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rLAMMPS lammps
pair_vashishta.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: Yongnan Xiong (HNU), xyn@hnu.edu.cn
Aidan Thompson (SNL)
Anders Hafreager (UiO), andershaf@gmail.com
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_vashishta.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
#define MAXLINE 1024
#define DELTA 4
/* ---------------------------------------------------------------------- */
PairVashishta
::
PairVashishta
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
single_enable
=
0
;
restartinfo
=
0
;
one_coeff
=
1
;
manybody_flag
=
1
;
nelements
=
0
;
elements
=
NULL
;
nparams
=
maxparam
=
0
;
params
=
NULL
;
elem2param
=
NULL
;
map
=
NULL
;
neigh3BodyMax
=
0
;
neigh3BodyCount
=
NULL
;
neigh3Body
=
NULL
;
useTable
=
false
;
nTablebits
=
12
;
forceTable
=
NULL
;
potentialTable
=
NULL
;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairVashishta
::~
PairVashishta
()
{
if
(
elements
)
for
(
int
i
=
0
;
i
<
nelements
;
i
++
)
delete
[]
elements
[
i
];
delete
[]
elements
;
memory
->
destroy
(
params
);
memory
->
destroy
(
elem2param
);
memory
->
destroy
(
forceTable
);
memory
->
destroy
(
potentialTable
);
memory
->
destroy
(
neigh3BodyCount
);
memory
->
destroy
(
neigh3Body
);
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
delete
[]
map
;
}
}
void
PairVashishta
::
modify_params
(
int
narg
,
char
**
arg
)
{
if
(
narg
==
0
)
error
->
all
(
FLERR
,
"Illegal pair_modify command"
);
int
iarg
=
0
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"table"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal pair_modify command"
);
nTablebits
=
force
->
inumeric
(
FLERR
,
arg
[
iarg
+
1
]);
if
((
nTablebits
<
0
)
||
(
nTablebits
>
sizeof
(
int
)
*
CHAR_BIT
-
1
))
error
->
all
(
FLERR
,
"Illegal interpolation table size"
);
if
(
nTablebits
==
0
)
{
useTable
=
false
;
}
else
{
useTable
=
true
;
}
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"tabinner"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
error
->
all
(
FLERR
,
"Illegal pair_modify command"
);
tabinner
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
1
]);
if
(
tabinner
<=
0.0
)
error
->
all
(
FLERR
,
"Illegal inner cutoff for tabulation"
);
iarg
+=
2
;
}
}
updateTables
();
}
void
PairVashishta
::
validateNeigh3Body
()
{
if
(
atom
->
nlocal
>
neigh3BodyMax
)
{
neigh3BodyMax
=
atom
->
nmax
;
memory
->
destroy
(
neigh3BodyCount
);
memory
->
destroy
(
neigh3Body
);
memory
->
create
(
neigh3BodyCount
,
neigh3BodyMax
,
"pair:vashishta:neigh3BodyCount"
);
memory
->
create
(
neigh3Body
,
neigh3BodyMax
,
1000
,
"pair:vashishta:neigh3Body"
);
// TODO: pick this number more wisely?
}
}
void
PairVashishta
::
updateTables
()
{
memory
->
destroy
(
forceTable
);
memory
->
destroy
(
potentialTable
);
forceTable
=
NULL
;
potentialTable
=
NULL
;
if
(
!
