hillclimber 0.1.6__cp314-cp314t-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl

plumed/_lib/lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdrun/legacymdrunoptions.h

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+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright 1991- The GROMACS Authors
+ * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
+ * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * https://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at https://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out https://www.gromacs.org.
+ */
+/*! \libinternal \file
+ *
+ * \brief This file declares helper functionality for legacy option handling for mdrun
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \author Erik Lindahl <erik@kth.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_mdrun
+ * \inlibraryapi
+ */
+#ifndef GMX_MDRUN_LEGACYMDRUNOPTIONS_H
+#define GMX_MDRUN_LEGACYMDRUNOPTIONS_H
+
+#include "gromacs/commandline/filenm.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/domdec/options.h"
+#include "gromacs/hardware/hw_info.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
+
+#include "replicaexchange.h"
+
+/* PLUMED */
+#include "../../../Plumed.h"
+extern int    plumedswitch;
+extern plumed plumedmain; 
+/* END PLUMED */
+
+/* PLUMED HREX */
+extern int plumed_hrex;
+/* END PLUMED HREX */
+
+namespace gmx
+
+{
+
+/*! \libinternal
+ * \brief This class provides the same command-line option
+ * functionality to both CLI and API sessions.
+ *
+ * This class should not exist, but is necessary now to introduce
+ * support for the CLI and API without duplicating code. It should be
+ * eliminated following the TODOs below.
+ *
+ * \warning Instances provide lifetime scope for members that do not have
+ *  effective lifetime management or which are frequently accessed unsafely.
+ *  The caller is responsible for keeping a LegacyMdrunOptions object alive
+ *  for as long as any consumers, direct or transitive.
+ *
+ * \todo Modules in mdrun should acquire proper option handling so
+ *       that all of these declarations and defaults are local to the
+ *       modules.
+ *
+ * \todo Contextual aspects, such as working directory
+ *       and environment variable handling are more properly
+ *       the role of SimulationContext, and should be moved there.
+ */
+class LegacyMdrunOptions
+{
+public:
+    //! Ongoing collection of mdrun options
+    MdrunOptions mdrunOptions;
+    //! Options for the domain decomposition.
+    DomdecOptions domdecOptions;
+    //! Parallelism-related user options.
+    gmx_hw_opt_t hw_opt;
+    //! Command-line override for the duration of a neighbor list with the Verlet scheme.
+    int nstlist_cmdline = 0;
+    //! Parameters for replica-exchange simulations.
+    ReplicaExchangeParameters replExParams;
+
+    //! Filename options to fill from command-line argument values.
+    std::vector<t_filenm> filenames = { { { efTPR, nullptr, nullptr, ffREAD },
+                                          { efTRN, "-o", nullptr, ffWRITE },
+                                          { efCOMPRESSED, "-x", nullptr, ffOPTWR },
+                                          { efCPT, "-cpi", nullptr, ffOPTRD | ffALLOW_MISSING },
+                                          { efCPT, "-cpo", nullptr, ffOPTWR },
+                                          { efSTO, "-c", "confout", ffWRITE },
+                                          { efEDR, "-e", "ener", ffWRITE },
+                                          { efLOG, "-g", "md", ffWRITE },
+                                          { efXVG, "-dhdl", "dhdl", ffOPTWR },
+                                          { efXVG, "-field", "field", ffOPTWR },
+                                          { efXVG, "-table", "table", ffOPTRD },
+                                          { efXVG, "-tablep", "tablep", ffOPTRD },
+                                          { efXVG, "-tableb", "table", ffOPTRDMULT },
+                                          { efTRX, "-rerun", "rerun", ffOPTRD },
+                                          { efXVG, "-tpi", "tpi", ffOPTWR },
+                                          { efXVG, "-tpid", "tpidist", ffOPTWR },
+                                          { efEDI, "-ei", "sam", ffOPTRD },
+                                          { efXVG, "-eo", "edsam", ffOPTWR },
+                                          { efXVG, "-px", "pullx", ffOPTWR },
+                                          { efXVG, "-pf", "pullf", ffOPTWR },
+                                          { efXVG, "-ro", "rotation", ffOPTWR },
+                                          { efLOG, "-ra", "rotangles", ffOPTWR },
+                                          { efLOG, "-rs", "rotslabs", ffOPTWR },
+                                          { efLOG, "-rt", "rottorque", ffOPTWR },
+                                          { efMTX, "-mtx", "nm", ffOPTWR },
+                                          { efRND, "-multidir", nullptr, ffOPTRDMULT },
+                                          { efXVG, "-awh", "awhinit", ffOPTRD },
+                                          { efDAT, "-plumed", "plumed", ffOPTRD },  /* PLUMED */
+                                          { efDAT, "-membed", "membed", ffOPTRD },
+                                          { efTOP, "-mp", "membed", ffOPTRD },
+                                          { efNDX, "-mn", "membed", ffOPTRD },
+                                          { efXVG, "-if", "imdforces", ffOPTWR },
+                                          { efXVG, "-swap", "swapions", ffOPTWR } } };
+
+    //! Print a warning if any force is larger than this (in kJ/mol nm).
