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/ActionAtomistic.h"
23 : #include "core/ActionWithArguments.h"
24 : #include "core/ActionPilot.h"
25 : #include "core/ActionRegister.h"
26 : #include "tools/Pbc.h"
27 : #include "tools/File.h"
28 : #include "core/PlumedMain.h"
29 : #include "tools/Units.h"
30 : #include "tools/CheckInRange.h"
31 : #include <cstdio>
32 : #include <memory>
33 : #include "core/GenericMolInfo.h"
34 : #include "core/ActionSet.h"
35 : #include "xdrfile/xdrfile_xtc.h"
36 : #include "xdrfile/xdrfile_trr.h"
37 :
38 :
39 : namespace PLMD {
40 : namespace generic {
41 :
42 : //+PLUMEDOC PRINTANALYSIS DUMPATOMS
43 : /*
44 : Dump selected atoms on a file.
45 :
46 : This command can be used to output the positions of a particular set of atoms.
47 : The atoms required are output in a xyz or gro formatted file.
48 : If PLUMED has been compiled with xdrfile support, then also xtc and trr files can be written.
49 : To this aim one should install xdrfile library (http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library).
50 : If the xdrfile library is installed properly the PLUMED configure script should be able to
51 : detect it and enable it.
52 : The type of file is automatically detected from the file extension, but can be also
53 : enforced with TYPE.
54 : Importantly, if your
55 : input file contains actions that edit the atoms position (e.g. \ref WHOLEMOLECULES)
56 : and the DUMPATOMS command appears after this instruction, then the edited
57 : atom positions are output.
58 : You can control the buffering of output using the \ref FLUSH keyword on a separate line.
59 :
60 : Units of the printed file can be controlled with the UNITS keyword. By default PLUMED units as
61 : controlled in the \ref UNITS command are used, but one can override it e.g. with UNITS=A.
62 : Notice that gro/xtc/trr files can only contain coordinates in nm.
63 :
64 : \par Examples
65 :
66 : The following input instructs plumed to print out the positions of atoms
67 : 1-10 together with the position of the center of mass of atoms 11-20 every
68 : 10 steps to a file called file.xyz.
69 : \plumedfile
70 : COM ATOMS=11-20 LABEL=c1
71 : DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1
72 : \endplumedfile
73 : Notice that the coordinates in the xyz file will be expressed in nm, since these
74 : are the defaults units in PLUMED. If you want the xyz file to be expressed in A, you should use the
75 : following input
76 : \plumedfile
77 : COM ATOMS=11-20 LABEL=c1
78 : DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1 UNITS=A
79 : \endplumedfile
80 : As an alternative, you might want to set all the length used by PLUMED to Angstrom using the \ref UNITS
81 : action. However, this latter choice will affect all your input and output.
82 :
83 : The following input is very similar but dumps a .gro (gromacs) file,
84 : which also contains atom and residue names.
85 : \plumedfile
86 : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
87 : # this is required to have proper atom names:
88 : MOLINFO STRUCTURE=reference.pdb
89 : # if omitted, atoms will have "X" name...
90 :
91 : COM ATOMS=11-20 LABEL=c1
92 : DUMPATOMS STRIDE=10 FILE=file.gro ATOMS=1-10,c1
93 : # notice that last atom is a virtual one and will not have
94 : # a correct name in the resulting gro file
95 : \endplumedfile
96 :
97 : The `file.gro` will contain coordinates expressed in nm, since this is the convention for gro files.
98 :
99 : In case you have compiled PLUMED with `xdrfile` library, you might even write xtc or trr files as follows
100 : \plumedfile
101 : COM ATOMS=11-20 LABEL=c1
102 : DUMPATOMS STRIDE=10 FILE=file.xtc ATOMS=1-10,c1
103 : \endplumedfile
104 : Notice that xtc files are significantly smaller than gro and xyz files.
105 :
106 : Finally, consider that gro and xtc file store coordinates with limited precision set by the
107 : `PRECISION` keyword. Default value is 3, which means "3 digits after dot" in nm (1/1000 of a nm).
