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fix_qeq_shielded.cpp
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Tue, Aug 27, 10:31
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rLAMMPS lammps
fix_qeq_shielded.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_shielded.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 "kspace.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
FixQEqShielded
::
FixQEqShielded
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixQEq
(
lmp
,
narg
,
arg
)
{}
/* ---------------------------------------------------------------------- */
void
FixQEqShielded
::
init
()
{
if
(
!
atom
->
q_flag
)
error
->
all
(
FLERR
,
"Fix qeq/shielded requires atom attribute q"
);
ngroup
=
group
->
count
(
igroup
);
if
(
ngroup
==
0
)
error
->
all
(
FLERR
,
"Fix qeq/shielded 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
;
memory
->
create
(
shld
,
ntypes
+
1
,
ntypes
+
1
,
"qeq:shielding"
);
init_shielding
();
int
i
;
for
(
i
=
1
;
i
<=
ntypes
;
i
++
)
{
if
(
gamma
[
i
]
==
0.0
)
error
->
all
(
FLERR
,
"Invalid param file for fix qeq/shielded"
);
}
if
(
strstr
(
update
->
integrate_style
,
"respa"
))
nlevels_respa
=
((
Respa
*
)
update
->
integrate
)
->
nlevels
;
}
/* ---------------------------------------------------------------------- */
void
FixQEqShielded
::
init_shielding
()
{
int
i
,
j
;
double
d7
,
swa2
,
swa3
,
swb2
,
swb3
;
int
ntypes
=
atom
->
ntypes
;
for
(
i
=
1
;
i
<=
ntypes
;
++
i
)
for
(
j
=
1
;
j
<=
ntypes
;
++
j
)
shld
[
i
][
j
]
=
pow
(
gamma
[
i
]
*
gamma
[
j
],
-
1.5
);
if
(
fabs
(
swa
)
>
0.01
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"Fix qeq has non-zero lower Taper radius cutoff"
);
if
(
swb
<
0
)
error
->
all
(
FLERR
,
"Fix qeq has negative upper Taper radius cutoff"
);
else
if
(
swb
<
5
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"Fix qeq has very low Taper radius cutoff"
);
d7
=
pow
(
swb
-
swa
,
7
);
swa2
=
swa
*
swa
;
swa3
=
swa2
*
swa
;
swb2
=
swb
*
swb
;
swb3
=
swb2
*
swb
;
Tap
[
7
]
=
20.0
/
d7
;
Tap
[
6
]
=
-
70.0
*
(
swa
+
swb
)
/
d7
;
Tap
[
5
]
=
84.0
*
(
swa2
+
3.0
*
swa
*
swb
+
swb2
)
/
d7
;
Tap
[
4
]
=
-
35.0
*
(
swa3
+
9.0
*
swa2
*
swb
+
9.0
*
swa
*
swb2
+
swb3
)
/
d7
;
Tap
[
3
]
=
140.0
*
(
swa3
*
swb
+
3.0
*
swa2
*
swb2
+
swa
*
swb3
)
/
d7
;
Tap
[
2
]
=-
210.0
*
(
swa3
*
swb2
+
swa2
*
swb3
)
/
d7
;
Tap
[
1
]
=
140.0
*
swa3
*
swb3
/
d7
;
Tap
[
0
]
=
(
-
35.0
*
swa3
*
swb2
*
swb2
+
21.0
*
swa2
*
swb3
*
swb2
+
7.0
*
swa
*
swb3
*
swb3
+
swb3
*
swb3
*
swb
)
/
d7
;
}
/* ---------------------------------------------------------------------- */
void
FixQEqShielded
::
pre_force
(
int
vflag
)
{
if
(
update
->
ntimestep
%
nevery
)
return
;
nlocal
=
atom
->
nlocal
;
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
FixQEqShielded
::
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
FixQEqShielded
::
compute_H
()
{
int
inum
,
jnum
,
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
int
i
,
j
,
ii
,
jj
;
double
**
x
;
double
dx
,
dy
,
dz
,
r_sqr
,
r
;
int
*
type
=
atom
->
type
;
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// fill in the H matrix
m_fill
=
0
;
r_sqr
=
0
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
{
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
H
.
firstnbr
[
i
]
=
m_fill
;
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
dx
=
x
[
j
][
0
]
-
x
[
i
][
0
];
dy
=
x
[
j
][
1
]
-
x
[
i
][
1
];
dz
=
x
[
j
][
2
]
-
x
[
i
][
2
];
r_sqr
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
if
(
r_sqr
<=
cutoff_sq
)
{
H
.
jlist
[
m_fill
]
=
j
;
r
=
sqrt
(
r_sqr
);
H
.
val
[
m_fill
]
=
0.5
*
calculate_H
(
r
,
shld
[
type
[
i
]][
type
[
j
]]
);
m_fill
++
;
}
}
H
.
numnbrs
[
i
]
=
m_fill
-
H
.
firstnbr
[
i
];
}
}
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/shielded has insufficient QEq matrix size"
);
}
}
/* ---------------------------------------------------------------------- */
double
FixQEqShielded
::
calculate_H
(
double
r
,
double
gamma
)
{
double
Taper
,
denom
;
Taper
=
Tap
[
7
]
*
r
+
Tap
[
6
];
Taper
=
Taper
*
r
+
Tap
[
5
];
Taper
=
Taper
*
r
+
Tap
[
4
];
Taper
=
Taper
*
r
+
Tap
[
3
];
Taper
=
Taper
*
r
+
Tap
[
2
];
Taper
=
Taper
*
r
+
Tap
[
1
];
Taper
=
Taper
*
r
+
Tap
[
0
];
denom
=
r
*
r
*
r
+
gamma
;
denom
=
pow
(
denom
,
0.3333333333333
);
return
Taper
*
EV_TO_KCAL_PER_MOL
/
denom
;
}
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