Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2020 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 : using namespace std;
29 :
30 : namespace PLMD {
31 : namespace setup {
32 :
33 : //+PLUMEDOC GENERIC UNITS
34 : /*
35 : This command sets the internal units for the code.
36 :
37 : A new unit can be set by either
38 : specifying a conversion factor from the plumed default unit or by using a string
39 : corresponding to one of the defined units given below. This directive MUST
40 : appear at the BEGINNING of the plumed.dat file. The same units must be used
41 : throughout the plumed.dat file.
42 :
43 : Notice that all input/output will then be made using the specified units.
44 : That is: all the input parameters, all the output files, etc. The only
45 : exceptions are file formats for which there is a specific convention concerning
46 : the units. For example, trajectories written in .gro format (with \ref DUMPATOMS)
47 : are going to be always in nm.
48 :
49 : The following strings can be used to specify units. Note that the strings are
50 : case sensitive.
51 : - LENGTH: nm (default), A (for Angstrom), um (for micrometer), Bohr (0.052917721067 nm)
52 : - ENERGY: kj/mol (default), j/mol, kcal/mol (4.184 kj/mol), eV (96.48530749925792 kj/mol), Ha (for Hartree, 2625.499638 kj/mol)
53 : - TIME: ps (default), fs, ns, atomic (2.418884326509e-5 ps)
54 : - MASS: amu (default)
55 : - CHARGE: e (default)
56 :
57 :
58 : \par Examples
59 :
60 : \plumedfile
61 : # this is using Angstrom - kj/mol - fs
62 : UNITS LENGTH=A TIME=fs
63 :
64 : # compute distance between atoms 1 and 4
65 : d: DISTANCE ATOMS=1,4
66 :
67 : # print time and distance on a COLVAR file
68 : PRINT ARG=d FILE=COLVAR
69 :
70 : # dump atoms 1 to 100 on a 'out.gro' file
71 : DUMPATOMS FILE=out.gro STRIDE=10 ATOMS=1-100
72 :
73 : # dump atoms 1 to 100 on a 'out.xyz' file
74 : DUMPATOMS FILE=out.xyz STRIDE=10 ATOMS=1-100
75 : \endplumedfile
76 :
77 : In the `COLVAR` file, time and distance will appear in fs and A respectively, *irrespective* of which units
78 : you are using in the host MD code. The coordinates in the `out.gro` file will be expressed in nm,
79 : since `gro` files are by convention written in nm. The coordinates in the `out.xyz` file
80 : will be written in Angstrom *since we used the UNITS command setting Angstrom units*.
81 : Indeed, within PLUMED xyz files are using internal PLUMED units and not necessarily Angstrom!
82 :
83 : If a number, x, is found instead of a string, the new unit is equal to x times the default units.
84 : Using the following command as first line of the previous example would have lead to an identical result:
85 : \plumedfile
86 : UNITS LENGTH=0.1 TIME=0.001
87 : \endplumedfile
88 :
89 : */
90 : //+ENDPLUMEDOC
91 :
92 30 : class Units :
93 : public virtual ActionSetup
94 : {
95 : public:
96 : static void registerKeywords( Keywords& keys );
97 : explicit Units(const ActionOptions&ao);
98 : };
99 :
100 7386 : PLUMED_REGISTER_ACTION(Units,"UNITS")
101 :
102 16 : void Units::registerKeywords( Keywords& keys ) {
103 16 : ActionSetup::registerKeywords(keys);
104 64 : 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 64 : 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 64 : 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 64 : keys.add("optional","MASS","the units of masses. Specify a conversion factor from the default, amu");
108 64 : keys.add("optional","CHARGE","the units of charges. Specify a conversion factor from the default, e");
109 48 : keys.addFlag("NATURAL",false,"use natural units");
110 16 : }
111 :
112 15 : Units::Units(const ActionOptions&ao):
113 : Action(ao),
114 15 : ActionSetup(ao)
115 : {
116 30 : PLMD::Units u;
117 :
118 : std::string s;
119 :
120 : s="";
121 30 : parse("LENGTH",s);
122 15 : if(s.length()>0) u.setLength(s);
123 28 : if(u.getLengthString().length()>0 && u.getLengthString()=="nm") {
124 16 : log.printf(" length: %s\n",u.getLengthString().c_str());
125 : }
126 12 : else if(u.getLengthString().length()>0 && u.getLengthString()!="nm") {
127 10 : log.printf(" length: %s = %g nm\n",u.getLengthString().c_str(),u.getLength());
128 : }
129 : else {
130 2 : log.printf(" length: %g nm\n",u.getLength());
131 : }
132 :
133 : s="";
134 30 : parse("ENERGY",s);
135 15 : if(s.length()>0) u.setEnergy(s);
136 28 : if(u.getEnergyString().length()>0 && u.getEnergyString()=="kj/mol") {
137 24 : log.printf(" energy: %s\n",u.getEnergyString().c_str());
138 : }
139 4 : else if(u.getEnergyString().length()>0 && u.getEnergyString()!="kj/mol") {
140 2 : log.printf(" energy: %s = %g kj/mol\n",u.getEnergyString().c_str(),u.getEnergy());
141 : }
142 : else {
143 2 : log.printf(" energy: %g kj/mol\n",u.getEnergy());
144 : }
145 :
146 : s="";
147 30 : parse("TIME",s);
148 15 : if(s.length()>0) u.setTime(s);
149 28 : if(u.getTimeString().length()>0 && u.getTimeString()=="ps") {
150 24 : log.printf(" time: %s\n",u.getTimeString().c_str());
151 : }
152 4 : else if(u.getTimeString().length()>0 && u.getTimeString()!="ps") {
153 2 : log.printf(" time: %s = %g ps\n",u.getTimeString().c_str(),u.getTime());
154 : }
155 : else {
156 2 : log.printf(" time: %g ps\n",u.getTime());
157 : }
158 :
159 : s="";
160 30 : parse("CHARGE",s);
161 15 : if(s.length()>0) u.setCharge(s);
162 28 : if(u.getChargeString().length()>0 && u.getChargeString()=="e") {
163 26 : log.printf(" charge: %s\n",u.getChargeString().c_str());
164 : }
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 : }
168 : else {
169 2 : log.printf(" charge: %g e\n",u.getCharge());
170 : }
171 :
172 : s="";
173 30 : parse("MASS",s);
174 15 : if(s.length()>0) u.setMass(s);
175 29 : if(u.getMassString().length()>0 && u.getMassString()=="amu") {
176 14 : log.printf(" mass: %s\n",u.getMassString().c_str());
177 : }
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 : }
181 : else {
182 1 : log.printf(" mass: %g amu\n",u.getMass());
183 : }
184 :
185 15 : bool natural=false;
186 30 : parseFlag("NATURAL",natural);
187 30 : plumed.getAtoms().setNaturalUnits(natural);
188 :
189 15 : checkRead();
190 :
191 15 : plumed.getAtoms().setUnits(u);
192 15 : if(natural) {
193 6 : log.printf(" using natural units\n");
194 : } else {
195 9 : log.printf(" using physical units\n");
196 : }
197 30 : log.printf(" inside PLUMED, Boltzmann constant is %g\n",plumed.getAtoms().getKBoltzmann());
198 :
199 30 : plumed.getAtoms().updateUnits();
200 15 : }
201 :
202 : }
203 5517 : }
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