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pair_gran_hooke_history.cpp
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rLAMMPS lammps
pair_gran_hooke_history.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 authors: Leo Silbert (SNL), Gary Grest (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_gran_hooke_history.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "fix_pour.h"
#include "fix_deposit.h"
#include "fix_shear_history.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairGranHookeHistory
::
PairGranHookeHistory
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
single_enable
=
1
;
no_virial_fdotr_compute
=
1
;
history
=
1
;
fix_history
=
NULL
;
suffix
=
NULL
;
single_extra
=
4
;
svector
=
new
double
[
4
];
computeflag
=
0
;
neighprev
=
0
;
nmax
=
0
;
mass_rigid
=
NULL
;
// set comm size needed by this Pair if used with fix rigid
comm_forward
=
1
;
}
/* ---------------------------------------------------------------------- */
PairGranHookeHistory
::~
PairGranHookeHistory
()
{
delete
[]
svector
;
if
(
fix_history
)
modify
->
delete_fix
(
"SHEAR_HISTORY"
);
if
(
suffix
)
delete
[]
suffix
;
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
delete
[]
onerad_dynamic
;
delete
[]
onerad_frozen
;
delete
[]
maxrad_dynamic
;
delete
[]
maxrad_frozen
;
}
memory
->
destroy
(
mass_rigid
);
}
/* ---------------------------------------------------------------------- */
void
PairGranHookeHistory
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
fx
,
fy
,
fz
;
double
radi
,
radj
,
radsum
,
rsq
,
r
,
rinv
,
rsqinv
;
double
vr1
,
vr2
,
vr3
,
vnnr
,
vn1
,
vn2
,
vn3
,
vt1
,
vt2
,
vt3
;
double
wr1
,
wr2
,
wr3
;
double
vtr1
,
vtr2
,
vtr3
,
vrel
;
double
mi
,
mj
,
meff
,
damp
,
ccel
,
tor1
,
tor2
,
tor3
;
double
fn
,
fs
,
fs1
,
fs2
,
fs3
;
double
shrmag
,
rsht
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
int
*
touch
,
**
firsttouch
;
double
*
shear
,
*
allshear
,
**
firstshear
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
computeflag
=
1
;
int
shearupdate
=
1
;
if
(
update
->
setupflag
)
shearupdate
=
0
;
// update rigid body info for owned & ghost atoms if using FixRigid masses
// body[i] = which body atom I is in, -1 if none
// mass_body = mass of each rigid body
if
(
fix_rigid
&&
neighbor
->
ago
==
0
)
{
int
tmp
;
int
*
body
=
(
int
*
)
fix_rigid
->
extract
(
"body"
,
tmp
);
double
*
mass_body
=
(
double
*
)
fix_rigid
->
extract
(
"masstotal"
,
tmp
);
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy
(
mass_rigid
);
nmax
=
atom
->
nmax
;
memory
->
create
(
mass_rigid
,
nmax
,
"pair:mass_rigid"
);
}
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
body
[
i
]
>=
0
)
mass_rigid
[
i
]
=
mass_body
[
body
[
i
]];
else
mass_rigid
[
i
]
=
0.0
;
comm
->
forward_comm_pair
(
this
);
}
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
**
omega
=
atom
->
omega
;
double
**
torque
=
atom
->
torque
;
double
*
radius
=
atom
->
radius
;
double
*
rmass
