src/programs/legacymodules.cpp

   1 /*
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  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/eneconv.h"
  63 #include "gromacs/tools/make_ndx.h"
  64 #include "gromacs/tools/mk_angndx.h"
  65 #include "gromacs/tools/pme_error.h"
  66 #include "gromacs/tools/report_methods.h"
  67 #include "gromacs/tools/trjcat.h"
  68 #include "gromacs/tools/trjconv.h"
  69 #include "gromacs/tools/tune_pme.h"
  70
  71 #include "mdrun/mdrun_main.h"
  72 #include "mdrun/nonbonded_bench.h"
  73 #include "view/view.h"
  74
  75 namespace
  76 {
  77
  78 /*! \brief
  79  * Command line module that provides information about obsolescence.
  80  *
  81  * Prints a message directing the user to a wiki page describing replacement
  82  * options.
  83  */
  84 class ObsoleteToolModule : public gmx::ICommandLineModule
  85 {
  86     public:
  87         //! Creates an obsolete tool module for a tool with the given name.
  88         explicit ObsoleteToolModule(const char *name)
  89             : name_(name)
  90         {
  91         }
  92
  93         const char *name() const override
  94         {
  95             return name_;
  96         }
  97         const char *shortDescription() const override
  98         {
  99             return nullptr;
 100         }
 101
 102         void init(gmx::CommandLineModuleSettings * /*settings*/) override
 103         {
 104         }
 105         int run(int /*argc*/, char * /*argv*/[]) override
 106         {
 107             printMessage();
 108             return 0;
 109         }
 110         void writeHelp(const gmx::CommandLineHelpContext & /*context*/) const override
 111         {
 112             printMessage();
 113         }
 114
 115     private:
 116         void printMessage() const
 117         {
 118             std::fprintf(stderr,
 119                          "This tool is no longer present in GROMACS. Please see\n"
 120                          "  http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/user-guide/cmdline.html#command-changes\n"
 121                          "for ideas how to perform the same tasks with the "
 122                          "new tools.\n");
 123         }
 124
 125         const char             *name_;
 126 };
 127
 128 //! Initializer for a module that defaults to nice level zero.
 129 void initSettingsNoNice(gmx::CommandLineModuleSettings *settings)
 130 {
 131     settings->setDefaultNiceLevel(0);
 132 }
 133
 134 /*! \brief
 135  * Convenience function for creating and registering a module.
 136  *
 137  * \param[in] manager          Module manager to which to register the module.
 138  * \param[in] mainFunction     Main function to wrap.
 139  * \param[in] name             Name for the new module.
 140  * \param[in] shortDescription One-line description for the new module.
 141  */
 142 void registerModule(gmx::CommandLineModuleManager                *manager,
 143                     gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 144                     const char *name, const char *shortDescription)
 145 {
 146     manager->addModuleCMain(name, shortDescription, mainFunction);
 147 }
 148
 149 /*! \brief
 150  * Convenience function for creating and registering a module that defaults to
 151  * -nice 0.
 152  *
 153  * \param[in] manager          Module manager to which to register the module.
 154  * \param[in] mainFunction     Main function to wrap.
 155  * \param[in] name             Name for the new module.
 156  * \param[in] shortDescription One-line description for the new module.
 157  */
 158 void registerModuleNoNice(gmx::CommandLineModuleManager                *manager,
 159                           gmx::CommandLineModuleManager::CMainFunction  mainFunction,
 160                           const char *name, const char *shortDescription)
 161 {
 162     manager->addModuleCMainWithSettings(name, shortDescription, mainFunction,
 163                                         &initSettingsNoNice);
 164 }
 165
 166 /*! \brief
 167  * Convenience function for registering a module for an obsolete tool.
 168  *
 169  * \param[in] manager          Module manager to which to register the module.
 170  * \param[in] name             Name for the obsolete tool.
