2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
5 * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
6 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
7 * and including many others, as listed in the AUTHORS file in the
8 * top-level source directory and at http://www.gromacs.org.
10 * GROMACS is free software; you can redistribute it and/or
11 * modify it under the terms of the GNU Lesser General Public License
12 * as published by the Free Software Foundation; either version 2.1
13 * of the License, or (at your option) any later version.
15 * GROMACS is distributed in the hope that it will be useful,
16 * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 * Lesser General Public License for more details.
20 * You should have received a copy of the GNU Lesser General Public
21 * License along with GROMACS; if not, see
22 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
23 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25 * If you want to redistribute modifications to GROMACS, please
26 * consider that scientific software is very special. Version
27 * control is crucial - bugs must be traceable. We will be happy to
28 * consider code for inclusion in the official distribution, but
29 * derived work must not be called official GROMACS. Details are found
30 * in the README & COPYING files - if they are missing, get the
31 * official version at http://www.gromacs.org.
33 * To help us fund GROMACS development, we humbly ask that you cite
34 * the research papers on the package. Check out http://www.gromacs.org.
37 * Registers command-line modules for pre-5.0 binaries.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
43 #include "legacymodules.h"
47 #include "gromacs/commandline/cmdlinemodule.h"
48 #include "gromacs/commandline/cmdlinemodulemanager.h"
49 #include "gromacs/commandline/cmdlineoptionsmodule.h"
50 #include "gromacs/gmxana/gmx_ana.h"
51 #include "gromacs/gmxpreprocess/editconf.h"
52 #include "gromacs/gmxpreprocess/genconf.h"
53 #include "gromacs/gmxpreprocess/genion.h"
54 #include "gromacs/gmxpreprocess/genrestr.h"
55 #include "gromacs/gmxpreprocess/grompp.h"
56 #include "gromacs/gmxpreprocess/insert_molecules.h"
57 #include "gromacs/gmxpreprocess/pdb2gmx.h"
58 #include "gromacs/gmxpreprocess/solvate.h"
59 #include "gromacs/gmxpreprocess/x2top.h"
60 #include "gromacs/tools/check.h"
61 #include "gromacs/tools/convert_tpr.h"
62 #include "gromacs/tools/dump.h"
63 #include "gromacs/tools/eneconv.h"
64 #include "gromacs/tools/make_ndx.h"
65 #include "gromacs/tools/mk_angndx.h"
66 #include "gromacs/tools/pme_error.h"
67 #include "gromacs/tools/report_methods.h"
68 #include "gromacs/tools/trjcat.h"
69 #include "gromacs/tools/trjconv.h"
70 #include "gromacs/tools/tune_pme.h"
72 #include "mdrun/mdrun_main.h"
73 #include "mdrun/nonbonded_bench.h"
74 #include "view/view.h"
80 * Command line module that provides information about obsolescence.
82 * Prints a message directing the user to a wiki page describing replacement
85 class ObsoleteToolModule
: public gmx::ICommandLineModule
88 //! Creates an obsolete tool module for a tool with the given name.
89 explicit ObsoleteToolModule(const char* name
) : name_(name
) {}
91 const char* name() const override
{ return name_
; }
92 const char* shortDescription() const override
{ return nullptr; }
94 void init(gmx::CommandLineModuleSettings
* /*settings*/) override
{}
95 int run(int /*argc*/, char* /*argv*/[]) override
100 void writeHelp(const gmx::CommandLineHelpContext
& /*context*/) const override
106 static void printMessage()
109 "This tool is no longer present in GROMACS. Please see\n"
111 "http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/"
112 "user-guide/cmdline.html#command-changes\n"
113 "for ideas how to perform the same tasks with the "
120 //! Initializer for a module that defaults to nice level zero.
121 void initSettingsNoNice(gmx::CommandLineModuleSettings
* settings
)
123 settings
->setDefaultNiceLevel(0);
127 * Convenience function for creating and registering a module.
129 * \param[in] manager Module manager to which to register the module.
130 * \param[in] mainFunction Main function to wrap.
131 * \param[in] name Name for the new module.
132 * \param[in] shortDescription One-line description for the new module.
134 void registerModule(gmx::CommandLineModuleManager
* manager
,
135 gmx::CommandLineModuleManager::CMainFunction mainFunction
,
137 const char* shortDescription
)
139 manager
->addModuleCMain(name
, shortDescription
, mainFunction
);
143 * Convenience function for creating and registering a module that defaults to
146 * \param[in] manager Module manager to which to register the module.
