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rLAMMPS lammps
pair_bop.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 authors: D.K. Ward (donward@sandia.gov) and X.W. Zhou (Sandia)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
The formulation for this work follows (a) D.G. Pettifor, et al., Mat.
Sci. and Eng. A365, 2-13, (2004);(b) D.A. Murdick, et al., Phys.
Rev. B 73, 045206 (2006);(c) D.G. Pettifor and I.I. Oleinik., Phys
Rev. Lett. 84, 4124 (2000); (d) D.K. Ward, et al., Phys. Rev. B 85,
115206 (2012).
Copyright (2012) Sandia Corporation. Under the terms of Contract DE-
AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
rights in this software.
pairbop v 1.0 comes with no warranty of any kind. pairbop v 1.0 is a
copyrighted code that is distributed free-of-charge, under the terms
of the GNU Public License (GPL). See "Open-Source
Rules"_http://lammps.sandia.gov/open_source.html
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <mpi.h>
#include "pair_bop.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "domain.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include <ctype.h>
using
namespace
LAMMPS_NS
;
#define MAXLINE 1024
#define EPSILON 1.0e-6
/* ---------------------------------------------------------------------- */
PairBOP
::
PairBOP
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
single_enable
=
0
;
one_coeff
=
1
;
manybody_flag
=
1
;
ghostneigh
=
1
;
map
=
NULL
;
pi_a
=
NULL
;
pro_delta
=
NULL
;
pi_delta
=
NULL
;
pi_p
=
NULL
;
pi_c
=
NULL
;
r1
=
NULL
;
sigma_r0
=
NULL
;
pi_r0
=
NULL
;
phi_r0
=
NULL
;
sigma_rc
=
NULL
;
pi_rc
=
NULL
;
phi_rc
=
NULL
;
sigma_beta0
=
NULL
;
pi_beta0
=
NULL
;
phi0
=
NULL
;
sigma_n
=
NULL
;
pi_n
=
NULL
;
phi_m
=
NULL
;
sigma_nc
=
NULL
;
pi_nc
=
NULL
;
phi_nc
=
NULL
;
pro
=
NULL
;
sigma_delta
=
NULL
;
sigma_c
=
NULL
;
sigma_a
=
NULL
;
sigma_f
=
NULL
;
sigma_k
=
NULL
;
small3
=
NULL
;
rcut
=
NULL
;
rcut3
=
NULL
;
rcutsq
=
NULL
;
rcutsq3
=
NULL
;
dr
=
NULL
;
rdr
=
NULL
;
dr3
=
NULL
;
rdr3
=
NULL
;
disij
=
NULL
;
rij
=
NULL
;
neigh_index
=
NULL
;
neigh_index3
=
NULL
;
cosAng
=
NULL
;
betaS
=
NULL
;
dBetaS
=
NULL
;
betaP
=
NULL
;
dBetaP
=
NULL
;
repul
=
NULL
;
dRepul
=
NULL
;
itypeSigBk
=
NULL
;
itypePiBk
=
NULL
;
pBetaS
=
NULL
;
pBetaS1
=
NULL
;
pBetaS2
=
NULL
;
pBetaS3
=
NULL
;
pBetaS4
=
NULL
;
pBetaS5
=
NULL
;
pBetaS6
=
NULL
;
pLong
=
NULL
;
pLong1
=
NULL
;
pLong2
=
NULL
;
pLong3
=
NULL
;
pLong4
=
NULL
;
pLong5
=
NULL
;
pLong6
=
NULL
;
pBetaP
=
NULL
;
pBetaP1
=
NULL
;
pBetaP2
=
NULL
;
pBetaP3
=
NULL
;
pBetaP4
=
NULL
;
pBetaP5
=
NULL
;
pBetaP6
=
NULL
;
pRepul
=
NULL
;
pRepul1
=
NULL
;
pRepul2
=
NULL
;
pRepul3
=
NULL
;
pRepul4
=
NULL
;
pRepul5
=
NULL
;
pRepul6
=
NULL
;
FsigBO
=
NULL
;
FsigBO1
=
NULL
;
FsigBO2
=
NULL
;
FsigBO3
=
NULL
;
FsigBO4
=
NULL
;
FsigBO5
=
NULL
;
FsigBO6
=
NULL
;
rcmin
=
NULL
;
rcmax
=
NULL
;
rcmaxp
=
NULL
;
setflag
=
NULL
;
cutsq
=
NULL
;
cutghost
=
NULL
;
gfunc
=
NULL
;
gfunc1
=
NULL
;
gfunc2
=
NULL
;
gfunc3
=
NULL
;
gfunc4
=
NULL
;
gfunc5
=
NULL
;
gfunc6
=
NULL
;
gpara
=
NULL
;
bt_sg
=
NULL
;
bt_pi
=
NULL
;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairBOP
::~
PairBOP
()
{
if
(
allocated
)
{
memory_theta_destroy
();
if
(
otfly
==
0
)
memory
->
destroy
(
cos_index
);
delete
[]
map
;
memory
->
destroy
(
BOP_index
);
memory
->
destroy
(
BOP_total
);
memory
->
destroy
(
BOP_index3
);
memory
->
destroy
(
BOP_total3
);
memory
->
destroy
(
rcut
);
memory
->
destroy
(
rcut3
);
memory
->
destroy
(
rcutsq
);
memory
->
destroy
(
rcutsq3
);
memory
->
destroy
(
dr
);
memory
->
destroy
(
rdr
);
memory
->
destroy
(
dr3
);
memory
->
destroy
(
rdr3
);
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cutghost
);
memory
->
destroy
(
pBetaS
);
memory
->
destroy
(
pBetaS1
);
memory
->
destroy
(
pBetaS2
);
memory
->
destroy
(
pBetaS3
);
memory
->
destroy
(
pBetaS4
);
memory
->
destroy
(
pBetaS5
);
memory
->
destroy
(
pBetaS6
);
memory
->
destroy
(
pLong
);
memory
->
destroy
(
pLong1
);
memory
->
destroy
(
pLong2
);
memory
->
destroy
(
pLong3
);
memory
->
destroy
(
pLong4
);
memory
->
destroy
(
pLong5
);
memory
->
destroy
(
pLong6
);
memory
->
destroy
(
pBetaP
);
memory
->
destroy
(
pBetaP1
);
memory
->
destroy
(
pBetaP2
);
memory
->
destroy
(
pBetaP3
);
memory
->
destroy
(
pBetaP4
);
memory
->
destroy
(
pBetaP5
);
memory
->
destroy
(
pBetaP6
);
memory
->
destroy
(
pRepul
);
memory
->
destroy
(
pRepul1
);
memory
->
destroy
(
pRepul2
);
memory
->
destroy
(
pRepul3
);
memory
->
destroy
(
pRepul4
);
memory
->
destroy
(
pRepul5
);
memory
->
destroy
(
pRepul6
);
memory
->
destroy
(
FsigBO
);
memory
->
destroy
(
FsigBO1
);
memory
->
destroy
(
FsigBO2
);
memory
->
destroy
(
FsigBO3
);
memory
->
destroy
(
FsigBO4
);
memory
->
destroy
(
FsigBO5
);
memory
->
destroy
(
FsigBO6
);
memory
->
destroy
(
pi_a
);
memory
->
destroy
(
pro_delta
);
memory
->
destroy
(
pi_delta
);
memory
->
destroy
(
pi_p
);
memory
->
destroy
(
pi_c
);
memory
->
destroy
(
r1
);
memory
->
destroy
(
pro
);
memory
->
destroy
(
sigma_delta
);
memory
->
destroy
(
sigma_c
);
memory
->
destroy
(
sigma_a
);
memory
->
destroy
(
sigma_f
);
memory
->
destroy
(
sigma_k
);
memory
->
destroy
(
small3
);
memory
->
destroy
(
gfunc
);
memory
->
destroy
(
gfunc1
);
memory
->
destroy
(
gfunc2
);
memory
->
destroy
(
gfunc3
);
memory
->
destroy
(
gfunc4
);
memory
->
destroy
(
gfunc5
);
memory
->
destroy
(
gfunc6
);
memory
->
destroy
(
gpara
);
}
if
(
allocate_sigma
)
{
destroy_sigma
();
}
if
(
allocate_pi
)
{
destroy_pi
();
}
}
/* ---------------------------------------------------------------------- */
void
PairBOP
::
compute
(
int
eflag
,
int
vflag
)
{
int
pass
;
int
i
,
j
,
ii
,
jj
,
iij
,
i12
;
int
inum
,
temp_ij
,
ks
;
int
nlisti
;
int
itype
,
jtype
;
tagint
i_tag
,
j_tag
;
int
*
ilist
,
*
iilist
;
int
**
firstneigh
;
double
dpr1
,
ps
;
double
ftmp1
,
ftmp2
,
ftmp3
,
dE
;
double
dis_ij
[
3
],
rsq_ij
,
r_ij
;
double
betaS_ij
,
dBetaS_ij
;
double
betaP_ij
,
dBetaP_ij
;
double
repul_ij
,
dRepul_ij
;
double
value
,
dvalue
;
double
totE
;
double
rcut_min
;
double
**
f
=
atom
->
f
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
tagint
*
tag
=
atom
->
tag
;
int
newton_pair
=
force
->
newton_pair
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
int
cnt1
;
MPI_Comm_rank
(
world
,
&
me
);
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
firstneigh
=
list
->
firstneigh
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
// BOP Neighbor lists must be updated every timestep
maxnall
=
nall
;
gneigh
();
// For non on the fly calculations cos and derivatives
// are calculated in advance and stored
totE
=
0
;
piB_0
=
0
;
sigB_0
=
0
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
f
[
i
][
0
]
=
0
;
f
[
i
][
1
]
=
0
;
f
[
i
][
2
]
=
0
;
}
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
i_tag
=
tag
[
i
];
itype
=
map
[
type
[
i
]]
+
1
;
iilist
=
firstneigh
[
i
];
nlisti
=
BOP_total
[
i
];
for
(
jj
=
0
;
jj
<
nlisti
;
jj
++
)
{
temp_ij
=
BOP_index
[
i
]
+
jj
;
j
=
iilist
[
neigh_index
[
temp_ij
]];
j_tag
=
tag
[
j
];
jtype
=
map
[
type
[
j
]]
+
1
;
if
(
j_tag
>=
i_tag
)
{
sigB_0
=
sigmaBo
(
ii
,
jj
);
piB_0
=
PiBo
(
ii
,
jj
);
if
(
otfly
==
0
)
{
if
(
neigh_flag
[
temp_ij
])
{
dpr1
=
(
dRepul
[
temp_ij
]
-
2.0
*
dBetaS
[
temp_ij
]
*
sigB_0
-
2.0
*
dBetaP
[
temp_ij
]
*
piB_0
)
/
rij
[
temp_ij
];
ftmp1
=
dpr1
*
disij
[
0
][
temp_ij
];
ftmp2
=
dpr1
*
disij
[
1
][
temp_ij
];
ftmp3
=
dpr1
*
disij
[
2
][
temp_ij
];
f
[
i
][
0
]
=
f
[
i
][
0
]
+
ftmp1
;
f
[
i
][
1
]
=
f
[
i
][
1
]
+
ftmp2
;
f
[
i
][
2
]
=
f
[
i
][
2
]
+
ftmp3
;
f
[
j
][
0
]
=
f
[
j
][
0
]
-
ftmp1
;
f
[
j
][
1
]
=
f
[
j
][
1
]
-
ftmp2
;
f
[
j
][
2
]
=
f
[
j
][
2
]
-
ftmp3
;
// add repulsive and bond order components to total energy
// (d) Eq.1
dE
=-
2.0
*
betaS
[
temp_ij
]
*
sigB_0
-
2.0
*
betaP
[
temp_ij
]
*
piB_0
;
totE
+=
dE
+
repul
[
temp_ij
];
if
(
evflag
)
{
ev_tally_full
(
i
,
repul
[
temp_ij
],
dE
,
0.0
,
0.0
,
0.0
,
0.0
);
ev_tally_full
(
j
,
repul
[
temp_ij
],
dE
,
0.0
,
0.0
,
0.0
,
0.0
);
ev_tally_xyz
(
i
,
j
,
nlocal
,
newton_pair
,
0.0
,
0.0
,
-
ftmp1
,
-
ftmp2
,
-
ftmp3
,
disij
[
0
][
temp_ij
],
disij
[
1
][
temp_ij
],
disij
[
2
][
temp_ij
]);
}
}
}
else
{
if
(
itype
==
jtype
)
iij
=
itype
-
1
;
else
if
(
itype
<
jtype
)
iij
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
jtype
-
1
;
else
iij
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
itype
-
1
;
dis_ij
[
0
]
=
x
[
j
][
0
]
-
x
[
i
][
0
];
dis_ij
[
1
]
=
x
[
j
][
1
]
-
x
[
i
][
1
];
dis_ij
[
2
]
=
x
[
j
][
2
]
-
x
[
i
][
2
];
rsq_ij
=
dis_ij
[
0
]
*
dis_ij
[
0
]
+
dis_ij
[
1
]
*
dis_ij
[
1
]
+
dis_ij
[
2
]
*
dis_ij
[
2
];
r_ij
=
sqrt
(
rsq_ij
);
if
(
r_ij
<=
rcut
[
iij
])
{
ps
=
r_ij
*
rdr
[
iij
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_ij
=
((
pBetaS3
[
iij
][
ks
-
1
]
*
ps
+
pBetaS2
[
iij
][
ks
-
1
])
*
ps
+
pBetaS1
[
iij
][
ks
-
1
])
*
ps
+
pBetaS
[
iij
][
ks
-
1
];
dBetaS_ij
=
(
pBetaS6
[
iij
][
ks
-
1
]
*
ps
+
pBetaS5
[
iij
][
ks
-
1
])
*
ps
+
pBetaS4
[
iij
][
ks
-
1
];
betaP_ij
=
((
pBetaP3
[
iij
][
ks
-
1
]
*
ps
+
pBetaP2
[
iij
][
ks
-
1
])
*
ps
+
pBetaP1
[
iij
][
ks
-
1
])
*
ps
+
pBetaP
[
iij
][
ks
-
1
];
dBetaP_ij
=
(
pBetaP6
[
iij
][
ks
-
1
]
*
ps
+
pBetaP5
[
iij
][
ks
-
1
])
*
ps
+
pBetaP4
[
iij
][
ks
-
1
];
repul_ij
=
((
pRepul3
[
iij
][
ks
-
1
]
*
ps
+
pRepul2
[
iij
][
ks
-
1
])
*
ps
+
pRepul1
[
iij
][
ks
-
1
])
*
ps
+
pRepul
[
iij
][
ks
-
1
];
dRepul_ij
=
(
pRepul6
[
iij
][
ks
-
1
]
*
ps
+
pRepul5
[
iij
][
ks
-
1
])
*
ps
+
pRepul4
[
iij
][
ks
-
1
];
dpr1
=
(
dRepul_ij
-
2.0
*
dBetaS_ij
*
sigB_0
-
2.0
*
dBetaP_ij
*
piB_0
)
/
r_ij
;
ftmp1
=
dpr1
*
dis_ij
[
0
];
ftmp2
=
dpr1
*
dis_ij
[
1
];
ftmp3
=
dpr1
*
dis_ij
[
2
];
f
[
i
][
0
]
=
f
[
i
][
0
]
+
ftmp1
;
f
[
i
][
1
]
=
f
[
i
][
1
]
+
ftmp2
;
f
[
i
][
2
]
=
f
[
i
][
2
]
+
ftmp3
;
f
[
j
][
0
]
=
f
[
j
][
0
]
-
ftmp1
;
f
[
j
][
1
]
=
f
[
j
][
1
]
-
ftmp2
;
f
[
j
][
2
]
=
f
[
j
][
2
]
-
ftmp3
;
// add repulsive and bond order components to total energy
// (d) Eq. 1
dE
=-
2.0
*
betaS_ij
*
sigB_0
-
2.0
*
betaP_ij
*
piB_0
;
totE
+=
dE
+
repul_ij
;
if
(
evflag
)
{
ev_tally_full
(
i
,
repul_ij
,
dE
,
0.0
,
0.0
,
0.0
,
0.0
);
ev_tally_full
(
j
,
repul_ij
,
dE
,
0.0
,
0.0
,
0.0
,
0.0
);
ev_tally_xyz
(
i
,
j
,
nlocal
,
newton_pair
,
0.0
,
0.0
,
-
ftmp1
,
-
ftmp2
,
-
ftmp3
,
dis_ij
[
0
],
dis_ij
[
1
],
dis_ij
[
2
]);
}
}
}
}
}
}
cnt1
=
0
;
rcut_min
=
10000
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
i_tag
=
tag
[
i
];
itype
=
map
[
type
[
i
]]
+
1
;
iilist
=
firstneigh
[
i
];
nlisti
=
BOP_total3
[
i
];
for
(
jj
=
0
;
jj
<
nlisti
;
jj
++
)
{
temp_ij
=
BOP_index3
[
i
]
+
jj
;
j
=
iilist
[
neigh_index3
[
temp_ij
]];
j_tag
=
tag
[
j
];
if
(
i_tag
<
j_tag
)
{
jtype
=
map
[
type
[
j
]]
+
1
;
pass
=
0
;
if
(
itype
==
jtype
)
i12
=
itype
-
1
;
else
if
(
itype
<
jtype
)
i12
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
jtype
-
1
;
else
i12
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
itype
-
1
;
dis_ij
[
0
]
=
x
[
j
][
0
]
-
x
[
i
][
0
];
dis_ij
[
1
]
=
x
[
j
][
1
]
-
x
[
i
][
1
];
dis_ij
[
2
]
=
x
[
j
][
2
]
-
x
[
i
][
2
];
r_ij
=
sqrt
(
dis_ij
[
0
]
*
dis_ij
[
0
]
+
dis_ij
[
1
]
*
dis_ij
[
1
]
+
dis_ij
[
2
]
*
dis_ij
[
2
]);
if
(
r_ij
<
rcut_min
)
{
rcut_min
=
r_ij
;
}
if
(
r_ij
<=
rcut3
[
i12
])
pass
=
1
;
if
(
pass
==
1
)
{
ps
=
r_ij
*
rdr3
[
i12
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
value
=
((
pLong3
[
i12
][
ks
-
1
]
*
ps
+
pLong2
[
i12
][
ks
-
1
])
*
ps
+
pLong1
[
i12
][
ks
-
1
])
*
ps
+
pLong
[
i12
][
ks
-
1
];
if
(
value
<=
0.0
)
value
=
pLong
[
i12
][
ks
-
1
];
dvalue
=
(
pLong6
[
i12
][
ks
-
1
]
*
ps
+
pLong5
[
i12
][
ks
-
1
])
*
ps
+
pLong4
[
i12
][
ks
-
1
];
dpr1
=-
dvalue
/
r_ij
;
ftmp1
=
dpr1
*
dis_ij
[
0
];
ftmp2
=
dpr1
*
dis_ij
[
1
];
ftmp3
=
dpr1
*
dis_ij
[
2
];
f
[
i
][
0
]
=
f
[
i
][
0
]
+
ftmp1
;
f
[
i
][
1
]
=
f
[
i
][
1
]
+
ftmp2
;
f
[
i
][
2
]
=
f
[
i
][
2
]
+
ftmp3
;
f
[
j
][
0
]
=
f
[
j
][
0
]
-
ftmp1
;
f
[
j
][
1
]
=
f
[
j
][
1
]
-
ftmp2
;
f
[
j
][
2
]
=
f
[
j
][
2
]
-
ftmp3
;
totE
=
totE
-
value
;
if
(
evflag
)
{
ev_tally_full
(
i
,
0
,
-
value
,
0.0
,
0.0
,
0.0
,
0.0
);
ev_tally_full
(
j
,
0
,
-
value
,
0.0
,
0.0
,
0.0
,
0.0
);
ev_tally_xyz
(
i
,
j
,
nlocal
,
newton_pair
,
0.0
,
0.0
,
-
ftmp1
,
-
ftmp2
,
-
ftmp3
,
dis_ij
[
0
],
dis_ij
[
1
],
dis_ij
[
2
]);
}
cnt1
++
;
}
}
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
bop_step
=
1
;
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairBOP
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
memory
->
create
(
rcut
,
npairs
,
"BOP:rcut"
);
memory
->
create
(
rcut3
,
npairs
,
"BOP:rcut3"
);
memory
->
create
(
rcutsq
,
npairs
,
"BOP:rcutsq"
);
memory
->
create
(
rcutsq3
,
npairs
,
"BOP:rcutsq3"
);
memory
->
create
(
dr
,
npairs
,
"BOP:dr"
);
memory
->
create
(
rdr
,
npairs
,
"BOP:dr"
);
memory
->
create
(
dr3
,
npairs
,
"BOP:dr"
);
memory
->
create
(
rdr3
,
npairs
,
"BOP:dr"
);
memory
->
create
(
setflag
,
n
+
1
,
n
+
1
,
"pair:setflag"
);
memory
->
create
(
cutsq
,
n
+
1
,
n
+
1
,
"pair:cutsq"
);
memory
->
create
(
cutghost
,
n
+
1
,
n
+
1
,
"pair:cutghost"
);
memory
->
create
(
pBetaS
,
npairs
,
nr
,
"BOP:pBetaS"
);
memory
->
create
(
pBetaS1
,
npairs
,
nr
,
"BOP:pBetaS1"
);
memory
->
create
(
pBetaS2
,
npairs
,
nr
,
"BOP:pBetaS2"
);
memory
->
create
(
pBetaS3
,
npairs
,
nr
,
"BOP:pBetaS3"
);
memory
->
create
(
pBetaS4
,
npairs
,
nr
,
"BOP:pBetaS4"
);
memory
->
create
(
pBetaS5
,
npairs
,
nr
,
"BOP:pBetaS5"
);
memory
->
create
(
pBetaS6
,
npairs
,
nr
,
"BOP:pBetaS6"
);
memory
->
create
(
pLong
,
npairs
,
nr
,
"BOP:pLong"
);
memory
->
create
(
pLong1
,
npairs
,
nr
,
"BOP:pLong"
);
memory
->
create
(
pLong2
,
npairs
,
nr
,
"BOP:pLong"
);
memory
->
create
(
pLong3
,
npairs
,
nr
,
"BOP:pLong"
);
memory
->
create
(
pLong4
,
npairs
,
nr
,
"BOP:pLong"
);
memory
->
create
(
pLong5
,
npairs
,
nr
,
"BOP:pLong"
);
memory
->
create
(
pLong6
,
npairs
,
nr
,
"BOP:pLong"
);
memory
->
create
(
pBetaP
,
npairs
,
nr
,
"BOP:pBetaP"
);
memory
->
create
(
pBetaP1
,
npairs
,
nr
,
"BOP:pBetaP1"
);
memory
->
create
(
pBetaP2
,
npairs
,
nr
,
"BOP:pBetaP2"
);
memory
->
create
(
pBetaP3
,
npairs
,
nr
,
"BOP:pBetaP3"
);
memory
->
create
(
pBetaP4
,
npairs
,
nr
,
"BOP:pBetaP4"
);
memory
->
create
(
pBetaP5
,
npairs
,
nr
,
"BOP:pBetaP5"
);
memory
->
create
(
pBetaP6
,
npairs
,
nr
,
"BOP:pBetaP6"
);
memory
->
create
(
pRepul
,
npairs
,
nr
,
"BOP:pRepul"
);
memory
->
create
(
pRepul1
,
npairs
,
nr
,
"BOP:pRepul1"
);
memory
->
create
(
pRepul2
,
npairs
,
nr
,
"BOP:pRepul2"
);
memory
->
create
(
pRepul3
,
npairs
,
nr
,
"BOP:pRepul3"
);
memory
->
create
(
pRepul4
,
npairs
,
nr
,
"BOP:pRepul4"
);
memory
->
create
(
pRepul5
,
npairs
,
nr
,
"BOP:pRepul5"
);
memory
->
create
(
pRepul6
,
npairs
,
nr
,
"BOP:pRepul6"
);
memory
->
create
(
FsigBO
,
npairs
,
nBOt
,
"BOP:FsigBO"
);
memory
->
create
(
FsigBO1
,
npairs
,
nBOt
,
"BOP:FsigBO1"
);
memory
->
create
(
FsigBO2
,
npairs
,
nBOt
,
"BOP:FsigBO2"
);
memory
->
create
(
FsigBO3
,
npairs
,
nBOt
,
"BOP:FsigBO3"
);
memory
->
create
(
FsigBO4
,
npairs
,
nBOt
,
"BOP:FsigBO4"
);
memory
->
create
(
FsigBO5
,
npairs
,
nBOt
,
"BOP:FsigBO5"
);
memory
->
create
(
FsigBO6
,
npairs
,
nBOt
,
"BOP:FsigBO6"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairBOP
::
settings
(
int
narg
,
char
**
arg
)
{
otfly
=
1
;
int
iarg
=
0
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"save"
)
==
0
)
{
otfly
=
0
;
iarg
++
;
}
else
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs(Updated: D.K. Ward 05/06/10)
------------------------------------------------------------------------- */
void
PairBOP
::
coeff
(
int
narg
,
char
**
arg
)
{
int
i
,
j
;
int
n
=
atom
->
ntypes
;
MPI_Comm_rank
(
world
,
&
me
);
map
=
new
int
[
n
+
1
];
if
(
narg
!=
3
+
atom
->
ntypes
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
// ensure I,J args are * *
if
(
strcmp
(
arg
[
0
],
"*"
)
!=
0
||
strcmp
(
arg
[
1
],
"*"
)
!=
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
// read the potential file
nr
=
2000
;
nBOt
=
2000
;
ntheta
=
2000
;
bop_step
=
0
;
nb_pi
=
0
;
nb_sg
=
0
;
allocate_sigma
=
0
;
allocate_pi
=
0
;
allocate_neigh
=
0
;
update_list
=
0
;
maxnall
=
0
;
read_table
(
arg
[
2
]);
// match element names to BOP word types
if
(
me
==
0
)
{
for
(
i
=
3
;
i
<
narg
;
i
++
)
{
if
(
strcmp
(
arg
[
i
],
"NULL"
)
==
0
)
{
map
[
i
-
2
]
=
-
1
;
continue
;
}
for
(
j
=
0
;
j
<
bop_types
;
j
++
)
{
if
(
strcmp
(
arg
[
i
],
elements
[
j
])
==
0
)
break
;
}
map
[
i
-
2
]
=
j
;
}
}
MPI_Bcast
(
&
map
[
1
],
atom
->
ntypes
,
MPI_INT
,
0
,
world
);
if
(
me
==
0
)
{
if
(
elements
)
{
for
(
i
=
0
;
i
<
bop_types
;
i
++
)
delete
[]
elements
[
i
];
delete
[]
elements
;
}
}
// clear setflag since coeff() called once with I,J = * *
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
PairBOP
::
init_style
()
{
if
(
atom
->
tag_enable
==
0
)
error
->
all
(
FLERR
,
"Pair style BOP requires atom IDs"
);
if
(
force
->
newton_pair
==
0
)
error
->
all
(
FLERR
,
"Pair style BOP requires newton pair on"
);
// check that user sets comm->cutghostuser to 3x the max BOP cutoff
if
(
comm
->
cutghostuser
<
3.0
*
cutmax
-
EPSILON
)
{
char
str
[
128
];
sprintf
(
str
,
"Pair style bop requires comm ghost cutoff "
"at least 3x larger than %g"
,
cutmax
);
error
->
all
(
FLERR
,
str
);
}
// need a full neighbor list and 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
;
}
/* ---------------------------------------------------------------------- */
double
PairBOP
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
error
->
all
(
FLERR
,
"All pair coeffs are not set"
);
int
ii
=
map
[
i
]
+
1
;
int
jj
=
map
[
j
]
+
1
;
int
ij
;
if
(
ii
==
jj
)
ij
=
ii
-
1
;
else
if
(
ii
<
jj
)
ij
=
ii
*
bop_types
-
ii
*
(
ii
+
1
)
/
2
+
jj
-
1
;
else
ij
=
jj
*
bop_types
-
jj
*
(
jj
+
1
)
/
2
+
ii
-
1
;
if
(
rcut
[
ij
]
>
rcut3
[
ij
])
{
cutghost
[
i
][
j
]
=
rcut
[
ij
];
cutghost
[
j
][
i
]
=
cutghost
[
i
][
j
];
cutsq
[
i
][
j
]
=
rcut
[
ij
]
*
rcut
[
ij
];
cutsq
[
j
][
i
]
=
cutsq
[
i
][
j
];
return
rcut
[
ij
];
}
else
{
cutghost
[
i
][
j
]
=
rcut3
[
ij
];
cutghost
[
j
][
i
]
=
cutghost
[
i
][
j
];
cutsq
[
i
][
j
]
=
rcut3
[
ij
]
*
rcut3
[
ij
];
cutsq
[
j
][
i
]
=
cutsq
[
i
][
j
];
return
rcut3
[
ij
];
}
}
/* ----------------------------------------------------------------------
create BOP neighbor list from main neighbor list
BOP neighbor list stores neighbors of ghost atoms
BOP requires neighbor's of k if k is a neighbor of
j and j is a neighbor of i
------------------------------------------------------------------------- */
void
PairBOP
::
gneigh
()
{
int
i
,
ii
;
int
j
,
jj
,
kk
;
int
itype
,
jtype
,
i12
;
int
temp_ij
,
temp_ik
,
temp_ijk
;
int
n
,
ks
,
max_check
,
neigh_t
;
int
max_check3
;
int
nlisti
;
int
*
ilist
,
*
numneigh
;
int
*
iilist
;
int
**
firstneigh
;
int
nlocal
=
atom
->
nlocal
;
int
nall
=
nlocal
+
atom
->
nghost
;
double
dis
[
3
],
r
;
double
rj2
,
rk2
,
rsq
,
ps
;
double
rj1k1
,
rj2k2
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
if
(
allocate_neigh
==
0
)
{
memory
->
create
(
BOP_index
,
nall
,
"BOP_index"
);
memory
->
create
(
BOP_index3
,
nall
,
"BOP_index3"
);
memory
->
create
(
BOP_total
,
nall
,
"BOP_total"
);
memory
->
create
(
BOP_total3
,
nall
,
"BOP_total"
);
if
(
otfly
==
0
)
memory
->
create
(
cos_index
,
nall
,
"cos_index"
);
allocate_neigh
=
1
;
}
else
{
memory
->
grow
(
BOP_index
,
nall
,
"BOP_index"
);
memory
->
grow
(
BOP_index3
,
nall
,
"BOP_index3"
);
memory
->
grow
(
BOP_total
,
nall
,
"BOP_total"
);
memory
->
grow
(
BOP_total3
,
nall
,
"BOP_total3"
);
if
(
otfly
==
0
)
memory
->
grow
(
cos_index
,
nall
,
"cos_index"
);
allocate_neigh
=
1
;
}
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
if
(
bop_step
==
0
)
{
maxneigh
=
0
;
maxneigh3
=
0
;
maxnall
=
0
;
}
neigh_total
=
0
;
neigh_total3
=
0
;
cos_total
=
0
;
for
(
ii
=
0
;
ii
<
nall
;
ii
++
)
{
if
(
ii
<
nlocal
)
i
=
ilist
[
ii
];
else
i
=
ii
;
itype
=
map
[
type
[
i
]]
+
1
;
iilist
=
firstneigh
[
i
];
max_check
=
0
;
max_check3
=
0
;
for
(
jj
=
0
;
jj
<
numneigh
[
i
];
jj
++
)
{
j
=
iilist
[
jj
];
jtype
=
map
[
type
[
j
]]
+
1
;
if
(
itype
==
jtype
)
i12
=
itype
-
1
;
else
if
(
itype
<
jtype
)
i12
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
jtype
-
1
;
else
i12
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
itype
-
1
;
if
(
i12
>=
npairs
)
{
error
->
one
(
FLERR
,
"Too many atom pairs for pair bop"
);
}
dis
[
0
]
=
x
[
j
][
0
]
-
x
[
i
][
0
];
dis
[
1
]
=
x
[
j
][
1
]
-
x
[
i
][
1
];
dis
[
2
]
=
x
[
j
][
2
]
-
x
[
i
][
2
];
rsq
=
dis
[
0
]
*
dis
[
0
]
+
dis
[
1
]
*
dis
[
1
]
+
dis
[
2
]
*
dis
[
2
];
r
=
sqrt
(
rsq
);
if
(
r
<=
rcut
[
i12
])
{
max_check
++
;
}
if
(
r
<=
rcut3
[
i12
])
{
max_check3
++
;
}
}
BOP_index
[
i
]
=
neigh_total
;
BOP_index3
[
i
]
=
neigh_total3
;
BOP_total
[
i
]
=
max_check
;
BOP_total3
[
i
]
=
max_check3
;
neigh_total
+=
max_check
;
neigh_total3
+=
max_check3
;
if
(
max_check
>
maxneigh
||
max_check3
>
maxneigh3
){
maxneigh
=
max_check
;
maxneigh3
=
max_check3
;
}
if
(
otfly
==
0
)
{
cos_index
[
i
]
=
cos_total
;
cos_total
+=
max_check
*
(
max_check
-
1
)
/
2
;
}
}
maxnall
=
nall
;
if
(
update_list
!=
0
)
memory_theta_grow
();
else
memory_theta_create
();
neigh_t
=
0
;
for
(
ii
=
0
;
ii
<
nall
;
ii
++
)
{
if
(
ii
<
nlocal
)
i
=
ilist
[
ii
];
else
i
=
ii
;
itype
=
map
[
type
[
i
]]
+
1
;
iilist
=
firstneigh
[
i
];
max_check
=
0
;
max_check3
=
0
;
for
(
jj
=
0
;
jj
<
numneigh
[
i
];
jj
++
)
{
j
=
iilist
[
jj
];
jtype
=
map
[
type
[
j
]]
+
1
;
if
(
itype
==
jtype
)
i12
=
itype
-
1
;
else
if
(
itype
<
jtype
)
i12
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
jtype
-
1
;
else
i12
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
itype
-
1
;
if
(
i12
>=
npairs
)
{
error
->
one
(
FLERR
,
"Too many atom pairs for pair bop"
);
}
dis
[
0
]
=
x
[
j
][
0
]
-
x
[
i
][
0
];
dis
[
1
]
=
x
[
j
][
1
]
-
x
[
i
][
1
];
dis
[
2
]
=
x
[
j
][
2
]
-
x
[
i
][
2
];
rsq
=
dis
[
0
]
*
dis
[
0
]
+
dis
[
1
]
*
dis
[
1
]
+
dis
[
2
]
*
dis
[
2
];
r
=
sqrt
(
rsq
);
if
(
r
<=
rcut
[
i12
])
{
temp_ij
=
BOP_index
[
i
]
+
max_check
;
if
(
i
==
0
)
{
}
neigh_index
[
temp_ij
]
=
jj
;
neigh_flag
[
temp_ij
]
=
1
;
max_check
++
;
}
if
(
r
<=
rcut3
[
i12
])
{
temp_ij
=
BOP_index3
[
i
]
+
max_check3
;
neigh_index3
[
temp_ij
]
=
jj
;
neigh_flag3
[
temp_ij
]
=
1
;
max_check3
++
;
}
}
}
if
(
otfly
==
0
)
{
for
(
ii
=
0
;
ii
<
nall
;
ii
++
)
{
if
(
ii
<
nlocal
)
i
=
ilist
[
ii
];
else
i
=
ii
;
itype
=
map
[
type
[
i
]]
+
1
;
iilist
=
firstneigh
[
i
];
nlisti
=
BOP_total
[
i
];
max_check
=
0
;
for
(
jj
=
0
;
jj
<
nlisti
;
jj
++
)
{
temp_ij
=
BOP_index
[
i
]
+
jj
;
j
=
iilist
[
neigh_index
[
temp_ij
]];
if
(
temp_ij
>=
neigh_total
)
{
}
if
(
temp_ij
<
0
)
{
}
jtype
=
map
[
type
[
j
]]
+
1
;
if
(
itype
==
jtype
)
i12
=
itype
-
1
;
else
if
(
itype
<
jtype
)
i12
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
jtype
-
1
;
else
i12
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
itype
-
1
;
if
(
i12
>=
npairs
)
{
error
->
one
(
FLERR
,
"Too many atom pairs for pair bop"
);
}
disij
[
0
][
temp_ij
]
=
x
[
j
][
0
]
-
x
[
i
][
0
];
disij
[
1
][
temp_ij
]
=
x
[
j
][
1
]
-
x
[
i
][
1
];
disij
[
2
][
temp_ij
]
=
x
[
j
][
2
]
-
x
[
i
][
2
];
rsq
=
disij
[
0
][
temp_ij
]
*
disij
[
0
][
temp_ij
]
+
disij
[
1
][
temp_ij
]
*
disij
[
1
][
temp_ij
]
+
disij
[
2
][
temp_ij
]
*
disij
[
2
][
temp_ij
];
rij
[
temp_ij
]
=
sqrt
(
rsq
);
if
(
rij
[
temp_ij
]
<=
rcut
[
i12
])
{
max_check
++
;
}
else
neigh_flag
[
temp_ij
]
=
0
;
}
}
neigh_t
+=
max_check
;
for
(
ii
=
0
;
ii
<
nall
;
ii
++
)
{
if
(
ii
<
nlocal
)
i
=
ilist
[
ii
];
else
i
=
ii
;
itype
=
map
[
type
[
i
]]
+
1
;
iilist
=
firstneigh
[
i
];
nlisti
=
BOP_total
[
i
];
for
(
jj
=
0
;
jj
<
nlisti
;
jj
++
)
{
temp_ij
=
BOP_index
[
i
]
+
jj
;
j
=
iilist
[
neigh_index
[
temp_ij
]];
jtype
=
map
[
type
[
j
]]
+
1
;
if
(
itype
==
jtype
)
i12
=
itype
-
1
;
else
if
(
itype
<
jtype
)
i12
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
jtype
-
1
;
else
i12
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
itype
-
1
;
if
(
i12
>=
npairs
)
{
error
->
one
(
FLERR
,
"Too many atom pairs for pair bop"
);
}
ps
=
rij
[
temp_ij
]
*
rdr
[
i12
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS
[
temp_ij
]
=
((
pBetaS3
[
i12
][
ks
-
1
]
*
ps
+
pBetaS2
[
i12
][
ks
-
1
])
*
ps
+
pBetaS1
[
i12
][
ks
-
1
])
*
ps
+
pBetaS
[
i12
][
ks
-
1
];
dBetaS
[
temp_ij
]
=
(
pBetaS6
[
i12
][
ks
-
1
]
*
ps
+
pBetaS5
[
i12
][
ks
-
1
])
*
ps
+
pBetaS4
[
i12
][
ks
-
1
];
betaP
[
temp_ij
]
=
((
pBetaP3
[
i12
][
ks
-
1
]
*
ps
+
pBetaP2
[
i12
][
ks
-
1
])
*
ps
+
pBetaP1
[
i12
][
ks
-
1
])
*
ps
+
pBetaP
[
i12
][
ks
-
1
];
dBetaP
[
temp_ij
]
=
(
pBetaP6
[
i12
][
ks
-
1
]
*
ps
+
pBetaP5
[
i12
][
ks
-
1
])
*
ps
+
pBetaP4
[
i12
][
ks
-
1
];
repul
[
temp_ij
]
=
((
pRepul3
[
i12
][
ks
-
1
]
*
ps
+
pRepul2
[
i12
][
ks
-
1
])
*
ps
+
pRepul1
[
i12
][
ks
-
1
])
*
ps
+
pRepul
[
i12
][
ks
-
1
];
dRepul
[
temp_ij
]
=
(
pRepul6
[
i12
][
ks
-
1
]
*
ps
+
pRepul5
[
i12
][
ks
-
1
])
*
ps
+
pRepul4
[
i12
][
ks
-
1
];
}
}
for
(
ii
=
0
;
ii
<
nall
;
ii
++
)
{
n
=
0
;
if
(
ii
<
nlocal
)
i
=
ilist
[
ii
];
else
i
=
ii
;
iilist
=
firstneigh
[
i
];
nlisti
=
BOP_total
[
i
];
for
(
jj
=
0
;
jj
<
nlisti
;
jj
++
)
{
temp_ij
=
BOP_index
[
i
]
+
jj
;
j
=
iilist
[
neigh_index
[
temp_ij
]];
rj2
=
rij
[
temp_ij
]
*
rij
[
temp_ij
];
for
(
kk
=
jj
+
1
;
kk
<
nlisti
;
kk
++
)
{
if
(
cos_index
[
i
]
+
n
>=
cos_total
)
{
error
->
one
(
FLERR
,
"Too many atom triplets for pair bop"
);
}
temp_ik
=
BOP_index
[
i
]
+
kk
;
temp_ijk
=
cos_index
[
i
]
+
n
;
if
(
temp_ijk
>=
cos_total
)
{
error
->
one
(
FLERR
,
"Too many atom triplets for pair bop"
);
}
rk2
=
rij
[
temp_ik
]
*
rij
[
temp_ik
];
rj1k1
=
rij
[
temp_ij
]
*
rij
[
temp_ik
];
rj2k2
=
rj1k1
*
rj1k1
;
if
(
temp_ijk
>=
cos_total
)
{
error
->
one
(
FLERR
,
"Too many atom triplets for pair bop"
);
}
cosAng
[
temp_ijk
]
=
(
disij
[
0
][
temp_ij
]
*
disij
[
0
][
temp_ik
]
+
disij
[
1
][
temp_ij
]
*
disij
[
1
][
temp_ik
]
+
disij
[
2
][
temp_ij
]
*
disij
[
2
][
temp_ik
])
/
rj1k1
;
dcAng
[
temp_ijk
][
0
][
0
]
=
(
disij
[
0
][
temp_ik
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
0
][
temp_ij
]
*
rk2
)
/
(
rj2k2
);
dcAng
[
temp_ijk
][
1
][
0
]
=
(
disij
[
1
][
temp_ik
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
1
][
temp_ij
]
*
rk2
)
/
(
rj2k2
);
dcAng
[
temp_ijk
][
2
][
0
]
=
(
disij
[
2
][
temp_ik
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
2
][
temp_ij
]
*
rk2
)
/
(
rj2k2
);
dcAng
[
temp_ijk
][
0
][
1
]
=
(
disij
[
0
][
temp_ij
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
0
][
temp_ik
]
*
rj2
)
/
(
rj2k2
);
dcAng
[
temp_ijk
][
1
][
1
]
=
(
disij
[
1
][
temp_ij
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
1
][
temp_ik
]
*
rj2
)
/
(
rj2k2
);
dcAng
[
temp_ijk
][
2
][
1
]
=
(
disij
