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fix_smd_integrate_ulsph.cpp
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Wed, Oct 2, 21:19
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Fri, Oct 4, 21:19 (2 d)
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rLAMMPS lammps
fix_smd_integrate_ulsph.cpp
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/* ----------------------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
* This file is part of the USER-SMD package for LAMMPS.
* Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de
* Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI,
* Eckerstrasse 4, D-79104 Freiburg i.Br, Germany.
*
* ----------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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 "stdio.h"
#include "string.h"
#include "fix_smd_integrate_ulsph.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
#include "pair.h"
#include "domain.h"
#include <Eigen/Eigen>
using
namespace
Eigen
;
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
/* ---------------------------------------------------------------------- */
FixSMDIntegrateUlsph
::
FixSMDIntegrateUlsph
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
((
atom
->
e_flag
!=
1
)
||
(
atom
->
vfrac_flag
!=
1
))
error
->
all
(
FLERR
,
"fix smd/integrate_ulsph command requires atom_style with both energy and volume"
);
if
(
narg
<
3
)
error
->
all
(
FLERR
,
"Illegal number of arguments for fix smd/integrate_ulsph command"
);
adjust_radius_flag
=
false
;
xsphFlag
=
false
;
vlimit
=
-
1.0
;
int
iarg
=
3
;
if
(
comm
->
me
==
0
)
{
printf
(
"
\n
>>========>>========>>========>>========>>========>>========>>========>>========
\n
"
);
printf
(
"fix smd/integrate_ulsph is active for group: %s
\n
"
,
arg
[
1
]);
}
while
(
true
)
{
if
(
iarg
>=
narg
)
{
break
;
}
if
(
strcmp
(
arg
[
iarg
],
"xsph"
)
==
0
)
{
xsphFlag
=
true
;
if
(
comm
->
me
==
0
)
{
error
->
one
(
FLERR
,
"XSPH is currently not available"
);
printf
(
"... will use XSPH time integration
\n
"
);
}
}
else
if
(
strcmp
(
arg
[
iarg
],
"adjust_radius"
)
==
0
)
{
adjust_radius_flag
=
true
;
iarg
++
;
if
(
iarg
==
narg
)
{
error
->
all
(
FLERR
,
"expected three numbers following adjust_radius: factor, min, max"
);
}
adjust_radius_factor
=
force
->
numeric
(
FLERR
,
arg
[
iarg
]);
iarg
++
;
if
(
iarg
==
narg
)
{
error
->
all
(
FLERR
,
"expected three numbers following adjust_radius: factor, min, max"
);
}
min_nn
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
]);
iarg
++
;
if
(
iarg
==
narg
)
{
error
->
all
(
FLERR
,
"expected three numbers following adjust_radius: factor, min, max"
);
}
max_nn
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
]);
if
(
comm
->
me
==
0
)
{
printf
(
"... will adjust smoothing length dynamically with factor %g to achieve %d to %d neighbors per particle.
\n
"
,
adjust_radius_factor
,
min_nn
,
max_nn
);
}
}
else
if
(
strcmp
(
arg
[
iarg
],
"limit_velocity"
)
==
0
)
{
iarg
++
;
if
(
iarg
==
narg
)
{
error
->
all
(
FLERR
,
"expected number following limit_velocity"
);
}
vlimit
=
force
->
numeric
(
FLERR
,
arg
[
iarg
]);
if
(
comm
->
me
==
0
)
{
printf
(
"... will limit velocities to <= %g
\n
"
,
vlimit
);
}
}
else
{
char
msg
[
128
];
sprintf
(
msg
,
"Illegal keyword for smd/integrate_ulsph: %s
\n
"
,
arg
[
iarg
]);
error
->
all
(
FLERR
,
msg
);
}
iarg
++
;
}
if
(
comm
->
me
==
0
)
{
printf
(
">>========>>========>>========>>========>>========>>========>>========>>========
\n\n
"
);
}
// set comm sizes needed by this fix
atom
->
add_callback
(
0
);
time_integrate
=
1
;
}
/* ---------------------------------------------------------------------- */
int
FixSMDIntegrateUlsph
::
setmask
()
{
int
mask
=
0
;
mask
|=
INITIAL_INTEGRATE
;
mask
|=
FINAL_INTEGRATE
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixSMDIntegrateUlsph
::
init
()
{
dtv
=
update
->
dt
;
dtf
=
0.5
*
update
->
dt
*
force
->
ftm2v
;
vlimitsq
=
vlimit
*
vlimit
;
}
/* ----------------------------------------------------------------------
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
void
FixSMDIntegrateUlsph
::
initial_integrate
(
int
vflag
)
{
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
