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rLAMMPS lammps
pppm_cg.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 author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "atom.h"
#include "gridcomm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "neighbor.h"
#include "memory.h"
#include "pppm_cg.h"
#include "math_const.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
#define OFFSET 16384
#define SMALLQ 0.00001
enum
{
REVERSE_RHO
};
enum
{
FORWARD_IK
,
FORWARD_AD
,
FORWARD_IK_PERATOM
,
FORWARD_AD_PERATOM
};
#ifdef FFT_SINGLE
#define ZEROF 0.0f
#else
#define ZEROF 0.0
#endif
/* ---------------------------------------------------------------------- */
PPPMCG
::
PPPMCG
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
PPPM
(
lmp
,
narg
,
arg
),
is_charged
(
NULL
)
{
if
((
narg
<
1
)
||
(
narg
>
2
))
error
->
all
(
FLERR
,
"Illegal kspace_style pppm/cg command"
);
if
(
narg
==
2
)
smallq
=
fabs
(
force
->
numeric
(
FLERR
,
arg
[
1
]));
else
smallq
=
SMALLQ
;
num_charged
=
-
1
;
group_group_enable
=
1
;
}
/* ----------------------------------------------------------------------
free all memory
------------------------------------------------------------------------- */
PPPMCG
::~
PPPMCG
()
{
memory
->
destroy
(
is_charged
);
}
/* ----------------------------------------------------------------------
compute the PPPM long-range force, energy, virial
------------------------------------------------------------------------- */
void
PPPMCG
::
compute
(
int
eflag
,
int
vflag
)
{
// set energy/virial flags
// invoke allocate_peratom() if needed for first time
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
evflag_atom
=
eflag_global
=
vflag_global
=
eflag_atom
=
vflag_atom
=
0
;
if
(
evflag_atom
&&
!
peratom_allocate_flag
)
{
allocate_peratom
();
cg_peratom
->
ghost_notify
();
cg_peratom
->
setup
();
}
// if atom count has changed, update qsum and qsqsum
if
(
atom
->
natoms
!=
natoms_original
)
{
qsum_qsq
();
natoms_original
=
atom
->
natoms
;
}
// return if there are no charges
if
(
qsqsum
==
0.0
)
return
;
// convert atoms from box to lamda coords
if
(
triclinic
==
0
)
boxlo
=
domain
->
boxlo
;
else
{
boxlo
=
domain
->
boxlo_lamda
;
domain
->
x2lamda
(
atom
->
nlocal
);
}
// extend size of per-atom arrays if necessary
if
(
atom
->
nmax
>
nmax
)
{
memory
->
destroy
(
part2grid
);
memory
->
destroy
(
is_charged
);
nmax
=
atom
->
nmax
;
memory
->
create
(
part2grid
,
nmax
,
3
,
"pppm:part2grid"
);
memory
->
create
(
is_charged
,
nmax
,
"pppm/cg:is_charged"
);
}
// one time setup message
if
(
num_charged
<
0
)
{
bigint
charged_all
,
charged_num
;
double
charged_frac
,
charged_fmax
,
charged_fmin
;
num_charged
=
0
;
for
(
int
i
=
0
;
i
<
atom
->
nlocal
;
++
i
)
if
(
fabs
(
atom
->
q
[
i
])
>
smallq
)
++
num_charged
;
// get fraction of charged particles per domain
if
(
atom
->
nlocal
>
0
)
charged_frac
=
static_cast
<
double
>
(
num_charged
)
*
100.0
/
static_cast
<
double
>
(
atom
->
nlocal
);
else
charged_frac
=
0.0
;
MPI_Reduce
(
&
charged_frac
,
&
charged_fmax
,
1
,
MPI_DOUBLE
,
MPI_MAX
,
0
,
world
);
MPI_Reduce
(
&
charged_frac
,
&
charged_fmin
,
1
,
MPI_DOUBLE
,
MPI_MIN
,
0
,
world
);
// get fraction of charged particles overall
charged_num
=
num_charged
;
MPI_Reduce
(
&
charged_num
,
&
charged_all
,
1
,
MPI_LMP_BIGINT
,
MPI_SUM
,
0
,
world
);
charged_frac
=
static_cast
<
double
>
(
charged_all
)
*
100.0
/
static_cast
<
double
>
(
atom
->
natoms
);
if
(
me
==
0
)
{
if
(
screen
)
fprintf
(
screen
,
" PPPM/cg optimization cutoff: %g
\n
"
" Total charged atoms: %.1f%%
\n
"
