Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F88095275
atom_vec_smd.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Oct 16, 18:28
Size
35 KB
Mime Type
text/x-c
Expires
Fri, Oct 18, 18:28 (2 d)
Engine
blob
Format
Raw Data
Handle
21715718
Attached To
rLAMMPS lammps
atom_vec_smd.cpp
View Options
/* ----------------------------------------------------------------------
*
* *** 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 <math.h>
#include <stdlib.h>
#include <string.h>
#include "atom_vec_smd.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "force.h"
#include "fix.h"
#include "fix_adapt.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
#define NMAT_FULL 9
#define NMAT_SYMM 6
/* ---------------------------------------------------------------------- */
AtomVecSMD
::
AtomVecSMD
(
LAMMPS
*
lmp
)
:
AtomVec
(
lmp
)
{
molecular
=
0
;
comm_x_only
=
0
;
comm_f_only
=
0
;
size_forward
=
6
;
// variables that are changed by time integration
size_reverse
=
4
;
// f[3] + de
size_border
=
31
;
size_velocity
=
6
;
// v + vest
size_data_atom
=
13
;
// 7 + 3 x0 + 3 x
size_data_vel
=
4
;
xcol_data
=
11
;
atom
->
radius_flag
=
1
;
atom
->
rmass_flag
=
1
;
atom
->
vfrac_flag
=
1
;
atom
->
contact_radius_flag
=
1
;
atom
->
molecule_flag
=
1
;
atom
->
smd_data_9_flag
=
1
;
atom
->
e_flag
=
1
;
atom
->
vest_flag
=
1
;
atom
->
smd_stress_flag
=
1
;
atom
->
eff_plastic_strain_flag
=
1
;
atom
->
x0_flag
=
1
;
atom
->
damage_flag
=
1
;
atom
->
eff_plastic_strain_rate_flag
=
1
;
forceclearflag
=
1
;
atom
->
smd_flag
=
1
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecSMD
::
init
()
{
AtomVec
::
init
();
// do nothing here
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void
AtomVecSMD
::
grow
(
int
n
)
{
if
(
n
==
0
)
grow_nmax
();
else
nmax
=
n
;
atom
->
nmax
=
nmax
;
if
(
nmax
<
0
||
nmax
>
MAXSMALLINT
)
error
->
one
(
FLERR
,
"Per-processor system is too big"
);
//printf("in grow, nmax is now %d\n", nmax);
tag
=
memory
->
grow
(
atom
->
tag
,
nmax
,
"atom:tag"
);
type
=
memory
->
grow
(
atom
->
type
,
nmax
,
"atom:type"
);
mask
=
memory
->
grow
(
atom
->
mask
,
nmax
,
"atom:mask"
);
image
=
memory
->
grow
(
atom
->
image
,
nmax
,
"atom:image"
);
x
=
memory
->
grow
(
atom
->
x
,
nmax
,
3
,
"atom:x"
);
v
=
memory
->
grow
(
atom
->
v
,
nmax
,
3
,
"atom:v"
);
f
=
memory
->
grow
(
atom
->
f
,
nmax
*
comm
->
nthreads
,
3
,
"atom:f"
);
de
=
memory
->
grow
(
atom
->
de
,
nmax
*
comm
->
nthreads
,
"atom:de"
);
vfrac
=
memory
->
grow
(
atom
->
vfrac
,
nmax
,
"atom:vfrac"
);
rmass
=
memory
->
grow
(
atom
->
rmass
,
nmax
,
"atom:rmass"
);
x0
=
memory
->
grow
(
atom
->
x0
,
nmax
,
3
,
"atom:x0"
);
radius
=
memory
->
grow
(
atom
->
radius
,
nmax
,
"atom:radius"
);
contact_radius
=
memory
->
grow
(
atom
->
contact_radius
,
nmax
,
"atom:contact_radius"
);
molecule
=
memory
->
grow
(
atom
->
molecule
,
nmax
,
"atom:molecule"
);
smd_data_9
=
memory
->
grow
(
atom
->
smd_data_9
,
nmax
,
NMAT_FULL
,
"atom:defgrad_old"
);
e
=
memory
->
grow
(
atom
->
e
,
nmax
,
"atom:e"
);
vest
=
memory
->
grow
(
atom
->
vest
,
nmax
,
3
,
"atom:vest"
);
tlsph_stress
=
memory
->
grow
(
atom
->
smd_stress
,
nmax
,
NMAT_SYMM
,
"atom:tlsph_stress"
);
eff_plastic_strain
=
memory
->
grow
(
atom
->
eff_plastic_strain
,
nmax
,
"atom:eff_plastic_strain"
);
eff_plastic_strain_rate
=
memory
->
grow
(
atom
->
eff_plastic_strain_rate
,
nmax
,
"atom:eff_plastic_strain_rate"
);
damage
=
memory
->
grow
(
atom
->
damage
,
nmax
,
"atom:damage"
);
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
grow_arrays
(
nmax
);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void
AtomVecSMD
::
grow_reset
()
{
tag
=
atom
->
tag
;
type
=
atom
->
type
;
mask
=
atom
->
mask
;
image
=
atom
->
image
;
x
=
atom
->
x
;
v
=
atom
->
v
;
f
=
atom
->
f
;
radius
=
atom
->
radius
;
rmass
=
atom
->
rmass
;
vfrac
=
atom
->
vfrac
;
x0
=
atom
->
x0
;
contact_radius
=
atom
->
contact_radius
;
molecule
=
atom
->
molecule
;
smd_data_9
=
atom
->
smd_data_9
;
e
=
atom
->
e
;
de
=
atom
->
de
;
tlsph_stress
=
atom
->
smd_stress
;
eff_plastic_strain
=
atom
->
eff_plastic_strain
;
eff_plastic_strain_rate
=
atom
->
eff_plastic_strain_rate
;
damage
=
atom
->
damage
;
vest
=
atom
->
vest
;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void
AtomVecSMD
::
copy
(
int
i
,
int
j
,
int
delflag
)
{
tag
[
j
]
=
tag
[
i
];
type
[
j
]
=
type
[
i
];
mask
[
j
]
=
mask
[
i
];
image
[
j
]
=
image
[
i
];
x
[
j
][
0
]
=
x
[
i
][
0
];
x
[
j
][
1
]
=
x
[
i
][
1
];