useTable
)
return
;
int
ntable
=
1
<<
nTablebits
;
tabinnersq
=
tabinner
*
tabinner
;
deltaR2
=
(
cutmax
*
cutmax
-
tabinnersq
)
/
(
ntable
-
1
);
oneOverDeltaR2
=
1.0
/
deltaR2
;
memory
->
create
(
forceTable
,
nelements
,
nelements
,
ntable
+
1
,
"pair:vashishta:forceTable"
);
memory
->
create
(
potentialTable
,
nelements
,
nelements
,
ntable
+
1
,
"pair:vashishta:potentialTable"
);
for
(
int
i
=
0
;
i
<
nelements
;
i
++
)
{
for
(
int
j
=
0
;
j
<
nelements
;
j
++
)
{
int
ijparam
=
elem2param
[
i
][
j
][
j
];
for
(
int
idx
=
0
;
idx
<=
ntable
;
idx
++
)
{
double
rsq
=
tabinnersq
+
idx
*
deltaR2
;
double
fpair
,
eng
;
// call analytical version of two-body term function
twobody
(
params
[
ijparam
],
rsq
,
fpair
,
1
,
eng
,
false
);
forceTable
[
i
][
j
][
idx
]
=
fpair
;
potentialTable
[
i
][
j
][
idx
]
=
eng
;
}
}
}
}
/* ---------------------------------------------------------------------- */
void
PairVashishta
::
compute
(
int
eflag
,
int
vflag
)
{
validateNeigh3Body
();
int
i
,
j
,
k
,
ii
,
jj
,
kk
,
inum
,
jnum
,
jnumm1
;
int
itype
,
jtype
,
ktype
,
ijparam
,
ikparam
,
ijkparam
;
tagint
itag
,
jtag
;
double
xtmp
,
ytmp
,
ztmp
,
delx
,
dely
,
delz
,
evdwl
,
fpair
;
double
rsq
,
rsq1
,
rsq2
;
double
delr1
[
3
],
delr2
[
3
],
fj
[
3
],
fk
[
3
];
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
evdwl
=
0.0
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
else
evflag
=
vflag_fdotr
=
0
;
double
**
x
=
atom
->
x
;
double
**
f
=
atom
->
f
;
tagint
*
tag
=
atom
->
tag
;
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 full neighbor list of my atoms
for
(
ii
=
0
;
ii
<
inum
;
ii
++
)
{
i
=
ilist
[
ii
];
itag
=
tag
[
i
];
itype
=
map
[
type
[
i
]];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
neigh3BodyCount
[
i
]
=
0
;
// Reset the 3-body neighbor list
// two-body interactions, skip half of them
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
i
];
for
(
jj
=
0
;
jj
<
jnum
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
jtag
=
tag
[
j
];
jtype
=
map
[
type
[
j
]];
delx
=
xtmp
-
x
[
j
][
0
];
dely
=
ytmp
-
x
[
j
][
1
];
delz
=
ztmp
-
x
[
j
][
2
];
rsq
=
delx
*
delx
+
dely
*
dely
+
delz
*
delz
;
ijparam
=
elem2param
[
itype
][
jtype
][
jtype
];
if
(
rsq
<=
params
[
ijparam
].
cutsq2
)
{
neigh3Body
[
i
][
neigh3BodyCount
[
i
]]
=
j
;
neigh3BodyCount
[
i
]
++
;
}
if
(
rsq
>
params
[
ijparam
].
cutsq
)
continue
;
if
(
itag
>
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
0
)
continue
;
}
else
if
(
itag
<
jtag
)
{
if
((
itag
+
jtag
)
%
2
==
1
)
continue
;
}
else
{
if
(
x
[
j
][
2
]
<
ztmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
<
ytmp
)
continue
;
if
(
x
[
j
][
2
]
==
ztmp
&&
x
[
j
][
1
]
==
ytmp
&&
x
[
j
][
0
]
<
xtmp
)
continue
;
}
twobody
(
params
[
ijparam
],
rsq
,
fpair
,
eflag
,
evdwl
,
useTable
);
f
[
i
][
0
]
+=
delx
*
fpair
;
f
[
i
][
1
]
+=
dely
*
fpair
;
f
[
i
][
2
]
+=
delz
*
fpair
;
f
[
j
][
0
]
-=
delx
*
fpair
;
f
[
j
][
1
]
-=
dely
*
fpair
;
f
[
j
][
2
]
-=
delz
*
fpair
;
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
0.0
,
fpair
,
delx
,
dely
,
delz
);
}
jlist
=
neigh3Body
[
i
];
jnum
=
neigh3BodyCount
[
i
];
jnumm1
=
jnum
-
1
;
for
(
jj
=
0
;
jj
<
jnumm1
;
jj
++
)
{
j
=
jlist
[
jj
];
j
&=
NEIGHMASK
;
jtype
=
map
[
type
[
j
]];
ijparam
=
elem2param
[
itype
][
jtype
][
jtype
];
delr1
[
0
]
=
x
[
j
][
0
]
-
xtmp
;
delr1
[
1
]
=
x
[
j
][
1
]
-
ytmp
;
delr1
[
2
]
=
x
[
j
][
2
]
-
ztmp
;
rsq1
=
delr1
[
0
]
*
delr1
[
0
]
+
delr1
[
1
]
*
delr1
[
1
]
+
delr1
[
2
]
*
delr1
[
2
];
if
(
rsq1
>=
params
[
ijparam
].
