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Mon, Sep 2, 06:04
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rLAMMPS lammps
fix_msst.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: Laurence Fried (LLNL), Evan Reed (LLNL, Stanford)
implementation of the Multi-Scale Shock Method
See Reed, Fried, Joannopoulos, Phys Rev Lett, 90, 235503 (2003)
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "fix_msst.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "output.h"
#include "modify.h"
#include "compute.h"
#include "kspace.h"
#include "update.h"
#include "respa.h"
#include "domain.h"
#include "error.h"
#include "thermo.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
FixMSST
::
FixMSST
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
4
)
error
->
all
(
"Illegal fix msst command"
);
restart_global
=
1
;
box_change
=
1
;
time_integrate
=
1
;
scalar_flag
=
1
;
vector_flag
=
1
;
size_vector
=
4
;
global_freq
=
1
;
extscalar
=
1
;
extvector
=
0
;
// set defaults
velocity
=
0.0
;
dilation
[
0
]
=
dilation
[
1
]
=
dilation
[
2
]
=
1.0
;
p0
=
0.0
;
v0
=
1.0
;
e0
=
0.0
;
qmass
=
1.0e1
;
mu
=
0.0
;
direction
=
2
;
p0_set
=
0
;
v0_set
=
0
;
e0_set
=
0
;
tscale
=
0.01
;
if
(
strcmp
(
arg
[
3
],
"x"
)
==
0
)
direction
=
0
;
else
if
(
strcmp
(
arg
[
3
],
"y"
)
==
0
)
direction
=
1
;
else
if
(
strcmp
(
arg
[
3
],
"z"
)
==
0
)
direction
=
2
;
else
{
error
->
all
(
"Illegal fix msst command"
);
}
velocity
=
atof
(
arg
[
4
]);
if
(
velocity
<
0
)
error
->
all
(
"Illegal fix msst command"
);
for
(
int
iarg
=
5
;
iarg
<
narg
;
iarg
++
)
{
if
(
strcmp
(
arg
[
iarg
],
"q"
)
==
0
)
{
qmass
=
atof
(
arg
[
iarg
+
1
]);
iarg
++
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"mu"
)
==
0
)
{
mu
=
atof
(
arg
[
iarg
+
1
]);
iarg
++
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"p0"
)
==
0
)
{
p0
=
atof
(
arg
[
iarg
+
1
]);
iarg
++
;
p0_set
=
1
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"v0"
)
==
0
)
{
v0
=
atof
(
arg
[
iarg
+
1
]);
v0_set
=
1
;
iarg
++
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"e0"
)
==
0
)
{
e0
=
atof
(
arg
[
iarg
+
1
]);
e0_set
=
1
;
iarg
++
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"tscale"
)
==
0
)
{
tscale
=
atof
(
arg
[
iarg
+
1
]);
if
(
tscale
<
0.0
||
tscale
>
1.0
)
error
->
all
(
"Fix msst tscale must satisfy 0 <= tscale < 1"
);
iarg
++
;
}
else
error
->
all
(
"Illegal fix msst command"
);
}
if
(
comm
->
me
==
0
)
{
if
(
screen
)
{
fprintf
(
screen
,
"MSST parameters:
\n
"
);
if
(
direction
==
0
)
fprintf
(
screen
,
" Shock in x direction
\n
"
);
else
if
(
direction
==
1
)
fprintf
(
screen
,
" Shock in y direction
\n
"
);
else
if
(
direction
==
2
)
fprintf
(
screen
,
" Shock in z direction
\n
"
);
fprintf
(
screen
,
" Cell mass-like parameter qmass "
"(units of mass^2/length^4) = %12.5e
\n
"
,
qmass
);
fprintf
(
screen
,
" Shock velocity = %12.5e
\n
"
,
velocity
);
fprintf
(
screen
,
" Artificial viscosity "
