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rLAMMPS lammps
pair_sph_lj.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 "stdlib.h"
#include "pair_sph_lj.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "domain.h"
using
namespace
LAMMPS_NS
;
/* ---------------------------------------------------------------------- */
PairSPHLJ
::
PairSPHLJ
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
restartinfo
=
0
;
}
/* ---------------------------------------------------------------------- */
PairSPHLJ
::~
PairSPHLJ
()
{
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
memory
->
destroy
(
cut
);
memory
->
destroy
(
viscosity
);
}
}
/* ---------------------------------------------------------------------- */
void
PairSPHLJ
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
ii
,
jj
,
inum
,
jnum
,
itype
,
jtype
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
fpair
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
double
vxtmp
,
vytmp
,
vztmp
,
imass
,
jmass
,
fi
,
fj
,
fvisc
,
h
,
ih
,
ihsq
,
ihcub
;
double
rsq
,
wfd
,
delVdotDelR
,
mu
,
deltaE
,
ci
,
cj
,
lrc
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
double
**
v
=
atom
->
vest
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
double
*
rho
=
atom
->
rho
;
double
*
mass
=
atom
->
mass
;
double
*
de
=
atom
->
de
;
double
*
e
=
atom
->
e
;
double
*
cv
=
atom
->
cv
;
double
*
drho
=
atom
->
drho
;
int
*
type
=
atom
->
type
;
int
nlocal
=
atom
->
nlocal
;
int
newton_pair
=
force
->
newton_pair
;
inum
=
list
->
inum
;
ilist
=
list
->
ilist
;
numneigh
=
list
->
numneigh
;
firstneigh
=
list
->
firstneigh
;
// loop over neighbors of my atoms
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
vxtmp
=
v
[
i
][
0
];
vytmp
=
v
[
i
][
1
];
vztmp
=
v
[
i
][
2
];
itype
=
type
[
i
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
imass
=
mass
[
itype
];
// compute pressure of particle i with LJ EOS
LJEOS2
(
rho
[
i
],
e
[
i
],
cv
[
i
],
&
fi
,
&
ci
);
fi
/=
(
rho
[
i
]
*
rho
[
i
]);
//printf("fi = %f\n", fi);
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
jtype
=
type
[
j
];
jmass
=
mass
[
jtype
];
if
(
rsq
<
cutsq
[
itype
][
jtype
])
{
h
=
cut
[
itype
][
jtype
];
ih
=
1.0
/
h
;
ihsq
=
ih
*
ih
;
ihcub
=
ihsq
*
ih
;
wfd
=
h
-
sqrt
(
rsq
);
if
(
domain
->
dimension
==
3
)
{
// Lucy Kernel, 3d
// Note that wfd, the derivative of the weight function with respect to r,
// is lacking a factor of r.
// The missing factor of r is recovered by
// (1) using delV . delX instead of delV . (delX/r) and
// (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair
wfd
=
-
25.066903536973515383e0
*
wfd
*
wfd
*
ihsq
*
ihsq
*
ihsq
*
ih
;
}
else
{
// Lucy Kernel, 2d
wfd
=
-
19.098593171027440292e0
*
wfd
*
wfd
*
ihsq
*
ihsq
*
ihsq
;
}
// function call to LJ EOS
LJEOS2
(
rho
[
j
],
e
[
j
],
cv
[
j
],
&
fj
,
&
cj
);
fj
/=
(
rho
[
j
]
*
rho
[
j
]);
// apply long-range correction to model a LJ fluid with cutoff
// this implies that the modelled LJ fluid has cutoff == SPH cutoff
lrc
=
-
11.1701
*
(
ihcub
*
ihcub
*
ihcub
-
1.5
*
ihcub
);
fi
+=
lrc
;
fj
+=
lrc
;
// dot product of velocity delta and distance vector
delVdotDelR
=
delx
*
(
vxtmp
-
v
[
j
][
0
])
+
dely
*
(
vytmp
-
v
[
j
][
1
])
+
delz
*
(
vztmp
-
v
[
j
][
2
]);
// artificial viscosity (Monaghan 1992)
if
(
delVdotDelR
<
0.
)
{
mu
=
h
*
delVdotDelR
/
(
rsq
+
0.01
*
h
*
h
);
fvisc
=
-
viscosity
[
itype
][
jtype
]
*
(
ci
+
cj
)
*
mu
/
(
rho
[
i
]
+
rho
[
j
]);
}
else
{
fvisc
=
0.
