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pair_tersoff_mod.cpp
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rLAMMPS lammps
pair_tersoff_mod.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: Aidan Thompson (SNL) - original Tersoff implementation
Vitaly Dozhdikov (JIHT of RAS) - MOD addition
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_tersoff_mod.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "math_const.h"
using
namespace
LAMMPS_NS
;
using
namespace
MathConst
;
#define MAXLINE 1024
#define DELTA 4
/* ---------------------------------------------------------------------- */
PairTersoffMOD
::
PairTersoffMOD
(
LAMMPS
*
lmp
)
:
PairTersoff
(
lmp
)
{}
/* ---------------------------------------------------------------------- */
void
PairTersoffMOD
::
read_file
(
char
*
file
)
{
int
params_per_line
=
20
;
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 Tersoff potential file %s"
,
file
);
error
->
one
(
FLERR
,
str
);
}
}
// read each line out of file, skipping blank lines or leading '#'
// store line of 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 Tersoff 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 line
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
].
powerm
=
atof
(
words
[
3
]);
params
[
nparams
].
lam3
=
atof
(
words
[
4
]);
params
[
nparams
].
h
=
atof
(
words
[
5
]);
params
[
nparams
].
powern
=
atof
(
words
[
6
]);
params
[
nparams
].
beta
=
atof
(
words
[
7
]);
params
[
nparams
].
lam2
=
atof
(
words
[
8
]);
params
[
nparams
].
bigb
=
atof
(
words
[
9
]);
params
[
nparams
].
bigr
=
atof
(
words
[
10
]);
params
[
nparams
].
bigd
=
atof
(
words
[
11
]);
params
[
nparams
].
lam1
=
atof
(
words
[
12
]);
params
[
nparams
].
biga
=
atof
(
words
[
13
]);
params
[
nparams
].
powern_del
=
atof
(
words
[
14
]);
params
[
nparams
].
c1
=
atof
(
words
[
15
]);
params
[
nparams
].
c2
=
atof
(
words
[
16
]);
params
[
nparams
].
c3
=
atof
(
words
[
17
]);
params
[
nparams
].
c4
=
atof
(
words
[
18
]);
params
[
nparams
].
c5
=
atof
(
words
[
19
]);
// currently only allow m exponent of 1
params
[
nparams
].
powermint
=
int
(
params
[
nparams
].
powerm
);
if
(
params
[
nparams
].
lam3
<
0.0
||
params
[
nparams
].
powern
<
0.0
||
params
[
nparams
].
beta
<
0.0
||
params
[
nparams
].
lam2
<
0.0
||
params
[
nparams
].
bigb
<
0.0
||
params
[
nparams
].
bigr
<
0.0
||
params
[
nparams
].
bigd
<
0.0
||
params
[
nparams
].
bigd
>
params
[
nparams
].
bigr
||
params
[
nparams
].
lam3
<
0.0
||
params
[
nparams
].
biga
<
0.0
||
params
[
nparams
].
powerm
-
params
[
nparams
].
powermint
!=
0.0
||
(
params
[
nparams
].
powermint
!=
3
&&
params
[
nparams
].
powermint
!=
1
))
error
->
all
(
FLERR
,
"Illegal Tersoff parameter"
);
nparams
++
;
}
delete
[]
words
;
}
/* ---------------------------------------------------------------------- */
void
PairTersoffMOD
::
setup
()
{
int
i
,
j
,
k
,
m
,
n
;
// set elem2param for all element 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
for
(
m
=
0
;
m
<
nparams
;
m
++
)
{
params
[
m
].
cut
=
params
[
m
].
bigr
+
params
[
m
].
bigd
;
params
[
m
].
cutsq
=
params
[
m
].
cut
*
params
[
m
].
cut
;
params
[
m
].
ca1
=
pow
(
2.0
*
params
[
m
].
powern_del
*
1.0e-16
,
-
1.0
/
params
[
m
].
powern
);
params
[
m
].