+    real pforce = -1;
+
+    //! The value of the -append option
+    bool appendOption = true;
+
+    /*! \brief Output context for writing text files
+     *
+     * \todo Clarify initialization, ownership, and lifetime. */
+    gmx_output_env_t* oenv = nullptr;
+
+    /*! \brief Command line options, defaults, docs and storage for them to fill. */
+    /*! \{ */
+    rvec        realddxyz                                                           = { 0, 0, 0 };
+    const char* ddrank_opt_choices[static_cast<int>(DdRankOrder::Count) + 1]        = { nullptr,
+                                                                                 "interleave",
+                                                                                 "pp_pme",
+                                                                                 "cartesian",
+                                                                                 nullptr };
+    const char* dddlb_opt_choices[static_cast<int>(DlbOption::Count) + 1]           = { nullptr,
+                                                                              "auto",
+                                                                              "no",
+                                                                              "yes",
+                                                                              nullptr };
+    const char* thread_aff_opt_choices[static_cast<int>(ThreadAffinity::Count) + 1] = { nullptr,
+                                                                                        "auto",
+                                                                                        "on",
+                                                                                        "off",
+                                                                                        nullptr };
+    const char* nbpu_opt_choices[5]    = { nullptr, "auto", "cpu", "gpu", nullptr };
+    const char* pme_opt_choices[5]     = { nullptr, "auto", "cpu", "gpu", nullptr };
+    const char* pme_fft_opt_choices[5] = { nullptr, "auto", "cpu", "gpu", nullptr };
+    const char* bonded_opt_choices[5]  = { nullptr, "auto", "cpu", "gpu", nullptr };
+    const char* update_opt_choices[5]  = { nullptr, "auto", "cpu", "gpu", nullptr };
+    const char* devicesSelectedByUser  = "";
+    const char* userGpuTaskAssignment  = "";
+
+
+    ImdOptions& imdOptions = mdrunOptions.imdOptions;
+
+        t_pargs           pa[49] = {
+
+        { "-dd", FALSE, etRVEC, { &realddxyz }, "Domain decomposition grid, 0 is optimize" },
+        { "-ddorder", FALSE, etENUM, { ddrank_opt_choices }, "DD rank order" },
+        { "-npme",
+          FALSE,
+          etINT,
+          { &domdecOptions.numPmeRanks },
+          "Number of separate ranks to be used for PME, -1 is guess" },
+        { "-nt",
+          FALSE,
+          etINT,
+          { &hw_opt.nthreads_tot },
+          "Total number of threads to start (0 is guess)" },
+        { "-ntmpi",
+          FALSE,
+          etINT,
+          { &hw_opt.nthreads_tmpi },
+          "Number of thread-MPI ranks to start (0 is guess)" },
+        { "-ntomp",
+          FALSE,
+          etINT,
+          { &hw_opt.nthreads_omp },
+          "Number of OpenMP threads per MPI rank to start (0 is guess)" },
+        { "-ntomp_pme",
+          FALSE,
+          etINT,
+          { &hw_opt.nthreads_omp_pme },
+          "Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
+        { "-pin",
+          FALSE,
+          etENUM,
+          { thread_aff_opt_choices },
+          "Whether mdrun should try to set thread affinities" },
+        { "-pinoffset",
+          FALSE,
+          etINT,
