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rLAMMPS lammps
pair_edip.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: Luca Ferraro (CASPUR)
email: luca.ferraro@caspur.it
Environment Dependent Interatomic Potential
References:
1) J. F. Justo, M. Z. Bazant, E. Kaxiras, V. V. Bulatov, S. Yip
Phys. Rev. B 58, 2539 (1998)
------------------------------------------------------------------------- */
#include "math.h"
#include "float.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_edip.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"
using
namespace
LAMMPS_NS
;
#define MAXLINE 1024
#define DELTA 4
/* ---------------------------------------------------------------------- */
PairEDIP
::
PairEDIP
(
LAMMPS
*
lmp
)
:
Pair
(
lmp
)
{
single_enable
=
0
;
restartinfo
=
0
;
one_coeff
=
1
;
nelements
=
0
;
elements
=
NULL
;
nparams
=
maxparam
=
0
;
params
=
NULL
;
elem2param
=
NULL
;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairEDIP
::~
PairEDIP
()
{
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
;
deallocateGrids
();
deallocatePreLoops
();
}
}
/* ---------------------------------------------------------------------- */
void
PairEDIP
::
compute
(
int
eflag
,
int
vflag
)
{
int
i
,
j
,
k
,
ii
,
inum
,
jnum
;
int
itype
,
jtype
,
ktype
,
ijparam
,
ikparam
,
ijkparam
;
double
xtmp
,
ytmp
,
ztmp
,
evdwl
;
int
*
ilist
,
*
jlist
,
*
numneigh
,
**
firstneigh
;
register
int
preForceCoord_counter
;
double
invR_ij
;
double
invR_ik
;
double
directorCos_ij_x
;
double
directorCos_ij_y
;
double
directorCos_ij_z
;
double
directorCos_ik_x
;
double
directorCos_ik_y
;
double
directorCos_ik_z
;
double
cosTeta
;
int
interpolIDX
;
double
interpolTMP
;
double
interpolDeltaX
;
double
interpolY1
;
double
interpolY2
;
double
invRMinusCutoffA
;
double
sigmaInvRMinusCutoffA
;
double
gammInvRMinusCutoffA
;
double
cosTetaDiff
;
double
cosTetaDiffCosTetaDiff
;
double
cutoffFunction_ij
;
double
exp2B_ij
;
double
exp2BDerived_ij
;
double
pow2B_ij
;
double
pow2BDerived_ij
;
double
exp3B_ij
;
double
exp3BDerived_ij
;
double
exp3B_ik
;
double
exp3BDerived_ik
;
double
qFunction
;
double
qFunctionDerived
;
double
tauFunction
;
double
tauFunctionDerived
;
double
expMinusBetaZeta_iZeta_i
;
double
qFunctionCosTetaDiffCosTetaDiff
;
double
expMinusQFunctionCosTetaDiffCosTetaDiff
;
double
zeta_i
;
double
zeta_iDerived
;
double
zeta_iDerivedInvR_ij
;
double
forceModCoord_factor
;
double
forceModCoord
;
double
forceModCoord_ij
;
double
forceMod2B
;
double
forceMod3B_factor1_ij
;
double
forceMod3B_factor2_ij
;
double
forceMod3B_factor2
;
double
forceMod3B_factor1_ik
;
double
forceMod3B_factor2_ik
;
double
potentia3B_factor
;
double
potential2B_factor
;
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
;
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
++
)
{
zeta_i
=
0.0
;
int
numForceCoordPairs
=
0
;
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
];
// pre-loop to compute environment coordination f(Z)
for
(
int
neighbor_j
=
0
;
neighbor_j
<
jnum
;
neighbor_j
++
)
{
j
=
jlist
[
neighbor_j
];
j
&=
NEIGHMASK
;
double
dr_ij
[
3
],
r_ij
;
dr_ij
[
0
]
=
xtmp
-
x
[
j
][
0
];
dr_ij
[
1
]
=
ytmp
-
x
[
j
][
1
];
dr_ij
[
2
]
=
ztmp
-
x
[
j
][
2
];
r_ij
=
dr_ij
[
0
]
*
dr_ij
[
0
]
+
dr_ij
[
1
]
*
dr_ij
[
1
]
+
dr_ij
[
2
]
*
dr_ij
[
2
];
jtype
=
map
[
type
[
j
]];
ijparam
=
elem2param
[
itype
][
jtype
][
jtype
];
if
(
r_ij
>
params
[
ijparam
].