[
2
][
temp_ij
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
2
][
temp_ik
]
*
rj2
)
/
(
rj2k2
);
n
++
;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void
PairBOP
::
theta
()
{
int
i
,
j
,
ii
,
jj
,
kk
;
int
itype
,
jtype
,
i12
;
int
temp_ij
,
temp_ik
,
temp_ijk
;
int
n
,
nlocal
,
nall
,
ks
;
int
nlisti
;
int
*
ilist
;
int
*
iilist
;
int
**
firstneigh
;
double
rj2
,
rk2
,
rsq
,
ps
;
double
rj1k1
,
rj2k2
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
nlocal
=
atom
->
nlocal
;
nall
=
nlocal
+
atom
->
nghost
;
ilist
=
list
->
ilist
;
firstneigh
=
list
->
firstneigh
;
if
(
update_list
!=
0
)
memory_theta_grow
();
else
memory_theta_create
();
for
(
ii
=
0
;
ii
<
nall
;
ii
++
)
{
if
(
ii
<
nlocal
)
i
=
ilist
[
ii
];
else
i
=
ii
;
itype
=
map
[
type
[
i
]]
+
1
;
iilist
=
firstneigh
[
i
];
nlisti
=
BOP_total
[
i
];
for
(
jj
=
0
;
jj
<
nlisti
;
jj
++
)
{
temp_ij
=
BOP_index
[
i
]
+
jj
;
j
=
iilist
[
neigh_index
[
temp_ij
]];
jtype
=
map
[
type
[
j
]]
+
1
;
if
(
itype
==
jtype
)
i12
=
itype
-
1
;
else
if
(
itype
<
jtype
)
i12
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
jtype
-
1
;
else
i12
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
itype
-
1
;
if
(
i12
>=
npairs
)
{
error
->
one
(
FLERR
,
"Too many atom pairs for pair bop"
);
}
disij
[
0
][
temp_ij
]
=
x
[
j
][
0
]
-
x
[
i
][
0
];
disij
[
1
][
temp_ij
]
=
x
[
j
][
1
]
-
x
[
i
][
1
];
disij
[
2
][
temp_ij
]
=
x
[
j
][
2
]
-
x
[
i
][
2
];
rsq
=
disij
[
0
][
temp_ij
]
*
disij
[
0
][
temp_ij
]
+
disij
[
1
][
temp_ij
]
*
disij
[
1
][
temp_ij
]
+
disij
[
2
][
temp_ij
]
*
disij
[
2
][
temp_ij
];
rij
[
temp_ij
]
=
sqrt
(
rsq
);
if
(
rij
[
temp_ij
]
<=
rcut
[
i12
])
neigh_flag
[
temp_ij
]
=
1
;
else
neigh_flag
[
temp_ij
]
=
0
;
if
(
rij
[
temp_ij
]
<=
rcut3
[
i12
])
neigh_flag3
[
temp_ij
]
=
1
;
else
neigh_flag3
[
temp_ij
]
=
0
;
ps
=
rij
[
temp_ij
]
*
rdr
[
i12
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS
[
temp_ij
]
=
((
pBetaS3
[
i12
][
ks
-
1
]
*
ps
+
pBetaS2
[
i12
][
ks
-
1
])
*
ps
+
pBetaS1
[
i12
][
ks
-
1
])
*
ps
+
pBetaS
[
i12
][
ks
-
1
];
dBetaS
[
temp_ij
]
=
(
pBetaS6
[
i12
][
ks
-
1
]
*
ps
+
pBetaS5
[
i12
][
ks
-
1
])
*
ps
+
pBetaS4
[
i12
][
ks
-
1
];
betaP
[
temp_ij
]
=
((
pBetaP3
[
i12
][
ks
-
1
]
*
ps
+
pBetaP2
[
i12
][
ks
-
1
])
*
ps
+
pBetaP1
[
i12
][
ks
-
1
])
*
ps
+
pBetaP
[
i12
][
ks
-
1
];
dBetaP
[
temp_ij
]
=
(
pBetaP6
[
i12
][
ks
-
1
]
*
ps
+
pBetaP5
[
i12
][
ks
-
1
])
*
ps
+
pBetaP4
[
i12
][
ks
-
1
];
repul
[
temp_ij
]
=
((
pRepul3
[
i12
][
ks
-
1
]
*
ps
+
pRepul2
[
i12
][
ks
-
1
])
*
ps
+
pRepul1
[
i12
][
ks
-
1
])
*
ps
+
pRepul
[
i12
][
ks
-
1
];
dRepul
[
temp_ij
]
=
(
pRepul6
[
i12
][
ks
-
1
]
*
ps
+
pRepul5
[
i12
][
ks
-
1
])
*
ps
+
pRepul4
[
i12
][
ks
-
1
];
}
}
for
(
ii
=
0
;
ii
<
nall
;
ii
++
)
{
n
=
0
;
if
(
ii
<
nlocal
)
i
=
ilist
[
ii
];
else
i
=
ii
;
iilist
=
firstneigh
[
i
];
nlisti
=
BOP_total
[
i
];
for
(
jj
=
0
;
jj
<
nlisti
;
jj
++
)
{
temp_ij
=
BOP_index
[
i
]
+
jj
;
j
=
iilist
[
neigh_index
[
temp_ij
]];
rj2
=
rij
[
temp_ij
]
*
rij
[
temp_ij
];
for
(
kk
=
jj
+
1
;
kk
<
nlisti
;
kk
++
)
{
if
(
cos_index
[
i
]
+
n
>=
cos_total
)
{
error
->
one
(
FLERR
,
"Too many atom triplets for pair bop"
);
}
temp_ik
=
BOP_index
[
i
]
+
kk
;
temp_ijk
=
cos_index
[
i
]
+
n
;
if
(
temp_ijk
>=
cos_total
)
{
error
->
one
(
FLERR
,
"Too many atom triplets for pair bop"
);
}
rk2
=
rij
[
temp_ik
]
*
rij
[
temp_ik
];
rj1k1
=
rij
[
temp_ij
]
*
rij
[
temp_ik
];
rj2k2
=
rj1k1
*
rj1k1
;
if
(
temp_ijk
>=
cos_total
)
{
error
->
one
(
FLERR
,
"Too many atom triplets for pair bop"
);
}
cosAng
[
temp_ijk
]
=
(
disij
[
0
][
temp_ij
]
*
disij
[
0
][
temp_ik
]
+
disij
[
1
][
temp_ij
]
*
disij
[
1
][
temp_ik
]
+
disij
[
2
][
temp_ij
]
*
disij
[
2
][
temp_ik
])
/
rj1k1
;
dcAng
[
temp_ijk
][
0
][
0
]
=
(
disij
[
0
][
temp_ik
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
0
][
temp_ij
]
*
rk2
)
/
(
rj2k2
);
dcAng
[
temp_ijk
][
1
][
0
]
=
(
disij
[
1
][
temp_ik
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
1
][
temp_ij
]
*
rk2
)
/
(
rj2k2
);
dcAng
[
temp_ijk
][
2
][
0
]
=
(
disij
[
2
][
temp_ik
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
2
][
temp_ij
]
*
rk2
)
/
(
rj2k2
);
dcAng
[
temp_ijk
][
0
][
1
]
=
(
disij
[
0
][
temp_ij
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
0
][
temp_ik
]
*
rj2
)
/
(
rj2k2
);
dcAng
[
temp_ijk
][
1
][
1
]
=
(
disij
[
1
][
temp_ij
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
1
][
temp_ik
]
*
rj2
)
/
(
rj2k2
);
dcAng
[
temp_ijk
][
2
][
1
]
=
(
disij
[
2
][
temp_ij
]
*
rj1k1
-
cosAng
[
temp_ijk
]
*
disij
[
2
][
temp_ik
]
*
rj2
)
/
(
rj2k2
);
n
++
;
}
}
}
}
/* ---------------------------------------------------------------------- */
void
PairBOP
::
theta_mod
()
{
if
(
update_list
!=
0
)
memory_theta_grow
();
else
memory_theta_create
();
}
/* ---------------------------------------------------------------------- */
/* The formulation differs slightly to avoid negative square roots
in the calculation of Sigma^(1/2) of (a) Eq. 6 and (b) Eq. 11 */
/* ---------------------------------------------------------------------- */
/* The formulation differs slightly to avoid negative square roots
in the calculation of Theta_pi,ij of (a) Eq. 36 and (b) Eq. 18 */
double
PairBOP
::
sigmaBo
(
int
itmp
,
int
jtmp
)
{
int
nb_t
,
new_n_tot
;
int
i
,
j
,
k
,
kp
,
m
,
pp
,
kpj
,
kpk
,
kkp
;
int
ktmp
,
ltmp
,
mtmp
;
int
i_tag
,
j_tag
;
int
kp1
,
kp2
,
kp1type
;
int
iij
,
iik
,
ijk
,
ikkp
,
ji
,
iikp
,
ijkp
;
int
nkp
,
nk0
;
int
jNeik
,
kNeii
,
kNeij
,
kNeikp
;
int
kpNeij
,
kpNeik
,
lp1
;
int
new1
,
new2
,
nlocal
;
int
*
ilist
,
*
iilist
,
*
jlist
,
*
klist
,
*
kplist
;
int
**
firstneigh
;
int
temp_ij
,
temp_ik
,
temp_jkp
,
temp_kk
,
temp_jk
;
int
temp_ji
,
temp_kpj
,
temp_kkp
;
int
temp_ikp
,
temp_kpk
;
int
nb_ij
,
nb_ik
,
nb_ikp
;
int
nb_jk
,
nb_jkp
,
nb_kkp
;
int
kp_nsearch
,
nsearch
;
int
sig_flag
,
setting
,
ncmp
,
ks
;
int
itype
,
jtype
,
ktype
,
kptype
;
int
bt_i
,
bt_j
;
int
same_ikp
,
same_jkp
,
same_kpk
;
int
same_jkpj
,
same_kkpk
;
int
pass_ij
,
pass_ik
,
pass_jk
;
int
pass_jkp
,
pass_ikp
,
pass_kkp
;
int
njik
,
ngj
,
ngk
;
int
nijk
,
ngji
,
ngjk
;
int
nikj
,
ngki
,
ngkj
;
int
njikp
,
nglj
,
ngl
;
int
nkikp
,
nglk
,
nglkp
;
int
nikkp
,
ngli
,
nijkp
;
int
ngkkp
,
njkpk
,
ngkpj
;
int
ngjkp
,
ngkpk
,
ngi
;
int
nkjkp
,
njkkp
;
int
ang_ijk
,
ang_jik
,
ang_ikj
;
int
ang_jikp
,
ang_kikp
,
ang_ikkp
;
int
ang_ijkp
,
ang_jkpk
,
ang_kjkp
;
int
ang_jkkp
;
int
ni_ij
,
ni_ji
,
ni_ik
;
int
ni_jk
,
ni_ikN
,
ni_kj
;
int
ni_jkp
,
ni_kpj
,
ni_ikp
,
ni_kkp
;
int
ni_kpk
,
ni_kpnsearch
;
int
temp_ikN
,
temp_kj
;
int
nlisti
,
nlistj
,
nlistk
,
nlistkp
;
double
AA
,
BB
,
CC
,
DD
,
EE
,
EE1
,
FF
;
double
AAC
,
BBC
,
CCC
,
DDC
,
EEC
,
FFC
,
GGC
;
double
AACFF
,
UT
,
bndtmp
,
UTcom
;
double
amean
,
ps
;
double
gfactor1
,
gprime1
,
gsqprime
;
double
gfactorsq
,
gfactor2
,
gprime2
;
double
gfactorsq2
,
gsqprime2
;
double
gfactor3
,
gprime3
,
gfactor
,
rfactor
;
double
drfactor
,
gfactor4
,
gprime4
,
agpdpr3
;
double
rfactor0
,
rfactorrt
,
rfactor1rt
,
rfactor1
;
double
rcm1
,
rcm2
,
gcm1
,
gcm2
,
gcm3
;
double
agpdpr1
,
agpdpr2
,
app1
,
app2
,
app3
,
app4
;
double
dsigB1
,
dsigB2
,
xrun
;
double
part0
,
part1
,
part2
,
part3
,
part4
;
double
psign
,
bndtmp0
,
pp1
;
double
bndtmp1
,
bndtmp2
,
bndtmp3
,
bndtmp4
,
bndtmp5
;
double
dis_ij
[
3
],
rsq_ij
,
r_ij
;
double
betaS_ij
,
dBetaS_ij
;
double
dis_ik
[
3
],
rsq_ik
,
r_ik
;
double
betaS_ik
,
dBetaS_ik
;
double
dis_ikp
[
3
],
rsq_ikp
,
r_ikp
;
double
betaS_ikp
,
dBetaS_ikp
;
double
dis_jk
[
3
],
rsq_jk
,
r_jk
;
double
betaS_jk
,
dBetaS_jk
;
double
dis_jkp
[
3
],
rsq_jkp
,
r_jkp
;
double
betaS_jkp
,
dBetaS_jkp
;
double
dis_kkp
[
3
],
rsq_kkp
,
r_kkp
;
double
betaS_kkp
,
dBetaS_kkp
;
double
cosAng_jik
,
dcA_jik
[
3
][
2
];
double
cosAng_jikp
,
dcA_jikp
[
3
][
2
];
double
cosAng_kikp
,
dcA_kikp
[
3
][
2
];
double
cosAng_ijk
,
dcA_ijk
[
3
][
2
];
double
cosAng_ijkp
,
dcA_ijkp
[
3
][
2
];
double
cosAng_kjkp
,
dcA_kjkp
[
3
][
2
];
double
cosAng_ikj
,
dcA_ikj
[
3
][
2
];
double
cosAng_ikkp
,
dcA_ikkp
[
3
][
2
];
double
cosAng_jkkp
,
dcA_jkkp
[
3
][
2
];
double
cosAng_jkpk
,
dcA_jkpk
[
3
][
2
];
double
ftmp
[
3
],
xtmp
[
3
];
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
tagint
*
tag
=
atom
->
tag
;
int
newton_pair
=
force
->
newton_pair
;
int
*
type
=
atom
->
type
;
nlocal
=
atom
->
nlocal
;
ilist
=
list
->
ilist
;
firstneigh
=
list
->
firstneigh
;
MPI_Comm_rank
(
world
,
&
me
);
if
(
nb_sg
==
0
)
{
nb_sg
=
(
maxneigh
)
*
(
maxneigh
/
2
);
}
if
(
allocate_sigma
)
{
destroy_sigma
();
}
create_sigma
(
nb_sg
);
sigB
=
0
;
if
(
itmp
<
nlocal
)
{
i
=
ilist
[
itmp
];
}
else
{
i
=
itmp
;
}
i_tag
=
tag
[
i
];
itype
=
map
[
type
[
i
]]
+
1
;
memset
(
bt_sg
,
0
,
sizeof
(
struct
B_SG
)
*
nb_sg
);
for
(
m
=
0
;
m
<
nb_sg
;
m
++
)
{
bt_sg
[
m
].
i
=-
1
;
bt_sg
[
m
].
j
=-
1
;
bt_sg
[
m
].
temp
=-
1
;
}
nb_t
=
0
;
iilist
=
firstneigh
[
i
];
temp_ij
=
BOP_index
[
i
]
+
jtmp
;
ni_ij
=
neigh_index
[
temp_ij
];
j
=
iilist
[
ni_ij
];
jlist
=
firstneigh
[
j
];
j_tag
=
tag
[
j
];
jtype
=
map
[
type
[
j
]]
+
1
;
nb_ij
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_sg
)
{
new_n_tot
=
nb_sg
+
maxneigh
;
grow_sigma
(
nb_sg
,
new_n_tot
);
nb_sg
=
new_n_tot
;
}
bt_sg
[
nb_ij
].
temp
=
temp_ij
;
bt_sg
[
nb_ij
].
i
=
i
;
bt_sg
[
nb_ij
].
j
=
j
;
if
(
j_tag
>=
i_tag
)
{
if
(
itype
==
jtype
)
iij
=
itype
-
1
;
else
if
(
itype
<
jtype
)
iij
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
jtype
-
1
;
else
iij
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
itype
-
1
;
nlistj
=
BOP_total
[
j
];
for
(
ji
=
0
;
ji
<
nlistj
;
ji
++
)
{
temp_ji
=
BOP_index
[
j
]
+
ji
;
ni_ji
=
neigh_index
[
temp_ji
];
if
(
x
[
jlist
[
ni_ji
]][
0
]
==
x
[
i
][
0
])
{
if
(
x
[
jlist
[
ni_ji
]][
1
]
==
x
[
i
][
1
])
{
if
(
x
[
jlist
[
ni_ji
]][
2
]
==
x
[
i
][
2
])
{
break
;
}
}
}
}
pass_ij
=
0
;
if
(
otfly
==
1
)
{
dis_ij
[
0
]
=
x
[
j
][
0
]
-
x
[
i
][
0
];
dis_ij
[
1
]
=
x
[
j
][
1
]
-
x
[
i
][
1
];
dis_ij
[
2
]
=
x
[
j
][
2
]
-
x
[
i
][
2
];
rsq_ij
=
dis_ij
[
0
]
*
dis_ij
[
0
]
+
dis_ij
[
1
]
*
dis_ij
[
1
]
+
dis_ij
[
2
]
*
dis_ij
[
2
];
r_ij
=
sqrt
(
rsq_ij
);
if
(
r_ij
<
rcut
[
iij
])
{
pass_ij
=
1
;
ps
=
r_ij
*
rdr
[
iij
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_ij
=
((
pBetaS3
[
iij
][
ks
-
1
]
*
ps
+
pBetaS2
[
iij
][
ks
-
1
])
*
ps
+
pBetaS1
[
iij
][
ks
-
1
])
*
ps
+
pBetaS
[
iij
][
ks
-
1
];
dBetaS_ij
=
(
pBetaS6
[
iij
][
ks
-
1
]
*
ps
+
pBetaS5
[
iij
][
ks
-
1
])
*
ps
+
pBetaS4
[
iij
][
ks
-
1
];
}
}
else
{
if
(
neigh_flag
[
temp_ij
])
{
pass_ij
=
1
;
dis_ij
[
0
]
=
disij
[
0
][
temp_ij
];
dis_ij
[
1
]
=
disij
[
1
][
temp_ij
];
dis_ij
[
2
]
=
disij
[
2
][
temp_ij
];
r_ij
=
rij
[
temp_ij
];
betaS_ij
=
betaS
[
temp_ij
];
dBetaS_ij
=
dBetaS
[
temp_ij
];
}
}
if
(
pass_ij
==
1
)
{
nSigBk
=
0
;
//AA-EE1 are the components making up Eq. 30 (a)
AA
=
0.0
;
BB
=
0.0
;
CC
=
0.0
;
DD
=
0.0
;
EE
=
0.0
;
EE1
=
0.0
;
//FF is the Beta_sigma^2 term
FF
=
betaS_ij
*
betaS_ij
;
//agpdpr1 is derivative of FF w.r.t. r_ij
agpdpr1
=
2.0
*
betaS_ij
*
dBetaS_ij
/
r_ij
;
//dXX derivatives are taken with respect to all pairs contributing to the energy
//nb_ij is derivative w.r.t. ij pair
bt_sg
[
nb_ij
].
dFF
[
0
]
=
agpdpr1
*
dis_ij
[
0
];
bt_sg
[
nb_ij
].
dFF
[
1
]
=
agpdpr1
*
dis_ij
[
1
];
bt_sg
[
nb_ij
].
dFF
[
2
]
=
agpdpr1
*
dis_ij
[
2
];
//k is loop over all neighbors of i again with j neighbor of i
nlisti
=
BOP_total
[
i
];
for
(
ktmp
=
0
;
ktmp
<
nlisti
;
ktmp
++
)
{
temp_ik
=
BOP_index
[
i
]
+
ktmp
;
ni_ik
=
neigh_index
[
temp_ik
];
if
(
ktmp
!=
jtmp
)
{
k
=
iilist
[
ni_ik
];
klist
=
firstneigh
[
k
];
ktype
=
map
[
type
[
k
]]
+
1
;
if
(
itype
==
ktype
)
iik
=
itype
-
1
;
else
if
(
itype
<
ktype
)
iik
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
ktype
-
1
;
else
iik
=
ktype
*
bop_types
-
ktype
*
(
ktype
+
1
)
/
2
+
itype
-
1
;
//find neighbor of k that is equal to i
nlistk
=
BOP_total
[
k
];
for
(
kNeii
=
0
;
kNeii
<
nlistk
;
kNeii
++
)
{
temp_ikN
=
BOP_index
[
k
]
+
kNeii
;
ni_ikN
=
neigh_index
[
temp_ikN
];
if
(
x
[
klist
[
ni_ikN
]][
0
]
==
x
[
i
][
0
])
{
if
(
x
[
klist
[
ni_ikN
]][
1
]
==
x
[
i
][
1
])
{
if
(
x
[
klist
[
ni_ikN
]][
2
]
==
x
[
i
][
2
])
{
break
;
}
}
}
}
pass_ik
=
0
;
if
(
otfly
==
1
)
{
dis_ik
[
0
]
=
x
[
k
][
0
]
-
x
[
i
][
0
];
dis_ik
[
1
]
=
x
[
k
][
1
]
-
x
[
i
][
1
];
dis_ik
[
2
]
=
x
[
k
][
2
]
-
x
[
i
][
2
];
rsq_ik
=
dis_ik
[
0
]
*
dis_ik
[
0
]
+
dis_ik
[
1
]
*
dis_ik
[
1
]
+
dis_ik
[
2
]
*
dis_ik
[
2
];
r_ik
=
sqrt
(
rsq_ik
);
if
(
r_ik
<=
rcut
[
iik
])
{
pass_ik
=
1
;
ps
=
r_ik
*
rdr
[
iik
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_ik
=
((
pBetaS3
[
iik
][
ks
-
1
]
*
ps
+
pBetaS2
[
iik
][
ks
-
1
])
*
ps
+
pBetaS1
[
iik
][
ks
-
1
])
*
ps
+
pBetaS
[
iik
][
ks
-
1
];
dBetaS_ik
=
(
pBetaS6
[
iik
][
ks
-
1
]
*
ps
+
pBetaS5
[
iik
][
ks
-
1
])
*
ps
+
pBetaS4
[
iik
][
ks
-
1
];
}
}
else
{
if
(
neigh_flag
[
temp_ik
])
{
pass_ik
=
1
;
dis_ik
[
0
]
=
disij
[
0
][
temp_ik
];
dis_ik
[
1
]
=
disij
[
1
][
temp_ik
];
dis_ik
[
2
]
=
disij
[
2
][
temp_ik
];
r_ik
=
rij
[
temp_ik
];
betaS_ik
=
betaS
[
temp_ik
];
dBetaS_ik
=
dBetaS
[
temp_ik
];
}
}
if
(
pass_ik
==
1
)
{
//find neighbor of i that is equal to k
nlistj
=
BOP_total
[
j
];
for
(
jNeik
=
0
;
jNeik
<
nlistj
;
jNeik
++
)
{
temp_jk
=
BOP_index
[
j
]
+
jNeik
;
ni_jk
=
neigh_index
[
temp_jk
];
if
(
x
[
jlist
[
ni_jk
]][
0
]
==
x
[
k
][
0
])
{
if
(
x
[
jlist
[
ni_jk
]][
1
]
==
x
[
k
][
1
])
{
if
(
x
[
jlist
[
ni_jk
]][
2
]
==
x
[
k
][
2
])
{
break
;
}
}
}
}
//find neighbor of k that is equal to j
for
(
kNeij
=
0
;
kNeij
<
nlistk
;
kNeij
++
)
{
temp_kj
=
BOP_index
[
k
]
+
kNeij
;
ni_kj
=
neigh_index
[
temp_kj
];
if
(
x
[
klist
[
ni_kj
]][
0
]
==
x
[
j
][
0
])
{
if
(
x
[
klist
[
ni_kj
]][
1
]
==
x
[
j
][
1
])
{
if
(
x
[
klist
[
ni_kj
]][
2
]
==
x
[
j
][
2
])
{
break
;
}
}
}
}
pass_jk
=
0
;
if
(
otfly
==
1
)
{
dis_jk
[
0
]
=
x
[
k
][
0
]
-
x
[
j
][
0
];
dis_jk
[
1
]
=
x
[
k
][
1
]
-
x
[
j
][
1
];
dis_jk
[
2
]
=
x
[
k
][
2
]
-
x
[
j
][
2
];
rsq_jk
=
dis_jk
[
0
]
*
dis_jk
[
0
]
+
dis_jk
[
1
]
*
dis_jk
[
1
]
+
dis_jk
[
2
]
*
dis_jk
[
2
];
r_jk
=
sqrt
(
rsq_jk
);
}
else
{
if
(
neigh_flag
[
temp_jk
])
{
pass_jk
=
1
;
dis_jk
[
0
]
=
disij
[
0
][
temp_jk
];
dis_jk
[
1
]
=
disij
[
1
][
temp_jk
];
dis_jk
[
2
]
=
disij
[
2
][
temp_jk
];
r_jk
=
rij
[
temp_jk
];
}
}
sig_flag
=
0
;
for
(
nsearch
=
0
;
nsearch
<
nSigBk
;
nsearch
++
)
{
ncmp
=
itypeSigBk
[
nsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
k
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
k
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
k
][
2
])
{
nk0
=
nsearch
;
sig_flag
=
1
;
break
;
}
}
}
}
if
(
sig_flag
==
0
)
{
nSigBk
=
nSigBk
+
1
;
nk0
=
nSigBk
-
1
;
itypeSigBk
[
nk0
]
=
k
;
}
nb_ik
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_sg
)
{
new_n_tot
=
nb_sg
+
maxneigh
;
grow_sigma
(
nb_sg
,
new_n_tot
);
nb_sg
=
new_n_tot
;
}
bt_sg
[
nb_ik
].
temp
=
temp_ik
;
bt_sg
[
nb_ik
].
i
=
i
;
bt_sg
[
nb_ik
].
j
=
k
;
nb_jk
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_sg
)
{
new_n_tot
=
nb_sg
+
maxneigh
;
grow_sigma
(
nb_sg
,
new_n_tot
);
nb_sg
=
new_n_tot
;
}
bt_sg
[
nb_jk
].
temp
=
temp_jk
;
bt_sg
[
nb_jk
].
i
=
j
;
bt_sg
[
nb_jk
].
j
=
k
;
if
(
otfly
==
1
)
{
cosAng_jik
=
(
dis_ij
[
0
]
*
dis_ik
[
0
]
+
dis_ij
[
1
]
*
dis_ik
[
1
]
+
dis_ij
[
2
]
*
dis_ik
[
2
])
/
(
r_ij
*
r_ik
);
dcA_jik
[
0
][
0
]
=
(
dis_ik
[
0
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ij
[
0
]
*
r_ik
*
r_ik
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
dcA_jik
[
1
][
0
]
=
(
dis_ik
[
1
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ij
[
1
]
*
r_ik
*
r_ik
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
dcA_jik
[
2
][
0
]
=
(
dis_ik
[
2
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ij
[
2
]
*
r_ik
*
r_ik
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
dcA_jik
[
0
][
1
]
=
(
dis_ij
[
0
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ik
[
0
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
dcA_jik
[
1
][
1
]
=
(
dis_ij
[
1
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ik
[
1
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
dcA_jik
[
2
][
1
]
=
(
dis_ij
[
2
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ik
[
2
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
}
else
{
if
(
ktmp
!=
jtmp
)
{
if
(
jtmp
<
ktmp
)
{
njik
=
jtmp
*
(
2
*
nlisti
-
jtmp
-
1
)
/
2
+
(
ktmp
-
jtmp
)
-
1
;
ngj
=
0
;
ngk
=
1
;
}
else
{
njik
=
ktmp
*
(
2
*
nlisti
-
ktmp
-
1
)
/
2
+
(
jtmp
-
ktmp
)
-
1
;
ngj
=
1
;
ngk
=
0
;
}
ang_jik
=
cos_index
[
i
]
+
njik
;
cosAng_jik
=
cosAng
[
ang_jik
];
dcA_jik
[
0
][
0
]
=
dcAng
[
ang_jik
][
0
][
ngj
];
dcA_jik
[
1
][
0
]
=
dcAng
[
ang_jik
][
1
][
ngj
];
dcA_jik
[
2
][
0
]
=
dcAng
[
ang_jik
][
2
][
ngj
];
dcA_jik
[
0
][
1
]
=
dcAng
[
ang_jik
][
0
][
ngk
];
dcA_jik
[
1
][
1
]
=
dcAng
[
ang_jik
][
1
][
ngk
];
dcA_jik
[
2
][
1
]
=
dcAng
[
ang_jik
][
2
][
ngk
];
}
}
amean
=
cosAng_jik
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor1
=
((
gfunc3
[
jtype
][
itype
][
ktype
][
ks
]
*
ps
+
gfunc2
[
jtype
][
itype
][
ktype
][
ks
])
*
ps
+
gfunc1
[
jtype
][
itype
][
ktype
][
ks
])
*
ps
+
gfunc
[
jtype
][
itype
][
ktype
][
ks
];
gprime1
=
(
gfunc6
[
jtype
][
itype
][
ktype
][
ks
]
*
ps
+
gfunc5
[
jtype
][
itype
][
ktype
][
ks
])
*
ps
+
gfunc4
[
jtype
][
itype
][
ktype
][
ks
];
}
else
{
gfactor1
=
gpara
[
jtype
-
1
][
itype
-
1
][
ktype
-
1
][
0
];
gprime1
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime1
=
gprime1
+
(
double
)(
lp1
)
*
xrun
*
gpara
[
jtype
-
1
][
itype
-
1
][
ktype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor1
=
gfactor1
+
xrun
*
gpara
[
jtype
-
1
][
itype
-
1
][
ktype
-
1
][
lp1
];
}
}
gfactorsq
=
gfactor1
*
gfactor1
;
gsqprime
=
2.0
*
gfactor1
*
gprime1
;
//AA is Eq. 34 (a) or Eq. 10 (c) for the i atom
//1st CC is Eq. 11 (c) for i atom where j & k=neighbor of i
AA
=
AA
+
gfactorsq
*
betaS_ik
*
betaS_ik
;
//agpdpr1 is derivative of AA w.r.t. Beta(rik)
//app1 is derivative of AA w.r.t. cos(theta_jik)
agpdpr1
=
2.0
*
gfactorsq
*
betaS_ik
*
dBetaS_ik
/
r_ik
;
app1
=
betaS_ik
*
betaS_ik
*
gsqprime
;
bt_sg
[
nb_ij
].
dAA
[
0
]
+=
app1
*
dcA_jik
[
0
][
0
];
bt_sg
[
nb_ij
].
dAA
[
1
]
+=
app1
*
dcA_jik
[
1
][
0
];
bt_sg
[
nb_ij
].
dAA
[
2
]
+=
app1
*
dcA_jik
[
2
][
0
];
bt_sg
[
nb_ik
].
dAA
[
0
]
+=
app1
*
dcA_jik
[
0
][
1
]
+
agpdpr1
*
dis_ik
[
0
];
bt_sg
[
nb_ik
].
dAA
[
1
]
+=
app1
*
dcA_jik
[
1
][
1
]
+
agpdpr1
*
dis_ik
[
1
];
bt_sg
[
nb_ik
].
dAA
[
2
]
+=
app1
*
dcA_jik
[
2
][
1
]
+
agpdpr1
*
dis_ik
[
2
];
if
(
sigma_a
[
iij
]
!=
0.0
)
{
CC
=
CC
+
gfactorsq
*
betaS_ik
*
betaS_ik
*
betaS_ik
*
betaS_ik
;
agpdpr2
=
2.0
*
betaS_ik
*
betaS_ik
*
agpdpr1
;
app2
=
betaS_ik
*
betaS_ik
*
app1
;
bt_sg
[
nb_ij
].
dCC
[
0
]
+=
app2
*
dcA_jik
[
0
][
0
];
bt_sg
[
nb_ij
].
dCC
[
1
]
+=
app2
*
dcA_jik
[
1
][
0
];
bt_sg
[
nb_ij
].
dCC
[
2
]
+=
app2
*
dcA_jik
[
2
][
0
];
bt_sg
[
nb_ik
].
dCC
[
0
]
+=
app2
*
dcA_jik
[
0
][
1
]
+
agpdpr2
*
dis_ik
[
0
];
bt_sg
[
nb_ik
].
dCC
[
1
]
+=
app2
*
dcA_jik
[
1
][
1
]
+
agpdpr2
*
dis_ik
[
1
];
bt_sg
[
nb_ik
].
dCC
[
2
]
+=
app2
*
dcA_jik
[
2
][
1
]
+
agpdpr2
*
dis_ik
[
2
];
}
//k' is loop over neighbors all neighbors of j with k a neighbor
//of i and j a neighbor of i and determine which k' is k
if
(
sigma_f
[
iij
]
!=
0.5
&&
sigma_k
[
iij
]
!=
0.0
)
{
same_kpk
=
0
;
for
(
ltmp
=
0
;
ltmp
<
nlistj
;
ltmp
++
)
{
temp_jkp
=
BOP_index
[
j
]
+
ltmp
;
ni_jkp
=
neigh_index
[
temp_jkp
];
kp1
=
jlist
[
ni_jkp
];
kp1type
=
map
[
type
[
kp1
]]
+
1
;
if
(
x
[
kp1
][
0
]
==
x
[
k
][
0
])
{
if
(
x
[
kp1
][
1
]
==
x
[
k
][
1
])
{
if
(
x
[
kp1
][
2
]
==
x
[
k
][
2
])
{
same_kpk
=
1
;
break
;
}
}
}
}
if
(
same_kpk
){
//loop over neighbors of k
for
(
mtmp
=
0
;
mtmp
<
nlistk
;
mtmp
++
)
{
temp_kpj
=
BOP_index
[
k
]
+
mtmp
;
ni_kpj
=
neigh_index
[
temp_kpj
];
kp2
=
klist
[
ni_kpj
];
if
(
x
[
kp2
][
0
]
==
x
[
j
][
0
])
{
if
(
x
[
kp2
][
1
]
==
x
[
j
][
1
])
{
if
(
x
[
kp2
][
2
]
==
x
[
j
][
2
])
{
break
;
}
}
}
}
if
(
jtype
==
ktype
)
ijk
=
jtype
-
1
;
else
if
(
jtype
<
ktype
)
ijk
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
ktype
-
1
;
else
ijk
=
ktype
*
bop_types
-
ktype
*
(
ktype
+
1
)
/
2
+
jtype
-
1
;
if
(
jtype
==
kp1type
)
ijkp
=
jtype
-
1
;
else
if
(
jtype
<
kp1type
)
ijkp
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
kp1type
-
1
;
else
ijkp
=
kp1type
*
bop_types
-
kp1type
*
(
kp1type
+
1
)
/
2
+
jtype
-
1
;
pass_jkp
=
0
;
if
(
otfly
==
1
)
{
dis_jkp
[
0
]
=
x
[
kp1
][
0
]
-
x
[
j
][
0
];
dis_jkp
[
1
]
=
x
[
kp1
][
1
]
-
x
[
j
][
1
];
dis_jkp
[
2
]
=
x
[
kp1
][
2
]
-
x
[
j
][
2
];
rsq_jkp
=
dis_jkp
[
0
]
*
dis_jkp
[
0
]
+
dis_jkp
[
1
]
*
dis_jkp
[
1
]
+
dis_jkp
[
2
]
*
dis_jkp
[
2
];
r_jkp
=
sqrt
(
rsq_jkp
);
if
(
r_jkp
<=
rcut
[
ijkp
])
{
pass_jkp
=
1
;
ps
=
r_jkp
*
rdr
[
ijkp
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_jkp
=
((
pBetaS3
[
ijkp
][
ks
-
1
]
*
ps
+
pBetaS2
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS1
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS
[
ijkp
][
ks
-
1
];
dBetaS_jkp
=
(
pBetaS6
[
ijkp
][
ks
-
1
]
*
ps
+
pBetaS5
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS4
[
ijkp
][
ks
-
1
];
cosAng_ijk
=
(
-
dis_ij
[
0
]
*
dis_jk
[
0
]
-
dis_ij
[
1
]
*
dis_jk
[
1
]
-
dis_ij
[
2
]
*
dis_jk
[
2
])
/
(
r_ij
*
r_jk
);
dcA_ijk
[
0
][
0
]
=
(
dis_jk
[
0
]
*
r_ij
*
r_jk
-
cosAng_ijk
*-
dis_ij
[
0
]
*
r_jk
*
r_jk
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
1
][
0
]
=
(
dis_jk
[
1
]
*
r_ij
*
r_jk
-
cosAng_ijk
*-
dis_ij
[
1
]
*
r_jk
*
r_jk
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
2
][
0
]
=
(
dis_jk
[
2
]
*
r_ij
*
r_jk
-
cosAng_ijk
*-
dis_ij
[
2
]
*
r_jk
*
r_jk
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
0
][
1
]
=
(
-
dis_ij
[
0
]
*
r_ij
*
r_jk
-
cosAng_ijk
*
dis_jk
[
0
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
1
][
1
]
=
(
-
dis_ij
[
1
]
*
r_ij
*
r_jk
-
cosAng_ijk
*
dis_jk
[
1
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
2
][
1
]
=
(
-
dis_ij
[
2
]
*
r_ij
*
r_jk
-
cosAng_ijk
*
dis_jk
[
2
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
}
}
else
{
if
(
neigh_flag
[
temp_jkp
])
{
pass_jkp
=
1
;
dis_jkp
[
0
]
=
disij
[
0
][
temp_jkp
];
dis_jkp
[
1
]
=
disij
[
1
][
temp_jkp
];
dis_jkp
[
2
]
=
disij
[
2
][
temp_jkp
];
r_jkp
=
rij
[
temp_jkp
];
betaS_jkp
=
betaS
[
temp_jkp
];
dBetaS_jkp
=
dBetaS
[
temp_jkp
];
if
(
ji
<
ltmp
)
{
nijk
=
ji
*
(
2
*
nlistj
-
ji
-
1
)
/
2
+
(
ltmp
-
ji
)
-
1
;
ngji
=
0
;
ngjk
=
1
;
}
else
{
nijk
=
ltmp
*
(
2
*
nlistj
-
ltmp
-
1
)
/
2
+
(
ji
-
ltmp
)
-
1
;
ngji
=
1
;
ngjk
=
0
;
}
ang_ijk
=
cos_index
[
j
]
+
nijk
;
cosAng_ijk
=
cosAng
[
ang_ijk
];
dcA_ijk
[
0
][
0
]
=
dcAng
[
ang_ijk
][
0
][
ngji
];
dcA_ijk
[
1
][
0
]
=
dcAng
[
ang_ijk
][
1
][
ngji
];
dcA_ijk
[
2
][
0
]
=
dcAng
[
ang_ijk
][
2
][
ngji
];
dcA_ijk
[
0
][
1
]
=
dcAng
[
ang_ijk
][
0
][
ngjk
];
dcA_ijk
[
1
][
1
]
=
dcAng
[
ang_ijk
][
1
][
ngjk
];
dcA_ijk
[
2
][
1
]
=
dcAng
[
ang_ijk
][
2
][
ngjk
];
}
}
if
(
pass_jkp
==
1
)
{
amean
=
cosAng_ijk
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor2
=
((
gfunc3
[
itype
][
jtype
][
ktype
][
ks
]
*
ps
+
gfunc2
[
itype
][
jtype
][
ktype
][
ks
])
*
ps
+
gfunc1
[
itype
][
jtype
][
ktype
][
ks
])
*
ps
+
gfunc
[
itype
][
jtype
][
ktype
][
ks
];
gprime2
=
(
gfunc6
[
itype
][
jtype
][
ktype
][
ks
]
*
ps
+
gfunc5
[
itype
][
jtype
][
ktype
][
ks
])
*
ps
+
gfunc4
[
itype
][
jtype
][
ktype
][
ks
];
}
else
{
gfactor2
=
gpara
[
itype
-
1
][
jtype
-
1
][
ktype
-
1
][
0
];
gprime2
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime2
=
gprime2
+
(
lp1
)
*
xrun
*
gpara
[
itype
-
1
][
jtype
-
1
][
ktype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor2
=
gfactor2
+
xrun
*
gpara
[
itype
-
1
][
jtype
-
1
][
ktype
-
1
][
lp1
];
}
}
if
(
otfly
==
1
)
{
cosAng_ikj
=
(
dis_ik
[
0
]
*
dis_jk
[
0
]
+
dis_ik
[
1
]
*
dis_jk
[
1
]
+
dis_ik
[
2
]
*
dis_jk
[
2
])
/
(
r_ik
*
r_jk
);
dcA_ikj
[
0
][
0
]
=
(
-
dis_jk
[
0
]
*
r_ik
*
r_jk
-
cosAng_ikj
*-
dis_ik
[
0
]
*
r_jk
*
r_jk
)
/
(
r_ik
*
r_ik
*
r_jk
*
r_jk
);
dcA_ikj
[
1
][
0
]
=
(
-
dis_jk
[
1
]
*
r_ik
*
r_jk
-
cosAng_ikj
*-
dis_ik
[
1
]
*
r_jk
*
r_jk
)
/
(
r_ik
*
r_ik
*
r_jk
*
r_jk
);
dcA_ikj
[
2
][
0
]
=
(
-
dis_jk
[
2
]
*
r_ik
*
r_jk
-
cosAng_ikj
*-
dis_ik
[
2
]
*
r_jk
*
r_jk
)
/
(
r_ik
*
r_ik
*
r_jk
*
r_jk
);
dcA_ikj
[
0
][
1
]
=
(
-
dis_ik
[
0
]
*
r_ik
*
r_jk
-
cosAng_ikj
*-
dis_jk
[
0
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_jk
*
r_jk
);
dcA_ikj
[
1
][
1
]
=
(
-
dis_ik
[
1
]
*
r_ik
*
r_jk
-
cosAng_ikj
*-
dis_jk
[
1
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_jk
*
r_jk
);
dcA_ikj
[
2
][
1
]
=
(
-
dis_ik
[
2
]
*
r_ik
*
r_jk
-
cosAng_ikj
*-
dis_jk
[
2
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_jk
*
r_jk
);
}
else
{
if
(
kNeii
<
mtmp
)
{
nikj
=
kNeii
*
(
2
*
nlistk
-
kNeii
-
1
)
/
2
+
(
mtmp
-
kNeii
)
-
1
;
ngki
=
0
;
ngkj
=
1
;
}
else
{
nikj
=
mtmp
*
(
2
*
nlistk
-
mtmp
-
1
)
/
2
+
(
kNeii
-
mtmp
)
-
1
;
ngki
=
1
;
ngkj
=
0
;
}
ang_ikj
=
cos_index
[
k
]
+
nikj
;
cosAng_ikj
=
cosAng
[
ang_ikj
];
dcA_ikj
[
0
][
0
]
=
dcAng
[
ang_ikj
][
0
][
ngki
];
dcA_ikj
[
1
][
0
]
=
dcAng
[
ang_ikj
][
1
][
ngki
];
dcA_ikj
[
2
][
0
]
=
dcAng
[
ang_ikj
][
2
][
ngki
];
dcA_ikj
[
0
][
1
]
=
dcAng
[
ang_ikj
][
0
][
ngkj
];
dcA_ikj
[
1
][
1
]
=
dcAng
[
ang_ikj
][
1
][
ngkj
];
dcA_ikj
[
2
][
1
]
=
dcAng
[
ang_ikj
][
2
][
ngkj
];
}
amean
=
cosAng_ikj
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor3
=
((
gfunc3
[
itype
][
jtype
][
jtype
][
ks
]
*
ps
+
gfunc2
[
itype
][
ktype
][
jtype
][
ks
])
*
ps
+
gfunc1
[
itype
][
ktype
][
jtype
][
ks
])
*
ps
+
gfunc
[
itype
][
ktype
][
jtype
][
ks
];
gprime3
=
(
gfunc6
[
itype
][
ktype
][
jtype
][
ks
]
*
ps
+
gfunc5
[
itype
][
ktype
][
jtype
][
ks
])
*
ps
+
gfunc4
[
itype
][
ktype
][
jtype
][
ks
];
}
else
{
gfactor3
=
gpara
[
itype
-
1
][
ktype
-
1
][
jtype
-
1
][
0
];
gprime3
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime3
=
gprime3
+
(
lp1
)
*
xrun
*
gpara
[
itype
-
1
][
ktype
-
1
][
jtype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor3
=
gfactor3
+
xrun
*
gpara
[
itype
-
1
][
ktype
-
1
][
jtype
-
1
][
lp1
];
}
}
gfactor
=
gfactor1
*
gfactor2
*
gfactor3
;
rfactor
=
betaS_ik
*
betaS_jkp
;
//EE1 is (b) Eq. 12
EE1
=
EE1
+
gfactor
*
rfactor
;
//rcm1 is derivative of EE1 w.r.t Beta(r_ik)
//rcm2 is derivative of EE1 w.r.t Beta(r_jk')
//gcm1 is derivative of EE1 w.r.t cos(theta_jik)
//gcm2 is derivative of EE1 w.r.t cos(theta_ijk)
//gcm3 is derivative of EE1 w.r.t cos(theta_ikj)
rcm1
=
gfactor
*
betaS_jkp
*
dBetaS_ik
/
r_ik
;
rcm2
=
gfactor
*
betaS_ik
*
dBetaS_jkp
/
r_jkp
;
gcm1
=
rfactor
*
gprime1
*
gfactor2
*
gfactor3
;
gcm2
=
rfactor
*
gfactor1
*
gprime2
*
gfactor3
;
gcm3
=
rfactor
*
gfactor1
*
gfactor2
*
gprime3
;
bt_sg
[
nb_ij
].