=
atom
->
rmass
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
firsttouch
=
listgranhistory
->
firstneigh
;
firstshear
=
listgranhistory
->
firstdouble
;
// loop over neighbors of my atoms
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
radi
=
radius
[
i
];
touch
=
firsttouch
[
i
];
allshear
=
firstshear
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
radj
=
radius
[
j
];
radsum
=
radi
+
radj
;
if
(
rsq
>=
radsum
*
radsum
)
{
// unset non-touching neighbors
touch
[
jj
]
=
0
;
shear
=
&
allshear
[
3
*
jj
];
shear
[
0
]
=
0.0
;
shear
[
1
]
=
0.0
;
shear
[
2
]
=
0.0
;
}
else
{
r
=
sqrt
(
rsq
);
rinv
=
1.0
/
r
;
rsqinv
=
1.0
/
rsq
;
// relative translational velocity
vr1
=
v
[
i
][
0
]
-
v
[
j
][
0
];
vr2
=
v
[
i
][
1
]
-
v
[
j
][
1
];
vr3
=
v
[
i
][
2
]
-
v
[
j
][
2
];
// normal component
vnnr
=
vr1
*
delx
+
vr2
*
dely
+
vr3
*
delz
;
vn1
=
delx
*
vnnr
*
rsqinv
;
vn2
=
dely
*
vnnr
*
rsqinv
;
vn3
=
delz
*
vnnr
*
rsqinv
;
// tangential component
vt1
=
vr1
-
vn1
;
vt2
=
vr2
-
vn2
;
vt3
=
vr3
-
vn3
;
// relative rotational velocity
wr1
=
(
radi
*
omega
[
i
][
0
]
+
radj
*
omega
[
j
][
0
])
*
rinv
;
wr2
=
(
radi
*
omega
[
i
][
1
]
+
radj
*
omega
[
j
][
1
])
*
rinv
;
wr3
=
(
radi
*
omega
[
i
][
2
]
+
radj
*
omega
[
j
][
2
])
*
rinv
;
// meff = effective mass of pair of particles
// if I or J part of rigid body, use body mass
// if I or J is frozen, meff is other particle
if
(
rmass
)
{
mi
=
rmass
[
i
];
mj
=
rmass
[
j
];
}
else
{
mi
=
mass
[
type
[
i
]];
mj
=
mass
[
type
[
j
]];
}
if
(
fix_rigid
)
{
if
(
mass_rigid
[
i
]
>
0.0
)
mi
=
mass_rigid
[
i
];
if
(
mass_rigid
[
j
]
>
0.0
)
mj
=
mass_rigid
[
j
];
}
meff
=
mi
*
mj
/
(
mi
+
mj
);
if
(
mask
[
i
]
&
freeze_group_bit
)
meff
=
mj
;
if
(
mask
[
j
]
&
freeze_group_bit
)
meff
=
mi
;
// normal forces = Hookian contact + normal velocity damping
damp
=
meff
*
gamman
*
vnnr
*
rsqinv
;
ccel
=
kn
*
(
radsum
-
r
)
*
rinv
-
damp
;
// relative velocities
vtr1
=
vt1
-
(
delz
*
wr2
-
dely
*
wr3
);
vtr2
=
vt2
-
(
delx
*
wr3
-
delz
*
wr1
);
vtr3
=
vt3
-
(
dely
*
wr1
-
delx
*
wr2
);
vrel
=
vtr1
*
vtr1
+
vtr2
*
vtr2
+
vtr3
*
vtr3
;
vrel
=
sqrt
(
vrel
);
// shear history effects
touch
[
jj
]
=
1
;
shear
=
&
allshear
[
3
*
jj
];
if
(
shearupdate
)
{
shear
[
0
]
+=
vtr1
*
dt
;
shear
[
1
]
+=
vtr2
*
dt
;
shear
[
2
]
+=
vtr3
*
dt
;
}
shrmag
=
sqrt
(
shear
[
0
]
*
shear
[
0
]
+
shear
[
1
]
*
shear
[
1
]
+
shear
[
2
]
*
shear
[
2
]);
// rotate shear displacements
rsht
=
shear
[
0
]
*
delx
+
shear
[
1
]
*
dely
+
shear
[
2
]
*
delz
;
rsht
*=
rsqinv
;
if
(
shearupdate
)
{
shear
[
0
]
-=
rsht
*
delx
;
shear
[
1
]
-=
rsht
*
dely
;
shear
[
2
]
-=
rsht
*
delz
;
}
// tangential forces = shear + tangential velocity damping
fs1
=
-
(
kt
*
shear
[
0
]
+
meff
*
gammat
*
vtr1
);
fs2
=
-
(
kt
*
shear
[
1
]
+
meff
*
gammat
*
vtr2
);
fs3
=
-
(
kt
*
shear
[
2
]
+
meff
*
gammat
*
vtr3
);
// rescale frictional displacements and forces if needed
fs
=
sqrt
(
fs1
*
fs1
+
fs2
*
