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reaxc_reset_tools.cpp
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rLAMMPS lammps
reaxc_reset_tools.cpp
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/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Copyright (2010) Purdue University
Hasan Metin Aktulga, hmaktulga@lbl.gov
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
"Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
#include "pair_reax_c.h"
#if defined(PURE_REAX)
#include "reset_tools.h"
#include "list.h"
#include "tool_box.h"
#include "vector.h"
#elif defined(LAMMPS_REAX)
#include "reaxc_reset_tools.h"
#include "reaxc_list.h"
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
#endif
void
Reset_Atoms
(
reax_system
*
system
,
control_params
*
control
)
{
int
i
;
reax_atom
*
atom
;
system
->
numH
=
0
;
if
(
control
->
hbond_cut
>
0
)
for
(
i
=
0
;
i
<
system
->
n
;
++
i
)
{
atom
=
&
(
system
->
my_atoms
[
i
]);
if
(
system
->
reax_param
.
sbp
[
atom
->
type
].
p_hbond
==
1
)
atom
->
Hindex
=
system
->
numH
++
;
else
atom
->
Hindex
=
-
1
;
}
}
void
Reset_Energies
(
energy_data
*
en
)
{
en
->
e_bond
=
0
;
en
->
e_ov
=
0
;
en
->
e_un
=
0
;
en
->
e_lp
=
0
;
en
->
e_ang
=
0
;
en
->
e_pen
=
0
;
en
->
e_coa
=
0
;
en
->
e_hb
=
0
;
en
->
e_tor
=
0
;
en
->
e_con
=
0
;
en
->
e_vdW
=
0
;
en
->
e_ele
=
0
;
en
->
e_pol
=
0
;
en
->
e_pot
=
0
;
en
->
e_kin
=
0
;
en
->
e_tot
=
0
;
}
void
Reset_Temperatures
(
simulation_data
*
data
)
{
data
->
therm
.
T
=
0
;
}
void
Reset_Pressures
(
simulation_data
*
data
)
{
data
->
flex_bar
.
P_scalar
=
0
;
rtensor_MakeZero
(
data
->
flex_bar
.
P
);
data
->
iso_bar
.
P
=
0
;
rvec_MakeZero
(
data
->
int_press
);
rvec_MakeZero
(
data
->
my_ext_press
);
rvec_MakeZero
(
data
->
ext_press
);
}
void
Reset_Simulation_Data
(
simulation_data
*
data
,
int
virial
)
{
Reset_Energies
(
&
data
->
my_en
);
Reset_Energies
(
&
data
->
sys_en
);
Reset_Temperatures
(
data
);
//if( virial )
Reset_Pressures
(
data
);
}
void
Reset_Timing
(
reax_timing
*
rt
)
{
rt
->
total
=
Get_Time
();
rt
->
comm
=
0
;
rt
->
nbrs
=
0
;
rt
->
init_forces
=
0
;
rt
->
bonded
=
0
;
rt
->
nonb
=
0
;
rt
->
qEq
=
0
;
rt
->
s_matvecs
=
0
;
rt
->
t_matvecs
=
0
;
}
#ifdef TEST_FORCES
void
Reset_Test_Forces
(
reax_system
*
system
,
storage
*
workspace
)
{
memset
(
workspace
->
f_ele
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_vdw
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_bo
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_be
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_lp
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_ov
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_un
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_ang
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_coa
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_pen
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_hb
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_tor
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
f_con
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
}
#endif
void
Reset_Workspace
(
reax_system
*
system
,
storage
*
workspace
)
{
memset
(
workspace
->
total_bond_order
,
0
,
system
->
total_cap
*
sizeof
(
real
)
);
memset
(
workspace
->
dDeltap_self
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
memset
(
workspace
->
CdDelta
,
0
,
system
->
total_cap
*
sizeof
(
real
)
);
memset
(
workspace
->
f
,
0
,
system
->
total_cap
*
sizeof
(
rvec
)
);
#ifdef TEST_FORCES
memset
(
workspace
->
dDelta
,
0
,
sizeof
(
rvec
)
*
system
->
total_cap
);
Reset_Test_Forces
(
system
,
workspace
);
#endif
}
void
Reset_Grid
(
grid
*
g
)
{
int
i
,
j
,
k
;
for
(
i
=
0
;
i
<
g
->
ncells
[
0
];
i
++
)
for
(
j
=
0
;
j
<
g
->
ncells
[
1
];
j
++
)
for
(
k
=
0
;
k
<
g
->
ncells
[
2
];
k
++
)
{
g
->
cells
[
i
][
j
][
k
].
