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reaxc_multi_body.cpp
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rLAMMPS lammps
reaxc_multi_body.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_reaxc.h"
#include "reaxc_multi_body.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_vector.h"
void
Atom_Energy
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
output_controls
*
out_control
)
{
int
i
,
j
,
pj
,
type_i
,
type_j
;
double
Delta_lpcorr
,
dfvl
;
double
e_lp
,
expvd2
,
inv_expvd2
,
dElp
,
CElp
,
DlpVi
;
double
e_lph
,
Di
,
vov3
,
deahu2dbo
,
deahu2dsbo
;
double
e_ov
,
CEover1
,
CEover2
,
CEover3
,
CEover4
;
double
exp_ovun1
,
exp_ovun2
,
sum_ovun1
,
sum_ovun2
;
double
exp_ovun2n
,
exp_ovun6
,
exp_ovun8
;
double
inv_exp_ovun1
,
inv_exp_ovun2
,
inv_exp_ovun2n
,
inv_exp_ovun8
;
double
e_un
,
CEunder1
,
CEunder2
,
CEunder3
,
CEunder4
;
double
p_lp2
,
p_lp3
;
double
p_ovun2
,
p_ovun3
,
p_ovun4
,
p_ovun5
,
p_ovun6
,
p_ovun7
,
p_ovun8
;
double
eng_tmp
;
int
numbonds
;
single_body_parameters
*
sbp_i
;
two_body_parameters
*
twbp
;
bond_data
*
pbond
;
bond_order_data
*
bo_ij
;
reax_list
*
bonds
=
(
*
lists
)
+
BONDS
;
/* Initialize parameters */
p_lp3
=
system
->
reax_param
.
gp
.
l
[
5
];
p_ovun3
=
system
->
reax_param
.
gp
.
l
[
32
];
p_ovun4
=
system
->
reax_param
.
gp
.
l
[
31
];
p_ovun6
=
system
->
reax_param
.
gp
.
l
[
6
];
p_ovun7
=
system
->
reax_param
.
gp
.
l
[
8
];
p_ovun8
=
system
->
reax_param
.
gp
.
l
[
9
];
for
(
i
=
0
;
i
<
system
->
n
;
++
i
)
{
/* set the parameter pointer */
type_i
=
system
->
my_atoms
[
i
].
type
;
if
(
type_i
<
0
)
continue
;
sbp_i
=
&
(
system
->
reax_param
.
sbp
[
type_i
]);
/* lone-pair Energy */
p_lp2
=
sbp_i
->
p_lp2
;
expvd2
=
exp
(
-
75
*
workspace
->
Delta_lp
[
i
]
);
inv_expvd2
=
1.
/
(
1.
+
expvd2
);
numbonds
=
0
;
e_lp
=
0.0
;
for
(
pj
=
Start_Index
(
i
,
bonds
);
pj
<
End_Index
(
i
,
bonds
);
++
pj
)
numbonds
++
;
/* calculate the energy */
if
(
numbonds
>
0
||
control
->
enobondsflag
)
data
->
my_en
.
e_lp
+=
e_lp
=
p_lp2
*
workspace
->
Delta_lp
[
i
]
*
inv_expvd2
;
dElp
=
p_lp2
*
inv_expvd2
+
75
*
p_lp2
*
workspace
->
Delta_lp
[
i
]
*
expvd2
*
SQR
(
inv_expvd2
);
CElp
=
dElp
*
workspace
->
dDelta_lp
[
i
];
if
(
numbonds
>
0
||
control
->
enobondsflag
)
workspace
->
CdDelta
[
i
]
+=
CElp
;
// lp - 1st term
/* tally into per-atom energy */
if
(
system
->
pair_ptr
->
evflag
)
system
->
pair_ptr
->
ev_tally
(
i
,
i
,
system
->
n
,
1
,
e_lp
,
0.0
,
0.0
,
0.0
,
0.0
,
0.0
);
/* correction for C2 */
if
(
p_lp3
>
0.001
&&
!
strcmp
(
system
->
reax_param
.
sbp
[
type_i
].
name
,
"C"
)
)
for
(
pj
=
Start_Index
(
i
,
bonds
);
pj
<
End_Index
(
i
,
bonds
);
++
pj
)
{
j
=
bonds
->
select
.
bond_list
[
pj
].
nbr
;
type_j
=
system
->
my_atoms
[
j
].
type
;
if
(
type_j
<
0
)
continue
;
if
(
!
strcmp
(
system
->
reax_param
.
sbp
[
type_j
].
name
,
"C"
)
)
{
twbp
=
&
(
system
->
reax_param
.
tbp
[
type_i
][
type_j
]);
bo_ij
=
&
(
bonds
->
select
.
bond_list
[
pj
].
bo_data
);
Di
=
workspace
->
Delta
[
i
];
vov3
=
bo_ij
->
BO
-
Di
-
0.040
*
pow
(
Di
,
4.
