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rLAMMPS lammps
pair_airebo.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ase Henry (MIT)
Bugfixes and optimizations:
Marcel Fallet & Steve Stuart (Clemson), Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <mpi.h>
#include "pair_airebo.h"
#include "atom.h"
#include "neighbor.h"
#include "force.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "my_page.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
using
namespace
MathSpecial
;
#define MAXLINE 1024
#define TOL 1.0e-9
#define PGDELTA 1
/* ---------------------------------------------------------------------- */
PairAIREBO
::
PairAIREBO
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
single_enable
=
0
;
one_coeff
=
1
;
ghostneigh
=
1
;
maxlocal
=
0
;
REBO_numneigh
=
NULL
;
REBO_firstneigh
=
NULL
;
ipage
=
NULL
;
pgsize
=
oneatom
=
0
;
nC
=
nH
=
NULL
;
map
=
NULL
;
manybody_flag
=
1
;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairAIREBO
::~
PairAIREBO
()
{
memory
->
destroy
(
REBO_numneigh
);
memory
->
sfree
(
REBO_firstneigh
);
delete
[]
ipage
;
memory
->
destroy
(
nC
);
memory
->
destroy
(
nH
);
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cutghost
);
memory
->
destroy
(
cutljsq
);
memory
->
destroy
(
lj1
);
memory
->
destroy
(
lj2
);
memory
->
destroy
(
lj3
);
memory
->
destroy
(
lj4
);
delete
[]
map
;
}
}
/* ---------------------------------------------------------------------- */
void
PairAIREBO
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
vflag_atom
=
0
;
REBO_neigh
();
FREBO
(
eflag
,
vflag
);
if
(
ljflag
)
FLJ
(
eflag
,
vflag
);
if
(
torflag
)
TORSION
(
eflag
,
vflag
);
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairAIREBO
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
memory
->
create
(
setflag
,
n
+
1
,
n
+
1
,
"pair:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
memory
->
create
(
cutsq
,
n
+
1
,
n
+
1
,
"pair:cutsq"
);
memory
->
create
(
cutghost
,
n
+
1
,
n
+
1
,
"pair:cutghost"
);
// only sized by C,H = 2 types
memory
->
create
(
cutljsq
,
2
,
2
,
"pair:cutljsq"
);
memory
->
create
(
lj1
,
2
,
2
,
"pair:lj1"
);
memory
->
create
(
lj2
,
2
,
2
,
"pair:lj2"
);
memory
->
create
(
lj3
,
2
,
2
,
"pair:lj3"
);
memory
->
create
(
lj4
,
2
,
2
,
"pair:lj4"
);
map
=
new
int
[
n
+
1
];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairAIREBO
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
1
&&
narg
!=
3
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
cutlj
=
force
->
numeric
(
FLERR
,
arg
[
0
]);
ljflag
=
torflag
=
1
;
if
(
narg
==
3
)
{
ljflag
=
force
->
inumeric
(
FLERR
,
arg
[
1
]);
torflag
=
force
->
inumeric
(
FLERR
,
arg
[
2
]);
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairAIREBO
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
!
allocated
)
allocate
();
if
(
narg
!=
3
+
atom
->
ntypes
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
// insure I,J args are * *
if
(
strcmp
(
arg
[
0
],
"*"
)
!=
0
||
strcmp
(
arg
[
1
],
"*"
)
!=
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
// read args that map atom types to C and H
// map[i] = which element (0,1) the Ith atom type is, -1 if NULL
for
(
int
i
=
3
;
i
<
narg
;
i
++
)
{
if
(
strcmp
(
arg
[
i
],
"NULL"
)
==
0
)
{
map
[
i
-
2
]
=
-
1
;
continue
;
}
else
if
(
strcmp
(
arg
[
i
],
"C"
)
==
0
)
{
map
[
i
-
2
]
=
0
;
}
else
if
(
strcmp
(
arg
[
i
],
"H"
)
==
0
)
{
map
[
i
-
2
]
=
1
;
}
else
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
// read potential file and initialize fitting splines
read_file
(
arg
[
2
]);
spline_init
();
// clear setflag since coeff() called once with I,J = * *
int
n
=
atom
->
ntypes
;
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
// set setflag i,j for type pairs where both are mapped to elements
int
count
=
0
;
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
if
(
map
[
i
]
>=
0
&&
map
[
j
]
>=
0
)
{
setflag
[
i
][
j
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairAIREBO
::
init_style
()
{
if
(
atom
->
tag_enable
==
0
)
error
->
all
(
FLERR
,
"Pair style AIREBO requires atom IDs"
);
if
(
force
->
newton_pair
==
0
)
error
->
all
(
FLERR
,
"Pair style AIREBO requires newton pair on"
);
// need a full neighbor list, including neighbors of ghosts
int
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full
=
1
;
neighbor
->
requests
[
irequest
]
->
ghost
=
1
;
// local REBO neighbor list
// create pages if first time or if neighbor pgsize/oneatom has changed
int
create
=
0
;
if
(
ipage
==
NULL
)
create
=
1
;
if
(
pgsize
!=
neighbor
->
pgsize
)
create
=
1
;
if
(
oneatom
!=
neighbor
->
oneatom
)
create
=
1
;
if
(
create
)
{
delete
[]
ipage
;
pgsize
=
neighbor
->
pgsize
;
oneatom
=
neighbor
->
oneatom
;
int
nmypage
=
comm
->
nthreads
;
ipage
=
new
MyPage
<
int
>
[
nmypage
];
for
(
int
i
=
0
;
i
<
nmypage
;
i
++
)
ipage
[
i
].
init
(
oneatom
,
pgsize
,
PGDELTA
);
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairAIREBO
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
error
->
all
(
FLERR
,
"All pair coeffs are not set"
);
// convert to C,H types
int
ii
=
map
[
i
];
int
jj
=
map
[
j
];
// use C-C values for these cutoffs since C atoms are biggest
// cut3rebo = 3 REBO distances
cut3rebo
=
3.0
*
rcmax
[
0
][
0
];
// cutljrebosq = furthest distance from an owned atom a ghost atom can be
// to need its REBO neighs computed
// interaction = M-K-I-J-L-N with I = owned and J = ghost
// this insures N is in the REBO neigh list of L
// since I-J < rcLJmax and J-L < rmax
double
cutljrebo
=
rcLJmax
[
0
][
0
]
+
rcmax
[
0
][
0
];
cutljrebosq
=
cutljrebo
*
cutljrebo
;
// cutmax = furthest distance from an owned atom
// at which another atom will feel force, i.e. the ghost cutoff
// for REBO term in potential:
// interaction = M-K-I-J-L-N with I = owned and J = ghost
// I to N is max distance = 3 REBO distances
// for LJ term in potential:
// short interaction = M-K-I-J-L-N with I = owned, J = ghost, I-J < rcLJmax
// rcLJmax + 2*rcmax, since I-J < rcLJmax and J-L,L-N = REBO distances
// long interaction = I-J with I = owned and J = ghost
// cutlj*sigma, since I-J < LJ cutoff
// cutghost = REBO cutoff used in REBO_neigh() for neighbors of ghosts
double
cutmax
=
cut3rebo
;
if
(
ljflag
)
{
cutmax
=
MAX
(
cutmax
,
rcLJmax
[
0
][
0
]
+
2.0
*
rcmax
[
0
][
0
]);
cutmax
=
MAX
(
cutmax
,
cutlj
*
sigma
[
0
][
0
]);
}
cutghost
[
i
][
j
]
=
rcmax
[
ii
][
jj
];
cutljsq
[
ii
][
jj
]
=
cutlj
*
sigma
[
ii
][
jj
]
*
cutlj
*
sigma
[
ii
][
jj
];
lj1
[
ii
][
jj
]
=
48.0
*
epsilon
[
ii
][
jj
]
*
pow
(
sigma
[
ii
][
jj
],
12.0
);
lj2
[
ii
][
jj
]
=
24.0
*
epsilon
[
ii
][
jj
]
*
pow
(
sigma
[
ii
][
jj
],
6.0
);
lj3
[
ii
][
jj
]
=
4.0
*
epsilon
[
ii
][
jj
]
*
pow
(
sigma
[
ii
][
jj
],
12.0
);
lj4
[
ii
][
jj
]
=
4.0
*
epsilon
[
ii
][
jj
]
*
pow
(
sigma
[
ii
][
jj
],
6.0
);
cutghost
[
j
][
i
]
=
cutghost
[
i
][
j
];
cutljsq
[
jj
][
ii
]
=
cutljsq
[
ii
][
jj
];
lj1
[
jj
][
ii
]
=
lj1
[
ii
][
jj
];
lj2
[
jj
][
ii
]
=
lj2
[
ii
][
jj
];
lj3
[
jj
][
ii
]
=
lj3
[
ii
][
jj
];
lj4
[
jj
][
ii
]
=
lj4
[
ii
][
jj
];
return
cutmax
;
}
/* ----------------------------------------------------------------------
create REBO neighbor list from main neighbor list
REBO neighbor list stores neighbors of ghost atoms
------------------------------------------------------------------------- */
void
PairAIREBO
::
REBO_neigh
()
{
int
i
,
j
,
ii
,
jj
,
n
,
allnum
,
jnum
,
itype
,
jtype
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
rsq
,
dS
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
int
*
neighptr
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
if
(
atom
->
nmax
>
maxlocal
)
{
maxlocal
=
atom
->
nmax
;
memory
->
destroy
(
REBO_numneigh
);
memory
->
sfree
(
REBO_firstneigh
);
memory
->
destroy
(
nC
);
memory
->
destroy
(
nH
);
memory
->
create
(
REBO_numneigh
,
maxlocal
,
"AIREBO:numneigh"
);
REBO_firstneigh
=
(
int
**
)
memory
->
smalloc
(
maxlocal
*
sizeof
(
int
*
),
"AIREBO:firstneigh"
);
memory
->
create
(
nC
,
maxlocal
,
"AIREBO:nC"
);
memory
->
create
(
nH
,
maxlocal
,
"AIREBO:nH"
);
}
allnum
=
list
->
inum
+
list
->
gnum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// store all REBO neighs of owned and ghost atoms
// scan full neighbor list of I
ipage
->
reset
();
for
(
ii
=
0
;
ii
<
allnum
;
ii
++
)
{
i
=
ilist
[
ii
];
n
=
0
;
neighptr
=
ipage
->
vget
();
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
itype
=
map
[
type
[
i
]];
nC
[
i
]
=
nH
[
i
]
=
0.0
;
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
jtype
=
map
[
type
[
j
]];
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
if
(
rsq
<
rcmaxsq
[
itype
][
jtype
])
{
neighptr
[
n
++
]
=
j
;
if
(
jtype
==
0
)
nC
[
i
]
+=
Sp
(
sqrt
(
rsq
),
rcmin
[
itype
][
jtype
],
rcmax
[
itype
][
jtype
],
dS
);
else
nH
[
i
]
+=
Sp
(
sqrt
(
rsq
),
rcmin
[
itype
][
jtype
],
rcmax
[
itype
][
jtype
],
dS
);
}
}
REBO_firstneigh
[
i
]
=
neighptr
;
REBO_numneigh
[
i
]
=
n
;
ipage
->
vgot
(
n
);
if
(
ipage
->
status
())
error
->
one
(
FLERR
,
"Neighbor list overflow, boost neigh_modify one"
);
}
}
/* ----------------------------------------------------------------------
REBO forces and energy
------------------------------------------------------------------------- */
void
PairAIREBO
::
FREBO
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
k
,
m
,
ii
,
inum
,
itype
,
jtype
;
tagint
itag
,
jtag
;
double
delx
,
dely
,
delz
,
evdwl
,
fpair
,
xtmp
,
ytmp
,
ztmp
;
double
rsq
,
rij
,
wij
;
double
Qij
,
Aij
,
alphaij
,
VR
,
pre
,
dVRdi
,
VA
,
term
,
bij
,
dVAdi
,
dVA
;
double
dwij
,
del
[
3
];
int
*
ilist
,
*
REBO_neighs
;
evdwl
=
0.0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
*
type
=
atom
->
type
;
tagint
*
tag
=
atom
->
tag
;
int
nlocal
=
atom
->
nlocal
;
int
newton_pair
=
force
->
newton_pair
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
// two-body interactions from REBO neighbor list, skip half of them
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
itag
=
tag
[
i
];
itype
=
map
[
type
[
i
]];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
REBO_neighs
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
j
=
REBO_neighs
[
k
];
jtag
=
tag
[
j
];
if
(
itag
>
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
0
)
continue
;
}
else
if
(
itag
<
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
1
)
continue
;
}
else
{
if
(
x
[
j
][
2
]
<
ztmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
<
ytmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
==
ytmp
&&
x
[
j
][
0
]
<
xtmp
)
continue
;
}
jtype
=
map
[
type
[
j
]];
delx
=
x
[
i
][
0
]
-
x
[
j
][
0
];
dely
=
x
[
i
][
1
]
-
x
[
j
][
1
];
delz
=
x
[
i
][
2
]
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
rij
=
sqrt
(
rsq
);
wij
=
Sp
(
rij
,
rcmin
[
itype
][
jtype
],
rcmax
[
itype
][
jtype
],
dwij
);
if
(
wij
<=
TOL
)
continue
;
Qij
=
Q
[
itype
][
jtype
];
Aij
=
A
[
itype
][
jtype
];
alphaij
=
alpha
[
itype
][
jtype
];
VR
=
wij
*
(
1.0
+
(
Qij
/
rij
))
*
Aij
*
exp
(
-
alphaij
*
rij
);
pre
=
wij
*
Aij
*
exp
(
-
alphaij
*
rij
);
dVRdi
=
pre
*
((
-
alphaij
)
-
(
Qij
/
rsq
)
-
(
Qij
*
alphaij
/
rij
));
dVRdi
+=
VR
/
wij
*
dwij
;
VA
=
dVA
=
0.0
;
for
(
m
=
0
;
m
<
3
;
m
++
)
{
term
=
-
wij
*
BIJc
[
itype
][
jtype
][
m
]
*
exp
(
-
Beta
[
itype
][
jtype
][
m
]
*
rij
);
VA
+=
term
;
dVA
+=
-
Beta
[
itype
][
jtype
][
m
]
*
term
;
}
dVA
+=
VA
/
wij
*
dwij
;
del
[
0
]
=
delx
;
del
[
1
]
=
dely
;
del
[
2
]
=
delz
;
bij
=
bondorder
(
i
,
j
,
del
,
rij
,
VA
,
f
,
vflag_atom
);
dVAdi
=
bij
*
dVA
;
fpair
=
-
(
dVRdi
+
dVAdi
)
/
rij
;
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
f
[
j
][
0
]
-=
delx
*
fpair
;
f
[
j
][
1
]
-=
dely
*
fpair
;
f
[
j
][
2
]
-=
delz
*
fpair
;
if
(
eflag
)
evdwl
=
VR
+
bij
*
VA
;
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
/* ----------------------------------------------------------------------
compute LJ forces and energy
find 3- and 4-step paths between atoms I,J via REBO neighbor lists
------------------------------------------------------------------------- */
void
PairAIREBO
::
FLJ
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
k
,
m
,
ii
,
jj
,
kk
,
mm
,
inum
,
jnum
,
itype
,
jtype
,
ktype
,
mtype
;
int
atomi
,
atomj
,
atomk
,
atomm
;
int
testpath
,
npath
,
done
;
tagint
itag
,
jtag
;
double
evdwl
,
fpair
,
xtmp
,
ytmp
,
ztmp
;
double
rsq
,
best
,
wik
,
wkm
,
cij
,
rij
,
dwij
,
dwik
,
dwkj
,
dwkm
,
dwmj
;
double
delij
[
3
],
rijsq
,
delik
[
3
],
rik
,
deljk
[
3
];
double
rkj
,
wkj
,
dC
,
VLJ
,
dVLJ
,
VA
,
Str
,
dStr
,
Stb
;
double
vdw
,
slw
,
dvdw
,
dslw
,
drij
,
swidth
,
tee
,
tee2
;
double
rljmin
,
rljmax
,
sigcut
,
sigmin
,
sigwid
;
double
delkm
[
3
],
rkm
,
deljm
[
3
],
rmj
,
wmj
,
r2inv
,
r6inv
,
scale
,
delscale
[
3
];
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
int
*
REBO_neighs_i
,
*
REBO_neighs_k
;
double
delikS
[
3
],
deljkS
[
3
],
delkmS
[
3
],
deljmS
[
3
],
delimS
[
3
];
double
rikS
,
rkjS
,
rkmS
,
rmjS
,
wikS
,
dwikS
;
double
wkjS
,
dwkjS
,
wkmS
,
dwkmS
,
wmjS
,
dwmjS
;
double
fpair1
,
fpair2
,
fpair3
;
double
fi
[
3
],
fj
[
3
],
fk
[
3
],
fm
[
3
];
// I-J interaction from full neighbor list
// skip 1/2 of interactions since only consider each pair once
evdwl
=
0.0
;
rljmin
=
0.0
;
rljmax
=
0.0
;
sigcut
=
0.0
;
sigmin
=
0.0
;
sigwid
=
0.0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
tagint
*
tag
=
atom
->
tag
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
int
newton_pair
=
force
->
newton_pair
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// loop over neighbors of my atoms
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
itag
=
tag
[
i
];
itype
=
map
[
type
[
i
]];
atomi
=
i
;
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
jtag
=
tag
[
j
];
if
(
itag
>
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
0
)
continue
;
}
else
if
(
itag
<
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
1
)
continue
;
}
else
{
if
(
x
[
j
][
2
]
<
ztmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
<
ytmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
==
ytmp
&&
x
[
j
][
0
]
<
xtmp
)
continue
;
}
jtype
=
map
[
type
[
j
]];
atomj
=
j
;
delij
[
0
]
=
xtmp
-
x
[
j
][
0
];
delij
[
1
]
=
ytmp
-
x
[
j
][
1
];
delij
[
2
]
=
ztmp
-
x
[
j
][
2
];
rijsq
=
delij
[
0
]
*
delij
[
0
]
+
delij
[
1
]
*
delij
[
1
]
+
delij
[
2
]
*
delij
[
2
];
// if outside of LJ cutoff, skip
// if outside of 4-path cutoff, best = 0.0, no need to test paths
// if outside of 2-path cutoff but inside 4-path cutoff,
// best = 0.0, test 3-,4-paths
// if inside 2-path cutoff, best = wij, only test 3-,4-paths if best < 1
if
(
rijsq
>=
cutljsq
[
itype
][
jtype
])
continue
;
rij
=
sqrt
(
rijsq
);
if
(
rij
>=
cut3rebo
)
{
best
=
0.0
;
testpath
=
0
;
}
else
if
(
rij
>=
rcmax
[
itype
][
jtype
])
{
best
=
0.0
;
testpath
=
1
;
}
else
{
best
=
Sp
(
rij
,
rcmin
[
itype
][
jtype
],
rcmax
[
itype
][
jtype
],
dwij
);
npath
=
2
;
if
(
best
<
1.0
)
testpath
=
1
;
else
testpath
=
0
;
}
done
=
0
;
if
(
testpath
)
{
// test all 3-body paths = I-K-J
// I-K interactions come from atom I's REBO neighbors
// if wik > current best, compute wkj
// if best = 1.0, done
REBO_neighs_i
=
REBO_firstneigh
[
i
];
for
(
kk
=
0
;
kk
<
REBO_numneigh
[
i
]
&&
done
==
0
;
kk
++
)
{
k
=
REBO_neighs_i
[
kk
];
if
(
k
==
j
)
continue
;
ktype
=
map
[
type
[
k
]];
delik
[
0
]
=
x
[
i
][
0
]
-
x
[
k
][
0
];
delik
[
1
]
=
x
[
i
][
1
]
-
x
[
k
][
1
];
delik
[
2
]
=
x
[
i
][
2
]
-
x
[
k
][
2
];
rsq
=
delik
[
0
]
*
delik
[
0
]
+
delik
[
1
]
*
delik
[
1
]
+
delik
[
2
]
*
delik
[
2
];
if
(
rsq
<
rcmaxsq
[
itype
][
ktype
])
{
rik
=
sqrt
(
rsq
);
wik
=
Sp
(
rik
,
rcmin
[
itype
][
ktype
],
rcmax
[
itype
][
ktype
],
dwik
);
}
else
wik
=
0.0
;
if
(
wik
>
best
)
{
deljk
[
0
]
=
x
[
j
][
0
]
-
x
[
k
][
0
];
deljk
[
1
]
=
x
[
j
][
1
]
-
x
[
k
][
1
];
deljk
[
2
]
=
x
[
j
][
2
]
-
x
[
k
][
2
];
rsq
=
deljk
[
0
]
*
deljk
[
0
]
+
deljk
[
1
]
*
deljk
[
1
]
+
deljk
[
2
]
*
deljk
[
2
];
if
(
rsq
<
rcmaxsq
[
ktype
][
jtype
])
{
rkj
=
sqrt
(
rsq
);
wkj
=
Sp
(
rkj
,
rcmin
[
ktype
][
jtype
],
rcmax
[
ktype
][
jtype
],
dwkj
);
if
(
wik
*
wkj
>
best
)
{
best
=
wik
*
wkj
;
npath
=
3
;
atomk
=
k
;
delikS
[
0
]
=
delik
[
0
];
delikS
[
1
]
=
delik
[
1
];
delikS
[
2
]
=
delik
[
2
];
rikS
=
rik
;
wikS
=
wik
;
dwikS
=
dwik
;
deljkS
[
0
]
=
deljk
[
0
];
deljkS
[
1
]
=
deljk
[
1
];
deljkS
[
2
]
=
deljk
[
2
];
rkjS
=
rkj
;
wkjS
=
wkj
;
dwkjS
=
dwkj
;
if
(
best
==
1.0
)
{
done
=
1
;
break
;
}
}
}
// test all 4-body paths = I-K-M-J
// K-M interactions come from atom K's REBO neighbors
// if wik*wkm > current best, compute wmj
// if best = 1.0, done
REBO_neighs_k
=
REBO_firstneigh
[
k
];
for
(
mm
=
0
;
mm
<
REBO_numneigh
[
k
]
&&
done
==
0
;
mm
++
)
{
m
=
REBO_neighs_k
[
mm
];
if
(
m
==
i
||
m
==
j
)
continue
;
mtype
=
map
[
type
[
m
]];
delkm
[
0
]
=
x
[
k
][
0
]
-
x
[
m
][
0
];
delkm
[
1
]
=
x
[
k
][
1
]
-
x
[
m
][
1
];
delkm
[
2
]
=
x
[
k
][
2
]
-
x
[
m
][
2
];
rsq
=
delkm
[
0
]
*
delkm
[
0
]
+
delkm
[
1
]
*
delkm
[
1
]
+
delkm
[
2
]
*
delkm
[
2
];
if
(
rsq
<
rcmaxsq
[
ktype
][
mtype
])
{
rkm
=
sqrt
(
rsq
);
wkm
=
Sp
(
rkm
,
rcmin
[
ktype
][
mtype
],
rcmax
[
ktype
][
mtype
],
dwkm
);
}
else
wkm
=
0.0
;
if
(
wik
*
wkm
>
best
)
{
deljm
[
0
]
=
x
[
j
][
0
]
-
x
[
m
][
0
];
deljm
[
1
]
=
x
[
j
][
1
]
-
x
[
m
][
1
];
deljm
[
2
]
=
x
[
j
][
2
]
-
x
[
m
][
2
];
rsq
=
deljm
[
0
]
*
deljm
[
0
]
+
deljm
[
1
]
*
deljm
[
1
]
+
deljm
[
2
]
*
deljm
[
2
];
if
(
rsq
<
rcmaxsq
[
mtype
][
jtype
])
{
rmj
=
sqrt
(
rsq
);
wmj
=
Sp
(
rmj
,
rcmin
[
mtype
][
jtype
],
rcmax
[
mtype
][
jtype
],
dwmj
);
if
(
wik
*
wkm
*
wmj
>
best
)
{
best
=
wik
*
wkm
*
wmj
;
npath
=
4
;
atomk
=
k
;
delikS
[
0
]
=
delik
[
0
];
delikS
[
1
]
=
delik
[
1
];
delikS
[
2
]
=
delik
[
2
];
rikS
=
rik
;
wikS
=
wik
;
dwikS
=
dwik
;
atomm
=
m
;
delkmS
[
0
]
=
delkm
[
0
];
delkmS
[
1
]
=
delkm
[
1
];
delkmS
[
2
]
=
delkm
[
2
];
rkmS
=
rkm
;
wkmS
=
wkm
;
dwkmS
=
dwkm
;
deljmS
[
0
]
=
deljm
[
0
];
deljmS
[
1
]
=
deljm
[
1
];
deljmS
[
2
]
=
deljm
[
2
];
rmjS
=
rmj
;
wmjS
=
wmj
;
dwmjS
=
dwmj
;
if
(
best
==
1.0
)
{
done
=
1
;
break
;
}
}
}
}
}
}
}
}
cij
=
1.0
-
best
;
if
(
cij
==
0.0
)
continue
;
// compute LJ forces and energy
sigwid
=
0.84
;
sigcut
=
3.0
;
sigmin
=
sigcut
-
sigwid
;
rljmin
=
sigma
[
itype
][
jtype
];
rljmax
=
sigcut
*
rljmin
;
rljmin
=
sigmin
*
rljmin
;
if
(
rij
>
rljmax
)
{
slw
=
0.0
;
dslw
=
0.0
;
}
else
if
(
rij
>
rljmin
)
{
drij
=
rij
-
rljmin
;
swidth
=
rljmax
-
rljmin
;
tee
=
drij
/
swidth
;
tee2
=
tee
*
tee
;
slw
=
1.0
-
tee2
*
(
3.0
-
2.0
*
tee
);
dslw
=
6.0
*
tee
*
(
1.0
-
tee
)
/
rij
/
swidth
;
}
else
{
slw
=
1.0
;
dslw
=
0.0
;
}
r2inv
=
1.0
/
rijsq
;
r6inv
=
r2inv
*
r2inv
*
r2inv
;
vdw
=
r6inv
*
(
lj3
[
itype
][
jtype
]
*
r6inv
-
lj4
[
itype
][
jtype
]);
dvdw
=
-
r6inv
*
(
lj1
[
itype
][
jtype
]
*
r6inv
-
lj2
[
itype
][
jtype
])
/
rij
;
// VLJ now becomes vdw * slw, derivaties, etc.
