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reaxc_init_md.cpp
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rLAMMPS lammps
reaxc_init_md.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"
#include "reaxc_init_md.h"
#include "reaxc_allocate.h"
#include "reaxc_forces.h"
#include "reaxc_io_tools.h"
#include "reaxc_list.h"
#include "reaxc_lookup.h"
#include "reaxc_reset_tools.h"
#include "reaxc_system_props.h"
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
int
Init_System
(
reax_system
*
system
,
control_params
*
control
,
char
*
msg
)
{
int
i
;
reax_atom
*
atom
;
int
mincap
=
system
->
mincap
;
double
safezone
=
system
->
safezone
;
double
saferzone
=
system
->
saferzone
;
// determine the local and total capacity
system
->
local_cap
=
MAX
(
(
int
)(
system
->
n
*
safezone
),
mincap
);
system
->
total_cap
=
MAX
(
(
int
)(
system
->
N
*
safezone
),
mincap
);
/* estimate numH and Hcap */
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
->
type
>=
0
)
atom
->
Hindex
=
system
->
numH
++
;
else
atom
->
Hindex
=
-
1
;
}
system
->
Hcap
=
(
int
)(
MAX
(
system
->
numH
*
saferzone
,
mincap
));
return
SUCCESS
;
}
int
Init_Simulation_Data
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
char
*
msg
)
{
Reset_Simulation_Data
(
data
,
control
->
virial
);
/* initialize the timer(s) */
if
(
system
->
my_rank
==
MASTER_NODE
)
{
data
->
timing
.
start
=
Get_Time
(
);
}
data
->
step
=
data
->
prev_steps
=
0
;
return
SUCCESS
;
}
void
Init_Taper
(
control_params
*
control
,
storage
*
workspace
,
MPI_Comm
comm
)
{
double
d1
,
d7
;
double
swa
,
swa2
,
swa3
;
double
swb
,
swb2
,
swb3
;
swa
=
control
->
nonb_low
;
swb
=
control
->
nonb_cut
;
if
(
fabs
(
swa
)
>
0.01
)
fprintf
(
stderr
,
"Warning: non-zero lower Taper-radius cutoff
\n
"
);
if
(
swb
<
0
)
{
fprintf
(
stderr
,
"Negative upper Taper-radius cutoff
\n
"
);
MPI_Abort
(
comm
,
INVALID_INPUT
);
}
else
if
(
swb
<
5
)
fprintf
(
stderr
,
"Warning: very low Taper-radius cutoff: %f
\n
"
,
swb
);
d1
=
swb
-
swa
;
d7
=
pow
(
d1
,
7.0
);
swa2
=
SQR
(
swa
);
swa3
=
CUBE
(
swa
);
swb2
=
SQR
(
swb
);
swb3
=
CUBE
(
swb
);
workspace
->
Tap
[
7
]
=
20.0
/
d7
;
workspace
->
Tap
[
6
]
=
-
70.0
*
(
swa
+
swb
)
/
d7
;
workspace
->
Tap
[
5
]
=
84.0
*
(
swa2
+
3.0
*
swa
*
swb
+
swb2
)
/
d7
;
workspace
->
Tap
[
4
]
=
-
35.0
*
(
swa3
+
9.0
*
swa2
*
swb
+
9.0
*
swa
*
swb2
+
swb3
)
/
d7
;
workspace
->
Tap
[
3
]
=
140.0
*
(
swa3
*
swb
+
3.0
*
swa2
*
swb2
+
swa
*
swb3
)
/
d7
;
workspace
->
Tap
[
2
]
=-
210.0
*
(
swa3
*
swb2
+
swa2
*
swb3
)
/
d7
;
workspace
->
Tap
[
1
]
=
140.0
*
swa3
*
swb3
