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rLAMMPS lammps
compute_rdf.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Paul Crozier (SNL), Jeff Greathouse (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "compute_rdf.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "group.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
/* ---------------------------------------------------------------------- */
ComputeRDF
::
ComputeRDF
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
)
{
if
(
narg
<
4
||
(
narg
-
4
)
%
2
)
error
->
all
(
FLERR
,
"Illegal compute rdf command"
);
array_flag
=
1
;
extarray
=
0
;
nbin
=
force
->
inumeric
(
FLERR
,
arg
[
3
]);
if
(
nbin
<
1
)
error
->
all
(
FLERR
,
"Illegal compute rdf command"
);
if
(
narg
==
4
)
npairs
=
1
;
else
npairs
=
(
narg
-
4
)
/
2
;
size_array_rows
=
nbin
;
size_array_cols
=
1
+
2
*
npairs
;
int
ntypes
=
atom
->
ntypes
;
memory
->
create
(
rdfpair
,
npairs
,
ntypes
+
1
,
ntypes
+
1
,
"rdf:rdfpair"
);
memory
->
create
(
nrdfpair
,
ntypes
+
1
,
ntypes
+
1
,
"rdf:nrdfpair"
);
ilo
=
new
int
[
npairs
];
ihi
=
new
int
[
npairs
];
jlo
=
new
int
[
npairs
];
jhi
=
new
int
[
npairs
];
if
(
narg
==
4
)
{
ilo
[
0
]
=
1
;
ihi
[
0
]
=
ntypes
;
jlo
[
0
]
=
1
;
jhi
[
0
]
=
ntypes
;
npairs
=
1
;
}
else
{
npairs
=
0
;
int
iarg
=
4
;
while
(
iarg
<
narg
)
{
force
->
bounds
(
arg
[
iarg
],
atom
->
ntypes
,
ilo
[
npairs
],
ihi
[
npairs
]);
force
->
bounds
(
arg
[
iarg
+
1
],
atom
->
ntypes
,
jlo
[
npairs
],
jhi
[
npairs
]);
if
(
ilo
[
npairs
]
>
ihi
[
npairs
]
||
jlo
[
npairs
]
>
jhi
[
npairs
])
error
->
all
(
FLERR
,
"Illegal compute rdf command"
);
npairs
++
;
iarg
+=
2
;
}
}
int
i
,
j
;
for
(
i
=
1
;
i
<=
ntypes
;
i
++
)
for
(
j
=
1
;
j
<=
ntypes
;
j
++
)
nrdfpair
[
i
][
j
]
=
0
;
for
(
int
m
=
0
;
m
<
npairs
;
m
++
)
for
(
i
=
ilo
[
m
];
i
<=
ihi
[
m
];
i
++
)
for
(
j
=
jlo
[
m
];
j
<=
jhi
[
m
];
j
++
)
rdfpair
[
nrdfpair
[
i
][
j
]
++
][
i
][
j
]
=
m
;
memory
->
create
(
hist
,
npairs
,
nbin
,
"rdf:hist"
);
memory
->
create
(
histall
,
npairs
,
nbin
,
"rdf:histall"
);
memory
->
create
(
array
,
nbin
,
1
+
2
*
npairs
,
"rdf:array"
);
typecount
=
new
int
[
ntypes
+
1
];
icount
=
new
int
[
npairs
];
jcount
=
new
int
[
npairs
];
}
/* ---------------------------------------------------------------------- */
ComputeRDF
::~
ComputeRDF
()
{
memory
->
destroy
(
rdfpair
);
memory
->
destroy
(
nrdfpair
);
delete
[]
ilo
;
delete
[]
ihi
;
delete
[]
jlo
;
delete
[]
jhi
;
memory
->
destroy
(
hist
);
memory
->
destroy
(
histall
);
memory
->
destroy
(
array
);
delete
[]
typecount
;
delete
[]
icount
;
delete
[]
jcount
;
}
/* ---------------------------------------------------------------------- */
void
ComputeRDF
::
init
()
{
int
i
,
m
;
if
(
force
->
pair
)
delr
=
force
->
pair
->
cutforce
/
nbin
;
else
error
->
all
(
FLERR
,
"Compute rdf requires a pair style be defined"
);
delrinv
=
1.0
/
delr
;
// set 1st column of output array to bin coords
for
(
int
i
=
0
;
i
<
nbin
;
i
++
)
array
[
i
][
0
]
=
(
i
+
0.5
)
*
delr
;
// count atoms of each type that are also in group
int
*
mask
=
atom
->
mask
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
int
ntypes
=
atom
->
ntypes
;
for
(
i
=
1
;
i
<=
ntypes
;
i
++
)
typecount
[
i
]
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
typecount
[
type
[
i
]]
++
;
// icount = # of I atoms participating in I,J pairs for each histogram
// jcount = # of J atoms participating in I,J pairs for each histogram
for
(
m
=
0
;
m
<
npairs
;
m
++
)
{
icount
[
m
]
=
0
;
for
(
i
=
ilo
[
m
];
i
<=
ihi
[
m
];
i
++
)
icount
[
m
]
+=
typecount
[
i
];
jcount
[
m
]
=
0
;
for
(
i
=
jlo
[
m
];
i
<=
jhi
[
m
];
i
++
)
jcount
[
m
]
+=
typecount
[
i
];
}
int
*
scratch
=
new
int
[
npairs
];
MPI_Allreduce
(
icount
,
scratch
,
npairs
,
MPI_INT
,
MPI_SUM
,
world
);
for
(
i
=
0
;
i
<
npairs
;
i
++
)
icount
[
i
]
=
scratch
[
i
];
MPI_Allreduce
(
jcount
,
scratch
,
npairs
,
MPI_INT
,
MPI_SUM
,
world
);
for
(
i
=
0
;
i
<
npairs
;
i
++
)
jcount
[
i
]
=
scratch
[
i
];
delete
[]
scratch
;
// need an occasional half neighbor list
int
irequest
=
neighbor
->
request
((
void
*
)
this
);
neighbor
->
requests
[
irequest
]
->
pair
=
0
;
neighbor
->
requests
[
irequest
]
->
compute
=
1
;
neighbor
->
requests
[
irequest
]
->
occasional
=
1
;
}
/* ---------------------------------------------------------------------- */
void
ComputeRDF
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
list
=
ptr
;
}
/* ---------------------------------------------------------------------- */
void
ComputeRDF
::
compute_array
()
{
int
i
,
j
,
m
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
,
ipair
,
jpair
,
ibin
,
ihisto
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
r
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
factor_lj
,
factor_coul
;
invoked_array
=
update
->
ntimestep
;
// invoke half neighbor list (will copy or build if necessary)
neighbor
->
build_one
(
list
->
index
);
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// zero the histogram counts
for
(
i
=
0
;
i
<
npairs
;
i
++
)
for
(
j
=
0
;
j
<
nbin
;
j
++
)
hist
[
i
][
j
]
=
0
;
// tally the RDF
// both atom i and j must be in fix group
// itype,jtype must have been specified by user
// consider I,J as one interaction even if neighbor pair is stored on 2 procs
// tally I,J pair each time I is central atom, and each time J is central
double
**
x
=
atom
->
x
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
*
special_coul
=
force
->
special_coul
;
double
*
special_lj
=
force
->
special_lj
;
int
newton_pair
=
force
->
newton_pair
;
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
if
(
!
