Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F64469340
meam_dens_init.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Mon, May 27, 02:43
Size
12 KB
Mime Type
text/x-c
Expires
Wed, May 29, 02:43 (2 d)
Engine
blob
Format
Raw Data
Handle
17887190
Attached To
rLAMMPS lammps
meam_dens_init.cpp
View Options
#include "meam.h"
#include "math_special.h"
using
namespace
LAMMPS_NS
;
void
MEAM
::
meam_dens_setup
(
int
atom_nmax
,
int
nall
,
int
n_neigh
)
{
int
i
,
j
;
// grow local arrays if necessary
if
(
atom_nmax
>
nmax
)
{
memory
->
destroy
(
rho
);
memory
->
destroy
(
rho0
);
memory
->
destroy
(
rho1
);
memory
->
destroy
(
rho2
);
memory
->
destroy
(
rho3
);
memory
->
destroy
(
frhop
);
memory
->
destroy
(
gamma
);
memory
->
destroy
(
dgamma1
);
memory
->
destroy
(
dgamma2
);
memory
->
destroy
(
dgamma3
);
memory
->
destroy
(
arho2b
);
memory
->
destroy
(
arho1
);
memory
->
destroy
(
arho2
);
memory
->
destroy
(
arho3
);
memory
->
destroy
(
arho3b
);
memory
->
destroy
(
t_ave
);
memory
->
destroy
(
tsq_ave
);
nmax
=
atom_nmax
;
memory
->
create
(
rho
,
nmax
,
"pair:rho"
);
memory
->
create
(
rho0
,
nmax
,
"pair:rho0"
);
memory
->
create
(
rho1
,
nmax
,
"pair:rho1"
);
memory
->
create
(
rho2
,
nmax
,
"pair:rho2"
);
memory
->
create
(
rho3
,
nmax
,
"pair:rho3"
);
memory
->
create
(
frhop
,
nmax
,
"pair:frhop"
);
memory
->
create
(
gamma
,
nmax
,
"pair:gamma"
);
memory
->
create
(
dgamma1
,
nmax
,
"pair:dgamma1"
);
memory
->
create
(
dgamma2
,
nmax
,
"pair:dgamma2"
);
memory
->
create
(
dgamma3
,
nmax
,
"pair:dgamma3"
);
memory
->
create
(
arho2b
,
nmax
,
"pair:arho2b"
);
memory
->
create
(
arho1
,
nmax
,
3
,
"pair:arho1"
);
memory
->
create
(
arho2
,
nmax
,
6
,
"pair:arho2"
);
memory
->
create
(
arho3
,
nmax
,
10
,
"pair:arho3"
);
memory
->
create
(
arho3b
,
nmax
,
3
,
"pair:arho3b"
);
memory
->
create
(
t_ave
,
nmax
,
3
,
"pair:t_ave"
);
memory
->
create
(
tsq_ave
,
nmax
,
3
,
"pair:tsq_ave"
);
}
if
(
n_neigh
>
maxneigh
)
{
memory
->
destroy
(
scrfcn
);
memory
->
destroy
(
dscrfcn
);
memory
->
destroy
(
fcpair
);
maxneigh
=
n_neigh
;
memory
->
create
(
scrfcn
,
maxneigh
,
"pair:scrfcn"
);
memory
->
create
(
dscrfcn
,
maxneigh
,
"pair:dscrfcn"
);
memory
->
create
(
fcpair
,
maxneigh
,
"pair:fcpair"
);
}
// zero out local arrays
for
(
i
=
0
;
i
<
nall
;
i
++
)
{
rho0
[
i
]
=
0.0
;
arho2b
[
i
]
=
0.0
;
arho1
[
i
][
0
]
=
arho1
[
i
][
1
]
=
arho1
[
i
][
2
]
=
0.0
;
for
(
j
=
0
;
j
<
6
;
j
++
)
arho2
[
i
][
j
]
=
0.0
;
for
(
j
=
0
;
j
<
10
;
j
++
)
arho3
[
i
][
j
]
=
0.0
;
arho3b
[
i
][
0
]
=
arho3b
[
i
][
1
]
=
arho3b
[
i
][
2
]
=
0.0
;
t_ave
[
i
][
0
]
=
t_ave
[
i
][
1
]
=
t_ave
[
i
][
2
]
=
0.0
;
tsq_ave
[
i
][
0
]
=
tsq_ave
[
i
][
1
]
=
tsq_ave
[
i
][
2
]
=
0.0
;
}
}
void
MEAM
::
meam_dens_init
(
int
i
,
int
ntype
,
int
*
type
,
int
*
fmap
,
double
**
x
,
int
numneigh
,
int
*
firstneigh
,
int
numneigh_full
,
int