 171  */
 172 void registerObsoleteTool(gmx::CommandLineModuleManager *manager,
 173                           const char                    *name)
 174 {
 175     gmx::CommandLineModulePointer module(new ObsoleteToolModule(name));
 176     manager->addModule(std::move(module));
 177 }
 178
 179 } // namespace
 180
 181 void registerLegacyModules(gmx::CommandLineModuleManager *manager)
 182 {
 183     registerModule(manager, &gmx_check, "check",
 184                    "Check and compare files");
 185     gmx::ICommandLineOptionsModule::registerModuleFactory(
 186             manager, gmx::DumpInfo::name,
 187             gmx::DumpInfo::shortDescription,
 188             &gmx::DumpInfo::create);
 189     registerModule(manager, &gmx_grompp, "grompp",
 190                    "Make a run input file");
 191     registerModule(manager, &gmx_convert_tpr, "convert-tpr",
 192                    "Make a modifed run-input file");
 193     registerObsoleteTool(manager, "tpbconv");
 194     registerModule(manager, &gmx_x2top, "x2top",
 195                    "Generate a primitive topology from coordinates");
 196
 197     registerModuleNoNice(manager, &gmx::gmx_mdrun, "mdrun",
 198                          "Perform a simulation, do a normal mode analysis or an energy minimization");
 199
 200     gmx::ICommandLineOptionsModule::registerModuleFactory(
 201             manager, gmx::NonbondedBenchmarkInfo::name,
 202             gmx::NonbondedBenchmarkInfo::shortDescription,
 203             &gmx::NonbondedBenchmarkInfo::create);
 204
 205     gmx::ICommandLineOptionsModule::registerModuleFactory(
 206             manager, gmx::InsertMoleculesInfo::name(),
 207             gmx::InsertMoleculesInfo::shortDescription(),
 208             &gmx::InsertMoleculesInfo::create);
 209
 210     gmx::ICommandLineOptionsModule::registerModuleFactory(
 211             manager, gmx::ReportMethodsInfo::name,
 212             gmx::ReportMethodsInfo::shortDescription,
 213             &gmx::ReportMethodsInfo::create);
 214
 215     gmx::ICommandLineOptionsModule::registerModuleFactory(
 216             manager, gmx::pdb2gmxInfo::name,
 217             gmx::pdb2gmxInfo::shortDescription,
 218             &gmx::pdb2gmxInfo::create);
 219
 220     // Modules from gmx_ana.h.
 221     registerModule(manager, &gmx_do_dssp, "do_dssp",
 222                    "Assign secondary structure and calculate solvent accessible surface area");
 223     registerModule(manager, &gmx_editconf, "editconf",
 224                    "Convert and manipulates structure files");
 225     registerModule(manager, &gmx_eneconv, "eneconv",
 226                    "Convert energy files");
 227     registerModule(manager, &gmx_solvate, "solvate",
 228                    "Solvate a system");
 229     registerObsoleteTool(manager, "genbox");
 230     registerModule(manager, &gmx_genconf, "genconf",
 231                    "Multiply a conformation in 'random' orientations");
 232     registerModule(manager, &gmx_genion, "genion",
 233                    "Generate monoatomic ions on energetically favorable positions");
 234     registerModule(manager, &gmx_genrestr, "genrestr",
 235                    "Generate position restraints or distance restraints for index groups");
 236     registerModule(manager, &gmx_make_edi, "make_edi",
 237                    "Generate input files for essential dynamics sampling");
 238     registerModule(manager, &gmx_make_ndx, "make_ndx",
 239                    "Make index files");
 240     registerModule(manager, &gmx_mk_angndx, "mk_angndx",
 241                    "Generate index files for 'gmx angle'");
 242     registerModule(manager, &gmx_trjcat, "trjcat",
 243                    "Concatenate trajectory files");
 244     registerModule(manager, &gmx_trjconv, "trjconv",
 245                    "Convert and manipulates trajectory files");
 246     registerModule(manager, &gmx_trjorder, "trjorder",
 247                    "Order molecules according to their distance to a group");
 248     registerModule(manager, &gmx_xpm2ps, "xpm2ps",
 249                    "Convert XPM (XPixelMap) matrices to postscript or XPM");
 250
 251     registerModule(manager, &gmx_anaeig, "anaeig",
 252                    "Analyze eigenvectors/normal modes");
 253     registerModule(manager, &gmx_analyze, "analyze",
 254                    "Analyze data sets");
 255     registerModule(manager, &gmx_g_angle, "angle",
 256                    "Calculate distributions and correlations for angles and dihedrals");
 257     registerModule(manager, &gmx_awh, "awh",
 258                    "Extract data from an accelerated weight histogram (AWH) run");
 259     registerModule(manager, &gmx_bar, "bar",
 260                    "Calculate free energy difference estimates through Bennett's acceptance ratio");
 261     registerObsoleteTool(manager, "bond");
 262     registerObsoleteTool(manager, "dist");