**
vest
=
atom
->
vest
;
double
*
rmass
=
atom
->
rmass
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
i
,
itmp
;
double
dtfm
,
vsq
,
scale
;
double
vxsph_x
,
vxsph_y
,
vxsph_z
;
//printf("initial_integrate at timestep %d\n", update->ntimestep);
/*
* get smoothed velocities from ULSPH pair style
*/
Vector3d
*
smoothVel
=
(
Vector3d
*
)
force
->
pair
->
extract
(
"smd/ulsph/smoothVel_ptr"
,
itmp
);
if
(
xsphFlag
)
{
if
(
smoothVel
==
NULL
)
{
error
->
one
(
FLERR
,
"fix smd/integrate_ulsph failed to access smoothVel array"
);
}
}
if
(
igroup
==
atom
->
firstgroup
)
nlocal
=
atom
->
nfirst
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
rmass
[
i
];
v
[
i
][
0
]
+=
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
+=
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
+=
dtfm
*
f
[
i
][
2
];
if
(
vlimit
>
0.0
)
{
vsq
=
v
[
i
][
0
]
*
v
[
i
][
0
]
+
v
[
i
][
1
]
*
v
[
i
][
1
]
+
v
[
i
][
2
]
*
v
[
i
][
2
];
if
(
vsq
>
vlimitsq
)
{
scale
=
sqrt
(
vlimitsq
/
vsq
);
v
[
i
][
0
]
*=
scale
;
v
[
i
][
1
]
*=
scale
;
v
[
i
][
2
]
*=
scale
;
vest
[
i
][
0
]
=
v
[
i
][
0
];
vest
[
i
][
1
]
=
v
[
i
][
1
];
vest
[
i
][
2
]
=
v
[
i
][
2
];
}
}
if
(
xsphFlag
)
{
// construct XSPH velocity
vxsph_x
=
v
[
i
][
0
]
-
0.5
*
smoothVel
[
i
](
0
);
vxsph_y
=
v
[
i
][
1
]
-
0.5
*
smoothVel
[
i
](
1
);
vxsph_z
=
v
[
i
][
2
]
-
0.5
*
smoothVel
[
i
](
2
);
vest
[
i
][
0
]
=
vxsph_x
+
dtfm
*
f
[
i
][
0
];
vest
[
i
][
1
]
=
vxsph_y
+
dtfm
*
f
[
i
][
1
];
vest
[
i
][
2
]
=
vxsph_z
+
dtfm
*
f
[
i
][
2
];
x
[
i
][
0
]
+=
dtv
*
vxsph_x
;
x
[
i
][
1
]
+=
dtv
*
vxsph_y
;
x
[
i
][
2
]
+=
dtv
*
vxsph_z
;
}
else
{
// extrapolate velocity from half- to full-step
vest
[
i
][
0
]
=
v
[
i
][
0
]
+
dtfm
*
f
[
i
][
0
];
vest
[
i
][
1
]
=
v
[
i
][
1
]
+
dtfm
*
f
[
i
][
1
];
vest
[
i
][
2
]
=
v
[
i
][
2
]
+
dtfm
*
f
[
i
][
2
];
x
[
i
][
0
]
+=
dtv
*
v
[
i
][
0
];
x
[
i
][
1
]
+=
dtv
*
v
[
i
][
1
];
x
[
i
][
2
]
+=
dtv
*
v
[
i
][
2
];
}
}
}
}
/* ---------------------------------------------------------------------- */
void
FixSMDIntegrateUlsph
::
final_integrate
()
{
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
*
e
=
atom
->
e
;
double
*
de
=
atom
->
de
;
double
*
vfrac
=
atom
->
vfrac
;
double
*
radius
=
atom
->
radius
;
double
*
contact_radius
=
atom
->
contact_radius
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
igroup
==
atom
->
firstgroup
)
nlocal
=
atom
->
nfirst
;
double
dtfm
,
vsq
,
scale
;
double
*
rmass
=
atom
->
rmass
;
double
vol_increment
;
Matrix3d
D
;
/*
* get current number of SPH neighbors from ULSPH pair style
*/
int
itmp
;
int
*
nn
=
(
int
*
)
force
->
pair
->
extract
(
"smd/ulsph/numNeighs_ptr"
,
itmp
);
if
(
nn
==
NULL
)
{
error
->
one
(
FLERR
,
"fix smd/integrate_ulsph failed to accesss num_neighs array"
);
}
Matrix3d
*
L
=
(
Matrix3d
*
)
force
->
pair
->
extract
(
"smd/ulsph/velocityGradient_ptr"
,
itmp
);
if
(
L
==
NULL
)
{
error
->
one
(
FLERR
,
"fix smd/integrate_ulsph failed to accesss velocityGradient array"
);
}
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
rmass
[
i
];
v
[
i
][
0
]
+=
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
+=
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
+=
dtfm
*
f
[
i
][
2
];
if
(
vlimit
>
0.0
)
{
vsq
=
v
[
i
][
0
]
*
v
[
i
][
0
]
+
v
[
i
][
1
]
*
v
[
i
][
1
]
+
v
[
i
][
2
]
*
v
[
i
][
2
];
if
(
vsq
>
vlimitsq
)
{
scale
=
sqrt
(
vlimitsq
/
vsq
);
v
[
i
][
0
]
*=
scale
;
v
[
i
][
1
]
*=
scale
;
v
[
i
][
2
]
*=
scale
;
}
}
e
[
i
]
+=
dtf
*
de
[
i
];
if
(
adjust_radius_flag
)
{
if
(
nn
[
i
]
<
min_nn
)
{
radius
[
i
]
*=
adjust_radius_factor
;
}
else
if
(
nn
[
i
]
>
max_nn
)
{
radius
[
i
]
/=
adjust_radius_factor
;
}
radius
[
i
]
=
MAX
(
radius
[
i
],
1.25
*
contact_radius
[
i
]);
radius
[
i
]
=
MIN
(
radius
[
i
],
4.0
*
contact_radius
[
i
]);
}
D
=
0.5
*
(
L
[
i
]
+
L
[
i
].
transpose
());
vol_increment
=
vfrac
[
i
]
*
update
->
dt
*
D
.
trace
();
// Jacobian of deformation
vfrac
[
i
]
+=
vol_increment
;
}
}
}
/* ---------------------------------------------------------------------- */
void
FixSMDIntegrateUlsph
::
reset_dt
()
{
dtv
=
update
->
dt
;
dtf
=
0.5
*
update
->
dt
*
force
->
ftm2v
;
}
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