dEE1
[
0
]
+=
gcm1
*
dcA_jik
[
0
][
0
]
-
gcm2
*
dcA_ijk
[
0
][
0
];
bt_sg
[
nb_ij
].
dEE1
[
1
]
+=
gcm1
*
dcA_jik
[
1
][
0
]
-
gcm2
*
dcA_ijk
[
1
][
0
];
bt_sg
[
nb_ij
].
dEE1
[
2
]
+=
gcm1
*
dcA_jik
[
2
][
0
]
-
gcm2
*
dcA_ijk
[
2
][
0
];
bt_sg
[
nb_ik
].
dEE1
[
0
]
+=
gcm1
*
dcA_jik
[
0
][
1
]
+
rcm1
*
dis_ik
[
0
]
-
gcm3
*
dcA_ikj
[
0
][
0
];
bt_sg
[
nb_ik
].
dEE1
[
1
]
+=
gcm1
*
dcA_jik
[
1
][
1
]
+
rcm1
*
dis_ik
[
1
]
-
gcm3
*
dcA_ikj
[
1
][
0
];
bt_sg
[
nb_ik
].
dEE1
[
2
]
+=
gcm1
*
dcA_jik
[
2
][
1
]
+
rcm1
*
dis_ik
[
2
]
-
gcm3
*
dcA_ikj
[
2
][
0
];
bt_sg
[
nb_jk
].
dEE1
[
0
]
+=
gcm2
*
dcA_ijk
[
0
][
1
]
+
rcm2
*
dis_jkp
[
0
]
-
gcm3
*
dcA_ikj
[
0
][
1
];
bt_sg
[
nb_jk
].
dEE1
[
1
]
+=
gcm2
*
dcA_ijk
[
1
][
1
]
+
rcm2
*
dis_jkp
[
1
]
-
gcm3
*
dcA_ikj
[
1
][
1
];
bt_sg
[
nb_jk
].
dEE1
[
2
]
+=
gcm2
*
dcA_ijk
[
2
][
1
]
+
rcm2
*
dis_jkp
[
2
]
-
gcm3
*
dcA_ikj
[
2
][
1
];
}
}
}
// k and k' and j are all different neighbors of i
if
(
sigma_a
[
iij
]
!=
0
)
{
for
(
ltmp
=
0
;
ltmp
<
ktmp
;
ltmp
++
)
{
if
(
ltmp
!=
jtmp
)
{
temp_ikp
=
BOP_index
[
i
]
+
ltmp
;
ni_ikp
=
neigh_index
[
temp_ikp
];
kp
=
iilist
[
ni_ikp
];
kptype
=
map
[
type
[
kp
]]
+
1
;
if
(
itype
==
kptype
)
iikp
=
itype
-
1
;
else
if
(
itype
<
kptype
)
iikp
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
kptype
-
1
;
else
iikp
=
kptype
*
bop_types
-
kptype
*
(
kptype
+
1
)
/
2
+
itype
-
1
;
for
(
nsearch
=
0
;
nsearch
<
nSigBk
;
nsearch
++
)
{
ncmp
=
itypeSigBk
[
nsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
kp
][
2
])
{
break
;
}
}
}
}
pass_ikp
=
0
;
if
(
otfly
==
1
)
{
dis_ikp
[
0
]
=
x
[
kp
][
0
]
-
x
[
i
][
0
];
dis_ikp
[
1
]
=
x
[
kp
][
1
]
-
x
[
i
][
1
];
dis_ikp
[
2
]
=
x
[
kp
][
2
]
-
x
[
i
][
2
];
rsq_ikp
=
dis_ikp
[
0
]
*
dis_ikp
[
0
]
+
dis_ikp
[
1
]
*
dis_ikp
[
1
]
+
dis_ikp
[
2
]
*
dis_ikp
[
2
];
r_ikp
=
sqrt
(
rsq_ikp
);
if
(
r_ikp
<=
rcut
[
iikp
])
{
pass_ikp
=
1
;
ps
=
r_ikp
*
rdr
[
iikp
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_ikp
=
((
pBetaS3
[
iikp
][
ks
-
1
]
*
ps
+
pBetaS2
[
iikp
][
ks
-
1
])
*
ps
+
pBetaS1
[
iikp
][
ks
-
1
])
*
ps
+
pBetaS
[
iikp
][
ks
-
1
];
dBetaS_ikp
=
(
pBetaS6
[
iikp
][
ks
-
1
]
*
ps
+
pBetaS5
[
iikp
][
ks
-
1
])
*
ps
+
pBetaS4
[
iikp
][
ks
-
1
];
}
}
else
{
if
(
neigh_flag
[
temp_ikp
])
{
pass_ikp
=
1
;
dis_ikp
[
0
]
=
disij
[
0
][
temp_ikp
];
dis_ikp
[
1
]
=
disij
[
1
][
temp_ikp
];
dis_ikp
[
2
]
=
disij
[
2
][
temp_ikp
];
r_ikp
=
rij
[
temp_ikp
];
betaS_ikp
=
betaS
[
temp_ikp
];
dBetaS_ikp
=
dBetaS
[
temp_ikp
];
}
}
if
(
pass_ikp
==
1
)
{
nb_ikp
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_sg
)
{
new_n_tot
=
nb_sg
+
maxneigh
;
grow_sigma
(
nb_sg
,
new_n_tot
);
nb_sg
=
new_n_tot
;
}
bt_sg
[
nb_ikp
].
temp
=
temp_ikp
;
bt_sg
[
nb_ikp
].
i
=
i
;
bt_sg
[
nb_ikp
].
j
=
kp
;
if
(
otfly
==
1
)
{
cosAng_jikp
=
(
dis_ij
[
0
]
*
dis_ikp
[
0
]
+
dis_ij
[
1
]
*
dis_ikp
[
1
]
+
dis_ij
[
2
]
*
dis_ikp
[
2
])
/
(
r_ij
*
r_ikp
);
dcA_jikp
[
0
][
0
]
=
(
dis_ikp
[
0
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ij
[
0
]
*
r_ikp
*
r_ikp
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
1
][
0
]
=
(
dis_ikp
[
1
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ij
[
1
]
*
r_ikp
*
r_ikp
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
2
][
0
]
=
(
dis_ikp
[
2
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ij
[
2
]
*
r_ikp
*
r_ikp
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
0
][
1
]
=
(
dis_ij
[
0
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ikp
[
0
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
1
][
1
]
=
(
dis_ij
[
1
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ikp
[
1
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
2
][
1
]
=
(
dis_ij
[
2
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ikp
[
2
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
cosAng_kikp
=
(
dis_ik
[
0
]
*
dis_ikp
[
0
]
+
dis_ik
[
1
]
*
dis_ikp
[
1
]
+
dis_ik
[
2
]
*
dis_ikp
[
2
])
/
(
r_ik
*
r_ikp
);
dcA_kikp
[
0
][
0
]
=
(
dis_ikp
[
0
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ik
[
0
]
*
r_ikp
*
r_ikp
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
dcA_kikp
[
1
][
0
]
=
(
dis_ikp
[
1
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ik
[
1
]
*
r_ikp
*
r_ikp
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
dcA_kikp
[
2
][
0
]
=
(
dis_ikp
[
2
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ik
[
2
]
*
r_ikp
*
r_ikp
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
dcA_kikp
[
0
][
1
]
=
(
dis_ik
[
0
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ikp
[
0
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
dcA_kikp
[
1
][
1
]
=
(
dis_ik
[
1
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ikp
[
1
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
dcA_kikp
[
2
][
1
]
=
(
dis_ik
[
2
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ikp
[
2
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
}
else
{
if
(
jtmp
<
ltmp
)
{
njikp
=
jtmp
*
(
2
*
nlisti
-
jtmp
-
1
)
/
2
+
(
ltmp
-
jtmp
)
-
1
;
nglj
=
0
;
ngl
=
1
;
}
else
{
njikp
=
ltmp
*
(
2
*
nlisti
-
ltmp
-
1
)
/
2
+
(
jtmp
-
ltmp
)
-
1
;
nglj
=
1
;
ngl
=
0
;
}
if
(
ktmp
<
ltmp
)
{
nkikp
=
ktmp
*
(
2
*
nlisti
-
ktmp
-
1
)
/
2
+
(
ltmp
-
ktmp
)
-
1
;
nglk
=
0
;
nglkp
=
1
;
}
else
{
nkikp
=
ltmp
*
(
2
*
nlisti
-
ltmp
-
1
)
/
2
+
(
ktmp
-
ltmp
)
-
1
;
nglk
=
1
;
nglkp
=
0
;
}
ang_jikp
=
cos_index
[
i
]
+
njikp
;
cosAng_jikp
=
cosAng
[
ang_jikp
];
dcA_jikp
[
0
][
0
]
=
dcAng
[
ang_jikp
][
0
][
nglj
];
dcA_jikp
[
1
][
0
]
=
dcAng
[
ang_jikp
][
1
][
nglj
];
dcA_jikp
[
2
][
0
]
=
dcAng
[
ang_jikp
][
2
][
nglj
];
dcA_jikp
[
0
][
1
]
=
dcAng
[
ang_jikp
][
0
][
ngl
];
dcA_jikp
[
1
][
1
]
=
dcAng
[
ang_jikp
][
1
][
ngl
];
dcA_jikp
[
2
][
1
]
=
dcAng
[
ang_jikp
][
2
][
ngl
];
ang_kikp
=
cos_index
[
i
]
+
nkikp
;
cosAng_kikp
=
cosAng
[
ang_jikp
];
dcA_kikp
[
0
][
0
]
=
dcAng
[
ang_kikp
][
0
][
nglk
];
dcA_kikp
[
1
][
0
]
=
dcAng
[
ang_kikp
][
1
][
nglk
];
dcA_kikp
[
2
][
0
]
=
dcAng
[
ang_kikp
][
2
][
nglk
];
dcA_kikp
[
0
][
1
]
=
dcAng
[
ang_kikp
][
0
][
nglkp
];
dcA_kikp
[
1
][
1
]
=
dcAng
[
ang_kikp
][
1
][
nglkp
];
dcA_kikp
[
2
][
1
]
=
dcAng
[
ang_kikp
][
2
][
nglkp
];
}
amean
=
cosAng_jikp
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor2
=
((
gfunc3
[
jtype
][
itype
][
kptype
][
ks
]
*
ps
+
gfunc2
[
jtype
][
itype
][
kptype
][
ks
])
*
ps
+
gfunc1
[
jtype
][
itype
][
kptype
][
ks
])
*
ps
+
gfunc
[
jtype
][
itype
][
kptype
][
ks
];
gprime2
=
(
gfunc6
[
jtype
][
itype
][
kptype
][
ks
]
*
ps
+
gfunc5
[
jtype
][
itype
][
kptype
][
ks
])
*
ps
+
gfunc4
[
jtype
][
itype
][
kptype
][
ks
];
}
else
{
gfactor2
=
gpara
[
jtype
-
1
][
itype
-
1
][
kptype
-
1
][
0
];
gprime2
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime2
=
gprime2
+
(
lp1
)
*
xrun
*
gpara
[
jtype
-
1
][
itype
-
1
][
kptype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor2
=
gfactor2
+
xrun
*
gpara
[
jtype
-
1
][
itype
-
1
][
kptype
-
1
][
lp1
];
}
}
amean
=
cosAng_kikp
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor3
=
((
gfunc3
[
ktype
][
itype
][
kptype
][
ks
]
*
ps
+
gfunc2
[
ktype
][
itype
][
kptype
][
ks
])
*
ps
+
gfunc1
[
ktype
][
itype
][
kptype
][
ks
])
*
ps
+
gfunc
[
ktype
][
itype
][
kptype
][
ks
];
gprime3
=
(
gfunc6
[
ktype
][
itype
][
kptype
][
ks
]
*
ps
+
gfunc5
[
ktype
][
itype
][
kptype
][
ks
])
*
ps
+
gfunc4
[
ktype
][
itype
][
kptype
][
ks
];
}
else
{
gfactor3
=
gpara
[
ktype
-
1
][
itype
-
1
][
kptype
-
1
][
0
];
gprime3
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime3
=
gprime3
+
(
lp1
)
*
xrun
*
gpara
[
ktype
-
1
][
itype
-
1
][
kptype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor3
=
gfactor3
+
xrun
*
gpara
[
ktype
-
1
][
itype
-
1
][
kptype
-
1
][
lp1
];
}
}
gfactor
=
gfactor1
*
gfactor2
*
gfactor3
;
rfactorrt
=
betaS_ik
*
betaS_ikp
;
rfactor
=
rfactorrt
*
rfactorrt
;
//2nd CC is second term of Eq. 11 (c) for i atom where j , k & k' =neighbor of i
CC
=
CC
+
2.0
*
gfactor
*
rfactor
;
//agpdpr1 is derivative of CC 2nd term w.r.t. Beta(r_ik)
//agpdpr2 is derivative of CC 2nd term w.r.t. Beta(r_ik')
//app1 is derivative of CC 2nd term w.r.t. cos(theta_jik)
//app2 is derivative of CC 2nd term w.r.t. cos(theta_jik')
//app3 is derivative of CC 2nd term w.r.t. cos(theta_kik')
agpdpr1
=
4.0
*
gfactor
*
rfactorrt
*
betaS_ikp
*
dBetaS_ik
/
r_ik
;
agpdpr2
=
4.0
*
gfactor
*
rfactorrt
*
betaS_ik
*
dBetaS_ikp
/
r_ikp
;
app1
=
2.0
*
rfactor
*
gfactor2
*
gfactor3
*
gprime1
;
app2
=
2.0
*
rfactor
*
gfactor1
*
gfactor3
*
gprime2
;
app3
=
2.0
*
rfactor
*
gfactor1
*
gfactor2
*
gprime3
;
bt_sg
[
nb_ij
].
dCC
[
0
]
+=
app1
*
dcA_jik
[
0
][
0
]
+
app2
*
dcA_jikp
[
0
][
0
];
bt_sg
[
nb_ij
].
dCC
[
1
]
+=
app1
*
dcA_jik
[
1
][
0
]
+
app2
*
dcA_jikp
[
1
][
0
];
bt_sg
[
nb_ij
].
dCC
[
2
]
+=
app1
*
dcA_jik
[
2
][
0
]
+
app2
*
dcA_jikp
[
2
][
0
];
bt_sg
[
nb_ik
].
dCC
[
0
]
+=
app1
*
dcA_jik
[
0
][
1
]
+
app3
*
dcA_kikp
[
0
][
0
]
+
agpdpr1
*
dis_ik
[
0
];
bt_sg
[
nb_ik
].
dCC
[
1
]
+=
app1
*
dcA_jik
[
1
][
1
]
+
app3
*
dcA_kikp
[
1
][
0
]
+
agpdpr1
*
dis_ik
[
1
];
bt_sg
[
nb_ik
].
dCC
[
2
]
+=
app1
*
dcA_jik
[
2
][
1
]
+
app3
*
dcA_kikp
[
2
][
0
]
+
agpdpr1
*
dis_ik
[
2
];
bt_sg
[
nb_ikp
].
dCC
[
0
]
=
app2
*
dcA_jikp
[
0
][
1
]
+
app3
*
dcA_kikp
[
0
][
1
]
+
agpdpr2
*
dis_ikp
[
0
];
bt_sg
[
nb_ikp
].
dCC
[
1
]
=
app2
*
dcA_jikp
[
1
][
1
]
+
app3
*
dcA_kikp
[
1
][
1
]
+
agpdpr2
*
dis_ikp
[
1
];
bt_sg
[
nb_ikp
].
dCC
[
2
]
=
app2
*
dcA_jikp
[
2
][
1
]
+
app3
*
dcA_kikp
[
2
][
1
]
+
agpdpr2
*
dis_ikp
[
2
];
}
}
}
// j and k are different neighbors of i and k' is a neighbor k not equal to i
for
(
ltmp
=
0
;
ltmp
<
nlistk
;
ltmp
++
)
{
temp_kkp
=
BOP_index
[
k
]
+
ltmp
;
ni_kkp
=
neigh_index
[
temp_ik
];
kp
=
klist
[
ni_kkp
];;
kptype
=
map
[
type
[
kp
]]
+
1
;
same_ikp
=
0
;
same_jkp
=
0
;
if
(
x
[
i
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
i
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
i
][
2
]
==
x
[
kp
][
2
])
{
same_ikp
=
1
;
}
}
}
if
(
x
[
j
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
j
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
j
][
2
]
==
x
[
kp
][
2
])
{
same_jkp
=
1
;
}
}
}
if
(
!
same_ikp
&&!
same_jkp
)
{
if
(
ktype
==
kptype
)
ikkp
=
ktype
-
1
;
else
if
(
ktype
<
kptype
)
ikkp
=
ktype
*
bop_types
-
ktype
*
(
ktype
+
1
)
/
2
+
kptype
-
1
;
else
ikkp
=
kptype
*
bop_types
-
kptype
*
(
kptype
+
1
)
/
2
+
ktype
-
1
;
pass_kkp
=
0
;
if
(
otfly
==
1
)
{
dis_kkp
[
0
]
=
x
[
kp
][
0
]
-
x
[
k
][
0
];
dis_kkp
[
1
]
=
x
[
kp
][
1
]
-
x
[
k
][
1
];
dis_kkp
[
2
]
=
x
[
kp
][
2
]
-
x
[
k
][
2
];
rsq_kkp
=
dis_kkp
[
0
]
*
dis_kkp
[
0
]
+
dis_kkp
[
1
]
*
dis_kkp
[
1
]
+
dis_kkp
[
2
]
*
dis_kkp
[
2
];
r_kkp
=
sqrt
(
rsq_kkp
);
if
(
r_kkp
<=
rcut
[
ikkp
])
{
pass_kkp
=
1
;
ps
=
r_kkp
*
rdr
[
ikkp
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_kkp
=
((
pBetaS3
[
ikkp
][
ks
-
1
]
*
ps
+
pBetaS2
[
ikkp
][
ks
-
1
])
*
ps
+
pBetaS1
[
ikkp
][
ks
-
1
])
*
ps
+
pBetaS
[
ikkp
][
ks
-
1
];
dBetaS_kkp
=
(
pBetaS6
[
ikkp
][
ks
-
1
]
*
ps
+
pBetaS5
[
ikkp
][
ks
-
1
])
*
ps
+
pBetaS4
[
ikkp
][
ks
-
1
];
}
}
else
{
if
(
neigh_flag
[
temp_kkp
])
{
pass_kkp
=
1
;
dis_kkp
[
0
]
=
disij
[
0
][
temp_kkp
];
dis_kkp
[
1
]
=
disij
[
1
][
temp_kkp
];
dis_kkp
[
2
]
=
disij
[
2
][
temp_kkp
];
r_kkp
=
rij
[
temp_kkp
];
betaS_kkp
=
betaS
[
temp_kkp
];
dBetaS_kkp
=
dBetaS
[
temp_kkp
];
}
}
if
(
pass_kkp
==
1
)
{
sig_flag
=
0
;
for
(
nsearch
=
0
;
nsearch
<
nSigBk
;
nsearch
++
)
{
ncmp
=
itypeSigBk
[
nsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
kp
][
2
])
{
sig_flag
=
1
;
nkp
=
nsearch
;
break
;
}
}
}
}
if
(
sig_flag
==
0
)
{
nSigBk
=
nSigBk
+
1
;
nkp
=
nSigBk
-
1
;
itypeSigBk
[
nkp
]
=
kp
;
}
if
(
otfly
==
1
)
{
cosAng_ikkp
=
(
-
dis_ik
[
0
]
*
dis_kkp
[
0
]
-
dis_ik
[
1
]
*
dis_kkp
[
1
]
-
dis_ik
[
2
]
*
dis_kkp
[
2
])
/
(
r_ik
*
r_kkp
);
dcA_ikkp
[
0
][
0
]
=
(
dis_kkp
[
0
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*-
dis_ik
[
0
]
*
r_kkp
*
r_kkp
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
dcA_ikkp
[
1
][
0
]
=
(
dis_kkp
[
1
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*-
dis_ik
[
1
]
*
r_kkp
*
r_kkp
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
dcA_ikkp
[
2
][
0
]
=
(
dis_kkp
[
2
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*-
dis_ik
[
2
]
*
r_kkp
*
r_kkp
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
dcA_ikkp
[
0
][
1
]
=
(
-
dis_ik
[
0
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*
dis_kkp
[
0
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
dcA_ikkp
[
1
][
1
]
=
(
-
dis_ik
[
1
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*
dis_kkp
[
1
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
dcA_ikkp
[
2
][
1
]
=
(
-
dis_ik
[
2
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*
dis_kkp
[
2
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
}
else
{
if
(
kNeii
<
ltmp
)
{
nikkp
=
kNeii
*
(
2
*
nlistk
-
kNeii
-
1
)
/
2
+
(
ltmp
-
kNeii
)
-
1
;
nglkp
=
1
;
ngli
=
0
;
}
else
{
nikkp
=
ltmp
*
(
2
*
nlistk
-
ltmp
-
1
)
/
2
+
(
kNeii
-
ltmp
)
-
1
;
nglkp
=
0
;
ngli
=
1
;
}
ang_ikkp
=
cos_index
[
i
]
+
nikkp
;
cosAng_ikkp
=
cosAng
[
ang_ikkp
];
dcA_ikkp
[
0
][
0
]
=
dcAng
[
ang_ikkp
][
0
][
nglkp
];
dcA_ikkp
[
1
][
0
]
=
dcAng
[
ang_ikkp
][
1
][
nglkp
];
dcA_ikkp
[
2
][
0
]
=
dcAng
[
ang_ikkp
][
2
][
nglkp
];
dcA_ikkp
[
0
][
1
]
=
dcAng
[
ang_ikkp
][
0
][
ngli
];
dcA_ikkp
[
1
][
1
]
=
dcAng
[
ang_ikkp
][
1
][
ngli
];
dcA_ikkp
[
2
][
1
]
=
dcAng
[
ang_ikkp
][
2
][
ngli
];
}
nb_kkp
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_sg
)
{
new_n_tot
=
nb_sg
+
maxneigh
;
grow_sigma
(
nb_sg
,
new_n_tot
);
nb_sg
=
new_n_tot
;
}
bt_sg
[
nb_kkp
].
temp
=
temp_kkp
;
bt_sg
[
nb_kkp
].
i
=
k
;
bt_sg
[
nb_kkp
].
j
=
kp
;
amean
=
cosAng_ikkp
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor2
=
((
gfunc3
[
itype
][
ktype
][
kptype
][
ks
]
*
ps
+
gfunc2
[
itype
][
ktype
][
kptype
][
ks
])
*
ps
+
gfunc1
[
itype
][
ktype
][
kptype
][
ks
])
*
ps
+
gfunc
[
itype
][
ktype
][
kptype
][
ks
];
gprime2
=
(
gfunc6
[
itype
][
ktype
][
kptype
][
ks
]
*
ps
+
gfunc5
[
itype
][
ktype
][
kptype
][
ks
])
*
ps
+
gfunc4
[
itype
][
ktype
][
kptype
][
ks
];
}
else
{
gfactor2
=
gpara
[
itype
-
1
][
ktype
-
1
][
kptype
-
1
][
0
];
gprime2
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime2
=
gprime2
+
(
lp1
)
*
xrun
*
gpara
[
itype
-
1
][
ktype
-
1
][
kptype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor2
=
gfactor2
+
xrun
*
gpara
[
itype
-
1
][
ktype
-
1
][
kptype
-
1
][
lp1
];
}
}
gfactorsq2
=
gfactor2
*
gfactor2
;
gsqprime2
=
2.0
*
gfactor2
*
gprime2
;
gfactor
=
gfactorsq
*
gfactorsq2
;
rfactorrt
=
betaS_ik
*
betaS_kkp
;
rfactor
=
rfactorrt
*
rfactorrt
;
//3rd CC is third term of Eq. 11 (c) for i atom
//where j , k =neighbor of i & k' =neighbor of k
CC
=
CC
+
gfactor
*
rfactor
;
//agpdpr1 is derivative of CC 3rd term w.r.t. Beta(r_ik)
//agpdpr2 is derivative of CC 3rd term w.r.t. Beta(r_kk')
//app1 is derivative of CC 3rd term w.r.t. cos(theta_jik)
//app2 is derivative of CC 3rd term w.r.t. cos(theta_ikk')
agpdpr1
=
2.0
*
gfactor
*
rfactorrt
*
betaS_kkp
*
dBetaS_ik
/
r_ik
;
agpdpr2
=
2.0
*
gfactor
*
rfactorrt
*
betaS_ik
*
dBetaS_kkp
/
r_kkp
;
app1
=
rfactor
*
gfactorsq2
*
gsqprime
;
app2
=
rfactor
*
gfactorsq
*
gsqprime2
;
bt_sg
[
nb_ij
].
dCC
[
0
]
+=
app1
*
dcA_jik
[
0
][
0
];
bt_sg
[
nb_ij
].
dCC
[
1
]
+=
app1
*
dcA_jik
[
1
][
0
];
bt_sg
[
nb_ij
].
dCC
[
2
]
+=
app1
*
dcA_jik
[
2
][
0
];
bt_sg
[
nb_ik
].
dCC
[
0
]
+=
app1
*
dcA_jik
[
0
][
1
]
+
agpdpr1
*
dis_ik
[
0
]
-
app2
*
dcA_ikkp
[
0
][
0
];
bt_sg
[
nb_ik
].
dCC
[
1
]
+=
app1
*
dcA_jik
[
1
][
1
]
+
agpdpr1
*
dis_ik
[
1
]
-
app2
*
dcA_ikkp
[
1
][
0
];
bt_sg
[
nb_ik
].
dCC
[
2
]
+=
app1
*
dcA_jik
[
2
][
1
]
+
agpdpr1
*
dis_ik
[
2
]
-
app2
*
dcA_ikkp
[
2
][
0
];
bt_sg
[
nb_kkp
].
dCC
[
0
]
+=
app2
*
dcA_ikkp
[
0
][
1
]
+
agpdpr2
*
dis_kkp
[
0
];
bt_sg
[
nb_kkp
].
dCC
[
1
]
+=
app2
*
dcA_ikkp
[
1
][
1
]
+
agpdpr2
*
dis_kkp
[
1
];
bt_sg
[
nb_kkp
].
dCC
[
2
]
+=
app2
*
dcA_ikkp
[
2
][
1
]
+
agpdpr2
*
dis_kkp
[
2
];
}
}
}
//j and k are different neighbors of i and k' is a neighbor j not equal to k
for
(
ltmp
=
0
;
ltmp
<
nlistj
;
ltmp
++
)
{
sig_flag
=
0
;
temp_jkp
=
BOP_index
[
j
]
+
ltmp
;
ni_jkp
=
neigh_index
[
temp_jkp
];
kp
=
jlist
[
ni_jkp
];
kptype
=
map
[
type
[
kp
]]
+
1
;
kplist
=
firstneigh
[
kp
];
same_kkpk
=
0
;
same_jkpj
=
0
;
nlistkp
=
BOP_total
[
kp
];
for
(
kpNeij
=
0
;
kpNeij
<
nlistkp
;
kpNeij
++
)
{
temp_kpj
=
BOP_index
[
kp
]
+
kpNeij
;
ni_kpj
=
neigh_index
[
temp_kpj
];
kpj
=
kplist
[
ni_kpj
];
if
(
x
[
j
][
0
]
==
x
[
kpj
][
0
])
{
if
(
x
[
j
][
1
]
==
x
[
kpj
][
1
])
{
if
(
x
[
j
][
2
]
==
x
[
kpj
][
2
])
{
same_jkpj
=
1
;
break
;
}
}
}
}
for
(
kpNeik
=
0
;
kpNeik
<
nlistkp
;
kpNeik
++
)
{
temp_kpk
=
BOP_index
[
kp
]
+
kpNeik
;
ni_kpk
=
neigh_index
[
temp_kpk
];
kpk
=
kplist
[
ni_kpk
];
if
(
x
[
k
][
0
]
==
x
[
kpk
][
0
])
{
if
(
x
[
k
][
1
]
==
x
[
kpk
][
1
])
{
if
(
x
[
k
][
2
]
==
x
[
kpk
][
2
])
{
same_kkpk
=
1
;
break
;
}
}
}
}
if
(
!
same_jkpj
&&!
