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fix_qeq_slater.cpp
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rLAMMPS lammps
fix_qeq_slater.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "fix_qeq_slater.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "pair.h"
#include "kspace.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
using
namespace
FixConst
;
/* ---------------------------------------------------------------------- */
FixQEqSlater
::
FixQEqSlater
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixQEq
(
lmp
,
narg
,
arg
)
{
alpha
=
0.20
;
// optional arg
int
iarg
=
8
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"alpha"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal fix qeq/slater command"
);
alpha
=
atof
(
arg
[
iarg
+
1
]);
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal fix qeq/slater command"
);
}
if
(
streitz_flag
)
extract_streitz
();
}
/* ---------------------------------------------------------------------- */
void
FixQEqSlater
::
init
()
{
if
(
!
atom
->
q_flag
)
error
->
all
(
FLERR
,
"Fix qeq/slater requires atom attribute q"
);
ngroup
=
group
->
count
(
igroup
);
if
(
ngroup
==
0
)
error
->
all
(
FLERR
,
"Fix qeq/slater group has no atoms"
);
int
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
pair
=
0
;
neighbor
->
requests
[
irequest
]
->
fix
=
1
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full
=
1
;
int
ntypes
=
atom
->
ntypes
;
for
(
int
i
=
1
;
i
<=
ntypes
;
i
++
)
{
if
(
zeta
[
i
]
==
0.0
)
error
->
all
(
FLERR
,
"Invalid param file for fix qeq/slater"
);
}
if
(
strstr
(
update
->
integrate_style
,
"respa"
))
nlevels_respa
=
((
Respa
*
)
update
->
integrate
)
->
nlevels
;
}
/* ---------------------------------------------------------------------- */
void
FixQEqSlater
::
extract_streitz
()
{
Pair
*
pair
=
force
->
pair_match
(
"coul/streitz"
,
1
);
if
(
pair
==
NULL
)
error
->
all
(
FLERR
,
"No pair coul/streitz for fix qeq/slater"
);
int
tmp
;
chi
=
(
double
*
)
pair
->
extract
(
"chi"
,
tmp
);
eta
=
(
double
*
)
pair
->
extract
(
"eta"
,
tmp
);
gamma
=
(
double
*
)
pair
->
extract
(
"gamma"
,
tmp
);
zeta
=
(
double
*
)
pair
->
extract
(
"zeta"
,
tmp
);
zcore
=
(
double
*
)
pair
->
extract
(
"zcore"
,
tmp
);
if
(
chi
==
NULL
||
eta
==
NULL
||
gamma
==
NULL
||
zeta
==
NULL
||
zcore
==
NULL
)
error
->
all
(
FLERR
,
"Fix qeq/slater could not extract params from pair coul/streitz"
);
}
/* ---------------------------------------------------------------------- */
void
FixQEqSlater
::
pre_force
(
int
vflag
)
{
if
(
update
->
ntimestep
%
nevery
)
return
;
nlocal
=
atom
->
nlocal
;
nall
=
atom
->
nlocal
+
atom
->
nghost
;
if
(
atom
->
nmax
>
nmax
)
reallocate_storage
();
if
(
nlocal
>
n_cap
*
DANGER_ZONE
||
m_fill
>
m_cap
*
DANGER_ZONE
)
reallocate_matrix
();
init_matvec
();
matvecs
=
CG
(
b_s
,
s
);
// CG on s - parallel
matvecs
+=
CG
(
b_t
,
t
);
// CG on t - parallel
calculate_Q
();
if
(
force
->
kspace
)
force
->
kspace
->
qsum_qsq
();
}
/* ---------------------------------------------------------------------- */
void
FixQEqSlater
::
init_matvec
()
{
compute_H
();
int
inum
,
ii
,
i
;
int
*
ilist
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
for
(
ii
=
0
;
ii
<
inum
;
++
ii
)
{
i
=
ilist
[
ii
];
if
(
atom
->
mask
[
i
]
&
groupbit
)
{
Hdia_inv
[
i
]
=
1.
/
eta
[
atom
->
type
[
i
]
];
b_s
[
i
]
=
-
(
chi
[
atom
->
type
[
i
]]
+
chizj
[
i
]
);
b_t
[
i
]
=
-
1.0
;
t
[
i
]
=
t_hist
[
i
][
2
]
+
3
*
(
t_hist
[
i
][
0
]
-
t_hist
[
i
][
1
]
);
s
[
i
]
=
4
*
(
s_hist
[
i
][
0
]
+
s_hist
[
i
][
2
])
-
(
6
*
s_hist
[
i
][
1
]
+
s_hist
[
i
][
3
]);
}
}
pack_flag
=
2
;
comm
->
forward_comm_fix
(
this
);
//Dist_vector( s );
pack_flag
=
3
;
comm
->
forward_comm_fix
(
this
);
//Dist_vector( t );
}
/* ---------------------------------------------------------------------- */
void
FixQEqSlater
::
compute_H
()
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
r
,
rsq
,
delr
[
3
];
double
zei
,
zej
,
zj
,
zjtmp
;
int
*
type
=
atom
->
type
;
double
**
x
=
atom
->
x
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
m_fill
=
0
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
itype
=
type
[
i
];
zei
=
zeta
[
itype
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
H
.