VLJ
=
vdw
*
slw
;
dVLJ
=
dvdw
*
slw
+
vdw
*
dslw
;
Str
=
Sp2
(
rij
,
rcLJmin
[
itype
][
jtype
],
rcLJmax
[
itype
][
jtype
],
dStr
);
VA
=
Str
*
cij
*
VLJ
;
if
(
Str
>
0.0
)
{
scale
=
rcmin
[
itype
][
jtype
]
/
rij
;
delscale
[
0
]
=
scale
*
delij
[
0
];
delscale
[
1
]
=
scale
*
delij
[
1
];
delscale
[
2
]
=
scale
*
delij
[
2
];
Stb
=
bondorderLJ
(
i
,
j
,
delscale
,
rcmin
[
itype
][
jtype
],
VA
,
delij
,
rij
,
f
,
vflag_atom
);
}
else
Stb
=
0.0
;
fpair
=
-
(
dStr
*
(
Stb
*
cij
*
VLJ
-
cij
*
VLJ
)
+
dVLJ
*
(
Str
*
Stb
*
cij
+
cij
-
Str
*
cij
))
/
rij
;
f
[
i
][
0
]
+=
delij
[
0
]
*
fpair
;
f
[
i
][
1
]
+=
delij
[
1
]
*
fpair
;
f
[
i
][
2
]
+=
delij
[
2
]
*
fpair
;
f
[
j
][
0
]
-=
delij
[
0
]
*
fpair
;
f
[
j
][
1
]
-=
delij
[
1
]
*
fpair
;
f
[
j
][
2
]
-=
delij
[
2
]
*
fpair
;
if
(
eflag
)
evdwl
=
VA
*
Stb
+
(
1.0
-
Str
)
*
cij
*
VLJ
;
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
0.0
,
fpair
,
delij
[
0
],
delij
[
1
],
delij
[
2
]);
if
(
cij
<
1.0
)
{
dC
=
Str
*
Stb
*
VLJ
+
(
1.0
-
Str
)
*
VLJ
;
if
(
npath
==
2
)
{
fpair
=
dC
*
dwij
/
rij
;
f
[
atomi
][
0
]
+=
delij
[
0
]
*
fpair
;
f
[
atomi
][
1
]
+=
delij
[
1
]
*
fpair
;
f
[
atomi
][
2
]
+=
delij
[
2
]
*
fpair
;
f
[
atomj
][
0
]
-=
delij
[
0
]
*
fpair
;
f
[
atomj
][
1
]
-=
delij
[
1
]
*
fpair
;
f
[
atomj
][
2
]
-=
delij
[
2
]
*
fpair
;
if
(
vflag_atom
)
v_tally2
(
atomi
,
atomj
,
fpair
,
delij
);
}
else
if
(
npath
==
3
)
{
fpair1
=
dC
*
dwikS
*
wkjS
/
rikS
;
fi
[
0
]
=
delikS
[
0
]
*
fpair1
;
fi
[
1
]
=
delikS
[
1
]
*
fpair1
;
fi
[
2
]
=
delikS
[
2
]
*
fpair1
;
fpair2
=
dC
*
wikS
*
dwkjS
/
rkjS
;
fj
[
0
]
=
deljkS
[
0
]
*
fpair2
;
fj
[
1
]
=
deljkS
[
1
]
*
fpair2
;
fj
[
2
]
=
deljkS
[
2
]
*
fpair2
;
f
[
atomi
][
0
]
+=
fi
[
0
];
f
[
atomi
][
1
]
+=
fi
[
1
];
f
[
atomi
][
2
]
+=
fi
[
2
];
f
[
atomj
][
0
]
+=
fj
[
0
];
f
[
atomj
][
1
]
+=
fj
[
1
];
f
[
atomj
][
2
]
+=
fj
[
2
];
f
[
atomk
][
0
]
-=
fi
[
0
]
+
fj
[
0
];
f
[
atomk
][
1
]
-=
fi
[
1
]
+
fj
[
1
];
f
[
atomk
][
2
]
-=
fi
[
2
]
+
fj
[
2
];
if
(
vflag_atom
)
v_tally3
(
atomi
,
atomj
,
atomk
,
fi
,
fj
,
delikS
,
deljkS
);
}
else
if
(
npath
==
4
)
{
fpair1
=
dC
*
dwikS
*
wkmS
*
wmjS
/
rikS
;
fi
[
0
]
=
delikS
[
0
]
*
fpair1
;
fi
[
1
]
=
delikS
[
1
]
*
fpair1
;
fi
[
2
]
=
delikS
[
2
]
*
fpair1
;
fpair2
=
dC
*
wikS
*
dwkmS
*
wmjS
/
rkmS
;
fk
[
0
]
=
delkmS
[
0
]
*
fpair2
-
fi
[
0
];
fk
[
1
]
=
delkmS
[
1
]
*
fpair2
-
fi
[
1
];
fk
[
2
]
=
delkmS
[
2
]
*
fpair2
-
fi
[
2
];
fpair3
=
dC
*
wikS
*
wkmS
*
dwmjS
/
rmjS
;
fj
[
0
]
=
deljmS
[
0
]
*
fpair3
;
fj
[
1
]
=
deljmS
[
1
]
*
fpair3
;
fj
[
2
]
=
deljmS
[
2
]
*
fpair3
;
fm
[
0
]
=
-
delkmS
[
0
]
*
fpair2
-
fj
[
0
];
fm
[
1
]
=
-
delkmS
[
1
]
*
fpair2
-
fj
[
1
];
fm
[
2
]
=
-
delkmS
[
2
]
*
fpair2
-
fj
[
2
];
f
[
atomi
][
0
]
+=
fi
[
0
];
f
[
atomi
][
1
]
+=
fi
[
1
];
f
[
atomi
][
2
]
+=
fi
[
2
];
f
[
atomj
][
0
]
+=
fj
[
0
];
f
[
atomj
][
1
]
+=
fj
[
1
];
f
[
atomj
][
2
]
+=
fj
[
2
];
f
[
atomk
][
0
]
+=
fk
[
0
];
f
[
atomk
][
1
]
+=
fk
[
1
];
f
[
atomk
][
2
]
+=
fk
[
2
];
f
[
atomm
][
0
]
+=
fm
[
0
];
f
[
atomm
][
1
]
+=
fm
[
1
];
f
[
atomm
][
2
]
+=
fm
[
2
];
if
(
vflag_atom
)
{
delimS
[
0
]
=
delikS
[
0
]
+
delkmS
[
0
];
delimS
[
1
]
=
delikS
[
1
]
+
delkmS
[
1
];
delimS
[
2
]
=
delikS
[
2
]
+
delkmS
[
2
];
v_tally4
(
atomi
,
atomj
,
atomk
,
atomm
,
fi
,
fj
,
fk
,
delimS
,
deljmS
,
delkmS
);
}
}
}
}
}
}
/* ----------------------------------------------------------------------
torsional forces and energy
------------------------------------------------------------------------- */
void
PairAIREBO
::
TORSION
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
k
,
l
,
ii
,
inum
;
tagint
itag
,
jtag
;
double
evdwl
,
fpair
,
xtmp
,
ytmp
,
ztmp
;
double
cos321
;
double
w21
,
dw21
,
cos234
,
w34
,
dw34
;
double
cross321
[
3
],
cross321mag
,
cross234
[
3
],
cross234mag
;
double
w23
,
dw23
,
cw2
,
ekijl
,
Ec
;
double
cw
,
cwnum
,
cwnom
;
double
rij
,
rij2
,
rik
,
rjl
,
tspjik
,
dtsjik
,
tspijl
,
dtsijl
,
costmp
,
fcpc
;
double
sin321
,
sin234
,
rjk2
,
rik2
,
ril2
,
rjl2
;
double
rjk
,
ril
;
double
Vtors
;
double
dndij
[
3
],
tmpvec
[
3
],
dndik
[
3
],
dndjl
[
3
];
double
dcidij
,
dcidik
,
dcidjk
,
dcjdji
,
dcjdjl
,
dcjdil
;
double
dsidij
,
dsidik
,
dsidjk
,
dsjdji
,
dsjdjl
,
dsjdil
;
double
dxidij
,
dxidik
,
dxidjk
,
dxjdji
,
dxjdjl
,
dxjdil
;
double
ddndij
,
ddndik
,
ddndjk
,
ddndjl
,
ddndil
,
dcwddn
,
dcwdn
,
dvpdcw
,
Ftmp
[
3
];
double
del32
[
3
],
rsq
,
r32
,
del23
[
3
],
del21
[
3
],
r21
;
double
deljk
[
3
],
del34
[
3
],
delil
[
3
],
delkl
[
3
],
r23
,
r34
;
double
fi
[
3
],
fj
[
3
],
fk
[
3
],
fl
[
3
];
int
itype
,
jtype
,
ktype
,
ltype
,
kk
,
ll
,
jj
;
int
*
ilist
,
*
REBO_neighs_i
,
*
REBO_neighs_j
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
int
*
type
=
atom
->
type
;
tagint
*
tag
=
atom
->
tag
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
itag
=
tag
[
i
];
itype
=
map
[
type
[
i
]];
if
(
itype
!=
0
)
continue
;
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
REBO_neighs_i
=
REBO_firstneigh
[
i
];
for
(
jj
=
0
;
jj
<
REBO_numneigh
[
i
];
jj
++
)
{
j
=
REBO_neighs_i
[
jj
];
jtag
=
tag
[
j
];
if
(
itag
>
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
0
)
continue
;
}
else
if
(
itag
<
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
1
)
continue
;
}
else
{
if
(
x
[
j
][
2
]
<
ztmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
<
ytmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
==
ytmp
&&
x
[
j
][
0
]
<
xtmp
)
continue
;
}
jtype
=
map
[
type
[
j
]];
if
(
jtype
!=
0
)
continue
;
del32
[
0
]
=
x
[
j
][
0
]
-
x
[
i
][
0
];
del32
[
1
]
=
x
[
j
][
1
]
-
x
[
i
][
1
];
del32
[
2
]
=
x
[
j
][
2
]
-
x
[
i
][
2
];
rsq
=
del32
[
0
]
*
del32
[
0
]
+
del32
[
1
]
*
del32
[
1
]
+
del32
[
2
]
*
del32
[
2
];
r32
=
sqrt
(
rsq
);
del23
[
0
]
=
-
del32
[
0
];
del23
[
1
]
=
-
del32
[
1
];
del23
[
2
]
=
-
del32
[
2
];
r23
=
r32
;
w23
=
Sp
(
r23
,
rcmin
[
itype
][
jtype
],
rcmax
[
itype
][
jtype
],
dw23
);
for
(
kk
=
0
;
kk
<
REBO_numneigh
[
i
];
kk
++
)
{
k
=
REBO_neighs_i
[
kk
];
ktype
=
map
[
type
[
k
]];
if
(
k
==
j
)
continue
;
del21
[
0
]
=
x
[
i
][
0
]
-
x
[
k
][
0
];
del21
[
1
]
=
x
[
i
][
1
]
-
x
[
k
][
1
];
del21
[
2
]
=
x
[
i
][
2
]
-
x
[
k
][
2
];
rsq
=
del21
[
0
]
*
del21
[
0
]
+
del21
[
1
]
*
del21
[
1
]
+
del21
[
2
]
*
del21
[
2
];
r21
=
sqrt
(
rsq
);
cos321
=
-
((
del21
[
0
]
*
del32
[
0
])
+
(
del21
[
1
]
*
del32
[
1
])
+
(
del21
[
2
]
*
del32
[
2
]))
/
(
r21
*
r32
);
cos321
=
MIN
(
cos321
,
1.0
);
cos321
=
MAX
(
cos321
,
-
1.0
);
sin321
=
sqrt
(
1.0
-
cos321
*
cos321
);
if
(
sin321
<
TOL
)
continue
;
deljk
[
0
]
=
del21
[
0
]
-
del23
[
0
];
deljk
[
1
]
=
del21
[
1
]
-
del23
[
1
];
deljk
[
2
]
=
del21
[
2
]
-
del23
[
2
];
rjk2
=
deljk
[
0
]
*
deljk
[
0
]
+
deljk
[
1
]
*
deljk
[
1
]
+
deljk
[
2
]
*
deljk
[
2
];
rjk
=
sqrt
(
rjk2
);
rik2
=
r21
*
r21
;
w21
=
Sp
(
r21
,
rcmin
[
itype
][
ktype
],
rcmax
[
itype
][
ktype
],
dw21
);
rij
=
r32
;
rik
=
r21
;
rij2
=
r32
*
r32
;
rik2
=
r21
*
r21
;
costmp
=
0.5
*
(
rij2
+
rik2
-
rjk2
)
/
rij
/
rik
;
tspjik
=
Sp2
(
costmp
,
thmin
,
thmax
,
dtsjik
);
dtsjik
=
-
dtsjik
;
REBO_neighs_j
=
REBO_firstneigh
[
j
];
for
(
ll
=
0
;
ll
<
REBO_numneigh
[
j
];
ll
++
)
{
l
=
REBO_neighs_j
[
ll
];
ltype
=
map
[
type
[
l
]];
if
(
l
==
i
||
l
==
k
)
continue
;
del34
[
0
]
=
x
[
j
][
0
]
-
x
[
l
][
0
];
del34
[
1
]
=
x
[
j
][
1
]
-
x
[
l
][
1
];
del34
[
2
]
=
x
[
j
][
2
]
-
x
[
l
][
2
];
rsq
=
del34
[
0
]
*
del34
[
0
]
+
del34
[
1
]
*
del34
[
1
]
+
del34
[
2
]
*
del34
[
2
];
r34
=
sqrt
(
rsq
);
cos234
=
(
del32
[
0
]
*
del34
[
0
]
+
del32
[
1
]
*
del34
[
1
]
+
del32
[
2
]
*
del34
[
2
])
/
(
r32
*
r34
);
cos234
=
MIN
(
cos234
,
1.0
);
cos234
=
MAX
(
cos234
,
-
1.0
);
sin234
=
sqrt
(
1.0
-
cos234
*
cos234
);
if
(
sin234
<
TOL
)
continue
;
w34
=
Sp
(
r34
,
rcmin
[
jtype
][
ltype
],
rcmax
[
jtype
][
ltype
],
dw34
);
delil
[
0
]
=
del23
[
0
]
+
del34
[
0
];
delil
[
1
]
=
del23
[
1
]
+
del34
[
1
];
delil
[
2
]
=
del23
[
2
]
+
del34
[
2
];
ril2
=
delil
[
0
]
*
delil
[
0
]
+
delil
[
1
]
*
delil
[
1
]
+
delil
[
2
]
*
delil
[
2
];
ril
=
sqrt
(
ril2
);
rjl2
=
r34
*
r34
;
rjl
=
r34
;
rjl2
=
r34
*
r34
;
costmp
=
0.5
*
(
rij2
+
rjl2
-
ril2
)
/
rij
/
rjl
;
tspijl
=
Sp2
(
costmp
,
thmin
,
thmax
,
dtsijl
);
dtsijl
=
-
dtsijl
;
//need minus sign
cross321
[
0
]
=
(
del32
[
1
]
*
del21
[
2
])
-
(
del32
[
2
]
*
del21
[
1
]);
cross321
[
1
]
=
(
del32
[
2
]
*
del21
[
0
])
-
(
del32
[
0
]
*
del21
[
2
]);
cross321
[
2
]
=
(
del32
[
0
]
*
del21
[
1
])
-
(
del32
[
1
]
*
del21
[
0
]);
cross321mag
=
sqrt
(
cross321
[
0
]
*
cross321
[
0
]
+
cross321
[
1
]
*
cross321
[
1
]
+
cross321
[
2
]
*
cross321
[
2
]);
cross234
[
0
]
=
(
del23
[
1
]
*
del34
[
2
])
-
(
del23
[
2
]
*
del34
[
1
]);
cross234
[
1
]
=
(
del23
[
2
]
*
del34
[
0
])
-
(
del23
[
0
]
*
del34
[
2
]);
cross234
[
2
]
=
(
del23
[
0
]
*
del34
[
1
])
-
(
del23
[
1
]
*
del34
[
0
]);
cross234mag
=
sqrt
(
cross234
[
0
]
*
cross234
[
0
]
+
cross234
[
1
]
*
cross234
[
1
]
+
cross234
[
2
]
*
cross234
[
2
]);
cwnum
=
(
cross321
[
0
]
*
cross234
[
0
])
+
(
cross321
[
1
]
*
cross234
[
1
])
+
(
cross321
[
2
]
*
cross234
[
2
]);
cwnom
=
r21
*
r34
*
r32
*
r32
*
sin321
*
sin234
;
cw
=
cwnum
/
cwnom
;
cw2
=
(
.5
*
(
1.0
-
cw
));
ekijl
=
epsilonT
[
ktype
][
ltype
];
Ec
=
256.0
*
ekijl
/
405.0
;
Vtors
=
(
Ec
*
(
powint
(
cw2
,
5
)))
-
(
ekijl
/
10.0
);
if
(
eflag
)
evdwl
=
Vtors
*
w21
*
w23
*
w34
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
);
dndij
[
0
]
=
(
cross234
[
1
]
*
del21
[
2
])
-
(
cross234
[
2
]
*
del21
[
1
]);
dndij
[
1
]
=
(
cross234
[
2
]
*
del21
[
0
])
-
(
cross234
[
0
]
*
del21
[
2
]);
dndij
[
2
]
=
(
cross234
[
0
]
*
del21
[
1
])
-
(
cross234
[
1
]
*
del21
[
0
]);
tmpvec
[
0
]
=
(
del34
[
1
]
*
cross321
[
2
])
-
(
del34
[
2
]
*
cross321
[
1
]);
tmpvec
[
1
]
=
(
del34
[
2
]
*
cross321
[
0
])
-
(
del34
[
0
]
*
cross321
[
2
]);
tmpvec
[
2
]
=
(
del34
[
0
]
*
cross321
[
1
])
-
(
del34
[
1
]
*
cross321
[
0
]);
dndij
[
0
]
=
dndij
[
0
]
+
tmpvec
[
0
];
dndij
[
1
]
=
dndij
[
1
]
+
tmpvec
[
1
];
dndij
[
2
]
=
dndij
[
2
]
+
tmpvec
[
2
];
dndik
[
0
]
=
(
del23
[
1
]
*
cross234
[
2
])
-
(
del23
[
2
]
*
cross234
[
1
]);
dndik
[
1
]
=
(
del23
[
2
]
*
cross234
[
0
])
-
(
del23
[
0
]
*
cross234
[
2
]);
dndik
[
2
]
=
(
del23
[
0
]
*
cross234
[
1
])
-
(
del23
[
1
]
*
cross234
[
0
]);
dndjl
[
0
]
=
(
cross321
[
1
]
*
del23
[
2
])
-
(
cross321
[
2
]
*
del23
[
1
]);
dndjl
[
1
]
=
(
cross321
[
2
]
*
del23
[
0
])
-
(
cross321
[
0
]
*
del23
[
2
]);
dndjl
[
2
]
=
(
cross321
[
0
]
*
del23
[
1
])
-
(
cross321
[
1
]
*
del23
[
0
]);
dcidij
=
((
r23
*
r23
)
-
(
r21
*
r21
)
+
(
rjk
*
rjk
))
/
(
2.0
*
r23
*
r23
*
r21
);
dcidik
=
((
r21
*
r21
)
-
(
r23
*
r23
)
+
(
rjk
*
rjk
))
/
(
2.0
*
r23
*
r21
*
r21
);
dcidjk
=
(
-
rjk
)
/
(
r23
*
r21
);
dcjdji
=
((
r23
*
r23
)
-
(
r34
*
r34
)
+
(
ril
*
ril
))
/
(
2.0
*
r23
*
r23
*
r34
);
dcjdjl
=
((
r34
*
r34
)
-
(
r23
*
r23
)
+
(
ril
*
ril
))
/
(
2.0
*
r23
*
r34
*
r34
);
dcjdil
=
(
-
ril
)
/
(
r23
*
r34
);
dsidij
=
(
-
cos321
/
sin321
)
*
dcidij
;
dsidik
=
(
-
cos321
/
sin321
)
*
dcidik
;
dsidjk
=
(
-
cos321
/
sin321
)
*
dcidjk
;
dsjdji
=
(
-
cos234
/
sin234
)
*
dcjdji
;
dsjdjl
=
(
-
cos234
/
sin234
)
*
dcjdjl
;
dsjdil
=
(
-
cos234
/
sin234
)
*
dcjdil
;
dxidij
=
(
r21
*
sin321
)
+
(
r23
*
r21
*
dsidij
);
dxidik
=
(
r23
*
sin321
)
+
(
r23
*
r21
*
dsidik
);
dxidjk
=
(
r23
*
r21
*
dsidjk
);
dxjdji
=
(
r34
*
sin234
)
+
(
r23
*
r34
*
dsjdji
);
dxjdjl
=
(
r23
*
sin234
)
+
(
r23
*
r34
*
dsjdjl
);
dxjdil
=
(
r23
*
r34
*
dsjdil
);
ddndij
=
(
dxidij
*
cross234mag
)
+
(
cross321mag
*
dxjdji
);
ddndik
=
dxidik
*
cross234mag
;
ddndjk
=
dxidjk
*
cross234mag
;
ddndjl
=
cross321mag
*
dxjdjl
;
ddndil
=
cross321mag
*
dxjdil
;
dcwddn
=
-
cwnum
/
(
cwnom
*
cwnom
);
dcwdn
=
1.0
/
cwnom
;
dvpdcw
=
(
-
1.0
)
*
Ec
*
(
-
.5
)
*
5.0
*
powint
(
cw2
,
4
)
*
w23
*
w21
*
w34
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
);
Ftmp
[
0
]
=
dvpdcw
*
((
dcwdn
*
dndij
[
0
])
+
(
dcwddn
*
ddndij
*
del23
[
0
]
/
r23
));
Ftmp
[
1
]
=
dvpdcw
*
((
dcwdn
*
dndij
[
1
])
+
(
dcwddn
*
ddndij
*
del23
[
1
]
/
r23
));
Ftmp
[
2
]
=
dvpdcw
*
((
dcwdn
*
dndij
[
2
])
+
(
dcwddn
*
ddndij
*
del23
[
2
]
/
r23
));
fi
[
0
]
=
Ftmp
[
0
];
fi
[
1
]
=
Ftmp
[
1
];
fi
[
2
]
=
Ftmp
[
2
];
fj
[
0
]
=
-
Ftmp
[
0
];
fj
[
1
]
=
-
Ftmp
[
1
];
fj
[
2
]
=
-
Ftmp
[
2
];
Ftmp
[
0
]
=
dvpdcw
*
((
dcwdn
*
dndik
[
0
])
+
(
dcwddn
*
ddndik
*
del21
[
0
]
/
r21
));
Ftmp
[
1
]
=
dvpdcw
*
((
dcwdn
*
dndik
[
1
])
+
(
dcwddn
*
ddndik
*
del21
[
1
]
/
r21
));
Ftmp
[
2
]
=
dvpdcw
*
((
dcwdn
*
dndik
[
2
])
+
(
dcwddn
*
ddndik
*
del21
[
2
]
/
r21
));
fi
[
0
]
+=
Ftmp
[
0
];
fi
[
1
]
+=
Ftmp
[
1
];
fi
[
2
]
+=
Ftmp
[
2
];
fk
[
0
]
=
-
Ftmp
[
0
];
fk
[
1
]
=
-
Ftmp
[
1
];
fk
[
2
]
=
-
Ftmp
[
2
];
Ftmp
[
0
]
=
(
dvpdcw
*
dcwddn
*
ddndjk
*
deljk
[
0
])
/
rjk
;
Ftmp
[
1
]
=
(
dvpdcw
*
dcwddn
*
ddndjk
*
deljk
[
1
])
/
rjk
;
Ftmp
[
2
]
=
(
dvpdcw
*
dcwddn
*
ddndjk
*
deljk
[
2
])
/
rjk
;
fj
[
0
]
+=
Ftmp
[
0
];
fj
[
1
]
+=
Ftmp
[
1
];
fj
[
2
]
+=
Ftmp
[
2
];
fk
[
0
]
-=
Ftmp
[
0
];
fk
[
1
]
-=
Ftmp
[
1
];
fk
[
2
]
-=
Ftmp
[
2
];
Ftmp
[
0
]
=
dvpdcw
*
((
dcwdn
*
dndjl
[
0
])
+
(
dcwddn
*
ddndjl
*
del34
[
0
]
/
r34
));
Ftmp
[
1
]
=
dvpdcw
*
((
dcwdn
*
dndjl
[
1
])
+
(
dcwddn
*
ddndjl
*
del34
[
1
]
/
r34
));
Ftmp
[
2
]
=
dvpdcw
*
((
dcwdn
*
dndjl
[
2
])
+
(
dcwddn
*
ddndjl
*
del34
[
2
]
/
r34
));
fj
[
0
]
+=
Ftmp
[
0
];
fj
[
1
]
+=
Ftmp
[
1
];
fj
[
2
]
+=
Ftmp
[
2
];
fl
[
0
]
=
-
Ftmp
[
0
];
fl
[
1
]
=
-
Ftmp
[
1
];
fl
[
2
]
=
-
Ftmp
[
2
];
Ftmp
[
0
]
=
(
dvpdcw
*
dcwddn
*
ddndil
*
delil
[
0
])
/
ril
;
Ftmp
[
1
]
=
(
dvpdcw
*
dcwddn
*
ddndil
*
delil
[
1
])
/
ril
;
Ftmp
[
2
]
=
(
dvpdcw
*
dcwddn
*
ddndil
*
delil
[
2
])
/
ril
;
fi
[
0
]
+=
Ftmp
[
0
];
fi
[
1
]
+=
Ftmp
[
1
];
fi
[
2
]
+=
Ftmp
[
2
];
fl
[
0
]
-=
Ftmp
[
0
];
fl
[
1
]
-=
Ftmp
[
1
];
fl
[
2
]
-=
Ftmp
[
2
];
// coordination forces
fpair
=
Vtors
*
dw21
*
w23
*
w34
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
)
/
r21
;
fi
[
0
]
-=
del21
[
0
]
*
fpair
;
fi
[
1
]
-=
del21
[
1
]
*
fpair
;
fi
[
2
]
-=
del21
[
2
]
*
fpair
;
fk
[
0
]
+=
del21
[
0
]
*
fpair
;
fk
[
1
]
+=
del21
[
1
]
*
fpair
;
fk
[
2
]
+=
del21
[
2
]
*
fpair
;
fpair
=
Vtors
*
w21
*
dw23
*
w34
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
)
/
r23
;
fi
[
0
]
-=
del23
[
0
]
*
fpair
;
fi
[
1
]
-=
del23
[
1
]
*
fpair
;
fi
[
2
]
-=
del23
[
2
]
*
fpair
;
fj
[
0
]
+=
del23
[
0
]
*
fpair
;
fj
[
1
]
+=
del23
[
1
]
*
fpair
;
fj
[
2
]
+=
del23
[
2
]
*
fpair
;
fpair
=
Vtors
*
w21
*
w23
*
dw34
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
)
/
r34
;
fj
[
0
]
-=
del34
[
0
]
*
fpair
;
fj
[
1
]
-=
del34
[
1
]
*
fpair
;
fj
[
2
]
-=
del34
[
2
]
*
fpair
;
fl
[
0
]
+=
del34
[
0
]
*
fpair
;
fl
[
1
]
+=
del34
[
1
]
*
fpair
;
fl
[
2
]
+=
del34
[
2
]
*
fpair
;
// additional cut off function forces
fcpc
=
-
Vtors
*
w21
*
w23
*
w34
*
dtsjik
*
(
1.0
-
tspijl
);
fpair
=
fcpc
*
dcidij
/
rij
;
fi
[
0
]
+=
fpair
*
del23
[
0
];
fi
[
1
]
+=
fpair
*
del23
[
1
];
fi
[
2
]
+=
fpair
*
del23
[
2
];
fj
[
0
]
-=
fpair
*
del23
[
0
];
fj
[
1
]
-=
fpair
*
del23
[
1
];
fj
[
2
]
-=
fpair
*
del23
[
2
];
fpair
=
fcpc
*
dcidik
/
rik
;
fi
[
0
]
+=
fpair
*
del21
[
0
];
fi
[
1
]
+=
fpair
*
del21
[
1
];
fi
[
2
]
+=
fpair
*
del21
[
2
];
fk
[
0
]
-=
fpair
*
del21
[
0
];
fk
[
1
]
-=
fpair
*
del21
[
1
];
fk
[
2
]
-=
fpair
*
del21
[
2
];
fpair
=
fcpc
*
dcidjk
/
rjk
;
fj
[
0
]
+=
fpair
*
deljk
[
0
];
fj
[
1
]
+=
fpair
*
deljk
[
1
];
fj
[
2
]
+=
fpair
*
deljk
[
2
];
fk
[
0
]
-=
fpair
*
deljk
[
0
];
fk
[
1
]
-=
fpair
*
deljk
[
1
];
fk
[
2
]
-=
fpair
*
deljk
[
2
];
fcpc
=
-
Vtors
*
w21
*
w23
*
w34
*
(
1.0
-
tspjik
)
*
dtsijl
;
fpair
=
fcpc
*
dcjdji
/
rij
;
fi
[
0
]
+=
fpair
*
del23
[
0
];
fi
[
1
]
+=
fpair
*
del23
[
1
];
fi
[
2
]
+=
fpair
*
del23
[
2
];
fj
[
0
]
-=
fpair
*
del23
[
0
];
fj
[
1
]
-=
fpair
*
del23
[
1
];
fj
[
2
]
-=
fpair
*
del23
[
2
];
fpair
=
fcpc
*
dcjdjl
/
rjl
;
fj
[
0
]
+=
fpair
*
del34
[
0
];
fj
[
1
]
+=
fpair
*
del34
[
1
];
fj
[
2
]
+=
fpair
*
del34
[
2
];
fl
[
0
]
-=
fpair
*
del34
[
0
];
fl
[
1
]
-=
fpair
*
del34
[
1
];
fl
[
2
]
-=
fpair
*
del34
[
2
];
fpair
=
fcpc
*
dcjdil
/
ril
;
fi
[
0
]
+=
fpair
*
delil
[
0
];
fi
[
1
]
+=
fpair
*
delil
[
1
];
fi
[
2
]
+=
fpair
*
delil
[
2
];
fl
[
0
]
-=
fpair
*
delil
[
0
];
fl
[
1
]
-=
fpair
*
delil
[
1
];
fl
[
2
]
-=
fpair
*
delil
[
2
];
// sum per-atom forces into atom force array
f
[
i
][
0
]
+=
fi
[
0
];
f
[
i
][
1
]
+=
fi
[
1
];
f
[
i
][
2
]
+=
fi
[
2
];
f
[
j
][
0
]
+=
fj
[
0
];
f
[
j
][
1
]
+=
fj
[
1
];
f
[
j
][
2
]
+=
fj
[
2
];
f
[
k
][
0
]
+=
fk
[
0
];
f
[
k
][
1
]
+=
fk
[
1
];
f
[
k
][
2
]
+=
fk
[
2
];
f
[
l
][
0
]
+=
fl
[
0
];
f
[
l
][
1
]
+=
fl
[
1
];
f
[
l
][
2
]
+=
fl
[
2
];
if
(
evflag
)
{
delkl
[
0
]
=
delil
[
0
]
-
del21
[
0
];
delkl
[
1
]
=
delil
[
1
]
-
del21
[
1
];
delkl
[
2
]
=
delil
[
2
]
-
del21
[
2
];
ev_tally4
(
i
,
j
,
k
,
l
,
evdwl
,
fi
,
fj
,
fk
,
delil
,
del34
,
delkl
);
}
}
}
}
}
}
/* ----------------------------------------------------------------------
Bij function
------------------------------------------------------------------------- */
double
PairAIREBO
::
bondorder
(
int
i
,
int
j
,
double
rij
[
3
],
double
rijmag
,
double
VA
,
double
**
f
,
int
vflag_atom
)
{
int
atomi
,
atomj
,
k
,
n
,
l
,
atomk
,
atoml
,
atomn
,
atom1
,
atom2
,
atom3
,
atom4
;
int
itype
,
jtype
,
ktype
,
ltype
,
ntype
;
double
rik
[
3
],
rjl
[
3
],
rkn
[
3
],
rji
[
3
],
rki
[
3
],
rlj
[
3
],
rknmag
,
dNki
,
dwjl
,
bij
;
double
NijC
,
NijH
,
NjiC
,
NjiH
,
wik
,
dwik
,
dwkn
,
wjl
;
double
rikmag
,
rjlmag
,
cosjik
,
cosijl
,
g
,
tmp2
,
tmp3
;
double
Etmp
,
pij
,
tmp
,
wij
,
dwij
,
NconjtmpI
,
NconjtmpJ
,
Nki
,
Nlj
,
dS
;
double
lamdajik
,
lamdaijl
,
dgdc
,
dgdN
,
pji
,
Nijconj
,
piRC
;
double
dcosjikdri
[
3
],
dcosijldri
[
3
],
dcosjikdrk
[
3
];
double
dN2
[
2
],
dN3
[
3
];
double
dcosjikdrj
[
3
],
dcosijldrj
[
3
],
dcosijldrl
[
3
];
double
Tij
;
double
r32
[
3
],
r32mag
,
cos321
,
r43
[
3
],
r13
[
3
];
double
dNlj
;
double
om1234
,
rln
[
3
];
double
rlnmag
,
dwln
,
r23
[
3
],
r23mag
,
r21
[
3
],
r21mag
;
double
w21
,
dw21
,
r34
[
3
],
r34mag
,
cos234
,
w34
,
dw34
;
double
cross321
[
3
],
cross234
[
3
],
prefactor
,
SpN
;
double
fcijpc
,
fcikpc
,
fcjlpc
,
fcjkpc
,
fcilpc
;
double
dt2dik
[
3
],
dt2djl
[
3
],
dt2dij
[
3
],
aa
,
aaa1
,
aaa2
,
at2
,
cw
,
cwnum
,
cwnom
;
double
sin321
,
sin234
,
rr
,
rijrik
,
rijrjl
,
rjk2
,
rik2
,
ril2
,
rjl2
;
double
dctik
,
dctjk
,
dctjl
,
dctij
,
dctji
,
dctil
,
rik2i
,
rjl2i
,
sink2i
,
sinl2i
;
double
rjk
[
3
],
ril
[
3
],
dt1dik
,
dt1djk
,
dt1djl
,
dt1dil
,
dt1dij
;
double
F23
[
3
],
F12
[
3
],
F34
[
3
],
F31
[
3
],
F24
[
3
],
fi
[
3
],
fj
[
3
],
fk
[
3
],
fl
[
3
];
double
f1
[
3
],
f2
[
3
],
f3
[
3
],
f4
[
4
];
double
dcut321
,
PijS
,
PjiS
;
double
rij2
,
tspjik
,
dtsjik
,
tspijl
,
dtsijl
,
costmp
;
int
*
REBO_neighs
,
*
REBO_neighs_i
,
*
REBO_neighs_j
,
*
REBO_neighs_k
,
*
REBO_neighs_l
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
atomi
=
i
;
atomj
=
j
;
itype
=
map
[
type
[