same_kkpk
)
{
same_kkpk
=
0
;
for
(
kNeikp
=
0
;
kNeikp
<
nlistk
;
kNeikp
++
)
{
temp_kkp
=
BOP_index
[
k
]
+
kNeikp
;
ni_kkp
=
neigh_index
[
temp_kkp
];
kkp
=
kplist
[
ni_kkp
];
if
(
x
[
kp
][
0
]
==
x
[
kkp
][
0
])
{
if
(
x
[
kp
][
1
]
==
x
[
kkp
][
1
])
{
if
(
x
[
kp
][
2
]
==
x
[
kkp
][
2
])
{
sig_flag
=
1
;
break
;
}
}
}
}
if
(
sig_flag
==
1
)
{
for
(
nsearch
=
0
;
nsearch
<
nlistkp
;
nsearch
++
)
{
kp_nsearch
=
BOP_index
[
kp
]
+
nsearch
;
ni_kpnsearch
=
neigh_index
[
kp_nsearch
];
ncmp
=
kplist
[
ni_kpnsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
j
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
j
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
j
][
2
])
{
kpNeij
=
nsearch
;
}
}
}
if
(
x
[
ncmp
][
0
]
==
x
[
k
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
k
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
k
][
2
])
{
kpNeik
=
nsearch
;
}
}
}
}
if
(
jtype
==
kptype
)
ijkp
=
jtype
-
1
;
else
if
(
jtype
<
kptype
)
ijkp
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
kptype
-
1
;
else
ijkp
=
kptype
*
bop_types
-
kptype
*
(
kptype
+
1
)
/
2
+
jtype
-
1
;
if
(
ktype
==
kptype
)
ikkp
=
ktype
-
1
;
else
if
(
ktype
<
kptype
)
ikkp
=
ktype
*
bop_types
-
ktype
*
(
ktype
+
1
)
/
2
+
kptype
-
1
;
else
ikkp
=
kptype
*
bop_types
-
kptype
*
(
kptype
+
1
)
/
2
+
ktype
-
1
;
if
(
otfly
==
1
)
{
dis_jkp
[
0
]
=
x
[
kp
][
0
]
-
x
[
j
][
0
];
dis_jkp
[
1
]
=
x
[
kp
][
1
]
-
x
[
j
][
1
];
dis_jkp
[
2
]
=
x
[
kp
][
2
]
-
x
[
j
][
2
];
rsq_jkp
=
dis_jkp
[
0
]
*
dis_jkp
[
0
]
+
dis_jkp
[
1
]
*
dis_jkp
[
1
]
+
dis_jkp
[
2
]
*
dis_jkp
[
2
];
r_jkp
=
sqrt
(
rsq_jkp
);
ps
=
r_jkp
*
rdr
[
ijkp
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_jkp
=
((
pBetaS3
[
ijkp
][
ks
-
1
]
*
ps
+
pBetaS2
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS1
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS
[
ijkp
][
ks
-
1
];
dBetaS_jkp
=
(
pBetaS6
[
ijkp
][
ks
-
1
]
*
ps
+
pBetaS5
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS4
[
ijkp
][
ks
-
1
];
dis_kkp
[
0
]
=
x
[
kp
][
0
]
-
x
[
k
][
0
];
dis_kkp
[
1
]
=
x
[
kp
][
1
]
-
x
[
k
][
1
];
dis_kkp
[
2
]
=
x
[
kp
][
2
]
-
x
[
k
][
2
];
rsq_kkp
=
dis_kkp
[
0
]
*
dis_kkp
[
0
]
+
dis_kkp
[
1
]
*
dis_kkp
[
1
]
+
dis_kkp
[
2
]
*
dis_kkp
[
2
];
r_kkp
=
sqrt
(
rsq_kkp
);
ps
=
r_kkp
*
rdr
[
ikkp
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_kkp
=
((
pBetaS3
[
ikkp
][
ks
-
1
]
*
ps
+
pBetaS2
[
ikkp
][
ks
-
1
])
*
ps
+
pBetaS1
[
ikkp
][
ks
-
1
])
*
ps
+
pBetaS
[
ikkp
][
ks
-
1
];
dBetaS_kkp
=
(
pBetaS6
[
ikkp
][
ks
-
1
]
*
ps
+
pBetaS5
[
ikkp
][
ks
-
1
])
*
ps
+
pBetaS4
[
ikkp
][
ks
-
1
];
cosAng_ijkp
=
(
-
dis_ij
[
0
]
*
dis_jkp
[
0
]
-
dis_ij
[
1
]
*
dis_jkp
[
1
]
-
dis_ij
[
2
]
*
dis_jkp
[
2
])
/
(
r_ij
*
r_jkp
);
dcA_ijkp
[
0
][
0
]
=
(
dis_jkp
[
0
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*-
dis_ij
[
0
]
*
r_jkp
*
r_jkp
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
1
][
0
]
=
(
dis_jkp
[
1
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*-
dis_ij
[
1
]
*
r_jkp
*
r_jkp
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
2
][
0
]
=
(
dis_jkp
[
2
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*-
dis_ij
[
2
]
*
r_jkp
*
r_jkp
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
0
][
1
]
=
(
-
dis_ij
[
0
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*
dis_jkp
[
0
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
1
][
1
]
=
(
-
dis_ij
[
1
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*
dis_jkp
[
1
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
2
][
1
]
=
(
-
dis_ij
[
2
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*
dis_jkp
[
2
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
cosAng_ikkp
=
(
-
dis_ik
[
0
]
*
dis_kkp
[
0
]
-
dis_ik
[
1
]
*
dis_kkp
[
1
]
-
dis_ik
[
2
]
*
dis_kkp
[
2
])
/
(
r_ik
*
r_kkp
);
dcA_ikkp
[
0
][
0
]
=
(
dis_kkp
[
0
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*-
dis_ik
[
0
]
*
r_kkp
*
r_kkp
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
dcA_ikkp
[
1
][
0
]
=
(
dis_kkp
[
1
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*-
dis_ik
[
1
]
*
r_kkp
*
r_kkp
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
dcA_ikkp
[
2
][
0
]
=
(
dis_kkp
[
2
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*-
dis_ik
[
2
]
*
r_kkp
*
r_kkp
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
dcA_ikkp
[
0
][
1
]
=
(
-
dis_ik
[
0
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*
dis_kkp
[
0
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
dcA_ikkp
[
1
][
1
]
=
(
-
dis_ik
[
1
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*
dis_kkp
[
1
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
dcA_ikkp
[
2
][
1
]
=
(
-
dis_ik
[
2
]
*
r_ik
*
r_kkp
-
cosAng_ikkp
*
dis_kkp
[
2
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_kkp
*
r_kkp
);
cosAng_jkpk
=
(
dis_jkp
[
0
]
*
dis_kkp
[
0
]
+
dis_jkp
[
1
]
*
dis_kkp
[
1
]
+
dis_jkp
[
2
]
*
dis_kkp
[
2
])
/
(
r_jkp
*
r_kkp
);
dcA_jkpk
[
0
][
0
]
=
(
-
dis_kkp
[
0
]
*
r_jkp
*
r_kkp
-
cosAng_jkpk
*-
dis_jkp
[
0
]
*
r_kkp
*
r_kkp
)
/
(
r_jkp
*
r_jkp
*
r_kkp
*
r_kkp
);
dcA_jkpk
[
1
][
0
]
=
(
-
dis_kkp
[
1
]
*
r_jkp
*
r_kkp
-
cosAng_jkpk
*-
dis_jkp
[
1
]
*
r_kkp
*
r_kkp
)
/
(
r_jkp
*
r_jkp
*
r_kkp
*
r_kkp
);
dcA_jkpk
[
2
][
0
]
=
(
-
dis_kkp
[
2
]
*
r_jkp
*
r_kkp
-
cosAng_jkpk
*-
dis_jkp
[
2
]
*
r_kkp
*
r_kkp
)
/
(
r_jkp
*
r_jkp
*
r_kkp
*
r_kkp
);
dcA_jkpk
[
0
][
1
]
=
(
-
dis_jkp
[
0
]
*
r_jkp
*
r_kkp
-
cosAng_jkpk
*-
dis_kkp
[
0
]
*
r_jkp
*
r_jkp
)
/
(
r_jkp
*
r_jkp
*
r_kkp
*
r_kkp
);
dcA_jkpk
[
1
][
1
]
=
(
-
dis_jkp
[
1
]
*
r_jkp
*
r_kkp
-
cosAng_jkpk
*-
dis_kkp
[
1
]
*
r_jkp
*
r_jkp
)
/
(
r_jkp
*
r_jkp
*
r_kkp
*
r_kkp
);
dcA_jkpk
[
2
][
1
]
=
(
-
dis_jkp
[
2
]
*
r_jkp
*
r_kkp
-
cosAng_jkpk
*-
dis_kkp
[
2
]
*
r_jkp
*
r_jkp
)
/
(
r_jkp
*
r_jkp
*
r_kkp
*
r_kkp
);
}
else
{
dis_jkp
[
0
]
=
disij
[
0
][
temp_jkp
];
dis_jkp
[
1
]
=
disij
[
1
][
temp_jkp
];
dis_jkp
[
2
]
=
disij
[
2
][
temp_jkp
];
r_jkp
=
rij
[
temp_jkp
];
betaS_jkp
=
betaS
[
temp_jkp
];
dBetaS_jkp
=
dBetaS
[
temp_jkp
];
dis_kkp
[
0
]
=
disij
[
0
][
temp_kkp
];
dis_kkp
[
1
]
=
disij
[
1
][
temp_kkp
];
dis_kkp
[
2
]
=
disij
[
2
][
temp_kkp
];
r_kkp
=
rij
[
temp_kkp
];
betaS_kkp
=
betaS
[
temp_kkp
];
dBetaS_kkp
=
dBetaS
[
temp_kkp
];
if
(
ji
<
ltmp
)
{
nijkp
=
(
ji
)
*
nlistj
-
(
ji
+
1
)
*
(
ji
+
2
)
/
2
+
ltmp
;
ngji
=
0
;
ngjkp
=
1
;
}
else
{
nijkp
=
(
ltmp
)
*
nlistj
-
(
ltmp
+
1
)
*
(
ltmp
+
2
)
/
2
+
ji
;
ngji
=
1
;
ngjkp
=
0
;
}
if
(
kNeii
<
kNeikp
)
{
nikkp
=
(
kNeii
)
*
nlistk
-
(
kNeii
+
1
)
*
(
kNeii
+
2
)
/
2
+
kNeikp
;
ngki
=
0
;
ngkkp
=
1
;
}
else
{
nikkp
=
(
kNeikp
)
*
nlistk
-
(
kNeikp
+
1
)
*
(
kNeikp
+
2
)
/
2
+
kNeii
;
ngki
=
1
;
ngkkp
=
0
;
}
if
(
kpNeij
<
kpNeik
)
{
njkpk
=
(
kpNeij
)
*
nlistkp
-
(
kpNeij
+
1
)
*
(
kpNeij
+
2
)
/
2
+
kpNeik
;
ngkpj
=
0
;
ngkpk
=
1
;
}
else
{
njkpk
=
(
kpNeik
)
*
nlistkp
-
(
kpNeik
+
1
)
*
(
kpNeik
+
2
)
/
2
+
kpNeij
;
ngkpj
=
1
;
ngkpk
=
0
;
}
ang_ijkp
=
cos_index
[
j
]
+
nijkp
;
ang_ikkp
=
cos_index
[
k
]
+
nikkp
;
ang_jkpk
=
cos_index
[
kp
]
+
njkpk
;
cosAng_ijkp
=
cosAng
[
ang_ijkp
];
dcA_ijkp
[
0
][
0
]
=
dcAng
[
ang_ijkp
][
0
][
ngji
];
dcA_ijkp
[
1
][
0
]
=
dcAng
[
ang_ijkp
][
1
][
ngji
];
dcA_ijkp
[
2
][
0
]
=
dcAng
[
ang_ijkp
][
2
][
ngji
];
dcA_ijkp
[
0
][
1
]
=
dcAng
[
ang_ijkp
][
0
][
ngjkp
];
dcA_ijkp
[
1
][
1
]
=
dcAng
[
ang_ijkp
][
1
][
ngjkp
];
dcA_ijkp
[
2
][
1
]
=
dcAng
[
ang_ijkp
][
2
][
ngjkp
];
cosAng_ikkp
=
cosAng
[
ang_ikkp
];
dcA_ikkp
[
0
][
0
]
=
dcAng
[
ang_ikkp
][
0
][
ngki
];
dcA_ikkp
[
1
][
0
]
=
dcAng
[
ang_ikkp
][
1
][
ngki
];
dcA_ikkp
[
2
][
0
]
=
dcAng
[
ang_ikkp
][
2
][
ngki
];
dcA_ikkp
[
0
][
1
]
=
dcAng
[
ang_ikkp
][
0
][
ngkkp
];
dcA_ikkp
[
1
][
1
]
=
dcAng
[
ang_ikkp
][
1
][
ngkkp
];
dcA_ikkp
[
2
][
1
]
=
dcAng
[
ang_ikkp
][
2
][
ngkkp
];
cosAng_jkpk
=
cosAng
[
ang_jkpk
];
dcA_jkpk
[
0
][
0
]
=
dcAng
[
ang_jkpk
][
0
][
ngkpj
];
dcA_jkpk
[
1
][
0
]
=
dcAng
[
ang_jkpk
][
1
][
ngkpj
];
dcA_jkpk
[
2
][
0
]
=
dcAng
[
ang_jkpk
][
2
][
ngkpj
];
dcA_jkpk
[
0
][
1
]
=
dcAng
[
ang_jkpk
][
0
][
ngkpk
];
dcA_jkpk
[
1
][
1
]
=
dcAng
[
ang_jkpk
][
1
][
ngkpk
];
dcA_jkpk
[
2
][
1
]
=
dcAng
[
ang_jkpk
][
2
][
ngkpk
];
}
sig_flag
=
0
;
for
(
nsearch
=
0
;
nsearch
<
nSigBk
;
nsearch
++
)
{
ncmp
=
itypeSigBk
[
nsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
kp
][
2
])
{
nkp
=
nsearch
;
sig_flag
=
1
;
break
;
}
}
}
}
if
(
sig_flag
==
0
)
{
nSigBk
=
nSigBk
+
1
;
nkp
=
nSigBk
-
1
;
itypeSigBk
[
nkp
]
=
kp
;
}
temp_kpk
=
BOP_index
[
kp
]
+
kpNeik
;
nb_jkp
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_sg
)
{
new_n_tot
=
nb_sg
+
maxneigh
;
grow_sigma
(
nb_sg
,
new_n_tot
);
nb_sg
=
new_n_tot
;
}
bt_sg
[
nb_jkp
].
temp
=
temp_jkp
;
bt_sg
[
nb_jkp
].
i
=
j
;
bt_sg
[
nb_jkp
].
j
=
kp
;
nb_kkp
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_sg
)
{
new_n_tot
=
nb_sg
+
maxneigh
;
grow_sigma
(
nb_sg
,
new_n_tot
);
nb_sg
=
new_n_tot
;
}
bt_sg
[
nb_kkp
].
temp
=
temp_kkp
;
bt_sg
[
nb_kkp
].
i
=
k
;
bt_sg
[
nb_kkp
].
j
=
kp
;
amean
=
cosAng_ijkp
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor2
=
((
gfunc3
[
itype
][
jtype
][
kptype
][
ks
]
*
ps
+
gfunc2
[
itype
][
jtype
][
kptype
][
ks
])
*
ps
+
gfunc1
[
itype
][
jtype
][
kptype
][
ks
])
*
ps
+
gfunc
[
itype
][
jtype
][
kptype
][
ks
];
gprime2
=
(
gfunc6
[
itype
][
jtype
][
kptype
][
ks
]
*
ps
+
gfunc5
[
itype
][
jtype
][
kptype
][
ks
])
*
ps
+
gfunc4
[
itype
][
jtype
][
kptype
][
ks
];
}
else
{
gfactor2
=
gpara
[
itype
-
1
][
jtype
-
1
][
kptype
-
1
][
0
];
gprime2
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime2
=
gprime2
+
(
lp1
)
*
xrun
*
gpara
[
itype
-
1
][
jtype
-
1
][
kptype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor2
=
gfactor2
+
xrun
*
gpara
[
itype
-
1
][
jtype
-
1
][
kptype
-
1
][
lp1
];
}
}
amean
=
cosAng_ikkp
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor3
=
((
gfunc3
[
itype
][
ktype
][
kptype
][
ks
]
*
ps
+
gfunc2
[
itype
][
ktype
][
kptype
][
ks
])
*
ps
+
gfunc1
[
itype
][
ktype
][
kptype
][
ks
])
*
ps
+
gfunc
[
itype
][
ktype
][
kptype
][
ks
];
gprime3
=
(
gfunc6
[
itype
][
ktype
][
kptype
][
ks
]
*
ps
+
gfunc5
[
itype
][
ktype
][
kptype
][
ks
])
*
ps
+
gfunc4
[
itype
][
ktype
][
kptype
][
ks
];
}
else
{
gfactor3
=
gpara
[
itype
-
1
][
ktype
-
1
][
kptype
-
1
][
0
];
gprime3
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime3
=
gprime3
+
(
lp1
)
*
xrun
*
gpara
[
itype
-
1
][
ktype
-
1
][
kptype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor3
=
gfactor3
+
xrun
*
gpara
[
itype
-
1
][
ktype
-
1
][
kptype
-
1
][
lp1
];
}
}
amean
=
cosAng_jkpk
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor4
=
((
gfunc3
[
jtype
][
kptype
][
ktype
][
ks
]
*
ps
+
gfunc2
[
jtype
][
kptype
][
ktype
][
ks
])
*
ps
+
gfunc1
[
jtype
][
kptype
][
ktype
][
ks
])
*
ps
+
gfunc
[
jtype
][
kptype
][
ktype
][
ks
];
gprime4
=
(
gfunc6
[
jtype
][
kptype
][
ktype
][
ks
]
*
ps
+
gfunc5
[
jtype
][
kptype
][
ktype
][
ks
])
*
ps
+
gfunc4
[
jtype
][
kptype
][
ktype
][
ks
];
}
else
{
gfactor4
=
gpara
[
jtype
-
1
][
kptype
-
1
][
ktype
-
1
][
0
];
gprime4
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime4
=
gprime4
+
(
lp1
)
*
xrun
*
gpara
[
jtype
-
1
][
kptype
-
1
][
ktype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor4
=
gfactor4
+
xrun
*
gpara
[
jtype
-
1
][
kptype
-
1
][
ktype
-
1
][
lp1
];
}
}
gfactor
=
gfactor1
*
gfactor2
*
gfactor3
*
gfactor4
;
rfactor0
=
(
betaS_ik
+
small2
)
*
(
betaS_jkp
+
small2
)
*
(
betaS_kkp
+
small2
);
rfactor
=
pow
(
rfactor0
,
2.0
/
3.0
);
drfactor
=
2.0
/
3.0
*
pow
(
rfactor0
,
-
1.0
/
3.0
);
//EE is Eq. 25(notes)
EE
=
EE
+
gfactor
*
rfactor
;
//agpdpr1 is derivative of agpdpr1 w.r.t. Beta(r_ik)
//agpdpr2 is derivative of agpdpr1 w.r.t. Beta(r_jk')
//agpdpr3 is derivative of agpdpr1 w.r.t. Beta(r_kk')
//app1 is derivative of agpdpr1 w.r.t. cos(theta_jik)
//app2 is derivative of agpdpr1 w.r.t. cos(theta_ijk')
//app3 is derivative of agpdpr1 w.r.t. cos(theta_ikk')
//app4 is derivative of agpdpr1 w.r.t. cos(theta_jk'k)
agpdpr1
=
gfactor
*
drfactor
*
(
betaS_jkp
+
small2
)
*
(
betaS_kkp
+
small2
)
*
dBetaS_ik
/
r_ik
;
agpdpr2
=
gfactor
*
drfactor
*
(
betaS_ik
+
small2
)
*
(
betaS_kkp
+
small2
)
*
dBetaS_jkp
/
r_jkp
;
agpdpr3
=
gfactor
*
drfactor
*
(
betaS_ik
+
small2
)
*
(
betaS_jkp
+
small2
)
*
dBetaS_kkp
/
r_kkp
;
app1
=
rfactor
*
gfactor2
*
gfactor3
*
gfactor4
*
gprime1
;
app2
=
rfactor
*
gfactor1
*
gfactor3
*
gfactor4
*
gprime2
;
app3
=
rfactor
*
gfactor1
*
gfactor2
*
gfactor4
*
gprime3
;
app4
=
rfactor
*
gfactor1
*
gfactor2
*
gfactor3
*
gprime4
;
bt_sg
[
nb_ij
].
dEE
[
0
]
+=
app1
*
dcA_jik
[
0
][
0
]
-
app2
*
dcA_ijkp
[
0
][
0
];
bt_sg
[
nb_ij
].
dEE
[
1
]
+=
app1
*
dcA_jik
[
1
][
0
]
-
app2
*
dcA_ijkp
[
1
][
0
];
bt_sg
[
nb_ij
].
dEE
[
2
]
+=
app1
*
dcA_jik
[
2
][
0
]
-
app2
*
dcA_ijkp
[
2
][
0
];
bt_sg
[
nb_ik
].
dEE
[
0
]
+=
app1
*
dcA_jik
[
0
][
1
]
+
agpdpr1
*
dis_ik
[
0
]
-
app3
*
dcA_ikkp
[
0
][
0
];
bt_sg
[
nb_ik
].
dEE
[
1
]
+=
app1
*
dcA_jik
[
1
][
1
]
+
agpdpr1
*
dis_ik
[
1
]
-
app3
*
dcA_ikkp
[
1
][
0
];
bt_sg
[
nb_ik
].
dEE
[
2
]
+=
app1
*
dcA_jik
[
2
][
1
]
+
agpdpr1
*
dis_ik
[
2
]
-
app3
*
dcA_ikkp
[
2
][
0
];
bt_sg
[
nb_jkp
].
dEE
[
0
]
+=
app2
*
dcA_ijkp
[
0
][
1
]
+
agpdpr2
*
dis_jkp
[
0
]
-
app4
*
dcA_jkpk
[
0
][
0
];
bt_sg
[
nb_jkp
].
dEE
[
1
]
+=
app2
*
dcA_ijkp
[
1
][
1
]
+
agpdpr2
*
dis_jkp
[
1
]
-
app4
*
dcA_jkpk
[
1
][
0
];
bt_sg
[
nb_jkp
].
dEE
[
2
]
+=
app2
*
dcA_ijkp
[
2
][
1
]
+
agpdpr2
*
dis_jkp
[
2
]
-
app4
*
dcA_jkpk
[
2
][
0
];
bt_sg
[
nb_kkp
].
dEE
[
0
]
+=
app3
*
dcA_ikkp
[
0
][
1
]
+
agpdpr3
*
dis_kkp
[
0
]
-
app4
*
dcA_jkpk
[
0
][
1
];
bt_sg
[
nb_kkp
].
dEE
[
1
]
+=
app3
*
dcA_ikkp
[
1
][
1
]
+
agpdpr3
*
dis_kkp
[
1
]
-
app4
*
dcA_jkpk
[
1
][
1
];
bt_sg
[
nb_kkp
].
dEE
[
2
]
+=
app3
*
dcA_ikkp
[
2
][
1
]
+
agpdpr3
*
dis_kkp
[
2
]
-
app4
*
dcA_jkpk
[
2
][
1
];
}
}
}
}
}
}
}
//j is a neighbor of i and k is a neighbor of j not equal to i
for
(
ktmp
=
0
;
ktmp
<
nlistj
;
ktmp
++
)
{
if
(
ktmp
!=
ji
)
{
temp_jk
=
BOP_index
[
j
]
+
ktmp
;
ni_jk
=
neigh_index
[
temp_jk
];
k
=
jlist
[
ni_jk
];
klist
=
firstneigh
[
k
];
ktype
=
map
[
type
[
k
]]
+
1
;
nlistk
=
BOP_total
[
k
];
for
(
kNeij
=
0
;
kNeij
<
nlistk
;
kNeij
++
)
{
if
(
x
[
klist
[
kNeij
]][
0
]
==
x
[
j
][
0
])
{
if
(
x
[
klist
[
kNeij
]][
1
]
==
x
[
j
][
1
])
{
if
(
x
[
klist
[
kNeij
]][
2
]
==
x
[
j
][
2
])
{
break
;
}
}
}
}
if
(
jtype
==
ktype
)
ijk
=
jtype
-
1
;
else
if
(
jtype
<
ktype
)
ijk
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
ktype
-
1
;
else
ijk
=
ktype
*
bop_types
-
ktype
*
(
ktype
+
1
)
/
2
+
jtype
-
1
;
sig_flag
=
0
;
for
(
nsearch
=
0
;
nsearch
<
nSigBk
;
nsearch
++
)
{
ncmp
=
itypeSigBk
[
nsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
k
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
k
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
k
][
2
])
{
new1
=
nsearch
;
sig_flag
=
1
;
break
;
}
}
}
}
if
(
sig_flag
==
0
)
{
nSigBk
=
nSigBk
+
1
;
new1
=
nSigBk
-
1
;
itypeSigBk
[
new1
]
=
k
;
}
pass_jk
=
0
;
if
(
otfly
==
1
)
{
dis_jk
[
0
]
=
x
[
k
][
0
]
-
x
[
j
][
0
];
dis_jk
[
1
]
=
x
[
k
][
1
]
-
x
[
j
][
1
];
dis_jk
[
2
]
=
x
[
k
][
2
]
-
x
[
j
][
2
];
rsq_jk
=
dis_jk
[
0
]
*
dis_jk
[
0
]
+
dis_jk
[
1
]
*
dis_jk
[
1
]
+
dis_jk
[
2
]
*
dis_jk
[
2
];
r_jk
=
sqrt
(
rsq_jk
);
if
(
r_jk
<=
rcut
[
ijk
])
{
pass_jk
=
1
;
ps
=
r_jk
*
rdr
[
ijk
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_jk
=
((
pBetaS3
[
ijk
][
ks
-
1
]
*
ps
+
pBetaS2
[
ijk
][
ks
-
1
])
*
ps
+
pBetaS1
[
ijk
][
ks
-
1
])
*
ps
+
pBetaS
[
ijk
][
ks
-
1
];
dBetaS_jk
=
(
pBetaS6
[
ijk
][
ks
-
1
]
*
ps
+
pBetaS5
[
ijk
][
ks
-
1
])
*
ps
+
pBetaS4
[
ijk
][
ks
-
1
];
cosAng_ijk
=
(
-
dis_ij
[
0
]
*
dis_jk
[
0
]
-
dis_ij
[
1
]
*
dis_jk
[
1
]
-
dis_ij
[
2
]
*
dis_jk
[
2
])
/
(
r_ij
*
r_jk
);
dcA_ijk
[
0
][
0
]
=
(
dis_jk
[
0
]
*
r_ij
*
r_jk
-
cosAng_ijk
*-
dis_ij
[
0
]
*
r_jk
*
r_jk
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
1
][
0
]
=
(
dis_jk
[
1
]
*
r_ij
*
r_jk
-
cosAng_ijk
*-
dis_ij
[
1
]
*
r_jk
*
r_jk
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
2
][
0
]
=
(
dis_jk
[
2
]
*
r_ij
*
r_jk
-
cosAng_ijk
*-
dis_ij
[
2
]
*
r_jk
*
r_jk
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
0
][
1
]
=
(
-
dis_ij
[
0
]
*
r_ij
*
r_jk
-
cosAng_ijk
*
dis_jk
[
0
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
1
][
1
]
=
(
-
dis_ij
[
1
]
*
r_ij
*
r_jk
-
cosAng_ijk
*
dis_jk
[
1
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
2
][
1
]
=
(
-
dis_ij
[
2
]
*
r_ij
*
r_jk
-
cosAng_ijk
*
dis_jk
[
2
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
}
}
else
{
if
(
neigh_flag
[
temp_jk
])
{
pass_jk
=
1
;
dis_jk
[
0
]
=
disij
[
0
][
temp_jk
];
dis_jk
[
1
]
=
disij
[
1
][
temp_jk
];
dis_jk
[
2
]
=
disij
[
2
][
temp_jk
];
r_jk
=
rij
[
temp_jk
];
betaS_jk
=
betaS
[
temp_jk
];
dBetaS_jk
=
dBetaS
[
temp_jk
];
if
(
ktmp
<
ji
)
{
nijk
=
ktmp
*
(
2
*
nlistj
-
ktmp
-
1
)
/
2
+
(
ji
-
ktmp
)
-
1
;
ngi
=
1
;
ngk
=
0
;
}
else
{
nijk
=
ji
*
(
2
*
nlistj
-
ji
-
1
)
/
2
+
(
ktmp
-
ji
)
-
1
;
ngi
=
0
;
ngk
=
1
;
}
ang_ijk
=
cos_index
[
j
]
+
nijk
;
cosAng_ijk
=
cosAng
[
ang_ijk
];
dcA_ijk
[
0
][
0
]
=
dcAng
[
ang_ijk
][
0
][
ngi
];
dcA_ijk
[
1
][
0
]
=
dcAng
[
ang_ijk
][
1
][
ngi
];
dcA_ijk
[
2
][
0
]
=
dcAng
[
ang_ijk
][
2
][
ngi
];
dcA_ijk
[
0
][
1
]
=
dcAng
[
ang_ijk
][
0
][
ngk
];
dcA_ijk
[
1
][
1
]
=
dcAng
[
ang_ijk
][
1
][
ngk
];
dcA_ijk
[
2
][
1
]
=
dcAng
[
ang_ijk
][
2
][
ngk
];
}
}
if
(
pass_jk
==
1
)
{
nb_jk
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_sg
)
{
new_n_tot
=
nb_sg
+
maxneigh
;
grow_sigma
(
nb_sg
,
new_n_tot
);
nb_sg
=
new_n_tot
;
}
bt_sg
[
nb_jk
].
temp
=
temp_jk
;
bt_sg
[
nb_jk
].
i
=
j
;
bt_sg
[
nb_jk
].
j
=
k
;
amean
=
cosAng_ijk
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor1
=
((
gfunc3
[
itype
][
jtype
][
ktype
][
ks
]
*
ps
+
gfunc2
[
itype
][
jtype
][
ktype
][
ks
])
*
ps
+
gfunc1
[
itype
][
jtype
][
ktype
][
ks
])
*
ps
+
gfunc
[
itype
][
jtype
][
ktype
][
ks
];
gprime1
=
(
gfunc6
[
itype
][
jtype
][
ktype
][
ks
]
*
ps
+
gfunc5
[
itype
][
jtype
][
ktype
][
ks
])
*
ps
+
gfunc4
[
itype
][
jtype
][
ktype
][
ks
];
}
else
{
gfactor1
=
gpara
[
itype
-
1
][
jtype
-
1
][
ktype
-
1
][
0
];
gprime1
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime1
=
gprime1
+
(
lp1
)
*
xrun
*
gpara
[
itype
-
1
][
jtype
-
1
][
ktype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor1
=
gfactor1
+
xrun
*
gpara
[
itype
-
1
][
jtype
-
1
][
ktype
-
1
][
lp1
];
}
}
gfactorsq
=
gfactor1
*
gfactor1
;
gsqprime
=
2.0
*
gfactor1
*
gprime1
;
rfactor1rt
=
betaS_jk
*
betaS_jk
;
rfactor1
=
rfactor1rt
*
rfactor1rt
;
//BB is Eq. 34 (a) or Eq. 10 (c) for the j atom
//1st DD is Eq. 11 (c) for j atom where i & k=neighbor of j
BB
=
BB
+
gfactorsq
*
rfactor1rt
;
//agpdpr1 is derivative of BB w.r.t. Beta(r_jk)
//app1 is derivative of BB w.r.t. cos(theta_ijk)
agpdpr1
=
2.0
*
gfactorsq
*
betaS_jk
*
dBetaS_jk
/
r_jk
;
app1
=
rfactor1rt
*
gsqprime
;
bt_sg
[
nb_ij
].
dBB
[
0
]
-=
app1
*
dcA_ijk
[
0
][
0
];
bt_sg
[
nb_ij
].
dBB
[
1
]
-=
app1
*
dcA_ijk
[
1
][
0
];
bt_sg
[
nb_ij
].
dBB
[
2
]
-=
app1
*
dcA_ijk
[
2
][
0
];
bt_sg
[
nb_jk
].
dBB
[
0
]
+=
app1
*
dcA_ijk
[
0
][
1
]
+
agpdpr1
*
dis_jk
[
0
];
bt_sg
[
nb_jk
].
dBB
[
1
]
+=
app1
*
dcA_ijk
[
1
][
1
]
+
agpdpr1
*
dis_jk
[
1
];
bt_sg
[
nb_jk
].
dBB
[
2
]
+=
app1
*
dcA_ijk
[
2
][
1
]
+
agpdpr1
*
dis_jk
[
2
];
if
(
sigma_a
[
iij
]
!=
0
)
{
app2
=
rfactor1rt
*
app1
;
agpdpr2
=
2.0
*
rfactor1rt
*
agpdpr1
;
DD
=
DD
+
gfactorsq
*
rfactor1
;
bt_sg
[
nb_ij
].
dDD
[
0
]
-=
app2
*
dcA_ijk
[
0
][
0
];
bt_sg
[
nb_ij
].
dDD
[
1
]
-=
app2
*
dcA_ijk
[
1
][
0
];
bt_sg
[
nb_ij
].
dDD
[
2
]
-=
app2
*
dcA_ijk
[
2
][
0
];
bt_sg
[
nb_jk
].
dDD
[
0
]
+=
app2
*
dcA_ijk
[
0
][
1
]
+
agpdpr2
*
dis_jk
[
0
];
bt_sg
[
nb_jk
].
dDD
[
1
]
+=
app2
*
dcA_ijk
[
1
][
1
]
+
agpdpr2
*
dis_jk
[
1
];
bt_sg
[
nb_jk
].
dDD
[
2
]
+=
app2
*
dcA_ijk
[
2
][
1
]
+
agpdpr2
*
dis_jk
[
2
];
//j is a neighbor of i, k and k' prime different neighbors of j not equal to i
for
(
ltmp
=
0
;
ltmp
<
ktmp
;
ltmp
++
)
{
if
(
ltmp
!=
ji
)
{
temp_jkp
=
BOP_index
[
j
]
+
ltmp
;
ni_jkp
=
neigh_index
[
temp_jkp
];
kp
=
jlist
[
ni_jkp
];
kptype
=
map
[
type
[
kp
]]
+
1
;
if
(
jtype
==
kptype
)
ijkp
=
jtype
-
1
;
else
if
(
jtype
<
kptype
)
ijkp
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
kptype
-
1
;
else
ijkp
=
kptype
*
bop_types
-
kptype
*
(
kptype
+
1
)
/
2
+
jtype
-
1
;
for
(
nsearch
=
0
;
nsearch
<
nSigBk
;
nsearch
++
)
{
ncmp
=
itypeSigBk
[
nsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
kp
][
2
])
{
new2
=
nsearch
;
break
;
}
}
}
}
pass_jkp
=
0
;
if
(
otfly
==
1
)
{
dis_jkp
[
0
]
=
x
[
kp
][
0
]
-
x
[
j
][
0
];
dis_jkp
[
1
]
=
x
[
kp
][
1
]
-
x
[
j
][
1
];
dis_jkp
[
2
]
=
x
[
kp
][
2
]
-
x
[
j
][
2
];
rsq_jkp
=
dis_jkp
[
0
]
*
dis_jkp
[
0
]
+
dis_jkp
[
1
]
*
dis_jkp
[
1
]
+
dis_jkp
[
2
]
*
dis_jkp
[
2
];
r_jkp
=
sqrt
(
rsq_jkp
);
if
(
r_jkp
<=
rcut
[
ijkp
])
{
pass_jkp
=
1
;
ps
=
r_jkp
*
rdr
[
ijkp
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_jkp
=
((
pBetaS3
[
ijkp
][
ks
-
1
]
*
ps
+
pBetaS2
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS1
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS
[
ijkp
][
ks
-
1
];
dBetaS_jkp
=
(
pBetaS6
[
ijkp
][
ks
-
1
]
*
ps
+
pBetaS5
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS4
[
ijkp
][
ks
-
1
];
cosAng_ijkp
=
(
-
dis_ij
[
0
]
*
dis_jkp
[
0
]
-
dis_ij
[
1
]
*
dis_jkp
[
1
]
-
dis_ij
[
2
]
*
dis_jkp
[
2
])
/
(
r_ij
*
r_jkp
);
dcA_ijkp
[
0
][
0
]
=
(
dis_jkp
[
0
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*-
dis_ij
[
0
]
*
r_jkp
*
r_jkp
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
1
][
0
]
=
(
dis_jkp
[
1
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*-
dis_ij
[
1
]
*
r_jkp
*
r_jkp
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
2
][
0
]
=
(
dis_jkp
[
2
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*-
dis_ij
[
2
]
*
r_jkp
*
r_jkp
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
0
][
1
]
=
(
-
dis_ij
[
0
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*
dis_jkp
[
0
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
1
][
1
]
=
(
-
dis_ij
[
1
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*
dis_jkp
[
1
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
2
][
1
]
=
(
-
dis_ij
[
2
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*
dis_jkp
[
2
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
cosAng_kjkp
=
(
dis_jk
[
0
]
*
dis_jkp
[
0
]
+
dis_jk
[
1
]
*
dis_jkp
[
1
]
+
dis_jk
[
2
]
*
dis_jkp
[
2
])
/
(
r_jk
*
r_jkp
);
dcA_kjkp
[
0
][
0
]
=
(
dis_jkp
[
0
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jk
[
0
]
*
r_jkp
*
r_jkp
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
dcA_kjkp
[
1
][
0
]
=
(
dis_jkp
[
1
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jk
[
1
]
*
r_jkp
*
r_jkp
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
dcA_kjkp
[
2
][
0
]
=
(
dis_jkp
[
2
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jk
[
2
]
*
r_jkp
*
r_jkp
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
dcA_kjkp
[
0
][
1
]
=
(
dis_jk
[
0
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jkp
[
0
]
*
r_jk
*
r_jk
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
dcA_kjkp
[
1
][
1
]
=
(
dis_jk
[
1
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jkp
[
1
]
*
r_jk
*
r_jk
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
dcA_kjkp
[
2
][
1
]
=
(
dis_jk
[
2
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jkp
[
2
]
*
r_jk
*
r_jk
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
}
}
else
{
if
(
neigh_flag
[
temp_jkp
])
{
pass_jkp
=
1
;
dis_jkp
[
0
]
=
disij
[
0
][
temp_jkp
];
dis_jkp
[
1
]
=
disij
[
1
][
temp_jkp
];
dis_jkp
[
2
]
=
disij
[
2
][
temp_jkp
];
r_jkp
=
rij
[
temp_jkp
];
betaS_jkp
=
betaS
[
temp_jkp
];
dBetaS_jkp
=
dBetaS
[
temp_jkp
];
if
(
ji
<
ltmp
)
{
nijkp
=
ji
*
(
2
*
nlistj
-
ji
-
1
)
/
2
+
(
ltmp
-
ji
)
-
1
;
ngli
=
0
;
ngl
=
1
;
}
else
{
nijkp
=
ltmp
*
(
2
*
nlistj
-
ltmp
-
1
)
/
2
+
(
ji
-
ltmp
)
-
1
;
ngli
=
1
;
ngl
=
0
;
}
if
(
ktmp
<
ltmp
)
{
nkjkp
=
ktmp
*
(
2
*
nlistj
-
ktmp
-
1
)
/
2
+
(
ltmp
-
ktmp
)
-
1
;
ngjk
=
0
;
ngjkp
=
1
;
}
else
{
nkjkp
=
ltmp
*
(
2
*
nlistj
-
ltmp
-
1
)
/
2
+
(
ktmp
-
ltmp
)
-
1
;
ngjk
=
1
;
ngjkp
=
0
;
}
ang_ijkp
=
cos_index
[
j
]
+
nijkp
;
cosAng_ijkp
=
cosAng
[
ang_ijkp
];
dcA_ijkp
[
0
][
0
]
=
dcAng
[
ang_ijkp
][
0
][
ngli
];
dcA_ijkp
[
1
][
0
]
=
dcAng
[
ang_ijkp
][
1
][
ngli
];
dcA_ijkp
[
2
][
0
]
=
dcAng
[
ang_ijkp
][
2
][
ngli
];
dcA_ijkp
[
0
][
1
]
=
dcAng
[
ang_ijkp
][
0
][
ngl
];
dcA_ijkp
[
1
][
1
]
=
dcAng
[
ang_ijkp
][
1
][
ngl
];
dcA_ijkp
[
2
][
1
]
=
dcAng
[
ang_ijkp
][
2
][
ngl
];
ang_kjkp
=
cos_index
[
j
]
+
nkjkp
;
cosAng_kjkp
=
cosAng
[
ang_kjkp
];
dcA_kjkp
[
0
][
0
]
=
dcAng
[
ang_kjkp
][
0
][
ngjk
];
dcA_kjkp
[
1
][
0
]
=
dcAng
[
ang_kjkp
][
1
][
ngjk
];
dcA_kjkp
[
2
][
0
]
=
dcAng
[
ang_kjkp
][
2
][
ngjk
];
dcA_kjkp
[
0
][
1
]
=
dcAng
[
ang_kjkp
][
0
][
ngjkp
];
dcA_kjkp
[
1
][
1
]
=
dcAng
[
ang_kjkp
][
1
][
ngjkp
];
dcA_kjkp
[
2
][
1
]
=
dcAng
[
ang_kjkp
][
2
][
ngjkp
];
}
}
if
(
pass_jkp
==
1
)
{
nb_jkp
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_sg
)
{
new_n_tot
=
nb_sg
+
maxneigh
;
grow_sigma
(
nb_sg
,
new_n_tot
);
nb_sg
=
new_n_tot
;
}
bt_sg
[
nb_jkp
].
temp
=
temp_jkp
;
bt_sg
[
nb_jkp
].
i
=
j
;
bt_sg
[
nb_jkp
].
j
=
kp
;
amean
=
cosAng_ijkp
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor2
=
((
gfunc3
[
itype
][
jtype
][
kptype
][
ks
]
*
ps
+
gfunc2
[
itype
][
jtype
][
kptype
][
ks
])
*
ps
+
gfunc1
[
itype
][
jtype
][
kptype
][
ks
])
*
ps
+
gfunc
[
itype
][
jtype
][
kptype
][
ks
];
gprime2
=
(
gfunc6
[
itype
][
jtype
][
kptype
][
ks
]
*
ps
+
gfunc5
[
itype
][
jtype
][
kptype
][
ks
])
*
ps
+
gfunc4
[
itype
][
jtype
][
kptype
][
ks
];
}
else
{
gfactor2
=
gpara
[
itype
-
1
][
jtype
-
1
][
kptype
-
1
][
0
];
gprime2
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime2
=
gprime2
+
(
lp1
)
*
xrun
*
gpara
[
itype
-
1
][
jtype
-
1
][
kptype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor2
=
gfactor2
+
xrun
*
gpara
[
itype
-
1
][
jtype
-
1
][
kptype
-
1
][
lp1
];
}
}
amean
=
cosAng_kjkp
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor3
=
((
gfunc3
[
ktype
][
jtype
][
kptype
][
ks
]
*
ps
+
gfunc2
[
ktype
][
jtype
][
kptype
][
ks
])
*
ps
+
gfunc1
[
ktype
][
jtype
][
kptype
][
ks
])
*
ps
+
gfunc
[
ktype
][
jtype
][
kptype
][
ks
];
gprime3
=
(
gfunc6
[
ktype
][
jtype
][
kptype
][
ks
]
*
ps
+
gfunc5
[
ktype
][
jtype
][
kptype
][
ks
])
*
ps
+
gfunc4
[
ktype
][
jtype
][
kptype
][
ks
];
}
else
{
gfactor3
=
gpara
[
ktype
-
1
][
jtype
-
1
][
kptype
-
1
][
0
];
gprime3
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime3
=
gprime3
+
(
lp1
)
*
xrun
*
gpara
[
ktype
-
1
][
jtype
-
1
][
kptype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor3
=
gfactor3
+
xrun
*
gpara
[
ktype
-
1
][
jtype
-
1
][
kptype
-
1
][
lp1
];
}
}
gfactor
=
gfactor1
*
gfactor2
*
gfactor3
;
rfactorrt
=
betaS_jk
*
betaS_jkp
;
rfactor
=
rfactorrt
*
rfactorrt
;
//2nd DD is Eq. 11 (c) for j atom where i , k & k'=neighbor of j
DD
=
DD
+
2.0
*
gfactor
*
rfactor
;
//agpdpr1 is derivative of DD w.r.t. Beta(r_jk)
//agpdpr2 is derivative of DD w.r.t. Beta(r_jk')
//app1 is derivative of DD w.r.t. cos(theta_ijk)
//app2 is derivative of DD w.r.t. cos(theta_ijkp)
//app3 is derivative of DD w.r.t. cos(theta_kjkp)
agpdpr1
=
4.0
*
gfactor
*
rfactorrt
*
betaS_jkp
*
dBetaS_jk
/
r_jk
;
agpdpr2
=
4.0
*
gfactor
*
rfactorrt
*
betaS_jk
*
dBetaS_jkp
/
r_jkp
;
app1
=
2.0
*
rfactor
*
gfactor2
*
gfactor3
*
gprime1
;
app2
=
2.0
*
rfactor
*
gfactor1
*
gfactor3
*
gprime2
;
app3
=
2.0
*
rfactor
*
gfactor1
*
gfactor2
*
gprime3
;
bt_sg
[
nb_ij
].
dDD
[
0
]
-=
app1
*
dcA_ijk
[
0
][
0
]
+
app2
*
dcA_ijkp
[
0
][
0
];
bt_sg
[
nb_ij
].
dDD
[
1
]
-=
app1
*
dcA_ijk
[
1
][
0
]
+
app2
*
dcA_ijkp
[
1
][
0
];
bt_sg
[
nb_ij
].
dDD
[
2
]
-=
app1
*
dcA_ijk
[
2
][
0
]
+
app2
*
dcA_ijkp
[
2
][
0
];
bt_sg
[
nb_jk
].
dDD
[
0
]
+=
app1
*
dcA_ijk
[
0
][
1
]
+
app3
*
dcA_kjkp
[
0
][
0
]
+
agpdpr1
*
dis_jk
[
0
];
bt_sg
[
nb_jk
].
dDD
[
1
]
+=
app1
*
dcA_ijk
[
1
][
1
]
+
app3
*
dcA_kjkp
[
1
][
0
]
+
agpdpr1
*
dis_jk
[
1
];
bt_sg
[
nb_jk
].
dDD
[
2
]
+=
app1
*
dcA_ijk
[
2
][
1
]
+
app3
*
dcA_kjkp
[
2
][
0
]
+
agpdpr1
*
dis_jk
[
2
];
bt_sg
[
nb_jkp
].
dDD
[
0
]
+=
app2
*
dcA_ijkp
[
0
][
1
]
+
app3
*
dcA_kjkp
[
0
][
1
]
+
agpdpr2
*
dis_jkp
[
0
];
bt_sg
[
nb_jkp
].
dDD
[
1
]
+=
app2
*
dcA_ijkp
[
1
][
1
]
+
app3
*
dcA_kjkp
[
1
][
1
]
+
agpdpr2
*
dis_jkp
[
1
];
bt_sg
[
nb_jkp
].