firstnbr
[
i
]
=
m_fill
;
zjtmp
=
0.0
;
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
jtype
=
type
[
j
];
zej
=
zeta
[
jtype
];
zj
=
zcore
[
jtype
];
delr
[
0
]
=
x
[
i
][
0
]
-
x
[
j
][
0
];
delr
[
1
]
=
x
[
i
][
1
]
-
x
[
j
][
1
];
delr
[
2
]
=
x
[
i
][
2
]
-
x
[
j
][
2
];
rsq
=
delr
[
0
]
*
delr
[
0
]
+
delr
[
1
]
*
delr
[
1
]
+
delr
[
2
]
*
delr
[
2
];
if
(
rsq
>
cutoff_sq
)
continue
;
r
=
sqrt
(
rsq
);
H
.
jlist
[
m_fill
]
=
j
;
H
.
val
[
m_fill
]
=
calculate_H
(
zei
,
zej
,
zj
,
r
,
zjtmp
);
m_fill
++
;
}
H
.
numnbrs
[
i
]
=
m_fill
-
H
.
firstnbr
[
i
];
chizj
[
i
]
=
zjtmp
;
}
if
(
m_fill
>=
H
.
m
)
{
char
str
[
128
];
sprintf
(
str
,
"H matrix size has been exceeded: m_fill=%d H.m=%d
\n
"
,
m_fill
,
H
.
m
);
error
->
warning
(
FLERR
,
str
);
error
->
all
(
FLERR
,
"Fix qeq/slater has insufficient QEq matrix size"
);
}
}
/* ---------------------------------------------------------------------- */
double
FixQEqSlater
::
calculate_H
(
double
zei
,
double
zej
,
double
zj
,
double
r
,
double
&
zjtmp
)
{
double
rinv
=
1.0
/
r
;
double
exp2zir
=
exp
(
-
2.0
*
zei
*
r
);
double
zei2
=
zei
*
zei
;
double
zei4
=
zei2
*
zei2
;
double
zei6
=
zei2
*
zei4
;
double
exp2zjr
=
exp
(
-
2.0
*
zej
*
r
);
double
zej2
=
zej
*
zej
;
double
zej4
=
zej2
*
zej2
;
double
zej6
=
zej2
*
zej4
;
double
sm1
=
11.0
/
8.0
;
double
sm2
=
3.00
/
4.0
;
double
sm3
=
1.00
/
6.0
;
double
erfcr
=
erfc
(
alpha
*
r
);
double
qqrd2e
=
force
->
qqrd2e
;
double
etmp1
,
etmp2
;
double
e1
,
e2
,
e3
,
e4
;
double
ci_jfi
,
ci_fifj
;
e1
=
e2
=
e3
=
e4
=
0.0
;
etmp1
=
etmp2
=
0.0
;
ci_jfi
=
-
zei
*
exp2zir
-
rinv
*
exp2zir
;
if
(
zei
==
zej
)
{
ci_fifj
=
-
exp2zir
*
(
rinv
+
zei
*
(
sm1
+
sm2
*
zei
*
r
+
sm3
*
zei2
*
r
*
r
));
}
else
{
e1
=
zei
*
zej4
/
((
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zei
-
zej
)
*
(
zei
-
zej
));
e2
=
zej
*
zei4
/
((
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zej
-
zei
)
*
(
zej
-
zei
));
e3
=
(
3.0
*
zei2
*
zej4
-
zej6
)
/
((
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zei
-
zej
)
*
(
zei
-
zej
)
*
(
zei
-
zej
));
e4
=
(
3.0
*
zej2
*
zei4
-
zei6
)
/
((
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zej
-
zei
)
*
(
zej
-
zei
)
*
(
zej
-
zei
));
ci_fifj
=
-
exp2zir
*
(
e1
+
e3
/
r
)
-
exp2zjr
*
(
e2
+
e4
/
r
);
}
etmp1
=
1.00
*
(
ci_jfi
-
ci_fifj
);
etmp2
=
0.50
*
(
ci_fifj
+
erfcr
*
rinv
);
zjtmp
+=
qqrd2e
*
zj
*
etmp1
;
return
qqrd2e
*
etmp2
;
}
/* ---------------------------------------------------------------------- */
double
FixQEqSlater
::
calculate_H_wolf
(
double
zei
,
double
zej
,
double
zj
,
double
r
,
double
&
zjtmp
)
{
double
rinv
=
1.0
/
r
;
double
exp2zir
=
exp
(
-
2.0
*
zei
*
r
);
double
zei2
=
zei
*
zei
;
double
zei4
=
zei2
*
zei2
;
double
zei6
=
zei2
*
zei4
;
double
exp2zjr
=
exp
(
-
2.0
*
zej
*
r
);
double
