hillclimber 0.1.5__cp313-cp313-musllinux_1_2_aarch64.whl

plumed/_lib/lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/legacymdrunoptions.cpp

@@ -0,0 +1,208 @@
+/*
+ * 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.
+ */
+/*! \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/arrayref.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 separated.
+        hw_opt.devicesSelectedByUser = devicesSelectedByUser;
+        hw_opt.userGpuTaskAssignment = userGpuTaskAssignment;
+
+        const char* env = getenv("GMX_GPU_ID");
+        if (env != nullptr)
+        {
+            if (!hw_opt.devicesSelectedByUser.empty())
+            {
+                gmx_fatal(FARGS, "GMX_GPU_ID and -gpu_id can not be used at the same time");
+            }
+            hw_opt.devicesSelectedByUser = 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.devicesSelectedByUser.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", ssize(filenames), 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

plumed/_lib/lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed

@@ -0,0 +1,175 @@
+/*
+ * 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.
+ */
+/*! \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/arrayref.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 separated.
+        hw_opt.devicesSelectedByUser = devicesSelectedByUser;
+        hw_opt.userGpuTaskAssignment = userGpuTaskAssignment;
+
+        const char* env = getenv("GMX_GPU_ID");
+        if (env != nullptr)
+        {
+            if (!hw_opt.devicesSelectedByUser.empty())
+            {
+                gmx_fatal(FARGS, "GMX_GPU_ID and -gpu_id can not be used at the same time");
+            }
+            hw_opt.devicesSelectedByUser = 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.devicesSelectedByUser.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]);
+
+    return 1;
+}
+
+LegacyMdrunOptions::~LegacyMdrunOptions()
+{
+    output_env_done(oenv);
+}
+
+} // namespace gmx