108 : The following will write a larger xtc file with high resolution coordinates:
109 : \plumedfile
110 : COM ATOMS=11-20 LABEL=c1
111 : DUMPATOMS STRIDE=10 FILE=file.xtc ATOMS=1-10,c1 PRECISION=7
112 : \endplumedfile
113 :
114 :
115 :
116 : */
117 : //+ENDPLUMEDOC
118 :
119 : class DumpAtoms:
120 : public ActionAtomistic,
121 : public ActionWithArguments,
122 : public ActionPilot
123 : {
124 : OFile of;
125 : double lenunit;
126 : int iprecision;
127 : CheckInRange bounds;
128 : std::vector<std::string> names;
129 : std::vector<unsigned> residueNumbers;
130 : std::vector<std::string> residueNames;
131 : std::string type;
132 : std::string fmt_gro_pos;
133 : std::string fmt_gro_box;
134 : std::string fmt_xyz;
135 : xdrfile::XDRFILE* xd;
136 : public:
137 : explicit DumpAtoms(const ActionOptions&);
138 : ~DumpAtoms();
139 : static void registerKeywords( Keywords& keys );
140 : void calculateNumericalDerivatives( ActionWithValue* a=NULL ) override;
141 194 : bool actionHasForces() override { return false; }
142 : void lockRequests() override;
143 : void unlockRequests() override;
144 9093 : void calculate() override {}
145 9093 : void apply() override {}
146 : void update() override ;
147 : };
148 :
149 : PLUMED_REGISTER_ACTION(DumpAtoms,"DUMPATOMS")
150 :
151 222 : void DumpAtoms::registerKeywords( Keywords& keys ) {
152 222 : Action::registerKeywords( keys );
153 222 : ActionPilot::registerKeywords( keys );
154 222 : ActionAtomistic::registerKeywords( keys );
155 222 : ActionWithArguments::registerKeywords( keys ); keys.use("ARG");
156 444 : keys.add("compulsory","STRIDE","1","the frequency with which the atoms should be output");
157 444 : keys.add("atoms", "ATOMS", "the atom indices whose positions you would like to print out");
158 444 : keys.add("compulsory", "FILE", "file on which to output coordinates; extension is automatically detected");
159 444 : keys.add("compulsory", "UNITS","PLUMED","the units in which to print out the coordinates. PLUMED means internal PLUMED units");
160 444 : keys.add("optional", "PRECISION","The number of digits in trajectory file");
161 444 : keys.add("optional", "TYPE","file type, either xyz, gro, xtc, or trr, can override an automatically detected file extension");
162 444 : keys.add("optional","LESS_THAN_OR_EQUAL","when printing with arguments that are vectors only print components of vectors have a value less than or equal to this value");
163 444 : keys.add("optional","GREATER_THAN_OR_EQUAL","when printing with arguments that are vectors only print components of vectors have a value greater than or equal to this value");
164 222 : keys.use("RESTART");
165 222 : keys.use("UPDATE_FROM");
166 222 : keys.use("UPDATE_UNTIL");
167 222 : }
168 :
169 220 : DumpAtoms::DumpAtoms(const ActionOptions&ao):
170 : Action(ao),
171 : ActionAtomistic(ao),
172 : ActionWithArguments(ao),
173 : ActionPilot(ao),
174 220 : iprecision(3)
175 : {
176 : std::vector<AtomNumber> atoms;
177 : std::string file;
178 440 : parse("FILE",file);
179 220 : if(file.length()==0) error("name out output file was not specified");
180 220 : type=Tools::extension(file);
181 220 : log<<" file name "<<file<<"\n";
182 453 : if(type=="gro" || type=="xyz" || type=="xtc" || type=="trr") {
183 197 : log<<" file extension indicates a "<<type<<" file\n";
184 : } else {
185 23 : log<<" file extension not detected, assuming xyz\n";
186 : type="xyz";
187 : }
188 : std::string ntype;
189 440 : parse("TYPE",ntype);
190 220 : if(ntype.length()>0) {
191 5 : if(ntype!="xyz" && ntype!="gro" && ntype!="xtc" && ntype!="trr"
192 0 : ) error("TYPE cannot be understood");
193 2 : log<<" file type enforced to be "<<ntype<<"\n";
194 : type=ntype;
195 : }
196 :
197 : fmt_gro_pos="%8.3f";
198 : fmt_gro_box="%12.7f";
199 : fmt_xyz="%f";
200 :
201 : std::string precision;
202 440 : parse("PRECISION",precision);
203 220 : if(precision.length()>0) {
204 136 : Tools::convert(precision,iprecision);