*
firstneigh_full
,
int
fnoffset
)
{
// Compute screening function and derivatives
getscreen
(
i
,
&
scrfcn
[
fnoffset
],
&
dscrfcn
[
fnoffset
],
&
fcpair
[
fnoffset
],
x
,
numneigh
,
firstneigh
,
numneigh_full
,
firstneigh_full
,
ntype
,
type
,
fmap
);
// Calculate intermediate density terms to be communicated
calc_rho1
(
i
,
ntype
,
type
,
fmap
,
x
,
numneigh
,
firstneigh
,
&
scrfcn
[
fnoffset
],
&
fcpair
[
fnoffset
]);
}
// ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
void
MEAM
::
getscreen
(
int
i
,
double
*
scrfcn
,
double
*
dscrfcn
,
double
*
fcpair
,
double
**
x
,
int
numneigh
,
int
*
firstneigh
,
int
numneigh_full
,
int
*
firstneigh_full
,
int
ntype
,
int
*
type
,
int
*
fmap
)
{
int
jn
,
j
,
kn
,
k
;
int
elti
,
eltj
,
eltk
;
double
xitmp
,
yitmp
,
zitmp
,
delxij
,
delyij
,
delzij
,
rij2
,
rij
;
double
xjtmp
,
yjtmp
,
zjtmp
,
delxik
,
delyik
,
delzik
,
rik2
/*,rik*/
;
double
xktmp
,
yktmp
,
zktmp
,
delxjk
,
delyjk
,
delzjk
,
rjk2
/*,rjk*/
;
double
xik
,
xjk
,
sij
,
fcij
,
sfcij
,
dfcij
,
sikj
,
dfikj
,
cikj
;
double
Cmin
,
Cmax
,
delc
,
/*ebound,*/
rbound
,
a
,
coef1
,
coef2
;
double
dCikj
;
double
rnorm
,
fc
,
dfc
,
drinv
;
drinv
=
1.0
/
this
->
delr_meam
;
elti
=
fmap
[
type
[
i
]];
if
(
elti
<
0
)
return
;
xitmp
=
x
[
i
][
0
];
yitmp
=
x
[
i
][
1
];
zitmp
=
x
[
i
][
2
];
for
(
jn
=
0
;
jn
<
numneigh
;
jn
++
)
{
j
=
firstneigh
[
jn
];
eltj
=
fmap
[
type
[
j
]];
if
(
eltj
<
0
)
continue
;
// First compute screening function itself, sij
xjtmp
=
x
[
j
][
0
];
yjtmp
=
x
[
j
][
1
];
zjtmp
=
x
[
j
][
2
];
delxij
=
xjtmp
-
xitmp
;
delyij
=
yjtmp
-
yitmp
;
delzij
=
zjtmp
-
zitmp
;
rij2
=
delxij
*
delxij
+
delyij
*
delyij
+
delzij
*
delzij
;
rij
=
sqrt
(
rij2
);
if
(
rij
>
this
->
rc_meam
)
{
fcij
=
0.0
;
dfcij
=
0.0
;
sij
=
0.0
;
}
else
{
rnorm
=
(
this
->
rc_meam
-
rij
)
*
drinv
;
sij
=
1.0
;
// if rjk2 > ebound*rijsq, atom k is definitely outside the ellipse
const
double
rbound
=
this
->
ebound_meam
[
elti
][
eltj
]
*
rij2
;
for
(
kn
=
0
;
kn
<
numneigh_full
;
kn
++
)
{
k
=
firstneigh_full
[
kn
];
eltk
=
fmap
[
type
[
k
]];
if
(
eltk
<
0
)
continue
;
if
(
k
==
j
)
continue
;
delxjk
=
x
[
k
][
0
]
-
xjtmp
;
delyjk
=
x
[
k
][
1
]
-
yjtmp
;
delzjk
=
x
[
k
][
2
]
-
zjtmp
;
rjk2
=
delxjk
*
delxjk
+
delyjk
*
delyjk
+
delzjk
*
delzjk
;
if
(
rjk2
>
rbound
)
continue
;
delxik
=
x
[
k
][
0
]
-
xitmp
;
delyik
=
x
[
k
][
1
]
-
yitmp
;
delzik
=
x
[
k
][
2
]
-
zitmp
;
rik2
=
delxik
*
delxik
+
delyik
*
delyik
+
delzik
*
delzik
;
if
(
rik2
>
rbound
)
continue
;
xik
=
rik2
/
rij2
;
xjk
=
rjk2
/
rij2
;
a
=
1
-
(
xik
-
xjk
)
*
(
xik
-
xjk
);
// if a < 0, then ellipse equation doesn't describe this case and
// atom k can't possibly screen i-j
if
(
a
<=
0.0
)
continue
;
cikj
=
(
2.0
*
(
xik
+
xjk
)
+
a
-
2.0
)
/
a
;
Cmax
=
this
->
Cmax_meam
[
elti
][
eltj
][
eltk
];
Cmin
=
this
->
Cmin_meam
[
elti
][
eltj
][
eltk
];
if
(