);
if
(
vov3
>
3.
)
{
data
->
my_en
.
e_lp
+=
e_lph
=
p_lp3
*
SQR
(
vov3
-
3.0
);
deahu2dbo
=
2.
*
p_lp3
*
(
vov3
-
3.
);
deahu2dsbo
=
2.
*
p_lp3
*
(
vov3
-
3.
)
*
(
-
1.
-
0.16
*
pow
(
Di
,
3.
));
bo_ij
->
Cdbo
+=
deahu2dbo
;
workspace
->
CdDelta
[
i
]
+=
deahu2dsbo
;
/* tally into per-atom energy */
if
(
system
->
pair_ptr
->
evflag
)
system
->
pair_ptr
->
ev_tally
(
i
,
j
,
system
->
n
,
1
,
e_lph
,
0.0
,
0.0
,
0.0
,
0.0
,
0.0
);
}
}
}
}
for
(
i
=
0
;
i
<
system
->
n
;
++
i
)
{
type_i
=
system
->
my_atoms
[
i
].
type
;
if
(
type_i
<
0
)
continue
;
sbp_i
=
&
(
system
->
reax_param
.
sbp
[
type_i
]);
/* over-coordination energy */
if
(
sbp_i
->
mass
>
21.0
)
dfvl
=
0.0
;
else
dfvl
=
1.0
;
// only for 1st-row elements
p_ovun2
=
sbp_i
->
p_ovun2
;
sum_ovun1
=
sum_ovun2
=
0
;
for
(
pj
=
Start_Index
(
i
,
bonds
);
pj
<
End_Index
(
i
,
bonds
);
++
pj
)
{
j
=
bonds
->
select
.
bond_list
[
pj
].
nbr
;
type_j
=
system
->
my_atoms
[
j
].
type
;
if
(
type_j
<
0
)
continue
;
bo_ij
=
&
(
bonds
->
select
.
bond_list
[
pj
].
bo_data
);
twbp
=
&
(
system
->
reax_param
.
tbp
[
type_i
][
type_j
]);
sum_ovun1
+=
twbp
->
p_ovun1
*
twbp
->
De_s
*
bo_ij
->
BO
;
sum_ovun2
+=
(
workspace
->
Delta
[
j
]
-
dfvl
*
workspace
->
Delta_lp_temp
[
j
])
*
(
bo_ij
->
BO_pi
+
bo_ij
->
BO_pi2
);
}
exp_ovun1
=
p_ovun3
*
exp
(
p_ovun4
*
sum_ovun2
);
inv_exp_ovun1
=
1.0
/
(
1
+
exp_ovun1
);
Delta_lpcorr
=
workspace
->
Delta
[
i
]
-
(
dfvl
*
workspace
->
Delta_lp_temp
[
i
])
*
inv_exp_ovun1
;
exp_ovun2
=
exp
(
p_ovun2
*
Delta_lpcorr
);
inv_exp_ovun2
=
1.0
/
(
1.0
+
exp_ovun2
);
DlpVi
=
1.0
/
(
Delta_lpcorr
+
sbp_i
->
valency
+
1e-8
);
CEover1
=
Delta_lpcorr
*
DlpVi
*
inv_exp_ovun2
;
data
->
my_en
.
e_ov
+=
e_ov
=
sum_ovun1
*
CEover1
;
CEover2
=
sum_ovun1
*
DlpVi
*
inv_exp_ovun2
*
(
1.0
-
Delta_lpcorr
*
(
DlpVi
+
p_ovun2
*
exp_ovun2
*
inv_exp_ovun2
));
CEover3
=
CEover2
*
(
1.0
-
dfvl
*
workspace
->
dDelta_lp
[
i
]
*
inv_exp_ovun1
);
CEover4
=
CEover2
*
(
dfvl
*
workspace
->
Delta_lp_temp
[
i
])
*
p_ovun4
*
exp_ovun1
*
SQR
(
inv_exp_ovun1
);
/* under-coordination potential */
p_ovun2
=
sbp_i
->
p_ovun2
;
p_ovun5
=
sbp_i
->
p_ovun5
;
exp_ovun2n
=
1.0
/
exp_ovun2
;
exp_ovun6
=
exp
(
p_ovun6
*
Delta_lpcorr
);
exp_ovun8
=
p_ovun7
*
exp
(
p_ovun8
*
sum_ovun2
);
inv_exp_ovun2n
=
1.0
/
(
1.0
+
exp_ovun2n
);
inv_exp_ovun8
=
1.0
/
(
1.0
+
exp_ovun8
);
numbonds
=
0
;
e_un
=
0.0
;
for
(
pj
=
Start_Index
(
i
,
bonds
);
pj
<
End_Index
(
i
,
bonds
);
++
pj
)
numbonds
++
;
if
(
numbonds
>
0
||
control
->
enobondsflag
)
data
->
my_en
.
