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rLAMMPS lammps
reaxc_forces.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_forces.h"
#include "reaxc_bond_orders.h"
#include "reaxc_bonds.h"
#include "reaxc_hydrogen_bonds.h"
#include "reaxc_io_tools.h"
#include "reaxc_list.h"
#include "reaxc_lookup.h"
#include "reaxc_multi_body.h"
#include "reaxc_nonbonded.h"
#include "reaxc_tool_box.h"
#include "reaxc_torsion_angles.h"
#include "reaxc_valence_angles.h"
#include "reaxc_vector.h"
interaction_function
Interaction_Functions
[
NUM_INTRS
];
void
Dummy_Interaction
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
output_controls
*
out_control
)
{
}
void
Init_Force_Functions
(
control_params
*
control
)
{
Interaction_Functions
[
0
]
=
BO
;
Interaction_Functions
[
1
]
=
Bonds
;
//Dummy_Interaction;
Interaction_Functions
[
2
]
=
Atom_Energy
;
//Dummy_Interaction;
Interaction_Functions
[
3
]
=
Valence_Angles
;
//Dummy_Interaction;
Interaction_Functions
[
4
]
=
Torsion_Angles
;
//Dummy_Interaction;
if
(
control
->
hbond_cut
>
0
)
Interaction_Functions
[
5
]
=
Hydrogen_Bonds
;
else
Interaction_Functions
[
5
]
=
Dummy_Interaction
;
Interaction_Functions
[
6
]
=
Dummy_Interaction
;
//empty
Interaction_Functions
[
7
]
=
Dummy_Interaction
;
//empty
Interaction_Functions
[
8
]
=
Dummy_Interaction
;
//empty
Interaction_Functions
[
9
]
=
Dummy_Interaction
;
//empty
}
void
Compute_Bonded_Forces
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
output_controls
*
out_control
,
MPI_Comm
comm
)
{
int
i
;
/* Implement all force calls as function pointers */
for
(
i
=
0
;
i
<
NUM_INTRS
;
i
++
)
{
(
Interaction_Functions
[
i
])(
system
,
control
,
data
,
workspace
,
lists
,
out_control
);
}
}
void
Compute_NonBonded_Forces
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
output_controls
*
out_control
,
MPI_Comm
comm
)
{
/* van der Waals and Coulomb interactions */
if
(
control
->
tabulate
==
0
)
vdW_Coulomb_Energy
(
system
,
control
,
data
,
workspace
,
lists
,
out_control
);
else
Tabulated_vdW_Coulomb_Energy
(
system
,
control
,
data
,
workspace
,
lists
,
out_control
);
}
void
Compute_Total_Force
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
mpi_datatypes
*
mpi_data
)
{
int
i
,
pj
;
reax_list
*
bonds
=
(
*
lists
)
+
BONDS
;
for
(
i
=
0
;
i
<
system
->
N
;
++
i
)
for
(
pj
=
Start_Index
(
i
,
bonds
);
pj
<
End_Index
(
i
,
bonds
);
++
pj
)
if
(
i
<
bonds
->
select
.
bond_list
[
pj
].
nbr
)
{
if
(
control
->
virial
==
0
)
Add_dBond_to_Forces
(
system
,
i
,
pj
,
workspace
,
lists
);
else
Add_dBond_to_Forces_NPT
(
i
,
pj
,
data
,
workspace
,
lists
);
}
}
void
Validate_Lists
(
reax_system
*
system
,
storage
*
workspace
,
reax_list
**
lists
,
int
step
,
int
n
,
int
N
,
int
numH
,
MPI_Comm
comm
)
{
int
i
,
comp
,
Hindex
;
reax_list
*
bonds
,
*
hbonds
;
double
saferzone
=
system
->
saferzone
;
/* bond list */
if
(
N
>
0
)
{
bonds
=
*
lists
+
BONDS
;
for
(
i
=
0
;
i
<
N
;
++
i
)
{
system
->
my_atoms
[
i
].
num_bonds
=
MAX
(
Num_Entries
(
i
,
bonds
)
*
2
,
MIN_BONDS
);
if
(
i
<
N
-
1
)
comp
=
Start_Index
(
i
+
1
,
bonds
);
else
comp
=
bonds
->
num_intrs
;
if
(
End_Index
(
i
,
bonds
)
>
comp
)
{
fprintf
(
stderr
,
"step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d
\n
"
,
step
,
i
,
End_Index
(
i
,
bonds
),
comp
);
MPI_Abort
(
comm
,
INSUFFICIENT_MEMORY
);
}
}
}
/* hbonds list */
if
(
numH
>
0
)
{
hbonds
=
*
lists
+
HBONDS
;
for
(
i
=
0
;
i
<
N
;
++
i
)
{
Hindex
=
system
->
my_atoms
[
i
].
