Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2018 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 "wrapper/Plumed.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 "tools/Units.h"
34 : #include "tools/PDB.h"
35 : #include "tools/FileBase.h"
36 : #include "tools/IFile.h"
37 :
38 : // when using molfile plugin
39 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
40 : #ifndef __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS
41 : /* Use the internal ones. Alternatively:
42 : * ifeq (,$(findstring __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS,$(CPPFLAGS)))
43 : * CPPFLAGS+=-I../molfile
44 : */
45 : #include "molfile/libmolfile_plugin.h"
46 : #include "molfile/molfile_plugin.h"
47 : using namespace PLMD::molfile;
48 : #else
49 : #include <libmolfile_plugin.h>
50 : #include <molfile_plugin.h>
51 : #endif
52 : #endif
53 :
54 : #ifdef __PLUMED_HAS_XDRFILE
55 : #include <xdrfile/xdrfile_trr.h>
56 : #include <xdrfile/xdrfile_xtc.h>
57 : #endif
58 :
59 : using namespace std;
60 :
61 : namespace PLMD {
62 : namespace cltools {
63 :
64 : //+PLUMEDOC TOOLS driver-float
65 : /*
66 : Equivalent to \ref driver, but using single precision reals.
67 :
68 : The purpose of this tool is just to test what PLUMED does when linked from
69 : a single precision code.
70 :
71 : \par Examples
72 :
73 : \verbatim
74 : plumed driver-float --plumed plumed.dat --ixyz trajectory.xyz
75 : \endverbatim
76 :
77 : See also examples in \ref driver
78 :
79 : */
80 : //+ENDPLUMEDOC
81 : //
82 :
83 :
84 : //+PLUMEDOC TOOLS driver
85 : /*
86 : driver is a tool that allows one to to use plumed to post-process an existing trajectory.
87 :
88 : The input to driver is specified using the command line arguments described below.
89 :
90 : In addition, you can use the special \subpage READ command inside your plumed input
91 : to read in colvar files that were generated during your MD simulation. The values
92 : read in can then be treated like calculated colvars.
93 :
94 : \warning
95 : Notice that by default the driver has no knowledge about the masses and charges
96 : of your atoms! Thus, if you want to compute quantities depending charges (e.g. \ref DHENERGY)
97 : or masses (e.g. \ref COM) you should pass the proper information to the driver.
98 : You can do it either with the --pdb option or with the --mc option. The latter
99 : will read a file produced by \ref DUMPMASSCHARGE .
100 :
101 :
102 : \par Examples
103 :
104 : The following command tells plumed to postprocess the trajectory contained in `trajectory.xyz`
105 : by performing the actions described in the input file `plumed.dat`. If an action that takes the
106 : stride keyword is given a stride equal to \f$n\f$ then it will be performed only on every \f$n\f$th
107 : frames in the trajectory file.
108 : \verbatim
109 : plumed driver --plumed plumed.dat --ixyz trajectory.xyz
110 : \endverbatim
111 :
112 : Notice that `xyz` files are expected to be in internal PLUMED units, that is by default nm.
113 : You can change this behavior by using the `--length-units` option:
114 : \verbatim
115 : plumed driver --plumed plumed.dat --ixyz trajectory.xyz --length-units A
116 : \endverbatim
117 : The strings accepted by the `--length-units` options are the same ones accepted by the \ref UNITS action.
118 : Other file formats typically have their default coordinates (e.g., `gro` files are always in nm)
119 : and it thus should not be necessary to use the `--length-units` option. Additionally,
120 : consider that the units used by the `driver` might be different by the units used in the PLUMED input
121 : file `plumed.dat`. For instance consider the command:
122 : \verbatim
123 : plumed driver --plumed plumed.dat --ixyz trajectory.xyz --length-units A
124 : \endverbatim
125 : where `plumed.dat` is
126 : \verbatim
127 : # no explicit UNITS action here
128 : d: DISTANCE ATOMS=1,2
129 : PRINT ARG=d FILE=colvar
130 : \endverbatim
131 : In this case, the driver reads the `xyz` file assuming it to contain coordinates in Angstrom units.
132 : However, the resulting `colvar` file contains a distance expressed in nm.
133 :
134 : The following command tells plumed to postprocess the trajectory contained in trajectory.xyz.
135 : by performing the actions described in the input file plumed.dat.
136 : \verbatim
137 : plumed driver --plumed plumed.dat --ixyz trajectory.xyz --trajectory-stride 100 --timestep 0.001
138 : \endverbatim
139 : Here though
140 : `--trajectory-stride` is set equal to the frequency with which frames were output during the trajectory
141 : and the `--timestep` is equal to the simulation timestep. As such the `STRIDE` parameters in the `plumed.dat`
142 : files are referred to the original timestep and any files output resemble those that would have been generated
143 : had we run the calculation we are running with driver when the MD simulation was running.
144 :
145 : PLUMED can read natively xyz files (in PLUMED units) and gro files (in nm). In addition,
146 : PLUMED includes by default support for a
147 : subset of the trajectory file formats supported by VMD, e.g. xtc and dcd:
148 :
149 : \verbatim
150 : plumed driver --plumed plumed.dat --pdb diala.pdb --mf_xtc traj.xtc --trajectory-stride 100 --timestep 0.001
151 : \endverbatim
152 :
153 : where `--mf_` prefixes the extension of one of the accepted molfile plugin format.
154 : If PLUMED has been \ref Installation "installed" with full molfile support, other formats will be available.
155 : Just type `plumed driver --help` to see which plugins are available.
156 :
157 : Molfile plugin require periodic cell to be triangular (i.e. first vector oriented along x and
158 : second vector in xy plane). This is true for many MD codes. However, it could be false
159 : if you rotate the coordinates in your trajectory before reading them in the driver.
160 : Also notice that some formats (e.g. amber crd) do not specify atom number. In this case you can use
161 : the `--natoms` option:
162 : \verbatim
163 : plumed driver --plumed plumed.dat --imf_crd trajectory.crd --natoms 128
164 : \endverbatim
165 :
166 : Check the available molfile plugins and limitations at [this link](http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/).
167 :
168 : Additionally, you can use the xdrfile implementation of xtc and trr. To this aim, just
169 : download and install properly the xdrfile library (see [this link](http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library)).
170 : If the xdrfile library is installed properly the PLUMED configure script should be able to
171 : detect it and enable it.
