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fix_temp_berendsen.cpp
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Wed, Oct 9, 05:12
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rLAMMPS lammps
fix_temp_berendsen.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.
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "fix_temp_berendsen.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "group.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
enum
{
NOBIAS
,
BIAS
};
enum
{
CONSTANT
,
EQUAL
};
/* ---------------------------------------------------------------------- */
FixTempBerendsen
::
FixTempBerendsen
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
6
)
error
->
all
(
FLERR
,
"Illegal fix temp/berendsen command"
);
// Berendsen thermostat should be applied every step
dynamic_group_allow
=
1
;
nevery
=
1
;
scalar_flag
=
1
;
global_freq
=
nevery
;
extscalar
=
1
;
tstr
=
NULL
;
if
(
strstr
(
arg
[
3
],
"v_"
)
==
arg
[
3
])
{
int
n
=
strlen
(
&
arg
[
3
][
2
])
+
1
;
tstr
=
new
char
[
n
];
strcpy
(
tstr
,
&
arg
[
3
][
2
]);
tstyle
=
EQUAL
;
}
else
{
t_start
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
t_target
=
t_start
;
tstyle
=
CONSTANT
;
}
t_stop
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
t_period
=
force
->
numeric
(
FLERR
,
arg
[
5
]);
// error checks
if
(
t_period
<=
0.0
)
error
->
all
(
FLERR
,
"Fix temp/berendsen period must be > 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
];
newarg
[
2
]
=
(
char
*
)
"temp"
;
modify
->
add_compute
(
3
,
newarg
);
delete
[]
newarg
;
tflag
=
1
;
energy
=
0
;
}
/* ---------------------------------------------------------------------- */
FixTempBerendsen
::~
FixTempBerendsen
()
{
delete
[]
tstr
;
// delete temperature if fix created it
if
(
tflag
)
modify
->
delete_compute
(
id_temp
);
delete
[]
id_temp
;
}
/* ---------------------------------------------------------------------- */
int
FixTempBerendsen
::
setmask
()
{
int
mask
=
0
;
mask
|=
END_OF_STEP
;
mask
|=
THERMO_ENERGY
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixTempBerendsen
::
init
()
{
// check variable
if
(
tstr
)
{
tvar
=
input
->
variable
->
find
(
tstr
);
if
(
tvar
<
0
)
error
->
all
(
FLERR
,
"Variable name for fix temp/berendsen does not exist"
);
if
(
input
->
variable
->
equalstyle
(
tvar
))
tstyle
=
EQUAL
;
else
error
->
all
(
FLERR
,
"Variable for fix temp/berendsen is invalid style"
);
}
int
icompute
=
modify
->
find_compute
(
id_temp
);
if
(
icompute
<
0
)
error
->
all
(
FLERR
,
"Temperature ID for fix temp/berendsen does not exist"
);
temperature
=
modify
->
compute
[
icompute
];
if
(
temperature
->
tempbias
)
which
=
BIAS
;
else
which
=
NOBIAS
;
}
/* ---------------------------------------------------------------------- */
void
FixTempBerendsen
::
end_of_step
()
{
double
t_current
=
temperature
->
compute_scalar
();
double
tdof
=
temperature
->
dof
;
// there is nothing to do, if there are no degrees of freedom
if
(
tdof
<
1
)
return
;
if
(
t_current
==
0.0
)
error
->
all
(
FLERR
,
"Computed temperature for fix temp/berendsen cannot be 0.0"
);
double
delta
=
update
->
ntimestep
-
update
->
beginstep
;
if
(
delta
!=
0.0
)
delta
/=
update
->
endstep
-
update
->
beginstep
;
// set current t_target
// if variable temp, evaluate variable, wrap with clear/add
if
(
tstyle
==
CONSTANT
)
t_target
=
t_start
+
delta
*
(
t_stop
-
t_start
);
else
{
modify
->
clearstep_compute
();
t_target
=
input
->
variable
->
compute_equal
(
tvar
);
if
(
t_target
<
0.0
)
error
->
one
(
FLERR
,
"Fix temp/berendsen variable returned negative temperature"
);
modify
->
addstep_compute
(
update
->
ntimestep
+
nevery
);
}
// rescale velocities by lamda
// for BIAS:
// temperature is current, so do not need to re-compute
// OK to not test returned v = 0, since lamda is multiplied by v
double
lamda
=
sqrt
(
1.0
+
update
->
dt
/
t_period
*
(
t_target
/
t_current
-
1.0
));
double
efactor
=
0.5
*
force
->
boltz
*
tdof
;
energy
+=
t_current
*
(
1.0
-
lamda
*
lamda
)
*
efactor
;
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
which
==
NOBIAS
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
v
[
i
][
0
]
*=
lamda
;
v
[
i
][
1
]
*=
lamda
;
v
[
i
][
2
]
*=
lamda
;
}
}
}
else
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
temperature
->
remove_bias
(
i
,
v
[
i
]);
v
[
i
][
0
]
*=
lamda
;
v
[
i
][
1
]
*=
lamda
;
v
[
i
][
2
]
*=
lamda
;
temperature
->
restore_bias
(
i
,
v
[
i
]);
}
}
}
}
/* ---------------------------------------------------------------------- */
int
FixTempBerendsen
::
modify_param
(
int
narg
,
char
**
arg
)
{
if
(
strcmp
(
arg
[
0
],
"temp"
)
==
0
)
{
if
(
narg
<
2
)
error
->
all
(
FLERR
,
"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
(
FLERR
,
"Could not find fix_modify temperature ID"
);
temperature
=
modify
->
compute
[
icompute
];
if
(
temperature
->
tempflag
==
0
)
error
->
all
(
FLERR
,
"Fix_modify temperature ID does not compute temperature"
);
if
(
temperature
->
igroup
!=
igroup
&&
comm
->
me
==
0
)
error
->
warning
(
FLERR
,
"Group for fix_modify temp != fix group"
);
return
2
;
}
return
0
;
}
/* ---------------------------------------------------------------------- */
void
FixTempBerendsen
::
reset_target
(
double
t_new
)
{
t_target
=
t_start
=
t_stop
=
t_new
;
}
/* ---------------------------------------------------------------------- */
double
FixTempBerendsen
::
compute_scalar
()
{
return
energy
;
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */
void
*
FixTempBerendsen
::
extract
(
const
char
*
str
,
int
&
dim
)
{
dim
=
0
;
if
(
strcmp
(
str
,
"t_target"
)
==
0
)
{
return
&
t_target
;
}
return
NULL
;
}
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