147 * \param[in] mainFunction Main function to wrap.
148 * \param[in] name Name for the new module.
149 * \param[in] shortDescription One-line description for the new module.
151 void registerModuleNoNice(gmx::CommandLineModuleManager
* manager
,
152 gmx::CommandLineModuleManager::CMainFunction mainFunction
,
154 const char* shortDescription
)
156 manager
->addModuleCMainWithSettings(name
, shortDescription
, mainFunction
, &initSettingsNoNice
);
160 * Convenience function for registering a module for an obsolete tool.
162 * \param[in] manager Module manager to which to register the module.
163 * \param[in] name Name for the obsolete tool.
165 void registerObsoleteTool(gmx::CommandLineModuleManager
* manager
, const char* name
)
167 gmx::CommandLineModulePointer
module(new ObsoleteToolModule(name
));
168 manager
->addModule(std::move(module
));
173 void registerLegacyModules(gmx::CommandLineModuleManager
* manager
)
175 registerModule(manager
, &gmx_check
, "check", "Check and compare files");
176 gmx::ICommandLineOptionsModule::registerModuleFactory(
177 manager
, gmx::DumpInfo::name
, gmx::DumpInfo::shortDescription
, &gmx::DumpInfo::create
);
178 registerModule(manager
, &gmx_grompp
, "grompp", "Make a run input file");
179 gmx::ICommandLineOptionsModule::registerModuleFactory(manager
, gmx::ConvertTprInfo::name
,
180 gmx::ConvertTprInfo::shortDescription
,
181 &gmx::ConvertTprInfo::create
);
182 registerObsoleteTool(manager
, "tpbconv");
183 registerModule(manager
, &gmx_x2top
, "x2top", "Generate a primitive topology from coordinates");
185 registerModuleNoNice(
186 manager
, &gmx::gmx_mdrun
, "mdrun",
187 "Perform a simulation, do a normal mode analysis or an energy minimization");
189 gmx::ICommandLineOptionsModule::registerModuleFactory(
190 manager
, gmx::NonbondedBenchmarkInfo::name
,
191 gmx::NonbondedBenchmarkInfo::shortDescription
, &gmx::NonbondedBenchmarkInfo::create
);
193 gmx::ICommandLineOptionsModule::registerModuleFactory(manager
, gmx::InsertMoleculesInfo::name(),
194 gmx::InsertMoleculesInfo::shortDescription(),
195 &gmx::InsertMoleculesInfo::create
);
197 gmx::ICommandLineOptionsModule::registerModuleFactory(manager
, gmx::ReportMethodsInfo::name
,
198 gmx::ReportMethodsInfo::shortDescription
,
199 &gmx::ReportMethodsInfo::create
);
201 gmx::ICommandLineOptionsModule::registerModuleFactory(manager
, gmx::pdb2gmxInfo::name
,
202 gmx::pdb2gmxInfo::shortDescription
,
203 &gmx::pdb2gmxInfo::create
);
205 // Modules from gmx_ana.h.