cikj
>=
Cmax
)
continue
;
// note that cikj may be slightly negative (within numerical
// tolerance) if atoms are colinear, so don't reject that case here
// (other negative cikj cases were handled by the test on "a" above)
else
if
(
cikj
<=
Cmin
)
{
sij
=
0.0
;
break
;
}
else
{
delc
=
Cmax
-
Cmin
;
cikj
=
(
cikj
-
Cmin
)
/
delc
;
sikj
=
fcut
(
cikj
);
}
sij
*=
sikj
;
}
fc
=
dfcut
(
rnorm
,
dfc
);
fcij
=
fc
;
dfcij
=
dfc
*
drinv
;
}
// Now compute derivatives
dscrfcn
[
jn
]
=
0.0
;
sfcij
=
sij
*
fcij
;
if
(
iszero
(
sfcij
)
||
iszero
(
sfcij
-
1.0
))
goto
LABEL_100
;
rbound
=
this
->
ebound_meam
[
elti
][
eltj
]
*
rij2
;
for
(
kn
=
0
;
kn
<
numneigh_full
;
kn
++
)
{
k
=
firstneigh_full
[
kn
];
if
(
k
==
j
)
continue
;
eltk
=
fmap
[
type
[
k
]];
if
(
eltk
<
0
)
continue
;
xktmp
=
x
[
k
][
0
];
yktmp
=
x
[
k
][
1
];
zktmp
=
x
[
k
][
2
];
delxjk
=
xktmp
-
xjtmp
;
delyjk
=
yktmp
-
yjtmp
;
delzjk
=
zktmp
-
zjtmp
;
rjk2
=
delxjk
*
delxjk
+
delyjk
*
delyjk
+
delzjk
*
delzjk
;
if
(
rjk2
>
rbound
)
continue
;
delxik
=
xktmp
-
xitmp
;
delyik
=
yktmp
-
yitmp
;
delzik
=
zktmp
-
zitmp
;
rik2
=
delxik
*
delxik
+
delyik
*
delyik
+
delzik
*
delzik
;
if
(
rik2
>
rbound
)
continue
;
xik
=
rik2
/
rij2
;
xjk
=
rjk2
/
rij2
;
a
=
1
-
(
xik
-
xjk
)
*
(
xik
-
xjk
);
// if a < 0, then ellipse equation doesn't describe this case and
// atom k can't possibly screen i-j
if
(
a
<=
0.0
)
continue
;
cikj
=
(
2.0
*
(
xik
+
xjk
)
+
a
-
2.0
)
/
a
;
Cmax
=
this
->
Cmax_meam
[
elti
][
eltj
][
eltk
];
Cmin
=
this
->
Cmin_meam
[
elti
][
eltj
][
eltk
];
if
(
cikj
>=
Cmax
)
{
continue
;
// Note that cikj may be slightly negative (within numerical
// tolerance) if atoms are colinear, so don't reject that case
// here
// (other negative cikj cases were handled by the test on "a"
// above)
// Note that we never have 0<cikj<Cmin here, else sij=0
// (rejected above)
}
else
{
delc
=
Cmax
-
Cmin
;
cikj
=
(
cikj
-
Cmin
)
/
delc
;
sikj
=
dfcut
(
cikj
,
dfikj
);
coef1
=
dfikj
/
(
delc
*
sikj
);
dCikj
=
dCfunc
(
rij2
,
rik2
,
rjk2
);
dscrfcn
[
jn
]
=
dscrfcn
[
jn
]
+
coef1
*
dCikj
;
}
}
coef1
=
sfcij
;
coef2
=
sij
*
dfcij
/
rij
;
dscrfcn
[
jn
]
=
dscrfcn
[
jn
]
*
coef1
-
coef2
;
LABEL_100:
scrfcn
[
jn
]
=
sij
;
fcpair
[
jn
]
=
fcij
;
}
}
// ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
void
MEAM
::
calc_rho1
(
int
i
,
int
ntype
,
int
*
type
,
int
*
fmap
,
double
**
x
,
int
numneigh
,
int
*
firstneigh
,
double
*
scrfcn
,
double
*
fcpair
)
{
int
jn
,
j
,
m
,
n
,
p
,
elti
,
eltj
;
int
nv2
,
nv3
;
double
xtmp
,
ytmp
,
ztmp
,
delij
[
3
],
rij2
,
rij
,
sij
;
double
ai
,
aj
,
rhoa0j
,
rhoa1j
,
rhoa2j
,
rhoa3j
,
A1j
,
A2j
,
A3j
;
// double G,Gbar,gam,shp[3+1];
double
ro0i
,
ro0j
;
double
rhoa0i
,
rhoa1i
,
rhoa2i
,
rhoa3i
,
A1i
,
A2i
,
A3i
;
elti
=
fmap
[
type
[
i
]];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
for
(
jn
=
0
;
jn
<
numneigh
;
jn
++
)
{
if
(
!