cutsq2
)
continue
;
for
(
kk
=
jj
+
1
;
kk
<
jnum
;
kk
++
)
{
k
=
jlist
[
kk
];
k
&=
NEIGHMASK
;
ktype
=
map
[
type
[
k
]];
ikparam
=
elem2param
[
itype
][
ktype
][
ktype
];
ijkparam
=
elem2param
[
itype
][
jtype
][
ktype
];
delr2
[
0
]
=
x
[
k
][
0
]
-
xtmp
;
delr2
[
1
]
=
x
[
k
][
1
]
-
ytmp
;
delr2
[
2
]
=
x
[
k
][
2
]
-
ztmp
;
rsq2
=
delr2
[
0
]
*
delr2
[
0
]
+
delr2
[
1
]
*
delr2
[
1
]
+
delr2
[
2
]
*
delr2
[
2
];
if
(
rsq2
>=
params
[
ikparam
].
cutsq2
)
continue
;
threebody
(
&
params
[
ijparam
],
&
params
[
ikparam
],
&
params
[
ijkparam
],
rsq1
,
rsq2
,
delr1
,
delr2
,
fj
,
fk
,
eflag
,
evdwl
);
f
[
i
][
0
]
-=
fj
[
0
]
+
fk
[
0
];
f
[
i
][
1
]
-=
fj
[
1
]
+
fk
[
1
];
f
[
i
][
2
]
-=
fj
[
2
]
+
fk
[
2
];
f
[
j
][
0
]
+=
fj
[
0
];
f
[
j
][
1
]
+=
fj
[
1
];
f
[
j
][
2
]
+=
fj
[
2
];
f
[
k
][
0
]
+=
fk
[
0
];
f
[
k
][
1
]
+=
fk
[
1
];
f
[
k
][
2
]
+=
fk
[
2
];
if
(
evflag
)
ev_tally3
(
i
,
j
,
k
,
evdwl
,
0.0
,
fj
,
fk
,
delr1
,
delr2
);
}
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ---------------------------------------------------------------------- */
void
PairVashishta
::
allocate
()
{
allocated
=
1
;
int
n
=
atom
->
ntypes
;
memory
->
create
(
setflag
,
n
+
1
,
n
+
1
,
"pair:setflag"
);
memory
->
create
(
cutsq
,
n
+
1
,
n
+
1
,
"pair:cutsq"
);
map
=
new
int
[
n
+
1
];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void
PairVashishta
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
0
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairVashishta
::
coeff
(
int
narg
,
char
**
arg
)
{
int
i
,
j
,
n
;
if
(
!
