src/programs/legacymodules.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS 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 GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \internal \brief
  36  * Registers command-line modules for pre-5.0 binaries.
  37  *
  38  * \author Teemu Murtola <teemu.murtola@gmail.com>
  39  */
  40 #include "gmxpre.h"
  41
  42 #include "legacymodules.h"
  43
  44 #include <cstdio>
  45
  46 #include "gromacs/commandline/cmdlinemodule.h"
  47 #include "gromacs/commandline/cmdlinemodulemanager.h"
  48 #include "gromacs/commandline/cmdlineoptionsmodule.h"
  49 #include "gromacs/gmxana/gmx_ana.h"
  50 #include "gromacs/gmxpreprocess/editconf.h"
  51 #include "gromacs/gmxpreprocess/genconf.h"
  52 #include "gromacs/gmxpreprocess/genion.h"
  53 #include "gromacs/gmxpreprocess/genrestr.h"
  54 #include "gromacs/gmxpreprocess/grompp.h"
  55 #include "gromacs/gmxpreprocess/insert-molecules.h"
  56 #include "gromacs/gmxpreprocess/pdb2gmx.h"
  57 #include "gromacs/gmxpreprocess/solvate.h"
  58 #include "gromacs/gmxpreprocess/x2top.h"
  59 #include "gromacs/tools/check.h"
  60 #include "gromacs/tools/convert_tpr.h"
  61 #include "gromacs/tools/dump.h"
  62 #include "gromacs/tools/report-methods.h"
  63
  64 #include "mdrun/mdrun_main.h"
  65 #include "view/view.h"
  66
  67 namespace
  68 {
  69
  70 /*! \brief
  71  * Command line module that provides information about obsolescence.
  72  *
  73  * Prints a message directing the user to a wiki page describing replacement
  74  * options.
  75  */
  76 class ObsoleteToolModule : public gmx::ICommandLineModule
  77 {
  78     public:
  79         //! Creates an obsolete tool module for a tool with the given name.
  80         explicit ObsoleteToolModule(const char *name)
  81             : name_(name)
  82         {
  83         }
  84
  85         const char *name() const override
  86         {
  87             return name_;
  88         }
  89         const char *shortDescription() const override
  90         {
  91             return nullptr;
  92         }
  93
  94         void init(gmx::CommandLineModuleSettings * /*settings*/) override
  95         {
  96         }
  97         int run(int /*argc*/, char * /*argv*/[]) override
  98         {
  99             printMessage();
 100             return 0;
 101         }
 102         void writeHelp(const gmx::CommandLineHelpContext & /*context*/) const override
 103         {
 104             printMessage();
 105         }
 106
 107     private:
 108         void printMessage() const
 109         {
 110             std::fprintf(stderr,
 111                          "This tool is no longer present in GROMACS. Please see\n"
 112                          "  http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/user-guide/cmdline.html#command-changes\n"
 113                          "for ideas how to perform the same tasks with the "
 114                          "new tools.\n");
 115         }
 116
 117         const char             *name_;
 118 };
 119
 120 //! Initializer for a module that defaults to nice level zero.
 121 void initSettingsNoNice(gmx::CommandLineModuleSettings *settings)
 122 {
 123     settings->setDefaultNiceLevel(0);
 124 }
 125
 126 /*! \brief
 127  * Convenience function for creating and registering a module.
 128  *
 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.
 133  */
 134 void registerModule(gmx::CommandLineModuleManager                *manager,
 135                     gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 136                     const char *name, const char *shortDescription)
 137 {
 138     manager->addModuleCMain(name, shortDescription, mainFunction);
 139 }
 140
 141 /*! \brief
 142  * Convenience function for creating and registering a module that defaults to
 143  * -nice 0.
 144  *
 145  * \param[in] manager          Module manager to which to register the module.
 146  * \param[in] mainFunction     Main function to wrap.
 147  * \param[in] name             Name for the new module.
 148  * \param[in] shortDescription One-line description for the new module.
 149  */
 150 void registerModuleNoNice(gmx::CommandLineModuleManager                *manager,
 151                           gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 152                           const char *name, const char *shortDescription)
 153 {
 154     manager->addModuleCMainWithSettings(name, shortDescription, mainFunction,
 155                                         &initSettingsNoNice);
 156 }
 157
 158 /*! \brief
 159  * Convenience function for registering a module for an obsolete tool.
 160  *
 161  * \param[in] manager          Module manager to which to register the module.
 162  * \param[in] name             Name for the obsolete tool.
