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 : #include "core/ActionAtomistic.h"
23 : #include "core/ActionPilot.h"
24 : #include "core/ActionRegister.h"
25 : #include "tools/Pbc.h"
26 : #include "tools/File.h"
27 : #include "core/PlumedMain.h"
28 : #include "core/Atoms.h"
29 : #include "tools/Units.h"
30 : #include <cstdio>
31 : #include "core/SetupMolInfo.h"
32 : #include "core/ActionSet.h"
33 :
34 : #if defined(__PLUMED_HAS_XDRFILE)
35 : #include <xdrfile/xdrfile_xtc.h>
36 : #include <xdrfile/xdrfile_trr.h>
37 : #endif
38 :
39 :
40 : using namespace std;
41 :
42 : namespace PLMD
43 : {
44 : namespace generic {
45 :
46 : //+PLUMEDOC PRINTANALYSIS DUMPATOMS
47 : /*
48 : Dump selected atoms on a file.
49 :
50 : This command can be used to output the positions of a particular set of atoms.
51 : The atoms required are ouput in a xyz or gro formatted file.
52 : If PLUMED has been compiled with xdrfile support, then also xtc and trr files can be written.
53 : To this aim one should install xdrfile library (http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library).
54 : If the xdrfile library is installed properly the PLUMED configure script should be able to
55 : detect it and enable it.
56 : The type of file is automatically detected from the file extension, but can be also
57 : enforced with TYPE.
58 : Importantly, if your
59 : input file contains actions that edit the atoms position (e.g. \ref WHOLEMOLECULES)
60 : and the DUMPATOMS command appears after this instruction, then the edited
61 : atom positions are output.
62 : You can control the buffering of output using the \ref FLUSH keyword on a separate line.
63 :
64 : Units of the printed file can be controlled with the UNITS keyword. By default PLUMED units as
65 : controlled in the \ref UNITS command are used, but one can override it e.g. with UNITS=A.
66 : Notice that gro/xtc/trr files can only contain coordinates in nm.
67 :
68 : \par Examples
69 :
70 : The following input instructs plumed to print out the positions of atoms
71 : 1-10 together with the position of the center of mass of atoms 11-20 every
72 : 10 steps to a file called file.xyz.
73 : \plumedfile
74 : COM ATOMS=11-20 LABEL=c1
75 : DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1
76 : \endplumedfile
77 : Notice that the coordinates in the xyz file will be expressed in nm, since these
78 : are the defaults units in PLUMED. If you want the xyz file to be expressed in A, you should use the
79 : following input
80 : \plumedfile
81 : COM ATOMS=11-20 LABEL=c1
82 : DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1 UNITS=A
83 : \endplumedfile
84 : As an alternative, you might want to set all the lentght used by PLUMED to Angstrom using the \ref UNITS
85 : action. However, this latter choice will affect all your input and output.
86 :
87 : The following input is very similar but dumps a .gro (gromacs) file,
88 : which also contains atom and residue names.
89 : \plumedfile
90 : # this is required to have proper atom names:
91 : MOLINFO STRUCTURE=reference.pdb
92 : # if omitted, atoms will have "X" name...
93 :
94 : COM ATOMS=11-20 LABEL=c1
95 : DUMPATOMS STRIDE=10 FILE=file.gro ATOMS=1-10,c1
96 : # notice that last atom is a virtual one and will not have
97 : # a correct name in the resulting gro file
98 : \endplumedfile
99 :
100 : The `file.gro` will contain coordinates expressed in nm, since this is the convention for gro files.
101 :
102 : In case you have compiled PLUMED with `xdrfile` library, you might even write xtc or trr files as follows
103 : \plumedfile
104 : COM ATOMS=11-20 LABEL=c1
105 : DUMPATOMS STRIDE=10 FILE=file.xtc ATOMS=1-10,c1
106 : \endplumedfile
107 : Notice that xtc files are significantly smaller than gro and xyz files.