cutsq
)
continue
;
r_ij
=
sqrt
(
r_ij
);
invR_ij
=
1.0
/
r_ij
;
preInvR_ij
[
neighbor_j
]
=
invR_ij
;
invRMinusCutoffA
=
1.0
/
(
r_ij
-
cutoffA
);
sigmaInvRMinusCutoffA
=
sigma
*
invRMinusCutoffA
;
gammInvRMinusCutoffA
=
gamm
*
invRMinusCutoffA
;
interpolDeltaX
=
r_ij
-
GRIDSTART
;
interpolTMP
=
(
interpolDeltaX
*
GRIDDENSITY
);
interpolIDX
=
(
int
)
interpolTMP
;
interpolY1
=
exp3B
[
interpolIDX
];
interpolY2
=
exp3B
[
interpolIDX
+
1
];
exp3B_ij
=
interpolY1
+
(
interpolY2
-
interpolY1
)
*
(
interpolTMP
-
interpolIDX
);
exp3BDerived_ij
=
-
exp3B_ij
*
gammInvRMinusCutoffA
*
invRMinusCutoffA
;
preExp3B_ij
[
neighbor_j
]
=
exp3B_ij
;
preExp3BDerived_ij
[
neighbor_j
]
=
exp3BDerived_ij
;
interpolY1
=
exp2B
[
interpolIDX
];
interpolY2
=
exp2B
[
interpolIDX
+
1
];
exp2B_ij
=
interpolY1
+
(
interpolY2
-
interpolY1
)
*
(
interpolTMP
-
interpolIDX
);
exp2BDerived_ij
=
-
exp2B_ij
*
sigmaInvRMinusCutoffA
*
invRMinusCutoffA
;
preExp2B_ij
[
neighbor_j
]
=
exp2B_ij
;
preExp2BDerived_ij
[
neighbor_j
]
=
exp2BDerived_ij
;
interpolY1
=
pow2B
[
interpolIDX
];
interpolY2
=
pow2B
[
interpolIDX
+
1
];
pow2B_ij
=
interpolY1
+
(
interpolY2
-
interpolY1
)
*
(
interpolTMP
-
interpolIDX
);
prePow2B_ij
[
neighbor_j
]
=
pow2B_ij
;
// zeta and its derivative
if
(
r_ij
<
cutoffC
)
zeta_i
+=
1.0
;
else
{
interpolY1
=
cutoffFunction
[
interpolIDX
];
interpolY2
=
cutoffFunction
[
interpolIDX
+
1
];
cutoffFunction_ij
=
interpolY1
+
(
interpolY2
-
interpolY1
)
*
(
interpolTMP
-
interpolIDX
);
zeta_i
+=
cutoffFunction_ij
;
interpolY1
=
cutoffFunctionDerived
[
interpolIDX
];
interpolY2
=
cutoffFunctionDerived
[
interpolIDX
+
1
];
zeta_iDerived
=
interpolY1
+
(
interpolY2
-
interpolY1
)
*
(
interpolTMP
-
interpolIDX
);
zeta_iDerivedInvR_ij
=
zeta_iDerived
*
invR_ij
;
preForceCoord_counter
=
numForceCoordPairs
*
5
;
preForceCoord
[
preForceCoord_counter
+
0
]
=
zeta_iDerivedInvR_ij
;
preForceCoord
[
preForceCoord_counter
+
1
]
=
dr_ij
[
0
];
preForceCoord
[
preForceCoord_counter
+
2
]
=
dr_ij
[
1
];
preForceCoord
[
preForceCoord_counter
+
3
]
=
dr_ij
[
2
];
preForceCoord
[
preForceCoord_counter
+
4
]
=
j
;
numForceCoordPairs
++
;
}
}
// quantities depending on zeta_i
interpolDeltaX
=
zeta_i
;
interpolTMP
=
(
interpolDeltaX
*
GRIDDENSITY
);
interpolIDX
=
(
int
)
interpolTMP
;
interpolY1
=
expMinusBetaZeta_iZeta_iGrid
[
interpolIDX
];
interpolY2
=
expMinusBetaZeta_iZeta_iGrid
[
interpolIDX
+
1
];
expMinusBetaZeta_iZeta_i
=
interpolY1
+
(
interpolY2
-
interpolY1
)
*
(
interpolTMP
-
interpolIDX
);
interpolY1
=
qFunctionGrid
[
interpolIDX
];
interpolY2
=
qFunctionGrid
[
interpolIDX
+
1
];
qFunction
=
interpolY1
+
(
interpolY2
-
interpolY1
)
*
(
interpolTMP
-
interpolIDX
);
interpolY1
=