" Min/max charged atoms/proc: %.1f%% %.1f%%
\n
"
,
smallq
,
charged_frac
,
charged_fmin
,
charged_fmax
);
if
(
logfile
)
fprintf
(
logfile
,
" PPPM/cg optimization cutoff: %g
\n
"
" Total charged atoms: %.1f%%
\n
"
" Min/max charged atoms/proc: %.1f%% %.1f%%
\n
"
,
smallq
,
charged_frac
,
charged_fmin
,
charged_fmax
);
}
}
// only need to rebuild this list after a neighbor list update
if
(
neighbor
->
ago
==
0
)
{
num_charged
=
0
;
for
(
int
i
=
0
;
i
<
atom
->
nlocal
;
++
i
)
{
if
(
fabs
(
atom
->
q
[
i
])
>
smallq
)
{
is_charged
[
num_charged
]
=
i
;
++
num_charged
;
}
}
}
// find grid points for all my particles
// map my particle charge onto my local 3d density grid
particle_map
();
make_rho
();
// all procs communicate density values from their ghost cells
// to fully sum contribution in their 3d bricks
// remap from 3d decomposition to FFT decomposition
cg
->
reverse_comm
(
this
,
REVERSE_RHO
);
brick2fft
();
// compute potential gradient on my FFT grid and
// portion of e_long on this proc's FFT grid
// return gradients (electric fields) in 3d brick decomposition
// also performs per-atom calculations via poisson_peratom()
poisson
();
// all procs communicate E-field values
// to fill ghost cells surrounding their 3d bricks
if
(
differentiation_flag
==
1
)
cg
->
forward_comm
(
this
,
FORWARD_AD
);
else
cg
->
forward_comm
(
this
,
FORWARD_IK
);
// extra per-atom energy/virial communication
if
(
evflag_atom
)
{
if
(
differentiation_flag
==
1
&&
vflag_atom
)
cg_peratom
->
forward_comm
(
this
,
FORWARD_AD_PERATOM
);
else
if
(
differentiation_flag
==
0
)
cg_peratom
->
forward_comm
(
this
,
FORWARD_IK_PERATOM
);
}
// calculate the force on my particles
fieldforce
();
// extra per-atom energy/virial communication
if
(
evflag_atom
)
fieldforce_peratom
();
// sum global energy across procs and add in volume-dependent term
const
double
qscale
=
qqrd2e
*
scale
;
if
(
eflag_global
)
{
double
energy_all
;
MPI_Allreduce
(
&
energy
,
&
energy_all
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
energy
=
energy_all
;
energy
*=
0.5
*
volume
;
energy
-=
g_ewald
*
qsqsum
/
MY_PIS
+
MY_PI2
*
qsum
*
qsum
/
(
g_ewald
*
g_ewald
*
volume
);
energy
*=
qscale
;
}
// sum global virial across procs
if
(
vflag_global
)
{
double
virial_all
[
6
];
MPI_Allreduce
(
virial
,
virial_all
,
6
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
for
(
int
i
=
0
;
i
<
6
;
i
++
)
virial
[
i
]
=
0.5
*
qscale
*
volume
*
virial_all
[
i
];
}
// per-atom energy/virial
// energy includes self-energy correction
if
(
evflag_atom
)
{
const
double
*
const
q
=
atom
->
q
;
if
(
eflag_atom
)
{
for
(
int
j
=
0
;
j
<
num_charged
;
j
++
)
{
const
int
i
=
is_charged
[
j
];
eatom
[
i
]
*=
0.5
;
eatom
[
i
]
-=
g_ewald
*
q
[
i
]
*
q
[
i
]
/
MY_PIS
+
MY_PI2
*
q
[
i
]
*
qsum
/
(
g_ewald
*
g_ewald
*
volume
);
eatom
[
i
]
*=
qscale
;
}
}
if
(
vflag_atom
)
{
for
(
int
n
=
0
;
n
<
num_charged
;
n
++
)
{
const
int
i
=
is_charged
[
n
];
for
(
int
j
=
0
;
j
<
6
;
j
++
)
vatom
[
i
][
j
]
*=
0.5
*
qscale
;
}
}
}
// 2d slab correction
if
(
slabflag
==
1
)
slabcorr
();
// convert atoms back from lamda to box coords
if
(
triclinic
)
domain
->
lamda2x
(
atom
->
nlocal
);
}
/* ----------------------------------------------------------------------
find center grid pt for each of my particles
check that full stencil for the particle will fit in my 3d brick
store central grid pt indices in part2grid array
------------------------------------------------------------------------- */
void
PPPMCG
::
particle_map
()
{
int
nx
,
ny
,
nz
;
double
**
x
=
atom
->
x
;
if
(
!