"(units of mass/length/time) = %12.5e
\n
"
,
mu
);
if
(
p0_set
)
fprintf
(
screen
,
" Initial pressure specified to be %12.5e
\n
"
,
p0
);
else
fprintf
(
screen
,
" Initial pressure calculated on first step
\n
"
);
if
(
v0_set
)
fprintf
(
screen
,
" Initial volume specified to be %12.5e
\n
"
,
v0
);
else
fprintf
(
screen
,
" Initial volume calculated on first step
\n
"
);
if
(
e0_set
)
fprintf
(
screen
,
" Initial energy specified to be %12.5e
\n
"
,
e0
);
else
fprintf
(
screen
,
" Initial energy calculated on first step
\n
"
);
}
if
(
logfile
)
{
fprintf
(
logfile
,
"MSST parameters:
\n
"
);
if
(
direction
==
0
)
fprintf
(
logfile
,
" Shock in x direction
\n
"
);
else
if
(
direction
==
1
)
fprintf
(
logfile
,
" Shock in y direction
\n
"
);
else
if
(
direction
==
2
)
fprintf
(
logfile
,
" Shock in z direction
\n
"
);
fprintf
(
logfile
,
" Cell mass-like parameter qmass "
"(units of mass^2/length^4) = %12.5e
\n
"
,
qmass
);
fprintf
(
logfile
,
" Shock velocity = %12.5e
\n
"
,
velocity
);
fprintf
(
logfile
,
" Artificial viscosity "
"(units of mass/length/time) = %12.5e
\n
"
,
mu
);
if
(
p0_set
)
fprintf
(
logfile
,
" Initial pressure specified to be %12.5e
\n
"
,
p0
);
else
fprintf
(
logfile
,
" Initial pressure calculated on first step
\n
"
);
if
(
v0_set
)
fprintf
(
logfile
,
" Initial volume specified to be %12.5e
\n
"
,
v0
);
else
fprintf
(
logfile
,
" Initial volume calculated on first step
\n
"
);
if
(
e0_set
)
fprintf
(
logfile
,
" Initial energy specified to be %12.5e
\n
"
,
e0
);
else
fprintf
(
logfile
,
" Initial energy calculated on first step
\n
"
);
}
}
// check for periodicity in controlled dimensions
if
(
domain
->
nonperiodic
)
error
->
all
(
"Fix msst requires a periodic box"
);
// create a new compute temp style
// id = fix-ID + temp
// compute group = all since pressure is always global (group all)
// and thus its KE/temperature contribution should use group all
int
n
=
strlen
(
id
)
+
6
;
id_temp
=
new
char
[
n
];
strcpy
(
id_temp
,
id
);
strcat
(
id_temp
,
"_temp"
);
char
**
newarg
=
new
char
*
[
3
];
newarg
[
0
]
=
id_temp
;
newarg
[
1
]
=
"all"
;
newarg
[
2
]
=
"temp"
;
modify
->
add_compute
(
3
,
newarg
);
delete
[]
newarg
;
tflag
=
1
;
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
n
=
strlen
(
id
)
+
7
;
id_press
=
new
char
[
n
];
strcpy
(
id_press
,
id
);
strcat
(
id_press
,
"_press"
);
newarg
=
new
char
*
[
4
];
newarg
[
0
]
=
id_press
;
newarg
[
1
]
=
"all"
;
newarg
[
2
]
=
"pressure"
;
newarg
[
3
]
=
id_temp
;
modify
->
add_compute
(
4
,
newarg
);
delete
[]
newarg
;
pflag
=
1
;
// create a new compute potential energy compute
n
=
strlen
(
id
)
+
3
;
id_pe
=
new
char
[
n
];
strcpy
(
id_pe
,
id
);
strcat
(
id_pe
,
"_pe"
);
newarg
=
new
char
*
[
3
];
newarg
[
0
]
=
id_pe
;
newarg
[
1
]
=
(
char
*
)
"all"
;
newarg
[
2
]
=
(
char
*
)
"pe"
;
modify
->
add_compute
(
3
,
newarg
);
delete
[]
newarg
;
peflag
=
1
;
// initialize the time derivative of the volume.