 163  */
 164 void registerObsoleteTool(gmx::CommandLineModuleManager *manager,
 165                           const char                    *name)
 166 {
 167     gmx::CommandLineModulePointer module(new ObsoleteToolModule(name));
 168     manager->addModule(std::move(module));
 169 }
 170
 171 } // namespace
 172
 173 void registerLegacyModules(gmx::CommandLineModuleManager *manager)
 174 {
 175     // Modules from this directory (were in src/kernel/).
 176     registerModule(manager, &gmx_check, "check",
 177                    "Check and compare files");
 178     registerModule(manager, &gmx_dump, "dump",
 179                    "Make binary files human readable");
 180     registerModule(manager, &gmx_grompp, "grompp",
 181                    "Make a run input file");
 182     registerModule(manager, &gmx_convert_tpr, "convert-tpr",
 183                    "Make a modifed run-input file");
 184     registerObsoleteTool(manager, "tpbconv");
 185     registerModule(manager, &gmx_x2top, "x2top",
 186                    "Generate a primitive topology from coordinates");
 187
 188     registerModuleNoNice(manager, &gmx::gmx_mdrun, "mdrun",
 189                          "Perform a simulation, do a normal mode analysis or an energy minimization");
 190
 191     gmx::ICommandLineOptionsModule::registerModuleFactory(
 192             manager, gmx::InsertMoleculesInfo::name(),
 193             gmx::InsertMoleculesInfo::shortDescription(),
 194             &gmx::InsertMoleculesInfo::create);
 195
 196     gmx::ICommandLineOptionsModule::registerModuleFactory(
 197             manager, gmx::ReportMethodsInfo::name,
 198             gmx::ReportMethodsInfo::shortDescription,
 199             &gmx::ReportMethodsInfo::create);
 200
 201     gmx::ICommandLineOptionsModule::registerModuleFactory(
 202             manager, gmx::pdb2gmxInfo::name,
 203             gmx::pdb2gmxInfo::shortDescription,
 204             &gmx::pdb2gmxInfo::create);
 205
 206     // Modules from gmx_ana.h.
 207     registerModule(manager, &gmx_do_dssp, "do_dssp",
 208                    "Assign secondary structure and calculate solvent accessible surface area");
 209     registerModule(manager, &gmx_editconf, "editconf",
 210                    "Convert and manipulates structure files");
 211     registerModule(manager, &gmx_eneconv, "eneconv",
 212                    "Convert energy files");
 213     registerModule(manager, &gmx_solvate, "solvate",
 214                    "Solvate a system");
 215     registerObsoleteTool(manager, "genbox");
 216     registerModule(manager, &gmx_genconf, "genconf",
 217                    "Multiply a conformation in 'random' orientations");
 218     registerModule(manager, &gmx_genion, "genion",
 219                    "Generate monoatomic ions on energetically favorable positions");
 220     registerModule(manager, &gmx_genrestr, "genrestr",
 221                    "Generate position restraints or distance restraints for index groups");
 222     registerModule(manager, &gmx_make_edi, "make_edi",
 223                    "Generate input files for essential dynamics sampling");
 224     registerModule(manager, &gmx_make_ndx, "make_ndx",
 225                    "Make index files");
 226     registerModule(manager, &gmx_mk_angndx, "mk_angndx",
 227                    "Generate index files for 'gmx angle'");
 228     registerModule(manager, &gmx_trjcat, "trjcat",
 229                    "Concatenate trajectory files");
 230     registerModule(manager, &gmx_trjconv, "trjconv",
 231                    "Convert and manipulates trajectory files");
 232     registerModule(manager, &gmx_trjorder, "trjorder",
 233                    "Order molecules according to their distance to a group");
 234     registerModule(manager, &gmx_xpm2ps, "xpm2ps",
 235                    "Convert XPM (XPixelMap) matrices to postscript or XPM");
 236
 237     registerModule(manager, &gmx_anaeig, "anaeig",
 238                    "Analyze eigenvectors/normal modes");
 239     registerModule(manager, &gmx_analyze, "analyze",
 240                    "Analyze data sets");
 241     registerModule(manager, &gmx_g_angle, "angle",
 242                    "Calculate distributions and correlations for angles and dihedrals");
 243     registerModule(manager, &gmx_awh, "awh",
 244                    "Extract data from an accelerated weight histogram (AWH) run");
 245     registerModule(manager, &gmx_bar, "bar",
 246                    "Calculate free energy difference estimates through Bennett's acceptance ratio");
 247     registerObsoleteTool(manager, "bond");
 248     registerObsoleteTool(manager, "dist");
 249     registerObsoleteTool(manager, "sas");
 250     registerObsoleteTool(manager, "sgangle");
 251
 252     registerModule(manager, &gmx_bundle, "bundle",
 253                    "Analyze bundles of axes, e.g., helices");