allocated
)
allocate
();
if
(
narg
!=
3
+
atom
->
ntypes
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
// insure I,J args are * *
if
(
strcmp
(
arg
[
0
],
"*"
)
!=
0
||
strcmp
(
arg
[
1
],
"*"
)
!=
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
// nelements = # of unique elements
// elements = list of element names
if
(
elements
)
{
for
(
i
=
0
;
i
<
nelements
;
i
++
)
delete
[]
elements
[
i
];
delete
[]
elements
;
}
elements
=
new
char
*
[
atom
->
ntypes
];
for
(
i
=
0
;
i
<
atom
->
ntypes
;
i
++
)
elements
[
i
]
=
NULL
;
nelements
=
0
;
for
(
i
=
3
;
i
<
narg
;
i
++
)
{
if
(
strcmp
(
arg
[
i
],
"NULL"
)
==
0
)
{
map
[
i
-
2
]
=
-
1
;
continue
;
}
for
(
j
=
0
;
j
<
nelements
;
j
++
)
if
(
strcmp
(
arg
[
i
],
elements
[
j
])
==
0
)
break
;
map
[
i
-
2
]
=
j
;
if
(
j
==
nelements
)
{
n
=
strlen
(
arg
[
i
])
+
1
;
elements
[
j
]
=
new
char
[
n
];
strcpy
(
elements
[
j
],
arg
[
i
]);
nelements
++
;
}
}
// read potential file and initialize potential parameters
read_file
(
arg
[
2
]);
setup_params
();
// clear setflag since coeff() called once with I,J = * *
n
=
atom
->
ntypes
;
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
setflag
[
i
][
j
]
=
0
;
// set setflag i,j for type pairs where both are mapped to elements
int
count
=
0
;
for
(
int
i
=
1
;
i
<=
n
;
i
++
)
for
(
int
j
=
i
;
j
<=
n
;
j
++
)
if
(
map
[
i
]
>=
0
&&
map
[
j
]
>=
0
)
{
setflag
[
i
][
j
]
=
1
;
count
++
;
}
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Incorrect args for pair coefficients"
);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairVashishta
::
init_style
()
{
if
(
atom
->
tag_enable
==
0
)
error
->
all
(
FLERR
,
"Pair style Vashishta requires atom IDs"
);
if
(
force
->
newton_pair
==
0
)
error
->
all
(
FLERR
,
"Pair style Vashishta requires newton pair on"
);
// need a full neighbor list
int
irequest
=
neighbor
->
request
(
this
);
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full
=
1
;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairVashishta
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
error
->
all
(
FLERR
,
"All pair coeffs are not set"
);
return
cutmax
;
}
/* ---------------------------------------------------------------------- */
void
PairVashishta
::
read_file
(
char
*
file
)
{
int
params_per_line
=
17
;
char
**
words
=
new
char
*
[
params_per_line
+
1
];
memory
->
sfree
(
params
);
params
=
NULL
;
nparams
=
maxparam
=
0
;
// open file on proc 0
FILE
*
fp
;
if
(
comm
->
me
==
0
)
{
fp
=
force
->
open_potential
(
file
);
if
(
fp
==
NULL
)
{
char
str
[
128
];
sprintf
(
str
,
"Cannot open Vashishta potential file %s"
,
file
);
error
->
one
(
FLERR
,
str
);
}
}
// read each set of params from potential file
// one set of params can span multiple lines
// store params if all 3 element tags are in element list
int
n
,
nwords
,
ielement
,
jelement
,
kelement
;
char
line
[
MAXLINE
],
*
ptr
;
int
eof
=
0
;
while
(
1
)
{
if
(
comm
->
me
==
0
)
{
ptr
=
fgets
(
line
,
MAXLINE
,
fp
);
if
(
ptr
==
NULL
)
{
eof
=
1
;
fclose
(
fp
);
}
else
n
=
strlen
(
line
)
+
1
;
}
MPI_Bcast
(
&
eof
