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fix_nvt.cpp
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rLAMMPS lammps
fix_nvt.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: Mark Stevens (SNL)
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "fix_nvt.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "group.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
FixNVT
::
FixNVT
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
6
)
error
->
all
(
"Illegal fix nvt command"
);
restart_global
=
1
;
scalar_flag
=
1
;
scalar_vector_freq
=
1
;
extscalar
=
1
;
t_start
=
atof
(
arg
[
3
]);
t_stop
=
atof
(
arg
[
4
]);
double
t_period
=
atof
(
arg
[
5
]);
if
(
narg
==
6
)
drag
=
0.0
;
else
if
(
narg
==
8
&&
strcmp
(
arg
[
6
],
"drag"
)
==
0
)
drag
=
atof
(
arg
[
7
]);
else
error
->
all
(
"Illegal fix nvt command"
);
// error checks
// convert input period to frequency
if
(
t_start
<
0.0
||
t_stop
<=
0.0
)
error
->
all
(
"Target T for fix nvt cannot be 0.0"
);
if
(
t_period
<=
0.0
)
error
->
all
(
"Fix nvt period must be > 0.0"
);
t_freq
=
1.0
/
t_period
;
eta
=
eta_dot
=
0.0
;
// create a new compute temp style
// id = fix-ID + temp, compute group = fix group
int
n
=
strlen
(
id
)
+
6
;
id_temp
=
new
char
[
n
];
strcpy
(
id_temp
,
id
);
strcat
(
id_temp
,
"_temp"
);
char
**
newarg
=
new
char
*
[
3
];
newarg
[
0
]
=
id_temp
;
newarg
[
1
]
=
group
->
names
[
igroup
];
if
(
strcmp
(
style
,
"nvt"
)
==
0
)
newarg
[
2
]
=
(
char
*
)
"temp"
;
else
if
(
strcmp
(
style
,
"nvt/asphere"
)
==
0
)
newarg
[
2
]
=
(
char
*
)
"temp/asphere"
;
else
if
(
strcmp
(
style
,
"nvt/sllod"
)
==
0
)
newarg
[
2
]
=
(
char
*
)
"temp/deform"
;
modify
->
add_compute
(
3
,
newarg
);
delete
[]
newarg
;
tflag
=
1
;
}
/* ---------------------------------------------------------------------- */
FixNVT
::~
FixNVT
()
{
// delete temperature if fix created it
if
(
tflag
)
modify
->
delete_compute
(
id_temp
);
delete
[]
id_temp
;
}
/* ---------------------------------------------------------------------- */
int
FixNVT
::
setmask
()
{
int
mask
=
0
;
mask
|=
INITIAL_INTEGRATE
;
mask
|=
FINAL_INTEGRATE
;
mask
|=
THERMO_ENERGY
;
mask
|=
INITIAL_INTEGRATE_RESPA
;
mask
|=
FINAL_INTEGRATE_RESPA
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixNVT
::
init
()
{
if
(
atom
->
mass
==
NULL
)
error
->
all
(
"Cannot use fix nvt without per-type mass defined"
);
int
icompute
=
modify
->
find_compute
(
id_temp
);
if
(
icompute
<
0
)
error
->
all
(
"Temp ID for fix nvt does not exist"
);
temperature
=
modify
->
compute
[
icompute
];
// set timesteps and frequencies
dtv
=
update
->
dt
;
dtf
=
0.5
*
update
->
dt
*
force
->
ftm2v
;
dtq
=
0.5
*
update
->
dt
;
dthalf
=
0.5
*
update
->
dt
;
drag_factor
=
1.0
-
(
update
->
dt
*
t_freq
*
drag
);
if
(
strcmp
(
update
->
integrate_style
,
"respa"
)
==
0
)
{
nlevels_respa
=
((
Respa
*
)
update
->
integrate
)
->
nlevels
;
step_respa
=
((
Respa
*
)
update
->
integrate
)
->
step
;
}
}
/* ---------------------------------------------------------------------- */
void