tauFunctionGrid
[
interpolIDX
];
interpolY2
=
tauFunctionGrid
[
interpolIDX
+
1
];
tauFunction
=
interpolY1
+
(
interpolY2
-
interpolY1
)
*
(
interpolTMP
-
interpolIDX
);
interpolY1
=
tauFunctionDerivedGrid
[
interpolIDX
];
interpolY2
=
tauFunctionDerivedGrid
[
interpolIDX
+
1
];
tauFunctionDerived
=
interpolY1
+
(
interpolY2
-
interpolY1
)
*
(
interpolTMP
-
interpolIDX
);
qFunctionDerived
=
-
mu
*
qFunction
;
forceModCoord_factor
=
2.0
*
beta
*
zeta_i
*
expMinusBetaZeta_iZeta_i
;
forceModCoord
=
0.0
;
// two-body interactions, skip half of them
for
(
int
neighbor_j
=
0
;
neighbor_j
<
jnum
;
neighbor_j
++
)
{
double
dr_ij
[
3
],
r_ij
,
f_ij
[
3
];
j
=
jlist
[
neighbor_j
];
j
&=
NEIGHMASK
;
dr_ij
[
0
]
=
x
[
j
][
0
]
-
xtmp
;
dr_ij
[
1
]
=
x
[
j
][
1
]
-
ytmp
;
dr_ij
[
2
]
=
x
[
j
][
2
]
-
ztmp
;
r_ij
=
dr_ij
[
0
]
*
dr_ij
[
0
]
+
dr_ij
[
1
]
*
dr_ij
[
1
]
+
dr_ij
[
2
]
*
dr_ij
[
2
];
jtype
=
map
[
type
[
j
]];
ijparam
=
elem2param
[
itype
][
jtype
][
jtype
];
if
(
r_ij
>
params
[
ijparam
].
cutsq
)
continue
;
r_ij
=
sqrt
(
r_ij
);
invR_ij
=
preInvR_ij
[
neighbor_j
];
pow2B_ij
=
prePow2B_ij
[
neighbor_j
];
potential2B_factor
=
pow2B_ij
-
expMinusBetaZeta_iZeta_i
;
exp2B_ij
=
preExp2B_ij
[
neighbor_j
];
pow2BDerived_ij
=
-
rho
*
invR_ij
*
pow2B_ij
;
forceModCoord
+=
(
forceModCoord_factor
*
exp2B_ij
);
exp2BDerived_ij
=
preExp2BDerived_ij
[
neighbor_j
];
forceMod2B
=
exp2BDerived_ij
*
potential2B_factor
+
exp2B_ij
*
pow2BDerived_ij
;
directorCos_ij_x
=
invR_ij
*
dr_ij
[
0
];
directorCos_ij_y
=
invR_ij
*
dr_ij
[
1
];
directorCos_ij_z
=
invR_ij
*
dr_ij
[
2
];
exp3B_ij
=
preExp3B_ij
[
neighbor_j
];
exp3BDerived_ij
=
preExp3BDerived_ij
[
neighbor_j
];
f_ij
[
0
]
=
forceMod2B
*
directorCos_ij_x
;
f_ij
[
1
]
=
forceMod2B
*
directorCos_ij_y
;
f_ij
[
2
]
=
forceMod2B
*
directorCos_ij_z
;
f
[
j
][
0
]
-=
f_ij
[
0
];
f
[
j
][
1
]
-=
f_ij
[
1
];
f
[
j
][
2
]
-=
f_ij
[
2
];
f
[
i
][
0
]
+=
f_ij
[
0
];
f
[
i
][
1
]
+=
f_ij
[
1
];
f
[
i
][
2
]
+=
f_ij
[
2
];
// potential energy
evdwl
=
(
exp2B_ij
*
potential2B_factor
);
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
0.0
,
-
forceMod2B
*
invR_ij
,
dr_ij
[
0
],
dr_ij
[
1
],
dr_ij
[
2
]);
// three-body Forces
for
(
int
neighbor_k
=
neighbor_j
+
1
;
neighbor_k
<
jnum
;
neighbor_k
++
)
{
double
dr_ik
[
3
],
r_ik
,
f_ik
[
3
];
k
=
jlist
[
neighbor_k
];
k
&=
NEIGHMASK
;
ktype
=
map
[
type
[
k
]];
ikparam
=
elem2param
[
itype
][
ktype
][
ktype
];
ijkparam
=
elem2param
[
itype
][
jtype
][
ktype
];
dr_ik
[
0
]
=
x
[
k
][
0
]
-
xtmp
;
dr_ik
[
1
]
=
x
[
k
][
1
]
-
ytmp
;
dr_ik
[
2
]
=
x
[
k
][
2
]
-
ztmp
;
r_ik
=
dr_ik
[
0
]
*
dr_ik
[
0
]
+
dr_ik
[
1
]
*
dr_ik
[
1
]
+
dr_ik
[
2
]
*
dr_ik
[
2
];
if
(
r_ik
>
params
[
ikparam
].