;
}
// total pair force & thermal energy increment
fpair
=
-
imass
*
jmass
*
(
fi
+
fj
+
fvisc
)
*
wfd
;
deltaE
=
-
0.5
*
fpair
*
delVdotDelR
;
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
// and change in density
drho
[
i
]
+=
jmass
*
delVdotDelR
*
wfd
;
// change in thermal energy
de
[
i
]
+=
deltaE
;
if
(
newton_pair
||
j
<
nlocal
)
{
f
[
j
][
0
]
-=
delx
*
fpair
;
f
[
j
][
1
]
-=
dely
*
fpair
;
f
[
j
][
2
]
-=
delz
*
fpair
;
de
[
j
]
+=
deltaE
;
drho
[
j
]
+=
imass
*
delVdotDelR
*
wfd
;
}
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
0.0
,
0.0
,
fpair
,
delx
,
dely
,
delz
);
}
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void
PairSPHLJ
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
memory
->
create
(
setflag
,
n
+
1
,
n
+
1
,
"pair:setflag"
);
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
memory
->
create
(
cutsq
,
n
+
1
,
n
+
1
,
"pair:cutsq"
);
memory
->
create
(
cut
,
n
+
1
,
n
+
1
,
"pair:cut"
);
memory
->
create
(
viscosity
,
n
+
1
,
n
+
1
,
"pair:viscosity"
);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairSPHLJ
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
0
)
error
->
all
(
FLERR
,
"Illegal number of setting arguments for pair_style sph/lj"
);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairSPHLJ
::
coeff
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
4
)
error
->
all
(
FLERR
,
"Incorrect args for pair_style sph/lj coefficients"
);
if
(
!
allocated
)
allocate
();
int
ilo
,
ihi
,
jlo
,
jhi
;
force
->
bounds
(
arg
[
0
],
atom
->
ntypes
,
ilo
,
ihi
);
force
->
bounds
(
arg
[
1
],
atom
->
ntypes
,
jlo
,
jhi
);
double
viscosity_one
=
force
->
numeric
(
arg
[
2
]);
double
cut_one
=
force
->
numeric
(
arg
[
3
]);
int
count
=
0
;
for
(
int
i
=
ilo
;
i
<=
ihi
;
i
++
)
{
for
(
int
j
=
MAX
(
jlo
,
i
);
j
<=
jhi
;
j
++
)
{
viscosity
[
i
][
j
]
=
viscosity_one
;
printf
(
"setting cut[%d][%d] = %f
\n
"
,
i
,
j
,
cut_one
);
cut
[
i
][
j
]
=
cut_one
;
setflag
[
i
][
j
]
=
1
;
count
++
;
}
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairSPHLJ
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
{
error
->
all
(
FLERR
,
"All pair sph/lj coeffs are not set"
);
}
cut
[
j
][
i
]
=
cut
[
i
][
j
];
viscosity
[
j
][
i
]
=
viscosity
[
i
][
j
];
return
cut
[
i
][
j
];
}
/* ---------------------------------------------------------------------- */
double
PairSPHLJ
::
single
(
int
i
,
int
j
,
int
itype
,
int
jtype
,
double
rsq
,
double
factor_coul
,
double
factor_lj
,
double
&
fforce
)
{
fforce
=
0.0
;
return
0.0
;
}
/*double PairSPHLJ::LJEOS2(double rho, double e, double cv) {
double T = e / cv;
if (T < 1.e-2) T = 1.e-2;
//printf("%f %f\n", T, rho);
double iT = 0.1e1 / T;
//double itpow1_4 = exp(0.25 * log(iT)); //pow(iT, 0.1e1 / 0.4e1);
double itpow1_4 = pow(iT, 0.1e1 / 0.4e1);
double x = rho * itpow1_4;
double xsq = x * x;
double xpow3 = xsq * x;
double xpow4 = xsq * xsq;
double xpow9 = xpow3 * xpow3 * xpow3;
return (0.1e1 + rho * (0.3629e1 + 0.7264e1 * x + 0.104925e2 * xsq + 0.11460e2
* xpow3 + 0.21760e1 * xpow9 - itpow1_4 * itpow1_4 * (0.5369e1 + 0.13160e2