172 : Notice that the xdrfile implementation of xtc and trr
173 : is more robust than the molfile one, since it provides support for generic cell shapes.
174 : In addition, it allows \ref DUMPATOMS to write compressed xtc files.
175 :
176 :
177 : */
178 : //+ENDPLUMEDOC
179 : //
180 :
181 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
182 2523 : static vector<molfile_plugin_t *> plugins;
183 2523 : static map <string, unsigned> pluginmap;
184 15138 : static int register_cb(void *v, vmdplugin_t *p) {
185 : //const char *key = p->name;
186 15138 : std::pair<std::map<string,unsigned>::iterator,bool> ret;
187 15138 : ret = pluginmap.insert ( std::pair<string,unsigned>(string(p->name),plugins.size()) );
188 15138 : 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 15138 : plugins.push_back(reinterpret_cast<molfile_plugin_t *>(p));
193 : }
194 15138 : return VMDPLUGIN_SUCCESS;
195 : }
196 : #endif
197 :
198 : template<typename real>
199 576 : 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, Plumed& 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 1682 : void Driver<real>::registerKeywords( Keywords& keys ) {
212 1682 : CLTool::registerKeywords( keys ); keys.isDriver();
213 1682 : keys.addFlag("--help-debug",false,"print special options that can be used to create regtests");
214 1682 : keys.add("compulsory","--plumed","plumed.dat","specify the name of the plumed input file");
215 1682 : keys.add("compulsory","--timestep","1.0","the timestep that was used in the calculation that produced this trajectory in picoseconds");
216 1682 : 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 3364 : );
222 1682 : keys.add("compulsory","--multi","0","set number of replicas for multi environment (needs mpi)");
223 1682 : keys.addFlag("--noatoms",false,"don't read in a trajectory. Just use colvar files as specified in plumed.dat");
224 1682 : keys.add("atoms","--ixyz","the trajectory in xyz format");
225 1682 : keys.add("atoms","--igro","the trajectory in gro format");
226 : #ifdef __PLUMED_HAS_XDRFILE
227 1682 : keys.add("atoms","--ixtc","the trajectory in xtc format (xdrfile implementation)");
228 1682 : keys.add("atoms","--itrr","the trajectory in trr format (xdrfile implementation)");
229 : #endif
230 1682 : keys.add("optional","--length-units","units for length, either as a string or a number");
231 1682 : keys.add("optional","--mass-units","units for mass in pdb and mc file, either as a string or a number");
232 1682 : keys.add("optional","--charge-units","units for charge in pdb and mc file, either as a string or a number");
233 1682 : keys.add("optional","--dump-forces","dump the forces on a file");
234 1682 : keys.add("optional","--dump-forces-fmt","( default=%%f ) the format to use to dump the forces");
235 1682 : keys.addFlag("--dump-full-virial",false,"with --dump-forces, it dumps the 9 components of the virial");
236 1682 : keys.add("optional","--pdb","provides a pdb with masses and charges");
237 1682 : keys.add("optional","--mc","provides a file with masses and charges as produced with DUMPMASSCHARGE");
238 1682 : keys.add("optional","--box","comma-separated box dimensions (3 for orthorombic, 9 for generic)");
239 1682 : keys.add("optional","--natoms","provides number of atoms - only used if file format does not contain number of atoms");
240 1682 : keys.add("optional","--debug-forces","output a file containing the forces due to the bias evaluated using numerical derivatives "
241 3364 : "and using the analytical derivatives implemented in plumed");
242 1682 : keys.add("hidden","--debug-float","[yes/no] turns on the single precision version (to check float interface)");
243 1682 : keys.add("hidden","--debug-dd","[yes/no] use a fake domain decomposition");
244 1682 : keys.add("hidden","--debug-pd","[yes/no] use a fake particle decomposition");
245 1682 : keys.add("hidden","--debug-grex","use a fake gromacs-like replica exchange, specify exchange stride");
246 1682 : keys.add("hidden","--debug-grex-log","log file for debug=grex");
247 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
248 1682 : MOLFILE_INIT_ALL
249 1682 : MOLFILE_REGISTER_ALL(NULL, register_cb)
250 16820 : for(int i=0; i<plugins.size(); i++) {
251 15138 : string kk="--mf_"+string(plugins[i]->name);
252 30276 : string mm=" molfile: the trajectory in "+string(plugins[i]->name)+" format " ;
253 : //cerr<<"REGISTERING "<<kk<<mm<<endl;
254 15138 : keys.add("atoms",kk,mm);
255 : }
256 : #endif
257 1682 : }
258 : template<typename real>
259 288 : Driver<real>::Driver(const CLToolOptions& co ):
260 288 : CLTool(co)
261 : {
262 288 : inputdata=commandline;
263 288 : }
264 : template<typename real>
265 0 : string Driver<real>::description()const { return "analyze trajectories with plumed"; }
266 :
267 : template<typename real>
268 288 : int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
269 :
270 288 : Units units;
271 576 : PDB pdb;
272 :
273 : // Parse everything
