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fix_heat.cpp
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rLAMMPS lammps
fix_heat.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: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_heat.h"
#include "atom.h"
#include "domain.h"
#include "region.h"
#include "group.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
enum
{
CONSTANT
,
EQUAL
,
ATOM
};
/* ---------------------------------------------------------------------- */
FixHeat
::
FixHeat
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
),
idregion
(
NULL
),
hstr
(
NULL
),
vheat
(
NULL
),
vscale
(
NULL
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Illegal fix heat command"
);
scalar_flag
=
1
;
global_freq
=
1
;
extscalar
=
0
;
nevery
=
force
->
inumeric
(
FLERR
,
arg
[
3
]);
if
(
nevery
<=
0
)
error
->
all
(
FLERR
,
"Illegal fix heat command"
);
hstr
=
NULL
;
if
(
strstr
(
arg
[
4
],
"v_"
)
==
arg
[
4
])
{
int
n
=
strlen
(
&
arg
[
4
][
2
])
+
1
;
hstr
=
new
char
[
n
];
strcpy
(
hstr
,
&
arg
[
4
][
2
]);
}
else
{
heat_input
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
hstyle
=
CONSTANT
;
}
// optional args
iregion
=
-
1
;
int
iarg
=
5
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"region"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal fix heat command"
);
iregion
=
domain
->
find_region
(
arg
[
iarg
+
1
]);
if
(
iregion
==
-
1
)
error
->
all
(
FLERR
,
"Region ID for fix heat does not exist"
);
int
n
=
strlen
(
arg
[
iarg
+
1
])
+
1
;
idregion
=
new
char
[
n
];
strcpy
(
idregion
,
arg
[
iarg
+
1
]);
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal fix heat command"
);
}
scale
=
1.0
;
maxatom
=
0
;
}
/* ---------------------------------------------------------------------- */
FixHeat
::~
FixHeat
()
{
delete
[]
hstr
;
delete
[]
idregion
;
memory
->
destroy
(
vheat
);
memory
->
destroy
(
vscale
);
}
/* ---------------------------------------------------------------------- */
int
FixHeat
::
setmask
()
{
int
mask
=
0
;
mask
|=
END_OF_STEP
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixHeat
::
init
()
{
// set index and check validity of region
if
(
iregion
>=
0
)
{
iregion
=
domain
->
find_region
(
idregion
);
if
(
iregion
==
-
1
)
error
->
all
(
FLERR
,
"Region ID for fix heat does not exist"
);
}
// check variable
if
(
hstr
)
{
hvar
=
input
->
variable
->
find
(
hstr
);
if
(
hvar
<
0
)
error
->
all
(
FLERR
,
"Variable name for fix heat does not exist"
);
if
(
input
->
variable
->
equalstyle
(
hvar
))
hstyle
=
EQUAL
;
else
if
(
input
->
variable
->
atomstyle
(
hvar
))
hstyle
=
ATOM
;
else
error
->
all
(
FLERR
,
"Variable for fix heat is invalid style"
);
}
// check for rigid bodies in region (done here for performance reasons)
if
(
modify
->
check_rigid_region_overlap
(
groupbit
,
domain
->
regions
[
iregion
]))
error
->
warning
(
FLERR
,
"Cannot apply fix heat to atoms in rigid bodies"
);
// cannot have 0 atoms in group
if
(
group
->
count
(
igroup
)
==
0
)
error
->
all
(
FLERR
,
"Fix heat group has no atoms"
);
masstotal
=
group
->
mass
(
igroup
);
if
(
masstotal
<=
0.0
)
error
->
all
(
FLERR
,