x
[
j
][
2
]
=
x
[
i
][
2
];
v
[
j
][
0
]
=
v
[
i
][
0
];
v
[
j
][
1
]
=
v
[
i
][
1
];
v
[
j
][
2
]
=
v
[
i
][
2
];
vfrac
[
j
]
=
vfrac
[
i
];
rmass
[
j
]
=
rmass
[
i
];
x0
[
j
][
0
]
=
x0
[
i
][
0
];
x0
[
j
][
1
]
=
x0
[
i
][
1
];
x0
[
j
][
2
]
=
x0
[
i
][
2
];
radius
[
j
]
=
radius
[
i
];
contact_radius
[
j
]
=
contact_radius
[
i
];
molecule
[
j
]
=
molecule
[
i
];
e
[
j
]
=
e
[
i
];
eff_plastic_strain
[
j
]
=
eff_plastic_strain
[
i
];
eff_plastic_strain_rate
[
j
]
=
eff_plastic_strain_rate
[
i
];
vest
[
j
][
0
]
=
vest
[
i
][
0
];
vest
[
j
][
1
]
=
vest
[
i
][
1
];
vest
[
j
][
2
]
=
vest
[
i
][
2
];
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
smd_data_9
[
j
][
k
]
=
smd_data_9
[
i
][
k
];
}
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
tlsph_stress
[
j
][
k
]
=
tlsph_stress
[
i
][
k
];
}
damage
[
j
]
=
damage
[
i
];
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
copy_arrays
(
i
,
j
,
delflag
);
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_comm
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
error
->
one
(
FLERR
,
"atom vec tlsph can only be used with ghost velocities turned on"
);
return
-
1
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_comm_vel
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
// communicate quantities to ghosts, which are changed by time-integration AND are required on ghost atoms.
//no need to pack stress or defgrad information here, as these quantities are not required for ghost atoms.
// Inside pair_style tlsph, these quantities are computed and communicated to ghosts.
// no need to communicate x0 here, as it is not changed by time integration
// if x0 is changed when the ref config is updated, this communication is performed in the fix_integrate/tlsph
// similarily, rmass could be removed here.
// radius should be communicated here for future time-integration of the radius with ulsph (not implemented yet)
int
i
,
j
,
m
;
double
dx
,
dy
,
dz
,
dvx
,
dvy
,
dvz
;
m
=
0
;
if
(
pbc_flag
==
0
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
];
buf
[
m
++
]
=
x
[
j
][
1
];
buf
[
m
++
]
=
x
[
j
][
2
];
//3
buf
[
m
++
]
=
radius
[
j
];
buf
[
m
++
]
=
vfrac
[
j
];
// 5
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
// 8
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
j
][
2
];
// 11
buf
[
m
++
]
=
e
[
j
];
// 12
}
}
else
{
if
(
domain
->
triclinic
==
0
)
{
dx
=
pbc
[
0
]
*
domain
->
xprd
;
dy
=
pbc
[
1
]
*
domain
->
yprd
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
else
{
dx
=
pbc
[
0
]
*
domain
->
xprd
+
pbc
[
5
]
*
domain
->
xy
+
pbc
[
4
]
*
domain
->
xz
;
dy
=
pbc
[
1
]
*
domain
->
yprd
+
pbc
[
3
]
*
domain
->
yz
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
if
(
!
deform_vremap
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
buf
[
m
++
]
=
radius
[
j
];
buf
[
m
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
// 8
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
j
][
2
];
// 11
buf
[
m
++
]
=
e
[
j
];
// 12
}
}
else
{
dvx
=
pbc
[
0
]
*
h_rate
[
0
]
+
pbc
[
5
]
*
h_rate
[
5
]
+
pbc
[
4
]
*
h_rate
[
4
];
dvy
=
pbc
[
1
]
*
h_rate
[
1
]
+
pbc
[
3
]
*
h_rate
[
3
];
dvz
=
pbc
[
2
]
*
h_rate
[
2
];
// printf("\ndvx = %f, dvy=%f, dvz=%f\n", dvx, dvy, dvz);
// printf("dx = %f, dy=%f, dz=%f\n", dx, dy, dz);
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
buf
[
m
++
]
=
radius
[
j
];
buf
[
m
++
]
=
vfrac
[
j
];
if
(
mask
[
i
]
&
deform_groupbit
)
{
buf
[
m
++
]
=
v
[
j
][
0
]
+
dvx
;
buf
[
m
++
]
=
v
[
j
][
1
]
+
dvy
;
buf
[
m
++
]
=
v
[
j
][
2
]
+
dvz
;
buf
[
m
++
]
=
vest
[
j
][
0
]
+
dvx
;
buf
[
m
++
]
=
vest
[
j
][
1
]
+
dvy
;
buf
[
m
++
]
=
vest
[
j
][
2
]
+
dvz
;
}
else
{
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
// 8
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
j
][
2
];
// 11
}
buf
[
m
++
]
=
e
[
j
];
// 12
}
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_comm_hybrid
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
radius
[
j
];
buf
[
m
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
j
][
2
];
buf
[
m
++
]
=
e
[
j
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecSMD
::
unpack_comm
(
int
n
,
int
first
,
double
*
buf
)
{
error
->
one
(
FLERR
,
"atom vec tlsph can only be used with ghost velocities turned on"
);
}
/* ---------------------------------------------------------------------- */
void
AtomVecSMD
::
unpack_comm_vel
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
x
[
i
][
0
]
=
buf
[
m
++
];
x
[
i