dDD
[
2
]
+=
app2
*
dcA_ijkp
[
2
][
1
]
+
app3
*
dcA_kjkp
[
2
][
1
]
+
agpdpr2
*
dis_jkp
[
2
];
}
}
}
//j is a neighbor of i, k is a neighbor of j not equal to i and k'
//is a neighbor of k not equal to j or i
for
(
ltmp
=
0
;
ltmp
<
nlistk
;
ltmp
++
)
{
temp_kkp
=
BOP_index
[
k
]
+
ltmp
;
ni_kkp
=
neigh_index
[
temp_kkp
];
kp
=
klist
[
ni_kkp
];
kptype
=
map
[
type
[
kp
]]
+
1
;
same_ikp
=
0
;
same_jkp
=
0
;
if
(
x
[
i
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
i
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
i
][
2
]
==
x
[
kp
][
2
])
{
same_ikp
=
1
;
}
}
}
if
(
x
[
j
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
j
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
j
][
2
]
==
x
[
kp
][
2
])
{
same_jkp
=
1
;
}
}
}
if
(
!
same_ikp
&&!
same_jkp
)
{
if
(
ktype
==
kptype
)
ikkp
=
ktype
-
1
;
else
if
(
ktype
<
kptype
)
ikkp
=
ktype
*
bop_types
-
ktype
*
(
ktype
+
1
)
/
2
+
kptype
-
1
;
else
ikkp
=
kptype
*
bop_types
-
kptype
*
(
kptype
+
1
)
/
2
+
ktype
-
1
;
for
(
kNeij
=
0
;
kNeij
<
nlistk
;
kNeij
++
)
{
temp_kj
=
BOP_index
[
k
]
+
kNeij
;
ni_kj
=
neigh_index
[
temp_kj
];
if
(
x
[
klist
[
ni_kj
]][
0
]
==
x
[
j
][
0
])
{
if
(
x
[
klist
[
ni_kj
]][
1
]
==
x
[
j
][
1
])
{
if
(
x
[
klist
[
ni_kj
]][
2
]
==
x
[
j
][
2
])
{
break
;
}
}
}
}
sig_flag
=
0
;
for
(
nsearch
=
0
;
nsearch
<
nSigBk
;
nsearch
++
)
{
ncmp
=
itypeSigBk
[
nsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
kp
][
2
])
{
new2
=
nsearch
;
sig_flag
=
1
;
break
;
}
}
}
}
if
(
sig_flag
==
0
)
{
nSigBk
=
nSigBk
+
1
;
new2
=
nSigBk
-
1
;
itypeSigBk
[
new2
]
=
kp
;
}
pass_kkp
=
0
;
if
(
otfly
==
1
)
{
dis_kkp
[
0
]
=
x
[
kp
][
0
]
-
x
[
k
][
0
];
dis_kkp
[
1
]
=
x
[
kp
][
1
]
-
x
[
k
][
1
];
dis_kkp
[
2
]
=
x
[
kp
][
2
]
-
x
[
k
][
2
];
rsq_kkp
=
dis_kkp
[
0
]
*
dis_kkp
[
0
]
+
dis_kkp
[
1
]
*
dis_kkp
[
1
]
+
dis_kkp
[
2
]
*
dis_kkp
[
2
];
r_kkp
=
sqrt
(
rsq_kkp
);
if
(
r_kkp
<=
rcut
[
ikkp
])
{
pass_kkp
=
1
;
ps
=
r_kkp
*
rdr
[
ikkp
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_kkp
=
((
pBetaS3
[
ikkp
][
ks
-
1
]
*
ps
+
pBetaS2
[
ikkp
][
ks
-
1
])
*
ps
+
pBetaS1
[
ikkp
][
ks
-
1
])
*
ps
+
pBetaS
[
ikkp
][
ks
-
1
];
dBetaS_kkp
=
(
pBetaS6
[
ikkp
][
ks
-
1
]
*
ps
+
pBetaS5
[
ikkp
][
ks
-
1
])
*
ps
+
pBetaS4
[
ikkp
][
ks
-
1
];
cosAng_jkkp
=
(
-
dis_jk
[
0
]
*
dis_kkp
[
0
]
-
dis_jk
[
1
]
*
dis_kkp
[
1
]
-
dis_jk
[
2
]
*
dis_kkp
[
2
])
/
(
r_jk
*
r_kkp
);
dcA_jkkp
[
0
][
0
]
=
(
dis_kkp
[
0
]
*
r_jk
*
r_kkp
-
cosAng_jkkp
*-
dis_jk
[
0
]
*
r_kkp
*
r_kkp
)
/
(
r_jk
*
r_jk
*
r_kkp
*
r_kkp
);
dcA_jkkp
[
1
][
0
]
=
(
dis_kkp
[
1
]
*
r_jk
*
r_kkp
-
cosAng_jkkp
*-
dis_jk
[
1
]
*
r_kkp
*
r_kkp
)
/
(
r_jk
*
r_jk
*
r_kkp
*
r_kkp
);
dcA_jkkp
[
2
][
0
]
=
(
dis_kkp
[
2
]
*
r_jk
*
r_kkp
-
cosAng_jkkp
*-
dis_jk
[
2
]
*
r_kkp
*
r_kkp
)
/
(
r_jk
*
r_jk
*
r_kkp
*
r_kkp
);
dcA_jkkp
[
0
][
1
]
=
(
-
dis_jk
[
0
]
*
r_jk
*
r_kkp
-
cosAng_jkkp
*
dis_kkp
[
0
]
*
r_jk
*
r_jk
)
/
(
r_jk
*
r_jk
*
r_kkp
*
r_kkp
);
dcA_jkkp
[
1
][
1
]
=
(
-
dis_jk
[
1
]
*
r_jk
*
r_kkp
-
cosAng_jkkp
*
dis_kkp
[
1
]
*
r_jk
*
r_jk
)
/
(
r_jk
*
r_jk
*
r_kkp
*
r_kkp
);
dcA_jkkp
[
2
][
1
]
=
(
-
dis_jk
[
2
]
*
r_jk
*
r_kkp
-
cosAng_jkkp
*
dis_kkp
[
2
]
*
r_jk
*
r_jk
)
/
(
r_jk
*
r_jk
*
r_kkp
*
r_kkp
);
}
}
else
{
if
(
neigh_flag
[
temp_kkp
])
{
pass_kkp
=
1
;
dis_kkp
[
0
]
=
disij
[
0
][
temp_kkp
];
dis_kkp
[
1
]
=
disij
[
1
][
temp_kkp
];
dis_kkp
[
2
]
=
disij
[
2
][
temp_kkp
];
r_kkp
=
rij
[
temp_kkp
];
betaS_kkp
=
betaS
[
temp_kkp
];
dBetaS_kkp
=
dBetaS
[
temp_kkp
];
if
(
kNeij
<
ltmp
)
{
njkkp
=
kNeij
*
(
2
*
nlistk
-
kNeij
-
1
)
/
2
+
(
ltmp
-
kNeij
)
-
1
;
nglkp
=
1
;
nglj
=
0
;
}
else
{
njkkp
=
ltmp
*
(
2
*
nlistk
-
ltmp
-
1
)
/
2
+
(
kNeij
-
ltmp
)
-
1
;
nglkp
=
0
;
nglj
=
1
;
}
ang_jkkp
=
cos_index
[
k
]
+
njkkp
;
cosAng_jkkp
=
cosAng
[
ang_jkkp
];
dcA_jkkp
[
0
][
0
]
=
dcAng
[
ang_jkkp
][
0
][
nglj
];
dcA_jkkp
[
1
][
0
]
=
dcAng
[
ang_jkkp
][
1
][
nglj
];
dcA_jkkp
[
2
][
0
]
=
dcAng
[
ang_jkkp
][
2
][
nglj
];
dcA_jkkp
[
0
][
1
]
=
dcAng
[
ang_jkkp
][
0
][
nglkp
];
dcA_jkkp
[
1
][
1
]
=
dcAng
[
ang_jkkp
][
1
][
nglkp
];
dcA_jkkp
[
2
][
1
]
=
dcAng
[
ang_jkkp
][
2
][
nglkp
];
}
}
if
(
pass_kkp
==
1
)
{
nb_kkp
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_sg
)
{
new_n_tot
=
nb_sg
+
maxneigh
;
grow_sigma
(
nb_sg
,
new_n_tot
);
nb_sg
=
new_n_tot
;
}
bt_sg
[
nb_kkp
].
temp
=
temp_kkp
;
bt_sg
[
nb_kkp
].
i
=
k
;
bt_sg
[
nb_kkp
].
j
=
kp
;
amean
=
cosAng_jkkp
;
if
(
amean
<-
1.0
)
amean
=-
1.0
;
if
(
npower
<=
2
)
{
ps
=
(
amean
-
1.0
)
*
rdtheta
+
1.0
;
ks
=
(
int
)
ps
;
if
(
ntheta
-
1
<
ks
)
ks
=
ntheta
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
ks
=
ks
-
1
;
gfactor2
=
((
gfunc3
[
jtype
][
ktype
][
kptype
][
ks
]
*
ps
+
gfunc2
[
jtype
][
ktype
][
kptype
][
ks
])
*
ps
+
gfunc1
[
jtype
][
ktype
][
kptype
][
ks
])
*
ps
+
gfunc
[
jtype
][
ktype
][
kptype
][
ks
];
gprime2
=
(
gfunc6
[
jtype
][
ktype
][
kptype
][
ks
]
*
ps
+
gfunc5
[
jtype
][
ktype
][
kptype
][
ks
])
*
ps
+
gfunc4
[
jtype
][
ktype
][
kptype
][
ks
];
}
else
{
gfactor2
=
gpara
[
jtype
-
1
][
ktype
-
1
][
kptype
-
1
][
0
];
gprime2
=
0.0
;
xrun
=
1.0
;
for
(
lp1
=
1
;
lp1
<
npower
+
1
;
lp1
++
)
{
gprime2
=
gprime2
+
(
lp1
)
*
xrun
*
gpara
[
jtype
-
1
][
ktype
-
1
][
kptype
-
1
][
lp1
];
xrun
=
xrun
*
amean
;
gfactor2
=
gfactor2
+
xrun
*
gpara
[
jtype
-
1
][
ktype
-
1
][
kptype
-
1
][
lp1
];
}
}
gfactorsq2
=
gfactor2
*
gfactor2
;
gsqprime2
=
2.0
*
gfactor2
*
gprime2
;
gfactor
=
gfactorsq
*
gfactorsq2
;
rfactorrt
=
betaS_jk
*
betaS_kkp
;
rfactor
=
rfactorrt
*
rfactorrt
;
//3rd DD is Eq. 11 (c) for j atom where i & k=neighbor of j & k'=neighbor of k
DD
=
DD
+
gfactor
*
rfactor
;
//agpdpr1 is derivative of DD 3rd term w.r.t. Beta(r_jk)
//agpdpr2 is derivative of DD 3rd term w.r.t. Beta(r_kk')
//app1 is derivative of DD 3rd term w.r.t. cos(theta_ijk)
//app2 is derivative of DD 3rd term w.r.t. cos(theta_jkkp)
agpdpr1
=
2.0
*
gfactor
*
rfactorrt
*
betaS_kkp
*
dBetaS_jk
/
r_jk
;
agpdpr2
=
2.0
*
gfactor
*
rfactorrt
*
betaS_jk
*
dBetaS_kkp
/
r_kkp
;
app1
=
rfactor
*
gfactorsq2
*
gsqprime
;
app2
=
rfactor
*
gfactorsq
*
gsqprime2
;
bt_sg
[
nb_ij
].
dDD
[
0
]
-=
app1
*
dcA_ijk
[
0
][
0
];
bt_sg
[
nb_ij
].
dDD
[
1
]
-=
app1
*
dcA_ijk
[
1
][
0
];
bt_sg
[
nb_ij
].
dDD
[
2
]
-=
app1
*
dcA_ijk
[
2
][
0
];
bt_sg
[
nb_jk
].
dDD
[
0
]
+=
app1
*
dcA_ijk
[
0
][
1
]
+
agpdpr1
*
dis_jk
[
0
]
-
app2
*
dcA_jkkp
[
0
][
0
];
bt_sg
[
nb_jk
].
dDD
[
1
]
+=
app1
*
dcA_ijk
[
1
][
1
]
+
agpdpr1
*
dis_jk
[
1
]
-
app2
*
dcA_jkkp
[
1
][
0
];
bt_sg
[
nb_jk
].
dDD
[
2
]
+=
app1
*
dcA_ijk
[
2
][
1
]
+
agpdpr1
*
dis_jk
[
2
]
-
app2
*
dcA_jkkp
[
2
][
0
];
bt_sg
[
nb_kkp
].
dDD
[
0
]
+=
app2
*
dcA_jkkp
[
0
][
1
]
+
agpdpr2
*
dis_kkp
[
0
];
bt_sg
[
nb_kkp
].
dDD
[
1
]
+=
app2
*
dcA_jkkp
[
1
][
1
]
+
agpdpr2
*
dis_kkp
[
1
];
bt_sg
[
nb_kkp
].
dDD
[
2
]
+=
app2
*
dcA_jkkp
[
2
][
1
]
+
agpdpr2
*
dis_kkp
[
2
];
}
}
}
}
}
}
}
sig_flag
=
0
;
if
(
FF
<=
0.000001
)
{
sigB
=
0.0
;
sig_flag
=
1
;
}
if
(
sig_flag
==
0
){
if
(
sigma_a
[
iij
]
==
0
){
if
(
sig_flag
==
0
)
{
if
(
AA
<
0.0
)
AA
=
0.0
;
if
(
BB
<
0.0
)
BB
=
0.0
;
AAC
=
AA
+
BB
;
for
(
m
=
0
;
m
<
nb_t
;
m
++
)
{
if
((
bt_sg
[
m
].
i
>-
1
)
&&
(
bt_sg
[
m
].
j
>-
1
))
{
bt_sg
[
m
].
dAAC
[
0
]
=
bt_sg
[
m
].
dAA
[
0
]
+
bt_sg
[
m
].
dBB
[
0
];
bt_sg
[
m
].
dAAC
[
1
]
=
bt_sg
[
m
].
dAA
[
1
]
+
bt_sg
[
m
].
dBB
[
1
];
bt_sg
[
m
].
dAAC
[
2
]
=
bt_sg
[
m
].
dAA
[
2
]
+
bt_sg
[
m
].
dBB
[
2
];
}
}
bndtmp
=
(
FF
+
sigma_delta
[
iij
]
*
sigma_delta
[
iij
]
+
sigma_c
[
iij
]
*
AAC
+
small4
);
bndtmp0
=
1.0
/
sqrt
(
bndtmp
);
sigB1
=
betaS_ij
*
bndtmp0
;
bndtmp
=-
0.5
*
bndtmp0
*
bndtmp0
*
bndtmp0
;
bndtmp1
=
bndtmp0
+
betaS_ij
*
bndtmp
*
2.0
*
betaS_ij
;
bndtmp1
=
bndtmp1
*
dBetaS_ij
/
r_ij
;
bndtmp2
=
betaS_ij
*
bndtmp
*
sigma_c
[
iij
];
setting
=
0
;
for
(
m
=
0
;
m
<
nb_t
;
m
++
)
{
if
((
bt_sg
[
m
].
i
>-
1
)
&&
(
bt_sg
[
m
].
j
>-
1
))
{
temp_kk
=
bt_sg
[
m
].
temp
;
if
(
temp_kk
==
temp_ij
&&
setting
==
0
)
{
bt_sg
[
m
].
dSigB1
[
0
]
=
bndtmp1
*
dis_ij
[
0
]
+
bndtmp2
*
bt_sg
[
m
].
dAAC
[
0
];
bt_sg
[
m
].
dSigB1
[
1
]
=
bndtmp1
*
dis_ij
[
1
]
+
bndtmp2
*
bt_sg
[
m
].
dAAC
[
1
];
bt_sg
[
m
].
dSigB1
[
2
]
=
bndtmp1
*
dis_ij
[
2
]
+
bndtmp2
*
bt_sg
[
m
].
dAAC
[
2
];
setting
=
1
;
}
else
if
(
temp_kk
==
temp_ji
&&
setting
==
0
)
{
bt_sg
[
m
].
dSigB1
[
0
]
=-
bndtmp1
*
dis_ij
[
0
]
+
bndtmp2
*
bt_sg
[
m
].
dAAC
[
0
];
bt_sg
[
m
].
dSigB1
[
1
]
=-
bndtmp1
*
dis_ij
[
1
]
+
bndtmp2
*
bt_sg
[
m
].
dAAC
[
1
];
bt_sg
[
m
].
dSigB1
[
2
]
=-
bndtmp1
*
dis_ij
[
2
]
+
bndtmp2
*
bt_sg
[
m
].
dAAC
[
2
];
setting
=
1
;
}
else
{
bt_sg
[
m
].
dSigB1
[
0
]
=
bndtmp2
*
bt_sg
[
m
].
dAAC
[
0
];
bt_sg
[
m
].
dSigB1
[
1
]
=
bndtmp2
*
bt_sg
[
m
].
dAAC
[
1
];
bt_sg
[
m
].
dSigB1
[
2
]
=
bndtmp2
*
bt_sg
[
m
].
dAAC
[
2
];
}
}
}
}
}
else
{
if
(
sig_flag
==
0
)
{
if
(
AA
<
0.0
)
AA
=
0.0
;
if
(
BB
<
0.0
)
BB
=
0.0
;
if
(
CC
<
0.0
)
CC
=
0.0
;
if
(
DD
<
0.0
)
DD
=
0.0
;
// AA and BB are the representations of (a) Eq. 34 and (b) Eq. 9
// for atoms i and j respectively
AAC
=
AA
+
BB
;
BBC
=
AA
*
BB
;
CCC
=
AA
*
AA
+
BB
*
BB
;
DDC
=
CC
+
DD
;
//EEC is a modified form of (a) Eq. 33
if
(
DDC
<
CCC
)
DDC
=
CCC
;
EEC
=
(
DDC
-
CCC
)
/
(
AAC
+
2.0
*
small1
);
AACFF
=
1.0
/
(
AAC
+
2.0
*
small1
);
for
(
m
=
0
;
m
<
nb_t
;
m
++
)
{
if
((
bt_sg
[
m
].
i
>-
1
)
&&
(
bt_sg
[
m
].
j
>-
1
))
{
bt_sg
[
m
].
dAAC
[
0
]
=
bt_sg
[
m
].
dAA
[
0
]
+
bt_sg
[
m
].
dBB
[
0
];
bt_sg
[
m
].
dAAC
[
1
]
=
bt_sg
[
m
].
dAA
[
1
]
+
bt_sg
[
m
].
dBB
[
1
];
bt_sg
[
m
].
dAAC
[
2
]
=
bt_sg
[
m
].
dAA
[
2
]
+
bt_sg
[
m
].
dBB
[
2
];
bt_sg
[
m
].
dBBC
[
0
]
=
bt_sg
[
m
].
dAA
[
0
]
*
BB
+
AA
*
bt_sg
[
m
].
dBB
[
0
];
bt_sg
[
m
].
dBBC
[
1
]
=
bt_sg
[
m
].
dAA
[
1
]
*
BB
+
AA
*
bt_sg
[
m
].
dBB
[
1
];
bt_sg
[
m
].
dBBC
[
2
]
=
bt_sg
[
m
].
dAA
[
2
]
*
BB
+
AA
*
bt_sg
[
m
].
dBB
[
2
];
bt_sg
[
m
].
dCCC
[
0
]
=
2.0
*
AA
*
bt_sg
[
m
].
dAA
[
0
]
+
2.0
*
BB
*
bt_sg
[
m
].
dBB
[
0
];
bt_sg
[
m
].
dCCC
[
1
]
=
2.0
*
AA
*
bt_sg
[
m
].
dAA
[
1
]
+
2.0
*
BB
*
bt_sg
[
m
].
dBB
[
1
];
bt_sg
[
m
].
dCCC
[
2
]
=
2.0
*
AA
*
bt_sg
[
m
].
dAA
[
2
]
+
2.0
*
BB
*
bt_sg
[
m
].
dBB
[
2
];
bt_sg
[
m
].
dDDC
[
0
]
=
bt_sg
[
m
].
dCC
[
0
]
+
bt_sg
[
m
].
dDD
[
0
];
bt_sg
[
m
].
dDDC
[
1
]
=
bt_sg
[
m
].
dCC
[
1
]
+
bt_sg
[
m
].
dDD
[
1
];
bt_sg
[
m
].
dDDC
[
2
]
=
bt_sg
[
m
].
dCC
[
2
]
+
bt_sg
[
m
].
dDD
[
2
];
bt_sg
[
m
].
dEEC
[
0
]
=
(
bt_sg
[
m
].
dDDC
[
0
]
-
bt_sg
[
m
].
dCCC
[
0
]
-
EEC
*
bt_sg
[
m
].
dAAC
[
0
])
*
AACFF
;
bt_sg
[
m
].
dEEC
[
1
]
=
(
bt_sg
[
m
].
dDDC
[
1
]
-
bt_sg
[
m
].
dCCC
[
1
]
-
EEC
*
bt_sg
[
m
].
dAAC
[
1
])
*
AACFF
;
bt_sg
[
m
].
dEEC
[
2
]
=
(
bt_sg
[
m
].
dDDC
[
2
]
-
bt_sg
[
m
].
dCCC
[
2
]
-
EEC
*
bt_sg
[
m
].
dAAC
[
2
])
*
AACFF
;
}
}
UT
=
EEC
*
FF
+
BBC
+
small3
[
iij
];
UT
=
1.0
/
sqrt
(
UT
);
// FFC is slightly modified form of (a) Eq. 31
// GGC is slightly modified form of (a) Eq. 32
// bndtmp is a slightly modified form of (a) Eq. 30 and (b) Eq. 8
FFC
=
BBC
*
UT
;
GGC
=
EEC
*
UT
;
bndtmp
=
(
FF
+
sigma_delta
[
iij
]
*
sigma_delta
[
iij
])
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
)
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
)
+
sigma_c
[
iij
]
*
(
AAC
+
sigma_a
[
iij
]
*
EE
+
sigma_a
[
iij
]
*
FFC
*
(
2.0
+
GGC
))
+
small4
;
UTcom
=-
0.5
*
UT
*
UT
*
UT
;
for
(
m
=
0
;
m
<
nb_t
;
m
++
)
{
if
((
bt_sg
[
m
].
i
>-
1
)
&&
(
bt_sg
[
m
].
j
>-
1
))
{
bt_sg
[
m
].
dUT
[
0
]
=
UTcom
*
(
bt_sg
[
m
].
dEEC
[
0
]
*
FF
+
EEC
*
bt_sg
[
m
].
dFF
[
0
]
+
bt_sg
[
m
].
dBBC
[
0
]);
bt_sg
[
m
].
dUT
[
1
]
=
UTcom
*
(
bt_sg
[
m
].
dEEC
[
1
]
*
FF
+
EEC
*
bt_sg
[
m
].
dFF
[
1
]
+
bt_sg
[
m
].
dBBC
[
1
]);
bt_sg
[
m
].
dUT
[
2
]
=
UTcom
*
(
bt_sg
[
m
].
dEEC
[
2
]
*
FF
+
EEC
*
bt_sg
[
m
].
dFF
[
2
]
+
bt_sg
[
m
].
dBBC
[
2
]);
bt_sg
[
m
].
dFFC
[
0
]
=
bt_sg
[
m
].
dBBC
[
0
]
*
UT
+
BBC
*
bt_sg
[
m
].
dUT
[
0
];
bt_sg
[
m
].
dFFC
[
1
]
=
bt_sg
[
m
].
dBBC
[
1
]
*
UT
+
BBC
*
bt_sg
[
m
].
dUT
[
1
];
bt_sg
[
m
].
dFFC
[
2
]
=
bt_sg
[
m
].
dBBC
[
2
]
*
UT
+
BBC
*
bt_sg
[
m
].
dUT
[
2
];
bt_sg
[
m
].
dGGC
[
0
]
=
bt_sg
[
m
].
dEEC
[
0
]
*
UT
+
EEC
*
bt_sg
[
m
].
dUT
[
0
];
bt_sg
[
m
].
dGGC
[
1
]
=
bt_sg
[
m
].
dEEC
[
1
]
*
UT
+
EEC
*
bt_sg
[
m
].
dUT
[
1
];
bt_sg
[
m
].
dGGC
[
2
]
=
bt_sg
[
m
].
dEEC
[
2
]
*
UT
+
EEC
*
bt_sg
[
m
].
dUT
[
2
];
}
}
psign
=
1.0
;
if
(
1.0
+
sigma_a
[
iij
]
*
GGC
<
0.0
)
psign
=-
1.0
;
bndtmp0
=
1.0
/
sqrt
(
bndtmp
);
sigB1
=
psign
*
betaS_ij
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
)
*
bndtmp0
;
bndtmp
=-
0.5
*
bndtmp0
*
bndtmp0
*
bndtmp0
;
bndtmp1
=
psign
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
)
*
bndtmp0
+
psign
*
betaS_ij
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
)
*
bndtmp
*
2.0
*
betaS_ij
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
)
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
);
bndtmp1
=
bndtmp1
*
dBetaS_ij
/
r_ij
;
bndtmp2
=
psign
*
betaS_ij
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
)
*
bndtmp
*
sigma_c
[
iij
];
bndtmp3
=
psign
*
betaS_ij
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
)
*
bndtmp
*
sigma_c
[
iij
]
*
sigma_a
[
iij
];
bndtmp4
=
psign
*
betaS_ij
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
)
*
bndtmp
*
sigma_c
[
iij
]
*
sigma_a
[
iij
]
*
(
2.0
+
GGC
);
bndtmp5
=
sigma_a
[
iij
]
*
psign
*
betaS_ij
*
bndtmp0
+
psign
*
betaS_ij
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
)
*
bndtmp
*
(
2.0
*
(
FF
+
sigma_delta
[
iij
]
*
sigma_delta
[
iij
])
*
(
1.0
+
sigma_a
[
iij
]
*
GGC
)
*
sigma_a
[
iij
]
+
sigma_c
[
iij
]
*
sigma_a
[
iij
]
*
FFC
);
setting
=
0
;
for
(
m
=
0
;
m
<
nb_t
;
m
++
)
{
if
((
bt_sg
[
m
].
i
>-
1
)
&&
(
bt_sg
[
m
].
j
>-
1
))
{
temp_kk
=
bt_sg
[
m
].
temp
;
if
(
temp_kk
==
temp_ij
&&
setting
==
0
)
{
bt_sg
[
m
].
dSigB1
[
0
]
=
bndtmp1
*
dis_ij
[
0
]
+
(
bndtmp2
*
bt_sg
[
m
].
dAAC
[
0
]
+
bndtmp3
*
bt_sg
[
m
].
dEE
[
0
]
+
bndtmp4
*
bt_sg
[
m
].
dFFC
[
0
]
+
bndtmp5
*
bt_sg
[
m
].
dGGC
[
0
]);
bt_sg
[
m
].
dSigB1
[
1
]
=
bndtmp1
*
dis_ij
[
1
]
+
(
bndtmp2
*
bt_sg
[
m
].
dAAC
[
1
]
+
bndtmp3
*
bt_sg
[
m
].
dEE
[
1
]
+
bndtmp4
*
bt_sg
[
m
].
dFFC
[
1
]
+
bndtmp5
*
bt_sg
[
m
].
dGGC
[
1
]);
bt_sg
[
m
].
dSigB1
[
2
]
=
bndtmp1
*
dis_ij
[
2
]
+
(
bndtmp2
*
bt_sg
[
m
].
dAAC
[
2
]
+
bndtmp3
*
bt_sg
[
m
].
dEE
[
2
]
+
bndtmp4
*
bt_sg
[
m
].
dFFC
[
2
]
+
bndtmp5
*
bt_sg
[
m
].
dGGC
[
2
]);
setting
=
1
;
}
else
if
(
temp_kk
==
temp_ji
&&
setting
==
0
)
{
bt_sg
[
m
].
dSigB1
[
0
]
=-
bndtmp1
*
dis_ij
[
0
]
+
(
bndtmp2
*
bt_sg
[
m
].
dAAC
[
0
]
+
bndtmp3
*
bt_sg
[
m
].
dEE
[
0
]
+
bndtmp4
*
bt_sg
[
m
].
dFFC
[
0
]
+
bndtmp5
*
bt_sg
[
m
].
dGGC
[
0
]);
bt_sg
[
m
].
dSigB1
[
1
]
=-
bndtmp1
*
dis_ij
[
1
]
+
(
bndtmp2
*
bt_sg
[
m
].
dAAC
[
1
]
+
bndtmp3
*
bt_sg
[
m
].
dEE
[
1
]
+
bndtmp4
*
bt_sg
[
m
].
dFFC
[
1
]
+
bndtmp5
*
bt_sg
[
m
].
dGGC
[
1
]);
bt_sg
[
m
].
dSigB1
[
2
]
=-
bndtmp1
*
dis_ij
[
2
]
+
(
bndtmp2
*
bt_sg
[
m
].
dAAC
[
2
]
+
bndtmp3
*
bt_sg
[
m
].
dEE
[
2
]
+
bndtmp4
*
bt_sg
[
m
].
dFFC
[
2
]
+
bndtmp5
*
bt_sg
[
m
].
dGGC
[
2
]);
setting
=
1
;
}
else
{
bt_sg
[
m
].
dSigB1
[
0
]
=
(
bndtmp2
*
bt_sg
[
m
].
dAAC
[
0
]
+
bndtmp3
*
bt_sg
[
m
].
dEE
[
0
]
+
bndtmp4
*
bt_sg
[
m
].
dFFC
[
0
]
+
bndtmp5
*
bt_sg
[
m
].
dGGC
[
0
]);
bt_sg
[
m
].
dSigB1
[
1
]
=
(
bndtmp2
*
bt_sg
[
m
].
dAAC
[
1
]
+
bndtmp3
*
bt_sg
[
m
].
dEE
[
1
]
+
bndtmp4
*
bt_sg
[
m
].
dFFC
[
1
]
+
bndtmp5
*
bt_sg
[
m
].
dGGC
[
1
]);
bt_sg
[
m
].
dSigB1
[
2
]
=
(
bndtmp2
*
bt_sg
[
m
].
dAAC
[
2
]
+
bndtmp3
*
bt_sg
[
m
].
dEE
[
2
]
+
bndtmp4
*
bt_sg
[
m
].
dFFC
[
2
]
+
bndtmp5
*
bt_sg
[
m
].
dGGC
[
2
]);
}
}
}
}
}
//This loop is to ensure there is not an error for atoms with no neighbors (deposition)
// sigB is the final expression for (a) Eq. 6 and (b) Eq. 11
if
(
nb_t
==
0
)
{
if
(
j
>
i
)
{
bt_sg
[
0
].
dSigB1
[
0
]
=
bndtmp1
*
dis_ij
[
0
];
bt_sg
[
0
].
dSigB1
[
1
]
=
bndtmp1
*
dis_ij
[
1
];
bt_sg
[
0
].
dSigB1
[
2
]
=
bndtmp1
*
dis_ij
[
2
];
}
else
{
bt_sg
[
0
].
dSigB1
[
0
]
=-
bndtmp1
*
dis_ij
[
0
];
bt_sg
[
0
].
dSigB1
[
1
]
=-
bndtmp1
*
dis_ij
[
1
];
bt_sg
[
0
].
dSigB1
[
2
]
=-
bndtmp1
*
dis_ij
[
2
];
}
for
(
pp
=
0
;
pp
<
3
;
pp
++
)
{
bt_sg
[
0
].
dAA
[
pp
]
=
0.0
;
bt_sg
[
0
].
dBB
[
pp
]
=
0.0
;
bt_sg
[
0
].
dAAC
[
pp
]
=
0.0
;
bt_sg
[
0
].
dSigB1
[
pp
]
=
0.0
;
bt_sg
[
0
].
dSigB
[
pp
]
=
0.0
;
if
(
sigma_f
[
iij
]
!=
0.5
&&
sigma_k
[
iij
]
!=
0.0
)
{
bt_sg
[
0
].
dCC
[
pp
]
=
0.0
;
bt_sg
[
0
].
dDD
[
pp
]
=
0.0
;
bt_sg
[
0
].
dEE
[
pp
]
=
0.0
;
bt_sg
[
0
].
dEE1
[
pp
]
=
0.0
;
bt_sg
[
0
].
dFF
[
pp
]
=
0.0
;
bt_sg
[
0
].
dBBC
[
pp
]
=
0.0
;
bt_sg
[
0
].
dCCC
[
pp
]
=
0.0
;
bt_sg
[
0
].
dDDC
[
pp
]
=
0.0
;
bt_sg
[
0
].
dEEC
[
pp
]
=
0.0
;
bt_sg
[
0
].
dFFC
[
pp
]
=
0.0
;
bt_sg
[
0
].
dGGC
[
pp
]
=
0.0
;
bt_sg
[
0
].
dUT
[
pp
]
=
0.0
;
}
}
bt_sg
[
0
].
i
=
i
;
bt_sg
[
0
].
j
=
j
;
bt_sg
[
0
].
temp
=
temp_ij
;
nb_t
++
;
if
(
nb_t
>
nb_sg
)
{
new_n_tot
=
nb_sg
+
maxneigh
;
grow_sigma
(
nb_sg
,
new_n_tot
);
nb_sg
=
new_n_tot
;
}
}
ps
=
sigB1
*
rdBO
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nBOt
-
1
<
ks
)
ks
=
nBOt
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
dsigB1
=
((
FsigBO3
[
iij
][
ks
-
1
]
*
ps
+
FsigBO2
[
iij
][
ks
-
1
])
*
ps
+
FsigBO1
[
iij
][
ks
-
1
])
*
ps
+
FsigBO
[
iij
][
ks
-
1
];
dsigB2
=
(
FsigBO6
[
iij
][
ks
-
1
]
*
ps
+
FsigBO5
[
iij
][
ks
-
1
])
*
ps
+
FsigBO4
[
iij
][
ks
-
1
];
for
(
m
=
0
;
m
<
nb_t
;
m
++
)
{
if
((
bt_sg
[
m
].
i
>-
1
)
&&
(
bt_sg
[
m
].
j
>-
1
))
{
temp_kk
=
bt_sg
[
m
].
temp
;
bt_i
=
bt_sg
[
m
].
i
;
bt_j
=
bt_sg
[
m
].
j
;
if
(
sigma_f
[
iij
]
==
0.5
&&
sigma_k
[
iij
]
==
0.0
)
{
sigB
=
dsigB1
;
pp1
=
2.0
*
betaS_ij
;
for
(
pp
=
0
;
pp
<
3
;
pp
++
)
{
bt_sg
[
m
].
dSigB
[
pp
]
=
dsigB2
*
bt_sg
[
m
].
dSigB1
[
pp
];
}
for
(
pp
=
0
;
pp
<
3
;
pp
++
)
{
ftmp
[
pp
]
=
pp1
*
bt_sg
[
m
].
dSigB
[
pp
];
f
[
bt_i
][
pp
]
-=
ftmp
[
pp
];
f
[
bt_j
][
pp
]
+=
ftmp
[
pp
];
}
if
(
evflag
)
{
ev_tally_xyz
(
bt_i
,
bt_j
,
nlocal
,
newton_pair
,
0.0
,
0.0
,
ftmp
[
0
],
ftmp
[
1
]
,
ftmp
[
2
],
xtmp
[
0
],
xtmp
[
1
],
xtmp
[
2
]);
}
}
else
{
part0
=
(
FF
+
0.5
*
AAC
+
small5
);
part1
=
(
sigma_f
[
iij
]
-
0.5
)
*
sigma_k
[
iij
];
part2
=
1.0
-
part1
*
EE1
/
part0
;
part3
=
dsigB1
*
part1
/
part0
;
part4
=
part3
/
part0
*
EE1
;
// sigB is the final expression for (a) Eq. 6 and (b) Eq. 11
sigB
=
dsigB1
*
part2
;
pp1
=
2.0
*
betaS_ij
;
xtmp
[
0
]
=
x
[
bt_j
][
0
]
-
x
[
bt_i
][
0
];
xtmp
[
1
]
=
x
[
bt_j
][
1
]
-
x
[
bt_i
][
1
];
xtmp
[
2
]
=
x
[
bt_j
][
2
]
-
x
[
bt_i
][
2
];
for
(
pp
=
0
;
pp
<
3
;
pp
++
)
{
bt_sg
[
m
].
dSigB
[
pp
]
=
dsigB2
*
part2
*
bt_sg
[
m
].
dSigB1
[
pp
]
-
part3
*
bt_sg
[
m
].
dEE1
[
pp
]
+
part4
*
(
bt_sg
[
m
].
dFF
[
pp
]
+
0.5
*
bt_sg
[
m
].
dAAC
[
pp
]);
}
for
(
pp
=
0
;
pp
<
3
;
pp
++
)
{
ftmp
[
pp
]
=
pp1
*
bt_sg
[
m
].
dSigB
[
pp
];
f
[
bt_i
][
pp
]
-=
ftmp
[
pp
];
f
[
bt_j
][
pp
]
+=
ftmp
[
pp
];
}
if
(
evflag
)
{
ev_tally_xyz
(
bt_i
,
bt_j
,
nlocal
,
newton_pair
,
0.0
,
0.0
,
ftmp
[
0
],
ftmp
[
1
]
,
ftmp
[
2
],
xtmp
[
0
],
xtmp
[
1
],
xtmp
[
2
]);
}
}
}
}
}
}
}
return
(
sigB
);
}
/* ---------------------------------------------------------------------- */
/* The formulation differs slightly to avoid negative square roots
in the calculation of Theta_pi,ij of (a) Eq. 36 and (b) Eq. 18
see (d) */
/* ---------------------------------------------------------------------- */
double
PairBOP
::
PiBo
(
int
itmp
,
int
jtmp
)
{
int
new_n_tot
;
int
i
,
j
,
k
,
kp
,
m
,
n
,
pp
,
nb_t
;
int
iij
,
iik
,
iikp
,
ji
,
ki
,
ijkp
,
ijk
;
int
nsearch
,
ncmp
;
tagint
i_tag
,
j_tag
;
int
ltmp
,
ktmp
;
int
pi_flag
,
ks
;
int
nlocal
;
int
*
ilist
,
*
iilist
,
*
jlist
;
int
**
firstneigh
;
int
itype
,
jtype
,
ktype
,
kptype
;
int
temp_ij
,
temp_ik
,
temp_ikp
;
int
temp_jk
,
temp_jkp
;
int
nb_ij
,
nb_ik
,
nb_jk
,
nb_ikp
,
nb_jkp
;
int
bt_i
,
bt_j
;
int
pass_ij
,
pass_ik
,
pass_ikp
;
int
pass_jkp
,
pass_jk
;
int
njik
,
ngj
,
ngk
;
int
nkikp
,
njikp
,
nglj
;
int
ngl
,
ngi
,
nkjkp
;
int
nijkp
,
ngli
,
nijk
;
int
ang_jik
,
ang_jikp
,
ang_kikp
;
int
ang_ijk
,
ang_ijkp
,
ang_kjkp
;
int
ni_ij
,
ni_ji
,
ni_ik
,
ni_ikp
;
int
ni_ki
,
ni_jk
,
ni_jkp
;
int
temp_ji
,
temp_ki
;
int
nlistj
,
nlisti
;
double
AA
,
BB
,
CC
;
double
cosSq
,
sinFactor
,
cosFactor
;
double
cosSq1
,
dotV
,
BBrt
,
AB1
,
AB2
;
double
BBrtR
,
ABrtR1
,
ABrtR2
;
double
angFactor
,
angFactor1
,
angFactor2
;
double
angFactor3
,
angFactor4
,
angRfactor
;
double
dAngR1
,
dAngR2
,
agpdpr3
;
double
agpdpr1
,
agpdpr2
,
app1
,
app2
,
app3
;
double
betaCapSq1
,
dbetaCapSq1
;
double
betaCapSq2
,
dbetaCapSq2
;
double
betaCapSum
,
ps
;
double
ftmp
[
3
],
xtmp
[
3
];
double
dPiB1
,
dPiB2
,
dPiB3
,
pp2
;
double
dis_ij
[
3
],
rsq_ij
,
r_ij
;
double
betaP_ij
,
dBetaP_ij
;
double
dis_ik
[
3
],
rsq_ik
,
r_ik
;
double
betaS_ik
,
dBetaS_ik
;
double
betaP_ik
,
dBetaP_ik
;
double
dis_ikp
[
3
],
rsq_ikp
,
r_ikp
;
double
betaS_ikp
,
dBetaS_ikp
;
double
betaP_ikp
,
dBetaP_ikp
;
double
dis_jk
[
3
],
rsq_jk
,
r_jk
;
double
betaS_jk
,
dBetaS_jk
;
double
betaP_jk
,
dBetaP_jk
;
double
dis_jkp
[
3
],
rsq_jkp
,
r_jkp
;
double
betaS_jkp
,
dBetaS_jkp
;
double
betaP_jkp
,
dBetaP_jkp
;
double
cosAng_jik
,
dcA_jik
[
3
][
2
];
double
cosAng_jikp
,
dcA_jikp
[
3
][
2
];
double
cosAng_kikp
,
dcA_kikp
[
3
][
2
];
double
cosAng_ijk
,
dcA_ijk
[
3
][
2
];
double
cosAng_ijkp
,
dcA_ijkp
[
3
][
2
];
double
cosAng_kjkp
,
dcA_kjkp
[
3
][
2
];
int
newton_pair
=
force
->
newton_pair
;
double
**
f
=
atom
->
f
;
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
tagint
*
tag
=
atom
->
tag
;
nlocal
=
atom
->
nlocal
;
firstneigh
=
list
->
firstneigh
;
ilist
=
list
->
ilist
;
n
=
0
;
if
(
nb_pi
>
16
)
{
nb_pi
=
16
;
}
if
(
nb_pi
==
0
)
{
nb_pi
=
(
maxneigh
)
*
(
maxneigh
/
2
);
}
// Loop over all local atoms for i
if
(
allocate_pi
)
{
destroy_pi
();
}
create_pi
(
nb_pi
);
piB
=
0
;
i
=
ilist
[
itmp
];
i_tag
=
tag
[
i
];
itype
=
map
[
type
[
i
]]
+
1
;
// j is a loop over all neighbors of i
iilist
=
firstneigh
[
i
];
for
(
m
=
0
;
m
<
nb_pi
;
m
++
)
{
for
(
pp
=
0
;
pp
<
3
;
pp
++
)
{
bt_pi
[
m
].
