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compute_bond_local.cpp
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rLAMMPS lammps
compute_bond_local.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.
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include "compute_bond_local.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "update.h"
#include "domain.h"
#include "force.h"
#include "bond.h"
#include "math_extra.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define DELTA 10000
#define EPSILON 1.0e-12
enum
{
DIST
,
VELVIB
,
OMEGA
,
ENGTRANS
,
ENGVIB
,
ENGROT
,
ENGPOT
,
FORCE
};
/* ---------------------------------------------------------------------- */
ComputeBondLocal
::
ComputeBondLocal
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Compute
(
lmp
,
narg
,
arg
),
bstyle
(
NULL
),
vlocal
(
NULL
),
alocal
(
NULL
)
{
if
(
narg
<
4
)
error
->
all
(
FLERR
,
"Illegal compute bond/local command"
);
if
(
atom
->
avec
->
bonds_allow
==
0
)
error
->
all
(
FLERR
,
"Compute bond/local used when bonds are not allowed"
);
local_flag
=
1
;
comm_forward
=
3
;
nvalues
=
narg
-
3
;
if
(
nvalues
==
1
)
size_local_cols
=
0
;
else
size_local_cols
=
nvalues
;
bstyle
=
new
int
[
nvalues
];
nvalues
=
0
;
for
(
int
iarg
=
3
;
iarg
<
narg
;
iarg
++
)
{
if
(
strcmp
(
arg
[
iarg
],
"dist"
)
==
0
)
bstyle
[
nvalues
++
]
=
DIST
;
else
if
(
strcmp
(
arg
[
iarg
],
"engpot"
)
==
0
)
bstyle
[
nvalues
++
]
=
ENGPOT
;
else
if
(
strcmp
(
arg
[
iarg
],
"force"
)
==
0
)
bstyle
[
nvalues
++
]
=
FORCE
;
else
if
(
strcmp
(
arg
[
iarg
],
"engvib"
)
==
0
)
bstyle
[
nvalues
++
]
=
ENGVIB
;
else
if
(
strcmp
(
arg
[
iarg
],
"engrot"
)
==
0
)
bstyle
[
nvalues
++
]
=
ENGROT
;
else
if
(
strcmp
(
arg
[
iarg
],
"engtrans"
)
==
0
)
bstyle
[
nvalues
++
]
=
ENGTRANS
;
else
if
(
strcmp
(
arg
[
iarg
],
"omega"
)
==
0
)
bstyle
[
nvalues
++
]
=
OMEGA
;
else
if
(
strcmp
(
arg
[
iarg
],
"velvib"
)
==
0
)
bstyle
[
nvalues
++
]
=
VELVIB
;
else
error
->
all
(
FLERR
,
"Invalid keyword in compute bond/local command"
);
}
// set singleflag if need to call bond->single()
// set velflag if compute any quantities based on velocities
singleflag
=
0
;
velflag
=
0
;
for
(
int
i
=
0
;
i
<
nvalues
;
i
++
)
{
if
(
bstyle
[
i
]
==
ENGPOT
||
bstyle
[
i
]
==
FORCE
)
singleflag
=
1
;
if
(
bstyle
[
i
]
==
VELVIB
||
bstyle
[
i
]
==
OMEGA
||
bstyle
[
i
]
==
ENGTRANS
||
bstyle
[
i
]
==
ENGVIB
||
bstyle
[
i
]
==
ENGROT
)
velflag
=
1
;
}
nmax
=
0
;
vlocal
=
NULL
;
alocal
=
NULL
;
}
/* ---------------------------------------------------------------------- */
ComputeBondLocal
::~
ComputeBondLocal
()
{
memory
->
destroy
(
vlocal
);
memory
->
destroy
(
alocal
);
delete
[]
bstyle
;
}
/* ---------------------------------------------------------------------- */
void
ComputeBondLocal
::
init
()
{
if
(
force
->
bond
==
NULL
)
error
->
all
(
FLERR
,
"No bond style is defined for compute bond/local"
);
// set ghostvelflag if need to acquire ghost atom velocities
if
(
velflag
&&
!