ISFINITE
(
boxlo
[
0
])
||
!
ISFINITE
(
boxlo
[
1
])
||
!
ISFINITE
(
boxlo
[
2
]))
error
->
one
(
FLERR
,
"Non-numeric box dimensions - simulation unstable"
);
int
flag
=
0
;
for
(
int
j
=
0
;
j
<
num_charged
;
j
++
)
{
int
i
=
is_charged
[
j
];
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// current particle coord can be outside global and local box
// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
nx
=
static_cast
<
int
>
((
x
[
i
][
0
]
-
boxlo
[
0
])
*
delxinv
+
shift
)
-
OFFSET
;
ny
=
static_cast
<
int
>
((
x
[
i
][
1
]
-
boxlo
[
1
])
*
delyinv
+
shift
)
-
OFFSET
;
nz
=
static_cast
<
int
>
((
x
[
i
][
2
]
-
boxlo
[
2
])
*
delzinv
+
shift
)
-
OFFSET
;
part2grid
[
i
][
0
]
=
nx
;
part2grid
[
i
][
1
]
=
ny
;
part2grid
[
i
][
2
]
=
nz
;
// check that entire stencil around nx,ny,nz will fit in my 3d brick
if
(
nx
+
nlower
<
nxlo_out
||
nx
+
nupper
>
nxhi_out
||
ny
+
nlower
<
nylo_out
||
ny
+
nupper
>
nyhi_out
||
nz
+
nlower
<
nzlo_out
||
nz
+
nupper
>
nzhi_out
)
flag
=
1
;
}
if
(
flag
)
error
->
one
(
FLERR
,
"Out of range atoms - cannot compute PPPM"
);
}
/* ----------------------------------------------------------------------
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
in global grid
------------------------------------------------------------------------- */
void
PPPMCG
::
make_rho
()
{
int
i
,
l
,
m
,
n
,
nx
,
ny
,
nz
,
mx
,
my
,
mz
;
FFT_SCALAR
dx
,
dy
,
dz
,
x0
,
y0
,
z0
;
// clear 3d density array
memset
(
&
(
density_brick
[
nzlo_out
][
nylo_out
][
nxlo_out
]),
0
,
ngrid
*
sizeof
(
FFT_SCALAR
));
// loop over my charges, add their contribution to nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
double
*
q
=
atom
->
q
;
double
**
x
=
atom
->
x
;
for
(
int
j
=
0
;
j
<
num_charged
;
j
++
)
{
i
=
is_charged
[
j
];
nx
=
part2grid
[
i
][
0
];
ny
=
part2grid
[
i
][
1
];
nz
=
part2grid
[
i
][
2
];
dx
=
nx
+
shiftone
-
(
x
[
i
][
0
]
-
boxlo
[
0
])
*
delxinv
;
dy
=
ny
+
shiftone
-
(
x
[
i
][
1
]
-
boxlo
[
1
])
*
delyinv
;
dz
=
nz
+
shiftone
-
(
x
[
i
][
2
]
-
boxlo
[
2
])
*
delzinv
;
compute_rho1d
(
dx
,
dy
,
dz
);
z0
=
delvolinv
*
q
[
i
];
for
(
n
=
nlower
;
n
<=
nupper
;
n
++
)
{
mz
=
n
+
nz
;
y0
=
z0
*
rho1d
[
2
][
n
];
for
(
m
=
nlower
;
m
<=
nupper
;
m
++
)
{
my
=
m
+
ny
;
x0
=
y0
*
rho1d
[
1
][
m
];
for
(
l
=
nlower
;
l
<=
nupper
;
l
++
)
{
mx
=
l
+
nx
;
density_brick
[
mz
][
my
][
mx
]
+=
x0
*
rho1d
[
0
][
l
];
}
}
}
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles for ik
------------------------------------------------------------------------- */