dAA
[
pp
]
=
0.0
;
bt_pi
[
m
].
dBB
[
pp
]
=
0.0
;
bt_pi
[
m
].
dPiB
[
pp
]
=
0.0
;
}
bt_pi
[
m
].
i
=-
1
;
bt_pi
[
m
].
j
=-
1
;
}
nb_t
=
0
;
temp_ij
=
BOP_index
[
i
]
+
jtmp
;
ni_ij
=
neigh_index
[
temp_ij
];
j
=
iilist
[
ni_ij
];
jlist
=
firstneigh
[
j
];
j_tag
=
tag
[
j
];
jtype
=
map
[
type
[
j
]]
+
1
;
ftmp
[
0
]
=
0.0
;
ftmp
[
1
]
=
0.0
;
ftmp
[
2
]
=
0.0
;
if
(
j_tag
>=
i_tag
)
{
if
(
itype
==
jtype
)
iij
=
itype
-
1
;
else
if
(
itype
<
jtype
)
iij
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
jtype
-
1
;
else
iij
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
itype
-
1
;
if
(
pi_a
[
iij
]
==
0
)
{
nPiBk
=
0
;
piB
=
0
;
}
else
{
AA
=
0.0
;
BB
=
0.0
;
nPiBk
=
0
;
nlistj
=
BOP_total
[
j
];
for
(
ji
=
0
;
ji
<
nlistj
;
ji
++
)
{
temp_ji
=
BOP_index
[
j
]
+
ji
;
ni_ji
=
neigh_index
[
temp_ji
];
if
(
x
[
jlist
[
ni_ji
]][
0
]
==
x
[
i
][
0
])
{
if
(
x
[
jlist
[
ni_ji
]][
1
]
==
x
[
i
][
1
])
{
if
(
x
[
jlist
[
ni_ji
]][
2
]
==
x
[
i
][
2
])
{
break
;
}
}
}
}
nb_ij
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_pi
)
{
new_n_tot
=
nb_pi
+
maxneigh
;
grow_pi
(
nb_pi
,
new_n_tot
);
nb_pi
=
new_n_tot
;
}
bt_pi
[
nb_ij
].
i
=
i
;
bt_pi
[
nb_ij
].
j
=
j
;
bt_pi
[
nb_ij
].
temp
=
temp_ij
;
pass_ij
=
0
;
if
(
otfly
==
1
)
{
dis_ij
[
0
]
=
x
[
j
][
0
]
-
x
[
i
][
0
];
dis_ij
[
1
]
=
x
[
j
][
1
]
-
x
[
i
][
1
];
dis_ij
[
2
]
=
x
[
j
][
2
]
-
x
[
i
][
2
];
rsq_ij
=
dis_ij
[
0
]
*
dis_ij
[
0
]
+
dis_ij
[
1
]
*
dis_ij
[
1
]
+
dis_ij
[
2
]
*
dis_ij
[
2
];
r_ij
=
sqrt
(
rsq_ij
);
if
(
r_ij
<=
rcut
[
iij
])
{
pass_ij
=
1
;
ps
=
r_ij
*
rdr
[
iij
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaP_ij
=
((
pBetaP3
[
iij
][
ks
-
1
]
*
ps
+
pBetaP2
[
iij
][
ks
-
1
])
*
ps
+
pBetaP1
[
iij
][
ks
-
1
])
*
ps
+
pBetaP
[
iij
][
ks
-
1
];
dBetaP_ij
=
(
pBetaP6
[
iij
][
ks
-
1
]
*
ps
+
pBetaP5
[
iij
][
ks
-
1
])
*
ps
+
pBetaP4
[
iij
][
ks
-
1
];
}
}
else
{
if
(
neigh_flag
[
temp_ij
])
{
pass_ij
=
1
;
dis_ij
[
0
]
=
disij
[
0
][
temp_ij
];
dis_ij
[
1
]
=
disij
[
1
][
temp_ij
];
dis_ij
[
2
]
=
disij
[
2
][
temp_ij
];
r_ij
=
rij
[
temp_ij
];
betaP_ij
=
betaP
[
temp_ij
];
dBetaP_ij
=
dBetaP
[
temp_ij
];
}
}
// j and k are different neighbors of i
AA
=
0.0
;
BB
=
0.0
;
if
(
pass_ij
==
1
)
{
nPiBk
=
0
;
nlisti
=
BOP_total
[
i
];
for
(
ktmp
=
0
;
ktmp
<
nlisti
;
ktmp
++
)
{
if
(
ktmp
!=
jtmp
)
{
temp_ik
=
BOP_index
[
i
]
+
ktmp
;
ni_ik
=
neigh_index
[
temp_ik
];
k
=
iilist
[
ni_ik
];
ktype
=
map
[
type
[
k
]]
+
1
;
if
(
itype
==
ktype
)
iik
=
itype
-
1
;
else
if
(
itype
<
ktype
)
iik
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
ktype
-
1
;
else
iik
=
ktype
*
bop_types
-
ktype
*
(
ktype
+
1
)
/
2
+
itype
-
1
;
pass_ik
=
0
;
if
(
otfly
==
1
)
{
dis_ik
[
0
]
=
x
[
k
][
0
]
-
x
[
i
][
0
];
dis_ik
[
1
]
=
x
[
k
][
1
]
-
x
[
i
][
1
];
dis_ik
[
2
]
=
x
[
k
][
2
]
-
x
[
i
][
2
];
rsq_ik
=
dis_ik
[
0
]
*
dis_ik
[
0
]
+
dis_ik
[
1
]
*
dis_ik
[
1
]
+
dis_ik
[
2
]
*
dis_ik
[
2
];
r_ik
=
sqrt
(
rsq_ik
);
if
(
r_ik
<=
rcut
[
iik
])
{
pass_ik
=
1
;
ps
=
r_ik
*
rdr
[
iik
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_ik
=
((
pBetaS3
[
iik
][
ks
-
1
]
*
ps
+
pBetaS2
[
iik
][
ks
-
1
])
*
ps
+
pBetaS1
[
iik
][
ks
-
1
])
*
ps
+
pBetaS
[
iik
][
ks
-
1
];
dBetaS_ik
=
(
pBetaS6
[
iik
][
ks
-
1
]
*
ps
+
pBetaS5
[
iik
][
ks
-
1
])
*
ps
+
pBetaS4
[
iik
][
ks
-
1
];
betaP_ik
=
((
pBetaP3
[
iik
][
ks
-
1
]
*
ps
+
pBetaP2
[
iik
][
ks
-
1
])
*
ps
+
pBetaP1
[
iik
][
ks
-
1
])
*
ps
+
pBetaP
[
iik
][
ks
-
1
];
dBetaP_ik
=
(
pBetaP6
[
iik
][
ks
-
1
]
*
ps
+
pBetaP5
[
iik
][
ks
-
1
])
*
ps
+
pBetaP4
[
iik
][
ks
-
1
];
cosAng_jik
=
(
dis_ij
[
0
]
*
dis_ik
[
0
]
+
dis_ij
[
1
]
*
dis_ik
[
1
]
+
dis_ij
[
2
]
*
dis_ik
[
2
])
/
(
r_ij
*
r_ik
);
dcA_jik
[
0
][
0
]
=
(
dis_ik
[
0
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ij
[
0
]
*
r_ik
*
r_ik
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
dcA_jik
[
1
][
0
]
=
(
dis_ik
[
1
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ij
[
1
]
*
r_ik
*
r_ik
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
dcA_jik
[
2
][
0
]
=
(
dis_ik
[
2
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ij
[
2
]
*
r_ik
*
r_ik
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
dcA_jik
[
0
][
1
]
=
(
dis_ij
[
0
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ik
[
0
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
dcA_jik
[
1
][
1
]
=
(
dis_ij
[
1
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ik
[
1
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
dcA_jik
[
2
][
1
]
=
(
dis_ij
[
2
]
*
r_ij
*
r_ik
-
cosAng_jik
*
dis_ik
[
2
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ik
*
r_ik
);
}
}
else
{
if
(
neigh_flag
[
temp_ik
])
{
pass_ik
=
1
;
dis_ik
[
0
]
=
disij
[
0
][
temp_ik
];
dis_ik
[
1
]
=
disij
[
1
][
temp_ik
];
dis_ik
[
2
]
=
disij
[
2
][
temp_ik
];
r_ik
=
rij
[
temp_ik
];
betaS_ik
=
betaS
[
temp_ik
];
dBetaS_ik
=
dBetaS
[
temp_ik
];
betaP_ik
=
betaP
[
temp_ik
];
dBetaP_ik
=
dBetaP
[
temp_ik
];
if
(
jtmp
<
ktmp
)
{
njik
=
jtmp
*
(
2
*
nlisti
-
jtmp
-
1
)
/
2
+
(
ktmp
-
jtmp
)
-
1
;
ngj
=
0
;
ngk
=
1
;
}
else
{
njik
=
ktmp
*
(
2
*
nlisti
-
ktmp
-
1
)
/
2
+
(
jtmp
-
ktmp
)
-
1
;
ngj
=
1
;
ngk
=
0
;
}
ang_jik
=
cos_index
[
i
]
+
njik
;
cosAng_jik
=
cosAng
[
ang_jik
];
dcA_jik
[
0
][
0
]
=
dcAng
[
ang_jik
][
0
][
ngj
];
dcA_jik
[
1
][
0
]
=
dcAng
[
ang_jik
][
1
][
ngj
];
dcA_jik
[
2
][
0
]
=
dcAng
[
ang_jik
][
2
][
ngj
];
dcA_jik
[
0
][
1
]
=
dcAng
[
ang_jik
][
0
][
ngk
];
dcA_jik
[
1
][
1
]
=
dcAng
[
ang_jik
][
1
][
ngk
];
dcA_jik
[
2
][
1
]
=
dcAng
[
ang_jik
][
2
][
ngk
];
}
}
if
(
pass_ik
==
1
)
{
nb_ik
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_pi
)
{
new_n_tot
=
nb_pi
+
maxneigh
;
grow_pi
(
nb_pi
,
new_n_tot
);
nb_pi
=
new_n_tot
;
}
bt_pi
[
nb_ik
].
i
=
i
;
bt_pi
[
nb_ik
].
j
=
k
;
bt_pi
[
nb_ik
].
temp
=
temp_ik
;
cosSq
=
cosAng_jik
*
cosAng_jik
;
sinFactor
=
.5
*
(
1.0
-
cosSq
)
*
pi_p
[
itype
-
1
]
*
betaS_ik
;
cosFactor
=
.5
*
(
1.0
+
cosSq
)
*
betaP_ik
;
betaCapSq1
=
pi_p
[
itype
-
1
]
*
betaS_ik
*
betaS_ik
-
betaP_ik
*
betaP_ik
;
dbetaCapSq1
=
2.0
*
pi_p
[
itype
-
1
]
*
betaS_ik
*
dBetaS_ik
-
2.0
*
betaP_ik
*
dBetaP_ik
;
//AA is Eq. 37 (a) and Eq. 19 (b) or i atoms
//1st BB is first term of Eq. 38 (a) where j and k =neighbors i
AA
=
AA
+
sinFactor
*
betaS_ik
+
cosFactor
*
betaP_ik
;
BB
=
BB
+
.25
*
(
1.0
-
cosSq
)
*
(
1.0
-
cosSq
)
*
betaCapSq1
*
betaCapSq1
;
//agpdpr1 is derivative of AA w.r.t. for atom i w.r.t. Beta(r_ik)
//agpdpr2 is derivative of BB w.r.t. for atom i w.r.t. Beta(r_ik)
//app1 is derivative of AA w.r.t. for atom i w.r.t. cos(theta_jik)
//app2 is derivative of BB w.r.t. for atom i w.r.t. cos(theta_jik)
agpdpr1
=
(
2.0
*
sinFactor
*
dBetaS_ik
+
2.0
*
cosFactor
*
dBetaP_ik
)
/
r_ik
;
app1
=
cosAng_jik
*
(
-
pi_p
[
itype
-
1
]
*
betaS_ik
*
betaS_ik
+
betaP_ik
*
betaP_ik
);
app2
=-
(
1.0
-
cosSq
)
*
cosAng_jik
*
betaCapSq1
*
betaCapSq1
;
agpdpr2
=
.5
*
(
1.0
-
cosSq
)
*
(
1.0
-
cosSq
)
*
betaCapSq1
*
dbetaCapSq1
/
r_ik
;
itypePiBk
[
nPiBk
]
=
k
;
bt_pi
[
nb_ij
].
dAA
[
0
]
+=
app1
*
dcA_jik
[
0
][
0
];
bt_pi
[
nb_ij
].
dAA
[
1
]
+=
app1
*
dcA_jik
[
1
][
0
];
bt_pi
[
nb_ij
].
dAA
[
2
]
+=
app1
*
dcA_jik
[
2
][
0
];
bt_pi
[
nb_ij
].
dBB
[
0
]
+=
app2
*
dcA_jik
[
0
][
0
];
bt_pi
[
nb_ij
].
dBB
[
1
]
+=
app2
*
dcA_jik
[
1
][
0
];
bt_pi
[
nb_ij
].
dBB
[
2
]
+=
app2
*
dcA_jik
[
2
][
0
];
bt_pi
[
nb_ik
].
dAA
[
0
]
+=
agpdpr1
*
dis_ik
[
0
]
+
app1
*
dcA_jik
[
0
][
1
];
bt_pi
[
nb_ik
].
dAA
[
1
]
+=
agpdpr1
*
dis_ik
[
1
]
+
app1
*
dcA_jik
[
1
][
1
];
bt_pi
[
nb_ik
].
dAA
[
2
]
+=
agpdpr1
*
dis_ik
[
2
]
+
app1
*
dcA_jik
[
2
][
1
];
bt_pi
[
nb_ik
].
dBB
[
0
]
+=
app2
*
dcA_jik
[
0
][
1
]
+
agpdpr2
*
dis_ik
[
0
];
bt_pi
[
nb_ik
].
dBB
[
1
]
+=
app2
*
dcA_jik
[
1
][
1
]
+
agpdpr2
*
dis_ik
[
1
];
bt_pi
[
nb_ik
].
dBB
[
2
]
+=
app2
*
dcA_jik
[
2
][
1
]
+
agpdpr2
*
dis_ik
[
2
];
// j and k and k' are different neighbors of i
for
(
ltmp
=
0
;
ltmp
<
ktmp
;
ltmp
++
)
{
if
(
ltmp
!=
jtmp
)
{
temp_ikp
=
BOP_index
[
i
]
+
ltmp
;
ni_ikp
=
neigh_index
[
temp_ikp
];
kp
=
iilist
[
ni_ikp
];
kptype
=
map
[
type
[
kp
]]
+
1
;
for
(
nsearch
=
0
;
nsearch
<
nPiBk
;
nsearch
++
)
{
ncmp
=
itypePiBk
[
nsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
kp
][
2
])
{
break
;
}
}
}
}
if
(
itype
==
kptype
)
iikp
=
itype
-
1
;
else
if
(
itype
<
kptype
)
iikp
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
kptype
-
1
;
else
iikp
=
kptype
*
bop_types
-
kptype
*
(
kptype
+
1
)
/
2
+
itype
-
1
;
pass_ikp
=
0
;
if
(
otfly
==
1
)
{
dis_ikp
[
0
]
=
x
[
kp
][
0
]
-
x
[
i
][
0
];
dis_ikp
[
1
]
=
x
[
kp
][
1
]
-
x
[
i
][
1
];
dis_ikp
[
2
]
=
x
[
kp
][
2
]
-
x
[
i
][
2
];
rsq_ikp
=
dis_ikp
[
0
]
*
dis_ikp
[
0
]
+
dis_ikp
[
1
]
*
dis_ikp
[
1
]
+
dis_ikp
[
2
]
*
dis_ikp
[
2
];
r_ikp
=
sqrt
(
rsq_ikp
);
if
(
r_ikp
<=
rcut
[
iikp
])
{
pass_ikp
=
1
;
ps
=
r_ikp
*
rdr
[
iikp
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_ikp
=
((
pBetaS3
[
iikp
][
ks
-
1
]
*
ps
+
pBetaS2
[
iikp
][
ks
-
1
])
*
ps
+
pBetaS1
[
iikp
][
ks
-
1
])
*
ps
+
pBetaS
[
iikp
][
ks
-
1
];
dBetaS_ikp
=
(
pBetaS6
[
iikp
][
ks
-
1
]
*
ps
+
pBetaS5
[
iikp
][
ks
-
1
])
*
ps
+
pBetaS4
[
iikp
][
ks
-
1
];
betaP_ikp
=
((
pBetaP3
[
iikp
][
ks
-
1
]
*
ps
+
pBetaP2
[
iikp
][
ks
-
1
])
*
ps
+
pBetaP1
[
iikp
][
ks
-
1
])
*
ps
+
pBetaP
[
iikp
][
ks
-
1
];
dBetaP_ikp
=
(
pBetaP6
[
iikp
][
ks
-
1
]
*
ps
+
pBetaP5
[
iikp
][
ks
-
1
])
*
ps
+
pBetaP4
[
iikp
][
ks
-
1
];
cosAng_jikp
=
(
dis_ij
[
0
]
*
dis_ikp
[
0
]
+
dis_ij
[
1
]
*
dis_ikp
[
1
]
+
dis_ij
[
2
]
*
dis_ikp
[
2
])
/
(
r_ij
*
r_ikp
);
dcA_jikp
[
0
][
0
]
=
(
dis_ikp
[
0
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ij
[
0
]
*
r_ikp
*
r_ikp
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
1
][
0
]
=
(
dis_ikp
[
1
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ij
[
1
]
*
r_ikp
*
r_ikp
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
2
][
0
]
=
(
dis_ikp
[
2
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ij
[
2
]
*
r_ikp
*
r_ikp
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
0
][
1
]
=
(
dis_ij
[
0
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ikp
[
0
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
1
][
1
]
=
(
dis_ij
[
1
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ikp
[
1
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
2
][
1
]
=
(
dis_ij
[
2
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ikp
[
2
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
cosAng_kikp
=
(
dis_ik
[
0
]
*
dis_ikp
[
0
]
+
dis_ik
[
1
]
*
dis_ikp
[
1
]
+
dis_ik
[
2
]
*
dis_ikp
[
2
])
/
(
r_ik
*
r_ikp
);
dcA_kikp
[
0
][
0
]
=
(
dis_ikp
[
0
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ik
[
0
]
*
r_ikp
*
r_ikp
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
dcA_kikp
[
1
][
0
]
=
(
dis_ikp
[
1
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ik
[
1
]
*
r_ikp
*
r_ikp
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
dcA_kikp
[
2
][
0
]
=
(
dis_ikp
[
2
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ik
[
2
]
*
r_ikp
*
r_ikp
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
dcA_kikp
[
0
][
1
]
=
(
dis_ik
[
0
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ikp
[
0
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
dcA_kikp
[
1
][
1
]
=
(
dis_ik
[
1
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ikp
[
1
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
dcA_kikp
[
2
][
1
]
=
(
dis_ik
[
2
]
*
r_ik
*
r_ikp
-
cosAng_kikp
*
dis_ikp
[
2
]
*
r_ik
*
r_ik
)
/
(
r_ik
*
r_ik
*
r_ikp
*
r_ikp
);
}
}
else
{
if
(
neigh_flag
[
temp_ikp
])
{
pass_ikp
=
1
;
dis_ikp
[
0
]
=
disij
[
0
][
temp_ikp
];
dis_ikp
[
1
]
=
disij
[
1
][
temp_ikp
];
dis_ikp
[
2
]
=
disij
[
2
][
temp_ikp
];
r_ikp
=
rij
[
temp_ikp
];
betaS_ikp
=
betaS
[
temp_ikp
];
dBetaS_ikp
=
dBetaS
[
temp_ikp
];
betaP_ikp
=
betaP
[
temp_ikp
];
dBetaP_ikp
=
dBetaP
[
temp_ikp
];
nkikp
=
ltmp
*
(
2
*
nlisti
-
ltmp
-
1
)
/
2
+
(
ktmp
-
ltmp
)
-
1
;
if
(
jtmp
<
ltmp
)
{
njikp
=
jtmp
*
(
2
*
nlisti
-
jtmp
-
1
)
/
2
+
(
ltmp
-
jtmp
)
-
1
;
nglj
=
0
;
ngl
=
1
;
}
else
{
njikp
=
ltmp
*
(
2
*
nlisti
-
ltmp
-
1
)
/
2
+
(
jtmp
-
ltmp
)
-
1
;
nglj
=
1
;
ngl
=
0
;
}
ang_jikp
=
cos_index
[
i
]
+
njikp
;
cosAng_jikp
=
cosAng
[
ang_jikp
];
dcA_jikp
[
0
][
0
]
=
dcAng
[
ang_jikp
][
0
][
nglj
];
dcA_jikp
[
1
][
0
]
=
dcAng
[
ang_jikp
][
1
][
nglj
];
dcA_jikp
[
2
][
0
]
=
dcAng
[
ang_jikp
][
2
][
nglj
];
dcA_jikp
[
0
][
1
]
=
dcAng
[
ang_jikp
][
0
][
ngl
];
dcA_jikp
[
1
][
1
]
=
dcAng
[
ang_jikp
][
1
][
ngl
];
dcA_jikp
[
2
][
1
]
=
dcAng
[
ang_jikp
][
2
][
ngl
];
ang_kikp
=
cos_index
[
i
]
+
nkikp
;
cosAng_kikp
=
cosAng
[
ang_kikp
];
dcA_kikp
[
0
][
0
]
=
dcAng
[
ang_kikp
][
0
][
1
];
dcA_kikp
[
1
][
0
]
=
dcAng
[
ang_kikp
][
1
][
1
];
dcA_kikp
[
2
][
0
]
=
dcAng
[
ang_kikp
][
2
][
1
];
dcA_kikp
[
0
][
1
]
=
dcAng
[
ang_kikp
][
0
][
0
];
dcA_kikp
[
1
][
1
]
=
dcAng
[
ang_kikp
][
1
][
0
];
dcA_kikp
[
2
][
1
]
=
dcAng
[
ang_kikp
][
2
][
0
];
}
}
if
(
pass_ikp
==
1
)
{
nb_ikp
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_pi
)
{
new_n_tot
=
nb_pi
+
maxneigh
;
grow_pi
(
nb_pi
,
new_n_tot
);
nb_pi
=
new_n_tot
;
}
bt_pi
[
nb_ikp
].
i
=
i
;
bt_pi
[
nb_ikp
].
j
=
kp
;
bt_pi
[
nb_ikp
].
temp
=
temp_ikp
;
betaCapSq2
=
pi_p
[
itype
-
1
]
*
betaS_ikp
*
betaS_ikp
-
betaP_ikp
*
betaP_ikp
;
dbetaCapSq2
=
2.0
*
pi_p
[
itype
-
1
]
*
betaS_ikp
*
dBetaS_ikp
-
2.0
*
betaP_ikp
*
dBetaP_ikp
;
cosSq1
=
cosAng_jikp
*
cosAng_jikp
;
angFactor
=
cosAng_kikp
-
cosAng_jikp
*
cosAng_jik
;
angFactor1
=
4.0
*
angFactor
;
angFactor2
=-
angFactor1
*
cosAng_jikp
+
2.0
*
cosAng_jik
*
(
1.0
-
cosSq1
);
angFactor3
=-
angFactor1
*
cosAng_jik
+
2.0
*
cosAng_jikp
*
(
1.0
-
cosSq
);
angFactor4
=
2.0
*
angFactor
*
angFactor
-
(
1.0
-
cosSq
)
*
(
1.0
-
cosSq1
);
betaCapSum
=
.5
*
betaCapSq1
*
betaCapSq2
;
//2nd BB is third term of Eq. 38 (a) where j , k and k'=neighbors i
BB
=
BB
+
betaCapSum
*
angFactor4
;
//agpdpr1 is derivative of BB w.r.t. for atom i w.r.t. Beta(r_ik)
//agpdpr2 is derivative of BB w.r.t. for atom i w.r.t. Beta(r_ik')
//app1 is derivative of BB 3rd term w.r.t. cos(theta_kik')
//app2 is derivative of BB 3rd term w.r.t. cos(theta_jik)
//app3 is derivative of BB 3rd term w.r.t. cos(theta_jik')
app1
=
betaCapSum
*
angFactor1
;
app2
=
betaCapSum
*
angFactor2
;
app3
=
betaCapSum
*
angFactor3
;
agpdpr1
=
.5
*
angFactor4
*
dbetaCapSq1
*
betaCapSq2
/
r_ik
;
agpdpr2
=
.5
*
angFactor4
*
betaCapSq1
*
dbetaCapSq2
/
r_ikp
;
bt_pi
[
nb_ij
].
dBB
[
0
]
+=
app2
*
dcA_jik
[
0
][
0
]
+
app3
*
dcA_jikp
[
0
][
0
];
bt_pi
[
nb_ij
].
dBB
[
1
]
+=
app2
*
dcA_jik
[
1
][
0
]
+
app3
*
dcA_jikp
[
1
][
0
];
bt_pi
[
nb_ij
].
dBB
[
2
]
+=
app2
*
dcA_jik
[
2
][
0
]
+
app3
*
dcA_jikp
[
2
][
0
];
bt_pi
[
nb_ik
].
dBB
[
0
]
+=
agpdpr1
*
dis_ik
[
0
]
+
app1
*
dcA_kikp
[
0
][
0
]
+
app2
*
dcA_jik
[
0
][
1
];
bt_pi
[
nb_ik
].
dBB
[
1
]
+=
agpdpr1
*
dis_ik
[
1
]
+
app1
*
dcA_kikp
[
1
][
0
]
+
app2
*
dcA_jik
[
1
][
1
];
bt_pi
[
nb_ik
].
dBB
[
2
]
+=
agpdpr1
*
dis_ik
[
2
]
+
app1
*
dcA_kikp
[
2
][
0
]
+
app2
*
dcA_jik
[
2
][
1
];
bt_pi
[
nb_ikp
].
dBB
[
0
]
+=
agpdpr2
*
dis_ikp
[
0
]
+
app1
*
dcA_kikp
[
0
][
1
]
+
app3
*
dcA_jikp
[
0
][
1
];
bt_pi
[
nb_ikp
].
dBB
[
1
]
+=
agpdpr2
*
dis_ikp
[
1
]
+
app1
*
dcA_kikp
[
1
][
1
]
+
app3
*
dcA_jikp
[
1
][
1
];
bt_pi
[
nb_ikp
].
dBB
[
2
]
+=
agpdpr2
*
dis_ikp
[
2
]
+
app1
*
dcA_kikp
[
2
][
1
]
+
app3
*
dcA_jikp
[
2
][
1
];
}
}
}
nPiBk
=
nPiBk
+
1
;
}
}
}
//j is a neighbor of i and k is a neighbor of j and equal to i
for
(
ki
=
0
;
ki
<
nlistj
;
ki
++
)
{
temp_ki
=
BOP_index
[
j
]
+
ki
;
ni_ki
=
neigh_index
[
temp_ki
];
k
=
jlist
[
ni_ki
];
if
(
x
[
k
][
0
]
==
x
[
i
][
0
])
{
if
(
x
[
k
][
1
]
==
x
[
i
][
1
])
{
if
(
x
[
k
][
2
]
==
x
[
i
][
2
])
{
break
;
}
}
}
}
//j is a neighbor of i and k is a neighbor of j not equal to i
for
(
ktmp
=
0
;
ktmp
<
nlistj
;
ktmp
++
)
{
if
(
ktmp
!=
ki
)
{
temp_jk
=
BOP_index
[
j
]
+
ktmp
;
ni_jk
=
neigh_index
[
temp_jk
];
k
=
jlist
[
ni_jk
];
ktype
=
map
[
type
[
k
]]
+
1
;
pi_flag
=
0
;
for
(
nsearch
=
0
;
nsearch
<
nPiBk
;
nsearch
++
)
{
ncmp
=
itypePiBk
[
nsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
k
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
k
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
k
][
2
])
{
pi_flag
=
1
;
break
;
}
}
}
}
if
(
pi_flag
==
0
)
{
itypePiBk
[
nPiBk
]
=
k
;
}
if
(
jtype
==
ktype
)
ijk
=
jtype
-
1
;
else
if
(
jtype
<
ktype
)
ijk
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
ktype
-
1
;
else
ijk
=
ktype
*
bop_types
-
ktype
*
(
ktype
+
1
)
/
2
+
jtype
-
1
;
pass_jk
=
0
;
if
(
otfly
==
1
)
{
dis_jk
[
0
]
=
x
[
k
][
0
]
-
x
[
j
][
0
];
dis_jk
[
1
]
=
x
[
k
][
1
]
-
x
[
j
][
1
];
dis_jk
[
2
]
=
x
[
k
][
2
]
-
x
[
j
][
2
];
rsq_jk
=
dis_jk
[
0
]
*
dis_jk
[
0
]
+
dis_jk
[
1
]
*
dis_jk
[
1
]
+
dis_jk
[
2
]
*
dis_jk
[
2
];
r_jk
=
sqrt
(
rsq_jk
);
if
(
r_jk
<=
rcut
[
ijk
])
{
pass_jk
=
1
;
ps
=
r_jk
*
rdr
[
ijk
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_jk
=
((
pBetaS3
[
ijk
][
ks
-
1
]
*
ps
+
pBetaS2
[
ijk
][
ks
-
1
])
*
ps
+
pBetaS1
[
ijk
][
ks
-
1
])
*
ps
+
pBetaS
[
ijk
][
ks
-
1
];
dBetaS_jk
=
(
pBetaS6
[
ijk
][
ks
-
1
]
*
ps
+
pBetaS5
[
ijk
][
ks
-
1
])
*
ps
+
pBetaS4
[
ijk
][
ks
-
1
];
betaP_jk
=
((
pBetaP3
[
ijk
][
ks
-
1
]
*
ps
+
pBetaP2
[
ijk
][
ks
-
1
])
*
ps
+
pBetaP1
[
ijk
][
ks
-
1
])
*
ps
+
pBetaP
[
ijk
][
ks
-
1
];
dBetaP_jk
=
(
pBetaP6
[
ijk
][
ks
-
1
]
*
ps
+
pBetaP5
[
ijk
][
ks
-
1
])
*
ps
+
pBetaP4
[
ijk
][
ks
-
1
];
cosAng_ijk
=
(
-
dis_ij
[
0
]
*
dis_jk
[
0
]
-
dis_ij
[
1
]
*
dis_jk
[
1
]
-
dis_ij
[
2
]
*
dis_jk
[
2
])
/
(
r_ij
*
r_jk
);
dcA_ijk
[
0
][
0
]
=
(
dis_jk
[
0
]
*
r_ij
*
r_jk
-
cosAng_ijk
*-
dis_ij
[
0
]
*
r_jk
*
r_jk
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
1
][
0
]
=
(
dis_jk
[
1
]
*
r_ij
*
r_jk
-
cosAng_ijk
*-
dis_ij
[
1
]
*
r_jk
*
r_jk
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
2
][
0
]
=
(
dis_jk
[
2
]
*
r_ij
*
r_jk
-
cosAng_ijk
*-
dis_ij
[
2
]
*
r_jk
*
r_jk
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
0
][
1
]
=
(
-
dis_ij
[
0
]
*
r_ij
*
r_jk
-
cosAng_ijk
*
dis_jk
[
0
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
1
][
1
]
=
(
-
dis_ij
[
1
]
*
r_ij
*
r_jk
-
cosAng_ijk
*
dis_jk
[
1
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
dcA_ijk
[
2
][
1
]
=
(
-
dis_ij
[
2
]
*
r_ij
*
r_jk
-
cosAng_ijk
*
dis_jk
[
2
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jk
*
r_jk
);
}
}
else
{
if
(
neigh_flag
[
temp_jk
])
{
pass_jk
=
1
;
dis_jk
[
0
]
=
disij
[
0
][
temp_jk
];
dis_jk
[
1
]
=
disij
[
1
][
temp_jk
];
dis_jk
[
2
]
=
disij
[
2
][
temp_jk
];
r_jk
=
rij
[
temp_jk
];
betaS_jk
=
betaS
[
temp_jk
];
dBetaS_jk
=
dBetaS
[
temp_jk
];
betaP_jk
=
betaP
[
temp_jk
];
dBetaP_jk
=
dBetaP
[
temp_jk
];
if
(
ktmp
<
ki
)
{
nijk
=
ktmp
*
(
2
*
nlistj
-
ktmp
-
1
)
/
2
+
(
ki
-
ktmp
)
-
1
;
ngi
=
1
;
ngk
=
0
;
}
else
{
nijk
=
ki
*
(
2
*
nlistj
-
ki
-
1
)
/
2
+
(
ktmp
-
ki
)
-
1
;
ngi
=
0
;
ngk
=
1
;
}
ang_ijk
=
cos_index
[
j
]
+
nijk
;
cosAng_ijk
=
cosAng
[
ang_ijk
];
dcA_ijk
[
0
][
0
]
=
dcAng
[
ang_ijk
][
0
][
ngi
];
dcA_ijk
[
1
][
0
]
=
dcAng
[
ang_ijk
][
1
][
ngi
];
dcA_ijk
[
2
][
0
]
=
dcAng
[
ang_ijk
][
2
][
ngi
];
dcA_ijk
[
0
][
1
]
=
dcAng
[
ang_ijk
][
0
][
ngk
];
dcA_ijk
[
1
][
1
]
=
dcAng
[
ang_ijk
][
1
][
ngk
];
dcA_ijk
[
2
][
1
]
=
dcAng
[
ang_ijk
][
2
][
ngk
];
}
}
if
(
pass_jk
==
1
)
{
nb_jk
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_pi
)
{
new_n_tot
=
nb_pi
+
maxneigh
;
grow_pi
(
nb_pi
,
new_n_tot
);
nb_pi
=
new_n_tot
;
}
bt_pi
[
nb_jk
].
i
=
j
;
bt_pi
[
nb_jk
].
j
=
k
;
bt_pi
[
nb_jk
].
temp
=
temp_jk
;
cosSq
=
cosAng_ijk
*
cosAng_ijk
;
sinFactor
=
.5
*
(
1.0
-
cosSq
)
*
pi_p
[
jtype
-
1
]
*
betaS_jk
;
cosFactor
=
.5
*
(
1.0
+
cosSq
)
*
betaP_jk
;
betaCapSq1
=
pi_p
[
jtype
-
1
]
*
betaS_jk
*
betaS_jk
-
betaP_jk
*
betaP_jk
;
dbetaCapSq1
=
2.0
*
pi_p
[
jtype
-
1
]
*
betaS_jk
*
dBetaS_jk
-
2.0
*
betaP_jk
*
dBetaP_jk
;
//AA is Eq. 37 (a) and Eq. 19 (b) for j atoms
//3rd BB is 2nd term of Eq. 38 (a) where i and k =neighbors j
AA
=
AA
+
sinFactor
*
betaS_jk
+
cosFactor
*
betaP_jk
;
BB
=
BB
+
.25
*
(
1.0
-
cosSq
)
*
(
1.0
-
cosSq
)
*
betaCapSq1
*
betaCapSq1
;
agpdpr1
=
(
2.0
*
sinFactor
*
dBetaS_jk
+
2.0
*
cosFactor
*
dBetaP_jk
)
/
r_jk
;
//agpdpr1 is derivative of AA for atom j w.r.t. Beta(r_jk)
//agpdpr2 is derivative of BB for atom j w.r.t. Beta(r_jk)
//app1 is derivative of AA for j atom w.r.t. cos(theta_ijk)
//app2 is derivative of BB 2nd term w.r.t. cos(theta_ijk)
agpdpr2
=
.5
*
(
1.0
-
cosSq
)
*
(
1.0
-
cosSq
)
*
betaCapSq1
*
dbetaCapSq1
/
r_jk
;
app1
=
cosAng_ijk
*
(
-
pi_p
[
jtype
-
1
]
*
betaS_jk
*
betaS_jk
+
betaP_jk
*
betaP_jk
);
app2
=-
(
1.0
-
cosSq
)
*
cosAng_ijk
*
betaCapSq1
*
betaCapSq1
;
bt_pi
[
nb_ij
].
dAA
[
0
]
-=
app1
*
dcA_ijk
[
0
][
0
];
bt_pi
[
nb_ij
].
dAA
[
1
]
-=
app1
*
dcA_ijk
[
1
][
0
];
bt_pi
[
nb_ij
].
dAA
[
2
]
-=
app1
*
dcA_ijk
[
2
][
0
];
bt_pi
[
nb_ij
].
dBB
[
0
]
-=
app2
*
dcA_ijk
[
0
][
0
];
bt_pi
[
nb_ij
].
dBB
[
1
]
-=
app2
*
dcA_ijk
[
1
][
0
];
bt_pi
[
nb_ij
].
dBB
[
2
]
-=
app2
*
dcA_ijk
[
2
][
0
];
bt_pi
[
nb_jk
].
dAA
[
0
]
+=
agpdpr1
*
dis_jk
[
0
]
+
app1
*
dcA_ijk
[
0
][
1
];
bt_pi
[
nb_jk
].
dAA
[
1
]
+=
agpdpr1
*
dis_jk
[
1
]
+
app1
*
dcA_ijk
[
1
][
1
];
bt_pi
[
nb_jk
].
dAA
[
2
]
+=
agpdpr1
*
dis_jk
[
2
]
+
app1
*
dcA_ijk
[
2
][
1
];
bt_pi
[
nb_jk
].
dBB
[
0
]
+=
app2
*
dcA_ijk
[
0
][
1
]
+
agpdpr2
*
dis_jk
[
0
];
bt_pi
[
nb_jk
].
dBB
[
1
]
+=
app2
*
dcA_ijk
[
1
][
1
]
+
agpdpr2
*
dis_jk
[
1
];
bt_pi
[
nb_jk
].