omega
[
0
]
=
omega
[
1
]
=
omega
[
2
]
=
0.0
;
nrigid
=
0
;
rfix
=
NULL
;
old_velocity
=
new
double
*
[
atom
->
nlocal
];
for
(
int
j
=
0
;
j
<
atom
->
nlocal
;
j
++
)
{
old_velocity
[
j
]
=
new
double
[
3
];
}
atoms_allocated
=
atom
->
nlocal
;
}
/* ---------------------------------------------------------------------- */
FixMSST
::~
FixMSST
()
{
delete
[]
rfix
;
// delete temperature and pressure if fix created them
if
(
tflag
)
modify
->
delete_compute
(
id_temp
);
if
(
pflag
)
modify
->
delete_compute
(
id_press
);
if
(
peflag
)
modify
->
delete_compute
(
id_pe
);
delete
[]
id_temp
;
delete
[]
id_press
;
delete
[]
id_pe
;
for
(
int
j
=
0
;
j
<
atoms_allocated
;
j
++
)
{
delete
[]
old_velocity
[
j
];
}
delete
[]
old_velocity
;
}
/* ---------------------------------------------------------------------- */
int
FixMSST
::
setmask
()
{
int
mask
=
0
;
mask
|=
INITIAL_INTEGRATE
;
mask
|=
FINAL_INTEGRATE
;
mask
|=
THERMO_ENERGY
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixMSST
::
init
()
{
if
(
atom
->
mass
==
NULL
)
error
->
all
(
"Cannot use fix msst without per-type mass defined"
);
// set compute ptrs
int
itemp
=
modify
->
find_compute
(
id_temp
);
int
ipress
=
modify
->
find_compute
(
id_press
);
int
ipe
=
modify
->
find_compute
(
id_pe
);
if
(
itemp
<
0
||
ipress
<
0
||
ipe
<
0
)
error
->
all
(
"Could not find fix msst compute ID"
);
if
(
modify
->
compute
[
itemp
]
->
tempflag
==
0
)
error
->
all
(
"Fix msst compute ID does not compute temperature"
);
if
(
modify
->
compute
[
ipress
]
->
pressflag
==
0
)
error
->
all
(
"Fix msst compute ID does not compute pressure"
);
if
(
modify
->
compute
[
ipe
]
->
peflag
==
0
)
error
->
all
(
"Fix msst compute ID does not compute potential energy"
);
temperature
=
modify
->
compute
[
itemp
];
pressure
=
modify
->
compute
[
ipress
];
pe
=
modify
->
compute
[
ipe
];
dtv
=
update
->
dt
;
dtf
=
0.5
*
update
->
dt
*
force
->
ftm2v
;
dthalf
=
0.5
*
update
->
dt
;
boltz
=
force
->
boltz
;
nktv2p
=
force
->
nktv2p
;
mvv2e
=
force
->
mvv2e
;
double
mass
=
0.0
;
for
(
int
i
=
0
;
i
<
atom
->
nlocal
;
i
++
)
mass
+=
atom
->
mass
[
atom
->
type
[
i
]];
MPI_Allreduce
(
&
mass
,
&
total_mass
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
total_mass
=
total_mass
;
if
(
force
->
kspace
)
kspace_flag
=
1
;
else
kspace_flag
=
0
;
// detect if any fix rigid exist so rigid bodies move when box is dilated
// 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
;
}
}
/* ----------------------------------------------------------------------
compute T,P before integrator starts
------------------------------------------------------------------------- */
void
FixMSST
::
setup
(
int
vflag
)
{
lagrangian_position
=
0.0
;
temperature
->
compute_vector
();
pressure
->
compute_vector
();
couple
();
velocity_sum
=
compute_vsum
();
if
(
v0_set
==
0
)
{
v0
=
compute_vol
();
v0_set
=
1
;
if
(
comm
->
me
==
0
)
{
if
(
screen
)
fprintf
(
screen
,
"Fix MSST v0 = %12.5e
\n
"
,
v0
);
if
(
logfile
)
fprintf
(
logfile
,
"Fix MSST v0 = %12.5e
\n
"
,
v0
);
}
}
if
(
p0_set
==
0
)
{
p0
=
p_current