+          { &hw_opt.core_pinning_offset },
+          "The lowest logical core number to which mdrun should pin the first thread" },
+        { "-pinstride",
+          FALSE,
+          etINT,
+          { &hw_opt.core_pinning_stride },
+          "Pinning distance in logical cores for threads, use 0 to minimize the number of threads "
+          "per physical core" },
+        { "-gpu_id",
+          FALSE,
+          etSTR,
+          { &devicesSelectedByUser },
+          "List of unique GPU device IDs available to use" },
+        { "-gputasks",
+          FALSE,
+          etSTR,
+          { &userGpuTaskAssignment },
+          "List of GPU device IDs, mapping each task on a node to a device. "
+          "Tasks include PP and PME (if present)." },
+        { "-ddcheck",
+          FALSE,
+          etBOOL,
+          { &domdecOptions.ddBondedChecking },
+          "Check for all bonded interactions with DD" },
+        { "-ddbondcomm",
+          FALSE,
+          etBOOL,
+          { &domdecOptions.useBondedCommunication },
+          "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
+        { "-rdd",
+          FALSE,
+          etREAL,
+          { &domdecOptions.minimumCommunicationRange },
+          "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial "
+          "coordinates" },
+        { "-rcon",
+          FALSE,
+          etREAL,
+          { &domdecOptions.constraintCommunicationRange },
+          "Maximum distance for P-LINCS (nm), 0 is estimate" },
+        { "-dlb", FALSE, etENUM, { dddlb_opt_choices }, "Dynamic load balancing (with DD)" },
+        { "-dds",
+          FALSE,
+          etREAL,
+          { &domdecOptions.dlbScaling },
+          "Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in "
+          "order to "
+          "provide a margin in which dynamic load balancing can act while preserving the minimum "
+          "cell size." },
+        { "-ddcsx",
+          FALSE,
+          etSTR,
+          { &domdecOptions.cellSizeX },
+          "HIDDENA string containing a vector of the relative sizes in the x "
+          "direction of the corresponding DD cells. Only effective with static "
+          "load balancing." },
+        { "-ddcsy",
+          FALSE,
+          etSTR,
+          { &domdecOptions.cellSizeY },
+          "HIDDENA string containing a vector of the relative sizes in the y "
+          "direction of the corresponding DD cells. Only effective with static "
+          "load balancing." },
+        { "-ddcsz",
+          FALSE,
+          etSTR,
+          { &domdecOptions.cellSizeZ },
+          "HIDDENA string containing a vector of the relative sizes in the z "
+          "direction of the corresponding DD cells. Only effective with static "
+          "load balancing." },
+        { "-nb", FALSE, etENUM, { nbpu_opt_choices }, "Calculate non-bonded interactions on" },
+        { "-nstlist",
+          FALSE,
+          etINT,
+          { &nstlist_cmdline },
+          "Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
+        { "-tunepme",
+          FALSE,
+          etBOOL,
+          { &mdrunOptions.tunePme },
+          "Optimize PME load between PP/PME ranks or GPU/CPU" },
+        { "-pme", FALSE, etENUM, { pme_opt_choices }, "Perform PME calculations on" },
+        { "-pmefft", FALSE, etENUM, { pme_fft_opt_choices }, "Perform PME FFT calculations on" },
+        { "-bonded", FALSE, etENUM, { bonded_opt_choices }, "Perform bonded calculations on" },
+        { "-update", FALSE, etENUM, { update_opt_choices }, "Perform update and constraints on" },
+        { "-v", FALSE, etBOOL, { &mdrunOptions.verbose }, "Be loud and noisy" },
+        { "-pforce", FALSE, etREAL, { &pforce }, "Print all forces larger than this (kJ/mol nm)" },