206 registerModule(manager
, &gmx_do_dssp
, "do_dssp",
207 "Assign secondary structure and calculate solvent accessible surface area");
208 registerModule(manager
, &gmx_editconf
, "editconf", "Convert and manipulates structure files");
209 registerModule(manager
, &gmx_eneconv
, "eneconv", "Convert energy files");
210 registerModule(manager
, &gmx_solvate
, "solvate", "Solvate a system");
211 registerObsoleteTool(manager
, "genbox");
212 registerModule(manager
, &gmx_genconf
, "genconf",
213 "Multiply a conformation in 'random' orientations");
214 registerModule(manager
, &gmx_genion
, "genion",
215 "Generate monoatomic ions on energetically favorable positions");
216 registerModule(manager
, &gmx_genrestr
, "genrestr",
217 "Generate position restraints or distance restraints for index groups");
218 registerModule(manager
, &gmx_make_edi
, "make_edi",
219 "Generate input files for essential dynamics sampling");
220 registerModule(manager
, &gmx_make_ndx
, "make_ndx", "Make index files");
221 registerModule(manager
, &gmx_mk_angndx
, "mk_angndx", "Generate index files for 'gmx angle'");
222 registerModule(manager
, &gmx_trjcat
, "trjcat", "Concatenate trajectory files");
223 registerModule(manager
, &gmx_trjconv
, "trjconv", "Convert and manipulates trajectory files");
224 registerModule(manager
, &gmx_trjorder
, "trjorder",
225 "Order molecules according to their distance to a group");
226 registerModule(manager
, &gmx_xpm2ps
, "xpm2ps",
227 "Convert XPM (XPixelMap) matrices to postscript or XPM");
229 registerModule(manager
, &gmx_anaeig
, "anaeig", "Analyze eigenvectors/normal modes");
230 registerModule(manager
, &gmx_analyze
, "analyze", "Analyze data sets");
231 registerModule(manager
, &gmx_g_angle
, "angle",
232 "Calculate distributions and correlations for angles and dihedrals");
233 registerModule(manager
, &gmx_awh
, "awh",
234 "Extract data from an accelerated weight histogram (AWH) run");
235 registerModule(manager
, &gmx_bar
, "bar",
236 "Calculate free energy difference estimates through Bennett's acceptance ratio");
237 registerObsoleteTool(manager
, "bond");
238 registerObsoleteTool(manager
, "dist");
239 registerObsoleteTool(manager
, "sas");
240 registerObsoleteTool(manager
, "sgangle");
242 registerModule(manager
, &gmx_bundle
, "bundle", "Analyze bundles of axes, e.g., helices");
243 registerModule(manager
, &gmx_chi
, "chi",
244 "Calculate everything you want to know about chi and other dihedrals");
245 registerModule(manager
, &gmx_cluster
, "cluster", "Cluster structures");
246 registerModule(manager
, &gmx_clustsize
, "clustsize",
247 "Calculate size distributions of atomic clusters");
248 registerModule(manager
, &gmx_confrms
, "confrms", "Fit two structures and calculates the RMSD");
249 registerModule(manager
, &gmx_covar
, "covar", "Calculate and diagonalize the covariance matrix");
250 registerModule(manager
, &gmx_current
, "current",
251 "Calculate dielectric constants and current autocorrelation function");
252 registerModule(manager
, &gmx_density
, "density", "Calculate the density of the system");
253 registerModule(manager
, &gmx_densmap
, "densmap",
254 "Calculate 2D planar or axial-radial density maps");
255 registerModule(manager
, &gmx_densorder
, "densorder", "Calculate surface fluctuations");
256 registerModule(manager
, &gmx_dielectric
, "dielectric",
257 "Calculate frequency dependent dielectric constants");
258 registerModule(manager
, &gmx_dipoles
, "dipoles", "Compute the total dipole plus fluctuations");
259 registerModule(manager
, &gmx_disre
, "disre", "Analyze distance restraints");
260 registerModule(manager
, &gmx_dos
, "dos",
261 "Analyze density of states and properties based on that");
262 registerModule(manager
, &gmx_dyecoupl
, "dyecoupl", "Extract dye dynamics from trajectories");
263 registerModule(manager
, &gmx_enemat
, "enemat", "Extract an energy matrix from an energy file");
264 registerModule(manager
, &gmx_energy
, "energy",
265 "Writes energies to xvg files and display averages");
266 registerModule(manager
, &gmx_filter
, "filter",
267 "Frequency filter trajectories, useful for making smooth movies");
268 registerModule(manager
, &gmx_gyrate
, "gyrate", "Calculate the radius of gyration");
269 registerModule(manager
, &gmx_h2order
, "h2order", "Compute the orientation of water molecules");
270 registerModule(manager
, &gmx_hbond
, "hbond", "Compute and analyze hydrogen bonds");
271 registerModule(manager
, &gmx_helix
, "helix", "Calculate basic properties of alpha helices");
272 registerModule(manager
, &gmx_helixorient
, "helixorient",