,
1
,
MPI_INT
,
0
,
world
);
if
(
eof
)
break
;
MPI_Bcast
(
&
n
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
line
,
n
,
MPI_CHAR
,
0
,
world
);
// strip comment, skip line if blank
if
((
ptr
=
strchr
(
line
,
'#'
)))
*
ptr
=
'\0'
;
nwords
=
atom
->
count_words
(
line
);
if
(
nwords
==
0
)
continue
;
// concatenate additional lines until have params_per_line words
while
(
nwords
<
params_per_line
)
{
n
=
strlen
(
line
);
if
(
comm
->
me
==
0
)
{
ptr
=
fgets
(
&
line
[
n
],
MAXLINE
-
n
,
fp
);
if
(
ptr
==
NULL
)
{
eof
=
1
;
fclose
(
fp
);
}
else
n
=
strlen
(
line
)
+
1
;
}
MPI_Bcast
(
&
eof
,
1
,
MPI_INT
,
0
,
world
);
if
(
eof
)
break
;
MPI_Bcast
(
&
n
,
1
,
MPI_INT
,
0
,
world
);
MPI_Bcast
(
line
,
n
,
MPI_CHAR
,
0
,
world
);
if
((
ptr
=
strchr
(
line
,
'#'
)))
*
ptr
=
'\0'
;
nwords
=
atom
->
count_words
(
line
);
}
if
(
nwords
!=
params_per_line
)
error
->
all
(
FLERR
,
"Incorrect format in Vashishta potential file"
);
// words = ptrs to all words in line
nwords
=
0
;
words
[
nwords
++
]
=
strtok
(
line
,
"
\t\n\r\f
"
);
while
((
words
[
nwords
++
]
=
strtok
(
NULL
,
"
\t\n\r\f
"
)))
continue
;
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next entry in file
for
(
ielement
=
0
;
ielement
<
nelements
;
ielement
++
)
if
(
strcmp
(
words
[
0
],
elements
[
ielement
])
==
0
)
break
;
if
(
ielement
==
nelements
)
continue
;
for
(
jelement
=
0
;
jelement
<
nelements
;
jelement
++
)
if
(
strcmp
(
words
[
1
],
elements
[
jelement
])
==
0
)
break
;
if
(
jelement
==
nelements
)
continue
;
for
(
kelement
=
0
;
kelement
<
nelements
;
kelement
++
)
if
(
strcmp
(
words
[
2
],
elements
[
kelement
])
==
0
)
break
;
if
(
kelement
==
nelements
)
continue
;
// load up parameter settings and error check their values
if
(
nparams
==
maxparam
)
{
maxparam
+=
DELTA
;
params
=
(
Param
*
)
memory
->
srealloc
(
params
,
maxparam
*
sizeof
(
Param
),
"pair:params"
);
}
params
[
nparams
].
ielement
=
ielement
;
params
[
nparams
].
jelement
=
jelement
;
params
[
nparams
].
kelement
=
kelement
;
params
[
nparams
].
bigh
=
atof
(
words
[
3
]);
params
[
nparams
].
eta
=
atof
(
words
[
4
]);
params
[
nparams
].
zi
=
atof
(
words
[
5
]);
params
[
nparams
].
zj
=
atof
(
words
[
6
]);
params
[
nparams
].
lambda1
=
atof
(
words
[
7
]);
params
[
nparams
].
bigd
=
atof
(
words
[
8
]);
params
[
nparams
].
lambda4
=
atof
(
words
[
9
]);
params
[
nparams
].
bigw
=
atof
(
words
[
10
]);
params
[
nparams
].
cut
=
atof
(
words
[
11
]);
params
[
nparams
].
bigb
=
atof
(
words
[
12
]);
params
[
nparams
].
gamma
=
atof
(
words
[
13
]);
params
[
nparams
].
r0
=
atof
(
words
[
14
]);
params
[
nparams
].
bigc
=
atof
(
words
[
15
]);
params
[
nparams
].
costheta
=
atof
(
words
[
16
]);
if
(
params
[
nparams
].
bigb
<
0.0
||
params
[
nparams
].
gamma
<
0.0
||
params
[
nparams
].
r0
<
0.0
||
params
[
nparams
].
bigc
<
0.0
||
params
[
nparams
].
bigh
<
0.0
||
params
[
nparams
].
eta
<
0.0
||
params
[
nparams
].
lambda1
<
0.0
||
params
[
nparams
].
bigd
<
0.0
||
params
[
nparams
].
lambda4
<
0.0
||
params
[
nparams
].
bigw
<
0.0
||
params
[
nparams
].