][
1
]
=
buf
[
m
++
];
x
[
i
][
2
]
=
buf
[
m
++
];
//3
radius
[
i
]
=
buf
[
m
++
];
vfrac
[
i
]
=
buf
[
m
++
];
// 5
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
// 8
vest
[
i
][
0
]
=
buf
[
m
++
];
vest
[
i
][
1
]
=
buf
[
m
++
];
vest
[
i
][
2
]
=
buf
[
m
++
];
// 11
e
[
i
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
unpack_comm_hybrid
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
radius
[
i
]
=
buf
[
m
++
];
vfrac
[
i
]
=
buf
[
m
++
];
vest
[
i
][
0
]
=
buf
[
m
++
];
vest
[
i
][
1
]
=
buf
[
m
++
];
vest
[
i
][
2
]
=
buf
[
m
++
];
e
[
i
]
=
buf
[
m
++
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_reverse
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
printf
(
"in pack_reverse
\n
"
);
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
buf
[
m
++
]
=
f
[
i
][
0
];
buf
[
m
++
]
=
f
[
i
][
1
];
buf
[
m
++
]
=
f
[
i
][
2
];
buf
[
m
++
]
=
de
[
i
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_reverse_hybrid
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
buf
[
m
++
]
=
de
[
i
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecSMD
::
unpack_reverse
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
f
[
j
][
0
]
+=
buf
[
m
++
];
f
[
j
][
1
]
+=
buf
[
m
++
];
f
[
j
][
2
]
+=
buf
[
m
++
];
de
[
j
]
+=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
unpack_reverse_hybrid
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
de
[
j
]
+=
buf
[
m
++
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_border
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
error
->
one
(
FLERR
,
"atom vec tlsph can only be used with ghost velocities turned on"
);
return
-
1
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_border_vel
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
double
dx
,
dy
,
dz
,
dvx
,
dvy
,
dvz
;
//printf("AtomVecSMD::pack_border_vel\n");
m
=
0
;
if
(
pbc_flag
==
0
)
{
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
];
buf
[
m
++
]
=
x
[
j
][
1
];
buf
[
m
++
]
=
x
[
j
][
2
];
// 3
buf
[
m
++
]
=
x0
[
j
][
0
];
buf
[
m
++
]
=
x0
[
j
][
1
];
buf
[
m
++
]
=
x0
[
j
][
2
];
// 6
buf
[
m
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
molecule
[
j
]).
d
;
// 10
buf
[
m
++
]
=
radius
[
j
];
buf
[
m
++
]
=
rmass
[
j
];
buf
[
m
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
contact_radius
[
j
];
buf
[
m
++
]
=
e
[
j
];
buf
[
m
++
]
=
eff_plastic_strain
[
j
];
// 16
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
buf
[
m
++
]
=
smd_data_9
[
j
][
k
];
}
// 25
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
buf
[
m
++
]
=
tlsph_stress
[
j
][
k
];
}
// 31
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
// 34
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
j
][
2
];
// 37
}
}
else
{
if
(
domain
->
triclinic
==
0
)
{
dx
=
pbc
[
0
]
*
domain
->
xprd
;
dy
=
pbc
[
1
]
*
domain
->
yprd
;
dz
=
pbc
[
2
]
*
domain
->
zprd
;
}
else
{
dx
=
pbc
[
0
];
dy
=
pbc
[
1
];
dz
=
pbc
[
2
];
}
if
(
!
deform_vremap
)
{
//printf("dx = %f\n", dx);
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
// 3
buf
[
m
++
]
=
x0
[
j
][
0
];
// this is correct
buf
[
m
++
]
=
x0
[
j
][
1
];
buf
[
m
++
]
=
x0
[
j
][
2
];
// 6
buf
[
m
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
molecule
[
j
]).
d
;
// 10
buf
[
m
++
]
=
radius
[
j
];
buf
[
m
++
]
=
rmass
[
j
];
buf
[
m
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
contact_radius
[
j
];
buf
[
m
++
]
=
e
[
j
];
buf
[
m
++
]
=
eff_plastic_strain
[
j
];
// 17
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
buf
[
m
++
]
=
smd_data_9
[
j
][
k
];
}
// 26
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
buf
[
m
++
]
=
tlsph_stress
[
j
][
k
];
}
// 32
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
// 35
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
j
][
2
];
// 38
}
}
else
{
dvx
=
pbc
[
0
]
*
h_rate
[
0
]
+
pbc
[
5
]
*
h_rate
[
5
]
+
pbc
[
4
]
*
h_rate
[
4
];
dvy
=
pbc
[
1
]
*
h_rate
[
1
]
+
pbc
[
3
]
*
h_rate
[
3
];
dvz
=
pbc
[
2
]
*
h_rate
[
2
];
// printf("\ndvx = %f, dvy=%f, dvz=%f\n", dvx, dvy, dvz);
// printf("dx = %f, dy=%f, dz=%f\n", dx, dy, dz);
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x
[
j
][
0
]
+
dx
;
buf
[
m
++
]
=
x
[
j
][
1
]
+
dy
;
buf
[
m
++
]
=
x
[
j
][
2
]
+
dz
;
// 3
buf
[
m
++
]
=
x0
[
j
][
0
];
buf
[
m
++
]
=
x0
[
j
][
1
];
buf
[
m
++
]
=
x0
[
j
][
2
];
// 6
buf
[
m
++
]
=
ubuf
(
tag
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
j
]).
d
;
buf
[
m
++
]
=
ubuf
(
molecule
[
j
]).
