hillclimber 0.1.5__cp313-cp313-musllinux_1_2_aarch64.whl

plumed/_lib/lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/replicaexchange.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 Declares the routines for replica exchange.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_mdrun
+ */
+#ifndef GMX_MDRUN_REPLICAEXCHANGE_H
+#define GMX_MDRUN_REPLICAEXCHANGE_H
+
+#include <cstdio>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_enerdata_t;
+struct gmx_multisim_t;
+struct t_commrec;
+struct t_inputrec;
+class t_state;
+
+/*! \libinternal
+ * \brief The parameters for the replica exchange algorithm. */
+struct ReplicaExchangeParameters
+{
+    //! Interval in steps at which to attempt exchanges, 0 means no replica exchange.
+    int exchangeInterval = 0;
+    //! The number of exchanges to attempt at an exchange step.
+    int numExchanges = 0;
+    //! The random seed, -1 means generate a seed.
+    int randomSeed = -1;
+};
+
+//! Abstract type for replica exchange
+typedef struct gmx_repl_ex* gmx_repl_ex_t;
+
+/*! \brief Setup function.
+ *
+ * Should only be called on the main ranks */
+gmx_repl_ex_t init_replica_exchange(FILE*                            fplog,
+                                    const gmx_multisim_t*            ms,
+                                    int                              numAtomsInSystem,
+                                    const t_inputrec*                ir,
+                                    const ReplicaExchangeParameters& replExParams);
+
+/*! \brief Attempts replica exchange.
+ *
+ * Should be called on all ranks.  When running each replica in
+ * parallel, this routine collects the state on the main rank before
+ * exchange.  With domain decomposition, the global state after
+ * exchange is stored in state and still needs to be redistributed
+ * over the ranks.
+ *
+ * \returns TRUE if the state has been exchanged.
+ */
+gmx_bool replica_exchange(FILE*                 fplog,
+                          const t_commrec*      cr,
+                          const gmx_multisim_t* ms,
+                          gmx_repl_ex_t         re,
+                          t_state*              state,
+                          const gmx_enerdata_t* enerd,
+                          t_state*              state_local,
+                          int64_t               step,
+                          real                  time);
+
+/*! \brief Prints replica exchange statistics to the log file.
+ *
+ * Should only be called on the main ranks */
+void print_replica_exchange_statistics(FILE* fplog, gmx_repl_ex_t re);
+
+/* PLUMED HREX */
+extern int replica_exchange_get_repl(const gmx_repl_ex_t re);
+extern int replica_exchange_get_nrepl(const gmx_repl_ex_t re);
+extern void pd_collect_state(const t_commrec *cr, t_state *state);
+extern void exchange_state(const gmx_multisim_t *ms, int b, t_state *state);
+extern void copy_state_serial(const t_state *src, t_state *dest);
+/* END PLUMED HREX */
+
+#endif

plumed/_lib/lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/replicaexchange.h.preplumed

@@ -0,0 +1,106 @@
+/*
+ * 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 Declares the routines for replica exchange.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_mdrun
+ */
+#ifndef GMX_MDRUN_REPLICAEXCHANGE_H
+#define GMX_MDRUN_REPLICAEXCHANGE_H
+
+#include <cstdio>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_enerdata_t;
+struct gmx_multisim_t;
+struct t_commrec;
+struct t_inputrec;
+class t_state;
+
+/*! \libinternal
+ * \brief The parameters for the replica exchange algorithm. */
+struct ReplicaExchangeParameters
+{
+    //! Interval in steps at which to attempt exchanges, 0 means no replica exchange.
+    int exchangeInterval = 0;
+    //! The number of exchanges to attempt at an exchange step.
+    int numExchanges = 0;
+    //! The random seed, -1 means generate a seed.
+    int randomSeed = -1;
+};
+
+//! Abstract type for replica exchange
+typedef struct gmx_repl_ex* gmx_repl_ex_t;
+
+/*! \brief Setup function.
+ *
+ * Should only be called on the main ranks */
+gmx_repl_ex_t init_replica_exchange(FILE*                            fplog,
+                                    const gmx_multisim_t*            ms,
+                                    int                              numAtomsInSystem,
+                                    const t_inputrec*                ir,
+                                    const ReplicaExchangeParameters& replExParams);
+
+/*! \brief Attempts replica exchange.
+ *
+ * Should be called on all ranks.  When running each replica in
+ * parallel, this routine collects the state on the main rank before
+ * exchange.  With domain decomposition, the global state after
+ * exchange is stored in state and still needs to be redistributed
+ * over the ranks.
+ *
+ * \returns TRUE if the state has been exchanged.
+ */
+gmx_bool replica_exchange(FILE*                 fplog,
+                          const t_commrec*      cr,
+                          const gmx_multisim_t* ms,
+                          gmx_repl_ex_t         re,
+                          t_state*              state,
+                          const gmx_enerdata_t* enerd,
+                          t_state*              state_local,
+                          int64_t               step,
+                          real                  time);
+
+/*! \brief Prints replica exchange statistics to the log file.
+ *
+ * Should only be called on the main ranks */
+void print_replica_exchange_statistics(FILE* fplog, gmx_repl_ex_t re);
+
+#endif