 254     registerModule(manager, &gmx_chi, "chi",
 255                    "Calculate everything you want to know about chi and other dihedrals");
 256     registerModule(manager, &gmx_cluster, "cluster",
 257                    "Cluster structures");
 258     registerModule(manager, &gmx_clustsize, "clustsize",
 259                    "Calculate size distributions of atomic clusters");
 260     registerModule(manager, &gmx_confrms, "confrms",
 261                    "Fit two structures and calculates the RMSD");
 262     registerModule(manager, &gmx_covar, "covar",
 263                    "Calculate and diagonalize the covariance matrix");
 264     registerModule(manager, &gmx_current, "current",
 265                    "Calculate dielectric constants and current autocorrelation function");
 266     registerModule(manager, &gmx_density, "density",
 267                    "Calculate the density of the system");
 268     registerModule(manager, &gmx_densmap, "densmap",
 269                    "Calculate 2D planar or axial-radial density maps");
 270     registerModule(manager, &gmx_densorder, "densorder",
 271                    "Calculate surface fluctuations");
 272     registerModule(manager, &gmx_dielectric, "dielectric",
 273                    "Calculate frequency dependent dielectric constants");
 274     registerModule(manager, &gmx_dipoles, "dipoles",
 275                    "Compute the total dipole plus fluctuations");
 276     registerModule(manager, &gmx_disre, "disre",
 277                    "Analyze distance restraints");
 278     registerModule(manager, &gmx_dos, "dos",
 279                    "Analyze density of states and properties based on that");
 280     registerModule(manager, &gmx_dyecoupl, "dyecoupl",
 281                    "Extract dye dynamics from trajectories");
 282     registerModule(manager, &gmx_enemat, "enemat",
 283                    "Extract an energy matrix from an energy file");
 284     registerModule(manager, &gmx_energy, "energy",
 285                    "Writes energies to xvg files and display averages");
 286     registerModule(manager, &gmx_filter, "filter",
 287                    "Frequency filter trajectories, useful for making smooth movies");
 288     registerModule(manager, &gmx_gyrate, "gyrate",
 289                    "Calculate the radius of gyration");
 290     registerModule(manager, &gmx_h2order, "h2order",
 291                    "Compute the orientation of water molecules");
 292     registerModule(manager, &gmx_hbond, "hbond",
 293                    "Compute and analyze hydrogen bonds");
 294     registerModule(manager, &gmx_helix, "helix",
 295                    "Calculate basic properties of alpha helices");
 296     registerModule(manager, &gmx_helixorient, "helixorient",
 297                    "Calculate local pitch/bending/rotation/orientation inside helices");
 298     registerModule(manager, &gmx_hydorder, "hydorder",
 299                    "Compute tetrahedrality parameters around a given atom");
 300     registerModule(manager, &gmx_lie, "lie",
 301                    "Estimate free energy from linear combinations");
 302     registerModule(manager, &gmx_mdmat, "mdmat",
 303                    "Calculate residue contact maps");
 304     registerModule(manager, &gmx_mindist, "mindist",
 305                    "Calculate the minimum distance between two groups");
 306     registerModule(manager, &gmx_msd, "msd",
 307                    "Calculates mean square displacements");
 308     registerModule(manager, &gmx_nmeig, "nmeig",
 309                    "Diagonalize the Hessian for normal mode analysis");
 310     registerModule(manager, &gmx_nmens, "nmens",
 311                    "Generate an ensemble of structures from the normal modes");
 312     registerModule(manager, &gmx_nmr, "nmr",
 313                    "Analyze nuclear magnetic resonance properties from an energy file");
 314     registerModule(manager, &gmx_nmtraj, "nmtraj",
 315                    "Generate a virtual oscillating trajectory from an eigenvector");
 316     registerModule(manager, &gmx_order, "order",
 317                    "Compute the order parameter per atom for carbon tails");
 318     registerModule(manager, &gmx_pme_error, "pme_error",
 319                    "Estimate the error of using PME with a given input file");
 320     registerModule(manager, &gmx_polystat, "polystat",
 321                    "Calculate static properties of polymers");
 322     registerModule(manager, &gmx_potential, "potential",
 323                    "Calculate the electrostatic potential across the box");
 324     registerModule(manager, &gmx_principal, "principal",
 325                    "Calculate principal axes of inertia for a group of atoms");
 326     registerModule(manager, &gmx_rama, "rama",