fs2
+
fs3
*
fs3
);
fn
=
xmu
*
fabs
(
ccel
*
r
);
if
(
fs
>
fn
)
{
if
(
shrmag
!=
0.0
)
{
shear
[
0
]
=
(
fn
/
fs
)
*
(
shear
[
0
]
+
meff
*
gammat
*
vtr1
/
kt
)
-
meff
*
gammat
*
vtr1
/
kt
;
shear
[
1
]
=
(
fn
/
fs
)
*
(
shear
[
1
]
+
meff
*
gammat
*
vtr2
/
kt
)
-
meff
*
gammat
*
vtr2
/
kt
;
shear
[
2
]
=
(
fn
/
fs
)
*
(
shear
[
2
]
+
meff
*
gammat
*
vtr3
/
kt
)
-
meff
*
gammat
*
vtr3
/
kt
;
fs1
*=
fn
/
fs
;
fs2
*=
fn
/
fs
;
fs3
*=
fn
/
fs
;
}
else
fs1
=
fs2
=
fs3
=
0.0
;
}
// forces & torques
fx
=
delx
*
ccel
+
fs1
;
fy
=
dely
*
ccel
+
fs2
;
fz
=
delz
*
ccel
+
fs3
;
f
[
i
][
0
]
+=
fx
;
f
[
i
][
1
]
+=
fy
;
f
[
i
][
2
]
+=
fz
;
tor1
=
rinv
*
(
dely
*
fs3
-
delz
*
fs2
);
tor2
=
rinv
*
(
delz
*
fs1
-
delx
*
fs3
);
tor3
=
rinv
*
(
delx
*
fs2
-
dely
*
fs1
);
torque
[
i
][
0
]
-=
radi
*
tor1
;
torque
[
i
][
1
]
-=
radi
*
tor2
;
torque
[
i
][
2
]
-=
radi
*
tor3
;
if
(
j
<
nlocal
)
{
f
[
j
][
0
]
-=
fx
;
f
[
j
][
1
]
-=
fy
;
f
[
j
][
2
]
-=
fz
;
torque
[
j
][
0
]
-=
radj
*
tor1
;
torque
[
j
][
1
]
-=
radj
*
tor2
;
torque
[
j
][
2
]
-=
radj
*
tor3
;
}
if
(
evflag
)
ev_tally_xyz
(
i
,
j
,
nlocal
,
0
,
0.0
,
0.0
,
fx
,
fy
,
fz
,
delx
,
dely
,
delz
);
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairGranHookeHistory
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
memory
->
create
(
setflag
,
n
+
1
,
n
+
1
,
"pair:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
memory
->
create
(
cutsq
,
n
+
1
,
n
+
1
,
"pair:cutsq"
);
onerad_dynamic
=
new
double
[
n
+
1
];
onerad_frozen
=
new
double
[
n
+
1
];
maxrad_dynamic
=
new
double
[
n
+
1
];
maxrad_frozen
=
new
double
[
n
+
1
];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairGranHookeHistory
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
6
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
kn
=
force
->
numeric
(
FLERR
,
arg
[
0
]);
if
(
strcmp
(
arg
[
1
],
"NULL"
)
==
0
)
kt
=
kn
*
2.0
/
7.0
;
else
kt
=
force
->
numeric
(
FLERR
,
arg
[
1
]);
gamman
=
force
->
numeric
(
FLERR
,
arg
[
2
]);
if
(
strcmp
(
arg
[
3
],
"NULL"
)
==
0
)
gammat
=
0.5
*
gamman
;
else
gammat
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
xmu
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
dampflag
=
force
->
inumeric
(
FLERR
,
arg
[
5
]);
if
(
dampflag
==
0
)
gammat
=
0.0
;
if
(
kn
<
0.0
||
kt
<
0.0
||
gamman
<
0.0
||
gammat
<
0.0
||
xmu
<
0.0
||
xmu
>
10000.0
||
dampflag
<
0
||
dampflag
>
1
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairGranHookeHistory
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
>
2
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
,
jlo
,
jhi
;
force
->
bounds
(
arg
[
0
],
atom
->
ntypes
,
ilo
,
ihi
);
force
->
bounds
(
arg
[
1
],
atom
->
ntypes
,
jlo
,
jhi
);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
for
(
int
j
=
MAX
(
jlo
,
i
);
j
<=
jhi
;
j
++
)
{
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairGranHookeHistory
::
init_style
()
{
int
i
;
// error and warning checks
if
(
!
