Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F84868629
reaxc_bond_orders.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Sep 25, 08:21
Size
22 KB
Mime Type
text/x-c
Expires
Fri, Sep 27, 08:21 (2 d)
Engine
blob
Format
Raw Data
Handle
21098763
Attached To
rLAMMPS lammps
reaxc_bond_orders.cpp
View Options
/*----------------------------------------------------------------------
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_types.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_vector.h"
void
Add_dBond_to_Forces_NPT
(
int
i
,
int
pj
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
)
{
reax_list
*
bonds
=
(
*
lists
)
+
BONDS
;
bond_data
*
nbr_j
,
*
nbr_k
;
bond_order_data
*
bo_ij
,
*
bo_ji
;
dbond_coefficients
coef
;
rvec
temp
,
ext_press
;
ivec
rel_box
;
int
pk
,
k
,
j
;
/* Initializations */
nbr_j
=
&
(
bonds
->
select
.
bond_list
[
pj
]);
j
=
nbr_j
->
nbr
;
bo_ij
=
&
(
nbr_j
->
bo_data
);
bo_ji
=
&
(
bonds
->
select
.
bond_list
[
nbr_j
->
sym_index
].
bo_data
);
coef
.
C1dbo
=
bo_ij
->
C1dbo
*
(
bo_ij
->
Cdbo
+
bo_ji
->
Cdbo
);
coef
.
C2dbo
=
bo_ij
->
C2dbo
*
(
bo_ij
->
Cdbo
+
bo_ji
->
Cdbo
);
coef
.
C3dbo
=
bo_ij
->
C3dbo
*
(
bo_ij
->
Cdbo
+
bo_ji
->
Cdbo
);
coef
.
C1dbopi
=
bo_ij
->
C1dbopi
*
(
bo_ij
->
Cdbopi
+
bo_ji
->
Cdbopi
);
coef
.
C2dbopi
=
bo_ij
->
C2dbopi
*
(
bo_ij
->
Cdbopi
+
bo_ji
->
Cdbopi
);
coef
.
C3dbopi
=
bo_ij
->
C3dbopi
*
(
bo_ij
->
Cdbopi
+
bo_ji
->
Cdbopi
);
coef
.
C4dbopi
=
bo_ij
->
C4dbopi
*
(
bo_ij
->
Cdbopi
+
bo_ji
->
Cdbopi
);
coef
.
C1dbopi2
=
bo_ij
->
C1dbopi2
*
(
bo_ij
->
Cdbopi2
+
bo_ji
->
Cdbopi2
);
coef
.
C2dbopi2
=
bo_ij
->
C2dbopi2
*
(
bo_ij
->
Cdbopi2
+
bo_ji
->
Cdbopi2
);
coef
.
C3dbopi2
=
bo_ij
->
C3dbopi2
*
(
bo_ij
->
Cdbopi2
+
bo_ji
->
Cdbopi2
);
coef
.
C4dbopi2
=
bo_ij
->
C4dbopi2
*
(
bo_ij
->
Cdbopi2
+
bo_ji
->
Cdbopi2
);
coef
.
C1dDelta
=
bo_ij
->
C1dbo
*
(
workspace
->
CdDelta
[
i
]
+
workspace
->
CdDelta
[
j
]);
coef
.
C2dDelta
=
bo_ij
->
C2dbo
*
(
workspace
->
CdDelta
[
i
]
+
workspace
->
CdDelta
[
j
]);
coef
.
C3dDelta
=
bo_ij
->
C3dbo
*
(
workspace
->
CdDelta
[
i
]
+
workspace
->
CdDelta
[
j
]);
for
(
pk
=
Start_Index
(
i
,
bonds
);
pk
<
End_Index
(
i
,
bonds
);
++
pk
)
{
nbr_k
=
&
(
bonds
->
select
.
bond_list
[
pk
]);
k
=
nbr_k
->
nbr
;
rvec_Scale
(
temp
,
-
coef
.
C2dbo
,
nbr_k
->
bo_data
.
dBOp
);
/*2nd, dBO*/
rvec_ScaledAdd
(
temp
,
-
coef
.
C2dDelta
,
nbr_k
->
bo_data
.
dBOp
);
/*dDelta*/
rvec_ScaledAdd
(
temp
,
-
coef
.
C3dbopi
,
nbr_k
->
bo_data
.
dBOp
);
/*3rd, dBOpi*/
rvec_ScaledAdd
(
temp
,
-
coef
.
C3dbopi2
,
nbr_k
->
bo_data
.
dBOp
);
/*3rd, dBOpi2*/
/* force */
rvec_Add
(
workspace
->
f
[
k
],
temp
);
/* pressure */
rvec_iMultiply
(
ext_press
,
nbr_k
->
rel_box
,
temp
);
rvec_Add
(
data
->
my_ext_press
,
ext_press
);
}
/* then atom i itself */
rvec_Scale
(
temp
,
coef
.
C1dbo
,
bo_ij
->
dBOp
);
/*1st,dBO*/
rvec_ScaledAdd
(
temp
,
coef
.