108 :
109 : Finally, consider that gro and xtc file store coordinates with limited precision set by the
110 : `PRECISION` keyword. Default value is 3, which means "3 digits after dot" in nm (1/1000 of a nm).
111 : The following will write a larger xtc file with high resolution coordinates:
112 : \plumedfile
113 : COM ATOMS=11-20 LABEL=c1
114 : DUMPATOMS STRIDE=10 FILE=file.xtc ATOMS=1-10,c1 PRECISION=7
115 : \endplumedfile
116 :
117 :
118 :
119 : */
120 : //+ENDPLUMEDOC
121 :
122 : class DumpAtoms:
123 : public ActionAtomistic,
124 : public ActionPilot
125 : {
126 : OFile of;
127 : double lenunit;
128 : int iprecision;
129 : std::vector<std::string> names;
130 : std::vector<unsigned> residueNumbers;
131 : std::vector<std::string> residueNames;
132 : std::string type;
133 : std::string fmt_gro_pos;
134 : std::string fmt_gro_box;
135 : std::string fmt_xyz;
136 : #if defined(__PLUMED_HAS_XDRFILE)
137 : XDRFILE* xd;
138 : #endif
139 : public:
140 : explicit DumpAtoms(const ActionOptions&);
141 : ~DumpAtoms();
142 : static void registerKeywords( Keywords& keys );
143 483 : void calculate() {}
144 483 : void apply() {}
145 : void update();
146 : };
147 :
148 6507 : PLUMED_REGISTER_ACTION(DumpAtoms,"DUMPATOMS")
149 :
150 56 : void DumpAtoms::registerKeywords( Keywords& keys ) {
151 56 : Action::registerKeywords( keys );
152 56 : ActionPilot::registerKeywords( keys );
153 56 : ActionAtomistic::registerKeywords( keys );
154 280 : keys.add("compulsory","STRIDE","1","the frequency with which the atoms should be output");
155 224 : keys.add("atoms", "ATOMS", "the atom indices whose positions you would like to print out");
156 224 : keys.add("compulsory", "FILE", "file on which to output coordinates; extension is automatically detected");
157 280 : keys.add("compulsory", "UNITS","PLUMED","the units in which to print out the coordinates. PLUMED means internal PLUMED units");
158 224 : keys.add("optional", "PRECISION","The number of digits in trajectory file");
159 : #if defined(__PLUMED_HAS_XDRFILE)
160 224 : keys.add("optional", "TYPE","file type, either xyz, gro, xtc, or trr, can override an automatically detected file extension");
161 : #else
162 : keys.add("optional", "TYPE","file type, either xyz or gro, can override an automatically detected file extension");
163 : #endif
164 112 : keys.use("RESTART");
165 112 : keys.use("UPDATE_FROM");
166 112 : keys.use("UPDATE_UNTIL");
167 56 : }
168 :
169 55 : DumpAtoms::DumpAtoms(const ActionOptions&ao):
170 : Action(ao),
171 : ActionAtomistic(ao),
172 : ActionPilot(ao),
173 385 : iprecision(3)
174 : {
175 : vector<AtomNumber> atoms;
176 : string file;
177 110 : parse("FILE",file);
178 55 : if(file.length()==0) error("name out output file was not specified");
179 110 : type=Tools::extension(file);
180 55 : log<<" file name "<<file<<"\n";
181 133 : if(type=="gro" || type=="xyz" || type=="xtc" || type=="trr") {
182 80 : log<<" file extension indicates a "<<type<<" file\n";
183 : } else {
184 15 : log<<" file extension not detected, assuming xyz\n";
185 : type="xyz";
186 : }
187 : string ntype;
188 110 : parse("TYPE",ntype);
189 55 : if(ntype.length()>0) {
