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rLAMMPS lammps
pair_mgpt.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: Tomas Oppelstrup, LLNL (oppelstrup2@llnl.gov)
and John Moriarty, LLNL (moriarty2@llnl.gov)
Fast MGPT algorithm developed by Tomas Oppelstrup (2015) based on the
matrix MGPT v4.4 FORTRAN routine of John Moriarty (2006) as converted
to C++ for LAMMPS application by Jamie Marian and Alexander Stukowski
(2011). See LLNL copyright notice at bottom of this file.
------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <cassert>
#include "pair_mgpt.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
//#define TIMING_ON
#ifdef TIMING_ON
#include <sys/time.h>
#include <time.h>
//#include "rdtsc.h"
#ifdef __bgq__
#include <hwi/include/bqc/A2_inlines.h>
#endif
static
double
gettime
(
int
x
=
0
)
{
if
(
1
)
{
/*
struct timeval tv;
gettimeofday(&tv,NULL);
return tv.tv_sec + 1e-6 * tv.tv_usec;
*/
/*
const double x = 1.0 / CLOCKS_PER_SEC;
return clock() * x;
*/
//const double invfreq = 1.0 / 2394.108e6;
/*
const double invfreq = 1.0 / 700e6;
unsigned long long int x = rdtsc();
return x*invfreq;
*/
const
double
invfreq
=
1.0
/
1.6e9
;
unsigned
long
long
int
x
=
GetTimeBase
();
return
x
*
invfreq
;
}
else
return
0.0
;
}
#else
static
double
gettime
(
int
x
=
0
)
{
return
0.0
;
}
#endif
/* ---------------------------------------------------------------------- */
PairMGPT
::
PairMGPT
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
single_enable
=
0
;
one_coeff
=
1
;
ghostneigh
=
1
;
}
PairMGPT
::~
PairMGPT
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cutghost
);
}
}
/* ---------------------------------------------------------------------- */
static
double
t_make_b2
=
0.0
,
n_make_b2
=
0.0
;
template
<
typename
intype
,
typename
outtype
,
int
ni
,
int
nj
>
void
fmatconv
(
intype
*
array
)
{
outtype
*
cast
=
(
outtype
*
)
array
;
for
(
int
i
=
0
;
i
<
ni
;
i
++
)
for
(
int
j
=
0
;
j
<
nj
;
j
++
)
cast
[
i
*
nj
+
j
]
=
array
[
i
*
nj
+
j
];
}
void
PairMGPT
::
make_bond
(
const
double
xx
[][
3
],
int
i
,
int
j
,
bond_data
*
bptr
)
{
double
rrij
[
3
],
rij
;
int
p
;
double
t0
,
t1
;
/* Check that alignment requirements for SIMD code are fullfilled */
assert
(
(((
unsigned
long
long
int
)
(
bptr
->
H
.
m
))
&
31
)
==
0
);
assert
(
(((
unsigned
long
long
int
)
(
bptr
->
Hx
.
m
))
&
31
)
==
0
);
assert
(
(((
unsigned
long
long
int
)
(
bptr
->
Hy
.
m
))
&
31
)
==
0
);
assert
(
(((
unsigned
long
long
int
)
(
bptr
->
Hz
.
m
))
&
31
)
==
0
);
rij
=
0.0
;
for
(
p
=
0
;
p
<
3
;
p
++
)
{
rrij
[
p
]
=
xx
[
i
][
p
]
-
xx
[
j
][
p
];
rij
=
rij
+
rrij
[
p
]
*
rrij
[
p
];
}
/* Zero all matrix elements */
for
(
i
=
0
;
i
<
8
;
i
++
)
for
(
j
=
0
;
j
<
8
;
j
++
)
{
bptr
->
H
.
m
[
i
][
j
]
=
0.0
;
bptr
->
Hx
.
m
[
i
][
j
]
=
0.0
;
bptr
->
Hy
.
m
[
i
][
j
]
=
0.0
;
bptr
->
Hz
.
m
[
i
][
j
]
=
0.0
;
bptr
->
Hz
.
m
[
j
][
i
]
=
0.0
;
}
if
(
rij
<=
rcrit
*
rcrit
)
{
t0
=
gettime
();
if
(
lang
==
3
)
{
hamltn_5_raw
(
rrij
[
0
],
rrij
[
1
],
rrij
[
2
],
bptr
->
H
.
m
,
bptr
->
Hx
.
m
,
bptr
->
Hy
.
m
,
bptr
->
Hz
.
m
,
&
bptr
->
fl_deriv_sum
);
}
else
{
hamltn_7_raw
(
rrij
[
0
],
rrij
[
1
],
rrij
[
2
],
bptr
->
H
.
m
,
bptr
->
Hx
.
m
,
bptr
->
Hy
.
m
,
bptr
->
Hz
.
m
,
&
bptr
->
fl_deriv_sum
);
}
t1
=
gettime
();
t_make_b2
+=
t1
-
t0
;
n_make_b2
++
;
}
else
{
bptr
->
fl_deriv_sum
=
0.0
;
}
if
(
linalg
.
single
)
{
fmatconv
<
double
,
float
,
7
,
8
>
(
&
(
bptr
->
H
.
m
[
1
][
0
]));
fmatconv
<
double
,
float
,
7
,
8
>
(
&
(
bptr
->
Hx
.
m
[
1
][
0
]));
fmatconv
<
double
,
float
,
7
,
8
>
(
&
(
bptr
->
Hy
.
m
[
1
][
0
]));
fmatconv
<
double
,
float
,
7
,
8
>
(
&
(
bptr
->
Hz
.
m
[
1
][
0
]));
}
}
static
double
t_trace
=
0.0
,
n_trace
=
0.0
;
/*
static inline double mtrace(int n,double A[8][8],double B[8][8]) {
double t0,t1;
double s;
t0 = gettime();
if(n == 5) s = mtrace_5(A,B);
else if(n == 7) s = mtrace_7(A,B);
else {
s = 0.0;
for(int i = 1; i<=n; i++)
for(int j = 1; j<=n; j++)
s = s + A[i][j]*B[i][j];
}
t1 = gettime();
t_trace += t1-t0;
n_trace++;
return s;
}
*/
void
PairMGPT
::
make_triplet
(
bond_data
*
ij_bond
,
bond_data
*
ik_bond
,
triplet_data
*
triptr
)
{
if
(
1
)
{
const
trmul_fun
tr_mul
=
linalg
.
tr_mul
;
tr_mul
(
&
(
ij_bond
->
H
.
m
[
1
][
0
]),
&
(
ik_bond
->
H
.
m
[
1
][
0
])
,
&
(
triptr
->
H1H2
.
m
[
1
][
0
])
);
tr_mul
(
&
(
ij_bond
->
Hx
.
m
[
1
][
0
]),
&
(
ik_bond
->
H
.
m
[
1
][
0
])
,
&
(
triptr
->
H1xH2
.
m
[
1
][
0
]));
tr_mul
(
&
(
ij_bond
->
Hy
.
m
[
1
][
0
]),
&
(
ik_bond
->
H
.
m
[
1
][
0
])
,
&
(
triptr
->
H1yH2
.
m
[
1
][
0
]));
tr_mul
(
&
(
ij_bond
->
Hz
.
m
[
1
][
0
]),
&
(
ik_bond
->
H
.
m
[
1
][
0
])
,
&
(
triptr
->
H1zH2
.
m
[
1
][
0
]));
tr_mul
(
&
(
ij_bond
->
H
.
m
[
1
][
0
])
,
&
(
ik_bond
->
Hx
.
m
[
1
][
0
]),
&
(
triptr
->
H1H2x
.
m
[
1
][
0
]));
tr_mul
(
&
(
ij_bond
->
H
.
m
[
1
][
0
])
,
&
(
ik_bond
->
Hy
.
m
[
1
][
0
]),
&
(
triptr
->
H1H2y
.
m
[
1
][
0
]));
tr_mul
(
&
(
ij_bond
->
H
.
m
[
1
][
0
])
,
&
(
ik_bond
->
Hz
.
m
[
1
][
0
]),
&
(
triptr
->
H1H2z
.
m
[
1
][
0
]));
}
else
{
transprod
(
ij_bond
->
H
,
ik_bond
->
H
,
triptr
->
H1H2
);
transprod
(
ij_bond
->
Hx
,
ik_bond
->
H
,
triptr
->
H1xH2
);
transprod
(
ij_bond
->
Hy
,
ik_bond
->
H
,
triptr
->
H1yH2
);
transprod
(
ij_bond
->
Hz
,
ik_bond
->
H
,
triptr
->
H1zH2
);
transprod
(
ij_bond
->
H
,
ik_bond
->
Hx
,
triptr
->
H1H2x
);
transprod
(
ij_bond
->
H
,
ik_bond
->
Hy
,
triptr
->
H1H2y
);
transprod
(
ij_bond
->
H
,
ik_bond
->
Hz
,
triptr
->
H1H2z
);
}
}
static
double
t_make_t
=
0.0
,
t_make_b
=
0.0
,
n_make
=
0.0
;
PairMGPT
::
triplet_data
*
PairMGPT
::
get_triplet
(
const
double
xx
[][
3
],
int
i
,
int
j
,
int
k
,
Hash
<
bond_data
,
Doublet
>
*
bhash
,
triplet_data
*
twork
,
double
*
dvir_ij_p
,
double
*
dvir_ik_p
)
{
const
int
recompute
=
0
;
static
bond_data
bij_work
,
bik_work
;
double
t0
,
t1
;
bond_data
*
bij
=
0
,
*
bik
=
0
;
triplet_data
*
tptr
=
0
;
t0
=
gettime
();
if
(
recompute
==
0
)
{
bij
=
bhash
->
Lookup
(
Doublet
(
i
,
j
));
bik
=
bhash
->
Lookup
(
Doublet
(
i
,
k
));
}
if
(
bij
==
0
)
{
if
(
recompute
==
0
)
bij
=
bhash
->
Insert
(
Doublet
(
i
,
j
));
else
bij
=
&
bij_work
;
if
(
i
<
j
)
make_bond
(
xx
,
i
,
j
,
bij
);
else
make_bond
(
xx
,
j
,
i
,
bij
);
}
if
(
bik
==
0
)
{
if
(
recompute
==
0
)
bik
=
bhash
->
Insert
(
Doublet
(
i
,
k
));
else
bik
=
&
bik_work
;
if
(
i
<
k
)
make_bond
(
xx
,
i
,
k
,
bik
);
else
make_bond
(
xx
,
k
,
i
,
bik
);
}
t1
=
gettime
();
t_make_b
+=
t1
-
t0
;
t0
=
gettime
();
if
(
bij
!=
0
&&
bij
!=
0
)
{
tptr
=
twork
;
make_triplet
(
bij
,
bik
,
tptr
);
*
dvir_ij_p
=
bij
->
fl_deriv_sum
;
*
dvir_ik_p
=
bik
->
fl_deriv_sum
;
}
else
{
*
dvir_ij_p
=
0.0
;
*
dvir_ik_p
=
0.0
;
}
t1
=
gettime
();
t_make_t
+=
t1
-
t0
;
n_make
++
;
return
tptr
;
}
double
PairMGPT
::
numderiv3t
(
double
xx
[][
3
],
int
i
,
int
j
,
int
k
,
int
p
)
{
static
bond_data
Bij
,
Bjk
,
Bki
;
const
double
delta
=
1e-5
;
const
double
xsave
=
xx
[
i
][
p
];
double
e1
,
e2
;
const
double
vc
=
splinepot
.
vc
;
xx
[
i
][
p
]
=
xsave
+
delta
;
make_bond
(
xx
,
i
,
j
,
&
Bij
);
make_bond
(
xx
,
j
,
k
,
&
Bjk
);
make_bond
(
xx
,
k
,
i
,
&
Bki
);
e1
=
trace
(
prodmat
(
Bij
.
H
,
Bjk
.
H
),
Bki
.
H
)
*
(
vc
/
anorm3
);
xx
[
i
][
p
]
=
xsave
-
delta
;
make_bond
(
xx
,
i
,
j
,
&
Bij
);
if
(
0
)
{
/* This bond doesn't change when i is perturbed */
make_bond
(
xx
,
j
,
k
,
&
Bjk
);
}
make_bond
(
xx
,
k
,
i
,
&
Bki
);
e2
=
trace
(
prodmat
(
Bij
.
H
,
Bjk
.
H
),
Bki
.
H
)
*
(
vc
/
anorm3
);
xx
[
i
][
p
]
=
xsave
;
return
(
e1
-
e2
)
/
(
2.0
*
delta
);
}
double
PairMGPT
::
numderiv3v
(
double
xx
[][
3
],
int
i
,
int
j
,
int
k
,
int
p
,
int
ipert
)
{
static
bond_data
Bij
,
Bik
;
const
double
delta
=
1e-5
;
const
double
xsave
=
xx
[
ipert
][
p
];
double
e1
,
e2
;
const
double
vd
=
splinepot
.
vd
;
xx
[
ipert
][
p
]
=
xsave
+
delta
;
make_bond
(
xx
,
i
,
j
,
&
Bij
);
make_bond
(
xx
,
i
,
k
,
&
Bik
);
e1
=
trace
(
prodmat
(
Bij
.
H
,
Bij
.
H
),
prodmat
(
Bik
.
H
,
Bik
.
H
))
*
(
vd
/
anorm4
);
xx
[
ipert
][
p
]
=
xsave
-
delta
;
make_bond
(
xx
,
i
,
j
,
&
Bij
);
make_bond
(
xx
,
i
,
k
,
&
Bik
);
e2
=
trace
(
prodmat
(
Bij
.
H
,
Bij
.
H
),
prodmat
(
Bik
.
H
,
Bik
.
H
))
*
(
vd
/
anorm4
);
xx
[
ipert
][
p
]
=
xsave
;
return
(
e1
-
e2
)
/
(
2.0
*
delta
);
}
double
PairMGPT
::
numderiv4
(
double
xx
[][
3
],
int
i
,
int
j
,
int
k
,
int
m
,
int
p
)
{
static
bond_data
Bij
,
Bjk
,
Bkm
,
Bmi
;
const
double
delta
=
1e-5
;
const
double
xsave
=
xx
[
i
][
p
];
double
e1
,
e2
;
const
double
ve
=
splinepot
.
ve
;
xx
[
i
][
p
]
=
xsave
+
delta
;
make_bond
(
xx
,
i
,
j
,
&
Bij
);
make_bond
(
xx
,
j
,
k
,
&
Bjk
);
make_bond
(
xx
,
k
,
m
,
&
Bkm
);
make_bond
(
xx
,
m
,
i
,
&
Bmi
);
e1
=
trace
(
prodmat
(
Bij
.
H
,
Bjk
.
H
),
prodmat
(
Bkm
.
H
,
Bmi
.
H
))
*
(
ve
/
anorm4
);
xx
[
i
][
p
]
=
xsave
-
delta
;
make_bond
(
xx
,
i
,
j
,
&
Bij
);
if
(
0
)
{
/* Only the i coordinates changed... */
make_bond
(
xx
,
j
,
k
,
&
Bjk
);
make_bond
(
xx
,
k
,
m
,
&
Bkm
);
}
make_bond
(
xx
,
m
,
i
,
&
Bmi
);
e2
=
trace
(
prodmat
(
Bij
.
H
,
Bjk
.
H
),
prodmat
(
Bkm
.
H
,
Bmi
.