205 136 : log<<" with precision "<<iprecision<<"\n";
206 : std::string a,b;
207 136 : Tools::convert(iprecision+5,a);
208 136 : Tools::convert(iprecision,b);
209 272 : fmt_gro_pos="%"+a+"."+b+"f";
210 : fmt_gro_box=fmt_gro_pos;
211 : fmt_xyz=fmt_gro_box;
212 : }
213 :
214 440 : parseAtomList("ATOMS",atoms);
215 :
216 440 : std::string unitname; parse("UNITS",unitname);
217 220 : if(unitname!="PLUMED") {
218 17 : Units myunit; myunit.setLength(unitname);
219 32 : if(myunit.getLength()!=1.0 && type=="gro") error("gro files should be in nm");
220 32 : if(myunit.getLength()!=1.0 && type=="xtc") error("xtc files should be in nm");
221 32 : if(myunit.getLength()!=1.0 && type=="trr") error("trr files should be in nm");
222 17 : lenunit=getUnits().getLength()/myunit.getLength();
223 528 : } else if(type=="gro" || type=="xtc" || type=="trr") lenunit=getUnits().getLength();
224 147 : else lenunit=1.0;
225 :
226 220 : of.link(*this);
227 220 : of.open(file);
228 : std::string path=of.getPath();
229 220 : log<<" Writing on file "<<path<<"\n";
230 : std::string mode=of.getMode();
231 220 : if(type=="xtc") {
232 6 : of.close();
233 6 : xd=xdrfile::xdrfile_open(path.c_str(),mode.c_str());
234 214 : } else if(type=="trr") {
235 4 : of.close();
236 4 : xd=xdrfile::xdrfile_open(path.c_str(),mode.c_str());
237 : }
238 220 : log.printf(" printing the following atoms in %s :", unitname.c_str() );
239 30852 : for(unsigned i=0; i<atoms.size(); ++i) log.printf(" %d",atoms[i].serial() );
240 220 : log.printf("\n");
241 :
242 220 : if( getNumberOfArguments()>0 ) {
243 39 : if( type!="xyz" ) error("can only print atomic properties when outputting xyz files");
244 :
245 : std::vector<std::string> argnames;
246 119 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
247 80 : if( getPntrToArgument(i)->getRank()!=1 || getPntrToArgument(i)->hasDerivatives() ) error("arguments for xyz output should be vectors");
248 80 : if( getPntrToArgument(i)->getNumberOfValues()!=atoms.size() ) error("number of elements in vector " + getPntrToArgument(i)->getName() + " is not equal to number of atoms output");
249 80 : getPntrToArgument(i)->buildDataStore(true); argnames.push_back( getPntrToArgument(i)->getName() );
250 : }
251 : std::vector<std::string> str_upper, str_lower; std::string errors;
252 117 : parseVector("LESS_THAN_OR_EQUAL",str_upper); parseVector("GREATER_THAN_OR_EQUAL",str_lower);
253 39 : if( !bounds.setBounds( getNumberOfArguments(), str_lower, str_upper, errors ) ) error( errors );
254 52 : if( bounds.wereSet() ) log.printf(" %s \n", bounds.report( argnames ).c_str() );
255 39 : }
256 :
257 220 : requestAtoms(atoms, false);
258 220 : auto* moldat=plumed.getActionSet().selectLatest<GenericMolInfo*>(this);
259 220 : if( moldat ) {
260 56 : log<<" MOLINFO DATA found with label " <<moldat->getLabel()<<", using proper atom names\n";
261 56 : names.resize(atoms.size());
262 5835 : for(unsigned i=0; i<atoms.size(); i++) if(atoms[i].index()<moldat->getPDBsize()) names[i]=moldat->getAtomName(atoms[i]);
263 56 : residueNumbers.resize(atoms.size());
264 5835 : for(unsigned i=0; i<residueNumbers.size(); ++i) if(atoms[i].index()<moldat->getPDBsize()) residueNumbers[i]=moldat->getResidueNumber(atoms[i]);
265 56 : residueNames.resize(atoms.size());
266 5835 : for(unsigned i=0; i<residueNames.size(); ++i) if(atoms[i].index()<moldat->getPDBsize()) residueNames[i]=moldat->getResidueName(atoms[i]);
267 : }
268 220 : }
269 :
270 0 : void DumpAtoms::calculateNumericalDerivatives( ActionWithValue* a ) {
271 0 : plumed_merror("this should never be called");
272 : }
273 :
274 9093 : void DumpAtoms::lockRequests() {
275 : ActionWithArguments::lockRequests();
276 : ActionAtomistic::lockRequests();
277 9093 : }
278 :
279 9093 : void DumpAtoms::unlockRequests() {
280 : ActionWithArguments::unlockRequests();
281 : ActionAtomistic::unlockRequests();
282 9093 : }
283 :
284 8998 : void DumpAtoms::update() {
