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reaxc_bonds.cpp
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rLAMMPS lammps
reaxc_bonds.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"
#include "reaxc_bonds.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
void
Bonds
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
output_controls
*
out_control
)
{
int
i
,
j
,
pj
,
natoms
;
int
start_i
,
end_i
;
int
type_i
,
type_j
;
double
ebond
,
pow_BOs_be2
,
exp_be12
,
CEbo
;
double
gp3
,
gp4
,
gp7
,
gp10
,
gp37
;
double
exphu
,
exphua1
,
exphub1
,
exphuov
,
hulpov
,
estriph
;
double
decobdbo
,
decobdboua
,
decobdboub
;
single_body_parameters
*
sbp_i
,
*
sbp_j
;
two_body_parameters
*
twbp
;
bond_order_data
*
bo_ij
;
reax_list
*
bonds
;
bonds
=
(
*
lists
)
+
BONDS
;
gp3
=
system
->
reax_param
.
gp
.
l
[
3
];
gp4
=
system
->
reax_param
.
gp
.
l
[
4
];
gp7
=
system
->
reax_param
.
gp
.
l
[
7
];
gp10
=
system
->
reax_param
.
gp
.
l
[
10
];
gp37
=
(
int
)
system
->
reax_param
.
gp
.
l
[
37
];
natoms
=
system
->
n
;
for
(
i
=
0
;
i
<
natoms
;
++
i
)
{
start_i
=
Start_Index
(
i
,
bonds
);
end_i
=
End_Index
(
i
,
bonds
);
for
(
pj
=
start_i
;
pj
<
end_i
;
++
pj
)
{
j
=
bonds
->
select
.
bond_list
[
pj
].
nbr
;
if
(
system
->
my_atoms
[
i
].
orig_id
>
system
->
my_atoms
[
j
].
orig_id
)
continue
;
if
(
system
->
my_atoms
[
i
].
orig_id
==
system
->
my_atoms
[
j
].
orig_id
)
{
if
(
system
->
my_atoms
[
j
].
x
[
2
]
<
system
->
my_atoms
[
i
].
x
[
2
])
continue
;
if
(
system
->
my_atoms
[
j
].
x
[
2
]
==
system
->
my_atoms
[
i
].
x
[
2
]
&&
system
->
my_atoms
[
j
].
x
[
1
]
<
system
->
my_atoms
[
i
].
x
[
1
])
continue
;
if
(
system
->
my_atoms
[
j
].
x
[
2
]
==
system
->
my_atoms
[
i
].
x
[
2
]
&&
system
->
my_atoms
[
j
].
x
[
1
]
==
system
->
my_atoms
[
i
].
x
[
1
]
&&
system
->
my_atoms
[
j
].
x
[
0
]
<
system
->
my_atoms
[
i
].
x
[
0
])
continue
;
}
/* set the pointers */
type_i
=
system
->
my_atoms
[
i
].
type
;
type_j
=
system
->
my_atoms
[
j
].
type
;
sbp_i
=
&
(
system
->
reax_param
.
sbp
[
type_i
]
);
sbp_j
=
&
(
system
->
reax_param
.
sbp
[
type_j
]
);
twbp
=
&
(
system
->
reax_param
.
tbp
[
type_i
][
type_j
]
);
bo_ij
=
&
(
bonds
->
select
.
bond_list
[
pj
].
bo_data
);
/* calculate the constants */
pow_BOs_be2
=
pow
(
bo_ij
->
BO_s
,
twbp
->
p_be2
);
exp_be12
=
exp
(
twbp
->
p_be1
*
(
1.0
-
pow_BOs_be2
)
);
CEbo
=
-
twbp
->
De_s
*
exp_be12
*
(
1.0
-
twbp
->
p_be1
*
twbp
->
p_be2
*
pow_BOs_be2
);
/* calculate the Bond Energy */
data
->
my_en
.
e_bond
+=
ebond
=
-
twbp
->
De_s
*
bo_ij
->
BO_s
*
exp_be12
-
twbp
->
De_p
*
bo_ij
->
BO_pi
-
twbp
->
De_pp
*
bo_ij
->
BO_pi2
;
/* tally into per-atom energy */
if
(
system
->
pair_ptr
->
evflag
)
system
->
pair_ptr
->
ev_tally
(
i
,
j
,
natoms
,
1
,
ebond
,
0.0
,
0.0
,
0.0
,
0.0
,
0.0
);
/* calculate derivatives of Bond Orders */
bo_ij
->
Cdbo
+=
CEbo
;
bo_ij
->
Cdbopi
-=
(
CEbo
+
twbp
->
De_p
);
bo_ij
->
Cdbopi2
-=
(
CEbo
+
twbp
->
De_pp
);
/* Stabilisation terminal triple bond */
if
(
bo_ij
->
BO
>=
1.00
)
{
if
(
gp37
==
2
||
(
sbp_i
->
mass
==
12.0000
&&
sbp_j
->
mass
==
15.9990
)
||
(
sbp_j
->
mass
==
12.0000
&&
sbp_i
->
mass
==
15.9990
)
)
{
exphu
=
exp
(
-
gp7
*
SQR
(
bo_ij
->
BO
-
2.50
)
);
exphua1
=
exp
(
-
gp3
*
(
workspace
->
total_bond_order
[
i
]
-
bo_ij
->
BO
));
exphub1
=
exp
(
-
gp3
*
(
workspace
->
total_bond_order
[
j
]
-
bo_ij
->
BO
));
exphuov
=
exp
(
gp4
*
(
workspace
->
Delta
[
i
]
+
workspace
->
Delta
[
j
]));
hulpov
=
1.0
/
(
1.0
+
25.0
*
exphuov
);
estriph
=
gp10
*
exphu
*
hulpov
*
(
exphua1
+
exphub1
);
data
->
my_en
.
e_bond
+=
estriph
;
decobdbo
=
gp10
*
exphu
*
hulpov
*
(
exphua1
+
exphub1
)
*
(
gp3
-
2.0
*
gp7
*
(
bo_ij
->
BO
-
2.50
)
);
decobdboua
=
-
gp10
*
exphu
*
hulpov
*
(
gp3
*
exphua1
+
25.0
*
gp4
*
exphuov
*
hulpov
*
(
exphua1
+
exphub1
));
decobdboub
=
-
gp10
*
exphu
*
hulpov
*
(
gp3
*
exphub1
+
25.0
*
gp4
*
exphuov
*
hulpov
*
(
exphua1
+
exphub1
));
/* tally into per-atom energy */
if
(
system
->
pair_ptr
->
evflag
)
system
->
pair_ptr
->
ev_tally
(
i
,
j
,
natoms
,
1
,
estriph
,
0.0
,
0.0
,
0.0
,
0.0
,
0.0
);
bo_ij
->
Cdbo
+=
decobdbo
;
workspace
->
CdDelta
[
i
]
+=
decobdboua
;
workspace
->
CdDelta
[
j
]
+=
decobdboub
;
}
}
}
}
}
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