Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2019 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 :
23 : #include "core/ActionRegister.h"
24 : #include "core/ActionAtomistic.h"
25 : #include "core/Atoms.h"
26 : #include "tools/IFile.h"
27 : #include "tools/Tools.h"
28 : #include <string>
29 : #include <vector>
30 : #include <algorithm>
31 :
32 : using namespace std;
33 :
34 : namespace PLMD {
35 : namespace generic {
36 :
37 : //+PLUMEDOC GENERIC GROUP
38 : /*
39 : Define a group of atoms so that a particular list of atoms can be referenced with a single label
40 : in definitions of CVs or virtual atoms.
41 :
42 : Atoms can be listed as comma separated numbers (i.e. `1,2,3,10,45,7,9`) , simple positive ranges
43 : (i.e. `20-40`), ranges with a stride either positive or negative (i.e. `20-40:2` or `80-50:-2`) or as
44 : comma separated combinations of all the former methods (`1,2,4,5,10-20,21-40:2,80-50:-2`).
45 :
46 : Moreover, lists can be imported from ndx files (GROMACS format). Use `NDX_FILE` to set the name of
47 : the index file and `NDX_GROUP` to set the name of the group to be imported (default is first one).
48 :
49 : It is also possible to remove atoms from a list and or sort them using keywords `REMOVE`, `SORT`, and `UNIQUE`.
50 : The flow is the following:
51 : - If `ATOMS` is present, then take the ordered list of atoms from the `ATOMS` keyword as a starting list.
52 : - If `NDX_FILE` is present, then append to it the list obtained from the gromacs group.
53 : - If `REMOVE` is present, then remove the first occurence of each of these atoms from the list.
54 : If one tries to remove an atom that was not listed plumed adds a notice in the output.
55 : An atom that is present twice in the original list might be removed twice.
56 : - If `SORT` is present, then the resulting list is sorted by increasing serial number.
57 : - If `UNIQUE` is present, then the resuling list is sorted by increasing serial number _and_ duplicate elements are removed.
58 :
59 : Notice that this command just creates a shortcut, and does not imply any real calculation.
60 : So, having a huge group defined does not slow down your calculation in any way.
61 : It is just convenient to better organize input files. Might be used in combination with
62 : the \ref INCLUDE command so as to store long group definitions in a separate file.
63 :
64 :
65 : \par Examples
66 :
67 : This command create a group of atoms containing atoms 1, 4, 7, 11 and 14 (labeled 'o'), and another containing
68 : atoms 2, 3, 5, 6, 8, 9, 12, and 13 (labeled 'h'):
69 : \plumedfile
70 : o: GROUP ATOMS=1,4,7,11,14
71 : h: GROUP ATOMS=2,3,5,6,8,9,12,13
72 : # compute the coordination among the two groups
73 : c: COORDINATION GROUPA=o GROUPB=h R_0=0.3
74 : # same could have been obtained without GROUP, just writing:
75 : # c: COORDINATION GROUPA=1,4,7,11,14 GROUPB=2,3,5,6,8,9,12,13
76 :
77 : # print the coordination on file 'colvar'
78 : PRINT ARG=c FILE=colvar
79 : \endplumedfile
80 :
81 : Groups can be conveniently stored in a separate file.
82 : E.g. one could create a file named `groups.dat` which reads
83 : \plumedfile
84 : o: GROUP ATOMS=1,4,7,11,14
85 : h: GROUP ATOMS=2,3,5,6,8,9,12,13
86 : \endplumedfile
87 : and then include it in the main 'plumed.dat' file
88 : \plumedfile
89 : INCLUDE FILE=groups.dat
90 : # compute the coordination among the two groups
91 : c: COORDINATION GROUPA=o GROUPB=h R_0=0.3
92 : # print the coordination on file 'colvar'
93 : PRINT ARG=c FILE=colvar
94 : \endplumedfile
95 : The `groups.dat` file could be very long and include lists of thousand atoms without cluttering the main plumed.dat file.