cutsq
)
continue
;
r_ik
=
sqrt
(
r_ik
);
invR_ik
=
preInvR_ij
[
neighbor_k
];
directorCos_ik_x
=
invR_ik
*
dr_ik
[
0
];
directorCos_ik_y
=
invR_ik
*
dr_ik
[
1
];
directorCos_ik_z
=
invR_ik
*
dr_ik
[
2
];
cosTeta
=
directorCos_ij_x
*
directorCos_ik_x
+
directorCos_ij_y
*
directorCos_ik_y
+
directorCos_ij_z
*
directorCos_ik_z
;
cosTetaDiff
=
cosTeta
+
tauFunction
;
cosTetaDiffCosTetaDiff
=
cosTetaDiff
*
cosTetaDiff
;
qFunctionCosTetaDiffCosTetaDiff
=
cosTetaDiffCosTetaDiff
*
qFunction
;
expMinusQFunctionCosTetaDiffCosTetaDiff
=
exp
(
-
qFunctionCosTetaDiffCosTetaDiff
);
potentia3B_factor
=
lambda
*
((
1.0
-
expMinusQFunctionCosTetaDiffCosTetaDiff
)
+
eta
*
qFunctionCosTetaDiffCosTetaDiff
);
exp3B_ik
=
preExp3B_ij
[
neighbor_k
];
exp3BDerived_ik
=
preExp3BDerived_ij
[
neighbor_k
];
forceMod3B_factor1_ij
=
-
exp3BDerived_ij
*
exp3B_ik
*
potentia3B_factor
;
forceMod3B_factor2
=
2.0
*
lambda
*
exp3B_ij
*
exp3B_ik
*
qFunction
*
cosTetaDiff
*
(
eta
+
expMinusQFunctionCosTetaDiffCosTetaDiff
);
forceMod3B_factor2_ij
=
forceMod3B_factor2
*
invR_ij
;
f_ij
[
0
]
=
forceMod3B_factor1_ij
*
directorCos_ij_x
+
forceMod3B_factor2_ij
*
(
cosTeta
*
directorCos_ij_x
-
directorCos_ik_x
);
f_ij
[
1
]
=
forceMod3B_factor1_ij
*
directorCos_ij_y
+
forceMod3B_factor2_ij
*
(
cosTeta
*
directorCos_ij_y
-
directorCos_ik_y
);
f_ij
[
2
]
=
forceMod3B_factor1_ij
*
directorCos_ij_z
+
forceMod3B_factor2_ij
*
(
cosTeta
*
directorCos_ij_z
-
directorCos_ik_z
);
forceMod3B_factor1_ik
=
-
exp3BDerived_ik
*
exp3B_ij
*
potentia3B_factor
;
forceMod3B_factor2_ik
=
forceMod3B_factor2
*
invR_ik
;
f_ik
[
0
]
=
forceMod3B_factor1_ik
*
directorCos_ik_x
+
forceMod3B_factor2_ik
*
(
cosTeta
*
directorCos_ik_x
-
directorCos_ij_x
);
f_ik
[
1
]
=
forceMod3B_factor1_ik
*
directorCos_ik_y
+
forceMod3B_factor2_ik
*
(
cosTeta
*
directorCos_ik_y
-
directorCos_ij_y
);
f_ik
[
2
]
=
forceMod3B_factor1_ik
*
directorCos_ik_z
+
forceMod3B_factor2_ik
*
(
cosTeta
*
directorCos_ik_z
-
directorCos_ij_z
);
forceModCoord
+=
(
forceMod3B_factor2
*
(
tauFunctionDerived
-
0.5
*
mu
*
cosTetaDiff
));
f
[
j
][
0
]
+=
f_ij
[
0
];
f
[
j
][
1
]
+=
f_ij
[
1
];
f
[
j
][
2
]
+=
f_ij
[
2
];
f
[
k
][
0
]
+=
f_ik
[
0
];
f
[
k
][
1
]
+=
f_ik
[
1
];
f
[
k
][
2
]
+=
f_ik
[
2
];
f
[
i
][
0
]
-=
f_ij
[
0
]
+
f_ik
[
0
];
f
[
i
][
1
]
-=
f_ij
[
1
]
+
f_ik
[
1
];
f
[
i
][
2
]
-=
f_ij
[
2
]
+
f_ik
[
2
];
// potential energy
evdwl
=
(
exp3B_ij
*
exp3B_ik
*
potentia3B_factor
);
if
(
evflag
)
ev_tally3
(
i
,
j
,
k
,
evdwl
,
0.0
,
f_ij
,
f_ik
,
dr_ij
,
dr_ik
);
}
}
// forces due to environment coordination f(Z)
for
(
int
idx
=
0
;
idx
<
numForceCoordPairs
;
idx
++
)
{
double
dr_ij
[
3
],
f_ij
[
3
];
preForceCoord_counter
=
idx
*
5
;
zeta_iDerivedInvR_ij
=
preForceCoord
[
preForceCoord_counter
+
0
];
dr_ij
[
0
]
=
preForceCoord
[
preForceCoord_counter
+
1
];
dr_ij
[
1
]
=
preForceCoord
[
preForceCoord_counter
+
2
];
dr_ij
[
2
]
=
preForceCoord
[
preForceCoord_counter
+
3
];
j
=
static_cast
<
int
>
(
preForceCoord
[
preForceCoord_counter
+
4
]);
forceModCoord_ij
=
forceModCoord
