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rLAMMPS lammps
reaxc_lookup.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_lookup.h"
#include "reaxc_nonbonded.h"
#include "reaxc_tool_box.h"
LR_lookup_table
**
LR
;
void
Tridiagonal_Solve
(
const
double
*
a
,
const
double
*
b
,
double
*
c
,
double
*
d
,
double
*
x
,
unsigned
int
n
){
int
i
;
double
id
;
c
[
0
]
/=
b
[
0
];
/* Division by zero risk. */
d
[
0
]
/=
b
[
0
];
/* Division by zero would imply a singular matrix. */
for
(
i
=
1
;
i
<
n
;
i
++
){
id
=
(
b
[
i
]
-
c
[
i
-
1
]
*
a
[
i
]);
/* Division by zero risk. */
c
[
i
]
/=
id
;
/* Last value calculated is redundant. */
d
[
i
]
=
(
d
[
i
]
-
d
[
i
-
1
]
*
a
[
i
])
/
id
;
}
x
[
n
-
1
]
=
d
[
n
-
1
];
for
(
i
=
n
-
2
;
i
>=
0
;
i
--
)
x
[
i
]
=
d
[
i
]
-
c
[
i
]
*
x
[
i
+
1
];
}
void
Natural_Cubic_Spline
(
const
double
*
h
,
const
double
*
f
,
cubic_spline_coef
*
coef
,
unsigned
int
n
,
MPI_Comm
comm
)
{
int
i
;
double
*
a
,
*
b
,
*
c
,
*
d
,
*
v
;
/* allocate space for the linear system */
a
=
(
double
*
)
smalloc
(
n
*
sizeof
(
double
),
"cubic_spline:a"
,
comm
);
b
=
(
double
*
)
smalloc
(
n
*
sizeof
(
double
),
"cubic_spline:a"
,
comm
);
c
=
(
double
*
)
smalloc
(
n
*
sizeof
(
double
),
"cubic_spline:a"
,
comm
);
d
=
(
double
*
)
smalloc
(
n
*
sizeof
(
double
),
"cubic_spline:a"
,
comm
);
v
=
(
double
*
)
smalloc
(
n
*
sizeof
(
double
),
"cubic_spline:a"
,
comm
);
/* build the linear system */
a
[
0
]
=
a
[
1
]
=
a
[
n
-
1
]
=
0
;
for
(
i
=
2
;
i
<
n
-
1
;
++
i
)
a
[
i
]
=
h
[
i
-
1
];
b
[
0
]
=
b
[
n
-
1
]
=
0
;
for
(
i
=
1
;
i
<
n
-
1
;
++
i
)
b
[
i
]
=
2
*
(
h
[
i
-
1
]
+
h
[
i
]);
c
[
0
]
=
c
[
n
-
2
]
=
c
[
n
-
1
]
=
0
;
for
(
i
=
1
;
i
<
n
-
2
;
++
i
)
c
[
i
]
=
h
[
i
];
d
[
0
]
=
d
[
n
-
1
]
=
0
;
for
(
i
=
1
;
i
<
n
-
1
;
++
i
)
d
[
i
]
=
6
*
((
f
[
i
+
1
]
-
f
[
i
])
/
h
[
i
]
-
(
f
[
i
]
-
f
[
i
-
1
])
/
h
[
i
-
1
]);
v
[
0
]
=
0
;
v
[
n
-
1
]
=
0
;
Tridiagonal_Solve
(
&
(
a
[
1
]),
&
(
b
[
1
]),
&
(
c
[
1
]),
&
(
d
[
1
]),
&
(
v
[
1
]),
n
-
2
);
for
(
i
=
1
;
i
<
n
;
++
i
){
coef
[
i
-
1
].
d
=
(
v
[
i
]
-
v
[
i
-
1
])
/
(
6
*
h
[
i
-
1
]);
coef
[
i
-
1
].
c
=
v
[
i
]
/
2
;
coef
[
i
-
1
].
b
=
(
f
[
i
]
-
f
[
i
-
1
])
/
h
[
i
-
1
]
+
h
[
i
-
1
]
*
(
2
*
v
[
i
]
+
v
[
i
-
1
])
/
6
;
coef
[
i
-
1
].