i
]];
jtype
=
map
[
type
[
j
]];
wij
=
Sp
(
rijmag
,
rcmin
[
itype
][
jtype
],
rcmax
[
itype
][
jtype
],
dwij
);
NijC
=
nC
[
i
]
-
(
wij
*
kronecker
(
jtype
,
0
));
NijH
=
nH
[
i
]
-
(
wij
*
kronecker
(
jtype
,
1
));
NjiC
=
nC
[
j
]
-
(
wij
*
kronecker
(
itype
,
0
));
NjiH
=
nH
[
j
]
-
(
wij
*
kronecker
(
itype
,
1
));
bij
=
0.0
;
tmp
=
0.0
;
tmp2
=
0.0
;
tmp3
=
0.0
;
dgdc
=
0.0
;
dgdN
=
0.0
;
NconjtmpI
=
0.0
;
NconjtmpJ
=
0.0
;
Etmp
=
0.0
;
REBO_neighs
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
atomk
=
REBO_neighs
[
k
];
if
(
atomk
!=
atomj
)
{
ktype
=
map
[
type
[
atomk
]];
rik
[
0
]
=
x
[
atomi
][
0
]
-
x
[
atomk
][
0
];
rik
[
1
]
=
x
[
atomi
][
1
]
-
x
[
atomk
][
1
];
rik
[
2
]
=
x
[
atomi
][
2
]
-
x
[
atomk
][
2
];
rikmag
=
sqrt
((
rik
[
0
]
*
rik
[
0
])
+
(
rik
[
1
]
*
rik
[
1
])
+
(
rik
[
2
]
*
rik
[
2
]));
lamdajik
=
4.0
*
kronecker
(
itype
,
1
)
*
((
rho
[
ktype
][
1
]
-
rikmag
)
-
(
rho
[
jtype
][
1
]
-
rijmag
));
wik
=
Sp
(
rikmag
,
rcmin
[
itype
][
ktype
],
rcmax
[
itype
][
ktype
],
dS
);
Nki
=
nC
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
0
))
+
nH
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
1
));
cosjik
=
((
rij
[
0
]
*
rik
[
0
])
+
(
rij
[
1
]
*
rik
[
1
])
+
(
rij
[
2
]
*
rik
[
2
]))
/
(
rijmag
*
rikmag
);
cosjik
=
MIN
(
cosjik
,
1.0
);
cosjik
=
MAX
(
cosjik
,
-
1.0
);
// evaluate splines g and derivatives dg
g
=
gSpline
(
cosjik
,(
NijC
+
NijH
),
itype
,
&
dgdc
,
&
dgdN
);
Etmp
=
Etmp
+
(
wik
*
g
*
exp
(
lamdajik
));
tmp3
=
tmp3
+
(
wik
*
dgdN
*
exp
(
lamdajik
));
NconjtmpI
=
NconjtmpI
+
(
kronecker
(
ktype
,
0
)
*
wik
*
Sp
(
Nki
,
Nmin
,
Nmax
,
dS
));
}
}
PijS
=
0.0
;
dN2
[
0
]
=
0.0
;
dN2
[
1
]
=
0.0
;
PijS
=
PijSpline
(
NijC
,
NijH
,
itype
,
jtype
,
dN2
);
pij
=
pow
(
1.0
+
Etmp
+
PijS
,
-
0.5
);
tmp
=
-
0.5
*
cube
(
pij
);
// pij forces
REBO_neighs
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
atomk
=
REBO_neighs
[
k
];
if
(
atomk
!=
atomj
)
{
ktype
=
map
[
type
[
atomk
]];
rik
[
0
]
=
x
[
atomi
][
0
]
-
x
[
atomk
][
0
];
rik
[
1
]
=
x
[
atomi
][
1
]
-
x
[
atomk
][
1
];
rik
[
2
]
=
x
[
atomi
][
2
]
-
x
[
atomk
][
2
];
rikmag
=
sqrt
((
rik
[
0
]
*
rik
[
0
])
+
(
rik
[
1
]
*
rik
[
1
])
+
(
rik
[
2
]
*
rik
[
2
]));
lamdajik
=
4.0
*
kronecker
(
itype
,
1
)
*
((
rho
[
ktype
][
1
]
-
rikmag
)
-
(
rho
[
jtype
][
1
]
-
rijmag
));
wik
=
Sp
(
rikmag
,
rcmin
[
itype
][
ktype
],
rcmax
[
itype
][
ktype
],
dwik
);
cosjik
=
(
rij
[
0
]
*
rik
[
0
]
+
rij
[
1
]
*
rik
[
1
]
+
rij
[
2
]
*
rik
[
2
])
/
(
rijmag
*
rikmag
);
cosjik
=
MIN
(
cosjik
,
1.0
);
cosjik
=
MAX
(
cosjik
,
-
1.0
);
dcosjikdri
[
0
]
=
((
rij
[
0
]
+
rik
[
0
])
/
(
rijmag
*
rikmag
))
-
(
cosjik
*
((
rij
[
0
]
/
(
rijmag
*
rijmag
))
+
(
rik
[
0
]
/
(
rikmag
*
rikmag
))));
dcosjikdri
[
1
]
=
((
rij
[
1
]
+
rik
[
1
])
/
(
rijmag
*
rikmag
))
-
(
cosjik
*
((
rij
[
1
]
/
(
rijmag
*
rijmag
))
+
(
rik
[
1
]
/
(
rikmag
*
rikmag
))));
dcosjikdri
[
2
]
=
((
rij
[
2
]
+
rik
[
2
])
/
(
rijmag
*
rikmag
))
-
(
cosjik
*
((
rij
[
2
]
/
(
rijmag
*
rijmag
))
+
(
rik
[
2
]
/
(
rikmag
*
rikmag
))));
dcosjikdrk
[
0
]
=
(
-
rij
[
0
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rik
[
0
]
/
(
rikmag
*
rikmag
)));
dcosjikdrk
[
1
]
=
(
-
rij
[
1
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rik
[
1
]
/
(
rikmag
*
rikmag
)));
dcosjikdrk
[
2
]
=
(
-
rij
[
2
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rik
[
2
]
/
(
rikmag
*
rikmag
)));
dcosjikdrj
[
0
]
=
(
-
rik
[
0
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rij
[
0
]
/
(
rijmag
*
rijmag
)));
dcosjikdrj
[
1
]
=
(
-
rik
[
1
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rij
[
1
]
/
(
rijmag
*
rijmag
)));
dcosjikdrj
[
2
]
=
(
-
rik
[
2
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rij
[
2
]
/
(
rijmag
*
rijmag
)));
g
=
gSpline
(
cosjik
,(
NijC
+
NijH
),
itype
,
&
dgdc
,
&
dgdN
);
tmp2
=
VA
*
.5
*
(
tmp
*
wik
*
dgdc
*
exp
(
lamdajik
));
fj
[
0
]
=
-
tmp2
*
dcosjikdrj
[
0
];
fj
[
1
]
=
-
tmp2
*
dcosjikdrj
[
1
];
fj
[
2
]
=
-
tmp2
*
dcosjikdrj
[
2
];
fi
[
0
]
=
-
tmp2
*
dcosjikdri
[
0
];
fi
[
1
]
=
-
tmp2
*
dcosjikdri
[
1
];
fi
[
2
]
=
-
tmp2
*
dcosjikdri
[
2
];
fk
[
0
]
=
-
tmp2
*
dcosjikdrk
[
0
];
fk
[
1
]
=
-
tmp2
*
dcosjikdrk
[
1
];
fk
[
2
]
=
-
tmp2
*
dcosjikdrk
[
2
];
tmp2
=
VA
*
.5
*
(
tmp
*
wik
*
g
*
exp
(
lamdajik
)
*
4.0
*
kronecker
(
itype
,
1
));
fj
[
0
]
-=
tmp2
*
(
-
rij
[
0
]
/
rijmag
);
fj
[
1
]
-=
tmp2
*
(
-
rij
[
1
]
/
rijmag
);
fj
[
2
]
-=
tmp2
*
(
-
rij
[
2
]
/
rijmag
);
fi
[
0
]
-=
tmp2
*
((
-
rik
[
0
]
/
rikmag
)
+
(
rij
[
0
]
/
rijmag
));
fi
[
1
]
-=
tmp2
*
((
-
rik
[
1
]
/
rikmag
)
+
(
rij
[
1
]
/
rijmag
));
fi
[
2
]
-=
tmp2
*
((
-
rik
[
2
]
/
rikmag
)
+
(
rij
[
2
]
/
rijmag
));
fk
[
0
]
-=
tmp2
*
(
rik
[
0
]
/
rikmag
);
fk
[
1
]
-=
tmp2
*
(
rik
[
1
]
/
rikmag
);
fk
[
2
]
-=
tmp2
*
(
rik
[
2
]
/
rikmag
);
// coordination forces
// dwik forces
tmp2
=
VA
*
.5
*
(
tmp
*
dwik
*
g
*
exp
(
lamdajik
))
/
rikmag
;
fi
[
0
]
-=
tmp2
*
rik
[
0
];
fi
[
1
]
-=
tmp2
*
rik
[
1
];
fi
[
2
]
-=
tmp2
*
rik
[
2
];
fk
[
0
]
+=
tmp2
*
rik
[
0
];
fk
[
1
]
+=
tmp2
*
rik
[
1
];
fk
[
2
]
+=
tmp2
*
rik
[
2
];
// PIJ forces
tmp2
=
VA
*
.5
*
(
tmp
*
dN2
[
ktype
]
*
dwik
)
/
rikmag
;
fi
[
0
]
-=
tmp2
*
rik
[
0
];
fi
[
1
]
-=
tmp2
*
rik
[
1
];
fi
[
2
]
-=
tmp2
*
rik
[
2
];
fk
[
0
]
+=
tmp2
*
rik
[
0
];
fk
[
1
]
+=
tmp2
*
rik
[
1
];
fk
[
2
]
+=
tmp2
*
rik
[
2
];
// dgdN forces
tmp2
=
VA
*
.5
*
(
tmp
*
tmp3
*
dwik
)
/
rikmag
;
fi
[
0
]
-=
tmp2
*
rik
[
0
];
fi
[
1
]
-=
tmp2
*
rik
[
1
];
fi
[
2
]
-=
tmp2
*
rik
[
2
];
fk
[
0
]
+=
tmp2
*
rik
[
0
];
fk
[
1
]
+=
tmp2
*
rik
[
1
];
fk
[
2
]
+=
tmp2
*
rik
[
2
];
f
[
atomi
][
0
]
+=
fi
[
0
];
f
[
atomi
][
1
]
+=
fi
[
1
];
f
[
atomi
][
2
]
+=
fi
[
2
];
f
[
atomj
][
0
]
+=
fj
[
0
];
f
[
atomj
][
1
]
+=
fj
[
1
];
f
[
atomj
][
2
]
+=
fj
[
2
];
f
[
atomk
][
0
]
+=
fk
[
0
];
f
[
atomk
][
1
]
+=
fk
[
1
];
f
[
atomk
][
2
]
+=
fk
[
2
];
if
(
vflag_atom
)
{
rji
[
0
]
=
-
rij
[
0
];
rji
[
1
]
=
-
rij
[
1
];
rji
[
2
]
=
-
rij
[
2
];
rki
[
0
]
=
-
rik
[
0
];
rki
[
1
]
=
-
rik
[
1
];
rki
[
2
]
=
-
rik
[
2
];
v_tally3
(
atomi
,
atomj
,
atomk
,
fj
,
fk
,
rji
,
rki
);
}
}
}
tmp
=
0.0
;
tmp2
=
0.0
;
tmp3
=
0.0
;
Etmp
=
0.0
;
REBO_neighs
=
REBO_firstneigh
[
j
];
for
(
l
=
0
;
l
<
REBO_numneigh
[
j
];
l
++
)
{
atoml
=
REBO_neighs
[
l
];
if
(
atoml
!=
atomi
)
{
ltype
=
map
[
type
[
atoml
]];
rjl
[
0
]
=
x
[
atomj
][
0
]
-
x
[
atoml
][
0
];
rjl
[
1
]
=
x
[
atomj
][
1
]
-
x
[
atoml
][
1
];
rjl
[
2
]
=
x
[
atomj
][
2
]
-
x
[
atoml
][
2
];
rjlmag
=
sqrt
((
rjl
[
0
]
*
rjl
[
0
])
+
(
rjl
[
1
]
*
rjl
[
1
])
+
(
rjl
[
2
]
*
rjl
[
2
]));
lamdaijl
=
4.0
*
kronecker
(
jtype
,
1
)
*
((
rho
[
ltype
][
1
]
-
rjlmag
)
-
(
rho
[
itype
][
1
]
-
rijmag
));
wjl
=
Sp
(
rjlmag
,
rcmin
[
jtype
][
ltype
],
rcmax
[
jtype
][
ltype
],
dS
);
Nlj
=
nC
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
0
))
+
nH
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
1
));
cosijl
=
-
1.0
*
((
rij
[
0
]
*
rjl
[
0
])
+
(
rij
[
1
]
*
rjl
[
1
])
+
(
rij
[
2
]
*
rjl
[
2
]))
/
(
rijmag
*
rjlmag
);
cosijl
=
MIN
(
cosijl
,
1.0
);
cosijl
=
MAX
(
cosijl
,
-
1.0
);
// evaluate splines g and derivatives dg
g
=
gSpline
(
cosijl
,
NjiC
+
NjiH
,
jtype
,
&
dgdc
,
&
dgdN
);
Etmp
=
Etmp
+
(
wjl
*
g
*
exp
(
lamdaijl
));
tmp3
=
tmp3
+
(
wjl
*
dgdN
*
exp
(
lamdaijl
));
NconjtmpJ
=
NconjtmpJ
+
(
kronecker
(
ltype
,
0
)
*
wjl
*
Sp
(
Nlj
,
Nmin
,
Nmax
,
dS
));
}
}
PjiS
=
0.0
;
dN2
[
0
]
=
0.0
;
dN2
[
1
]
=
0.0
;
PjiS
=
PijSpline
(
NjiC
,
NjiH
,
jtype
,
itype
,
dN2
);
pji
=
pow
(
1.0
+
Etmp
+
PjiS
,
-
0.5
);
tmp
=
-
0.5
*
cube
(
pji
);
REBO_neighs
=
REBO_firstneigh
[
j
];
for
(
l
=
0
;
l
<
REBO_numneigh
[
j
];
l
++
)
{
atoml
=
REBO_neighs
[
l
];
if
(
atoml
!=
atomi
)
{
ltype
=
map
[
type
[
atoml
]];
rjl
[
0
]
=
x
[
atomj
][
0
]
-
x
[
atoml
][
0
];
rjl
[
1
]
=
x
[
atomj
][
1
]
-
x
[
atoml
][
1
];
rjl
[
2
]
=
x
[
atomj
][
2
]
-
x
[
atoml
][
2
];
rjlmag
=
sqrt
((
rjl
[
0
]
*
rjl
[
0
])
+
(
rjl
[
1
]
*
rjl
[
1
])
+
(
rjl
[
2
]
*
rjl
[
2
]));
lamdaijl
=
4.0
*
kronecker
(
jtype
,
1
)
*
((
rho
[
ltype
][
1
]
-
rjlmag
)
-
(
rho
[
itype
][
1
]
-
rijmag
));
wjl
=
Sp
(
rjlmag
,
rcmin
[
jtype
][
ltype
],
rcmax
[
jtype
][
ltype
],
dwjl
);
cosijl
=
(
-
1.0
*
((
rij
[
0
]
*
rjl
[
0
])
+
(
rij
[
1
]
*
rjl
[
1
])
+
(
rij
[
2
]
*
rjl
[
2
])))
/
(
rijmag
*
rjlmag
);
cosijl
=
MIN
(
cosijl
,
1.0
);
cosijl
=
MAX
(
cosijl
,
-
1.0
);
dcosijldri
[
0
]
=
(
-
rjl
[
0
]
/
(
rijmag
*
rjlmag
))
-
(
cosijl
*
rij
[
0
]
/
(
rijmag
*
rijmag
));
dcosijldri
[
1
]
=
(
-
rjl
[
1
]
/
(
rijmag
*
rjlmag
))
-
(
cosijl
*
rij
[
1
]
/
(
rijmag
*
rijmag
));
dcosijldri
[
2
]
=
(
-
rjl
[
2
]
/
(
rijmag
*
rjlmag
))
-
(
cosijl
*
rij
[
2
]
/
(
rijmag
*
rijmag
));
dcosijldrj
[
0
]
=
((
-
rij
[
0
]
+
rjl
[
0
])
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
((
rij
[
0
]
/
square
(
rijmag
))
-
(
rjl
[
0
]
/
(
rjlmag
*
rjlmag
))));
dcosijldrj
[
1
]
=
((
-
rij
[
1
]
+
rjl
[
1
])
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
((
rij
[
1
]
/
square
(
rijmag
))
-
(
rjl
[
1
]
/
(
rjlmag
*
rjlmag
))));
dcosijldrj
[
2
]
=
((
-
rij
[
2
]
+
rjl
[
2
])
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
((
rij
[
2
]
/
square
(
rijmag
))
-
(
rjl
[
2
]
/
(
rjlmag
*
rjlmag
))));
dcosijldrl
[
0
]
=
(
rij
[
0
]
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
rjl
[
0
]
/
(
rjlmag
*
rjlmag
));
dcosijldrl
[
1
]
=
(
rij
[
1
]
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
rjl
[
1
]
/
(
rjlmag
*
rjlmag
));
dcosijldrl
[
2
]
=
(
rij
[
2
]
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
rjl
[
2
]
/
(
rjlmag
*
rjlmag
));
// evaluate splines g and derivatives dg
g
=
gSpline
(
cosijl
,
NjiC
+
NjiH
,
jtype
,
&
dgdc
,
&
dgdN
);
tmp2
=
VA
*
.5
*
(
tmp
*
wjl
*
dgdc
*
exp
(
lamdaijl
));
fi
[
0
]
=
-
tmp2
*
dcosijldri
[
0
];
fi
[
1
]
=
-
tmp2
*
dcosijldri
[
1
];
fi
[
2
]
=
-
tmp2
*
dcosijldri
[
2
];
fj
[
0
]
=
-
tmp2
*
dcosijldrj
[
0
];
fj
[
1
]
=
-
tmp2
*
dcosijldrj
[
1
];
fj
[
2
]
=
-
tmp2
*
dcosijldrj
[
2
];
fl
[
0
]
=
-
tmp2
*
dcosijldrl
[
0
];
fl
[
1
]
=
-
tmp2
*
dcosijldrl
[
1
];
fl
[
2
]
=
-
tmp2
*
dcosijldrl
[
2
];
tmp2
=
VA
*
.5
*
(
tmp
*
wjl
*
g
*
exp
(
lamdaijl
)
*
4.0
*
kronecker
(
jtype
,
1
));
fi
[
0
]
-=
tmp2
*
(
rij
[
0
]
/
rijmag
);
fi
[
1
]
-=
tmp2
*
(
rij
[
1
]
/
rijmag
);
fi
[
2
]
-=
tmp2
*
(
rij
[
2
]
/
rijmag
);
fj
[
0
]
-=
tmp2
*
((
-
rjl
[
0
]
/
rjlmag
)
-
(
rij
[
0
]
/
rijmag
));
fj
[
1
]
-=
tmp2
*
((
-
rjl
[
1
]
/
rjlmag
)
-
(
rij
[
1
]
/
rijmag
));
fj
[
2
]
-=
tmp2
*
((
-
rjl
[
2
]
/
rjlmag
)
-
(
rij
[
2
]
/
rijmag
));
fl
[
0
]
-=
tmp2
*
(
rjl
[
0
]
/
rjlmag
);
fl
[
1
]
-=
tmp2
*
(
rjl
[
1
]
/
rjlmag
);
fl
[
2
]
-=
tmp2
*
(
rjl
[
2
]
/
rjlmag
);
// coordination forces
// dwik forces
tmp2
=
VA
*
.5
*
(
tmp
*
dwjl
*
g
*
exp
(
lamdaijl
))
/
rjlmag
;
fj
[
0
]
-=
tmp2
*
rjl
[
0
];
fj
[
1
]
-=
tmp2
*
rjl
[
1
];
fj
[
2
]
-=
tmp2
*
rjl
[
2
];
fl
[
0
]
+=
tmp2
*
rjl
[
0
];
fl
[
1
]
+=
tmp2
*
rjl
[
1
];
fl
[
2
]
+=
tmp2
*
rjl
[
2
];
// PIJ forces
tmp2
=
VA
*
.5
*
(
tmp
*
dN2
[
ltype
]
*
dwjl
)
/
rjlmag
;
fj
[
0
]
-=
tmp2
*
rjl
[
0
];
fj
[
1
]
-=
tmp2
*
rjl
[
1
];
fj
[
2
]
-=
tmp2
*
rjl
[
2
];
fl
[
0
]
+=
tmp2
*
rjl
[
0
];
fl
[
1
]
+=
tmp2
*
rjl
[
1
];
fl
[
2
]
+=
tmp2
*
rjl
[
2
];
// dgdN forces
tmp2
=
VA
*
.5
*
(
tmp
*
tmp3
*
dwjl
)
/
rjlmag
;
fj
[
0
]
-=
tmp2
*
rjl
[
0
];
fj
[
1
]
-=
tmp2
*
rjl
[
1
];
fj
[
2
]
-=
tmp2
*
rjl
[
2
];
fl
[
0
]
+=
tmp2
*
rjl
[
0
];
fl
[
1
]
+=
tmp2
*
rjl
[
1
];
fl
[
2
]
+=
tmp2
*
rjl
[
2
];
f
[
atomi
][
0
]
+=
fi
[
0
];
f
[
atomi
][
1
]
+=
fi
[
1
];
f
[
atomi
][
2
]
+=
fi
[
2
];
f
[
atomj
][
0
]
+=
fj
[
0
];
f
[
atomj
][
1
]
+=
fj
[
1
];
f
[
atomj
][
2
]
+=
fj
[
2
];
f
[
atoml
][
0
]
+=
fl
[
0
];
f
[
atoml
][
1
]
+=
fl
[
1
];
f
[
atoml
][
2
]
+=
fl
[
2
];
if
(
vflag_atom
)
{
rlj
[
0
]
=
-
rjl
[
0
];
rlj
[
1
]
=
-
rjl
[
1
];
rlj
[
2
]
=
-
rjl
[
2
];
v_tally3
(
atomi
,
atomj
,
atoml
,
fi
,
fl
,
rij
,
rlj
);
}
}
}
// evaluate Nij conj
Nijconj
=
1.0
+
(
NconjtmpI
*
NconjtmpI
)
+
(
NconjtmpJ
*
NconjtmpJ
);
piRC
=
piRCSpline
(
NijC
+
NijH
,
NjiC
+
NjiH
,
Nijconj
,
itype
,
jtype
,
dN3
);
// piRC forces
REBO_neighs_i
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
atomk
=
REBO_neighs_i
[
k
];
if
(
atomk
!=
atomj
)
{
ktype
=
map
[
type
[
atomk
]];
rik
[
0
]
=
x
[
atomi
][
0
]
-
x
[
atomk
][
0
];
rik
[
1
]
=
x
[
atomi
][
1
]
-
x
[
atomk
][
1
];
rik
[
2
]
=
x
[
atomi
][
2
]
-
x
[
atomk
][
2
];
rikmag
=
sqrt
((
rik
[
0
]
*
rik
[
0
])
+
(
rik
[
1
]
*
rik
[
1
])
+
(
rik
[
2
]
*
rik
[
2
]));
wik
=
Sp
(
rikmag
,
rcmin
[
itype
][
ktype
],
rcmax
[
itype
][
ktype
],
dwik
);
Nki
=
nC
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
0
))
+
nH
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
1
));
SpN
=
Sp
(
Nki
,
Nmin
,
Nmax
,
dNki
);
tmp2
=
VA
*
dN3
[
0
]
*
dwik
/
rikmag
;
f
[
atomi
][
0
]
-=
tmp2
*
rik
[
0
];
f
[
atomi
][
1
]
-=
tmp2
*
rik
[
1
];
f
[
atomi
][
2
]
-=
tmp2
*
rik
[
2
];
f
[
atomk
][
0
]
+=
tmp2
*
rik
[
0
];
f
[
atomk
][
1
]
+=
tmp2
*
rik
[
1
];
f
[
atomk
][
2
]
+=
tmp2
*
rik
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomi
,
atomk
,
-
tmp2
,
rik
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpI
*
dwik
*
SpN
)
/
rikmag
;
f
[
atomi
][
0
]
-=
tmp2
*
rik
[
0
];
f
[
atomi
][
1
]
-=
tmp2
*
rik
[
1
];
f
[
atomi
][
2
]
-=
tmp2
*
rik
[
2
];
f
[
atomk
][
0
]
+=
tmp2
*
rik
[
0
];
f
[
atomk
][
1
]
+=
tmp2
*
rik
[
1
];
f
[
atomk
][
2
]
+=
tmp2
*
rik
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomi
,
atomk
,
-
tmp2
,
rik
);
if
(
fabs
(
dNki
)
>
TOL
)
{
REBO_neighs_k
=
REBO_firstneigh
[
atomk
];
for
(
n
=
0
;
n
<
REBO_numneigh
[
atomk
];
n
++
)
{
atomn
=
REBO_neighs_k
[
n
];
if
(
atomn
!=
atomi
)
{
ntype
=
map
[
type
[
atomn
]];
rkn
[
0
]
=
x
[
atomk
][
0
]
-
x
[
atomn
][
0
];
rkn
[
1
]
=
x
[
atomk
][
1
]
-
x
[
atomn
][
1
];
rkn
[
2
]
=
x
[
atomk
][
2
]
-
x
[
atomn
][
2
];
rknmag
=
sqrt
((
rkn
[
0
]
*
rkn
[
0
])
+
(
rkn
[
1
]
*
rkn
[
1
])
+
(
rkn
[
2
]
*
rkn
[
2
]));
Sp
(
rknmag
,
rcmin
[
ktype
][
ntype
],
rcmax
[
ktype
][
ntype
],
dwkn
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpI
*
wik
*
dNki
*
dwkn
)
/
rknmag
;
f
[
atomk
][
0
]
-=
tmp2
*
rkn
[
0
];
f
[
atomk
][
1
]
-=
tmp2
*
rkn
[
1
];
f
[
atomk
][
2
]
-=
tmp2
*
rkn
[
2
];
f
[
atomn
][
0
]
+=
tmp2
*
rkn
[
0
];
f
[
atomn
][
1
]
+=
tmp2
*
rkn
[
1
];
f
[
atomn
][
2
]
+=
tmp2
*
rkn
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomk
,
atomn
,
-
tmp2
,
rkn
);
}
}
}
}
}
// piRC forces
REBO_neighs
=
REBO_firstneigh
[
atomj
];
for
(
l
=
0
;
l
<
REBO_numneigh
[
atomj
];
l
++
)
{
atoml
=
REBO_neighs
[
l
];
if
(
atoml
!=
atomi
)
{
ltype
=
map
[
type
[
atoml
]];
rjl
[
0
]
=
x
[
atomj
][
0
]
-
x
[
atoml
][
0
];
rjl
[
1
]
=
x
[
atomj
][
1
]
-
x
[
atoml
][
1
];
rjl
[
2
]
=
x
[
atomj
][
2
]
-
x
[
atoml
][
2
];
rjlmag
=
sqrt
((
rjl
[
0
]
*
rjl
[
0
])
+
(
rjl
[
1
]
*
rjl
[
1
])
+
(
rjl
[
2
]
*
rjl
[
2
]));
wjl
=
Sp
(
rjlmag
,
rcmin
[
jtype
][
ltype
],
rcmax
[
jtype
][
ltype
],
dwjl
);
Nlj
=
nC
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
0
))
+
nH
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
1
));
SpN
=
Sp
(
Nlj
,
Nmin
,
Nmax
,
dNlj
);
tmp2
=
VA
*
dN3
[
1
]
*
dwjl
/
rjlmag
;
f
[
atomj
][
0
]
-=
tmp2
*
rjl
[
0
];
f
[
atomj
][
1
]
-=
tmp2
*
rjl
[
1
];
f
[
atomj
][
2
]
-=
tmp2
*
rjl
[
2
];
f
[
atoml
][
0
]
+=
tmp2
*
rjl
[
0
];
f
[
atoml
][
1
]
+=
tmp2
*
rjl
[
1
];
f
[
atoml
][
2
]
+=
tmp2
*
rjl
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomj
,
atoml
,
-
tmp2
,
rjl
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpJ
*
dwjl
*
SpN
)
/
rjlmag
;
f
[
atomj
][
0
]
-=
tmp2
*
rjl
[
0
];
f
[
atomj
][
1
]
-=
tmp2
*
rjl
[
1
];
f
[
atomj
][
2
]
-=
tmp2
*
rjl
[
2
];
f
[
atoml
][
0
]
+=
tmp2
*
rjl
[
0
];
f
[
atoml
][
1
]
+=
tmp2
*
rjl
[
1
];
f
[
atoml
][
2
]
+=
tmp2
*
rjl
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomj
,
atoml
,
-
tmp2
,
rjl
);
if
(
fabs
(
dNlj
)
>
TOL
)
{
REBO_neighs_l
=
REBO_firstneigh
[
atoml
];
for
(
n
=
0
;
n
<
REBO_numneigh
[
atoml
];
n
++
)
{
atomn
=
REBO_neighs_l
[
n
];
if
(
atomn
!=
atomj
)
{
ntype
=
map
[
type
[
atomn
]];
rln
[
0
]
=
x
[
atoml
][
0
]
-
x
[
atomn
][
0
];
rln
[
1
]
=
x
[
atoml
][
1
]
-
x
[
atomn
][
1
];
rln
[
2
]
=
x
[
atoml
][
2
]
-
x
[
atomn
][
2
];
rlnmag
=
sqrt
((
rln
[
0
]
*
rln
[
0
])
+
(
rln
[
1
]
*
rln
[
1
])
+
(
rln
[
2
]
*
rln
[
2
]));
Sp
(
rlnmag
,
rcmin
[
ltype
][
ntype
],
rcmax
[
ltype
][
ntype
],
dwln
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpJ
*
wjl
*
dNlj
*
dwln
)
/
rlnmag
;
f
[
atoml
][
0
]
-=
tmp2
*
rln
[
0
];
f
[
atoml
][
1
]
-=
tmp2
*
rln
[
1
];
f
[
atoml
][
2
]
-=
tmp2
*
rln
[
2
];
f
[
atomn
][
0
]
+=
tmp2
*
rln
[
0
];
f
[
atomn
][
1
]
+=
tmp2
*
rln
[
1
];
f
[
atomn
][
2
]
+=
tmp2
*
rln
[
2
];
if
(
vflag_atom
)
v_tally2
(
atoml
,
atomn
,
-
tmp2
,
rln
);
}
}
}
}
}
Tij
=
0.0
;
dN3
[
0
]
=
0.0
;
dN3
[
1
]
=
0.0
;
dN3
[
2
]
=
0.0
;
if
(
itype
==
0
&&
jtype
==
0
)
Tij
=
TijSpline
((
NijC
+
NijH
),(
NjiC
+
NjiH
),
Nijconj
,
dN3
);
Etmp
=
0.0
;
if
(
fabs
(
Tij
)
>
TOL
)
{
atom2
=
atomi
;
atom3
=
atomj
;
r32
[
0
]
=
x
[
atom3
][
0
]
-
x
[
atom2
][
0
];
r32
[
1
]
=
x
[
atom3
][
1
]
-
x
[
atom2
][
1
];
r32
[
2
]
=
x
[
atom3
][
2
]
-
x
[
atom2
][
2
];
r32mag
=
sqrt
((
r32
[
0
]
*
r32
[
0
])
+
(
r32
[
1
]
*
r32
[
1
])
+
(
r32
[
2
]
*
r32
[
2
]));
r23
[
0
]
=
-
r32
[
0
];
r23
[
1
]
=
-
r32
[
1
];
r23
[
2
]
=
-
r32
[
2
];
r23mag
=
r32mag
;
REBO_neighs_i
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
atomk
=
REBO_neighs_i
[
k
];
atom1
=
atomk
;
ktype
=
map
[
type
[
atomk
]];
if
(
atomk
!=
atomj
)
{
r21
[
0
]
=
x
[
atom2
][
0
]
-
x
[
atom1
][
0
];
r21
[
1
]
=
x
[
atom2
][
1
]
-
x
[
atom1
][
1
];
r21
[
2
]
=
x
[
atom2
][
2
]
-
x
[
atom1
][
2
];
r21mag
=
sqrt
(
r21
[
0
]
*
r21
[
0
]
+
r21
[
1
]
*
r21
[
1
]
+
r21
[
2
]
*
r21
[
2
]);
cos321
=
-
1.0
*
((
r21
[
0
]
*
r32
[
0
])
+
(
r21
[
1
]
*
r32
[
1
])
+
(
r21
[
2
]
*
r32
[
2
]))
/
(
r21mag
*
r32mag
);
cos321
=
MIN
(
cos321
,
1.0
);
cos321
=
MAX
(
cos321
,
-
1.0
);
Sp2
(
cos321
,
thmin
,
thmax
,
dcut321
);
sin321
=
sqrt
(
1.0
-
cos321
*
cos321
);
sink2i
=
1.0
/
(
sin321
*
sin321
);
rik2i
=
1.0
/
(
r21mag
*
r21mag
);
if
(
sin321
!=
0.0
)
{
rr
=
(
r23mag
*
r23mag
)
-
(
r21mag
*
r21mag
);
rjk
[
0
]
=
r21
[
0
]
-
r23
[
0
];
rjk
[
1
]
=
r21
[
1
]
-
r23
[
1
];
rjk
[
2
]
=
r21
[
2
]
-
r23
[
2
];
rjk2
=
(
rjk
[
0
]
*
rjk
[
0
])
+
(
rjk
[
1
]
*
rjk
[
1
])
+
(
rjk
[
2
]
*
rjk
[
2
]);
rijrik
=
2.0
*
r23mag
*
r21mag
;
rik2
=
r21mag
*
r21mag
;
dctik
=
(
-
rr
+
rjk2
)
/
(
rijrik
*
rik2
);
dctij
=
(
rr
+
rjk2
)
/
(
rijrik
*
r23mag
*
r23mag
);
dctjk
=
-
2.0
/
rijrik
;
w21
=
Sp
(
r21mag
,
rcmin
[
itype
][
ktype
],
rcmaxp
[
itype
][
ktype
],
dw21
);
rijmag
=
r32mag
;
rikmag
=
r21mag
;
rij2
=
r32mag
*
r32mag
;
rik2
=
r21mag
*
r21mag
;
costmp
=
0.5
*
(
rij2
+
rik2
-
rjk2
)
/
rijmag
/
rikmag
;
tspjik
=
Sp2
(
costmp
,
thmin
,
thmax
,
dtsjik
);
dtsjik
=
-
dtsjik
;
REBO_neighs_j
=
REBO_firstneigh
[
j
];
for
(
l
=
0
;
l
<
REBO_numneigh
[
j
];
l
++
)
{
atoml
=
REBO_neighs_j
[
l
];
atom4
=
atoml
;
ltype
=
map
[
type
[
atoml
]];
if
(
!
