Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F87578689
lmpspk.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
Sun, Oct 13, 12:36
Size
5 KB
Mime Type
text/x-c
Expires
Tue, Oct 15, 12:36 (2 d)
Engine
blob
Format
Raw Data
Handle
21566587
Attached To
rLAMMPS lammps
lmpspk.cpp
View Options
// lmpspk = umbrella driver to couple LAMMPS + SPPARKS
// for a strain-induced grain growth model
// Syntax: lmpspk Niter Ndelta Sfactor in.spparks
// Niter = # of outer iterations
// Ndelta = time to run MC in each iteration
// Sfactor = multiplier on strain effect
// in.spparks = SPPARKS input script
#include "mpi.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "lammps_data_write.h"
#include "many2many.h"
#include "memory.h"
#include "error.h"
#define QUOTE_(x) #x
#define QUOTE(x) QUOTE_(x)
#include "spkpath.h"
#include QUOTE(SPKPATH/src/spparks.h)
#include QUOTE(SPKPATH/src/library.h)
#include QUOTE(SPKPATH/src/input.h)
#include "lmppath.h"
#include QUOTE(LMPPATH/src/lammps.h)
#include QUOTE(LMPPATH/src/library.h)
#include QUOTE(LMPPATH/src/input.h)
#include QUOTE(LMPPATH/src/modify.h)
#include QUOTE(LMPPATH/src/compute.h)
using
namespace
SPPARKS_NS
;
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
int
main
(
int
narg
,
char
**
arg
)
{
int
i
,
n
;
char
str
[
128
];
// setup MPI
MPI_Init
(
&
narg
,
&
arg
);
MPI_Comm
comm
=
MPI_COMM_WORLD
;
int
me
,
nprocs
;
MPI_Comm_rank
(
comm
,
&
me
);
MPI_Comm_size
(
comm
,
&
nprocs
);
Memory
*
memory
=
new
Memory
(
comm
);
Error
*
error
=
new
Error
(
comm
);
// command-line args
if
(
narg
!=
5
)
error
->
all
(
"Syntax: lmpspk Niter Ndelta Sfactor in.spparks"
);
int
niter
=
atoi
(
arg
[
1
]);
double
delta
=
atof
(
arg
[
2
]);
double
sfactor
=
atof
(
arg
[
3
]);
n
=
strlen
(
arg
[
4
])
+
1
;
char
*
spparks_input
=
new
char
[
n
];
strcpy
(
spparks_input
,
arg
[
4
]);
// instantiate LAMMPS and SPPARKS
SPPARKS
*
spk
=
new
SPPARKS
(
0
,
NULL
,
MPI_COMM_WORLD
);
LAMMPS
*
lmp
=
new
LAMMPS
(
0
,
NULL
,
MPI_COMM_WORLD
);
// create simulation in SPPARKS from in.spparks
spk
->
input
->
file
(
spparks_input
);
// extract permanent info from SPPARKS
int
dimension
,
nglobal
,
nlocal_spparks
,
nspins
;
double
boxxlo
,
boxxhi
,
boxylo
,
boxyhi
,
boxzlo
,
boxzhi
;
int
*
id_spparks
,
*
spins
;
double
**
xyz
;
double
*
strain
;
dimension
=
*
((
int
*
)
spparks_extract
(
spk
,
"dimension"
));
nglobal
=
*
((
int
*
)
spparks_extract
(
spk
,
"nglobal"
));
nlocal_spparks
=
*
((
int
*
)
spparks_extract
(
spk
,
"nlocal"
));
boxxlo
=
*
((
double
*
)
spparks_extract
(
spk
,
"boxxlo"
));
boxxhi
=
*
((
double
*
)
spparks_extract
(
spk
,
"boxxhi"
));
boxylo
=
*
((
double
*
)
spparks_extract
(
spk
,
"boxylo"
));
boxyhi
=
*
((
double
*
)
spparks_extract
(
spk
,
"boxyhi"
));
if
(
dimension
==
3
)
{
boxzlo
=
*
((
double
*
)
spparks_extract
(
spk
,
"boxzlo"
));
boxzhi
=
*
((
double
*
)
spparks_extract
(
spk
,
"boxzhi"
));
}
else
{
boxzlo
=
-
0.5
;
boxzhi
=
0.5
;
}
id_spparks
=
(
int
*
)
spparks_extract
(
spk
,
"id"
);
spins
=
(
int
*
)
spparks_extract
(
spk
,
"site"
);
xyz
=
(
double
**
)
spparks_extract
(
spk
,
"xyz"
);
nspins
=
*
((
int
*
)
spparks_extract
(
spk
,
"nspins"
));
strain
=
(
double
*
)
spparks_extract
(
spk
,
"strain"
);
// write a LAMMPS input script using SPPARKS params