d
;
// 10
buf
[
m
++
]
=
radius
[
j
];
buf
[
m
++
]
=
rmass
[
j
];
buf
[
m
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
contact_radius
[
j
];
buf
[
m
++
]
=
e
[
j
];
buf
[
m
++
]
=
eff_plastic_strain
[
j
];
// 16
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
buf
[
m
++
]
=
smd_data_9
[
j
][
k
];
}
// 25
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
buf
[
m
++
]
=
tlsph_stress
[
j
][
k
];
}
// 31
if
(
mask
[
i
]
&
deform_groupbit
)
{
buf
[
m
++
]
=
v
[
j
][
0
]
+
dvx
;
buf
[
m
++
]
=
v
[
j
][
1
]
+
dvy
;
buf
[
m
++
]
=
v
[
j
][
2
]
+
dvz
;
// 34
buf
[
m
++
]
=
vest
[
j
][
0
]
+
dvx
;
buf
[
m
++
]
=
vest
[
j
][
1
]
+
dvy
;
buf
[
m
++
]
=
vest
[
j
][
2
]
+
dvz
;
// 37
}
else
{
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
// 34
buf
[
m
++
]
=
vest
[
j
][
0
];
buf
[
m
++
]
=
vest
[
j
][
1
];
buf
[
m
++
]
=
vest
[
j
][
2
];
// 37
}
}
}
}
if
(
atom
->
nextra_border
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_border
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_border
[
iextra
]]
->
pack_border
(
n
,
list
,
&
buf
[
m
]);
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_border_hybrid
(
int
n
,
int
*
list
,
double
*
buf
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
x0
[
j
][
0
];
buf
[
m
++
]
=
x0
[
j
][
1
];
buf
[
m
++
]
=
x0
[
j
][
2
];
// 3
buf
[
m
++
]
=
ubuf
(
molecule
[
j
]).
d
;
// 4
buf
[
m
++
]
=
radius
[
j
];
buf
[
m
++
]
=
rmass
[
j
];
buf
[
m
++
]
=
vfrac
[
j
];
buf
[
m
++
]
=
contact_radius
[
j
];
buf
[
m
++
]
=
e
[
j
];
buf
[
m
++
]
=
eff_plastic_strain
[
j
];
// 11
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
buf
[
m
++
]
=
smd_data_9
[
j
][
k
];
}
// 20
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
buf
[
m
++
]
=
tlsph_stress
[
j
][
k
];
}
// 26
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecSMD
::
unpack_border
(
int
n
,
int
first
,
double
*
buf
)
{
error
->
one
(
FLERR
,
"atom vec tlsph can only be used with ghost velocities turned on"
);
}
/* ---------------------------------------------------------------------- */
void
AtomVecSMD
::
unpack_border_vel
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
if
(
i
==
nmax
)
grow
(
0
);
x
[
i
][
0
]
=
buf
[
m
++
];
x
[
i
][
1
]
=
buf
[
m
++
];
x
[
i
][
2
]
=
buf
[
m
++
];
// 3
x0
[
i
][
0
]
=
buf
[
m
++
];
x0
[
i
][
1
]
=
buf
[
m
++
];
x0
[
i
][
2
]
=
buf
[
m
++
];
// 6
tag
[
i
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
type
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
mask
[
i
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
molecule
[
i
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
// 10
radius
[
i
]
=
buf
[
m
++
];
rmass
[
i
]
=
buf
[
m
++
];
vfrac
[
i
]
=
buf
[
m
++
];
contact_radius
[
i
]
=
buf
[
m
++
];
e
[
i
]
=
buf
[
m
++
];
eff_plastic_strain
[
i
]
=
buf
[
m
++
];
// 16
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
smd_data_9
[
i
][
k
]
=
buf
[
m
++
];
}
// 25
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
tlsph_stress
[
i
][
k
]
=
buf
[
m
++
];
}
// 31
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
// 34
vest
[
i
][
0
]
=
buf
[
m
++
];
vest
[
i
][
1
]
=
buf
[
m
++
];
vest
[
i
][
2
]
=
buf
[
m
++
];
// 37
}
if
(
atom
->
nextra_border
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_border
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_border
[
iextra
]]
->
unpack_border
(
n
,
first
,
&
buf
[
m
]);
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
unpack_border_hybrid
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
x0
[
i
][
0
]
=
buf
[
m
++
];
x0
[
i
][
1
]
=
buf
[
m
++
];
x0
[
i
][
2
]
=
buf
[
m
++
];
// 3
molecule
[
i
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
// 4
radius
[
i
]
=
buf
[
m
++
];
rmass
[
i
]
=
buf
[
m
++
];
vfrac
[
i
]
=
buf
[
m
++
];
contact_radius
[
i
]
=
buf
[
m
++
];
e
[
i
]
=
buf
[
m
++
];
eff_plastic_strain
[
i
]
=
buf
[
m
++
];
// 11
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
smd_data_9
[
i
][
k
]
=
buf
[
m
++
];
}
// 20
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
tlsph_stress
[
i
][
k
]
=
buf
[
m
++
];
}
// 26
}
return
m
;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_exchange
(
int
i
,
double
*
buf
)
{
int
m
=
1
;
//printf("in AtomVecSMD::pack_exchange tag %d\n", tag[i]);
buf
[
m
++
]
=
x
[
i
][
0
];
buf
[
m
++
]
=
x
[
i
][
1
];
buf
[
m
++
]
=
x
[
i
][
2
];
// 3
buf
[
m
++
]
=
x0
[
i
][
0
];
buf
[
m
++
]
=
x0
[
i
][
1
];
buf
[
m
++
]
=
x0
[
i
][
2
];
// 6
buf
[
m
++
]
=
ubuf
(
tag
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
image
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
molecule
[
i
]).