(
atoml
==
atomi
||
atoml
==
atomk
))
{
r34
[
0
]
=
x
[
atom3
][
0
]
-
x
[
atom4
][
0
];
r34
[
1
]
=
x
[
atom3
][
1
]
-
x
[
atom4
][
1
];
r34
[
2
]
=
x
[
atom3
][
2
]
-
x
[
atom4
][
2
];
r34mag
=
sqrt
((
r34
[
0
]
*
r34
[
0
])
+
(
r34
[
1
]
*
r34
[
1
])
+
(
r34
[
2
]
*
r34
[
2
]));
cos234
=
(
r32
[
0
]
*
r34
[
0
]
+
r32
[
1
]
*
r34
[
1
]
+
r32
[
2
]
*
r34
[
2
])
/
(
r32mag
*
r34mag
);
cos234
=
MIN
(
cos234
,
1.0
);
cos234
=
MAX
(
cos234
,
-
1.0
);
sin234
=
sqrt
(
1.0
-
cos234
*
cos234
);
sinl2i
=
1.0
/
(
sin234
*
sin234
);
rjl2i
=
1.0
/
(
r34mag
*
r34mag
);
if
(
sin234
!=
0.0
)
{
w34
=
Sp
(
r34mag
,
rcmin
[
jtype
][
ltype
],
rcmaxp
[
jtype
][
ltype
],
dw34
);
rr
=
(
r23mag
*
r23mag
)
-
(
r34mag
*
r34mag
);
ril
[
0
]
=
r23
[
0
]
+
r34
[
0
];
ril
[
1
]
=
r23
[
1
]
+
r34
[
1
];
ril
[
2
]
=
r23
[
2
]
+
r34
[
2
];
ril2
=
(
ril
[
0
]
*
ril
[
0
])
+
(
ril
[
1
]
*
ril
[
1
])
+
(
ril
[
2
]
*
ril
[
2
]);
rijrjl
=
2.0
*
r23mag
*
r34mag
;
rjl2
=
r34mag
*
r34mag
;
dctjl
=
(
-
rr
+
ril2
)
/
(
rijrjl
*
rjl2
);
dctji
=
(
rr
+
ril2
)
/
(
rijrjl
*
r23mag
*
r23mag
);
dctil
=
-
2.0
/
rijrjl
;
rjlmag
=
r34mag
;
rjl2
=
r34mag
*
r34mag
;
costmp
=
0.5
*
(
rij2
+
rjl2
-
ril2
)
/
rijmag
/
rjlmag
;
tspijl
=
Sp2
(
costmp
,
thmin
,
thmax
,
dtsijl
);
dtsijl
=
-
dtsijl
;
prefactor
=
VA
*
Tij
;
cross321
[
0
]
=
(
r32
[
1
]
*
r21
[
2
])
-
(
r32
[
2
]
*
r21
[
1
]);
cross321
[
1
]
=
(
r32
[
2
]
*
r21
[
0
])
-
(
r32
[
0
]
*
r21
[
2
]);
cross321
[
2
]
=
(
r32
[
0
]
*
r21
[
1
])
-
(
r32
[
1
]
*
r21
[
0
]);
cross234
[
0
]
=
(
r23
[
1
]
*
r34
[
2
])
-
(
r23
[
2
]
*
r34
[
1
]);
cross234
[
1
]
=
(
r23
[
2
]
*
r34
[
0
])
-
(
r23
[
0
]
*
r34
[
2
]);
cross234
[
2
]
=
(
r23
[
0
]
*
r34
[
1
])
-
(
r23
[
1
]
*
r34
[
0
]);
cwnum
=
(
cross321
[
0
]
*
cross234
[
0
])
+
(
cross321
[
1
]
*
cross234
[
1
])
+
(
cross321
[
2
]
*
cross234
[
2
]);
cwnom
=
r21mag
*
r34mag
*
r23mag
*
r23mag
*
sin321
*
sin234
;
om1234
=
cwnum
/
cwnom
;
cw
=
om1234
;
Etmp
+=
((
1.0
-
square
(
om1234
))
*
w21
*
w34
)
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
);
dt1dik
=
(
rik2i
)
-
(
dctik
*
sink2i
*
cos321
);
dt1djk
=
(
-
dctjk
*
sink2i
*
cos321
);
dt1djl
=
(
rjl2i
)
-
(
dctjl
*
sinl2i
*
cos234
);
dt1dil
=
(
-
dctil
*
sinl2i
*
cos234
);
dt1dij
=
(
2.0
/
(
r23mag
*
r23mag
))
-
(
dctij
*
sink2i
*
cos321
)
-
(
dctji
*
sinl2i
*
cos234
);
dt2dik
[
0
]
=
(
-
r23
[
2
]
*
cross234
[
1
])
+
(
r23
[
1
]
*
cross234
[
2
]);
dt2dik
[
1
]
=
(
-
r23
[
0
]
*
cross234
[
2
])
+
(
r23
[
2
]
*
cross234
[
0
]);
dt2dik
[
2
]
=
(
-
r23
[
1
]
*
cross234
[
0
])
+
(
r23
[
0
]
*
cross234
[
1
]);
dt2djl
[
0
]
=
(
-
r23
[
1
]
*
cross321
[
2
])
+
(
r23
[
2
]
*
cross321
[
1
]);
dt2djl
[
1
]
=
(
-
r23
[
2
]
*
cross321
[
0
])
+
(
r23
[
0
]
*
cross321
[
2
]);
dt2djl
[
2
]
=
(
-
r23
[
0
]
*
cross321
[
1
])
+
(
r23
[
1
]
*
cross321
[
0
]);
dt2dij
[
0
]
=
(
r21
[
2
]
*
cross234
[
1
])
-
(
r34
[
2
]
*
cross321
[
1
])
-
(
r21
[
1
]
*
cross234
[
2
])
+
(
r34
[
1
]
*
cross321
[
2
]);
dt2dij
[
1
]
=
(
r21
[
0
]
*
cross234
[
2
])
-
(
r34
[
0
]
*
cross321
[
2
])
-
(
r21
[
2
]
*
cross234
[
0
])
+
(
r34
[
2
]
*
cross321
[
0
]);
dt2dij
[
2
]
=
(
r21
[
1
]
*
cross234
[
0
])
-
(
r34
[
1
]
*
cross321
[
0
])
-
(
r21
[
0
]
*
cross234
[
1
])
+
(
r34
[
0
]
*
cross321
[
1
]);
aa
=
(
prefactor
*
2.0
*
cw
/
cwnom
)
*
w21
*
w34
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
);
aaa1
=
-
prefactor
*
(
1.0
-
square
(
om1234
))
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
);
aaa2
=
aaa1
*
w21
*
w34
;
at2
=
aa
*
cwnum
;
fcijpc
=
(
-
dt1dij
*
at2
)
+
(
aaa2
*
dtsjik
*
dctij
*
(
1.0
-
tspijl
))
+
(
aaa2
*
dtsijl
*
dctji
*
(
1.0
-
tspjik
));
fcikpc
=
(
-
dt1dik
*
at2
)
+
(
aaa2
*
dtsjik
*
dctik
*
(
1.0
-
tspijl
));
fcjlpc
=
(
-
dt1djl
*
at2
)
+
(
aaa2
*
dtsijl
*
dctjl
*
(
1.0
-
tspjik
));
fcjkpc
=
(
-
dt1djk
*
at2
)
+
(
aaa2
*
dtsjik
*
dctjk
*
(
1.0
-
tspijl
));
fcilpc
=
(
-
dt1dil
*
at2
)
+
(
aaa2
*
dtsijl
*
dctil
*
(
1.0
-
tspjik
));
F23
[
0
]
=
(
fcijpc
*
r23
[
0
])
+
(
aa
*
dt2dij
[
0
]);
F23
[
1
]
=
(
fcijpc
*
r23
[
1
])
+
(
aa
*
dt2dij
[
1
]);
F23
[
2
]
=
(
fcijpc
*
r23
[
2
])
+
(
aa
*
dt2dij
[
2
]);
F12
[
0
]
=
(
fcikpc
*
r21
[
0
])
+
(
aa
*
dt2dik
[
0
]);
F12
[
1
]
=
(
fcikpc
*
r21
[
1
])
+
(
aa
*
dt2dik
[
1
]);
F12
[
2
]
=
(
fcikpc
*
r21
[
2
])
+
(
aa
*
dt2dik
[
2
]);
F34
[
0
]
=
(
fcjlpc
*
r34
[
0
])
+
(
aa
*
dt2djl
[
0
]);
F34
[
1
]
=
(
fcjlpc
*
r34
[
1
])
+
(
aa
*
dt2djl
[
1
]);
F34
[
2
]
=
(
fcjlpc
*
r34
[
2
])
+
(
aa
*
dt2djl
[
2
]);
F31
[
0
]
=
(
fcjkpc
*
rjk
[
0
]);
F31
[
1
]
=
(
fcjkpc
*
rjk
[
1
]);
F31
[
2
]
=
(
fcjkpc
*
rjk
[
2
]);
F24
[
0
]
=
(
fcilpc
*
ril
[
0
]);
F24
[
1
]
=
(
fcilpc
*
ril
[
1
]);
F24
[
2
]
=
(
fcilpc
*
ril
[
2
]);
f1
[
0
]
=
-
F12
[
0
]
-
F31
[
0
];
f1
[
1
]
=
-
F12
[
1
]
-
F31
[
1
];
f1
[
2
]
=
-
F12
[
2
]
-
F31
[
2
];
f2
[
0
]
=
F23
[
0
]
+
F12
[
0
]
+
F24
[
0
];
f2
[
1
]
=
F23
[
1
]
+
F12
[
1
]
+
F24
[
1
];
f2
[
2
]
=
F23
[
2
]
+
F12
[
2
]
+
F24
[
2
];
f3
[
0
]
=
-
F23
[
0
]
+
F34
[
0
]
+
F31
[
0
];
f3
[
1
]
=
-
F23
[
1
]
+
F34
[
1
]
+
F31
[
1
];
f3
[
2
]
=
-
F23
[
2
]
+
F34
[
2
]
+
F31
[
2
];
f4
[
0
]
=
-
F34
[
0
]
-
F24
[
0
];
f4
[
1
]
=
-
F34
[
1
]
-
F24
[
1
];
f4
[
2
]
=
-
F34
[
2
]
-
F24
[
2
];
// coordination forces
tmp2
=
VA
*
Tij
*
((
1.0
-
(
om1234
*
om1234
)))
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
)
*
dw21
*
w34
/
r21mag
;
f2
[
0
]
-=
tmp2
*
r21
[
0
];
f2
[
1
]
-=
tmp2
*
r21
[
1
];
f2
[
2
]
-=
tmp2
*
r21
[
2
];
f1
[
0
]
+=
tmp2
*
r21
[
0
];
f1
[
1
]
+=
tmp2
*
r21
[
1
];
f1
[
2
]
+=
tmp2
*
r21
[
2
];
tmp2
=
VA
*
Tij
*
((
1.0
-
(
om1234
*
om1234
)))
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
)
*
w21
*
dw34
/
r34mag
;
f3
[
0
]
-=
tmp2
*
r34
[
0
];
f3
[
1
]
-=
tmp2
*
r34
[
1
];
f3
[
2
]
-=
tmp2
*
r34
[
2
];
f4
[
0
]
+=
tmp2
*
r34
[
0
];
f4
[
1
]
+=
tmp2
*
r34
[
1
];
f4
[
2
]
+=
tmp2
*
r34
[
2
];
f
[
atom1
][
0
]
+=
f1
[
0
];
f
[
atom1
][
1
]
+=
f1
[
1
];
f
[
atom1
][
2
]
+=
f1
[
2
];
f
[
atom2
][
0
]
+=
f2
[
0
];
f
[
atom2
][
1
]
+=
f2
[
1
];
f
[
atom2
][
2
]
+=
f2
[
2
];
f
[
atom3
][
0
]
+=
f3
[
0
];
f
[
atom3
][
1
]
+=
f3
[
1
];
f
[
atom3
][
2
]
+=
f3
[
2
];
f
[
atom4
][
0
]
+=
f4
[
0
];
f
[
atom4
][
1
]
+=
f4
[
1
];
f
[
atom4
][
2
]
+=
f4
[
2
];
if
(
vflag_atom
)
{
r13
[
0
]
=
-
rjk
[
0
];
r13
[
1
]
=
-
rjk
[
1
];
r13
[
2
]
=
-
rjk
[
2
];
r43
[
0
]
=
-
r34
[
0
];
r43
[
1
]
=
-
r34
[
1
];
r43
[
2
]
=
-
r34
[
2
];
v_tally4
(
atom1
,
atom2
,
atom3
,
atom4
,
f1
,
f2
,
f4
,
r13
,
r23
,
r43
);
}
}
}
}
}
}
}
// Tij forces now that we have Etmp
REBO_neighs
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
atomk
=
REBO_neighs
[
k
];
if
(
atomk
!=
atomj
)
{
ktype
=
map
[
type
[
atomk
]];
rik
[
0
]
=
x
[
atomi
][
0
]
-
x
[
atomk
][
0
];
rik
[
1
]
=
x
[
atomi
][
1
]
-
x
[
atomk
][
1
];
rik
[
2
]
=
x
[
atomi
][
2
]
-
x
[
atomk
][
2
];
rikmag
=
sqrt
((
rik
[
0
]
*
rik
[
0
])
+
(
rik
[
1
]
*
rik
[
1
])
+
(
rik
[
2
]
*
rik
[
2
]));
wik
=
Sp
(
rikmag
,
rcmin
[
itype
][
ktype
],
rcmax
[
itype
][
ktype
],
dwik
);
Nki
=
nC
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
0
))
+
nH
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
1
));
SpN
=
Sp
(
Nki
,
Nmin
,
Nmax
,
dNki
);
tmp2
=
VA
*
dN3
[
0
]
*
dwik
*
Etmp
/
rikmag
;
f
[
atomi
][
0
]
-=
tmp2
*
rik
[
0
];
f
[
atomi
][
1
]
-=
tmp2
*
rik
[
1
];
f
[
atomi
][
2
]
-=
tmp2
*
rik
[
2
];
f
[
atomk
][
0
]
+=
tmp2
*
rik
[
0
];
f
[
atomk
][
1
]
+=
tmp2
*
rik
[
1
];
f
[
atomk
][
2
]
+=
tmp2
*
rik
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomi
,
atomk
,
-
tmp2
,
rik
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpI
*
dwik
*
SpN
)
*
Etmp
/
rikmag
;
f
[
atomi
][
0
]
-=
tmp2
*
rik
[
0
];
f
[
atomi
][
1
]
-=
tmp2
*
rik
[
1
];
f
[
atomi
][
2
]
-=
tmp2
*
rik
[
2
];
f
[
atomk
][
0
]
+=
tmp2
*
rik
[
0
];
f
[
atomk
][
1
]
+=
tmp2
*
rik
[
1
];
f
[
atomk
][
2
]
+=
tmp2
*
rik
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomi
,
atomk
,
-
tmp2
,
rik
);
if
(
fabs
(
dNki
)
>
TOL
)
{
REBO_neighs_k
=
REBO_firstneigh
[
atomk
];
for
(
n
=
0
;
n
<
REBO_numneigh
[
atomk
];
n
++
)
{
atomn
=
REBO_neighs_k
[
n
];
ntype
=
map
[
type
[
atomn
]];
if
(
atomn
!=
atomi
)
{
rkn
[
0
]
=
x
[
atomk
][
0
]
-
x
[
atomn
][
0
];
rkn
[
1
]
=
x
[
atomk
][
1
]
-
x
[
atomn
][
1
];
rkn
[
2
]
=
x
[
atomk
][
2
]
-
x
[
atomn
][
2
];
rknmag
=
sqrt
((
rkn
[
0
]
*
rkn
[
0
])
+
(
rkn
[
1
]
*
rkn
[
1
])
+
(
rkn
[
2
]
*
rkn
[
2
]));
Sp
(
rknmag
,
rcmin
[
ktype
][
ntype
],
rcmax
[
ktype
][
ntype
],
dwkn
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpI
*
wik
*
dNki
*
dwkn
)
*
Etmp
/
rknmag
;
f
[
atomk
][
0
]
-=
tmp2
*
rkn
[
0
];
f
[
atomk
][
1
]
-=
tmp2
*
rkn
[
1
];
f
[
atomk
][
2
]
-=
tmp2
*
rkn
[
2
];
f
[
atomn
][
0
]
+=
tmp2
*
rkn
[
0
];
f
[
atomn
][
1
]
+=
tmp2
*
rkn
[
1
];
f
[
atomn
][
2
]
+=
tmp2
*
rkn
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomk
,
atomn
,
-
tmp2
,
rkn
);
}
}
}
}
}
// Tij forces
REBO_neighs
=
REBO_firstneigh
[
j
];
for
(
l
=
0
;
l
<
REBO_numneigh
[
j
];
l
++
)
{
atoml
=
REBO_neighs
[
l
];
if
(
atoml
!=
atomi
)
{
ltype
=
map
[
type
[
atoml
]];
rjl
[
0
]
=
x
[
atomj
][
0
]
-
x
[
atoml
][
0
];
rjl
[
1
]
=
x
[
atomj
][
1
]
-
x
[
atoml
][
1
];
rjl
[
2
]
=
x
[
atomj
][
2
]
-
x
[
atoml
][
2
];
rjlmag
=
sqrt
((
rjl
[
0
]
*
rjl
[
0
])
+
(
rjl
[
1
]
*
rjl
[
1
])
+
(
rjl
[
2
]
*
rjl
[
2
]));
wjl
=
Sp
(
rjlmag
,
rcmin
[
jtype
][
ltype
],
rcmax
[
jtype
][
ltype
],
dwjl
);
Nlj
=
nC
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
0
))
+
nH
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
1
));
SpN
=
Sp
(
Nlj
,
Nmin
,
Nmax
,
dNlj
);
tmp2
=
VA
*
dN3
[
1
]
*
dwjl
*
Etmp
/
rjlmag
;
f
[
atomj
][
0
]
-=
tmp2
*
rjl
[
0
];
f
[
atomj
][
1
]
-=
tmp2
*
rjl
[
1
];
f
[
atomj
][
2
]
-=
tmp2
*
rjl
[
2
];
f
[
atoml
][
0
]
+=
tmp2
*
rjl
[
0
];
f
[
atoml
][
1
]
+=
tmp2
*
rjl
[
1
];
f
[
atoml
][
2
]
+=
tmp2
*
rjl
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomj
,
atoml
,
-
tmp2
,
rjl
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpJ
*
dwjl
*
SpN
)
*
Etmp
/
rjlmag
;
f
[
atomj
][
0
]
-=
tmp2
*
rjl
[
0
];
f
[
atomj
][
1
]
-=
tmp2
*
rjl
[
1
];
f
[
atomj
][
2
]
-=
tmp2
*
rjl
[
2
];
f
[
atoml
][
0
]
+=
tmp2
*
rjl
[
0
];
f
[
atoml
][
1
]
+=
tmp2
*
rjl
[
1
];
f
[
atoml
][
2
]
+=
tmp2
*
rjl
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomj
,
atoml
,
-
tmp2
,
rjl
);
if
(
fabs
(
dNlj
)
>
TOL
)
{
REBO_neighs_l
=
REBO_firstneigh
[
atoml
];
for
(
n
=
0
;
n
<
REBO_numneigh
[
atoml
];
n
++
)
{
atomn
=
REBO_neighs_l
[
n
];
ntype
=
map
[
type
[
atomn
]];
if
(
atomn
!=
atomj
)
{
rln
[
0
]
=
x
[
atoml
][
0
]
-
x
[
atomn
][
0
];
rln
[
1
]
=
x
[
atoml
][
1
]
-
x
[
atomn
][
1
];
rln
[
2
]
=
x
[
atoml
][
2
]
-
x
[
atomn
][
2
];
rlnmag
=
sqrt
((
rln
[
0
]
*
rln
[
0
])
+
(
rln
[
1
]
*
rln
[
1
])
+
(
rln
[
2
]
*
rln
[
2
]));
Sp
(
rlnmag
,
rcmin
[
ltype
][
ntype
],
rcmax
[
ltype
][
ntype
],
dwln
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpJ
*
wjl
*
dNlj
*
dwln
)
*
Etmp
/
rlnmag
;
f
[
atoml
][
0
]
-=
tmp2
*
rln
[
0
];
f
[
atoml
][
1
]
-=
tmp2
*
rln
[
1
];
f
[
atoml
][
2
]
-=
tmp2
*
rln
[
2
];
f
[
atomn
][
0
]
+=
tmp2
*
rln
[
0
];
f
[
atomn
][
1
]
+=
tmp2
*
rln
[
1
];
f
[
atomn
][
2
]
+=
tmp2
*
rln
[
2
];
if
(
vflag_atom
)
v_tally2
(
atoml
,
atomn
,
-
tmp2
,
rln
);
}
}
}
}
}
}
bij
=
(
0.5
*
(
pij
+
pji
))
+
piRC
+
(
Tij
*
Etmp
);
return
bij
;
}
/* ----------------------------------------------------------------------
Bij* function
------------------------------------------------------------------------- */
double
PairAIREBO
::
bondorderLJ
(
int
i
,
int
j
,
double
rij
[
3
],
double
rijmag
,
double
VA
,
double
rij0
[
3
],
double
rij0mag
,
double
**
f
,
int
vflag_atom
)
{
int
k
,
n
,
l
,
atomk
,
atoml
,
atomn
,
atom1
,
atom2
,
atom3
,
atom4
;
int
atomi
,
atomj
,
itype
,
jtype
,
ktype
,
ltype
,
ntype
;
double
rik
[
3
],
rjl
[
3
],
rkn
[
3
],
rknmag
,
dNki
;
double
NijC
,
NijH
,
NjiC
,
NjiH
,
wik
,
dwik
,
dwkn
,
wjl
;
double
rikmag
,
rjlmag
,
cosjik
,
cosijl
,
g
,
tmp2
,
tmp3
;
double
Etmp
,
pij
,
tmp
,
wij
,
dwij
,
NconjtmpI
,
NconjtmpJ
;
double
Nki
,
Nlj
,
dS
,
lamdajik
,
lamdaijl
,
dgdc
,
dgdN
,
pji
,
Nijconj
,
piRC
;
double
dcosjikdri
[
3
],
dcosijldri
[
3
],
dcosjikdrk
[
3
];
double
dN2
[
2
],
dN3
[
3
];
double
dcosijldrj
[
3
],
dcosijldrl
[
3
],
dcosjikdrj
[
3
],
dwjl
;
double
Tij
,
crosskij
[
3
],
crosskijmag
;
double
crossijl
[
3
],
crossijlmag
,
omkijl
;
double
tmppij
,
tmppji
,
dN2PIJ
[
2
],
dN2PJI
[
2
],
dN3piRC
[
3
],
dN3Tij
[
3
];
double
bij
,
tmp3pij
,
tmp3pji
,
Stb
,
dStb
;
double
r32
[
3
],
r32mag
,
cos321
;
double
om1234
,
rln
[
3
];
double
rlnmag
,
dwln
,
r23
[
3
],
r23mag
,
r21
[
3
],
r21mag
;
double
w21
,
dw21
,
r34
[
3
],
r34mag
,
cos234
,
w34
,
dw34
;
double
cross321
[
3
],
cross234
[
3
],
prefactor
,
SpN
;
double
fcijpc
,
fcikpc
,
fcjlpc
,
fcjkpc
,
fcilpc
;
double
dt2dik
[
3
],
dt2djl
[
3
],
dt2dij
[
3
],
aa
,
aaa1
,
aaa2
,
at2
,
cw
,
cwnum
,
cwnom
;
double
sin321
,
sin234
,
rr
,
rijrik
,
rijrjl
,
rjk2
,
rik2
,
ril2
,
rjl2
;
double
dctik
,
dctjk
,
dctjl
,
dctij
,
dctji
,
dctil
,
rik2i
,
rjl2i
,
sink2i
,
sinl2i
;
double
rjk
[
3
],
ril
[
3
],
dt1dik
,
dt1djk
,
dt1djl
,
dt1dil
,
dt1dij
;
double
dNlj
;
double
PijS
,
PjiS
;
double
rij2
,
tspjik
,
dtsjik
,
tspijl
,
dtsijl
,
costmp
;
int
*
REBO_neighs
,
*
REBO_neighs_i
,
*
REBO_neighs_j
,
*
REBO_neighs_k
,
*
REBO_neighs_l
;
double
F12
[
3
],
F23
[
3
],
F34
[
3
],
F31
[
3
],
F24
[
3
];
double
fi
[
3
],
fj
[
3
],
fk
[
3
],
fl
[
3
],
f1
[
3
],
f2
[
3
],
f3
[
3
],
f4
[
4
];
double
rji
[
3
],
rki
[
3
],
rlj
[
3
],
r13
[
3
],
r43
[
3
];
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
atomi
=
i
;
atomj
=
j
;
itype
=
map
[
type
[
atomi
]];
jtype
=
map
[
type
[
atomj
]];
wij
=
Sp
(
rij0mag
,
rcmin
[
itype
][
jtype
],
rcmax
[
itype
][
jtype
],
dwij
);
NijC
=
nC
[
atomi
]
-
(
wij
*
kronecker
(
jtype
,
0
));
NijH
=
nH
[
atomi
]
-
(
wij
*
kronecker
(
jtype
,
1
));
NjiC
=
nC
[
atomj
]
-
(
wij
*
kronecker
(
itype
,
0
));
NjiH
=
nH
[
atomj
]
-
(
wij
*
kronecker
(
itype
,
1
));
bij
=
0.0
;
tmp
=
0.0
;
tmp2
=
0.0
;
tmp3
=
0.0
;
dgdc
=
0.0
;
dgdN
=
0.0
;
NconjtmpI
=
0.0
;
NconjtmpJ
=
0.0
;
Etmp
=
0.0
;
Stb
=
0.0
;
dStb
=
0.0
;
REBO_neighs
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
atomk
=
REBO_neighs
[
k
];
if
(
atomk
!=
atomj
)
{
ktype
=
map
[
type
[
atomk
]];
rik
[
0
]
=
x
[
atomi
][
0
]
-
x
[
atomk
][
0
];
rik
[
1
]
=
x
[
atomi
][
1
]
-
x
[
atomk
][
1
];
rik
[
2
]
=
x
[
atomi
][
2
]
-
x
[
atomk
][
2
];
rikmag
=
sqrt
((
rik
[
0
]
*
rik
[
0
])
+
(
rik
[
1
]
*
rik
[
1
])
+
(
rik
[
2
]
*
rik
[
2
]));
lamdajik
=
4.0
*
kronecker
(
itype
,
1
)
*
((
rho
[
ktype
][
1
]
-
rikmag
)
-
(
rho
[
jtype
][
1
]
-
rijmag
));
wik
=
Sp
(
rikmag
,
rcmin
[
itype
][
ktype
],
rcmax
[
itype
][
ktype
],
dS
);
Nki
=
nC
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
0
))
+
nH
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
1
));
cosjik
=
((
rij
[
0
]
*
rik
[
0
])
+
(
rij
[
1
]
*
rik
[
1
])
+
(
rij
[
2
]
*
rik
[
2
]))
/
(
rijmag
*
rikmag
);
cosjik
=
MIN
(
cosjik
,
1.0
);
cosjik
=
MAX
(
cosjik
,
-
1.0
);
// evaluate splines g and derivatives dg
g
=
gSpline
(
cosjik
,(
NijC
+
NijH
),
itype
,
&
dgdc
,
&
dgdN
);
Etmp
+=
(
wik
*
g
*
exp
(
lamdajik
));
tmp3
+=
(
wik
*
dgdN
*
exp
(
lamdajik
));
NconjtmpI
=
NconjtmpI
+
(
kronecker
(
ktype
,
0
)
*
wik
*
Sp
(
Nki
,
Nmin
,
Nmax
,
dS
));
}
}
PijS
=
0.0
;
dN2PIJ
[
0
]
=
0.0
;
dN2PIJ
[
1
]
=
0.0
;
PijS
=
PijSpline
(
NijC
,
NijH
,
itype
,
jtype
,
dN2PIJ
);
pij
=
pow
(
1.0
+
Etmp
+
PijS
,
-
0.5
);
tmppij
=
-
.5
*
cube
(
pij
);
tmp3pij
=
tmp3
;
tmp
=
0.0
;
tmp2
=
0.0
;
tmp3
=
0.0
;
Etmp
=
0.0
;
REBO_neighs
=
REBO_firstneigh
[
j
];
for
(
l
=
0
;
l
<
REBO_numneigh
[
j
];
l
++
)
{
atoml
=
REBO_neighs
[
l
];
if
(
atoml
!=
atomi
)
{
ltype
=
map
[
type
[
atoml
]];
rjl
[
0
]
=
x
[
atomj
][
0
]
-
x
[
atoml
][
0
];
rjl
[
1
]
=
x
[
atomj
][
1
]
-
x
[
atoml
][
1
];
rjl
[
2
]
=
x
[
atomj
][
2
]
-
x
[
atoml
][
2
];
rjlmag
=
sqrt
((
rjl
[
0
]
*
rjl
[
0
])
+
(
rjl
[
1
]
*
rjl
[
1
])
+
(
rjl
[
2
]
*
rjl
[
2
]));
lamdaijl
=
4.0
*
kronecker
(
jtype
,
1
)
*
((
rho
[
ltype
][
1
]
-
rjlmag
)
-
(
rho
[
itype
][
1
]
-
rijmag
));
wjl
=
Sp
(
rjlmag
,
rcmin
[
jtype
][
ltype
],
rcmax
[
jtype
][
ltype
],
dS
);
Nlj
=
nC
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
0
))
+
nH
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
1
));
cosijl
=
-
1.0
*
((
rij
[
0
]
*
rjl
[
0
])
+
(
rij
[
1
]
*
rjl
[
1
])
+
(
rij
[
2
]
*
rjl
[
2
]))
/
(
rijmag
*
rjlmag
);
cosijl
=
MIN
(
cosijl
,
1.0
);
cosijl
=
MAX
(
cosijl
,
-
1.0
);
// evaluate splines g and derivatives dg
g
=
gSpline
(
cosijl
,
NjiC
+
NjiH
,
jtype
,
&
dgdc
,
&
dgdN
);
Etmp
+=
(
wjl
*
g
*
exp
(
lamdaijl
));
tmp3
+=
(
wjl
*
dgdN
*
exp
(
lamdaijl
));
NconjtmpJ
=
NconjtmpJ
+
(
kronecker
(
