Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2020 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 "CLTool.h"
23 : #include "CLToolRegister.h"
24 : #include "tools/Tools.h"
25 : #include "core/PlumedMain.h"
26 : #include "tools/Communicator.h"
27 : #include "tools/Random.h"
28 : #include "tools/Pbc.h"
29 : #include <cstdio>
30 : #include <cstring>
31 : #include <vector>
32 : #include <map>
33 : #include <memory>
34 : #include "tools/Units.h"
35 : #include "tools/PDB.h"
36 : #include "tools/FileBase.h"
37 : #include "tools/IFile.h"
38 :
39 : // when using molfile plugin
40 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
41 : #ifndef __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS
42 : /* Use the internal ones. Alternatively:
43 : * ifeq (,$(findstring __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS,$(CPPFLAGS)))
44 : * CPPFLAGS+=-I../molfile
45 : */
46 : #include "molfile/libmolfile_plugin.h"
47 : #include "molfile/molfile_plugin.h"
48 : using namespace PLMD::molfile;
49 : #else
50 : #include <libmolfile_plugin.h>
51 : #include <molfile_plugin.h>
52 : #endif
53 : #endif
54 :
55 : #ifdef __PLUMED_HAS_XDRFILE
56 : #include <xdrfile/xdrfile_trr.h>
57 : #include <xdrfile/xdrfile_xtc.h>
58 : #endif
59 :
60 : using namespace std;
61 :
62 : namespace PLMD {
63 : namespace cltools {
64 :
65 : //+PLUMEDOC TOOLS driver-float
66 : /*
67 : Equivalent to \ref driver, but using single precision reals.
68 :
69 : The purpose of this tool is just to test what PLUMED does when linked from
70 : a single precision code.
71 :
72 : \par Examples
73 :
74 : \verbatim
75 : plumed driver-float --plumed plumed.dat --ixyz trajectory.xyz
76 : \endverbatim
77 :
78 : See also examples in \ref driver
79 :
80 : */
81 : //+ENDPLUMEDOC
82 : //
83 :
84 :
85 : //+PLUMEDOC TOOLS driver
86 : /*
87 : driver is a tool that allows one to to use plumed to post-process an existing trajectory.
88 :
89 : The input to driver is specified using the command line arguments described below.
90 :
91 : In addition, you can use the special \subpage READ command inside your plumed input
92 : to read in colvar files that were generated during your MD simulation. The values
93 : read in can then be treated like calculated colvars.
94 :
95 : \warning
96 : Notice that by default the driver has no knowledge about the masses and charges
97 : of your atoms! Thus, if you want to compute quantities depending charges (e.g. \ref DHENERGY)
98 : or masses (e.g. \ref COM) you should pass the proper information to the driver.
99 : You can do it either with the --pdb option or with the --mc option. The latter
100 : will read a file produced by \ref DUMPMASSCHARGE .
101 :
102 :
103 : \par Examples
104 :
105 : The following command tells plumed to post process the trajectory contained in `trajectory.xyz`
106 : by performing the actions described in the input file `plumed.dat`. If an action that takes the
107 : stride keyword is given a stride equal to \f$n\f$ then it will be performed only on every \f$n\f$th
108 : frames in the trajectory file.
109 : \verbatim
110 : plumed driver --plumed plumed.dat --ixyz trajectory.xyz
111 : \endverbatim
112 :
113 : Notice that `xyz` files are expected to be in internal PLUMED units, that is by default nm.
114 : You can change this behavior by using the `--length-units` option:
115 : \verbatim
116 : plumed driver --plumed plumed.dat --ixyz trajectory.xyz --length-units A
117 : \endverbatim
118 : The strings accepted by the `--length-units` options are the same ones accepted by the \ref UNITS action.
119 : Other file formats typically have their default coordinates (e.g., `gro` files are always in nm)
120 : and it thus should not be necessary to use the `--length-units` option. Additionally,
121 : consider that the units used by the `driver` might be different by the units used in the PLUMED input
122 : file `plumed.dat`. For instance consider the command:
123 : \verbatim
124 : plumed driver --plumed plumed.dat --ixyz trajectory.xyz --length-units A
125 : \endverbatim
126 : where `plumed.dat` is
127 : \plumedfile
128 : # no explicit UNITS action here
129 : d: DISTANCE ATOMS=1,2
130 : PRINT ARG=d FILE=colvar
131 : \endplumedfile
132 : In this case, the driver reads the `xyz` file assuming it to contain coordinates in Angstrom units.
133 : However, the resulting `colvar` file contains a distance expressed in nm.
134 :
135 : The following command tells plumed to post process the trajectory contained in trajectory.xyz.
136 : by performing the actions described in the input file plumed.dat.
137 : \verbatim
138 : plumed driver --plumed plumed.dat --ixyz trajectory.xyz --trajectory-stride 100 --timestep 0.001
139 : \endverbatim
140 : Here though
141 : `--trajectory-stride` is set equal to the frequency with which frames were output during the trajectory
142 : and the `--timestep` is equal to the simulation timestep. As such the `STRIDE` parameters in the `plumed.dat`
143 : files are referred to the original timestep and any files output resemble those that would have been generated
144 : had we run the calculation we are running with driver when the MD simulation was running.
145 :
146 : PLUMED can read xyz files (in PLUMED units) and gro files (in nm). In addition,
147 : PLUMED includes by default support for a
148 : subset of the trajectory file formats supported by VMD, e.g. xtc and dcd:
149 :
150 : \verbatim
151 : plumed driver --plumed plumed.dat --pdb diala.pdb --mf_xtc traj.xtc --trajectory-stride 100 --timestep 0.001
152 : \endverbatim
153 :
154 : where `--mf_` prefixes the extension of one of the accepted molfile plugin format.
155 : If PLUMED has been \ref Installation "installed" with full molfile support, other formats will be available.
156 : Just type `plumed driver --help` to see which plugins are available.
157 :
158 : Molfile plugin require periodic cell to be triangular (i.e. first vector oriented along x and
159 : second vector in xy plane). This is true for many MD codes. However, it could be false
160 : if you rotate the coordinates in your trajectory before reading them in the driver.
161 : Also notice that some formats (e.g. amber crd) do not specify atom number. In this case you can use
162 : the `--natoms` option:
163 : \verbatim
164 : plumed driver --plumed plumed.dat --imf_crd trajectory.crd --natoms 128
165 : \endverbatim
166 :
167 : Check the available molfile plugins and limitations at [this link](http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/).
168 :
169 : Additionally, you can use the xdrfile implementation of xtc and trr. To this aim, just
170 : download and install properly the xdrfile library (see [this link](http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library)).