e_un
+=
e_un
=
-
p_ovun5
*
(
1.0
-
exp_ovun6
)
*
inv_exp_ovun2n
*
inv_exp_ovun8
;
CEunder1
=
inv_exp_ovun2n
*
(
p_ovun5
*
p_ovun6
*
exp_ovun6
*
inv_exp_ovun8
+
p_ovun2
*
e_un
*
exp_ovun2n
);
CEunder2
=
-
e_un
*
p_ovun8
*
exp_ovun8
*
inv_exp_ovun8
;
CEunder3
=
CEunder1
*
(
1.0
-
dfvl
*
workspace
->
dDelta_lp
[
i
]
*
inv_exp_ovun1
);
CEunder4
=
CEunder1
*
(
dfvl
*
workspace
->
Delta_lp_temp
[
i
])
*
p_ovun4
*
exp_ovun1
*
SQR
(
inv_exp_ovun1
)
+
CEunder2
;
/* tally into per-atom energy */
if
(
system
->
pair_ptr
->
evflag
)
{
eng_tmp
=
e_ov
;
if
(
numbonds
>
0
||
control
->
enobondsflag
)
eng_tmp
+=
e_un
;
system
->
pair_ptr
->
ev_tally
(
i
,
i
,
system
->
n
,
1
,
eng_tmp
,
0.0
,
0.0
,
0.0
,
0.0
,
0.0
);
}
/* forces */
workspace
->
CdDelta
[
i
]
+=
CEover3
;
// OvCoor - 2nd term
if
(
numbonds
>
0
||
control
->
enobondsflag
)
workspace
->
CdDelta
[
i
]
+=
CEunder3
;
// UnCoor - 1st term
for
(
pj
=
Start_Index
(
i
,
bonds
);
pj
<
End_Index
(
i
,
bonds
);
++
pj
)
{
pbond
=
&
(
bonds
->
select
.
bond_list
[
pj
]);
j
=
pbond
->
nbr
;
bo_ij
=
&
(
pbond
->
bo_data
);
twbp
=
&
(
system
->
reax_param
.
tbp
[
system
->
my_atoms
[
i
].
type
]
[
system
->
my_atoms
[
pbond
->
nbr
].
type
]);
bo_ij
->
Cdbo
+=
CEover1
*
twbp
->
p_ovun1
*
twbp
->
De_s
;
// OvCoor-1st
workspace
->
CdDelta
[
j
]
+=
CEover4
*
(
1.0
-
dfvl
*
workspace
->
dDelta_lp
[
j
])
*
(
bo_ij
->
BO_pi
+
bo_ij
->
BO_pi2
);
// OvCoor-3a
bo_ij
->
Cdbopi
+=
CEover4
*
(
workspace
->
Delta
[
j
]
-
dfvl
*
workspace
->
Delta_lp_temp
[
j
]);
// OvCoor-3b
bo_ij
->
Cdbopi2
+=
CEover4
*
(
workspace
->
Delta
[
j
]
-
dfvl
*
workspace
->
Delta_lp_temp
[
j
]);
// OvCoor-3b
workspace
->
CdDelta
[
j
]
+=
CEunder4
*
(
1.0
-
dfvl
*
workspace
->
dDelta_lp
[
j
])
*
(
bo_ij
->
BO_pi
+
bo_ij
->
BO_pi2
);
// UnCoor - 2a
bo_ij
->
Cdbopi
+=
CEunder4
*
(
workspace
->
Delta
[
j
]
-
dfvl
*
workspace
->
Delta_lp_temp
[
j
]);
// UnCoor-2b
bo_ij
->
Cdbopi2
+=
CEunder4
*
(
workspace
->
Delta
[
j
]
-
dfvl
*
workspace
->
Delta_lp_temp
[
j
]);
// UnCoor-2b
}
}
}
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