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pair_nb3b_harmonic.cpp
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rLAMMPS lammps
pair_nb3b_harmonic.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: Todd R. Zeitler (SNL)
(based on Stillinger-Weber pair style)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_nb3b_harmonic.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
#define SMALL 0.001
#define PI 3.141592653589793238462643383279
/* ---------------------------------------------------------------------- */
PairNb3bHarmonic
::
PairNb3bHarmonic
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
single_enable
=
0
;
one_coeff
=
1
;
manybody_flag
=
1
;
nelements
=
0
;
elements
=
NULL
;
nparams
=
maxparam
=
0
;
params
=
NULL
;
elem2param
=
NULL
;
map
=
NULL
;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairNb3bHarmonic
::~
PairNb3bHarmonic
()
{
if
(
elements
)
for
(
int
i
=
0
;
i
<
nelements
;
i
++
)
delete
[]
elements
[
i
];
delete
[]
elements
;
memory
->
destroy
(
params
);
memory
->
destroy
(
elem2param
);
if
(
allocated
)
{
memory
->
destroy
(
setflag
);
memory
->
destroy
(
cutsq
);
delete
[]
map
;
}
}
/* ---------------------------------------------------------------------- */
void
PairNb3bHarmonic
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
k
,
ii
,
jj
,
kk
,
inum
,
jnum
,
jnumm1
;
int
itype
,
jtype
,
ktype
,
ijparam
,
ikparam
,
ijkparam
;
double
xtmp
,
ytmp
,
ztmp
,
evdwl
;
double
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
;
int
*
type
=
atom
->
type
;
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
];
itype
=
map
[
type
[
i
]];
xtmp
=
x
[
i
][
0
];
ytmp
=
x
[
i
][
1
];
ztmp
=
x
[
i
][
2
];
jlist
=
firstneigh
[
i
];
jnum
=
numneigh
[
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
].
cutsq
)
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
].
cutsq
)
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
PairNb3bHarmonic
::
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
PairNb3bHarmonic
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
0
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairNb3bHarmonic
::
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
PairNb3bHarmonic
::
init_style
()
{
if
(
atom
->
tag_enable
==
0
)
error
->
all
(
FLERR
,
"Pair style nb3b/harmonic requires atom IDs"
);
if
(
force
->
newton_pair
==
0
)
error
->
all
(
FLERR
,
"Pair style nb3b/harmonic requires newton pair on"
);
// need a full neighbor list
int
irequest
=
neighbor
->
request
(
this
,
instance_me
);
neighbor
->
requests
[
irequest
]
->
half
=
0
;
neighbor
->
requests
[
irequest
]
->
full
=
1
;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double
PairNb3bHarmonic
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
error
->
all
(
FLERR
,
"All pair coeffs are not set"
);
return
cutmax
;
}
/* ---------------------------------------------------------------------- */
void
PairNb3bHarmonic
::
read_file
(
char
*
file
)
{
int
params_per_line
=
6
;
char
**
words
=
new
char
*
[
params_per_line
+
1
];
memory
->
sfree
(
params
);
params
=
NULL
;
nparams
=
maxparam
=
0
;
// open file on proc 0
FILE
*
fp
=
NULL
;
if
(
comm
->
me
==
0
)
{
fp
=
force
->
open_potential
(
file
);
if
(
fp
==
NULL
)
{
char
str
[
128
];
sprintf
(
str
,
"Cannot open nb3b/harmonic 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 nb3b/harmonic 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
].
k_theta
=
atof
(
words
[
3
]);
params
[
nparams
].
theta0
=
atof
(
words
[
4
]);
params
[
nparams
].
cutoff
=
atof
(
words
[
5
]);
if
(
params
[
nparams
].
k_theta
<
0.0
||
params
[
nparams
].
theta0
<
0.0
||
params
[
nparams
].
cutoff
<
0.0
)
error
->
all
(
FLERR
,
"Illegal nb3b/harmonic parameter"
);
nparams
++
;
}
delete
[]
words
;
}
/* ---------------------------------------------------------------------- */
void
PairNb3bHarmonic
::
setup_params
()
{
int
i
,
j
,
k
,
m
,
n
;
double
rtmp
;
// 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
// (cut = a*sigma)
for
(
m
=
0
;
m
<
nparams
;
m
++
)
{
params
[
m
].
cut
=
params
[
m
].
cutoff
;
params
[
m
].
cutsq
=
params
[
m
].
cut
*
params
[
m
].
cut
;
params
[
m
].
theta0
=
params
[
m
].
theta0
/
180.0
*
PI
;
}
// set cutmax to max of all params
cutmax
=
0.0
;
for
(
m
=
0
;
m
<
nparams
;
m
++
)
{
rtmp
=
sqrt
(
params
[
m
].
cutsq
);
if
(
rtmp
>
cutmax
)
cutmax
=
rtmp
;
}
}
/* ---------------------------------------------------------------------- */
void
PairNb3bHarmonic
::
threebody
(
Param
*
paramij
,
Param
*
paramik
,
Param
*
paramijk
,
double
rsq1
,
double
rsq2
,
double
*
delr1
,
double
*
delr2
,
double
*
fj
,
double
*
fk
,
int
eflag
,
double
&
eng
)
{
double
dtheta
,
tk
;
double
r1
,
r2
,
c
,
s
,
a
,
a11
,
a12
,
a22
;
// angle (cos and sin)
r1
=
sqrt
(
rsq1
);
r2
=
sqrt
(
rsq2
);
c
=
delr1
[
0
]
*
delr2
[
0
]
+
delr1
[
1
]
*
delr2
[
1
]
+
delr1
[
2
]
*
delr2
[
2
];
c
/=
r1
*
r2
;
if
(
c
>
1.0
)
c
=
1.0
;
if
(
c
<
-
1.0
)
c
=
-
1.0
;
s
=
sqrt
(
1.0
-
c
*
c
);
if
(
s
<
SMALL
)
s
=
SMALL
;
s
=
1.0
/
s
;
// force & energy
dtheta
=
acos
(
c
)
-
paramijk
->
theta0
;
tk
=
paramijk
->
k_theta
*
dtheta
;
if
(
eflag
)
eng
=
tk
*
dtheta
;
a
=
-
2.0
*
tk
*
s
;
a11
=
a
*
c
/
rsq1
;
a12
=
-
a
/
(
r1
*
r2
);
a22
=
a
*
c
/
rsq2
;
fj
[
0
]
=
a11
*
delr1
[
0
]
+
a12
*
delr2
[
0
];
fj
[
1
]
=
a11
*
delr1
[
1
]
+
a12
*
delr2
[
1
];
fj
[
2
]
=
a11
*
delr1
[
2
]
+
a12
*
delr2
[
2
];
fk
[
0
]
=
a22
*
delr2
[
0
]
+
a12
*
delr1
[
0
];
fk
[
1
]
=
a22
*
delr2
[
1
]
+
a12
*
delr1
[
1
];
fk
[
2
]
=
a22
*
delr2
[
2
]
+
a12
*
delr1
[
2
];
}
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