d
;
// 11
buf
[
m
++
]
=
radius
[
i
];
buf
[
m
++
]
=
rmass
[
i
];
buf
[
m
++
]
=
vfrac
[
i
];
buf
[
m
++
]
=
contact_radius
[
i
];
buf
[
m
++
]
=
e
[
i
];
buf
[
m
++
]
=
eff_plastic_strain
[
i
];
// 18
buf
[
m
++
]
=
eff_plastic_strain_rate
[
i
];
// 19
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
buf
[
m
++
]
=
smd_data_9
[
i
][
k
];
}
// 27
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
buf
[
m
++
]
=
tlsph_stress
[
i
][
k
];
}
// 33
buf
[
m
++
]
=
v
[
i
][
0
];
buf
[
m
++
]
=
v
[
i
][
1
];
buf
[
m
++
]
=
v
[
i
][
2
];
// 36
buf
[
m
++
]
=
vest
[
i
][
0
];
buf
[
m
++
]
=
vest
[
i
][
1
];
buf
[
m
++
]
=
vest
[
i
][
2
];
// 39
buf
[
m
++
]
=
damage
[
i
];
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
pack_exchange
(
i
,
&
buf
[
m
]);
buf
[
0
]
=
m
;
return
m
;
}
/* ---------------------------------------------------------------------- */
int
AtomVecSMD
::
unpack_exchange
(
double
*
buf
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
int
m
=
1
;
x
[
nlocal
][
0
]
=
buf
[
m
++
];
x
[
nlocal
][
1
]
=
buf
[
m
++
];
x
[
nlocal
][
2
]
=
buf
[
m
++
];
// 3
x0
[
nlocal
][
0
]
=
buf
[
m
++
];
x0
[
nlocal
][
1
]
=
buf
[
m
++
];
x0
[
nlocal
][
2
]
=
buf
[
m
++
];
// 6
tag
[
nlocal
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
type
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
mask
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
image
[
nlocal
]
=
(
imageint
)
ubuf
(
buf
[
m
++
]).
i
;
molecule
[
nlocal
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
// 11
radius
[
nlocal
]
=
buf
[
m
++
];
rmass
[
nlocal
]
=
buf
[
m
++
];
vfrac
[
nlocal
]
=
buf
[
m
++
];
contact_radius
[
nlocal
]
=
buf
[
m
++
];
e
[
nlocal
]
=
buf
[
m
++
];
eff_plastic_strain
[
nlocal
]
=
buf
[
m
++
];
// 18
eff_plastic_strain_rate
[
nlocal
]
=
buf
[
m
++
];
// 19
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
smd_data_9
[
nlocal
][
k
]
=
buf
[
m
++
];
}
// 27
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
tlsph_stress
[
nlocal
][
k
]
=
buf
[
m
++
];
}
// 33
v
[
nlocal
][
0
]
=
buf
[
m
++
];
v
[
nlocal
][
1
]
=
buf
[
m
++
];
v
[
nlocal
][
2
]
=
buf
[
m
++
];
// 36
vest
[
nlocal
][
0
]
=
buf
[
m
++
];
vest
[
nlocal
][
1
]
=
buf
[
m
++
];
vest
[
nlocal
][
2
]
=
buf
[
m
++
];
// 39
damage
[
nlocal
]
=
buf
[
m
++
];
//40
if
(
atom
->
nextra_grow
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_grow
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_grow
[
iextra
]]
->
unpack_exchange
(
nlocal
,
&
buf
[
m
]);
atom
->
nlocal
++
;
return
m
;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int
AtomVecSMD
::
size_restart
()
{
int
i
;
int
nlocal
=
atom
->
nlocal
;
int
n
=
43
*
nlocal
;
// count pack_restart + 1 (size of buffer)
if
(
atom
->
nextra_restart
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_restart
;
iextra
++
)
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
n
+=
modify
->
fix
[
atom
->
extra_restart
[
iextra
]]
->
size_restart
(
i
);
return
n
;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_restart
(
int
i
,
double
*
buf
)
{
int
m
=
1
;
// 1
buf
[
m
++
]
=
x
[
i
][
0
];
buf
[
m
++
]
=
x
[
i
][
1
];
buf
[
m
++
]
=
x
[
i
][
2
];
// 4
buf
[
m
++
]
=
x0
[
i
][
0
];
buf
[
m
++
]
=
x0
[
i
][
1
];
buf
[
m
++
]
=
x0
[
i
][
2
];
// 7
buf
[
m
++
]
=
ubuf
(
tag
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
type
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
mask
[
i
]).
d
;
// 10
buf
[
m
++
]
=
ubuf
(
image
[
i
]).
d
;
buf
[
m
++
]
=
ubuf
(
molecule
[
i
]).
d
;
buf
[
m
++
]
=
radius
[
i
];
buf
[
m
++
]
=
rmass
[
i
];
buf
[
m
++
]
=
vfrac
[
i
];
// 15
buf
[
m
++
]
=
contact_radius
[
i
];
buf
[
m
++
]
=
e
[
i
];
buf
[
m
++
]
=
eff_plastic_strain
[
i
];
buf
[
m
++
]
=
eff_plastic_strain_rate
[
i
];
// 19
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
buf
[
m
++
]
=
smd_data_9
[
i
][
k
];
}
// 28
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
buf
[
m
++
]
=
tlsph_stress
[
i
][
k
];
}
// 34
buf
[
m
++
]
=
v
[
i
][
0
];
buf
[
m
++
]
=
v
[
i
][
1
];
buf
[
m
++
]
=
v
[
i
][
2
];
// 37
buf
[
m
++
]
=
vest
[
i
][
0
];
buf
[
m
++
]
=
vest
[
i
][
1
];
buf
[
m
++
]
=
vest
[
i
][
2
];
// 40
buf
[
m
++
]
=
damage
[
i
];
// 41
if
(
atom
->
nextra_restart
)
for
(
int
iextra
=
0
;
iextra
<
atom
->
nextra_restart
;
iextra
++
)
m
+=
modify
->
fix
[
atom
->
extra_restart
[
iextra
]]
->
pack_restart
(
i
,
&
buf
[
m
]);
buf
[
0
]
=
m
;
return
m
;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int
AtomVecSMD
::
unpack_restart
(
double
*
buf
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
{
grow
(
0
);
if
(
atom
->
nextra_store
)
memory
->
grow
(
atom
->
extra
,
nmax
,
atom
->
nextra_store
,
"atom:extra"
);
}
int
m
=
1
;
x
[
nlocal
][
0
]
=
buf
[
m
++
];
x
[
nlocal
][
1
]
=
buf
[
m
++
];
x
[
nlocal
][
2
]
=
buf
[
m
++
];
// 3
x0
[
nlocal
][
0
]
=
buf
[
m
++
];
x0
[
nlocal
][
1
]
=
buf
[
m
++
];
x0
[
nlocal
][
2
]
=
buf
[
m
++
];
// 6
tag
[
nlocal
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
type
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
mask
[
nlocal
]
=
(
int
)
ubuf
(
buf
[
m
++
]).