a
=
f
[
i
];
}
sfree
(
a
,
"cubic_spline:a"
);
sfree
(
b
,
"cubic_spline:b"
);
sfree
(
c
,
"cubic_spline:c"
);
sfree
(
d
,
"cubic_spline:d"
);
sfree
(
v
,
"cubic_spline:v"
);
}
void
Complete_Cubic_Spline
(
const
double
*
h
,
const
double
*
f
,
double
v0
,
double
vlast
,
cubic_spline_coef
*
coef
,
unsigned
int
n
,
MPI_Comm
comm
)
{
int
i
;
double
*
a
,
*
b
,
*
c
,
*
d
,
*
v
;
/* allocate space for the linear system */
a
=
(
double
*
)
smalloc
(
n
*
sizeof
(
double
),
"cubic_spline:a"
,
comm
);
b
=
(
double
*
)
smalloc
(
n
*
sizeof
(
double
),
"cubic_spline:a"
,
comm
);
c
=
(
double
*
)
smalloc
(
n
*
sizeof
(
double
),
"cubic_spline:a"
,
comm
);
d
=
(
double
*
)
smalloc
(
n
*
sizeof
(
double
),
"cubic_spline:a"
,
comm
);
v
=
(
double
*
)
smalloc
(
n
*
sizeof
(
double
),
"cubic_spline:a"
,
comm
);
/* build the linear system */
a
[
0
]
=
0
;
for
(
i
=
1
;
i
<
n
;
++
i
)
a
[
i
]
=
h
[
i
-
1
];
b
[
0
]
=
2
*
h
[
0
];
for
(
i
=
1
;
i
<
n
;
++
i
)
b
[
i
]
=
2
*
(
h
[
i
-
1
]
+
h
[
i
]);
c
[
n
-
1
]
=
0
;
for
(
i
=
0
;
i
<
n
-
1
;
++
i
)
c
[
i
]
=
h
[
i
];
d
[
0
]
=
6
*
(
f
[
1
]
-
f
[
0
])
/
h
[
0
]
-
6
*
v0
;
d
[
n
-
1
]
=
6
*
vlast
-
6
*
(
f
[
n
-
1
]
-
f
[
n
-
2
]
/
h
[
n
-
2
]);
for
(
i
=
1
;
i
<
n
-
1
;
++
i
)
d
[
i
]
=
6
*
((
f
[
i
+
1
]
-
f
[
i
])
/
h
[
i
]
-
(
f
[
i
]
-
f
[
i
-
1
])
/
h
[
i
-
1
]);
Tridiagonal_Solve
(
&
(
a
[
0
]),
&
(
b
[
0
]),
&
(
c
[
0
]),
&
(
d
[
0
]),
&
(
v
[
0
]),
n
);
for
(
i
=
1
;
i
<
n
;
++
i
){
coef
[
i
-
1
].
d
=
(
v
[
i
]
-
v
[
i
-
1
])
/
(
6
*
h
[
i
-
1
]);
coef
[
i
-
1
].
c
=
v
[
i
]
/
2
;
coef
[
i
-
1
].
b
=
(
f
[
i
]
-
f
[
i
-
1
])
/
h
[
i
-
1
]
+
h
[
i
-
1
]
*
(
2
*
v
[
i
]
+
v
[
i
-
1
])
/
6
;
coef
[
i
-
1
].
a
=
f
[
i
];
}
sfree
(
a
,
"cubic_spline:a"
);
sfree
(
b
,
"cubic_spline:b"
);
sfree
(
c
,
"cubic_spline:c"
);
sfree
(
d
,
"cubic_spline:d"
);
sfree
(
v
,
"cubic_spline:v"
);
}
void
LR_Lookup
(
LR_lookup_table
*
t
,
double
r
,
LR_data
*
y
)
{
int
i
;
double
base
,
dif
;
i
=
(
int
)(
r
*
t
->
inv_dx
);
if
(
i
==
0
)
++
i
;
base
=
(
double
)(
i
+
1
)
*
t
->
dx
;
dif
=
r
-
base
;
y
->
e_vdW
=
((
t
->
vdW
[
i
].
d
*
dif
+
t
->
vdW
[
i
].
c
)
*
dif
+
t
->
vdW
[
i
].
b
)
*
dif
+
t
->
vdW
[
i
].
a
;
y
->
CEvd
=
((
t
->
CEvd
[
i
].
d
*
dif
+
t
->
CEvd
[
i
].
c
)
*
dif
+
t
->
CEvd
[
i
].
b
)
*
dif
+
t
->
CEvd
[
i
].
a
;
y
->
e_ele
=
((
t
->
ele
[
i
].
d
*
dif
+
t
->
ele
[
i
].
c
)
*
dif
+
t
->
ele
[
i
].
b
)
*
dif
+
t
->
ele
[
i
].
a
;
y
->
CEclmb
=
((
t
->
CEclmb
[
i
].
d
*
dif
+
t
->
CEclmb
[
i
].
c
)
*
dif
+
t
->
CEclmb
[
i
].
b
)
*
dif
+
t
->
CEclmb
[
i
].