273 "Calculate local pitch/bending/rotation/orientation inside helices");
274 registerModule(manager
, &gmx_hydorder
, "hydorder",
275 "Compute tetrahedrality parameters around a given atom");
276 registerModule(manager
, &gmx_lie
, "lie", "Estimate free energy from linear combinations");
277 registerModule(manager
, &gmx_mdmat
, "mdmat", "Calculate residue contact maps");
278 registerModule(manager
, &gmx_mindist
, "mindist",
279 "Calculate the minimum distance between two groups");
280 registerModule(manager
, &gmx_msd
, "msd", "Calculates mean square displacements");
281 registerModule(manager
, &gmx_nmeig
, "nmeig", "Diagonalize the Hessian for normal mode analysis");
282 registerModule(manager
, &gmx_nmens
, "nmens",
283 "Generate an ensemble of structures from the normal modes");
284 registerModule(manager
, &gmx_nmr
, "nmr",
285 "Analyze nuclear magnetic resonance properties from an energy file");
286 registerModule(manager
, &gmx_nmtraj
, "nmtraj",
287 "Generate a virtual oscillating trajectory from an eigenvector");
288 registerModule(manager
, &gmx_order
, "order",
289 "Compute the order parameter per atom for carbon tails");
290 registerModule(manager
, &gmx_pme_error
, "pme_error",
291 "Estimate the error of using PME with a given input file");
292 registerModule(manager
, &gmx_polystat
, "polystat", "Calculate static properties of polymers");
293 registerModule(manager
, &gmx_potential
, "potential",
294 "Calculate the electrostatic potential across the box");
295 registerModule(manager
, &gmx_principal
, "principal",
296 "Calculate principal axes of inertia for a group of atoms");
297 registerModule(manager
, &gmx_rama
, "rama", "Compute Ramachandran plots");
298 registerModule(manager
, &gmx_rms
, "rms",
299 "Calculate RMSDs with a reference structure and RMSD matrices");
300 registerModule(manager
, &gmx_rmsdist
, "rmsdist",
301 "Calculate atom pair distances averaged with power -2, -3 or -6");
302 registerModule(manager
, &gmx_rmsf
, "rmsf", "Calculate atomic fluctuations");
303 registerModule(manager
, &gmx_rotacf
, "rotacf",
304 "Calculate the rotational correlation function for molecules");
305 registerModule(manager
, &gmx_rotmat
, "rotmat",
306 "Plot the rotation matrix for fitting to a reference structure");
307 registerModule(manager
, &gmx_saltbr
, "saltbr", "Compute salt bridges");
308 registerModule(manager
, &gmx_sans
, "sans", "Compute small angle neutron scattering spectra");
309 registerModule(manager
, &gmx_saxs
, "saxs", "Compute small angle X-ray scattering spectra");
310 registerModule(manager
, &gmx_sham
, "sham",
311 "Compute free energies or other histograms from histograms");
312 registerModule(manager
, &gmx_sigeps
, "sigeps",
313 "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
314 registerModule(manager
, &gmx_sorient
, "sorient", "Analyze solvent orientation around solutes");
315 registerModule(manager
, &gmx_spatial
, "spatial", "Calculate the spatial distribution function");
316 registerModule(manager
, &gmx_spol
, "spol",
317 "Analyze solvent dipole orientation and polarization around solutes");
318 registerModule(manager
, &gmx_tcaf
, "tcaf", "Calculate viscosities of liquids");
319 registerModule(manager
, &gmx_traj
, "traj",
320 "Plot x, v, f, box, temperature and rotational energy from trajectories");
321 registerModule(manager
, &gmx_tune_pme
, "tune_pme",
322 "Time mdrun as a function of PME ranks to optimize settings");
323 registerModule(manager
, &gmx_vanhove
, "vanhove",
324 "Compute Van Hove displacement and correlation functions");
325 registerModule(manager
, &gmx_velacc
, "velacc", "Calculate velocity autocorrelation functions");
326 registerModule(manager
, &gmx_wham
, "wham",
327 "Perform weighted histogram analysis after umbrella sampling");
328 registerModule(manager
, &gmx_wheel
, "wheel", "Plot helical wheels");
329 registerModuleNoNice(manager
, &gmx_view
, "view", "View a trajectory on an X-Windows terminal");
332 gmx::CommandLineModuleGroup group
=
333 manager
->addModuleGroup("Generating topologies and coordinates");
334 group
.addModuleWithDescription("editconf", "Edit the box and write subgroups");
335 group
.addModule("x2top");
336 group
.addModule("solvate");
337 group
.addModule("insert-molecules");
338 group
.addModule("genconf");
339 group
.addModule("genion");
340 group
.addModule("genrestr");
341 group
.addModule("pdb2gmx");
344 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Running a simulation");
345 group
.addModule("grompp");
346 group
.addModule("mdrun");
347 group
.addModule("convert-tpr");