190 5 : if(ntype!="xyz" && ntype!="gro" && ntype!="xtc" && ntype!="trr"
191 0 : ) error("TYPE cannot be understood");
192 2 : log<<" file type enforced to be "<<ntype<<"\n";
193 : type=ntype;
194 : }
195 : #ifndef __PLUMED_HAS_XDRFILE
196 : if(type=="xtc" || type=="trr") error("types xtc and trr require PLUMED to be linked with the xdrfile library. Please install it and recompile PLUMED.");
197 : #endif
198 :
199 : fmt_gro_pos="%8.3f";
200 : fmt_gro_box="%12.7f";
201 : fmt_xyz="%f";
202 :
203 : string precision;
204 110 : parse("PRECISION",precision);
205 55 : if(precision.length()>0) {
206 9 : Tools::convert(precision,iprecision);
207 9 : log<<" with precision "<<iprecision<<"\n";
208 : string a,b;
209 9 : Tools::convert(iprecision+5,a);
210 9 : Tools::convert(iprecision,b);
211 45 : fmt_gro_pos="%"+a+"."+b+"f";
212 : fmt_gro_box=fmt_gro_pos;
213 : fmt_xyz=fmt_gro_box;
214 : }
215 :
216 110 : parseAtomList("ATOMS",atoms);
217 :
218 110 : std::string unitname; parse("UNITS",unitname);
219 55 : if(unitname!="PLUMED") {
220 8 : Units myunit; myunit.setLength(unitname);
221 6 : if(myunit.getLength()!=1.0 && type=="gro") error("gro files should be in nm");
222 6 : if(myunit.getLength()!=1.0 && type=="xtc") error("xtc files should be in nm");
223 6 : if(myunit.getLength()!=1.0 && type=="trr") error("trr files should be in nm");
224 8 : lenunit=plumed.getAtoms().getUnits().getLength()/myunit.getLength();
225 167 : } else if(type=="gro" || type=="xtc" || type=="trr") lenunit=plumed.getAtoms().getUnits().getLength();
226 21 : else lenunit=1.0;
227 :
228 55 : checkRead();
229 55 : of.link(*this);
230 55 : of.open(file);
231 : std::string path=of.getPath();
232 55 : log<<" Writing on file "<<path<<"\n";
233 : #ifdef __PLUMED_HAS_XDRFILE
234 : std::string mode=of.getMode();
235 55 : if(type=="xtc") {
236 6 : of.close();
237 6 : xd=xdrfile_open(path.c_str(),mode.c_str());
238 49 : } else if(type=="trr") {
239 4 : of.close();
240 4 : xd=xdrfile_open(path.c_str(),mode.c_str());
241 : }
242 : #endif
243 110 : log.printf(" printing the following atoms in %s :", unitname.c_str() );
244 47051 : for(unsigned i=0; i<atoms.size(); ++i) log.printf(" %d",atoms[i].serial() );
245 55 : log.printf("\n");
246 55 : requestAtoms(atoms);
247 110 : std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
248 55 : if( moldat.size()==1 ) {
249 26 : log<<" MOLINFO DATA found, using proper atom names\n";
250 26 : names.resize(atoms.size());
251 19756 : for(unsigned i=0; i<atoms.size(); i++) names[i]=moldat[0]->getAtomName(atoms[i]);
252 26 : residueNumbers.resize(atoms.size());
253 13188 : for(unsigned i=0; i<residueNumbers.size(); ++i) residueNumbers[i]=moldat[0]->getResidueNumber(atoms[i]);
254 26 : residueNames.resize(atoms.size());
255 19756 : for(unsigned i=0; i<residueNames.size(); ++i) residueNames[i]=moldat[0]->getResidueName(atoms[i]);
256 : }
257 55 : }
258 :
259 483 : void DumpAtoms::update() {
260 966 : if(type=="xyz") {
261 282 : of.printf("%d\n",getNumberOfAtoms());
262 141 : const Tensor & t(getPbc().getBox());
263 141 : if(getPbc().isOrthorombic()) {
264 944 : of.printf((" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+"\n").c_str(),lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2));