iszero
(
scrfcn
[
jn
]))
{
j
=
firstneigh
[
jn
];
sij
=
scrfcn
[
jn
]
*
fcpair
[
jn
];
delij
[
0
]
=
x
[
j
][
0
]
-
xtmp
;
delij
[
1
]
=
x
[
j
][
1
]
-
ytmp
;
delij
[
2
]
=
x
[
j
][
2
]
-
ztmp
;
rij2
=
delij
[
0
]
*
delij
[
0
]
+
delij
[
1
]
*
delij
[
1
]
+
delij
[
2
]
*
delij
[
2
];
if
(
rij2
<
this
->
cutforcesq
)
{
eltj
=
fmap
[
type
[
j
]];
rij
=
sqrt
(
rij2
);
ai
=
rij
/
this
->
re_meam
[
elti
][
elti
]
-
1.0
;
aj
=
rij
/
this
->
re_meam
[
eltj
][
eltj
]
-
1.0
;
ro0i
=
this
->
rho0_meam
[
elti
];
ro0j
=
this
->
rho0_meam
[
eltj
];
rhoa0j
=
ro0j
*
MathSpecial
::
fm_exp
(
-
this
->
beta0_meam
[
eltj
]
*
aj
)
*
sij
;
rhoa1j
=
ro0j
*
MathSpecial
::
fm_exp
(
-
this
->
beta1_meam
[
eltj
]
*
aj
)
*
sij
;
rhoa2j
=
ro0j
*
MathSpecial
::
fm_exp
(
-
this
->
beta2_meam
[
eltj
]
*
aj
)
*
sij
;
rhoa3j
=
ro0j
*
MathSpecial
::
fm_exp
(
-
this
->
beta3_meam
[
eltj
]
*
aj
)
*
sij
;
rhoa0i
=
ro0i
*
MathSpecial
::
fm_exp
(
-
this
->
beta0_meam
[
elti
]
*
ai
)
*
sij
;
rhoa1i
=
ro0i
*
MathSpecial
::
fm_exp
(
-
this
->
beta1_meam
[
elti
]
*
ai
)
*
sij
;
rhoa2i
=
ro0i
*
MathSpecial
::
fm_exp
(
-
this
->
beta2_meam
[
elti
]
*
ai
)
*
sij
;
rhoa3i
=
ro0i
*
MathSpecial
::
fm_exp
(
-
this
->
beta3_meam
[
elti
]
*
ai
)
*
sij
;
if
(
this
->
ialloy
==
1
)
{
rhoa1j
=
rhoa1j
*
this
->
t1_meam
[
eltj
];
rhoa2j
=
rhoa2j
*
this
->
t2_meam
[
eltj
];
rhoa3j
=
rhoa3j
*
this
->
t3_meam
[
eltj
];
rhoa1i
=
rhoa1i
*
this
->
t1_meam
[
elti
];
rhoa2i
=
rhoa2i
*
this
->
t2_meam
[
elti
];
rhoa3i
=
rhoa3i
*
this
->
t3_meam
[
elti
];
}
rho0
[
i
]
=
rho0
[
i
]
+
rhoa0j
;
rho0
[
j
]
=
rho0
[
j
]
+
rhoa0i
;
// For ialloy = 2, use single-element value (not average)
if
(
this
->
ialloy
!=
2
)
{
t_ave
[
i
][
0
]
=
t_ave
[
i
][
0
]
+
this
->
t1_meam
[
eltj
]
*
rhoa0j
;
t_ave
[
i
][
1
]
=
t_ave
[
i
][
1
]
+
this
->
t2_meam
[
eltj
]
*
rhoa0j
;
t_ave
[
i
][
2
]
=
t_ave
[
i
][
2
]
+
this
->
t3_meam
[
eltj
]
*