Hindex
;
if
(
Hindex
>
-
1
)
{
system
->
my_atoms
[
i
].
num_hbonds
=
(
int
)(
MAX
(
Num_Entries
(
Hindex
,
hbonds
)
*
saferzone
,
MIN_HBONDS
));
//if( Num_Entries(i, hbonds) >=
//(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/){
// workspace->realloc.hbonds = 1;
if
(
Hindex
<
numH
-
1
)
comp
=
Start_Index
(
Hindex
+
1
,
hbonds
);
else
comp
=
hbonds
->
num_intrs
;
if
(
End_Index
(
Hindex
,
hbonds
)
>
comp
)
{
fprintf
(
stderr
,
"step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d
\n
"
,
step
,
Hindex
,
End_Index
(
Hindex
,
hbonds
),
comp
);
MPI_Abort
(
comm
,
INSUFFICIENT_MEMORY
);
}
}
}
}
}
void
Init_Forces_noQEq
(
reax_system
*
system
,
control_params
*
control
,
simulation_data
*
data
,
storage
*
workspace
,
reax_list
**
lists
,
output_controls
*
out_control
,
MPI_Comm
comm
)
{
int
i
,
j
,
pj
;
int
start_i
,
end_i
;
int
type_i
,
type_j
;
int
btop_i
,
btop_j
,
num_bonds
,
num_hbonds
;
int
ihb
,
jhb
,
ihb_top
,
jhb_top
;
int
local
,
flag
,
renbr
;
double
cutoff
;
reax_list
*
far_nbrs
,
*
bonds
,
*
hbonds
;
single_body_parameters
*
sbp_i
,
*
sbp_j
;
two_body_parameters
*
twbp
;
far_neighbor_data
*
nbr_pj
;
reax_atom
*
atom_i
,
*
atom_j
;
far_nbrs
=
*
lists
+
FAR_NBRS
;
bonds
=
*
lists
+
BONDS
;
hbonds
=
*
lists
+
HBONDS
;
for
(
i
=
0
;
i
<
system
->
n
;
++
i
)
workspace
->
bond_mark
[
i
]
=
0
;
for
(
i
=
system
->
n
;
i
<
system
->
N
;
++
i
)
{
workspace
->
bond_mark
[
i
]
=
1000
;
// put ghost atoms to an infinite distance
}
num_bonds
=
0
;
num_hbonds
=
0
;
btop_i
=
btop_j
=
0
;
renbr
=
(
data
->
step
-
data
->
prev_steps
)
%
control
->
reneighbor
==
0
;
for
(
i
=
0
;
i
<
system
->
N
;
++
i
)
{
atom_i
=
&
(
system
->
my_atoms
[
i
]);
type_i
=
atom_i
->
type
;
if
(
type_i
<
0
)
continue
;
start_i
=
Start_Index
(
i
,
far_nbrs
);
end_i
=
End_Index
(
i
,
far_nbrs
);
btop_i
=
End_Index
(
i
,
bonds
);
sbp_i
=
&
(
system
->
reax_param
.
sbp
[
type_i
]);
if
(
i
<
system
->
n
)
{
local
=
1
;
cutoff
=
MAX
(
control
->
hbond_cut
,
control
->
bond_cut
);
}
else
{
local
=
0
;
cutoff
=
control
->
bond_cut
;
}
ihb
=
-
1
;
ihb_top
=
-
1
;
if
(
local
&&
control
->
hbond_cut
>
0
)
{
ihb
=
sbp_i
->
p_hbond
;
if
(
ihb
==
1
)
ihb_top
=
End_Index
(
atom_i
->
Hindex
,
hbonds
);
else
ihb_top
=
-
1
;
}
/* update i-j distance - check if j is within cutoff */
for
(
pj
=
start_i
;
pj
<
end_i
;
++
pj
)
{
nbr_pj
=
&
(
far_nbrs
->
select
.
far_nbr_list
[
pj
]
);
j
=
nbr_pj
->
nbr
;
atom_j
=
&
(
system
->
my_atoms
[
j
]);
if
(
renbr
)
{
if
(
nbr_pj
->
d
<=
cutoff
)
flag
=
1
;
else
flag
=
0
;
}
else
{
nbr_pj
->
dvec
[
0
]
=
atom_j
->
x
[
0
]
-
atom_i
->
x
[
0
];
nbr_pj
->
dvec
[
1
]
=
atom_j
->
x
[
1
]
-
atom_i
->
x
[
1
];
nbr_pj
->
dvec
[
2
]
=
atom_j
->
x
[
2
]
-
atom_i
->
x
[
2
];
nbr_pj
->
d
=
rvec_Norm_Sqr
(
nbr_pj
->
dvec
);
if
(
nbr_pj
->
d
<=
SQR
(
cutoff
)
)
{
nbr_pj
->
d
=
sqrt
(
nbr_pj
->
d
);
flag
=
1
;
}
else
{
flag
=
0
;
}
}
if
(
flag
)
{
type_j
=
atom_j
->
type
;
if
(
type_j
<
0
)
continue
;
sbp_j
=
&
(
system
->
reax_param
.
