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fix_ave_time.cpp
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Created
Fri, Jul 19, 22:05
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11 KB
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text/x-c
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Sun, Jul 21, 22:05 (2 d)
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blob
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19170571
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rLAMMPS lammps
fix_ave_time.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: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "fix_ave_time.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
enum
{
COMPUTE
,
FIX
};
enum
{
SCALAR
,
VECTOR
,
BOTH
};
enum
{
ONE
,
RUNNING
,
WINDOW
};
/* ---------------------------------------------------------------------- */
FixAveTime
::
FixAveTime
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
8
)
error
->
all
(
"Illegal fix ave/time command"
);
MPI_Comm_rank
(
world
,
&
me
);
nevery
=
atoi
(
arg
[
3
]);
nrepeat
=
atoi
(
arg
[
4
]);
nfreq
=
atoi
(
arg
[
5
]);
if
(
strcmp
(
arg
[
6
],
"compute"
)
==
0
)
which
=
COMPUTE
;
else
if
(
strcmp
(
arg
[
6
],
"fix"
)
==
0
)
which
=
FIX
;
else
error
->
all
(
"Illegal fix ave/time command"
);
int
n
=
strlen
(
arg
[
7
])
+
1
;
id
=
new
char
[
n
];
strcpy
(
id
,
arg
[
7
]);
// option defaults
sflag
=
1
;
vflag
=
0
;
fp
=
NULL
;
ave
=
ONE
;
// optional args
int
iarg
=
8
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"type"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
"Illegal fix ave/time command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"scalar"
)
==
0
)
{
sflag
=
1
;
vflag
=
0
;
}
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"vector"
)
==
0
)
{
sflag
=
0
;
vflag
=
1
;
}
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"both"
)
==
0
)
sflag
=
vflag
=
1
;
else
error
->
all
(
"Illegal fix ave/time command"
);
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"file"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
"Illegal fix ave/time command"
);
if
(
me
==
0
)
{
fp
=
fopen
(
arg
[
iarg
+
1
],
"w"
);
if
(
fp
==
NULL
)
{
char
str
[
128
];
sprintf
(
str
,
"Cannot open fix ave/time file %s"
,
arg
[
iarg
+
1
]);
error
->
one
(
str
);
}
}
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"ave"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
"Illegal fix ave/time command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"one"
)
==
0
)
ave
=
ONE
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"running"
)
==
0
)
ave
=
RUNNING
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"window"
)
==
0
)
ave
=
WINDOW
;
else
error
->
all
(
"Illegal fix ave/time command"
);
if
(
ave
==
WINDOW
)
{
if
(
iarg
+
3
>
narg
)
error
->
all
(
"Illegal fix ave/time command"
);
nwindow
=
atoi
(
arg
[
iarg
+
2
]);
if
(
nwindow
<=
0
)
error
->
all
(
"Illegal fix ave/time command"
);
}
iarg
+=
2
;
if
(
ave
==
WINDOW
)
iarg
++
;
}
else
error
->
all
(
"Illegal fix ave/time command"
);
}
// setup and error check
if
(
nevery
<=
0
)
error
->
all
(
"Illegal fix ave/time command"
);
if
(
nfreq
<
nevery
||
nfreq
%
nevery
||
(
nrepeat
-
1
)
*
nevery
>=
nfreq
)
error
->
all
(
"Illegal fix ave/time command"
);
int
icompute
,
ifix
;
if
(
which
==
COMPUTE
)
{
icompute
=
modify
->
find_compute
(
id
);
if
(
icompute
<
0
)
error
->
all
(
"Compute ID for fix ave/time does not exist"
);
}
else
{
ifix
=
modify
->
find_fix
(
id
);
if
(
ifix
<
0
)
error
->
all
(
"Fix ID for fix ave/time does not exist"
);
}
if
(
which
==
COMPUTE
)
{
if
(
sflag
&&
modify
->
compute
[
icompute
]
->
scalar_flag
==
0
)
error
->
all
(
"Fix ave/time compute does not calculate a scalar"
);
if
(
vflag
&&
modify
->
compute
[
icompute
]
->
vector_flag
==
0
)
error
->
all
(
"Fix ave/time compute does not calculate a vector"
);
}
else
{
if
(
sflag
&&
modify
->
fix
[
ifix
]
->
scalar_flag
==
0
)
error
->
all
(
"Fix ave/time fix does not calculate a scalar"
);
if
(
vflag
&&
modify
->
fix
[
ifix
]
->
vector_flag
==
0
)
error
->
all
(
"Fix ave/time fix does not calculate a vector"
);
}
if
(
which
==
COMPUTE
&&
modify
->
compute
[
icompute
]
->
pressflag
)
pressure_every
=
nevery
;
// setup list of computes to call, including pre-computes
compute
=
NULL
;
if
(
which
==
COMPUTE
)
{
ncompute
=
1
+
modify
->
compute
[
icompute
]
->
npre
;
compute
=
new
Compute
*
[
ncompute
];
}
else
ncompute
=
0
;
// print header into file
if
(
fp
&&
me
==
0
)
{
if
(
which
==
COMPUTE
)
fprintf
(
fp
,
"Time-averaged data for fix %s, group %s, and compute %s
\n
"
,
id
,
group
->
names
[
modify
->
compute
[
icompute
]
->
igroup
],
id
);
else
fprintf
(
fp
,
"Time-averaged data for fix %s, group %s, and fix %s
\n
"
,
id
,
group
->
names
[
modify
->
fix
[
ifix
]
->
igroup
],
id
);
if
(
sflag
and
!