[
direction
];
p0_set
=
1
;
if
(
comm
->
me
==
0
)
{
if
(
screen
)
fprintf
(
screen
,
"Fix MSST p0 = %12.5e
\n
"
,
p0
);
if
(
logfile
)
fprintf
(
logfile
,
"Fix MSST p0 = %12.5e
\n
"
,
p0
);
}
}
if
(
e0_set
==
0
)
{
e0
=
compute_etotal
();
e0_set
=
1
;
if
(
comm
->
me
==
0
)
{
if
(
screen
)
fprintf
(
screen
,
"Fix MSST e0 = to be %12.5e
\n
"
,
e0
);
if
(
logfile
)
fprintf
(
logfile
,
"Fix MSST e0 = to be %12.5e
\n
"
,
e0
);
}
}
temperature
->
compute_vector
();
double
*
ke_tensor
=
temperature
->
vector
;
double
ke_temp
=
ke_tensor
[
0
]
+
ke_tensor
[
1
]
+
ke_tensor
[
2
];
if
(
ke_temp
>
0.0
&&
tscale
>
0.0
)
{
// transfer energy from atom velocities to cell volume motion
// to bias initial compression
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
double
sqrt_initial_temperature_scaling
=
sqrt
(
1.0
-
tscale
);
double
fac1
=
tscale
*
total_mass
/
qmass
*
ke_temp
/
force
->
mvv2e
;
omega
[
direction
]
=-
1
*
sqrt
(
fac1
);
double
fac2
=
omega
[
direction
]
/
v0
;
if
(
comm
->
me
==
0
&&
tscale
!=
1.0
)
{
if
(
screen
)
fprintf
(
screen
,
"Fix MSST initial strain rate of %12.5e established "
"by reducing temperature by factor of %12.5e
\n
"
,
fac2
,
tscale
);
if
(
logfile
)
fprintf
(
logfile
,
"Fix MSST initial strain rate of %12.5e established "
"by reducing temperature by factor of %12.5e
\n
"
,
fac2
,
tscale
);
}
for
(
int
i
=
0
;
i
<
atom
->
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
for
(
int
k
=
0
;
k
<
3
;
k
++
)
{
v
[
i
][
k
]
*=
sqrt_initial_temperature_scaling
;
}
}
}
}
// trigger virial computation on next timestep
pressure
->
addstep
(
update
->
ntimestep
+
1
);
}
/* ----------------------------------------------------------------------
1st half of Verlet update
------------------------------------------------------------------------- */
void
FixMSST
::
initial_integrate
(
int
vflag
)
{
int
sd
;
double
p_msst
;
// MSST driving pressure.
int
i
,
k
;
double
vol
;
int
nlocal
=
atom
->
nlocal
;
int
*
mask
=
atom
->
mask
;
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
double
**
x
=
atom
->
x
;
// check to see if old_velocity is correctly allocated
check_alloc
(
nlocal
);
sd
=
direction
;
// compute new pressure and volume.
temperature
->
compute_vector
();
pressure
->
compute_vector
();
couple
();
vol
=
compute_vol
();
// propagate the time derivative of
// the volume 1/2 step at fixed vol, r, rdot.
p_msst
=
nktv2p
*
mvv2e
*
velocity
*
velocity
*
total_mass
*
(
v0
-
vol
)
/
(
v0
*
v0
);
double
A
=
total_mass
*
(
p_current
[
sd
]
-
p0
-
p_msst
)
/
(
qmass
*
nktv2p
*
mvv2e
);
double
B
=
total_mass
*
mu
/
(
qmass
*
vol
);
// prevent blow-up of the volume.
if
(
vol
>
v0
&&
A
>
0.0
)
{
A
=
-
A
;
}
// use taylor expansion to avoid singularity at B == 0.
if
(
B
*
dthalf
>
1.0e-06
)
{
omega
[
sd
]
=
(
omega
[
sd
]
+
A
*
(
exp
(
B
*
dthalf
)
-
1.0
)
/
B
)
*
exp
(
-
B
*
dthalf
);
}
else
{
omega
[
sd
]
=
omega
[
sd
]
+
(
A
-
B
*
omega
[
sd
])
*
dthalf
+
0.5
*
(
B
*
B
*
omega
[
sd
]
-
A
*
B
)
*
dthalf
*
dthalf
;
}
// propagate velocity sum 1/2 step by
// temporarily propagating the velocities.