sbp
[
type_j
]);
twbp
=
&
(
system
->
reax_param
.
tbp
[
type_i
][
type_j
]);
if
(
local
)
{
/* hydrogen bond lists */
if
(
control
->
hbond_cut
>
0
&&
(
ihb
==
1
||
ihb
==
2
)
&&
nbr_pj
->
d
<=
control
->
hbond_cut
)
{
// fprintf( stderr, "%d %d\n", atom1, atom2 );
jhb
=
sbp_j
->
p_hbond
;
if
(
ihb
==
1
&&
jhb
==
2
)
{
hbonds
->
select
.
hbond_list
[
ihb_top
].
nbr
=
j
;
hbonds
->
select
.
hbond_list
[
ihb_top
].
scl
=
1
;
hbonds
->
select
.
hbond_list
[
ihb_top
].
ptr
=
nbr_pj
;
++
ihb_top
;
++
num_hbonds
;
}
else
if
(
j
<
system
->
n
&&
ihb
==
2
&&
jhb
==
1
)
{
jhb_top
=
End_Index
(
atom_j
->
Hindex
,
hbonds
);
hbonds
->
select
.
hbond_list
[
jhb_top
].
nbr
=
i
;
hbonds
->
select
.
hbond_list
[
jhb_top
].
scl
=
-
1
;
hbonds
->
select
.
hbond_list
[
jhb_top
].
ptr
=
nbr_pj
;
Set_End_Index
(
atom_j
->
Hindex
,
jhb_top
+
1
,
hbonds
);
++
num_hbonds
;
}
}
}
if
(
//(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
nbr_pj
->
d
<=
control
->
bond_cut
&&
BOp
(
workspace
,
bonds
,
control
->
bo_cut
,
i
,
btop_i
,
nbr_pj
,
sbp_i
,
sbp_j
,
twbp
)
)
{
num_bonds
+=
2
;
++
btop_i
;
if
(
workspace
->
bond_mark
[
j
]
>
workspace
->
bond_mark
[
i
]
+
1
)
workspace
->
bond_mark
[
j
]
=
workspace
->
bond_mark
[
i
]
+
1
;
else
if
(
workspace
->
bond_mark
[
i
]
>
workspace
->
bond_mark
[
j
]
+
1
)
{
workspace
->
bond_mark
[
i
]
=
workspace
->
bond_mark
[
j
]
+
1
;
}
}
}
}
Set_End_Index
(
i
,
btop_i
,
bonds
);
if
(
local
&&
ihb
==
1
)
Set_End_Index
(
atom_i
->
Hindex
,
ihb_top
,
hbonds
);
}
workspace
->
realloc
.
num_bonds
=
num_bonds
;
workspace
->
realloc
.
num_hbonds
=
num_hbonds
;
Validate_Lists
(
system
,
workspace
,
lists
,
data
->
step
,
system
->
n
,
system
->
N
,
system
->
numH
,
comm
);
}
void
Estimate_Storages
(
reax_system
*
system
,
control_params
*
control
,
reax_list
**
lists
,
int
*
Htop
,
int
*
hb_top
,
int
*
bond_top
,
int
*
num_3body
,
MPI_Comm
comm
)
{
int
i
,
j
,
pj
;
int
start_i
,
end_i
;
int
type_i
,
type_j
;
int
ihb
,
jhb
;
int
local
;
double
cutoff
;
double
r_ij
;
double
C12
,
C34
,
C56
;
double
BO
,
BO_s
,
BO_pi
,
BO_pi2
;
reax_list
*
far_nbrs
;
single_body_parameters
*
sbp_i
,
*
sbp_j
;
two_body_parameters
*
twbp
;
far_neighbor_data
*
nbr_pj
;
reax_atom
*
atom_i
,
*
atom_j
;
int
mincap
=
system
->
mincap
;
double
safezone
=
system
->
safezone
;
double
saferzone
=
system
->
saferzone
;
far_nbrs
=
*
lists
+
FAR_NBRS
;
*
Htop
=
0
;
memset
(
hb_top
,
0
,
sizeof
(
int
)
*
system
->
local_cap
);
memset
(
bond_top
,
0
,
sizeof
(
int
)
*
system
->
total_cap
);
*
num_3body
=
0
;
for
(
i
=
0
;
i
<
system
->
N
;
++
i
)
{
atom_i
=
&
(
system
->
my_atoms
[
i
]);
type_i
=
atom_i
->
type
;
if
(
type_i
<
0
)
continue
;
start_i
=
Start_Index
(
i
,
far_nbrs
);
end_i
=
End_Index
(
i
,
far_nbrs
);
sbp_i
=
&
(
system
->
reax_param
.
