src/programs/legacymodules.cpp

   1 /*
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  36 /*! \internal \brief
  37  * Registers command-line modules for pre-5.0 binaries.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  */
  41 #include "gmxpre.h"
  42
  43 #include "legacymodules.h"
  44
  45 #include <cstdio>
  46
  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"
  71
  72 #include "mdrun/mdrun_main.h"
  73 #include "mdrun/nonbonded_bench.h"
  74 #include "view/view.h"
  75
  76 namespace
  77 {
  78
  79 /*! \brief
  80  * Command line module that provides information about obsolescence.
  81  *
  82  * Prints a message directing the user to a wiki page describing replacement
  83  * options.
  84  */
  85 class ObsoleteToolModule : public gmx::ICommandLineModule
  86 {
  87 public:
  88     //! Creates an obsolete tool module for a tool with the given name.
  89     explicit ObsoleteToolModule(const char* name) : name_(name) {}
  90
  91     const char* name() const override { return name_; }
  92     const char* shortDescription() const override { return nullptr; }
  93
  94     void init(gmx::CommandLineModuleSettings* /*settings*/) override {}
  95     int  run(int /*argc*/, char* /*argv*/[]) override
  96     {
  97         printMessage();
  98         return 0;
  99     }
 100     void writeHelp(const gmx::CommandLineHelpContext& /*context*/) const override
 101     {
 102         printMessage();
 103     }
 104
 105 private:
 106     static void printMessage()
 107     {
 108         std::fprintf(stderr,
 109                      "This tool is no longer present in GROMACS. Please see\n"
 110                      "  "
 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 "
 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,
 137                     const char*                                  shortDescription)
 138 {
 139     manager->addModuleCMain(name, shortDescription, mainFunction);
 140 }
 141
 142 /*! \brief
 143  * Convenience function for creating and registering a module that defaults to
 144  * -nice 0.
 145  *
 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.
 150  */
 151 void registerModuleNoNice(gmx::CommandLineModuleManager*               manager,
 152                           gmx::CommandLineModuleManager::CMainFunction mainFunction,
 153                           const char*                                  name,
 154                           const char*                                  shortDescription)
 155 {
 156     manager->addModuleCMainWithSettings(name, shortDescription, mainFunction, &initSettingsNoNice);
 157 }
 158
 159 /*! \brief
 160  * Convenience function for registering a module for an obsolete tool.
 161  *
 162  * \param[in] manager          Module manager to which to register the module.
 163  * \param[in] name             Name for the obsolete tool.
 164  */
 165 void registerObsoleteTool(gmx::CommandLineModuleManager* manager, 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     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");
 184
 185     registerModuleNoNice(
 186             manager, &gmx::gmx_mdrun, "mdrun",
 187             "Perform a simulation, do a normal mode analysis or an energy minimization");
 188
 189     gmx::ICommandLineOptionsModule::registerModuleFactory(
 190             manager, gmx::NonbondedBenchmarkInfo::name,
 191             gmx::NonbondedBenchmarkInfo::shortDescription, &gmx::NonbondedBenchmarkInfo::create);
 192
 193     gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::InsertMoleculesInfo::name(),
 194                                                           gmx::InsertMoleculesInfo::shortDescription(),
 195                                                           &gmx::InsertMoleculesInfo::create);
 196
 197     gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::ReportMethodsInfo::name,
 198                                                           gmx::ReportMethodsInfo::shortDescription,
 199                                                           &gmx::ReportMethodsInfo::create);
 200
 201     gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::pdb2gmxInfo::name,
 202                                                           gmx::pdb2gmxInfo::shortDescription,
 203                                                           &gmx::pdb2gmxInfo::create);
 204
 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");
 228
 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");
 241
 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");
 330
 331     {
 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");
 342     }
 343     {
 344         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Running a simulation");
 345         group.addModule("grompp");
 346         group.addModule("mdrun");
 347         group.addModule("convert-tpr");
 348     }
 349     {
 350         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Viewing trajectories");
 351         group.addModule("nmtraj");
 352         group.addModule("view");
 353     }
 354     {
 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");
 360     }
 361     {
 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");
 369     }
 370     {
 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");
 389     }
 390     {
 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");
 396     }
 397     {
 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");
 404     }
 405     {
 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");
 418     }
 419     {
 420         gmx::CommandLineModuleGroup group =
 421                 manager->addModuleGroup("Analyzing bonded interactions");
 422         group.addModule("angle");
 423         group.addModule("mk_angndx");
 424     }
 425     {
 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");
 437     }
 438     {
 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");
 449     }
 450     {
 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");
 458     }
 459     {
 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");
 467     }
 468     {
 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");
 478     }
 479     {
 480         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Covariance analysis");
 481         group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
 482         group.addModule("covar");
 483         group.addModule("make_edi");
 484     }
 485     {
 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");
 494     }
 495 }