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fix_qeq_comb.cpp
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Sat, Jul 6, 13:05
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8 KB
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text/x-c
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Mon, Jul 8, 13:05 (1 d, 23 h)
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18830979
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rLAMMPS lammps
fix_qeq_comb.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: Ray Shan (Sandia, tnshan@sandia.gov)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "pair_comb.h"
#include "pair_comb3.h"
#include "fix_qeq_comb.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "group.h"
#include "respa.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include "iostream"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
/* ---------------------------------------------------------------------- */
FixQEQComb
::
FixQEQComb
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
5
)
error
->
all
(
FLERR
,
"Illegal fix qeq/comb command"
);
peratom_flag
=
1
;
size_peratom_cols
=
0
;
peratom_freq
=
1
;
nevery
=
force
->
inumeric
(
FLERR
,
arg
[
3
]);
precision
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
if
(
nevery
<=
0
||
precision
<=
0.0
)
error
->
all
(
FLERR
,
"Illegal fix qeq/comb command"
);
MPI_Comm_rank
(
world
,
&
me
);
// optional args
fp
=
NULL
;
int
iarg
=
5
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"file"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal fix qeq/comb command"
);
if
(
me
==
0
)
{
fp
=
fopen
(
arg
[
iarg
+
1
],
"w"
);
if
(
fp
==
NULL
)
{
char
str
[
128
];
sprintf
(
str
,
"Cannot open fix qeq/comb file %s"
,
arg
[
iarg
+
1
]);
error
->
one
(
FLERR
,
str
);
}
}
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal fix qeq/comb command"
);
}
nmax
=
atom
->
nmax
;
memory
->
create
(
qf
,
nmax
,
"qeq:qf"
);
memory
->
create
(
q1
,
nmax
,
"qeq:q1"
);
memory
->
create
(
q2
,
nmax
,
"qeq:q2"
);
vector_atom
=
qf
;
// zero the vector since dump may access it on timestep 0
// zero the vector since a variable may access it before first run
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
qf
[
i
]
=
0.0
;
comb
=
NULL
;
comb3
=
NULL
;
comm_forward
=
1
;
}
/* ---------------------------------------------------------------------- */
FixQEQComb
::~
FixQEQComb
()
{
if
(
me
==
0
&&
fp
)
fclose
(
fp
);
memory
->
destroy
(
qf
);
memory
->
destroy
(
q1
);
memory
->
destroy
(
q2
);
}
/* ---------------------------------------------------------------------- */
int
FixQEQComb
::
setmask
()
{
int
mask
=
0
;
mask
|=
POST_FORCE
;
mask
|=
POST_FORCE_RESPA
;
mask
|=
MIN_POST_FORCE
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixQEQComb
::
init
()
{
if
(
!
atom
->
q_flag
)
error
->
all
(
FLERR
,
"Fix qeq/comb requires atom attribute q"
);
comb
=
(
PairComb
*
)
force
->
pair_match
(
"comb"
,
1
);
comb3
=
(
PairComb3
*
)
force
->
pair_match
(
"comb3"
,
1
);
if
(
comb
==
NULL
&&
comb3
==
NULL
)
error
->
all
(
FLERR
,
"Must use pair_style comb or comb3 with fix qeq/comb"
);
if
(
strstr
(
update
->
integrate_style
,
"respa"
))
nlevels_respa
=
((
Respa
*
)
update
->
integrate
)
->
nlevels
;
ngroup
=
group
->
count
(
igroup
);
if
(
ngroup
==
0
)
error
->
all
(
FLERR
,
"Fix qeq/comb group has no atoms"
);
int
irequest
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest
]
->
pair
=
0
;
neighbor
->
requests
[
irequest
]
->
fix
=
1
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full
=
1
;
}
/* ---------------------------------------------------------------------- */
void
FixQEQComb
::
setup
(
int
vflag
)
{
firstflag
=
1
;
if
(
strstr
(
update
->
integrate_style
,
"verlet"
))
post_force
(
vflag
);
else
{
((
Respa
*
)
update
->
integrate
)
->
copy_flevel_f
(
nlevels_respa
-
1
);
post_force_respa
(
vflag
,
nlevels_respa
-
1
,
0
);
((
Respa
*
)
update
->