sbp
[
type_i
]);
if
(
i
<
system
->
n
)
{
local
=
1
;
cutoff
=
control
->
nonb_cut
;
++
(
*
Htop
);
ihb
=
sbp_i
->
p_hbond
;
}
else
{
local
=
0
;
cutoff
=
control
->
bond_cut
;
ihb
=
-
1
;
}
for
(
pj
=
start_i
;
pj
<
end_i
;
++
pj
)
{
nbr_pj
=
&
(
far_nbrs
->
select
.
far_nbr_list
[
pj
]
);
j
=
nbr_pj
->
nbr
;
atom_j
=
&
(
system
->
my_atoms
[
j
]);
if
(
nbr_pj
->
d
<=
cutoff
)
{
type_j
=
system
->
my_atoms
[
j
].
type
;
if
(
type_j
<
0
)
continue
;
r_ij
=
nbr_pj
->
d
;
sbp_j
=
&
(
system
->
reax_param
.
sbp
[
type_j
]);
twbp
=
&
(
system
->
reax_param
.
tbp
[
type_i
][
type_j
]);
if
(
local
)
{
if
(
j
<
system
->
n
||
atom_i
->
orig_id
<
atom_j
->
orig_id
)
//tryQEq ||1
++
(
*
Htop
);
/* hydrogen bond lists */
if
(
control
->
hbond_cut
>
0.1
&&
(
ihb
==
1
||
ihb
==
2
)
&&
nbr_pj
->
d
<=
control
->
hbond_cut
)
{
jhb
=
sbp_j
->
p_hbond
;
if
(
ihb
==
1
&&
jhb
==
2
)
++
hb_top
[
i
];
else
if
(
j
<
system
->
n
&&
ihb
==
2
&&
jhb
==
1
)
++
hb_top
[
j
];
}
}
/* uncorrected bond orders */
if
(
nbr_pj
->
d
<=
control
->
bond_cut
)
{
if
(
sbp_i
->
r_s
>
0.0
&&
sbp_j
->
r_s
>
0.0
)
{
C12
=
twbp
->
p_bo1
*
pow
(
r_ij
/
twbp
->
r_s
,
twbp
->
p_bo2
);
BO_s
=
(
1.0
+
control
->
bo_cut
)
*
exp
(
C12
);
}
else
BO_s
=
C12
=
0.0
;
if
(
sbp_i
->
r_pi
>
0.0
&&
sbp_j
->
r_pi
>
0.0
)
{
C34
=
twbp
->
p_bo3
*
pow
(
r_ij
/
twbp
->
r_p
,
twbp
->
p_bo4
);
BO_pi
=
exp
(
C34
);
}
else
BO_pi
=
C34
=
0.0
;
if
(
sbp_i
->
r_pi_pi
>
0.0
&&
sbp_j
->
r_pi_pi
>
0.0
)
{
C56
=
twbp
->
p_bo5
*
pow
(
r_ij
/
twbp
->
r_pp
,
twbp
->
p_bo6
);
BO_pi2
=
exp
(
C56
);
}
else
BO_pi2
=
C56
=
0.0
;
/* Initially BO values are the uncorrected ones, page 1 */
BO
=
BO_s
+
BO_pi
+
BO_pi2
;
if
(
BO
>=
control
->
bo_cut
)
{
++
bond_top
[
i
];
++
bond_top
[
j
];
}
}
}
}
}
*
Htop
=
(
int
)(
MAX
(
*
Htop
*
safezone
,
mincap
*
MIN_HENTRIES
));
for
(
i
=
0
;
i
<
system
->
n
;
++
i
)
hb_top
[
i
]
=
(
int
)(
MAX
(
hb_top
[
i
]
*
saferzone
,
MIN_HBONDS
));
for
(
i
=
0
;
i
<
system
->
N
;
++
i
)
{
*
num_3body
+=
SQR
(
bond_top
[
i
]);
bond_top
[
i
]
=
MAX
(
bond_top
[
i
]
*
2
,
MIN_BONDS
);
}
}
void
Compute_Forces
(
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
=
mpi_data
->
world
;
Init_Forces_noQEq
(
system
,
control
,
data
,
workspace
,
lists
,
out_control
,
comm
);
/********* bonded interactions ************/
Compute_Bonded_Forces
(
system
,
control
,
data
,
workspace
,
lists
,
out_control
,
mpi_data
->
world
);
/********* nonbonded interactions ************/
Compute_NonBonded_Forces
(
system
,
control
,
data
,
workspace
,
lists
,
out_control
,
mpi_data
->
world
);
/*********** total force ***************/
Compute_Total_Force
(
system
,
control
,
data
,
workspace
,
lists
,
mpi_data
);
}
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