zej2
=
zej
*
zej
;
double
zej4
=
zej2
*
zej2
;
double
zej6
=
zej2
*
zej4
;
double
sm1
=
11.0
/
8.0
;
double
sm2
=
3.00
/
4.0
;
double
sm3
=
1.00
/
6.0
;
double
e1
,
e2
,
e3
,
e4
;
double
rc
=
cutoff
;
double
rcinv
=
1.0
/
rc
;
double
rcinv2
=
rcinv
*
rcinv
;
double
exp2zirsh
=
exp
(
-
2.0
*
zei
*
rc
);
double
exp2zjrsh
=
exp
(
-
2.0
*
zej
*
rc
);
double
eshift
,
fshift
,
ci_jfi
,
ci_fifj
;
double
etmp1
,
etmp2
,
etmp3
;
double
a
=
alpha
;
double
erfcr
=
erfc
(
a
*
r
);
double
erfcrc
=
erfc
(
a
*
rc
);
double
qqrd2e
=
force
->
qqrd2e
;
etmp1
=
etmp2
=
etmp3
=
0.0
;
e1
=
e2
=
e3
=
e4
=
0.0
;
eshift
=
-
zei
*
exp2zirsh
-
rcinv
*
exp2zirsh
;
fshift
=
2.0
*
zei2
*
exp2zirsh
+
rcinv2
*
exp2zirsh
+
2.0
*
zei
*
rcinv
*
exp2zirsh
;
ci_jfi
=
-
zei
*
exp2zir
-
rinv
*
exp2zir
-
eshift
-
(
r
-
rc
)
*
fshift
;
if
(
zei
==
zej
)
{
eshift
=
-
exp2zirsh
*
(
rcinv
+
zei
*
(
sm1
+
sm2
*
zei
*
rc
+
sm3
*
zei2
*
rc
*
rc
));
ci_fifj
=
-
exp2zir
*
(
rinv
+
zei
*
(
sm1
+
sm2
*
zei
*
r
+
sm3
*
zei2
*
r
*
r
))
-
eshift
-
(
r
-
rc
)
*
fshift
;
}
else
{
e1
=
zei
*
zej4
/
((
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zei
-
zej
)
*
(
zei
-
zej
));
e2
=
zej
*
zei4
/
((
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zej
-
zei
)
*
(
zej
-
zei
));
e3
=
(
3.0
*
zei2
*
zej4
-
zej6
)
/
((
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zei
-
zej
)
*
(
zei
-
zej
)
*
(
zei
-
zej
));
e4
=
(
3.0
*
zej2
*
zei4
-
zei6
)
/
((
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zei
+
zej
)
*
(
zej
-
zei
)
*
(
zej
-
zei
)
*
(
zej
-
zei
));
eshift
=
-
exp2zirsh
*
(
e1
+
e3
/
rc
)
-
exp2zjrsh
*
(
e2
+
e4
/
rc
);
ci_fifj
=
-
exp2zir
*
(
e1
+
e3
/
r
)
-
exp2zjr
*
(
e2
+
e4
/
r
)
-
eshift
-
(
r
-
rc
)
*
fshift
;
}
etmp1
=
erfcr
/
r
-
erfcrc
/
rc
;
etmp2
=
1.00
*
(
ci_jfi
-
ci_fifj
);
etmp3
=
0.50
*
(
etmp1
+
ci_fifj
);
zjtmp
+=
qqrd2e
*
zj
*
etmp2
;
return
qqrd2e
*
etmp3
;
}
/* ---------------------------------------------------------------------- */
void
FixQEqSlater
::
sparse_matvec
(
sparse_matrix
*
A
,
double
*
x
,
double
*
b
)
{
int
i
,
j
,
itr_j
;
nlocal
=
atom
->
nlocal
;
nall
=
atom
->
nlocal
+
atom
->
nghost
;
double
r
=
cutoff
;
double
woself
=
0.50
*
erfc
(
alpha
*
r
)
/
r
+
alpha
/
MY_PIS
;
for
(
i
=
0
;
i
<
nlocal
;
++
i
)
{
if
(
atom
->
mask
[
i
]
&
groupbit
)
b
[
i
]
=
(
eta
[
atom
->
type
[
i
]]
-
2.0
*
force
->
qqr2e
*
woself
)
*
x
[
i
];
}
for
(
i
=
nlocal
;
i
<
nall
;
++
i
)
{
if
(
atom
->
mask
[
i
]
&
groupbit
)
b
[
i
]
=
0
;
}
for
(
i
=
0
;
i
<
nlocal
;
++
i
)
{
if
(
atom
->
mask
[
i
]
&
groupbit
)
{
for
(
itr_j
=
A
->
firstnbr
[
i
];
itr_j
<
A
->
firstnbr
[
i
]
+
A
->
numnbrs
[
i
];
itr_j
++
)
{
j
=
A
->
jlist
[
itr_j
];
b
[
i
]
+=
A
->
val
[
itr_j
]
*
x
[
j
];
b
[
j
]
+=
A
->
val
[
itr_j
]
*
x
[
i
];
}
}
}
}
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