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reaxc_nonbonded.cpp
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rLAMMPS lammps
reaxc_nonbonded.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_types.h"
#include "reaxc_nonbonded.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_vector.h"
void
vdW_Coulomb_Energy
(
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
,
flag
;
rc_tagint
orig_i
,
orig_j
;
real
p_vdW1
,
p_vdW1i
;
real
powr_vdW1
,
powgi_vdW1
;
real
tmp
,
r_ij
,
fn13
,
exp1
,
exp2
;
real
Tap
,
dTap
,
dfn13
,
CEvd
,
CEclmb
,
de_core
;
real
dr3gamij_1
,
dr3gamij_3
;
real
e_ele
,
e_vdW
,
e_core
,
SMALL
=
0.0001
;
real
e_lg
,
de_lg
,
r_ij5
,
r_ij6
,
re6
;
rvec
temp
,
ext_press
;
two_body_parameters
*
twbp
;
far_neighbor_data
*
nbr_pj
;
reax_list
*
far_nbrs
;
// Tallying variables:
real
pe_vdw
,
f_tmp
,
delij
[
3
];
natoms
=
system
->
n
;
far_nbrs
=
(
*
lists
)
+
FAR_NBRS
;
p_vdW1
=
system
->
reax_param
.
gp
.
l
[
28
];
p_vdW1i
=
1.0
/
p_vdW1
;
e_core
=
0
;
e_vdW
=
0
;
e_lg
=
de_lg
=
0.0
;
for
(
i
=
0
;
i
<
natoms
;
++
i
)
{
if
(
system
->
my_atoms
[
i
].
type
<
0
)
continue
;
start_i
=
Start_Index
(
i
,
far_nbrs
);
end_i
=
End_Index
(
i
,
far_nbrs
);
orig_i
=
system
->
my_atoms
[
i
].
orig_id
;
for
(
pj
=
start_i
;
pj
<
end_i
;
++
pj
)
{
nbr_pj
=
&
(
far_nbrs
->
select
.
far_nbr_list
[
pj
]);
j
=
nbr_pj
->
nbr
;
if
(
system
->
my_atoms
[
j
].
type
<
0
)
continue
;
orig_j
=
system
->
my_atoms
[
j
].
orig_id
;
flag
=
0
;
if
(
nbr_pj
->
d
<=
control
->
nonb_cut
)
{
if
(
j
<
natoms
)
flag
=
1
;
else
if
(
orig_i
<
orig_j
)
flag
=
1
;
else
if
(
orig_i
==
orig_j
)
{
if
(
nbr_pj
->
dvec
[
2
]
>
SMALL
)
flag
=
1
;
else
if
(
fabs
(
nbr_pj
->
dvec
[
2
])
<
SMALL
)
{
if
(
nbr_pj
->
dvec
[
1
]
>
SMALL
)
flag
=
1
;
else
if
(
fabs
(
nbr_pj
->
dvec
[
1
])
<
SMALL
&&
nbr_pj
->
dvec
[
0
]
>
SMALL
)
flag
=
1
;
}
}
}
if
(
flag
)
{
r_ij
=
nbr_pj
->
d
;
twbp
=
&
(
system
->
reax_param
.
tbp
[
system
->
my_atoms
[
i
].
type
]
[
system
->
my_atoms
[
j
].
type
]);
Tap
=
workspace
->
Tap
[
7
]
*
r_ij
+
workspace
->
Tap
[
6
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
5
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
4
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
3
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
2
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
1
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
0
];
dTap
=
7
*
workspace
->
Tap
[
7
]
*
r_ij
+
6
*
workspace
->
Tap
[
6
];
dTap
=
dTap
*
r_ij
+
5
*
workspace
->
Tap
[
5
];
dTap
=
dTap
*
r_ij
+
4
*
workspace
->
Tap
[
4
];
dTap
=
dTap
*
r_ij
+
3
*
workspace
->
Tap
[
3
];
dTap
=
dTap
*
r_ij
+
2
*
workspace
->
Tap
[
2
];
dTap
+=
workspace
->
Tap
[
1
]
/
r_ij
;
/*vdWaals Calculations*/
if
(
system
->
reax_param
.
gp
.
vdw_type
==
1
||
system
->
reax_param
.
gp
.