comm
->
ghost_velocity
)
ghostvelflag
=
1
;
else
ghostvelflag
=
0
;
// do initial memory allocation so that memory_usage() is correct
initflag
=
1
;
ncount
=
compute_bonds
(
0
);
initflag
=
0
;
if
(
ncount
>
nmax
)
reallocate
(
ncount
);
size_local_rows
=
ncount
;
}
/* ---------------------------------------------------------------------- */
void
ComputeBondLocal
::
compute_local
()
{
invoked_local
=
update
->
ntimestep
;
// count local entries and compute bond info
ncount
=
compute_bonds
(
0
);
if
(
ncount
>
nmax
)
reallocate
(
ncount
);
size_local_rows
=
ncount
;
ncount
=
compute_bonds
(
1
);
}
/* ----------------------------------------------------------------------
count bonds and compute bond info on this proc
only count bond once if newton_bond is off
all atoms in interaction must be in group
all atoms in interaction must be known to proc
if bond is deleted (type = 0), do not count
if bond is turned off (type < 0), still count
if flag is set, compute requested info about bond
if bond is turned off (type < 0), energy = 0.0
------------------------------------------------------------------------- */
int
ComputeBondLocal
::
compute_bonds
(
int
flag
)
{
int
i
,
m
,
n
,
nb
,
atom1
,
atom2
,
imol
,
iatom
,
btype
;
tagint
tagprev
;
double
dx
,
dy
,
dz
,
rsq
;
double
mass1
,
mass2
,
masstotal
,
invmasstotal
;
double
xcm
[
3
],
vcm
[
3
];
double
delr1
[
3
],
delr2
[
3
],
delv1
[
3
],
delv2
[
3
];
double
r12
[
3
],
vpar1
,
vpar2
;
double
vvib
,
vrotsq
;
double
inertia
,
omegasq
;
double
mvv2e
;
double
engpot
,
engtrans
,
engvib
,
engrot
,
fbond
;
double
*
ptr
;
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
int
*
type
=
atom
->
type
;
double
*
mass
=
atom
->
mass
;
double
*
rmass
=
atom
->
rmass
;
tagint
*
tag
=
atom
->
tag
;
int
*
num_bond
=
atom
->
num_bond
;
tagint
**
bond_atom
=
atom
->
bond_atom
;
int
**
bond_type
=
atom
->
bond_type
;
int
*
mask
=
atom
->
mask
;
int
*
molindex
=
atom
->
molindex
;
int
*
molatom
=
atom
->
molatom
;
Molecule
**
onemols
=
atom
->
avec
->
onemols
;
int
nlocal
=
atom
->
nlocal
;
int
newton_bond
=
force
->
newton_bond
;
int
molecular
=
atom
->
molecular
;
Bond
*
bond
=
force
->
bond
;
// communicate ghost velocities if needed
if
(
ghostvelflag
&&
!
initflag
)
comm
->
forward_comm_compute
(
this
);
// loop over all atoms and their bonds
m
=
n
=
0
;
for
(
atom1
=
0
;
atom1
<
nlocal
;
atom1
++
)
{
if
(
!
(
mask
[
atom1
]
&
groupbit
))
continue
;
if
(
molecular
==
1
)
nb
=
num_bond
[
atom1
];
else
{
if
(
molindex
[
atom1
]
<
0
)
continue
;
imol
=
molindex
[
atom1
];
iatom
=
molatom
[
atom1
];
nb
=
onemols
[
imol
]
->
num_bond
[
iatom
];
}
for
(
i
=
0
;
i
<
nb
;
i
++
)
{
if
(
molecular
==
1
)
{
btype
=
bond_type
[
atom1
][
i
];
atom2
=
atom
->
map
(
bond_atom
[
atom1
][
i
]);
}
else
{
tagprev
=
tag
[
atom1
]
-
iatom
-
1
;
btype
=
onemols
[
imol
]
->
bond_type
[
iatom
][
i
];
atom2
=
atom
->
map
(
onemols
[
imol
]
->
bond_atom
[
iatom
][
i
]
+
tagprev
);
}
if
(
atom2
<
0
||
!
