/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2011-2019, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * 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
 * http://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 http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */
/*! \internal \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
 */
#include "gmxpre.h"

#include "legacymdrunoptions.h"

#include <cstring>

#include "gromacs/math/functions.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/fatalerror.h"

namespace gmx
{

/*! \brief Return whether the command-line parameter that
 *  will trigger a multi-simulation is set */
static bool is_multisim_option_set(int argc, const char* const argv[])
{
    for (int i = 0; i < argc; ++i)
    {
        if (strcmp(argv[i], "-multidir") == 0)
        {
            return true;
        }
    }
    return false;
}

int LegacyMdrunOptions::updateFromCommandLine(int argc, char** argv, ArrayRef<const char*> desc)
{
    unsigned long PCA_Flags = PCA_CAN_SET_DEFFNM;
    // With -multidir, the working directory still needs to be
    // changed, so we can't check for the existence of files during
    // parsing.  It isn't useful to do any completion based on file
    // system contents, either.
    if (is_multisim_option_set(argc, argv))
    {
        PCA_Flags |= PCA_DISABLE_INPUT_FILE_CHECKING;
    }

    if (!parse_common_args(&argc, argv, PCA_Flags, ssize(filenames), filenames.data(), asize(pa),
                           pa, ssize(desc), desc.data(), 0, nullptr, &oenv))
    {
        return 0;
    }

    // Handle the options that permits the user to either declare
    // which compatible GPUs are availble for use, or to select a GPU
    // task assignment. Either could be in an environment variable (so
    // that there is a way to customize it, when using MPI in
    // heterogeneous contexts).
    {
        // TODO Argument parsing can't handle std::string. We should
        // fix that by changing the parsing, once more of the roles of
        // handling, validating and implementing defaults for user
        // command-line options have been seperated.
        hw_opt.gpuIdsAvailable       = gpuIdsAvailable;
        hw_opt.userGpuTaskAssignment = userGpuTaskAssignment;

        const char* env = getenv("GMX_GPU_ID");
        if (env != nullptr)
        {
            if (!hw_opt.gpuIdsAvailable.empty())
            {
                gmx_fatal(FARGS, "GMX_GPU_ID and -gpu_id can not be used at the same time");
            }
            hw_opt.gpuIdsAvailable = env;
        }

        env = getenv("GMX_GPUTASKS");
        if (env != nullptr)
        {
            if (!hw_opt.userGpuTaskAssignment.empty())
            {
                gmx_fatal(FARGS, "GMX_GPUTASKS and -gputasks can not be used at the same time");
            }
            hw_opt.userGpuTaskAssignment = env;
        }

        if (!hw_opt.gpuIdsAvailable.empty() && !hw_opt.userGpuTaskAssignment.empty())
        {
            gmx_fatal(FARGS, "-gpu_id and -gputasks cannot be used at the same time");
        }
    }

    hw_opt.threadAffinity = static_cast<ThreadAffinity>(nenum(thread_aff_opt_choices));

    if (!opt2parg_bSet("-append", asize(pa), pa))
    {
        mdrunOptions.appendingBehavior = AppendingBehavior::Auto;
    }
    else
    {
        if (opt2parg_bool("-append", asize(pa), pa))
        {
            mdrunOptions.appendingBehavior = AppendingBehavior::Appending;
        }
        else
        {
            mdrunOptions.appendingBehavior = AppendingBehavior::NoAppending;
        }
    }

    mdrunOptions.rerun            = opt2bSet("-rerun", ssize(filenames), filenames.data());
    mdrunOptions.ntompOptionIsSet = opt2parg_bSet("-ntomp", asize(pa), pa);

    domdecOptions.rankOrder    = static_cast<DdRankOrder>(nenum(ddrank_opt_choices));
    domdecOptions.dlbOption    = static_cast<DlbOption>(nenum(dddlb_opt_choices));
    domdecOptions.numCells[XX] = roundToInt(realddxyz[XX]);
    domdecOptions.numCells[YY] = roundToInt(realddxyz[YY]);
    domdecOptions.numCells[ZZ] = roundToInt(realddxyz[ZZ]);

    /* PLUMED */
    plumedswitch=0;
    if (opt2bSet("-plumed", static_cast<int>(filenames.size()), filenames.data())) plumedswitch=1;
    if(plumedswitch){
      int real_precision=sizeof(real);
      real energyUnits=1.0;
      real lengthUnits=1.0;
      real timeUnits=1.0;
  
      if(!plumed_installed()){
        gmx_fatal(FARGS,"Plumed is not available. Check your PLUMED_KERNEL variable.");
      }
      plumedmain=plumed_create();
      plumed_cmd(plumedmain,"setRealPrecision",&real_precision);
      // this is not necessary for gromacs units:
      plumed_cmd(plumedmain,"setMDEnergyUnits",&energyUnits);
      plumed_cmd(plumedmain,"setMDLengthUnits",&lengthUnits);
      plumed_cmd(plumedmain,"setMDTimeUnits",&timeUnits);
      //
      plumed_cmd(plumedmain,"setPlumedDat",ftp2fn(efDAT,static_cast<int>(filenames.size()), filenames.data()));
      plumedswitch=1;
    }
    /* PLUMED HREX*/
    if(getenv("PLUMED_HREX")) plumed_hrex=1;
    if(plumed_hrex){
      if(!plumedswitch) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) requires -plumed");
      if(replExParams.exchangeInterval==0) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) replica exchange");
      if(replExParams.numExchanges!=0) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) not compatible with -nex");
    }
    /* END PLUMED HREX */

    /* END PLUMED */

    return 1;
}

LegacyMdrunOptions::~LegacyMdrunOptions()
{
    output_env_done(oenv);
}

} // namespace gmx