a
;
y
->
H
=
y
->
e_ele
*
EV_to_KCALpMOL
/
C_ele
;
}
int
Init_Lookup_Tables
(
reax_system
*
system
,
control_params
*
control
,
storage
*
workspace
,
mpi_datatypes
*
mpi_data
,
char
*
msg
)
{
int
i
,
j
,
r
;
int
num_atom_types
;
int
existing_types
[
MAX_ATOM_TYPES
],
aggregated
[
MAX_ATOM_TYPES
];
double
dr
;
double
*
h
,
*
fh
,
*
fvdw
,
*
fele
,
*
fCEvd
,
*
fCEclmb
;
double
v0_vdw
,
v0_ele
,
vlast_vdw
,
vlast_ele
;
MPI_Comm
comm
;
/* initializations */
v0_vdw
=
0
;
v0_ele
=
0
;
vlast_vdw
=
0
;
vlast_ele
=
0
;
comm
=
mpi_data
->
world
;
num_atom_types
=
system
->
reax_param
.
num_atom_types
;
dr
=
control
->
nonb_cut
/
control
->
tabulate
;
h
=
(
double
*
)
smalloc
(
(
control
->
tabulate
+
2
)
*
sizeof
(
double
),
"lookup:h"
,
comm
);
fh
=
(
double
*
)
smalloc
(
(
control
->
tabulate
+
2
)
*
sizeof
(
double
),
"lookup:fh"
,
comm
);
fvdw
=
(
double
*
)
smalloc
(
(
control
->
tabulate
+
2
)
*
sizeof
(
double
),
"lookup:fvdw"
,
comm
);
fCEvd
=
(
double
*
)
smalloc
(
(
control
->
tabulate
+
2
)
*
sizeof
(
double
),
"lookup:fCEvd"
,
comm
);
fele
=
(
double
*
)
smalloc
(
(
control
->
tabulate
+
2
)
*
sizeof
(
double
),
"lookup:fele"
,
comm
);
fCEclmb
=
(
double
*
)
smalloc
(
(
control
->
tabulate
+
2
)
*
sizeof
(
double
),
"lookup:fCEclmb"
,
comm
);
LR
=
(
LR_lookup_table
**
)
scalloc
(
num_atom_types
,
sizeof
(
LR_lookup_table
*
),
"lookup:LR"
,
comm
);
for
(
i
=
0
;
i
<
num_atom_types
;
++
i
)
LR
[
i
]
=
(
LR_lookup_table
*
)
scalloc
(
num_atom_types
,
sizeof
(
LR_lookup_table
),
"lookup:LR[i]"
,
comm
);
for
(
i
=
0
;
i
<
MAX_ATOM_TYPES
;
++
i
)
existing_types
[
i
]
=
0
;
for
(
i
=
0
;
i
<
system
->
n
;
++
i
)
existing_types
[
system
->
my_atoms
[
i
].
type
]
=
1
;
MPI_Allreduce
(
existing_types
,
aggregated
,
MAX_ATOM_TYPES
,
MPI_INT
,
MPI_SUM
,
mpi_data
->
world
);
for
(
i
=
0
;
i
<
num_atom_types
;
++
i
)
{
if
(
aggregated
[
i
]
)
{
for
(
j
=
i
;
j
<
num_atom_types
;
++
j
)
{
if
(
aggregated
[
j
]
)
{
LR
[
i
][
j
].
xmin
=
0
;
LR
[
i
][
j
].
xmax
=
control
->
nonb_cut
;
LR
[
i
][
j
].
n
=
control
->
tabulate
+
2
;
LR
[
i
][
j
].
dx
=
dr
;
LR
[
i
][
j
].
inv_dx
=
control
->
tabulate
/
control
->
nonb_cut
;
LR
[
i
][
j
].
y
=
(
LR_data
*
)
smalloc
(
LR
[
i
][
j
].
n
*
sizeof
(
LR_data
),
"lookup:LR[i,j].y"
,
comm
);
LR
[
i
][
j
].
H
=
(
cubic_spline_coef
*
)
smalloc
(
LR
[
i
][
j
].
n
*
sizeof
(
cubic_spline_coef
),
"lookup:LR[i,j].H"
,
comm
);
LR
[
i
][
j
].
vdW
=
(
cubic_spline_coef
*
)
smalloc
(
LR
[
i
][
j
].
n
*
sizeof
(
cubic_spline_coef
),
"lookup:LR[i,j].vdW"
,
comm
);
LR
[
i
][
j
].