(
mask
[
atom2
]
&
groupbit
))
continue
;
if
(
newton_bond
==
0
&&
tag
[
atom1
]
>
tag
[
atom2
])
continue
;
if
(
btype
==
0
)
continue
;
if
(
!
flag
)
{
m
++
;
continue
;
}
dx
=
x
[
atom1
][
0
]
-
x
[
atom2
][
0
];
dy
=
x
[
atom1
][
1
]
-
x
[
atom2
][
1
];
dz
=
x
[
atom1
][
2
]
-
x
[
atom2
][
2
];
domain
->
minimum_image
(
dx
,
dy
,
dz
);
rsq
=
dx
*
dx
+
dy
*
dy
+
dz
*
dz
;
if
(
btype
==
0
)
{
engpot
=
fbond
=
0.0
;
engvib
=
engrot
=
engtrans
=
omegasq
=
vvib
=
0.0
;
}
else
{
if
(
singleflag
)
engpot
=
bond
->
single
(
btype
,
rsq
,
atom1
,
atom2
,
fbond
);
if
(
velflag
)
{
if
(
rmass
)
{
mass1
=
rmass
[
atom1
];
mass2
=
rmass
[
atom2
];
}
else
{
mass1
=
mass
[
type
[
atom1
]];
mass2
=
mass
[
type
[
atom2
]];
}
masstotal
=
mass1
+
mass2
;
invmasstotal
=
1.0
/
(
masstotal
);
xcm
[
0
]
=
(
mass1
*
x
[
atom1
][
0
]
+
mass2
*
x
[
atom2
][
0
])
*
invmasstotal
;
xcm
[
1
]
=
(
mass1
*
x
[
atom1
][
1
]
+
mass2
*
x
[
atom2
][
1
])
*
invmasstotal
;
xcm
[
2
]
=
(
mass1
*
x
[
atom1
][
2
]
+
mass2
*
x
[
atom2
][
2
])
*
invmasstotal
;
vcm
[
0
]
=
(
mass1
*
v
[
atom1
][
0
]
+
mass2
*
v
[
atom2
][
0
])
*
invmasstotal
;
vcm
[
1
]
=
(
mass1
*
v
[
atom1
][
1
]
+
mass2
*
v
[
atom2
][
1
])
*
invmasstotal
;
vcm
[
2
]
=
(
mass1
*
v
[
atom1
][
2
]
+
mass2
*
v
[
atom2
][
2
])
*
invmasstotal
;
engtrans
=
0.5
*
masstotal
*
MathExtra
::
lensq3
(
vcm
);
// r12 = unit bond vector from atom1 to atom2
MathExtra
::
sub3
(
x
[
atom2
],
x
[
atom1
],
r12
);
MathExtra
::
norm3
(
r12
);
// delr = vector from COM to each atom
// delv = velocity of each atom relative to COM
MathExtra
::
sub3
(
x
[
atom1
],
xcm
,
delr1
);
MathExtra
::
sub3
(
x
[
atom2
],
xcm
,
delr2
);
MathExtra
::
sub3
(
v
[
atom1
],
vcm
,
delv1
);
MathExtra
::
sub3
(
v
[
atom2
],
vcm
,
delv2
);
// vpar = component of delv parallel to bond vector
vpar1
=
MathExtra
::
dot3
(
delv1
,
r12
);
vpar2
=
MathExtra
::
dot3
(
delv2
,
r12
);
engvib
=
0.5
*
(
mass1
*
vpar1
*
vpar1
+
mass2
*
vpar2
*
vpar2
);
// vvib = relative velocity of 2 atoms along bond direction
// vvib < 0 for 2 atoms moving towards each other
// vvib > 0 for 2 atoms moving apart
vvib
=
vpar2
-
vpar1
;
// vrotsq = tangential speed squared of atom1 only
// omegasq = omega squared, and is the same for atom1 and atom2
inertia
=
mass1
*
MathExtra
::
lensq3
(
delr1
)
+
mass2
*
MathExtra
::
lensq3
(
delr2
);
vrotsq
=
MathExtra
::
lensq3
(
delv1
)
-
vpar1
*
vpar1
;
omegasq
=
vrotsq