96 :
97 : A GROMACS index file can also be imported
98 : \plumedfile
99 : # import group named 'protein' from file index.ndx
100 : pro: GROUP NDX_FILE=index.ndx NDX_GROUP=protein
101 : # dump all the atoms of the protein on a trajectory file
102 : DUMPATOMS ATOMS=pro FILE=traj.gro
103 : \endplumedfile
104 :
105 : A list can be edited with `REMOVE`. For instance, if you
106 : are using a water model with three atoms per molecule, you can
107 : easily construct the list of hydrogens in this manner
108 : \plumedfile
109 : # take one atom every three, that is oxygens
110 : ox: GROUP ATOMS=1-90:3
111 : # take the remaining atoms, that is hydrogens
112 : hy: GROUP ATOMS=1-90 REMOVE=ox
113 : DUMPATOMS ATOMS=ox FILE=ox.gro
114 : DUMPATOMS ATOMS=hy FILE=hy.gro
115 : \endplumedfile
116 :
117 :
118 : */
119 : //+ENDPLUMEDOC
120 :
121 : class Group:
122 : public ActionAtomistic
123 : {
124 :
125 : public:
126 : explicit Group(const ActionOptions&ao);
127 : ~Group();
128 : static void registerKeywords( Keywords& keys );
129 0 : void calculate() {}
130 0 : void apply() {}
131 : };
132 :
133 6539 : PLUMED_REGISTER_ACTION(Group,"GROUP")
134 :
135 87 : Group::Group(const ActionOptions&ao):
136 : Action(ao),
137 87 : ActionAtomistic(ao)
138 : {
139 : vector<AtomNumber> atoms;
140 174 : parseAtomList("ATOMS",atoms);
141 : std::string ndxfile,ndxgroup;
142 174 : parse("NDX_FILE",ndxfile);
143 174 : parse("NDX_GROUP",ndxgroup);
144 93 : if(ndxfile.length()>0 && atoms.size()>0) error("either use explicit atom list or import from index file");
145 168 : if(ndxfile.length()==0 && ndxgroup.size()>0) error("NDX_GROUP can be only used is NDX_FILE is also used");
146 :
147 87 : if(ndxfile.length()>0) {
148 16 : if(ndxgroup.size()>0) log<<" importing group '"+ndxgroup+"'";
149 1 : else log<<" importing first group";
150 6 : log<<" from index file "<<ndxfile<<"\n";
151 :
152 12 : IFile ifile;
153 6 : ifile.open(ndxfile);
154 : std::string line;
155 : std::string groupname;
156 : bool firstgroup=true;
157 : bool groupfound=false;
158 2468 : while(ifile.getline(line)) {
159 2462 : std::vector<std::string> words=Tools::getWords(line);
160 2487 : if(words.size()>=3 && words[0]=="[" && words[2]=="]") {
161 44 : if(groupname.length()>0) firstgroup=false;
162 : groupname=words[1];
163 83 : if(groupname==ndxgroup || ndxgroup.length()==0) groupfound=true;
164 2505 : } else if(groupname==ndxgroup || (firstgroup && ndxgroup.length()==0)) {
165 5928 : for(unsigned i=0; i<words.size(); i++) {
166 1888 : AtomNumber at; Tools::convert(words[i],at);
167 1888 : atoms.push_back(at);
168 : }
169 : }
170 : }
171 6 : if(!groupfound) error("group has not been found in index file");
172 : }
173 :
174 : std::vector<AtomNumber> remove;
175 174 : parseAtomList("REMOVE",remove);
176 87 : if(remove.size()>0) {
177 : std::vector<AtomNumber> notfound;
178 : unsigned k=0;
179 1 : log<<" removing these atoms from the list:";
180 14 : for(unsigned i=0; i<remove.size(); i++) {
181 4 : const auto it = find(atoms.begin(),atoms.end(),remove[i]);
182 4 : if(it!=atoms.end()) {
183 3 : if(k%25==0) log<<"\n";
184 6 : log<<" "<<(*it).serial();
185 3 : k++;
186 : atoms.erase(it);
187 1 : } else notfound.push_back(remove[i]);
188 : }
189 1 : log<<"\n";
190 1 : if(notfound.size()>0) {
191 1 : log<<" the following atoms were not found:";
192 5 : for(unsigned i=0; i<notfound.size(); i++) log<<" "<<notfound[i].serial();
193 1 : log<<"\n";
194 : }
195 : }
196 :
197 87 : bool sortme=false;
198 174 : parseFlag("SORT",sortme);
199 87 : if(sortme) {
200 1 : log<<" atoms are sorted\n";
201 : sort(atoms.begin(),atoms.end());
202 : }
203 87 : bool unique=false;
204 174 : parseFlag("UNIQUE",unique);
205 87 : if(unique) {
206 1 : log<<" sorting atoms and removing duplicates\n";
207 1 : Tools::removeDuplicates(atoms);
208 : }
209 :
210 174 : this->atoms.insertGroup(getLabel(),atoms);
211 87 : log.printf(" list of atoms:");
212 52218 : for(unsigned i=0; i<atoms.size(); i++) {
213 17348 : if(i%25==0) log<<"\n";
214 34696 : log<<" "<<atoms[i].serial();
215 : }
216 87 : log.printf("\n");
217 87 : }
218 :
219 88 : void Group::registerKeywords( Keywords& keys ) {
220 88 : Action::registerKeywords( keys );
221 88 : ActionAtomistic::registerKeywords( keys );
222 352 : keys.add("atoms", "ATOMS", "the numerical indexes for the set of atoms in the group");
223 352 : keys.add("atoms", "REMOVE","remove these atoms from the list");
224 264 : keys.addFlag("SORT",false,"sort the resulting list");
225 264 : keys.addFlag("UNIQUE",false,"sort atoms and remove duplicated ones");
226 352 : keys.add("optional", "NDX_FILE", "the name of index file (gromacs syntax)");
227 352 : keys.add("optional", "NDX_GROUP", "the name of the group to be imported (gromacs syntax) - first group found is used by default");
228 88 : }
229 :
230 261 : Group::~Group() {
231 174 : atoms.removeGroup(getLabel());
232 174 : }
233 :
234 : }
235 4839 : }
236 :
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