vdw_type
==
3
)
{
// shielding
powr_vdW1
=
pow
(
r_ij
,
p_vdW1
);
powgi_vdW1
=
pow
(
1.0
/
twbp
->
gamma_w
,
p_vdW1
);
fn13
=
pow
(
powr_vdW1
+
powgi_vdW1
,
p_vdW1i
);
exp1
=
exp
(
twbp
->
alpha
*
(
1.0
-
fn13
/
twbp
->
r_vdW
)
);
exp2
=
exp
(
0.5
*
twbp
->
alpha
*
(
1.0
-
fn13
/
twbp
->
r_vdW
)
);
e_vdW
=
twbp
->
D
*
(
exp1
-
2.0
*
exp2
);
data
->
my_en
.
e_vdW
+=
Tap
*
e_vdW
;
dfn13
=
pow
(
powr_vdW1
+
powgi_vdW1
,
p_vdW1i
-
1.0
)
*
pow
(
r_ij
,
p_vdW1
-
2.0
);
CEvd
=
dTap
*
e_vdW
-
Tap
*
twbp
->
D
*
(
twbp
->
alpha
/
twbp
->
r_vdW
)
*
(
exp1
-
exp2
)
*
dfn13
;
}
else
{
// no shielding
exp1
=
exp
(
twbp
->
alpha
*
(
1.0
-
r_ij
/
twbp
->
r_vdW
)
);
exp2
=
exp
(
0.5
*
twbp
->
alpha
*
(
1.0
-
r_ij
/
twbp
->
r_vdW
)
);
e_vdW
=
twbp
->
D
*
(
exp1
-
2.0
*
exp2
);
data
->
my_en
.
e_vdW
+=
Tap
*
e_vdW
;
CEvd
=
dTap
*
e_vdW
-
Tap
*
twbp
->
D
*
(
twbp
->
alpha
/
twbp
->
r_vdW
)
*
(
exp1
-
exp2
)
/
r_ij
;
}
if
(
system
->
reax_param
.
gp
.
vdw_type
==
2
||
system
->
reax_param
.
gp
.
vdw_type
==
3
)
{
// innner wall
e_core
=
twbp
->
ecore
*
exp
(
twbp
->
acore
*
(
1.0
-
(
r_ij
/
twbp
->
rcore
)));
data
->
my_en
.
e_vdW
+=
Tap
*
e_core
;
de_core
=
-
(
twbp
->
acore
/
twbp
->
rcore
)
*
e_core
;
CEvd
+=
dTap
*
e_core
+
Tap
*
de_core
/
r_ij
;
// lg correction, only if lgvdw is yes
if
(
control
->
lgflag
)
{
r_ij5
=
pow
(
r_ij
,
5.0
);
r_ij6
=
pow
(
r_ij
,
6.0
);
re6
=
pow
(
twbp
->
lgre
,
6.0
);
e_lg
=
-
(
twbp
->
lgcij
/
(
r_ij6
+
re6
));
data
->
my_en
.
e_vdW
+=
Tap
*
e_lg
;
de_lg
=
-
6.0
*
e_lg
*
r_ij5
/
(
r_ij6
+
re6
)
;
CEvd
+=
dTap
*
e_lg
+
Tap
*
de_lg
/
r_ij
;
}
}
/*Coulomb Calculations*/
dr3gamij_1
=
(
r_ij
*
r_ij
*
r_ij
+
twbp
->
gamma
);
dr3gamij_3
=
pow
(
dr3gamij_1
,
0.33333333333333
);
tmp
=
Tap
/
dr3gamij_3
;
data
->
my_en
.
e_ele
+=
e_ele
=
C_ele
*
system
->
my_atoms
[
i
].
q
*
system
->
my_atoms
[
j
].
q
*
tmp
;
CEclmb
=
C_ele
*
system
->
my_atoms
[
i
].
q
*
system
->
my_atoms
[
j
].
q
*
(
dTap
-
Tap
*
r_ij
/
dr3gamij_1
)
/
dr3gamij_3
;
/* tally into per-atom energy */
if
(
system
->
pair_ptr
->
evflag
||
system
->
pair_ptr
->
vflag_atom
)
{
pe_vdw
=
Tap
*
(
e_vdW
+
e_core
+
e_lg
);
rvec_ScaledSum
(
delij
,
1.
,
system
->
my_atoms
[
i
].
x
,
-
1.
,
system
->
my_atoms
[
j
].
x
);
f_tmp
=
-
(
CEvd
+
CEclmb
);
system
->
pair_ptr
->
ev_tally
(
i
,
j
,
natoms
,
1
,
pe_vdw
,
e_ele
,
f_tmp
,
delij
[
0
],
delij
[
1
],
delij
[
2
]);
}
if
(
control
->
virial
==
0
)
{
rvec_ScaledAdd
(
workspace
->
f
[
i
],
-
(
CEvd
+
CEclmb
),
nbr_pj
->
dvec
);
rvec_ScaledAdd
(
workspace
->
f
[
j
],
+
(
CEvd
+
CEclmb
),
nbr_pj
->
dvec
);
}
else
{
/* NPT, iNPT or sNPT */
rvec_Scale
(
temp
,
CEvd
+
CEclmb
,
nbr_pj
->
dvec
);
rvec_ScaledAdd
(
workspace
->
f
[
i
],
-
1.
