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ntopo_improper_template.cpp
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Thu, Sep 12, 08:26
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rLAMMPS lammps
ntopo_improper_template.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Templatel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <mpi.h>
#include "ntopo_improper_template.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "domain.h"
#include "update.h"
#include "output.h"
#include "thermo.h"
#include "molecule.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
NTopoImproperTemplate
::
NTopoImproperTemplate
(
LAMMPS
*
lmp
)
:
NTopo
(
lmp
)
{
allocate_improper
();
}
/* ---------------------------------------------------------------------- */
void
NTopoImproperTemplate
::
build
()
{
int
i
,
m
,
atom1
,
atom2
,
atom3
,
atom4
;
int
imol
,
iatom
;
tagint
tagprev
;
int
*
num_improper
;
tagint
**
improper_atom1
,
**
improper_atom2
,
**
improper_atom3
,
**
improper_atom4
;
int
**
improper_type
;
Molecule
**
onemols
=
atom
->
avec
->
onemols
;
tagint
*
tag
=
atom
->
tag
;
int
*
molindex
=
atom
->
molindex
;
int
*
molatom
=
atom
->
molatom
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
int
lostbond
=
output
->
thermo
->
lostbond
;
int
nmissing
=
0
;
nimproperlist
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
molindex
[
i
]
<
0
)
continue
;
imol
=
molindex
[
i
];
iatom
=
molatom
[
i
];
tagprev
=
tag
[
i
]
-
iatom
-
1
;
num_improper
=
onemols
[
imol
]
->
num_improper
;
improper_atom1
=
onemols
[
imol
]
->
improper_atom1
;
improper_atom2
=
onemols
[
imol
]
->
improper_atom2
;
improper_atom3
=
onemols
[
imol
]
->
improper_atom3
;
improper_atom4
=
onemols
[
imol
]
->
improper_atom4
;
improper_type
=
onemols
[
imol
]
->
improper_type
;
for
(
m
=
0
;
m
<
num_improper
[
iatom
];
m
++
)
{
atom1
=
atom
->
map
(
improper_atom1
[
iatom
][
m
]
+
tagprev
);
atom2
=
atom
->
map
(
improper_atom2
[
iatom
][
m
]
+
tagprev
);
atom3
=
atom
->
map
(
improper_atom3
[
iatom
][
m
]
+
tagprev
);
atom4
=
atom
->
map
(
improper_atom4
[
iatom
][
m
]
+
tagprev
);
if
(
atom1
==
-
1
||
atom2
==
-
1
||
atom3
==
-
1
||
atom4
==
-
1
)
{
nmissing
++
;
if
(
lostbond
==
ERROR
)
{
char
str
[
128
];
sprintf
(
str
,
"Improper atoms "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" "
TAGINT_FORMAT
" missing on proc %d at step "
BIGINT_FORMAT
,
improper_atom1
[
iatom
][
m
]
+
tagprev
,
improper_atom2
[
iatom
][
m
]
+
tagprev
,
improper_atom3
[
iatom
][
m
]
+
tagprev
,
improper_atom4
[
iatom
][
m
]
+
tagprev
,
me
,
update
->
ntimestep
);
error
->
one
(
FLERR
,
str
);
}
continue
;
}
atom1
=
domain
->
closest_image
(
i
,
atom1
);
atom2
=
domain
->
closest_image
(
i
,
atom2
);
atom3
=
domain
->
closest_image
(
i
,
atom3
);
atom4
=
domain
->
closest_image
(
i
,
atom4
);
if
(
newton_bond
||
(
i
<=
atom1
&&
i
<=
atom2
&&
i
<=
atom3
&&
i
<=
atom4
))
{
if
(
nimproperlist
==
maximproper
)
{
maximproper
+=
DELTA
;
memory
->
grow
(
improperlist
,
maximproper
,
5
,
"neigh_topo:improperlist"
);
}
improperlist
[
nimproperlist
][
0
]
=
atom1
;
improperlist
[
nimproperlist
][
1
]
=
atom2
;
improperlist
[
nimproperlist
][
2
]
=
atom3
;
improperlist
[
nimproperlist
][
3
]
=
atom4
;
improperlist
[
nimproperlist
][
4
]
=
improper_type
[
iatom
][
m
];
nimproperlist
++
;
}
}
}
if
(
cluster_check
)
dihedral_check
(
nimproperlist
,
improperlist
);
if
(
lostbond
==
IGNORE
)
return
;
int
all
;
MPI_Allreduce
(
&
nmissing
,
&
all
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
if
(
all
)
{
char
str
[
128
];
sprintf
(
str
,
"Improper atoms missing at step "
BIGINT_FORMAT
,
update
->
ntimestep
);
if
(
me
==
0
)
error
->
warning
(
FLERR
,
str
);
}
}
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