H
))
*
(
ve
/
anorm4
);
xx
[
i
][
p
]
=
xsave
;
return
(
e1
-
e2
)
/
(
2.0
*
delta
);
}
static
double
dtol
=
1e-6
;
void
PairMGPT
::
force_debug_3t
(
double
xx
[][
3
],
int
i0
,
int
j0
,
int
k0
,
int
i
,
int
j
,
int
k
,
double
dfix
,
double
dfiy
,
double
dfiz
,
double
dfjx
,
double
dfjy
,
double
dfjz
,
double
dfkx
,
double
dfky
,
double
dfkz
)
{
double
dfi
[
3
],
dfj
[
3
],
dfk
[
3
];
dfi
[
0
]
=
dfix
;
dfi
[
1
]
=
dfiy
;
dfi
[
2
]
=
dfiz
;
dfj
[
0
]
=
dfjx
;
dfj
[
1
]
=
dfjy
;
dfj
[
2
]
=
dfjz
;
dfk
[
0
]
=
dfkx
;
dfk
[
1
]
=
dfky
;
dfk
[
2
]
=
dfkz
;
for
(
int
p
=
0
;
p
<
3
;
p
++
)
{
/* Compute numerical derivatives by displacing atoms i,j,k */
double
ndfi
,
ndfj
,
ndfk
;
ndfi
=
-
numderiv3t
(
xx
,
i
,
j
,
k
,
p
);
ndfj
=
-
numderiv3t
(
xx
,
j
,
k
,
i
,
p
);
ndfk
=
-
numderiv3t
(
xx
,
k
,
i
,
j
,
p
);
if
((
fabs
(
dfi
[
p
]
-
ndfi
)
>
dtol
&&
fabs
(
dfi
[
p
]
-
ndfi
)
>
dtol
*
fabs
(
ndfi
))
||
(
fabs
(
dfj
[
p
]
-
ndfj
)
>
dtol
&&
fabs
(
dfj
[
p
]
-
ndfj
)
>
dtol
*
fabs
(
ndfj
))
||
(
fabs
(
dfk
[
p
]
-
ndfk
)
>
dtol
&&
fabs
(
dfk
[
p
]
-
ndfk
)
>
dtol
*
fabs
(
ndfk
)))
{
printf
(
"Force error in T12 & T23 & T31 :: i,j,k = %d,%d,%d
\n
"
,
i0
,
j0
,
k0
);
printf
(
" dE/d%c[i] = %20.10e %20.10e
\n
"
,
'x'
+
p
,
ndfi
,
dfi
[
p
]);
printf
(
" dE/d%c[j] = %20.10e %20.10e
\n
"
,
'x'
+
p
,
ndfj
,
dfj
[
p
]);
printf
(
" dE/d%c[k] = %20.10e %20.10e
\n
"
,
'x'
+
p
,
ndfk
,
dfk
[
p
]);
printf
(
"
\n
"
);
}
}
}
void
PairMGPT
::
force_debug_3v
(
double
xx
[][
3
],
int
i0
,
int
j0
,
int
k0
,
int
i
,
int
j
,
int
k
,
double
dfix
,
double
dfiy
,
double
dfiz
,
double
dfjx
,
double
dfjy
,
double
dfjz
,
double
dfkx
,
double
dfky
,
double
dfkz
)
{
double
dfi
[
3
],
dfj
[
3
],
dfk
[
3
];
dfi
[
0
]
=
dfix
;
dfi
[
1
]
=
dfiy
;
dfi
[
2
]
=
dfiz
;
dfj
[
0
]
=
dfjx
;
dfj
[
1
]
=
dfjy
;
dfj
[
2
]
=
dfjz
;
dfk
[
0
]
=
dfkx
;
dfk
[
1
]
=
dfky
;
dfk
[
2
]
=
dfkz
;
for
(
int
p
=
0
;
p
<
3
;
p
++
)
{
/* Compute numerical derivatives by displacing atoms i,j,k */
double
ndfi
,
ndfj
,
ndfk
;
ndfi
=
-
numderiv3v
(
xx
,
i
,
j
,
k
,
p
,
i0
);
ndfj
=
-
numderiv3v
(
xx
,
i
,
j
,
k
,
p
,
j0
);
ndfk
=
-
numderiv3v
(
xx
,
i
,
j
,
k
,
p
,
k0
);
if
((
fabs
(
dfi
[
p
]
-
ndfi
)
>
dtol
&&
fabs
(
dfi
[
p
]
-
ndfi
)
>
dtol
*
fabs
(
ndfi
))
||
(
fabs
(
dfj
[
p
]
-
ndfj
)
>
dtol
&&
fabs
(
dfj
[
p
]
-
ndfj
)
>
dtol
*
fabs
(
ndfj
))
||
(
fabs
(
dfk
[
p
]
-
ndfk
)
>
dtol
&&
fabs
(
dfk
[
p
]
-
ndfk
)
>
dtol
*
fabs
(
ndfk
)))
{
printf
(
"Force error in T12 :: i,j,k = %d,%d,%d
\n
"
,
i0
,
j0
,
k0
);
printf
(
" dE/d%c[i] = %20.10e %20.10e
\n
"
,
'x'
+
p
,
ndfi
,
dfi
[
p
]);
printf
(
" dE/d%c[j] = %20.10e %20.10e
\n
"
,
'x'
+
p
,
ndfj
,
dfj
[
p
]);
printf
(
" dE/d%c[k] = %20.10e %20.10e
\n
"
,
'x'
+
p
,
ndfk
,
dfk
[
p
]);
printf
(
"
\n
"
);
}
}
}
void
PairMGPT
::
force_debug_4
(
double
xx
[][
3
],
int
i0
,
int
j0
,
int
k0
,
int
m0
,
int
i
,
int
j
,
int
k
,
int
m
,
double
dfix
,
double
dfiy
,
double
dfiz
,
double
dfjx
,
double
dfjy
,
double
dfjz
,
double
dfkx
,
double
dfky
,
double
dfkz
,
double
dfmx
,
double
dfmy
,
double
dfmz
)
{
double
dfi
[
3
],
dfj
[
3
],
dfk
[
3
],
dfm
[
3
];
dfi
[
0
]
=
dfix
;
dfi
[
1
]
=
dfiy
;
dfi
[
2
]
=
dfiz
;
dfj
[
0
]
=
dfjx
;
dfj
[
1
]
=
dfjy
;
dfj
[
2
]
=
dfjz
;
dfk
[
0
]
=
dfkx
;
dfk
[
1
]
=
dfky
;
dfk
[
2
]
=
dfkz
;
dfm
[
0
]
=
dfmx
;
dfm
[
1
]
=
dfmy
;
dfm
[
2
]
=
dfmz
;
const
int
ii0
[]
=
{
i0
,
j0
,
k0
,
m0
},
ii
[]
=
{
i
,
j
,
k
,
m
,
i
,
j
,
k
};
for
(
int
p
=
0
;
p
<
3
;
p
++
)
{
/* Compute numerical derivatives by displacing atoms i,j,k,m */
double
ndfi
,
ndfj
,
ndfk
,
ndfm
;
if
(
1
)
{
double
ndf
[]
=
{
0.0
,
0.0
,
0.0
,
0.0
};
for
(
int
s
=
0
;
s
<
4
;
s
++
)
for
(
int
t
=
0
;
t
<
4
;
t
++
)
if
(
ii
[
s
]
==
ii0
[
t
])
ndf
[
t
]
=
-
numderiv4
(
xx
,
ii
[
s
],
ii
[
s
+
1
],
ii
[
s
+
2
],
ii
[
s
+
3
],
p
);
ndfi
=
ndf
[
0
];
ndfj
=
ndf
[
1
];
ndfk
=
ndf
[
2
];
ndfm
=
ndf
[
3
];
}
else
{
ndfi
=
-
numderiv4
(
xx
,
i
,
j
,
k
,
m
,
p
);
ndfj
=
-
numderiv4
(
xx
,
j
,
k
,
m
,
i
,
p
);
ndfk
=
-
numderiv4
(
xx
,
k
,
m
,
i
,
j
,
p
);
ndfm
=
-
numderiv4
(
xx
,
m
,
i
,
j
,
k
,
p
);
}
if
((
fabs
(
dfi
[
p
]
-
ndfi
)
>
dtol
&&
fabs
(
dfi
[
p
]
-
ndfi
)
>
dtol
*
fabs
(
ndfi
))
||
(
fabs
(
dfj
[
p
]
-
ndfj
)
>
dtol
&&
fabs
(
dfj
[
p
]
-
ndfj
)
>
dtol
*
fabs
(
ndfj
))
||
(
fabs
(
dfk
[
p
]
-
ndfk
)
>
dtol
&&
fabs
(
dfk
[
p
]
-
ndfk
)
>
dtol
*
fabs
(
ndfk
))
||
(
fabs
(
dfm
[
p
]
-
ndfm
)
>
dtol
&&
fabs
(
dfm
[
p
]
-
ndfm
)
>
dtol
*
fabs
(
ndfm
)))
{
printf
(
"Force error in T31 & T64 :: i,j,k,m = %d,%d,%d,%d
\n
"
,
i0
,
j0
,
k0
,
m0
);
printf
(
" dE/d%c[i] = %20.10e %20.10e
\n
"
,
'x'
+
p
,
ndfi
,
dfi
[
p
]);
printf
(
" dE/d%c[j] = %20.10e %20.10e
\n
"
,
'x'
+
p
,
ndfj
,
dfj
[
p
]);
printf
(
" dE/d%c[k] = %20.10e %20.10e
\n
"
,
'x'
+
p
,
ndfk
,
dfk
[
p
]);
printf
(
" dE/d%c[m] = %20.10e %20.10e
\n
"
,
'x'
+
p
,
ndfm
,
dfm
[
p
]);
printf
(
"
\n
"
);
}
}
}
/*
#define trd_update_4(T12,T45,coord) \
do { \
trd1 = transtrace(T12->H1##coord##H2,T45->H1H2 ); \
trd2 = transtrace(T12->H1H2##coord,T45->H1H2 ); \
trd3 = transtrace(T12->H1H2 ,T45->H1##coord##H2); \
trd4 = transtrace(T12->H1H2 ,T45->H1H2##coord ); \
} while(0)
*/
#define trd_update_4(T12,T45) \
do { \
tr_trace3(&(T45->H1H2.m[1][0]), \
&(T12->H1xH2.m[1][0]),&utr1x.d, \
&(T12->H1yH2.m[1][0]),&utr1y.d, \
&(T12->H1zH2.m[1][0]),&utr1z.d); \
tr_trace3(&(T45->H1H2.m[1][0]), \
&(T12->H1H2x.m[1][0]),&utr2x.d, \
&(T12->H1H2y.m[1][0]),&utr2y.d, \
&(T12->H1H2z.m[1][0]),&utr2z.d); \
tr_trace3(&(T12->H1H2.m[1][0]), \
&(T45->H1xH2.m[1][0]),&utr3x.d, \
&(T45->H1yH2.m[1][0]),&utr3y.d, \
&(T45->H1zH2.m[1][0]),&utr3z.d); \
tr_trace3(&(T12->H1H2.m[1][0]), \
&(T45->H1H2x.m[1][0]),&utr4x.d, \
&(T45->H1H2y.m[1][0]),&utr4y.d, \
&(T45->H1H2z.m[1][0]),&utr4z.d); \
if(linalg.single) { \
trd1x = utr1x.f; trd2x = utr2x.f; trd3x = utr3x.f; trd4x = utr4x.f; \
trd1y = utr1y.f; trd2y = utr2y.f; trd3y = utr3y.f; trd4y = utr4y.f; \
trd1z = utr1z.f; trd2z = utr2z.f; trd3z = utr3z.f; trd4z = utr4z.f; \
} else { \
trd1x = utr1x.d; trd2x = utr2x.d; trd3x = utr3x.d; trd4x = utr4x.d; \
trd1y = utr1y.d; trd2y = utr2y.d; trd3y = utr3y.d; trd4y = utr4y.d; \
trd1z = utr1z.d; trd2z = utr2z.d; trd3z = utr3z.d; trd4z = utr4z.d; \
} \
} while(0)
#define dfix_update_4a(coord) \
do { \
dfi##coord = ( (-sij)*trd1##coord + (-sim)*trd3##coord ) * (ve / anorm4); \
dfj##coord = ( ( sij)*trd1##coord + (-sjk)*trd2##coord ) * (ve / anorm4); \
dfk##coord = ( ( sjk)*trd2##coord + (-skm)*trd4##coord ) * (ve / anorm4); \
dfm##coord = ( ( sim)*trd3##coord + ( skm)*trd4##coord ) * (ve / anorm4); \
} while(0)
#define dfix_update_4b(coord) \
do { \
dfi##coord = ( ( ski)*trd1##coord + (-sim)*trd3##coord ) * (ve / anorm4); \
dfj##coord = ( (-sjk)*trd2##coord + (-sjm)*trd4##coord ) * (ve / anorm4); \
dfk##coord = ( (-ski)*trd1##coord + ( sjk)*trd2##coord ) * (ve / anorm4); \
dfm##coord = ( ( sim)*trd3##coord + ( sjm)*trd4##coord ) * (ve / anorm4); \
} while(0);
#define dfix_update_4c(coord) \
do { \
dfi##coord = ( (-sij)*trd1##coord + ( ski)*trd2##coord ) * (ve / anorm4); \
dfj##coord = ( ( sij)*trd1##coord + (-sjm)*trd3##coord ) * (ve / anorm4); \
dfk##coord = ( (-ski)*trd2##coord + (-skm)*trd4##coord ) * (ve / anorm4); \
dfm##coord = ( ( sjm)*trd3##coord + ( skm)*trd4##coord ) * (ve / anorm4); \
} while(0);
#define accumulate_forces_2(w) \
do { \
fix = fix + dfix*(w); \
fiy = fiy + dfiy*(w); \
fiz = fiz + dfiz*(w); \
\
fjx = fjx + dfjx*(w); \
fjy = fjy + dfjy*(w); \
fjz = fjz + dfjz*(w); \
} while(0)
#define accumulate_forces_3(w) \
do { \
accumulate_forces_2(w); \
fkx = fkx + dfkx*(w); \
fky = fky + dfky*(w); \
fkz = fkz + dfkz*(w); \
} while(0)
#define accumulate_forces_4(w) \
do { \
accumulate_forces_3(w); \
fmx = fmx + dfmx*(w); \
fmy = fmy + dfmy*(w); \
fmz = fmz + dfmz*(w); \
} while(0)
#define restrict __restrict__
#ifdef __bg__
#define const
#endif
static
int
ntr_calls
=
0
;
static
trtrace3_fun
tr_internal
;
static
void
tr_count
(
const
double
*
restrict
A
,
const
double
*
restrict
B1
,
double
*
restrict
t1
,
const
double
*
restrict
B2
,
double
*
restrict
t2
,
const
double
*
restrict
B3
,
double
*
restrict
t3
)
{
tr_internal
(
A
,
B1
,
t1
,
B2
,
t2
,
B3
,
t3
);
ntr_calls
++
;
}
#ifdef __bg__
#undef const
#endif
#undef restrict
int
PairMGPT
::
Matrix
::
sz
;
void
PairMGPT
::
compute_x
(
const
int
*
nnei
,
const
int
*
const
*
nlist
,
double
*
e_s
,
double
*
e_p
,
double
*
e_t
,
double
*
e_q
,
int
evflag
,
int
newton_pair
)
{
Hash
<
bond_data
,
Doublet
>
bond_hash
(
100000
);
int
i
,
j
,
k
,
m
,
ix
,
jx
,
kx
,
mx
,
itag
,
jtag
,
p
;
double
e_single
,
e_pair
,
e_triplet
,
e_triplet_c
,
e_quad
;
double
volvir2
;
double
nbc
=
0.0
,
tbl
=
0.0
,
tbm
=
0.0
;
const
int
lmax_local
=
lmax
;
//if(evflag) printf("##### ev flag is set... wasting cycles...\n");
*
e_s
=
-
99.0
;
*
e_p
=
-
99.0
;
*
e_t
=
-
99.0
;
*
e_q
=
-
99.0
;
double
t0
,
t1
;
t0
=
gettime
(
1
);
e_single
=
e_pair
=
e_triplet
=
e_triplet_c
=
e_quad
=
0.0
;
volvir2
=
0.0
;
t_make_t
=
t_make_b
=
t_make_b2
=
t_trace
=
0.0
;
n_make
=
n_make_b2
=
n_trace
=
0.0
;
double
tx0
,
tx1
,
tsort
=
0.0
,
tpair
=
0.0
,
tlookup
=
0.0
;
double
ttriplet
=
0.0
,
tquad
=
0.0
,
tmem
=
0.0
;
double
ntsort
=
0.0
,
ntpair
=
0.0
,
ntlookup
=
0.0
;
double
nttriplet
=
0.0
,
ntquad
=
0.0
,
ntmem
=
0.0
,
ntquaditer
=
0.0
;
double
mcount
=
0.0
,
mcount2
=
0.0
,
qcount
=
0.0
;
double
fix
,
fjx
,
fkx
,
fmx
,
dfix
,
dfjx
,
dfkx
,
dfmx
;
double
fiy
,
fjy
,
fky
,
fmy
,
dfiy
,
dfjy
,
dfky
,
dfmy
;
double
fiz
,
fjz
,
fkz
,
fmz
,
dfiz
,
dfjz
,
dfkz
,
dfmz
;
double
fsave
[
4
][
3
]
=
{
{
0.0
}
}
/* {{0.0}} is to get rid of uninitialized use warning */
;
//const int numerical_pair_forces = (nbody_flag/16)%2;
const
int
pair_forces
=
(
nbody_flag
/
2
)
%
2
,
three_body_forces
=
(
nbody_flag
/
4
)
%
2
,
four_body_forces
=
(
nbody_flag
/
8
)
%
2
;
const
int
pair_energies
=
(
nbody_flag
/
2
)
%
2
,
three_body_energies
=
(
nbody_flag
/
4
)
%
2
,
four_body_energies
=
(
nbody_flag
/
8
)
%
2
;
const
int
single_energies
=
nbody_flag
%
2
;
const
int
triplet_debug
=
0
,
quad_debug
=
0
;
/* Energy and force scale factor for unit conversion. */
const
double
e_scale
=
0.5
;
#ifdef NEIGHMASK
#define NIDX(x) (x)
#else
#define NIDX(x) ((x) & NEIGHMASK)
#endif
int
nneitot
,
*
first
,
*
nlist_short
;
double
w2
,
w3
,
w4
;
triplet_data
T12work
,
T23work
,
T31work
,
T45work
,
T56work
,
T64work
;
triplet_data
*
T12
,
*
T23
,
*
T31
,
*
T45
,
*
T56
,
*
T64
;
int
c_ij
,
c_jk
,
c_ki
,
c_im
,
c_jm
,
c_km
;
int
mi
,
mj
,
mk
;
double
tr0
,
tr1
,
tr2
,
tr3
;
double
v33
,
v43
;
double
rcut2_pair
=
rmax
*
rmax
,
rcut2_bond
=
rcrit
*
rcrit
,
rij2
;
int
ntot
,
nloc
;
double
dvir_ij
,
dvir_jk
,
dvir_ki
,
dvir_im
,
dvir_jm
,
dvir_km
;
double
vir3t
=
0.0
,
vir3v
=
0.0
,
vir4
=
0.0
;
double
(
*
xx
)[
3
],(
*
ff
)[
3
],(
*
ss
)[
3
];
#ifdef TIMING_ON
tr_internal
=
linalg
.
tr_trace
;
ntr_calls
=
0
;
const
trtrace3_fun
tr_trace3
=
tr_count
;
#else
const
trtrace3_fun
tr_trace3
=
linalg
.
tr_trace
;
#endif
union
{
double
d
;
float
f
;
}
utr1x
,
utr2x
,
utr3x
,
utr4x
,
utr1y
,
utr2y
,
utr3y
,
utr4y
,
utr1z
,
utr2z
,
utr3z
,
utr4z
;
double
trd1x
,
trd2x
,
trd3x
,
trd4x
;
double
trd1y
,
trd2y
,
trd3y
,
trd4y
;
double
trd1z
,
trd2z
,
trd3z
,
trd4z
;
tx0
=
gettime
();
double
rhoinv
;
{
double
vtot
=
1.0
;
double
ntot
=
atom
->
natoms
;
for
(
i
=
0
;
i
<
3
;
i
++
)
vtot
=
vtot
*
(
domain
->
boxhi
[
i
]
-
domain
->
boxlo
[
i
]);
rhoinv
=
vtot
/
ntot
;
}
/* Make sure triplet data work area is aligned and zeroed out. */
{
assert
(
T12work
.
align_check
()
==
0
);
assert
(
T23work
.
align_check
()
==
0
);
assert
(
T31work
.
align_check
()
==
0
);
assert
(
T45work
.
align_check
()
==
0
);
assert
(
T56work
.
align_check
()
==
0
);
assert
(
T64work
.
align_check
()
==
0
);
T12work
.
zero
();
T23work
.
zero
();
T31work
.
zero
();
T45work
.
zero
();
T56work
.
zero
();
T64work
.
zero
();
}
ntot
=
atom
->
nlocal
+
atom
->
nghost
;
nloc
=
atom
->
nlocal
;
//printf("[%3d] Allocating local array, size is %d atoms...\n",comm->me,j);
xx
=
(
double
(
*
)[
3
])
memory
->
smalloc
(
sizeof
(
double
[
3
])
*
ntot
,
"mgpt: local position vector."
