micrometer), Bohr (0.052917721067 nm)
50 : - ENERGY: kj/mol (default), j/mol, kcal/mol (4.184 kj/mol), eV (96.48530749925792 kj/mol), Ha (for Hartree, 2625.499638 kj/mol)
51 : - TIME: ps (default), fs, ns, atomic (2.418884326509e-5 ps)
52 : - MASS: amu (default)
53 : - CHARGE: e (default)
54 :
55 :
56 : \par Examples
57 :
58 : \plumedfile
59 : # this is using Angstrom - kj/mol - fs
60 : UNITS LENGTH=A TIME=fs
61 :
62 : # compute distance between atoms 1 and 4
63 : d: DISTANCE ATOMS=1,4
64 :
65 : # print time and distance on a COLVAR file
66 : PRINT ARG=d FILE=COLVAR
67 :
68 : # dump atoms 1 to 100 on a 'out.gro' file
69 : DUMPATOMS FILE=out.gro STRIDE=10 ATOMS=1-100
70 :
71 : # dump atoms 1 to 100 on a 'out.xyz' file
72 : DUMPATOMS FILE=out.xyz STRIDE=10 ATOMS=1-100
73 : \endplumedfile
74 :
75 : In the `COLVAR` file, time and distance will appear in fs and A respectively, *irrespective* of which units
76 : you are using in the host MD code. The coordinates in the `out.gro` file will be expressed in nm,
77 : since `gro` files are by convention written in nm. The coordinates in the `out.xyz` file
78 : will be written in Angstrom *since we used the UNITS command setting Angstrom units*.
79 : Indeed, within PLUMED xyz files are using internal PLUMED units and not necessarily Angstrom!
80 :
81 : If a number, x, is found instead of a string, the new unit is equal to x times the default units.
82 : Using the following command as first line of the previous example would have lead to an identical result:
83 : \plumedfile
84 : UNITS LENGTH=0.1 TIME=0.001
85 : \endplumedfile
86 :
87 : */
88 : //+ENDPLUMEDOC
89 :
90 : class Units :
91 : public virtual ActionSetup
92 : {
93 : public:
94 : static void registerKeywords( Keywords& keys );
95 : explicit Units(const ActionOptions&ao);
96 : };
97 :
98 10457 : PLUMED_REGISTER_ACTION(Units,"UNITS")
99 :
100 20 : void Units::registerKeywords( Keywords& keys ) {
101 20 : ActionSetup::registerKeywords(keys);
102 40 : keys.add("optional","LENGTH","the units of lengths. Either specify a conversion factor from the default, nm, or use one of the defined units, A (for angstroms), um (for micrometer), and Bohr.");
103 40 : keys.add("optional","ENERGY","the units of energy. Either specify a conversion factor from the default, kj/mol, or use one of the defined units, j/mol, kcal/mol and Ha (for Hartree)");
104 40 : keys.add("optional","TIME","the units of time. Either specify a conversion factor from the default, ps, or use one of the defined units, ns, fs, and atomic");
105 40 : keys.add("optional","MASS","the units of masses. Specify a conversion factor from the default, amu");
106 40 : keys.add("optional","CHARGE","the units of charges. Specify a conversion factor from the default, e");
107 40 : keys.addFlag("NATURAL",false,"use natural units");
108 20 : }
109 :
110 19 : Units::Units(const ActionOptions&ao):
111 : Action(ao),
112 19 : ActionSetup(ao)
113 : {
114 19 : PLMD::Units u;
115 :
116 : std::string s;
117 :
118 : s="";
119 38 : parse("LENGTH",s);
120 19 : if(s.length()>0) u.setLength(s);
121 36 : if(u.getLengthString().length()>0 && u.getLengthString()=="nm") {
122 8 : log.printf(" length: %s\n",u.getLengthString().c_str());
123 : }
124 20 : else if(u.getLengthString().length()>0 && u.getLengthString()!="nm") {
125 9 : log.printf(" length: %s = %g nm\n",u.getLengthString().c_str(),u.getLength());
126 : }
127 : else {
128 2 : log.printf(" length: %g nm\n",u.getLength());
129 : }
130 :
131 : s="";
132 38 : parse("ENERGY",s);
133 19 : if(s.length()>0) u.setEnergy(s);
134 36 : if(u.getEnergyString().length()>0 && u.getEnergyString()=="kj/mol") {
135 12 : log.printf(" energy: %s\n",u.getEnergyString().c_str());
136 : }
137 12 : else if(u.getEnergyString().length()>0 && u.getEnergyString()!="kj/mol") {
138 5 : log.printf(" energy: %s = %g kj/mol\n",u.getEnergyString().c_str(),u.getEnergy());
139 : }
140 : else {
141 2 : log.printf(" energy: %g kj/mol\n",u.getEnergy());
142 : }
143 :
144 : s="";
145 38 : parse("TIME",s);
146 19 : if(s.length()>0) u.setTime(s);
147 36 : if(u.getTimeString().length()>0 && u.getTimeString()=="ps") {
148 14 : log.printf(" time: %s\n",u.getTimeString().c_str());
149 : }
150 8 : else if(u.getTimeString().length()>0 && u.getTimeString()!="ps") {
151 3 : log.printf(" time: %s = %g ps\n",u.getTimeString().c_str(),u.getTime());
152 : }
153 : else {
154 2 : log.printf(" time: %g ps\n",u.getTime());
155 : }
156 :
157 : s="";
158 38 : parse("CHARGE",s);
159 19 : if(s.length()>0) u.setCharge(s);
160 36 : if(u.getChargeString().length()>0 && u.getChargeString()=="e") {
161 17 : log.printf(" charge: %s\n",u.getChargeString().c_str());
162 : }
163 2 : else if(u.getChargeString().length()>0 && u.getChargeString()!="e") {
164 0 : log.printf(" charge: %s = %g e\n",u.getChargeString().c_str(),u.getCharge());
165 : }
166 : else {
167 2 : log.printf(" charge: %g e\n",u.getCharge());
168 : }
169 :
170 : s="";
171 38 : parse("MASS",s);
172 19 : if(s.length()>0) u.setMass(s);
173 37 : if(u.getMassString().length()>0 && u.getMassString()=="amu") {
174 18 : log.printf(" mass: %s\n",u.getMassString().c_str());
175 : }
176 1 : else if(u.getMassString().length()>0 && u.getMassString()!="amu") {
177 0 : log.printf(" mass: %s = %g amu\n",u.getMassString().c_str(),u.getMass());
178 : }
179 : else {
180 1 : log.printf(" mass: %g amu\n",u.getMass());
181 : }
182 :
183 19 : bool natural=false;
184 19 : parseFlag("NATURAL",natural);
185 19 : plumed.getAtoms().setNaturalUnits(natural);
186 :
187 19 : checkRead();
188 :
189 19 : plumed.getAtoms().setUnits(u);
190 19 : if(natural) {
191 6 : log.printf(" using natural units\n");
192 : } else {
193 13 : log.printf(" using physical units\n");
194 : }
195 19 : log.printf(" inside PLUMED, Boltzmann constant is %g\n",plumed.getAtoms().getKBoltzmann());
196 :
197 19 : plumed.getAtoms().updateUnits();
198 19 : }
199 :
200 : }
201 : }
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