 263     registerObsoleteTool(manager, "sas");
 264     registerObsoleteTool(manager, "sgangle");
 265
 266     registerModule(manager, &gmx_bundle, "bundle",
 267                    "Analyze bundles of axes, e.g., helices");
 268     registerModule(manager, &gmx_chi, "chi",
 269                    "Calculate everything you want to know about chi and other dihedrals");
 270     registerModule(manager, &gmx_cluster, "cluster",
 271                    "Cluster structures");
 272     registerModule(manager, &gmx_clustsize, "clustsize",
 273                    "Calculate size distributions of atomic clusters");
 274     registerModule(manager, &gmx_confrms, "confrms",
 275                    "Fit two structures and calculates the RMSD");
 276     registerModule(manager, &gmx_covar, "covar",
 277                    "Calculate and diagonalize the covariance matrix");
 278     registerModule(manager, &gmx_current, "current",
 279                    "Calculate dielectric constants and current autocorrelation function");
 280     registerModule(manager, &gmx_density, "density",
 281                    "Calculate the density of the system");
 282     registerModule(manager, &gmx_densmap, "densmap",
 283                    "Calculate 2D planar or axial-radial density maps");
 284     registerModule(manager, &gmx_densorder, "densorder",
 285                    "Calculate surface fluctuations");
 286     registerModule(manager, &gmx_dielectric, "dielectric",
 287                    "Calculate frequency dependent dielectric constants");
 288     registerModule(manager, &gmx_dipoles, "dipoles",
 289                    "Compute the total dipole plus fluctuations");
 290     registerModule(manager, &gmx_disre, "disre",
 291                    "Analyze distance restraints");
 292     registerModule(manager, &gmx_dos, "dos",
 293                    "Analyze density of states and properties based on that");
 294     registerModule(manager, &gmx_dyecoupl, "dyecoupl",
 295                    "Extract dye dynamics from trajectories");
 296     registerModule(manager, &gmx_enemat, "enemat",
 297                    "Extract an energy matrix from an energy file");
 298     registerModule(manager, &gmx_energy, "energy",
 299                    "Writes energies to xvg files and display averages");
 300     registerModule(manager, &gmx_filter, "filter",
 301                    "Frequency filter trajectories, useful for making smooth movies");
 302     registerModule(manager, &gmx_gyrate, "gyrate",
 303                    "Calculate the radius of gyration");
 304     registerModule(manager, &gmx_h2order, "h2order",
 305                    "Compute the orientation of water molecules");
 306     registerModule(manager, &gmx_hbond, "hbond",
 307                    "Compute and analyze hydrogen bonds");
 308     registerModule(manager, &gmx_helix, "helix",
 309                    "Calculate basic properties of alpha helices");
 310     registerModule(manager, &gmx_helixorient, "helixorient",
 311                    "Calculate local pitch/bending/rotation/orientation inside helices");
 312     registerModule(manager, &gmx_hydorder, "hydorder",
 313                    "Compute tetrahedrality parameters around a given atom");
 314     registerModule(manager, &gmx_lie, "lie",
 315                    "Estimate free energy from linear combinations");
 316     registerModule(manager, &gmx_mdmat, "mdmat",
 317                    "Calculate residue contact maps");
 318     registerModule(manager, &gmx_mindist, "mindist",
 319                    "Calculate the minimum distance between two groups");
 320     registerModule(manager, &gmx_msd, "msd",
 321                    "Calculates mean square displacements");
 322     registerModule(manager, &gmx_nmeig, "nmeig",
 323                    "Diagonalize the Hessian for normal mode analysis");
 324     registerModule(manager, &gmx_nmens, "nmens",
 325                    "Generate an ensemble of structures from the normal modes");
 326     registerModule(manager, &gmx_nmr, "nmr",
 327                    "Analyze nuclear magnetic resonance properties from an energy file");
 328     registerModule(manager, &gmx_nmtraj, "nmtraj",
 329                    "Generate a virtual oscillating trajectory from an eigenvector");
 330     registerModule(manager, &gmx_order, "order",
 331                    "Compute the order parameter per atom for carbon tails");
 332     registerModule(manager, &gmx_pme_error, "pme_error",
 333                    "Estimate the error of using PME with a given input file");
 334     registerModule(manager, &gmx_polystat, "polystat",
 335                    "Calculate static properties of polymers");
 336     registerModule(manager, &gmx_potential, "potential",
 337                    "Calculate the electrostatic potential across the box");
 338     registerModule(manager, &gmx_principal, "principal",