350 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Viewing trajectories");
351 group
.addModule("nmtraj");
352 group
.addModule("view");
355 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Processing energies");
356 group
.addModule("enemat");
357 group
.addModule("energy");
358 group
.addModuleWithDescription("mdrun",
359 "(Re)calculate energies for trajectory frames with -rerun");
362 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Converting files");
363 group
.addModule("editconf");
364 group
.addModule("eneconv");
365 group
.addModule("sigeps");
366 group
.addModule("trjcat");
367 group
.addModule("trjconv");
368 group
.addModule("xpm2ps");
371 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Tools");
372 group
.addModule("analyze");
373 group
.addModule("awh");
374 group
.addModule("filter");
375 group
.addModule("lie");
376 group
.addModule("pme_error");
377 group
.addModule("sham");
378 group
.addModule("spatial");
379 group
.addModule("traj");
380 group
.addModule("tune_pme");
381 group
.addModule("wham");
382 group
.addModule("check");
383 group
.addModule("dump");
384 group
.addModule("make_ndx");
385 group
.addModule("mk_angndx");
386 group
.addModule("trjorder");
387 group
.addModule("xpm2ps");
388 group
.addModule("report-methods");
391 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Distances between structures");
392 group
.addModule("cluster");
393 group
.addModule("confrms");
394 group
.addModule("rms");
395 group
.addModule("rmsf");
398 gmx::CommandLineModuleGroup group
=
399 manager
->addModuleGroup("Distances in structures over time");
400 group
.addModule("mindist");
401 group
.addModule("mdmat");
402 group
.addModule("polystat");
403 group
.addModule("rmsdist");
406 gmx::CommandLineModuleGroup group
=
407 manager
->addModuleGroup("Mass distribution properties over time");
408 group
.addModule("gyrate");
409 group
.addModule("msd");
410 group
.addModule("polystat");
411 group
.addModule("rdf");
412 group
.addModule("rotacf");
413 group
.addModule("rotmat");
414 group
.addModule("sans");
415 group
.addModule("saxs");
416 group
.addModule("traj");
417 group
.addModule("vanhove");
420 gmx::CommandLineModuleGroup group
=
421 manager
->addModuleGroup("Analyzing bonded interactions");
422 group
.addModule("angle");
423 group
.addModule("mk_angndx");
426 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Structural properties");
427 group
.addModule("bundle");
428 group
.addModule("clustsize");
429 group
.addModule("disre");
430 group
.addModule("hbond");
431 group
.addModule("order");
432 group
.addModule("principal");
433 group
.addModule("rdf");
434 group
.addModule("saltbr");
435 group
.addModule("sorient");
436 group
.addModule("spol");
439 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Kinetic properties");
440 group
.addModule("bar");
441 group
.addModule("current");
442 group
.addModule("dos");
443 group
.addModule("dyecoupl");
444 group
.addModule("principal");
445 group
.addModule("tcaf");
446 group
.addModule("traj");
447 group
.addModule("vanhove");
448 group
.addModule("velacc");
451 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Electrostatic properties");
452 group
.addModule("current");
453 group
.addModule("dielectric");
454 group
.addModule("dipoles");
455 group
.addModule("potential");
456 group
.addModule("spol");
457 group
.addModule("genion");
460 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Protein-specific analysis");
461 group
.addModule("do_dssp");
462 group
.addModule("chi");
463 group
.addModule("helix");
464 group
.addModule("helixorient");
465 group
.addModule("rama");
466 group
.addModule("wheel");
469 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Interfaces");
470 group
.addModule("bundle");
471 group
.addModule("density");
472 group
.addModule("densmap");
473 group
.addModule("densorder");
474 group
.addModule("h2order");
475 group
.addModule("hydorder");
476 group
.addModule("order");
477 group
.addModule("potential");
480 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Covariance analysis");
481 group
.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
482 group
.addModule("covar");
483 group
.addModule("make_edi");
486 gmx::CommandLineModuleGroup group
= manager
->addModuleGroup("Normal modes");
487 group
.addModuleWithDescription("anaeig", "Analyze the normal modes");
488 group
.addModule("nmeig");
489 group
.addModule("nmtraj");
490 group
.addModule("nmens");
491 group
.addModule("grompp");
492 group
.addModuleWithDescription("mdrun",
493 "Find a potential energy minimum and calculate the Hessian");