rhoa0j
;
t_ave
[
j
][
0
]
=
t_ave
[
j
][
0
]
+
this
->
t1_meam
[
elti
]
*
rhoa0i
;
t_ave
[
j
][
1
]
=
t_ave
[
j
][
1
]
+
this
->
t2_meam
[
elti
]
*
rhoa0i
;
t_ave
[
j
][
2
]
=
t_ave
[
j
][
2
]
+
this
->
t3_meam
[
elti
]
*
rhoa0i
;
}
if
(
this
->
ialloy
==
1
)
{
tsq_ave
[
i
][
0
]
=
tsq_ave
[
i
][
0
]
+
this
->
t1_meam
[
eltj
]
*
this
->
t1_meam
[
eltj
]
*
rhoa0j
;
tsq_ave
[
i
][
1
]
=
tsq_ave
[
i
][
1
]
+
this
->
t2_meam
[
eltj
]
*
this
->
t2_meam
[
eltj
]
*
rhoa0j
;
tsq_ave
[
i
][
2
]
=
tsq_ave
[
i
][
2
]
+
this
->
t3_meam
[
eltj
]
*
this
->
t3_meam
[
eltj
]
*
rhoa0j
;
tsq_ave
[
j
][
0
]
=
tsq_ave
[
j
][
0
]
+
this
->
t1_meam
[
elti
]
*
this
->
t1_meam
[
elti
]
*
rhoa0i
;
tsq_ave
[
j
][
1
]
=
tsq_ave
[
j
][
1
]
+
this
->
t2_meam
[
elti
]
*
this
->
t2_meam
[
elti
]
*
rhoa0i
;
tsq_ave
[
j
][
2
]
=
tsq_ave
[
j
][
2
]
+
this
->
t3_meam
[
elti
]
*
this
->
t3_meam
[
elti
]
*
rhoa0i
;
}
arho2b
[
i
]
=
arho2b
[
i
]
+
rhoa2j
;
arho2b
[
j
]
=
arho2b
[
j
]
+
rhoa2i
;
A1j
=
rhoa1j
/
rij
;
A2j
=
rhoa2j
/
rij2
;
A3j
=
rhoa3j
/
(
rij2
*
rij
);
A1i
=
rhoa1i
/
rij
;
A2i
=
rhoa2i
/
rij2
;
A3i
=
rhoa3i
/
(
rij2
*
rij
);
nv2
=
0
;
nv3
=
0
;
for
(
m
=
0
;
m
<
3
;
m
++
)
{
arho1
[
i
][
m
]
=
arho1
[
i
][
m
]
+
A1j
*
delij
[
m
];
arho1
[
j
][
m
]
=
arho1
[
j
][
m
]
-
A1i
*
delij
[
m
];
arho3b
[
i
][
m
]
=
arho3b
[
i
][
m
]
+
rhoa3j
*
delij
[
m
]
/
rij
;
arho3b
[
j
][
m
]
=
arho3b
[
j
][
m
]
-
rhoa3i
*
delij
[
m
]
/
rij
;
for
(
n
=
m
;
n
<
3
;
n
++
)
{
arho2
[
i
][
nv2
]
=
arho2
[
i
][
nv2
]
+
A2j
*
delij
[
m
]
*
delij
[
n
];
arho2
[
j
][
nv2
]
=
arho2
[
j
][
nv2
]
+
A2i
*
delij
[
m
]
*
delij
[
n
];
nv2
=
nv2
+
1
;
for
(
p
=
n
;
p
<
3
;
p
++
)
{
arho3
[
i
][
nv3
]
=
arho3
[
i
][
nv3
]
+
A3j
*
delij
[
m
]
*
delij
[
n
]
*
delij
[
p
];
arho3
[
j
][
nv3
]
=
arho3
[
j
][
nv3
]
-
A3i
*
delij
[
m
]
*
delij
[
n
]
*
delij
[
p
];
nv3
=
nv3
+
1
;
}
}
}
}
}
}
}
Event Timeline
Log In to Comment