);
ff
=
(
double
(
*
)[
3
])
memory
->
smalloc
(
sizeof
(
double
[
3
])
*
ntot
,
"mgpt: local force vector."
);
//printf("[%3d] Initializing arrays...\n",comm->me);
const
int
triclinic
=
domain
->
triclinic
;
double
alpha
[
3
]
=
{
0.0
,
0.0
,
0.0
};
if
(
triclinic
)
{
double
E
[
3
][
3
],
EX
[
3
][
3
];
int
cyc
[]
=
{
0
,
1
,
2
,
0
,
1
};
ss
=
(
double
(
*
)[
3
])
memory
->
smalloc
(
sizeof
(
double
[
3
])
*
ntot
,
"mgpt: local reduced coordinate vector."
);
for
(
i
=
0
;
i
<
3
;
i
++
)
{
for
(
j
=
0
;
j
<
3
;
j
++
)
E
[
i
][
j
]
=
0.0
;
E
[
i
][
i
]
=
domain
->
subhi_lamda
[
i
]
-
domain
->
sublo_lamda
[
i
];
domain
->
lamda2x
(
E
[
i
],
EX
[
i
]);
}
for
(
i
=
0
;
i
<
3
;
i
++
)
{
int
i1
=
cyc
[
i
+
1
],
i2
=
cyc
[
i
+
2
];
double
dot
=
0.0
,
ns2
=
0.0
;
for
(
j
=
0
;
j
<
3
;
j
++
)
{
int
j1
=
cyc
[
j
+
1
],
j2
=
cyc
[
j
+
2
];
double
cj
=
EX
[
i1
][
j1
]
*
EX
[
i2
][
j2
]
-
EX
[
i1
][
j2
]
*
EX
[
i2
][
j1
];
ns2
=
ns2
+
cj
*
cj
;
dot
=
dot
+
EX
[
i
][
j
]
*
cj
;
}
alpha
[
i
]
=
E
[
i
][
i
]
/
(
dot
/
sqrt
(
ns2
));
if
(
comm
->
me
==
0
)
{
static
int
count
=
0
;
if
(
count
<
3
)
printf
(
"@@@ alpha(%d) = %15.5e
\n
"
,
i
+
1
,
alpha
[
i
]);
count
++
;
}
if
(
alpha
[
i
]
<
0.0
)
alpha
[
i
]
=
-
alpha
[
i
];
}
}
else
ss
=
xx
;
nneitot
=
0
;
for
(
ix
=
0
;
ix
<
ntot
;
ix
++
)
{
for
(
p
=
0
;
p
<
3
;
p
++
)
{
xx
[
ix
][
p
]
=
atom
->
x
[
ix
][
p
];
ff
[
ix
][
p
]
=
0.0
;
}
if
(
triclinic
)
domain
->
x2lamda
(
xx
[
ix
],
ss
[
ix
]);
nneitot
=
nneitot
+
nnei
[
ix
];
}
first
=
(
int
*
)
memory
->
smalloc
(
sizeof
(
int
)
*
(
ntot
+
1
),
"mgpt: first"
);
nlist_short
=
(
int
*
)
memory
->
smalloc
(
sizeof
(
int
)
*
nneitot
,
"mgpt: nlist_short"
);
tx1
=
gettime
();
tmem
+=
tx1
-
tx0
;
ntmem
++
;
//printf("[%3d] Starting calculation...\n",comm->me);
fix
=
fjx
=
fkx
=
fmx
=
0.0
;
fiy
=
fjy
=
fky
=
fmy
=
0.0
;
fiz
=
fjz
=
fkz
=
fmz
=
0.0
;
int
c_p
=
0
,
c_t
=
0
,
c_q
=
0
;
if
(
0
)
if
(
domain
->
triclinic
)
{
if
(
comm
->
me
==
0
)
printf
(
"Can not handle triclinic box yet
\n
"
);
error
->
all
(
__FILE__
,
__LINE__
,
"Can not handle triclinic cell with mgpt yet."
);
}
/*
for(i = 0; i<nloc; i++) {
printf("Atom %3d:: %10.3f %10.3f %10.3f\n",
i,xx[i][0],xx[i][1],xx[i][2]);
}
*/
first
[
0
]
=
0
;
for
(
i
=
0
;
i
<
ntot
;
i
++
)
{
fix
=
fiy
=
fiz
=
0.0
;
first
[
i
+
1
]
=
first
[
i
];
const
int
c1
=
c1_outside
(
ss
[
i
],
triclinic
,
alpha
);
tx0
=
gettime
();
for
(
jx
=
0
;
jx
<
nnei
[
i
];
jx
++
)
{
fjx
=
fjy
=
fjz
=
0.0
;
j
=
NIDX
(
nlist
[
i
][
jx
]
);
rij2
=
0.0
;
for
(
p
=
0
;
p
<
3
;
p
++
)
{
double
t
=
xx
[
i
][
p
]
-
xx
[
j
][
p
];
rij2
=
rij2
+
t
*
t
;
}
if
(
c1
==
0
&&
rij2
<
rcut2_pair
)
{
if
(
j
<
i
)
{
w2
=
get_weight
(
triclinic
,
ss
[
i
],
ss
[
j
]);
if
(
w2
>
0.0
)
{
/*
Compute pair energy/force
*/
double
de_pair
,
df
,
rij
=
sqrt
(
rij2
);
splinepot
.
eval_pot
(
rij
,
&
de_pair
,
&
df
);
de_pair
=
de_pair
*
e_scale
*
w2
;
df
=
df
/
rij
*
w2
;
if
(
pair_energies
==
0
)
de_pair
=
0.0
;
e_pair
=
e_pair
+
de_pair
;
c_p
++
;
if
(
pair_forces
==
0
)
df
=
0.0
;
if
(
volpres_flag
&&
pair_energies
)
{
double
dvir
;
splinepot
.
eval_vir
(
rij
,
&
dvir
);
volvir2
=
volvir2
-
dvir
*
w2
;
/* Per-atom virial contribution of volumetric energy term */
if
(
vflag_atom
)
for
(
int
pp
=
0
;
pp
<
3
;
pp
++
)
{
//virial[i] = virial[i] + rhoinv*e_scale*volvir2;
vatom
[
i
][
pp
]
-=
0.5
*
rhoinv
*
e_scale
*
dvir
*
w2
;
vatom
[
j
][
pp
]
-=
0.5
*
rhoinv
*
e_scale
*
dvir
*
w2
;
}
}
double
drijx
=
xx
[
j
][
0
]
-
xx
[
i
][
0
];
double
drijy
=
xx
[
j
][
1
]
-
xx
[
i
][
1
];
double
drijz
=
xx
[
j
][
2
]
-
xx
[
i
][
2
];
fix
=
fix
+
df
*
drijx
;
fjx
=
fjx
-
df
*
drijx
;
fiy
=
fiy
+
df
*
drijy
;
fjy
=
fjy
-
df
*
drijy
;
fiz
=
fiz
+
df
*
drijz
;
fjz
=
fjz
-
df
*
drijz
;
if
(
evflag
)
{
//ev_tally(i,j,nloc,newton_pair,de_pair,0.0,df,-drijx,-drijy,-drijz);
/* To fix stress-per-atom scaling, and sign */
ev_tally
(
i
,
j
,
nloc
,
newton_pair
,
de_pair
,
0.0
,
-
df
*
e_scale
,
-
drijx
,
-
drijy
,
-
drijz
);
}
ff
[
j
][
0
]
+=
fjx
*
e_scale
;
ff
[
j
][
1
]
+=
fjy
*
e_scale
;
ff
[
j
][
2
]
+=
fjz
*
e_scale
;
}
}
}
if
(
rij2
<
rcut2_bond
&&
c2_outside
(
ss
[
i
],
ss
[
j
],
triclinic
,
alpha
)
==
0
)
{
/*
Add j to short neighbor list for i.
Insert j to keep list sorted.
*/
p
=
first
[
i
+
1
]
-
1
;
while
(
p
>=
first
[
i
]
&&
nlist_short
[
p
]
>
j
)
{
nlist_short
[
p
+
1
]
=
nlist_short
[
p
];
p
=
p
-
1
;
}
nlist_short
[
p
+
1
]
=
j
;
first
[
i
+
1
]
=
first
[
i
+
1
]
+
1
;
if
(
first
[
i
+
1
]
>
nneitot
)
{
printf
(
"nneitot = %d, short list full. i=%d
\n
"
,
nneitot
,
i
);
error
->
one
(
__FILE__
,
__LINE__
,
"Shit! Short list full
\n
"
);
}
}
}
ff
[
i
][
0
]
+=
fix
*
e_scale
;
ff
[
i
][
1
]
+=
fiy
*
e_scale
;
ff
[
i
][
2
]
+=
fiz
*
e_scale
;
tx1
=
gettime
();
tpair
+=
tx1
-
tx0
;
ntpair
+=
nnei
[
i
];
}
for
(
i
=
0
;
i
<
ntot
;
i
++
)
{
fix
=
fiy
=
fiz
=
0.0
;
/*
Use short lists for triplets and quadruplets.
For open (2-bonded) triplets, can only use k<j, but not k<i.
For closed (3-bonded) triplets, we can assume k<j<i.
Quadruplets:
Always use k<j<i, and require m<i.
If 5-bonded with im bond, ignore the quadruplet.
If 6-bonded, require m<k.
For 4-bonded quadruplets, we can still use k<j, but also
assume max(m,j)<i
*/
if
(
three_body_energies
||
three_body_forces
||
four_body_energies
||
four_body_forces
)
for
(
jx
=
first
[
i
];
jx
<
first
[
i
+
1
];
jx
++
)
{
fjx
=
fjy
=
fjz
=
0.0
;
j
=
nlist_short
[
jx
];
for
(
kx
=
first
[
i
];
kx
<
jx
;
kx
++
)
{
fkx
=
fky
=
fkz
=
0.0
;
k
=
nlist_short
[
kx
];
/*
Search lists of j and k, and see if
1) j is in k-list (closed triplet)
2) j and k have a common neighbor (closed quadruplet)
*/
c_ij
=
c_ki
=
1
;
const
int
sij
=
(
i
<
j
)
?
1
:
-
1
;
const
int
sjk
=
(
j
<
k
)
?
1
:
-
1
;
const
int
ski
=
(
k
<
i
)
?
1
:
-
1
;
T12
=
T23
=
T31
=
0
;
mj
=
first
[
j
];
/*
Since i is in the j-list, and i > k and the list
is sorted, the loop below terminates:-)
*/
while
(
mj
<
first
[
j
+
1
]
&&
nlist_short
[
mj
]
<
k
)
mj
=
mj
+
1
;
if
(
mj
<
first
[
j
+
1
]
&&
nlist_short
[
mj
]
==
k
)
{
/* Closed triplet */
c_jk
=
1
;
if
(
j
>
i
)
continue
;
/* Require k<j<i for closed triplets */
}
else
{
/* Open triplet */
c_jk
=
0
;
}
tx0
=
gettime
();
w3
=
get_weight
(
triclinic
,
ss
[
i
],
ss
[
j
],
ss
[
k
]);
int
triplet_defer
;
if
(
w3
>
0.0
)
{
triplet_defer
=
0
;
dvir_ij
=
dvir_jk
=
dvir_ki
=
0.0
;
if
(
c_ij
&&
c_jk
)
T12
=
get_triplet
(
xx
,
j
,
i
,
k
,
&
bond_hash
,
&
T12work
,
&
dvir_ij
,
&
dvir_jk
);
if
(
c_ki
&&
c_jk
)
T23
=
get_triplet
(
xx
,
k
,
i
,
j
,
&
bond_hash
,
&
T23work
,
&
dvir_ki
,
&
dvir_jk
);
if
(
c_ij
&&
c_ki
)
T31
=
get_triplet
(
xx
,
i
,
j
,
k
,
&
bond_hash
,
&
T31work
,
&
dvir_ij
,
&
dvir_ki
);
if
(
evflag
)
{
fsave
[
0
][
0
]
=
fix
;
fsave
[
0
][
1
]
=
fiy
;
fsave
[
0
][
2
]
=
fiz
;
fsave
[
1
][
0
]
=
fjx
;
fsave
[
1
][
1
]
=
fjy
;
fsave
[
1
][
2
]
=
fjz
;
fsave
[
2
][
0
]
=
fkx
;
fsave
[
2
][
1
]
=
fky
;
fsave
[
2
][
2
]
=
fkz
;
fix
=
fiy
=
fiz
=
0.0
;
fjx
=
fjy
=
fjz
=
0.0
;
fkx
=
fky
=
fkz
=
0.0
;
}
tr0
=
tr1
=
tr2
=
tr3
=
0.0
;
double
xvir3t
,
xvir3v
;
xvir3t
=
xvir3v
=
0.0
;
if
(
T12
&&
T23
)
{
bond_data
*
bki
=
bond_hash
.
Lookup
(
Doublet
(
k
,
i
));
if
(
three_body_energies
&&
evflag
)
{
tr0
=
transtrace
(
T12
->
H1H2
,
bki
->
H
);
double
dvir
=
((
dvir_ij
+
dvir_jk
+
bki
->
fl_deriv_sum
)
*
splinepot
.
vc
+
splinepot
.
dvc
)
*
tr0
*
w3
/
anorm3
;
vir3t
=
vir3t
+
dvir
;
xvir3t
=
xvir3t
+
dvir
;
}
mcount2
++
;
{
const
double
vc
=
splinepot
.
vc
;
tr_trace3
(
&
(
bki
->
H
.
m
[
1
][
0
]),
&
(
T12
->
H1xH2
.
m
[
1
][
0
]),
&
utr1x
.
d
,
&
(
T12
->
H1yH2
.
m
[
1
][
0
]),
&
utr1y
.
d
,
&
(
T12
->
H1zH2
.
m
[
1
][
0
]),
&
utr1z
.
d
);
tr_trace3
(
&
(
bki
->
H
.
m
[
1
][
0
]),
&
(
T12
->
H1H2x
.
m
[
1
][
0
]),
&
utr2x
.
d
,
&
(
T12
->
H1H2y
.
m
[
1
][
0
]),
&
utr2y
.
d
,
&
(
T12
->
H1H2z
.
m
[
1
][
0
]),
&
utr2z
.
d
);
tr_trace3
(
&
(
T12
->
H1H2
.
m
[
1
][
0
]),
&
(
bki
->
Hx
.
m
[
1
][
0
]),
&
utr3x
.
d
,
&
(
bki
->
Hy
.
m
[
1
][
0
]),
&
utr3y
.
d
,
&
(
bki
->
Hz
.
m
[
1
][
0
]),
&
utr3z
.
d
);
if
(
linalg
.
single
)
{
trd1x
=
utr1x
.
f
;
trd2x
=
utr2x
.
f
;
trd3x
=
utr3x
.
f
;
trd1y
=
utr1y
.
f
;
trd2y
=
utr2y
.
f
;
trd3y
=
utr3y
.
f
;
trd1z
=
utr1z
.
f
;
trd2z
=
utr2z
.
f
;
trd3z
=
utr3z
.
f
;
}
else
{
trd1x
=
utr1x
.
d
;
trd2x
=
utr2x
.
d
;
trd3x
=
utr3x
.
d
;
trd1y
=
utr1y
.
d
;
trd2y
=
utr2y
.
d
;
trd3y
=
utr3y
.
d
;
trd1z
=
utr1z
.
d
;
trd2z
=
utr2z
.
d
;
trd3z
=
utr3z
.
d
;
}
dfix
=
(
(
-
sij
)
*
trd1x
+
(
ski
)
*
trd3x
)
*
(
vc
/
anorm3
);
dfjx
=
(
(
sij
)
*
trd1x
+
(
-
sjk
)
*
trd2x
)
*
(
vc
/
anorm3
);
dfkx
=
(
(
sjk
)
*
trd2x
+
(
-
ski
)
*
trd3x
)
*
(
vc
/
anorm3
);
dfiy
=
(
(
-
sij
)
*
trd1y
+
(
ski
)
*
trd3y
)
*
(
vc
/
anorm3
);
dfjy
=
(
(
sij
)
*
trd1y
+
(
-
sjk
)
*
trd2y
)
*
(
vc
/
anorm3
);
dfky
=
(
(
sjk
)
*
trd2y
+
(
-
ski
)
*
trd3y
)
*
(
vc
/
anorm3
);
dfiz
=
(
(
-
sij
)
*
trd1z
+
(
ski
)
*
trd3z
)
*
(
vc
/
anorm3
);
dfjz
=
(
(
sij
)
*
trd1z
+
(
-
sjk
)
*
trd2z
)
*
(
vc
/
anorm3
);
dfkz
=
(
(
sjk
)
*
trd2z
+
(
-
ski
)
*
trd3z
)
*
(
vc
/
anorm3
);
}
if
(
triplet_debug
)
force_debug_3t
(
xx
,
i
,
j
,
k
,
i
,
j
,
k
,
dfix
,
dfiy
,
dfiz
,
dfjx
,
dfjy
,
dfjz
,
dfkx
,
dfky
,
dfkz
);
if
(
three_body_forces
)
accumulate_forces_3
(
w3
);
}
if
(
T12
!=
0
)
{
//printf("T12 i,j,k = %d,%d,%d\n",i,j,k);
mcount
++
;
if
(
three_body_energies
&&
evflag
)
{
tr1
=
transtrace
(
T12
->
H1H2
,
T12
->
H1H2
);
double
dvir
=
(
2.0
*
(
dvir_ij
+
dvir_jk
)
*
splinepot
.
vd
+
splinepot
.
dvd
)
*
tr1
*
w3
/
anorm4
;
vir3v
=
vir3v
+
dvir
;
xvir3v
=
xvir3v
+
dvir
;
}
{
const
double
vd
=
splinepot
.