*
zeta_iDerivedInvR_ij
;
f_ij
[
0
]
=
forceModCoord_ij
*
dr_ij
[
0
];
f_ij
[
1
]
=
forceModCoord_ij
*
dr_ij
[
1
];
f_ij
[
2
]
=
forceModCoord_ij
*
dr_ij
[
2
];
f
[
j
][
0
]
-=
f_ij
[
0
];
f
[
j
][
1
]
-=
f_ij
[
1
];
f
[
j
][
2
]
-=
f_ij
[
2
];
f
[
i
][
0
]
+=
f_ij
[
0
];
f
[
i
][
1
]
+=
f_ij
[
1
];
f
[
i
][
2
]
+=
f_ij
[
2
];
// potential energy
evdwl
=
0.0
;
if
(
evflag
)
ev_tally
(
i
,
j
,
nlocal
,
newton_pair
,
evdwl
,
0.0
,
forceModCoord_ij
,
dr_ij
[
0
],
dr_ij
[
1
],
dr_ij
[
2
]);
}
}
if
(
vflag_fdotr
)
virial_fdotr_compute
();
}
/* ---------------------------------------------------------------------- */
void
PairEDIP
::
allocateGrids
(
void
)
{
int
numGridPointsOneCutoffFunction
;
int
numGridPointsNotOneCutoffFunction
;
int
numGridPointsCutoffFunction
;
int
numGridPointsR
;
int
numGridPointsRTotal
;
int
numGridPointsQFunctionGrid
;
int
numGridPointsExpMinusBetaZeta_iZeta_i
;
int
numGridPointsTauFunctionGrid
;
double
maxArgumentTauFunctionGrid
;
double
maxArgumentQFunctionGrid
;
double
maxArgumentExpMinusBetaZeta_iZeta_i
;
double
const
leftLimitToZero
=
-
DBL_MIN
*
1000.0
;
// tauFunctionGrid
maxArgumentTauFunctionGrid
=
leadDimInteractionList
;
numGridPointsTauFunctionGrid
=
(
int
)
((
maxArgumentTauFunctionGrid
)
*
GRIDDENSITY
)
+
2
;
memory
->
create
(
tauFunctionGrid
,
numGridPointsTauFunctionGrid
,
"edip:tauFunctionGrid"
);
memory
->
create
(
tauFunctionDerivedGrid
,
numGridPointsTauFunctionGrid
,
"edip:tauFunctionDerivedGrid"
);
// expMinusBetaZeta_iZeta_iGrid
maxArgumentExpMinusBetaZeta_iZeta_i
=
leadDimInteractionList
;
numGridPointsExpMinusBetaZeta_iZeta_i
=
(
int
)
((
maxArgumentExpMinusBetaZeta_iZeta_i
)
*
GRIDDENSITY
)
+
2
;
memory
->
create
(
expMinusBetaZeta_iZeta_iGrid
,
numGridPointsExpMinusBetaZeta_iZeta_i
,
"edip:expMinusBetaZeta_iZeta_iGrid"
);
// qFunctionGrid
maxArgumentQFunctionGrid
=
leadDimInteractionList
;
numGridPointsQFunctionGrid
=
(
int
)
((
maxArgumentQFunctionGrid
)
*
GRIDDENSITY
)
+
2
;
memory
->
create
(
qFunctionGrid
,
numGridPointsQFunctionGrid
,
"edip:qFunctionGrid"
);
// cutoffFunction
numGridPointsOneCutoffFunction
=
(
int
)
((
cutoffC
-
GRIDSTART
)
*
GRIDDENSITY
);
numGridPointsNotOneCutoffFunction
=
(
int
)
((
cutoffA
-
cutoffC
)
*
GRIDDENSITY
);
numGridPointsCutoffFunction
=
numGridPointsOneCutoffFunction
+
numGridPointsNotOneCutoffFunction
+
2
;
memory
->
create
(
cutoffFunction
,
numGridPointsCutoffFunction
,
"edip:cutoffFunction"
);
memory
->
create
(
cutoffFunctionDerived
,
numGridPointsCutoffFunction
,
"edip:cutoffFunctionDerived"
);
// pow2B
numGridPointsR
=
(
int
)
((
cutoffA
+
leftLimitToZero
-
GRIDSTART
)
*
GRIDDENSITY
);
numGridPointsRTotal
=
numGridPointsR
+
2
;
memory
->
create
(
pow2B
,
numGridPointsRTotal
,
"edip:pow2B"
);
memory
->
create
(
exp2B
,
numGridPointsRTotal
,
"edip:exp2B"
);
memory
->
create
(
exp3B
,
numGridPointsRTotal
,
"edip:exp3B"
);
}
/* ----------------------------------------------------------------------
pre-calculated structures
------------------------------------------------------------------------- */