 327                    "Compute Ramachandran plots");
 328     registerModule(manager, &gmx_rms, "rms",
 329                    "Calculate RMSDs with a reference structure and RMSD matrices");
 330     registerModule(manager, &gmx_rmsdist, "rmsdist",
 331                    "Calculate atom pair distances averaged with power -2, -3 or -6");
 332     registerModule(manager, &gmx_rmsf, "rmsf",
 333                    "Calculate atomic fluctuations");
 334     registerModule(manager, &gmx_rotacf, "rotacf",
 335                    "Calculate the rotational correlation function for molecules");
 336     registerModule(manager, &gmx_rotmat, "rotmat",
 337                    "Plot the rotation matrix for fitting to a reference structure");
 338     registerModule(manager, &gmx_saltbr, "saltbr",
 339                    "Compute salt bridges");
 340     registerModule(manager, &gmx_sans, "sans",
 341                    "Compute small angle neutron scattering spectra");
 342     registerModule(manager, &gmx_saxs, "saxs",
 343                    "Compute small angle X-ray scattering spectra");
 344     registerModule(manager, &gmx_sham, "sham",
 345                    "Compute free energies or other histograms from histograms");
 346     registerModule(manager, &gmx_sigeps, "sigeps",
 347                    "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
 348     registerModule(manager, &gmx_sorient, "sorient",
 349                    "Analyze solvent orientation around solutes");
 350     registerModule(manager, &gmx_spatial, "spatial",
 351                    "Calculate the spatial distribution function");
 352     registerModule(manager, &gmx_spol, "spol",
 353                    "Analyze solvent dipole orientation and polarization around solutes");
 354     registerModule(manager, &gmx_tcaf, "tcaf",
 355                    "Calculate viscosities of liquids");
 356     registerModule(manager, &gmx_traj, "traj",
 357                    "Plot x, v, f, box, temperature and rotational energy from trajectories");
 358     registerModule(manager, &gmx_tune_pme, "tune_pme",
 359                    "Time mdrun as a function of PME ranks to optimize settings");
 360     registerModule(manager, &gmx_vanhove, "vanhove",
 361                    "Compute Van Hove displacement and correlation functions");
 362     registerModule(manager, &gmx_velacc, "velacc",
 363                    "Calculate velocity autocorrelation functions");
 364     registerModule(manager, &gmx_wham, "wham",
 365                    "Perform weighted histogram analysis after umbrella sampling");
 366     registerModule(manager, &gmx_wheel, "wheel",
 367                    "Plot helical wheels");
 368     registerModuleNoNice(manager, &gmx_view, "view",
 369                          "View a trajectory on an X-Windows terminal");
 370
 371     {
 372         gmx::CommandLineModuleGroup group =
 373             manager->addModuleGroup("Generating topologies and coordinates");
 374         group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
 375         group.addModule("x2top");
 376         group.addModule("solvate");
 377         group.addModule("insert-molecules");
 378         group.addModule("genconf");
 379         group.addModule("genion");
 380         group.addModule("genrestr");
 381         group.addModule("pdb2gmx");
 382     }
 383     {
 384         gmx::CommandLineModuleGroup group =
 385             manager->addModuleGroup("Running a simulation");
 386         group.addModule("grompp");
 387         group.addModule("mdrun");
 388         group.addModule("convert-tpr");
 389     }
 390     {
 391         gmx::CommandLineModuleGroup group =
 392             manager->addModuleGroup("Viewing trajectories");
 393         group.addModule("nmtraj");
 394         group.addModule("view");
 395     }
 396     {
 397         gmx::CommandLineModuleGroup group =
 398             manager->addModuleGroup("Processing energies");
 399         group.addModule("enemat");
 400         group.addModule("energy");
 401         group.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
 402     }
 403     {
 404         gmx::CommandLineModuleGroup group =
 405             manager->addModuleGroup("Converting files");
 406         group.addModule("editconf");
 407         group.addModule("eneconv");
 408         group.addModule("sigeps");
 409         group.addModule("trjcat");
 410         group.addModule("trjconv");
 411         group.addModule("xpm2ps");
 412     }
 413     {
 414         gmx::CommandLineModuleGroup group =
 415             manager->addModuleGroup("Tools");
 416         group.addModule("analyze");
 417         group.addModule("awh");
 418         group.addModule("filter");
 419         group.addModule("lie");
 420         group.addModule("pme_error");
 421         group.addModule("sham");