void
PPPMCG
::
fieldforce_ik
()
{
int
i
,
l
,
m
,
n
,
nx
,
ny
,
nz
,
mx
,
my
,
mz
;
FFT_SCALAR
dx
,
dy
,
dz
,
x0
,
y0
,
z0
;
FFT_SCALAR
ekx
,
eky
,
ekz
;
// loop over my charges, interpolate electric field from nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
// ek = 3 components of E-field on particle
double
*
q
=
atom
->
q
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
for
(
int
j
=
0
;
j
<
num_charged
;
j
++
)
{
i
=
is_charged
[
j
];
nx
=
part2grid
[
i
][
0
];
ny
=
part2grid
[
i
][
1
];
nz
=
part2grid
[
i
][
2
];
dx
=
nx
+
shiftone
-
(
x
[
i
][
0
]
-
boxlo
[
0
])
*
delxinv
;
dy
=
ny
+
shiftone
-
(
x
[
i
][
1
]
-
boxlo
[
1
])
*
delyinv
;
dz
=
nz
+
shiftone
-
(
x
[
i
][
2
]
-
boxlo
[
2
])
*
delzinv
;
compute_rho1d
(
dx
,
dy
,
dz
);
ekx
=
eky
=
ekz
=
ZEROF
;
for
(
n
=
nlower
;
n
<=
nupper
;
n
++
)
{
mz
=
n
+
nz
;
z0
=
rho1d
[
2
][
n
];
for
(
m
=
nlower
;
m
<=
nupper
;
m
++
)
{
my
=
m
+
ny
;
y0
=
z0
*
rho1d
[
1
][
m
];
for
(
l
=
nlower
;
l
<=
nupper
;
l
++
)
{
mx
=
l
+
nx
;
x0
=
y0
*
rho1d
[
0
][
l
];
ekx
-=
x0
*
vdx_brick
[
mz
][
my
][
mx
];
eky
-=
x0
*
vdy_brick
[
mz
][
my
][
mx
];
ekz
-=
x0
*
vdz_brick
[
mz
][
my
][
mx
];
}
}
}
// convert E-field to force
const
double
qfactor
=
qqrd2e
*
scale
*
q
[
i
];
f
[
i
][
0
]
+=
qfactor
*
ekx
;
f
[
i
][
1
]
+=
qfactor
*
eky
;
if
(
slabflag
!=
2
)
f
[
i
][
2
]
+=
qfactor
*
ekz
;
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles for ad
------------------------------------------------------------------------- */
void
PPPMCG
::
fieldforce_ad
()
{
int
i
,
l
,
m
,
n
,
nx
,
ny
,
nz
,
mx
,
my
,
mz
;
FFT_SCALAR
dx
,
dy
,
dz
;
FFT_SCALAR
ekx
,
eky
,
ekz
;
double
s1
,
s2
,
s3
;
double
sf
=
0.0
;
double
*
prd
;
if
(
triclinic
==
0
)
prd
=
domain
->
prd
;
else
prd
=
domain
->
prd_lamda
;
double
xprd
=
prd
[
0
];
double
yprd
=
prd
[
1
];
double
zprd
=
prd
[
2
];
double
hx_inv
=
nx_pppm
/
xprd
;
double
hy_inv
=
ny_pppm
/
yprd
;
double
hz_inv
=
nz_pppm
/
zprd
;
// loop over my charges, interpolate electric field from nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
// ek = 3 components of E-field on particle
double
*
q
=
atom
->
q
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
for
(
int
j
=
0
;
j
<
num_charged
;
j
++
)
{
i
=
is_charged
[
j
];
nx
=
part2grid
[
i
][
0
];
ny
=
part2grid
[
i
][
1
];
nz
=
part2grid
[
i
][
2
];
dx
=
nx
+
shiftone
-
(
x
[
i
][
0
]
-
boxlo
[
0
])
*
delxinv
;
dy
=
ny
+
shiftone
-
(
x
[
i
][
1
]
-
boxlo
[
1
])
*
delyinv
;
dz
=
nz
+
shiftone
-
(
x
[
i
][
2
]
-
boxlo