,
temp
);
rvec_Add
(
workspace
->
f
[
j
],
temp
);
rvec_iMultiply
(
ext_press
,
nbr_pj
->
rel_box
,
temp
);
rvec_Add
(
data
->
my_ext_press
,
ext_press
);
}
}
}
}
Compute_Polarization_Energy
(
system
,
data
);
}
void
Tabulated_vdW_Coulomb_Energy
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
output_controls
*
out_control
)
{
int
i
,
j
,
pj
,
r
,
natoms
;
int
type_i
,
type_j
,
tmin
,
tmax
;
int
start_i
,
end_i
,
flag
;
rc_tagint
orig_i
,
orig_j
;
real
r_ij
,
base
,
dif
;
real
e_vdW
,
e_ele
;
real
CEvd
,
CEclmb
,
SMALL
=
0.0001
;
real
f_tmp
,
delij
[
3
];
rvec
temp
,
ext_press
;
far_neighbor_data
*
nbr_pj
;
reax_list
*
far_nbrs
;
LR_lookup_table
*
t
;
natoms
=
system
->
n
;
far_nbrs
=
(
*
lists
)
+
FAR_NBRS
;
e_ele
=
e_vdW
=
0
;
for
(
i
=
0
;
i
<
natoms
;
++
i
)
{
type_i
=
system
->
my_atoms
[
i
].
type
;
if
(
type_i
<
0
)
continue
;
start_i
=
Start_Index
(
i
,
far_nbrs
);
end_i
=
End_Index
(
i
,
far_nbrs
);
orig_i
=
system
->
my_atoms
[
i
].
orig_id
;
for
(
pj
=
start_i
;
pj
<
end_i
;
++
pj
)
{
nbr_pj
=
&
(
far_nbrs
->
select
.
far_nbr_list
[
pj
]);
j
=
nbr_pj
->
nbr
;
type_j
=
system
->
my_atoms
[
j
].
type
;
if
(
type_j
<
0
)
continue
;
orig_j
=
system
->
my_atoms
[
j
].
orig_id
;
flag
=
0
;
if
(
nbr_pj
->
d
<=
control
->
nonb_cut
)
{
if
(
j
<
natoms
)
flag
=
1
;
else
if
(
orig_i
<
orig_j
)
flag
=
1
;
else
if
(
orig_i
==
orig_j
)
{
if
(
nbr_pj
->
dvec
[
2
]
>
SMALL
)
flag
=
1
;
else
if
(
fabs
(
nbr_pj
->
dvec
[
2
])
<
SMALL
)
{
if
(
nbr_pj
->
dvec
[
1
]
>
SMALL
)
flag
=
1
;
else
if
(
fabs
(
nbr_pj
->
dvec
[
1
])
<
SMALL
&&
nbr_pj
->
dvec
[
0
]
>
SMALL
)
flag
=
1
;
}
}
}
if
(
flag
)
{
r_ij
=
nbr_pj
->
d
;
tmin
=
MIN
(
type_i
,
type_j
);
tmax
=
MAX
(
type_i
,
type_j
);
t
=
&
(
LR
[
tmin
][
tmax
]
);
/* Cubic Spline Interpolation */
r
=
(
int
)(
r_ij
*
t
->
inv_dx
);
if
(
r
==
0
)
++
r
;
base
=
(
real
)(
r
+
1
)
*
t
->
dx
;
dif
=
r_ij
-
base
;
e_vdW
=
((
t
->
vdW
[
r
].
d
*
dif
+
t
->
vdW
[
r
].
c
)
*
dif
+
t
->
vdW
[
r
].
b
)
*
dif
+
t
->
vdW
[
r
].
a
;
e_ele
=
((
t
->
ele
[
r
].
d
*
dif
+
t
->
ele
[
r
].
c
)
*
dif
+
t
->
ele
[
r
].
b
)
*
dif
+
t
->
ele
[
r
].
a
;
e_ele
*=
system
->
my_atoms
[
i
].
q
*
system
->
my_atoms
[
j
].
q
;
data
->
my_en
.
e_vdW
+=
e_vdW
;
data
->
my_en
.
e_ele
+=
e_ele
;
CEvd
=
((
t
->
CEvd
[
r
].