/
d7
;
workspace
->
Tap
[
0
]
=
(
-
35.0
*
swa3
*
swb2
*
swb2
+
21.0
*
swa2
*
swb3
*
swb2
+
7.0
*
swa
*
swb3
*
swb3
+
swb3
*
swb3
*
swb
)
/
d7
;
}
int
Init_Workspace
(
reax_system
*
system
,
control_params
*
control
,
storage
*
workspace
,
MPI_Comm
comm
,
char
*
msg
)
{
int
ret
;
ret
=
Allocate_Workspace
(
system
,
control
,
workspace
,
system
->
local_cap
,
system
->
total_cap
,
comm
,
msg
);
if
(
ret
!=
SUCCESS
)
return
ret
;
memset
(
&
(
workspace
->
realloc
),
0
,
sizeof
(
reallocate_data
)
);
Reset_Workspace
(
system
,
workspace
);
/* Initialize the Taper function */
Init_Taper
(
control
,
workspace
,
comm
);
return
SUCCESS
;
}
/************** setup communication data structures **************/
int
Init_MPI_Datatypes
(
reax_system
*
system
,
storage
*
workspace
,
mpi_datatypes
*
mpi_data
,
MPI_Comm
comm
,
char
*
msg
)
{
/* setup the world */
mpi_data
->
world
=
comm
;
MPI_Comm_size
(
comm
,
&
(
system
->
wsize
)
);
return
SUCCESS
;
}
int
Init_Lists
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
mpi_datatypes
*
mpi_data
,
char
*
msg
)
{
int
i
,
total_hbonds
,
total_bonds
,
bond_cap
,
num_3body
,
cap_3body
,
Htop
;
int
*
hb_top
,
*
bond_top
;
MPI_Comm
comm
;
int
mincap
=
system
->
mincap
;
double
safezone
=
system
->
safezone
;
double
saferzone
=
system
->
saferzone
;
comm
=
mpi_data
->
world
;
bond_top
=
(
int
*
)
calloc
(
system
->
total_cap
,
sizeof
(
int
)
);
hb_top
=
(
int
*
)
calloc
(
system
->
local_cap
,
sizeof
(
int
)
);
Estimate_Storages
(
system
,
control
,
lists
,
&
Htop
,
hb_top
,
bond_top
,
&
num_3body
,
comm
);
if
(
control
->
hbond_cut
>
0
)
{
/* init H indexes */
total_hbonds
=
0
;
for
(
i
=
0
;
i
<
system
->
n
;
++
i
)
{
system
->
my_atoms
[
i
].
num_hbonds
=
hb_top
[
i
];
total_hbonds
+=
hb_top
[
i
];
}
total_hbonds
=
(
int
)(
MAX
(
total_hbonds
*
saferzone
,
mincap
*
MIN_HBONDS
));
if
(
!
Make_List
(
system
->
Hcap
,
total_hbonds
,
TYP_HBOND
,
*
lists
+
HBONDS
,
comm
)
)
{
fprintf
(
stderr
,
"not enough space for hbonds list. terminating!
\n
"
);
MPI_Abort
(
comm
,
INSUFFICIENT_MEMORY
);
}
}
total_bonds
=
0
;
for
(
i
=
0
;
i
<
system
->
N
;
++
i
)
{
system
->
my_atoms
[
i
].
num_bonds
=
bond_top
[
i
];
total_bonds
+=
bond_top
[
i
];
}
bond_cap
=
(
int
)(
MAX
(
total_bonds
*
safezone
,
mincap
*
MIN_BONDS
));
if
(
!
Make_List
(
system
->
total_cap
,
bond_cap
,
TYP_BOND
,
*
lists
+
BONDS
,
comm
)
)
{
fprintf
(
stderr
,
"not enough space for bonds list. terminating!
\n
"
);
MPI_Abort
(
comm
,
INSUFFICIENT_MEMORY
);
}
/* 3bodies list */
cap_3body
=
(
int
)(
MAX
(
num_3body
*
safezone
,
MIN_3BODIES
));
if
(
!