velocity_sum
=
compute_vsum
();
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
for
(
k
=
0
;
k
<
3
;
k
++
)
{
double
C
=
f
[
i
][
k
]
*
force
->
ftm2v
/
mass
[
type
[
i
]];
double
D
=
mu
*
omega
[
sd
]
*
omega
[
sd
]
/
(
velocity_sum
*
mass
[
type
[
i
]]
*
vol
);
old_velocity
[
i
][
k
]
=
v
[
i
][
k
];
if
(
k
==
direction
)
{
D
=
D
-
2.0
*
omega
[
sd
]
/
vol
;
}
if
(
fabs
(
dthalf
*
D
)
>
1.0e-06
)
{
double
expd
=
exp
(
D
*
dthalf
);
v
[
i
][
k
]
=
expd
*
(
C
+
D
*
v
[
i
][
k
]
-
C
/
expd
)
/
D
;
}
else
{
v
[
i
][
k
]
=
v
[
i
][
k
]
+
(
C
+
D
*
v
[
i
][
k
]
)
*
dthalf
+
0.5
*
(
D
*
D
*
v
[
i
][
k
]
+
C
*
D
)
*
dthalf
*
dthalf
;
}
}
}
}
velocity_sum
=
compute_vsum
();
// reset the velocities.
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
for
(
k
=
0
;
k
<
3
;
k
++
)
{
v
[
i
][
k
]
=
old_velocity
[
i
][
k
];
}
}
}
// propagate velocities 1/2 step using the new velocity sum.
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
for
(
k
=
0
;
k
<
3
;
k
++
)
{
double
C
=
f
[
i
][
k
]
*
force
->
ftm2v
/
mass
[
type
[
i
]];
double
D
=
mu
*
omega
[
sd
]
*
omega
[
sd
]
/
(
velocity_sum
*
mass
[
type
[
i
]]
*
vol
);
if
(
k
==
direction
)
{
D
=
D
-
2.0
*
omega
[
sd
]
/
vol
;
}
if
(
fabs
(
dthalf
*
D
)
>
1.0e-06
)
{
double
expd
=
exp
(
D
*
dthalf
);
v
[
i
][
k
]
=
expd
*
(
C
+
D
*
v
[
i
][
k
]
-
C
/
expd
)
/
D
;
}
else
{
v
[
i
][
k
]
=
v
[
i
][
k
]
+
(
C
+
D
*
v
[
i
][
k
]
)
*
dthalf
+
0.5
*
(
D
*
D
*
v
[
i
][
k
]
+
C
*
D
)
*
dthalf
*
dthalf
;
}
}
}
}
// propagate the volume 1/2 step.
double
vol1
=
vol
+
omega
[
sd
]
*
dthalf
;
// rescale positions and change box size.
dilation
[
sd
]
=
vol1
/
vol
;
remap
(
0
);
// propagate particle positions 1 time step.
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
x
[
i
][
0
]
+=
dtv
*
v
[
i
][
0
];
x
[
i
][
1
]
+=
dtv
*
v
[
i
][
1
];
x
[
i
][
2
]
+=
dtv
*
v
[
i
][
2
];
}
}
// propagate the volume 1/2 step.
double
vol2
=
vol1
+
omega
[
sd
]
*
dthalf
;
// rescale positions and change box size.
dilation
[
sd
]
=
vol2
/
vol1
;
remap
(
0
);
if
(
kspace_flag
)
force
->
kspace
->
setup
();
}
/* ----------------------------------------------------------------------
2nd half of Verlet update
------------------------------------------------------------------------- */
void
FixMSST
::
final_integrate
()
{
int
i
;
// v update only for atoms in MSST group
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
vol
=
compute_vol
();
double
p_msst
;
int
sd
=
direction
;
// propagate particle velocities 1/2 step.
