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FundamentalAtomicQuantity.cpp
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Tue, Jun 4, 18:43
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Thu, Jun 6, 18:43 (2 d)
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rLAMMPS lammps
FundamentalAtomicQuantity.cpp
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#include "FundamentalAtomicQuantity.h"
using
std
::
string
;
namespace
ATC
{
//--------------------------------------------------------
//--------------------------------------------------------
// Class FundamentalAtomQuantity
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
FundamentalAtomQuantity
::
FundamentalAtomQuantity
(
ATC_Method
*
atc
,
LammpsInterface
::
FundamentalAtomQuantity
atomQuantity
,
AtomType
atomType
)
:
ShallowAtomQuantity
<
double
>
(
atc
,
0
,
atomType
),
atomQuantity_
(
atomQuantity
),
unitsConversion_
(
lammpsInterface_
->
atom_quantity_conversion
(
atomQuantity_
))
{
nCols_
=
lammpsInterface_
->
atom_quantity_ndof
(
atomQuantity_
);
}
//--------------------------------------------------------
// set_lammps_to_quantity
//--------------------------------------------------------
void
FundamentalAtomQuantity
::
set_lammps_to_quantity
()
const
{
if
(
unitsConversion_
==
1.
)
{
// is there a way to avoid equal testing a double?
PerAtomQuantity
<
double
>::
set_lammps_to_quantity
();
}
else
{
// perform unit conversion
if
(
quantity_
.
nRows
()
>
0
)
{
// full matrix copy
if
(
atomType_
==
ALL
||
atomType_
==
PROC_GHOST
)
{
if
(
nCols_
==
1
)
{
// scalar
double
*
lammpsQuantity
=
lammps_scalar
();
for
(
int
i
=
0
;
i
<
atc_
.
nlocal_total
();
i
++
)
lammpsQuantity
[
i
]
=
quantity_
(
i
,
0
)
/
unitsConversion_
;
}
else
{
// vector
double
**
lammpsQuantity
=
lammps_vector
();
for
(
int
i
=
0
;
i
<
atc_
.
nlocal_total
();
i
++
)
for
(
int
j
=
0
;
j
<
nCols_
;
j
++
)
lammpsQuantity
[
i
][
j
]
=
quantity_
(
i
,
j
)
/
unitsConversion_
;
}
}
// mapped copy
else
{
int
atomIndex
;
if
(
nCols_
==
1
)
{
// scalar
double
*
lammpsQuantity
=
lammps_scalar
();
for
(
int
i
=
0
;
i
<
quantity_
.
nRows
();
i
++
)
{
atomIndex
=
quantityToLammps_
(
i
);
lammpsQuantity
[
atomIndex
]
=
quantity_
(
i
,
0
)
/
unitsConversion_
;
}
}
else
{
// vector
double
**
lammpsQuantity
=
lammps_vector
();
for
(
int
i
=
0
;
i
<
quantity_
.
nRows
();
i
++
)
{
atomIndex
=
quantityToLammps_
(
i
);
for
(
int
j
=
0
;
j
<
nCols_
;
j
++
)
{
lammpsQuantity
[
atomIndex
][
j
]
=
quantity_
(
i
,
j
)
/
unitsConversion_
;
}
}
}
}
}
}
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class AtomMass
// Access-only operations when mass is
// defined per type.
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
AtomMass
::
AtomMass
(
ATC_Method
*
atc
,
AtomType
atomType
)
:
FundamentalAtomQuantity
(
atc
,
LammpsInterface
::
ATOM_MASS
,
atomType
)
{
// do nothing
}
//--------------------------------------------------------
// set_quantity_to_lammps
//--------------------------------------------------------
void
AtomMass
::
set_quantity_to_lammps
()
const
{
const
int
*
type
=
lammpsInterface_
->
atom_type
();
const
double
*
mass
=
lammpsInterface_
->
atom_mass
();
if
(
atomType_
==
ALL
||
atomType_
==
PROC_GHOST
)
{
for
(
int
i
=
0
;
i
<
quantity_
.
nRows
();
i
++
)
quantity_
(
i
,
0
)
=
mass
[
type
[
i
]];
}
else
{
int
atomIndex
;
for
(
int
i
=
0
;
i
<
quantity_
.
nRows
();
i
++
)
{
atomIndex
=
quantityToLammps_
(
i
);
quantity_
(
i
,
0
)
=
mass
[
type
[
atomIndex
]];
}
}
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class ComputedAtomQuantity
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
ComputedAtomQuantity
::
ComputedAtomQuantity
(
ATC_Method
*
atc
,
const
string
&
tag
,
double
unitsConversion
,
AtomType
atomType
)
:
ShallowAtomQuantity
<
double
>
(
atc
,
0
,
atomType
),
computePointer_
(
NULL
),
computeTag_
(
tag
),
unitsConversion_
(
unitsConversion
)
{
// register compute with lammps interface and provide pointer for syncing
computePointer_
=
lammpsInterface_
->
compute_pointer
(
computeTag_
.
c_str
());
nCols_
=
lammpsInterface_
->
compute_ncols_peratom
(
computePointer_
);
}
//--------------------------------------------------------
// force_reset
//--------------------------------------------------------
void
ComputedAtomQuantity
::
force_reset
()
{
// only reset if the compute needs it this timestep
if
(
lammpsInterface_
->
compute_matchstep
(
computePointer_
,
lammpsInterface_
->
ntimestep
()))
{
if
(
!
isFixed_
)
{
lammpsInterface_
->
reset_invoked_flag
(
computePointer_
);
}
ShallowAtomQuantity
<
double
>::
force_reset
();
}
}
}
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