FixNVT
::
setup
()
{
t_target
=
t_start
;
// used by compute_scalar()
t_current
=
temperature
->
compute_scalar
();
}
/* ---------------------------------------------------------------------- */
void
FixNVT
::
initial_integrate
()
{
double
dtfm
;
double
delta
=
update
->
ntimestep
-
update
->
beginstep
;
delta
/=
update
->
endstep
-
update
->
beginstep
;
t_target
=
t_start
+
delta
*
(
t_stop
-
t_start
);
// update eta_dot
f_eta
=
t_freq
*
t_freq
*
(
t_current
/
t_target
-
1.0
);
eta_dot
+=
f_eta
*
dthalf
;
eta_dot
*=
drag_factor
;
eta
+=
dtv
*
eta_dot
;
factor
=
exp
(
-
dthalf
*
eta_dot
);
// update v and x of only atoms in NVT group
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
mass
[
type
[
i
]];
v
[
i
][
0
]
=
v
[
i
][
0
]
*
factor
+
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
=
v
[
i
][
1
]
*
factor
+
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
=
v
[
i
][
2
]
*
factor
+
dtfm
*
f
[
i
][
2
];
x
[
i
][
0
]
+=
dtv
*
v
[
i
][
0
];
x
[
i
][
1
]
+=
dtv
*
v
[
i
][
1
];
x
[
i
][
2
]
+=
dtv
*
v
[
i
][
2
];
}
}
}
/* ---------------------------------------------------------------------- */
void
FixNVT
::
final_integrate
()
{
double
dtfm
;
// update v of only atoms in NVT group
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
mass
[
type
[
i
]]
*
factor
;
v
[
i
][
0
]
=
v
[
i
][
0
]
*
factor
+
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
=
v
[
i
][
1
]
*
factor
+
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
=
v
[
i
][
2
]
*
factor
+
dtfm
*
f
[
i
][
2
];
}
}
// compute current T
t_current
=
temperature
->
compute_scalar
();
// update eta_dot
f_eta
=
t_freq
*
t_freq
*
(
t_current
/
t_target
-
1.0
);
eta_dot
+=
f_eta
*
dthalf
;
eta_dot
*=
drag_factor
;
}
/* ---------------------------------------------------------------------- */
void
FixNVT
::
initial_integrate_respa
(
int
ilevel
,
int
flag
)
{
if
(
flag
)
return
;
// only used by NPT,NPH
// set timesteps by level
double
dtfm
;
dtv
=
step_respa
[
ilevel
];
dtf
=
0.5
*
step_respa
[
ilevel
]
*
force
->
ftm2v
;
dthalf
=
0.5
*
step_respa
[
ilevel
];
// atom quantities
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
// outermost level - update eta_dot and apply to v
// all other levels - NVE update of v
if
(
ilevel
==
nlevels_respa
-
1
)
{
double
delta
=
update
->
ntimestep
-
update
->
beginstep
;
delta
/=
update
->
endstep
-
update
->
beginstep
;
t_target
=
t_start
+
delta
*
(
t_stop
-
t_start
);
// update eta_dot
f_eta
=
t_freq
*
t_freq
*
(
t_current
/
t_target
-
1.0
);
eta_dot
+=
f_eta
*
dthalf
;
eta_dot
*=
drag_factor
;
eta
+=
dtv
*
eta_dot
;
factor
=
exp
(
-
dthalf
*
eta_dot
);
}
else
factor
=
1.0
;
// update v of only atoms in NVT group
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
mass
[
type
[
i
]];
v
[
i
][
0
]
=
v
[
i
][
0
]
*
factor
+
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
=
v
[
i
][
1
]
*
factor
+
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
=
v
[
i
][
2
]
*
factor
+
dtfm
*
f
[
i
][
2
];
}
}
// innermost level - also update x of only atoms in NVT group