C2dbo
,
workspace
->
dDeltap_self
[
i
]
);
/*2nd,dBO*/
rvec_ScaledAdd
(
temp
,
coef
.
C1dDelta
,
bo_ij
->
dBOp
);
/*1st,dBO*/
rvec_ScaledAdd
(
temp
,
coef
.
C2dDelta
,
workspace
->
dDeltap_self
[
i
]
);
/*2nd,dBO*/
rvec_ScaledAdd
(
temp
,
coef
.
C1dbopi
,
bo_ij
->
dln_BOp_pi
);
/*1st,dBOpi*/
rvec_ScaledAdd
(
temp
,
coef
.
C2dbopi
,
bo_ij
->
dBOp
);
/*2nd,dBOpi*/
rvec_ScaledAdd
(
temp
,
coef
.
C3dbopi
,
workspace
->
dDeltap_self
[
i
]);
/*3rd,dBOpi*/
rvec_ScaledAdd
(
temp
,
coef
.
C1dbopi2
,
bo_ij
->
dln_BOp_pi2
);
/*1st,dBO_pi2*/
rvec_ScaledAdd
(
temp
,
coef
.
C2dbopi2
,
bo_ij
->
dBOp
);
/*2nd,dBO_pi2*/
rvec_ScaledAdd
(
temp
,
coef
.
C3dbopi2
,
workspace
->
dDeltap_self
[
i
]
);
/*3rd*/
/* force */
rvec_Add
(
workspace
->
f
[
i
],
temp
);
for
(
pk
=
Start_Index
(
j
,
bonds
);
pk
<
End_Index
(
j
,
bonds
);
++
pk
)
{
nbr_k
=
&
(
bonds
->
select
.
bond_list
[
pk
]);
k
=
nbr_k
->
nbr
;
rvec_Scale
(
temp
,
-
coef
.
C3dbo
,
nbr_k
->
bo_data
.
dBOp
);
/*3rd,dBO*/
rvec_ScaledAdd
(
temp
,
-
coef
.
C3dDelta
,
nbr_k
->
bo_data
.
dBOp
);
/*dDelta*/
rvec_ScaledAdd
(
temp
,
-
coef
.
C4dbopi
,
nbr_k
->
bo_data
.
dBOp
);
/*4th,dBOpi*/
rvec_ScaledAdd
(
temp
,
-
coef
.
C4dbopi2
,
nbr_k
->
bo_data
.
dBOp
);
/*4th,dBOpi2*/
/* force */
rvec_Add
(
workspace
->
f
[
k
],
temp
);
/* pressure */
if
(
k
!=
i
)
{
ivec_Sum
(
rel_box
,
nbr_k
->
rel_box
,
nbr_j
->
rel_box
);
//rel_box(k, i)
rvec_iMultiply
(
ext_press
,
rel_box
,
temp
);
rvec_Add
(
data
->
my_ext_press
,
ext_press
);
}
}
/* then atom j itself */
rvec_Scale
(
temp
,
-
coef
.
C1dbo
,
bo_ij
->
dBOp
);
/*1st, dBO*/
rvec_ScaledAdd
(
temp
,
coef
.
C3dbo
,
workspace
->
dDeltap_self
[
j
]
);
/*2nd, dBO*/
rvec_ScaledAdd
(
temp
,
-
coef
.
C1dDelta
,
bo_ij
->
dBOp
);
/*1st, dBO*/
rvec_ScaledAdd
(
temp
,
coef
.
C3dDelta
,
workspace
->
dDeltap_self
[
j
]);
/*2nd, dBO*/
rvec_ScaledAdd
(
temp
,
-
coef
.
C1dbopi
,
bo_ij
->
dln_BOp_pi
);
/*1st,dBOpi*/
rvec_ScaledAdd
(
temp
,
-
coef
.
C2dbopi
,
bo_ij
->
dBOp
);
/*2nd,dBOpi*/
rvec_ScaledAdd
(
temp
,
coef
.
C4dbopi
,
workspace
->
dDeltap_self
[
j
]);
/*3rd,dBOpi*/
rvec_ScaledAdd
(
temp
,
-
coef
.
C1dbopi2
,
bo_ij
->
dln_BOp_pi2
);
/*1st,dBOpi2*/
rvec_ScaledAdd
(
temp
,
-
coef
.
C2dbopi2
,
bo_ij
->
dBOp
);
/*2nd,dBOpi2*/
rvec_ScaledAdd
(
temp
,
coef
.