ltype
,
0
)
*
wjl
*
Sp
(
Nlj
,
Nmin
,
Nmax
,
dS
));
}
}
PjiS
=
0.0
;
dN2PJI
[
0
]
=
0.0
;
dN2PJI
[
1
]
=
0.0
;
PjiS
=
PijSpline
(
NjiC
,
NjiH
,
jtype
,
itype
,
dN2PJI
);
pji
=
pow
(
1.0
+
Etmp
+
PjiS
,
-
0.5
);
tmppji
=
-
.5
*
cube
(
pji
);
tmp3pji
=
tmp3
;
// evaluate Nij conj
Nijconj
=
1.0
+
(
NconjtmpI
*
NconjtmpI
)
+
(
NconjtmpJ
*
NconjtmpJ
);
piRC
=
piRCSpline
(
NijC
+
NijH
,
NjiC
+
NjiH
,
Nijconj
,
itype
,
jtype
,
dN3piRC
);
Tij
=
0.0
;
dN3Tij
[
0
]
=
0.0
;
dN3Tij
[
1
]
=
0.0
;
dN3Tij
[
2
]
=
0.0
;
if
(
itype
==
0
&&
jtype
==
0
)
Tij
=
TijSpline
((
NijC
+
NijH
),(
NjiC
+
NjiH
),
Nijconj
,
dN3Tij
);
Etmp
=
0.0
;
if
(
fabs
(
Tij
)
>
TOL
)
{
REBO_neighs_i
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
atomk
=
REBO_neighs_i
[
k
];
ktype
=
map
[
type
[
atomk
]];
if
(
atomk
!=
atomj
)
{
rik
[
0
]
=
x
[
atomi
][
0
]
-
x
[
atomk
][
0
];
rik
[
1
]
=
x
[
atomi
][
1
]
-
x
[
atomk
][
1
];
rik
[
2
]
=
x
[
atomi
][
2
]
-
x
[
atomk
][
2
];
rikmag
=
sqrt
((
rik
[
0
]
*
rik
[
0
])
+
(
rik
[
1
]
*
rik
[
1
])
+
(
rik
[
2
]
*
rik
[
2
]));
cos321
=
((
rij
[
0
]
*
rik
[
0
])
+
(
rij
[
1
]
*
rik
[
1
])
+
(
rij
[
2
]
*
rik
[
2
]))
/
(
rijmag
*
rikmag
);
cos321
=
MIN
(
cos321
,
1.0
);
cos321
=
MAX
(
cos321
,
-
1.0
);
rjk
[
0
]
=
rik
[
0
]
-
rij
[
0
];
rjk
[
1
]
=
rik
[
1
]
-
rij
[
1
];
rjk
[
2
]
=
rik
[
2
]
-
rij
[
2
];
rjk2
=
(
rjk
[
0
]
*
rjk
[
0
])
+
(
rjk
[
1
]
*
rjk
[
1
])
+
(
rjk
[
2
]
*
rjk
[
2
]);
rij2
=
rijmag
*
rijmag
;
rik2
=
rikmag
*
rikmag
;
costmp
=
0.5
*
(
rij2
+
rik2
-
rjk2
)
/
rijmag
/
rikmag
;
tspjik
=
Sp2
(
costmp
,
thmin
,
thmax
,
dtsjik
);
if
(
sqrt
(
1.0
-
cos321
*
cos321
)
>
sqrt
(
TOL
))
{
wik
=
Sp
(
rikmag
,
rcmin
[
itype
][
ktype
],
rcmaxp
[
itype
][
ktype
],
dwik
);
REBO_neighs_j
=
REBO_firstneigh
[
j
];
for
(
l
=
0
;
l
<
REBO_numneigh
[
j
];
l
++
)
{
atoml
=
REBO_neighs_j
[
l
];
ltype
=
map
[
type
[
atoml
]];
if
(
!
(
atoml
==
atomi
||
atoml
==
atomk
))
{
rjl
[
0
]
=
x
[
atomj
][
0
]
-
x
[
atoml
][
0
];
rjl
[
1
]
=
x
[
atomj
][
1
]
-
x
[
atoml
][
1
];
rjl
[
2
]
=
x
[
atomj
][
2
]
-
x
[
atoml
][
2
];
rjlmag
=
sqrt
(
rjl
[
0
]
*
rjl
[
0
]
+
rjl
[
1
]
*
rjl
[
1
]
+
rjl
[
2
]
*
rjl
[
2
]);
cos234
=
-
((
rij
[
0
]
*
rjl
[
0
])
+
(
rij
[
1
]
*
rjl
[
1
])
+
(
rij
[
2
]
*
rjl
[
2
]))
/
(
rijmag
*
rjlmag
);
cos234
=
MIN
(
cos234
,
1.0
);
cos234
=
MAX
(
cos234
,
-
1.0
);
ril
[
0
]
=
rij
[
0
]
+
rjl
[
0
];
ril
[
1
]
=
rij
[
1
]
+
rjl
[
1
];
ril
[
2
]
=
rij
[
2
]
+
rjl
[
2
];
ril2
=
(
ril
[
0
]
*
ril
[
0
])
+
(
ril
[
1
]
*
ril
[
1
])
+
(
ril
[
2
]
*
ril
[
2
]);
rijrjl
=
2.0
*
rijmag
*
rjlmag
;
rjl2
=
rjlmag
*
rjlmag
;
costmp
=
0.5
*
(
rij2
+
rjl2
-
ril2
)
/
rijmag
/
rjlmag
;
tspijl
=
Sp2
(
costmp
,
thmin
,
thmax
,
dtsijl
);
if
(
sqrt
(
1.0
-
cos234
*
cos234
)
>
sqrt
(
TOL
))
{
wjl
=
Sp
(
rjlmag
,
rcmin
[
jtype
][
ltype
],
rcmaxp
[
jtype
][
ltype
],
dS
);
crosskij
[
0
]
=
(
rij
[
1
]
*
rik
[
2
]
-
rij
[
2
]
*
rik
[
1
]);
crosskij
[
1
]
=
(
rij
[
2
]
*
rik
[
0
]
-
rij
[
0
]
*
rik
[
2
]);
crosskij
[
2
]
=
(
rij
[
0
]
*
rik
[
1
]
-
rij
[
1
]
*
rik
[
0
]);
crosskijmag
=
sqrt
(
crosskij
[
0
]
*
crosskij
[
0
]
+
crosskij
[
1
]
*
crosskij
[
1
]
+
crosskij
[
2
]
*
crosskij
[
2
]);
crossijl
[
0
]
=
(
rij
[
1
]
*
rjl
[
2
]
-
rij
[
2
]
*
rjl
[
1
]);
crossijl
[
1
]
=
(
rij
[
2
]
*
rjl
[
0
]
-
rij
[
0
]
*
rjl
[
2
]);
crossijl
[
2
]
=
(
rij
[
0
]
*
rjl
[
1
]
-
rij
[
1
]
*
rjl
[
0
]);
crossijlmag
=
sqrt
(
crossijl
[
0
]
*
crossijl
[
0
]
+
crossijl
[
1
]
*
crossijl
[
1
]
+
crossijl
[
2
]
*
crossijl
[
2
]);
omkijl
=
-
1.0
*
(((
crosskij
[
0
]
*
crossijl
[
0
])
+
(
crosskij
[
1
]
*
crossijl
[
1
])
+
(
crosskij
[
2
]
*
crossijl
[
2
]))
/
(
crosskijmag
*
crossijlmag
));
Etmp
+=
((
1.0
-
square
(
omkijl
))
*
wik
*
wjl
)
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
);
}
}
}
}
}
}
}
bij
=
(
.5
*
(
pij
+
pji
))
+
piRC
+
(
Tij
*
Etmp
);
Stb
=
Sp2
(
bij
,
bLJmin
[
itype
][
jtype
],
bLJmax
[
itype
][
jtype
],
dStb
);
VA
=
VA
*
dStb
;
if
(
dStb
!=
0.0
)
{
tmp
=
tmppij
;
dN2
[
0
]
=
dN2PIJ
[
0
];
dN2
[
1
]
=
dN2PIJ
[
1
];
tmp3
=
tmp3pij
;
// pij forces
REBO_neighs_i
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
atomk
=
REBO_neighs_i
[
k
];
ktype
=
map
[
type
[
atomk
]];
if
(
atomk
!=
atomj
)
{
lamdajik
=
0.0
;
rik
[
0
]
=
x
[
atomi
][
0
]
-
x
[
atomk
][
0
];
rik
[
1
]
=
x
[
atomi
][
1
]
-
x
[
atomk
][
1
];
rik
[
2
]
=
x
[
atomi
][
2
]
-
x
[
atomk
][
2
];
rikmag
=
sqrt
(
rik
[
0
]
*
rik
[
0
]
+
rik
[
1
]
*
rik
[
1
]
+
rik
[
2
]
*
rik
[
2
]);
lamdajik
=
4.0
*
kronecker
(
itype
,
1
)
*
((
rho
[
ktype
][
1
]
-
rikmag
)
-
(
rho
[
jtype
][
1
]
-
rijmag
));
wik
=
Sp
(
rikmag
,
rcmin
[
itype
][
ktype
],
rcmax
[
itype
][
ktype
],
dwik
);
cosjik
=
((
rij
[
0
]
*
rik
[
0
])
+
(
rij
[
1
]
*
rik
[
1
])
+
(
rij
[
2
]
*
rik
[
2
]))
/
(
rijmag
*
rikmag
);
cosjik
=
MIN
(
cosjik
,
1.0
);
cosjik
=
MAX
(
cosjik
,
-
1.0
);
dcosjikdri
[
0
]
=
((
rij
[
0
]
+
rik
[
0
])
/
(
rijmag
*
rikmag
))
-
(
cosjik
*
((
rij
[
0
]
/
(
rijmag
*
rijmag
))
+
(
rik
[
0
]
/
(
rikmag
*
rikmag
))));
dcosjikdri
[
1
]
=
((
rij
[
1
]
+
rik
[
1
])
/
(
rijmag
*
rikmag
))
-
(
cosjik
*
((
rij
[
1
]
/
(
rijmag
*
rijmag
))
+
(
rik
[
1
]
/
(
rikmag
*
rikmag
))));
dcosjikdri
[
2
]
=
((
rij
[
2
]
+
rik
[
2
])
/
(
rijmag
*
rikmag
))
-
(
cosjik
*
((
rij
[
2
]
/
(
rijmag
*
rijmag
))
+
(
rik
[
2
]
/
(
rikmag
*
rikmag
))));
dcosjikdrk
[
0
]
=
(
-
rij
[
0
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rik
[
0
]
/
(
rikmag
*
rikmag
)));
dcosjikdrk
[
1
]
=
(
-
rij
[
1
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rik
[
1
]
/
(
rikmag
*
rikmag
)));
dcosjikdrk
[
2
]
=
(
-
rij
[
2
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rik
[
2
]
/
(
rikmag
*
rikmag
)));
dcosjikdrj
[
0
]
=
(
-
rik
[
0
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rij
[
0
]
/
(
rijmag
*
rijmag
)));
dcosjikdrj
[
1
]
=
(
-
rik
[
1
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rij
[
1
]
/
(
rijmag
*
rijmag
)));
dcosjikdrj
[
2
]
=
(
-
rik
[
2
]
/
(
rijmag
*
rikmag
))
+
(
cosjik
*
(
rij
[
2
]
/
(
rijmag
*
rijmag
)));
g
=
gSpline
(
cosjik
,(
NijC
+
NijH
),
itype
,
&
dgdc
,
&
dgdN
);
tmp2
=
VA
*
.5
*
(
tmp
*
wik
*
dgdc
*
exp
(
lamdajik
));
fj
[
0
]
=
-
tmp2
*
dcosjikdrj
[
0
];
fj
[
1
]
=
-
tmp2
*
dcosjikdrj
[
1
];
fj
[
2
]
=
-
tmp2
*
dcosjikdrj
[
2
];
fi
[
0
]
=
-
tmp2
*
dcosjikdri
[
0
];
fi
[
1
]
=
-
tmp2
*
dcosjikdri
[
1
];
fi
[
2
]
=
-
tmp2
*
dcosjikdri
[
2
];
fk
[
0
]
=
-
tmp2
*
dcosjikdrk
[
0
];
fk
[
1
]
=
-
tmp2
*
dcosjikdrk
[
1
];
fk
[
2
]
=
-
tmp2
*
dcosjikdrk
[
2
];
tmp2
=
VA
*
.5
*
(
tmp
*
wik
*
g
*
exp
(
lamdajik
)
*
4.0
*
kronecker
(
itype
,
1
));
fj
[
0
]
-=
tmp2
*
(
-
rij
[
0
]
/
rijmag
);
fj
[
1
]
-=
tmp2
*
(
-
rij
[
1
]
/
rijmag
);
fj
[
2
]
-=
tmp2
*
(
-
rij
[
2
]
/
rijmag
);
fi
[
0
]
-=
tmp2
*
((
-
rik
[
0
]
/
rikmag
)
+
(
rij
[
0
]
/
rijmag
));
fi
[
1
]
-=
tmp2
*
((
-
rik
[
1
]
/
rikmag
)
+
(
rij
[
1
]
/
rijmag
));
fi
[
2
]
-=
tmp2
*
((
-
rik
[
2
]
/
rikmag
)
+
(
rij
[
2
]
/
rijmag
));
fk
[
0
]
-=
tmp2
*
(
rik
[
0
]
/
rikmag
);
fk
[
1
]
-=
tmp2
*
(
rik
[
1
]
/
rikmag
);
fk
[
2
]
-=
tmp2
*
(
rik
[
2
]
/
rikmag
);
// coordination forces
// dwik forces
tmp2
=
VA
*
.5
*
(
tmp
*
dwik
*
g
*
exp
(
lamdajik
))
/
rikmag
;
fi
[
0
]
-=
tmp2
*
rik
[
0
];
fi
[
1
]
-=
tmp2
*
rik
[
1
];
fi
[
2
]
-=
tmp2
*
rik
[
2
];
fk
[
0
]
+=
tmp2
*
rik
[
0
];
fk
[
1
]
+=
tmp2
*
rik
[
1
];
fk
[
2
]
+=
tmp2
*
rik
[
2
];
// PIJ forces
tmp2
=
VA
*
.5
*
(
tmp
*
dN2
[
ktype
]
*
dwik
)
/
rikmag
;
fi
[
0
]
-=
tmp2
*
rik
[
0
];
fi
[
1
]
-=
tmp2
*
rik
[
1
];
fi
[
2
]
-=
tmp2
*
rik
[
2
];
fk
[
0
]
+=
tmp2
*
rik
[
0
];
fk
[
1
]
+=
tmp2
*
rik
[
1
];
fk
[
2
]
+=
tmp2
*
rik
[
2
];
// dgdN forces
tmp2
=
VA
*
.5
*
(
tmp
*
tmp3
*
dwik
)
/
rikmag
;
fi
[
0
]
-=
tmp2
*
rik
[
0
];
fi
[
1
]
-=
tmp2
*
rik
[
1
];
fi
[
2
]
-=
tmp2
*
rik
[
2
];
fk
[
0
]
+=
tmp2
*
rik
[
0
];
fk
[
1
]
+=
tmp2
*
rik
[
1
];
fk
[
2
]
+=
tmp2
*
rik
[
2
];
f
[
atomi
][
0
]
+=
fi
[
0
];
f
[
atomi
][
1
]
+=
fi
[
1
];
f
[
atomi
][
2
]
+=
fi
[
2
];
f
[
atomj
][
0
]
+=
fj
[
0
];
f
[
atomj
][
1
]
+=
fj
[
1
];
f
[
atomj
][
2
]
+=
fj
[
2
];
f
[
atomk
][
0
]
+=
fk
[
0
];
f
[
atomk
][
1
]
+=
fk
[
1
];
f
[
atomk
][
2
]
+=
fk
[
2
];
if
(
vflag_atom
)
{
rji
[
0
]
=
-
rij
[
0
];
rji
[
1
]
=
-
rij
[
1
];
rji
[
2
]
=
-
rij
[
2
];
rki
[
0
]
=
-
rik
[
0
];
rki
[
1
]
=
-
rik
[
1
];
rki
[
2
]
=
-
rik
[
2
];
v_tally3
(
atomi
,
atomj
,
atomk
,
fj
,
fk
,
rji
,
rki
);
}
}
}
tmp
=
tmppji
;
tmp3
=
tmp3pji
;
dN2
[
0
]
=
dN2PJI
[
0
];
dN2
[
1
]
=
dN2PJI
[
1
];
REBO_neighs
=
REBO_firstneigh
[
j
];
for
(
l
=
0
;
l
<
REBO_numneigh
[
j
];
l
++
)
{
atoml
=
REBO_neighs
[
l
];
if
(
atoml
!=
atomi
)
{
ltype
=
map
[
type
[
atoml
]];
rjl
[
0
]
=
x
[
atomj
][
0
]
-
x
[
atoml
][
0
];
rjl
[
1
]
=
x
[
atomj
][
1
]
-
x
[
atoml
][
1
];
rjl
[
2
]
=
x
[
atomj
][
2
]
-
x
[
atoml
][
2
];
rjlmag
=
sqrt
((
rjl
[
0
]
*
rjl
[
0
])
+
(
rjl
[
1
]
*
rjl
[
1
])
+
(
rjl
[
2
]
*
rjl
[
2
]));
lamdaijl
=
4.0
*
kronecker
(
jtype
,
1
)
*
((
rho
[
ltype
][
1
]
-
rjlmag
)
-
(
rho
[
itype
][
1
]
-
rijmag
));
wjl
=
Sp
(
rjlmag
,
rcmin
[
jtype
][
ltype
],
rcmax
[
jtype
][
ltype
],
dwjl
);
cosijl
=
(
-
1.0
*
((
rij
[
0
]
*
rjl
[
0
])
+
(
rij
[
1
]
*
rjl
[
1
])
+
(
rij
[
2
]
*
rjl
[
2
])))
/
(
rijmag
*
rjlmag
);
cosijl
=
MIN
(
cosijl
,
1.0
);
cosijl
=
MAX
(
cosijl
,
-
1.0
);
dcosijldri
[
0
]
=
(
-
rjl
[
0
]
/
(
rijmag
*
rjlmag
))
-
(
cosijl
*
rij
[
0
]
/
(
rijmag
*
rijmag
));
dcosijldri
[
1
]
=
(
-
rjl
[
1
]
/
(
rijmag
*
rjlmag
))
-
(
cosijl
*
rij
[
1
]
/
(
rijmag
*
rijmag
));
dcosijldri
[
2
]
=
(
-
rjl
[
2
]
/
(
rijmag
*
rjlmag
))
-
(
cosijl
*
rij
[
2
]
/
(
rijmag
*
rijmag
));
dcosijldrj
[
0
]
=
((
-
rij
[
0
]
+
rjl
[
0
])
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
((
rij
[
0
]
/
square
(
rijmag
))
-
(
rjl
[
0
]
/
(
rjlmag
*
rjlmag
))));
dcosijldrj
[
1
]
=
((
-
rij
[
1
]
+
rjl
[
1
])
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
((
rij
[
1
]
/
square
(
rijmag
))
-
(
rjl
[
1
]
/
(
rjlmag
*
rjlmag
))));
dcosijldrj
[
2
]
=
((
-
rij
[
2
]
+
rjl
[
2
])
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
((
rij
[
2
]
/
square
(
rijmag
))
-
(
rjl
[
2
]
/
(
rjlmag
*
rjlmag
))));
dcosijldrl
[
0
]
=
(
rij
[
0
]
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
rjl
[
0
]
/
(
rjlmag
*
rjlmag
));
dcosijldrl
[
1
]
=
(
rij
[
1
]
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
rjl
[
1
]
/
(
rjlmag
*
rjlmag
));
dcosijldrl
[
2
]
=
(
rij
[
2
]
/
(
rijmag
*
rjlmag
))
+
(
cosijl
*
rjl
[
2
]
/
(
rjlmag
*
rjlmag
));
// evaluate splines g and derivatives dg
g
=
gSpline
(
cosijl
,
NjiC
+
NjiH
,
jtype
,
&
dgdc
,
&
dgdN
);
tmp2
=
VA
*
.5
*
(
tmp
*
wjl
*
dgdc
*
exp
(
lamdaijl
));
fi
[
0
]
=
-
tmp2
*
dcosijldri
[
0
];
fi
[
1
]
=
-
tmp2
*
dcosijldri
[
1
];
fi
[
2
]
=
-
tmp2
*
dcosijldri
[
2
];
fj
[
0
]
=
-
tmp2
*
dcosijldrj
[
0
];
fj
[
1
]
=
-
tmp2
*
dcosijldrj
[
1
];
fj
[
2
]
=
-
tmp2
*
dcosijldrj
[
2
];
fl
[
0
]
=
-
tmp2
*
dcosijldrl
[
0
];
fl
[
1
]
=
-
tmp2
*
dcosijldrl
[
1
];
fl
[
2
]
=
-
tmp2
*
dcosijldrl
[
2
];
tmp2
=
VA
*
.5
*
(
tmp
*
wjl
*
g
*
exp
(
lamdaijl
)
*
4.0
*
kronecker
(
jtype
,
1
));
fi
[
0
]
-=
tmp2
*
(
rij
[
0
]
/
rijmag
);
fi
[
1
]
-=
tmp2
*
(
rij
[
1
]
/
rijmag
);
fi
[
2
]
-=
tmp2
*
(
rij
[
2
]
/
rijmag
);
fj
[
0
]
-=
tmp2
*
((
-
rjl
[
0
]
/
rjlmag
)
-
(
rij
[
0
]
/
rijmag
));
fj
[
1
]
-=
tmp2
*
((
-
rjl
[
1
]
/
rjlmag
)
-
(
rij
[
1
]
/
rijmag
));
fj
[
2
]
-=
tmp2
*
((
-
rjl
[
2
]
/
rjlmag
)
-
(
rij
[
2
]
/
rijmag
));
fl
[
0
]
-=
tmp2
*
(
rjl
[
0
]
/
rjlmag
);
fl
[
1
]
-=
tmp2
*
(
rjl
[
1
]
/
rjlmag
);
fl
[
2
]
-=
tmp2
*
(
rjl
[
2
]
/
rjlmag
);
// coordination forces
// dwik forces
tmp2
=
VA
*
.5
*
(
tmp
*
dwjl
*
g
*
exp
(
lamdaijl
))
/
rjlmag
;
fj
[
0
]
-=
tmp2
*
rjl
[
0
];
fj
[
1
]
-=
tmp2
*
rjl
[
1
];
fj
[
2
]
-=
tmp2
*
rjl
[
2
];
fl
[
0
]
+=
tmp2
*
rjl
[
0
];
fl
[
1
]
+=
tmp2
*
rjl
[
1
];
fl
[
2
]
+=
tmp2
*
rjl
[
2
];
// PIJ forces
tmp2
=
VA
*
.5
*
(
tmp
*
dN2
[
ltype
]
*
dwjl
)
/
rjlmag
;
fj
[
0
]
-=
tmp2
*
rjl
[
0
];
fj
[
1
]
-=
tmp2
*
rjl
[
1
];
fj
[
2
]
-=
tmp2
*
rjl
[
2
];
fl
[
0
]
+=
tmp2
*
rjl
[
0
];
fl
[
1
]
+=
tmp2
*
rjl
[
1
];
fl
[
2
]
+=
tmp2
*
rjl
[
2
];
// dgdN forces
tmp2
=
VA
*
.5
*
(
tmp
*
tmp3
*
dwjl
)
/
rjlmag
;
fj
[
0
]
-=
tmp2
*
rjl
[
0
];
fj
[
1
]
-=
tmp2
*
rjl
[
1
];
fj
[
2
]
-=
tmp2
*
rjl
[
2
];
fl
[
0
]
+=
tmp2
*
rjl
[
0
];
fl
[
1
]
+=
tmp2
*
rjl
[
1
];
fl
[
2
]
+=
tmp2
*
rjl
[
2
];
f
[
atomi
][
0
]
+=
fi
[
0
];
f
[
atomi
][
1
]
+=
fi
[
1
];
f
[
atomi
][
2
]
+=
fi
[
2
];
f
[
atomj
][
0
]
+=
fj
[
0
];
f
[
atomj
][
1
]
+=
fj
[
1
];
f
[
atomj
][
2
]
+=
fj
[
2
];
f
[
atoml
][
0
]
+=
fl
[
0
];
f
[
atoml
][
1
]
+=
fl
[
1
];
f
[
atoml
][
2
]
+=
fl
[
2
];
if
(
vflag_atom
)
{
rlj
[
0
]
=
-
rjl
[
0
];
rlj
[
1
]
=
-
rjl
[
1
];
rlj
[
2
]
=
-
rjl
[
2
];
v_tally3
(
atomi
,
atomj
,
atoml
,
fi
,
fl
,
rij
,
rlj
);
}
}
}
// piRC forces
dN3
[
0
]
=
dN3piRC
[
0
];
dN3
[
1
]
=
dN3piRC
[
1
];
dN3
[
2
]
=
dN3piRC
[
2
];
REBO_neighs_i
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
atomk
=
REBO_neighs_i
[
k
];
if
(
atomk
!=
atomj
)
{
ktype
=
map
[
type
[
atomk
]];
rik
[
0
]
=
x
[
atomi
][
0
]
-
x
[
atomk
][
0
];
rik
[
1
]
=
x
[
atomi
][
1
]
-
x
[
atomk
][
1
];
rik
[
2
]
=
x
[
atomi
][
2
]
-
x
[
atomk
][
2
];
rikmag
=
sqrt
((
rik
[
0
]
*
rik
[
0
])
+
(
rik
[
1
]
*
rik
[
1
])
+
(
rik
[
2
]
*
rik
[
2
]));
wik
=
Sp
(
rikmag
,
rcmin
[
itype
][
ktype
],
rcmax
[
itype
][
ktype
],
dwik
);
Nki
=
nC
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
0
))
+
nH
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
1
));
SpN
=
Sp
(
Nki
,
Nmin
,
Nmax
,
dNki
);
tmp2
=
VA
*
dN3
[
0
]
*
dwik
/
rikmag
;
f
[
atomi
][
0
]
-=
tmp2
*
rik
[
0
];
f
[
atomi
][
1
]
-=
tmp2
*
rik
[
1
];
f
[
atomi
][
2
]
-=
tmp2
*
rik
[
2
];
f
[
atomk
][
0
]
+=
tmp2
*
rik
[
0
];
f
[
atomk
][
1
]
+=
tmp2
*
rik
[
1
];
f
[
atomk
][
2
]
+=
tmp2
*
rik
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomi
,
atomk
,
-
tmp2
,
rik
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpI
*
dwik
*
SpN
)
/
rikmag
;
f
[
atomi
][
0
]
-=
tmp2
*
rik
[
0
];
f
[
atomi
][
1
]
-=
tmp2
*
rik
[
1
];
f
[
atomi
][
2
]
-=
tmp2
*
rik
[
2
];
f
[
atomk
][
0
]
+=
tmp2
*
rik
[
0
];
f
[
atomk
][
1
]
+=
tmp2
*
rik
[
1
];
f
[
atomk
][
2
]
+=
tmp2
*
rik
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomi
,
atomk
,
-
tmp2
,
rik
);
if
(
fabs
(
dNki
)
>
TOL
)
{
REBO_neighs_k
=
REBO_firstneigh
[
atomk
];
for
(
n
=
0
;
n
<
REBO_numneigh
[
atomk
];
n
++
)
{
atomn
=
REBO_neighs_k
[
n
];
if
(
atomn
!=
atomi
)
{
ntype
=
map
[
type
[
atomn
]];
rkn
[
0
]
=
x
[
atomk
][
0
]
-
x
[
atomn
][
0
];
rkn
[
1
]
=
x
[
atomk
][
1
]
-
x
[
atomn
][
1
];
rkn
[
2
]
=
x
[
atomk
][
2
]
-
x
[
atomn
][
2
];
rknmag
=
sqrt
((
rkn
[
0
]
*
rkn
[
0
])
+
(
rkn
[
1
]
*
rkn
[
1
])
+
(
rkn
[
2
]
*
rkn
[
2
]));
Sp
(
rknmag
,
rcmin
[
ktype
][
ntype
],
rcmax
[
ktype
][
ntype
],
dwkn
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpI
*
wik
*
dNki
*
dwkn
)
/
rknmag
;
f
[
atomk
][
0
]
-=
tmp2
*
rkn
[
0
];
f
[
atomk
][
1
]
-=
tmp2
*
rkn
[
1
];
f
[
atomk
][
2
]
-=
tmp2
*
rkn
[
2
];
f
[
atomn
][
0
]
+=
tmp2
*
rkn
[
0
];
f
[
atomn
][
1
]
+=
tmp2
*
rkn
[
1
];
f
[
atomn
][
2
]
+=
tmp2
*
rkn
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomk
,
atomn
,
-
tmp2
,
rkn
);
}
}
}
}
}
// piRC forces to J side
REBO_neighs
=
REBO_firstneigh
[
j
];
for
(
l
=
0
;
l
<
REBO_numneigh
[
j
];
l
++
)
{
atoml
=
REBO_neighs
[
l
];
if
(
atoml
!=
atomi
)
{
ltype
=
map
[
type
[
atoml
]];
rjl
[
0
]
=
x
[
atomj
][
0
]
-
x
[
atoml
][
0
];
rjl
[
1
]
=
x
[
atomj
][
1
]
-
x
[
atoml
][
1
];
rjl
[
2
]
=
x
[
atomj
][
2
]
-
x
[
atoml
][
2
];
rjlmag
=
sqrt
((
rjl
[
0
]
*
rjl
[
0
])
+
(
rjl
[
1
]
*
rjl
[
1
])
+
(
rjl
[
2
]
*
rjl
[
2
]));
wjl
=
Sp
(
rjlmag
,
rcmin
[
jtype
][
ltype
],
rcmax
[
jtype
][
ltype
],
dwjl
);
Nlj
=
nC
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
0
))
+
nH
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
1
));
SpN
=
Sp
(
Nlj
,
Nmin
,
Nmax
,
dNlj
);
tmp2
=
VA
*
dN3
[
1
]
*
dwjl
/
rjlmag
;
f
[
atomj
][
0
]
-=
tmp2
*
rjl
[
0
];
f
[
atomj
][
1
]
-=
tmp2
*
rjl
[
1
];
f
[
atomj
][
2
]
-=
tmp2
*
rjl
[
2
];
f
[
atoml
][
0
]
+=
tmp2
*
rjl
[
0
];
f
[
atoml
][
1
]
+=
tmp2
*
rjl
[
1
];
f
[
atoml
][
2
]
+=
tmp2
*
rjl
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomj
,
atoml
,
-
tmp2
,
rjl
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpJ
*
dwjl
*
SpN
)
/
rjlmag
;
f
[
atomj
][
0
]
-=
tmp2
*
rjl
[
0
];
f
[
atomj
][
1
]
-=
tmp2
*
rjl
[
1
];
f
[
atomj
][
2
]
-=
tmp2
*
rjl
[
2
];
f
[
atoml
][
0
]
+=
tmp2
*
rjl
[
0
];
f
[
atoml
][
1
]
+=
tmp2
*
rjl
[
1
];
f
[
atoml
][
2
]
+=
tmp2
*
rjl
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomj
,
atoml
,
-
tmp2
,
rjl
);
if
(
fabs
(
dNlj
)
>
TOL
)
{
REBO_neighs_l
=
REBO_firstneigh
[
atoml
];
for
(
n
=
0
;
n
<
REBO_numneigh