"Fix heat group has invalid mass"
);
}
/* ---------------------------------------------------------------------- */
void
FixHeat
::
end_of_step
()
{
int
i
;
double
heat
,
ke
,
massone
;
double
vsub
[
3
],
vcm
[
3
];
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
*
type
=
atom
->
type
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
// reallocate per-atom arrays if necessary
if
(
hstyle
==
ATOM
&&
atom
->
nmax
>
maxatom
)
{
maxatom
=
atom
->
nmax
;
memory
->
destroy
(
vheat
);
memory
->
destroy
(
vscale
);
memory
->
create
(
vheat
,
maxatom
,
"heat:vheat"
);
memory
->
create
(
vscale
,
maxatom
,
"heat:vscale"
);
}
// evaluate variable
if
(
hstyle
!=
CONSTANT
)
{
modify
->
clearstep_compute
();
if
(
hstyle
==
EQUAL
)
heat_input
=
input
->
variable
->
compute_equal
(
hvar
);
else
input
->
variable
->
compute_atom
(
hvar
,
igroup
,
vheat
,
1
,
0
);
modify
->
addstep_compute
(
update
->
ntimestep
+
nevery
);
}
// vcm = center-of-mass velocity of scaled atoms
if
(
iregion
<
0
)
{
ke
=
group
->
ke
(
igroup
)
*
force
->
ftm2v
;
group
->
vcm
(
igroup
,
masstotal
,
vcm
);
}
else
{
masstotal
=
group
->
mass
(
igroup
,
iregion
);
if
(
masstotal
==
0.0
)
error
->
all
(
FLERR
,
"Fix heat group has no atoms"
);
ke
=
group
->
ke
(
igroup
,
iregion
)
*
force
->
ftm2v
;
group
->
vcm
(
igroup
,
masstotal
,
vcm
,
iregion
);
}
double
vcmsq
=
vcm
[
0
]
*
vcm
[
0
]
+
vcm
[
1
]
*
vcm
[
1
]
+
vcm
[
2
]
*
vcm
[
2
];
// add heat via scale factor on velocities for CONSTANT and EQUAL cases
// scale = velocity scale factor to accomplish eflux change in energy
// vsub = velocity subtracted from each atom to preserve momentum
// overall KE cannot go negative
Region
*
region
=
NULL
;
if
(
iregion
>=
0
)
{
region
=
domain
->
regions
[
iregion
];
region
->
prematch
();
}
if
(
hstyle
!=
ATOM
)
{
heat
=
heat_input
*
nevery
*
update
->
dt
*
force
->
ftm2v
;
double
escale
=
(
ke
+
heat
-
0.5
*
vcmsq
*
masstotal
)
/
(
ke
-
0.5
*
vcmsq
*
masstotal
);
if
(
escale
<
0.0
)
error
->
all
(
FLERR
,
"Fix heat kinetic energy went negative"
);
scale
=
sqrt
(
escale
);
vsub
[
0
]
=
(
scale
-
1.0
)
*
vcm
[
0
];
vsub
[
1
]
=
(
scale
-
1.0
)
*
vcm
[
1
];
vsub
[
2
]
=
(
scale
-
1.0
)
*
vcm
[
2
];
if
(
iregion
<
0
)
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
v
[
i
][
0
]
=
scale
*
v
[
i
][
0
]
-
vsub
[
0
];
v
[
i
][
1
]
=
scale
*
v
[
i
][
1
]
-
vsub
[
1
];
v
[
i
][
2
]
=
scale
*
v
[
i
][
2
]
-
vsub
[
2
];
}
}
else
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
&&
region
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
{
v
[
i
][
0
]
=
scale
*
v
[
i
][
0
]
-
vsub
[
0
];
v
[
i
][
1
]
=
scale
*
v
[
i
][
1
]
-
vsub
[
1
];
v
[
i
][
2
]
=
scale
*
v
[
i
][
2
]
-
vsub
[
2
];
}
}
// add heat via per-atom scale factor on velocities for ATOM case
// vscale = velocity scale factor to accomplish eflux change in energy
// vsub = velocity subtracted from each atom to preserve momentum
// KE of an atom cannot go negative
}
else
{
vsub
[
0
]
=
vsub
[
1
]
=
vsub
[
2
]
=
0.0
;
if
(
iregion
<
0
)
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
heat
=
vheat
[
i
]
*
nevery
*
update
->
dt
*
force
->
ftm2v
