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rLAMMPS lammps
setup.cpp
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/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 2.0
// Copyright (2014) Sandia Corporation
//
// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#include <system.h>
#include <cmath>
#include <cstdio>
#include <cstdlib>
/* initialize atoms on fcc lattice in parallel fashion */
#define MAX(a,b) (a>b?a:b)
#define MIN(a,b) (a<b?a:b)
int
create_system
(
System
&
system
,
int
nx
,
int
ny
,
int
nz
,
double
rho
)
{
/* Box Setup */
double
lattice
=
pow
((
4.0
/
rho
),
(
1.0
/
3.0
));
system
.
box
.
xprd
=
nx
*
lattice
;
system
.
box
.
yprd
=
ny
*
lattice
;
system
.
box
.
zprd
=
nz
*
lattice
;
system
.
box
.
xlo
=
0
;
system
.
box
.
ylo
=
0
;
system
.
box
.
zlo
=
0
;
system
.
box
.
xhi
=
system
.
box
.
xprd
;
system
.
box
.
yhi
=
system
.
box
.
yprd
;
system
.
box
.
zhi
=
system
.
box
.
zprd
;
int
ghost_dist
=
int
(
system
.
neigh_cut
/
lattice
)
+
1
;
/* total # of atoms */
system
.
nlocal
=
4
*
nx
*
ny
*
nz
;
system
.
nghost
=
4
*
(
nx
+
2
*
ghost_dist
)
*
(
ny
+
2
*
ghost_dist
)
*
(
nz
+
2
*
ghost_dist
)
-
system
.
nlocal
;
system
.
natoms
=
system
.
nlocal
+
system
.
nghost
;
system
.
d_x
=
t_x_array
(
"X"
,
system
.
natoms
);
system
.
h_x
=
Kokkos
::
create_mirror_view
(
system
.
d_x
);
system
.
f
=
t_f_array
(
"F"
,
system
.
natoms
);
/* determine loop bounds of lattice subsection that overlaps my sub-box
insure loop bounds do not exceed nx,ny,nz */
double
alat
=
pow
((
4.0
/
rho
),
(
1.0
/
3.0
));
int
ilo
=
static_cast
<
int
>
(
system
.
box
.
xlo
/
(
0.5
*
alat
)
-
1
);
int
ihi
=
static_cast
<
int
>
(
system
.
box
.
xhi
/
(
0.5
*
alat
)
+
1
);
int
jlo
=
static_cast
<
int
>
(
system
.
box
.
ylo
/
(
0.5
*
alat
)
-
1
);
int
jhi
=
static_cast
<
int
>
(
system
.
box
.
yhi
/
(
0.5
*
alat
)
+
1
);
int
klo
=
static_cast
<
int
>
(
system
.
box
.
zlo
/
(
0.5
*
alat
)
-
1
);
int
khi
=
static_cast
<
int
>
(
system
.
box
.
zhi
/
(
0.5
*
alat
)
+
1
);
ilo
=
MAX
(
ilo
,
0
);
ihi
=
MIN
(
ihi
,
2
*
nx
-
1
);
jlo
=
MAX
(
jlo
,
0
);
jhi
=
MIN
(
jhi
,
2
*
ny
-
1
);
klo
=
MAX
(
klo
,
0
);
khi
=
MIN
(
khi
,
2
*
nz
-
1
);
/* generates positions of atoms on fcc sublattice*/
srand
(
3718273
);
/* create non-ghost atoms */
{
double
xtmp
,
ytmp
,
ztmp
;
int
sx
=
0
;
int
sy
=
0
;
int
sz
=
0
;
int
ox
=
0
;
int
oy
=
0
;
int
oz
=
0
;
int
subboxdim
=
8
;
int
n
=
0
;
int
iflag
=
0
;
while
(
oz
*
subboxdim
<=
khi
)
{
const
int
k
=
oz
*
subboxdim
+
sz
;
const
int
j
=
oy
*
subboxdim
+
sy
;
const
int
i
=
ox
*
subboxdim
+
sx
;
if
(
iflag
)
continue
;
if
(((
i
+
j
+
k
)
%
2
==
0
)
&&
(
i
>=
ilo
)
&&
(
i
<=
ihi
)
&&
(
j
>=
jlo
)
&&
(
j
<=
jhi
)
&&
(
k
>=
klo
)
&&
(
k
<=
khi
))
{
const
int
nold
=
n
;
while
(
nold
==
n
)
{
xtmp
=
0.5
*
alat
*
i
+
system
.
delta
/
1000
*
(
rand
()
%
1000
-
500
);
ytmp
=
0.5
*
alat
*
j
+
system
.