[
atoml
];
n
++
)
{
atomn
=
REBO_neighs_l
[
n
];
if
(
atomn
!=
atomj
)
{
ntype
=
map
[
type
[
atomn
]];
rln
[
0
]
=
x
[
atoml
][
0
]
-
x
[
atomn
][
0
];
rln
[
1
]
=
x
[
atoml
][
1
]
-
x
[
atomn
][
1
];
rln
[
2
]
=
x
[
atoml
][
2
]
-
x
[
atomn
][
2
];
rlnmag
=
sqrt
((
rln
[
0
]
*
rln
[
0
])
+
(
rln
[
1
]
*
rln
[
1
])
+
(
rln
[
2
]
*
rln
[
2
]));
Sp
(
rlnmag
,
rcmin
[
ltype
][
ntype
],
rcmax
[
ltype
][
ntype
],
dwln
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpJ
*
wjl
*
dNlj
*
dwln
)
/
rlnmag
;
f
[
atoml
][
0
]
-=
tmp2
*
rln
[
0
];
f
[
atoml
][
1
]
-=
tmp2
*
rln
[
1
];
f
[
atoml
][
2
]
-=
tmp2
*
rln
[
2
];
f
[
atomn
][
0
]
+=
tmp2
*
rln
[
0
];
f
[
atomn
][
1
]
+=
tmp2
*
rln
[
1
];
f
[
atomn
][
2
]
+=
tmp2
*
rln
[
2
];
if
(
vflag_atom
)
v_tally2
(
atoml
,
atomn
,
-
tmp2
,
rln
);
}
}
}
}
}
if
(
fabs
(
Tij
)
>
TOL
)
{
dN3
[
0
]
=
dN3Tij
[
0
];
dN3
[
1
]
=
dN3Tij
[
1
];
dN3
[
2
]
=
dN3Tij
[
2
];
atom2
=
atomi
;
atom3
=
atomj
;
r32
[
0
]
=
x
[
atom3
][
0
]
-
x
[
atom2
][
0
];
r32
[
1
]
=
x
[
atom3
][
1
]
-
x
[
atom2
][
1
];
r32
[
2
]
=
x
[
atom3
][
2
]
-
x
[
atom2
][
2
];
r32mag
=
sqrt
((
r32
[
0
]
*
r32
[
0
])
+
(
r32
[
1
]
*
r32
[
1
])
+
(
r32
[
2
]
*
r32
[
2
]));
r23
[
0
]
=
-
r32
[
0
];
r23
[
1
]
=
-
r32
[
1
];
r23
[
2
]
=
-
r32
[
2
];
r23mag
=
r32mag
;
REBO_neighs_i
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
atomk
=
REBO_neighs_i
[
k
];
atom1
=
atomk
;
ktype
=
map
[
type
[
atomk
]];
if
(
atomk
!=
atomj
)
{
r21
[
0
]
=
x
[
atom2
][
0
]
-
x
[
atom1
][
0
];
r21
[
1
]
=
x
[
atom2
][
1
]
-
x
[
atom1
][
1
];
r21
[
2
]
=
x
[
atom2
][
2
]
-
x
[
atom1
][
2
];
r21mag
=
sqrt
(
r21
[
0
]
*
r21
[
0
]
+
r21
[
1
]
*
r21
[
1
]
+
r21
[
2
]
*
r21
[
2
]);
cos321
=
((
r21
[
0
]
*
rij
[
0
])
+
(
r21
[
1
]
*
rij
[
1
])
+
(
r21
[
2
]
*
rij
[
2
]))
/
(
r21mag
*
rijmag
);
cos321
=
MIN
(
cos321
,
1.0
);
cos321
=
MAX
(
cos321
,
-
1.0
);
sin321
=
sqrt
(
1.0
-
cos321
*
cos321
);
sink2i
=
1.0
/
(
sin321
*
sin321
);
rik2i
=
1.0
/
(
r21mag
*
r21mag
);
if
(
sin321
!=
0.0
)
{
rr
=
(
rijmag
*
rijmag
)
-
(
r21mag
*
r21mag
);
rjk
[
0
]
=
r21
[
0
]
-
rij
[
0
];
rjk
[
1
]
=
r21
[
1
]
-
rij
[
1
];
rjk
[
2
]
=
r21
[
2
]
-
rij
[
2
];
rjk2
=
(
rjk
[
0
]
*
rjk
[
0
])
+
(
rjk
[
1
]
*
rjk
[
1
])
+
(
rjk
[
2
]
*
rjk
[
2
]);
rijrik
=
2.0
*
rijmag
*
r21mag
;
rik2
=
r21mag
*
r21mag
;
dctik
=
(
-
rr
+
rjk2
)
/
(
rijrik
*
rik2
);
dctij
=
(
rr
+
rjk2
)
/
(
rijrik
*
rijmag
*
rijmag
);
dctjk
=
-
2.0
/
rijrik
;
w21
=
Sp
(
r21mag
,
rcmin
[
itype
][
ktype
],
rcmaxp
[
itype
][
ktype
],
dw21
);
rikmag
=
r21mag
;
rij2
=
r32mag
*
r32mag
;
rik2
=
r21mag
*
r21mag
;
costmp
=
0.5
*
(
rij2
+
rik2
-
rjk2
)
/
rijmag
/
rikmag
;
tspjik
=
Sp2
(
costmp
,
thmin
,
thmax
,
dtsjik
);
dtsjik
=
-
dtsjik
;
REBO_neighs_j
=
REBO_firstneigh
[
j
];
for
(
l
=
0
;
l
<
REBO_numneigh
[
j
];
l
++
)
{
atoml
=
REBO_neighs_j
[
l
];
atom4
=
atoml
;
ltype
=
map
[
type
[
atoml
]];
if
(
!
(
atoml
==
atomi
||
atoml
==
atomk
))
{
r34
[
0
]
=
x
[
atom3
][
0
]
-
x
[
atom4
][
0
];
r34
[
1
]
=
x
[
atom3
][
1
]
-
x
[
atom4
][
1
];
r34
[
2
]
=
x
[
atom3
][
2
]
-
x
[
atom4
][
2
];
r34mag
=
sqrt
(
r34
[
0
]
*
r34
[
0
]
+
r34
[
1
]
*
r34
[
1
]
+
r34
[
2
]
*
r34
[
2
]);
cos234
=
-
1.0
*
((
rij
[
0
]
*
r34
[
0
])
+
(
rij
[
1
]
*
r34
[
1
])
+
(
rij
[
2
]
*
r34
[
2
]))
/
(
rijmag
*
r34mag
);
cos234
=
MIN
(
cos234
,
1.0
);
cos234
=
MAX
(
cos234
,
-
1.0
);
sin234
=
sqrt
(
1.0
-
cos234
*
cos234
);
sinl2i
=
1.0
/
(
sin234
*
sin234
);
rjl2i
=
1.0
/
(
r34mag
*
r34mag
);
if
(
sin234
!=
0.0
)
{
w34
=
Sp
(
r34mag
,
rcmin
[
jtype
][
ltype
],
rcmaxp
[
jtype
][
ltype
],
dw34
);
rr
=
(
r23mag
*
r23mag
)
-
(
r34mag
*
r34mag
);
ril
[
0
]
=
r23
[
0
]
+
r34
[
0
];
ril
[
1
]
=
r23
[
1
]
+
r34
[
1
];
ril
[
2
]
=
r23
[
2
]
+
r34
[
2
];
ril2
=
(
ril
[
0
]
*
ril
[
0
])
+
(
ril
[
1
]
*
ril
[
1
])
+
(
ril
[
2
]
*
ril
[
2
]);
rijrjl
=
2.0
*
r23mag
*
r34mag
;
rjl2
=
r34mag
*
r34mag
;
dctjl
=
(
-
rr
+
ril2
)
/
(
rijrjl
*
rjl2
);
dctji
=
(
rr
+
ril2
)
/
(
rijrjl
*
r23mag
*
r23mag
);
dctil
=
-
2.0
/
rijrjl
;
rjlmag
=
r34mag
;
rjl2
=
r34mag
*
r34mag
;
costmp
=
0.5
*
(
rij2
+
rjl2
-
ril2
)
/
rijmag
/
rjlmag
;
tspijl
=
Sp2
(
costmp
,
thmin
,
thmax
,
dtsijl
);
dtsijl
=
-
dtsijl
;
//need minus sign
prefactor
=
VA
*
Tij
;
cross321
[
0
]
=
(
r32
[
1
]
*
r21
[
2
])
-
(
r32
[
2
]
*
r21
[
1
]);
cross321
[
1
]
=
(
r32
[
2
]
*
r21
[
0
])
-
(
r32
[
0
]
*
r21
[
2
]);
cross321
[
2
]
=
(
r32
[
0
]
*
r21
[
1
])
-
(
r32
[
1
]
*
r21
[
0
]);
cross234
[
0
]
=
(
r23
[
1
]
*
r34
[
2
])
-
(
r23
[
2
]
*
r34
[
1
]);
cross234
[
1
]
=
(
r23
[
2
]
*
r34
[
0
])
-
(
r23
[
0
]
*
r34
[
2
]);
cross234
[
2
]
=
(
r23
[
0
]
*
r34
[
1
])
-
(
r23
[
1
]
*
r34
[
0
]);
cwnum
=
(
cross321
[
0
]
*
cross234
[
0
])
+
(
cross321
[
1
]
*
cross234
[
1
])
+
(
cross321
[
2
]
*
cross234
[
2
]);
cwnom
=
r21mag
*
r34mag
*
r23mag
*
r23mag
*
sin321
*
sin234
;
om1234
=
cwnum
/
cwnom
;
cw
=
om1234
;
Etmp
+=
((
1.0
-
square
(
om1234
))
*
w21
*
w34
)
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
);
dt1dik
=
(
rik2i
)
-
(
dctik
*
sink2i
*
cos321
);
dt1djk
=
(
-
dctjk
*
sink2i
*
cos321
);
dt1djl
=
(
rjl2i
)
-
(
dctjl
*
sinl2i
*
cos234
);
dt1dil
=
(
-
dctil
*
sinl2i
*
cos234
);
dt1dij
=
(
2.0
/
(
r23mag
*
r23mag
))
-
(
dctij
*
sink2i
*
cos321
)
-
(
dctji
*
sinl2i
*
cos234
);
dt2dik
[
0
]
=
(
-
r23
[
2
]
*
cross234
[
1
])
+
(
r23
[
1
]
*
cross234
[
2
]);
dt2dik
[
1
]
=
(
-
r23
[
0
]
*
cross234
[
2
])
+
(
r23
[
2
]
*
cross234
[
0
]);
dt2dik
[
2
]
=
(
-
r23
[
1
]
*
cross234
[
0
])
+
(
r23
[
0
]
*
cross234
[
1
]);
dt2djl
[
0
]
=
(
-
r23
[
1
]
*
cross321
[
2
])
+
(
r23
[
2
]
*
cross321
[
1
]);
dt2djl
[
1
]
=
(
-
r23
[
2
]
*
cross321
[
0
])
+
(
r23
[
0
]
*
cross321
[
2
]);
dt2djl
[
2
]
=
(
-
r23
[
0
]
*
cross321
[
1
])
+
(
r23
[
1
]
*
cross321
[
0
]);
dt2dij
[
0
]
=
(
r21
[
2
]
*
cross234
[
1
])
-
(
r34
[
2
]
*
cross321
[
1
])
-
(
r21
[
1
]
*
cross234
[
2
])
+
(
r34
[
1
]
*
cross321
[
2
]);
dt2dij
[
1
]
=
(
r21
[
0
]
*
cross234
[
2
])
-
(
r34
[
0
]
*
cross321
[
2
])
-
(
r21
[
2
]
*
cross234
[
0
])
+
(
r34
[
2
]
*
cross321
[
0
]);
dt2dij
[
2
]
=
(
r21
[
1
]
*
cross234
[
0
])
-
(
r34
[
1
]
*
cross321
[
0
])
-
(
r21
[
0
]
*
cross234
[
1
])
+
(
r34
[
0
]
*
cross321
[
1
]);
aa
=
(
prefactor
*
2.0
*
cw
/
cwnom
)
*
w21
*
w34
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
);
aaa1
=
-
prefactor
*
(
1.0
-
square
(
om1234
))
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
);
aaa2
=
aaa1
*
w21
*
w34
;
at2
=
aa
*
cwnum
;
fcijpc
=
(
-
dt1dij
*
at2
)
+
(
aaa2
*
dtsjik
*
dctij
*
(
1.0
-
tspijl
))
+
(
aaa2
*
dtsijl
*
dctji
*
(
1.0
-
tspjik
));
fcikpc
=
(
-
dt1dik
*
at2
)
+
(
aaa2
*
dtsjik
*
dctik
*
(
1.0
-
tspijl
));
fcjlpc
=
(
-
dt1djl
*
at2
)
+
(
aaa2
*
dtsijl
*
dctjl
*
(
1.0
-
tspjik
));
fcjkpc
=
(
-
dt1djk
*
at2
)
+
(
aaa2
*
dtsjik
*
dctjk
*
(
1.0
-
tspijl
));
fcilpc
=
(
-
dt1dil
*
at2
)
+
(
aaa2
*
dtsijl
*
dctil
*
(
1.0
-
tspjik
));
F23
[
0
]
=
(
fcijpc
*
r23
[
0
])
+
(
aa
*
dt2dij
[
0
]);
F23
[
1
]
=
(
fcijpc
*
r23
[
1
])
+
(
aa
*
dt2dij
[
1
]);
F23
[
2
]
=
(
fcijpc
*
r23
[
2
])
+
(
aa
*
dt2dij
[
2
]);
F12
[
0
]
=
(
fcikpc
*
r21
[
0
])
+
(
aa
*
dt2dik
[
0
]);
F12
[
1
]
=
(
fcikpc
*
r21
[
1
])
+
(
aa
*
dt2dik
[
1
]);
F12
[
2
]
=
(
fcikpc
*
r21
[
2
])
+
(
aa
*
dt2dik
[
2
]);
F34
[
0
]
=
(
fcjlpc
*
r34
[
0
])
+
(
aa
*
dt2djl
[
0
]);
F34
[
1
]
=
(
fcjlpc
*
r34
[
1
])
+
(
aa
*
dt2djl
[
1
]);
F34
[
2
]
=
(
fcjlpc
*
r34
[
2
])
+
(
aa
*
dt2djl
[
2
]);
F31
[
0
]
=
(
fcjkpc
*
rjk
[
0
]);
F31
[
1
]
=
(
fcjkpc
*
rjk
[
1
]);
F31
[
2
]
=
(
fcjkpc
*
rjk
[
2
]);
F24
[
0
]
=
(
fcilpc
*
ril
[
0
]);
F24
[
1
]
=
(
fcilpc
*
ril
[
1
]);
F24
[
2
]
=
(
fcilpc
*
ril
[
2
]);
f1
[
0
]
=
-
F12
[
0
]
-
F31
[
0
];
f1
[
1
]
=
-
F12
[
1
]
-
F31
[
1
];
f1
[
2
]
=
-
F12
[
2
]
-
F31
[
2
];
f2
[
0
]
=
F23
[
0
]
+
F12
[
0
]
+
F24
[
0
];
f2
[
1
]
=
F23
[
1
]
+
F12
[
1
]
+
F24
[
1
];
f2
[
2
]
=
F23
[
2
]
+
F12
[
2
]
+
F24
[
2
];
f3
[
0
]
=
-
F23
[
0
]
+
F34
[
0
]
+
F31
[
0
];
f3
[
1
]
=
-
F23
[
1
]
+
F34
[
1
]
+
F31
[
1
];
f3
[
2
]
=
-
F23
[
2
]
+
F34
[
2
]
+
F31
[
2
];
f4
[
0
]
=
-
F34
[
0
]
-
F24
[
0
];
f4
[
1
]
=
-
F34
[
1
]
-
F24
[
1
];
f4
[
2
]
=
-
F34
[
2
]
-
F24
[
2
];
// coordination forces
tmp2
=
VA
*
Tij
*
((
1.0
-
(
om1234
*
om1234
)))
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
)
*
dw21
*
w34
/
r21mag
;
f2
[
0
]
-=
tmp2
*
r21
[
0
];
f2
[
1
]
-=
tmp2
*
r21
[
1
];
f2
[
2
]
-=
tmp2
*
r21
[
2
];
f1
[
0
]
+=
tmp2
*
r21
[
0
];
f1
[
1
]
+=
tmp2
*
r21
[
1
];
f1
[
2
]
+=
tmp2
*
r21
[
2
];
tmp2
=
VA
*
Tij
*
((
1.0
-
(
om1234
*
om1234
)))
*
(
1.0
-
tspjik
)
*
(
1.0
-
tspijl
)
*
w21
*
dw34
/
r34mag
;
f3
[
0
]
-=
tmp2
*
r34
[
0
];
f3
[
1
]
-=
tmp2
*
r34
[
1
];
f3
[
2
]
-=
tmp2
*
r34
[
2
];
f4
[
0
]
+=
tmp2
*
r34
[
0
];
f4
[
1
]
+=
tmp2
*
r34
[
1
];
f4
[
2
]
+=
tmp2
*
r34
[
2
];
f
[
atom1
][
0
]
+=
f1
[
0
];
f
[
atom1
][
1
]
+=
f1
[
1
];
f
[
atom1
][
2
]
+=
f1
[
2
];
f
[
atom2
][
0
]
+=
f2
[
0
];
f
[
atom2
][
1
]
+=
f2
[
1
];
f
[
atom2
][
2
]
+=
f2
[
2
];
f
[
atom3
][
0
]
+=
f3
[
0
];
f
[
atom3
][
1
]
+=
f3
[
1
];
f
[
atom3
][
2
]
+=
f3
[
2
];
f
[
atom4
][
0
]
+=
f4
[
0
];
f
[
atom4
][
1
]
+=
f4
[
1
];
f
[
atom4
][
2
]
+=
f4
[
2
];
if
(
vflag_atom
)
{
r13
[
0
]
=
-
rjk
[
0
];
r13
[
1
]
=
-
rjk
[
1
];
r13
[
2
]
=
-
rjk
[
2
];
r43
[
0
]
=
-
r34
[
0
];
r43
[
1
]
=
-
r34
[
1
];
r43
[
2
]
=
-
r34
[
2
];
v_tally4
(
atom1
,
atom2
,
atom3
,
atom4
,
f1
,
f2
,
f4
,
r13
,
r23
,
r43
);
}
}
}
}
}
}
}
REBO_neighs
=
REBO_firstneigh
[
i
];
for
(
k
=
0
;
k
<
REBO_numneigh
[
i
];
k
++
)
{
atomk
=
REBO_neighs
[
k
];
if
(
atomk
!=
atomj
)
{
ktype
=
map
[
type
[
atomk
]];
rik
[
0
]
=
x
[
atomi
][
0
]
-
x
[
atomk
][
0
];
rik
[
1
]
=
x
[
atomi
][
1
]
-
x
[
atomk
][
1
];
rik
[
2
]
=
x
[
atomi
][
2
]
-
x
[
atomk
][
2
];
rikmag
=
sqrt
((
rik
[
0
]
*
rik
[
0
])
+
(
rik
[
1
]
*
rik
[
1
])
+
(
rik
[
2
]
*
rik
[
2
]));
wik
=
Sp
(
rikmag
,
rcmin
[
itype
][
ktype
],
rcmax
[
itype
][
ktype
],
dwik
);
Nki
=
nC
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
0
))
+
nH
[
atomk
]
-
(
wik
*
kronecker
(
itype
,
1
));
SpN
=
Sp
(
Nki
,
Nmin
,
Nmax
,
dNki
);
tmp2
=
VA
*
dN3
[
0
]
*
dwik
*
Etmp
/
rikmag
;
f
[
atomi
][
0
]
-=
tmp2
*
rik
[
0
];
f
[
atomi
][
1
]
-=
tmp2
*
rik
[
1
];
f
[
atomi
][
2
]
-=
tmp2
*
rik
[
2
];
f
[
atomk
][
0
]
+=
tmp2
*
rik
[
0
];
f
[
atomk
][
1
]
+=
tmp2
*
rik
[
1
];
f
[
atomk
][
2
]
+=
tmp2
*
rik
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomi
,
atomk
,
-
tmp2
,
rik
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpI
*
dwik
*
SpN
)
*
Etmp
/
rikmag
;
f
[
atomi
][
0
]
-=
tmp2
*
rik
[
0
];
f
[
atomi
][
1
]
-=
tmp2
*
rik
[
1
];
f
[
atomi
][
2
]
-=
tmp2
*
rik
[
2
];
f
[
atomk
][
0
]
+=
tmp2
*
rik
[
0
];
f
[
atomk
][
1
]
+=
tmp2
*
rik
[
1
];
f
[
atomk
][
2
]
+=
tmp2
*
rik
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomi
,
atomk
,
-
tmp2
,
rik
);
if
(
fabs
(
dNki
)
>
TOL
)
{
REBO_neighs_k
=
REBO_firstneigh
[
atomk
];
for
(
n
=
0
;
n
<
REBO_numneigh
[
atomk
];
n
++
)
{
atomn
=
REBO_neighs_k
[
n
];
ntype
=
map
[
type
[
atomn
]];
if
(
atomn
!=
atomi
)
{
rkn
[
0
]
=
x
[
atomk
][
0
]
-
x
[
atomn
][
0
];
rkn
[
1
]
=
x
[
atomk
][
1
]
-
x
[
atomn
][
1
];
rkn
[
2
]
=
x
[
atomk
][
2
]
-
x
[
atomn
][
2
];
rknmag
=
sqrt
((
rkn
[
0
]
*
rkn
[
0
])
+
(
rkn
[
1
]
*
rkn
[
1
])
+
(
rkn
[
2
]
*
rkn
[
2
]));
Sp
(
rknmag
,
rcmin
[
ktype
][
ntype
],
rcmax
[
ktype
][
ntype
],
dwkn
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpI
*
wik
*
dNki
*
dwkn
)
*
Etmp
/
rknmag
;
f
[
atomk
][
0
]
-=
tmp2
*
rkn
[
0
];
f
[
atomk
][
1
]
-=
tmp2
*
rkn
[
1
];
f
[
atomk
][
2
]
-=
tmp2
*
rkn
[
2
];
f
[
atomn
][
0
]
+=
tmp2
*
rkn
[
0
];
f
[
atomn
][
1
]
+=
tmp2
*
rkn
[
1
];
f
[
atomn
][
2
]
+=
tmp2
*
rkn
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomk
,
atomn
,
-
tmp2
,
rkn
);
}
}
}
}
}
// Tij forces
REBO_neighs
=
REBO_firstneigh
[
j
];
for
(
l
=
0
;
l
<
REBO_numneigh
[
j
];
l
++
)
{
atoml
=
REBO_neighs
[
l
];
if
(
atoml
!=
atomi
)
{
ltype
=
map
[
type
[
atoml
]];
rjl
[
0
]
=
x
[
atomj
][
0
]
-
x
[
atoml
][
0
];
rjl
[
1
]
=
x
[
atomj
][
1
]
-
x
[
atoml
][
1
];
rjl
[
2
]
=
x
[
atomj
][
2
]
-
x
[
atoml
][
2
];
rjlmag
=
sqrt
((
rjl
[
0
]
*
rjl
[
0
])
+
(
rjl
[
1
]
*
rjl
[
1
])
+
(
rjl
[
2
]
*
rjl
[
2
]));
wjl
=
Sp
(
rjlmag
,
rcmin
[
jtype
][
ltype
],
rcmax
[
jtype
][
ltype
],
dwjl
);
Nlj
=
nC
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
0
))
+
nH
[
atoml
]
-
(
wjl
*
kronecker
(
jtype
,
1
));
SpN
=
Sp
(
Nlj
,
Nmin
,
Nmax
,
dNlj
);
tmp2
=
VA
*
dN3
[
1
]
*
dwjl
*
Etmp
/
rjlmag
;
f
[
atomj
][
0
]
-=
tmp2
*
rjl
[
0
];
f
[
atomj
][
1
]
-=
tmp2
*
rjl
[
1
];
f
[
atomj
][
2
]
-=
tmp2
*
rjl
[
2
];
f
[
atoml
][
0
]
+=
tmp2
*
rjl
[
0
];
f
[
atoml
][
1
]
+=
tmp2
*
rjl
[
1
];
f
[
atoml
][
2
]
+=
tmp2
*
rjl
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomj
,
atoml
,
-
tmp2
,
rjl
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpJ
*
dwjl
*
SpN
)
*
Etmp
/
rjlmag
;
f
[
atomj
][
0
]
-=
tmp2
*
rjl
[
0
];
f
[
atomj
][
1
]
-=
tmp2
*
rjl
[
1
];
f
[
atomj
][
2
]
-=
tmp2
*
rjl
[
2
];
f
[
atoml
][
0
]
+=
tmp2
*
rjl
[
0
];
f
[
atoml
][
1
]
+=
tmp2
*
rjl
[
1
];
f
[
atoml
][
2
]
+=
tmp2
*
rjl
[
2
];
if
(
vflag_atom
)
v_tally2
(
atomj
,
atoml
,
-
tmp2
,
rjl
);
if
(
fabs
(
dNlj
)
>
TOL
)
{
REBO_neighs_l
=
REBO_firstneigh
[
atoml
];
for
(
n
=
0
;
n
<
REBO_numneigh
[
atoml
];
n
++
)
{
atomn
=
REBO_neighs_l
[
n
];
ntype
=
map
[
type
[
atomn
]];
if
(
atomn
!=
atomj
)
{
rln
[
0
]
=
x
[
atoml
][
0
]
-
x
[
atomn
][
0
];
rln
[
1
]
=
x
[
atoml
][
1
]
-
x
[
atomn
][
1
];
rln
[
2
]
=
x
[
atoml
][
2
]
-
x
[
atomn
][
2
];
rlnmag
=
sqrt
((
rln
[
0
]
*
rln
[
0
])
+
(
rln
[
1
]
*
rln
[
1
])
+
(
rln
[
2
]
*
rln
[
2
]));
Sp
(
rlnmag
,
rcmin
[
ltype
][
ntype
],
rcmax
[
ltype
][
ntype
],
dwln
);
tmp2
=
VA
*
dN3
[
2
]
*
(
2.0
*
NconjtmpJ
*
wjl
*
dNlj
*
dwln
)
*
Etmp
/
rlnmag
;
f
[
atoml
][
0
]
-=
tmp2
*
rln
[
0
];
f
[
atoml
][
1
]
-=
tmp2
*
rln
[
1
];
f
[
atoml
][
2
]
-=
tmp2
*
rln
[
2
];
f
[
atomn
][
0
]
+=
tmp2
*
rln
[
0
];
f
[
atomn
][
1
]
+=
tmp2
*
rln
[
1
];
f
[
atomn
][
2
]
+=
tmp2
*
rln
[
2
];
if
(
vflag_atom
)
v_tally2
(
atoml
,
atomn
,
-
tmp2
,
rln
);
}
}
}
}
}
}
}
return
Stb
;
}
/* ----------------------------------------------------------------------
G spline
------------------------------------------------------------------------- */
double
PairAIREBO
::
gSpline
(
double
costh
,
double
Nij
,
int
typei
,
double
*
dgdc
,
double
*
dgdN
)
{
double
coeffs
[
6
],
dS
,
g1
,
g2
,
dg1
,
dg2
,
cut
,
g
;
int
i
,
j
;
i
=
0
;
j
=
0
;
g
=
0.0
;
cut
=
0.0
;
dS
=
0.0
;
dg1
=
0.0
;
dg2
=
0.0
;
*
dgdc
=
0.0
;
*
dgdN
=
0.0
;
// central atom is Carbon
if
(
typei
==
0
)
{
if
(
costh
<
gCdom
[
0
])
costh
=
gCdom
[
0
];
if
(
costh
>
gCdom
[
4
])
costh
=
gCdom
[
4
];
if
(
Nij
>=
NCmax
)
{
for
(
i
=
0
;
i
<
4
;
i
++
)
{
if
(
costh
>=
gCdom
[
i
]
&&
costh
<=
gCdom
[
i
+
1
])
{
for
(
j
=
0
;
j
<
6
;
j
++
)
coeffs
[
j
]
=
gC2
[
i
][
j
];
}
}
g2
=
Sp5th
(
costh
,
coeffs
,
&
dg2
);
g
=
g2
;
*
dgdc
=
dg2
;
*
dgdN
=
0.0
;
}
if
(
Nij
<=
NCmin
)
{
for
(
i
=
0
;
i
<
4
;
i
++
)
{
if
(
costh
>=
gCdom
[
i
]
&&
costh
<=
gCdom
[
i
+
1
])
{
for
(
j
=
0
;
j
<
6
;
j
++
)
coeffs
[
j
]
=
gC1
[
i
][
j
];
}
}
g1
=
Sp5th
(
costh
,
coeffs
,
&
dg1
);
g
=
g1
;
*
dgdc
=
dg1
;
*
dgdN
=
0.0
;
}
if
(
Nij
>
NCmin
&&
Nij
<
NCmax
)
{
for
(
i
=
0
;
i
<
4
;
i
++
)
{
if
(
costh
>=
gCdom
[
i
]
&&
costh
<=
gCdom
[
i
+
1
])
{
for
(
j
=
0
;
j
<
6
;
j
++
)
coeffs
[
j
]
=
gC1
[
i
][
j
];
}
}
g1
=
Sp5th
(
costh
,
coeffs
,
&
dg1
);
for
(
i
=
0
;
i
<
4
;
i
++
)
{
if
(
costh
>=
gCdom
[
i
]
&&
costh
<=
gCdom
[
i
+
1
])
{
for
(
j
=
0
;
j
<
6
;
j
++
)
coeffs
[
j
]
=
gC2
[
i
][
j
];
}
}
g2
=
Sp5th
(
costh
,
coeffs
,
&
dg2
);
cut
=
Sp
(
Nij
,
NCmin
,
NCmax
,
dS
);
g
=
g2
+
cut
*
(
g1
-
g2
);
*
dgdc
=
dg2
+
(
cut
*
(
dg1
-
dg2
));
*
dgdN
=
dS
*
(
g1
-
g2
);
}
}
// central atom is Hydrogen
if
(
typei
==
1
)
{
if
(
costh
<
gHdom
[
0
])
costh
=
gHdom
[
0
];
if
(
costh
>
gHdom
[
3
])
costh
=
gHdom
[
3
];
for
(
i
=
0
;
i
<
3
;
i
++
)
{
if
(
costh
>=
gHdom
[
i
]
&&
costh
<=
gHdom
[
i
+
1
])
{
for
(
j
=
0
;
j
<
6
;
j
++
)
coeffs
[
j
]
=
gH
[
i
][
j
];
}
}
g
=
Sp5th
(
costh
,
coeffs
,
&
dg1
);
*
dgdN
=
0.0
;
*
dgdc
=
dg1
;
}
return
g
;
}
/* ----------------------------------------------------------------------
Pij spline
------------------------------------------------------------------------- */
double
PairAIREBO
::
PijSpline
(
double
NijC
,
double
NijH
,
int
typei
,
int
typej
,
double
dN2
[
2
])
{
int
x
,
y
,
i
,
done
;
double
Pij
,
coeffs
[
16
];
for
(
i
=
0
;
i
<
16
;
i
++
)
coeffs
[
i
]
=
0.0
;
x
=
0
;
y
=
0
;
dN2
[
0
]
=
0.0
;
dN2
[
1
]
=
0.0
;
done
=
0
;
// if inputs are out of bounds set them back to a point in bounds
if
(
typei
==
0
&&
typej
==
0
)
{
if
(
NijC
<
pCCdom
[
0
][
0
])
NijC
=
pCCdom
[
0
][