if
(
me
==
0
)
{
FILE
*
fp
=
fopen
(
"in.lammps"
,
"w"
);
if
(
fp
==
NULL
)
error
->
one
(
"Could not create LAMMPS input script"
);
fprintf
(
fp
,
"units lj
\n
"
);
sprintf
(
str
,
"dimension %d
\n
"
,
dimension
);
fprintf
(
fp
,
str
);
fprintf
(
fp
,
"atom_style atomic
\n\n
"
);
fprintf
(
fp
,
"read_data data.lammps
\n
"
);
fprintf
(
fp
,
"mass * 1.0
\n\n
"
);
fprintf
(
fp
,
"pair_style lj/cut 2.5
\n
"
);
fprintf
(
fp
,
"pair_coeff * * 1.0 1.2
\n
"
);
for
(
i
=
0
;
i
<
nspins
;
i
++
)
{
sprintf
(
str
,
"pair_coeff %d %d 1.0 1.0
\n
"
,
i
+
1
,
i
+
1
);
fprintf
(
fp
,
str
);
}
fprintf
(
fp
,
"
\n
"
);
fprintf
(
fp
,
"compute da all displace/atom
\n\n
"
);
fprintf
(
fp
,
"dump 1 all atom 10 dump.md
\n
"
);
fprintf
(
fp
,
"thermo 1
\n
"
);
fclose
(
fp
);
}
// write a LAMMPS data file using SPPARKS data
LAMMPSDataWrite
*
lwd
=
new
LAMMPSDataWrite
(
MPI_COMM_WORLD
);
lwd
->
file
(
"data.lammps"
);
lwd
->
header
(
"%d atoms"
,
nglobal
);
lwd
->
header
(
"%d atom types"
,
nspins
);
lwd
->
header
(
"%g %g xlo xhi"
,
boxxlo
,
boxxhi
);
lwd
->
header
(
"%g %g ylo yhi"
,
boxylo
,
boxyhi
);
lwd
->
header
(
"%g %g zlo zhi"
,
boxzlo
,
boxzhi
);
lwd
->
atoms
(
nlocal_spparks
);
lwd
->
atoms
(
id_spparks
);
lwd
->
atoms
(
spins
);
lwd
->
atoms
(
3
,
xyz
);
lwd
->
execute
();
delete
lwd
;
// create simulation in LAMMPS from created input script
lmp
->
input
->
file
(
"in.lammps"
);
// create transfer operators
Many2Many
*
spk2lmp
=
new
Many2Many
(
MPI_COMM_WORLD
);
Many2Many
*
lmp2spk
=
new
Many2Many
(
MPI_COMM_WORLD
);
// timestep loop
// run SPPARKS for delta time
// use SPPARKS spins to reset LAMMPS atom types
// perform LAMMPS minimization
// use atom displacements to reset strain values in SPPARKS
// realloc displace as necessary since nlocal_lammps may change
// re-create both xfers every iteration since LAMMPS may migrate atoms
int
nmax
=
0
;
double
*
displace
=
NULL
;
int
nlocal_lammps
;
int
*
id_lammps
,
*
type
;
double
**
displace_lammps
;
for
(
int
iter
=
0
;
iter
<
niter
;
iter
++
)
{
sprintf
(
str
,
"run %g"
,
delta
);
spk
->
input
->
one
(
str
);
nlocal_lammps
=
*
((
int
*
)
lammps_extract_global
(
lmp
,
"nlocal"
));
id_lammps
=
(
int
*
)
lammps_extract_atom
(
lmp
,
"id"
);
type
=
(
int
*
)
lammps_extract_atom
(
lmp
,
"type"
);
spk2lmp
->
setup
(
nlocal_spparks
,
id_spparks
,
nlocal_lammps
,
id_lammps
);
spk2lmp
->
exchange
(
spins
,
type
);
lmp
->
input
->
one
(
"minimize 0.001 0.001 10 1000"
);
nlocal_lammps
=
*
((
int
*
)
lammps_extract_global
(
lmp
,
"nlocal"
));
id_lammps
=
(
int
*
)
lammps_extract_atom
(
lmp
,
"id"
);
displace_lammps
=
(
double
**
)
lammps_extract_compute
(
lmp
,
"da"
,
1
,
2
);
if
(
nlocal_lammps
>
nmax
)
{
memory
->
sfree
(
displace
);
nmax
=
nlocal_lammps
;
displace
=
(
double
*
)
memory
->
smalloc
(
nmax
*
sizeof
(
double
),
"lmpspk:displace"
);
}
for
(
i
=
0
;
i
<
nlocal_lammps
;
i
++
)
displace
[
i
]
=
sfactor
*
displace_lammps
[
i
][
3
];
lmp2spk
->
setup
(
nlocal_lammps
,
id_lammps
,
nlocal_spparks
,
id_spparks
);
lmp2spk
->
exchange
(
displace
,
strain
);
}
memory
->
sfree
(
displace
);
// clean up
delete
spk2lmp
;
delete
lmp2spk
;
delete
spk
;
delete
lmp
;
delete
[]
spparks_input
;
delete
memory
;
delete
error
;
MPI_Finalize
();
}
Event Timeline
Log In to Comment