void
PairEDIP
::
allocatePreLoops
(
void
)
{
int
nthreads
=
comm
->
nthreads
;
memory
->
create
(
preInvR_ij
,
nthreads
*
leadDimInteractionList
,
"edip:preInvR_ij"
);
memory
->
create
(
preExp3B_ij
,
nthreads
*
leadDimInteractionList
,
"edip:preExp3B_ij"
);
memory
->
create
(
preExp3BDerived_ij
,
nthreads
*
leadDimInteractionList
,
"edip:preExp3BDerived_ij"
);
memory
->
create
(
preExp2B_ij
,
nthreads
*
leadDimInteractionList
,
"edip:preExp2B_ij"
);
memory
->
create
(
preExp2BDerived_ij
,
nthreads
*
leadDimInteractionList
,
"edip:preExp2BDerived_ij"
);
memory
->
create
(
prePow2B_ij
,
nthreads
*
leadDimInteractionList
,
"edip:prePow2B_ij"
);
memory
->
create
(
preForceCoord
,
5
*
nthreads
*
leadDimInteractionList
,
"edip:preForceCoord"
);
}
/* ----------------------------------------------------------------------
deallocate grids
------------------------------------------------------------------------- */
void
PairEDIP
::
deallocateGrids
(
void
)
{
memory
->
destroy
(
cutoffFunction
);
memory
->
destroy
(
cutoffFunctionDerived
);
memory
->
destroy
(
pow2B
);
memory
->
destroy
(
exp2B
);
memory
->
destroy
(
exp3B
);
memory
->
destroy
(
qFunctionGrid
);
memory
->
destroy
(
expMinusBetaZeta_iZeta_iGrid
);
memory
->
destroy
(
tauFunctionGrid
);
memory
->
destroy
(
tauFunctionDerivedGrid
);
}
/* ----------------------------------------------------------------------
deallocate preLoops
------------------------------------------------------------------------- */
void
PairEDIP
::
deallocatePreLoops
(
void
)
{
memory
->
destroy
(
preInvR_ij
);
memory
->
destroy
(
preExp3B_ij
);
memory
->
destroy
(
preExp3BDerived_ij
);
memory
->
destroy
(
preExp2B_ij
);
memory
->
destroy
(
preExp2BDerived_ij
);
memory
->
destroy
(
prePow2B_ij
);
memory
->
destroy
(
preForceCoord
);
}
/* ---------------------------------------------------------------------- */
void
PairEDIP
::
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
PairEDIP
::
settings
(
int
narg
,
char
**
arg
)
{
if
(
narg
!=
0
)
error
->
all
(
FLERR
,
"Illegal pair_style command"
);
}
/* ---------------------------------------------------------------------- */
void
PairEDIP
::
initGrids
(
void
)
{
int
l
;
int
numGridPointsOneCutoffFunction
;
int
numGridPointsNotOneCutoffFunction
;
int
numGridPointsCutoffFunction
;
int
numGridPointsR
;
int
numGridPointsRTotal
;
int
numGridPointsQFunctionGrid
;
int
numGridPointsExpMinusBetaZeta_iZeta_i
;
int
numGridPointsTauFunctionGrid
;
double
maxArgumentTauFunctionGrid
;
double
maxArgumentQFunctionGrid
;
double
maxArgumentExpMinusBetaZeta_iZeta_i
;
double
r
;
double
temp
;
double
temp3
;
double
temp4
;
double
deltaArgumentR
;
double
deltaArgumentCutoffFunction
;
double
deltaArgumentQFunctionGrid
;
double
deltaArgumentTauFunctionGrid
;
double
deltaArgumentExpMinusBetaZeta_iZeta_i
;
double
const
leftLimitToZero
=
-
DBL_MIN
*
1000.0
;
// tauFunctionGrid
maxArgumentTauFunctionGrid
=
leadDimInteractionList
;
numGridPointsTauFunctionGrid
=
(
int
)
((
maxArgumentTauFunctionGrid
)
*
GRIDDENSITY
)
+