+        { "-reprod",
+          FALSE,
+          etBOOL,
+          { &mdrunOptions.reproducible },
+          "Try to avoid optimizations that affect binary reproducibility" },
+        { "-cpt",
+          FALSE,
+          etREAL,
+          { &mdrunOptions.checkpointOptions.period },
+          "Checkpoint interval (minutes)" },
+        { "-cpnum",
+          FALSE,
+          etBOOL,
+          { &mdrunOptions.checkpointOptions.keepAndNumberCheckpointFiles },
+          "Keep and number checkpoint files" },
+        { "-append",
+          FALSE,
+          etBOOL,
+          { &appendOption },
+          "Append to previous output files when continuing from checkpoint instead of adding the "
+          "simulation part number to all file names" },
+        { "-nsteps",
+          FALSE,
+          etINT64,
+          { &mdrunOptions.numStepsCommandline },
+          "Run this number of steps (-1 means infinite, -2 means use mdp option, smaller is "
+          "invalid)" },
+        { "-maxh",
+          FALSE,
+          etREAL,
+          { &mdrunOptions.maximumHoursToRun },
+          "Terminate after 0.99 times this time (hours)" },
+        { "-replex",
+          FALSE,
+          etINT,
+          { &replExParams.exchangeInterval },
+          "Attempt replica exchange periodically with this period (steps)" },
+        { "-nex",
+          FALSE,
+          etINT,
+          { &replExParams.numExchanges },
+          "Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). "
+          " -nex zero or not specified gives neighbor replica exchange." },
+        { "-reseed",
+          FALSE,
+          etINT,
+          { &replExParams.randomSeed },
+          "Seed for replica exchange, -1 is generate a seed" },
+        { "-hrex",  FALSE, etBOOL, {&plumed_hrex}, /* PLUMED HREX */
+              "Enable hamiltonian replica exchange" },
+        { "-imdport", FALSE, etINT, { &imdOptions.port }, "HIDDENIMD listening port" },
+        { "-imdwait",
+          FALSE,
+          etBOOL,
+          { &imdOptions.wait },
+          "HIDDENPause the simulation while no IMD client is connected" },
+        { "-imdterm",
+          FALSE,
+          etBOOL,
+          { &imdOptions.terminatable },
+          "HIDDENAllow termination of the simulation from IMD client" },
+        { "-imdpull",
+          FALSE,
+          etBOOL,
+          { &imdOptions.pull },
+          "HIDDENAllow pulling in the simulation from IMD client" },
+        { "-rerunvsite",
+          FALSE,
+          etBOOL,
+          { &mdrunOptions.rerunConstructVsites },
+          "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
+        { "-confout",
+          FALSE,
+          etBOOL,
+          { &mdrunOptions.writeConfout },
+          "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last "
+          "step" },
+        { "-stepout",
+          FALSE,
+          etINT,
+          { &mdrunOptions.verboseStepPrintInterval },
+          "HIDDENFrequency of writing the remaining wall clock time for the run" },
+        { "-resetstep",
+          FALSE,
+          etINT,
+          { &mdrunOptions.timingOptions.resetStep },
+          "HIDDENReset cycle counters after these many time steps" },
+        { "-resethway",
+          FALSE,
+          etBOOL,
+          { &mdrunOptions.timingOptions.resetHalfway },
+          "HIDDENReset the cycle counters after half the number of steps or halfway "
+          "[TT]-maxh[tt]" }
+    };
+    /*! \} */
+
+    //! Parses the command-line input and prepares to start mdrun.
+    int updateFromCommandLine(int argc, char** argv, ArrayRef<const char*> desc);
+
+    ~LegacyMdrunOptions();
+};
+
+} // end namespace gmx
+
+#endif