atom
->
sphere_flag
)
error
->
all
(
FLERR
,
"Pair granular requires atom style sphere"
);
if
(
comm
->
ghost_velocity
==
0
)
error
->
all
(
FLERR
,
"Pair granular requires ghost atoms store velocity"
);
// need a granular neigh list and optionally a granular history neigh list
int
irequest
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
gran
=
1
;
if
(
history
)
{
irequest
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest
]
->
id
=
1
;
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
granhistory
=
1
;
neighbor
->
requests
[
irequest
]
->
dnum
=
3
;
}
dt
=
update
->
dt
;
// if shear history is stored:
// check if newton flag is valid
// if first init, create Fix needed for storing shear history
if
(
history
&&
force
->
newton_pair
==
1
)
error
->
all
(
FLERR
,
"Pair granular with shear history requires newton pair off"
);
if
(
history
&&
fix_history
==
NULL
)
{
char
**
fixarg
=
new
char
*
[
3
];
fixarg
[
0
]
=
(
char
*
)
"SHEAR_HISTORY"
;
fixarg
[
1
]
=
(
char
*
)
"all"
;
fixarg
[
2
]
=
(
char
*
)
"SHEAR_HISTORY"
;
modify
->
add_fix
(
3
,
fixarg
,
suffix
);
delete
[]
fixarg
;
fix_history
=
(
FixShearHistory
*
)
modify
->
fix
[
modify
->
nfix
-
1
];
fix_history
->
pair
=
this
;
}
// check for FixFreeze and set freeze_group_bit
for
(
i
=
0
;
i
<
modify
->
nfix
;
i
++
)
if
(
strcmp
(
modify
->
fix
[
i
]
->
style
,
"freeze"
)
==
0
)
break
;
if
(
i
<
modify
->
nfix
)
freeze_group_bit
=
modify
->
fix
[
i
]
->
groupbit
;
else
freeze_group_bit
=
0
;
// check for FixPour and set pour_type and pour_maxrad
int
pour_type
=
0
;
double
pour_maxrad
=
0.0
;
for
(
i
=
0
;
i
<
modify
->
nfix
;
i
++
)
if
(
strcmp
(
modify
->
fix
[
i
]
->
style
,
"pour"
)
==
0
)
break
;
if
(
i
<
modify
->
nfix
)
{
pour_type
=
((
FixPour
*
)
modify
->
fix
[
i
])
->
ntype
;
pour_maxrad
=
((
FixPour
*
)
modify
->
fix
[
i
])
->
radius_max
;
}
// check for FixDeposit and set deposit_type and deposit_maxrad
int
deposit_type
=
0
;
double
deposit_maxrad
=
0.0
;
for
(
i
=
0
;
i
<
modify
->
nfix
;
i
++
)
if
(
strcmp
(
modify
->
fix
[
i
]
->
style
,
"deposit"
)
==
0
)
break
;
if
(
i
<
modify
->
nfix
)
{
deposit_type
=
((
FixDeposit
*
)
modify
->
fix
[
i
])
->
ntype
;
deposit_maxrad
=
0.5
;
}
// check for FixRigid
fix_rigid
=
NULL
;
for
(
i
=
0
;
i
<
modify
->
nfix
;
i
++
)
if
(
modify
->
fix
[
i
]
->
rigid_flag
)
break
;
if
(
i
<
modify
->
nfix
)
fix_rigid
=
modify
->
fix
[
i
];
// set maxrad_dynamic and maxrad_frozen for each type
// include future FixPour and FixDeposit particles as dynamic
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
onerad_dynamic
[
i
]
=
onerad_frozen
[
i
]
=
0.0
;
if
(
pour_type
)
onerad_dynamic
[
pour_type
]
=
pour_maxrad
;
if
(
deposit_type