i
;
image
[
nlocal
]
=
(
imageint
)
ubuf
(
buf
[
m
++
]).
i
;
molecule
[
nlocal
]
=
(
tagint
)
ubuf
(
buf
[
m
++
]).
i
;
// 11
radius
[
nlocal
]
=
buf
[
m
++
];
rmass
[
nlocal
]
=
buf
[
m
++
];
vfrac
[
nlocal
]
=
buf
[
m
++
];
//14
contact_radius
[
nlocal
]
=
buf
[
m
++
];
//15
e
[
nlocal
]
=
buf
[
m
++
];
eff_plastic_strain
[
nlocal
]
=
buf
[
m
++
];
// 18
eff_plastic_strain_rate
[
nlocal
]
=
buf
[
m
++
];
// 29
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
smd_data_9
[
nlocal
][
k
]
=
buf
[
m
++
];
}
// 28
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
tlsph_stress
[
nlocal
][
k
]
=
buf
[
m
++
];
}
// 34
v
[
nlocal
][
0
]
=
buf
[
m
++
];
v
[
nlocal
][
1
]
=
buf
[
m
++
];
v
[
nlocal
][
2
]
=
buf
[
m
++
];
// 37
vest
[
nlocal
][
0
]
=
buf
[
m
++
];
vest
[
nlocal
][
1
]
=
buf
[
m
++
];
vest
[
nlocal
][
2
]
=
buf
[
m
++
];
// 40
damage
[
nlocal
]
=
buf
[
m
++
];
//41
//printf("nlocal in restart is %d\n", nlocal);
double
**
extra
=
atom
->
extra
;
if
(
atom
->
nextra_store
)
{
int
size
=
static_cast
<
int
>
(
buf
[
0
])
-
m
;
for
(
int
i
=
0
;
i
<
size
;
i
++
)
extra
[
nlocal
][
i
]
=
buf
[
m
++
];
}
atom
->
nlocal
++
;
//printf("returning m=%d in unpack_restart\n", m);
return
m
;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void
AtomVecSMD
::
create_atom
(
int
itype
,
double
*
coord
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
{
printf
(
"nlocal = %d, nmax = %d, calling grow
\n
"
,
nlocal
,
nmax
);
grow
(
0
);
printf
(
"... finished growing
\n
"
);
}
tag
[
nlocal
]
=
0
;
type
[
nlocal
]
=
itype
;
x
[
nlocal
][
0
]
=
coord
[
0
];
x
[
nlocal
][
1
]
=
coord
[
1
];
x
[
nlocal
][
2
]
=
coord
[
2
];
x0
[
nlocal
][
0
]
=
coord
[
0
];
x0
[
nlocal
][
1
]
=
coord
[
1
];
x0
[
nlocal
][
2
]
=
coord
[
2
];
mask
[
nlocal
]
=
1
;
image
[
nlocal
]
=
((
imageint
)
IMGMAX
<<
IMG2BITS
)
|
((
imageint
)
IMGMAX
<<
IMGBITS
)
|
IMGMAX
;
v
[
nlocal
][
0
]
=
0.0
;
v
[
nlocal
][
1
]
=
0.0
;
v
[
nlocal
][
2
]
=
0.0
;
vest
[
nlocal
][
0
]
=
0.0
;
vest
[
nlocal
][
1
]
=
0.0
;
vest
[
nlocal
][
2
]
=
0.0
;
vfrac
[
nlocal
]
=
1.0
;
rmass
[
nlocal
]
=
1.0
;
radius
[
nlocal
]
=
0.5
;
contact_radius
[
nlocal
]
=
0.5
;
molecule
[
nlocal
]
=
1
;
e
[
nlocal
]
=
0.0
;
eff_plastic_strain
[
nlocal
]
=
0.0
;
eff_plastic_strain_rate
[
nlocal
]
=
0.0
;
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
smd_data_9
[
nlocal
][
k
]
=
0.0
;
}
smd_data_9
[
nlocal
][
0
]
=
1.0
;
// xx
smd_data_9
[
nlocal
][
4
]
=
1.0
;
// yy
smd_data_9
[
nlocal
][
8
]
=
1.0
;
// zz
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
tlsph_stress
[
nlocal
][
k
]
=
0.0
;
}
damage
[
nlocal
]
=
0.0
;
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void
AtomVecSMD
::
data_atom
(
double
*
coord
,
imageint
imagetmp
,
char
**
values
)
{
int
nlocal
=
atom
->
nlocal
;
if
(
nlocal
==
nmax
)
grow
(
0
);
tag
[
nlocal
]
=
ATOTAGINT
(
values
[
0
]);
type
[
nlocal
]
=
atoi
(
values
[
1
]);
if
(
type
[
nlocal
]
<=
0
||
type
[
nlocal
]
>
atom
->
ntypes
)
error
->
one
(
FLERR
,
"Invalid atom type in Atoms section of data file"
);
molecule
[
nlocal
]
=
ATOTAGINT
(
values
[
2
]);
if
(
molecule
[
nlocal
]
<=
0
)
error
->
one
(
FLERR
,
"Invalid molecule in Atoms section of data file"
);
vfrac
[
nlocal
]
=
atof
(
values
[
3
]);
if
(
vfrac
[
nlocal
]
<
0.0
)
error
->
one
(
FLERR
,
"Invalid volume in Atoms section of data file"
);
rmass
[
nlocal
]
=
atof
(
values
[
4
]);
if
(
rmass
[
nlocal
]
==
0.0
)
error
->
one
(
FLERR
,