dBB
[
2
]
+=
app2
*
dcA_ijk
[
2
][
1
]
+
agpdpr2
*
dis_jk
[
2
];
//j is a neighbor of i and k and k' are different neighbors of j not equal to i
for
(
ltmp
=
0
;
ltmp
<
ktmp
;
ltmp
++
)
{
if
(
ltmp
!=
ki
)
{
temp_jkp
=
BOP_index
[
j
]
+
ltmp
;
ni_jkp
=
neigh_index
[
temp_jkp
];
kp
=
jlist
[
ni_jkp
];
kptype
=
map
[
type
[
kp
]]
+
1
;
for
(
nsearch
=
0
;
nsearch
<
nPiBk
;
nsearch
++
)
{
ncmp
=
itypePiBk
[
nsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
kp
][
2
])
{
break
;
}
}
}
}
if
(
jtype
==
kptype
)
ijkp
=
jtype
-
1
;
else
if
(
jtype
<
kptype
)
ijkp
=
jtype
*
bop_types
-
jtype
*
(
jtype
+
1
)
/
2
+
kptype
-
1
;
else
ijkp
=
kptype
*
bop_types
-
kptype
*
(
kptype
+
1
)
/
2
+
jtype
-
1
;
pass_jkp
=
0
;
if
(
otfly
==
1
)
{
dis_jkp
[
0
]
=
x
[
kp
][
0
]
-
x
[
j
][
0
];
dis_jkp
[
1
]
=
x
[
kp
][
1
]
-
x
[
j
][
1
];
dis_jkp
[
2
]
=
x
[
kp
][
2
]
-
x
[
j
][
2
];
rsq_jkp
=
dis_jkp
[
0
]
*
dis_jkp
[
0
]
+
dis_jkp
[
1
]
*
dis_jkp
[
1
]
+
dis_jkp
[
2
]
*
dis_jkp
[
2
];
r_jkp
=
sqrt
(
rsq_jkp
);
if
(
r_jkp
<=
rcut
[
ijkp
])
{
pass_jkp
=
1
;
ps
=
r_jkp
*
rdr
[
ijkp
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_jkp
=
((
pBetaS3
[
ijkp
][
ks
-
1
]
*
ps
+
pBetaS2
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS1
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS
[
ijkp
][
ks
-
1
];
dBetaS_jkp
=
(
pBetaS6
[
ijkp
][
ks
-
1
]
*
ps
+
pBetaS5
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaS4
[
ijkp
][
ks
-
1
];
betaP_jkp
=
((
pBetaP3
[
ijkp
][
ks
-
1
]
*
ps
+
pBetaP2
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaP1
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaP
[
ijkp
][
ks
-
1
];
dBetaP_jkp
=
(
pBetaP6
[
ijkp
][
ks
-
1
]
*
ps
+
pBetaP5
[
ijkp
][
ks
-
1
])
*
ps
+
pBetaP4
[
ijkp
][
ks
-
1
];
cosAng_ijkp
=
(
-
dis_ij
[
0
]
*
dis_jkp
[
0
]
-
dis_ij
[
1
]
*
dis_jkp
[
1
]
-
dis_ij
[
2
]
*
dis_jkp
[
2
])
/
(
r_ij
*
r_jkp
);
dcA_ijkp
[
0
][
0
]
=
(
dis_jkp
[
0
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*-
dis_ij
[
0
]
*
r_jkp
*
r_jkp
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
1
][
0
]
=
(
dis_jkp
[
1
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*-
dis_ij
[
1
]
*
r_jkp
*
r_jkp
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
2
][
0
]
=
(
dis_jkp
[
2
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*-
dis_ij
[
2
]
*
r_jkp
*
r_jkp
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
0
][
1
]
=
(
-
dis_ij
[
0
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*
dis_jkp
[
0
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
1
][
1
]
=
(
-
dis_ij
[
1
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*
dis_jkp
[
1
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
dcA_ijkp
[
2
][
1
]
=
(
-
dis_ij
[
2
]
*
r_ij
*
r_jkp
-
cosAng_ijkp
*
dis_jkp
[
2
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_jkp
*
r_jkp
);
cosAng_kjkp
=
(
dis_jk
[
0
]
*
dis_jkp
[
0
]
+
dis_jk
[
1
]
*
dis_jkp
[
1
]
+
dis_jk
[
2
]
*
dis_jkp
[
2
])
/
(
r_jk
*
r_jkp
);
dcA_kjkp
[
0
][
0
]
=
(
dis_jkp
[
0
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jk
[
0
]
*
r_jkp
*
r_jkp
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
dcA_kjkp
[
1
][
0
]
=
(
dis_jkp
[
1
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jk
[
1
]
*
r_jkp
*
r_jkp
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
dcA_kjkp
[
2
][
0
]
=
(
dis_jkp
[
2
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jk
[
2
]
*
r_jkp
*
r_jkp
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
dcA_kjkp
[
0
][
1
]
=
(
dis_jk
[
0
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jkp
[
0
]
*
r_jk
*
r_jk
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
dcA_kjkp
[
1
][
1
]
=
(
dis_jk
[
1
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jkp
[
1
]
*
r_jk
*
r_jk
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
dcA_kjkp
[
2
][
1
]
=
(
dis_jk
[
2
]
*
r_jk
*
r_jkp
-
cosAng_kjkp
*
dis_jkp
[
2
]
*
r_jk
*
r_jk
)
/
(
r_jk
*
r_jk
*
r_jkp
*
r_jkp
);
}
}
else
{
if
(
neigh_flag
[
temp_jkp
])
{
pass_jkp
=
1
;
dis_jkp
[
0
]
=
disij
[
0
][
temp_jkp
];
dis_jkp
[
1
]
=
disij
[
1
][
temp_jkp
];
dis_jkp
[
2
]
=
disij
[
2
][
temp_jkp
];
r_jkp
=
rij
[
temp_jkp
];
betaS_jkp
=
betaS
[
temp_jkp
];
dBetaS_jkp
=
dBetaS
[
temp_jkp
];
betaP_jkp
=
betaP
[
temp_jkp
];
dBetaP_jkp
=
dBetaP
[
temp_jkp
];
nkjkp
=
ltmp
*
(
2
*
nlistj
-
ltmp
-
1
)
/
2
+
(
ktmp
-
ltmp
)
-
1
;
if
(
ki
<
ltmp
)
{
nijkp
=
ki
*
(
2
*
nlistj
-
ki
-
1
)
/
2
+
(
ltmp
-
ki
)
-
1
;
ngli
=
0
;
ngl
=
1
;
}
else
{
nijkp
=
ltmp
*
(
2
*
nlistj
-
ltmp
-
1
)
/
2
+
(
ki
-
ltmp
)
-
1
;
ngli
=
1
;
ngl
=
0
;
}
ang_ijkp
=
cos_index
[
j
]
+
nijkp
;
cosAng_ijkp
=
cosAng
[
ang_ijkp
];
dcA_ijkp
[
0
][
0
]
=
dcAng
[
ang_ijkp
][
0
][
ngli
];
dcA_ijkp
[
1
][
0
]
=
dcAng
[
ang_ijkp
][
1
][
ngli
];
dcA_ijkp
[
2
][
0
]
=
dcAng
[
ang_ijkp
][
2
][
ngli
];
dcA_ijkp
[
0
][
1
]
=
dcAng
[
ang_ijkp
][
0
][
ngl
];
dcA_ijkp
[
1
][
1
]
=
dcAng
[
ang_ijkp
][
1
][
ngl
];
dcA_ijkp
[
2
][
1
]
=
dcAng
[
ang_ijkp
][
2
][
ngl
];
ang_kjkp
=
cos_index
[
j
]
+
nkjkp
;
cosAng_kjkp
=
cosAng
[
ang_kjkp
];
dcA_kjkp
[
0
][
0
]
=
dcAng
[
ang_kjkp
][
0
][
1
];
dcA_kjkp
[
1
][
0
]
=
dcAng
[
ang_kjkp
][
1
][
1
];
dcA_kjkp
[
2
][
0
]
=
dcAng
[
ang_kjkp
][
2
][
1
];
dcA_kjkp
[
0
][
1
]
=
dcAng
[
ang_kjkp
][
0
][
0
];
dcA_kjkp
[
1
][
1
]
=
dcAng
[
ang_kjkp
][
1
][
0
];
dcA_kjkp
[
2
][
1
]
=
dcAng
[
ang_kjkp
][
2
][
0
];
}
}
if
(
pass_jkp
)
{
nb_jkp
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_pi
)
{
new_n_tot
=
nb_pi
+
maxneigh
;
grow_pi
(
nb_pi
,
new_n_tot
);
nb_pi
=
new_n_tot
;
}
bt_pi
[
nb_jkp
].
i
=
j
;
bt_pi
[
nb_jkp
].
j
=
kp
;
bt_pi
[
nb_jkp
].
temp
=
temp_jkp
;
betaCapSq2
=
pi_p
[
jtype
-
1
]
*
betaS_jkp
*
betaS_jkp
-
betaP_jkp
*
betaP_jkp
;
dbetaCapSq2
=
2.0
*
pi_p
[
jtype
-
1
]
*
betaS_jkp
*
dBetaS_jkp
-
2.0
*
betaP_jkp
*
dBetaP_jkp
;
cosSq1
=
cosAng_ijkp
*
cosAng_ijkp
;
angFactor
=
cosAng_kjkp
-
cosAng_ijkp
*
cosAng_ijk
;
angFactor1
=
4.0
*
angFactor
;
angFactor2
=-
angFactor1
*
cosAng_ijkp
+
2.0
*
cosAng_ijk
*
(
1.0
-
cosSq1
);
angFactor3
=-
angFactor1
*
cosAng_ijk
+
2.0
*
cosAng_ijkp
*
(
1.0
-
cosSq
);
angFactor4
=
2.0
*
angFactor
*
angFactor
-
(
1.0
-
cosSq
)
*
(
1.0
-
cosSq1
);
betaCapSum
=
.5
*
betaCapSq1
*
betaCapSq2
;
//4th BB is 4th term of Eq. 38 (a) where i , k and k' =neighbors j
BB
=
BB
+
betaCapSum
*
angFactor4
;
//app1 is derivative of BB 4th term w.r.t. cos(theta_kjk')
//app2 is derivative of BB 4th term w.r.t. cos(theta_ijk)
//app3 is derivative of BB 4th term w.r.t. cos(theta_ijk')
//agpdpr1 is derivative of BB 4th term for atom j w.r.t. Beta(r_jk)
//agpdpr2 is derivative of BB 4th term for atom j w.r.t. Beta(r_jk')
app1
=
betaCapSum
*
angFactor1
;
app2
=
betaCapSum
*
angFactor2
;
app3
=
betaCapSum
*
angFactor3
;
agpdpr1
=
.5
*
angFactor4
*
dbetaCapSq1
*
betaCapSq2
/
r_jk
;
agpdpr2
=
.5
*
angFactor4
*
betaCapSq1
*
dbetaCapSq2
/
r_jkp
;
bt_pi
[
nb_ij
].
dBB
[
0
]
-=
app3
*
dcA_ijkp
[
0
][
0
]
+
app2
*
dcA_ijk
[
0
][
0
];
bt_pi
[
nb_ij
].
dBB
[
1
]
-=
app3
*
dcA_ijkp
[
1
][
0
]
+
app2
*
dcA_ijk
[
1
][
0
];
bt_pi
[
nb_ij
].
dBB
[
2
]
-=
app3
*
dcA_ijkp
[
2
][
0
]
+
app2
*
dcA_ijk
[
2
][
0
];
bt_pi
[
nb_jk
].
dBB
[
0
]
+=
agpdpr1
*
dis_jk
[
0
]
+
app1
*
dcA_kjkp
[
0
][
0
]
+
app2
*
dcA_ijk
[
0
][
1
];
bt_pi
[
nb_jk
].
dBB
[
1
]
+=
agpdpr1
*
dis_jk
[
1
]
+
app1
*
dcA_kjkp
[
1
][
0
]
+
app2
*
dcA_ijk
[
1
][
1
];
bt_pi
[
nb_jk
].
dBB
[
2
]
+=
agpdpr1
*
dis_jk
[
2
]
+
app1
*
dcA_kjkp
[
2
][
0
]
+
app2
*
dcA_ijk
[
2
][
1
];
bt_pi
[
nb_jkp
].
dBB
[
0
]
+=
agpdpr2
*
dis_jkp
[
0
]
+
app1
*
dcA_kjkp
[
0
][
1
]
+
app3
*
dcA_ijkp
[
0
][
1
];
bt_pi
[
nb_jkp
].
dBB
[
1
]
+=
agpdpr2
*
dis_jkp
[
1
]
+
app1
*
dcA_kjkp
[
1
][
1
]
+
app3
*
dcA_ijkp
[
1
][
1
];
bt_pi
[
nb_jkp
].
dBB
[
2
]
+=
agpdpr2
*
dis_jkp
[
2
]
+
app1
*
dcA_kjkp
[
2
][
1
]
+
app3
*
dcA_ijkp
[
2
][
1
];
}
}
}
//j and k' are different neighbors of i and k is a neighbor of j not equal to i
for
(
ltmp
=
0
;
ltmp
<
nlisti
;
ltmp
++
)
{
if
(
ltmp
!=
jtmp
)
{
temp_ikp
=
BOP_index
[
i
]
+
ltmp
;
ni_ikp
=
neigh_index
[
temp_ikp
];
kp
=
iilist
[
ni_ikp
];
kptype
=
map
[
type
[
kp
]]
+
1
;
for
(
nsearch
=
0
;
nsearch
<
nPiBk
;
nsearch
++
)
{
ncmp
=
itypePiBk
[
nsearch
];
if
(
x
[
ncmp
][
0
]
==
x
[
kp
][
0
])
{
if
(
x
[
ncmp
][
1
]
==
x
[
kp
][
1
])
{
if
(
x
[
ncmp
][
2
]
==
x
[
kp
][
2
])
{
break
;
}
}
}
}
if
(
itype
==
kptype
)
iikp
=
itype
-
1
;
else
if
(
itype
<
kptype
)
iikp
=
itype
*
bop_types
-
itype
*
(
itype
+
1
)
/
2
+
kptype
-
1
;
else
iikp
=
kptype
*
bop_types
-
kptype
*
(
kptype
+
1
)
/
2
+
itype
-
1
;
pass_ikp
=
0
;
if
(
otfly
==
1
)
{
dis_ikp
[
0
]
=
x
[
kp
][
0
]
-
x
[
i
][
0
];
dis_ikp
[
1
]
=
x
[
kp
][
1
]
-
x
[
i
][
1
];
dis_ikp
[
2
]
=
x
[
kp
][
2
]
-
x
[
i
][
2
];
rsq_ikp
=
dis_ikp
[
0
]
*
dis_ikp
[
0
]
+
dis_ikp
[
1
]
*
dis_ikp
[
1
]
+
dis_ikp
[
2
]
*
dis_ikp
[
2
];
r_ikp
=
sqrt
(
rsq_ikp
);
if
(
r_ikp
<=
rcut
[
iikp
])
{
pass_ikp
=
1
;
ps
=
r_ikp
*
rdr
[
iikp
]
+
1.0
;
ks
=
(
int
)
ps
;
if
(
nr
-
1
<
ks
)
ks
=
nr
-
1
;
ps
=
ps
-
ks
;
if
(
ps
>
1.0
)
ps
=
1.0
;
betaS_ikp
=
((
pBetaS3
[
iikp
][
ks
-
1
]
*
ps
+
pBetaS2
[
iikp
][
ks
-
1
])
*
ps
+
pBetaS1
[
iikp
][
ks
-
1
])
*
ps
+
pBetaS
[
iikp
][
ks
-
1
];
dBetaS_ikp
=
(
pBetaS6
[
iikp
][
ks
-
1
]
*
ps
+
pBetaS5
[
iikp
][
ks
-
1
])
*
ps
+
pBetaS4
[
iikp
][
ks
-
1
];
betaP_ikp
=
((
pBetaP3
[
iikp
][
ks
-
1
]
*
ps
+
pBetaP2
[
iikp
][
ks
-
1
])
*
ps
+
pBetaP1
[
iikp
][
ks
-
1
])
*
ps
+
pBetaP
[
iikp
][
ks
-
1
];
dBetaP_ikp
=
(
pBetaP6
[
iikp
][
ks
-
1
]
*
ps
+
pBetaP5
[
iikp
][
ks
-
1
])
*
ps
+
pBetaP4
[
iikp
][
ks
-
1
];
cosAng_jikp
=
(
dis_ij
[
0
]
*
dis_ikp
[
0
]
+
dis_ij
[
1
]
*
dis_ikp
[
1
]
+
dis_ij
[
2
]
*
dis_ikp
[
2
])
/
(
r_ij
*
r_ikp
);
dcA_jikp
[
0
][
0
]
=
(
dis_ikp
[
0
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ij
[
0
]
*
r_ikp
*
r_ikp
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
1
][
0
]
=
(
dis_ikp
[
1
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ij
[
1
]
*
r_ikp
*
r_ikp
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
2
][
0
]
=
(
dis_ikp
[
2
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ij
[
2
]
*
r_ikp
*
r_ikp
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
0
][
1
]
=
(
dis_ij
[
0
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ikp
[
0
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
1
][
1
]
=
(
dis_ij
[
1
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ikp
[
1
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
dcA_jikp
[
2
][
1
]
=
(
dis_ij
[
2
]
*
r_ij
*
r_ikp
-
cosAng_jikp
*
dis_ikp
[
2
]
*
r_ij
*
r_ij
)
/
(
r_ij
*
r_ij
*
r_ikp
*
r_ikp
);
}
}
else
{
if
(
neigh_flag
[
temp_ikp
])
{
pass_ikp
=
1
;
dis_ikp
[
0
]
=
disij
[
0
][
temp_ikp
];
dis_ikp
[
1
]
=
disij
[
1
][
temp_ikp
];
dis_ikp
[
2
]
=
disij
[
2
][
temp_ikp
];
r_ikp
=
rij
[
temp_ikp
];
betaS_ikp
=
betaS
[
temp_ikp
];
dBetaS_ikp
=
dBetaS
[
temp_ikp
];
betaP_ikp
=
betaP
[
temp_ikp
];
dBetaP_ikp
=
dBetaP
[
temp_ikp
];
if
(
ltmp
<
jtmp
)
{
njikp
=
ltmp
*
(
2
*
nlisti
-
ltmp
-
1
)
/
2
+
(
jtmp
-
ltmp
)
-
1
;
ngl
=
1
;
nglj
=
0
;
}
else
{
njikp
=
jtmp
*
(
2
*
nlisti
-
jtmp
-
1
)
/
2
+
(
ltmp
-
jtmp
)
-
1
;
ngl
=
0
;
nglj
=
1
;
}
ang_jikp
=
cos_index
[
i
]
+
njikp
;
cosAng_jikp
=
cosAng
[
ang_jikp
];
dcA_jikp
[
0
][
0
]
=
dcAng
[
ang_jikp
][
0
][
ngl
];
dcA_jikp
[
1
][
0
]
=
dcAng
[
ang_jikp
][
1
][
ngl
];
dcA_jikp
[
2
][
0
]
=
dcAng
[
ang_jikp
][
2
][
ngl
];
dcA_jikp
[
0
][
1
]
=
dcAng
[
ang_jikp
][
0
][
nglj
];
dcA_jikp
[
1
][
1
]
=
dcAng
[
ang_jikp
][
1
][
nglj
];
dcA_jikp
[
2
][
1
]
=
dcAng
[
ang_jikp
][
2
][
nglj
];
}
}
if
(
pass_ikp
==
1
)
{
nb_ikp
=
nb_t
;
nb_t
++
;
if
(
nb_t
>
nb_pi
)
{
new_n_tot
=
nb_pi
+
maxneigh
;
grow_pi
(
nb_pi
,
new_n_tot
);
nb_pi
=
new_n_tot
;
}
bt_pi
[
nb_ikp
].
i
=
i
;
bt_pi
[
nb_ikp
].
j
=
kp
;
bt_pi
[
nb_ikp
].
temp
=
temp_ikp
;
betaCapSq2
=
pi_p
[
itype
-
1
]
*
betaS_ikp
*
betaS_ikp
-
betaP_ikp
*
betaP_ikp
;
dbetaCapSq2
=
2.0
*
pi_p
[
itype
-
1
]
*
betaS_ikp
*
dBetaS_ikp
-
2.0
*
betaP_ikp
*
dBetaP_ikp
;
dotV
=
(
dis_jk
[
0
]
*
dis_ikp
[
0
]
+
dis_jk
[
1
]
*
dis_ikp
[
1
]
+
dis_jk
[
2
]
*
dis_ikp
[
2
])
/
(
r_jk
*
r_ikp
);
cosSq1
=
cosAng_jikp
*
cosAng_jikp
;
angFactor
=
dotV
+
cosAng_jikp
*
cosAng_ijk
;
angRfactor
=
4.0
*
angFactor
*
dotV
;
dAngR1
=-
angRfactor
/
r_jk
;
dAngR2
=-
angRfactor
/
r_ikp
;
angFactor1
=
4.0
*
angFactor
*
cosAng_jikp
+
2.0
*
cosAng_ijk
*
(
1.0
-
cosSq1
);
angFactor2
=
4.0
*
angFactor
*
cosAng_ijk
+
2.0
*
cosAng_jikp
*
(
1.0
-
cosSq
);
angFactor3
=
2.0
*
angFactor
*
angFactor
-
(
1.0
-
cosSq
)
*
(
1.0
-
cosSq1
);
betaCapSum
=
.5
*
betaCapSq1
*
betaCapSq2
;
//5th BB is 5th term of Eq. 38 (a) Eq. 21 (b) where i , k and k' =neighbors j
BB
=
BB
+
betaCapSum
*
angFactor3
;
//app1 is derivative of BB 5th term w.r.t. cos(theta_ijk)
//app2 is derivative of BB 5th term w.r.t. cos(theta_jik')
//agpdpr1 is derivative of BB 5th term for atom j w.r.t. Beta(r_jk)
//agpdpr2 is derivative of BB 5th term for atom j w.r.t. Beta(r_ik')
//agpdpr3 is derivative of BB 5th term for atom j w.r.t. dot(r_ik',r_ij)
app1
=
betaCapSum
*
angFactor1
;
app2
=
betaCapSum
*
angFactor2
;
agpdpr1
=
(
.5
*
angFactor3
*
dbetaCapSq1
*
betaCapSq2
+
betaCapSum
*
dAngR1
)
/
r_jk
;
agpdpr2
=
(
.5
*
angFactor3
*
betaCapSq1
*
dbetaCapSq2
+
betaCapSum
*
dAngR2
)
/
r_ikp
;
agpdpr3
=
4.0
*
betaCapSum
*
angFactor
/
(
r_ikp
*
r_jk
);
bt_pi
[
nb_ij
].
dBB
[
0
]
+=
+
app2
*
dcA_jikp
[
0
][
0
]
-
app1
*
dcA_ijk
[
0
][
0
];
bt_pi
[
nb_ij
].
dBB
[
1
]
+=
+
app2
*
dcA_jikp
[
1
][
0
]
-
app1
*
dcA_ijk
[
1
][
0
];
bt_pi
[
nb_ij
].
dBB
[
2
]
+=
+
app2
*
dcA_jikp
[
2
][
0
]
-
app1
*
dcA_ijk
[
2
][
0
];
bt_pi
[
nb_ikp
].
dBB
[
0
]
+=
agpdpr2
*
dis_ikp
[
0
]
+
agpdpr3
*
dis_jk
[
0
]
+
app2
*
dcA_jikp
[
0
][
1
];
bt_pi
[
nb_ikp
].
dBB
[
1
]
+=
agpdpr2
*
dis_ikp
[
1
]
+
agpdpr3
*
dis_jk
[
1
]
+
app2
*
dcA_jikp
[
1
][
1
];
bt_pi
[
nb_ikp
].
dBB
[
2
]
+=
agpdpr2
*
dis_ikp
[
2
]
+
agpdpr3
*
dis_jk
[
2
]
+
app2
*
dcA_jikp
[
2
][
1
];
bt_pi
[
nb_jk
].
dBB
[
0
]
+=
agpdpr1
*
dis_jk
[
0
]
+
agpdpr3
*
dis_ikp
[
0
]
+
app1
*
dcA_ijk
[
0
][
1
];
bt_pi
[
nb_jk
].
dBB
[
1
]
+=
agpdpr1
*
dis_jk
[
1
]
+
agpdpr3
*
dis_ikp
[
1
]
+
app1
*
dcA_ijk
[
1
][
1
];
bt_pi
[
nb_jk
].
dBB
[
2
]
+=
agpdpr1
*
dis_jk
[
2
]
+
agpdpr3
*
dis_ikp
[
2
]
+
app1
*
dcA_ijk
[
2
][
1
];
}
}
}
if
(
pi_flag
==
0
)
nPiBk
=
nPiBk
+
1
;
}
}
}
n
++
;
pp2
=
2.0
*
betaP_ij
;
for
(
m
=
0
;
m
<
nb_t
;
m
++
)
{
bt_i
=
bt_pi
[
m
].
i
;
bt_j
=
bt_pi
[
m
].
j
;
CC
=
betaP_ij
*
betaP_ij
+
pi_delta
[
iij
]
*
pi_delta
[
iij
];
BBrt
=
sqrt
(
BB
+
small6
);
AB1
=
CC
+
pi_c
[
iij
]
*
(
AA
+
BBrt
)
+
small7
;
AB2
=
CC
+
pi_c
[
iij
]
*
(
AA
-
BBrt
+
sqrt
(
small6
))
+
small7
;
BBrtR
=
1.0
/
BBrt
;
ABrtR1
=
1.0
/
sqrt
(
AB1
);
ABrtR2
=
1.0
/
sqrt
(
AB2
);
piB
=
(
ABrtR1
+
ABrtR2
)
*
pi_a
[
iij
]
*
betaP_ij
;
dPiB1
=-
.5
*
(
pow
(
ABrtR1
,
3
)
+
pow
(
ABrtR2
,
3
))
*
pi_c
[
iij
]
*
pi_a
[
iij
]
*
betaP_ij
;
dPiB2
=
.25
*
BBrtR
*
(
pow
(
ABrtR2
,
3
)
-
pow
(
ABrtR1
,
3
))
*
pi_c
[
iij
]
*
pi_a
[
iij
]
*
betaP_ij
;
dPiB3
=
((
ABrtR1
+
ABrtR2
)
*
pi_a
[
iij
]
-
(
pow
(
ABrtR1
,
3
)
+
pow
(
ABrtR2
,
3
))
*
pi_a
[
iij
]
*
betaP_ij
*
betaP_ij
)
*
dBetaP_ij
/
r_ij
;
xtmp
[
0
]
=
x
[
bt_j
][
0
]
-
x
[
bt_i
][
0
];
xtmp
[
1
]
=
x
[
bt_j
][
1
]
-
x
[
bt_i
][
1
];
xtmp
[
2
]
=
x
[
bt_j
][
2
]
-
x
[
bt_i
][
2
];
for
(
pp
=
0
;
pp
<
3
;
pp
++
)
{
bt_pi
[
m
].
dPiB
[
pp
]
=
+
dPiB1
*
bt_pi
[
m
].
dAA
[
pp
]
+
dPiB2
*
bt_pi
[
m
].
dBB
[
pp
];
ftmp
[
pp
]
=
pp2
*
bt_pi
[
m
].
dPiB
[
pp
];
f
[
bt_i
][
pp
]
-=
ftmp
[
pp
];
f
[
bt_j
][
pp
]
+=
ftmp
[
pp
];
}
if
(
evflag
)
{
ev_tally_xyz
(
bt_i
,
bt_j
,
nlocal
,
newton_pair
,
0.0
,
0.0
,
ftmp
[
0
],
ftmp
[
1
]
,
ftmp
[
2
],
xtmp
[
0
],
xtmp
[
1
],
xtmp
[
2
]);
}
}
for
(
pp
=
0
;
pp
<
3
;
pp
++
)
{
ftmp
[
pp
]
=
pp2
*
dPiB3
*
dis_ij
[
pp
];
f
[
i
][
pp
]
-=
ftmp
[
pp
];
f
[
j
][
pp
]
+=
ftmp
[
pp
];
}
if
(
evflag
)
{
ev_tally_xyz
(
i
,
j
,
nlocal
,
newton_pair
,
0.0
,
0.0
,
ftmp
[
0
],
ftmp
[
1
]
,
ftmp
[
2
],
dis_ij
[
0
],
dis_ij
[
1
],
dis_ij
[
2
]);
}
}
}
}
destroy_pi
();
return
(
piB
);
}
/* ----------------------------------------------------------------------
read BOP potential file
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void
PairBOP
::
read_table
(
char
*
filename
)
{
int
i
,
j
,
k
,
n
,
m
;
int
buf1
,
pass
;
int
nws
,
ws
;
double
buf2
;
char
s
[
MAXLINE
],
buf
[
2
];
MPI_Comm_rank
(
world
,
&
me
);
if
(
me
==
0
)
{
FILE
*
fp
=
force
->
open_potential
(
filename
);
if
(
fp
==
NULL
)
{
char
str
[
128
];
sprintf
(
str
,
"Cannot open BOP potential file %s"
,
filename
);
error
->
one
(
FLERR
,
str
);
}
fgets
(
s
,
MAXLINE
,
fp
);
// skip first comment line
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%d"
,
&
bop_types
);
elements
=
new
char
*
[
bop_types
];
for
(
i
=
0
;
i
<
bop_types
;
i
++
)
elements
[
i
]
=
NULL
;
for
(
i
=
0
;
i
<
bop_types
;
i
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
nws
=
0
;
ws
=
1
;
for
(
j
=
0
;
j
<
strlen
(
s
);
j
++
)
{
if
(
ws
==
1
)
{
if
(
isspace
(
s
[
j
]))
{
ws
=
1
;
}
else
{
ws
=
0
;
}
}
else
{
if
(
isspace
(
s
[
j
]))
{
ws
=
1
;
nws
++
;
}
else
{
ws
=
0
;
}
}
}
if
(
nws
!=
3
){
error
->
all
(
FLERR
,
"Incorrect table format check for element types"
);
}
sscanf
(
s
,
"%d %lf %s"
,
&
buf1
,
&
buf2
,
buf
);
n
=
strlen
(
buf
)
+
1
;
elements
[
i
]
=
new
char
[
n
];
strcpy
(
elements
[
i
],
buf
);
}
nws
=
0
;
ws
=
1
;
fgets
(
s
,
MAXLINE
,
fp
);
for
(
j
=
0
;
j
<
strlen
(
s
);
j
++
)
{
if
(
ws
==
1
)
{
if
(
isspace
(
s
[
j
]))
{
ws
=
1
;
}
else
{
ws
=
0
;
}
}
else
{
if
(
isspace
(
s
[
j
]))
{
ws
=
1
;
nws
++
;
}
else
{
ws
=
0
;
}
}
}
if
(
nws
==
3
)
{
sscanf
(
s
,
"%d %d %d"
,
&
nr
,
&
ntheta
,
&
nBOt
);
npower
=
2
;
if
(
ntheta
<=
10
)
npower
=
ntheta
;
}
else
{
sscanf
(
s
,
"%d %d"
,
&
nr
,
&
nBOt
);
ntheta
=
0
;
npower
=
3
;
}
fclose
(
fp
);
npairs
=
bop_types
*
(
bop_types
+
1
)
/
2
;
}
MPI_Bcast
(
&
nr
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
nBOt
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
ntheta
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
bop_types
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
npairs
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
npower
,
1
,
MPI_INT
,
0
,
world
);
memory
->
create
(
pi_a
,
npairs
,
"BOP:pi_a"
);
memory
->
create
(
pro_delta
,
bop_types
,
"BOP:pro_delta"
);
memory
->
create
(
pi_delta
,
npairs
,
"BOP:pi_delta"
);
memory
->
create
(
pi_p
,
bop_types
,
"BOP:pi_p"
);
memory
->
create
(
pi_c
,
npairs
,
"BOP:pi_c"
);
memory
->
create
(
r1
,
npairs
,
"BOP:r1"
);
memory
->
create
(
pro
,
bop_types
,
"BOP:pro"
);
memory
->
create
(
sigma_delta
,
npairs
,
"BOP:sigma_delta"
);
memory
->
create
(
sigma_c
,
npairs
,
"BOP:sigma_c"
);
memory
->
create
(
sigma_a
,
npairs
,
"BOP:sigma_a"
);
memory
->
create
(
sigma_f
,
npairs
,
"BOP:sigma_f"
);
memory
->
create
(
sigma_k
,
npairs
,
"BOP:sigma_k"
);
memory
->
create
(
small3
,
npairs
,
"BOP:small3"
);
memory
->
create
(
gfunc
,
bop_types
,
bop_types
,
bop_types
,
ntheta
,
"BOP:gfunc"
);
memory
->
create
(
gfunc1
,
bop_types
,
bop_types
,
bop_types
,
ntheta
,
"BOP:gfunc1"
);
memory
->
create
(
gfunc2
,
bop_types
,
bop_types
,
bop_types
,
ntheta
,
"BOP:gfunc2"
);
memory
->
create
(
gfunc3
,
bop_types
,
bop_types
,
bop_types
,
ntheta
,
"BOP:gfunc3"
);
memory
->
create
(
gfunc4
,
bop_types
,
bop_types
,
bop_types
,
ntheta
,
"BOP:gfunc4"
);
memory
->
create
(
gfunc5
,
bop_types
,
bop_types
,
bop_types
,
ntheta
,
"BOP:gfunc5"
);
memory
->
create
(
gfunc6
,
bop_types
,
bop_types
,
bop_types
,
ntheta
,
"BOP:gfunc6"
);
memory
->
create
(
gpara
,
bop_types
,
bop_types
,
bop_types
,
npower
+
1
,
"BOP:gpara"
);
allocate
();
if
(
me
==
0
)
{
FILE
*
fp
=
force
->
open_potential
(
filename
);
if
(
fp
==
NULL
)
{
char
str
[
128
];
sprintf
(
str
,
"Cannot open BOP potential file %s"
,
filename
);
error
->
one
(
FLERR
,
str
);
}
fgets
(
s
,
MAXLINE
,
fp
);
// skip first comment line
for
(
i
=
0
;
i
<
bop_types
+
2
;
i
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
}
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf%lf%lf"
,
&
small1
,
&
small2
,
&
small3g
,
&
small4
,
&
small5
,
&
small6
,
&
small7
);
for
(
i
=
0
;
i
<
bop_types
;
i
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf"
,
&
pi_p
[
i
]);
}
cutmax
=
0
;
for
(
i
=
0
;
i
<
npairs
;
i
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf"
,
&
rcut
[
i
]);
if
(
rcut
[
i
]
>
cutmax
)
cutmax
=
rcut
[
i
];
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf"
,
&
sigma_c
[
i
],
&
sigma_a
[
i
],
&
pi_c
[
i
],
&
pi_a
[
i
]);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf"
,
&
sigma_delta
[
i
],
&
pi_delta
[
i
]);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf"
,
&
sigma_f
[
i
],
&
sigma_k
[
i
],
&
small3
[
i
]);
}
if
(
nws
==
3
)
{
for
(
i
=
0
;
i
<
bop_types
;
i
++
)
for
(
j
=
0
;
j
<
bop_types
;
j
++
)
for
(
k
=
j
;
k
<
bop_types
;
k
++
)
{
if
(
npower
<=
2
)
{
for
(
m
=
0
;
m
<
ntheta
;
m
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
gfunc
[
j
][
i
][
k
][
n
],
&
gfunc
[
j
][
i
][
k
][
n
+
1
]
,
&
gfunc
[
j
][
i
][
k
][
n
+
2
],
&
gfunc
[
j
][
i
][
k
][
n
+
3
],
&
gfunc
[
j
][
i
][
k
][
n
+
4
]);
n
+=
4
;
}
}
else
{
if
(
npower
==
3
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
0
],
&
gpara
[
j
][
i
][
k
][
1
],
&
gpara
[
j
][
i
][
k
][
2
],
&
gpara
[
j
][
i
][
k
][
3
]);
}
else
if
(
npower
==
4
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
0
],
&
gpara
[
j
][
i
][
k
][
1
],
&
gpara
[
j
][
i
][
k
][
2
],
&
gpara
[
j
][
i
][
k
][
3
],
&
gpara
[
j
][
i
][
k
][
4
]);
}
else
if
(
npower
==
5
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
0
],
&
gpara
[
j
][
i
][
k
][
1
],
&
gpara
[
j
][
i
][
k
][
2
],
&
gpara
[
j
][
i
][
k
][
3
],
&
gpara
[
j
][
i
][
k
][
4
]);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf"
,
&
gpara
[
j
][
i
][
k
][
5
]);
}
else
if
(
npower
==
6
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
0
],
&
gpara
[
j
][
i
][
k
][
1
],
&
gpara
[
j
][
i
][
k
][
2
],
&
gpara
[
j
][
i
][
k
][
3
],
&
gpara
[
j
][
i
][
k
][
4
]);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
5
],
&
gpara
[
j
][
i
][
k
][
6
]);
}
else
if
(
npower
==
7
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
0
],
&
gpara
[
j
][
i
][
k
][
1
],
&
gpara
[
j
][
i
][
k
][
2
],
&
gpara
[
j
][
i
][
k
][
3
],
&
gpara
[
j
][
i
][
k
][
4
]);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
5
],
&
gpara
[
j
][
i
][
k
][
6
],
&
gpara
[
j
][
i
][
k
][
7
]);
}
else
if
(
npower
==
8
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
0
],
&
gpara
[
j
][
i
][
k
][
1
],
&
gpara
[
j
][
i
][
k
][
2
],
&
gpara
[
j
][
i
][
k
][
3
],
&
gpara
[
j
][
i
][
k
][
4
]);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
5
],
&
gpara
[
j
][
i
][
k
][
6
],
&
gpara
[
j
][
i
][
k
][
7
],
&
gpara
[
j
][
i
][
k
][
8
]);
}
else
if
(
npower
==
9
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
0
],
&
gpara
[
j
][
i
][
k
][
1
],
&
gpara
[
j
][
i
][
k
][
2
],
&
gpara
[
j
][
i
][
k
][
3
],
&
gpara
[
j
][
i
][
k
][
4
]);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
5
],
&
gpara
[
j
][
i
][
k
][
6
],
&
gpara
[
j
][
i
][
k
][
7
],
&
gpara
[
j
][
i
][
k
][
8
],
&
gpara
[
j
][
i
][
k
][
9
]);
}
else
if
(
npower
==
10
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
0
],
&
gpara
[
j
][
i
][
k
][
1
],
&
gpara
[
j
][
i
][
k
][
2
],
&
gpara
[
j
][
i
][
k
][
3
],
&
gpara
[
j
][
i
][
k
][
4
]);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
gpara
[
j
][
i
][
k
][
5
],
&
gpara
[
j
][
i
][
k
][
6
],
&
gpara
[
j
][
i
][
k
][
7
],
&
gpara
[
j
][
i
][
k
][
8
],
&
gpara
[
j
][
i
][
k
][
9
]);
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf"
,
&
gpara
[
j
][
i
][
k
][
10
]);
}
}
}
}
else
{
for
(
i
=
0
;
i
<
bop_types
;
i
++
)
for
(
j
=
0
;
j
<
bop_types
;
j
++
)
for
(
k
=
0
;
k
<
bop_types
;
k
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf"
,
&
gpara
[
i
][
j
][
k
][
0
],
&
gpara
[
i
][
j
][
k
][
1
],
&
gpara
[
i
][
j
][
k
][
2
]);
gpara
[
j
][
i
][
k
][
3
]
=
0
;
}
}
for
(
i
=
0
;
i
<
npairs
;
i
++
)
{
for
(
j
=
0
;
j
<
nr
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
pRepul
[
i
][
j
],
&
pRepul
[
i
][
j
+
1
]
,
&
pRepul
[
i
][
j
+
2
],
&
pRepul
[
i
][
j
+
3
],
&
pRepul
[
i
][
j
+
4
]);
j
+=
4
;
}
}
for
(
i
=
0
;
i
<
npairs
;
i
++
)
{
for
(
j
=
0
;
j
<
nr
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
pBetaS
[
i
][
j
],
&
pBetaS
[
i
][
j
+
1
]
,
&
pBetaS
[
i
][
j
+
2
],
&
pBetaS
[
i
][
j
+
3
],
&
pBetaS
[
i
][
j
+
4
]);
j
+=
4
;
}
}
for
(
i
=
0
;
i
<
npairs
;
i
++
)
{
for
(
j
=
0
;
j
<
nr
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
pBetaP
[
i
][
j
],
&
pBetaP
[
i
][
j
+
1
]
,
&
pBetaP
[
i
][
j
+
2
],
&
pBetaP
[
i
][
j
+
3
],
&
pBetaP
[
i
][
j
+
4
]);
j
+=
4
;
}
}
for
(
i
=
0
;
i
<
npairs
;
i
++
)
{
for
(
j
=
0
;
j
<
nBOt
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
FsigBO
[
i
][
j
],
&
FsigBO
[
i
][
j
+
1
]
,
&
FsigBO
[
i
][
j
+
2
],
&
FsigBO
[
i
][
j
+
3
],
&
FsigBO
[
i
][
j
+
4
]);
j
+=
4
;
}
}
for
(
i
=
0
;
i
<
bop_types
;
i
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf"
,
&
pro_delta
[
i
]);
}
for
(
i
=
0
;
i
<
bop_types
;
i
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf"
,
&
pro
[
i
]);
}
for
(
i
=
0
;
i
<
npairs
;
i
++
)
{
rcut3
[
i
]
=
0.0
;
}
pass
=
0
;
i
=
0
;
if
(
nws
==
3
)
{
while
(
fgets
(
s
,
MAXLINE
,
fp
)
!=
NULL
&&
i
<
npairs
)
{
sscanf
(
s
,
"%lf"
,
&
rcut3
[
i
]);
pass
=
1
;
i
++
;
}
if
(
pass
==
1
)
{
for
(
i
=
0
;
i
<
npairs
;
i
++
)
{
for
(
j
=
0
;
j
<
nr
;
j
++
)
{
fgets
(
s
,
MAXLINE
,
fp
);
sscanf
(
s
,
"%lf%lf%lf%lf%lf"
,
&
pLong
[
i
][
j
],
&
pLong
[
i
][
j
+
1
]
,
&
pLong
[
i
][
j
+
2
],
&
pLong
[
i
][
j
+
3
],
&
pLong
[
i
][
j
+
4
]);
j
+=
4
;
}
}
}
}
rcutall
=
0.0
;
for
(
i
=
0
;
i
<
npairs
;
i
++
)
{
if
(
rcut
[
i
]
>
rcutall
)
rcutall
=
rcut
[
i
];
if
(
rcut3
[
i
]
>
rcutall
)
rcutall
=
rcut3
[
i
];
rcutsq
[
i
]
=
rcut
[
i
]
*
rcut
[
i
];
rcutsq3
[
i
]
=
rcut3
[
i
]
*
rcut3
[
i
];
dr
[
i
]
=
rcut
[
i
]
/
((
double
)
nr
-
1.0
);
rdr
[
i
]
=
1.0
/
dr
[
i
];
dr3
[
i
]
=
rcut3
[
i
]
/
((
double
)
nr
-
1.0
);
rdr3
[
i
]
=
1.0
/
dr3
[
i
];
}
rctroot
=
rcutall
;
dtheta
=
2.0
/
((
double
)
ntheta
-
1.0
);
rdtheta
=
1.0
/
dtheta
;
dBO
=
1.0
/
((
double
)
nBOt
-
1.0
);
rdBO
=
1.0
/
(
double
)
dBO
;
for
(
i
=
0
;
i
<
npairs
;
i
++
)
{
pBetaS1
[
i
][
0
]
=
pBetaS
[
i
][
1
]
-
pBetaS
[
i
][
0
];
pBetaS1
[
i
][
1
]
=
0.5
*
(
pBetaS
[
i
][
2
]
-
pBetaS
[
i
][
0
]);
pBetaS1
[
i
][
nr
-
2
]
=
0.5
*
(
pBetaS
[
i
][
nr
-
1
]
-
pBetaS
[
i
][
nr
-
3
]);
pBetaS1
[
i
][
nr
-
1
]
=
pBetaS
[
i
][
nr
-
1
]
-
pBetaS
[
i
][
nr
-
2
];
pBetaP1
[
i
][
0
]
=
pBetaP
[
i
][
1
]
-
pBetaP
[
i
][
0
];
pBetaP1
[
i
][
1
]
=
0.5
*
(
pBetaP
[
i
][
2
]
-
pBetaP
[
i
][
0
]);
pBetaP1
[
i
][
nr
-
2
]
=
0.5
*
(
pBetaP
[
i
][
nr
-
1
]
-
pBetaP
[
i
][
nr
-
3
]);
pBetaP1
[
i
][
nr
-
1
]
=
pBetaP
[
i
][
nr
-
1
]
-
pBetaP
[
i
][
nr
-
2
];
pRepul1
[
i
][
0
]
=
pRepul
[
i
][
1
]
-
pRepul
[
i
][
0
];
pRepul1
[
i
][
1
]
=
0.5
*
(
pRepul
[
i
][
2
]
-
pRepul
[
i
][
0
]);
pRepul1
[
i
][
nr
-
2
]
=
0.5
*
(
pRepul
[
i
][
nr
-
1
]
-
pRepul
[
i
][
nr
-
3
]);
pRepul1
[