d
*
dif
+
t
->
CEvd
[
r
].
c
)
*
dif
+
t
->
CEvd
[
r
].
b
)
*
dif
+
t
->
CEvd
[
r
].
a
;
CEclmb
=
((
t
->
CEclmb
[
r
].
d
*
dif
+
t
->
CEclmb
[
r
].
c
)
*
dif
+
t
->
CEclmb
[
r
].
b
)
*
dif
+
t
->
CEclmb
[
r
].
a
;
CEclmb
*=
system
->
my_atoms
[
i
].
q
*
system
->
my_atoms
[
j
].
q
;
/* tally into per-atom energy */
if
(
system
->
pair_ptr
->
evflag
||
system
->
pair_ptr
->
vflag_atom
)
{
rvec_ScaledSum
(
delij
,
1.
,
system
->
my_atoms
[
i
].
x
,
-
1.
,
system
->
my_atoms
[
j
].
x
);
f_tmp
=
-
(
CEvd
+
CEclmb
);
system
->
pair_ptr
->
ev_tally
(
i
,
j
,
natoms
,
1
,
e_vdW
,
e_ele
,
f_tmp
,
delij
[
0
],
delij
[
1
],
delij
[
2
]);
}
if
(
control
->
virial
==
0
)
{
rvec_ScaledAdd
(
workspace
->
f
[
i
],
-
(
CEvd
+
CEclmb
),
nbr_pj
->
dvec
);
rvec_ScaledAdd
(
workspace
->
f
[
j
],
+
(
CEvd
+
CEclmb
),
nbr_pj
->
dvec
);
}
else
{
// NPT, iNPT or sNPT
rvec_Scale
(
temp
,
CEvd
+
CEclmb
,
nbr_pj
->
dvec
);
rvec_ScaledAdd
(
workspace
->
f
[
i
],
-
1.
,
temp
);
rvec_Add
(
workspace
->
f
[
j
],
temp
);
rvec_iMultiply
(
ext_press
,
nbr_pj
->
rel_box
,
temp
);
rvec_Add
(
data
->
my_ext_press
,
ext_press
);
}
}
}
}
Compute_Polarization_Energy
(
system
,
data
);
}
void
Compute_Polarization_Energy
(
reax_system
*
system
,
simulation_data
*
data
)
{
int
i
,
type_i
;
real
q
,
en_tmp
;
data
->
my_en
.
e_pol
=
0.0
;
for
(
i
=
0
;
i
<
system
->
n
;
i
++
)
{
type_i
=
system
->
my_atoms
[
i
].
type
;
if
(
type_i
<
0
)
continue
;
q
=
system
->
my_atoms
[
i
].
q
;
en_tmp
=
KCALpMOL_to_EV
*
(
system
->
reax_param
.
sbp
[
type_i
].
chi
*
q
+
(
system
->
reax_param
.
sbp
[
type_i
].
eta
/
2.
)
*
SQR
(
q
));
data
->
my_en
.
e_pol
+=
en_tmp
;
/* tally into per-atom energy */
if
(
system
->
pair_ptr
->
evflag
)
system
->
pair_ptr
->
ev_tally
(
i
,
i
,
system
->
n
,
1
,
0.0
,
en_tmp
,
0.0
,
0.0
,
0.0
,
0.0
);
}
}
void
LR_vdW_Coulomb
(
reax_system
*
system
,
storage
*
workspace
,
control_params
*
control
,
int
i
,
int
j
,
real
r_ij
,
LR_data
*
lr
)
{
real
p_vdW1
=
system
->
reax_param
.
gp
.
l
[
28
];
real
p_vdW1i
=
1.0
/
p_vdW1
;
real
powr_vdW1
,
powgi_vdW1
;
real
tmp
,
fn13
,
exp1
,
exp2
;
real
Tap
,
dTap
,
dfn13
;
real
dr3gamij_1
,
dr3gamij_3
;
real
e_core
,
de_core
;
real
e_lg
,
de_lg
,
r_ij5
,
r_ij6
,
re6
;
two_body_parameters
*
twbp
;
twbp
=
&
(
system
->
reax_param
.