integrate
)
->
copy_f_flevel
(
nlevels_respa
-
1
);
}
firstflag
=
0
;
}
/* ---------------------------------------------------------------------- */
void
FixQEQComb
::
min_post_force
(
int
vflag
)
{
post_force
(
vflag
);
}
/* ---------------------------------------------------------------------- */
void
FixQEQComb
::
post_force
(
int
vflag
)
{
int
i
,
ii
,
iloop
,
loopmax
,
inum
,
*
ilist
;
double
heatpq
,
qmass
,
dtq
,
dtq2
;
double
enegchkall
,
enegmaxall
;
if
(
update
->
ntimestep
%
nevery
)
return
;
// reallocate work arrays if necessary
// qf = charge force
// q1 = charge displacement
// q2 = tmp storage of charge force for next iteration
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy
(
qf
);
memory
->
destroy
(
q1
);
memory
->
destroy
(
q2
);
nmax
=
atom
->
nmax
;
memory
->
create
(
qf
,
nmax
,
"qeq:qf"
);
memory
->
create
(
q1
,
nmax
,
"qeq:q1"
);
memory
->
create
(
q2
,
nmax
,
"qeq:q2"
);
vector_atom
=
qf
;
}
// more loops for first-time charge equilibrium
iloop
=
0
;
if
(
firstflag
)
loopmax
=
200
;
else
loopmax
=
100
;
// charge-equilibration loop
if
(
me
==
0
&&
fp
)
fprintf
(
fp
,
"Charge equilibration on step "
BIGINT_FORMAT
"
\n
"
,
update
->
ntimestep
);
heatpq
=
0.05
;
qmass
=
0.016
;
dtq
=
0.01
;
dtq2
=
0.5
*
dtq
*
dtq
/
qmass
;
double
enegchk
=
0.0
;
double
enegtot
=
0.0
;
double
enegmax
=
0.0
;
double
*
q
=
atom
->
q
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
comb
)
{
inum
=
comb
->
list
->
inum
;
ilist
=
comb
->
list
->
ilist
;
}
if
(
comb3
)
{
inum
=
comb3
->
list
->
inum
;
ilist
=
comb3
->
list
->
ilist
;
}
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
q1
[
i
]
=
q2
[
i
]
=
qf
[
i
]
=
0.0
;
}
for
(
iloop
=
0
;
iloop
<
loopmax
;
iloop
++
)
{
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
{
q1
[
i
]
+=
qf
[
i
]
*
dtq2
-
heatpq
*
q1
[
i
];
q
[
i
]
+=
q1
[
i
];
}
}
comm
->
forward_comm_fix
(
this
);
if
(
comb
)
enegtot
=
comb
->
yasu_char
(
qf
,
igroup
);
if
(
comb3
)
enegtot
=
comb3
->
combqeq
(
qf
,
igroup
);
enegtot
/=
ngroup
;
enegchk
=
enegmax
=
0.0
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
{
q2
[
i
]
=
enegtot
-
qf
[
i
];
enegmax
=
MAX
(
enegmax
,
fabs
(
q2
[
i
]));
enegchk
+=
fabs
(
q2
[
i
]);
qf
[
i
]
=
q2
[
i
];
}
}
MPI_Allreduce
(
&
enegchk
,
&
enegchkall
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
enegchk
=
enegchkall
/
ngroup
;
MPI_Allreduce
(
&
enegmax
,
&
enegmaxall
,
1
,
MPI_DOUBLE
,
MPI_MAX
,
world
);
enegmax
=
enegmaxall
;
if
(
enegchk
<=
precision
&&
enegmax
<=
100.0
*
precision
)
break
;
if
(
me
==
0
&&
fp
)
fprintf
(
fp
,
" iteration: %d, enegtot %.6g, "
"enegmax %.6g, fq deviation: %.6g
\n
"
,
iloop
,
enegtot
,
enegmax
,
enegchk
);
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
mask
[
i
]
&
groupbit
)
q1
[
i
]
+=
qf
[
i
]
*
dtq2
-
heatpq
*
q1
[
i
];
}
}
if
(
me
==
0
&&
fp
)
{
if
(
iloop
==
loopmax
)
fprintf
(
fp
,
"Charges did not converge in %d iterations
\n
"
,
iloop
);
else
fprintf
(
fp
,
"Charges converged in %d iterations to %.10f tolerance
\n
"
,
iloop
,
enegchk
);
}
}
/* ---------------------------------------------------------------------- */
void
FixQEQComb
::
post_force_respa
(
int
vflag
,
int
ilevel
,
int
iloop
)
{
if
(
ilevel
==
nlevels_respa
-
1
)
post_force
(
vflag
);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double
FixQEQComb
::
memory_usage
()
{
double
bytes
=
atom
->
nmax
*
3
*
sizeof
(
double
);
return
bytes
;
}
/* ---------------------------------------------------------------------- */
int
FixQEQComb
::
pack_comm
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
atom
->
q
[
j
];
}
return
1
;
}
/* ---------------------------------------------------------------------- */
void
FixQEQComb
::
unpack_comm
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
atom
->
q
[
i
]
=
buf
[
m
++
];
}
/* ---------------------------------------------------------------------- */
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