cut
<
0.0
)
error
->
all
(
FLERR
,
"Illegal Vashishta parameter"
);
nparams
++
;
}
delete
[]
words
;
}
/* ---------------------------------------------------------------------- */
void
PairVashishta
::
setup_params
()
{
int
i
,
j
,
k
,
m
,
n
;
// set elem2param for all triplet combinations
// must be a single exact match to lines read from file
// do not allow for ACB in place of ABC
memory
->
destroy
(
elem2param
);
memory
->
create
(
elem2param
,
nelements
,
nelements
,
nelements
,
"pair:elem2param"
);
for
(
i
=
0
;
i
<
nelements
;
i
++
)
for
(
j
=
0
;
j
<
nelements
;
j
++
)
for
(
k
=
0
;
k
<
nelements
;
k
++
)
{
n
=
-
1
;
for
(
m
=
0
;
m
<
nparams
;
m
++
)
{
if
(
i
==
params
[
m
].
ielement
&&
j
==
params
[
m
].
jelement
&&
k
==
params
[
m
].
kelement
)
{
if
(
n
>=
0
)
error
->
all
(
FLERR
,
"Potential file has duplicate entry"
);
n
=
m
;
}
}
if
(
n
<
0
)
error
->
all
(
FLERR
,
"Potential file is missing an entry"
);
elem2param
[
i
][
j
][
k
]
=
n
;
}
// compute parameter values derived from inputs
// set cutsq using shortcut to reduce neighbor list for accelerated
// calculations. cut must remain unchanged as it is a potential parameter
double
tmp_par
;
for
(
m
=
0
;
m
<
nparams
;
m
++
)
{
params
[
m
].
cutsq
=
params
[
m
].
cut
*
params
[
m
].
cut
;
params
[
m
].
cutsq2
=
params
[
m
].
r0
*
params
[
m
].
r0
;
tmp_par
=
params
[
m
].
lambda1
;
params
[
m
].
lam1inv
=
(
tmp_par
==
0.0
)
?
0.0
:
1.0
/
tmp_par
;
tmp_par
=
params
[
m
].
lambda4
;
params
[
m
].
lam4inv
=
(
tmp_par
==
0.0
)
?
0.0
:
1.0
/
tmp_par
;
params
[
m
].
zizj
=
params
[
m
].
zi
*
params
[
m
].
zj
*
force
->
qqr2e
;
// note that bigd does not have 1/2 factor
params
[
m
].
mbigd
=
params
[
m
].
bigd
;
params
[
m
].
heta
=
params
[
m
].
bigh
*
params
[
m
].
eta
;
params
[
m
].
big2b
=
2.0
*
params
[
m
].
bigb
;
params
[
m
].
big6w
=
6.0
*
params
[
m
].
bigw
;
tmp_par
=
params
[
m
].
cut
;
params
[
m
].
rcinv
=
(
tmp_par
==
0.0
)
?
0.0
:
1.0
/
tmp_par
;
params
[
m
].
rc2inv
=
params
[
m
].
rcinv
*
params
[
m
].
rcinv
;
params
[
m
].
rc4inv
=
params
[
m
].
rc2inv
*
params
[
m
].
rc2inv
;
params
[
m
].
rc6inv
=
params
[
m
].
rc2inv
*
params
[
m
].
rc4inv
;
params
[
m
].
rceta
=
pow
(
params
[
m
].
rcinv
,
params
[
m
].
eta
);
params
[
m
].
lam1rc
=
params
[
m
].
cut
*
params
[
m
].
lam1inv
;
params
[
m
].
lam4rc
=
params
[
m
].
cut
*
params
[
m
].
lam4inv
;
params
[
m
].
vrcc2
=
params
[
m
].
zizj
*
params
[
m
].
rcinv
*
exp
(
-
params
[
m
].
lam1rc
);
params
[
m
].
vrcc3
=
params
[
m
].
mbigd
*
params
[
m
].
rc4inv
*
exp
(
-
params
[
m
].
lam4rc
);
params
[
m
].
vrc
=
params
[
m
].
bigh
*
params
[
m
].
rceta
+
params
[
m
].
vrcc2
-
params
[
m
].
vrcc3
-
params
[
m
].
bigw
*
params
[
m
].
rc6inv
;
params
[
m
].