vd
;
tr_trace3
(
&
(
T12
->
H1H2
.
m
[
1
][
0
]),
&
(
T12
->
H1xH2
.
m
[
1
][
0
]),
&
utr1x
.
d
,
&
(
T12
->
H1yH2
.
m
[
1
][
0
]),
&
utr1y
.
d
,
&
(
T12
->
H1zH2
.
m
[
1
][
0
]),
&
utr1z
.
d
);
tr_trace3
(
&
(
T12
->
H1H2
.
m
[
1
][
0
]),
&
(
T12
->
H1H2x
.
m
[
1
][
0
]),
&
utr2x
.
d
,
&
(
T12
->
H1H2y
.
m
[
1
][
0
]),
&
utr2y
.
d
,
&
(
T12
->
H1H2z
.
m
[
1
][
0
]),
&
utr2z
.
d
);
if
(
linalg
.
single
)
{
trd1x
=
utr1x
.
f
;
trd2x
=
utr2x
.
f
;
trd1y
=
utr1y
.
f
;
trd2y
=
utr2y
.
f
;
trd1z
=
utr1z
.
f
;
trd2z
=
utr2z
.
f
;
}
else
{
trd1x
=
utr1x
.
d
;
trd2x
=
utr2x
.
d
;
trd1y
=
utr1y
.
d
;
trd2y
=
utr2y
.
d
;
trd1z
=
utr1z
.
d
;
trd2z
=
utr2z
.
d
;
}
dfix
=
2.0
*
(
-
sij
)
*
trd1x
*
(
vd
/
anorm4
);
dfkx
=
2.0
*
(
sjk
)
*
trd2x
*
(
vd
/
anorm4
);
dfjx
=
-
(
dfix
+
dfkx
);
dfiy
=
2.0
*
(
-
sij
)
*
trd1y
*
(
vd
/
anorm4
);
dfky
=
2.0
*
(
sjk
)
*
trd2y
*
(
vd
/
anorm4
);
dfjy
=
-
(
dfiy
+
dfky
);
dfiz
=
2.0
*
(
-
sij
)
*
trd1z
*
(
vd
/
anorm4
);
dfkz
=
2.0
*
(
sjk
)
*
trd2z
*
(
vd
/
anorm4
);
dfjz
=
-
(
dfiz
+
dfkz
);
}
if
(
triplet_debug
)
/* Compare forces to numerical derivatives */
force_debug_3v
(
xx
,
i
,
j
,
k
,
j
,
i
,
k
,
dfix
,
dfiy
,
dfiz
,
dfjx
,
dfjy
,
dfjz
,
dfkx
,
dfky
,
dfkz
);
if
(
three_body_forces
)
accumulate_forces_3
(
w3
);
}
if
(
T23
!=
0
)
{
//printf("T23 i,j,k = %d,%d,%d\n",i,j,k);
mcount
++
;
if
(
three_body_energies
&&
evflag
)
{
tr2
=
transtrace
(
T23
->
H1H2
,
T23
->
H1H2
);
double
dvir
=
(
2.0
*
(
dvir_jk
+
dvir_ki
)
*
splinepot
.
vd
+
splinepot
.
dvd
)
*
tr2
*
w3
/
anorm4
;
vir3v
=
vir3v
+
dvir
;
xvir3v
=
xvir3v
+
dvir
;
}
{
const
double
vd
=
splinepot
.
vd
;
tr_trace3
(
&
(
T23
->
H1H2
.
m
[
1
][
0
]),
&
(
T23
->
H1xH2
.
m
[
1
][
0
]),
&
utr1x
.
d
,
&
(
T23
->
H1yH2
.
m
[
1
][
0
]),
&
utr1y
.
d
,
&
(
T23
->
H1zH2
.
m
[
1
][
0
]),
&
utr1z
.
d
);
tr_trace3
(
&
(
T23
->
H1H2
.
m
[
1
][
0
]),
&
(
T23
->
H1H2x
.
m
[
1
][
0
]),
&
utr2x
.
d
,
&
(
T23
->
H1H2y
.
m
[
1
][
0
]),
&
utr2y
.
d
,
&
(
T23
->
H1H2z
.
m
[
1
][
0
]),
&
utr2z
.
d
);
if
(
linalg
.
single
)
{
trd1x
=
utr1x
.
f
;
trd2x
=
utr2x
.
f
;
trd1y
=
utr1y
.
f
;
trd2y
=
utr2y
.
f
;
trd1z
=
utr1z
.
f
;
trd2z
=
utr2z
.
f
;
}
else
{
trd1x
=
utr1x
.
d
;
trd2x
=
utr2x
.
d
;
trd1y
=
utr1y
.
d
;
trd2y
=
utr2y
.
d
;
trd1z
=
utr1z
.
d
;
trd2z
=
utr2z
.
d
;
}
dfix
=
2.0
*
(
ski
)
*
trd1x
*
(
vd
/
anorm4
);
dfjx
=
2.0
*
(
-
sjk
)
*
trd2x
*
(
vd
/
anorm4
);
dfkx
=
-
(
dfix
+
dfjx
);
dfiy
=
2.0
*
(
ski
)
*
trd1y
*
(
vd
/
anorm4
);
dfjy
=
2.0
*
(
-
sjk
)
*
trd2y
*
(
vd
/
anorm4
);
dfky
=
-
(
dfiy
+
dfjy
);
dfiz
=
2.0
*
(
ski
)
*
trd1z
*
(
vd
/
anorm4
);
dfjz
=
2.0
*
(
-
sjk
)
*
trd2z
*
(
vd
/
anorm4
);
dfkz
=
-
(
dfiz
+
dfjz
);
}
if
(
triplet_debug
)
/* Compare forces to numerical derivatives */
force_debug_3v
(
xx
,
i
,
j
,
k
,
k
,
i
,
j
,
dfix
,
dfiy
,
dfiz
,
dfjx
,
dfjy
,
dfjz
,
dfkx
,
dfky
,
dfkz
);
if
(
three_body_forces
)
accumulate_forces_3
(
w3
);
}
if
(
T31
!=
0
)
{
//printf("T31 i,j,k = %d,%d,%d\n",i,j,k);
mcount
++
;
if
(
three_body_energies
&&
evflag
)
{
tr3
=
transtrace
(
T31
->
H1H2
,
T31
->
H1H2
);
double
dvir
=
(
2.0
*
(
dvir_ki
+
dvir_ij
)
*
splinepot
.
vd
+
splinepot
.
dvd
)
*
tr3
*
w3
/
anorm4
;
vir3v
=
vir3v
+
dvir
;
xvir3v
=
xvir3v
+
dvir
;
}
{
const
double
vd
=
splinepot
.
vd
;
tr_trace3
(
&
(
T31
->
H1H2
.
m
[
1
][
0
]),
&
(
T31
->
H1xH2
.
m
[
1
][
0
]),
&
utr1x
.
d
,
&
(
T31
->
H1yH2
.
m
[
1
][
0
]),
&
utr1y
.
d
,
&
(
T31
->
H1zH2
.
m
[
1
][
0
]),
&
utr1z
.
d
);
tr_trace3
(
&
(
T31
->
H1H2
.
m
[
1
][
0
]),
&
(
T31
->
H1H2x
.
m
[
1
][
0
]),
&
utr2x
.
d
,
&
(
T31
->
H1H2y
.
m
[
1
][
0
]),
&
utr2y
.
d
,
&
(
T31
->
H1H2z
.
m
[
1
][
0
]),
&
utr2z
.
d
);
if
(
linalg
.
single
)
{
trd1x
=
utr1x
.
f
;
trd2x
=
utr2x
.
f
;
trd1y
=
utr1y
.
f
;
trd2y
=
utr2y
.
f
;
trd1z
=
utr1z
.
f
;
trd2z
=
utr2z
.
f
;
}
else
{
trd1x
=
utr1x
.
d
;
trd2x
=
utr2x
.
d
;
trd1y
=
utr1y
.
d
;
trd2y
=
utr2y
.
d
;
trd1z
=
utr1z
.
d
;
trd2z
=
utr2z
.
d
;
}
dfjx
=
2.0
*
(
sij
)
*
trd1x
*
(
vd
/
anorm4
);
dfkx
=
2.0
*
(
-
ski
)
*
trd2x
*
(
vd
/
anorm4
);
dfix
=
-
(
dfjx
+
dfkx
);
dfjy
=
2.0
*
(
sij
)
*
trd1y
*
(
vd
/
anorm4
);
dfky
=
2.0
*
(
-
ski
)
*
trd2y
*
(
vd
/
anorm4
);
dfiy
=
-
(
dfjy
+
dfky
);
dfjz
=
2.0
*
(
sij
)
*
trd1z
*
(
vd
/
anorm4
);
dfkz
=
2.0
*
(
-
ski
)
*
trd2z
*
(
vd
/
anorm4
);
dfiz
=
-
(
dfjz
+
dfkz
);
}
if
(
triplet_debug
)
/* Compare forces to numerical derivatives */
force_debug_3v
(
xx
,
i
,
j
,
k
,
i
,
j
,
k
,
dfix
,
dfiy
,
dfiz
,
dfjx
,
dfjy
,
dfjz
,
dfkx
,
dfky
,
dfkz
);
if
(
three_body_forces
)
accumulate_forces_3
(
w3
);
}
v33
=
tr0
/
anorm3
;
v43
=
(
tr1
+
tr2
+
tr3
)
/
anorm4
;
double
de_triplet
=
(
splinepot
.
vc
*
v33
+
splinepot
.
vd
*
v43
)
*
e_scale
*
w3
;
e_triplet
=
e_triplet
+
de_triplet
;
e_triplet_c
=
e_triplet_c
+
splinepot
.
vc
*
v33
*
e_scale
*
w3
;
c_t
++
;
//printf("xxxx %6d %6d %6d :: %20.10e\n",1,2,3,de_triplet);
if
(
evflag
)
{
double
drji
[
3
],
drki
[
3
];
double
fj
[
3
]
=
{
fjx
,
fjy
,
fjz
},
fk
[
3
]
=
{
fkx
,
fky
,
fkz
};
for
(
int
p
=
0
;
p
<
3
;
p
++
)
{
drji
[
p
]
=
xx
[
j
][
p
]
-
xx
[
i
][
p
];
drki
[
p
]
=
xx
[
k
][
p
]
-
xx
[
i
][
p
];
/* To fix stress-per-atom scaling. */
fj
[
p
]
*=
e_scale
;
fk
[
p
]
*=
e_scale
;
}
ev_tally3
(
i
,
j
,
k
,
de_triplet
,
0.0
,
fj
,
fk
,
drji
,
drki
);
if
(
volpres_flag
&&
vflag_atom
)
{
//virial[i] = virial[i] - (vir3v + vir3t) * rhoinv*e_scale;
double
dvir
=
-
(
xvir3v
+
xvir3t
)
*
rhoinv
*
e_scale
*
(
1.0
/
3.0
);
for
(
int
pp
=
0
;
pp
<
3
;
pp
++
)
{
vatom
[
i
][
pp
]
+=
dvir
;
vatom
[
j
][
pp
]
+=
dvir
;
vatom
[
k
][
pp
]
+=
dvir
;
}
}
fix
=
fix
+
fsave
[
0
][
0
];
fiy
=
fiy
+
fsave
[
0
][
1
];
fiz
=
fiz
+
fsave
[
0
][
2
];
fjx
=
fjx
+
fsave
[
1
][
0
];
fjy
=
fjy
+
fsave
[
1
][
1
];
fjz
=
fjz
+
fsave
[
1
][
2
];
fkx
=
fkx
+
fsave
[
2
][
0
];
fky
=
fky
+
fsave
[
2
][
1
];
fkz
=
fkz
+
fsave
[
2
][
2
];
}
tx1
=
gettime
();
ttriplet
+=
tx1
-
tx0
;
nttriplet
++
;
}
else
{
triplet_defer
=
1
;
}
if
(
four_body_energies
||
four_body_forces
)
if
(
j
<
i
)
{
/* Search for quadruplet */
tx0
=
gettime
();
mj
=
first
[
j
];
mk
=
first
[
k
];
/*
i is in both the j-list and the k-list, and i > k,
and lists are sorted, so the loop terminates.
*/
while
(
nlist_short
[
mj
]
<
i
&&
nlist_short
[
mk
]
<
i
)
{
if
(
mj
>=
first
[
j
+
1
]
||
mk
>=
first
[
k
+
1
])
{
printf
(
"Illegal quad...
\n
"
" j=%d first[j]=%d first[j+1]=%d mj=%d
\n
"
" k=%d first[k]=%d first[k+1]=%d mk=%d
\n
"
,
j
,
first
[
j
],
first
[
j
+
1
],
mj
,
k
,
first
[
k
],
first
[
k
+
1
],
mk
);
error
->
one
(
__FILE__
,
__LINE__
,
"Shit, brkoen quad loop"
);
}
if
(
nlist_short
[
mj
]
==
nlist_short
[
mk
])
{
/* Closed quadruplet */
m
=
nlist_short
[
mj
];
c_jm
=
c_km
=
1
;
const
int
sim
=
(
i
<
m
)
?
1
:
-
1
;
const
int
sjm
=
(
j
<
m
)
?
1
:
-
1
;
const
int
skm
=
(
k
<
m
)
?
1
:
-
1
;
w4
=
get_weight
(
triclinic
,
ss
[
i
],
ss
[
j
],
ss
[
k
],
ss
[
m
]);
if
(
w4
>
0.0
)
{
/* Alrady know ij,jk,ki,jm,km bonds. Look for im bond. */
mi
=
first
[
i
];
while
(
mi
<
first
[
i
+
1
]
&&
nlist_short
[
mi
]
<
m
)
mi
=
mi
+
1
;
if
(
mi
<
first
[
i
+
1
]
&&
nlist_short
[
mi
]
==
m
)
c_im
=
1
;
else
c_im
=
0
;
if
(
c_im
==
0
||
c_jk
==
0
||
(
c_jk
&&
c_im
&&
m
<
k
))
{
if
(
triplet_defer
)
{
dvir_ij
=
dvir_jk
=
dvir_ki
=
0.0
;
if
(
c_ij
&&
c_jk
)
T12
=
get_triplet
(
xx
,
j
,
i
,
k
,
&
bond_hash
,
&
T12work
,
&
dvir_ij
,
&
dvir_jk
);
if
(
c_ki
&&
c_jk
)
T23
=
get_triplet
(
xx
,
k
,
i
,
j
,
&
bond_hash
,
&
T23work
,
&
dvir_ki
,
&
dvir_jk
);
if
(
c_ij
&&
c_ki
)
T31
=
get_triplet
(
xx
,
i
,
j
,
k
,
&
bond_hash
,
&
T31work
,
&
dvir_ij
,
&
dvir_ki
);
triplet_defer
=
0
;
}
fmx
=
fmy
=
fmz
=
0.0
;
double
xvir4
=
0.0
;
if
(
evflag
)
{
fsave
[
0
][
0
]
=
fix
;
fsave
[
0
][
1
]
=
fiy
;
fsave
[
0
][
2
]
=
fiz
;
fsave
[
1
][
0
]
=
fjx
;
fsave
[
1
][
1
]
=
fjy
;
fsave
[
1
][
2
]
=
fjz
;
fsave
[
2
][
0
]
=
fkx
;
fsave
[
2
][
1
]
=
fky
;
fsave
[
2
][
2
]
=
fkz
;
fsave
[
3
][
0
]
=
fmx
;
fsave
[
3
][
1
]
=
fmy
;
fsave
[
3
][
2
]
=
fmz
;
fix
=
fiy
=
fiz
=
0.0
;
fjx
=
fjy
=
fjz
=
0.0
;
fkx
=
fky
=
fkz
=
0.0
;
fmx
=
fmy
=
fmz
=
0.0
;
}
tr1
=
tr2
=
tr3
=
0.0
;
dvir_im
=
dvir_jm
=
dvir_km
=
0.0
;
T45
=
T56
=
T64
=
0
;
if
(
T12
!=
0
&&
c_km
&&
c_im
)
T45
=
get_triplet
(
xx
,
m
,
i
,
k
,
&
bond_hash
,
&
T45work
,
&
dvir_im
,
&
dvir_km
);
if
(
T23
!=
0
&&
c_im
&&
c_jm
)
T56
=
get_triplet
(
xx
,
m
,
i
,
j
,
&
bond_hash
,
&
T56work
,
&
dvir_im
,
&
dvir_jm
);
if
(
T31
!=
0
&&
c_jm
&&
c_km
)
T64
=
get_triplet
(
xx
,
m
,
j
,
k
,
&
bond_hash
,
&
T64work
,
&
dvir_jm
,
&
dvir_km
);
if
(
T12
!=
0
&&
T45
!=
0
)
{
if
(
four_body_energies
&&
evflag
)
{
tr1
=
transtrace
(
T12
->
H1H2
,
T45
->
H1H2
);
double
dvir
=
(
(
dvir_ij
+
dvir_jk
+
dvir_im
+
dvir_km
)
*
splinepot
.
ve
+
splinepot
.
dve
)
*
tr1
*
w4
/
anorm4
;
vir4
=
vir4
+
dvir
;
xvir4
=
xvir4
+
dvir
;
}
qcount
++
;
{
const
double
ve
=
splinepot
.
ve
;
trd_update_4
(
T12
,
T45
);
dfix_update_4a
(
x
);
dfix_update_4a
(
y
);
dfix_update_4a
(
z
);
}
if
(
quad_debug
)
/* Compare forces to numerical derivatives */
force_debug_4
(
xx
,
i
,
j
,
k
,
m
,
i
,
j
,
k
,
m
,
dfix
,
dfiy
,
dfiz
,
dfjx
,
dfjy
,
dfjz
,
dfkx
,
dfky
,
dfkz
,
dfmx
,
dfmy
,
dfmz
);
if
(
four_body_forces
)
accumulate_forces_4
(
w4
);
}
if
(
T23
!=
0
&&
T56
!=
0
)
{
if
(
four_body_energies
&&
evflag
)
{
tr2
=
transtrace
(
T23
->
H1H2
,
T56
->
H1H2
);
double
dvir
=
(
(
dvir_ki
+
dvir_jk
+
dvir_im
+
dvir_jm
)
*
splinepot
.