"Invalid mass in Atoms section of data file"
);
radius
[
nlocal
]
=
atof
(
values
[
5
]);
if
(
radius
[
nlocal
]
<
0.0
)
error
->
one
(
FLERR
,
"Invalid radius in Atoms section of data file"
);
contact_radius
[
nlocal
]
=
atof
(
values
[
6
]);
if
(
contact_radius
[
nlocal
]
<
0.0
)
error
->
one
(
FLERR
,
"Invalid contact radius in Atoms section of data file"
);
e
[
nlocal
]
=
0.0
;
x0
[
nlocal
][
0
]
=
atof
(
values
[
7
]);
x0
[
nlocal
][
1
]
=
atof
(
values
[
8
]);
x0
[
nlocal
][
2
]
=
atof
(
values
[
9
]);
x
[
nlocal
][
0
]
=
coord
[
0
];
x
[
nlocal
][
1
]
=
coord
[
1
];
x
[
nlocal
][
2
]
=
coord
[
2
];
image
[
nlocal
]
=
imagetmp
;
mask
[
nlocal
]
=
1
;
v
[
nlocal
][
0
]
=
0.0
;
v
[
nlocal
][
1
]
=
0.0
;
v
[
nlocal
][
2
]
=
0.0
;
vest
[
nlocal
][
0
]
=
0.0
;
vest
[
nlocal
][
1
]
=
0.0
;
vest
[
nlocal
][
2
]
=
0.0
;
damage
[
nlocal
]
=
0.0
;
eff_plastic_strain
[
nlocal
]
=
0.0
;
eff_plastic_strain_rate
[
nlocal
]
=
0.0
;
for
(
int
k
=
0
;
k
<
NMAT_FULL
;
k
++
)
{
smd_data_9
[
nlocal
][
k
]
=
0.0
;
}
for
(
int
k
=
0
;
k
<
NMAT_SYMM
;
k
++
)
{
tlsph_stress
[
nlocal
][
k
]
=
0.0
;
}
smd_data_9
[
nlocal
][
0
]
=
1.0
;
// xx
smd_data_9
[
nlocal
][
4
]
=
1.0
;
// yy
smd_data_9
[
nlocal
][
8
]
=
1.0
;
// zz
atom
->
nlocal
++
;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int
AtomVecSMD
::
data_atom_hybrid
(
int
nlocal
,
char
**
values
)
{
error
->
one
(
FLERR
,
"hybrid atom style functionality not yet implemented for atom style tlsph"
);
return
-
1
;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void
AtomVecSMD
::
data_vel
(
int
m
,
char
**
values
)
{
v
[
m
][
0
]
=
atof
(
values
[
0
]);
v
[
m
][
1
]
=
atof
(
values
[
1
]);
v
[
m
][
2
]
=
atof
(
values
[
2
]);
vest
[
m
][
0
]
=
atof
(
values
[
0
]);
vest
[
m
][
1
]
=
atof
(
values
[
1
]);
vest
[
m
][
2
]
=
atof
(
values
[
2
]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int
AtomVecSMD
::
data_vel_hybrid
(
int
m
,
char
**
values
)
{
error
->
one
(
FLERR
,
"hybrid atom style functionality not yet implemented for atom style tlsph"
);
return
0
;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void
AtomVecSMD
::
pack_data
(
double
**
buf
)
{
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
buf
[
i
][
0
]
=
ubuf
(
tag
[
i
]).
d
;
buf
[
i
][
1
]
=
ubuf
(
type
[
i
]).
d
;
buf
[
i
][
2
]
=
ubuf
(
molecule
[
i
]).
d
;
buf
[
i
][
3
]
=
vfrac
[
i
];
buf
[
i
][
4
]
=
rmass
[
i
];
buf
[
i
][
5
]
=
radius
[
i
];
buf
[
i
][
6
]
=
contact_radius
[
i
];
buf
[
i
][
7
]
=
x
[
i
][
0
];
buf
[
i
][
8
]
=
x
[
i
][
1
];
buf
[
i
][
9
]
=
x
[
i
][
2
];
buf
[
i
][
10
]
=
ubuf
((
image
[
i
]
&
IMGMASK
)
-
IMGMAX
).
d
;
buf
[
i
][
11
]
=
ubuf
((
image
[
i
]
>>
IMGBITS
&
IMGMASK
)
-
IMGMAX
).
d
;
buf
[
i
][
12
]
=
ubuf
((
image
[
i
]
>>
IMG2BITS
)
-
IMGMAX
).
d
;
}
}
/* ----------------------------------------------------------------------
pack hybrid atom info for data file
------------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_data_hybrid
(
int
i
,
double
*
buf
)
{
error
->
one
(
FLERR
,
"hybrid atom style functionality not yet implemented for atom style tlsph"
);
return
-
1
;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void
AtomVecSMD
::
write_data
(
FILE
*
fp
,
int
n
,
double
**
buf
)
{
for
(
int
i
=
0
;
i
<
n
;
i
++
)
fprintf
(
fp
,
TAGINT_FORMAT
" %d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d
\n
"
,
(
tagint
)
ubuf
(
buf
[
i
][
0
]).
i
,
(
int
)
ubuf
(
buf
[
i
][
1
]).
i
,
(
int
)
ubuf
(
buf
[
i
][
2
]).