if
(
ilevel
==
0
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
x
[
i
][
0
]
+=
dtv
*
v
[
i
][
0
];
x
[
i
][
1
]
+=
dtv
*
v
[
i
][
1
];
x
[
i
][
2
]
+=
dtv
*
v
[
i
][
2
];
}
}
}
}
/* ---------------------------------------------------------------------- */
void
FixNVT
::
final_integrate_respa
(
int
ilevel
)
{
double
dtfm
;
// set timesteps by level
dtf
=
0.5
*
step_respa
[
ilevel
]
*
force
->
ftm2v
;
dthalf
=
0.5
*
step_respa
[
ilevel
];
// outermost level - update eta_dot and apply to v via final_integrate()
// all other levels - NVE update of v
if
(
ilevel
==
nlevels_respa
-
1
)
final_integrate
();
else
{
// update v of only atoms in NVT group
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
mass
[
type
[
i
]];
v
[
i
][
0
]
+=
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
+=
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
+=
dtfm
*
f
[
i
][
2
];
}
}
}
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void
FixNVT
::
write_restart
(
FILE
*
fp
)
{
int
n
=
0
;
double
list
[
2
];
list
[
n
++
]
=
eta
;
list
[
n
++
]
=
eta_dot
;
if
(
comm
->
me
==
0
)
{
int
size
=
n
*
sizeof
(
double
);
fwrite
(
&
size
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
list
,
sizeof
(
double
),
n
,
fp
);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void
FixNVT
::
restart
(
char
*
buf
)
{
int
n
=
0
;
double
*
list
=
(
double
*
)
buf
;
eta
=
list
[
n
++
];
eta_dot
=
list
[
n
++
];
}
/* ---------------------------------------------------------------------- */
int
FixNVT
::
modify_param
(
int
narg
,
char
**
arg
)
{
if
(
strcmp
(
arg
[
0
],
"temp"
)
==
0
)
{
if
(
narg
<
2
)
error
->
all
(
"Illegal fix_modify command"
);
if
(
tflag
)
{
modify
->
delete_compute
(
id_temp
);
tflag
=
0
;
}
delete
[]
id_temp
;
int
n
=
strlen
(
arg
[
1
])
+
1
;
id_temp
=
new
char
[
n
];
strcpy
(
id_temp
,
arg
[
1
]);
int
icompute
=
modify
->
find_compute
(
id_temp
);
if
(
icompute
<
0
)
error
->
all
(
"Could not find fix_modify temp ID"
);
temperature
=
modify
->
compute
[
icompute
];
if
(
temperature
->
tempflag
==
0
)
error
->
all
(
"Fix_modify temp ID does not compute temperature"
);
if
(
temperature
->
igroup
!=
igroup
&&
comm
->
me
==
0
)
error
->
warning
(
"Group for fix_modify temp != fix group"
);
return
2
;
}
return
0
;
}
/* ---------------------------------------------------------------------- */
void
FixNVT
::
reset_target
(
double
t_new
)
{
t_start
=
t_stop
=
t_new
;
}
/* ---------------------------------------------------------------------- */
void
FixNVT
::
reset_dt
()
{
dtv
=
update
->
dt
;
dtf
=
0.5
*
update
->
dt
*
force
->
ftm2v
;
dtq
=
0.5
*
update
->
dt
;
dthalf
=
0.5
*
update
->
dt
;
drag_factor
=
1.0
-
(
update
->
dt
*
t_freq
*
drag
);
}
/* ---------------------------------------------------------------------- */
double
FixNVT
::
compute_scalar
()
{
double
ke
=
temperature
->
dof
*
force
->
boltz
*
t_target
;
double
energy
=
ke
*
(
eta
+
0.5
*
eta_dot
*
eta_dot
/
(
t_freq
*
t_freq
));
return
energy
;
}
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