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fix.cpp
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Tue, Sep 3, 12:28
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Thu, Sep 5, 12:28 (1 d, 23 h)
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rLAMMPS lammps
fix.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 <ctype.h>
#include "fix.h"
#include "atom.h"
#include "group.h"
#include "force.h"
#include "comm.h"
#include "atom_masks.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
// allocate space for static class instance variable and initialize it
int
Fix
::
instance_total
=
0
;
/* ---------------------------------------------------------------------- */
Fix
::
Fix
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Pointers
(
lmp
),
id
(
NULL
),
style
(
NULL
),
eatom
(
NULL
),
vatom
(
NULL
)
{
instance_me
=
instance_total
++
;
// fix ID, group, and style
// ID must be all alphanumeric chars or underscores
int
n
=
strlen
(
arg
[
0
])
+
1
;
id
=
new
char
[
n
];
strcpy
(
id
,
arg
[
0
]);
for
(
int
i
=
0
;
i
<
n
-
1
;
i
++
)
if
(
!
isalnum
(
id
[
i
])
&&
id
[
i
]
!=
'_'
)
error
->
all
(
FLERR
,
"Fix ID must be alphanumeric or underscore characters"
);
igroup
=
group
->
find
(
arg
[
1
]);
if
(
igroup
==
-
1
)
error
->
all
(
FLERR
,
"Could not find fix group ID"
);
groupbit
=
group
->
bitmask
[
igroup
];
n
=
strlen
(
arg
[
2
])
+
1
;
style
=
new
char
[
n
];
strcpy
(
style
,
arg
[
2
]);
restart_global
=
restart_peratom
=
restart_file
=
0
;
force_reneighbor
=
0
;
box_change_size
=
box_change_shape
=
box_change_domain
=
0
;
thermo_energy
=
0
;
rigid_flag
=
0
;
peatom_flag
=
0
;
virial_flag
=
0
;
no_change_box
=
0
;
time_integrate
=
0
;
time_depend
=
0
;
create_attribute
=
0
;
restart_pbc
=
0
;
wd_header
=
wd_section
=
0
;
dynamic_group_allow
=
0
;
dof_flag
=
0
;
special_alter_flag
=
0
;
enforce2d_flag
=
0
;
respa_level_support
=
0
;
respa_level
=
-
1
;
scalar_flag
=
vector_flag
=
array_flag
=
0
;
peratom_flag
=
local_flag
=
0
;
size_vector_variable
=
size_array_rows_variable
=
0
;
comm_forward
=
comm_reverse
=
comm_border
=
0
;
restart_reset
=
0
;
// reasonable defaults
// however, each fix that uses these values should explicitly set them
nevery
=
1
;
global_freq
=
1
;
// per-atom virial
// set vflag_atom = 0 b/c some fixes grow vatom in grow_arrays()
// which may occur outside of timestepping
maxeatom
=
maxvatom
=
0
;
vflag_atom
=
0
;
// CUDA and KOKKOS per-fix data masks
datamask
=
ALL_MASK
;
datamask_ext
=
ALL_MASK
;
execution_space
=
Host
;
datamask_read
=
ALL_MASK
;
datamask_modify
=
ALL_MASK
;
copymode
=
0
;
}
/* ---------------------------------------------------------------------- */
Fix
::~
Fix
()
{
if
(
copymode
)
return
;
delete
[]
id
;
delete
[]
style
;
memory
->
destroy
(
eatom
);
memory
->
destroy
(
vatom
);
}
/* ----------------------------------------------------------------------
process params common to all fixes here
if unknown param, call modify_param specific to the fix
------------------------------------------------------------------------- */
void
Fix
::
modify_params
(
int
narg
,
char
**
arg
)
{
if
(
narg
==
0
)
error
->
all
(
FLERR
,
"Illegal fix_modify command"
);
int
iarg
=
0
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"energy"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal fix_modify command"
);
if
(
strcmp
(
arg
[
iarg
+
1
],
"no"
)
==
0
)
thermo_energy
=
0
;
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"yes"
)
==
0
)
thermo_energy
=
1
;
else
error
->
all
(
FLERR
,
"Illegal fix_modify command"
);
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"respa"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal fix_modify command"
);
if
(
!