ve
+
splinepot
.
dve
)
*
tr2
*
w4
/
anorm4
;
vir4
=
vir4
+
dvir
;
xvir4
=
xvir4
+
dvir
;
}
qcount
++
;
{
const
double
ve
=
splinepot
.
ve
;
trd_update_4
(
T23
,
T56
);
dfix_update_4b
(
x
);
dfix_update_4b
(
y
);
dfix_update_4b
(
z
);
}
if
(
quad_debug
)
/* Compare forces to numerical derivatives */
force_debug_4
(
xx
,
i
,
j
,
k
,
m
,
i
,
m
,
j
,
k
,
dfix
,
dfiy
,
dfiz
,
dfjx
,
dfjy
,
dfjz
,
dfkx
,
dfky
,
dfkz
,
dfmx
,
dfmy
,
dfmz
);
if
(
four_body_forces
)
accumulate_forces_4
(
w4
);
}
if
(
T31
!=
0
&&
T64
!=
0
)
{
if
(
four_body_energies
&&
evflag
)
{
tr3
=
transtrace
(
T31
->
H1H2
,
T64
->
H1H2
);
double
dvir
=
(
(
dvir_ki
+
dvir_ij
+
dvir_jm
+
dvir_km
)
*
splinepot
.
ve
+
splinepot
.
dve
)
*
tr3
*
w4
/
anorm4
;
vir4
=
vir4
+
dvir
;
xvir4
=
xvir4
+
dvir
;
}
qcount
++
;
{
const
double
ve
=
splinepot
.
ve
;
/* X */
trd_update_4
(
T31
,
T64
);
dfix_update_4c
(
x
);
dfix_update_4c
(
y
);
dfix_update_4c
(
z
);
}
if
(
quad_debug
)
/* Compare forces to numerical derivatives */
force_debug_4
(
xx
,
i
,
j
,
k
,
m
,
i
,
j
,
m
,
k
,
dfix
,
dfiy
,
dfiz
,
dfjx
,
dfjy
,
dfjz
,
dfkx
,
dfky
,
dfkz
,
dfmx
,
dfmy
,
dfmz
);
if
(
four_body_forces
)
accumulate_forces_4
(
w4
);
}
double
de_quad
=
splinepot
.
ve
*
(
tr1
+
tr2
+
tr3
)
/
anorm4
*
e_scale
*
w4
;
e_quad
=
e_quad
+
de_quad
;
if
((
T12
&&
T45
)
||
(
T23
&&
T56
)
||
(
T31
&&
T64
))
{
c_q
++
;
}
if
(
evflag
)
{
double
drim
[
3
],
drjm
[
3
],
drkm
[
3
];
double
fi
[
3
]
=
{
fix
,
fiy
,
fiz
};
double
fj
[
3
]
=
{
fjx
,
fjy
,
fjz
};
double
fk
[
3
]
=
{
fkx
,
fky
,
fkz
};
for
(
int
p
=
0
;
p
<
3
;
p
++
)
{
drim
[
p
]
=
xx
[
i
][
p
]
-
xx
[
m
][
p
];
drjm
[
p
]
=
xx
[
j
][
p
]
-
xx
[
m
][
p
];
drkm
[
p
]
=
xx
[
k
][
p
]
-
xx
[
m
][
p
];
fi
[
p
]
*=
e_scale
;
fj
[
p
]
*=
e_scale
;
fk
[
p
]
*=
e_scale
;
}
ev_tally4
(
i
,
j
,
k
,
m
,
de_quad
,
fi
,
fj
,
fk
,
drim
,
drjm
,
drkm
);
if
(
volpres_flag
&&
vflag_atom
)
{
//virial[i] = virial[i] - vir4 * rhoinv*e_scale;
double
dvir
=
-
xvir4
*
rhoinv
*
e_scale
*
(
1.0
/
4.0
);
for
(
int
pp
=
0
;
pp
<
3
;
pp
++
)
{
vatom
[
i
][
pp
]
+=
dvir
;
vatom
[
j
][
pp
]
+=
dvir
;
vatom
[
k
][
pp
]
+=
dvir
;
vatom
[
m
][
pp
]
+=
dvir
;
}
}
fix
=
fix
+
fsave
[
0
][
0
];
fiy
=
fiy
+
fsave
[
0
][
1
];
fiz
=
fiz
+
fsave
[
0
][
2
];
fjx
=
fjx
+
fsave
[
1
][
0
];
fjy
=
fjy
+
fsave
[
1
][
1
];
fjz
=
fjz
+
fsave
[
1
][
2
];
fkx
=
fkx
+
fsave
[
2
][
0
];
fky
=
fky
+
fsave
[
2
][
1
];
fkz
=
fkz
+
fsave
[
2
][
2
];
fmx
=
fmx
+
fsave
[
3
][
0
];
fmy
=
fmy
+
fsave
[
3
][
1
];
fmz
=
fmz
+
fsave
[
3
][
2
];
}
ff
[
m
][
0
]
+=
fmx
*
e_scale
;
ff
[
m
][
1
]
+=
fmy
*
e_scale
;
ff
[
m
][
2
]
+=
fmz
*
e_scale
;
}
}
mj
=
mj
+
1
;
mk
=
mk
+
1
;
}
else
if
(
nlist_short
[
mj
]
<
nlist_short
[
mk
])
{
mj
=
mj
+
1
;
}
else
{
mk
=
mk
+
1
;
}
}
tx1
=
gettime
();
tquad
+=
tx1
-
tx0
;
ntquad
++
;
ntquaditer
++
;
}
ff
[
k
][
0
]
+=
fkx
*
e_scale
;
ff
[
k
][
1
]
+=
fky
*
e_scale
;
ff
[
k
][
2
]
+=
fkz
*
e_scale
;
}
#undef transtrace
ff
[
j
][
0
]
+=
fjx
*
e_scale
;
ff
[
j
][
1
]
+=
fjy
*
e_scale
;
ff
[
j
][
2
]
+=
fjz
*
e_scale
;
}
ff
[
i
][
0
]
+=
fix
*
e_scale
;
ff
[
i
][
1
]
+=
fiy
*
e_scale
;
ff
[
i
][
2
]
+=
fiz
*
e_scale
;
if
(
single_energies
==
1
&&
i
<
nloc
)
{
const
double
evol0
=
splinepot
.
evol0
;
if
(
eflag_global
)
{
e_single
=
e_single
+
evol0
*
e_scale
;
eng_vdwl
=
eng_vdwl
+
evol0
*
e_scale
;
}
if
(
eflag_atom
)
eatom
[
i
]
=
eatom
[
i
]
+
evol0
*
e_scale
;
if
(
volpres_flag
&&
vflag_atom
)
{
for
(
int
pp
=
0
;
pp
<
3
;
pp
++
)
vatom
[
i
][
pp
]
=
vatom
[
i
][
pp
]
-
rhoinv
*
splinepot
.
devol0
*
e_scale
;
}
}
}
tx0
=
gettime
();
for
(
i
=
0
;
i
<
ntot
;
i
++
)
for
(
p
=
0
;
p
<
3
;
p
++
)
atom
->
f
[
i
][
p
]
=
atom
->
f
[
i
][
p
]
+
ff
[
i
][
p
];
memory
->
sfree
(
nlist_short
);
memory
->
sfree
(
first
);
if
(
ss
!=
xx
)
memory
->
sfree
(
ss
);
memory
->
sfree
(
ff
);
memory
->
sfree
(
xx
);
tx1
=
gettime
();
tmem
+=
tx1
-
tx0
;
ntmem
++
;
t1
=
gettime
(
1
);
//printf("compute_x: c_p = %d c_t = %d c_q = %d\n",c_p,c_t,c_q);
#ifdef TIMING_ON
if
(
comm
->
me
==
0
)
{
double
tsum
=
(
tmem
+
tsort
+
tpair
+
tlookup
+
ttriplet
+
tquad
);
double
nsum
=
(
ntmem
+
ntsort
+
ntpair
+
ntlookup
+
nttriplet
+
ntquad
);
//double adj = ((t1-t0)-tsum)/nsum;
/* Use adj = 6ns for RDTSC, and 58ns for gettimeofday,
on monkfish.llnl.gov, 2.4GHz Intel
Use adj = 35.945ns for RDTSC on uBGL (assumed rate set to 700MHz)
*/
double
adj
=
35.945e-9
;
double
memadj
=
tmem
-
adj
*
ntmem
,
sortadj
=
tsort
-
adj
*
ntsort
,
pairadj
=
tpair
-
adj
*
ntpair
,
lookupadj
=
tlookup
-
adj
*
ntlookup
,
tripletadj
=
ttriplet
-
adj
*
nttriplet
,
quadadj
=
tquad
-
adj
*
ntquad
,
make_b_adj
=
t_make_b
-
adj
*
n_make
,
make_t_adj
=
t_make_t
-
adj
*
n_make
,
make_b2_adj
=
t_make_b2
-
adj
*
n_make_b2
,
trace_adj
=
t_trace
-
adj
*
n_trace
;
printf
(
"mgpt engy = %10.3fms
\n
"
,(
t1
-
t0
)
*
1e3
);
printf
(
" mem = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns
\n
"
,
tmem
*
1e3
,
ntmem
,
memadj
*
1e3
,
memadj
/
ntmem
*
1e9
);
printf
(
" sort = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns
\n
"
,
tsort
*
1e3
,
ntsort
,
sortadj
*
1e3
,
sortadj
/
ntsort
*
1e9
);
printf
(
" pair = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns
\n
"
,
tpair
*
1e3
,
ntpair
,
pairadj
*
1e3
,
pairadj
/
ntpair
*
1e9
);
printf
(
" lookup = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns
\n
"
,
tlookup
*
1e3
,
ntlookup
,
lookupadj
*
1e3
,
lookupadj
/
ntlookup
*
1e9
);
printf
(
" triplet = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns
\n
"
,
ttriplet
*
1e3
,
nttriplet
,
tripletadj
*
1e3
,
tripletadj
/
nttriplet
*
1e9
);
printf
(
" quad = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns
\n
"
,
tquad
*
1e3
,
ntquaditer
,
quadadj
*
1e3
,
quadadj
/
ntquaditer
*
1e9
);
printf
(
" sum = %10.3fms adj = %10.3fms
\n
"
,
tsum
*
1e3
,(
tsum
-
adj
*
nsum
)
*
1e3
);
printf
(
"
\n
make_b = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns
\n
"
,
t_make_b
*
1e3
,
n_make
,
make_b_adj
*
1e3
,
make_b_adj
/
n_make
*
1e9
);
printf
(
" make_b2 = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns
\n
"
,
t_make_b2
*
1e3
,
n_make_b2
,
make_b2_adj
*
1e3
,
make_b2_adj
/
n_make_b2
*
1e9
);
printf
(
" make_t = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns
\n\n
"
,
t_make_t
*
1e3
,
n_make
,
make_t_adj
*
1e3
,
make_t_adj
/
n_make
*
1e9
);
printf
(
" trace = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns
\n\n
"
,
t_trace
*
1e3
,
n_trace
,
trace_adj
*
1e3
,
trace_adj
/
n_trace
*
1e9
);
printf
(
"mcount (transpose + trace for triplet) = %.0f , %.0f qcount = %.0f lmax = %d
\n
"
,
mcount
,
mcount2
,
qcount
,
lmax
);
printf
(
"nbc=%.0f tbl=%.3fms tbm=%.3fms one tbl=%.3fns one tbm=%.3fns
\n
"
,
nbc
,(
tbl
-
adj
*
nbc
)
*
1e3
,(
tbm
-
adj
*
nbc
)
*
1e3
,(
tbl
/
nbc
-
adj
)
*
1e9
,
(
tbm
/
nbc
-
adj
)
*
1e9
);
printf
(
"
\n\n
Forces:
\n
"
);
printf
(
"fix = %.3f fiy=%.3f fiz=%.3f
\n
"
,
fix
,
fiy
,
fiz
);
printf
(
"fjx = %.3f fjy=%.3f fjz=%.3f
\n
"
,
fjx
,
fjy
,
fjz
);
printf
(
"fkx = %.3f fky=%.3f fkz=%.3f
\n
"
,
fkx
,
fky
,
fkz
);
printf
(
"
\n
"
);
printf
(
"Bonds : nsearch=%d maxlen=%d avg.len=%.3f
\n
"
,
bond_hash
.
NSearch
(),
bond_hash
.
MaxLength
(),
bond_hash
.
NStep
()
/
(
double
)
bond_hash
.
NSearch
());
printf
(
"compute_x: c_p = %d c_t = %d c_q = %d
\n
"
,
c_p
,
c_t
,
c_q
);
printf
(
"@@ Total number of trace3 calls is %d, total number of make_triplet is %.1f
\n
"
,
ntr_calls
,
n_make
);
{
Hash
<
bond_data
,
Doublet
>::
Iterator
iter
=
bond_hash
.
begin
();
int
nitem
=
0
,
nhit
=
0
;
while
(
iter
!=
bond_hash
.
end
())
{
nitem
++
;
nhit
+=
iter
.
link
()
->
hits
;
iter
.
next
();
}
printf
(
"bond_hash hits: nitems=%d nhits=%d hits/item = %.3f
\n
"
,
nitem
,
nhit
,
nhit
/
(
double
)
nitem
);
}
}
#endif
if
(
volpres_flag
)
{
/*
Include contributions to the pressure due to derivatines
of the energy with respect to the potential input volume.
*/
/* The following lines have moved to beginning of functions,
since they are used in calculating per-atom virial contributions */
/*
double vtot = 1.0;
double ntot = atom->natoms;
for(i = 0; i<3; i++)
vtot = vtot * (domain->boxhi[i] - domain->boxlo[i]);
double rhoinv = vtot / ntot;
*/
if
(
single_energies
)
// Virial correction for self energy
for
(
i
=
0
;
i
<
3
;
i
++
)
{
//virial[i] = virial[i] + nloc*pot_input_vol*pvol0*e_scale;
virial
[
i
]
=
virial
[
i
]
-
nloc
*
rhoinv
*
splinepot
.
devol0
*
e_scale
;
}
if
(
pair_energies
)
// Virial correction for pair energy
for
(
i
=
0
;
i
<
3
;
i
++
)
virial
[
i
]
=
virial
[
i
]
+
rhoinv
*
e_scale
*
volvir2
;
if
(
three_body_energies
)
// Virial correction for three body enegries
for
(
i
=
0
;
i
<
3
;
i
++
)
{
//virial[i] = virial[i] - pot_input_vol*(e_triplet_c*pc + (e_triplet-e_triplet_c)*pd);
virial
[
i
]
=
virial
[
i
]
-
(
vir3v
+
vir3t
)
*
rhoinv
*
e_scale
;
}
if
(
four_body_energies
)
// Virial correction for four body enegries
for
(
i
=
0
;
i
<
3
;
i
++
)
{
//virial[i] = virial[i] - pot_input_vol*e_quad*pe;
virial
[
i
]
=
virial
[
i
]
-
vir4
*
rhoinv
*
e_scale
;
}
}
*
e_s
=
e_single
;
*
e_p
=
e_pair
;
*
e_t
=
e_triplet
;
*
e_q
=
e_quad
;
}
void
PairMGPT
::
compute
(
int
eflag
,
int
vflag
)
{
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
eflag_global
=
vflag_global
=
eflag_atom
=
vflag_atom
=
0
;
int
newton_pair
=
force
->
newton_pair
;
double
e_s
,
e_p
,
e_t
,
e_q
;
//printf("newton_pair = %d, newton = %d, tag_enable = %d\n",force->newton_pair,force->newton,atom->tag_enable);
if
(
newton_pair
==
0
)
{
printf
(
"This is a problem. MGPT requires newton_pair flag to be on. Exiting...
\n
"
);
exit
(
1
);
}
if
(
atom
->
tag_enable
==
0
)
{
printf
(
"This is a problem. MGPT requires tag_enable flag to be on. Exiting...