171 : If the xdrfile library is installed properly the PLUMED configure script should be able to
172 : detect it and enable it.
173 : Notice that the xdrfile implementation of xtc and trr
174 : is more robust than the molfile one, since it provides support for generic cell shapes.
175 : In addition, it allows \ref DUMPATOMS to write compressed xtc files.
176 :
177 :
178 : */
179 : //+ENDPLUMEDOC
180 : //
181 :
182 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
183 5517 : static vector<molfile_plugin_t *> plugins;
184 5517 : static map <string, unsigned> pluginmap;
185 33102 : static int register_cb(void *v, vmdplugin_t *p) {
186 : //const char *key = p->name;
187 99306 : const auto ret = pluginmap.insert ( std::pair<string,unsigned>(string(p->name),plugins.size()) );
188 33102 : if (ret.second==false) {
189 : //cerr<<"MOLFILE: found duplicate plugin for "<<key<<" : not inserted "<<endl;
190 : } else {
191 : //cerr<<"MOLFILE: loading plugin "<<key<<" number "<<plugins.size()-1<<endl;
192 66204 : plugins.push_back(reinterpret_cast<molfile_plugin_t *>(p));
193 : }
194 33102 : return VMDPLUGIN_SUCCESS;
195 : }
196 : #endif
197 :
198 : template<typename real>
199 579 : class Driver : public CLTool {
200 : public:
201 : static void registerKeywords( Keywords& keys );
202 : explicit Driver(const CLToolOptions& co );
203 : int main(FILE* in,FILE*out,Communicator& pc);
204 : void evaluateNumericalDerivatives( const long int& step, PlumedMain& p, const std::vector<real>& coordinates,
205 : const std::vector<real>& masses, const std::vector<real>& charges,
206 : std::vector<real>& cell, const double& base, std::vector<real>& numder );
207 : string description()const;
208 : };
209 :
210 : template<typename real>
211 3678 : void Driver<real>::registerKeywords( Keywords& keys ) {
212 3678 : CLTool::registerKeywords( keys ); keys.isDriver();
213 11034 : keys.addFlag("--help-debug",false,"print special options that can be used to create regtests");
214 18390 : keys.add("compulsory","--plumed","plumed.dat","specify the name of the plumed input file");
215 18390 : keys.add("compulsory","--timestep","1.0","the timestep that was used in the calculation that produced this trajectory in picoseconds");
216 18390 : keys.add("compulsory","--trajectory-stride","1","the frequency with which frames were output to this trajectory during the simulation"
217 : #ifdef __PLUMED_HAS_XDRFILE
218 : " (0 means that the number of the step is read from the trajectory file,"
219 : " currently working only for xtc/trr files read with --ixtc/--trr)"
220 : #endif
221 : );
222 18390 : keys.add("compulsory","--multi","0","set number of replicas for multi environment (needs MPI)");
223 11034 : keys.addFlag("--noatoms",false,"don't read in a trajectory. Just use colvar files as specified in plumed.dat");
224 11034 : keys.addFlag("--parse-only",false,"read the plumed input file and stop");
225 14712 : keys.add("atoms","--ixyz","the trajectory in xyz format");
226 14712 : keys.add("atoms","--igro","the trajectory in gro format");
227 : #ifdef __PLUMED_HAS_XDRFILE
228 14712 : keys.add("atoms","--ixtc","the trajectory in xtc format (xdrfile implementation)");
229 14712 : keys.add("atoms","--itrr","the trajectory in trr format (xdrfile implementation)");
230 : #endif
231 14712 : keys.add("optional","--length-units","units for length, either as a string or a number");
232 14712 : keys.add("optional","--mass-units","units for mass in pdb and mc file, either as a string or a number");
233 14712 : keys.add("optional","--charge-units","units for charge in pdb and mc file, either as a string or a number");
234 14712 : keys.add("optional","--kt","set \\f$k_B T\\f$, it will not be necessary to specify temperature in input file");
235 14712 : keys.add("optional","--dump-forces","dump the forces on a file");
236 14712 : keys.add("optional","--dump-forces-fmt","( default=%%f ) the format to use to dump the forces");
237 11034 : keys.addFlag("--dump-full-virial",false,"with --dump-forces, it dumps the 9 components of the virial");
238 14712 : keys.add("optional","--pdb","provides a pdb with masses and charges");
239 14712 : keys.add("optional","--mc","provides a file with masses and charges as produced with DUMPMASSCHARGE");
240 14712 : keys.add("optional","--box","comma-separated box dimensions (3 for orthorhombic, 9 for generic)");
241 14712 : keys.add("optional","--natoms","provides number of atoms - only used if file format does not contain number of atoms");
242 14712 : keys.add("optional","--initial-step","provides a number for the initial step, default is 0");
243 14712 : keys.add("optional","--debug-forces","output a file containing the forces due to the bias evaluated using numerical derivatives "
244 : "and using the analytical derivatives implemented in plumed");
245 14712 : keys.add("hidden","--debug-float","[yes/no] turns on the single precision version (to check float interface)");
246 14712 : keys.add("hidden","--debug-dd","[yes/no] use a fake domain decomposition");
247 14712 : keys.add("hidden","--debug-pd","[yes/no] use a fake particle decomposition");
248 14712 : keys.add("hidden","--debug-grex","use a fake gromacs-like replica exchange, specify exchange stride");