vflag
)
fprintf
(
fp
,
"TimeStep Value
\n
"
);
else
if
(
!
sflag
and
vflag
)
fprintf
(
fp
,
"TimeStep Vector-values
\n
"
);
else
if
(
!
sflag
and
vflag
)
fprintf
(
fp
,
"TimeStep Scalar-value Vector-values
\n
"
);
}
// allocate memory for averaging
vector
=
vector_total
=
NULL
;
if
(
vflag
)
{
if
(
which
==
COMPUTE
)
size_vector
=
modify
->
compute
[
icompute
]
->
size_vector
;
else
size_vector
=
modify
->
fix
[
ifix
]
->
size_vector
;
vector
=
new
double
[
size_vector
];
vector_total
=
new
double
[
size_vector
];
}
scalar_list
=
NULL
;
vector_list
=
NULL
;
if
(
sflag
&&
ave
==
WINDOW
)
scalar_list
=
new
double
[
nwindow
];
if
(
vflag
&&
ave
==
WINDOW
)
vector_list
=
memory
->
create_2d_double_array
(
nwindow
,
size_vector
,
"ave/time:vector_list"
);
// enable this fix to produce a global scalar and/or vector
if
(
sflag
)
scalar_flag
=
1
;
if
(
vflag
)
vector_flag
=
1
;
scalar_vector_freq
=
nfreq
;
if
(
which
==
COMPUTE
)
extensive
=
modify
->
compute
[
icompute
]
->
extensive
;
else
extensive
=
modify
->
fix
[
ifix
]
->
extensive
;
// initializations
// set scalar and vector total to zero since they accumulate
irepeat
=
0
;
iwindow
=
window_limit
=
0
;
norm
=
0
;
scalar_total
=
0.0
;
if
(
vflag
)
for
(
int
i
=
0
;
i
<
size_vector
;
i
++
)
vector_total
[
i
]
=
0.0
;
// nvalid = next step on which end_of_step does something
// can be this timestep if multiple of nfreq and nrepeat = 1
// else backup from next multiple of nfreq
nvalid
=
(
update
->
ntimestep
/
nfreq
)
*
nfreq
+
nfreq
;
if
(
nvalid
-
nfreq
==
update
->
ntimestep
&&
nrepeat
==
1
)
nvalid
=
update
->
ntimestep
;
else
nvalid
-=
(
nrepeat
-
1
)
*
nevery
;
if
(
nvalid
<
update
->
ntimestep
)
error
->
all
(
"Fix ave/time cannot be started on this timestep"
);
}
/* ---------------------------------------------------------------------- */
FixAveTime
::~
FixAveTime
()
{
delete
[]
id
;
if
(
fp
&&
me
==
0
)
fclose
(
fp
);
delete
[]
compute
;
delete
[]
vector
;
delete
[]
vector_total
;
delete
[]
scalar_list
;
memory
->
destroy_2d_double_array
(
vector_list
);
}
/* ---------------------------------------------------------------------- */
int
FixAveTime
::
setmask
()
{
int
mask
=
0
;
mask
|=
END_OF_STEP
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixAveTime
::
init
()
{
// set ptrs to compute and its pre-computes called each end-of-step
// put pre-computes in list before compute
if
(
which
==
COMPUTE
)
{
int
icompute
=
modify
->
find_compute
(
id
);
if
(
icompute
<
0
)
error
->
all
(
"Compute ID for fix ave/time does not exist"
);
ncompute
=
0
;
if
(
modify
->
compute
[
icompute
]
->
npre
)
for
(
int
i
=
0
;
i
<
modify
->
compute
[
icompute
]
->
npre
;
i
++
)
{
int
ic
=
modify
->
find_compute
(
modify
->
compute
[
icompute
]
->
id_pre
[
i
]);
if
(
ic
<
0
)
error
->
all
(
"Precompute ID for fix ave/time does not exist"
);
compute
[
ncompute
++
]
=
modify
->
compute
[
ic
];
}
compute
[
ncompute
++
]
=
modify
->
compute
[
icompute
];
}
// set ptr to fix ID
// check that fix frequency is acceptable
if
(
which
==
FIX
)
{
int
ifix
=
modify
->
find_fix
(
id
);
if
(
ifix
<
0
)
error
->
all
(
"Fix ID for fix ave/time does not exist"
);
fix
=
modify
->
fix
[
ifix
];
if
(
nevery
%
fix
->
scalar_vector_freq
)
error
->
all
(
"Fix ave/time and fix not computed at compatible times"
);
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void
