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MoleculeSet.cpp
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Sat, Sep 7, 02:15
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9 KB
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Mon, Sep 9, 02:15 (2 d)
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blob
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rLAMMPS lammps
MoleculeSet.cpp
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// ATC_Method headers
#include "MoleculeSet.h"
#include "ATC_Method.h"
#include "LammpsInterface.h"
#include "ATC_Error.h"
#include <queue>
#include <utility>
#include <sstream>
using
std
::
multimap
;
using
std
::
map
;
using
std
::
pair
;
using
std
::
set
;
using
std
::
stringstream
;
namespace
ATC
{
//--------------------------------------------------------
//--------------------------------------------------------
// Class MoleculeSet
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
MoleculeSet
::
MoleculeSet
(
ATC_Method
*
atc
,
int
groupBit
)
:
atc_
(
atc
),
groupBit_
(
groupBit
),
lammps_
(
atc
->
lammps_interface
())
{
// do nothing
}
//--------------------------------------------------------
// Destructor
//--------------------------------------------------------
MoleculeSet
::~
MoleculeSet
()
{
clear
();
}
//--------------------------------------------------------
// clear
//--------------------------------------------------------
void
MoleculeSet
::
clear
()
{
moleculeToAtoms_
.
clear
();
localMoleculeToAtoms_
.
clear
();
}
//--------------------------------------------------------
// initialize
//--------------------------------------------------------
void
MoleculeSet
::
initialize
(
map
<
int
,
double
>
*
globalAtomsPerMolecule
)
{
// determine the total number of molecules in this group
// essentially ripped Compute::molecules_in_group from lammps
// find lo/hi molecule ID for any atom in group
int
i
;
int
*
molecule
=
lammps_
->
atom_to_molecule
();
const
int
*
mask
=
lammps_
->
atom_mask
();
int
nlocal
=
lammps_
->
nlocal
();
int
lo
=
lammps_
->
natoms
();
int
hi
=
-
1
;
int
flag
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupBit_
)
{
if
(
molecule
[
i
]
==
0
)
flag
=
1
;
lo
=
MIN
(
lo
,
molecule
[
i
]);
hi
=
MAX
(
hi
,
molecule
[
i
]);
}
}
int
flagall
;
lammps_
->
int_allsum
(
&
flag
,
&
flagall
);
if
(
flagall
)
throw
ATC_Error
(
"Atom with molecule ID = 0 included in atc molecule group"
);
int
globalLo
,
globalHi
;
lammps_
->
int_allmin
(
&
lo
,
&
globalLo
);
lammps_
->
int_allmax
(
&
hi
,
&
globalHi
);
if
(
globalLo
==
lammps_
->
natoms
())
throw
ATC_Error
(
"MoleculeSet:initialize - no molecules correspond to the group"
);
// molmap = vector of length nlen
// set to 1 for IDs that appear in group across all procs, else 0
int
nlen
=
globalHi
-
globalLo
+
1
;
int
*
localCount
=
new
int
[
nlen
];
for
(
i
=
0
;
i
<
nlen
;
i
++
)
localCount
[
i
]
=
0
;
for
(
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupBit_
)
localCount
[
molecule
[
i
]
-
globalLo
]
++
;
int
*
globalCount
=
new
int
[
nlen
];
lammps_
->
int_allsum
(
localCount
,
globalCount
,
nlen
);
// nmolecules = # of non-zero IDs in molmap
// molmap[i] = index of molecule, skipping molecules not in group with -1
nMoleculesTotal_
=
0
;
for
(
i
=
0
;
i
<
nlen
;
i
++
)
if
(
globalCount
[
i
])
nMoleculesTotal_
++
;
if
(
globalAtomsPerMolecule
)
{
for
(
i
=
0
;
i
<
nlen
;
i
++
)
if
(
globalCount
[
i
])
globalAtomsPerMolecule
->
insert
(
pair
<
int
,
double
>
(
i
+
globalLo
,
double
(
globalCount
[
i
])));
}
// deallocate storage
delete
[]
localCount
;
delete
[]
globalCount
;
}
//--------------------------------------------------------
// atoms_by_global_molecule
//--------------------------------------------------------
set
<
int
>
MoleculeSet
::
atoms_by_global_molecule
(
int
id
)
const
{
if
(
need_reset
())
reset
();
typedef
multimap
<
int
,
set
<
int
>
>::
const_iterator
MMIT
;
typedef
set
<
int
>::
const_iterator
SIT
;
pair
<
MMIT
,
MMIT
>
mol
=
moleculeToAtoms_
.
equal_range
(
id
);
set
<
int
>
realAtoms
;
const
set
<
int
>
*
myAtoms
;
for
(
MMIT
molIt
=
mol
.
first
;
molIt
!=
mol
.
second
;
molIt
++
)
{
myAtoms
=
&
(
molIt
->
second
);
for
(
SIT
atomIt
=
myAtoms
->
begin
();
atomIt
!=
myAtoms
->
end
();
atomIt
++
)
realAtoms
.
insert
(
*
atomIt
);
}
return
realAtoms
;
}
//--------------------------------------------------------
// atoms_by_local_molecule
//--------------------------------------------------------
const
set
<
int
>
&
MoleculeSet
::
atoms_by_local_molecule
(
int
id
)
const
{
if
(
need_reset
())
reset
();
return
localMoleculeToAtoms_
[
id
]
->
second
;
}
//--------------------------------------------------------
// set_local_molecules_to_atoms
//--------------------------------------------------------
void
MoleculeSet
::
set_local_molecules_to_atoms
()
const
{
localMoleculeToAtoms_
.