dvrc
=
params
[
m
].
vrcc3
*
(
4.0
*
params
[
m
].
rcinv
+
params
[
m
].
lam4inv
)
+
params
[
m
].
big6w
*
params
[
m
].
rc6inv
*
params
[
m
].
rcinv
-
params
[
m
].
heta
*
params
[
m
].
rceta
*
params
[
m
].
rcinv
-
params
[
m
].
vrcc2
*
(
params
[
m
].
rcinv
+
params
[
m
].
lam1inv
);
params
[
m
].
c0
=
params
[
m
].
cut
*
params
[
m
].
dvrc
-
params
[
m
].
vrc
;
}
// set cutmax to max of all params
cutmax
=
0.0
;
for
(
m
=
0
;
m
<
nparams
;
m
++
)
{
if
(
params
[
m
].
cut
>
cutmax
)
cutmax
=
params
[
m
].
cut
;
if
(
params
[
m
].
r0
>
cutmax
)
cutmax
=
params
[
m
].
r0
;
}
updateTables
();
}
/* ---------------------------------------------------------------------- */
void
PairVashishta
::
twobody
(
const
Param
&
param
,
double
rsq
,
double
&
fforce
,
int
eflag
,
double
&
eng
,
bool
tabulated
)
{
if
(
tabulated
)
{
if
(
rsq
<
tabinnersq
)
{
sprintf
(
estr
,
"Pair distance < table inner cutoff: "
"ijtype %d %d dist %g"
,
param
.
ielement
+
1
,
param
.
jelement
+
1
,
sqrt
(
rsq
));
error
->
one
(
FLERR
,
estr
);
}
const
int
tableIndex
=
(
rsq
-
tabinnersq
)
*
oneOverDeltaR2
;
// double - int will only keep the 0.xxxx part
const
double
fraction
=
(
rsq
-
tabinnersq
)
*
oneOverDeltaR2
-
tableIndex
;
double
force0
=
forceTable
[
param
.
ielement
][
param
.
jelement
][
tableIndex
];
double
force1
=
forceTable
[
param
.
ielement
][
param
.
jelement
][
tableIndex
+
1
];
fforce
=
(
1.0
-
fraction
)
*
force0
+
fraction
*
force1
;
// force is linearly interpolated between the two values
if
(
evflag
)
{
double
energy0
=
potentialTable
[
param
.
ielement
][
param
.
jelement
][
tableIndex
];
double
energy1
=
potentialTable
[
param
.
ielement
][
param
.
jelement
][
tableIndex
+
1
];
eng
=
(
1.0
-
fraction
)
*
energy0
+
fraction
*
energy1
;
}
}
else
{
double
r
,
rinvsq
,
r4inv
,
r6inv
,
reta
,
lam1r
,
lam4r
,
vc2
,
vc3
;
r
=
sqrt
(
rsq
);
rinvsq
=
1.0
/
rsq
;
r4inv
=
rinvsq
*
rinvsq
;
r6inv
=
rinvsq
*
r4inv
;
reta
=
pow
(
r
,
-
param
.
eta
);
lam1r
=
r
*
param
.
lam1inv
;
lam4r
=
r
*
param
.
lam4inv
;
vc2
=
param
.
zizj
*
exp
(
-
lam1r
)
/
r
;
vc3
=
param
.
mbigd
*
r4inv
*
exp
(
-
lam4r
);
fforce
=
(
param
.
dvrc
*
r
-
(
4.0
*
vc3
+
lam4r
*
vc3
+
param
.
big6w
*
r6inv
-
param
.
heta
*
reta
-
vc2
-
lam1r
*
vc2
)
)
*
rinvsq
;
if
(
eflag
)
eng
=
param
.
bigh
*
reta
+
vc2
-
vc3
-
param
.
bigw
*
r6inv
-
r
*
param
.
dvrc
+
param
.