249 14712 : keys.add("hidden","--debug-grex-log","log file for debug=grex");
250 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
251 3678 : MOLFILE_INIT_ALL
252 3678 : MOLFILE_REGISTER_ALL(NULL, register_cb)
253 106662 : for(unsigned i=0; i<plugins.size(); i++) {
254 66204 : string kk="--mf_"+string(plugins[i]->name);
255 99306 : string mm=" molfile: the trajectory in "+string(plugins[i]->name)+" format " ;
256 66204 : keys.add("atoms",kk,mm);
257 : }
258 : #endif
259 3678 : }
260 : template<typename real>
261 579 : Driver<real>::Driver(const CLToolOptions& co ):
262 579 : CLTool(co)
263 : {
264 579 : inputdata=commandline;
265 579 : }
266 : template<typename real>
267 0 : string Driver<real>::description()const { return "analyze trajectories with plumed"; }
268 :
269 : template<typename real>
270 579 : int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
271 :
272 1158 : Units units;
273 1158 : PDB pdb;
274 :
275 : // Parse everything
276 1158 : bool printhelpdebug; parseFlag("--help-debug",printhelpdebug);
277 579 : if( printhelpdebug ) {
278 : fprintf(out,"%s",
279 : "Additional options for debug (only to be used in regtest):\n"
280 : " [--debug-float yes] : turns on the single precision version (to check float interface)\n"
281 : " [--debug-dd yes] : use a fake domain decomposition\n"
282 : " [--debug-pd yes] : use a fake particle decomposition\n"
283 : );
284 : return 0;
285 : }
286 : // Are we reading trajectory data
287 1158 : bool noatoms; parseFlag("--noatoms",noatoms);
288 1158 : bool parseOnly; parseFlag("--parse-only",parseOnly);
289 :
290 : std::string fakein;
291 : bool debug_float=false;
292 : fakein="";
293 1158 : if(parse("--debug-float",fakein)) {
294 0 : if(fakein=="yes") debug_float=true;
295 0 : else if(fakein=="no") debug_float=false;
296 0 : else error("--debug-float should have argument yes or no");
297 : }
298 :
299 : if(debug_float && sizeof(real)!=sizeof(float)) {
300 0 : auto cl=cltoolRegister().create(CLToolOptions("driver-float"));
301 : cl->setInputData(this->getInputData());
302 0 : int ret=cl->main(in,out,pc);
303 : return ret;
304 : }
305 :
306 : bool debug_pd=false;
307 : fakein="";
308 1158 : if(parse("--debug-pd",fakein)) {
309 12 : if(fakein=="yes") debug_pd=true;
310 0 : else if(fakein=="no") debug_pd=false;
311 0 : else error("--debug-pd should have argument yes or no");
312 : }
313 : if(debug_pd) fprintf(out,"DEBUGGING PARTICLE DECOMPOSITION\n");
314 :
315 : bool debug_dd=false;
316 : fakein="";
317 1158 : if(parse("--debug-dd",fakein)) {
318 58 : if(fakein=="yes") debug_dd=true;
319 0 : else if(fakein=="no") debug_dd=false;
320 0 : else error("--debug-dd should have argument yes or no");
321 : }
322 : if(debug_dd) fprintf(out,"DEBUGGING DOMAIN DECOMPOSITION\n");
323 :
324 579 : if( debug_pd || debug_dd ) {
325 70 : if(noatoms) error("cannot debug without atoms");
326 : }
327 :
328 : // set up for multi replica driver:
329 579 : int multi=0;
330 1158 : parse("--multi",multi);
331 1158 : Communicator intracomm;
332 1158 : Communicator intercomm;
333 579 : if(multi) {
334 150 : int ntot=pc.Get_size();
335 150 : int nintra=ntot/multi;
336 150 : if(multi*nintra!=ntot) error("invalid number of processes for multi environment");
337 150 : pc.Split(pc.Get_rank()/nintra,pc.Get_rank(),intracomm);
338 150 : pc.Split(pc.Get_rank()%nintra,pc.Get_rank(),intercomm);
339 : } else {
340 429 : intracomm.Set_comm(pc.Get_comm());
341 : }
342 :
343 : // set up for debug replica exchange:
344 1158 : bool debug_grex=parse("--debug-grex",fakein);
345 579 : int grex_stride=0;
346 : FILE*grex_log=NULL;
347 579 : if(debug_grex) {
348 30 : if(noatoms) error("must have atoms to debug_grex");
349 30 : if(multi<2) error("--debug_grex needs --multi with at least two replicas");
350 30 : Tools::convert(fakein,grex_stride);
351 30 : string n; Tools::convert(intercomm.Get_rank(),n);
352 : string file;
353 60 : parse("--debug-grex-log",file);
354 30 : if(file.length()>0) {
355 60 : file+="."+n;
356 30 : grex_log=fopen(file.c_str(),"w");
357 : }
358 : }
359 :
360 : // Read the plumed input file name
361 1158 : string plumedFile; parse("--plumed",plumedFile);
362 : // the timestep
363 1158 : double t; parse("--timestep",t);
364 579 : real timestep=real(t);
365 : // the stride
366 1158 : unsigned stride; parse("--trajectory-stride",stride);
367 : // are we writing forces
368 579 : string dumpforces(""), debugforces(""), dumpforcesFmt("%f");;
369 579 : bool dumpfullvirial=false;
370 579 : if(!noatoms) {
371 1076 : parse("--dump-forces",dumpforces);
372 1076 : parse("--debug-forces",debugforces);
373 : }
374 1167 : if(dumpforces!="" || debugforces!="" ) parse("--dump-forces-fmt",dumpforcesFmt);
375 938 : if(dumpforces!="") parseFlag("--dump-full-virial",dumpfullvirial);
376 579 : if( debugforces!="" && (debug_dd || debug_pd) ) error("cannot debug forces and domain/particle decomposition at same time");
377 0 : if( debugforces!="" && sizeof(real)!=sizeof(double) ) error("cannot debug forces in single precision mode");
378 :
379 579 : real kt=-1.0;
380 1158 : parse("--kt",kt);
381 : string trajectory_fmt;
382 :
383 : bool use_molfile=false;
384 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