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
for
(
int
k
=
0
;
k
<
3
;
k
++
)
{
double
C
=
f
[
i
][
k
]
*
force
->
ftm2v
/
mass
[
type
[
i
]];
double
D
=
mu
*
omega
[
sd
]
*
omega
[
sd
]
/
(
velocity_sum
*
mass
[
type
[
i
]]
*
vol
);
if
(
k
==
direction
)
{
D
=
D
-
2.0
*
omega
[
sd
]
/
vol
;
}
if
(
fabs
(
dthalf
*
D
)
>
1.0e-06
)
{
double
expd
=
exp
(
D
*
dthalf
);
v
[
i
][
k
]
=
expd
*
(
C
+
D
*
v
[
i
][
k
]
-
C
/
expd
)
/
D
;
}
else
{
v
[
i
][
k
]
=
v
[
i
][
k
]
+
(
C
+
D
*
v
[
i
][
k
]
)
*
dthalf
+
0.5
*
(
D
*
D
*
v
[
i
][
k
]
+
C
*
D
)
*
dthalf
*
dthalf
;
}
}
}
}
// compute new pressure and volume.
temperature
->
compute_vector
();
pressure
->
compute_vector
();
couple
();
velocity_sum
=
compute_vsum
();
vol
=
compute_vol
();
// propagate the time derivative of the volume 1/2 step at fixed V, r, rdot.
p_msst
=
nktv2p
*
mvv2e
*
velocity
*
velocity
*
total_mass
*
(
v0
-
vol
)
/
(
v0
*
v0
);
double
A
=
total_mass
*
(
p_current
[
sd
]
-
p0
-
p_msst
)
/
(
qmass
*
nktv2p
*
mvv2e
);
double
B
=
total_mass
*
mu
/
(
qmass
*
vol
);
// prevent blow-up of the volume.
if
(
vol
>
v0
&&
A
>
0.0
)
{
A
=
-
A
;
}
// use taylor expansion to avoid singularity at B == 0.
if
(
B
*
dthalf
>
1.0e-06
)
{
omega
[
sd
]
=
(
omega
[
sd
]
+
A
*
(
exp
(
B
*
dthalf
)
-
1.0
)
/
B
)
*
exp
(
-
B
*
dthalf
);
}
else
{
omega
[
sd
]
=
omega
[
sd
]
+
(
A
-
B
*
omega
[
sd
])
*
dthalf
+
0.5
*
(
B
*
B
*
omega
[
sd
]
-
A
*
B
)
*
dthalf
*
dthalf
;
}
// calculate Lagrangian position of computational cell
lagrangian_position
-=
velocity
*
vol
/
v0
*
update
->
dt
;
// trigger virial computation on next timestep
pressure
->
addstep
(
update
->
ntimestep
+
1
);
}
/* ---------------------------------------------------------------------- */
void
FixMSST
::
couple
()
{
double
*
tensor
=
pressure
->
vector
;
p_current
[
0
]
=
tensor
[
0
];
p_current
[
1
]
=
tensor
[
1
];
p_current
[
2
]
=
tensor
[
2
];
}
/* ----------------------------------------------------------------------
change box size
remap owned or owned+ghost atoms depending on flag
if rigid bodies exist, scale rigid body centers-of-mass
------------------------------------------------------------------------- */
void
FixMSST
::
remap
(
int
flag
)
{
int
i
,
n
;
double
oldlo
,
oldhi
,
ctr
;
double
**
v
=
atom
->
v
;
if
(
flag
)
n
=
atom
->
nlocal
+
atom
->
nghost
;
else
n
=
atom
->
nlocal
;
// convert pertinent atoms and rigid bodies to lamda coords
domain
->
x2lamda
(
n
);
if
(
nrigid
)
for
(
i
=
0
;
i
<
nrigid
;
i
++
)
modify
->
fix
[
rfix
[
i
]]
->
deform
(
0
);
// reset global and local box to new size/shape
for
(
i
=
0
;
i
<
3
;
i
++
)
{
if
(
direction
==
i
)
{
oldlo
=
domain
->
boxlo
[
i
];
oldhi
=
domain
->
boxhi
[
i
];
ctr
=
0.5
*
(
oldlo
+
oldhi
);
domain
->
boxlo
[
i
]
=
(
oldlo
-
ctr
)
*
dilation
[
i
]
+
ctr
;
domain
->
boxhi
[
i
]
=
(
oldhi
-
ctr
)
*
dilation
[
i
]
+
ctr
;
}
}
domain
->
set_global_box
();
domain
->
set_local_box
();
// convert pertinent atoms and rigid bodies back to box coords
domain
->
lamda2x
(
n
);
if
(
nrigid
)
for
(
i
=
0
;
i
<
nrigid
;
i
++
)
modify
->
fix
[
rfix
[
i
]]
->
deform
(
1
);
for
(
i
=
0
;
i
<
n
;
i
++
)
{
v
[
i
][
direction
]
=
v
[
i
][
direction
]
*
dilation
[
direction
];
}
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void