[
2
])
*
delzinv
;
compute_rho1d
(
dx
,
dy
,
dz
);
compute_drho1d
(
dx
,
dy
,
dz
);
ekx
=
eky
=
ekz
=
ZEROF
;
for
(
n
=
nlower
;
n
<=
nupper
;
n
++
)
{
mz
=
n
+
nz
;
for
(
m
=
nlower
;
m
<=
nupper
;
m
++
)
{
my
=
m
+
ny
;
for
(
l
=
nlower
;
l
<=
nupper
;
l
++
)
{
mx
=
l
+
nx
;
ekx
+=
drho1d
[
0
][
l
]
*
rho1d
[
1
][
m
]
*
rho1d
[
2
][
n
]
*
u_brick
[
mz
][
my
][
mx
];
eky
+=
rho1d
[
0
][
l
]
*
drho1d
[
1
][
m
]
*
rho1d
[
2
][
n
]
*
u_brick
[
mz
][
my
][
mx
];
ekz
+=
rho1d
[
0
][
l
]
*
rho1d
[
1
][
m
]
*
drho1d
[
2
][
n
]
*
u_brick
[
mz
][
my
][
mx
];
}
}
}
ekx
*=
hx_inv
;
eky
*=
hy_inv
;
ekz
*=
hz_inv
;
// convert E-field to force and substract self forces
const
double
qfactor
=
qqrd2e
*
scale
;
s1
=
x
[
i
][
0
]
*
hx_inv
;
s2
=
x
[
i
][
1
]
*
hy_inv
;
s3
=
x
[
i
][
2
]
*
hz_inv
;
sf
=
sf_coeff
[
0
]
*
sin
(
2
*
MY_PI
*
s1
);
sf
+=
sf_coeff
[
1
]
*
sin
(
4
*
MY_PI
*
s1
);
sf
*=
2
*
q
[
i
]
*
q
[
i
];
f
[
i
][
0
]
+=
qfactor
*
(
ekx
*
q
[
i
]
-
sf
);
sf
=
sf_coeff
[
2
]
*
sin
(
2
*
MY_PI
*
s2
);
sf
+=
sf_coeff
[
3
]
*
sin
(
4
*
MY_PI
*
s2
);
sf
*=
2
*
q
[
i
]
*
q
[
i
];
f
[
i
][
1
]
+=
qfactor
*
(
eky
*
q
[
i
]
-
sf
);
sf
=
sf_coeff
[
4
]
*
sin
(
2
*
MY_PI
*
s3
);
sf
+=
sf_coeff
[
5
]
*
sin
(
4
*
MY_PI
*
s3
);
sf
*=
2
*
q
[
i
]
*
q
[
i
];
if
(
slabflag
!=
2
)
f
[
i
][
2
]
+=
qfactor
*
(
ekz
*
q
[
i
]
-
sf
);
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get per-atom energy/virial
------------------------------------------------------------------------- */
void
PPPMCG
::
fieldforce_peratom
()
{
int
i
,
l
,
m
,
n
,
nx
,
ny
,
nz
,
mx
,
my
,
mz
;
FFT_SCALAR
dx
,
dy
,
dz
,
x0
,
y0
,
z0
;
FFT_SCALAR
u
,
v0
,
v1
,
v2
,
v3
,
v4
,
v5
;
// loop over my charges, interpolate from nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
double
*
q
=
atom
->
q
;
double
**
x
=
atom
->
x
;
for
(
int
j
=
0
;
j
<
num_charged
;
j
++
)
{
i
=
is_charged
[
j
];
nx
=
part2grid
[
i
][
0
];
ny
=
part2grid
[
i
][
1
];
nz
=
part2grid
[
i
][
2
];
dx
=
nx
+
shiftone
-
(
x
[
i
][
0
]
-
boxlo
[
0
])
*
delxinv
;
dy
=
ny
+
shiftone
-
(
x
[
i
][
1
]
-
boxlo
[
1
])
*
delyinv
;
dz
=
nz
+
shiftone
-
(
x
[
i
][
2
]
-
boxlo
[
2
])
*
delzinv
;
compute_rho1d
(
dx
,
dy
,
dz
);
u
=
v0
=
v1
=
v2
=
v3
=
v4
=
v5
=
ZEROF
;
for
(
n
=
nlower
;
n
<=
nupper
;
n
++
)
{
mz
=
n
+
nz
;
z0
=
rho1d
[
2
][
n
];
for
(
m
=
nlower
;
m
<=
nupper
;
m
++
)
{
my
=
m
+
ny
;
y0
=
z0
*
rho1d
[
1
][
m
];
for
(
l
=
nlower
;
l
<=
nupper
;
l
++
)
{
mx
=
l
+
nx
;
x0
=
y0
*
rho1d
[
0
][
l
];
if
(
eflag_atom
)
u
+=
x0
*
u_brick
[
mz
][