(
mask
[
i
]
&
groupbit
))
continue
;
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
itype
=
type
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
factor_lj
=
special_lj
[
sbmask
(
j
)];
factor_coul
=
special_coul
[
sbmask
(
j
)];
j
&=
NEIGHMASK
;
// if both weighting factors are 0, skip this pair
// could be 0 and still be in neigh list for long-range Coulombics
// want consistency with non-charged pairs which wouldn't be in list
if
(
factor_lj
==
0.0
&&
factor_coul
==
0.0
)
continue
;
if
(
!
(
mask
[
j
]
&
groupbit
))
continue
;
jtype
=
type
[
j
];
ipair
=
nrdfpair
[
itype
][
jtype
];
jpair
=
nrdfpair
[
jtype
][
itype
];
if
(
!
ipair
&&
!
jpair
)
continue
;
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
r
=
sqrt
(
delx
*
delx
+
dely
*
dely
+
delz
*
delz
);
ibin
=
static_cast
<
int
>
(
r
*
delrinv
);
if
(
ibin
>=
nbin
)
continue
;
if
(
ipair
)
for
(
ihisto
=
0
;
ihisto
<
ipair
;
ihisto
++
)
hist
[
rdfpair
[
ihisto
][
itype
][
jtype
]][
ibin
]
+=
1.0
;
if
(
newton_pair
||
j
<
nlocal
)
{
if
(
jpair
)
for
(
ihisto
=
0
;
ihisto
<
jpair
;
ihisto
++
)
hist
[
rdfpair
[
ihisto
][
jtype
][
itype
]][
ibin
]
+=
1.0
;
}
}
}
// sum histograms across procs
MPI_Allreduce
(
hist
[
0
],
histall
[
0
],
npairs
*
nbin
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
// convert counts to g(r) and coord(r) and copy into output array
// nideal = # of J atoms surrounding single I atom in a single bin
// assuming J atoms are at uniform density
double
constant
,
nideal
,
gr
,
ncoord
,
rlower
,
rupper
;
if
(
domain
->
dimension
==
3
)
{
constant
=
4.0
*
MY_PI
/
(
3.0
*
domain
->
xprd
*
domain
->
yprd
*
domain
->
zprd
);
for
(
m
=
0
;
m
<
npairs
;
m
++
)
{
ncoord
=
0.0
;
for
(
ibin
=
0
;
ibin
<
nbin
;
ibin
++
)
{
rlower
=
ibin
*
delr
;
rupper
=
(
ibin
+
1
)
*
delr
;
nideal
=
constant
*
(
rupper
*
rupper
*
rupper
-
rlower
*
rlower
*
rlower
)
*
jcount
[
m
];
if
(
icount
[
m
]
*
nideal
!=
0.0
)
gr
=
histall
[
m
][
ibin
]
/
(
icount
[
m
]
*
nideal
);
else
gr
=
0.0
;
ncoord
+=
gr
*
nideal
;
array
[
ibin
][
1
+
2
*
m
]
=
gr
;
array
[
ibin
][
2
+
2
*
m
]
=
ncoord
;
}
}
}
else
{
constant
=
MY_PI
/
(
domain
->
xprd
*
domain
->
yprd
);
for
(
m
=
0
;
m
<
npairs
;
m
++
)
{
ncoord
=
0.0
;
for
(
ibin
=
0
;
ibin
<
nbin
;
ibin
++
)
{
rlower
=
ibin
*
delr
;
rupper
=
(
ibin
+
1
)
*
delr
;
nideal
=
constant
*
(
rupper
*
rupper
-
rlower
*
rlower
)
*
jcount
[
m
];
if
(
icount
[
m
]
*
nideal
!=
0.0
)
gr
=
histall
[
m
][
ibin
]
/
(
icount
[
m
]
*
nideal
);
else
gr
=
0.0
;
ncoord
+=
gr
*
nideal
;
array
[
ibin
][
1
+
2
*
m
]
=
gr
;
array
[
ibin
][
2
+
2
*
m
]
=
ncoord
;
}
}
}
}
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