385 : molfile_plugin_t *api=NULL;
386 : void *h_in=NULL;
387 : molfile_timestep_t ts_in; // this is the structure that has the timestep
388 : // a std::unique_ptr<float> with the same scope as ts_in
389 : // it is necessary in order to store the pointer to ts_in.coords
390 : std::unique_ptr<float[]> ts_in_coords;
391 579 : ts_in.coords=ts_in_coords.get();
392 579 : ts_in.velocities=NULL;
393 579 : ts_in.A=-1; // we use this to check whether cell is provided or not
394 : #endif
395 :
396 : // Read in an xyz file
397 579 : string trajectoryFile(""), pdbfile(""), mcfile("");
398 579 : bool pbc_cli_given=false; vector<double> pbc_cli_box(9,0.0);
399 579 : int command_line_natoms=-1;
400 :
401 579 : if(!noatoms) {
402 1076 : std::string traj_xyz; parse("--ixyz",traj_xyz);
403 1076 : std::string traj_gro; parse("--igro",traj_gro);
404 : std::string traj_xtc;
405 : std::string traj_trr;
406 : #ifdef __PLUMED_HAS_XDRFILE
407 1076 : parse("--ixtc",traj_xtc);
408 1076 : parse("--itrr",traj_trr);
409 : #endif
410 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
411 15602 : for(unsigned i=0; i<plugins.size(); i++) {
412 9684 : string molfile_key="--mf_"+string(plugins[i]->name);
413 : string traj_molfile;
414 4842 : parse(molfile_key,traj_molfile);
415 4842 : if(traj_molfile.length()>0) {
416 72 : fprintf(out,"\nDRIVER: Found molfile format trajectory %s with name %s\n",plugins[i]->name,traj_molfile.c_str());
417 : trajectoryFile=traj_molfile;
418 144 : trajectory_fmt=string(plugins[i]->name);
419 : use_molfile=true;
420 72 : api = plugins[i];
421 : }
422 : }
423 : #endif
424 : { // check that only one fmt is specified
425 : int nn=0;
426 538 : if(traj_xyz.length()>0) nn++;
427 538 : if(traj_gro.length()>0) nn++;
428 538 : if(traj_xtc.length()>0) nn++;
429 538 : if(traj_trr.length()>0) nn++;
430 538 : if(nn>1) {
431 0 : fprintf(stderr,"ERROR: cannot provide more than one trajectory file\n");
432 0 : if(grex_log)fclose(grex_log);
433 : return 1;
434 : }
435 : }
436 899 : if(traj_xyz.length()>0 && trajectoryFile.length()==0) {
437 : trajectoryFile=traj_xyz;
438 : trajectory_fmt="xyz";
439 : }
440 638 : if(traj_gro.length()>0 && trajectoryFile.length()==0) {
441 : trajectoryFile=traj_gro;
442 : trajectory_fmt="gro";
443 : }
444 540 : if(traj_xtc.length()>0 && trajectoryFile.length()==0) {
445 : trajectoryFile=traj_xtc;
446 : trajectory_fmt="xdr-xtc";
447 : }
448 541 : if(traj_trr.length()>0 && trajectoryFile.length()==0) {
449 : trajectoryFile=traj_trr;
450 : trajectory_fmt="xdr-trr";
451 : }
452 538 : if(trajectoryFile.length()==0&&!parseOnly) {
453 0 : fprintf(stderr,"ERROR: missing trajectory data\n");
454 0 : if(grex_log)fclose(grex_log);
455 : return 1;
456 : }
457 1614 : string lengthUnits(""); parse("--length-units",lengthUnits);
458 538 : if(lengthUnits.length()>0) units.setLength(lengthUnits);
459 1076 : string chargeUnits(""); parse("--charge-units",chargeUnits);
460 538 : if(chargeUnits.length()>0) units.setCharge(chargeUnits);
461 1076 : string massUnits(""); parse("--mass-units",massUnits);
462 538 : if(massUnits.length()>0) units.setMass(massUnits);
463 :
464 1076 : parse("--pdb",pdbfile);
465 538 : if(pdbfile.length()>0) {
466 69 : bool check=pdb.read(pdbfile,false,1.0);
467 69 : if(!check) error("error reading pdb file");
468 : }
469 :
470 1076 : parse("--mc",mcfile);
471 :
472 1076 : string pbc_cli_list; parse("--box",pbc_cli_list);
473 538 : if(pbc_cli_list.length()>0) {
474 : pbc_cli_given=true;
475 36 : vector<string> words=Tools::getWords(pbc_cli_list,",");
476 18 : if(words.size()==3) {
477 180 : for(int i=0; i<3; i++) sscanf(words[i].c_str(),"%100lf",&(pbc_cli_box[4*i]));
478 0 : } else if(words.size()==9) {
479 0 : for(int i=0; i<9; i++) sscanf(words[i].c_str(),"%100lf",&(pbc_cli_box[i]));
480 : } else {
481 0 : string msg="ERROR: cannot parse command-line box "+pbc_cli_list;
482 0 : fprintf(stderr,"%s\n",msg.c_str());
483 : return 1;
484 : }
485 :
486 : }
487 :
488 1076 : parse("--natoms",command_line_natoms);
489 :
490 : }
491 :
492 :
493 579 : if(debug_dd && debug_pd) error("cannot use debug-dd and debug-pd at the same time");
494 579 : if(debug_pd || debug_dd) {
495 70 : if( !Communicator::initialized() ) error("needs mpi for debug-pd");
496 : }
497 :
498 1158 : PlumedMain p;
499 579 : int rr=sizeof(real);
500 1158 : p.cmd("setRealPrecision",&rr);
501 : int checknatoms=-1;
502 579 : long int step=0;
503 1158 : parse("--initial-step",step);
504 :
505 579 : if(Communicator::initialized()) {
506 246 : if(multi) {
507 252 : if(intracomm.Get_rank()==0) p.cmd("GREX setMPIIntercomm",&intercomm.Get_comm());
508 300 : p.cmd("GREX setMPIIntracomm",&intracomm.Get_comm());
509 300 : p.cmd("GREX init");
510 : }
511 492 : p.cmd("setMPIComm",&intracomm.Get_comm());
512 : }
513 1158 : p.cmd("setMDLengthUnits",&units.getLength());
514 1158 : p.cmd("setMDChargeUnits",&units.getCharge());
515 1158 : p.cmd("setMDMassUnits",&units.getMass());
516 1158 : p.cmd("setMDEngine","driver");
517 1158 : p.cmd("setTimestep",×tep);
518 1158 : p.cmd("setPlumedDat",plumedFile.c_str());
519 1158 : p.cmd("setLog",out);
520 :
521 : int natoms;
522 :
523 579 : if(parseOnly) {
524 0 : if(command_line_natoms<0) error("--parseOnly requires setting the number of atoms with --natoms");