0
];
if
(
NijC
>
pCCdom
[
0
][
1
])
NijC
=
pCCdom
[
0
][
1
];
if
(
NijH
<
pCCdom
[
1
][
0
])
NijH
=
pCCdom
[
1
][
0
];
if
(
NijH
>
pCCdom
[
1
][
1
])
NijH
=
pCCdom
[
1
][
1
];
if
(
fabs
(
NijC
-
floor
(
NijC
))
<
TOL
&&
fabs
(
NijH
-
floor
(
NijH
))
<
TOL
)
{
Pij
=
PCCf
[(
int
)
NijC
][(
int
)
NijH
];
dN2
[
0
]
=
PCCdfdx
[(
int
)
NijC
][(
int
)
NijH
];
dN2
[
1
]
=
PCCdfdy
[(
int
)
NijC
][(
int
)
NijH
];
done
=
1
;
}
if
(
done
==
0
)
{
x
=
(
int
)
(
floor
(
NijC
));
y
=
(
int
)
(
floor
(
NijH
));
for
(
i
=
0
;
i
<
16
;
i
++
)
coeffs
[
i
]
=
pCC
[
x
][
y
][
i
];
Pij
=
Spbicubic
(
NijC
,
NijH
,
coeffs
,
dN2
);
}
}
// if inputs are out of bounds set them back to a point in bounds
if
(
typei
==
0
&&
typej
==
1
){
if
(
NijC
<
pCHdom
[
0
][
0
])
NijC
=
pCHdom
[
0
][
0
];
if
(
NijC
>
pCHdom
[
0
][
1
])
NijC
=
pCHdom
[
0
][
1
];
if
(
NijH
<
pCHdom
[
1
][
0
])
NijH
=
pCHdom
[
1
][
0
];
if
(
NijH
>
pCHdom
[
1
][
1
])
NijH
=
pCHdom
[
1
][
1
];
if
(
fabs
(
NijC
-
floor
(
NijC
))
<
TOL
&&
fabs
(
NijH
-
floor
(
NijH
))
<
TOL
)
{
Pij
=
PCHf
[(
int
)
NijC
][(
int
)
NijH
];
dN2
[
0
]
=
PCHdfdx
[(
int
)
NijC
][(
int
)
NijH
];
dN2
[
1
]
=
PCHdfdy
[(
int
)
NijC
][(
int
)
NijH
];
done
=
1
;
}
if
(
done
==
0
)
{
x
=
(
int
)
(
floor
(
NijC
));
y
=
(
int
)
(
floor
(
NijH
));
for
(
i
=
0
;
i
<
16
;
i
++
)
coeffs
[
i
]
=
pCH
[
x
][
y
][
i
];
Pij
=
Spbicubic
(
NijC
,
NijH
,
coeffs
,
dN2
);
}
}
if
(
typei
==
1
&&
typej
==
0
)
{
Pij
=
0.0
;
dN2
[
0
]
=
0.0
;
dN2
[
1
]
=
0.0
;
}
if
(
typei
==
1
&&
typej
==
1
)
{
Pij
=
0.0
;
dN2
[
0
]
=
0.0
;
dN2
[
1
]
=
0.0
;
}
return
Pij
;
}
/* ----------------------------------------------------------------------
PiRC spline
------------------------------------------------------------------------- */
double
PairAIREBO
::
piRCSpline
(
double
Nij
,
double
Nji
,
double
Nijconj
,
int
typei
,
int
typej
,
double
dN3
[
3
])
{
int
x
,
y
,
z
,
i
,
done
;
double
piRC
,
coeffs
[
64
];
x
=
0
;
y
=
0
;
z
=
0
;
i
=
0
;
done
=
0
;
for
(
i
=
0
;
i
<
64
;
i
++
)
coeffs
[
i
]
=
0.0
;
if
(
typei
==
0
&&
typej
==
0
)
{
//if the inputs are out of bounds set them back to a point in bounds
if
(
Nij
<
piCCdom
[
0
][
0
])
Nij
=
piCCdom
[
0
][
0
];
if
(
Nij
>
piCCdom
[
0
][
1
])
Nij
=
piCCdom
[
0
][
1
];
if
(
Nji
<
piCCdom
[
1
][
0
])
Nji
=
piCCdom
[
1
][
0
];
if
(
Nji
>
piCCdom
[
1
][
1
])
Nji
=
piCCdom
[
1
][
1
];
if
(
Nijconj
<
piCCdom
[
2
][
0
])
Nijconj
=
piCCdom
[
2
][
0
];
if
(
Nijconj
>
piCCdom
[
2
][
1
])
Nijconj
=
piCCdom
[
2
][
1
];
if
(
fabs
(
Nij
-
floor
(
Nij
))
<
TOL
&&
fabs
(
Nji
-
floor
(
Nji
))
<
TOL
&&
fabs
(
Nijconj
-
floor
(
Nijconj
))
<
TOL
)
{
piRC
=
piCCf
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
0
]
=
piCCdfdx
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
1
]
=
piCCdfdy
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
2
]
=
piCCdfdz
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
done
=
1
;
}
if
(
done
==
0
)
{
for
(
i
=
0
;
i
<
piCCdom
[
0
][
1
];
i
++
)
if
(
Nij
>=
(
double
)
i
&&
Nij
<=
(
double
)
i
+
1
||
Nij
==
(
double
)
i
)
x
=
i
;
for
(
i
=
0
;
i
<
piCCdom
[
1
][
1
];
i
++
)
if
(
Nji
>=
(
double
)
i
&&
Nji
<=
(
double
)
i
+
1
||
Nji
==
(
double
)
i
)
y
=
i
;
for
(
i
=
0
;
i
<
piCCdom
[
2
][
1
];
i
++
)
if
(
Nijconj
>=
(
double
)
i
&&
Nijconj
<=
(
double
)
i
+
1
||
Nijconj
==
(
double
)
i
)
z
=
i
;
for
(
i
=
0
;
i
<
64
;
i
++
)
coeffs
[
i
]
=
piCC
[
x
][
y
][
z
][
i
];
piRC
=
Sptricubic
(
Nij
,
Nji
,
Nijconj
,
coeffs
,
dN3
);
}
}
// CH interaction
if
(
typei
==
0
&&
typej
==
1
||
typei
==
1
&&
typej
==
0
)
{
// if the inputs are out of bounds set them back to a point in bounds
if
(
Nij
<
piCHdom
[
0
][
0
]
||
Nij
>
piCHdom
[
0
][
1
]
||
Nji
<
piCHdom
[
1
][
0
]
||
Nji
>
piCHdom
[
1
][
1
]
||
Nijconj
<
piCHdom
[
2
][
0
]
||
Nijconj
>
piCHdom
[
2
][
1
])
{
if
(
Nij
<
piCHdom
[
0
][
0
])
Nij
=
piCHdom
[
0
][
0
];
if
(
Nij
>
piCHdom
[
0
][
1
])
Nij
=
piCHdom
[
0
][
1
];
if
(
Nji
<
piCHdom
[
1
][
0
])
Nji
=
piCHdom
[
1
][
0
];
if
(
Nji
>
piCHdom
[
1
][
1
])
Nji
=
piCHdom
[
1
][
1
];
if
(
Nijconj
<
piCHdom
[
2
][
0
])
Nijconj
=
piCHdom
[
2
][
0
];
if
(
Nijconj
>
piCHdom
[
2
][
1
])
Nijconj
=
piCHdom
[
2
][
1
];
}
if
(
fabs
(
Nij
-
floor
(
Nij
))
<
TOL
&&
fabs
(
Nji
-
floor
(
Nji
))
<
TOL
&&
fabs
(
Nijconj
-
floor
(
Nijconj
))
<
TOL
)
{
piRC
=
piCHf
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
0
]
=
piCHdfdx
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
1
]
=
piCHdfdy
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
2
]
=
piCHdfdz
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
done
=
1
;
}
if
(
done
==
0
)
{
for
(
i
=
0
;
i
<
piCHdom
[
0
][
1
];
i
++
)
if
(
Nij
>=
i
&&
Nij
<=
i
+
1
)
x
=
i
;
for
(
i
=
0
;
i
<
piCHdom
[
1
][
1
];
i
++
)
if
(
Nji
>=
i
&&
Nji
<=
i
+
1
)
y
=
i
;
for
(
i
=
0
;
i
<
piCHdom
[
2
][
1
];
i
++
)
if
(
Nijconj
>=
i
&&
Nijconj
<=
i
+
1
)
z
=
i
;
for
(
i
=
0
;
i
<
64
;
i
++
)
coeffs
[
i
]
=
piCH
[
x
][
y
][
z
][
i
];
piRC
=
Sptricubic
(
Nij
,
Nji
,
Nijconj
,
coeffs
,
dN3
);
}
}
if
(
typei
==
1
&&
typej
==
1
)
{
if
(
Nij
<
piHHdom
[
0
][
0
]
||
Nij
>
piHHdom
[
0
][
1
]
||
Nji
<
piHHdom
[
1
][
0
]
||
Nji
>
piHHdom
[
1
][
1
]
||
Nijconj
<
piHHdom
[
2
][
0
]
||
Nijconj
>
piHHdom
[
2
][
1
])
{
Nij
=
0.0
;
Nji
=
0.0
;
Nijconj
=
0.0
;
}
if
(
fabs
(
Nij
-
floor
(
Nij
))
<
TOL
&&
fabs
(
Nji
-
floor
(
Nji
))
<
TOL
&&
fabs
(
Nijconj
-
floor
(
Nijconj
))
<
TOL
)
{
piRC
=
piHHf
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
0
]
=
piHHdfdx
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
1
]
=
piHHdfdy
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
2
]
=
piHHdfdz
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
done
=
1
;
}
if
(
done
==
0
)
{
for
(
i
=
0
;
i
<
piHHdom
[
0
][
1
];
i
++
)
if
(
Nij
>=
i
&&
Nij
<=
i
+
1
)
x
=
i
;
for
(
i
=
0
;
i
<
piHHdom
[
1
][
1
];
i
++
)
if
(
Nji
>=
i
&&
Nji
<=
i
+
1
)
y
=
i
;
for
(
i
=
0
;
i
<
piHHdom
[
2
][
1
];
i
++
)
if
(
Nijconj
>=
i
&&
Nijconj
<=
i
+
1
)
z
=
i
;
for
(
i
=
0
;
i
<
64
;
i
++
)
coeffs
[
i
]
=
piHH
[
x
][
y
][
z
][
i
];
piRC
=
Sptricubic
(
Nij
,
Nji
,
Nijconj
,
coeffs
,
dN3
);
}
}
return
piRC
;
}
/* ----------------------------------------------------------------------
Tij spline
------------------------------------------------------------------------- */
double
PairAIREBO
::
TijSpline
(
double
Nij
,
double
Nji
,
double
Nijconj
,
double
dN3
[
3
])
{
int
x
,
y
,
z
,
i
,
done
;
double
Tijf
,
coeffs
[
64
];
x
=
0
;
y
=
0
;
z
=
0
;
i
=
0
;
Tijf
=
0.0
;
done
=
0
;
for
(
i
=
0
;
i
<
64
;
i
++
)
coeffs
[
i
]
=
0.0
;
//if the inputs are out of bounds set them back to a point in bounds
if
(
Nij
<
Tijdom
[
0
][
0
])
Nij
=
Tijdom
[
0
][
0
];
if
(
Nij
>
Tijdom
[
0
][
1
])
Nij
=
Tijdom
[
0
][
1
];
if
(
Nji
<
Tijdom
[
1
][
0
])
Nji
=
Tijdom
[
1
][
0
];
if
(
Nji
>
Tijdom
[
1
][
1
])
Nji
=
Tijdom
[
1
][
1
];
if
(
Nijconj
<
Tijdom
[
2
][
0
])
Nijconj
=
Tijdom
[
2
][
0
];
if
(
Nijconj
>
Tijdom
[
2
][
1
])
Nijconj
=
Tijdom
[
2
][
1
];
if
(
fabs
(
Nij
-
floor
(
Nij
))
<
TOL
&&
fabs
(
Nji
-
floor
(
Nji
))
<
TOL
&&
fabs
(
Nijconj
-
floor
(
Nijconj
))
<
TOL
)
{
Tijf
=
Tf
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
0
]
=
Tdfdx
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
1
]
=
Tdfdy
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
dN3
[
2
]
=
Tdfdz
[(
int
)
Nij
][(
int
)
Nji
][(
int
)
Nijconj
];
done
=
1
;
}
if
(
done
==
0
)
{
for
(
i
=
0
;
i
<
Tijdom
[
0
][
1
];
i
++
)
if
(
Nij
>=
i
&&
Nij
<=
i
+
1
)
x
=
i
;
for
(
i
=
0
;
i
<
Tijdom
[
1
][
1
];
i
++
)
if
(
Nji
>=
i
&&
Nji
<=
i
+
1
)
y
=
i
;
for
(
i
=
0
;
i
<
Tijdom
[
2
][
1
];
i
++
)
if
(
Nijconj
>=
i
&&
Nijconj
<=
i
+
1
)
z
=
i
;
for
(
i
=
0
;
i
<
64
;
i
++
)
coeffs
[
i
]
=
Tijc
[
x
][
y
][
z
][
i
];
Tijf
=
Sptricubic
(
Nij
,
Nji
,
Nijconj
,
coeffs
,
dN3
);
}
return
Tijf
;
}
/* ----------------------------------------------------------------------
read AIREBO potential file
------------------------------------------------------------------------- */
void
PairAIREBO
::
read_file
(
char
*
filename
)
{
int
i
,
j
,
k
,
l
,
limit
;
char
s
[
MAXLINE
];
// REBO Parameters (AIREBO)
double
rcmin_CC
,
rcmin_CH
,
rcmin_HH
,
rcmax_CC
,
rcmax_CH
,
rcmax_HH
,
rcmaxp_CC
,
rcmaxp_CH
,
rcmaxp_HH
;
double
Q_CC
,
Q_CH
,
Q_HH
,
alpha_CC
,
alpha_CH
,
alpha_HH
,
A_CC
,
A_CH
,
A_HH
;
double
BIJc_CC1
,
BIJc_CC2
,
BIJc_CC3
,
BIJc_CH1
,
BIJc_CH2
,
BIJc_CH3
,
BIJc_HH1
,
BIJc_HH2
,
BIJc_HH3
;
double
Beta_CC1
,
Beta_CC2
,
Beta_CC3
,
Beta_CH1
,
Beta_CH2
,
Beta_CH3
,
Beta_HH1
,
Beta_HH2
,
Beta_HH3
;
double
rho_CC
,
rho_CH
,
rho_HH
;
// LJ Parameters (AIREBO)
double
rcLJmin_CC
,
rcLJmin_CH
,
rcLJmin_HH
,
rcLJmax_CC
,
rcLJmax_CH
,
rcLJmax_HH
,
bLJmin_CC
;
double
bLJmin_CH
,
bLJmin_HH
,
bLJmax_CC
,
bLJmax_CH
,
bLJmax_HH
,
epsilon_CC
,
epsilon_CH
,
epsilon_HH
;
double
sigma_CC
,
sigma_CH
,
sigma_HH
,
epsilonT_CCCC
,
epsilonT_CCCH
,
epsilonT_HCCH
;
MPI_Comm_rank
(
world
,
&
me
);
// read file on proc 0
if
(
me
==
0
)
{
FILE
*
fp
=
force
->
open_potential
(
filename
);
if
(
fp
==
NULL
)
{
char
str
[
128
];
sprintf
(
str
,
"Cannot open AIREBO potential file %s"
,
filename
);
error
->
one
(
FLERR
,
str
);
}
// skip initial comment lines
while
(
1
)
{
fgets
(
s
,
MAXLINE
,
fp
);
if
(
s
[
0
]
!=
'#'
)
break
;
}
// read parameters
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcmin_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcmin_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcmin_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcmax_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcmax_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcmax_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcmaxp_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcmaxp_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcmaxp_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
smin
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Nmin
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Nmax
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
NCmin
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
NCmax
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Q_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Q_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Q_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
alpha_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
alpha_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
alpha_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
A_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
A_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
A_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
BIJc_CC1
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
BIJc_CC2
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
BIJc_CC3
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
BIJc_CH1
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
BIJc_CH2
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
BIJc_CH3
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
BIJc_HH1
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
BIJc_HH2
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
BIJc_HH3
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Beta_CC1
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Beta_CC2
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Beta_CC3
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Beta_CH1
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Beta_CH2
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Beta_CH3
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Beta_HH1
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Beta_HH2
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Beta_HH3
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rho_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rho_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rho_HH
);
// LJ parameters
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcLJmin_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcLJmin_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcLJmin_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcLJmax_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcLJmax_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
rcLJmax_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
bLJmin_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
bLJmin_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
bLJmin_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
bLJmax_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
bLJmax_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
bLJmax_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
epsilon_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
epsilon_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
epsilon_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
sigma_CC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
sigma_CH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
sigma_HH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
epsilonT_CCCC
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
epsilonT_CCCH
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
epsilonT_HCCH
);
// gC spline
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
// number-1 = # of domains for the spline
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%d"
,
&
limit
);
for
(
i
=
0
;
i
<
limit
;
i
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
gCdom
[
i
]);
}
fgets
(
s
,
MAXLINE
,
fp
);
for
(
i
=
0
;
i
<
limit
-
1
;
i
++
)
{
for
(
j
=
0
;
j
<
6
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
gC1
[
i
][
j
]);
}
}
fgets
(
s
,
MAXLINE
,
fp
);
for
(
i
=
0
;
i
<
limit
-
1
;
i
++
)
{
for
(
j
=
0
;
j
<
6
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
gC2
[
i
][
j
]);
}
}
// gH spline
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%d"
,
&
limit
);
for
(
i
=
0
;
i
<
limit
;
i
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
gHdom
[
i
]);
}
fgets
(
s
,
MAXLINE
,
fp
);
for
(
i
=
0
;
i
<
limit
-
1
;
i
++
)
{
for
(
j
=
0
;
j
<
6
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
gH
[
i
][
j
]);
}
}
// pCC spline
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%d"
,
&
limit
);
for
(
i
=
0
;
i
<
limit
/
2
;
i
++
)
{
for
(
j
=
0
;
j
<
limit
/
2
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
pCCdom
[
i
][
j
]);
}
}
fgets
(
s
,
MAXLINE
,
fp
);
for
(
i
=
0
;
i
<
(
int
)
pCCdom
[
0
][
1
];
i
++
)
{
for
(
j
=
0
;
j
<
(
int
)
pCCdom
[
1
][
1
];
j
++
)
{
for
(
k
=
0
;
k
<
16
;
k
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
pCC
[
i
][
j
][
k
]);
}
}
}
// pCH spline
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%d"
,
&
limit
);
for
(
i
=
0
;
i
<
limit
/
2
;
i
++
)
{
for
(
j
=
0
;
j
<
limit
/
2
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
pCHdom
[
i
][
j
]);
}
}
fgets
(
s
,
MAXLINE
,
fp
);
for
(
i
=
0
;
i
<
(
int
)
pCHdom
[
0
][
1
];
i
++
)
{
for
(
j
=
0
;
j
<
(
int
)
pCHdom
[
1
][
1
];
j
++
)
{
for
(
k
=
0
;
k
<
16
;
k
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
pCH
[
i
][
j
][
k
]);
}
}
}
// piCC cpline
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%d"
,
&
limit
);
for
(
i
=
0
;
i
<
limit
/
2
;
i
++
)
{
for
(
j
=
0
;
j
<
limit
/
3
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
piCCdom
[
i
][
j
]);
}
}
fgets
(
s
,
MAXLINE
,
fp
);
for
(
i
=
0
;
i
<
(
int
)
piCCdom
[
0
][
1
];
i
++
)
{
for
(
j
=
0
;
j
<
(
int
)
piCCdom
[
1
][
1
];
j
++
)
{
for
(
k
=
0
;
k
<
(
int
)
piCCdom
[
2
][
1
];
k
++
)
{
for
(
l
=
0
;
l
<
64
;
l
=
l
+
1
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
piCC
[
i
][
j
][
k
][
l
]);
}
}
}
}
// piCH spline
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%d"
,
&
limit
);
for
(
i
=
0
;
i
<
limit
/
2
;
i
++
)
{
for
(
j
=
0
;
j
<
limit
/
3
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
piCHdom
[
i
][
j
]);
}
}
fgets
(
s
,
MAXLINE
,
fp
);
for
(
i
=
0
;
i
<
(
int
)
piCHdom
[
0
][
1
];
i
++
)
{
for
(
j
=
0
;
j
<
(
int
)
piCHdom
[
1
][
1
];
j
++
)
{
for
(
k
=
0
;
k
<
(
int
)
piCHdom
[
2
][
1
];
k
++
)
{
for
(
l
=
0
;
l
<
64
;
l
=
l
+
1
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
piCH
[
i
][
j
][
k
][
l
]);
}
}
}
}
// piHH spline
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%d"
,
&
limit
);
for
(
i
=
0
;
i
<
limit
/
2
;
i
++
)
{
for
(
j
=
0
;
j
<
limit
/
3
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
piHHdom
[
i
][
j
]);
}
}
fgets
(
s
,
MAXLINE
,
fp
);
for
(
i
=
0
;
i
<
(
int
)
piHHdom
[
0
][
1
];
i
++
)
{
for
(
j
=
0
;
j
<
(
int
)
piHHdom
[
1
][
1
];
j
++
)
{
for
(
k
=
0
;
k
<
(
int
)