/
MathExtra
::
lensq3
(
delr1
);
engrot
=
0.5
*
inertia
*
omegasq
;
// sanity check: engtotal = engtrans + engvib + engrot
//engtot = 0.5 * (mass1*MathExtra::lensq3(v[atom1]) +
// mass2*MathExtra::lensq3(v[atom2]));
//if (fabs(engtot-engtrans-engvib-engrot) > EPSILON)
// error->one(FLERR,"Sanity check on 3 energy components failed");
// scale energies by units
mvv2e
=
force
->
mvv2e
;
engtrans
*=
mvv2e
;
engvib
*=
mvv2e
;
engrot
*=
mvv2e
;
}
if
(
nvalues
==
1
)
ptr
=
&
vlocal
[
m
];
else
ptr
=
alocal
[
m
];
for
(
n
=
0
;
n
<
nvalues
;
n
++
)
{
switch
(
bstyle
[
n
])
{
case
DIST:
ptr
[
n
]
=
sqrt
(
rsq
);
break
;
case
ENGPOT:
ptr
[
n
]
=
engpot
;
break
;
case
FORCE:
ptr
[
n
]
=
sqrt
(
rsq
)
*
fbond
;
break
;
case
ENGVIB:
ptr
[
n
]
=
engvib
;
break
;
case
ENGROT:
ptr
[
n
]
=
engrot
;
break
;
case
ENGTRANS:
ptr
[
n
]
=
engtrans
;
break
;
case
OMEGA:
ptr
[
n
]
=
sqrt
(
omegasq
);
break
;
case
VELVIB:
ptr
[
n
]
=
vvib
;
break
;
}
}
}
m
++
;
}
}
return
m
;
}
/* ---------------------------------------------------------------------- */
int
ComputeBondLocal
::
pack_forward_comm
(
int
n
,
int
*
list
,
double
*
buf
,
int
pbc_flag
,
int
*
pbc
)
{
int
i
,
j
,
m
;
double
**
v
=
atom
->
v
;
m
=
0
;
for
(
i
=
0
;
i
<
n
;
i
++
)
{
j
=
list
[
i
];
buf
[
m
++
]
=
v
[
j
][
0
];
buf
[
m
++
]
=
v
[
j
][
1
];
buf
[
m
++
]
=
v
[
j
][
2
];
}
return
m
;
}
/* ---------------------------------------------------------------------- */
void
ComputeBondLocal
::
unpack_forward_comm
(
int
n
,
int
first
,
double
*
buf
)
{
int
i
,
m
,
last
;
double
**
v
=
atom
->
v
;
m
=
0
;
last
=
first
+
n
;
for
(
i
=
first
;
i
<
last
;
i
++
)
{
v
[
i
][
0
]
=
buf
[
m
++
];
v
[
i
][
1
]
=
buf
[
m
++
];
v
[
i
][
2
]
=
buf
[
m
++
];
}
}
/* ---------------------------------------------------------------------- */
void
ComputeBondLocal
::
reallocate
(
int
n
)
{
// grow vector_local or array_local
while
(
nmax
<
n
)
nmax
+=
DELTA
;
if
(
nvalues
==
1
)
{
memory
->
destroy
(
vlocal
);
memory
->
create
(
vlocal
,
nmax
,
"bond/local:vector_local"
);
vector_local
=
vlocal
;
}
else
{
memory
->
destroy
(
alocal
);
memory
->
create
(
alocal
,
nmax
,
nvalues
,
"bond/local:array_local"
);
array_local
=
alocal
;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double
ComputeBondLocal
::
memory_usage
()
{
double
bytes
=
nmax
*
nvalues
*
sizeof
(
double
);
return
bytes
;
}
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