)
onerad_dynamic
[
deposit_type
]
=
MAX
(
onerad_dynamic
[
deposit_type
],
deposit_maxrad
);
double
*
radius
=
atom
->
radius
;
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
freeze_group_bit
)
onerad_frozen
[
type
[
i
]]
=
MAX
(
onerad_frozen
[
type
[
i
]],
radius
[
i
]);
else
onerad_dynamic
[
type
[
i
]]
=
MAX
(
onerad_dynamic
[
type
[
i
]],
radius
[
i
]);
MPI_Allreduce
(
&
onerad_dynamic
[
1
],
&
maxrad_dynamic
[
1
],
atom
->
ntypes
,
MPI_DOUBLE
,
MPI_MAX
,
world
);
MPI_Allreduce
(
&
onerad_frozen
[
1
],
&
maxrad_frozen
[
1
],
atom
->
ntypes
,
MPI_DOUBLE
,
MPI_MAX
,
world
);
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
optional granular history list
------------------------------------------------------------------------- */
void
PairGranHookeHistory
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
if
(
id
==
0
)
list
=
ptr
;
else
if
(
id
==
1
)
listgranhistory
=
ptr
;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairGranHookeHistory
::
init_one
(
int
i
,
int
j
)
{
if
(
!
allocated
)
allocate
();
// cutoff = sum of max I,J radii for
// dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
double
cutoff
=
maxrad_dynamic
[
i
]
+
maxrad_dynamic
[
j
];
cutoff
=
MAX
(
cutoff
,
maxrad_frozen
[
i
]
+
maxrad_dynamic
[
j
]);
cutoff
=
MAX
(
cutoff
,
maxrad_dynamic
[
i
]
+
maxrad_frozen
[
j
]);
return
cutoff
;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairGranHookeHistory
::
write_restart
(
FILE
*
fp
)
{
write_restart_settings
(
fp
);
int
i
,
j
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
fwrite
(
&
setflag
[
i
][
j
],
sizeof
(
int
),
1
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairGranHookeHistory
::
read_restart
(
FILE
*
fp
)
{
read_restart_settings
(
fp
);
allocate
();
int
i
,
j
;
int
me
=
comm
->
me
;
for
(
i
=
1
;
i
<=
atom
->
ntypes
;
i
++
)
for
(
j
=
i
;
j
<=
atom
->
ntypes
;
j
++
)
{
if
(
me
==
0
)
fread
(
&
setflag
[
i
][
j
],
sizeof
(
int
),
1
,
fp
);
MPI_Bcast
(
&
setflag
[
i
][
j
],
1
,
MPI_INT
,
0
,
world
);
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void
PairGranHookeHistory
::
write_restart_settings
(
FILE
*
fp
)
{
fwrite
(
&
kn
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
kt
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
gamman
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
gammat
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
xmu
,
sizeof
(
double
),
1
,
fp
);
fwrite
(
&
dampflag
,
sizeof
(
int
),
1
,
fp
);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void
PairGranHookeHistory
::
read_restart_settings
(
FILE
*
fp
)
{
if
(
comm
->
me
==
0
)
{
fread
(
&
kn
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
kt