clear
();
localMoleculeToAtoms_
.
reserve
(
moleculeToAtoms_
.
size
());
multimap
<
int
,
set
<
int
>
>::
const_iterator
molecule
;
for
(
molecule
=
moleculeToAtoms_
.
begin
();
molecule
!=
moleculeToAtoms_
.
end
();
molecule
++
)
localMoleculeToAtoms_
.
push_back
(
molecule
);
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class SmallMoleculeSet
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
SmallMoleculeSet
::
SmallMoleculeSet
(
ATC_Method
*
atc
,
int
groupBit
,
PerAtomQuantity
<
int
>
*
bondList
,
PerAtomQuantity
<
int
>
*
numBond
)
:
MoleculeSet
(
atc
,
groupBit
),
bondList_
(
bondList
)
{
}
//--------------------------------------------------------
// Destructor
//--------------------------------------------------------
SmallMoleculeSet
::~
SmallMoleculeSet
()
{
}
//--------------------------------------------------------
// clear
//--------------------------------------------------------
void
SmallMoleculeSet
::
clear
()
{
MoleculeSet
::
clear
();
}
//--------------------------------------------------------
// initialize
//--------------------------------------------------------
void
SmallMoleculeSet
::
initialize
(
std
::
map
<
int
,
double
>
*
globalAtomsPerMolecule
)
{
// make sure newton_bond is off, otherwise use large molecule set
if
(
lammps_
->
newton_bond
())
throw
ATC_Error
(
"Cannot use newton_bond with small molecules"
);
MoleculeSet
::
initialize
(
globalAtomsPerMolecule
);
}
//--------------------------------------------------------
// reset
//--------------------------------------------------------
void
SmallMoleculeSet
::
reset
()
const
{
stringstream
message
;
using
std
::
queue
;
moleculeToAtoms_
.
clear
();
lammps_
->
forward_comm_fix
();
int
*
numBond
=
lammps_
->
num_bond
();
int
**
bondAtom
=
lammps_
->
bond_atom
();
// add in real atoms for molecules
int
*
molecule
=
lammps_
->
atom_to_molecule
();
const
int
*
mask
=
lammps_
->
atom_mask
();
int
nlocal
=
lammps_
->
nlocal
();
_atomFound_
.
resize
(
atc_
->
nproc_ghost
());
_atomFound_
=
false
;
int
nmol
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
queue
<
int
>
myQueue
;
if
((
mask
[
i
]
&
groupBit_
)
&&
!
_atomFound_
(
i
))
{
set
<
int
>
myAtoms
;
myAtoms
.
insert
(
i
);
_atomFound_
(
i
)
=
true
;
for
(
int
j
=
0
;
j
<
numBond
[
i
];
j
++
)
{
int
localIdx
=
lammps_
->
local_to_global_map
(
bondAtom
[
i
][
j
]);
if
(
!
_atomFound_
(
localIdx
))
{
myQueue
.
push
(
localIdx
);
_atomFound_
(
localIdx
)
=
true
;
}
}
while
(
!
myQueue
.
empty
())
{
int
myIdx
=
myQueue
.
front
();
myQueue
.
pop
();
myAtoms
.
insert
(
myIdx
);
for
(
int
j
=
0
;
j
<
numBond
[
myIdx
];
j
++
)
{
int
localIdx
=
lammps_
->
local_to_global_map
(
bondAtom
[
myIdx
][
j
]);
if
(
!
_atomFound_
(
localIdx
))
{
myQueue
.
push
(
localIdx
);
_atomFound_
(
localIdx
)
=
true
;
}
}
}
nmol
++
;
moleculeToAtoms_
.
insert
(
pair
<
int
,
set
<
int
>
>
(
molecule
[
i
],
myAtoms
));
}
}
// set local molecule order
MoleculeSet
::
set_local_molecules_to_atoms
();
needReset_
=
false
;
}
//--------------------------------------------------------
// atoms_by_global_molecule
//--------------------------------------------------------
set
<
int
>
SmallMoleculeSet
::
atoms_by_global_molecule
(
int
id
)
const
{
// take all atoms and prune out ghosts
set
<
int
>
realAtoms
=
MoleculeSet
::
atoms_by_global_molecule
(
id
);
remove_proc_ghosts
(
realAtoms
);
return
realAtoms
;
}
//--------------------------------------------------------
// local_fraction
//--------------------------------------------------------
double
SmallMoleculeSet
::
local_fraction
(
int
id
)
const
{
if
(
need_reset
())
reset
();
set
<
int
>
realAtoms
=
(
localMoleculeToAtoms_
[
id
])
->
second
;
int
totalAtoms
=
realAtoms
.
size
();
remove_proc_ghosts
(
realAtoms
);
return
double
(
realAtoms
.
size
())
/
double
(
totalAtoms
);
}
//--------------------------------------------------------
// remove_proc_ghosts
//--------------------------------------------------------
void
SmallMoleculeSet
::
remove_proc_ghosts
(
set
<
int
>
&
atomSet
)
const
{
int
nlocalIdx
=
lammps_
->
nlocal
()
-
1
;
set
<
int
>::
const_iterator
atomIt
;
for
(
atomIt
=
atomSet
.
begin
();
atomIt
!=
atomSet
.
end
();
atomIt
++
)
{
if
(
*
atomIt
>
nlocalIdx
)
atomSet
.
erase
(
atomIt
);
}
}
};
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