ca4
=
1.0
/
params
[
m
].
ca1
;
}
// 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
;
}
/* ---------------------------------------------------------------------- */
double
PairTersoffMOD
::
zeta
(
Param
*
param
,
double
rsqij
,
double
rsqik
,
double
*
delrij
,
double
*
delrik
)
{
double
rij
,
rik
,
costheta
,
arg
,
ex_delr
;
rij
=
sqrt
(
rsqij
);
rik
=
sqrt
(
rsqik
);
costheta
=
(
delrij
[
0
]
*
delrik
[
0
]
+
delrij
[
1
]
*
delrik
[
1
]
+
delrij
[
2
]
*
delrik
[
2
])
/
(
rij
*
rik
);
if
(
param
->
powermint
==
3
)
arg
=
pow
(
param
->
lam3
*
(
rij
-
rik
),
3.0
);
else
arg
=
param
->
lam3
*
(
rij
-
rik
);
if
(
arg
>
69.0776
)
ex_delr
=
1.e30
;
else
if
(
arg
<
-
69.0776
)
ex_delr
=
0.0
;
else
ex_delr
=
exp
(
arg
);
return
ters_fc
(
rik
,
param
)
*
ters_gijk_mod
(
costheta
,
param
)
*
ex_delr
;
}
/* ---------------------------------------------------------------------- */
double
PairTersoffMOD
::
ters_fc
(
double
r
,
Param
*
param
)
{
double
ters_R
=
param
->
bigr
;
double
ters_D
=
param
->
bigd
;
if
(
r
<
ters_R
-
ters_D
)
return
1.0
;
if
(
r
>
ters_R
+
ters_D
)
return
0.0
;
return
0.5
*
(
1.0
-
1.125
*
sin
(
MY_PI2
*
(
r
-
ters_R
)
/
ters_D
)
-
0.125
*
sin
(
3
*
MY_PI2
*
(
r
-
ters_R
)
/
ters_D
));
}
/* ---------------------------------------------------------------------- */
double
PairTersoffMOD
::
ters_fc_d
(
double
r
,
Param
*
param
)
{
double
ters_R
=
param
->
bigr
;
double
ters_D
=
param
->
bigd
;
if
(
r
<
ters_R
-
ters_D
)
return
0.0
;
if
(
r
>
ters_R
+
ters_D
)
return
0.0
;
return
-
(
0.375
*
MY_PI4
/
ters_D
)
*
(
3
*
cos
(
MY_PI2
*
(
r
-
ters_R
)
/
ters_D
)
+
cos
(
3
*
MY_PI2
*
(
r
-
ters_R
)
/
ters_D
));
}
/* ---------------------------------------------------------------------- */
double
PairTersoffMOD
::
ters_bij
(
double
zeta
,
Param
*
param
)
{
double
tmp
=
param
->
beta
*
zeta
;
if
(
tmp
>
param
->
ca1
)
return
pow
(
tmp
,
-
param
->
powern
/
(
2.0
*
param
->
powern_del
));
if
(
tmp
<
param
->
ca4
)
return
1.0
;
return
pow
(
1.0
+
pow
(
tmp
,
param
->
powern
),
-
1.0
/
(
2.0
*
param
->
powern_del
));
}
/* ---------------------------------------------------------------------- */
double
PairTersoffMOD
::
ters_bij_d
(
double
zeta
,
Param
*
param
)
{
double
tmp
=
param
->
beta
*
zeta
;
if
(
tmp
>
param
->
ca1
)
return
-
0.5
*
(
param
->
powern
/
param
->
powern_del
)
*
pow
(
tmp
,
-
0.5
*
(
param
->
powern
/
param
->
powern_del
))
/
zeta
;
if