525 0 : natoms=command_line_natoms;
526 : }
527 :
528 :
529 1158 : FILE* fp=NULL; FILE* fp_forces=NULL; OFile fp_dforces;
530 : #ifdef __PLUMED_HAS_XDRFILE
531 : XDRFILE* xd=NULL;
532 : #endif
533 579 : if(!noatoms&&!parseOnly) {
534 538 : if (trajectoryFile=="-")
535 : fp=in;
536 : else {
537 538 : if(multi) {
538 : string n;
539 150 : Tools::convert(intercomm.Get_rank(),n);
540 300 : std::string testfile=FileBase::appendSuffix(trajectoryFile,"."+n);
541 150 : FILE* tmp_fp=fopen(testfile.c_str(),"r");
542 150 : if(tmp_fp) { fclose(tmp_fp); trajectoryFile=testfile.c_str();}
543 : }
544 538 : if(use_molfile==true) {
545 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
546 144 : h_in = api->open_file_read(trajectoryFile.c_str(), trajectory_fmt.c_str(), &natoms);
547 72 : if(natoms==MOLFILE_NUMATOMS_UNKNOWN) {
548 2 : if(command_line_natoms>=0) natoms=command_line_natoms;
549 0 : else error("this file format does not provide number of atoms; use --natoms on the command line");
550 : }
551 72 : ts_in_coords.reset(new float [3*natoms]);
552 72 : ts_in.coords = ts_in_coords.get();
553 : #endif
554 930 : } else if(trajectory_fmt=="xdr-xtc" || trajectory_fmt=="xdr-trr") {
555 : #ifdef __PLUMED_HAS_XDRFILE
556 5 : xd=xdrfile_open(trajectoryFile.c_str(),"r");
557 5 : if(!xd) {
558 0 : string msg="ERROR: Error opening trajectory file "+trajectoryFile;
559 0 : fprintf(stderr,"%s\n",msg.c_str());
560 : return 1;
561 : }
562 7 : if(trajectory_fmt=="xdr-xtc") read_xtc_natoms(&trajectoryFile[0],&natoms);
563 8 : if(trajectory_fmt=="xdr-trr") read_trr_natoms(&trajectoryFile[0],&natoms);
564 : #endif
565 : } else {
566 461 : fp=fopen(trajectoryFile.c_str(),"r");
567 461 : if(!fp) {
568 0 : string msg="ERROR: Error opening trajectory file "+trajectoryFile;
569 0 : fprintf(stderr,"%s\n",msg.c_str());
570 : return 1;
571 : }
572 : }
573 : }
574 538 : if(dumpforces.length()>0) {
575 359 : if(Communicator::initialized() && pc.Get_size()>1) {
576 : string n;
577 186 : Tools::convert(pc.Get_rank(),n);
578 372 : dumpforces+="."+n;
579 : }
580 359 : fp_forces=fopen(dumpforces.c_str(),"w");
581 : }
582 538 : if(debugforces.length()>0) {
583 10 : if(Communicator::initialized() && pc.Get_size()>1) {
584 : string n;
585 6 : Tools::convert(pc.Get_rank(),n);
586 12 : debugforces+="."+n;
587 : }
588 10 : fp_dforces.open(debugforces);
589 : }
590 : }
591 :
592 : std::string line;
593 : std::vector<real> coordinates;
594 : std::vector<real> forces;
595 : std::vector<real> masses;
596 : std::vector<real> charges;
597 : std::vector<real> cell;
598 : std::vector<real> virial;
599 : std::vector<real> numder;
600 :
601 : // variables to test particle decomposition
602 : int pd_nlocal;
603 : int pd_start;
604 : // variables to test random decomposition (=domain decomposition)
605 : std::vector<int> dd_gatindex;
606 : std::vector<int> dd_g2l;
607 : std::vector<real> dd_masses;
608 : std::vector<real> dd_charges;
609 : std::vector<real> dd_forces;
610 : std::vector<real> dd_coordinates;
611 : int dd_nlocal;
612 : // random stream to choose decompositions
613 579 : Random rnd;
614 :
615 31770 : while(true) {
616 32349 : if(!noatoms&&!parseOnly) {
617 30022 : if(use_molfile==true) {
618 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
619 : int rc;
620 6515 : rc = api->read_next_timestep(h_in, natoms, &ts_in);
621 6515 : if(rc==MOLFILE_EOF) {
622 : break;
623 : }
624 : #endif
625 25689 : } else if(trajectory_fmt=="xyz" || trajectory_fmt=="gro") {
626 23438 : if(!Tools::getline(fp,line)) break;
627 : }
628 : }
629 :
630 : bool first_step=false;
631 31820 : if(!noatoms&&!parseOnly) {
632 54628 : if(use_molfile==false && (trajectory_fmt=="xyz" || trajectory_fmt=="gro")) {
633 22981 : if(trajectory_fmt=="gro") if(!Tools::getline(fp,line)) error("premature end of trajectory file");
634 22981 : sscanf(line.c_str(),"%100d",&natoms);
635 : }
636 : }
637 31820 : if(checknatoms<0 && !noatoms) {
638 538 : pd_nlocal=natoms;
639 538 : pd_start=0;
640 : first_step=true;
641 1076 : masses.assign(natoms,std::numeric_limits<real>::quiet_NaN());
642 1076 : charges.assign(natoms,std::numeric_limits<real>::quiet_NaN());
643 : //case pdb: structure
644 538 : if(pdbfile.length()>0) {
645 13449 : for(unsigned i=0; i<pdb.size(); ++i) {
646 13380 : AtomNumber an=pdb.getAtomNumbers()[i];
647 : unsigned index=an.index();
648 6690 : if( index>=unsigned(natoms) ) error("atom index in pdb exceeds the number of atoms in trajectory");
649 20070 : masses[index]=pdb.getOccupancy()[i];
650 13380 : charges[index]=pdb.getBeta()[i];
651 : }
652 : }
653 538 : if(mcfile.length()>0) {
654 10 : IFile ifile;
655 5 : ifile.open(mcfile);
656 : int index; double mass; double charge;
657 2840 : while(ifile.scanField("index",index).scanField("mass",mass).scanField("charge",charge).scanField()) {
658 1128 : masses[index]=mass;
659 1128 : charges[index]=charge;
660 : }
661 : }
662 31282 : } else if( checknatoms<0 && noatoms ) {
663 41 : natoms=0;
664 : }
665 31820 : if( checknatoms<0 ) {
666 579 : if(kt>=0) {
667 2 : p.cmd("setKbT",&kt);
668 : }
669 579 : checknatoms=natoms;
670 1158 : p.cmd("setNatoms",&natoms);
671 1158 : p.cmd("init");
672 579 : if(parseOnly) break;
673 : }