 339                    "Calculate principal axes of inertia for a group of atoms");
 340     registerModule(manager, &gmx_rama, "rama",
 341                    "Compute Ramachandran plots");
 342     registerModule(manager, &gmx_rms, "rms",
 343                    "Calculate RMSDs with a reference structure and RMSD matrices");
 344     registerModule(manager, &gmx_rmsdist, "rmsdist",
 345                    "Calculate atom pair distances averaged with power -2, -3 or -6");
 346     registerModule(manager, &gmx_rmsf, "rmsf",
 347                    "Calculate atomic fluctuations");
 348     registerModule(manager, &gmx_rotacf, "rotacf",
 349                    "Calculate the rotational correlation function for molecules");
 350     registerModule(manager, &gmx_rotmat, "rotmat",
 351                    "Plot the rotation matrix for fitting to a reference structure");
 352     registerModule(manager, &gmx_saltbr, "saltbr",
 353                    "Compute salt bridges");
 354     registerModule(manager, &gmx_sans, "sans",
 355                    "Compute small angle neutron scattering spectra");
 356     registerModule(manager, &gmx_saxs, "saxs",
 357                    "Compute small angle X-ray scattering spectra");
 358     registerModule(manager, &gmx_sham, "sham",
 359                    "Compute free energies or other histograms from histograms");
 360     registerModule(manager, &gmx_sigeps, "sigeps",
 361                    "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
 362     registerModule(manager, &gmx_sorient, "sorient",
 363                    "Analyze solvent orientation around solutes");
 364     registerModule(manager, &gmx_spatial, "spatial",
 365                    "Calculate the spatial distribution function");
 366     registerModule(manager, &gmx_spol, "spol",
 367                    "Analyze solvent dipole orientation and polarization around solutes");
 368     registerModule(manager, &gmx_tcaf, "tcaf",
 369                    "Calculate viscosities of liquids");
 370     registerModule(manager, &gmx_traj, "traj",
 371                    "Plot x, v, f, box, temperature and rotational energy from trajectories");
 372     registerModule(manager, &gmx_tune_pme, "tune_pme",
 373                    "Time mdrun as a function of PME ranks to optimize settings");
 374     registerModule(manager, &gmx_vanhove, "vanhove",
 375                    "Compute Van Hove displacement and correlation functions");
 376     registerModule(manager, &gmx_velacc, "velacc",
 377                    "Calculate velocity autocorrelation functions");
 378     registerModule(manager, &gmx_wham, "wham",
 379                    "Perform weighted histogram analysis after umbrella sampling");
 380     registerModule(manager, &gmx_wheel, "wheel",
 381                    "Plot helical wheels");
 382     registerModuleNoNice(manager, &gmx_view, "view",
 383                          "View a trajectory on an X-Windows terminal");
 384
 385     {
 386         gmx::CommandLineModuleGroup group =
 387             manager->addModuleGroup("Generating topologies and coordinates");
 388         group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
 389         group.addModule("x2top");
 390         group.addModule("solvate");
 391         group.addModule("insert-molecules");
 392         group.addModule("genconf");
 393         group.addModule("genion");
 394         group.addModule("genrestr");
 395         group.addModule("pdb2gmx");
 396     }
 397     {
 398         gmx::CommandLineModuleGroup group =
 399             manager->addModuleGroup("Running a simulation");
 400         group.addModule("grompp");
 401         group.addModule("mdrun");
 402         group.addModule("convert-tpr");
 403     }
 404     {
 405         gmx::CommandLineModuleGroup group =
 406             manager->addModuleGroup("Viewing trajectories");
 407         group.addModule("nmtraj");
 408         group.addModule("view");
 409     }
 410     {
 411         gmx::CommandLineModuleGroup group =
 412             manager->addModuleGroup("Processing energies");
 413         group.addModule("enemat");
 414         group.addModule("energy");
 415         group.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
 416     }
 417     {
 418         gmx::CommandLineModuleGroup group =
 419             manager->addModuleGroup("Converting files");
 420         group.addModule("editconf");
 421         group.addModule("eneconv");
 422         group.addModule("sigeps");
 423         group.addModule("trjcat");
 424         group.addModule("trjconv");
 425         group.addModule("xpm2ps");
 426     }
 427     {
 428         gmx::CommandLineModuleGroup group =
 429             manager->addModuleGroup("Tools");
 430         group.addModule("analyze");
 431         group.addModule("awh");
 432         group.addModule("filter");
 433         group.addModule("lie");