FixAveTime
::
setup
()
{
end_of_step
();
}
/* ---------------------------------------------------------------------- */
void
FixAveTime
::
end_of_step
()
{
int
i
;
// skip if not step which requires doing something
if
(
update
->
ntimestep
!=
nvalid
)
return
;
// zero if first step
if
(
irepeat
==
0
)
{
scalar
=
0.0
;
if
(
vflag
)
for
(
i
=
0
;
i
<
size_vector
;
i
++
)
vector
[
i
]
=
0.0
;
}
// accumulate results of compute or fix to local copy
if
(
which
==
COMPUTE
)
{
if
(
sflag
)
{
double
value
;
for
(
i
=
0
;
i
<
ncompute
;
i
++
)
value
=
compute
[
i
]
->
compute_scalar
();
scalar
+=
value
;
}
if
(
vflag
)
{
for
(
i
=
0
;
i
<
ncompute
;
i
++
)
compute
[
i
]
->
compute_vector
();
double
*
cvector
=
compute
[
ncompute
-
1
]
->
vector
;
for
(
i
=
0
;
i
<
size_vector
;
i
++
)
vector
[
i
]
+=
cvector
[
i
];
}
}
else
{
if
(
sflag
)
scalar
+=
fix
->
compute_scalar
();
if
(
vflag
)
for
(
i
=
0
;
i
<
size_vector
;
i
++
)
vector
[
i
]
+=
fix
->
compute_vector
(
i
);
}
// done if irepeat < nrepeat
irepeat
++
;
nvalid
+=
nevery
;
if
(
irepeat
<
nrepeat
)
return
;
// average the final result for the Nfreq timestep
double
repeat
=
nrepeat
;
if
(
sflag
)
scalar
/=
repeat
;
if
(
vflag
)
for
(
i
=
0
;
i
<
size_vector
;
i
++
)
vector
[
i
]
/=
repeat
;
// reset irepeat and nvalid
irepeat
=
0
;
nvalid
=
update
->
ntimestep
+
nfreq
-
(
nrepeat
-
1
)
*
nevery
;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, comine with nwindow most recent Nfreq timestep values
if
(
ave
==
ONE
)
{
if
(
sflag
)
scalar_total
=
scalar
;
if
(
vflag
)
for
(
i
=
0
;
i
<
size_vector
;
i
++
)
vector_total
[
i
]
=
vector
[
i
];
norm
=
1
;
}
else
if
(
ave
==
RUNNING
)
{
if
(
sflag
)
scalar_total
+=
scalar
;
if
(
vflag
)
for
(
i
=
0
;
i
<
size_vector
;
i
++
)
vector_total
[
i
]
+=
vector
[
i
];
norm
++
;
}
else
if
(
ave
==
WINDOW
)
{
if
(
sflag
)
{
scalar_total
+=
scalar
;
if
(
window_limit
)
scalar_total
-=
scalar_list
[
iwindow
];
scalar_list
[
iwindow
]
=
scalar
;
}
if
(
vflag
)
{
for
(
i
=
0
;
i
<
size_vector
;
i
++
)
{
vector_total
[
i
]
+=
vector
[
i
];
if
(
window_limit
)
vector_total
[
i
]
-=
vector_list
[
iwindow
][
i
];
vector_list
[
iwindow
][
i
]
=
vector
[
i
];
}
}
iwindow
++
;
if
(
iwindow
==
nwindow
)
{
iwindow
=
0
;
window_limit
=
1
;
}
if
(
window_limit
)
norm
=
nwindow
;
else
norm
=
iwindow
;
}
// output result to file
if
(
fp
&&
me
==
0
)
{
fprintf
(
fp
,
"%d"
,
update
->
ntimestep
);
if
(
sflag
)
fprintf
(
fp
,
" %g"
,
scalar_total
/
norm
);
if
(
vflag
)
for
(
i
=
0
;
i
<
size_vector
;
i
++
)
fprintf
(
fp
,
" %g"
,
vector_total
[
i
]
/
norm
);
fprintf
(
fp
,
"
\n
"
);
fflush
(
fp
);
}
}
/* ----------------------------------------------------------------------
return scalar value
could be ONE, RUNNING, or WINDOW value
------------------------------------------------------------------------- */
double
FixAveTime
::
compute_scalar
()
{
if
(
norm
)
return
scalar_total
/
norm
;
return
0.0
;
}
/* ----------------------------------------------------------------------
return Nth vector value
could be ONE, RUNNING, or WINDOW value
------------------------------------------------------------------------- */
double
FixAveTime
::
compute_vector
(
int
n
)
{
if
(
norm
)
return
vector_total
[
n
]
/
norm
;
else
return
0.0
;
}
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