tbp
[
i
][
j
]);
e_core
=
0
;
de_core
=
0
;
e_lg
=
de_lg
=
0.0
;
/* calculate taper and its derivative */
Tap
=
workspace
->
Tap
[
7
]
*
r_ij
+
workspace
->
Tap
[
6
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
5
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
4
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
3
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
2
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
1
];
Tap
=
Tap
*
r_ij
+
workspace
->
Tap
[
0
];
dTap
=
7
*
workspace
->
Tap
[
7
]
*
r_ij
+
6
*
workspace
->
Tap
[
6
];
dTap
=
dTap
*
r_ij
+
5
*
workspace
->
Tap
[
5
];
dTap
=
dTap
*
r_ij
+
4
*
workspace
->
Tap
[
4
];
dTap
=
dTap
*
r_ij
+
3
*
workspace
->
Tap
[
3
];
dTap
=
dTap
*
r_ij
+
2
*
workspace
->
Tap
[
2
];
dTap
+=
workspace
->
Tap
[
1
]
/
r_ij
;
/*vdWaals Calculations*/
if
(
system
->
reax_param
.
gp
.
vdw_type
==
1
||
system
->
reax_param
.
gp
.
vdw_type
==
3
)
{
// shielding
powr_vdW1
=
pow
(
r_ij
,
p_vdW1
);
powgi_vdW1
=
pow
(
1.0
/
twbp
->
gamma_w
,
p_vdW1
);
fn13
=
pow
(
powr_vdW1
+
powgi_vdW1
,
p_vdW1i
);
exp1
=
exp
(
twbp
->
alpha
*
(
1.0
-
fn13
/
twbp
->
r_vdW
)
);
exp2
=
exp
(
0.5
*
twbp
->
alpha
*
(
1.0
-
fn13
/
twbp
->
r_vdW
)
);
lr
->
e_vdW
=
Tap
*
twbp
->
D
*
(
exp1
-
2.0
*
exp2
);
dfn13
=
pow
(
powr_vdW1
+
powgi_vdW1
,
p_vdW1i
-
1.0
)
*
pow
(
r_ij
,
p_vdW1
-
2.0
);
lr
->
CEvd
=
dTap
*
twbp
->
D
*
(
exp1
-
2.0
*
exp2
)
-
Tap
*
twbp
->
D
*
(
twbp
->
alpha
/
twbp
->
r_vdW
)
*
(
exp1
-
exp2
)
*
dfn13
;
}
else
{
// no shielding
exp1
=
exp
(
twbp
->
alpha
*
(
1.0
-
r_ij
/
twbp
->
r_vdW
)
);
exp2
=
exp
(
0.5
*
twbp
->
alpha
*
(
1.0
-
r_ij
/
twbp
->
r_vdW
)
);
lr
->
e_vdW
=
Tap
*
twbp
->
D
*
(
exp1
-
2.0
*
exp2
);
lr
->
CEvd
=
dTap
*
twbp
->
D
*
(
exp1
-
2.0
*
exp2
)
-
Tap
*
twbp
->
D
*
(
twbp
->
alpha
/
twbp
->
r_vdW
)
*
(
exp1
-
exp2
)
/
r_ij
;
}
if
(
system
->
reax_param
.
gp
.
vdw_type
==
2
||
system
->
reax_param
.
gp
.
vdw_type
==
3
)
{
// innner wall
e_core
=
twbp
->
ecore
*
exp
(
twbp
->
acore
*
(
1.0
-
(
r_ij
/
twbp
->
rcore
)));
lr
->
e_vdW
+=
Tap
*
e_core
;
de_core
=
-
(
twbp
->
acore
/
twbp
->
rcore
)
*
e_core
;
lr
->
CEvd
+=
dTap
*
e_core
+
Tap
*
de_core
/
r_ij
;
// lg correction, only if lgvdw is yes
if
(
control
->
lgflag
)
{
r_ij5
=
pow
(
r_ij
,
5.0
);
r_ij6
=
pow
(
r_ij
,
6.0
);
re6
=
pow
(
twbp
->
lgre
,
6.0
);
e_lg
=
-
(
twbp
->
lgcij
/
(
r_ij6
+
re6
));
lr
->
e_vdW
+=
Tap
*
e_lg
;
de_lg
=
-
6.0
*
e_lg
*
r_ij5
/
(
r_ij6
+
re6
)
;
lr
->
CEvd
+=
dTap
*
e_lg
+
Tap
*
de_lg
/
r_ij
;
}
}
/* Coulomb calculations */
dr3gamij_1
=
(
r_ij
*
r_ij
*
r_ij
+
twbp
->
gamma
);
dr3gamij_3
=
pow
(
dr3gamij_1
,
0.33333333333333
);
tmp
=
Tap
/
dr3gamij_3
;
lr
->
H
=
EV_to_KCALpMOL
*
tmp
;
lr
->
e_ele
=
C_ele
*
tmp
;
lr
->
CEclmb
=
C_ele
*
(
dTap
-
Tap
*
r_ij
/
dr3gamij_1
)
/
dr3gamij_3
;
}
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