\n
"
);
exit
(
1
);
}
compute_x
(
listfull
->
numneigh
,
listfull
->
firstneigh
,
&
e_s
,
&
e_p
,
&
e_t
,
&
e_q
,
evflag
,
newton_pair
);
if
(
0
)
{
// Stupid force calculation / verification
int
ii
,
nmax
=-
1
;
for
(
ii
=
0
;
ii
<
listfull
->
inum
+
listfull
->
gnum
;
ii
++
)
{
int
i
=
listfull
->
ilist
[
ii
];
if
(
i
>
nmax
)
nmax
=
i
;
}
nmax
++
;
double
*
ffwork
=
new
double
[
3
*
nmax
];
double
*
ffloc
=
new
double
[
3
*
listfull
->
inum
];
double
*
ffloc2
=
new
double
[
3
*
listfull
->
inum
];
double
**
ffptr
=
new
double
*
[
nmax
];
for
(
ii
=
0
;
ii
<
listfull
->
inum
+
listfull
->
gnum
;
ii
++
)
ffptr
[
ii
]
=
&
ffwork
[
3
*
ii
];
printf
(
"Computing boundary forces
\n
"
);
for
(
ii
=
0
;
ii
<
listfull
->
inum
;
ii
++
)
{
ffloc2
[
3
*
ii
]
=
0.0
;
ffloc2
[
3
*
ii
+
1
]
=
0.0
;
ffloc2
[
3
*
ii
+
2
]
=
0.0
;
int
i
=
listfull
->
ilist
[
ii
];
for
(
int
jj
=
0
;
jj
<
listfull
->
inum
+
listfull
->
gnum
;
jj
++
)
{
int
j
=
listfull
->
ilist
[
jj
];
if
(
atom
->
tag
[
i
]
==
atom
->
tag
[
j
])
for
(
int
p
=
0
;
p
<
3
;
p
++
)
ffloc2
[
3
*
ii
+
p
]
+=
atom
->
f
[
j
][
p
];
}
}
printf
(
"Starting main displacement force calculation
\n
"
);
for
(
ii
=
0
;
ii
<
listfull
->
inum
;
ii
++
)
{
int
i
=
listfull
->
ilist
[
ii
];
double
**
atom_f_save
=
atom
->
f
;
atom
->
f
=
ffptr
;
for
(
int
p
=
0
;
p
<
3
;
p
++
)
{
double
xsave
=
atom
->
x
[
i
][
p
];
const
double
delta
=
1e-3
;
atom
->
x
[
i
][
p
]
=
xsave
+
delta
;
for
(
int
jj
=
0
;
jj
<
3
*
nmax
;
jj
++
)
ffwork
[
jj
]
=
0.0
;
compute_x
(
listfull
->
numneigh
,
listfull
->
firstneigh
,
&
e_s
,
&
e_p
,
&
e_t
,
&
e_q
,
evflag
,
newton_pair
);
double
e1
=
e_s
+
e_p
+
e_t
+
e_q
;
atom
->
x
[
i
][
p
]
=
xsave
-
delta
;
for
(
int
jj
=
0
;
jj
<
3
*
nmax
;
jj
++
)
ffwork
[
jj
]
=
0.0
;
compute_x
(
listfull
->
numneigh
,
listfull
->
firstneigh
,
&
e_s
,
&
e_p
,
&
e_t
,
&
e_q
,
evflag
,
newton_pair
);
double
e2
=
e_s
+
e_p
+
e_t
+
e_q
;
ffloc
[
3
*
ii
+
p
]
=
-
(
e1
-
e2
)
/
(
2
*
delta
);
atom
->
x
[
i
][
p
]
=
xsave
;
}
atom
->
f
=
atom_f_save
;
printf
(
"Force on i=%4d:
\n
"
,
i
);
printf
(
" Position %20.10e %20.10e %20.10e
\n
"
,
atom
->
x
[
i
][
0
],
atom
->
x
[
i
][
1
],
atom
->
x
[
i
][
2
]);
printf
(
" Exact %20.10e %20.10e %20.10e
\n
"
,
atom
->
f
[
i
][
0
],
atom
->
f
[
i
][
1
],
atom
->
f
[
i
][
2
]);
printf
(
" Numerical %20.10e %20.10e %20.10e
\n
"
,
ffloc
[
3
*
ii
+
0
],
ffloc
[
3
*
ii
+
1
],
ffloc
[
3
*
ii
+
2
]);
printf
(
" Boundary %20.10e %20.10e %20.10e
\n
"
,
ffloc2
[
3
*
ii
+
0
],
ffloc2
[
3
*
ii
+
1
],
ffloc2
[
3
*
ii
+
2
]);
}
delete
[]
ffloc2
;
delete
[]
ffloc
;
delete
[]
ffptr
;
delete
[]
ffwork
;
}
if
(
0
)
{
printf
(
"
\n
Forces MGPT:
\n
"
);
const
int
iimax
=
(
listfull
->
inum
<
10
)
?
listfull
->
inum
:
10
;
for
(
int
ii
=
0
;
ii
<
iimax
;
ii
++
)
{
int
i
=
listfull
->
ilist
[
ii
];
printf
(
"%4d = %20.10e %20.10e %20.10e
\n
"
,
i
,
atom
->
f
[
i
][
0
],
atom
->
f
[
i
][
1
],
atom
->
f
[
i
][
2
]);
}
printf
(
"
\n\n
"
);
}
if
(
vflag_fdotr
)
{
//printf("##### Using virial_compute!!!\n");
virial_fdotr_compute
();
}
}
void
PairMGPT
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
memory
->
create
(
setflag
,
n
+
1
,
n
+
1
,
"pair:setflag"
);
for
(
int
i
=
0
;
i
<=
n
;
i
++
)
for
(
int
j
=
0
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
memory
->
create
(
cutsq
,
n
+
1
,
n
+
1
,
"pair:cutsq"
);
memory
->
create
(
cutghost
,
n
+
1
,
n
+
1
,
"pair:cutsq"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairMGPT
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
0
)
error
->
all
(
__FILE__
,
__LINE__
,
"Illegal pair_style command"
);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairMGPT
::
coeff
(
int
narg
,
char
**
arg
)
{
int
single_precision
=
0
;
if
(
narg
<
5
)
error
->
all
(
__FILE__
,
__LINE__
,
"Not enough arguments for mgpt (MGPT) pair coefficients."
);
if
(
!
allocated
)
allocate
();
// Make sure I,J args are * *
if
(
strcmp
(
arg
[
0
],
"*"
)
!=
0
||
strcmp
(
arg
[
1
],
"*"
)
!=
0
)
error
->
all
(
__FILE__
,
__LINE__
,
"Incorrect args for pair coefficients"
);
double
vol
;
if
(
sscanf
(
arg
[
4
],
"%lg"
,
&
vol
)
!=
1
||
vol
<=
0.0
)
error
->
all
(
__FILE__
,
__LINE__
,
"Invalid volume in mgpt (MGPT) pair coefficients."
);
volpres_flag
=
1
;
single_precision
=
0
;
/* Parse arguments */
{
int
volpres_tag
=
0
,
precision_tag
=
0
,
nbody_tag
=
0
;
int
iarg
=
5
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"volpress"
)
==
0
)
{
/* Volumetric pressure flag */
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"yes"
)
==
0
)
volpres_flag
=
1
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"no"
)
==
0
)
volpres_flag
=
0
;
else
{
char
line
[
1024
];
sprintf
(
line
,
"(In %s:%d) Invalid value for volumetric pressure argument.
\n
"
"It should be
\"
volpress yes
\"
or
\"
volpress no
\"
.
\n
"
"The value is
\"
%s
\"
.
\n
"
,
__FILE__
,
__LINE__
,
arg
[
iarg
+
1
]);
error
->
all
(
__FILE__
,
__LINE__
,
line
);
}
volpres_tag
=
1
;
iarg
+=
2
;
if
(
comm
->
me
==
0
)
printf
(
"* volpress: volpres_flag = %d [%s %s]
\n
"
,
volpres_flag
,
arg
[
iarg
-
2
],
arg
[
iarg
-
1
]);
}
else
if
(
strcmp
(
arg
[
iarg
],
"nbody"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
if
(
strspn
(
arg
[
iarg
+
1
],
"1234"
)
==
strlen
(
arg
[
iarg
+
1
]))
{
nbody_flag
=
0
;
for
(
int
i
=
0
;
i
<
4
;
i
++
)
if
(
strchr
(
arg
[
iarg
+
1
],
'1'
+
i
)
!=
NULL
)
{
nbody_flag
=
nbody_flag
+
(
1
<<
i
);
if
(
comm
->
me
==
0
)
printf
(
"Explicitly adding %d-tuple forces.
\n
"
,
i
+
1
);
}
}
else
{
char
line
[
1024
];
sprintf
(
line
,
"(In %s:%d) Invalid value for nbody flag.
\n
"
"It should be e.g.
\"
nbody=1234
\"
(for single, pair, triple, and quad forces/energiers)
\n
"
"For e.g. only pair and triple forces/energies, use
\"
nbody=23
\"
.
\n
"
"The default is
\"
nbody=1234
\"
.
\n
"
"The current value is
\"
%s
\"
.
\n
"
,
__FILE__
,
__LINE__
,
arg
[
iarg
+
1
]);
error
->
all
(
__FILE__
,
__LINE__
,
line
);
}
nbody_tag
=
1
;
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"precision"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"single"
)
==
0
)
single_precision
=
1
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"double"
)
==
0
)
single_precision
=
0
;
else
{
char
line
[
1024
];
sprintf
(
line
,
"(In %s:%d) Invalid value for precision argument.
\n
"
"It should be
\"
precision single
\"
or
\"
precision double
\"
.
\n
"
"The value is
\"
%s
\"
.
\n
"
,
__FILE__
,
__LINE__
,
arg
[
iarg
+
1
]);
error
->
all
(
__FILE__
,
__LINE__
,
line
);
}
precision_tag
=
1
;
iarg
+=
2
;
if
(
comm
->
me
==
0
)
printf
(
"* precision: single_flag = %d [%s %s]
\n
"
,
single_precision
,
arg
[
iarg
-
2
],
arg
[
iarg
-
1
]);
}
else
{
char
line
[
1024
];
sprintf
(
line
,
"(In %s:%d) Invalid argument. Allowed arguments are:
\n
"
" volpress {yes|no} , default = yes
\n
"
" precision {single|double} , default = double
\n
"
" nbody {[1234,]*} , default = whichever terms potential require
\n
"
"The invalid argument is
\"
%s
\"
.
\n
"
,
__FILE__
,
__LINE__
,
arg
[
iarg
]);
error
->
all
(
__FILE__
,
__LINE__
,
line
);
}
}
if
(
comm
->
me
==
0
)
printf
(
"Volumetric pressure is %s.
\n
"
,
volpres_flag
?
"on"
:
"off"
);
if
(
comm
->
me
==
0
)
{
FILE
*
parmin_fp
=
force
->
open_potential
(
arg
[
2
]);
FILE
*
potin_fp
=
force
->
open_potential
(
arg
[
3
]);
if
(
parmin_fp
==
NULL
||
potin_fp
==
NULL
)
{
char
str
[
128
];
sprintf
(
str
,
"Cannot open MGPT potential files %s %s"
,
arg
[
2
],
arg
[
3
]);
error
->
one
(
FLERR
,
str
);
}
fclose
(
parmin_fp
);
fclose
(
potin_fp
);
splinepot
.
readpot
(
arg
[
2
],
arg
[
3
],
vol
);
printf
(
"evol0 = %.10e
\n
"
,
splinepot
.
evol0
);
/* Set up default and requested nbody forces to include */
{
int
nbody_default
=
(
1
<<
0
)
+
(
1
<<
1
)
+
(
1
<<
2
)
+
(
1
<<
3
);
if
(
splinepot
.
vd
==
0.0
&&
splinepot
.
dvd
==
0.0
)
nbody_default
-=
(
1
<<
2
);
// No 3-body contributions
if
(
splinepot
.
ve
==
0.0
&&
splinepot
.
dve
==
0.0
)
nbody_default
-=
(
1
<<
3
);
// No 4-body contributions
if
(
nbody_tag
==
0
)
nbody_flag
=
nbody_default
;
if
(
nbody_flag
!=
nbody_default
)
{
printf
(
"Warning: nbody=%d (suggested=%d) set to disregard multibody-forces in potential.
\n
"
,
nbody_flag
,
nbody_default
);
}
}
}
}
MPI_Bcast
(
&
nbody_flag
,
sizeof
(
nbody_flag
),
MPI_BYTE
,
0
,
world
);
/*
Broadcast structure to all processes. In receiving
processes, pointes will be screwed up. We allocate
memory, and then broadcast contents of arrays.
*/
MPI_Bcast
(
&
splinepot
,
sizeof
(
splinepot
),
MPI_BYTE
,
0
,
world
);
if
(
comm
->
me
!=
0
)
{
splinepot
.
vpair_spline
=
new
double
[
splinepot
.
nr
-
1
][
4
];
splinepot
.
dvpair_spline
=
new
double
[
splinepot
.
nr
-
1
][
4
];
}
MPI_Bcast
(
splinepot
.
vpair_spline
,
4
*
(
splinepot
.
nr
-
1
),
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
splinepot
.
dvpair_spline
,
4
*
(
splinepot
.
nr
-
1
),
MPI_DOUBLE
,
0
,
world
);
anorm3
=
splinepot
.
anorm3
;
anorm4
=
splinepot
.
anorm4
;
lmax
=
splinepot
.
lmax
;
lang
=
splinepot
.
lang
;
//ipot = splinepot.ipot;
for
(
int
i
=
0
;
i
<
(
int
)
(
sizeof
(
ddl
)
/
sizeof
(
double
));
i
++
)
ddl
[
i
]
=
splinepot
.
ddl
[
i
];
for
(
int
i
=
0
;
i
<
lmax
;
i
++
)
{
for
(
int
j
=
0
;
j
<
lmax
;
j
++
)
del0
.
m
[
i
+
1
][
j
+
1
]
=
0.0
;
del0
.
m
[
i
+
1
][
i
+
1
]
=
1.0
;
}
/* Set matrix param, cutoff, LAMMPS param */
Matrix
::
sz
=
lmax
;
rcrit
=
splinepot
.
rcrit
;
rmax
=
splinepot
.
rmax
;
cutoff
=
rmax
;
if
(
rcrit
>
rmax
)
cutoff
=
rcrit
;
// Set LAMMPS pair interaction flags.
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
{
for
(
int
j
=
1
;
j
<=
atom
->
ntypes
;
j
++
)
{
setflag
[
i
][
j
]
=
1
;
cutsq
[
i
][
j
]
=
cutoff
;
cutghost
[
i
][
j
]
=
cutoff
;
}
}
// Set atomic mass.
for
(
int
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
atom
->
set_mass
(
FLERR
,
i
,
splinepot
.
mass
);
// Initialize linear algebra routines.
linalg
=
mgpt_linalg
(
lmax
,
single_precision
);
if
(
comm
->
me
==
0
)
printf
(
"%s"
,
linalg
.
msg
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairMGPT
::
init_style
()
{
if
(
force
->
newton_pair
==
0
)
error
->
all
(
__FILE__
,
__LINE__
,
"Pair style mgpt requires newton pair on."
);
// Need full neighbor list.
int
irequest_full
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest_full
]
->
id
=
1
;
neighbor
->
requests
[
irequest_full
]
->
half
=
0
;
neighbor
->
requests
[
irequest_full
]
->
full
=
1
;
neighbor
->
requests
[
irequest_full
]
->
ghost
=
1
;
// Also need half neighbor list.
int
irequest_half
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest_half
]
->
id
=
2
;
neighbor
->
requests
[
irequest_half
]
->
half
=
0
;
neighbor
->
requests
[
irequest_half
]
->
half_from_full
=
1
;
neighbor
->
requests
[
irequest_half
]
->
otherlist
=
irequest_full
;
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
half or full
------------------------------------------------------------------------- */
void
PairMGPT
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
if
(
id
==
1
)
listfull
=
ptr
;
else
if
(
id
==
2
)
listhalf
=
ptr
;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairMGPT
::
init_one
(
int
i
,
int
j
)
{
return
cutoff
;
}
/************************************************************************
**** REIMPLEMENTATION OF FL AND HAMLTN WITH ANALYTICAL DERIVATIVES ****
************************************************************************/
/*
Reimplementation of bond length potential, including
derivatives with respect to x,y, and z.
*/
void
PairMGPT
::
fl_deriv_new
(
double
r
,
double
ri
,
double
xhat
,
double
yhat
,
double
zhat
,
double
&
fl_0
,
double
&
fl_x
,
double
&
fl_y
,
double
&
fl_z
,
double
&
fl_rp
,
double
&
fl_p1
,
double
&
fl_r0
,
double
&
fl_al
)
{
const
double
rp
=
splinepot
.
rp
,
p1
=
splinepot
.
p1
,
r0
=
splinepot
.
r00
,
al
=
splinepot
.
al
;
const
int
mode
=
splinepot
.
mode
;
const
double
pn
=
splinepot
.
pn
;
double
t
,
tx
,
ty
,
tz
,
t_rp_ti
,
t_p1_ti
;
double
s
;
/*
// Original code
double term;
double pn=1.0;
if (mode <= 4)
term = pow(rp/r, p1);
else
term = exp(-p1*(pow(r/rp, pn) - 1.0)/pn);
*/
double
rpi
=
1.0
/
rp
;
if
(
mode
<=
4
)
{
t
=
pow
(
rp
*
ri
,
p1
);
s
=
-
p1
*
t
*
ri
;
t_rp_ti
=
p1
*
rpi
;
t_p1_ti
=
log
(
rp
*
ri
);
}
else
{
if
(
pn
==
1.0
)
{
double
p1_rpi
=
-
p1
*
rpi
;
t
=
exp
(
p1
+
r
*
p1_rpi
);
s
=
p1_rpi
*
t
;
t_rp_ti
=
-
r
*
p1_rpi
*
rpi
;
t_p1_ti
=
1.0
-
r
*
rpi
;
}
else
{
double
pni
=
1.0
/
pn
;
double
rprpn
=
pow
(
r
*
rpi
,
pn
);
t
=
exp
(
-
p1
*
pni
*
(
rprpn
-
1.0
));
s
=
-
p1
*
rprpn
*
ri
*
t
;
t_rp_ti
=
p1
*
rprpn
*
rpi
;
t_p1_ti
=
pni
-
pni
*
rprpn
;
// -pni*(rprpn - 1.0);
}
}
tx
=
s
*
xhat
;
ty
=
s
*
yhat
;
tz
=
s
*
zhat
;
fl_rp
=
t_rp_ti
;
fl_p1
=
t_p1_ti
;
if
(
r
<=
r0
)
{
fl_0
=
t
;
fl_x
=
tx
;
fl_y
=
ty
;
fl_z
=
tz
;
fl_r0
=
0.0
;
fl_al
=
0.0
;
}
else
{
double
q
,
qx
,
qy
,
qz
,
exp_q
,
q_r0
,
q_al
;
double
r0i
,
u
;
r0i
=
1.0
/
r0
;
u
=
r
*
r0i
-
1.0
;
q
=
al
*
u
*
u
;
s
=
2
*
al
*
u
*
r0i
;
qx
=
s
*
xhat
;
qy
=
s
*
yhat
;
qz
=
s
*
zhat
;
q_r0
=
-
2.0
*
al
*
u
*
r
*
r0i
*
r0i
;
q_al
=
u
*
u
;
exp_q
=
exp
(
-
q
);
if
(
mode
<=
2
)
{
fl_0
=
exp_q
*
t
;
fl_x
=
exp_q
*
(
tx
-
t
*
qx
);
fl_y
=
exp_q
*
(
ty
-
t
*
qy
);
fl_z
=
exp_q
*
(
tz
-
t
*
qz
);
fl_r0
=
-
q_r0
;
fl_al
=
-
q_al
;
}
else
{
fl_0
=
exp_q
*
(
1.0
+
q
)
*
t
;
fl_x
=
exp_q
*
(
tx
+
q
*
(
tx
-
t
*
qx
));
fl_y
=
exp_q
*
(
ty
+
q
*
(
ty
-
t
*
qy
));
fl_z
=
exp_q
*
(
tz
+
q
*
(
tz
-
t
*
qz
));
fl_r0
=
-
q_r0
*
q
/
(
1.0
+
q
);
fl_al
=
-
q_al
*
q
/
(
1.0
+
q
);
}
}
}
/*
Macros to build elements of the bond matrix, and also
its derivatives with repsect to x,y, and z.
