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 "tools/Exception.h"
26 :
27 : namespace PLMD {
28 : namespace setup {
29 :
30 : //+PLUMEDOC GENERIC UNITS
31 : /*
32 : This command sets the internal units for the code.
33 :
34 : The default units in the plumed input and output files are discussed [here](parsing.md). If you would like
35 : to use units that are different from these defaults you can use the UNITS command. This directive MUST
36 : appear at the BEGINNING of the plumed.dat file and same units must be used throughout the plumed.dat file.
37 :
38 : The following input demonstrates one way that you can use the UNITS command to change the units.
39 :
40 : ```plumed
41 : # this is using Angstrom - kj/mol - fs
42 : UNITS LENGTH=A TIME=fs
43 :
44 : # compute distance between atoms 1 and 4
45 : d: DISTANCE ATOMS=1,4
46 :
47 : # print time and distance on a COLVAR file
48 : # times and distances in this file will be in fs and A respectively
49 : PRINT ARG=d FILE=COLVAR
50 :
51 : # dump atoms 1 to 100 on a 'out.gro' file
52 : # The positions in the gro file here will be written
53 : # in nm because this is the convention for gro files.
54 : DUMPATOMS FILE=out.gro STRIDE=10 ATOMS=1-100
55 :
56 : # dump atoms 1 to 100 on a 'out.xyz' file
57 : # The position in the xyz file here will be written
58 : # in A as there is no conventional units for xyz files
59 : # and the plumed length units has been set to Angstroms.
60 : DUMPATOMS FILE=out.xyz STRIDE=10 ATOMS=1-100
61 : ```
62 :
63 : In the example input above strings are used to set the units. The following table details all the strings
64 : that can be used when setting units. Note that the strings are case sensitive.
65 :
66 : | Quantity | Default | Alternatives |
67 : |:---------|:--------|:-------------|
68 : | Length | nm | A (for Angstrom), um (for micrometer), Bohr (0.052917721067 nm) |
69 : | Energy | kj/mol | j/mol, kcal/mol (4.184 kj/mol), eV (96.48530749925792 kj/mol), Ha (for Hartree, 2625.499638 kj/mol) |
70 : | Time | ps | fs, ns, atomic (2.418884326509e-5 ps) |
71 : | Mass | amu | |
72 : | Charge | e | |
73 :
74 : If you want to use a unit that is not specified in the table above you can specify a factor for converting the default unit to
75 : your chosen unit. As an example of how this works in practice the example below converts lengths and times into A and fs by
76 : giving explicit values for the conversion factors.
77 :
78 : ```plumed
79 : UNITS LENGTH=0.1 TIME=0.001
80 : ```
81 :
82 : The input above tells PLUMED that lengths in nm should be divided by 0.1 so as to convert them to Anstroms. Times in ps
83 : should be divded by 0.001 to convert them from ps to fs.
84 :
85 : To reitterate, the default or the units specified in the UNITS command are used in all input and output
86 : files. The only exceptions are file formats for which there is a specific convention concerning
87 : the units. For example, trajectories written in .gro format (with [DUMPATOMS](DUMPATOMS.md)) will
88 : always in nm.