674 31820 : if(checknatoms!=natoms) {
675 0 : std::string stepstr; Tools::convert(step,stepstr);
676 0 : error("number of atoms in frame " + stepstr + " does not match number of atoms in first frame");
677 : }
678 :
679 63640 : coordinates.assign(3*natoms,real(0.0));
680 63640 : forces.assign(3*natoms,real(0.0));
681 63640 : cell.assign(9,real(0.0));
682 63640 : virial.assign(9,real(0.0));
683 :
684 31820 : if( first_step || rnd.U01()>0.5) {
685 16603 : if(debug_pd) {
686 152 : int npe=intracomm.Get_size();
687 152 : vector<int> loc(npe,0);
688 152 : vector<int> start(npe,0);
689 1064 : for(int i=0; i<npe-1; i++) {
690 456 : int cc=(natoms*2*rnd.U01())/npe;
691 912 : if(start[i]+cc>natoms) cc=natoms-start[i];
692 456 : loc[i]=cc;
693 1368 : start[i+1]=start[i]+loc[i];
694 : }
695 456 : loc[npe-1]=natoms-start[npe-1];
696 152 : intracomm.Bcast(loc,0);
697 152 : intracomm.Bcast(start,0);
698 304 : pd_nlocal=loc[intracomm.Get_rank()];
699 304 : pd_start=start[intracomm.Get_rank()];
700 152 : if(intracomm.Get_rank()==0) {
701 : fprintf(out,"\nDRIVER: Reassigning particle decomposition\n");
702 494 : fprintf(out,"DRIVER: "); for(int i=0; i<npe; i++) fprintf(out,"%d ",loc[i]); printf("\n");
703 494 : fprintf(out,"DRIVER: "); for(int i=0; i<npe; i++) fprintf(out,"%d ",start[i]); printf("\n");
704 : }
705 304 : p.cmd("setAtomsNlocal",&pd_nlocal);
706 304 : p.cmd("setAtomsContiguous",&pd_start);
707 16451 : } else if(debug_dd) {
708 946 : int npe=intracomm.Get_size();
709 946 : int rank=intracomm.Get_rank();
710 1892 : dd_charges.assign(natoms,0.0);
711 1892 : dd_masses.assign(natoms,0.0);
712 1892 : dd_gatindex.assign(natoms,-1);
713 1892 : dd_g2l.assign(natoms,-1);
714 1892 : dd_coordinates.assign(3*natoms,0.0);
715 1892 : dd_forces.assign(3*natoms,0.0);
716 946 : dd_nlocal=0;
717 103966 : for(int i=0; i<natoms; ++i) {
718 51510 : double r=rnd.U01()*npe;
719 110396 : int n; for(n=0; n<npe; n++) if(n+1>r)break;
720 51510 : plumed_assert(n<npe);
721 51510 : if(n==rank) {
722 38334 : dd_gatindex[dd_nlocal]=i;
723 38334 : dd_g2l[i]=dd_nlocal;
724 38334 : dd_charges[dd_nlocal]=charges[i];
725 38334 : dd_masses[dd_nlocal]=masses[i];
726 19167 : dd_nlocal++;
727 : }
728 : }
729 946 : if(intracomm.Get_rank()==0) {
730 : fprintf(out,"\nDRIVER: Reassigning domain decomposition\n");
731 : }
732 1892 : p.cmd("setAtomsNlocal",&dd_nlocal);
733 1892 : p.cmd("setAtomsGatindex",&dd_gatindex[0]);
734 : }
735 : }
736 :
737 31820 : int plumedStopCondition=0;
738 31820 : if(!noatoms) {
739 29493 : if(use_molfile) {
740 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
741 6443 : if(pbc_cli_given==false) {
742 6440 : if(ts_in.A>0.0) { // this is negative if molfile does not provide box
743 : // info on the cell: convert using pbcset.tcl from pbctools in vmd distribution
744 6437 : real cosBC=cos(ts_in.alpha*pi/180.);
745 : //double sinBC=sin(ts_in.alpha*pi/180.);
746 6437 : real cosAC=cos(ts_in.beta*pi/180.);
747 6437 : real cosAB=cos(ts_in.gamma*pi/180.);
748 6437 : real sinAB=sin(ts_in.gamma*pi/180.);
749 6437 : real Ax=ts_in.A;
750 6437 : real Bx=ts_in.B*cosAB;
751 6437 : real By=ts_in.B*sinAB;
752 6437 : real Cx=ts_in.C*cosAC;
753 6437 : real Cy=(ts_in.C*ts_in.B*cosBC-Cx*Bx)/By;
754 6437 : real Cz=sqrt(ts_in.C*ts_in.C-Cx*Cx-Cy*Cy);
755 12874 : cell[0]=Ax/10.; cell[1]=0.; cell[2]=0.;
756 6437 : cell[3]=Bx/10.; cell[4]=By/10.; cell[5]=0.;
757 6437 : cell[6]=Cx/10.; cell[7]=Cy/10.; cell[8]=Cz/10.;
758 : } else {
759 6 : cell[0]=0.0; cell[1]=0.0; cell[2]=0.0;
760 3 : cell[3]=0.0; cell[4]=0.0; cell[5]=0.0;
761 3 : cell[6]=0.0; cell[7]=0.0; cell[8]=0.0;
762 : }
763 : } else {
764 57 : for(unsigned i=0; i<9; i++)cell[i]=pbc_cli_box[i];
765 : }
766 : // info on coords
767 : // the order is xyzxyz...
768 6536861 : for(int i=0; i<3*natoms; i++) {
769 6530418 : coordinates[i]=real(ts_in.coords[i]/10.); //convert to nm
770 : //cerr<<"COOR "<<coordinates[i]<<endl;
771 : }
772 : #endif
773 46070 : } else if(trajectory_fmt=="xdr-xtc" || trajectory_fmt=="xdr-trr") {
774 : #ifdef __PLUMED_HAS_XDRFILE
775 : int localstep;
776 : float time;
777 : matrix box;
778 69 : std::unique_ptr<rvec[]> pos(new rvec[natoms]);
779 : float prec,lambda;
780 : int ret=exdrOK;
781 69 : if(trajectory_fmt=="xdr-xtc") ret=read_xtc(xd,natoms,&localstep,&time,box,pos.get(),&prec);
782 69 : if(trajectory_fmt=="xdr-trr") ret=read_trr(xd,natoms,&localstep,&time,&lambda,box,pos.get(),NULL,NULL);
783 69 : if(stride==0) step=localstep;
784 69 : if(ret==exdrENDOFFILE) break;
785 67 : if(ret!=exdrOK) break;
786 832 : for(unsigned i=0; i<3; i++) for(unsigned j=0; j<3; j++) cell[3*i+j]=box[i][j];
787 10976 : for(int i=0; i<natoms; i++) for(unsigned j=0; j<3; j++)
788 24552 : coordinates[3*i+j]=real(pos[i][j]);
789 : #endif
790 : } else {
791 22981 : if(trajectory_fmt=="xyz") {
792 20965 : if(!Tools::getline(fp,line)) error("premature end of trajectory file");
793 :
794 20965 : std::vector<double> celld(9,0.0);
795 20965 : if(pbc_cli_given==false) {
796 20759 : std::vector<std::string> words;
797 41518 : words=Tools::getWords(line);
798 20759 : if(words.size()==3) {
799 20186 : sscanf(line.c_str(),"%100lf %100lf %100lf",&celld[0],&celld[4],&celld[8]);
800 573 : } else if(words.size()==9) {