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
gamman
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
gammat
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
xmu
,
sizeof
(
double
),
1
,
fp
);
fread
(
&
dampflag
,
sizeof
(
int
),
1
,
fp
);
}
MPI_Bcast
(
&
kn
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
kt
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gamman
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
gammat
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
xmu
,
1
,
MPI_DOUBLE
,
0
,
world
);
MPI_Bcast
(
&
dampflag
,
1
,
MPI_INT
,
0
,
world
);
}
/* ---------------------------------------------------------------------- */
void
PairGranHookeHistory
::
reset_dt
()
{
dt
=
update
->
dt
;
}
/* ---------------------------------------------------------------------- */
double
PairGranHookeHistory
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
double
radi
,
radj
,
radsum
;
double
r
,
rinv
,
rsqinv
,
delx
,
dely
,
delz
;
double
vr1
,
vr2
,
vr3
,
vnnr
,
vn1
,
vn2
,
vn3
,
vt1
,
vt2
,
vt3
,
wr1
,
wr2
,
wr3
;
double
mi
,
mj
,
meff
,
damp
,
ccel
,
polyhertz
;
double
vtr1
,
vtr2
,
vtr3
,
vrel
,
shrmag
,
rsht
;
double
fs1
,
fs2
,
fs3
,
fs
,
fn
;
double
*
radius
=
atom
->
radius
;
radi
=
radius
[
i
];
radj
=
radius
[
j
];
radsum
=
radi
+
radj
;
if
(
rsq
>=
radsum
*
radsum
)
{
fforce
=
0.0
;
svector
[
0
]
=
svector
[
1
]
=
svector
[
2
]
=
svector
[
3
]
=
0.0
;
return
0.0
;
}
r
=
sqrt
(
rsq
);
rinv
=
1.0
/
r
;
rsqinv
=
1.0
/
rsq
;
// relative translational velocity
double
**
v
=
atom
->
v
;
vr1
=
v
[
i
][
0
]
-
v
[
j
][
0
];
vr2
=
v
[
i
][
1
]
-
v
[
j
][
1
];
vr3
=
v
[
i
][
2
]
-
v
[
j
][
2
];
// normal component
double
**
x
=
atom
->
x
;
delx
=
x
[
i
][
0
]
-
x
[
j
][
0
];
dely
=
x
[
i
][
1
]
-
x
[
j
][
1
];
delz
=
x
[
i
][
2
]
-
x
[
j
][
2
];
vnnr
=
vr1
*
delx
+
vr2
*
dely
+
vr3
*
delz
;
vn1
=
delx
*
vnnr
*
rsqinv
;
vn2
=
dely
*
vnnr
*
rsqinv
;
vn3
=
delz
*
vnnr
*
rsqinv
;
// tangential component
vt1
=
vr1
-
vn1
;
vt2
=
vr2
-
vn2
;
vt3
=
vr3
-
vn3
;
// relative rotational velocity
double
**
omega
=
atom
->
omega
;
wr1
=
(
radi
*
omega
[
i
][
0
]
+
radj
*
omega
[
j
][
0
])
*
rinv
;
wr2
=
(
radi
*
omega
[
i
][
1
]
+
radj
*
omega
[
j
][
1
])
*
rinv
;
wr3
=
(
radi
*
omega
[
i
][
2
]
+
radj
*
omega
[
j
][
2
])
*
rinv
;
// meff = effective mass of pair of particles
// if I or J part of rigid body, use body mass
// if I or J is frozen, meff is other particle
double
*
rmass
=
atom
->
rmass
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
if
(
rmass
)
{
mi
=
rmass
[
i
];
mj
=
rmass
[
j
];
}
else
{
mi
=
mass
[
type
[
i
]];
mj
=
mass
[
type
[
j
]];
}
if
(
fix_rigid
)
{
// NOTE: insure mass_rigid is current for owned+ghost atoms?
