-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 4.0.5
- * Written by Christoph Junghans, Brad Lambeth, and possibly others.
* Copyright (c) 2009 Christoph Junghans, Brad Lambeth.
- * All rights reserved.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2011,2014, 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.
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+ * in the README & COPYING files - if they are missing, get the
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* To help us fund GROMACS development, we humbly ask that you cite
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+/*! \internal \file
+ * \brief Implementation of the AdResS method.
*/
-
#ifndef _adress_h_
#define _adress_h_
-/** \file adress.h
- *
- * \brief Implementation of the AdResS method
- *
- */
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+
+#ifdef __cplusplus
+extern "C"
+{
+#endif
-#include "types/simple.h"
-#include "typedefs.h"
+struct t_pbc;
/** \brief calculates the AdResS weight of a particle
*
* eAdressSphere - spherical splitting with ref as center
* else - weight = 1 - explicit simulation
* \param[in] adressr radius/size of the explicit zone
- * \param[in] adressw size of the hybrid zone
+ * \param[in] adressw size of the hybrid zone
* \param[in] ref center of the explicit zone
* for adresstype 1 - unused
* for adresstype 2 - only ref[0] is used
- * \param[in] pbc for calculating shortest distance to ref
+ * \param[in] pbc pbc struct for calculating shortest distance
+ * \param[in] fr the forcerec containing all the parameters
*
* \return weight of the particle
*
*/
-real
-adress_weight(rvec x,
- int adresstype,
- real adressr,
- real adressw,
- rvec * ref,
- t_pbc * pbc,
+real
+adress_weight(rvec x,
+ int adresstype,
+ real adressr,
+ real adressw,
+ rvec * ref,
+ struct t_pbc * pbc,
t_forcerec * fr);
/** \brief update the weight of all coarse-grained particles in several charge groups for com vsites
* \param[in,out] fplog log file in case of debug
* \param[in] cg0 first charge group to update
* \param[in] cg1 last+1 charge group to update
- * \param[in] cgs block containing the cg index
- * \param[in] x array with all the particle positions
+ * \param[in] cgs block containing the cg index
+ * \param[in] x array with all the particle positions
* \param[in] fr the forcerec containing all the parameters
* \param[in,out] mdatoms the struct containing all the atoms properties
* \param[in] pbc for shortest distance in adress_weight
rvec x[],
t_forcerec * fr,
t_mdatoms * mdatoms,
- t_pbc * pbc);
+ struct t_pbc * pbc);
/** \brief update the weight of all coarse-grained particles for cog vsites
*
* \param[in] ip contains interaction parameters, in this case the number of constructing atoms n for vsitesn
* \param[in] ilist list of interaction types, in this case the virtual site types are what's important
- * \param[in] x array with all the particle positions
+ * \param[in] x array with all the particle positions
* \param[in] fr the forcerec containing all the parameters
* \param[in,out] mdatoms the struct containing all the atoms properties
* \param[in] pbc for shortest distance in adress_weight
rvec x[],
t_forcerec * fr,
t_mdatoms * mdatoms,
- t_pbc * pbc);
+ struct t_pbc * pbc);
+
/** \brief update the weight of all coarse-grained particles in several charge groups for atom vsites
*
* \param[in] cg0 first charge group to update
* \param[in] cg1 last+1 charge group to update
- * \param[in] cgs block containing the cg index
- * \param[in] x array with all the particle positions
+ * \param[in] cgs block containing the cg index
+ * \param[in] x array with all the particle positions
* \param[in] fr the forcerec containing all the parameters
* \param[in,out] mdatoms the struct containing all the atoms properties
* \param[in] pbc for shortest distance in adress_weight
rvec x[],
t_forcerec * fr,
t_mdatoms * mdatoms,
- t_pbc * pbc);
+ struct t_pbc * pbc);
+/** \brief update the weight on per atom basis of all coarse-grained particles in several charge groups for atom vsites
+ *
+ * \param[in] cg0 first charge group to update
+ * \param[in] cg1 last+1 charge group to update
+ * \param[in] cgs block containing the cg index
+ * \param[in] x array with all the particle positions
+ * \param[in] fr the forcerec containing all the parameters
+ * \param[in,out] mdatoms the struct containing all the atoms properties
+ * \param[in] pbc for shortest distance in adress_weight
+ */
void
update_adress_weights_atom_per_atom(int cg0,
- int cg1,
- t_block * cgs,
- rvec x[],
- t_forcerec * fr,
- t_mdatoms * mdatoms,
- t_pbc * pbc);
+ int cg1,
+ t_block * cgs,
+ rvec x[],
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ struct t_pbc * pbc);
/** \brief add AdResS IC thermodynamic force to f_novirsum
*
* \param[in] cg0 first charge group to update
* \param[in] cg1 last+1 charge group to update
- * \param[in] cgs block containing the cg index
- * \param[in] x array with all the particle positions
+ * \param[in] cgs block containing the cg index
+ * \param[in] x array with all the particle positions
* \param[in,out] f the force array pointing at f_novirsum from sim_util.c
* \param[in] fr the forcerec containing all the parameters
* \param[in] mdatoms the struct containing all the atoms properties
rvec f[],
t_forcerec * fr,
t_mdatoms * mdatoms,
- t_pbc * pbc);
+ struct t_pbc * pbc);
+
+/** \brief checks weather a cpu calculates only coarse-grained or explicit interactions
+ *
+ * \param[in] n_ex number of explicit particles
+ * \param[in] n_hyb number of hybrid particles
+ * \param[in] n_cg number of coarse-grained particles
+ * \param[in,out] mdatoms the struct containing all the atoms properties
+ */
void adress_set_kernel_flags(int n_ex, int n_hyb, int n_cg, t_mdatoms * mdatoms);
-/* functions to look up if a energy group is explicit or coarse-grained*/
+/** \brief looks up if a energy group is explicit
+ * \param[in] fr the forcerec containing all the parameters
+ * \param[in] egp_nr energy group number
+ * \return boolean if explicit or not
+ */
gmx_bool egp_explicit(t_forcerec * fr, int egp_nr);
+
+/** \brief looks up if a energy group is coarse-grained
+ * \param[in] fr the forcerec containing all the parameters
+ * \param[in] egp_nr energy group number
+ * \return boolean if coarse-grained or not
+ */
gmx_bool egp_coarsegrained(t_forcerec * fr, int egp_nr);
+
+#ifdef __cplusplus
+}
+#endif
+
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff