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 : public:
93 : static void registerKeywords( Keywords& keys );
94 : explicit Units(const ActionOptions&ao);
95 : };
96 :
97 13825 : PLUMED_REGISTER_ACTION(Units,"UNITS")
98 :
99 24 : void Units::registerKeywords( Keywords& keys ) {
100 24 : ActionSetup::registerKeywords(keys);
101 48 : 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.");
102 48 : 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)");
103 48 : 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");
104 48 : keys.add("optional","MASS","the units of masses. Specify a conversion factor from the default, amu");
105 48 : keys.add("optional","CHARGE","the units of charges. Specify a conversion factor from the default, e");
106 48 : keys.addFlag("NATURAL",false,"use natural units");
107 24 : }
108 :
109 20 : Units::Units(const ActionOptions&ao):
110 : Action(ao),
111 20 : ActionSetup(ao) {
112 20 : PLMD::Units u;
113 :
114 : std::string s;
115 :
116 : s="";
117 40 : parse("LENGTH",s);
118 20 : if(s.length()>0) {
119 12 : u.setLength(s);
120 : }
121 38 : if(u.getLengthString().length()>0 && u.getLengthString()=="nm") {
122 8 : log.printf(" length: %s\n",u.getLengthString().c_str());
123 22 : } else if(u.getLengthString().length()>0 && u.getLengthString()!="nm") {
124 10 : log.printf(" length: %s = %g nm\n",u.getLengthString().c_str(),u.getLength());
125 : } else {
126 2 : log.printf(" length: %g nm\n",u.getLength());
127 : }
128 :
129 : s="";
130 40 : parse("ENERGY",s);
131 20 : if(s.length()>0) {
132 7 : u.setEnergy(s);
133 : }
134 38 : if(u.getEnergyString().length()>0 && u.getEnergyString()=="kj/mol") {
135 13 : log.printf(" energy: %s\n",u.getEnergyString().c_str());
136 12 : } else if(u.getEnergyString().length()>0 && u.getEnergyString()!="kj/mol") {
137 5 : log.printf(" energy: %s = %g kj/mol\n",u.getEnergyString().c_str(),u.getEnergy());
138 : } else {
139 2 : log.printf(" energy: %g kj/mol\n",u.getEnergy());
140 : }
141 :
142 : s="";
143 40 : parse("TIME",s);
144 20 : if(s.length()>0) {
145 7 : u.setTime(s);
146 : }
147 38 : if(u.getTimeString().length()>0 && u.getTimeString()=="ps") {
148 15 : log.printf(" time: %s\n",u.getTimeString().c_str());
149 8 : } else if(u.getTimeString().length()>0 && u.getTimeString()!="ps") {
150 3 : log.printf(" time: %s = %g ps\n",u.getTimeString().c_str(),u.getTime());
151 : } else {
152 2 : log.printf(" time: %g ps\n",u.getTime());
153 : }
154 :
155 : s="";
156 40 : parse("CHARGE",s);
157 20 : if(s.length()>0) {
158 3 : u.setCharge(s);
159 : }
160 38 : if(u.getChargeString().length()>0 && u.getChargeString()=="e") {
161 18 : log.printf(" charge: %s\n",u.getChargeString().c_str());
162 2 : } else if(u.getChargeString().length()>0 && u.getChargeString()!="e") {
163 0 : log.printf(" charge: %s = %g e\n",u.getChargeString().c_str(),u.getCharge());
164 : } else {
165 2 : log.printf(" charge: %g e\n",u.getCharge());
166 : }
167 :
168 : s="";
169 40 : parse("MASS",s);
170 20 : if(s.length()>0) {
171 2 : u.setMass(s);
172 : }
173 39 : if(u.getMassString().length()>0 && u.getMassString()=="amu") {
174 19 : log.printf(" mass: %s\n",u.getMassString().c_str());
175 1 : } else if(u.getMassString().length()>0 && u.getMassString()!="amu") {
176 0 : log.printf(" mass: %s = %g amu\n",u.getMassString().c_str(),u.getMass());
177 : } else {
178 1 : log.printf(" mass: %g amu\n",u.getMass());
179 : }
180 :
181 20 : bool natural=false;
182 20 : parseFlag("NATURAL",natural);
183 20 : plumed.getAtoms().setNaturalUnits(natural);
184 :
185 20 : checkRead();
186 :
187 20 : plumed.getAtoms().setUnits(u);
188 20 : if(natural) {
189 6 : log.printf(" using natural units\n");
190 : } else {
191 14 : log.printf(" using physical units\n");
192 : }
193 20 : log.printf(" inside PLUMED, Boltzmann constant is %g\n",plumed.getAtoms().getKBoltzmann());
194 :
195 20 : plumed.getAtoms().updateUnits();
196 20 : }
197 :
198 : }
199 : }
|