C4dbopi2
,
workspace
->
dDeltap_self
[
j
]);
/*3rd,dBOpi2*/
/* force */
rvec_Add
(
workspace
->
f
[
j
],
temp
);
/* pressure */
rvec_iMultiply
(
ext_press
,
nbr_j
->
rel_box
,
temp
);
rvec_Add
(
data
->
my_ext_press
,
ext_press
);
}
void
Add_dBond_to_Forces
(
reax_system
*
system
,
int
i
,
int
pj
,
storage
*
workspace
,
reax_list
**
lists
)
{
reax_list
*
bonds
=
(
*
lists
)
+
BONDS
;
bond_data
*
nbr_j
,
*
nbr_k
;
bond_order_data
*
bo_ij
,
*
bo_ji
;
dbond_coefficients
coef
;
int
pk
,
k
,
j
;
/* Virial Tallying variables */
rvec
fi_tmp
,
fj_tmp
,
fk_tmp
,
delij
,
delji
,
delki
,
delkj
,
temp
;
/* Initializations */
nbr_j
=
&
(
bonds
->
select
.
bond_list
[
pj
]);
j
=
nbr_j
->
nbr
;
bo_ij
=
&
(
nbr_j
->
bo_data
);
bo_ji
=
&
(
bonds
->
select
.
bond_list
[
nbr_j
->
sym_index
].
bo_data
);
coef
.
C1dbo
=
bo_ij
->
C1dbo
*
(
bo_ij
->
Cdbo
+
bo_ji
->
Cdbo
);
coef
.
C2dbo
=
bo_ij
->
C2dbo
*
(
bo_ij
->
Cdbo
+
bo_ji
->
Cdbo
);
coef
.
C3dbo
=
bo_ij
->
C3dbo
*
(
bo_ij
->
Cdbo
+
bo_ji
->
Cdbo
);
coef
.
C1dbopi
=
bo_ij
->
C1dbopi
*
(
bo_ij
->
Cdbopi
+
bo_ji
->
Cdbopi
);
coef
.
C2dbopi
=
bo_ij
->
C2dbopi
*
(
bo_ij
->
Cdbopi
+
bo_ji
->
Cdbopi
);
coef
.
C3dbopi
=
bo_ij
->
C3dbopi
*
(
bo_ij
->
Cdbopi
+
bo_ji
->
Cdbopi
);
coef
.
C4dbopi
=
bo_ij
->
C4dbopi
*
(
bo_ij
->
Cdbopi
+
bo_ji
->
Cdbopi
);
coef
.
C1dbopi2
=
bo_ij
->
C1dbopi2
*
(
bo_ij
->
Cdbopi2
+
bo_ji
->
Cdbopi2
);
coef
.
C2dbopi2
=
bo_ij
->
C2dbopi2
*
(
bo_ij
->
Cdbopi2
+
bo_ji
->
Cdbopi2
);
coef
.
C3dbopi2
=
bo_ij
->
C3dbopi2
*
(
bo_ij
->
Cdbopi2
+
bo_ji
->
Cdbopi2
);
coef
.
C4dbopi2
=
bo_ij
->
C4dbopi2
*
(
bo_ij
->
Cdbopi2
+
bo_ji
->
Cdbopi2
);
coef
.
C1dDelta
=
bo_ij
->
C1dbo
*
(
workspace
->
CdDelta
[
i
]
+
workspace
->
CdDelta
[
j
]);
coef
.
C2dDelta
=
bo_ij
->
C2dbo
*
(
workspace
->
CdDelta
[
i
]
+
workspace
->
CdDelta
[
j
]);
coef
.
C3dDelta
=
bo_ij
->
C3dbo
*
(
workspace
->
CdDelta
[
i
]
+
workspace
->
CdDelta
[
j
]);
// forces on i
rvec_Scale
(
temp
,
coef
.
C1dbo
,
bo_ij
->
dBOp
);
rvec_ScaledAdd
(
temp
,
coef
.
C2dbo
,
workspace
->
dDeltap_self
[
i
]
);
rvec_ScaledAdd
(
temp
,
coef
.
C1dDelta
,
bo_ij
->
dBOp
);
rvec_ScaledAdd
(
temp
,
coef
.
C2dDelta
,
workspace
->
dDeltap_self
[
i
]
);
rvec_ScaledAdd
(
temp
,
coef
.
C1dbopi
,
bo_ij
->
dln_BOp_pi
);
rvec_ScaledAdd
(
temp
,
coef
.
C2dbopi
,
bo_ij
->
dBOp
);
rvec_ScaledAdd
(
temp
,
coef
.
C3dbopi
,
workspace
->
dDeltap_self
[
i
]);
rvec_ScaledAdd
(
temp
,
coef
.
C1dbopi2
,
bo_ij
->
dln_BOp_pi2
);
rvec_ScaledAdd
(
temp
,
coef
.
C2dbopi2
,
bo_ij
->
dBOp
);
rvec_ScaledAdd
(
temp
,
coef
.
C3dbopi2
,
workspace
->
dDeltap_self
[
i
]
);
rvec_Add
(
workspace
->
f
[
i
],
temp
);
if
(
system
->
pair_ptr
->
vflag_atom
)
{
rvec_Scale
(
fi_tmp
,
-
1.0
,
temp
);
rvec_ScaledSum
(
delij
,
1.
,
system
->
my_atoms
[
i
].
x
,
-
1.
,
system
->
my_atoms
[
j
].
x
);
system
->
pair_ptr
->
v_tally
(
i
,
fi_tmp
,
delij
);
}
// forces on j
rvec_Scale
(
temp
,
-
coef
.