FixMSST
::
write_restart
(
FILE
*
fp
)
{
int
n
=
0
;
double
list
[
4
];
list
[
n
++
]
=
omega
[
direction
];
list
[
n
++
]
=
e0
;
list
[
n
++
]
=
v0
;
list
[
n
++
]
=
p0
;
if
(
comm
->
me
==
0
)
{
int
size
=
n
*
sizeof
(
double
);
fwrite
(
&
size
,
sizeof
(
int
),
1
,
fp
);
fwrite
(
&
list
,
sizeof
(
double
),
n
,
fp
);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void
FixMSST
::
restart
(
char
*
buf
)
{
int
n
=
0
;
double
*
list
=
(
double
*
)
buf
;
omega
[
direction
]
=
list
[
n
++
];
e0
=
list
[
n
++
];
v0
=
list
[
n
++
];
p0
=
list
[
n
++
];
p0_set
=
1
;
v0_set
=
1
;
e0_set
=
1
;
}
/* ---------------------------------------------------------------------- */
int
FixMSST
::
modify_param
(
int
narg
,
char
**
arg
)
{
if
(
strcmp
(
arg
[
0
],
"temp"
)
==
0
)
{
if
(
narg
<
2
)
error
->
all
(
"Illegal fix_modify command"
);
if
(
tflag
)
{
modify
->
delete_compute
(
id_temp
);
tflag
=
0
;
}
delete
[]
id_temp
;
int
n
=
strlen
(
arg
[
1
])
+
1
;
id_temp
=
new
char
[
n
];
strcpy
(
id_temp
,
arg
[
1
]);
int
icompute
=
modify
->
find_compute
(
id_temp
);
if
(
icompute
<
0
)
error
->
all
(
"Could not find fix_modify temperature ID"
);
temperature
=
modify
->
compute
[
icompute
];
if
(
temperature
->
tempflag
==
0
)
error
->
all
(
"Fix_modify temperature ID does not compute temperature"
);
if
(
temperature
->
igroup
!=
0
&&
comm
->
me
==
0
)
error
->
warning
(
"Temperature for MSST is not for group all"
);
return
2
;
}
else
if
(
strcmp
(
arg
[
0
],
"press"
)
==
0
)
{
if
(
narg
<
2
)
error
->
all
(
"Illegal fix_modify command"
);
if
(
pflag
)
{
modify
->
delete_compute
(
id_press
);
pflag
=
0
;
}
delete
[]
id_press
;
int
n
=
strlen
(
arg
[
1
])
+
1
;
id_press
=
new
char
[
n
];
strcpy
(
id_press
,
arg
[
1
]);
int
icompute
=
modify
->
find_compute
(
id_press
);
if
(
icompute
<
0
)
error
->
all
(
"Could not find fix_modify pressure ID"
);
pressure
=
modify
->
compute
[
icompute
];
if
(
pressure
->
pressflag
==
0
)
error
->
all
(
"Fix_modify pressure ID does not compute pressure"
);
return
2
;
}
return
0
;
}
/* ---------------------------------------------------------------------- */
double
FixMSST
::
compute_scalar
()
{
// compute new pressure and volume.
temperature
->
compute_vector
();
pressure
->
compute_vector
();
couple
();
double
volume
=
compute_vol
();
double
energy
=
0.0
;
int
i
;
i
=
direction
;
energy
=
qmass
*
omega
[
i
]
*
omega
[
i
]
/
(
2.0
*
total_mass
)
*
mvv2e
;
energy
-=
0.5
*
total_mass
*
velocity
*
velocity
*
(
1.0
-
volume
/
v0
)
*
(
1.0
-
volume
/
v0
)
*
mvv2e
;
energy
-=
p0
*
(
v0
-
volume
)
/
nktv2p
;
return
energy
;
}
/* ----------------------------------------------------------------------
return a single element from the following vector,
[dhug,dray,lgr_vel,lgr_pos]
------------------------------------------------------------------------- */
double
FixMSST
::
compute_vector
(
int
n
)
{
if
(
n
==
0
)
{
return
compute_hugoniot
();
}
else
if
(
n
==
1
)
{
return
compute_rayleigh
();
}
else
if
(
n
==
2
)
{
return
compute_lagrangian_speed
();
}
else
if
(
n
==
3
)
{
return
compute_lagrangian_position
();
}
return
0.0
;
}
/* ----------------------------------------------------------------------
Computes the deviation of the current point
from the Hugoniot in Kelvin for the MSST.
