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Implement Gromacs internal Whole Procedure

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This commit is contained in:
Niels Müller
2019-10-25 09:55:20 +02:00
parent b71961979f
commit 92addd3148
3 changed files with 55 additions and 8 deletions
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36
pygmx/topology.pxd
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@ -68,6 +68,9 @@ cdef extern from "gromacs/topology/idef.h":
ctypedef struct t_ilist:
pass
ctypedef struct t_idef:
pass
#cdef enum t_ft_enum:
# F_LJ
@ -143,14 +146,45 @@ cdef extern from "gromacs/topology/topology.h":
gmx_groups_t groups
t_symtab symtab # The symbol table */
ctypedef struct t_topology:
char **name # /* Name of the topology */
t_idef idef # /* The interaction function definition */
t_atoms atoms # /* The atoms */
t_atomtypes atomtypes # /* Atomtype properties */
t_block cgs # /* The charge groups */
t_block mols # /* The molecules */
gmx_bool bIntermolecularInteractions# /* Inter.mol. int. ? */
t_blocka excls # /* The exclusions */
t_symtab symtab # /* The symbol table */
ctypedef struct gmx_localtop_t:
t_idef idef # /* The interaction function definition */
#t_atomtypes atomtypes # /* Atomtype properties */
#t_block cgs # /* The charge groups */
# t_blocka excls # /* The exclusions */
void init_mtop(gmx_mtop_t *mtop)
void done_top(t_topology *top)
# cdef extern from "gromacs/topology/topology.h":
# generate a t_atoms struct for the system from gmx_mtop_t
# t_atoms* mtop2atoms(gmx_mtop_t *mtop)
cdef extern from "gromacs/topology/mtop_util.h":
t_atoms gmx_mtop_global_atoms(const gmx_mtop_t *mtop)
t_topology gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop, bint freeMTop)
gmx_localtop_t *gmx_mtop_generate_local_top(const gmx_mtop_t *mtop, bint freeEnergyInteractionsAtEnd)
cdef extern from "gromacs/pbcutil/rmpbc.h":
void rm_gropbc(const t_atoms *atoms, rvec x[], const matrix box);
ctypedef struct gmx_rmpbc_t:
pass
gmx_rmpbc_t gmx_rmpbc_init(const t_idef *idef, int ePBC, int natoms)
void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
void rm_gropbc(const t_atoms *atoms, rvec x[], const matrix box)
void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[])