c0
;
}
}
/* ---------------------------------------------------------------------- */
void
PairVashishta
::
threebody
(
Param
*
paramij
,
Param
*
paramik
,
Param
*
paramijk
,
double
rsq1
,
double
rsq2
,
double
*
delr1
,
double
*
delr2
,
double
*
fj
,
double
*
fk
,
int
eflag
,
double
&
eng
)
{
double
r1
,
rinvsq1
,
rainv1
,
gsrainv1
,
gsrainvsq1
,
expgsrainv1
;
double
r2
,
rinvsq2
,
rainv2
,
gsrainv2
,
gsrainvsq2
,
expgsrainv2
;
double
rinv12
,
cs
,
delcs
,
delcssq
,
facexp
,
facrad
,
frad1
,
frad2
,
pcsinv
,
pcsinvsq
,
pcs
;
double
facang
,
facang12
,
csfacang
,
csfac1
,
csfac2
;
r1
=
sqrt
(
rsq1
);
rinvsq1
=
1.0
/
rsq1
;
rainv1
=
1.0
/
(
r1
-
paramij
->
r0
);
gsrainv1
=
paramij
->
gamma
*
rainv1
;
gsrainvsq1
=
gsrainv1
*
rainv1
/
r1
;
expgsrainv1
=
exp
(
gsrainv1
);
r2
=
sqrt
(
rsq2
);
rinvsq2
=
1.0
/
rsq2
;
rainv2
=
1.0
/
(
r2
-
paramik
->
r0
);
gsrainv2
=
paramik
->
gamma
*
rainv2
;
gsrainvsq2
=
gsrainv2
*
rainv2
/
r2
;
expgsrainv2
=
exp
(
gsrainv2
);
rinv12
=
1.0
/
(
r1
*
r2
);
cs
=
(
delr1
[
0
]
*
delr2
[
0
]
+
delr1
[
1
]
*
delr2
[
1
]
+
delr1
[
2
]
*
delr2
[
2
])
*
rinv12
;
delcs
=
cs
-
paramijk
->
costheta
;
delcssq
=
delcs
*
delcs
;
pcsinv
=
paramijk
->
bigc
*
delcssq
+
1.0
;
pcsinvsq
=
pcsinv
*
pcsinv
;
pcs
=
delcssq
/
pcsinv
;
facexp
=
expgsrainv1
*
expgsrainv2
;
facrad
=
paramijk
->
bigb
*
facexp
*
pcs
;
frad1
=
facrad
*
gsrainvsq1
;
frad2
=
facrad
*
gsrainvsq2
;
facang
=
paramijk
->
big2b
*
facexp
*
delcs
/
pcsinvsq
;
facang12
=
rinv12
*
facang
;
csfacang
=
cs
*
facang
;
csfac1
=
rinvsq1
*
csfacang
;
fj
[
0
]
=
delr1
[
0
]
*
(
frad1
+
csfac1
)
-
delr2
[
0
]
*
facang12
;
fj
[
1
]
=
delr1
[
1
]
*
(
frad1
+
csfac1
)
-
delr2
[
1
]
*
facang12
;
fj
[
2
]
=
delr1
[
2
]
*
(
frad1
+
csfac1
)
-
delr2
[
2
]
*
facang12
;
csfac2
=
rinvsq2
*
csfacang
;
fk
[
0
]
=
delr2
[
0
]
*
(
frad2
+
csfac2
)
-
delr1
[
0
]
*
facang12
;
fk
[
1
]
=
delr2
[
1
]
*
(
frad2
+
csfac2
)
-
delr1
[
1
]
*
facang12
;
fk
[
2
]
=
delr2
[
2
]
*
(
frad2
+
csfac2
)
-
delr1
[
2
]
*
facang12
;
if
(
eflag
)
eng
=
facrad
;
}
/* ----------------------------------------------------------------------
* add memory usage for tabulation
* ---------------------------------------------------------------------- */
double
PairVashishta
::
memory_usage
()
{
double
bytes
=
Pair
::
memory_usage
();
if
(
useTable
)
bytes
+=
2
*
nelements
*
nelements
*
sizeof
(
double
)
*
(
1
<<
nTablebits
);
return
bytes
;
}
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