CEvd
=
(
cubic_spline_coef
*
)
smalloc
(
LR
[
i
][
j
].
n
*
sizeof
(
cubic_spline_coef
),
"lookup:LR[i,j].CEvd"
,
comm
);
LR
[
i
][
j
].
ele
=
(
cubic_spline_coef
*
)
smalloc
(
LR
[
i
][
j
].
n
*
sizeof
(
cubic_spline_coef
),
"lookup:LR[i,j].ele"
,
comm
);
LR
[
i
][
j
].
CEclmb
=
(
cubic_spline_coef
*
)
smalloc
(
LR
[
i
][
j
].
n
*
sizeof
(
cubic_spline_coef
),
"lookup:LR[i,j].CEclmb"
,
comm
);
for
(
r
=
1
;
r
<=
control
->
tabulate
;
++
r
)
{
LR_vdW_Coulomb
(
system
,
workspace
,
control
,
i
,
j
,
r
*
dr
,
&
(
LR
[
i
][
j
].
y
[
r
])
);
h
[
r
]
=
LR
[
i
][
j
].
dx
;
fh
[
r
]
=
LR
[
i
][
j
].
y
[
r
].
H
;
fvdw
[
r
]
=
LR
[
i
][
j
].
y
[
r
].
e_vdW
;
fCEvd
[
r
]
=
LR
[
i
][
j
].
y
[
r
].
CEvd
;
fele
[
r
]
=
LR
[
i
][
j
].
y
[
r
].
e_ele
;
fCEclmb
[
r
]
=
LR
[
i
][
j
].
y
[
r
].
CEclmb
;
}
// init the start-end points
h
[
r
]
=
LR
[
i
][
j
].
dx
;
v0_vdw
=
LR
[
i
][
j
].
y
[
1
].
CEvd
;
v0_ele
=
LR
[
i
][
j
].
y
[
1
].
CEclmb
;
fh
[
r
]
=
fh
[
r
-
1
];
fvdw
[
r
]
=
fvdw
[
r
-
1
];
fCEvd
[
r
]
=
fCEvd
[
r
-
1
];
fele
[
r
]
=
fele
[
r
-
1
];
fCEclmb
[
r
]
=
fCEclmb
[
r
-
1
];
vlast_vdw
=
fCEvd
[
r
-
1
];
vlast_ele
=
fele
[
r
-
1
];
Natural_Cubic_Spline
(
&
h
[
1
],
&
fh
[
1
],
&
(
LR
[
i
][
j
].
H
[
1
]),
control
->
tabulate
+
1
,
comm
);
Complete_Cubic_Spline
(
&
h
[
1
],
&
fvdw
[
1
],
v0_vdw
,
vlast_vdw
,
&
(
LR
[
i
][
j
].
vdW
[
1
]),
control
->
tabulate
+
1
,
comm
);
Natural_Cubic_Spline
(
&
h
[
1
],
&
fCEvd
[
1
],
&
(
LR
[
i
][
j
].
CEvd
[
1
]),
control
->
tabulate
+
1
,
comm
);
Complete_Cubic_Spline
(
&
h
[
1
],
&
fele
[
1
],
v0_ele
,
vlast_ele
,
&
(
LR
[
i
][
j
].
ele
[
1
]),
control
->
tabulate
+
1
,
comm
);
Natural_Cubic_Spline
(
&
h
[
1
],
&
fCEclmb
[
1
],
&
(
LR
[
i
][
j
].
CEclmb
[
1
]),
control
->
tabulate
+
1
,
comm
);
}
else
{
LR
[
i
][
j
].
n
=
0
;
}
}
}
}
free
(
h
);
free
(
fh
);
free
(
fvdw
);
free
(
fCEvd
);
free
(
fele
);
free
(
fCEclmb
);
return
1
;
}
void
Deallocate_Lookup_Tables
(
reax_system
*
system
)
{
int
i
,
j
;
int
ntypes
;
ntypes
=
system
->
reax_param
.
num_atom_types
;
for
(
i
=
0
;
i
<
ntypes
;
++
i
)
{
for
(
j
=
i
;
j
<
ntypes
;
++
j
)
if
(
LR
[
i
][
j
].
n
)
{
sfree
(
LR
[
i
][
j
].
y
,
"LR[i,j].y"
);
sfree
(
LR
[
i
][
j
].
H
,
"LR[i,j].H"
);
sfree
(
LR
[
i
][
j
].
vdW
,
"LR[i,j].vdW"
);
sfree
(
LR
[
i
][
j
].
CEvd
,
"LR[i,j].CEvd"
);
sfree
(
LR
[
i
][
j
].
ele
,
"LR[i,j].ele"
);
sfree
(
LR
[
i
][
j
].
CEclmb
,
"LR[i,j].CEclmb"
);
}
sfree
(
LR
[
i
],
"LR[i]"
);
}
sfree
(
LR
,
"LR"
);
}
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