89 :
90 : */
91 : //+ENDPLUMEDOC
92 :
93 : class Units :
94 : public virtual ActionSetup {
95 : public:
96 : static void registerKeywords( Keywords& keys );
97 : explicit Units(const ActionOptions&ao);
98 : };
99 :
100 : PLUMED_REGISTER_ACTION(Units,"UNITS")
101 :
102 36 : void Units::registerKeywords( Keywords& keys ) {
103 36 : ActionSetup::registerKeywords(keys);
104 36 : 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.");
105 36 : 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)");
106 36 : 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");
107 36 : keys.add("optional","MASS","the units of masses. Specify a conversion factor from the default, amu");
108 36 : keys.add("optional","CHARGE","the units of charges. Specify a conversion factor from the default, e");
109 36 : keys.addFlag("NATURAL",false,"use natural units");
110 36 : }
111 :
112 34 : Units::Units(const ActionOptions&ao):
113 : Action(ao),
114 34 : ActionSetup(ao) {
115 34 : PLMD::Units u;
116 :
117 : std::string s;
118 :
119 : s="";
120 68 : parse("LENGTH",s);
121 34 : if(s.length()>0) {
122 26 : u.setLength(s);
123 : }
124 66 : if(u.getLengthString().length()>0 && u.getLengthString()=="nm") {
125 8 : log.printf(" length: %s\n",u.getLengthString().c_str());
126 50 : } else if(u.getLengthString().length()>0 && u.getLengthString()!="nm") {
127 24 : log.printf(" length: %s = %g nm\n",u.getLengthString().c_str(),u.getLength());
128 : } else {
129 2 : log.printf(" length: %g nm\n",u.getLength());
130 : }
131 :
132 : s="";
133 68 : parse("ENERGY",s);
134 34 : if(s.length()>0) {
135 13 : u.setEnergy(s);
136 : }
137 66 : if(u.getEnergyString().length()>0 && u.getEnergyString()=="kj/mol") {
138 21 : log.printf(" energy: %s\n",u.getEnergyString().c_str());
139 24 : } else if(u.getEnergyString().length()>0 && u.getEnergyString()!="kj/mol") {
140 11 : log.printf(" energy: %s = %g kj/mol\n",u.getEnergyString().c_str(),u.getEnergy());
141 : } else {
142 2 : log.printf(" energy: %g kj/mol\n",u.getEnergy());
143 : }
144 :
145 : s="";
146 68 : parse("TIME",s);
147 34 : if(s.length()>0) {
148 13 : u.setTime(s);
149 : }
150 66 : if(u.getTimeString().length()>0 && u.getTimeString()=="ps") {
151 29 : log.printf(" time: %s\n",u.getTimeString().c_str());
152 8 : } else if(u.getTimeString().length()>0 && u.getTimeString()!="ps") {
153 3 : log.printf(" time: %s = %g ps\n",u.getTimeString().c_str(),u.getTime());
154 : } else {
155 2 : log.printf(" time: %g ps\n",u.getTime());
156 : }
157 :
158 : s="";
159 68 : parse("CHARGE",s);
160 34 : if(s.length()>0) {
161 3 : u.setCharge(s);
162 : }
163 66 : if(u.getChargeString().length()>0 && u.getChargeString()=="e") {
164 32 : log.printf(" charge: %s\n",u.getChargeString().c_str());
165 2 : } else if(u.getChargeString().length()>0 && u.getChargeString()!="e") {
166 0 : log.printf(" charge: %s = %g e\n",u.getChargeString().c_str(),u.getCharge());
167 : } else {
168 2 : log.printf(" charge: %g e\n",u.getCharge());
169 : }
170 :
171 : s="";
172 68 : parse("MASS",s);
173 34 : if(s.length()>0) {
174 2 : u.setMass(s);
175 : }
176 67 : if(u.getMassString().length()>0 && u.getMassString()=="amu") {
177 33 : log.printf(" mass: %s\n",u.getMassString().c_str());
178 1 : } else if(u.getMassString().length()>0 && u.getMassString()!="amu") {
179 0 : log.printf(" mass: %s = %g amu\n",u.getMassString().c_str(),u.getMass());
180 : } else {
181 1 : log.printf(" mass: %g amu\n",u.getMass());
182 : }
183 :
184 34 : bool natural=false;
185 34 : parseFlag("NATURAL",natural);
186 :
187 34 : checkRead();
188 :
189 34 : if(natural) {
190 6 : log.printf(" using natural units\n");
191 : } else {
192 28 : log.printf(" using physical units\n");
193 : }
194 34 : log.printf(" inside PLUMED, Boltzmann constant is %g\n",getKBoltzmann());
195 :
196 34 : plumed.setUnits(natural,u);
197 34 : }
198 :
199 : }
200 : }
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