274 288 : bool printhelpdebug; parseFlag("--help-debug",printhelpdebug);
275 288 : if( printhelpdebug ) {
276 0 : fprintf(out,"%s",
277 : "Additional options for debug (only to be used in regtest):\n"
278 : " [--debug-float yes] : turns on the single precision version (to check float interface)\n"
279 : " [--debug-dd yes] : use a fake domain decomposition\n"
280 : " [--debug-pd yes] : use a fake particle decomposition\n"
281 : );
282 0 : return 0;
283 : }
284 : // Are we reading trajectory data
285 288 : bool noatoms; parseFlag("--noatoms",noatoms);
286 :
287 576 : std::string fakein;
288 :
289 288 : bool debug_float=false;
290 288 : fakein="";
291 288 : if(parse("--debug-float",fakein)) {
292 0 : if(fakein=="yes") debug_float=true;
293 0 : else if(fakein=="no") debug_float=false;
294 0 : else error("--debug-float should have argument yes or no");
295 : }
296 :
297 288 : if(debug_float && sizeof(real)!=sizeof(float)) {
298 0 : CLTool* cl=cltoolRegister().create(CLToolOptions("driver-float")); //new Driver<float>(*this);
299 0 : cl->setInputData(this->getInputData());
300 0 : int ret=cl->main(in,out,pc);
301 0 : delete cl;
302 0 : return ret;
303 : }
304 :
305 288 : bool debug_pd=false;
306 288 : fakein="";
307 288 : if(parse("--debug-pd",fakein)) {
308 4 : if(fakein=="yes") debug_pd=true;
309 0 : else if(fakein=="no") debug_pd=false;
310 0 : else error("--debug-pd should have argument yes or no");
311 : }
312 288 : if(debug_pd) fprintf(out,"DEBUGGING PARTICLE DECOMPOSITION\n");
313 :
314 288 : bool debug_dd=false;
315 288 : fakein="";
316 288 : if(parse("--debug-dd",fakein)) {
317 30 : if(fakein=="yes") debug_dd=true;
318 0 : else if(fakein=="no") debug_dd=false;
319 0 : else error("--debug-dd should have argument yes or no");
320 : }
321 288 : if(debug_dd) fprintf(out,"DEBUGGING DOMAIN DECOMPOSITION\n");
322 :
323 288 : if( debug_pd || debug_dd ) {
324 34 : if(noatoms) error("cannot debug without atoms");
325 : }
326 :
327 : // set up for multi replica driver:
328 288 : int multi=0;
329 288 : parse("--multi",multi);
330 576 : Communicator intracomm;
331 576 : Communicator intercomm;
332 288 : if(multi) {
333 63 : int ntot=pc.Get_size();
334 63 : int nintra=ntot/multi;
335 63 : if(multi*nintra!=ntot) error("invalid number of processes for multi environment");
336 63 : pc.Split(pc.Get_rank()/nintra,pc.Get_rank(),intracomm);
337 63 : pc.Split(pc.Get_rank()%nintra,pc.Get_rank(),intercomm);
338 : } else {
339 225 : intracomm.Set_comm(pc.Get_comm());
340 : }
341 :
342 : // set up for debug replica exchange:
343 288 : bool debug_grex=parse("--debug-grex",fakein);
344 288 : int grex_stride=0;
345 288 : FILE*grex_log=NULL;
346 288 : if(debug_grex) {
347 18 : if(noatoms) error("must have atoms to debug_grex");
348 18 : if(multi<2) error("--debug_grex needs --multi with at least two replicas");
349 18 : Tools::convert(fakein,grex_stride);
350 18 : string n; Tools::convert(intercomm.Get_rank(),n);
351 36 : string file;
352 18 : parse("--debug-grex-log",file);
353 18 : if(file.length()>0) {
354 18 : file+="."+n;
355 18 : grex_log=fopen(file.c_str(),"w");
356 18 : }
357 : }
358 :
359 : // Read the plumed input file name
360 576 : string plumedFile; parse("--plumed",plumedFile);
361 : // the timestep
362 288 : double t; parse("--timestep",t);
363 288 : real timestep=real(t);
364 : // the stride
365 288 : unsigned stride; parse("--trajectory-stride",stride);
366 : // are we writing forces
367 576 : string dumpforces(""), debugforces(""), dumpforcesFmt("%f");;
368 288 : bool dumpfullvirial=false;
369 288 : if(!noatoms) {
370 287 : parse("--dump-forces",dumpforces);
371 287 : parse("--debug-forces",debugforces);
372 : }
373 288 : if(dumpforces!="" || debugforces!="" ) parse("--dump-forces-fmt",dumpforcesFmt);
374 288 : if(dumpforces!="") parseFlag("--dump-full-virial",dumpfullvirial);
375 288 : if( debugforces!="" && (debug_dd || debug_pd) ) error("cannot debug forces and domain/particle decomposition at same time");
376 288 : if( debugforces!="" && sizeof(real)!=sizeof(double) ) error("cannot debug forces in single precision mode");
377 :
378 576 : string trajectory_fmt;
379 :
380 288 : bool use_molfile=false;
381 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
382 288 : molfile_plugin_t *api=NULL;
383 288 : void *h_in=NULL;
384 : molfile_timestep_t ts_in; // this is the structure that has the timestep
385 288 : ts_in.coords=NULL;
386 288 : ts_in.A=-1; // we use this to check whether cell is provided or not
387 : #endif
388 :
389 : // Read in an xyz file
390 576 : string trajectoryFile(""), pdbfile(""), mcfile("");
391 576 : bool pbc_cli_given=false; vector<double> pbc_cli_box(9,0.0);
392 288 : int command_line_natoms=-1;
393 :
394 288 : if(!noatoms) {
395 287 : std::string traj_xyz; parse("--ixyz",traj_xyz);
396 574 : std::string traj_gro; parse("--igro",traj_gro);
397 574 : std::string traj_xtc;
398 574 : std::string traj_trr;
399 : #ifdef __PLUMED_HAS_XDRFILE
