hillclimber 0.1.6__cp313-cp313-macosx_15_0_x86_64.whl

plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.h

@@ -0,0 +1,103 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright 2017- 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.
+ */
+#ifndef GMX_MDLIB_EXPANDED_H
+#define GMX_MDLIB_EXPANDED_H
+
+#include <stdio.h>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+
+struct df_history_t;
+struct gmx_enerdata_t;
+struct t_expanded;
+struct t_extmass;
+struct t_inputrec;
+struct t_lambda;
+struct t_mdatoms;
+struct t_simtemp;
+class t_state;
+
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
+void init_npt_masses(const t_inputrec* ir, t_state* state, t_extmass* MassQ, bool bInit);
+
+void init_expanded_ensemble(bool bStateFromCP, const t_inputrec* ir, df_history_t* dfhist);
+
+int ExpandedEnsembleDynamics(FILE*                               log,
+                             t_inputrec*                         ir,
+                             const gmx_enerdata_t*               enerd,
+                             t_state*                            state,
+                             t_extmass*                          MassQ,
+                             int                                 fep_state,
+                             df_history_t*                       dfhist,
+                             int64_t                             step,
+                             rvec*                               v,
+                             real*                               realFepState,  /* PLUMED */
+                             int                                 homenr,
+                             gmx::ArrayRef<const unsigned short> cTC);
+
+/*!
+ * \brief Return a new lambda state using expanded ensemble
+ *
+ * \param log  File pointer to the log file
+ * \param ir  The input record
+ * \param enerd  Data for energy output.
+ * \param fep_state  The current lambda state
+ * \param dfhist  Free energy sampling history struct
+ * \param step  The current simulation step
+ * \return  The new lambda state
+ */
+int expandedEnsembleUpdateLambdaState(FILE*                 log,
+                                      const t_inputrec*     ir,
+                                      const gmx_enerdata_t* enerd,
+                                      int                   fep_state,
+                                      df_history_t*         dfhist,
+                                      int64_t               step,
+                                      real*                 realFepState); /* PLUMED */
+
+void PrintFreeEnergyInfoToFile(FILE*               outfile,
+                               const t_lambda*     fep,
+                               const t_expanded*   expand,
+                               const t_simtemp*    simtemp,
+                               const df_history_t* dfhist,
+                               int                 fep_state,
+                               int                 frequency,
+                               int64_t             step);
+
+#endif

plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdlib/expanded.h.preplumed

@@ -0,0 +1,99 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright 2017- 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.
+ */
+#ifndef GMX_MDLIB_EXPANDED_H
+#define GMX_MDLIB_EXPANDED_H
+
+#include <stdio.h>
+
+#include "gromacs/math/vectypes.h"
+
+struct df_history_t;
+struct gmx_enerdata_t;
+struct t_expanded;
+struct t_extmass;
+struct t_inputrec;
+struct t_lambda;
+struct t_simtemp;
+class t_state;
+
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
+
+void init_npt_masses(const t_inputrec* ir, t_state* state, t_extmass* MassQ, bool bInit);
+
+void init_expanded_ensemble(bool bStateFromCP, const t_inputrec* ir, df_history_t* dfhist);
+
+int ExpandedEnsembleDynamics(FILE*                               log,
+                             t_inputrec*                         ir,
+                             const gmx_enerdata_t*               enerd,
+                             t_state*                            state,
+                             t_extmass*                          MassQ,
+                             int                                 fep_state,
+                             df_history_t*                       dfhist,
+                             int64_t                             step,
+                             rvec*                               v,
+                             int                                 homenr,
+                             gmx::ArrayRef<const unsigned short> cTC);
+
+/*!
+ * \brief Return a new lambda state using expanded ensemble
+ *
+ * \param log  File pointer to the log file
+ * \param ir  The input record
+ * \param enerd  Data for energy output.
+ * \param fep_state  The current lambda state
+ * \param dfhist  Free energy sampling history struct
+ * \param step  The current simulation step
+ * \return  The new lambda state
+ */
+int expandedEnsembleUpdateLambdaState(FILE*                 log,
+                                      const t_inputrec*     ir,
+                                      const gmx_enerdata_t* enerd,
+                                      int                   fep_state,
+                                      df_history_t*         dfhist,
+                                      int64_t               step);
+
+void PrintFreeEnergyInfoToFile(FILE*               outfile,
+                               const t_lambda*     fep,
+                               const t_expanded*   expand,
+                               const t_simtemp*    simtemp,
+                               const df_history_t* dfhist,
+                               int                 fep_state,
+                               int                 frequency,
+                               int64_t             step);
+
+#endif