delta
/
1000
*
(
rand
()
%
1000
-
500
);
ztmp
=
0.5
*
alat
*
k
+
system
.
delta
/
1000
*
(
rand
()
%
1000
-
500
);
if
(
xtmp
>=
system
.
box
.
xlo
&&
xtmp
<
system
.
box
.
xhi
&&
ytmp
>=
system
.
box
.
ylo
&&
ytmp
<
system
.
box
.
yhi
&&
ztmp
>=
system
.
box
.
zlo
&&
ztmp
<
system
.
box
.
zhi
)
{
system
.
h_x
(
n
,
0
)
=
xtmp
;
system
.
h_x
(
n
,
1
)
=
ytmp
;
system
.
h_x
(
n
,
2
)
=
ztmp
;
n
++
;
}
}
}
sx
++
;
if
(
sx
==
subboxdim
)
{
sx
=
0
;
sy
++
;
}
if
(
sy
==
subboxdim
)
{
sy
=
0
;
sz
++
;
}
if
(
sz
==
subboxdim
)
{
sz
=
0
;
ox
++
;
}
if
(
ox
*
subboxdim
>
ihi
)
{
ox
=
0
;
oy
++
;
}
if
(
oy
*
subboxdim
>
jhi
)
{
oy
=
0
;
oz
++
;
}
}
/* check that correct # of atoms were created */
if
(
system
.
nlocal
!=
n
)
{
printf
(
"Created incorrect # of atoms
\n
"
);
return
1
;
}
}
/* create ghost atoms */
{
double
xtmp
,
ytmp
,
ztmp
;
int
ilo_g
=
ilo
-
2
*
ghost_dist
;
int
jlo_g
=
jlo
-
2
*
ghost_dist
;
int
klo_g
=
klo
-
2
*
ghost_dist
;
int
ihi_g
=
ihi
+
2
*
ghost_dist
;
int
jhi_g
=
jhi
+
2
*
ghost_dist
;
int
khi_g
=
khi
+
2
*
ghost_dist
;
int
subboxdim
=
8
;
int
sx
=
0
;
int
sy
=
0
;
int
sz
=
0
;
int
ox
=
subboxdim
*
ilo_g
;
int
oy
=
subboxdim
*
jlo_g
;
int
oz
=
subboxdim
*
klo_g
;
int
n
=
system
.
nlocal
;
int
iflag
=
0
;
while
(
oz
*
subboxdim
<=
khi_g
)
{
const
int
k
=
oz
*
subboxdim
+
sz
;
const
int
j
=
oy
*
subboxdim
+
sy
;
const
int
i
=
ox
*
subboxdim
+
sx
;
if
(
iflag
)
continue
;
if
(((
i
+
j
+
k
)
%
2
==
0
)
&&
(
i
>=
ilo_g
)
&&
(
i
<=
ihi_g
)
&&
(
j
>=
jlo_g
)
&&
(
j
<=
jhi_g
)
&&
(
k
>=
klo_g
)
&&
(
k
<=
khi_g
)
&&
((
i
<
ilo
)
||
(
i
>
ihi
)
||
(
j
<
jlo
)
||
(
j
>
jhi
)
||
(
k
<
klo
)
||
(
k
>
khi
))
)
{
xtmp
=
0.5
*
alat
*
i
;
ytmp
=
0.5
*
alat
*
j
;
ztmp
=
0.5
*
alat
*
k
;
system
.
h_x
(
n
,
0
)
=
xtmp
+
system
.
delta
/
1000
*
(
rand
()
%
1000
-
500
);;
system
.
h_x
(
n
,
1
)
=
ytmp
+
system
.
delta
/
1000
*
(
rand
()
%
1000
-
500
);;
system
.
h_x
(
n
,
2
)
=
ztmp
+
system
.
delta
/
1000
*
(
rand
()
%
1000
-
500
);;
n
++
;
}
sx
++
;
if
(
sx
==
subboxdim
)
{
sx
=
0
;
sy
++
;
}
if
(
sy
==
subboxdim
)
{
sy
=
0
;
sz
++
;
}
if
(
sz
==
subboxdim
)
{
sz
=
0
;
ox
++
;
//printf("%i %i %i // %i %i %i\n",ox,oy,oz,i,j,k);
}
if
(
ox
*
subboxdim
>
ihi_g
)
{
ox
=
subboxdim
*
ilo_g
;
oy
++
;
}
if
(
oy
*
subboxdim
>
jhi_g
)
{
oy
=
subboxdim
*
jlo_g
;
oz
++
;
}
}
}
Kokkos
::
deep_copy
(
system
.
d_x
,
system
.
h_x
);
return
0
;
}
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