(
tmp
<
param
->
ca4
)
return
0.0
;
double
tmp_n
=
pow
(
tmp
,
param
->
powern
);
return
-
0.5
*
(
param
->
powern
/
param
->
powern_del
)
*
pow
(
1.0
+
tmp_n
,
-
1.0
-
(
1.0
/
(
2.0
*
param
->
powern_del
)))
*
tmp_n
/
zeta
;
}
/* ---------------------------------------------------------------------- */
void
PairTersoffMOD
::
ters_zetaterm_d
(
double
prefactor
,
double
*
rij_hat
,
double
rij
,
double
*
rik_hat
,
double
rik
,
double
*
dri
,
double
*
drj
,
double
*
drk
,
Param
*
param
)
{
double
gijk
,
gijk_d
,
ex_delr
,
ex_delr_d
,
fc
,
dfc
,
cos_theta
,
tmp
;
double
dcosdri
[
3
],
dcosdrj
[
3
],
dcosdrk
[
3
];
fc
=
ters_fc
(
rik
,
param
);
dfc
=
ters_fc_d
(
rik
,
param
);
if
(
param
->
powermint
==
3
)
tmp
=
pow
(
param
->
lam3
*
(
rij
-
rik
),
3.0
);
else
tmp
=
param
->
lam3
*
(
rij
-
rik
);
if
(
tmp
>
69.0776
)
ex_delr
=
1.e30
;
else
if
(
tmp
<
-
69.0776
)
ex_delr
=
0.0
;
else
ex_delr
=
exp
(
tmp
);
if
(
param
->
powermint
==
3
)
ex_delr_d
=
3.0
*
pow
(
param
->
lam3
,
3.0
)
*
pow
(
rij
-
rik
,
2.0
)
*
ex_delr
;
else
ex_delr_d
=
param
->
lam3
*
ex_delr
;
cos_theta
=
vec3_dot
(
rij_hat
,
rik_hat
);
gijk
=
ters_gijk_mod
(
cos_theta
,
param
);
gijk_d
=
ters_gijk_d_mod
(
cos_theta
,
param
);
costheta_d
(
rij_hat
,
rij
,
rik_hat
,
rik
,
dcosdri
,
dcosdrj
,
dcosdrk
);
// compute the derivative wrt Ri
// dri = -dfc*gijk*ex_delr*rik_hat;
// dri += fc*gijk_d*ex_delr*dcosdri;
// dri += fc*gijk*ex_delr_d*(rik_hat - rij_hat);
vec3_scale
(
-
dfc
*
gijk
*
ex_delr
,
rik_hat
,
dri
);
vec3_scaleadd
(
fc
*
gijk_d
*
ex_delr
,
dcosdri
,
dri
,
dri
);
vec3_scaleadd
(
fc
*
gijk
*
ex_delr_d
,
rik_hat
,
dri
,
dri
);
vec3_scaleadd
(
-
fc
*
gijk
*
ex_delr_d
,
rij_hat
,
dri
,
dri
);
vec3_scale
(
prefactor
,
dri
,
dri
);
// compute the derivative wrt Rj
// drj = fc*gijk_d*ex_delr*dcosdrj;
// drj += fc*gijk*ex_delr_d*rij_hat;
vec3_scale
(
fc
*
gijk_d
*
ex_delr
,
dcosdrj
,
drj
);
vec3_scaleadd
(
fc
*
gijk
*
ex_delr_d
,
rij_hat
,
drj
,
drj
);
vec3_scale
(
prefactor
,
drj
,
drj
);
// compute the derivative wrt Rk
// drk = dfc*gijk*ex_delr*rik_hat;
// drk += fc*gijk_d*ex_delr*dcosdrk;
// drk += -fc*gijk*ex_delr_d*rik_hat;
vec3_scale
(
dfc
*
gijk
*
ex_delr
,
rik_hat
,
drk
);
vec3_scaleadd
(
fc
*
gijk_d
*
ex_delr
,
dcosdrk
,
drk
,
drk
);
vec3_scaleadd
(
-
fc
*
gijk
*
ex_delr_d
,
rik_hat
,
drk
,
drk
);
vec3_scale
(
prefactor
,
drk
,
drk
);
}
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