C1dbo
,
bo_ij
->
dBOp
);
rvec_ScaledAdd
(
temp
,
coef
.
C3dbo
,
workspace
->
dDeltap_self
[
j
]
);
rvec_ScaledAdd
(
temp
,
-
coef
.
C1dDelta
,
bo_ij
->
dBOp
);
rvec_ScaledAdd
(
temp
,
coef
.
C3dDelta
,
workspace
->
dDeltap_self
[
j
]);
rvec_ScaledAdd
(
temp
,
-
coef
.
C1dbopi
,
bo_ij
->
dln_BOp_pi
);
rvec_ScaledAdd
(
temp
,
-
coef
.
C2dbopi
,
bo_ij
->
dBOp
);
rvec_ScaledAdd
(
temp
,
coef
.
C4dbopi
,
workspace
->
dDeltap_self
[
j
]);
rvec_ScaledAdd
(
temp
,
-
coef
.
C1dbopi2
,
bo_ij
->
dln_BOp_pi2
);
rvec_ScaledAdd
(
temp
,
-
coef
.
C2dbopi2
,
bo_ij
->
dBOp
);
rvec_ScaledAdd
(
temp
,
coef
.
C4dbopi2
,
workspace
->
dDeltap_self
[
j
]);
rvec_Add
(
workspace
->
f
[
j
],
temp
);
if
(
system
->
pair_ptr
->
vflag_atom
)
{
rvec_Scale
(
fj_tmp
,
-
1.0
,
temp
);
rvec_ScaledSum
(
delji
,
1.
,
system
->
my_atoms
[
j
].
x
,
-
1.
,
system
->
my_atoms
[
i
].
x
);
system
->
pair_ptr
->
v_tally
(
j
,
fj_tmp
,
delji
);
}
// forces on k: i neighbor
for
(
pk
=
Start_Index
(
i
,
bonds
);
pk
<
End_Index
(
i
,
bonds
);
++
pk
)
{
nbr_k
=
&
(
bonds
->
select
.
bond_list
[
pk
]);
k
=
nbr_k
->
nbr
;
rvec_Scale
(
temp
,
-
coef
.
C2dbo
,
nbr_k
->
bo_data
.
dBOp
);
rvec_ScaledAdd
(
temp
,
-
coef
.
C2dDelta
,
nbr_k
->
bo_data
.
dBOp
);
rvec_ScaledAdd
(
temp
,
-
coef
.
C3dbopi
,
nbr_k
->
bo_data
.
dBOp
);
rvec_ScaledAdd
(
temp
,
-
coef
.
C3dbopi2
,
nbr_k
->
bo_data
.
dBOp
);
rvec_Add
(
workspace
->
f
[
k
],
temp
);
if
(
system
->
pair_ptr
->
vflag_atom
)
{
rvec_Scale
(
fk_tmp
,
-
1.0
,
temp
);
rvec_ScaledSum
(
delki
,
1.
,
system
->
my_atoms
[
k
].
x
,
-
1.
,
system
->
my_atoms
[
i
].
x
);
system
->
pair_ptr
->
v_tally
(
k
,
fk_tmp
,
delki
);
rvec_ScaledSum
(
delkj
,
1.
,
system
->
my_atoms
[
k
].
x
,
-
1.
,
system
->
my_atoms
[
j
].
x
);
system
->
pair_ptr
->
v_tally
(
k
,
fk_tmp
,
delkj
);
}
}
// forces on k: j neighbor
for
(
pk
=
Start_Index
(
j
,
bonds
);
pk
<
End_Index
(
j
,
bonds
);
++
pk
)
{
nbr_k
=
&
(
bonds
->
select
.
bond_list
[
pk
]);
k
=
nbr_k
->
nbr
;
rvec_Scale
(
temp
,
-
coef
.
C3dbo
,
nbr_k
->
bo_data
.
dBOp
);
rvec_ScaledAdd
(
temp
,
-
coef
.
C3dDelta
,
nbr_k
->
bo_data
.
dBOp
);
rvec_ScaledAdd
(
temp
,
-
coef
.
C4dbopi
,
nbr_k
->
bo_data
.
dBOp
);
rvec_ScaledAdd
(
temp
,
-
coef
.
C4dbopi2
,
nbr_k
->
bo_data
.
dBOp
);
rvec_Add
(
workspace
->
f
[
k
],
temp
);
if
(
system
->
pair_ptr
->
vflag_atom
)
{
rvec_Scale
(
fk_tmp
,
-
1.0
,
temp
);
rvec_ScaledSum
(
delki
,
1.
,
system
->
my_atoms
[
k
].
x
,
-
1.
,
system
->
my_atoms
[
i
].
x
);
system
->
pair_ptr
->
v_tally
(
k
,
fk_tmp
,
delki
);
rvec_ScaledSum
(
delkj
,
1.
,
system
->
my_atoms
[
k
].
x
,
-
1.
,
system
->
my_atoms
[
j
].
x
);
system
->
pair_ptr
->
v_tally
(
k
,
fk_tmp
,
delkj
);
}
}
}
int
BOp
(
storage
*
workspace
,
reax_list
*
bonds
,
double
bo_cut
,
int
i
,
int
btop_i
,
far_neighbor_data
*
nbr_pj
,
single_body_parameters
*
sbp_i
,
single_body_parameters
*
sbp_j
,
two_body_parameters
*
twbp
)
{
int
j
,
btop_j
;
double
r2
,
C12
,
C34
,
C56
;
double
Cln_BOp_s
,
Cln_BOp_pi
,
Cln_BOp_pi2
;
double
BO
,
BO_s
,
BO_pi
,
BO_pi2
;
bond_data
*
ibond
,
*
jbond
;
bond_order_data
*
bo_ij
,
*
bo_ji
;
j
=
nbr_pj
->
nbr
;
r2
=
SQR
(
nbr_pj
->
d
);
if
(
sbp_i
->
r_s
>
0.0
&&
sbp_j
->
r_s
>
0.0
)
{
C12
=
twbp
->
p_bo1
*
pow
(
nbr_pj
->
d
/
twbp
->
r_s
,
twbp
->
p_bo2
);
BO_s
=
(
1.0
+
bo_cut
)
*
exp
(
C12
);
}
else
BO_s
=
C12
=
0.0
;
if
(
sbp_i
->
r_pi
>
0.0
&&
sbp_j
->
r_pi
>
0.0
)
{
C34
=
twbp
->
p_bo3
*
pow
(
nbr_pj
->
d
/
twbp
->
r_p
,
twbp
->
p_bo4
);
BO_pi
=
exp
(
C34
);
}
else
BO_pi
=
C34
=
0.0
;
if
(
sbp_i
->
r_pi_pi
>
0.0
&&
sbp_j
->
r_pi_pi
>
0.0
)
{
C56
=
twbp
->
p_bo5
*
pow
(
nbr_pj
->
d
/
twbp
->
r_pp
,
twbp
->
p_bo6
);
BO_pi2
=
exp
(
C56
);
}
else
BO_pi2
=
C56
=
0.0
;
/* Initially BO values are the uncorrected ones, page 1 */
BO
=
BO_s
+
BO_pi
+
BO_pi2
;
if
(
BO
>=
bo_cut
)
{
/****** bonds i-j and j-i ******/
ibond
=
&
(
bonds
->
select
.
bond_list
[
btop_i
]
);
btop_j
=
End_Index
(
j
,
bonds
);
jbond
=
&
(
bonds
->
select
.
bond_list
[
btop_j
]);
ibond
->
nbr
=
j
;
jbond
->
nbr
=
i
;
ibond
->
d
=
nbr_pj
->
d
;
jbond
->
d
=
nbr_pj
->
d
;
rvec_Copy
(
ibond
->
dvec
,
nbr_pj
->
dvec
);
rvec_Scale
(
jbond
->
dvec
,
-
1
,
nbr_pj
->
dvec
);
ivec_Copy
(
ibond
->
rel_box
,
nbr_pj
->
rel_box
);
ivec_Scale
(
jbond
->
rel_box
,
-
1
,
nbr_pj
->
rel_box
);
ibond
->
dbond_index
=
btop_i
;
jbond
->
dbond_index
=
btop_i
;
ibond
->
sym_index
=
btop_j
;
jbond
->
sym_index
=
btop_i
;
Set_End_Index
(
j
,
btop_j
+
1
,
bonds
);
bo_ij
=
&
(
ibond
->
bo_data
);
bo_ji
=
&
(
jbond
->
bo_data
);
bo_ji
->
BO
=
bo_ij
->
BO
=
BO
;
bo_ji
->
BO_s
=
bo_ij
->
BO_s
=
BO_s
;
bo_ji
->
BO_pi
=
bo_ij
->
BO_pi
=
BO_pi
;
bo_ji
->
BO_pi2
=
bo_ij
->
BO_pi2
=
BO_pi2
;
/* Bond Order page2-3, derivative of total bond order prime */
Cln_BOp_s
=
twbp
->
p_bo2
*
C12
/
r2
;
Cln_BOp_pi
=
twbp
->
p_bo4
*
C34
/
r2
;
Cln_BOp_pi2
=
twbp
->
p_bo6
*
C56
/
r2
;
/* Only dln_BOp_xx wrt. dr_i is stored here, note that
dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */
rvec_Scale
(
bo_ij
->
dln_BOp_s
,
-
bo_ij
->
BO_s
*
Cln_BOp_s
,
ibond
->
dvec
);
rvec_Scale
(
bo_ij
->
dln_BOp_pi
,
-
bo_ij
->
BO_pi
*
Cln_BOp_pi
,
ibond
->
dvec
);
rvec_Scale
(
bo_ij
->
dln_BOp_pi2
,
-
bo_ij
->
BO_pi2
*
Cln_BOp_pi2
,
ibond
->
dvec
);
rvec_Scale
(
bo_ji
->
dln_BOp_s
,
-
1.
,
bo_ij
->
dln_BOp_s
);
rvec_Scale
(
bo_ji
->
dln_BOp_pi
,
-
1.
,
bo_ij
->
dln_BOp_pi
);
rvec_Scale
(
bo_ji
->
dln_BOp_pi2
,
-
1.
,
bo_ij
->
dln_BOp_pi2
);
rvec_Scale
(
bo_ij
->
dBOp
,
-
(
bo_ij
->
BO_s
*
Cln_BOp_s
+
bo_ij
->
BO_pi
*
Cln_BOp_pi
+
bo_ij
->
BO_pi2
*
Cln_BOp_pi2
),
ibond
->
dvec
);
rvec_Scale
(
bo_ji
->
dBOp
,
-
1.
,
bo_ij
->
dBOp
);
rvec_Add
(
workspace
->
dDeltap_self
[
i
],
bo_ij
->
dBOp
);
rvec_Add
(
workspace
->
dDeltap_self
[
j
],
bo_ji
->
dBOp
);
bo_ij
->
BO_s
-=
bo_cut
;
bo_ij
->
BO
-=
bo_cut
;
bo_ji
->
BO_s
-=
bo_cut
;
bo_ji
->
BO
-=
bo_cut
;
workspace
->
total_bond_order
[
i
]
+=
bo_ij
->
BO
;
//currently total_BOp
workspace
->
total_bond_order
[
j
]
+=
bo_ji
->
BO
;
//currently total_BOp
bo_ij
->
Cdbo
=
bo_ij
->
Cdbopi
=
bo_ij
->
Cdbopi2
=
0.0
;
bo_ji
->
Cdbo
=
bo_ji
->
Cdbopi
=
bo_ji
->
Cdbopi2
=
0.0
;
return
1
;
}
return
0
;
}
void
BO
(
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
;
int
start_i
,
end_i
,
sym_index
;
double
val_i
,
Deltap_i
,
Deltap_boc_i
;
double
val_j
,
Deltap_j
,
Deltap_boc_j
;
double
f1
,
f2
,
f3
,
f4
,
f5
,
f4f5
,
exp_f4
,
exp_f5
;
double
exp_p1i
,
exp_p2i
,
exp_p1j
,
exp_p2j
;
double
temp
,
u1_ij
,
u1_ji
,
Cf1A_ij
,
Cf1B_ij
,
Cf1_ij
,
Cf1_ji
;
double
Cf45_ij
,
Cf45_ji
,
p_lp1
;
//u_ij, u_ji
double
A0_ij
,
A1_ij
,
A2_ij
,
A2_ji
,
A3_ij
,
A3_ji
;
double
explp1
,
p_boc1
,
p_boc2
;
single_body_parameters
*
sbp_i
,
*
sbp_j
;
two_body_parameters
*
twbp
;
bond_order_data
*
bo_ij
,
*
bo_ji
;
reax_list
*
bonds
=
(
*
lists
)
+
BONDS
;
p_boc1
=
system
->
reax_param
.
gp
.
l
[
0
];
p_boc2
=
system
->
reax_param
.
gp
.
l
[
1
];
/* Calculate Deltaprime, Deltaprime_boc values */
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
]);
workspace
->
Deltap
[
i
]
=
workspace
->
total_bond_order
[
i
]
-
sbp_i
->
valency
;
workspace
->
Deltap_boc
[
i
]
=
workspace
->
total_bond_order
[
i
]
-
sbp_i
->
valency_val
;
workspace
->
total_bond_order
[
i
]
=
0
;
}
/* Corrected Bond Order calculations */
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
]);
val_i
=
sbp_i
->
valency
;
Deltap_i
=
workspace
->
Deltap
[
i
];
Deltap_boc_i
=
workspace
->
Deltap_boc
[
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
;
type_j
=
system
->
my_atoms
[
j
].
type
;
if
(
type_j
<
0
)
continue
;
bo_ij
=
&
(
bonds
->
select
.
bond_list
[
pj
].
bo_data
);
// fprintf( stderr, "\tj:%d - ubo: %8.3f\n", j+1, bo_ij->BO );
if
(
i
<
j
||
workspace
->
bond_mark
[
j
]
>
3
)
{
twbp
=
&
(
system
->
reax_param
.
tbp
[
type_i
][
type_j
]
);
if
(
twbp
->
ovc
<
0.001
&&
twbp
->
v13cor
<
0.001
)
{
bo_ij
->
C1dbo
=
1.000000
;
bo_ij
->
C2dbo
=
0.000000
;
bo_ij
->
C3dbo
=
0.000000
;
bo_ij
->
C1dbopi
=
bo_ij
->
BO_pi
;
bo_ij
->
C2dbopi
=
0.000000
;
bo_ij
->
C3dbopi
=
0.000000
;
bo_ij
->
C4dbopi
=
0.000000
;
bo_ij
->
C1dbopi2
=
bo_ij
->
BO_pi2
;
bo_ij
->
C2dbopi2
=
0.000000
;
bo_ij
->
C3dbopi2
=
0.000000
;
bo_ij
->
C4dbopi2
=
0.000000
;
}
else
{
val_j
=
system
->
reax_param
.
sbp
[
type_j
].
valency
;
Deltap_j
=
workspace
->
Deltap
[
j
];
Deltap_boc_j
=
workspace
->
Deltap_boc
[
j
];
/* on page 1 */
if
(
twbp
->
ovc
>=
0.001
)
{
/* Correction for overcoordination */
exp_p1i
=
exp
(
-
p_boc1
*
Deltap_i
);
exp_p2i
=
exp
(
-
p_boc2
*
Deltap_i
);
exp_p1j
=
exp
(
-
p_boc1
*
Deltap_j
);
exp_p2j
=
exp
(
-
p_boc2
*
Deltap_j
);
f2
=
exp_p1i
+
exp_p1j
;
f3
=
-
1.0
/
p_boc2
*
log
(
0.5
*
(
exp_p2i
+
exp_p2j
)
);
f1
=
0.5
*
(
(
val_i
+
f2
)
/
(
val_i
+
f2
+
f3
)
+
(
val_j
+
f2
)
/
(
val_j
+
f2
+
f3
)
);
temp
=
f2
+
f3
;
u1_ij
=
val_i
+
temp
;
u1_ji
=
val_j
+
temp
;
Cf1A_ij
=
0.5
*
f3
*
(
1.0
/
SQR
(
u1_ij
)
+
1.0
/
SQR
(
u1_ji
));
Cf1B_ij
=
-
0.5
*
((
u1_ij
-
f3
)
/
SQR
(
u1_ij
)
+
(
u1_ji
-
f3
)
/
SQR
(
u1_ji
));
Cf1_ij
=
0.50
*
(
-
p_boc1
*
exp_p1i
/
u1_ij
-
((
val_i
+
f2
)
/
SQR
(
u1_ij
))
*
(
-
p_boc1
*
exp_p1i
+
exp_p2i
/
(
exp_p2i
+
exp_p2j
)
)
+
-
p_boc1
*
exp_p1i
/
u1_ji
-
((
val_j
+
f2
)
/
SQR
(
u1_ji
))
*
(
-
p_boc1
*
exp_p1i
+
exp_p2i
/
(
exp_p2i
+
exp_p2j
)
));
Cf1_ji
=
-
Cf1A_ij
*
p_boc1
*
exp_p1j
+
Cf1B_ij
*
exp_p2j
/
(
exp_p2i
+
exp_p2j
);
}
else
{
/* No overcoordination correction! */
f1
=
1.0
;
Cf1_ij
=
Cf1_ji
=
0.0
;
}
if
(
twbp
->
v13cor
>=
0.001
)
{
/* Correction for 1-3 bond orders */
exp_f4
=
exp
(
-
(
twbp
->
p_boc4
*
SQR
(
bo_ij
->
BO
)
-
Deltap_boc_i
)
*
twbp
->
p_boc3
+
twbp
->
p_boc5
);
exp_f5
=
exp
(
-
(
twbp
->
p_boc4
*
SQR
(
bo_ij
->
BO
)
-
Deltap_boc_j
)
*
twbp
->
p_boc3
+
twbp
->
p_boc5
);
f4
=
1.
/
(
1.
+
exp_f4
);
f5
=
1.
/
(
1.
+
exp_f5
);
f4f5
=
f4
*
f5
;
/* Bond Order pages 8-9, derivative of f4 and f5 */
Cf45_ij
=
-
f4
*
exp_f4
;
Cf45_ji
=
-
f5
*
exp_f5
;
}
else
{
f4
=
f5
=
f4f5
=
1.0
;
Cf45_ij
=
Cf45_ji
=
0.0
;
}
/* Bond Order page 10, derivative of total bond order */
A0_ij
=
f1
*
f4f5
;
A1_ij
=
-
2
*
twbp
->
p_boc3
*
twbp
->
p_boc4
*
bo_ij
->
BO
*
(
Cf45_ij
+
Cf45_ji
);
A2_ij
=
Cf1_ij
/
f1
+
twbp
->
p_boc3
*
Cf45_ij
;
A2_ji
=
Cf1_ji
/
f1
+
twbp
->
p_boc3
*
Cf45_ji
;
A3_ij
=
A2_ij
+
Cf1_ij
/
f1
;
A3_ji
=
A2_ji
+
Cf1_ji
/
f1
;
/* find corrected bond orders and their derivative coef */
bo_ij
->
BO
=
bo_ij
->
BO
*
A0_ij
;
bo_ij
->
BO_pi
=
bo_ij
->
BO_pi
*
A0_ij
*
f1
;
bo_ij
->
BO_pi2
=
bo_ij
->
BO_pi2
*
A0_ij
*
f1
;
bo_ij
->
BO_s
=
bo_ij
->
BO
-
(
bo_ij
->
BO_pi
+
bo_ij
->
BO_pi2
);
bo_ij
->
C1dbo
=
A0_ij
+
bo_ij
->
BO
*
A1_ij
;
bo_ij
->
C2dbo
=
bo_ij
->
BO
*
A2_ij
;
bo_ij
->
C3dbo
=
bo_ij
->
BO
*
A2_ji
;
bo_ij
->
C1dbopi
=
f1
*
f1
*
f4
*
f5
;
bo_ij
->
C2dbopi
=
bo_ij
->
BO_pi
*
A1_ij
;
bo_ij
->
C3dbopi
=
bo_ij
->
BO_pi
*
A3_ij
;
bo_ij
->
C4dbopi
=
bo_ij
->
BO_pi
*
A3_ji
;
bo_ij
->
C1dbopi2
=
f1
*
f1
*
f4
*
f5
;
bo_ij
->
C2dbopi2
=
bo_ij
->
BO_pi2
*
A1_ij
;
bo_ij
->
C3dbopi2
=
bo_ij
->
BO_pi2
*
A3_ij
;
bo_ij
->
C4dbopi2
=
bo_ij
->
BO_pi2
*
A3_ji
;
}
/* neglect bonds that are < 1e-10 */
if
(
bo_ij
->
BO
<
1e-10
)
bo_ij
->
BO
=
0.0
;
if
(
bo_ij
->
BO_s
<
1e-10
)
bo_ij
->
BO_s
=
0.0
;
if
(
bo_ij
->
BO_pi
<
1e-10
)
bo_ij
->
BO_pi
=
0.0
;
if
(
bo_ij
->
BO_pi2
<
1e-10
)
bo_ij
->
BO_pi2
=
0.0
;
workspace
->
total_bond_order
[
i
]
+=
bo_ij
->
BO
;
//now keeps total_BO
}
else
{
/* We only need to update bond orders from bo_ji
everything else is set in uncorrected_bo calculations */
sym_index
=
bonds
->
select
.
bond_list
[
pj
].
sym_index
;
bo_ji
=
&
(
bonds
->
select
.
bond_list
[
sym_index
].
bo_data
);
bo_ij
->
BO
=
bo_ji
->
BO
;
bo_ij
->
BO_s
=
bo_ji
->
BO_s
;
bo_ij
->
BO_pi
=
bo_ji
->
BO_pi
;
bo_ij
->
BO_pi2
=
bo_ji
->
BO_pi2
;
workspace
->
total_bond_order
[
i
]
+=
bo_ij
->
BO
;
// now keeps total_BO
}
}
}
p_lp1
=
system
->
reax_param
.
gp
.
l
[
15
];
for
(
j
=
0
;
j
<
system
->
N
;
++
j
){
type_j
=
system
->
my_atoms
[
j
].
type
;
if
(
type_j
<
0
)
continue
;
sbp_j
=
&
(
system
->
reax_param
.
sbp
[
type_j
]);
workspace
->
Delta
[
j
]
=
workspace
->
total_bond_order
[
j
]
-
sbp_j
->
valency
;
workspace
->
Delta_e
[
j
]
=
workspace
->
total_bond_order
[
j
]
-
sbp_j
->
valency_e
;
workspace
->
Delta_boc
[
j
]
=
workspace
->
total_bond_order
[
j
]
-
sbp_j
->
valency_boc
;
workspace
->
Delta_val
[
j
]
=
workspace
->
total_bond_order
[
j
]
-
sbp_j
->
valency_val
;
workspace
->
vlpex
[
j
]
=
workspace
->
Delta_e
[
j
]
-
2.0
*
(
int
)(
workspace
->
Delta_e
[
j
]
/
2.0
);
explp1
=
exp
(
-
p_lp1
*
SQR
(
2.0
+
workspace
->
vlpex
[
j
]));
workspace
->
nlp
[
j
]
=
explp1
-
(
int
)(
workspace
->
Delta_e
[
j
]
/
2.0
);
workspace
->
Delta_lp
[
j
]
=
sbp_j
->
nlp_opt
-
workspace
->
nlp
[
j
];
workspace
->
Clp
[
j
]
=
2.0
*
p_lp1
*
explp1
*
(
2.0
+
workspace
->
vlpex
[
j
]);
workspace
->
dDelta_lp
[
j
]
=
workspace
->
Clp
[
j
];
if
(
sbp_j
->
mass
>
21.0
)
{
workspace
->
nlp_temp
[
j
]
=
0.5
*
(
sbp_j
->
valency_e
-
sbp_j
->
valency
);
workspace
->
Delta_lp_temp
[
j
]
=
sbp_j
->
nlp_opt
-
workspace
->
nlp_temp
[
j
];
workspace
->
dDelta_lp_temp
[
j
]
=
0.
;
}
else
{
workspace
->
nlp_temp
[
j
]
=
workspace
->
nlp
[
j
];
workspace
->
Delta_lp_temp
[
j
]
=
sbp_j
->
nlp_opt
-
workspace
->
nlp_temp
[
j
];
workspace
->
dDelta_lp_temp
[
j
]
=
workspace
->
Clp
[
j
];
}
}
}
Event Timeline
Log In to Comment