i
,
buf
[
i
][
3
],
buf
[
i
][
4
],
buf
[
i
][
5
],
buf
[
i
][
6
],
buf
[
i
][
7
],
buf
[
i
][
8
],
buf
[
i
][
9
],
(
int
)
ubuf
(
buf
[
i
][
7
]).
i
,
(
int
)
ubuf
(
buf
[
i
][
8
]).
i
,
(
int
)
ubuf
(
buf
[
i
][
9
]).
i
);
}
/* ----------------------------------------------------------------------
write hybrid atom info to data file
------------------------------------------------------------------------- */
int
AtomVecSMD
::
write_data_hybrid
(
FILE
*
fp
,
double
*
buf
)
{
error
->
one
(
FLERR
,
"hybrid atom style functionality not yet implemented for atom style tlsph"
);
return
-
1
;
}
/* ----------------------------------------------------------------------
pack velocity info for data file
------------------------------------------------------------------------- */
void
AtomVecSMD
::
pack_vel
(
double
**
buf
)
{
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
buf
[
i
][
0
]
=
ubuf
(
tag
[
i
]).
d
;
buf
[
i
][
1
]
=
v
[
i
][
0
];
buf
[
i
][
2
]
=
v
[
i
][
1
];
buf
[
i
][
3
]
=
v
[
i
][
2
];
}
}
/* ----------------------------------------------------------------------
pack hybrid velocity info for data file
------------------------------------------------------------------------- */
int
AtomVecSMD
::
pack_vel_hybrid
(
int
i
,
double
*
buf
)
{
error
->
one
(
FLERR
,
"hybrid atom style functionality not yet implemented for atom style tlsph"
);
return
0
;
}
/* ----------------------------------------------------------------------
write velocity info to data file
------------------------------------------------------------------------- */
void
AtomVecSMD
::
write_vel
(
FILE
*
fp
,
int
n
,
double
**
buf
)
{
for
(
int
i
=
0
;
i
<
n
;
i
++
)
fprintf
(
fp
,
TAGINT_FORMAT
" %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e
\n
"
,
(
tagint
)
ubuf
(
buf
[
i
][
0
]).
i
,
buf
[
i
][
1
],
buf
[
i
][
2
],
buf
[
i
][
3
],
buf
[
i
][
4
],
buf
[
i
][
5
],
buf
[
i
][
6
]);
}
/* ----------------------------------------------------------------------
write hybrid velocity info to data file
------------------------------------------------------------------------- */
int
AtomVecSMD
::
write_vel_hybrid
(
FILE
*
fp
,
double
*
buf
)
{
error
->
one
(
FLERR
,
"hybrid atom style functionality not yet implemented for atom style tlsph"
);
return
3
;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint
AtomVecSMD
::
memory_usage
()
{
bigint
bytes
=
0
;
if
(
atom
->
memcheck
(
"tag"
))
bytes
+=
memory
->
usage
(
tag
,
nmax
);
if
(
atom
->
memcheck
(
"type"
))
bytes
+=
memory
->
usage
(
type
,
nmax
);
if
(
atom
->
memcheck
(
"molecule"
))
bytes
+=
memory
->
usage
(
molecule
,
nmax
);
if
(
atom
->
memcheck
(
"mask"
))
bytes
+=
memory
->
usage
(
mask
,
nmax
);
if
(
atom
->
memcheck
(
"image"
))
bytes
+=
memory
->
usage
(
image
,
nmax
);
if
(
atom
->
memcheck
(
"x"
))
bytes
+=
memory
->
usage
(
x
,
nmax
,
3
);
if
(
atom
->
memcheck
(
"v"
))
bytes
+=
memory
->
usage
(
v
,
nmax
,
3
);
if
(
atom
->
memcheck
(
"vest"
))
bytes
+=
memory
->
usage
(
vest
,
nmax
,
3
);
if
(
atom
->
memcheck
(
"f"
))
bytes
+=
memory
->
usage
(
f
,
nmax
*
comm
->
nthreads
,
3
);
if
(
atom
->
memcheck
(
"radius"
))
bytes
+=
memory
->
usage
(
radius
,
nmax
);
if
(
atom
->
memcheck
(
"contact_radius"
))
bytes
+=
memory
->
usage
(
contact_radius
,
nmax
);
if
(
atom
->
memcheck
(
"vfrac"
))
bytes
+=
memory
->
usage
(
vfrac
,
nmax
);
if
(
atom
->
memcheck
(
"rmass"
))
bytes
+=
memory
->
usage
(
rmass
,
nmax
);
if
(
atom
->
memcheck
(
"eff_plastic_strain"
))
bytes
+=
memory
->
usage
(
eff_plastic_strain
,
nmax
);
if
(
atom
->
memcheck
(
"eff_plastic_strain_rate"
))
bytes
+=
memory
->
usage
(
eff_plastic_strain_rate
,
nmax
);
if
(
atom
->
memcheck
(
"e"
))
bytes
+=
memory
->
usage
(
e
,
nmax
);
if
(
atom
->
memcheck
(
"de"
))
bytes
+=
memory
->
usage
(
de
,
nmax
);
if
(
atom
->
memcheck
(
"smd_data_9"
))
bytes
+=
memory
->
usage
(
smd_data_9
,
nmax
,
NMAT_FULL
);
if
(
atom
->
memcheck
(
"tlsph_stress"
))
bytes
+=
memory
->
usage
(
tlsph_stress
,
nmax
,
NMAT_SYMM
);
if
(
atom
->
memcheck
(
"damage"
))
bytes
+=
memory
->
usage
(
damage
,
nmax
);
return
bytes
;
}
/* ---------------------------------------------------------------------- */
void
AtomVecSMD
::
force_clear
(
int
n
,
size_t
nbytes
)
{
//printf("clearing force on atom %d", n);
memset
(
&
de
[
n
],
0
,
nbytes
);
memset
(
&
f
[
0
][
0
],
0
,
3
*
nbytes
);
}
Event Timeline
Log In to Comment