 434         group.addModule("pme_error");
 435         group.addModule("sham");
 436         group.addModule("spatial");
 437         group.addModule("traj");
 438         group.addModule("tune_pme");
 439         group.addModule("wham");
 440         group.addModule("check");
 441         group.addModule("dump");
 442         group.addModule("make_ndx");
 443         group.addModule("mk_angndx");
 444         group.addModule("trjorder");
 445         group.addModule("xpm2ps");
 446         group.addModule("report-methods");
 447     }
 448     {
 449         gmx::CommandLineModuleGroup group =
 450             manager->addModuleGroup("Distances between structures");
 451         group.addModule("cluster");
 452         group.addModule("confrms");
 453         group.addModule("rms");
 454         group.addModule("rmsf");
 455     }
 456     {
 457         gmx::CommandLineModuleGroup group =
 458             manager->addModuleGroup("Distances in structures over time");
 459         group.addModule("mindist");
 460         group.addModule("mdmat");
 461         group.addModule("polystat");
 462         group.addModule("rmsdist");
 463     }
 464     {
 465         gmx::CommandLineModuleGroup group =
 466             manager->addModuleGroup("Mass distribution properties over time");
 467         group.addModule("gyrate");
 468         group.addModule("msd");
 469         group.addModule("polystat");
 470         group.addModule("rdf");
 471         group.addModule("rotacf");
 472         group.addModule("rotmat");
 473         group.addModule("sans");
 474         group.addModule("saxs");
 475         group.addModule("traj");
 476         group.addModule("vanhove");
 477     }
 478     {
 479         gmx::CommandLineModuleGroup group =
 480             manager->addModuleGroup("Analyzing bonded interactions");
 481         group.addModule("angle");
 482         group.addModule("mk_angndx");
 483     }
 484     {
 485         gmx::CommandLineModuleGroup group =
 486             manager->addModuleGroup("Structural properties");
 487         group.addModule("bundle");
 488         group.addModule("clustsize");
 489         group.addModule("disre");
 490         group.addModule("hbond");
 491         group.addModule("order");
 492         group.addModule("principal");
 493         group.addModule("rdf");
 494         group.addModule("saltbr");
 495         group.addModule("sorient");
 496         group.addModule("spol");
 497     }
 498     {
 499         gmx::CommandLineModuleGroup group =
 500             manager->addModuleGroup("Kinetic properties");
 501         group.addModule("bar");
 502         group.addModule("current");
 503         group.addModule("dos");
 504         group.addModule("dyecoupl");
 505         group.addModule("principal");
 506         group.addModule("tcaf");
 507         group.addModule("traj");
 508         group.addModule("vanhove");
 509         group.addModule("velacc");
 510     }
 511     {
 512         gmx::CommandLineModuleGroup group =
 513             manager->addModuleGroup("Electrostatic properties");
 514         group.addModule("current");
 515         group.addModule("dielectric");
 516         group.addModule("dipoles");
 517         group.addModule("potential");
 518         group.addModule("spol");
 519         group.addModule("genion");
 520     }
 521     {
 522         gmx::CommandLineModuleGroup group =
 523             manager->addModuleGroup("Protein-specific analysis");
 524         group.addModule("do_dssp");
 525         group.addModule("chi");
 526         group.addModule("helix");
 527         group.addModule("helixorient");
 528         group.addModule("rama");
 529         group.addModule("wheel");
 530     }
 531     {
 532         gmx::CommandLineModuleGroup group =
 533             manager->addModuleGroup("Interfaces");
 534         group.addModule("bundle");
 535         group.addModule("density");
 536         group.addModule("densmap");
 537         group.addModule("densorder");
 538         group.addModule("h2order");
 539         group.addModule("hydorder");
 540         group.addModule("order");
 541         group.addModule("potential");
 542     }
 543     {
 544         gmx::CommandLineModuleGroup group =
 545             manager->addModuleGroup("Covariance analysis");
 546         group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
 547         group.addModule("covar");
 548         group.addModule("make_edi");
 549     }
 550     {
 551         gmx::CommandLineModuleGroup group =
 552             manager->addModuleGroup("Normal modes");
 553         group.addModuleWithDescription("anaeig", "Analyze the normal modes");
 554         group.addModule("nmeig");
 555         group.addModule("nmtraj");
 556         group.addModule("nmens");
 557         group.addModule("grompp");
 558         group.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");
 559     }
 560 }