2
;
r
=
0.0
;
deltaArgumentTauFunctionGrid
=
1.0
/
GRIDDENSITY
;
for
(
l
=
0
;
l
<
numGridPointsTauFunctionGrid
;
l
++
)
{
tauFunctionGrid
[
l
]
=
u1
+
u2
*
u3
*
exp
(
-
u4
*
r
)
-
u2
*
exp
(
-
2.0
*
u4
*
r
);
tauFunctionDerivedGrid
[
l
]
=
-
u2
*
u3
*
u4
*
exp
(
-
u4
*
r
)
+
2.0
*
u2
*
u4
*
exp
(
-
2.0
*
u4
*
r
);
r
+=
deltaArgumentTauFunctionGrid
;
}
// expMinusBetaZeta_iZeta_iGrid
maxArgumentExpMinusBetaZeta_iZeta_i
=
leadDimInteractionList
;
numGridPointsExpMinusBetaZeta_iZeta_i
=
(
int
)
((
maxArgumentExpMinusBetaZeta_iZeta_i
)
*
GRIDDENSITY
)
+
2
;
r
=
0.0
;
deltaArgumentExpMinusBetaZeta_iZeta_i
=
1.0
/
GRIDDENSITY
;
for
(
l
=
0
;
l
<
numGridPointsExpMinusBetaZeta_iZeta_i
;
l
++
)
{
expMinusBetaZeta_iZeta_iGrid
[
l
]
=
exp
(
-
beta
*
r
*
r
);
r
+=
deltaArgumentExpMinusBetaZeta_iZeta_i
;
}
// qFunctionGrid
maxArgumentQFunctionGrid
=
leadDimInteractionList
;
numGridPointsQFunctionGrid
=
(
int
)
((
maxArgumentQFunctionGrid
)
*
GRIDDENSITY
)
+
2
;
r
=
0.0
;
deltaArgumentQFunctionGrid
=
1.0
/
GRIDDENSITY
;
for
(
l
=
0
;
l
<
numGridPointsQFunctionGrid
;
l
++
)
{
qFunctionGrid
[
l
]
=
Q0
*
exp
(
-
mu
*
r
);
r
+=
deltaArgumentQFunctionGrid
;
}
// cutoffFunction
numGridPointsOneCutoffFunction
=
(
int
)
((
cutoffC
-
GRIDSTART
)
*
GRIDDENSITY
);
numGridPointsNotOneCutoffFunction
=
(
int
)
((
cutoffA
-
cutoffC
)
*
GRIDDENSITY
);
numGridPointsCutoffFunction
=
numGridPointsOneCutoffFunction
+
numGridPointsNotOneCutoffFunction
+
2
;
r
=
GRIDSTART
;
deltaArgumentCutoffFunction
=
1.0
/
GRIDDENSITY
;
for
(
l
=
0
;
l
<
numGridPointsOneCutoffFunction
;
l
++
)
{
cutoffFunction
[
l
]
=
1.0
;
cutoffFunctionDerived
[
l
]
=
0.0
;
r
+=
deltaArgumentCutoffFunction
;
}
for
(
l
=
numGridPointsOneCutoffFunction
;
l
<
numGridPointsCutoffFunction
;
l
++
)
{
temp
=
(
cutoffA
-
cutoffC
)
/
(
r
-
cutoffC
);
temp3
=
temp
*
temp
*
temp
;
temp4
=
temp3
*
temp
;
cutoffFunction
[
l
]
=
exp
(
alpha
/
(
1.0
-
temp3
));
cutoffFunctionDerived
[
l
]
=
(
-
3
*
alpha
/
(
cutoffA
-
cutoffC
))
*
(
temp4
/
((
1
-
temp3
)
*
(
1
-
temp3
)))
*
exp
(
alpha
/
(
1.0
-
temp3
));
r
+=
deltaArgumentCutoffFunction
;
}
// pow2B
numGridPointsR
=
(
int
)
((
cutoffA
+
leftLimitToZero
-
GRIDSTART
)
*
GRIDDENSITY
);
numGridPointsRTotal
=
numGridPointsR
+
2
;
r
=
GRIDSTART
;
deltaArgumentR
=
1.0
/
GRIDDENSITY
;
for
(
l
=
0
;
l
<
numGridPointsR
;
l
++
)
{
pow2B
[
l
]
=
pow
((
B
/
r
),
rho
);
exp2B
[
l
]
=
A
*
exp
(
sigma
/
(
r
-
cutoffA
));
exp3B
[
l
]
=
exp
(
gamm
/
(
r
-
cutoffA
));
r
+=
deltaArgumentR
;
}
pow2B
[
numGridPointsR
]
=
pow
((
B
/
r
),
rho
);
exp2B
[
numGridPointsR
]
=
0
;
exp3B
[
numGridPointsR
]
=
0
;
r
+=
deltaArgumentR
;
pow2B
[
numGridPointsR
+
1
]
=
pow
((
B
/
r
),
rho
);
exp2B
[
numGridPointsR
+
1
]
=
0
;
exp3B
[
numGridPointsR
+
1
]
=
0
;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void
PairEDIP
::
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
();
// 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"
);
// allocate tables and internal structures
allocatePreLoops
();
allocateGrids
();
initGrids