my
][
mx
];
if
(
vflag_atom
)
{
v0
+=
x0
*
v0_brick
[
mz
][
my
][
mx
];
v1
+=
x0
*
v1_brick
[
mz
][
my
][
mx
];
v2
+=
x0
*
v2_brick
[
mz
][
my
][
mx
];
v3
+=
x0
*
v3_brick
[
mz
][
my
][
mx
];
v4
+=
x0
*
v4_brick
[
mz
][
my
][
mx
];
v5
+=
x0
*
v5_brick
[
mz
][
my
][
mx
];
}
}
}
}
if
(
eflag_atom
)
eatom
[
i
]
+=
q
[
i
]
*
u
;
if
(
vflag_atom
)
{
vatom
[
i
][
0
]
+=
q
[
i
]
*
v0
;
vatom
[
i
][
1
]
+=
q
[
i
]
*
v1
;
vatom
[
i
][
2
]
+=
q
[
i
]
*
v2
;
vatom
[
i
][
3
]
+=
q
[
i
]
*
v3
;
vatom
[
i
][
4
]
+=
q
[
i
]
*
v4
;
vatom
[
i
][
5
]
+=
q
[
i
]
*
v5
;
}
}
}
/* ----------------------------------------------------------------------
Slab-geometry correction term to dampen inter-slab interactions between
periodically repeating slabs. Yields good approximation to 2D Ewald if
adequate empty space is left between repeating slabs (J. Chem. Phys.
111, 3155). Slabs defined here to be parallel to the xy plane. Also
extended to non-neutral systems (J. Chem. Phys. 131, 094107).
------------------------------------------------------------------------- */
void
PPPMCG
::
slabcorr
()
{
int
i
,
j
;
// compute local contribution to global dipole moment
const
double
*
const
q
=
atom
->
q
;
const
double
*
const
*
const
x
=
atom
->
x
;
const
double
zprd
=
domain
->
zprd
;
double
dipole
=
0.0
;
for
(
j
=
0
;
j
<
num_charged
;
j
++
)
{
i
=
is_charged
[
j
];
dipole
+=
q
[
i
]
*
x
[
i
][
2
];
}
// sum local contributions to get global dipole moment
double
dipole_all
;
MPI_Allreduce
(
&
dipole
,
&
dipole_all
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
// need to make non-neutral systems and/or
// per-atom energy translationally invariant
double
dipole_r2
=
0.0
;
if
(
eflag_atom
||
fabs
(
qsum
)
>
SMALLQ
)
{
for
(
j
=
0
;
j
<
num_charged
;
j
++
)
{
i
=
is_charged
[
j
];
dipole_r2
+=
q
[
i
]
*
x
[
i
][
2
]
*
x
[
i
][
2
];
}
// sum local contributions
double
tmp
;
MPI_Allreduce
(
&
dipole_r2
,
&
tmp
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
dipole_r2
=
tmp
;
}
// compute corrections
const
double
e_slabcorr
=
MY_2PI
*
(
dipole_all
*
dipole_all
-
qsum
*
dipole_r2
-
qsum
*
qsum
*
zprd
*
zprd
/
12.0
)
/
volume
;
const
double
qscale
=
qqrd2e
*
scale
;
if
(
eflag_global
)
energy
+=
qscale
*
e_slabcorr
;
// per-atom energy
if
(
eflag_atom
)
{
const
double
efact
=
qscale
*
MY_2PI
/
volume
;
for
(
j
=
0
;
j
<
num_charged
;
j
++
)
{
i
=
is_charged
[
j
];
eatom
[
i
]
+=
efact
*
q
[
i
]
*
(
x
[
i
][
2
]
*
dipole_all
-
0.5
*
(
dipole_r2
+
qsum
*
x
[
i
][
2
]
*
x
[
i
][
2
])
-
qsum
*
zprd
*
