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fix_uniaxial.cpp
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Tue, Oct 15, 02:45
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rLAMMPS lammps
fix_uniaxial.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: Carsten Svaneborg
(Max Planck Institute for Complex Systems, Dresden, Germany)
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "fix_uniaxial.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "comm.h"
#include "kspace.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
FixUniaxial
::
FixUniaxial
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
6
)
error
->
all
(
"Illegal fix uniaxial command"
);
nevery
=
atoi
(
arg
[
3
]);
if
(
nevery
<=
0
)
error
->
all
(
"Illegal fix uniaxial command"
);
if
(
strcmp
(
arg
[
4
],
"x"
)
==
0
)
dir
=
0
;
else
if
(
strcmp
(
arg
[
4
],
"y"
)
==
0
)
dir
=
1
;
else
if
(
strcmp
(
arg
[
4
],
"z"
)
==
0
)
dir
=
2
;
else
error
->
all
(
"Illegal fix uniaxial command"
);
lambda_final
=
atof
(
arg
[
5
]);
if
(
lambda_final
<=
0
)
error
->
all
(
"Illegal fix uniaxial command"
);
if
(
domain
->
nonperiodic
)
error
->
all
(
"Cannot use fix uniaxial on non-periodic system"
);
if
(
domain
->
triclinic
)
error
->
all
(
"Cannot use fix uniaxial with triclinic box"
);
nrigid
=
0
;
rfix
=
NULL
;
}
/* ---------------------------------------------------------------------- */
FixUniaxial
::~
FixUniaxial
()
{
delete
[]
rfix
;
}
/* ---------------------------------------------------------------------- */
int
FixUniaxial
::
setmask
()
{
int
mask
=
0
;
mask
|=
END_OF_STEP
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixUniaxial
::
init
()
{
// store pointers to domain variable so can loop over dimensions
domainlo
[
0
]
=
&
domain
->
boxxlo
;
domainlo
[
1
]
=
&
domain
->
boxylo
;
domainlo
[
2
]
=
&
domain
->
boxzlo
;
domainhi
[
0
]
=
&
domain
->
boxxhi
;
domainhi
[
1
]
=
&
domain
->
boxyhi
;
domainhi
[
2
]
=
&
domain
->
boxzhi
;
domainprd
[
0
]
=
&
domain
->
xprd
;
domainprd
[
1
]
=
&
domain
->
yprd
;
domainprd
[
2
]
=
&
domain
->
zprd
;
double
L
=
pow
((
domain
->
boxxhi
-
domain
->
boxxlo
)
*
(
domain
->
boxyhi
-
domain
->
boxylo
)
*
(
domain
->
boxzhi
-
domain
->
boxzlo
)
,
1.0
/
3.0
);
// save box sizes for coordinate rescaling
// calculate strains and asymmetry parameter
// alpha=lampdai[first]/lampbdai[second] for the two perp directions
alpha0
=
1.0
;
for
(
int
m
=
0
;
m
<
3
;
m
++
)
{
domainloi
[
m
]
=
*
domainlo
[
m
];
domainhii
[
m
]
=
*
domainhi
[
m
];
lambdai
[
m
]
=
(
*
domainhi
[
m
]
-
*
domainlo
[
m
])
/
L
;
lambdaf
[
m
]
=
(
m
==
dir
?
lambda_final
:
1.0
/
sqrt
(
lambda_final
)
)
;
if
(
m
!=
dir
)
{
alpha0
*=
lambdai
[
m
];
alpha0
=
1.0
/
alpha0
;
}
}
if
(
comm
->
me
==
0
)
{
if
(
screen
)
{
fprintf
(
screen
,
"Initial strain = %g %g %g
\n
"
,
lambdai
[
0
],
lambdai
[
1
],
lambdai
[
2
]);
fprintf
(
screen
,
"Target strain = %g %g %g
\n
"
,
lambdaf
[
0
],
lambdaf
[
1
],
lambdaf
[
2
]);
}
if
(
logfile
)
{
fprintf
(
logfile
,
"Initial strain = %g %g %g
\n
"
,
lambdai
[
0
],
lambdai
[
1
],
lambdai
[
2
]);
fprintf
(
logfile
,
"Target strain = %g %g %g
\n
"
,
lambdaf
[
0
],
lambdaf
[
1
],
lambdaf
[
2
]);
}
}
if
(
force
->
kspace
)
kspace_flag
=
1
;
else
kspace_flag
=
0
;
// detect if any fix rigid exist so rigid bodies can be re-scaled
// rfix[] = indices to each fix rigid
delete
[]
rfix
;
nrigid
=
0
;
rfix
=
NULL
;
for
(
int
i
=
0
;
i
<
modify
->
nfix
;
i
++
)
if
(
strcmp
(
modify
->
fix
[
i
]
->
style
,
"rigid"
)
==
0
||
strcmp
(
modify
->
fix
[
i
]
->
style
,
"poems"
)
==
0
)
nrigid
++
;
if
(
nrigid
)
{
rfix
=
new
int
[
nrigid
];
nrigid
=
0
;
for
(
int
i
=
0
;
i
<
modify
->
nfix
;
i
++
)
if
(
strcmp
(
modify
->
fix
[
i
]
->
style
,
"rigid"
)
==
0
||
strcmp
(
modify
->
fix
[
i
]
->
style
,
"poems"
)
==
0
)
rfix
[
nrigid
++
]
=
i
;
}
}
/* ---------------------------------------------------------------------- */
void
FixUniaxial
::
end_of_step
()
{
int
i
,
m
;
double
oldlo
,
oldhi
,
newlo
,
newhi
,
ratio
;
double
delta
=
update
->
ntimestep
-
update
->
beginstep
;
delta
/=
update
->
endstep
-
update
->
beginstep
;
double
lvalue
[
3
];
// linear interpolation of strain in specified direction
lvalue
[
dir
]
=
lambdai
[
dir
]
*
(
1.0
-
delta
)
+
lambdaf
[
dir
]
*
delta
;
// linear interpolation of asymmetry parameter in the perp direction
double
alpha
=
alpha0
*
(
1
-
delta
)
+
delta
;
// calculate strains perpendicular to dir
for
(
m
=
0
;
m
<
3
;
m
++
)
if
(
m
!=
dir
)
{
lvalue
[
m
]
=
sqrt
(
alpha
/
lvalue
[
dir
]);
alpha
=
1.0
/
alpha
;
}
// apply appropriate rescaling in each dimension
double
**
x
=
atom
->
x
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
for
(
m
=
0
;
m
<
3
;
m
++
)
{
oldlo
=
*
domainlo
[
m
];
oldhi
=
*
domainhi
[
m
];
newlo
=
domainloi
[
m
]
*
lvalue
[
m
]
/
lambdai
[
m
];
newhi
=
domainhii
[
m
]
*
lvalue
[
m
]
/
lambdai
[
m
];
ratio
=
(
newhi
-
newlo
)
/
*
domainprd
[
m
];
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
x
[
i
][
m
]
=
newlo
+
(
x
[
i
][
m
]
-
oldlo
)
*
ratio
;
*
domainlo
[
m
]
=
newlo
;
*
domainhi
[
m
]
=
newhi
;
*
domainprd
[
m
]
=
newhi
-
newlo
;
if
(
nrigid
)
for
(
i
=
0
;
i
<
nrigid
;
i
++
)
modify
->
fix
[
rfix
[
i
]]
->
dilate
(
m
,
oldlo
,
oldhi
,
newlo
,
newhi
);
}
// redo KSpace coeffs since volume has changed
if
(
kspace_flag
)
force
->
kspace
->
setup
();
}
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