();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void
PairEDIP
::
init_style
()
{
if
(
atom
->
tag_enable
==
0
)
error
->
all
(
FLERR
,
"Pair style EDIP requires atom IDs"
);
if
(
force
->
newton_pair
==
0
)
error
->
all
(
FLERR
,
"Pair style EDIP 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
PairEDIP
::
init_one
(
int
i
,
int
j
)
{
if
(
setflag
[
i
][
j
]
==
0
)
error
->
all
(
FLERR
,
"All pair coeffs are not set"
);
return
cutmax
;
}
/* ---------------------------------------------------------------------- */
void
PairEDIP
::
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
=
fopen
(
file
,
"r"
);
if
(
fp
==
NULL
)
{
char
str
[
128
];
sprintf
(
str
,
"Cannot open EDIP 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 EDIP 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
].
A
=
atof
(
words
[
3
]);
params
[
nparams
].
B
=
atof
(
words
[
4
]);
params
[
nparams
].
cutoffA
=
atof
(
words
[
5
]);
params
[
nparams
].
cutoffC
=
atof
(
words
[
6
]);
params
[
nparams
].
alpha
=
atof
(
words
[
7
]);
params
[
nparams
].
beta
=
atof
(
words
[
8
]);
params
[
nparams
].
eta
=
atof
(
words
[
9
]);
params
[
nparams
].
gamm
=
atof
(
words
[
10
]);
params
[
nparams
].
lambda
=
atof
(
words
[
11
]);
params
[
nparams
].
mu
=
atof
(
words
[
12
]);
params
[
nparams
].
rho
=
atof
(
words
[
13
]);
params
[
nparams
].
sigma
=
atof
(
words
[
14
]);
params
[
nparams
].
Q0
=
atof
(
words
[
15
]);
params
[
nparams
].
u1
=
atof
(
words
[
16
]);
params
[
nparams
].
u2
=
atof
(
words
[
17
]);
params
[
nparams
].
u3
=
atof
(
words
[
18
]);
params
[
nparams
].
u4
=
atof
(
words
[
19
]);
if
(
params
[
nparams
].
A
<
0.0
||
params
[
nparams
].
B
<
0.0
||
params
[
nparams
].
cutoffA
<
0.0
||
params
[
nparams
].
cutoffC
<
0.0
||
params
[
nparams
].
alpha
<
0.0
||
params
[
nparams
].
beta
<
0.0
||
params
[
nparams
].
eta
<
0.0
||
params
[
nparams
].
gamm
<
0.0
||
params
[
nparams
].
lambda
<
0.0
||
params
[
nparams
].
mu
<
0.0
||
params
[
nparams
].
rho
<
0.0
||
params
[
nparams
].
sigma
<
0.0
)
error
->
all
(
FLERR
,
"Illegal EDIP parameter"
);
nparams
++
;
}
delete
[]
words
;
}
/* ---------------------------------------------------------------------- */
void
PairEDIP
::
setup
()
{
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
;
}
// set cutoff square
for
(
m
=
0
;
m
<
nparams
;
m
++
)
{
params
[
m
].
cutsq
=
params
[
m
].
cutoffA
*
params
[
m
].
cutoffA
;
}
// 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
;
}
// this should be removed for multi species parametrizations
A
=
params
[
0
].
A
;
B
=
params
[
0
].
B
;
rho
=
params
[
0
].
rho
;
cutoffA
=
params
[
0
].
cutoffA
;
cutoffC
=
params
[
0
].
cutoffC
;
sigma
=
params
[
0
].
sigma
;
lambda
=
params
[
0
].
lambda
;
gamm
=
params
[
0
].
gamm
;
eta
=
params
[
0
].
eta
;
Q0
=
params
[
0
].
Q0
;
mu
=
params
[
0
].
mu
;
beta
=
params
[
0
].
beta
;
alpha
=
params
[
0
].
alpha
;
u1
=
params
[
0
].
u1
;
u2
=
params
[
0
].
u2
;
u3
=
params
[
0
].
u3
;
u4
=
params
[
0
].
u4
;
}
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