if
(
mass_rigid
[
i
]
>
0.0
)
mi
=
mass_rigid
[
i
];
if
(
mass_rigid
[
j
]
>
0.0
)
mj
=
mass_rigid
[
j
];
}
meff
=
mi
*
mj
/
(
mi
+
mj
);
if
(
mask
[
i
]
&
freeze_group_bit
)
meff
=
mj
;
if
(
mask
[
j
]
&
freeze_group_bit
)
meff
=
mi
;
// normal forces = Hookian contact + normal velocity damping
damp
=
meff
*
gamman
*
vnnr
*
rsqinv
;
ccel
=
kn
*
(
radsum
-
r
)
*
rinv
-
damp
;
// relative velocities
vtr1
=
vt1
-
(
delz
*
wr2
-
dely
*
wr3
);
vtr2
=
vt2
-
(
delx
*
wr3
-
delz
*
wr1
);
vtr3
=
vt3
-
(
dely
*
wr1
-
delx
*
wr2
);
vrel
=
vtr1
*
vtr1
+
vtr2
*
vtr2
+
vtr3
*
vtr3
;
vrel
=
sqrt
(
vrel
);
// shear history effects
// neighprev = index of found neigh on previous call
// search entire jnum list of neighbors of I for neighbor J
// start from neighprev, since will typically be next neighbor
// reset neighprev to 0 as necessary
int
*
jlist
=
list
->
firstneigh
[
i
];
int
jnum
=
list
->
numneigh
[
i
];
int
*
touch
=
list
->
listgranhistory
->
firstneigh
[
i
];
double
*
allshear
=
list
->
listgranhistory
->
firstdouble
[
i
];
for
(
int
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
neighprev
++
;
if
(
neighprev
>=
jnum
)
neighprev
=
0
;
if
(
touch
[
neighprev
]
==
j
)
break
;
}
double
*
shear
=
&
allshear
[
3
*
neighprev
];
shrmag
=
sqrt
(
shear
[
0
]
*
shear
[
0
]
+
shear
[
1
]
*
shear
[
1
]
+
shear
[
2
]
*
shear
[
2
]);
// rotate shear displacements
rsht
=
shear
[
0
]
*
delx
+
shear
[
1
]
*
dely
+
shear
[
2
]
*
delz
;
rsht
*=
rsqinv
;
// tangential forces = shear + tangential velocity damping
fs1
=
-
(
kt
*
shear
[
0
]
+
meff
*
gammat
*
vtr1
);
fs2
=
-
(
kt
*
shear
[
1
]
+
meff
*
gammat
*
vtr2
);
fs3
=
-
(
kt
*
shear
[
2
]
+
meff
*
gammat
*
vtr3
);
// rescale frictional displacements and forces if needed
fs
=
sqrt
(
fs1
*
fs1
+
fs2
*
fs2
+
fs3
*
fs3
);
fn
=
xmu
*
fabs
(
ccel
*
r
);
if
(
fs
>
fn
)
{
if
(
shrmag
!=
0.0
)
{
fs1
*=
fn
/
fs
;
fs2
*=
fn
/
fs
;
fs3
*=
fn
/
fs
;
fs
*=
fn
/
fs
;
}
else
fs1
=
fs2
=
fs3
=
fs
=
0.0
;
}
// set all forces and return no energy
fforce
=
ccel
;
svector
[
0
]
=
fs1
;
svector
[
1
]
=
fs2
;
svector
[
2
]
=
fs3
;
svector
[
3
]
=
fs
;
return
0.0
;
}
/* ---------------------------------------------------------------------- */
int
PairGranHookeHistory
::
pack_comm
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
mass_rigid
[
j
];
}
return
1
;
}
/* ---------------------------------------------------------------------- */
void
PairGranHookeHistory
::
unpack_comm
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
mass_rigid
[
i
]
=
buf
[
m
++
];
}
/* ---------------------------------------------------------------------- */
void
*
PairGranHookeHistory
::
extract
(
const
char
*
str
,
int
&
dim
)
{
dim
=
0
;
if
(
strcmp
(
str
,
"computeflag"
)
==
0
)
return
(
void
*
)
&
computeflag
;
return
NULL
;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double
PairGranHookeHistory
::
memory_usage
()
{
double
bytes
=
nmax
*
sizeof
(
double
);
return
bytes
;
}
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