801 573 : sscanf(line.c_str(),"%100lf %100lf %100lf %100lf %100lf %100lf %100lf %100lf %100lf",
802 : &celld[0], &celld[1], &celld[2],
803 : &celld[3], &celld[4], &celld[5],
804 : &celld[6], &celld[7], &celld[8]);
805 0 : } else error("needed box in second line of xyz file");
806 : } else { // from command line
807 206 : celld=pbc_cli_box;
808 : }
809 398335 : for(unsigned i=0; i<9; i++)cell[i]=real(celld[i]);
810 : }
811 : int ddist=0;
812 : // Read coordinates
813 3459651 : for(int i=0; i<natoms; i++) {
814 1718335 : bool ok=Tools::getline(fp,line);
815 1718335 : if(!ok) error("premature end of trajectory file");
816 : double cc[3];
817 1718335 : if(trajectory_fmt=="xyz") {
818 : char dummy[1000];
819 1642749 : int ret=std::sscanf(line.c_str(),"%999s %100lf %100lf %100lf",dummy,&cc[0],&cc[1],&cc[2]);
820 1642749 : if(ret!=4) error("cannot read line"+line);
821 75586 : } else if(trajectory_fmt=="gro") {
822 : // do the gromacs way
823 75586 : if(!i) {
824 : //
825 : // calculate the distance between dots (as in gromacs gmxlib/confio.c, routine get_w_conf )
826 : //
827 : const char *p1, *p2, *p3;
828 : p1 = strchr(line.c_str(), '.');
829 2016 : if (p1 == NULL) error("seems there are no coordinates in the gro file");
830 2016 : p2 = strchr(&p1[1], '.');
831 2016 : if (p2 == NULL) error("seems there is only one coordinates in the gro file");
832 2016 : ddist = p2 - p1;
833 2016 : p3 = strchr(&p2[1], '.');
834 2016 : if (p3 == NULL)error("seems there are only two coordinates in the gro file");
835 2016 : if (p3 - p2 != ddist)error("not uniform spacing in fields in the gro file");
836 : }
837 151172 : Tools::convert(line.substr(20,ddist),cc[0]);
838 151172 : Tools::convert(line.substr(20+ddist,ddist),cc[1]);
839 151172 : Tools::convert(line.substr(20+ddist+ddist,ddist),cc[2]);
840 0 : } else plumed_error();
841 1718335 : if(!debug_pd || ( i>=pd_start && i<pd_start+pd_nlocal) ) {
842 3397790 : coordinates[3*i]=real(cc[0]);
843 3397790 : coordinates[3*i+1]=real(cc[1]);
844 3397790 : coordinates[3*i+2]=real(cc[2]);
845 : }
846 : }
847 22981 : if(trajectory_fmt=="gro") {
848 2016 : if(!Tools::getline(fp,line)) error("premature end of trajectory file");
849 4032 : std::vector<string> words=Tools::getWords(line);
850 2016 : if(words.size()<3) error("cannot understand box format");
851 2016 : Tools::convert(words[0],cell[0]);
852 2016 : Tools::convert(words[1],cell[4]);
853 2016 : Tools::convert(words[2],cell[8]);
854 2286 : if(words.size()>3) Tools::convert(words[3],cell[1]);
855 2286 : if(words.size()>4) Tools::convert(words[4],cell[2]);
856 2286 : if(words.size()>5) Tools::convert(words[5],cell[3]);
857 2286 : if(words.size()>6) Tools::convert(words[6],cell[5]);
858 2286 : if(words.size()>7) Tools::convert(words[7],cell[6]);
859 2286 : if(words.size()>8) Tools::convert(words[8],cell[7]);
860 : }
861 :
862 : }
863 :
864 58976 : p.cmd("setStepLong",&step);
865 58976 : p.cmd("setStopFlag",&plumedStopCondition);
866 :
867 29488 : if(debug_dd) {
868 72908 : for(int i=0; i<dd_nlocal; ++i) {
869 71144 : int kk=dd_gatindex[i];
870 106716 : dd_coordinates[3*i+0]=coordinates[3*kk+0];
871 106716 : dd_coordinates[3*i+1]=coordinates[3*kk+1];
872 106716 : dd_coordinates[3*i+2]=coordinates[3*kk+2];
873 : }
874 3528 : p.cmd("setForces",&dd_forces[0]);
875 3528 : p.cmd("setPositions",&dd_coordinates[0]);
876 3528 : p.cmd("setMasses",&dd_masses[0]);
877 3528 : p.cmd("setCharges",&dd_charges[0]);
878 : } else {
879 : // this is required to avoid troubles when the last domain
880 : // contains zero atoms
881 : // Basically, for empty domains we pass null pointers
882 : #define fix_pd(xx) (pd_nlocal!=0?&xx:NULL)
883 83172 : p.cmd("setForces",fix_pd(forces[3*pd_start]));
884 83172 : p.cmd("setPositions",fix_pd(coordinates[3*pd_start]));
885 83172 : p.cmd("setMasses",fix_pd(masses[pd_start]));
886 83172 : p.cmd("setCharges",fix_pd(charges[pd_start]));
887 : }
888 58976 : p.cmd("setBox",&cell[0]);
889 58976 : p.cmd("setVirial",&virial[0]);
890 : } else {
891 4654 : p.cmd("setStepLong",&step);
892 4654 : p.cmd("setStopFlag",&plumedStopCondition);
893 : }
894 63630 : p.cmd("calc");
895 :
896 : // this is necessary as only processor zero is adding to the virial:
897 31815 : intracomm.Bcast(virial,0);
898 31815 : if(debug_pd) intracomm.Sum(forces);
899 31815 : if(debug_dd) {
900 72908 : for(int i=0; i<dd_nlocal; i++) {
901 142288 : forces[3*dd_gatindex[i]+0]=dd_forces[3*i+0];
902 106716 : forces[3*dd_gatindex[i]+1]=dd_forces[3*i+1];
903 106716 : forces[3*dd_gatindex[i]+2]=dd_forces[3*i+2];
904 : }
905 3528 : dd_forces.assign(3*natoms,0.0);
906 1764 : intracomm.Sum(forces);
907 : }
908 31815 : if(debug_grex &&step%grex_stride==0) {
909 228 : p.cmd("GREX savePositions");
910 114 : if(intracomm.Get_rank()>0) {
911 114 : p.cmd("GREX prepare");
912 : } else {
913 57 : int r=intercomm.Get_rank();
914 57 : int n=intercomm.Get_size();
915 57 : int partner=r+(2*((r+step/grex_stride)%2))-1;
916 57 : if(partner<0)partner=0;
917 57 : if(partner>=n) partner=n-1;
918 114 : p.cmd("GREX setPartner",&partner);
919 114 : p.cmd("GREX calculate");
920 114 : p.cmd("GREX shareAllDeltaBias");
921 399 : for(int i=0; i<n; i++) {
922 171 : string s; Tools::convert(i,s);