* x + 0.18525e2 * xsq - 0.17076e2 * xpow3 + 0.9320e1 * xpow4) + iT
* (-0.3492e1 + 0.18698e2 * x - 0.35505e2 * xsq + 0.31816e2 * xpow3
- 0.11195e2 * xpow4)) * itpow1_4) * rho * T;
}*/
/* --------------------------------------------------------------------------------------------- */
/* Lennard-Jones EOS,
Francis H. Ree
"Analytic representation of thermodynamic data for the Lennard‐Jones fluid",
Journal of Chemical Physics 73 pp. 5401-5403 (1980)
*/
void
PairSPHLJ
::
LJEOS2
(
double
rho
,
double
e
,
double
cv
,
double
*
p
,
double
*
c
)
{
double
T
=
e
/
cv
;
double
beta
=
1.0
/
T
;
double
beta_sqrt
=
sqrt
(
beta
);
double
x
=
rho
*
sqrt
(
beta_sqrt
);
double
xsq
=
x
*
x
;
double
xpow3
=
xsq
*
x
;
double
xpow4
=
xsq
*
xsq
;
/* differential of Helmholtz free energy w.r.t. x */
double
diff_A_NkT
=
3.629
+
7.264
*
x
-
beta
*
(
3.492
-
18.698
*
x
+
35.505
*
xsq
-
31.816
*
xpow3
+
11.195
*
xpow4
)
-
beta_sqrt
*
(
5.369
+
13.16
*
x
+
18.525
*
xsq
-
17.076
*
xpow3
+
9.32
*
xpow4
)
+
10.4925
*
xsq
+
11.46
*
xpow3
+
2.176
*
xpow4
*
xpow4
*
x
;
/* differential of Helmholtz free energy w.r.t. x^2 */
double
d2A_dx2
=
7.264
+
20.985
*
x
\
+
beta
*
(
18.698
-
71.01
*
x
+
95.448
*
xsq
-
44.78
*
xpow3
)
\
-
beta_sqrt
*
(
13.16
+
37.05
*
x
-
51.228
*
xsq
+
37.28
*
xpow3
)
\
+
34.38
*
xsq
+
19.584
*
xpow4
*
xpow4
;
// p = rho k T * (1 + rho * d(A/(NkT))/drho)
// dx/drho = rho/x
*
p
=
rho
*
T
*
(
1.0
+
diff_A_NkT
*
x
);
// pressure
double
csq
=
T
*
(
1.0
+
2.0
*
diff_A_NkT
*
x
+
d2A_dx2
*
x
*
x
);
// soundspeed squared
if
(
csq
>
0.0
)
{
*
c
=
sqrt
(
csq
);
// soundspeed
}
else
{
*
c
=
0.0
;
}
}
/* ------------------------------------------------------------------------------ */
/* Jirí Kolafa, Ivo Nezbeda
* "The Lennard-Jones fluid: an accurate analytic and theoretically-based equation of state",
* Fluid Phase Equilibria 100 pp. 1-34 (1994) */
/*double PairSPHLJ::LJEOS2(double rho, double e, double cv) {
double T = e / cv;
double sT = sqrt(T);
double isT = 1.0 / sT;
double dC = -0.063920968 * log(T) + 0.011117524 / T - 0.076383859 / sT
+ 1.080142248 + 0.000693129 * sT;
double eta = 3.141592654 / 6. * rho * (dC * dC * dC);
double zHS = (1 + eta * (1 + eta * (1 - eta / 1.5 * (1 + eta))))
/ ((1. - eta) * (1. - eta) * (1. - eta));
double BC = (((((-0.58544978 * isT + 0.43102052) * isT + .87361369) * isT
- 4.13749995) * isT + 2.90616279) * isT - 7.02181962) / T + 0.02459877;
double gammaBH = 1.92907278;
double sum = ((2.01546797 * 2 + rho * ((-28.17881636) * 3 + rho
* (28.28313847 * 4 + rho * (-10.42402873) * 5))) + (-19.58371655 * 2
+ rho * (+75.62340289 * 3 + rho * ((-120.70586598) * 4 + rho
* (+93.92740328 * 5 + rho * (-27.37737354) * 6)))) / sqrt(T)
+ ((29.34470520 * 2 + rho * ((-112.35356937) * 3 + rho * (+170.64908980
* 4 + rho * ((-123.06669187) * 5 + rho * 34.42288969 * 6))))
+ ((-13.37031968) * 2 + rho * (65.38059570 * 3 + rho
* ((-115.09233113) * 4 + rho * (88.91973082 * 5 + rho
* (-25.62099890) * 6)))) / T) / T) * rho * rho;
return ((zHS + BC / exp(gammaBH * rho * rho) * rho * (1 - 2 * gammaBH * rho
* rho)) * T + sum) * rho;
}
*/
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