top
=
0
;
g
->
cells
[
i
][
j
][
k
].
str
=
0
;
g
->
cells
[
i
][
j
][
k
].
end
=
0
;
}
}
void
Reset_Out_Buffers
(
mpi_out_data
*
out_buf
,
int
n
)
{
int
i
;
for
(
i
=
0
;
i
<
n
;
++
i
)
out_buf
[
i
].
cnt
=
0
;
}
void
Reset_Neighbor_Lists
(
reax_system
*
system
,
control_params
*
control
,
storage
*
workspace
,
reax_list
**
lists
,
MPI_Comm
comm
)
{
int
i
,
total_bonds
,
Hindex
,
total_hbonds
;
reax_list
*
bonds
,
*
hbonds
;
/* bonds list */
if
(
system
->
N
>
0
){
bonds
=
(
*
lists
)
+
BONDS
;
total_bonds
=
0
;
/* reset start-end indexes */
for
(
i
=
0
;
i
<
system
->
N
;
++
i
)
{
Set_Start_Index
(
i
,
total_bonds
,
bonds
);
Set_End_Index
(
i
,
total_bonds
,
bonds
);
total_bonds
+=
system
->
my_atoms
[
i
].
num_bonds
;
}
/* is reallocation needed? */
if
(
total_bonds
>=
bonds
->
num_intrs
*
DANGER_ZONE
)
{
workspace
->
realloc
.
bonds
=
1
;
if
(
total_bonds
>=
bonds
->
num_intrs
)
{
fprintf
(
stderr
,
"p%d: not enough space for bonds! total=%d allocated=%d
\n
"
,
system
->
my_rank
,
total_bonds
,
bonds
->
num_intrs
);
MPI_Abort
(
comm
,
INSUFFICIENT_MEMORY
);
}
}
}
// fprintf( stderr, "p%d: n:%d num_intrs:%d num_H:%d\n",
// system->my_rank, hbonds->n, hbonds->num_intrs, workspace->num_H );
// MPI_Barrier( comm );
/* hbonds list */
if
(
control
->
hbond_cut
>
0
&&
system
->
numH
>
0
)
{
hbonds
=
(
*
lists
)
+
HBONDS
;
total_hbonds
=
0
;
/* reset start-end indexes */
for
(
i
=
0
;
i
<
system
->
n
;
++
i
)
{
Hindex
=
system
->
my_atoms
[
i
].
Hindex
;
if
(
Hindex
>
-
1
)
{
Set_Start_Index
(
Hindex
,
total_hbonds
,
hbonds
);
Set_End_Index
(
Hindex
,
total_hbonds
,
hbonds
);
total_hbonds
+=
system
->
my_atoms
[
i
].
num_hbonds
;
}
}
/* is reallocation needed? */
if
(
total_hbonds
>=
hbonds
->
num_intrs
*
0.90
/*DANGER_ZONE*/
)
{
workspace
->
realloc
.
hbonds
=
1
;
if
(
total_hbonds
>=
hbonds
->
num_intrs
)
{
fprintf
(
stderr
,
"p%d: not enough space for hbonds! total=%d allocated=%d
\n
"
,
system
->
my_rank
,
total_hbonds
,
hbonds
->
num_intrs
);
MPI_Abort
(
comm
,
INSUFFICIENT_MEMORY
);
}
}
}
// fprintf( stderr, "p%d: cleared hbonds\n", system->my_rank );
// MPI_Barrier( comm );
}
void
Reset
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
MPI_Comm
comm
)
{
Reset_Atoms
(
system
,
control
);
Reset_Simulation_Data
(
data
,
control
->
virial
);
Reset_Workspace
(
system
,
workspace
);
Reset_Neighbor_Lists
(
system
,
control
,
workspace
,
lists
,
comm
);
#if defined(DEBUG_FOCUS)
fprintf
(
stderr
,
"p%d @ step%d: reset done
\n
"
,
system
->
my_rank
,
data
->
step
);
MPI_Barrier
(
comm
);
#endif
}
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