 422         group.addModule("spatial");
 423         group.addModule("traj");
 424         group.addModule("tune_pme");
 425         group.addModule("wham");
 426         group.addModule("check");
 427         group.addModule("dump");
 428         group.addModule("make_ndx");
 429         group.addModule("mk_angndx");
 430         group.addModule("trjorder");
 431         group.addModule("xpm2ps");
 432         group.addModule("report-methods");
 433     }
 434     {
 435         gmx::CommandLineModuleGroup group =
 436             manager->addModuleGroup("Distances between structures");
 437         group.addModule("cluster");
 438         group.addModule("confrms");
 439         group.addModule("rms");
 440         group.addModule("rmsf");
 441     }
 442     {
 443         gmx::CommandLineModuleGroup group =
 444             manager->addModuleGroup("Distances in structures over time");
 445         group.addModule("mindist");
 446         group.addModule("mdmat");
 447         group.addModule("polystat");
 448         group.addModule("rmsdist");
 449     }
 450     {
 451         gmx::CommandLineModuleGroup group =
 452             manager->addModuleGroup("Mass distribution properties over time");
 453         group.addModule("gyrate");
 454         group.addModule("msd");
 455         group.addModule("polystat");
 456         group.addModule("rdf");
 457         group.addModule("rotacf");
 458         group.addModule("rotmat");
 459         group.addModule("sans");
 460         group.addModule("saxs");
 461         group.addModule("traj");
 462         group.addModule("vanhove");
 463     }
 464     {
 465         gmx::CommandLineModuleGroup group =
 466             manager->addModuleGroup("Analyzing bonded interactions");
 467         group.addModule("angle");
 468         group.addModule("mk_angndx");
 469     }
 470     {
 471         gmx::CommandLineModuleGroup group =
 472             manager->addModuleGroup("Structural properties");
 473         group.addModule("bundle");
 474         group.addModule("clustsize");
 475         group.addModule("disre");
 476         group.addModule("hbond");
 477         group.addModule("order");
 478         group.addModule("principal");
 479         group.addModule("rdf");
 480         group.addModule("saltbr");
 481         group.addModule("sorient");
 482         group.addModule("spol");
 483     }
 484     {
 485         gmx::CommandLineModuleGroup group =
 486             manager->addModuleGroup("Kinetic properties");
 487         group.addModule("bar");
 488         group.addModule("current");
 489         group.addModule("dos");
 490         group.addModule("dyecoupl");
 491         group.addModule("principal");
 492         group.addModule("tcaf");
 493         group.addModule("traj");
 494         group.addModule("vanhove");
 495         group.addModule("velacc");
 496     }
 497     {
 498         gmx::CommandLineModuleGroup group =
 499             manager->addModuleGroup("Electrostatic properties");
 500         group.addModule("current");
 501         group.addModule("dielectric");
 502         group.addModule("dipoles");
 503         group.addModule("potential");
 504         group.addModule("spol");
 505         group.addModule("genion");
 506     }
 507     {
 508         gmx::CommandLineModuleGroup group =
 509             manager->addModuleGroup("Protein-specific analysis");
 510         group.addModule("do_dssp");
 511         group.addModule("chi");
 512         group.addModule("helix");
 513         group.addModule("helixorient");
 514         group.addModule("rama");
 515         group.addModule("wheel");
 516     }
 517     {
 518         gmx::CommandLineModuleGroup group =
 519             manager->addModuleGroup("Interfaces");
 520         group.addModule("bundle");
 521         group.addModule("density");
 522         group.addModule("densmap");
 523         group.addModule("densorder");
 524         group.addModule("h2order");
 525         group.addModule("hydorder");
 526         group.addModule("order");
 527         group.addModule("potential");
 528     }
 529     {
 530         gmx::CommandLineModuleGroup group =
 531             manager->addModuleGroup("Covariance analysis");
 532         group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
 533         group.addModule("covar");
 534         group.addModule("make_edi");
 535     }
 536     {
 537         gmx::CommandLineModuleGroup group =
 538             manager->addModuleGroup("Normal modes");
 539         group.addModuleWithDescription("anaeig", "Analyze the normal modes");
 540         group.addModule("nmeig");
 541         group.addModule("nmtraj");
 542         group.addModule("nmens");
 543         group.addModule("grompp");
 544         group.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");
 545     }
 546 }