------------------------------------------------------------------------- */
double
FixMSST
::
compute_hugoniot
()
{
double
v
,
e
,
p
;
double
dhugo
;
e
=
compute_etotal
();
temperature
->
compute_vector
();
pressure
->
compute_vector
();
p
=
pressure
->
vector
[
direction
];
v
=
compute_vol
();
dhugo
=
(
0.5
*
(
p
+
p0
)
*
(
v0
-
v
))
/
force
->
nktv2p
+
e0
-
e
;
dhugo
/=
temperature
->
dof
*
force
->
boltz
;
return
dhugo
;
}
/* ----------------------------------------------------------------------
Computes the deviation of the current point from the Rayleigh
in pressure units for the MSST.
------------------------------------------------------------------------- */
double
FixMSST
::
compute_rayleigh
()
{
double
v
,
p
;
double
drayleigh
;
temperature
->
compute_vector
();
pressure
->
compute_vector
();
p
=
pressure
->
vector
[
direction
];
v
=
compute_vol
();
drayleigh
=
p
-
p0
-
total_mass
*
velocity
*
velocity
*
force
->
mvv2e
*
(
1.0
-
v
/
v0
)
*
force
->
nktv2p
/
v0
;
return
drayleigh
;
}
/* ----------------------------------------------------------------------
Computes the speed of the MSST computational cell in the
unshocked material rest-frame
------------------------------------------------------------------------- */
double
FixMSST
::
compute_lagrangian_speed
()
{
double
v
=
compute_vol
();
return
velocity
*
(
1.0
-
v
/
v0
);
}
/* ----------------------------------------------------------------------
Computes the distance behind the
shock front of the MSST computational cell.
------------------------------------------------------------------------- */
double
FixMSST
::
compute_lagrangian_position
()
{
return
lagrangian_position
;
}
/* ---------------------------------------------------------------------- */
double
FixMSST
::
compute_etotal
()
{
double
epot
,
ekin
,
etot
;
epot
=
pe
->
compute_scalar
();
if
(
thermo_energy
)
epot
-=
compute_scalar
();
ekin
=
temperature
->
compute_scalar
();
ekin
*=
0.5
*
temperature
->
dof
*
force
->
boltz
;
etot
=
epot
+
ekin
;
return
etot
;
}
/* ---------------------------------------------------------------------- */
double
FixMSST
::
compute_vol
()
{
if
(
domain
->
dimension
==
3
)
return
domain
->
xprd
*
domain
->
yprd
*
domain
->
zprd
;
else
return
domain
->
xprd
*
domain
->
yprd
;
}
/* ----------------------------------------------------------------------
Checks to see if the allocated size of old_velocity is >= n
The number of local atoms can change during a parallel run.
------------------------------------------------------------------------- */
void
FixMSST
::
check_alloc
(
int
n
)
{
if
(
atoms_allocated
<
n
)
{
for
(
int
j
=
0
;
j
<
atoms_allocated
;
j
++
)
{
delete
[]
old_velocity
[
j
];
}
delete
[]
old_velocity
;
old_velocity
=
new
double
*
[
n
];
for
(
int
j
=
0
;
j
<
n
;
j
++
)
old_velocity
[
j
]
=
new
double
[
3
];
atoms_allocated
=
n
;
}
}
double
FixMSST
::
compute_vsum
()
{
double
vsum
;
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
t
=
0.0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
t
+=
(
v
[
i
][
0
]
*
v
[
i
][
0
]
+
v
[
i
][
1
]
*
v
[
i
][
1
]
+
v
[
i
][
2
]
*
v
[
i
][
2
])
;
}
}
MPI_Allreduce
(
&
t
,
&
vsum
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
return
vsum
;
}
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