;
vscale
[
i
]
=
(
ke
+
heat
-
0.5
*
vcmsq
*
masstotal
)
/
(
ke
-
0.5
*
vcmsq
*
masstotal
);
if
(
vscale
[
i
]
<
0.0
)
error
->
all
(
FLERR
,
"Fix heat kinetic energy of an atom went negative"
);
scale
=
sqrt
(
vscale
[
i
]);
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
vsub
[
0
]
+=
(
scale
-
1.0
)
*
v
[
i
][
0
]
*
massone
;
vsub
[
1
]
+=
(
scale
-
1.0
)
*
v
[
i
][
1
]
*
massone
;
vsub
[
2
]
+=
(
scale
-
1.0
)
*
v
[
i
][
2
]
*
massone
;
}
}
vsub
[
0
]
/=
masstotal
;
vsub
[
1
]
/=
masstotal
;
vsub
[
2
]
/=
masstotal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
scale
=
sqrt
(
vscale
[
i
]);
v
[
i
][
0
]
=
scale
*
v
[
i
][
0
]
-
vsub
[
0
];
v
[
i
][
1
]
=
scale
*
v
[
i
][
1
]
-
vsub
[
1
];
v
[
i
][
2
]
=
scale
*
v
[
i
][
2
]
-
vsub
[
2
];
}
}
else
{
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
&&
region
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
{
heat
=
vheat
[
i
]
*
nevery
*
update
->
dt
*
force
->
ftm2v
;
vscale
[
i
]
=
(
ke
+
heat
-
0.5
*
vcmsq
*
masstotal
)
/
(
ke
-
0.5
*
vcmsq
*
masstotal
);
if
(
vscale
[
i
]
<
0.0
)
error
->
all
(
FLERR
,
"Fix heat kinetic energy of an atom went negative"
);
scale
=
sqrt
(
vscale
[
i
]);
if
(
rmass
)
massone
=
rmass
[
i
];
else
massone
=
mass
[
type
[
i
]];
vsub
[
0
]
+=
(
scale
-
1.0
)
*
v
[
i
][
0
]
*
massone
;
vsub
[
1
]
+=
(
scale
-
1.0
)
*
v
[
i
][
1
]
*
massone
;
vsub
[
2
]
+=
(
scale
-
1.0
)
*
v
[
i
][
2
]
*
massone
;
}
}
vsub
[
0
]
/=
masstotal
;
vsub
[
1
]
/=
masstotal
;
vsub
[
2
]
/=
masstotal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
&&
region
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
{
scale
=
sqrt
(
vscale
[
i
]);
v
[
i
][
0
]
=
scale
*
v
[
i
][
0
]
-
vsub
[
0
];
v
[
i
][
1
]
=
scale
*
v
[
i
][
1
]
-
vsub
[
1
];
v
[
i
][
2
]
=
scale
*
v
[
i
][
2
]
-
vsub
[
2
];
}
}
}
}
/* ---------------------------------------------------------------------- */
double
FixHeat
::
compute_scalar
()
{
double
average_scale
=
scale
;
if
(
hstyle
==
ATOM
)
{
double
scale_sum
=
0.0
;
int
ncount
=
0
;
int
*
mask
=
atom
->
mask
;
double
**
x
=
atom
->
x
;
int
nlocal
=
atom
->
nlocal
;
if
(
iregion
<
0
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
scale_sum
+=
sqrt
(
vscale
[
i
]);
ncount
++
;
}
}
}
else
{
Region
*
region
=
domain
->
regions
[
iregion
];
region
->
prematch
();
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
&&
region
->
match
(
x
[
i
][
0
],
x
[
i
][
1
],
x
[
i
][
2
]))
{
scale_sum
+=
sqrt
(
vscale
[
i
]);
ncount
++
;
}
}
}
double
scale_sum_all
=
0.0
;
int
ncount_all
=
0
;
MPI_Allreduce
(
&
scale_sum
,
&
scale_sum_all
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
MPI_Allreduce
(
&
ncount
,
&
ncount_all
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
if
(
ncount_all
==
0
)
average_scale
=
0.0
;
else
average_scale
=
scale_sum_all
/
static_cast
<
double
>
(
ncount_all
);
}
return
average_scale
;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double
FixHeat
::
memory_usage
()
{
double
bytes
=
0.0
;
if
(
hstyle
==
ATOM
)
bytes
=
atom
->
nmax
*
2
*
sizeof
(
double
);
return
bytes
;
}
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