piHHdom
[
2
][
1
];
k
++
)
{
for
(
l
=
0
;
l
<
64
;
l
=
l
+
1
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
piHH
[
i
][
j
][
k
][
l
]);
}
}
}
}
// Tij spline
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%d"
,
&
limit
);
for
(
i
=
0
;
i
<
limit
/
2
;
i
++
)
{
for
(
j
=
0
;
j
<
limit
/
3
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Tijdom
[
i
][
j
]);
}
}
fgets
(
s
,
MAXLINE
,
fp
);
for
(
i
=
0
;
i
<
(
int
)
Tijdom
[
0
][
1
];
i
++
)
{
for
(
j
=
0
;
j
<
(
int
)
Tijdom
[
1
][
1
];
j
++
)
{
for
(
k
=
0
;
k
<
(
int
)
Tijdom
[
2
][
1
];
k
++
)
{
for
(
l
=
0
;
l
<
64
;
l
=
l
+
1
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lg"
,
&
Tijc
[
i
][
j
][
k
][
l
]);
}
}
}
}
fclose
(
fp
);
}
// store read-in values in arrays
if
(
me
==
0
)
{
// REBO
rcmin
[
0
][
0
]
=
rcmin_CC
;
rcmin
[
0
][
1
]
=
rcmin_CH
;
rcmin
[
1
][
0
]
=
rcmin
[
0
][
1
];
rcmin
[
1
][
1
]
=
rcmin_HH
;
rcmax
[
0
][
0
]
=
rcmax_CC
;
rcmax
[
0
][
1
]
=
rcmax_CH
;
rcmax
[
1
][
0
]
=
rcmax
[
0
][
1
];
rcmax
[
1
][
1
]
=
rcmax_HH
;
rcmaxsq
[
0
][
0
]
=
rcmax
[
0
][
0
]
*
rcmax
[
0
][
0
];
rcmaxsq
[
1
][
0
]
=
rcmax
[
1
][
0
]
*
rcmax
[
1
][
0
];
rcmaxsq
[
0
][
1
]
=
rcmax
[
0
][
1
]
*
rcmax
[
0
][
1
];
rcmaxsq
[
1
][
1
]
=
rcmax
[
1
][
1
]
*
rcmax
[
1
][
1
];
rcmaxp
[
0
][
0
]
=
rcmaxp_CC
;
rcmaxp
[
0
][
1
]
=
rcmaxp_CH
;
rcmaxp
[
1
][
0
]
=
rcmaxp
[
0
][
1
];
rcmaxp
[
1
][
1
]
=
rcmaxp_HH
;
Q
[
0
][
0
]
=
Q_CC
;
Q
[
0
][
1
]
=
Q_CH
;
Q
[
1
][
0
]
=
Q
[
0
][
1
];
Q
[
1
][
1
]
=
Q_HH
;
alpha
[
0
][
0
]
=
alpha_CC
;
alpha
[
0
][
1
]
=
alpha_CH
;
alpha
[
1
][
0
]
=
alpha
[
0
][
1
];
alpha
[
1
][
1
]
=
alpha_HH
;
A
[
0
][
0
]
=
A_CC
;
A
[
0
][
1
]
=
A_CH
;
A
[
1
][
0
]
=
A
[
0
][
1
];
A
[
1
][
1
]
=
A_HH
;
rho
[
0
][
0
]
=
rho_CC
;
rho
[
0
][
1
]
=
rho_CH
;
rho
[
1
][
0
]
=
rho
[
0
][
1
];
rho
[
1
][
1
]
=
rho_HH
;
BIJc
[
0
][
0
][
0
]
=
BIJc_CC1
;
BIJc
[
0
][
0
][
1
]
=
BIJc_CC2
;
BIJc
[
0
][
0
][
2
]
=
BIJc_CC3
;
BIJc
[
0
][
1
][
0
]
=
BIJc_CH1
;
BIJc
[
0
][
1
][
1
]
=
BIJc_CH2
;
BIJc
[
0
][
1
][
2
]
=
BIJc_CH3
;
BIJc
[
1
][
0
][
0
]
=
BIJc_CH1
;
BIJc
[
1
][
0
][
1
]
=
BIJc_CH2
;
BIJc
[
1
][
0
][
2
]
=
BIJc_CH3
;
BIJc
[
1
][
1
][
0
]
=
BIJc_HH1
;
BIJc
[
1
][
1
][
1
]
=
BIJc_HH2
;
BIJc
[
1
][
1
][
2
]
=
BIJc_HH3
;
Beta
[
0
][
0
][
0
]
=
Beta_CC1
;
Beta
[
0
][
0
][
1
]
=
Beta_CC2
;
Beta
[
0
][
0
][
2
]
=
Beta_CC3
;
Beta
[
0
][
1
][
0
]
=
Beta_CH1
;
Beta
[
0
][
1
][
1
]
=
Beta_CH2
;
Beta
[
0
][
1
][
2
]
=
Beta_CH3
;
Beta
[
1
][
0
][
0
]
=
Beta_CH1
;
Beta
[
1
][
0
][
1
]
=
Beta_CH2
;
Beta
[
1
][
0
][
2
]
=
Beta_CH3
;
Beta
[
1
][
1
][
0
]
=
Beta_HH1
;
Beta
[
1
][
1
][
1
]
=
Beta_HH2
;
Beta
[
1
][
1
][
2
]
=
Beta_HH3
;
// LJ
rcLJmin
[
0
][
0
]
=
rcLJmin_CC
;
rcLJmin
[
0
][
1
]
=
rcLJmin_CH
;
rcLJmin
[
1
][
0
]
=
rcLJmin
[
0
][
1
];
rcLJmin
[
1
][
1
]
=
rcLJmin_HH
;
rcLJmax
[
0
][
0
]
=
rcLJmax_CC
;
rcLJmax
[
0
][
1
]
=
rcLJmax_CH
;
rcLJmax
[
1
][
0
]
=
rcLJmax
[
0
][
1
];
rcLJmax
[
1
][
1
]
=
rcLJmax_HH
;
rcLJmaxsq
[
0
][
0
]
=
rcLJmax
[
0
][
0
]
*
rcLJmax
[
0
][
0
];
rcLJmaxsq
[
1
][
0
]
=
rcLJmax
[
1
][
0
]
*
rcLJmax
[
1
][
0
];
rcLJmaxsq
[
0
][
1
]
=
rcLJmax
[
0
][
1
]
*
rcLJmax
[
0
][
1
];
rcLJmaxsq
[
1
][
1
]
=
rcLJmax
[
1
][
1
]
*
rcLJmax
[
1
][
1
];
bLJmin
[
0
][
0
]
=
bLJmin_CC
;
bLJmin
[
0
][
1
]
=
bLJmin_CH
;
bLJmin
[
1
][
0
]
=
bLJmin
[
0
][
1
];
bLJmin
[
1
][
1
]
=
bLJmin_HH
;
bLJmax
[
0
][
0
]
=
bLJmax_CC
;
bLJmax
[
0
][
1
]
=
bLJmax_CH
;
bLJmax
[
1
][
0
]
=
bLJmax
[
0
][
1
];
bLJmax
[
1
][
1
]
=
bLJmax_HH
;
epsilon
[
0
][
0
]
=
epsilon_CC
;
epsilon
[
0
][
1
]
=
epsilon_CH
;
epsilon
[
1
][
0
]
=
epsilon
[
0
][
1
];
epsilon
[
1
][
1
]
=
epsilon_HH
;
sigma
[
0
][
0
]
=
sigma_CC
;
sigma
[
0
][
1
]
=
sigma_CH
;
sigma
[
1
][
0
]
=
sigma
[
0
][
1
];
sigma
[
1
][
1
]
=
sigma_HH
;
// torsional
thmin
=
-
1.0
;
thmax
=
-
0.995
;
epsilonT
[
0
][
0
]
=
epsilonT_CCCC
;
epsilonT
[
0
][
1
]
=
epsilonT_CCCH
;
epsilonT
[
1
][
0
]
=
epsilonT
[
0
][
1
];
epsilonT
[
1
][
1
]
=
epsilonT_HCCH
;
}
// broadcast read-in and setup values
MPI_Bcast
(
&
thmin
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
thmax
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
smin
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
Nmin
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
Nmax
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
NCmin
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
NCmax
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcmin
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcmax
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcmaxsq
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcmaxp
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
Q
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
alpha
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
A
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rho
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
BIJc
[
0
][
0
][
0
],
12
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
Beta
[
0
][
0
][
0
],
12
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcLJmin
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcLJmax
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcLJmaxsq
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcLJmin
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcLJmin
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcLJmin
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcLJmax
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
bLJmin
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
bLJmax
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
epsilon
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
epsilonT
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gCdom
[
0
],
5
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gC1
[
0
][
0
],
24
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gC2
[
0
][
0
],
24
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gHdom
[
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gH
[
0
][
0
],
18
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pCCdom
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pCHdom
[
0
][
0
],
4
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pCC
[
0
][
0
][
0
],
256
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pCH
[
0
][
0
][
0
],
256
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
piCCdom
[
0
][
0
],
6
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
piCHdom
[
0
][
0
],
6
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
piHHdom
[
0
][
0
],
6
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
piCC
[
0
][
0
][
0
][
0
],
9216
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
piCH
[
0
][
0
][
0
][
0
],
9216
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
piHH
[
0
][
0
][
0
][
0
],
9216
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
Tijdom
[
0
][
0
],
6
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
Tijc
[
0
][
0
][
0
][
0
],
9216
,
MPI_DOUBLE
,
0
,
world
);
}
// ----------------------------------------------------------------------
// generic Spline functions
// ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
fifth order spline evaluation
------------------------------------------------------------------------- */
double
PairAIREBO
::
Sp5th
(
double
x
,
double
coeffs
[
6
],
double
*
df
)
{
double
f
,
d
;
const
double
x2
=
x
*
x
;
const
double
x3
=
x2
*
x
;
f
=
coeffs
[
0
];
f
+=
coeffs
[
1
]
*
x
;
d
=
coeffs
[
1
];
f
+=
coeffs
[
2
]
*
x2
;
d
+=
2.0
*
coeffs
[
2
]
*
x
;
f
+=
coeffs
[
3
]
*
x3
;
d
+=
3.0
*
coeffs
[
3
]
*
x2
;
f
+=
coeffs
[
4
]
*
x2
*
x2
;
d
+=
4.0
*
coeffs
[
4
]
*
x3
;
f
+=
coeffs
[
5
]
*
x2
*
x3
;
d
+=
5.0
*
coeffs
[
5
]
*
x2
*
x2
;
*
df
=
d
;
return
f
;
}
/* ----------------------------------------------------------------------
bicubic spline evaluation
------------------------------------------------------------------------- */
double
PairAIREBO
::
Spbicubic
(
double
x
,
double
y
,
double
coeffs
[
16
],
double
df
[
2
])
{
double
f
,
xn
,
yn
,
xn1
,
yn1
,
c
;
int
i
,
j
;
f
=
0.0
;
df
[
0
]
=
0.0
;
df
[
1
]
=
0.0
;
xn
=
1.0
;
for
(
i
=
0
;
i
<
4
;
i
++
)
{
yn
=
1.0
;
for
(
j
=
0
;
j
<
4
;
j
++
)
{
c
=
coeffs
[
i
*
4
+
j
];
f
+=
c
*
xn
*
yn
;
if
(
i
>
0
)
df
[
0
]
+=
c
*
((
double
)
i
)
*
xn1
*
yn
;
if
(
j
>
0
)
df
[
1
]
+=
c
*
((
double
)
j
)
*
xn
*
yn1
;
yn1
=
yn
;
yn
*=
y
;
}
xn1
=
xn
;
xn
*=
x
;
}
return
f
;
}
/* ----------------------------------------------------------------------
tricubic spline evaluation
------------------------------------------------------------------------- */
double
PairAIREBO
::
Sptricubic
(
double
x
,
double
y
,
double
z
,
double
coeffs
[
64
],
double
df
[
3
])
{
double
f
,
ir
,
jr
,
kr
,
xn
,
yn
,
zn
,
xn1
,
yn1
,
zn1
,
c
;
int
i
,
j
,
k
;
f
=
0.0
;
df
[
0
]
=
0.0
;
df
[
1
]
=
0.0
;
df
[
2
]
=
0.0
;
xn
=
1.0
;
for
(
i
=
0
;
i
<
4
;
i
++
)
{
ir
=
(
double
)
i
;
yn
=
1.0
;
for
(
j
=
0
;
j
<
4
;
j
++
)
{
jr
=
(
double
)
j
;
zn
=
1.0
;
for
(
k
=
0
;
k
<
4
;
k
++
)
{
kr
=
(
double
)
k
;
c
=
coeffs
[
16
*
i
+
4
*
j
+
k
];
f
+=
c
*
xn
*
yn
*
zn
;
if
(
i
>
0
)
df
[
0
]
+=
c
*
ir
*
xn1
*
yn
*
zn
;
if
(
j
>
0
)
df
[
1
]
+=
c
*
jr
*
xn
*
yn1
*
zn
;
if
(
k
>
0
)
df
[
2
]
+=
c
*
kr
*
xn
*
yn
*
zn1
;
zn1
=
zn
;
zn
*=
z
;
}
yn1
=
yn
;
yn
*=
y
;
}
xn1
=
xn
;
xn
*=
x
;
}
return
f
;
}
/* ----------------------------------------------------------------------
initialize spline knot values
------------------------------------------------------------------------- */
void
PairAIREBO
::
spline_init
()
{
int
i
,
j
,
k
;
for
(
i
=
0
;
i
<
5
;
i
++
)
{
for
(
j
=
0
;
j
<
5
;
j
++
)
{
PCCf
[
i
][
j
]
=
0.0
;
PCCdfdx
[
i
][
j
]
=
0.0
;
PCCdfdy
[
i
][
j
]
=
0.0
;
PCHf
[
i
][
j
]
=
0.0
;
PCHdfdx
[
i
][
j
]
=
0.0
;
PCHdfdy
[
i
][
j
]
=
0.0
;
}
}
PCCf
[
0
][
2
]
=
-
0.00050
;
PCCf
[
0
][
3
]
=
0.0161253646
;
PCCf
[
1
][
1
]
=
-
0.010960
;
PCCf
[
1
][
2
]
=
0.00632624824
;
PCCf
[
2
][
0
]
=
-
0.0276030
;
PCCf
[
2
][
1
]
=
0.00317953083
;
PCHf
[
0
][
1
]
=
0.209336733
;
PCHf
[
0
][
2
]
=
-
0.0644496154
;
PCHf
[
0
][
3
]
=
-
0.303927546
;
PCHf
[
1
][
0
]
=
0.010
;
PCHf
[
1
][
1
]
=
-
0.125123401
;
PCHf
[
1
][
2
]
=
-
0.298905246
;
PCHf
[
2
][
0
]
=
-
0.122042146
;
PCHf
[
2
][
1
]
=
-
0.300529172
;
PCHf
[
3
][
0
]
=
-
0.307584705
;
for
(
i
=
0
;
i
<
5
;
i
++
)
{
for
(
j
=
0
;
j
<
5
;
j
++
)
{
for
(
k
=
0
;
k
<
10
;
k
++
)
{
piCCf
[
i
][
j
][
k
]
=
0.0
;
piCCdfdx
[
i
][
j
][
k
]
=
0.0
;
piCCdfdy
[
i
][
j
][
k
]
=
0.0
;
piCCdfdz
[
i
][
j
][
k
]
=
0.0
;
piCHf
[
i
][
j
][
k
]
=
0.0
;
piCHdfdx
[
i
][
j
][
k
]
=
0.0
;
piCHdfdy
[
i
][
j
][
k
]
=
0.0
;
piCHdfdz
[
i
][
j
][
k
]
=
0.0
;
piHHf
[
i
][
j
][
k
]
=
0.0
;
piHHdfdx
[
i
][
j
][
k
]
=
0.0
;
piHHdfdy
[
i
][
j
][
k
]
=
0.0
;
piHHdfdz
[
i
][
j
][
k
]
=
0.0
;
Tf
[
i
][
j
][
k
]
=
0.0
;
Tdfdx
[
i
][
j
][
k
]
=
0.0
;
Tdfdy
[
i
][
j
][
k
]
=
0.0
;
Tdfdz
[
i
][
j
][
k
]
=
0.0
;
}
}
}
for
(
i
=
3
;
i
<
10
;
i
++
)
piCCf
[
0
][
0
][
i
]
=
0.0049586079
;
piCCf
[
1
][
0
][
1
]
=
0.021693495
;
piCCf
[
0
][
1
][
1
]
=
0.021693495
;
for
(
i
=
2
;
i
<
10
;
i
++
)
piCCf
[
1
][
0
][
i
]
=
0.0049586079
;
for
(
i
=
2
;
i
<
10
;
i
++
)
piCCf
[
0
][
1
][
i
]
=
0.0049586079
;
piCCf
[
1
][
1
][
1
]
=
0.05250
;
piCCf
[
1
][
1
][
2
]
=
-
0.002088750
;
for
(
i
=
3
;
i
<
10
;
i
++
)
piCCf
[
1
][
1
][
i
]
=
-
0.00804280
;
piCCf
[
2
][
0
][
1
]
=
0.024698831850
;
piCCf
[
0
][
2
][
1
]
=
0.024698831850
;
piCCf
[
2
][
0
][
2
]
=
-
0.00597133450
;
piCCf
[
0
][
2
][
2
]
=
-
0.00597133450
;
for
(
i
=
3
;
i
<
10
;
i
++
)
piCCf
[
2
][
0
][
i
]
=
0.0049586079
;
for
(
i
=
3
;
i
<
10
;
i
++
)
piCCf
[
0
][
2
][
i
]
=
0.0049586079
;
piCCf
[
2
][
1
][
1
]
=
0.00482478490
;
piCCf
[
1
][
2
][
1
]
=
0.00482478490
;
piCCf
[
2
][
1
][
2
]
=
0.0150
;
piCCf
[
1
][
2
][
2
]
=
0.0150
;
piCCf
[
2
][
1
][
3
]
=
-
0.010
;
piCCf
[
1
][
2
][
3
]
=
-
0.010
;
piCCf
[
2
][
1
][
4
]
=
-
0.01168893870
;
piCCf
[
1
][
2
][
4
]
=
-
0.01168893870
;
piCCf
[
2
][
1
][
5
]
=
-
0.013377877400
;
piCCf
[
1
][
2
][
5
]
=
-
0.013377877400
;
piCCf
[
2
][
1
][
6
]
=
-
0.015066816000
;
piCCf
[
1
][
2
][
6
]
=
-
0.015066816000
;
for
(
i
=
7
;
i
<
10
;
i
++
)
piCCf
[
2
][
1
][
i
]
=
-
0.015066816000
;
for
(
i
=
7
;
i
<
10
;
i
++
)
piCCf
[
1
][
2
][
i
]
=
-
0.015066816000
;
piCCf
[
2
][
2
][
1
]
=
0.0472247850
;
piCCf
[
2
][
2
][
2
]
=
0.0110
;
piCCf
[
2
][
2
][
3
]
=
0.0198529350
;
piCCf
[
2
][
2
][
4
]
=
0.01654411250
;
piCCf
[
2
][
2
][
5
]
=
0.013235290
;
piCCf
[
2
][
2
][
6
]
=
0.00992646749999
;
piCCf
[
2
][
2
][
7
]
=
0.006617644999
;
piCCf
[
2
][
2
][
8
]
=
0.00330882250
;
piCCf
[
3
][
0
][
1
]
=
-
0.05989946750
;
piCCf
[
0
][
3
][
1
]
=
-
0.05989946750
;
piCCf
[
3
][
0
][
2
]
=
-
0.05989946750
;
piCCf
[
0
][
3
][
2
]
=
-
0.05989946750
;
for
(
i
=
3
;
i
<
10
;
i
++
)
piCCf
[
3
][
0
][
i
]
=
0.0049586079
;
for
(
i
=
3
;
i
<
10
;
i
++
)
piCCf
[
0
][
3
][
i
]
=
0.0049586079
;
piCCf
[
3
][
1
][
2
]
=
-
0.0624183760
;
piCCf
[
1
][
3
][
2
]
=
-
0.0624183760
;
for
(
i
=
3
;
i
<
10
;
i
++
)
piCCf
[
3
][
1
][
i
]
=
-
0.0624183760
;
for
(
i
=
3
;
i
<
10
;
i
++
)
piCCf
[
1
][
3
][
i
]
=
-
0.0624183760
;
piCCf
[
3
][
2
][
1
]
=
-
0.02235469150
;
piCCf
[
2
][
3
][
1
]
=
-
0.02235469150
;
for
(
i
=
2
;
i
<
10
;
i
++
)
piCCf
[
3
][
2
][
i
]
=
-
0.02235469150
;
for
(
i
=
2
;
i
<
10
;
i
++
)
piCCf
[
2
][
3
][
i
]
=
-
0.02235469150
;
piCCdfdx
[
2
][
1
][
1
]
=
-
0.026250
;
piCCdfdx
[
2
][
1
][
5
]
=
-
0.0271880
;
piCCdfdx
[
2
][
1
][
6
]
=
-
0.0271880
;
for
(
i
=
7
;
i
<
10
;
i
++
)
piCCdfdx
[
2
][
1
][
i
]
=
-
0.0271880
;
piCCdfdx
[
1
][
3
][
2
]
=
0.0187723882
;
for
(
i
=
2
;
i
<
10
;
i
++
)
piCCdfdx
[
2
][
3
][
i
]
=
0.031209
;
piCCdfdy
[
1
][
2
][
1
]
=
-
0.026250
;
piCCdfdy
[
1
][
2
][
5
]
=
-
0.0271880
;
piCCdfdy
[
1
][
2
][
6
]
=
-
0.0271880
;
for
(
i
=
7
;
i
<
10
;
i
++
)
piCCdfdy
[
1
][
2
][
i
]
=
-
0.0271880
;
piCCdfdy
[
3
][
1
][
2
]
=
0.0187723882
;
for
(
i
=
2
;
i
<
10
;
i
++
)
piCCdfdy
[
3
][
2
][
i
]
=
0.031209
;
piCCdfdz
[
1
][
1
][
2
]
=
-
0.0302715
;
piCCdfdz
[
2
][
1
][
4
]
=
-
0.0100220
;
piCCdfdz
[
1
][
2
][
4
]
=
-
0.0100220
;
piCCdfdz
[
2
][
1
][
5
]
=
-
0.0100220
;
piCCdfdz
[
1
][
2
][
5
]
=
-
0.0100220
;
for
(
i
=
4
;
i
<
9
;
i
++
)
piCCdfdz
[
2
][
2
][
i
]
=
-
0.0033090
;
// make top end of piCC flat instead of zero
i
=
4
;
for
(
j
=
0
;
j
<
4
;
j
++
){
for
(
k
=
1
;
k
<
11
;
k
++
){
piCCf
[
i
][
j
][
k
]
=
piCCf
[
i
-
1
][
j
][
k
];
}
}
for
(
i
=
0
;
i
<
4
;
i
++
){
// also enforces some symmetry
for
(
j
=
i
+
1
;
j
<
5
;
j
++
){
for
(
k
=
1
;
k
<
11
;
k
++
){
piCCf
[
i
][
j
][
k
]
=
piCCf
[
j
][
i
][
k
];
}
}
}
for
(
k
=
1
;
k
<
11
;
k
++
)
piCCf
[
4
][
4
][
k
]
=
piCCf
[
3
][
4
][
k
];
k
=
10
;
for
(
i
=
0
;
i
<
5
;
i
++
){
for
(
j
=
0
;
j
<
5
;
j
++
){
piCCf
[
i
][
j
][
k
]
=
piCCf
[
i
][
j
][
k
-
1
];
}
}
piCHf
[
1
][
1
][
1
]
=
-
0.050
;
piCHf
[
1
][
1
][
2
]
=
-
0.050
;
piCHf
[
1
][
1
][
3
]
=
-
0.30
;
for
(
i
=
4
;
i
<
10
;
i
++
)
piCHf
[
1
][
1
][
i
]
=
-
0.050
;
for
(
i
=
5
;
i
<
10
;
i
++
)
piCHf
[
2
][
0
][
i
]
=
-
0.004523893758064
;
for
(
i
=
5
;
i
<
10
;
i
++
)
piCHf
[
0
][
2
][
i
]
=
-
0.004523893758064
;
piCHf
[
2
][
1
][
2
]
=
-
0.250
;
piCHf
[
1
][
2
][
2
]
=
-
0.250
;
piCHf
[
2
][
1
][
3
]
=
-
0.250
;
piCHf
[
1
][
2
][
3
]
=
-
0.250
;
piCHf
[
3
][
1
][
1
]
=
-
0.10
;
piCHf
[
1
][
3
][
1
]
=
-
0.10
;
piCHf
[
3
][
1
][
2
]
=
-
0.125
;
piCHf
[
1
][
3
][
2
]
=
-
0.125
;
piCHf
[
3
][
1
][
3
]
=
-
0.125
;
piCHf
[
1
][
3
][
3
]
=
-
0.125
;
for
(
i
=
4
;
i
<
10
;
i
++
)
piCHf
[
3
][
1
][
i
]
=
-
0.10
;
for
(
i
=
4
;
i
<
10
;
i
++
)
piCHf
[
1
][
3
][
i
]
=
-
0.10
;
// make top end of piCH flat instead of zero
// also enforces some symmetry
i
=
4
;
for
(
j
=
0
;
j
<
4
;
j
++
){
for
(
k
=
1
;
k
<
11
;
k
++
){
piCHf
[
i
][
j
][
k
]
=
piCHf
[
i
-
1
][
j
][
k
];
}
}
for
(
i
=
0
;
i
<
4
;
i
++
){
for
(
j
=
i
+
1
;
j
<
5
;
j
++
){
for
(
k
=
1
;
k
<
11
;
k
++
){
piCHf
[
i
][
j
][
k
]
=
piCHf
[
j
][
i
][
k
];
}
}
}
for
(
k
=
1
;
k
<
11
;
k
++
)
piCHf
[
4
][
4
][
k
]
=
piCHf
[
3
][
4
][
k
];
k
=
10
;
for
(
i
=
0
;
i
<
5
;
i
++
){
for
(
j
=
0
;
j
<
5
;
j
++
){
piCHf
[
i
][
j
][
k
]
=
piCHf
[
i
][
j
][
k
-
1
];
}
}
piHHf
[
1
][
1
][
1
]
=
0.124915958
;
Tf
[
2
][
2
][
1
]
=
-
0.035140
;
for
(
i
=
2
;
i
<
10
;
i
++
)
Tf
[
2
][
2
][
i
]
=
-
0.0040480
;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double
PairAIREBO
::
memory_usage
()
{
double
bytes
=
0.0
;
bytes
+=
maxlocal
*
sizeof
(
int
);
bytes
+=
maxlocal
*
sizeof
(
int
*
);
for
(
int
i
=
0
;
i
<
comm
->
nthreads
;
i
++
)
bytes
+=
ipage
[
i
].
size
();
bytes
+=
2
*
maxlocal
*
sizeof
(
double
);
return
bytes
;
}
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