285 8998 : if(type=="xyz") {
286 8412 : unsigned nat=0; std::vector<double> args( getNumberOfArguments() );
287 73985 : for(unsigned i=0; i<getNumberOfAtoms(); ++i) {
288 95475 : for(unsigned j=0; j<getNumberOfArguments(); ++j) args[j] = getPntrToArgument(j)->get(i);
289 65573 : if( bounds.check( args ) ) nat++;
290 : }
291 8412 : of.printf("%d\n",nat);
292 8412 : const Tensor & t(getPbc().getBox());
293 8412 : if(getPbc().isOrthorombic()) {
294 612 : of.printf((" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+"\n").c_str(),lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2));
295 : } else {
296 16212 : of.printf((" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz+"\n").c_str(),
297 8106 : lenunit*t(0,0),lenunit*t(0,1),lenunit*t(0,2),
298 8106 : lenunit*t(1,0),lenunit*t(1,1),lenunit*t(1,2),
299 8106 : lenunit*t(2,0),lenunit*t(2,1),lenunit*t(2,2)
300 : );
301 : }
302 73985 : for(unsigned i=0; i<getNumberOfAtoms(); ++i) {
303 95475 : for(unsigned j=0; j<getNumberOfArguments(); ++j) args[j] = getPntrToArgument(j)->get(i);
304 65573 : if( !bounds.check(args) ) continue;
305 : const char* defname="X";
306 : const char* name=defname;
307 61767 : if(names.size()>0) if(names[i].length()>0) name=names[i].c_str();
308 123534 : of.printf(("%s "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz).c_str(),name,lenunit*getPosition(i)(0),lenunit*getPosition(i)(1),lenunit*getPosition(i)(2));
309 87863 : for(unsigned j=0; j<getNumberOfArguments(); ++j) of.printf((" "+fmt_xyz).c_str(), getPntrToArgument(j)->get(i) );
310 61767 : of.printf("\n");
311 : }
312 586 : } else if(type=="gro") {
313 466 : const Tensor & t(getPbc().getBox());
314 466 : of.printf("Made with PLUMED t=%f\n",getTime()/getUnits().getTime());
315 466 : of.printf("%d\n",getNumberOfAtoms());
316 38404 : for(unsigned i=0; i<getNumberOfAtoms(); ++i) {
317 : const char* defname="X";
318 : const char* name=defname;
319 : unsigned residueNumber=0;
320 37938 : if(names.size()>0) if(names[i].length()>0) name=names[i].c_str();
321 37938 : if(residueNumbers.size()>0) residueNumber=residueNumbers[i];
322 37938 : std::string resname="";
323 37938 : if(residueNames.size()>0) resname=residueNames[i];
324 75876 : of.printf(("%5u%-5s%5s%5d"+fmt_gro_pos+fmt_gro_pos+fmt_gro_pos+"\n").c_str(),
325 : residueNumber%100000,resname.c_str(),name,getAbsoluteIndex(i).serial()%100000,
326 37938 : lenunit*getPosition(i)(0),lenunit*getPosition(i)(1),lenunit*getPosition(i)(2));
327 : }
328 932 : 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(),
329 466 : lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2),
330 466 : lenunit*t(0,1),lenunit*t(0,2),lenunit*t(1,0),
331 466 : lenunit*t(1,2),lenunit*t(2,0),lenunit*t(2,1));
332 168 : } else if(type=="xtc" || type=="trr") {
333 : xdrfile::matrix box;
334 120 : const Tensor & t(getPbc().getBox());
335 120 : int natoms=getNumberOfAtoms();
336 120 : int step=getStep();
337 120 : float time=getTime()/getUnits().getTime();
338 120 : float precision=Tools::fastpow(10.0,iprecision);
339 1560 : for(int i=0; i<3; i++) for(int j=0; j<3; j++) box[i][j]=lenunit*t(i,j);
340 : // here we cannot use a std::vector<rvec> since it does not compile.
341 : // we thus use a std::unique_ptr<rvec[]>
342 : auto pos = Tools::make_unique<xdrfile::rvec[]>(natoms);
343 25464 : for(int i=0; i<natoms; i++) for(int j=0; j<3; j++) pos[i][j]=lenunit*getPosition(i)(j);
344 120 : if(type=="xtc") {
345 72 : write_xtc(xd,natoms,step,time,box,&pos[0],precision);
346 48 : } else if(type=="trr") {
347 48 : write_trr(xd,natoms,step,time,0.0,box,&pos[0],NULL,NULL);
348 : }
349 0 : } else plumed_merror("unknown file type "+type);
350 8998 : }
351 :
352 440 : DumpAtoms::~DumpAtoms() {
353 220 : if(type=="xtc") {
354 6 : xdrfile_close(xd);
355 214 : } else if(type=="trr") {
356 4 : xdrfile_close(xd);
357 : }
358 1100 : }
359 :
360 :
361 : }
362 : }
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