respa_level_support
)
error
->
all
(
FLERR
,
"Illegal fix_modify command"
);
int
lvl
=
force
->
inumeric
(
FLERR
,
arg
[
1
]);
if
(
lvl
<
0
)
error
->
all
(
FLERR
,
"Illegal fix_modify command"
);
respa_level
=
lvl
-
1
;
iarg
+=
2
;
}
else
{
int
n
=
modify_param
(
narg
-
iarg
,
&
arg
[
iarg
]);
if
(
n
==
0
)
error
->
all
(
FLERR
,
"Illegal fix_modify command"
);
iarg
+=
n
;
}
}
}
/* ----------------------------------------------------------------------
setup for energy, virial computation
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
fixes call this if use ev_tally()
------------------------------------------------------------------------- */
void
Fix
::
ev_setup
(
int
eflag
,
int
vflag
)
{
int
i
,
n
;
evflag
=
1
;
eflag_either
=
eflag
;
eflag_global
=
eflag
%
2
;
eflag_atom
=
eflag
/
2
;
vflag_either
=
vflag
;
vflag_global
=
vflag
%
4
;
vflag_atom
=
vflag
/
4
;
// reallocate per-atom arrays if necessary
if
(
eflag_atom
&&
atom
->
nlocal
>
maxeatom
)
{
maxeatom
=
atom
->
nmax
;
memory
->
destroy
(
eatom
);
memory
->
create
(
eatom
,
maxeatom
,
"fix:eatom"
);
}
if
(
vflag_atom
&&
atom
->
nlocal
>
maxvatom
)
{
maxvatom
=
atom
->
nmax
;
memory
->
destroy
(
vatom
);
memory
->
create
(
vatom
,
maxvatom
,
6
,
"fix:vatom"
);
}
// zero accumulators
// no global energy variable to zero (unlike pair,bond,angle,etc)
// fixes tally it individually via fix_modify energy yes and compute_scalar()
if
(
vflag_global
)
for
(
i
=
0
;
i
<
6
;
i
++
)
virial
[
i
]
=
0.0
;
if
(
eflag_atom
)
{
n
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
n
;
i
++
)
eatom
[
i
]
=
0.0
;
}
if
(
vflag_atom
)
{
n
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
vatom
[
i
][
0
]
=
0.0
;
vatom
[
i
][
1
]
=
0.0
;
vatom
[
i
][
2
]
=
0.0
;
vatom
[
i
][
3
]
=
0.0
;
vatom
[
i
][
4
]
=
0.0
;
vatom
[
i
][
5
]
=
0.0
;
}
}
}
/* ----------------------------------------------------------------------
setup for virial computation
see integrate::ev_set() for values of vflag (0-6)
fixes call this if use v_tally()
------------------------------------------------------------------------- */
void
Fix
::
v_setup
(
int
vflag
)
{
int
i
,
n
;
evflag
=
1
;
vflag_global
=
vflag
%
4
;
vflag_atom
=
vflag
/
4
;
// reallocate per-atom array if necessary
if
(
vflag_atom
&&
atom
->
nlocal
>
maxvatom
)
{
maxvatom
=
atom
->
nmax
;
memory
->
destroy
(
vatom
);
memory
->
create
(
vatom
,
maxvatom
,
6
,
"fix:vatom"
);
}
// zero accumulators
if
(
vflag_global
)
for
(
i
=
0
;
i
<
6
;
i
++
)
virial
[
i
]
=
0.0
;
if
(
vflag_atom
)
{
n
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
vatom
[
i
][
0
]
=
0.0
;
vatom
[
i
][
1
]
=
0.0
;
vatom
[
i
][
2
]
=
0.0
;
vatom
[
i
][
3
]
=
0.0
;
vatom
[
i
][
4
]
=
0.0
;
vatom
[
i
][
5
]
=
0.0
;
}
}
}
/* ----------------------------------------------------------------------
tally per-atom energy and global/per-atom virial into accumulators
n = # of local owned atoms involved, with local indices in list
eng = total energy for the interaction involving total atoms
v = total virial for the interaction involving total atoms
increment per-atom energy of each atom in list by 1/total fraction
v_tally tallies virial
this method can be used when fix computes energy/forces in post_force()
e.g. fix cmap: compute energy and virial only on owned atoms
whether newton_bond is on or off
other procs will tally left-over fractions for atoms they own
------------------------------------------------------------------------- */
void
Fix
::
ev_tally
(
int
n
,
int
*
list
,
double
total
,
double
eng
,
double
*
v
)
{
if
(
eflag_atom
)
{
double
fraction
=
eng
/
total
;
for
(
int
i
=
0
;
i
<
n
;
i
++
)
eatom
[
list
[
i
]]
+=
fraction
;
}
v_tally
(
n
,
list
,
total
,
v
);
}
/* ----------------------------------------------------------------------
tally virial into global and per-atom accumulators
n = # of local owned atoms involved, with local indices in list
v = total virial for the interaction involving total atoms
increment global virial by n/total fraction
increment per-atom virial of each atom in list by 1/total fraction
this method can be used when fix computes forces in post_force()
e.g. fix shake, fix rigid: compute virial only on owned atoms
whether newton_bond is on or off
other procs will tally left-over fractions for atoms they own
------------------------------------------------------------------------- */
void
Fix
::
v_tally
(
int
n
,
int
*
list
,
double
total
,
double
*
v
)
{
int
m
;
if
(
vflag_global
)
{
double
fraction
=
n
/
total
;
virial
[
0
]
+=
fraction
*
v
[
0
];
virial
[
1
]
+=
fraction
*
v
[
1
];
virial
[
2
]
+=
fraction
*
v
[
2
];
virial
[
3
]
+=
fraction
*
v
[
3
];
virial
[
4
]
+=
fraction
*
v
[
4
];
virial
[
5
]
+=
fraction
*
v
[
5
];
}
if
(
vflag_atom
)
{
double
fraction
=
1.0
/
total
;
for
(
int
i
=
0
;
i
<
n
;
i
++
)
{
m
=
list
[
i
];
vatom
[
m
][
0
]
+=
fraction
*
v
[
0
];
vatom
[
m
][
1
]
+=
fraction
*
v
[
1
];
vatom
[
m
][
2
]
+=
fraction
*
v
[
2
];
vatom
[
m
][
3
]
+=
fraction
*
v
[
3
];
vatom
[
m
][
4
]
+=
fraction
*
v
[
4
];
vatom
[
m
][
5
]
+=
fraction
*
v
[
5
];
}
}
}
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