400 287 : parse("--ixtc",traj_xtc);
401 287 : parse("--itrr",traj_trr);
402 : #endif
403 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
404 2870 : for(int i=0; i<plugins.size(); i++) {
405 2583 : string molfile_key="--mf_"+string(plugins[i]->name);
406 5166 : string traj_molfile;
407 2583 : parse(molfile_key,traj_molfile);
408 2583 : if(traj_molfile.length()>0) {
409 14 : fprintf(out,"\nDRIVER: Found molfile format trajectory %s with name %s\n",plugins[i]->name,traj_molfile.c_str());
410 14 : trajectoryFile=traj_molfile;
411 14 : trajectory_fmt=string(plugins[i]->name);
412 14 : use_molfile=true;
413 14 : api = plugins[i];
414 : }
415 : }
416 : #endif
417 : { // check that only one fmt is specified
418 287 : int nn=0;
419 287 : if(traj_xyz.length()>0) nn++;
420 287 : if(traj_gro.length()>0) nn++;
421 287 : if(traj_xtc.length()>0) nn++;
422 287 : if(traj_trr.length()>0) nn++;
423 287 : if(nn>1) {
424 0 : fprintf(stderr,"ERROR: cannot provide more than one trajectory file\n");
425 0 : if(grex_log)fclose(grex_log);
426 0 : return 1;
427 : }
428 : }
429 287 : if(traj_xyz.length()>0 && trajectoryFile.length()==0) {
430 247 : trajectoryFile=traj_xyz;
431 247 : trajectory_fmt="xyz";
432 : }
433 287 : if(traj_gro.length()>0 && trajectoryFile.length()==0) {
434 22 : trajectoryFile=traj_gro;
435 22 : trajectory_fmt="gro";
436 : }
437 287 : if(traj_xtc.length()>0 && trajectoryFile.length()==0) {
438 1 : trajectoryFile=traj_xtc;
439 1 : trajectory_fmt="xdr-xtc";
440 : }
441 287 : if(traj_trr.length()>0 && trajectoryFile.length()==0) {
442 3 : trajectoryFile=traj_trr;
443 3 : trajectory_fmt="xdr-trr";
444 : }
445 287 : if(trajectoryFile.length()==0) {
446 0 : fprintf(stderr,"ERROR: missing trajectory data\n");
447 0 : if(grex_log)fclose(grex_log);
448 0 : return 1;
449 : }
450 574 : string lengthUnits(""); parse("--length-units",lengthUnits);
451 287 : if(lengthUnits.length()>0) units.setLength(lengthUnits);
452 574 : string chargeUnits(""); parse("--charge-units",chargeUnits);
453 287 : if(chargeUnits.length()>0) units.setCharge(chargeUnits);
454 574 : string massUnits(""); parse("--mass-units",massUnits);
455 287 : if(massUnits.length()>0) units.setMass(massUnits);
456 :
457 287 : parse("--pdb",pdbfile);
458 287 : if(pdbfile.length()>0) {
459 37 : bool check=pdb.read(pdbfile,false,1.0);
460 37 : if(!check) error("error reading pdb file");
461 : }
462 :
463 287 : parse("--mc",mcfile);
464 :
465 574 : string pbc_cli_list; parse("--box",pbc_cli_list);
466 287 : if(pbc_cli_list.length()>0) {
467 14 : pbc_cli_given=true;
468 14 : vector<string> words=Tools::getWords(pbc_cli_list,",");
469 14 : if(words.size()==3) {
470 14 : for(int i=0; i<3; i++) sscanf(words[i].c_str(),"%100lf",&(pbc_cli_box[4*i]));
471 0 : } else if(words.size()==9) {
472 0 : for(int i=0; i<9; i++) sscanf(words[i].c_str(),"%100lf",&(pbc_cli_box[i]));
473 : } else {
474 0 : string msg="ERROR: cannot parse command-line box "+pbc_cli_list;
475 0 : fprintf(stderr,"%s\n",msg.c_str());
476 0 : return 1;
477 14 : }
478 :
479 : }
480 :
481 574 : parse("--natoms",command_line_natoms);
482 :
483 : }
484 :
485 288 : if( debug_dd && debug_pd ) error("cannot use debug-dd and debug-pd at the same time");
486 288 : if(debug_pd || debug_dd) {
487 34 : if( !Communicator::initialized() ) error("needs mpi for debug-pd");
488 : }
489 :
490 576 : Plumed p;
491 288 : int rr=sizeof(real);
492 288 : p.cmd("setRealPrecision",&rr);
493 288 : int checknatoms=-1;
494 288 : long int step=0;
495 288 : if(Communicator::initialized()) {
496 115 : if(multi) {
497 63 : if(intracomm.Get_rank()==0) p.cmd("GREX setMPIIntercomm",&intercomm.Get_comm());
498 63 : p.cmd("GREX setMPIIntracomm",&intracomm.Get_comm());
499 63 : p.cmd("GREX init");
500 : }
501 115 : p.cmd("setMPIComm",&intracomm.Get_comm());
502 : }
503 288 : p.cmd("setMDLengthUnits",&units.getLength());
504 288 : p.cmd("setMDChargeUnits",&units.getCharge());
505 288 : p.cmd("setMDMassUnits",&units.getMass());
506 288 : p.cmd("setMDEngine","driver");
507 288 : p.cmd("setTimestep",×tep);
508 288 : p.cmd("setPlumedDat",plumedFile.c_str());
509 288 : p.cmd("setLog",out);
510 :
511 288 : if(multi) {
512 63 : string n;
513 63 : Tools::convert(intercomm.Get_rank(),n);
514 63 : trajectoryFile=FileBase::appendSuffix(trajectoryFile,"."+n);
515 : }
516 :
517 :
518 : int natoms;
519 :
520 576 : FILE* fp=NULL; FILE* fp_forces=NULL; OFile fp_dforces;
521 : #ifdef __PLUMED_HAS_XDRFILE
522 288 : XDRFILE* xd=NULL;
523 : #endif
524 288 : if(!noatoms) {
525 287 : if (trajectoryFile=="-")
526 0 : fp=in;
527 : else {
528 287 : if(use_molfile==true) {
529 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
530 14 : h_in = api->open_file_read(trajectoryFile.c_str(), trajectory_fmt.c_str(), &natoms);
531 14 : if(natoms==MOLFILE_NUMATOMS_UNKNOWN) {
532 2 : if(command_line_natoms>=0) natoms=command_line_natoms;
533 0 : else error("this file format does not provide number of atoms; use --natoms on the command line");