i
][
nr
-
1
]
=
pRepul
[
i
][
nr
-
1
]
-
pRepul
[
i
][
nr
-
2
];
FsigBO1
[
i
][
0
]
=
FsigBO
[
i
][
1
]
-
FsigBO
[
i
][
0
];
FsigBO1
[
i
][
1
]
=
0.5
*
(
FsigBO
[
i
][
2
]
-
FsigBO
[
i
][
0
]);
FsigBO1
[
i
][
nBOt
-
2
]
=
0.5
*
(
FsigBO
[
i
][
nBOt
-
1
]
-
FsigBO
[
i
][
nBOt
-
3
]);
FsigBO1
[
i
][
nBOt
-
1
]
=
FsigBO
[
i
][
nBOt
-
1
]
-
FsigBO
[
i
][
nBOt
-
2
];
pLong1
[
i
][
0
]
=
pLong
[
i
][
1
]
-
pLong
[
i
][
0
];
pLong1
[
i
][
1
]
=
0.5
*
(
pLong
[
i
][
2
]
-
pLong
[
i
][
0
]);
pLong1
[
i
][
nBOt
-
2
]
=
0.5
*
(
pLong
[
i
][
nr
-
1
]
-
pLong
[
i
][
nr
-
3
]);
pLong1
[
i
][
nBOt
-
1
]
=
pLong
[
i
][
nr
-
1
]
-
pLong
[
i
][
nr
-
2
];
for
(
k
=
2
;
k
<
nr
-
2
;
k
++
)
{
pBetaS1
[
i
][
k
]
=
((
pBetaS
[
i
][
k
-
2
]
-
pBetaS
[
i
][
k
+
2
])
+
8.0
*
(
pBetaS
[
i
][
k
+
1
]
-
pBetaS
[
i
][
k
-
1
]))
/
12.0
;
pBetaP1
[
i
][
k
]
=
((
pBetaP
[
i
][
k
-
2
]
-
pBetaP
[
i
][
k
+
2
])
+
8.0
*
(
pBetaP
[
i
][
k
+
1
]
-
pBetaP
[
i
][
k
-
1
]))
/
12.0
;
pRepul1
[
i
][
k
]
=
((
pRepul
[
i
][
k
-
2
]
-
pRepul
[
i
][
k
+
2
])
+
8.0
*
(
pRepul
[
i
][
k
+
1
]
-
pRepul
[
i
][
k
-
1
]))
/
12.0
;
pLong1
[
i
][
k
]
=
((
pLong
[
i
][
k
-
2
]
-
pLong
[
i
][
k
+
2
])
+
8.0
*
(
pLong
[
i
][
k
+
1
]
-
pLong
[
i
][
k
-
1
]))
/
12.0
;
}
for
(
k
=
2
;
k
<
nr
-
2
;
k
++
)
{
FsigBO1
[
i
][
k
]
=
((
FsigBO
[
i
][
k
-
2
]
-
FsigBO
[
i
][
k
+
2
])
+
8.0
*
(
FsigBO
[
i
][
k
+
1
]
-
FsigBO
[
i
][
k
-
1
]))
/
12.0
;
}
for
(
k
=
0
;
k
<
nr
-
1
;
k
++
)
{
pBetaS2
[
i
][
k
]
=
3.0
*
(
pBetaS
[
i
][
k
+
1
]
-
pBetaS
[
i
][
k
])
-
2.0
*
pBetaS1
[
i
][
k
]
-
pBetaS1
[
i
][
k
+
1
];
pBetaS3
[
i
][
k
]
=
pBetaS1
[
i
][
k
]
+
pBetaS1
[
i
][
k
+
1
]
-
2.0
*
(
pBetaS
[
i
][
k
+
1
]
-
pBetaS
[
i
][
k
]);
pBetaP2
[
i
][
k
]
=
3.0
*
(
pBetaP
[
i
][
k
+
1
]
-
pBetaP
[
i
][
k
])
-
2.0
*
pBetaP1
[
i
][
k
]
-
pBetaP1
[
i
][
k
+
1
];
pBetaP3
[
i
][
k
]
=
pBetaP1
[
i
][
k
]
+
pBetaP1
[
i
][
k
+
1
]
-
2.0
*
(
pBetaP
[
i
][
k
+
1
]
-
pBetaP
[
i
][
k
]);
pRepul2
[
i
][
k
]
=
3.0
*
(
pRepul
[
i
][
k
+
1
]
-
pRepul
[
i
][
k
])
-
2.0
*
pRepul1
[
i
][
k
]
-
pRepul1
[
i
][
k
+
1
];
pRepul3
[
i
][
k
]
=
pRepul1
[
i
][
k
]
+
pRepul1
[
i
][
k
+
1
]
-
2.0
*
(
pRepul
[
i
][
k
+
1
]
-
pRepul
[
i
][
k
]);
pLong2
[
i
][
k
]
=
3.0
*
(
pLong
[
i
][
k
+
1
]
-
pLong
[
i
][
k
])
-
2.0
*
pLong1
[
i
][
k
]
-
pLong1
[
i
][
k
+
1
];
pLong3
[
i
][
k
]
=
pLong1
[
i
][
k
]
+
pLong1
[
i
][
k
+
1
]
-
2.0
*
(
pLong
[
i
][
k
+
1
]
-
pLong
[
i
][
k
]);
}
for
(
k
=
0
;
k
<
nBOt
-
1
;
k
++
)
{
FsigBO2
[
i
][
k
]
=
3.0
*
(
FsigBO
[
i
][
k
+
1
]
-
FsigBO
[
i
][
k
])
-
2.0
*
FsigBO1
[
i
][
k
]
-
FsigBO1
[
i
][
k
+
1
];
FsigBO3
[
i
][
k
]
=
FsigBO1
[
i
][
k
]
+
FsigBO1
[
i
][
k
+
1
]
-
2.0
*
(
FsigBO
[
i
][
k
+
1
]
-
FsigBO
[
i
][
k
]);
}
pBetaS2
[
i
][
nr
-
1
]
=
0.0
;
pBetaS3
[
i
][
nr
-
1
]
=
0.0
;
pBetaP2
[
i
][
nr
-
1
]
=
0.0
;
pBetaP3
[
i
][
nr
-
1
]
=
0.0
;
pRepul2
[
i
][
nr
-
1
]
=
0.0
;
pRepul3
[
i
][
nr
-
1
]
=
0.0
;
pLong2
[
i
][
nr
-
1
]
=
0.0
;
pLong3
[
i
][
nr
-
1
]
=
0.0
;
FsigBO2
[
i
][
nBOt
-
1
]
=
0.0
;
FsigBO3
[
i
][
nBOt
-
1
]
=
0.0
;
for
(
k
=
0
;
k
<
nr
;
k
++
)
{
pBetaS4
[
i
][
k
]
=
pBetaS1
[
i
][
k
]
/
dr
[
i
];
pBetaS5
[
i
][
k
]
=
2.0
*
pBetaS2
[
i
][
k
]
/
dr
[
i
];
pBetaS6
[
i
][
k
]
=
3.0
*
pBetaS3
[
i
][
k
]
/
dr
[
i
];
pBetaP4
[
i
][
k
]
=
pBetaP1
[
i
][
k
]
/
dr
[
i
];
pBetaP5
[
i
][
k
]
=
2.0
*
pBetaP2
[
i
][
k
]
/
dr
[
i
];
pBetaP6
[
i
][
k
]
=
3.0
*
pBetaP3
[
i
][
k
]
/
dr
[
i
];
pRepul4
[
i
][
k
]
=
pRepul1
[
i
][
k
]
/
dr
[
i
];
pRepul5
[
i
][
k
]
=
2.0
*
pRepul2
[
i
][
k
]
/
dr
[
i
];
pRepul6
[
i
][
k
]
=
3.0
*
pRepul3
[
i
][
k
]
/
dr
[
i
];
pLong4
[
i
][
k
]
=
pLong1
[
i
][
k
]
/
dr3
[
i
];
pLong5
[
i
][
k
]
=
2.0
*
pLong2
[
i
][
k
]
/
dr3
[
i
];
pLong6
[
i
][
k
]
=
3.0
*
pLong3
[
i
][
k
]
/
dr3
[
i
];
}
for
(
k
=
0
;
k
<
nBOt
;
k
++
)
{
FsigBO4
[
i
][
k
]
=
FsigBO1
[
i
][
k
]
/
dBO
;
FsigBO5
[
i
][
k
]
=
2.0
*
FsigBO2
[
i
][
k
]
/
dBO
;
FsigBO6
[
i
][
k
]
=
3.0
*
FsigBO3
[
i
][
k
]
/
dBO
;
}
}
if
(
npower
<=
2
)
{
for
(
i
=
0
;
i
<
bop_types
;
i
++
)
{
for
(
j
=
0
;
j
<
bop_types
;
j
++
)
{
for
(
k
=
j
;
k
<
bop_types
;
k
++
)
{
gfunc1
[
j
][
i
][
k
][
0
]
=
gfunc
[
j
][
i
][
k
][
1
]
-
gfunc
[
j
][
i
][
k
][
0
];
gfunc1
[
j
][
i
][
k
][
1
]
=
0.5
*
(
gfunc
[
j
][
i
][
k
][
2
]
-
gfunc
[
j
][
i
][
k
][
0
]);
gfunc1
[
j
][
i
][
k
][
ntheta
-
2
]
=
0.5
*
(
gfunc
[
j
][
i
][
k
][
ntheta
-
1
]
-
gfunc
[
j
][
i
][
k
][
ntheta
-
3
]);
gfunc1
[
j
][
i
][
k
][
ntheta
-
1
]
=
0.5
*
(
gfunc
[
j
][
i
][
k
][
ntheta
-
1
]
-
gfunc
[
j
][
i
][
k
][
ntheta
-
2
]);
for
(
m
=
2
;
m
<
ntheta
-
2
;
m
++
)
{
gfunc1
[
j
][
i
][
k
][
m
]
=
((
gfunc
[
j
][
i
][
k
][
m
-
2
]
-
gfunc
[
j
][
i
][
k
][
m
+
2
])
+
8.0
*
(
gfunc
[
j
][
i
][
k
][
m
+
1
]
-
gfunc
[
j
][
i
][
k
][
m
+
1
]
-
gfunc
[
j
][
i
][
k
][
m
-
1
]))
/
12.0
;
}
for
(
m
=
0
;
m
<
ntheta
-
1
;
m
++
)
{
gfunc2
[
j
][
i
][
k
][
m
]
=
3.0
*
(
gfunc
[
j
][
i
][
k
][
m
+
1
]
-
gfunc
[
j
][
i
][
k
][
m
])
-
2.0
*
gfunc1
[
j
][
i
][
k
][
m
]
-
gfunc1
[
j
][
i
][
k
][
m
+
1
];
gfunc3
[
j
][
i
][
k
][
m
]
=
gfunc1
[
j
][
i
][
k
][
m
]
+
gfunc1
[
j
][
i
][
k
][
m
+
1
]
-
2.0
*
(
gfunc
[
j
][
i
][
k
][
m
+
1
]
-
gfunc
[
j
][
i
][
k
][
m
]);
}
gfunc2
[
j
][
i
][
k
][
ntheta
-
1
]
=
0.0
;
gfunc3
[
j
][
i
][
k
][
ntheta
-
1
]
=
0.0
;
for
(
m
=
0
;
m
<
ntheta
;
m
++
)
{
gfunc4
[
j
][
i
][
k
][
ntheta
-
1
]
=
gfunc1
[
j
][
i
][
k
][
m
]
/
dtheta
;
gfunc5
[
j
][
i
][
k
][
ntheta
-
1
]
=
2.0
*
gfunc2
[
j
][
i
][
k
][
m
]
/
dtheta
;
gfunc6
[
j
][
i
][
k
][
ntheta
-
1
]
=
3.0
*
gfunc3
[
j
][
i
][
k
][
m
]
/
dtheta
;
}
}
}
}
}
for
(
i
=
0
;
i
<
bop_types
;
i
++
)
{
for
(
j
=
0
;
j
<
bop_types
;
j
++
)
{
for
(
k
=
0
;
k
<
j
;
k
++
)
{
if
(
npower
<=
2
)
{
for
(
n
=
0
;
n
<
ntheta
;
n
++
)
{
gfunc
[
j
][
i
][
k
][
n
]
=
gfunc
[
k
][
i
][
j
][
n
];
gfunc1
[
j
][
i
][
k
][
n
]
=
gfunc1
[
k
][
i
][
j
][
n
];
gfunc2
[
j
][
i
][
k
][
n
]
=
gfunc2
[
k
][
i
][
j
][
n
];
gfunc3
[
j
][
i
][
k
][
n
]
=
gfunc3
[
k
][
i
][
j
][
n
];
gfunc4
[
j
][
i
][
k
][
n
]
=
gfunc4
[
k
][
i
][
j
][
n
];
gfunc5
[
j
][
i
][
k
][
n
]
=
gfunc5
[
k
][
i
][
j
][
n
];
gfunc6
[
j
][
i
][
k
][
n
]
=
gfunc6
[
k
][
i
][
j
][
n
];
}
}
else
{
for
(
n
=
0
;
n
<
npower
+
1
;
n
++
)
{
gpara
[
j
][
i
][
k
][
n
]
=
gpara
[
k
][
i
][
j
][
n
];
}
}
}
}
}
fclose
(
fp
);
}
MPI_Bcast
(
&
rdBO
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
dBO
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rdtheta
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
dtheta
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
bop_types
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
&
small1
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
small2
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
small3g
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
small4
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
small5
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
small6
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
small7
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pro
[
0
],
bop_types
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pro_delta
[
0
],
bop_types
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pi_p
[
0
],
bop_types
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
r1
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcut
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcut3
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcutsq
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rcutsq3
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
cutmax
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma_a
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma_c
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma_delta
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pi_a
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pi_c
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pi_delta
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma_f
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
sigma_k
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
small3
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
dr
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rdr
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
dr3
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
rdr3
[
0
],
npairs
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaS
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaS1
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaS2
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaS3
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaS4
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaS5
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaS6
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaP
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaP1
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaP2
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaP3
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaP4
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaP5
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pBetaP6
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pLong
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pLong1
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pLong2
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pLong3
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pLong4
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pLong5
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pLong6
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pRepul
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pRepul1
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pRepul2
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pRepul3
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pRepul4
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pRepul5
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
pRepul6
[
0
][
0
],
npairs
*
nr
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
FsigBO
[
0
][
0
],
npairs
*
nBOt
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
FsigBO1
[
0
][
0
],
npairs
*
nBOt
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
FsigBO2
[
0
][
0
],
npairs
*
nBOt
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
FsigBO3
[
0
][
0
],
npairs
*
nBOt
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
FsigBO4
[
0
][
0
],
npairs
*
nBOt
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
FsigBO5
[
0
][
0
],
npairs
*
nBOt
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
FsigBO6
[
0
][
0
],
npairs
*
nBOt
,
MPI_DOUBLE
,
0
,
world
);
if
(
npower
<=
2
){
MPI_Bcast
(
&
gfunc
[
0
][
0
][
0
][
0
],
bop_types
*
bop_types
*
bop_types
*
ntheta
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gfunc1
[
0
][
0
][
0
][
0
],
bop_types
*
bop_types
*
bop_types
*
ntheta
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gfunc2
[
0
][
0
][
0
][
0
],
bop_types
*
bop_types
*
bop_types
*
ntheta
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gfunc3
[
0
][
0
][
0
][
0
],
bop_types
*
bop_types
*
bop_types
*
ntheta
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gfunc4
[
0
][
0
][
0
][
0
],
bop_types
*
bop_types
*
bop_types
*
ntheta
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gfunc5
[
0
][
0
][
0
][
0
],
bop_types
*
bop_types
*
bop_types
*
ntheta
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gfunc6
[
0
][
0
][
0
][
0
],
bop_types
*
bop_types
*
bop_types
*
ntheta
,
MPI_DOUBLE
,
0
,
world
);
}
else
{
MPI_Bcast
(
&
gpara
[
0
][
0
][
0
][
0
],
bop_types
*
bop_types
*
bop_types
*
(
npower
+
1
),
MPI_DOUBLE
,
0
,
world
);
}
}
/* ---------------------------------------------------------------------- */
double
PairBOP
::
cutoff
(
double
rp
,
double
vrcut
,
int
mode
,
double
r
)
{
double
tmp
,
tmp_beta
,
tmp_alpha
,
cut_store
;
if
(
mode
==
1
)
{
tmp
=
(
rsmall
-
rbig
)
*
(
r
-
rp
)
/
(
vrcut
-
rp
)
+
rbig
;
cut_store
=
(
erfc
(
tmp
)
-
erfc
(
rsmall
))
/
(
erfc
(
rbig
)
-
erfc
(
rsmall
));
}
else
{
tmp_beta
=
log
(
log
(
rbig
)
/
log
(
rsmall
))
/
log
(
rp
/
vrcut
);
tmp_alpha
=-
log
(
rbig
)
/
pow
(
rp
,
tmp_beta
);
cut_store
=
(
exp
(
-
tmp_alpha
*
pow
(
r
,
tmp_beta
))
-
exp
(
-
tmp_alpha
*
pow
(
vrcut
,
tmp_beta
)))
/
(
exp
(
-
tmp_alpha
*
pow
(
rp
,
tmp_beta
))
-
exp
(
-
tmp_alpha
*
pow
(
vrcut
,
tmp_beta
)));
}
return
(
cut_store
);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double
PairBOP
::
memory_usage
()
{
int
nlocal
,
nghost
,
nall
;
int
n
=
atom
->
ntypes
;
nlocal
=
atom
->
nlocal
;
nghost
=
atom
->
nghost
;
nall
=
nlocal
+
nghost
;
double
bytes
=
0.0
;
// rcut
bytes
+=
npairs
*
sizeof
(
double
);
// rcut3
bytes
+=
npairs
*
sizeof
(
double
);
// rcutsq
bytes
+=
npairs
*
sizeof
(
double
);
// rcutsq3
bytes
+=
npairs
*
sizeof
(
double
);
// dr
bytes
+=
npairs
*
sizeof
(
double
);
// rdr
bytes
+=
npairs
*
sizeof
(
double
);
// dr3
bytes
+=
npairs
*
sizeof
(
double
);
// rdr3
bytes
+=
npairs
*
sizeof
(
double
);
// setflag
bytes
+=
(
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
int
);
// cutsq
bytes
+=
(
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
double
);
// cutghost
bytes
+=
(
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
double
);
// cutghost
bytes
+=
(
n
+
1
)
*
(
n
+
1
)
*
sizeof
(
double
);
// pBetaS
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaS1
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaS2
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaS3
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaS4
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaS5
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaS6
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pLong
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pLong1
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pLong2
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pLong3
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pLong4
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pLong5
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pLong6
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaP
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaP1
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaP2
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaP3
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaP4
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaP5
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pBetaP6
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pRepul
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pRepul1
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pRepul2
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pRepul3
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pRepul4
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pRepul5
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// pRepul6
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// FsigBO
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// FsigBO1
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// FsigBO2
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// FsigBO3
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// FsigBO4
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// FsigBO5
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// FsigBO6
bytes
+=
npairs
*
nr
*
sizeof
(
double
);
// itypeSigBk
bytes
+=
neigh_ct
*
sizeof
(
int
);
// itypePiBk
bytes
+=
neigh_ct
*
sizeof
(
int
);
// BOP_index
bytes
+=
nall
*
sizeof
(
double
);
// BOP_total
bytes
+=
nall
*
sizeof
(
double
);
if
(
otfly
==
0
)
{
// cosAng
bytes
+=
cos_total
*
sizeof
(
double
);
// dcAng
bytes
+=
cos_total
*
3
*
2
*
sizeof
(
double
);
// disij
bytes
+=
neigh_total
*
3
*
sizeof
(
double
);
// rij
bytes
+=
neigh_total
*
sizeof
(
double
);
// betaS
bytes
+=
neigh_total
*
sizeof
(
double
);
// dBetaS
bytes
+=
neigh_total
*
sizeof
(
double
);
// betaP
bytes
+=
neigh_total
*
sizeof
(
double
);
// dBetaP
bytes
+=
neigh_total
*
sizeof
(
double
);
// repul
bytes
+=
neigh_total
*
sizeof
(
double
);
// dRepul
bytes
+=
neigh_total
*
sizeof
(
double
);
// cos_index
bytes
+=
nall
*
sizeof
(
double
);
}
// pi_a
bytes
+=
npairs
*
sizeof
(
double
);
// pro
bytes
+=
bop_types
*
sizeof
(
double
);
// pi_delta
bytes
+=
npairs
*
sizeof
(
double
);
// pi_p
bytes
+=
npairs
*
sizeof
(
double
);
// pi_c
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_r0
bytes
+=
npairs
*
sizeof
(
double
);
// pi_r0
bytes
+=
npairs
*
sizeof
(
double
);
// phi_r0
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_rc
bytes
+=
npairs
*
sizeof
(
double
);
// pi_rc
bytes
+=
npairs
*
sizeof
(
double
);
// pi_a
bytes
+=
npairs
*
sizeof
(
double
);
// pro_delta
bytes
+=
bop_types
*
sizeof
(
double
);
// pi_delta
bytes
+=
npairs
*
sizeof
(
double
);
// pi_p
bytes
+=
npairs
*
sizeof
(
double
);
// pi_c
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_r0
bytes
+=
npairs
*
sizeof
(
double
);
// pi_r0
bytes
+=
npairs
*
sizeof
(
double
);
// phi_r0
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_rc
bytes
+=
npairs
*
sizeof
(
double
);
// pi_rc
bytes
+=
npairs
*
sizeof
(
double
);
// phi_rc
bytes
+=
npairs
*
sizeof
(
double
);
// r1
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_beta0
bytes
+=
npairs
*
sizeof
(
double
);
// pi_beta0
bytes
+=
npairs
*
sizeof
(
double
);
// phi0
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_n
bytes
+=
npairs
*
sizeof
(
double
);
// pi_n
bytes
+=
npairs
*
sizeof
(
double
);
// phi_m
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_nc
bytes
+=
npairs
*
sizeof
(
double
);
// pi_nc
bytes
+=
npairs
*
sizeof
(
double
);
// phi_nc
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_delta
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_c
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_a
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_f
bytes
+=
npairs
*
sizeof
(
double
);
// sigma_k
bytes
+=
npairs
*
sizeof
(
double
);
// small3
bytes
+=
npairs
*
sizeof
(
double
);
// bt_pi
bytes
+=
maxneigh
*
(
maxneigh
/
2
)
*
sizeof
(
B_PI
);
// bt_sigma
bytes
+=
maxneigh
*
(
maxneigh
/
2
)
*
sizeof
(
B_SG
);
if
(
npower
<=
2
)
{
// gfunc
bytes
+=
bop_types
*
bop_types
*
bop_types
*
ntheta
*
sizeof
(
double
);
// gfunc1
bytes
+=
bop_types
*
bop_types
*
bop_types
*
ntheta
*
sizeof
(
double
);
// gfunc2
bytes
+=
bop_types
*
bop_types
*
bop_types
*
ntheta
*
sizeof
(
double
);
// gfunc3
bytes
+=
bop_types
*
bop_types
*
bop_types
*
ntheta
*
sizeof
(
double
);
// gfunc4
bytes
+=
bop_types
*
bop_types
*
bop_types
*
ntheta
*
sizeof
(
double
);
// gfunc5
bytes
+=
bop_types
*
bop_types
*
bop_types
*
ntheta
*
sizeof
(
double
);
// gfunc6
bytes
+=
bop_types
*
bop_types
*
bop_types
*
ntheta
*
sizeof
(
double
);
}
else
{
bytes
+=
bop_types
*
bop_types
*
bop_types
*
npower
+
1
*
sizeof
(
double
);
}
return
bytes
;
}
/* ---------------------------------------------------------------------- */
void
PairBOP
::
memory_theta_create
()
{
neigh_ct
=
(
maxneigh
-
1
)
*
(
maxneigh
-
1
)
*
(
maxneigh
-
1
);
if
(
neigh_ct
<
1
)
neigh_ct
=
1
;
memory
->
create
(
itypeSigBk
,
neigh_ct
,
"itypeSigBk"
);
memory
->
create
(
itypePiBk
,
neigh_ct
,
"itypePiBk"
);
memory
->
create
(
neigh_flag
,
neigh_total
,
"neigh_flag"
);
memory
->
create
(
neigh_flag3
,
neigh_total3
,
"neigh_flag3"
);
memory
->
create
(
neigh_index
,
neigh_total
,
"neigh_index"
);
memory
->
create
(
neigh_index3
,
neigh_total3
,
"neigh_index3"
);
if
(
otfly
==
0
)
{
memory
->
create
(
cosAng
,
cos_total
,
"BOP:cosAng"
);
memory
->
create
(
dcAng
,
cos_total
,
3
,
2
,
"BOP:dcAng"
);
memory
->
create
(
disij
,
3
,
neigh_total
,
"disij"
);
memory
->
create
(
rij
,
neigh_total
,
"rij"
);
memory
->
create
(
betaS
,
neigh_total
,
"betaS"
);
memory
->
create
(
dBetaS
,
neigh_total
,
"dBetaS"
);
memory
->
create
(
betaP
,
neigh_total
,
"betaP"
);
memory
->
create
(
dBetaP
,
neigh_total
,
"dBetaP"
);
memory
->
create
(
repul
,
neigh_total
,
"repul"
);
memory
->
create
(
dRepul
,
neigh_total
,
"dRepul"
);
}
update_list
=
1
;
}
/* ---------------------------------------------------------------------- */
void
PairBOP
::
memory_theta_grow
()
{
neigh_ct
=
(
maxneigh
-
1
)
*
(
maxneigh
-
1
)
*
(
maxneigh
-
1
);
if
(
neigh_ct
<
1
)
neigh_ct
=
1
;
memory
->
grow
(
itypeSigBk
,
neigh_ct
,
"itypeSigBk"
);
memory
->
grow
(
itypePiBk
,
neigh_ct
,
"itypePiBk"
);
memory
->
grow
(
neigh_flag
,
neigh_total
,
"neigh_flag"
);
memory
->
grow
(
neigh_flag3
,
neigh_total3
,
"neigh_flag3"
);
memory
->
grow
(
neigh_index
,
neigh_total
,
"neigh_index"
);
memory
->
grow
(
neigh_index3
,
neigh_total3
,
"neigh_index3"
);
if
(
otfly
==
0
)
{
memory
->
grow
(
cosAng
,
cos_total
,
"BOP:cosAng"
);
memory
->
grow
(
dcAng
,
cos_total
,
3
,
2
,
"BOP:dcAng"
);
memory
->
grow
(
disij
,
3
,
neigh_total
,
"disij"
);
memory
->
grow
(
rij
,
neigh_total
,
"rij"
);
memory
->
grow
(
betaS
,
neigh_total
,
"betaS"
);
memory
->
grow
(
dBetaS
,
neigh_total
,
"dBetaS"
);
memory
->
grow
(
betaP
,
neigh_total
,
"betaP"
);
memory
->
grow
(
dBetaP
,
neigh_total
,
"dBetaP"
);
memory
->
grow
(
repul
,
neigh_total
,
"repul"
);
memory
->
grow
(
dRepul
,
neigh_total
,
"dRepul"
);
}
update_list
=
1
;
}
/* ---------------------------------------------------------------------- */
void
PairBOP
::
memory_theta_destroy
()
{
memory
->
destroy
(
itypeSigBk
);
memory
->
destroy
(
itypePiBk
);
memory
->
destroy
(
neigh_flag
);
memory
->
destroy
(
neigh_flag3
);
memory
->
destroy
(
neigh_index
);
memory
->
destroy
(
neigh_index3
);
if
(
otfly
==
0
)
{
memory
->
destroy
(
cosAng
);
memory
->
destroy
(
dcAng
);
memory
->
destroy
(
disij
);
memory
->
destroy
(
rij
);
memory
->
destroy
(
betaS
);
memory
->
destroy
(
dBetaS
);
memory
->
destroy
(
betaP
);
memory
->
destroy
(
dBetaP
);
memory
->
destroy
(
repul
);
memory
->
destroy
(
dRepul
);
}
update_list
=
0
;
}
/* ---------------------------------------------------------------------- */
void
PairBOP
::
create_pi
(
int
n_tot
)
{
bt_pi
=
(
B_PI
*
)
memory
->
smalloc
(
n_tot
*
sizeof
(
B_PI
),
"BOP:bt_pi"
);
allocate_pi
=
1
;
}
void
PairBOP
::
create_sigma
(
int
n_tot
)
{
bt_sg
=
(
B_SG
*
)
memory
->
smalloc
(
n_tot
*
sizeof
(
B_SG
),
"BOP:bt_sg"
);
allocate_sigma
=
1
;
}
void
PairBOP
::
destroy_pi
()
{
memory
->
destroy
(
bt_pi
);
allocate_pi
=
0
;
}
void
PairBOP
::
destroy_sigma
()
{
memory
->
destroy
(
bt_sg
);
allocate_sigma
=
0
;
}
/* ---------------------------------------------------------------------- */
void
PairBOP
::
grow_pi
(
int
n1
,
int
n2
)
{
int
i
,
j
;
B_PI
*
bt_temp
;
bt_temp
=
(
B_PI
*
)
memory
->
smalloc
(
n1
*
sizeof
(
B_PI
),
"BOP:b_temp"
);
for
(
i
=
0
;
i
<
n1
;
i
++
)
{
bt_temp
[
i
].
temp
=
bt_pi
[
i
].
temp
;
bt_temp
[
i
].
i
=
bt_pi
[
i
].
i
;
bt_temp
[
i
].
j
=
bt_pi
[
i
].
j
;
for
(
j
=
0
;
j
<
3
;
j
++
)
{
bt_temp
[
i
].
dAA
[
j
]
=
bt_pi
[
i
].
dAA
[
j
];
bt_temp
[
i
].
dBB
[
j
]
=
bt_pi
[
i
].
dBB
[
j
];
bt_temp
[
i
].
dPiB
[
j
]
=
bt_pi
[
i
].
dPiB
[
j
];
}
}
memory
->
destroy
(
bt_pi
);
bt_pi
=
NULL
;
bt_pi
=
(
B_PI
*
)
memory
->
smalloc
(
n2
*
sizeof
(
B_PI
),
"BOP:bt_pi"
);
for
(
i
=
0
;
i
<
n1
;
i
++
)
{
bt_pi
[
i
].
temp
=
bt_temp
[
i
].
temp
;
bt_pi
[
i
].
i
=
bt_temp
[
i
].
i
;
bt_pi
[
i
].
j
=
bt_temp
[
i
].
j
;
for
(
j
=
0
;
j
<
3
;
j
++
)
{
bt_pi
[
i
].
dAA
[
j
]
=
bt_temp
[
i
].
dAA
[
j
];
bt_pi
[
i
].
dBB
[
j
]
=
bt_temp
[
i
].
dBB
[
j
];
bt_pi
[
i
].
dPiB
[
j
]
=
bt_temp
[
i
].
dPiB
[
j
];
}
}
for
(
i
=
n1
;
i
<
n2
;
i
++
)
{
bt_pi
[
i
].
i
=
-
1
;
bt_pi
[
i
].
j
=
-
1
;
for
(
j
=
0
;
j
<
3
;
j
++
)
{
bt_pi
[
i
].
dAA
[
j
]
=
0.0
;
bt_pi
[
i
].
dBB
[
j
]
=
0.0
;
bt_pi
[
i
].
dPiB
[
j
]
=
0.0
;
}
}
memory
->
destroy
(
bt_temp
);
}
/* ---------------------------------------------------------------------- */
void
PairBOP
::
grow_sigma
(
int
n1
,
int
n2
)
{
int
i
,
j
;
B_SG
*
bt_temp
;
bt_temp
=
(
B_SG
*
)
memory
->
smalloc
(
n1
*
sizeof
(
B_SG
),
"BOP:bt_temp"
);
for
(
i
=
0
;
i
<
n1
;
i
++
)
{
bt_temp
[
i
].
temp
=
bt_sg
[
i
].
temp
;
bt_temp
[
i
].
i
=
bt_sg
[
i
].
i
;
bt_temp
[
i
].
j
=
bt_sg
[
i
].
j
;
for
(
j
=
0
;
j
<
3
;
j
++
)
{
bt_temp
[
i
].
dAA
[
j
]
=
bt_sg
[
i
].
dAA
[
j
];
bt_temp
[
i
].
dBB
[
j
]
=
bt_sg
[
i
].
dBB
[
j
];
bt_temp
[
i
].
dCC
[
j
]
=
bt_sg
[
i
].
dCC
[
j
];
bt_temp
[
i
].
dDD
[
j
]
=
bt_sg
[
i
].
dDD
[
j
];
bt_temp
[
i
].
dEE
[
j
]
=
bt_sg
[
i
].
dEE
[
j
];
bt_temp
[
i
].
dEE1
[
j
]
=
bt_sg
[
i
].
dEE1
[
j
];
bt_temp
[
i
].
dFF
[
j
]
=
bt_sg
[
i
].
dFF
[
j
];
bt_temp
[
i
].
dAAC
[
j
]
=
bt_sg
[
i
].
dAAC
[
j
];
bt_temp
[
i
].
dBBC
[
j
]
=
bt_sg
[
i
].
dBBC
[
j
];
bt_temp
[
i
].
dCCC
[
j
]
=
bt_sg
[
i
].
dCCC
[
j
];
bt_temp
[
i
].
dDDC
[
j
]
=
bt_sg
[
i
].
dDDC
[
j
];
bt_temp
[
i
].
dEEC
[
j
]
=
bt_sg
[
i
].
dEEC
[
j
];
bt_temp
[
i
].
dFFC
[
j
]
=
bt_sg
[
i
].
dFFC
[
j
];
bt_temp
[
i
].
dGGC
[
j
]
=
bt_sg
[
i
].
dGGC
[
j
];
bt_temp
[
i
].
dUT
[
j
]
=
bt_sg
[
i
].
dUT
[
j
];
bt_temp
[
i
].
dSigB1
[
j
]
=
bt_sg
[
i
].
dSigB1
[
j
];
bt_temp
[
i
].
dSigB
[
j
]
=
bt_sg
[
i
].
dSigB
[
j
];
}
}
memory
->
destroy
(
bt_sg
);
bt_sg
=
NULL
;
bt_sg
=
(
B_SG
*
)
memory
->
smalloc
(
n2
*
sizeof
(
B_SG
),
"BOP:bt_sg"
);
for
(
i
=
0
;
i
<
n1
;
i
++
)
{
bt_sg
[
i
].
temp
=
bt_temp
[
i
].
temp
;
bt_sg
[
i
].
i
=
bt_temp
[
i
].
i
;
bt_sg
[
i
].
j
=
bt_temp
[
i
].
j
;
for
(
j
=
0
;
j
<
3
;
j
++
)
{
bt_sg
[
i
].
dAA
[
j
]
=
bt_temp
[
i
].
dAA
[
j
];
bt_sg
[
i
].
dBB
[
j
]
=
bt_temp
[
i
].
dBB
[
j
];
bt_sg
[
i
].
dCC
[
j
]
=
bt_temp
[
i
].
dCC
[
j
];
bt_sg
[
i
].
dDD
[
j
]
=
bt_temp
[
i
].
dDD
[
j
];
bt_sg
[
i
].
dEE
[
j
]
=
bt_temp
[
i
].
dEE
[
j
];
bt_sg
[
i
].
dEE1
[
j
]
=
bt_temp
[
i
].
dEE1
[
j
];
bt_sg
[
i
].
dFF
[
j
]
=
bt_temp
[
i
].
dFF
[
j
];
bt_sg
[
i
].
dAAC
[
j
]
=
bt_temp
[
i
].
dAAC
[
j
];
bt_sg
[
i
].
dBBC
[
j
]
=
bt_temp
[
i
].
dBBC
[
j
];
bt_sg
[
i
].
dCCC
[
j
]
=
bt_temp
[
i
].
dCCC
[
j
];
bt_sg
[
i
].
dDDC
[
j
]
=
bt_temp
[
i
].
dDDC
[
j
];
bt_sg
[
i
].
dEEC
[
j
]
=
bt_temp
[
i
].
dEEC
[
j
];
bt_sg
[
i
].
dFFC
[
j
]
=
bt_temp
[
i
].
dFFC
[
j
];
bt_sg
[
i
].
dGGC
[
j
]
=
bt_temp
[
i
].
dGGC
[
j
];
bt_sg
[
i
].
dUT
[
j
]
=
bt_temp
[
i
].
dUT
[
j
];
bt_sg
[
i
].
dSigB1
[
j
]
=
bt_temp
[
i
].
dSigB1
[
j
];
bt_sg
[
i
].
dSigB
[
j
]
=
bt_temp
[
i
].
dSigB
[
j
];
}
}
for
(
i
=
n1
;
i
<
n2
;
i
++
)
{
bt_sg
[
i
].
i
=
-
1
;
bt_sg
[
i
].
j
=
-
1
;
for
(
j
=
0
;
j
<
3
;
j
++
)
{
bt_sg
[
i
].
dAA
[
j
]
=
0.0
;
bt_sg
[
i
].
dBB
[
j
]
=
0.0
;
bt_sg
[
i
].
dCC
[
j
]
=
0.0
;
bt_sg
[
i
].
dDD
[
j
]
=
0.0
;
bt_sg
[
i
].
dEE
[
j
]
=
0.0
;
bt_sg
[
i
].
dEE1
[
j
]
=
0.0
;
bt_sg
[
i
].
dFF
[
j
]
=
0.0
;
bt_sg
[
i
].
dAAC
[
j
]
=
0.0
;
bt_sg
[
i
].
dBBC
[
j
]
=
0.0
;
bt_sg
[
i
].
dCCC
[
j
]
=
0.0
;
bt_sg
[
i
].
dDDC
[
j
]
=
0.0
;
bt_sg
[
i
].
dEEC
[
j
]
=
0.0
;
bt_sg
[
i
].
dFFC
[
j
]
=
0.0
;
bt_sg
[
i
].
dGGC
[
j
]
=
0.0
;
bt_sg
[
i
].
dUT
[
j
]
=
0.0
;
bt_sg
[
i
].
dSigB1
[
j
]
=
0.0
;
bt_sg
[
i
].
dSigB
[
j
]
=
0.0
;
}
}
memory
->
destroy
(
bt_temp
);
}
Event Timeline
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