265 : } else {
266 644 : of.printf((" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+"\n").c_str(),
267 69 : lenunit*t(0,0),lenunit*t(0,1),lenunit*t(0,2),
268 69 : lenunit*t(1,0),lenunit*t(1,1),lenunit*t(1,2),
269 69 : lenunit*t(2,0),lenunit*t(2,1),lenunit*t(2,2)
270 : );
271 : }
272 62017 : for(unsigned i=0; i<getNumberOfAtoms(); ++i) {
273 : const char* defname="X";
274 : const char* name=defname;
275 39014 : if(names.size()>0) if(names[i].length()>0) name=names[i].c_str();
276 278442 : of.printf(("%s "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+"\n").c_str(),name,lenunit*getPosition(i)(0),lenunit*getPosition(i)(1),lenunit*getPosition(i)(2));
277 : }
278 342 : } else if(type=="gro") {
279 222 : const Tensor & t(getPbc().getBox());
280 444 : of.printf("Made with PLUMED t=%f\n",getTime()/plumed.getAtoms().getUnits().getTime());
281 222 : of.printf("%d\n",getNumberOfAtoms());
282 44292 : for(unsigned i=0; i<getNumberOfAtoms(); ++i) {
283 : const char* defname="X";
284 : const char* name=defname;
285 : unsigned residueNumber=0;
286 43269 : if(names.size()>0) if(names[i].length()>0) name=names[i].c_str();
287 43269 : if(residueNumbers.size()>0) residueNumber=residueNumbers[i];
288 22035 : std::string resname="";
289 22035 : if(residueNames.size()>0) resname=residueNames[i];
290 220350 : of.printf(("%5u%-5s%5s%5d"+fmt_gro_pos+fmt_gro_pos+fmt_gro_pos+"\n").c_str(),
291 : residueNumber%100000,resname.c_str(),name,getAbsoluteIndex(i).serial()%100000,
292 88140 : lenunit*getPosition(i)(0),lenunit*getPosition(i)(1),lenunit*getPosition(i)(2));
293 : }
294 5994 : of.printf((fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+" "+fmt_gro_box+"\n").c_str(),
295 666 : lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2),
296 666 : lenunit*t(0,1),lenunit*t(0,2),lenunit*t(1,0),
297 666 : lenunit*t(1,2),lenunit*t(2,0),lenunit*t(2,1));
298 : #if defined(__PLUMED_HAS_XDRFILE)
299 168 : } else if(type=="xtc" || type=="trr") {
300 : matrix box;
301 120 : const Tensor & t(getPbc().getBox());
302 120 : int natoms=getNumberOfAtoms();
303 120 : int step=getStep();
304 240 : float time=getTime()/plumed.getAtoms().getUnits().getTime();
305 240 : float precision=Tools::fastpow(10.0,iprecision);
306 480 : for(int i=0; i<3; i++) for(int j=0; j<3; j++) box[i][j]=lenunit*t(i,j);
307 120 : rvec* pos=new rvec [natoms];
308 : // Notice that code below cannot throw any exception.
309 : // Thus, this pointer is excepton safe
310 25464 : for(int i=0; i<natoms; i++) for(int j=0; j<3; j++) pos[i][j]=lenunit*getPosition(i)(j);
311 120 : if(type=="xtc") {
312 72 : write_xtc(xd,natoms,step,time,box,&pos[0],precision);
313 48 : } else if(type=="trr") {
314 48 : write_trr(xd,natoms,step,time,0.0,box,&pos[0],NULL,NULL);
315 : }
316 120 : delete [] pos;
317 : #endif
318 0 : } else plumed_merror("unknown file type "+type);
319 483 : }
320 :
321 275 : DumpAtoms::~DumpAtoms() {
322 : #ifdef __PLUMED_HAS_XDRFILE
323 110 : if(type=="xtc") {
324 6 : xdrfile_close(xd);
325 49 : } else if(type=="trr") {
326 4 : xdrfile_close(xd);
327 : }
328 : #endif
329 110 : }
330 :
331 :
332 : }
333 4839 : }
|
