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reaxc_list.cpp
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Thu, Aug 22, 09:40
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Sat, Aug 24, 09:40 (1 d, 21 h)
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rLAMMPS lammps
reaxc_list.cpp
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/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Copyright (2010) Purdue University
Hasan Metin Aktulga, hmaktulga@lbl.gov
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
"Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
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 of
the License, or (at your option) any later version.
This program 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 General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
#include "pair_reax_c.h"
#if defined(PURE_REAX)
#include "list.h"
#include "tool_box.h"
#elif defined(LAMMPS_REAX)
#include "reaxc_list.h"
#include "reaxc_tool_box.h"
#endif
/************* allocate list space ******************/
int
Make_List
(
int
n
,
int
num_intrs
,
int
type
,
reax_list
*
l
,
MPI_Comm
comm
)
{
l
->
allocated
=
1
;
l
->
n
=
n
;
l
->
num_intrs
=
num_intrs
;
l
->
index
=
(
int
*
)
smalloc
(
n
*
sizeof
(
int
),
"list:index"
,
comm
);
l
->
end_index
=
(
int
*
)
smalloc
(
n
*
sizeof
(
int
),
"list:end_index"
,
comm
);
l
->
type
=
type
;
#if defined(DEBUG_FOCUS)
fprintf
(
stderr
,
"list: n=%d num_intrs=%d type=%d
\n
"
,
n
,
num_intrs
,
type
);
#endif
switch
(
l
->
type
)
{
case
TYP_VOID:
l
->
select
.
v
=
(
void
*
)
smalloc
(
l
->
num_intrs
*
sizeof
(
void
*
),
"list:v"
,
comm
);
break
;
case
TYP_THREE_BODY:
l
->
select
.
three_body_list
=
(
three_body_interaction_data
*
)
smalloc
(
l
->
num_intrs
*
sizeof
(
three_body_interaction_data
),
"list:three_bodies"
,
comm
);
break
;
case
TYP_BOND:
l
->
select
.
bond_list
=
(
bond_data
*
)
smalloc
(
l
->
num_intrs
*
sizeof
(
bond_data
),
"list:bonds"
,
comm
);
break
;
case
TYP_DBO:
l
->
select
.
dbo_list
=
(
dbond_data
*
)
smalloc
(
l
->
num_intrs
*
sizeof
(
dbond_data
),
"list:dbonds"
,
comm
);
break
;
case
TYP_DDELTA:
l
->
select
.
dDelta_list
=
(
dDelta_data
*
)
smalloc
(
l
->
num_intrs
*
sizeof
(
dDelta_data
),
"list:dDeltas"
,
comm
);
break
;
case
TYP_FAR_NEIGHBOR:
l
->
select
.
far_nbr_list
=
(
far_neighbor_data
*
)
smalloc
(
l
->
num_intrs
*
sizeof
(
far_neighbor_data
),
"list:far_nbrs"
,
comm
);
break
;
case
TYP_HBOND:
l
->
select
.
hbond_list
=
(
hbond_data
*
)
smalloc
(
l
->
num_intrs
*
sizeof
(
hbond_data
),
"list:hbonds"
,
comm
);
break
;
default
:
fprintf
(
stderr
,
"ERROR: no %d list type defined!
\n
"
,
l
->
type
);
MPI_Abort
(
comm
,
INVALID_INPUT
);
}
return
SUCCESS
;
}
void
Delete_List
(
reax_list
*
l
,
MPI_Comm
comm
)
{
if
(
l
->
allocated
==
0
)
return
;
l
->
allocated
=
0
;
sfree
(
l
->
index
,
"list:index"
);
sfree
(
l
->
end_index
,
"list:end_index"
);
switch
(
l
->
type
)
{
case
TYP_VOID:
sfree
(
l
->
select
.
v
,
"list:v"
);
break
;
case
TYP_HBOND:
sfree
(
l
->
select
.
hbond_list
,
"list:hbonds"
);
break
;
case
TYP_FAR_NEIGHBOR:
sfree
(
l
->
select
.
far_nbr_list
,
"list:far_nbrs"
);
break
;
case
TYP_BOND:
sfree
(
l
->
select
.
bond_list
,
"list:bonds"
);
break
;
case
TYP_DBO:
sfree
(
l
->
select
.
dbo_list
,
"list:dbos"
);
break
;
case
TYP_DDELTA:
sfree
(
l
->
select
.
dDelta_list
,
"list:dDeltas"
);
break
;
case
TYP_THREE_BODY:
sfree
(
l
->
select
.
three_body_list
,
"list:three_bodies"
);
break
;
default
:
fprintf
(
stderr
,
"ERROR: no %d list type defined!
\n
"
,
l
->
type
);
MPI_Abort
(
comm
,
INVALID_INPUT
);
}
}
#if defined(PURE_REAX)
inline
int
Num_Entries
(
int
i
,
reax_list
*
l
)
{
return
l
->
end_index
[
i
]
-
l
->
index
[
i
];
}
inline
int
Start_Index
(
int
i
,
reax_list
*
l
)
{
return
l
->
index
[
i
];
}
inline
int
End_Index
(
int
i
,
reax_list
*
l
)
{
return
l
->
end_index
[
i
];
}
inline
void
Set_Start_Index
(
int
i
,
int
val
,
reax_list
*
l
)
{
l
->
index
[
i
]
=
val
;
}
inline
void
Set_End_Index
(
int
i
,
int
val
,
reax_list
*
l
)
{
l
->
end_index
[
i
]
=
val
;
}
#endif
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