zprd
/
12.0
);
}
}
// add on force corrections
const
double
ffact
=
qscale
*
(
-
MY_4PI
/
volume
);
double
*
const
*
const
f
=
atom
->
f
;
for
(
j
=
0
;
j
<
num_charged
;
j
++
)
{
i
=
is_charged
[
j
];
f
[
i
][
2
]
+=
ffact
*
q
[
i
]
*
(
dipole_all
-
qsum
*
x
[
i
][
2
]);
}
}
/* ----------------------------------------------------------------------
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
in global grid for group-group interactions
------------------------------------------------------------------------- */
void
PPPMCG
::
make_rho_groups
(
int
groupbit_A
,
int
groupbit_B
,
int
BA_flag
)
{
int
i
,
l
,
m
,
n
,
nx
,
ny
,
nz
,
mx
,
my
,
mz
;
FFT_SCALAR
dx
,
dy
,
dz
,
x0
,
y0
,
z0
;
// clear 3d density arrays
memset
(
&
(
density_A_brick
[
nzlo_out
][
nylo_out
][
nxlo_out
]),
0
,
ngrid
*
sizeof
(
FFT_SCALAR
));
memset
(
&
(
density_B_brick
[
nzlo_out
][
nylo_out
][
nxlo_out
]),
0
,
ngrid
*
sizeof
(
FFT_SCALAR
));
// loop over my charges, add their contribution to nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
const
double
*
const
q
=
atom
->
q
;
const
double
*
const
*
const
x
=
atom
->
x
;
const
int
*
const
mask
=
atom
->
mask
;
for
(
int
j
=
0
;
j
<
num_charged
;
j
++
)
{
i
=
is_charged
[
j
];
if
((
mask
[
i
]
&
groupbit_A
)
&&
(
mask
[
i
]
&
groupbit_B
))
if
(
BA_flag
)
continue
;
if
((
mask
[
i
]
&
groupbit_A
)
||
(
mask
[
i
]
&
groupbit_B
))
{
nx
=
part2grid
[
i
][
0
];
ny
=
part2grid
[
i
][
1
];
nz
=
part2grid
[
i
][
2
];
dx
=
nx
+
shiftone
-
(
x
[
i
][
0
]
-
boxlo
[
0
])
*
delxinv
;
dy
=
ny
+
shiftone
-
(
x
[
i
][
1
]
-
boxlo
[
1
])
*
delyinv
;
dz
=
nz
+
shiftone
-
(
x
[
i
][
2
]
-
boxlo
[
2
])
*
delzinv
;
compute_rho1d
(
dx
,
dy
,
dz
);
z0
=
delvolinv
*
q
[
i
];
for
(
n
=
nlower
;
n
<=
nupper
;
n
++
)
{
mz
=
n
+
nz
;
y0
=
z0
*
rho1d
[
2
][
n
];
for
(
m
=
nlower
;
m
<=
nupper
;
m
++
)
{
my
=
m
+
ny
;
x0
=
y0
*
rho1d
[
1
][
m
];
for
(
l
=
nlower
;
l
<=
nupper
;
l
++
)
{
mx
=
l
+
nx
;
// group A
if
(
mask
[
i
]
&
groupbit_A
)
density_A_brick
[
mz
][
my
][
mx
]
+=
x0
*
rho1d
[
0
][
l
];
// group B
if
(
mask
[
i
]
&
groupbit_B
)
density_B_brick
[
mz
][
my
][
mx
]
+=
x0
*
rho1d
[
0
][
l
];
}
}
}
}
}
}
/* ----------------------------------------------------------------------
memory usage of local arrays
------------------------------------------------------------------------- */
double
PPPMCG
::
memory_usage
()
{
double
bytes
=
PPPM
::
memory_usage
();
bytes
+=
nmax
*
sizeof
(
int
);
return
bytes
;
}
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