534 : }
535 14 : ts_in.coords = new float [3*natoms];
536 : #endif
537 273 : } else if(trajectory_fmt=="xdr-xtc" || trajectory_fmt=="xdr-trr") {
538 : #ifdef __PLUMED_HAS_XDRFILE
539 4 : xd=xdrfile_open(trajectoryFile.c_str(),"r");
540 4 : if(!xd) {
541 0 : string msg="ERROR: Error opening trajectory file "+trajectoryFile;
542 0 : fprintf(stderr,"%s\n",msg.c_str());
543 0 : return 1;
544 : }
545 4 : if(trajectory_fmt=="xdr-xtc") read_xtc_natoms(&trajectoryFile[0],&natoms);
546 4 : if(trajectory_fmt=="xdr-trr") read_trr_natoms(&trajectoryFile[0],&natoms);
547 : #endif
548 : } else {
549 269 : fp=fopen(trajectoryFile.c_str(),"r");
550 269 : if(!fp) {
551 0 : string msg="ERROR: Error opening trajectory file "+trajectoryFile;
552 0 : fprintf(stderr,"%s\n",msg.c_str());
553 : // cppcheck detects a false positive here. I suppress it:
554 : // cppcheck-suppress memleak
555 0 : return 1;
556 : }
557 : }
558 : }
559 287 : if(dumpforces.length()>0) {
560 183 : if(Communicator::initialized() && pc.Get_size()>1) {
561 87 : string n;
562 87 : Tools::convert(pc.Get_rank(),n);
563 87 : dumpforces+="."+n;
564 : }
565 183 : fp_forces=fopen(dumpforces.c_str(),"w");
566 : }
567 287 : if(debugforces.length()>0) {
568 3 : if(Communicator::initialized() && pc.Get_size()>1) {
569 0 : string n;
570 0 : Tools::convert(pc.Get_rank(),n);
571 0 : debugforces+="."+n;
572 : }
573 3 : fp_dforces.open(debugforces);
574 : }
575 : }
576 :
577 576 : std::string line;
578 576 : std::vector<real> coordinates;
579 576 : std::vector<real> forces;
580 576 : std::vector<real> masses;
581 576 : std::vector<real> charges;
582 576 : std::vector<real> cell;
583 576 : std::vector<real> virial;
584 576 : std::vector<real> numder;
585 :
586 : // variables to test particle decomposition
587 : int pd_nlocal;
588 : int pd_start;
589 : // variables to test random decomposition (=domain decomposition)
590 576 : std::vector<int> dd_gatindex;
591 576 : std::vector<int> dd_g2l;
592 576 : std::vector<real> dd_masses;
593 576 : std::vector<real> dd_charges;
594 576 : std::vector<real> dd_forces;
595 576 : std::vector<real> dd_coordinates;
596 : int dd_nlocal;
597 : // random stream to choose decompositions
598 576 : Random rnd;
599 :
600 : while(true) {
601 19546 : if(!noatoms) {
602 19000 : if(use_molfile==true) {
603 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
604 : int rc;
605 186 : rc = api->read_next_timestep(h_in, natoms, &ts_in);
606 : //if(rc==MOLFILE_SUCCESS){
607 : // printf(" read this one :success \n");
608 : //}
609 186 : if(rc==MOLFILE_EOF) {
610 : //printf(" read this one :eof or error \n");
611 302 : break;
612 : }
613 : #endif
614 18814 : } else if(trajectory_fmt=="xyz" || trajectory_fmt=="gro") {
615 18762 : if(!Tools::getline(fp,line)) break;
616 : }
617 : }
618 :
619 19263 : bool first_step=false;
620 19263 : if(!noatoms) {
621 18717 : if(use_molfile==false && (trajectory_fmt=="xyz" || trajectory_fmt=="gro")) {
622 18493 : if(trajectory_fmt=="gro") if(!Tools::getline(fp,line)) error("premature end of trajectory file");
623 18493 : sscanf(line.c_str(),"%100d",&natoms);
624 : }
625 : }
626 19263 : if(checknatoms<0 && !noatoms) {
627 287 : pd_nlocal=natoms;
628 287 : pd_start=0;
629 287 : first_step=true;
630 287 : masses.assign(natoms,NAN);
631 287 : charges.assign(natoms,NAN);
632 : //case pdb: structure
633 287 : if(pdbfile.length()>0) {
634 3271 : for(unsigned i=0; i<pdb.size(); ++i) {
635 3234 : AtomNumber an=pdb.getAtomNumbers()[i];
636 3234 : unsigned index=an.index();
637 3234 : if( index>=unsigned(natoms) ) error("atom index in pdb exceeds the number of atoms in trajectory");
638 3234 : masses[index]=pdb.getOccupancy()[i];
639 3234 : charges[index]=pdb.getBeta()[i];
640 : }
641 : }
642 287 : if(mcfile.length()>0) {
643 4 : IFile ifile;
644 4 : ifile.open(mcfile);
645 : int index; double mass; double charge;
646 440 : while(ifile.scanField("index",index).scanField("mass",mass).scanField("charge",charge).scanField()) {
647 432 : masses[index]=mass;
648 432 : charges[index]=charge;
649 4 : }
650 287 : }
651 18976 : } else if( checknatoms<0 && noatoms ) {
652 1 : natoms=0;
653 : }
654 19263 : if( checknatoms<0 ) {
655 288 : checknatoms=natoms;
656 288 : p.cmd("setNatoms",&natoms);
657 288 : p.cmd("init");
658 : }
659 19263 : if(checknatoms!=natoms) {
660 0 : std::string stepstr; Tools::convert(step,stepstr);
661 0 : error("number of atoms in frame " + stepstr + " does not match number of atoms in first frame");
662 : }
663 :
664 19263 : coordinates.assign(3*natoms,real(0.0));
665 19263 : forces.assign(3*natoms,real(0.0));
666 19263 : cell.assign(9,real(0.0));
667 19263 : virial.assign(9,real(0.0));
668 :
669 19263 : if( first_step || rnd.U01()>0.5) {
670 9819 : if(debug_pd) {
671 16 : int npe=intracomm.Get_size();
672 16 : vector<int> loc(npe,0);
673 32 : vector<int> start(npe,0);
674 64 : for(int i=0; i<npe-1; i++) {
675 48 : int cc=(natoms*2*rnd.U01())/npe;
