-/* -*- 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.
*
- *
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*/
+#ifndef GMX_LEGACYHEADERS_TYPES_GENBORN_H
+#define GMX_LEGACYHEADERS_TYPES_GENBORN_H
#ifdef __cplusplus
extern "C" {
#endif
-#include "simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
typedef struct
{
- int nbonds;
- int bond[10];
- real length[10];
+ int nbonds;
+ int bond[10];
+ real length[10];
} genborn_bonds_t;
typedef struct gbtmpnbls *gbtmpnbls_t;
/* Struct to hold all the information for GB */
typedef struct
{
- int nr; /* number of atoms, length of arrays below */
- int n12; /* number of 1-2 (bond) interactions */
- int n13; /* number of 1-3 (angle) terms */
- int n14; /* number of 1-4 (torsion) terms */
- int nalloc; /* Allocation of local arrays (with DD) */
-
-
- /* Arrays below that end with _globalindex are used for setting up initial values of
- * all gb parameters and values. They all have length natoms, which for DD is the
- * global atom number.
- * Values are then taken from these arrays to local copies, that have names without
- * _globalindex, in the routine make_local_gb(), which is called once for single
- * node runs, and for DD at every call to dd_partition_system
- */
-
- real *gpol; /* Atomic polarisation energies */
- real *gpol_globalindex; /* */
- real *gpol_still_work; /* Work array for Still model */
- real *gpol_hct_work; /* Work array for HCT/OBC models */
- real *bRad; /* Atomic Born radii */
- real *vsolv; /* Atomic solvation volumes */
- real *vsolv_globalindex; /* */
- real *gb_radius; /* Radius info, copied from atomtypes */
- real *gb_radius_globalindex;
-
- int *use; /* Array that till if this atom does GB */
- int *use_globalindex; /* Global array for parallelization */
-
- real es; /* Solvation energy and derivatives */
- real *asurf; /* Atomic surface area */
- rvec *dasurf; /* Surface area derivatives */
- real as; /* Total surface area */
-
- real *drobc; /* Parameters for OBC chain rule calculation */
- real *param; /* Precomputed factor rai*atype->S_hct for HCT/OBC */
- real *param_globalindex; /* */
-
- real *log_table; /* Table for logarithm lookup */
-
- real obc_alpha; /* OBC parameters */
- real obc_beta; /* OBC parameters */
- real obc_gamma; /* OBC parameters */
- real gb_doffset; /* Dielectric offset for Still/HCT/OBC */
- real gb_epsilon_solvent; /* */
- real epsilon_r; /* Used for inner dielectric */
-
- real sa_surface_tension; /* Surface tension for non-polar solvation */
-
- real *work; /* Used for parallel summation and in the chain rule, length natoms */
- real *buf; /* Used for parallel summation and in the chain rule, length natoms */
- int *count; /* Used for setting up the special gb nblist, length natoms */
- gbtmpnbls_t nblist_work; /* Used for setting up the special gb nblist, dim natoms*nblist_work_nalloc */
- int nblist_work_nalloc; /* Length of second dimension of nblist_work */
-}
+ int nr; /* number of atoms, length of arrays below */
+ int n12; /* number of 1-2 (bond) interactions */
+ int n13; /* number of 1-3 (angle) terms */
+ int n14; /* number of 1-4 (torsion) terms */
+ int nalloc; /* Allocation of local arrays (with DD) */
+
+
+ /* Arrays below that end with _globalindex are used for setting up initial values of
+ * all gb parameters and values. They all have length natoms, which for DD is the
+ * global atom number.
+ * Values are then taken from these arrays to local copies, that have names without
+ * _globalindex, in the routine make_local_gb(), which is called once for single
+ * node runs, and for DD at every call to dd_partition_system
+ */
+
+ real *gpol; /* Atomic polarisation energies */
+ real *gpol_globalindex; /* */
+ real *gpol_still_work; /* Work array for Still model */
+ real *gpol_hct_work; /* Work array for HCT/OBC models */
+ real *bRad; /* Atomic Born radii */
+ real *vsolv; /* Atomic solvation volumes */
+ real *vsolv_globalindex; /* */
+ real *gb_radius; /* Radius info, copied from atomtypes */
+ real *gb_radius_globalindex;
+
+ int *use; /* Array that till if this atom does GB */
+ int *use_globalindex; /* Global array for parallelization */
+
+ real es; /* Solvation energy and derivatives */
+ real *asurf; /* Atomic surface area */
+ rvec *dasurf; /* Surface area derivatives */
+ real as; /* Total surface area */
+
+ real *drobc; /* Parameters for OBC chain rule calculation */
+ real *param; /* Precomputed factor rai*atype->S_hct for HCT/OBC */
+ real *param_globalindex; /* */
+
+ real *log_table; /* Table for logarithm lookup */
+
+ real obc_alpha; /* OBC parameters */
+ real obc_beta; /* OBC parameters */
+ real obc_gamma; /* OBC parameters */
+ real gb_doffset; /* Dielectric offset for Still/HCT/OBC */
+ real gb_epsilon_solvent; /* */
+ real epsilon_r; /* Used for inner dielectric */
+
+ real sa_surface_tension; /* Surface tension for non-polar solvation */
+
+ real *work; /* Used for parallel summation and in the chain rule, length natoms */
+ real *buf; /* Used for parallel summation and in the chain rule, length natoms */
+ int *count; /* Used for setting up the special gb nblist, length natoms */
+ gbtmpnbls_t nblist_work; /* Used for setting up the special gb nblist, dim natoms*nblist_work_nalloc */
+ int nblist_work_nalloc; /* Length of second dimension of nblist_work */
+}
gmx_genborn_t;
#ifdef __cplusplus
}
#endif
-
+#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff