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reaxc_valence_angles.cpp
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rLAMMPS lammps
reaxc_valence_angles.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_valence_angles.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_vector.h"
static
double
Dot
(
double
*
v1
,
double
*
v2
,
int
k
)
{
double
ret
=
0.0
;
for
(
int
i
=
0
;
i
<
k
;
++
i
)
ret
+=
v1
[
i
]
*
v2
[
i
];
return
ret
;
}
void
Calculate_Theta
(
rvec
dvec_ji
,
double
d_ji
,
rvec
dvec_jk
,
double
d_jk
,
double
*
theta
,
double
*
cos_theta
)
{
(
*
cos_theta
)
=
Dot
(
dvec_ji
,
dvec_jk
,
3
)
/
(
d_ji
*
d_jk
);
if
(
*
cos_theta
>
1.
)
*
cos_theta
=
1.0
;
if
(
*
cos_theta
<
-
1.
)
*
cos_theta
=
-
1.0
;
(
*
theta
)
=
acos
(
*
cos_theta
);
}
void
Calculate_dCos_Theta
(
rvec
dvec_ji
,
double
d_ji
,
rvec
dvec_jk
,
double
d_jk
,
rvec
*
dcos_theta_di
,
rvec
*
dcos_theta_dj
,
rvec
*
dcos_theta_dk
)
{
int
t
;
double
sqr_d_ji
=
SQR
(
d_ji
);
double
sqr_d_jk
=
SQR
(
d_jk
);
double
inv_dists
=
1.0
/
(
d_ji
*
d_jk
);
double
inv_dists3
=
pow
(
inv_dists
,
3.0
);
double
dot_dvecs
=
Dot
(
dvec_ji
,
dvec_jk
,
3
);
double
Cdot_inv3
=
dot_dvecs
*
inv_dists3
;
for
(
t
=
0
;
t
<
3
;
++
t
)
{
(
*
dcos_theta_di
)[
t
]
=
dvec_jk
[
t
]
*
inv_dists
-
Cdot_inv3
*
sqr_d_jk
*
dvec_ji
[
t
];
(
*
dcos_theta_dj
)[
t
]
=
-
(
dvec_jk
[
t
]
+
dvec_ji
[
t
])
*
inv_dists
+
Cdot_inv3
*
(
sqr_d_jk
*
dvec_ji
[
t
]
+
sqr_d_ji
*
dvec_jk
[
t
]
);
(
*
dcos_theta_dk
)[
t
]
=
dvec_ji
[
t
]
*
inv_dists
-
Cdot_inv3
*
sqr_d_ji
*
dvec_jk
[
t
];
}
}
void
Valence_Angles
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
output_controls
*
out_control
)
{
int
i
,
j
,
pi
,
k
,
pk
,
t
;
int
type_i
,
type_j
,
type_k
;
int
start_j
,
end_j
,
start_pk
,
end_pk
;
int
cnt
,
num_thb_intrs
;
double
temp
,
temp_bo_jt
,
pBOjt7
;
double
p_val1
,
p_val2
,
p_val3
,
p_val4
,
p_val5
;
double
p_val6
,
p_val7
,
p_val8
,
p_val9
,
p_val10
;
double
p_pen1
,
p_pen2
,
p_pen3
,
p_pen4
;
double
p_coa1
,
p_coa2
,
p_coa3
,
p_coa4
;
double
trm8
,
expval6
,
expval7
,
expval2theta
,
expval12theta
,
exp3ij
,
exp3jk
;
double
exp_pen2ij
,
exp_pen2jk
,
exp_pen3
,
exp_pen4
,
trm_pen34
,
exp_coa2
;
double
dSBO1
,
dSBO2
,
SBO
,
SBO2
,
CSBO2
,
SBOp
,
prod_SBO
,
vlpadj
;
double
CEval1
,
CEval2
,
CEval3
,
CEval4
,
CEval5
,
CEval6
,
CEval7
,
CEval8
;
double
CEpen1
,
CEpen2
,
CEpen3
;
double
e_ang
,
e_coa
,
e_pen
;
double
CEcoa1
,
CEcoa2
,
CEcoa3
,
CEcoa4
,
CEcoa5
;
double
Cf7ij
,
Cf7jk
,
Cf8j
,
Cf9j
;
double
f7_ij
,
f7_jk
,
f8_Dj
,
f9_Dj
;
double
Ctheta_0
,
theta_0
,
theta_00
,
theta
,
cos_theta
,
sin_theta
;
double
BOA_ij
,
BOA_jk
;
rvec
force
,
ext_press
;
// Tallying variables
double
eng_tmp
,
fi_tmp
[
3
],
fj_tmp
[
3
],
fk_tmp
[
3
];
double
delij
[
3
],
delkj
[
3
];
three_body_header
*
thbh
;
three_body_parameters
*
thbp
;
three_body_interaction_data
*
p_ijk
,
*
p_kji
;
bond_data
*
pbond_ij
,
*
pbond_jk
,
*
pbond_jt
;
bond_order_data
*
bo_ij
,
*
bo_jk
,
*
bo_jt
;
reax_list
*
bonds
=
(
*
lists
)
+
BONDS
;
reax_list
*
thb_intrs
=
(
*
lists
)
+
THREE_BODIES
;
/* global parameters used in these calculations */
p_val6
=
system
->
reax_param
.
gp
.
l
[
14
];
p_val8
=
system
->
reax_param
.
gp
.
l
[
33
];
p_val9
=
system
->
reax_param
.
gp
.
l
[
16
];
p_val10
=
system
->
reax_param
.
gp
.
l
[
17
];
num_thb_intrs
=
0
;
for
(
j
=
0
;
j
<
system
->
N
;
++
j
)
{
// Ray: the first one with system->N
type_j
=
system
->
my_atoms
[
j
].
type
;
if
(
type_j
<
0
)
continue
;
start_j
=
Start_Index
(
j
,
bonds
);
end_j
=
End_Index
(
j
,
bonds
);
p_val3
=
system
->
reax_param
.
sbp
[
type_j
].
p_val3
;
p_val5
=
system
->
reax_param
.
sbp
[
type_j
].
p_val5
;
SBOp
=
0
,
prod_SBO
=
1
;
for
(
t
=
start_j
;
t
<
end_j
;
++
t
)
{
bo_jt
=
&
(
bonds
->
select
.
bond_list
[
t
].
bo_data
);
SBOp
+=
(
bo_jt
->
BO_pi
+
bo_jt
->
BO_pi2
);
temp
=
SQR
(
bo_jt
->
BO
);
temp
*=
temp
;
temp
*=
temp
;
prod_SBO
*=
exp
(
-
temp
);
}
if
(
workspace
->
vlpex
[
j
]
>=
0
){
vlpadj
=
0
;
dSBO2
=
prod_SBO
-
1
;
}
else
{
vlpadj
=
workspace
->
nlp
[
j
];
dSBO2
=
(
prod_SBO
-
1
)
*
(
1
-
p_val8
*
workspace
->
dDelta_lp
[
j
]);
}
SBO
=
SBOp
+
(
1
-
prod_SBO
)
*
(
-
workspace
->
Delta_boc
[
j
]
-
p_val8
*
vlpadj
);
dSBO1
=
-
8
*
prod_SBO
*
(
workspace
->
Delta_boc
[
j
]
+
p_val8
*
vlpadj
);
if
(
SBO
<=
0
)
SBO2
=
0
,
CSBO2
=
0
;
else
if
(
SBO
>
0
&&
SBO
<=
1
)
{
SBO2
=
pow
(
SBO
,
p_val9
);
CSBO2
=
p_val9
*
pow
(
SBO
,
p_val9
-
1
);
}
else
if
(
SBO
>
1
&&
SBO
<
2
)
{
SBO2
=
2
-
pow
(
2
-
SBO
,
p_val9
);
CSBO2
=
p_val9
*
pow
(
2
-
SBO
,
p_val9
-
1
);
}
else
SBO2
=
2
,
CSBO2
=
0
;
expval6
=
exp
(
p_val6
*
workspace
->
Delta_boc
[
j
]
);
for
(
pi
=
start_j
;
pi
<
end_j
;
++
pi
)
{
Set_Start_Index
(
pi
,
num_thb_intrs
,
thb_intrs
);
pbond_ij
=
&
(
bonds
->
select
.
bond_list
[
pi
]);
bo_ij
=
&
(
pbond_ij
->
bo_data
);
BOA_ij
=
bo_ij
->
BO
-
control
->
thb_cut
;
if
(
BOA_ij
/*bo_ij->BO*/
>
0.0
&&
(
j
<
system
->
n
||
pbond_ij
->
nbr
<
system
->
n
)
)
{
i
=
pbond_ij
->
nbr
;
type_i
=
system
->
my_atoms
[
i
].
type
;
for
(
pk
=
start_j
;
pk
<
pi
;
++
pk
)
{
start_pk
=
Start_Index
(
pk
,
thb_intrs
);
end_pk
=
End_Index
(
pk
,
thb_intrs
);
for
(
t
=
start_pk
;
t
<
end_pk
;
++
t
)
if
(
thb_intrs
->
select
.
three_body_list
[
t
].
thb
==
i
)
{
p_ijk
=
&
(
thb_intrs
->
select
.
three_body_list
[
num_thb_intrs
]
);
p_kji
=
&
(
thb_intrs
->
select
.
three_body_list
[
t
]);
p_ijk
->
thb
=
bonds
->
select
.
bond_list
[
pk
].
nbr
;
p_ijk
->
pthb
=
pk
;
p_ijk
->
theta
=
p_kji
->
theta
;
rvec_Copy
(
p_ijk
->
dcos_di
,
p_kji
->
dcos_dk
);
rvec_Copy
(
p_ijk
->
dcos_dj
,
p_kji
->
dcos_dj
);
rvec_Copy
(
p_ijk
->
dcos_dk
,
p_kji
->
dcos_di
);
++
num_thb_intrs
;
break
;
}
}
for
(
pk
=
pi
+
1
;
pk
<
end_j
;
++
pk
)
{
pbond_jk
=
&
(
bonds
->
select
.
bond_list
[
pk
]);
bo_jk
=
&
(
pbond_jk
->
bo_data
);
BOA_jk
=
bo_jk
->
BO
-
control
->
thb_cut
;
k
=
pbond_jk
->
nbr
;
type_k
=
system
->
my_atoms
[
k
].
type
;
p_ijk
=
&
(
thb_intrs
->
select
.
three_body_list
[
num_thb_intrs
]
);
Calculate_Theta
(
pbond_ij
->
dvec
,
pbond_ij
->
d
,
pbond_jk
->
dvec
,
pbond_jk
->
d
,
&
theta
,
&
cos_theta
);
Calculate_dCos_Theta
(
pbond_ij
->
dvec
,
pbond_ij
->
d
,
pbond_jk
->
dvec
,
pbond_jk
->
d
,
&
(
p_ijk
->
dcos_di
),
&
(
p_ijk
->
dcos_dj
),
&
(
p_ijk
->
dcos_dk
)
);
p_ijk
->
thb
=
k
;
p_ijk
->
pthb
=
pk
;
p_ijk
->
theta
=
theta
;
sin_theta
=
sin
(
theta
);
if
(
sin_theta
<
1.0e-5
)
sin_theta
=
1.0e-5
;
++
num_thb_intrs
;
if
(
(
j
<
system
->
n
)
&&
(
BOA_jk
>
0.0
)
&&
(
bo_ij
->
BO
>
control
->
thb_cut
)
&&
(
bo_jk
->
BO
>
control
->
thb_cut
)
&&
(
bo_ij
->
BO
*
bo_jk
->
BO
>
control
->
thb_cutsq
)
)
{
thbh
=
&
(
system
->
reax_param
.
thbp
[
type_i
][
type_j
][
type_k
]
);
for
(
cnt
=
0
;
cnt
<
thbh
->
cnt
;
++
cnt
)
{
if
(
fabs
(
thbh
->
prm
[
cnt
].
p_val1
)
>
0.001
)
{
thbp
=
&
(
thbh
->
prm
[
cnt
]
);
/* ANGLE ENERGY */
p_val1
=
thbp
->
p_val1
;
p_val2
=
thbp
->
p_val2
;
p_val4
=
thbp
->
p_val4
;
p_val7
=
thbp
->
p_val7
;
theta_00
=
thbp
->
theta_00
;
exp3ij
=
exp
(
-
p_val3
*
pow
(
BOA_ij
,
p_val4
)
);
f7_ij
=
1.0
-
exp3ij
;
Cf7ij
=
p_val3
*
p_val4
*
pow
(
BOA_ij
,
p_val4
-
1.0
)
*
exp3ij
;
exp3jk
=
exp
(
-
p_val3
*
pow
(
BOA_jk
,
p_val4
)
);
f7_jk
=
1.0
-
exp3jk
;
Cf7jk
=
p_val3
*
p_val4
*
pow
(
BOA_jk
,
p_val4
-
1.0
)
*
exp3jk
;
expval7
=
exp
(
-
p_val7
*
workspace
->
Delta_boc
[
j
]
);
trm8
=
1.0
+
expval6
+
expval7
;
f8_Dj
=
p_val5
-
(
(
p_val5
-
1.0
)
*
(
2.0
+
expval6
)
/
trm8
);
Cf8j
=
(
(
1.0
-
p_val5
)
/
SQR
(
trm8
)
)
*
(
p_val6
*
expval6
*
trm8
-
(
2.0
+
expval6
)
*
(
p_val6
*
expval6
-
p_val7
*
expval7
)
);
theta_0
=
180.0
-
theta_00
*
(
1.0
-
exp
(
-
p_val10
*
(
2.0
-
SBO2
)));
theta_0
=
DEG2RAD
(
theta_0
);
expval2theta
=
exp
(
-
p_val2
*
SQR
(
theta_0
-
theta
)
);
if
(
p_val1
>=
0
)
expval12theta
=
p_val1
*
(
1.0
-
expval2theta
);
else
// To avoid linear Me-H-Me angles (6/6/06)
expval12theta
=
p_val1
*
-
expval2theta
;
CEval1
=
Cf7ij
*
f7_jk
*
f8_Dj
*
expval12theta
;
CEval2
=
Cf7jk
*
f7_ij
*
f8_Dj
*
expval12theta
;
CEval3
=
Cf8j
*
f7_ij
*
f7_jk
*
expval12theta
;
CEval4
=
-
2.0
*
p_val1
*
p_val2
*
f7_ij
*
f7_jk
*
f8_Dj
*
expval2theta
*
(
theta_0
-
theta
);
Ctheta_0
=
p_val10
*
DEG2RAD
(
theta_00
)
*
exp
(
-
p_val10
*
(
2.0
-
SBO2
)
);
CEval5
=
-
CEval4
*
Ctheta_0
*
CSBO2
;
CEval6
=
CEval5
*
dSBO1
;
CEval7
=
CEval5
*
dSBO2
;
CEval8
=
-
CEval4
/
sin_theta
;
data
->
my_en
.
e_ang
+=
e_ang
=
f7_ij
*
f7_jk
*
f8_Dj
*
expval12theta
;
/* END ANGLE ENERGY*/
/* PENALTY ENERGY */
p_pen1
=
thbp
->
p_pen1
;
p_pen2
=
system
->
reax_param
.
gp
.
l
[
19
];
p_pen3
=
system
->
reax_param
.
gp
.
l
[
20
];
p_pen4
=
system
->
reax_param
.
gp
.
l
[
21
];
exp_pen2ij
=
exp
(
-
p_pen2
*
SQR
(
BOA_ij
-
2.0
)
);
exp_pen2jk
=
exp
(
-
p_pen2
*
SQR
(
BOA_jk
-
2.0
)
);
exp_pen3
=
exp
(
-
p_pen3
*
workspace
->
Delta
[
j
]
);
exp_pen4
=
exp
(
p_pen4
*
workspace
->
Delta
[
j
]
);
trm_pen34
=
1.0
+
exp_pen3
+
exp_pen4
;
f9_Dj
=
(
2.0
+
exp_pen3
)
/
trm_pen34
;
Cf9j
=
(
-
p_pen3
*
exp_pen3
*
trm_pen34
-
(
2.0
+
exp_pen3
)
*
(
-
p_pen3
*
exp_pen3
+
p_pen4
*
exp_pen4
)
)
/
SQR
(
trm_pen34
);
data
->
my_en
.
e_pen
+=
e_pen
=
p_pen1
*
f9_Dj
*
exp_pen2ij
*
exp_pen2jk
;
CEpen1
=
e_pen
*
Cf9j
/
f9_Dj
;
temp
=
-
2.0
*
p_pen2
*
e_pen
;
CEpen2
=
temp
*
(
BOA_ij
-
2.0
);
CEpen3
=
temp
*
(
BOA_jk
-
2.0
);
/* END PENALTY ENERGY */
/* COALITION ENERGY */
p_coa1
=
thbp
->
p_coa1
;
p_coa2
=
system
->
reax_param
.
gp
.
l
[
2
];
p_coa3
=
system
->
reax_param
.
gp
.
l
[
38
];
p_coa4
=
system
->
reax_param
.
gp
.
l
[
30
];
exp_coa2
=
exp
(
p_coa2
*
workspace
->
Delta_val
[
j
]
);
data
->
my_en
.
e_coa
+=
e_coa
=
p_coa1
/
(
1.
+
exp_coa2
)
*
exp
(
-
p_coa3
*
SQR
(
workspace
->
total_bond_order
[
i
]
-
BOA_ij
)
)
*
exp
(
-
p_coa3
*
SQR
(
workspace
->
total_bond_order
[
k
]
-
BOA_jk
)
)
*
exp
(
-
p_coa4
*
SQR
(
BOA_ij
-
1.5
)
)
*
exp
(
-
p_coa4
*
SQR
(
BOA_jk
-
1.5
)
);
CEcoa1
=
-
2
*
p_coa4
*
(
BOA_ij
-
1.5
)
*
e_coa
;
CEcoa2
=
-
2
*
p_coa4
*
(
BOA_jk
-
1.5
)
*
e_coa
;
CEcoa3
=
-
p_coa2
*
exp_coa2
*
e_coa
/
(
1
+
exp_coa2
);
CEcoa4
=
-
2
*
p_coa3
*
(
workspace
->
total_bond_order
[
i
]
-
BOA_ij
)
*
e_coa
;
CEcoa5
=
-
2
*
p_coa3
*
(
workspace
->
total_bond_order
[
k
]
-
BOA_jk
)
*
e_coa
;
/* END COALITION ENERGY */
/* FORCES */
bo_ij
->
Cdbo
+=
(
CEval1
+
CEpen2
+
(
CEcoa1
-
CEcoa4
));
bo_jk
->
Cdbo
+=
(
CEval2
+
CEpen3
+
(
CEcoa2
-
CEcoa5
));
workspace
->
CdDelta
[
j
]
+=
((
CEval3
+
CEval7
)
+
CEpen1
+
CEcoa3
);
workspace
->
CdDelta
[
i
]
+=
CEcoa4
;
workspace
->
CdDelta
[
k
]
+=
CEcoa5
;
for
(
t
=
start_j
;
t
<
end_j
;
++
t
)
{
pbond_jt
=
&
(
bonds
->
select
.
bond_list
[
t
]
);
bo_jt
=
&
(
pbond_jt
->
bo_data
);
temp_bo_jt
=
bo_jt
->
BO
;
temp
=
CUBE
(
temp_bo_jt
);
pBOjt7
=
temp
*
temp
*
temp_bo_jt
;
bo_jt
->
Cdbo
+=
(
CEval6
*
pBOjt7
);
bo_jt
->
Cdbopi
+=
CEval5
;
bo_jt
->
Cdbopi2
+=
CEval5
;
}
if
(
control
->
virial
==
0
)
{
rvec_ScaledAdd
(
workspace
->
f
[
i
],
CEval8
,
p_ijk
->
dcos_di
);
rvec_ScaledAdd
(
workspace
->
f
[
j
],
CEval8
,
p_ijk
->
dcos_dj
);
rvec_ScaledAdd
(
workspace
->
f
[
k
],
CEval8
,
p_ijk
->
dcos_dk
);
}
else
{
rvec_Scale
(
force
,
CEval8
,
p_ijk
->
dcos_di
);
rvec_Add
(
workspace
->
f
[
i
],
force
);
rvec_iMultiply
(
ext_press
,
pbond_ij
->
rel_box
,
force
);
rvec_Add
(
data
->
my_ext_press
,
ext_press
);
rvec_ScaledAdd
(
workspace
->
f
[
j
],
CEval8
,
p_ijk
->
dcos_dj
);
rvec_Scale
(
force
,
CEval8
,
p_ijk
->
dcos_dk
);
rvec_Add
(
workspace
->
f
[
k
],
force
);
rvec_iMultiply
(
ext_press
,
pbond_jk
->
rel_box
,
force
);
rvec_Add
(
data
->
my_ext_press
,
ext_press
);
}
/* tally into per-atom virials */
if
(
system
->
pair_ptr
->
vflag_atom
||
system
->
pair_ptr
->
evflag
)
{
/* Acquire vectors */
rvec_ScaledSum
(
delij
,
1.
,
system
->
my_atoms
[
i
].
x
,
-
1.
,
system
->
my_atoms
[
j
].
x
);
rvec_ScaledSum
(
delkj
,
1.
,
system
->
my_atoms
[
k
].
x
,
-
1.
,
system
->
my_atoms
[
j
].
x
);
rvec_Scale
(
fi_tmp
,
-
CEval8
,
p_ijk
->
dcos_di
);
rvec_Scale
(
fj_tmp
,
-
CEval8
,
p_ijk
->
dcos_dj
);
rvec_Scale
(
fk_tmp
,
-
CEval8
,
p_ijk
->
dcos_dk
);
eng_tmp
=
e_ang
+
e_pen
+
e_coa
;
if
(
system
->
pair_ptr
->
evflag
)
system
->
pair_ptr
->
ev_tally
(
j
,
j
,
system
->
N
,
1
,
eng_tmp
,
0.0
,
0.0
,
0.0
,
0.0
,
0.0
);
if
(
system
->
pair_ptr
->
vflag_atom
)
system
->
pair_ptr
->
v_tally3
(
i
,
j
,
k
,
fi_tmp
,
fk_tmp
,
delij
,
delkj
);
}
}
}
}
}
}
Set_End_Index
(
pi
,
num_thb_intrs
,
thb_intrs
);
}
}
if
(
num_thb_intrs
>=
thb_intrs
->
num_intrs
*
DANGER_ZONE
)
{
workspace
->
realloc
.
num_3body
=
num_thb_intrs
;
if
(
num_thb_intrs
>
thb_intrs
->
num_intrs
)
{
fprintf
(
stderr
,
"step%d-ran out of space on angle_list: top=%d, max=%d"
,
data
->
step
,
num_thb_intrs
,
thb_intrs
->
num_intrs
);
MPI_Abort
(
MPI_COMM_WORLD
,
INSUFFICIENT_MEMORY
);
}
}
}
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