676 48 : if(start[i]+cc>natoms) cc=natoms-start[i];
677 48 : loc[i]=cc;
678 48 : start[i+1]=start[i]+loc[i];
679 : }
680 16 : loc[npe-1]=natoms-start[npe-1];
681 16 : intracomm.Bcast(loc,0);
682 16 : intracomm.Bcast(start,0);
683 16 : pd_nlocal=loc[intracomm.Get_rank()];
684 16 : pd_start=start[intracomm.Get_rank()];
685 16 : if(intracomm.Get_rank()==0) {
686 4 : fprintf(out,"\nDRIVER: Reassigning particle decomposition\n");
687 4 : fprintf(out,"DRIVER: "); for(int i=0; i<npe; i++) fprintf(out,"%d ",loc[i]); printf("\n");
688 4 : fprintf(out,"DRIVER: "); for(int i=0; i<npe; i++) fprintf(out,"%d ",start[i]); printf("\n");
689 : }
690 16 : p.cmd("setAtomsNlocal",&pd_nlocal);
691 32 : p.cmd("setAtomsContiguous",&pd_start);
692 9803 : } else if(debug_dd) {
693 134 : int npe=intracomm.Get_size();
694 134 : int rank=intracomm.Get_rank();
695 134 : dd_charges.assign(natoms,0.0);
696 134 : dd_masses.assign(natoms,0.0);
697 134 : dd_gatindex.assign(natoms,-1);
698 134 : dd_g2l.assign(natoms,-1);
699 134 : dd_coordinates.assign(3*natoms,0.0);
700 134 : dd_forces.assign(3*natoms,0.0);
701 134 : dd_nlocal=0;
702 13196 : for(int i=0; i<natoms; ++i) {
703 13062 : double r=rnd.U01()*npe;
704 13062 : int n; for(n=0; n<npe; n++) if(n+1>r)break;
705 13062 : plumed_assert(n<npe);
706 13062 : if(n==rank) {
707 5883 : dd_gatindex[dd_nlocal]=i;
708 5883 : dd_g2l[i]=dd_nlocal;
709 5883 : dd_charges[dd_nlocal]=charges[i];
710 5883 : dd_masses[dd_nlocal]=masses[i];
711 5883 : dd_nlocal++;
712 : }
713 : }
714 134 : if(intracomm.Get_rank()==0) {
715 61 : fprintf(out,"\nDRIVER: Reassigning particle decomposition\n");
716 : }
717 134 : p.cmd("setAtomsNlocal",&dd_nlocal);
718 134 : p.cmd("setAtomsGatindex",&dd_gatindex[0]);
719 : }
720 : }
721 :
722 19263 : int plumedStopCondition=0;
723 19263 : if(!noatoms) {
724 18717 : if(use_molfile) {
725 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
726 172 : if(pbc_cli_given==false) {
727 172 : if(ts_in.A>0.0) { // this is negative if molfile does not provide box
728 : // info on the cell: convert using pbcset.tcl from pbctools in vmd distribution
729 170 : real cosBC=cos(ts_in.alpha*pi/180.);
730 : //double sinBC=sin(ts_in.alpha*pi/180.);
731 170 : real cosAC=cos(ts_in.beta*pi/180.);
732 170 : real cosAB=cos(ts_in.gamma*pi/180.);
733 170 : real sinAB=sin(ts_in.gamma*pi/180.);
734 170 : real Ax=ts_in.A;
735 170 : real Bx=ts_in.B*cosAB;
736 170 : real By=ts_in.B*sinAB;
737 170 : real Cx=ts_in.C*cosAC;
738 170 : real Cy=(ts_in.C*ts_in.B*cosBC-Cx*Bx)/By;
739 170 : real Cz=sqrt(ts_in.C*ts_in.C-Cx*Cx-Cy*Cy);
740 170 : cell[0]=Ax/10.; cell[1]=0.; cell[2]=0.;
741 170 : cell[3]=Bx/10.; cell[4]=By/10.; cell[5]=0.;
742 170 : cell[6]=Cx/10.; cell[7]=Cy/10.; cell[8]=Cz/10.;
743 : } else {
744 2 : cell[0]=0.0; cell[1]=0.0; cell[2]=0.0;
745 2 : cell[3]=0.0; cell[4]=0.0; cell[5]=0.0;
746 2 : cell[6]=0.0; cell[7]=0.0; cell[8]=0.0;
747 : }
748 : } else {
749 0 : for(unsigned i=0; i<9; i++)cell[i]=pbc_cli_box[i];
750 : }
751 : // info on coords
752 : // the order is xyzxyz...
753 1012447 : for(unsigned i=0; i<3*natoms; i++) {
754 1012275 : coordinates[i]=real(ts_in.coords[i]/10.); //convert to nm
755 : //cerr<<"COOR "<<coordinates[i]<<endl;
756 : }
757 : #endif
758 18545 : } else if(trajectory_fmt=="xdr-xtc" || trajectory_fmt=="xdr-trr") {
759 : #ifdef __PLUMED_HAS_XDRFILE
760 : int localstep;
761 : float time;
762 : matrix box;
763 52 : rvec* pos=new rvec[natoms];
764 : float prec,lambda;
765 52 : int ret=exdrOK;
766 52 : if(trajectory_fmt=="xdr-xtc") ret=read_xtc(xd,natoms,&localstep,&time,box,pos,&prec);
767 52 : if(trajectory_fmt=="xdr-trr") ret=read_trr(xd,natoms,&localstep,&time,&lambda,box,pos,NULL,NULL);
768 52 : if(stride==0) step=localstep;
769 56 : if(ret==exdrENDOFFILE) break;
770 51 : if(ret!=exdrOK) break;
771 48 : for(unsigned i=0; i<3; i++) for(unsigned j=0; j<3; j++) cell[3*i+j]=box[i][j];
772 7176 : for(unsigned i=0; i<natoms; i++) for(unsigned j=0; j<3; j++)
773 7128 : coordinates[3*i+j]=real(pos[i][j]);
774 48 : delete [] pos;
775 : #endif
776 : } else {
777 18493 : if(trajectory_fmt=="xyz") {
778 18015 : if(!Tools::getline(fp,line)) error("premature end of trajectory file");
779 :
780 18015 : std::vector<double> celld(9,0.0);
781 18015 : if(pbc_cli_given==false) {
782 17815 : std::vector<std::string> words;
783 17815 : words=Tools::getWords(line);
784 17815 : if(words.size()==3) {
785 17357 : sscanf(line.c_str(),"%100lf %100lf %100lf",&celld[0],&celld[4],&celld[8]);
786 458 : } else if(words.size()==9) {
787 458 : sscanf(line.c_str(),"%100lf %100lf %100lf %100lf %100lf %100lf %100lf %100lf %100lf",
788 : &celld[0], &celld[1], &celld[2],
789 : &celld[3], &celld[4], &celld[5],
790 458 : &celld[6], &celld[7], &celld[8]);
791 0 : } else error("needed box in second line of xyz file");
792 : } else { // from command line
793 200 : celld=pbc_cli_box;
794 : }
795 18015 : for(unsigned i=0; i<9; i++)cell[i]=real(celld[i]);
796 : }
797 18493 : int ddist=0;