*/
#define MAKE_ELEMENT_5(i,j) \
do { \
const double dl0 = del0.m[i][j]; \
const double dl4 = gsl_##i * gsl_##j; \
const double dl4x = gsl_##i##x * gsl_##j + gsl_##i * gsl_##j##x; \
const double dl4y = gsl_##i##y * gsl_##j + gsl_##i * gsl_##j##y; \
const double dl4z = gsl_##i##z * gsl_##j + gsl_##i * gsl_##j##z; \
\
const double tmp = w4*dl4 + w2*dl2 + w0*dl0; \
const double tmpx = w4*dl4x + w2*dl2x; \
const double tmpy = w4*dl4y + w2*dl2y; \
const double tmpz = w4*dl4z + w2*dl2z; \
const double tmpsum = tmpx*x + tmpy*y + tmpz*z; \
M [j][i] = M[i][j] = fl *tmp; \
Mx[j][i] = Mx[i][j] = fl_x*tmp + fl_ri*(tmpx - x*tmpsum); \
My[j][i] = My[i][j] = fl_y*tmp + fl_ri*(tmpy - y*tmpsum); \
Mz[j][i] = Mz[i][j] = fl_z*tmp + fl_ri*(tmpz - z*tmpsum); \
} while(0)
#define MAKE_ELEMENT_7(i,j) \
do { \
const double dl0 = del0.m[i][j]; \
const double dl6 = gsl_##i * gsl_##j; \
const double dl6x = gsl_##i##x * gsl_##j + gsl_##i * gsl_##j##x; \
const double dl6y = gsl_##i##y * gsl_##j + gsl_##i * gsl_##j##y; \
const double dl6z = gsl_##i##z * gsl_##j + gsl_##i * gsl_##j##z; \
\
const double tmp = w6*dl6 + w4*dl4 + w2*dl2 + w0*dl0; \
const double tmpx = w6*dl6x + w4*dl4x + w2*dl2x; \
const double tmpy = w6*dl6y + w4*dl4y + w2*dl2y; \
const double tmpz = w6*dl6z + w4*dl4z + w2*dl2z; \
const double tmpsum = tmpx*x + tmpy*y + tmpz*z; \
M [j][i] = M[i][j] = fl *tmp; \
Mx[j][i] = Mx[i][j] = fl_x*tmp + fl_ri*(tmpx - x*tmpsum); \
My[j][i] = My[i][j] = fl_y*tmp + fl_ri*(tmpy - y*tmpsum); \
Mz[j][i] = Mz[i][j] = fl_z*tmp + fl_ri*(tmpz - z*tmpsum); \
} while(0)
/* End of bond matrix macros */
/*
Construction of bond matrix, and its derivatives
with respect to the coordinates
*/
void
PairMGPT
::
hamltn_5_raw
(
const
double
xin
,
const
double
yin
,
const
double
zin
,
double
M
[
8
][
8
],
double
Mx
[
8
][
8
],
double
My
[
8
][
8
],
double
Mz
[
8
][
8
],
double
*
fl_deriv_sum_p
)
{
const
double
r
=
sqrt
(
xin
*
xin
+
yin
*
yin
+
zin
*
zin
),
ri
=
1.0
/
r
;
const
double
x
=
xin
*
ri
,
y
=
yin
*
ri
,
z
=
zin
*
ri
;
// d-d
// call delndd(x,y,z)
const
double
x2
=
x
*
x
,
y2
=
y
*
y
,
z2
=
z
*
z
;
const
double
xy
=
x
*
y
,
xz
=
x
*
z
,
yz
=
y
*
z
;
const
double
sr3
=
sqrt
(
3.0
),
sr3i
=
1.0
/
sr3
;
const
double
frac_1_3
=
1.0
/
3.0
,
frac_2_3
=
2.0
/
3.0
,
frac_4_3
=
4.0
/
3.0
;
const
double
ddl_1
=
ddl
[
1
],
ddl_2
=
ddl
[
2
],
ddl_3
=
ddl
[
3
];
const
double
w4
=
ddl_1
-
frac_4_3
*
ddl_2
+
frac_1_3
*
ddl_3
;
const
double
w2
=
ddl_2
-
ddl_3
;
const
double
w0
=
ddl_2
;
//del4
double
gsl_1
,
gsl_2
,
gsl_3
,
gsl_4
,
gsl_5
;
double
gsl_1x
,
gsl_2x
,
gsl_3x
,
gsl_4x
,
gsl_5x
;
double
gsl_1y
,
gsl_2y
,
gsl_3y
,
gsl_4y
,
gsl_5y
;
double
gsl_1z
,
gsl_2z
,
gsl_3z
,
gsl_4z
,
gsl_5z
;
double
dl2
,
dl2x
,
dl2y
,
dl2z
;
double
fl
,
fl_x
,
fl_y
,
fl_z
,
fl_ri
;
double
fl_rp
,
fl_p1
,
fl_r0
,
fl_al
;
gsl_1
=
0.5
*
(
3.0
*
z2
-
1.0
);
gsl_1x
=
0.0
;
gsl_1y
=
0.0
;
gsl_1z
=
3.0
*
z
;
gsl_2
=
sr3
*
xz
;
gsl_2x
=
sr3
*
z
;
gsl_2y
=
0.0
;
gsl_2z
=
sr3
*
x
;
gsl_3
=
sr3
*
yz
;
gsl_3x
=
0.0
;
gsl_3y
=
sr3
*
z
;
gsl_3z
=
sr3
*
y
;
gsl_4
=
sr3
*
(
x2
-
y2
)
*
0.5
;
gsl_4x
=
sr3
*
x
;
gsl_4y
=
-
sr3
*
y
;
gsl_4z
=
0.0
;
gsl_5
=
sr3
*
xy
;
gsl_5x
=
sr3
*
y
;
gsl_5y
=
sr3
*
x
;
gsl_5z
=
0.0
;
// Compute bond length potential
fl_deriv_new
(
r
,
ri
,
x
,
y
,
z
,
fl
,
fl_x
,
fl_y
,
fl_z
,
fl_rp
,
fl_p1
,
fl_r0
,
fl_al
);
fl_ri
=
fl
*
ri
;
*
fl_deriv_sum_p
=
fl_rp
*
splinepot
.
drp
+
fl_p1
*
splinepot
.
dp1
+
fl_r0
*
splinepot
.
dr00
+
fl_al
*
splinepot
.
dal
;
// del2
//del2.m[1][1] = z2 - 2.0/3.0;
dl2
=
z2
-
frac_2_3
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
2
*
z
;
MAKE_ELEMENT_5
(
1
,
1
);
//del2.m[1][2] = xz/sr3;
dl2
=
xz
*
sr3i
;
dl2x
=
z
*
sr3i
;
dl2y
=
0.0
;
dl2z
=
x
*
sr3i
;
MAKE_ELEMENT_5
(
1
,
2
);
//del2.m[1][3] = yz/sr3;
dl2
=
yz
*
sr3i
;
dl2x
=
0.0
;
dl2y
=
z
*
sr3i
;
dl2z
=
y
*
sr3i
;
MAKE_ELEMENT_5
(
1
,
3
);
//del2.m[1][4] = -(x2 - y2)*sr3i;
dl2
=
-
(
x2
-
y2
)
*
sr3i
;
dl2x
=
-
2.0
*
sr3i
*
x
;
dl2y
=
2.0
*
sr3i
*
y
;
dl2z
=
0.0
;
MAKE_ELEMENT_5
(
1
,
4
);
//del2.m[1][5] = -2.0*xy*sr3i;
dl2
=
-
2.0
*
xy
*
sr3i
;
dl2x
=
-
2.0
*
y
*
sr3i
;
dl2y
=
-
2.0
*
x
*
sr3i
;
dl2z
=
0.0
;
MAKE_ELEMENT_5
(
1
,
5
);
//del2.m[2][2] = -y2;
dl2
=
-
y2
;
dl2x
=
0.0
;
dl2y
=
-
2.0
*
y
;
dl2z
=
0.0
;
MAKE_ELEMENT_5
(
2
,
2
);
//del2.m[2][3] = xy;
dl2
=
xy
;
dl2x
=
y
;
dl2y
=
x
;
dl2z
=
0.0
;
MAKE_ELEMENT_5
(
2
,
3
);
//del2.m[2][4] = xz;
dl2
=
xz
;
dl2x
=
z
;
dl2y
=
0.0
;
dl2z
=
x
;
MAKE_ELEMENT_5
(
2
,
4
);
//del2.m[2][5] = yz;
dl2
=
yz
;
dl2x
=
0.0
;
dl2y
=
z
;
dl2z
=
y
;
MAKE_ELEMENT_5
(
2
,
5
);
//del2.m[3][3] = -x2;
dl2
=
-
x2
;
dl2x
=
-
2.0
*
x
;
dl2y
=
0.0
;
dl2z
=
0.0
;
MAKE_ELEMENT_5
(
3
,
3
);
//del2.m[3][4] = -yz;
dl2
=
-
yz
;
dl2x
=
0.0
;
dl2y
=
-
z
;
dl2z
=
-
y
;
MAKE_ELEMENT_5
(
3
,
4
);
//del2.m[3][5] = xz;
dl2
=
xz
;
dl2x
=
z
;
dl2y
=
0.0
;
dl2z
=
x
;
MAKE_ELEMENT_5
(
3
,
5
);
//del2.m[4][4] = -z2;
dl2
=
-
z2
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
-
2.0
*
z
;
MAKE_ELEMENT_5
(
4
,
4
);
//del2.m[4][5] = 0.0;
dl2
=
0.0
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
0.0
;
MAKE_ELEMENT_5
(
4
,
5
);
//del2.m[5][5] = -z2;
dl2
=
-
z2
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
-
2.0
*
z
;
MAKE_ELEMENT_5
(
5
,
5
);
}
void
PairMGPT
::
hamltn_7_raw
(
const
double
xin
,
const
double
yin
,
const
double
zin
,
double
M
[
8
][
8
],
double
Mx
[
8
][
8
],
double
My
[
8
][
8
],
double
Mz
[
8
][
8
],
double
*
fl_deriv_sum_p
)
{
const
double
r
=
sqrt
(
xin
*
xin
+
yin
*
yin
+
zin
*
zin
),
ri
=
1.0
/
r
;
const
double
x
=
xin
*
ri
,
y
=
yin
*
ri
,
z
=
zin
*
ri
;
// d-d
// call delndd(x,y,z)
const
double
x2
=
x
*
x
,
y2
=
y
*
y
,
z2
=
z
*
z
;
const
double
xy
=
x
*
y
,
xz
=
x
*
z
,
yz
=
y
*
z
;
const
double
x4
=
x2
*
x2
,
y4
=
y2
*
y2
;
//const double sr3 = sqrt(3.0);//,sr3i = 1.0/sr3;
//const double frac_1_3 = 1.0/3.0,frac_2_3 = 2.0/3.0,frac_4_3 = 4.0/3.0;
const
double
sr01
=
sqrt
(
0.1
);
const
double
sr015
=
sqrt
(
0.15
);
const
double
sr024
=
sqrt
(
0.24
);
const
double
sr0375
=
sqrt
(
0.375
);
const
double
sr06
=
sqrt
(
0.6
);
const
double
sr0625
=
sqrt
(
0.625
);
const
double
sr09
=
sqrt
(
0.9
);
const
double
sr15
=
sqrt
(
1.5
);
const
double
sr24
=
sqrt
(
2.4
);
const
double
sr36
=
sqrt
(
3.6
);
const
double
sr375
=
sqrt
(
3.75
);
const
double
sr96
=
sqrt
(
9.6
);
const
double
sr150
=
sqrt
(
15.0
);
const
double
ddl_1
=
ddl
[
1
],
ddl_2
=
ddl
[
2
],
ddl_3
=
ddl
[
3
],
ddl_4
=
ddl
[
4
];
const
double
w6
=
ddl_1
-
1.5
*
ddl_2
+
0.6
*
ddl_3
-
0.1
*
ddl_4
;
const
double
w4
=
0.625
*
ddl_2
-
ddl_3
+
0.375
*
ddl_4
;
const
double
w2
=
0.625
*
(
ddl_2
-
ddl_4
);
const
double
w0
=
0.625
*
ddl_2
+
0.375
*
ddl_4
;
//del6
double
gsl_1
,
gsl_2
,
gsl_3
,
gsl_4
,
gsl_5
,
gsl_6
,
gsl_7
;
double
gsl_1x
,
gsl_2x
,
gsl_3x
,
gsl_4x
,
gsl_5x
,
gsl_6x
,
gsl_7x
;
double
gsl_1y
,
gsl_2y
,
gsl_3y
,
gsl_4y
,
gsl_5y
,
gsl_6y
,
gsl_7y
;
double
gsl_1z
,
gsl_2z
,
gsl_3z
,
gsl_4z
,
gsl_5z
,
gsl_6z
,
gsl_7z
;
double
dl2
,
dl2x
,
dl2y
,
dl2z
;
double
dl4
,
dl4x
,
dl4y
,
dl4z
;
double
t1
;
double
fl
,
fl_x
,
fl_y
,
fl_z
,
fl_ri
;
double
fl_rp
,
fl_p1
,
fl_r0
,
fl_al
;
//gslf[1] = 0.5*(5.0*n2 - 3.0)*n;
gsl_1
=
0.5
*
(
5.0
*
z2
-
3.0
)
*
z
;
gsl_1x
=
0.0
;
gsl_1y
=
0.0
;
gsl_1z
=
7.5
*
z2
-
1.5
;
//gslf[2] = sr0375*(5.0*n2 - 1.0)*l;
gsl_2
=
sr0375
*
(
5.0
*
z2
-
1.0
)
*
x
;
gsl_2x
=
sr0375
*
(
5.0
*
z2
-
1.0
);
gsl_2y
=
0.0
;
gsl_2z
=
sr0375
*
10.0
*
xz
;
//gslf[3] = sr0375*(5.0*n2 - 1.0)*m;
gsl_3
=
sr0375
*
(
5.0
*
z2
-
1.0
)
*
y
;
gsl_3x
=
0.0
;
gsl_3y
=
sr0375
*
(
5.0
*
z2
-
1.0
);
gsl_3z
=
sr0375
*
10.0
*
yz
;
//gslf[4] = sr375*(l2 - m2)*n;
gsl_4
=
sr375
*
(
x2
-
y2
)
*
z
;
gsl_4x
=
2.0
*
sr375
*
xz
;
gsl_4y
=
-
2.0
*
sr375
*
yz
;
gsl_4z
=
sr375
*
(
x2
-
y2
);
//gslf[5] = sr150*lm*n;
gsl_5
=
sr150
*
xy
*
z
;
gsl_5x
=
sr150
*
yz
;
gsl_5y
=
sr150
*
xz
;
gsl_5z
=
sr150
*
xy
;
//gslf[6] = sr0625*(l2 - 3.0*m2)*l;
gsl_6
=
sr0625
*
(
x2
-
3.0
*
y2
)
*
x
;
gsl_6x
=
3.0
*
sr0625
*
(
x2
-
y2
);
gsl_6y
=
-
6.0
*
sr0625
*
xy
;
gsl_6z
=
0.0
;
//gslf[7] = sr0625*(3.0*l2 - m2)*m;
gsl_7
=
sr0625
*
(
3.0
*
x2
-
y2
)
*
y
;
gsl_7x
=
6.0
*
sr0625
*
xy
;
gsl_7y
=
3.0
*
sr0625
*
(
x2
-
y2
);
gsl_7z
=
0.0
;
// Compute bond length potential
fl_deriv_new
(
r
,
ri
,
x
,
y
,
z
,
fl
,
fl_x
,
fl_y
,
fl_z
,
fl_rp
,
fl_p1
,
fl_r0
,
fl_al
);
fl_ri
=
fl
*
ri
;
*
fl_deriv_sum_p
=
fl_rp
*
splinepot
.
drp
+
fl_p1
*
splinepot
.
dp1
+
fl_r0
*
splinepot
.
dr00
+
fl_al
*
splinepot
.