Make_List
(
bond_cap
,
cap_3body
,
TYP_THREE_BODY
,
*
lists
+
THREE_BODIES
,
comm
)
){
fprintf
(
stderr
,
"Problem in initializing angles list. Terminating!
\n
"
);
MPI_Abort
(
comm
,
INSUFFICIENT_MEMORY
);
}
free
(
hb_top
);
free
(
bond_top
);
return
SUCCESS
;
}
void
Initialize
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
output_controls
*
out_control
,
mpi_datatypes
*
mpi_data
,
MPI_Comm
comm
)
{
char
msg
[
MAX_STR
];
if
(
Init_MPI_Datatypes
(
system
,
workspace
,
mpi_data
,
comm
,
msg
)
==
FAILURE
)
{
fprintf
(
stderr
,
"p%d: init_mpi_datatypes: could not create datatypes
\n
"
,
system
->
my_rank
);
fprintf
(
stderr
,
"p%d: mpi_data couldn't be initialized! terminating.
\n
"
,
system
->
my_rank
);
MPI_Abort
(
mpi_data
->
world
,
CANNOT_INITIALIZE
);
}
if
(
Init_System
(
system
,
control
,
msg
)
==
FAILURE
){
fprintf
(
stderr
,
"p%d: %s
\n
"
,
system
->
my_rank
,
msg
);
fprintf
(
stderr
,
"p%d: system could not be initialized! terminating.
\n
"
,
system
->
my_rank
);
MPI_Abort
(
mpi_data
->
world
,
CANNOT_INITIALIZE
);
}
if
(
Init_Simulation_Data
(
system
,
control
,
data
,
msg
)
==
FAILURE
)
{
fprintf
(
stderr
,
"p%d: %s
\n
"
,
system
->
my_rank
,
msg
);
fprintf
(
stderr
,
"p%d: sim_data couldn't be initialized! terminating.
\n
"
,
system
->
my_rank
);
MPI_Abort
(
mpi_data
->
world
,
CANNOT_INITIALIZE
);
}
if
(
Init_Workspace
(
system
,
control
,
workspace
,
mpi_data
->
world
,
msg
)
==
FAILURE
)
{
fprintf
(
stderr
,
"p%d:init_workspace: not enough memory
\n
"
,
system
->
my_rank
);
fprintf
(
stderr
,
"p%d:workspace couldn't be initialized! terminating.
\n
"
,
system
->
my_rank
);
MPI_Abort
(
mpi_data
->
world
,
CANNOT_INITIALIZE
);
}
if
(
Init_Lists
(
system
,
control
,
data
,
workspace
,
lists
,
mpi_data
,
msg
)
==
FAILURE
)
{
fprintf
(
stderr
,
"p%d: %s
\n
"
,
system
->
my_rank
,
msg
);
fprintf
(
stderr
,
"p%d: system could not be initialized! terminating.
\n
"
,
system
->
my_rank
);
MPI_Abort
(
mpi_data
->
world
,
CANNOT_INITIALIZE
);
}
if
(
Init_Output_Files
(
system
,
control
,
out_control
,
mpi_data
,
msg
)
==
FAILURE
)
{
fprintf
(
stderr
,
"p%d: %s
\n
"
,
system
->
my_rank
,
msg
);
fprintf
(
stderr
,
"p%d: could not open output files! terminating...
\n
"
,
system
->
my_rank
);
MPI_Abort
(
mpi_data
->
world
,
CANNOT_INITIALIZE
);
}
if
(
control
->
tabulate
)
{
if
(
Init_Lookup_Tables
(
system
,
control
,
workspace
,
mpi_data
,
msg
)
==
FAILURE
)
{
fprintf
(
stderr
,
"p%d: %s
\n
"
,
system
->
my_rank
,
msg
);
fprintf
(
stderr
,
"p%d: couldn't create lookup table! terminating.
\n
"
,
system
->
my_rank
);
MPI_Abort
(
mpi_data
->
world
,
CANNOT_INITIALIZE
);
}
}
Init_Force_Functions
(
control
);
}
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