798 : // Read coordinates
799 1373437 : for(int i=0; i<natoms; i++) {
800 1354944 : bool ok=Tools::getline(fp,line);
801 1354944 : if(!ok) error("premature end of trajectory file");
802 : double cc[3];
803 1354944 : if(trajectory_fmt=="xyz") {
804 : char dummy[1000];
805 1314026 : int ret=std::sscanf(line.c_str(),"%999s %100lf %100lf %100lf",dummy,&cc[0],&cc[1],&cc[2]);
806 1314026 : if(ret!=4) error("cannot read line"+line);
807 40918 : } else if(trajectory_fmt=="gro") {
808 : // do the gromacs way
809 40918 : if(!i) {
810 : //
811 : // calculate the distance between dots (as in gromacs gmxlib/confio.c, routine get_w_conf )
812 : //
813 : const char *p1, *p2, *p3;
814 478 : p1 = strchr(line.c_str(), '.');
815 478 : if (p1 == NULL) error("seems there are no coordinates in the gro file");
816 478 : p2 = strchr(&p1[1], '.');
817 478 : if (p2 == NULL) error("seems there is only one coordinates in the gro file");
818 478 : ddist = p2 - p1;
819 478 : p3 = strchr(&p2[1], '.');
820 478 : if (p3 == NULL)error("seems there are only two coordinates in the gro file");
821 478 : if (p3 - p2 != ddist)error("not uniform spacing in fields in the gro file");
822 : }
823 40918 : Tools::convert(line.substr(20,ddist),cc[0]);
824 40918 : Tools::convert(line.substr(20+ddist,ddist),cc[1]);
825 40918 : Tools::convert(line.substr(20+ddist+ddist,ddist),cc[2]);
826 0 : } else plumed_error();
827 1354944 : if(!debug_pd || ( i>=pd_start && i<pd_start+pd_nlocal) ) {
828 1353324 : coordinates[3*i]=real(cc[0]);
829 1353324 : coordinates[3*i+1]=real(cc[1]);
830 1353324 : coordinates[3*i+2]=real(cc[2]);
831 : }
832 : }
833 18493 : if(trajectory_fmt=="gro") {
834 478 : if(!Tools::getline(fp,line)) error("premature end of trajectory file");
835 478 : std::vector<string> words=Tools::getWords(line);
836 478 : if(words.size()<3) error("cannot understand box format");
837 478 : Tools::convert(words[0],cell[0]);
838 478 : Tools::convert(words[1],cell[4]);
839 478 : Tools::convert(words[2],cell[8]);
840 478 : if(words.size()>3) Tools::convert(words[3],cell[1]);
841 478 : if(words.size()>4) Tools::convert(words[4],cell[2]);
842 478 : if(words.size()>5) Tools::convert(words[5],cell[3]);
843 478 : if(words.size()>6) Tools::convert(words[6],cell[5]);
844 478 : if(words.size()>7) Tools::convert(words[7],cell[6]);
845 478 : if(words.size()>8) Tools::convert(words[8],cell[7]);
846 : }
847 :
848 : }
849 :
850 18713 : p.cmd("setStepLong",&step);
851 18713 : p.cmd("setStopFlag",&plumedStopCondition);
852 :
853 18713 : if(debug_dd) {
854 10996 : for(int i=0; i<dd_nlocal; ++i) {
855 10764 : int kk=dd_gatindex[i];
856 10764 : dd_coordinates[3*i+0]=coordinates[3*kk+0];
857 10764 : dd_coordinates[3*i+1]=coordinates[3*kk+1];
858 10764 : dd_coordinates[3*i+2]=coordinates[3*kk+2];
859 : }
860 232 : p.cmd("setForces",&dd_forces[0]);
861 232 : p.cmd("setPositions",&dd_coordinates[0]);
862 232 : p.cmd("setMasses",&dd_masses[0]);
863 232 : p.cmd("setCharges",&dd_charges[0]);
864 : } else {
865 : // this is required to avoid troubles when the last domain
866 : // contains zero atoms
867 : // Basically, for empty domains we pass null pointers
868 : #define fix_pd(xx) (pd_nlocal!=0?&xx:NULL)
869 18481 : p.cmd("setForces",fix_pd(forces[3*pd_start]));
870 18481 : p.cmd("setPositions",fix_pd(coordinates[3*pd_start]));
871 18481 : p.cmd("setMasses",fix_pd(masses[pd_start]));
872 18481 : p.cmd("setCharges",fix_pd(charges[pd_start]));
873 : }
874 18713 : p.cmd("setBox",&cell[0]);
875 18713 : p.cmd("setVirial",&virial[0]);
876 : } else {
877 546 : p.cmd("setStepLong",&step);
878 546 : p.cmd("setStopFlag",&plumedStopCondition);
879 : }
880 19259 : p.cmd("calc");
881 :
882 : // this is necessary as only processor zero is adding to the virial:
883 19259 : intracomm.Bcast(virial,0);
884 19259 : if(debug_pd) intracomm.Sum(forces);
885 19259 : if(debug_dd) {
886 10996 : for(int i=0; i<dd_nlocal; i++) {
887 10764 : forces[3*dd_gatindex[i]+0]=dd_forces[3*i+0];
888 10764 : forces[3*dd_gatindex[i]+1]=dd_forces[3*i+1];
889 10764 : forces[3*dd_gatindex[i]+2]=dd_forces[3*i+2];
890 : }
891 232 : dd_forces.assign(3*natoms,0.0);
892 232 : intracomm.Sum(forces);
893 : }
894 19259 : if(debug_grex &&step%grex_stride==0) {
895 72 : p.cmd("GREX savePositions");
896 72 : if(intracomm.Get_rank()>0) {
897 36 : p.cmd("GREX prepare");
898 : } else {
899 36 : int r=intercomm.Get_rank();
900 36 : int n=intercomm.Get_size();
901 36 : int partner=r+(2*((r+step/grex_stride)%2))-1;
902 36 : if(partner<0)partner=0;
903 36 : if(partner>=n) partner=n-1;
904 36 : p.cmd("GREX setPartner",&partner);
905 36 : p.cmd("GREX calculate");
906 36 : p.cmd("GREX shareAllDeltaBias");
907 144 : for(int i=0; i<n; i++) {
908 108 : string s; Tools::convert(i,s);
909 108 : real a=NAN; s="GREX getDeltaBias "+s; p.cmd(s.c_str(),&a);
910 108 : if(grex_log) fprintf(grex_log," %f",a);
911 : }
912 36 : if(grex_log) fprintf(grex_log,"\n");
913 : }
914 : }
915 :
916 :
917 19259 : if(fp_forces) {