dal
;
// del2f
//del2f.m[1][1] = 0.4*(3.0*n2 - 1.0);
dl2
=
0.4
*
(
3.0
*
z2
-
1.0
);
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
2.4
*
z
;
//del4f.m[1][1] = 0.60*(5.0*n2 - 4.0)*n2;
dl4
=
0.60
*
(
5.0
*
z2
-
4.0
)
*
z2
;
dl4x
=
0.0
;
dl4y
=
0.0
;
dl4z
=
0.60
*
(
20.0
*
z2
-
8.0
)
*
z
;
MAKE_ELEMENT_7
(
1
,
1
);
//del2f.m[1][2] = sr024*ln;
dl2
=
sr024
*
xz
;
dl2x
=
sr024
*
z
;
dl2y
=
0.0
;
dl2z
=
sr024
*
x
;
//del4f.m[1][2] = sr024*(5.0*n2 - 2.0)*ln;
dl4
=
sr024
*
(
5.0
*
z2
-
2.0
)
*
xz
;
dl4x
=
sr024
*
(
5.0
*
z2
-
2.0
)
*
z
;
dl4y
=
0.0
;
dl4z
=
sr024
*
(
15.0
*
z2
-
2.0
)
*
x
;
MAKE_ELEMENT_7
(
1
,
2
);
//del2f.m[1][3] = sr024*mn;
dl2
=
sr024
*
yz
;
dl2x
=
0.0
;
dl2y
=
sr024
*
z
;
dl2z
=
sr024
*
y
;
//del4f.m[1][3] = sr024*(5.0*n2 - 2.0)*mn;
dl4
=
sr024
*
(
5.0
*
z2
-
2.0
)
*
yz
;
dl4x
=
0.0
;
dl4y
=
sr024
*
(
5.0
*
z2
-
2.0
)
*
z
;
dl4z
=
sr024
*
(
15.0
*
z2
-
2.0
)
*
y
;
MAKE_ELEMENT_7
(
1
,
3
);
//del2f.m[1][4] = -sr06*(l2 - m2);
dl2
=
-
sr06
*
(
x2
-
y2
);
dl2x
=
-
2.0
*
sr06
*
x
;
dl2y
=
2.0
*
sr06
*
y
;
dl2z
=
0.0
;
//del4f.m[1][4] = -sr06*(l2 - m2)*n2;
dl4
=
-
sr06
*
(
x2
-
y2
)
*
z2
;
dl4x
=
-
2.0
*
sr06
*
x
*
z2
;
dl4y
=
2.0
*
sr06
*
y
*
z2
;
dl4z
=
-
2.0
*
sr06
*
(
x2
-
y2
)
*
z
;
MAKE_ELEMENT_7
(
1
,
4
);
//del2f.m[1][5] = -sr24*lm;
dl2
=
-
sr24
*
xy
;
dl2x
=
-
sr24
*
y
;
dl2y
=
-
sr24
*
x
;
dl2z
=
0.0
;
//del4f.m[1][5] = -sr24*lm*n2;
dl4
=
-
sr24
*
xy
*
z2
;
dl4x
=
-
sr24
*
y
*
z2
;
dl4y
=
-
sr24
*
x
*
z2
;
dl4z
=
-
2.0
*
sr24
*
xy
*
z
;
MAKE_ELEMENT_7
(
1
,
5
);
//del2f.m[1][6] = 0.0;
dl2
=
0.0
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
0.0
;
//del4f.m[1][6] = sr36*(3.0*m2 - l2)*ln;
dl4
=
sr36
*
(
3.0
*
y2
-
x2
)
*
xz
;
dl4x
=
3.0
*
sr36
*
(
y2
-
x2
)
*
z
;
dl4y
=
6.0
*
sr36
*
y
*
xz
;
dl4z
=
sr36
*
(
3.0
*
y2
-
x2
)
*
x
;
MAKE_ELEMENT_7
(
1
,
6
);
//del2f.m[1][7] = 0.0;
dl2
=
0.0
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
0.0
;
//del4f.m[1][7] = -sr36*(3.0*l2 - m2)*mn;
dl4
=
-
sr36
*
(
3.0
*
x2
-
y2
)
*
yz
;
dl4x
=
-
6.0
*
sr36
*
x
*
yz
;
dl4y
=
-
3.0
*
sr36
*
(
x2
-
y2
)
*
z
;
dl4z
=
-
sr36
*
(
3.0
*
x2
-
y2
)
*
y
;
MAKE_ELEMENT_7
(
1
,
7
);
//del2f.m[2][2] = 0.3*(1.0 - 4.0*m2 + n2);
dl2
=
0.3
-
1.2
*
y2
+
0.3
*
z2
;
dl2x
=
0.0
;
dl2y
=
-
2.4
*
y
;
dl2z
=
0.6
*
z
;
//del4f.m[2][2] = -0.4*l*l - 2.5*(m2 - 0.6*l2)*n2;
dl4
=
-
0.4
*
x2
-
2.5
*
(
y2
-
0.6
*
x2
)
*
z2
;
dl4x
=
-
0.8
*
x
+
3.0
*
x
*
z2
;
dl4y
=
-
5.0
*
y
*
z2
;
dl4z
=
-
5.0
*
(
y2
-
0.6
*
x2
)
*
z
;
MAKE_ELEMENT_7
(
2
,
2
);
//del2f.m[2][3] = 1.2*lm;
dl2
=
1.2
*
xy
;
dl2x
=
1.2
*
y
;
dl2y
=
1.2
*
x
;
dl2z
=
0.0
;
//del4f.m[2][3] = 0.4*(10.0*n2 - 1.0)*lm;
dl4
=
(
4.0
*
z2
-
0.4
)
*
xy
;
dl4x
=
(
4.0
*
z2
-
0.4
)
*
y
;
dl4y
=
(
4.0
*
z2
-
0.4
)
*
x
;
dl4z
=
8.0
*
z
*
xy
;
MAKE_ELEMENT_7
(
2
,
3
);
//del2f.m[2][4] = sr09*ln;
dl2
=
sr09
*
xz
;
dl2x
=
sr09
*
z
;
dl2y
=
0.0
;
dl2z
=
sr09
*
x
;
//del4f.m[2][4] = sr01*(6.0*n2 - 8.0*m2 - 1.0)*ln;
dl4
=
sr01
*
(
6.0
*
z2
-
8.0
*
y2
-
1.0
)
*
xz
;
dl4x
=
sr01
*
(
6.0
*
z2
-
8.0
*
y2
-
1.0
)
*
z
;
dl4y
=
-
16.0
*
sr01
*
y
*
xz
;
dl4z
=
sr01
*
(
18.0
*
z2
-
8.0
*
y2
-
1.0
)
*
x
;
MAKE_ELEMENT_7
(
2
,
4
);
//del2f.m[2][5] = sr09*mn;
dl2
=
sr09
*
yz
;
dl2x
=
0.0
;
dl2y
=
sr09
*
z
;
dl2z
=
sr09
*
y
;
//del4f.m[2][5] = sr01*(2.0*n2 - 8.0*m2 + 3.0)*mn;
dl4
=
sr01
*
(
2.0
*
z2
-
8.0
*
y2
+
3.0
)
*
yz
;
dl4x
=
0.0
;
dl4y
=
sr01
*
(
2.0
*
z2
-
24.0
*
y2
+
3.0
)
*
z
;
dl4z
=
sr01
*
(
6.0
*
z2
-
8.0
*
y2
+
3.0
)
*
y
;
MAKE_ELEMENT_7
(
2
,
5
);
//del2f.m[2][6] = -sr015*(l2 - m2);
dl2
=
-
sr015
*
(
x2
-
y2
);
dl2x
=
-
2.0
*
sr015
*
x
;
dl2y
=
2.0
*
sr015
*
y
;
dl2z
=
0.0
;
//del4f.m[2][6] = sr375*(l2 - m2 - 1.4*l4 + 1.2*l2*m2 + m4);
dl4
=
sr375
*
(
x2
-
y2
-
1.4
*
x4
+
1.2
*
x2
*
y2
+
y4
);
dl4x
=
sr375
*
(
2.0
-
5.6
*
x2
+
2.4
*
y2
)
*
x
;
dl4y
=
sr375
*
(
-
2.0
+
2.4
*
x2
+
4.0
*
y2
)
*
y
;
dl4z
=
0.0
;
MAKE_ELEMENT_7
(
2
,
6
);
//del2f.m[2][7] = -sr06*lm;
dl2
=
-
sr06
*
xy
;
dl2x
=
-
sr06
*
y
;
dl2y
=
-
sr06
*
x
;
dl2z
=
0.0
;
//del4f.m[2][7] = sr96*(n2 - l2 + 0.25)*lm;
dl4
=
sr96
*
(
z2
-
x2
+
0.25
)
*
xy
;
dl4x
=
sr96
*
(
z2
-
3.0
*
x2
+
0.25
)
*
y
;
dl4y
=
sr96
*
(
z2
-
x2
+
0.25
)
*
x
;
dl4z
=
2.0
*
sr96
*
z
*
xy
;
MAKE_ELEMENT_7
(
2
,
7
);
//del2f.m[3][3] = 0.30*(1.0 - 4.0*l2 + n2);
dl2
=
0.3
-
1.2
*
x2
+
0.3
*
z2
;
dl2x
=
-
2.4
*
x
;
dl2y
=
0.0
;
dl2z
=
0.6
*
z
;
//del4f.m[3][3] = -0.4*m2 - 2.5*(l2 - 0.6*m2)*n2;
dl4
=
-
0.4
*
y2
-
2.5
*
(
x2
-
0.6
*
y2
)
*
z2
;
dl4x
=
-
5.0
*
x
*
z2
;
dl4y
=
y
*
(
3.0
*
z2
-
0.8
);
dl4z
=
-
5.0
*
(
x2
-
0.6
*
y2
)
*
z
;
MAKE_ELEMENT_7
(
3
,
3
);
//del2f.m[3][4] = -sr09*mn;
dl2
=
-
sr09
*
yz
;
dl2x
=
0.0
;
dl2y
=
-
sr09
*
z
;
dl2z
=
-
sr09
*
y
;
//del4f.m[3][4] = -sr01*(6.0*n2 - 8.0*l2 - 1.0)*mn;
dl4
=
-
sr01
*
(
6.0
*
z2
-
8.0
*
x2
-
1.0
)
*
yz
;
dl4x
=
16.0
*
sr01
*
x
*
yz
;
dl4y
=
-
sr01
*
(
6.0
*
z2
-
8.0
*
x2
-
1.0
)
*
z
;
dl4z
=
-
sr01
*
(
18.0
*
z2
-
8.0
*
x2
-
1.0
)
*
y
;
MAKE_ELEMENT_7
(
3
,
4
);
//del2f.m[3][5] = sr09*ln;
dl2
=
sr09
*
xz
;
dl2x
=
sr09
*
z
;
dl2y
=
0.0
;
dl2z
=
sr09
*
x
;
//del4f.m[3][5] = sr01*(2.0*n2 - 8.0*l2 + 3.0)*ln;
dl4
=
sr01
*
(
2.0
*
z2
-
8.0
*
x2
+
3.0
)
*
xz
;
dl4x
=
sr01
*
(
2.0
*
z2
-
24.0
*
x2
+
3.0
)
*
z
;
dl4y
=
0.0
;
dl4z
=
sr01
*
(
6.0
*
z2
-
8.0
*
x2
+
3.0
)
*
x
;
MAKE_ELEMENT_7
(
3
,
5
);
//del2f.m[3][6] = sr06*lm;
dl2
=
sr06
*
xy
;
dl2x
=
sr06
*
y
;
dl2y
=
sr06
*
x
;
dl2z
=
0.0
;
//del4f.m[3][6] = sr96*(m2 - n2 - 0.25)*lm;
dl4
=
sr96
*
(
y2
-
z2
-
0.25
)
*
xy
;
dl4x
=
sr96
*
(
y2
-
z2
-
0.25
)
*
y
;
dl4y
=
sr96
*
(
3.0
*
y2
-
z2
-
0.25
)
*
x
;
dl4z
=
-
2.0
*
sr96
*
z
*
xy
;
MAKE_ELEMENT_7
(
3
,
6
);
//del2f.m[3][7] = -sr015*(l2 - m2);
dl2
=
-
sr015
*
(
x2
-
y2
);
dl2x
=
-
2.0
*
sr015
*
x
;
dl2y
=
2.0
*
sr015
*
y
;
dl2z
=
0.0
;
//del4f.m[3][7] = sr375*(l2 - m2 + 1.4*m4 - 1.2*l2*m2 - l4);
dl4
=
sr375
*
(
x2
-
y2
+
1.4
*
y4
-
1.2
*
x2
*
y2
-
x4
);
dl4x
=
sr375
*
(
2.0
-
2.4
*
y2
-
4.0
*
x2
)
*
x
;
dl4y
=
sr375
*
(
-
2.0
+
5.6
*
y2
-
2.4
*
x2
)
*
y
;
dl4z
=
0.0
;
MAKE_ELEMENT_7
(
3
,
7
);
//del2f.m[4][4] = 0.0;
dl2
=
0.0
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
0.0
;
//del4f.m[4][4] = (2.0 - 3.0*n2)*n2 - 4.0*l2*m2;
dl4
=
(
2.0
-
3.0
*
z2
)
*
z2
-
4.0
*
x2
*
y2
;
dl4x
=
-
8.0
*
x
*
y2
;
dl4y
=
-
8.0
*
x2
*
y
;
dl4z
=
(
4.0
-
12.0
*
z2
)
*
z
;
MAKE_ELEMENT_7
(
4
,
4
);
//del2f.m[4][5] = 0.0;
dl2
=
0.0
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
0.0
;
//del4f.m[4][5] = 2.0*(l2 - m2)*lm;
dl4
=
2.0
*
(
x2
-
y2
)
*
xy
;
dl4x
=
2.0
*
(
3.0
*
x2
-
y2
)
*
y
;
dl4y
=
2.0
*
(
x2
-
3.0
*
y2
)
*
x
;
dl4z
=
0.0
;
MAKE_ELEMENT_7
(
4
,
5
);
//del2f.m[4][6] = sr15*ln;
dl2
=
sr15
*
xz
;
dl2x
=
sr15
*
z
;
dl2y
=
0.0
;
dl2z
=
sr15
*
x
;
//del4f.m[4][6] = -sr15*(2.0*n2 - 1.0)*ln;
dl4
=
-
sr15
*
(
2.0
*
z2
-
1.0
)
*
xz
;
dl4x
=
-
sr15
*
(
2.0
*
z2
-
1.0
)
*
z
;
dl4y
=
0.0
;
dl4z
=
-
sr15
*
(
6.0
*
z2
-
1.0
)
*
x
;
MAKE_ELEMENT_7
(
4
,
6
);
//del2f.m[4][7] = sr15*mn;
dl2
=
sr15
*
yz
;
dl2x
=
0.0
;
dl2y
=
sr15
*
z
;
dl2z
=
sr15
*
y
;
//del4f.m[4][7] = -sr15*(2.0*n2 - 1.0)*mn;
dl4
=
-
sr15
*
(
2.0
*
z2
-
1.0
)
*
yz
;
dl4x
=
0.0
;
dl4y
=
-
sr15
*
(
2.0
*
z2
-
1.0
)
*
z
;
dl4z
=
-
sr15
*
(
6.0
*
z2
-
1.0
)
*
y
;
MAKE_ELEMENT_7
(
4
,
7
);
//del2f.m[5][5] = 0.0;
dl2
=
0.0
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
0.0
;
//del4f.m[5][5] = -pow((2.0*n2 - 1.0),2) + 4.0*l2*m2;
t1
=
2.0
*
z2
-
1.0
;
dl4
=
-
t1
*
t1
+
4.0
*
x2
*
y2
;
dl4x
=
8.0
*
x
*
y2
;
dl4y
=
8.0
*
x2
*
y
;
dl4z
=
-
8.0
*
t1
*
z
;
MAKE_ELEMENT_7
(
5
,
5
);
//del2f.m[5][6] = -sr15*mn;
dl2
=
-
sr15
*
yz
;
dl2x
=
0.0
;
dl2y
=
-
sr15
*
z
;
dl2z
=
-
sr15
*
y
;
//del4f.m[5][6] = sr15*(2.0*n2 - 1.0)*mn;
dl4
=
sr15
*
(
2.0
*
z2
-
1.0
)
*
yz
;
dl4x
=
0.0
;
dl4y
=
sr15
*
(
2.0
*
z2
-
1.0
)
*
z
;
dl4z
=
sr15
*
(
6.0
*
z2
-
1.0
)
*
y
;
MAKE_ELEMENT_7
(
5
,
6
);
//del2f.m[5][7] = sr15*ln;
dl2
=
sr15
*
xz
;
dl2x
=
sr15
*
z
;
dl2y
=
0.0
;
dl2z
=
sr15
*
x
;
//del4f.m[5][7] = -sr15*(2.0*n2 - 1.0)*ln;
dl4
=
-
sr15
*
(
2.0
*
z2
-
1.0
)
*
xz
;
dl4x
=
-
sr15
*
(
2.0
*
z2
-
1.0
)
*
z
;
dl4y
=
0.0
;
dl4z
=
-
sr15
*
(
6.0
*
z2
-
1.0
)
*
x
;
MAKE_ELEMENT_7
(
5
,
7
);
//del2f.m[6][6] = -(3.0*n2 - 1.0)/2.0;
dl2
=
0.5
-
1.5
*
z2
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
-
3.0
*
z
;
//del4f.m[6][6] = 1.5*(n2 - 1.0)*n2;
dl4
=
(
1.5
*
z2
-
1.5
)
*
z2
;
dl4x
=
0.0
;
dl4y
=
0.0
;
dl4z
=
(
6.0
*
z2
-
3.0
)
*
z
;
MAKE_ELEMENT_7
(
6
,
6
);
//del2f.m[6][7] = 0.0;
dl2
=
0.0
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
0.0
;
//del4f.m[6][7] = 0.0;
dl4
=
0.0
;
dl4x
=
0.0
;
dl4y
=
0.0
;
dl4z
=
0.0
;
MAKE_ELEMENT_7
(
6
,
7
);
//del2f.m[7][7] = -(3.0*n2 - 1.0)/2.0;
dl2
=
0.5
-
1.5
*
z2
;
dl2x
=
0.0
;
dl2y
=
0.0
;
dl2z
=
-
3.0
*
z
;
//del4f.m[7][7] = 1.5*(n2 - 1.0)*n2;
dl4
=
(
1.5
*
z2
-
1.5
)
*
z2
;
dl4x
=
0.0
;
dl4y
=
0.0
;
dl4z
=
(
6.0
*
z2
-
3.0
)
*
z
;
MAKE_ELEMENT_7
(
7
,
7
);
}
/************************************************************************/
/* ----------------------------------------------------------------------
* Fast Model Generalized Pseudopotential Theory (MGPT) interatomic
* potential routine.
*
* Copyright (2015) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Tomas Oppelstrup (oppelstrup2@llnl.gov) and John Moriarty
* (moriarty2@llnl.gov)
* LLNL-CODE-674031 All rights reserved.
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU General Public License (as published by the
* Free Software Foundation) version 2, dated June 1991.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
* GNU General Public License for more details.
*
* LLNL Preamble Notice
* A. This notice is required to be provided under our contract with the
* U.S. Department of Energy (DOE). This work was performed under the auspices
* of the DOE by Lawrence Livermore National Laboratory under Contract No.
* DE-AC52-07NA27344.
*
* B. Neither the United States Government nor Lawrence Livermore National
* Security, LLC nor any of their employees, makes any warranty, express or
* implied, or assumes any liability or responsibility for the accuracy,
* completeness, or usefulness of any information, apparatus, product, or
* process disclosed, or represents that its use would not infringe
* privately-owned rights.
*
* C. Also, reference herein to any specific commercial products, process,
* or services by trade name, trademark, manufacturer or otherwise does not
* necessarily constitute or imply its endorsement, recommendation, or
* favoring by the United States Government or Lawrence Livermore National
* Security, LLC. The views and opinions of authors expressed herein do not
* necessarily state or reflect those of the United States Government or
* Lawrence Livermore National Security, LLC, and shall not be used for
* advertising or product endorsement purposes.
------------------------------------------------------------------------- */
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