923 684 : real a=std::numeric_limits<real>::quiet_NaN(); s="GREX getDeltaBias "+s; p.cmd(s.c_str(),&a);
924 171 : if(grex_log) fprintf(grex_log," %f",a);
925 : }
926 57 : if(grex_log) fprintf(grex_log,"\n");
927 : }
928 : }
929 :
930 :
931 31815 : if(fp_forces) {
932 18458 : fprintf(fp_forces,"%d\n",natoms);
933 313786 : string fmtv=dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+"\n";
934 92290 : string fmt=dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+"\n";
935 18458 : if(dumpfullvirial) {
936 350 : fprintf(fp_forces,fmtv.c_str(),virial[0],virial[1],virial[2],virial[3],virial[4],virial[5],virial[6],virial[7],virial[8]);
937 : } else {
938 18108 : fprintf(fp_forces,fmt.c_str(),virial[0],virial[4],virial[8]);
939 : }
940 36916 : fmt="X "+fmt;
941 3135886 : for(int i=0; i<natoms; i++)
942 6234856 : fprintf(fp_forces,fmt.c_str(),forces[3*i],forces[3*i+1],forces[3*i+2]);
943 : }
944 31815 : if(debugforces.length()>0) {
945 : // Now call the routine to work out the derivatives numerically
946 40 : numder.assign(3*natoms+9,real(0.0)); real base=0;
947 40 : p.cmd("getBias",&base);
948 20 : if( fabs(base)<epsilon ) printf("WARNING: bias for configuration appears to be zero so debugging forces is trivial");
949 20 : evaluateNumericalDerivatives( step, p, coordinates, masses, charges, cell, base, numder );
950 :
951 : // And output everything to a file
952 40 : fp_dforces.fmtField(" " + dumpforcesFmt);
953 320 : for(int i=0; i<3*natoms; ++i) {
954 300 : fp_dforces.printField("parameter",(int)i);
955 450 : fp_dforces.printField("analytical",forces[i]);
956 300 : fp_dforces.printField("numerical",-numder[i]);
957 150 : fp_dforces.printField();
958 : }
959 : // And print the virial
960 380 : for(int i=0; i<9; ++i) {
961 360 : fp_dforces.printField("parameter",3*natoms+i );
962 540 : fp_dforces.printField("analytical",virial[i] );
963 540 : fp_dforces.printField("numerical",-numder[3*natoms+i]);
964 180 : fp_dforces.printField();
965 : }
966 : }
967 :
968 31815 : if(plumedStopCondition) break;
969 :
970 31770 : step+=stride;
971 : }
972 1158 : if(!parseOnly) p.cmd("runFinalJobs");
973 :
974 579 : if(fp_forces) fclose(fp_forces);
975 579 : if(debugforces.length()>0) fp_dforces.close();
976 579 : if(fp && fp!=in)fclose(fp);
977 : #ifdef __PLUMED_HAS_XDRFILE
978 579 : if(xd) xdrfile_close(xd);
979 : #endif
980 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
981 579 : if(h_in) api->close_file_read(h_in);
982 : #endif
983 579 : if(grex_log) fclose(grex_log);
984 :
985 : return 0;
986 : }
987 :
988 : template<typename real>
989 20 : void Driver<real>::evaluateNumericalDerivatives( const long int& step, PlumedMain& p, const std::vector<real>& coordinates,
990 : const std::vector<real>& masses, const std::vector<real>& charges,
991 : std::vector<real>& cell, const double& base, std::vector<real>& numder ) {
992 :
993 20 : int natoms = coordinates.size() / 3; real delta = sqrt(epsilon);
994 20 : std::vector<Vector> pos(natoms); real bias=0;
995 20 : std::vector<real> fake_forces( 3*natoms ), fake_virial(9);
996 120 : for(int i=0; i<natoms; ++i) {
997 500 : for(unsigned j=0; j<3; ++j) pos[i][j]=coordinates[3*i+j];
998 : }
999 :
1000 120 : for(int i=0; i<natoms; ++i) {
1001 350 : for(unsigned j=0; j<3; ++j) {
1002 300 : pos[i][j]=pos[i][j]+delta;
1003 300 : p.cmd("setStepLong",&step);
1004 450 : p.cmd("setPositions",&pos[0][0]);
1005 450 : p.cmd("setForces",&fake_forces[0]);
1006 300 : p.cmd("setMasses",&masses[0]);
1007 300 : p.cmd("setCharges",&charges[0]);
1008 450 : p.cmd("setBox",&cell[0]);
1009 450 : p.cmd("setVirial",&fake_virial[0]);
1010 300 : p.cmd("prepareCalc");
1011 300 : p.cmd("performCalcNoUpdate");
1012 300 : p.cmd("getBias",&bias);
1013 300 : pos[i][j]=coordinates[3*i+j];
1014 300 : numder[3*i+j] = (bias - base) / delta;
1015 : }
1016 : }
1017 :
1018 : // Create the cell
1019 20 : Tensor box( cell[0], cell[1], cell[2], cell[3], cell[4], cell[5], cell[6], cell[7], cell[8] );
1020 : // And the virial
1021 20 : Pbc pbc; pbc.setBox( box ); Tensor nvirial;
1022 260 : for(unsigned i=0; i<3; i++) for(unsigned k=0; k<3; k++) {
1023 180 : double arg0=box(i,k);
1024 1080 : for(int j=0; j<natoms; ++j) pos[j]=pbc.realToScaled( pos[j] );
1025 360 : cell[3*i+k]=box(i,k)=box(i,k)+delta; pbc.setBox(box);
1026 1080 : for(int j=0; j<natoms; j++) pos[j]=pbc.scaledToReal( pos[j] );
1027 360 : p.cmd("setStepLong",&step);
1028 540 : p.cmd("setPositions",&pos[0][0]);
1029 540 : p.cmd("setForces",&fake_forces[0]);
1030 360 : p.cmd("setMasses",&masses[0]);
1031 360 : p.cmd("setCharges",&charges[0]);
1032 540 : p.cmd("setBox",&cell[0]);
1033 540 : p.cmd("setVirial",&fake_virial[0]);
1034 360 : p.cmd("prepareCalc");
1035 360 : p.cmd("performCalcNoUpdate");
1036 360 : p.cmd("getBias",&bias);
1037 360 : cell[3*i+k]=box(i,k)=arg0; pbc.setBox(box);
1038 3330 : for(int j=0; j<natoms; j++) for(unsigned n=0; n<3; ++n) pos[j][n]=coordinates[3*j+n];
1039 180 : nvirial(i,k) = ( bias - base ) / delta;
1040 : }
1041 20 : nvirial=-matmul(box.transpose(),nvirial);
1042 260 : for(unsigned i=0; i<3; i++) for(unsigned k=0; k<3; k++) numder[3*natoms+3*i+k] = nvirial(i,k);
1043 :
1044 20 : }
1045 :
1046 : }
1047 5517 : }
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