918 10599 : fprintf(fp_forces,"%d\n",natoms);
919 10599 : string fmtv=dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+"\n";
920 21198 : string fmt=dumpforcesFmt+" "+dumpforcesFmt+" "+dumpforcesFmt+"\n";
921 10599 : if(dumpfullvirial) {
922 117 : fprintf(fp_forces,fmtv.c_str(),virial[0],virial[1],virial[2],virial[3],virial[4],virial[5],virial[6],virial[7],virial[8]);
923 : } else {
924 10482 : fprintf(fp_forces,fmt.c_str(),virial[0],virial[4],virial[8]);
925 : }
926 10599 : fmt="X "+fmt;
927 477029 : for(int i=0; i<natoms; i++)
928 477029 : fprintf(fp_forces,fmt.c_str(),forces[3*i],forces[3*i+1],forces[3*i+2]);
929 : }
930 19259 : if(debugforces.length()>0) {
931 : // Now call the routine to work out the derivatives numerically
932 3 : numder.assign(3*natoms+9,real(0.0)); real base=0;
933 3 : p.cmd("getBias",&base);
934 3 : if( fabs(base)<epsilon ) printf("WARNING: bias for configuration appears to be zero so debugging forces is trivial");
935 3 : evaluateNumericalDerivatives( step, p, coordinates, masses, charges, cell, base, numder );
936 :
937 : // And output everything to a file
938 3 : fp_dforces.fmtField(" " + dumpforcesFmt);
939 36 : for(int i=0; i<3*natoms; ++i) {
940 33 : fp_dforces.printField("parameter",(int)i);
941 33 : fp_dforces.printField("analytical",forces[i]);
942 33 : fp_dforces.printField("numerical",-numder[i]);
943 33 : fp_dforces.printField();
944 : }
945 : // And print the virial
946 30 : for(int i=0; i<9; ++i) {
947 27 : fp_dforces.printField("parameter",3*natoms+i );
948 27 : fp_dforces.printField("analytical",virial[i] );
949 27 : fp_dforces.printField("numerical",-numder[3*natoms+i]);
950 27 : fp_dforces.printField();
951 : }
952 : }
953 :
954 19259 : if(noatoms && plumedStopCondition) break;
955 :
956 19258 : step+=stride;
957 : }
958 288 : p.cmd("runFinalJobs");
959 :
960 288 : if(fp_forces) fclose(fp_forces);
961 288 : if(debugforces.length()>0) fp_dforces.close();
962 288 : if(fp && fp!=in)fclose(fp);
963 : #ifdef __PLUMED_HAS_XDRFILE
964 288 : if(xd) xdrfile_close(xd);
965 : #endif
966 : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
967 288 : if(h_in) api->close_file_read(h_in);
968 288 : if(ts_in.coords) delete [] ts_in.coords;
969 : #endif
970 288 : if(grex_log) fclose(grex_log);
971 :
972 576 : return 0;
973 : }
974 :
975 : template<typename real>
976 3 : void Driver<real>::evaluateNumericalDerivatives( const long int& step, Plumed& p, const std::vector<real>& coordinates,
977 : const std::vector<real>& masses, const std::vector<real>& charges,
978 : std::vector<real>& cell, const double& base, std::vector<real>& numder ) {
979 :
980 3 : int natoms = coordinates.size() / 3; real delta = sqrt(epsilon);
981 3 : std::vector<Vector> pos(natoms); real bias=0;
982 6 : std::vector<real> fake_forces( 3*natoms ), fake_virial(9);
983 14 : for(int i=0; i<natoms; ++i) {
984 11 : for(unsigned j=0; j<3; ++j) pos[i][j]=coordinates[3*i+j];
985 : }
986 :
987 14 : for(int i=0; i<natoms; ++i) {
988 44 : for(unsigned j=0; j<3; ++j) {
989 33 : pos[i][j]=pos[i][j]+delta;
990 33 : p.cmd("setStepLong",&step);
991 33 : p.cmd("setPositions",&pos[0][0]);
992 33 : p.cmd("setForces",&fake_forces[0]);
993 33 : p.cmd("setMasses",&masses[0]);
994 33 : p.cmd("setCharges",&charges[0]);
995 33 : p.cmd("setBox",&cell[0]);
996 33 : p.cmd("setVirial",&fake_virial[0]);
997 33 : p.cmd("prepareCalc");
998 33 : p.cmd("performCalcNoUpdate");
999 33 : p.cmd("getBias",&bias);
1000 33 : pos[i][j]=coordinates[3*i+j];
1001 33 : numder[3*i+j] = (bias - base) / delta;
1002 : }
1003 : }
1004 :
1005 : // Create the cell
1006 3 : Tensor box( cell[0], cell[1], cell[2], cell[3], cell[4], cell[5], cell[6], cell[7], cell[8] );
1007 : // And the virial
1008 6 : Pbc pbc; pbc.setBox( box ); Tensor nvirial;
1009 30 : for(unsigned i=0; i<3; i++) for(unsigned k=0; k<3; k++) {
1010 27 : double arg0=box(i,k);
1011 27 : for(int j=0; j<natoms; ++j) pos[j]=pbc.realToScaled( pos[j] );
1012 27 : cell[3*i+k]=box(i,k)=box(i,k)+delta; pbc.setBox(box);
1013 27 : for(int j=0; j<natoms; j++) pos[j]=pbc.scaledToReal( pos[j] );
1014 27 : p.cmd("setStepLong",&step);
1015 27 : p.cmd("setPositions",&pos[0][0]);
1016 27 : p.cmd("setForces",&fake_forces[0]);
1017 27 : p.cmd("setMasses",&masses[0]);
1018 27 : p.cmd("setCharges",&charges[0]);
1019 27 : p.cmd("setBox",&cell[0]);
1020 27 : p.cmd("setVirial",&fake_virial[0]);
1021 27 : p.cmd("prepareCalc");
1022 27 : p.cmd("performCalcNoUpdate");
1023 27 : p.cmd("getBias",&bias);
1024 27 : cell[3*i+k]=box(i,k)=arg0; pbc.setBox(box);
1025 27 : for(int j=0; j<natoms; j++) for(unsigned n=0; n<3; ++n) pos[j][n]=coordinates[3*j+n];
1026 27 : nvirial(i,k) = ( bias - base ) / delta;
1027 : }
1028 3 : nvirial=-matmul(box.transpose(),nvirial);
1029 6 : for(unsigned i=0; i<3; i++) for(unsigned k=0; k<3; k++) numder[3*natoms+3*i+k] = nvirial(i,k);
1030 :
1031 3 : }
1032 :
1033 : }
1034 2523 : }
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