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rLAMMPS lammps
pair_bop.h
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/* -*- c++ -*- ----------------------------------------------------------
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.
The this work follows the formulation from (a) D.G. Pettifor, et al., Mat.
Sci. and Eng. A365, 2-13, (2004) and (b) D.A. Murdick, et al., Phys.
Rev. B 73, 045206 (2006). (c) D.K. Ward, et al., Phys. Rev. B 85, 115206
(2012)
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle
(
bop
,
PairBOP
)
#else
#ifndef LMP_PAIR_BOP_H
#define LMP_PAIR_BOP_H
#include "pair.h"
#include <time.h>
#include "update.h"
namespace
LAMMPS_NS
{
class
PairBOP
:
public
Pair
{
public:
PairBOP
(
class
LAMMPS
*
);
virtual
~
PairBOP
();
void
compute
(
int
,
int
);
void
settings
(
int
,
char
**
);
void
coeff
(
int
,
char
**
);
void
init_style
();
double
init_one
(
int
,
int
);
double
memory_usage
();
private:
int
me
;
int
maxneigh
;
// maximum size of neighbor list on this processor
int
maxneigh3
;
// maximum size of neighbor list on this processor
int
update_list
;
// check for changing maximum size of neighbor list
int
maxbopn
;
// maximum size of bop neighbor list for allocation
int
maxnall
;
// maximum size of bop neighbor list for allocation
int
*
map
;
// mapping from atom types to elements
int
nelements
;
// # of unique elments
int
nr
;
// increments for the BOP pair potential
int
ntheta
;
// increments for the angle function
int
npower
;
// power of the angular function
int
nBOt
;
// second BO increments
int
bop_types
;
// number of elments in potential
int
npairs
;
// number of element pairs
char
**
elements
;
// names of unique elements
int
***
elem2param
;
int
nparams
;
int
bop_step
;
int
allocate_pi
;
int
allocate_sigma
;
int
allocate_neigh
;
int
nb_pi
,
nb_sg
;
int
ago1
;
// int cnt1;
int
*
BOP_index
;
// index for neighbor list position
int
*
BOP_total
;
// index for neighbor list position
int
*
BOP_index3
;
// index for neighbor list position
int
*
BOP_total3
;
// index for neighbor list position
int
*
neigh_index
;
// index for neighbor list position
int
*
neigh_index3
;
// index for neighbor list position
int
neigh_total
;
// total number of neighbors stored
int
neigh_total3
;
// total number of neighbors stored
int
*
cos_index
;
// index for neighbor cosine if not using on the fly
int
*
neigh_flag
;
// index for neighbor cosine if not using on the fly
int
*
neigh_flag3
;
// index for neighbor cosine if not using on the fly
int
cos_total
;
// number of cosines stored if not using on the fly
int
neigh_ct
;
// limit for large arrays
/*Parameters variables*/
int
ncutoff
,
nfunc
;
int
a_flag
;
double
*
pi_a
,
*
pro_delta
,
*
pi_delta
;
double
*
pi_p
,
*
pi_c
,
*
sigma_r0
,
*
pi_r0
,
*
phi_r0
;
double
*
sigma_rc
,
*
pi_rc
,
*
phi_rc
,
*
r1
,
*
sigma_beta0
;
double
*
pi_beta0
,
*
phi0
,
*
sigma_n
,
*
pi_n
,
*
phi_m
;
double
*
sigma_nc
,
*
pi_nc
,
*
phi_nc
;
double
*
pro
,
*
sigma_delta
,
*
sigma_c
,
*
sigma_a
;
double
*
sigma_f
,
*
sigma_k
,
*
small3
;
double
small1
,
small2
,
small3g
,
small4
,
small5
,
small6
,
small7
;
double
which
,
alpha
,
alpha1
,
beta1
,
gamma1
,
alpha2
,
beta2
,
alpha3
;
double
beta3
,
rsmall
,
rbig
,
rcore
;
char
**
words
;
double
cutmax
;
//max cutoff for all elements
int
otfly
;
//Defines whether to do on the fly
//calculations of angles and distances
//on the fly will slow down calculations
//but requires less memory on = 1, off=0
/* Neigh variables */
double
*
rcut
,
*
rcut3
,
*
dr
,
*
rdr
,
*
dr3
,
*
rdr3
;
double
*
rcutsq
,
*
rcutsq3
;
double
**
disij
,
*
rij
;
double
rcutall
,
rctroot
;
/*Triple variables */
double
*
cosAng
,
***
dcosAng
,
***
dcAng
;
/*Double variables */
double
*
betaS
,
*
dBetaS
,
*
betaP
;
double
*
dBetaP
,
*
repul
,
*
dRepul
;
/*Sigma variables */
int
*
itypeSigBk
,
nSigBk
;
double
sigB
,
sigB_0
;
double
sigB1
;
/*Pi variables */
int
*
itypePiBk
,
nPiBk
;
double
piB
,
piB_0
;
/*Grids1 variables */
double
**
pBetaS
,
**
pBetaS1
,
**
pBetaS2
,
**
pBetaS3
;
double
**
pBetaS4
,
**
pBetaS5
,
**
pBetaS6
;
/*Grids2 variables */
double
**
pBetaP
,
**
pBetaP1
,
**
pBetaP2
,
**
pBetaP3
;
double
**
pBetaP4
,
**
pBetaP5
,
**
pBetaP6
;
/*Grids3 variables */
double
**
pRepul
,
**
pRepul1
,
**
pRepul2
,
**
pRepul3
;
double
**
pRepul4
,
**
pRepul5
,
**
pRepul6
;
double
**
pLong
,
**
pLong1
,
**
pLong2
,
**
pLong3
;
double
**
pLong4
,
**
pLong5
,
**
pLong6
;
double
****
gfunc
,
****
gpara
;
double
****
gfunc1
,
****
gfunc2
,
****
gfunc3
;
double
****
gfunc4
,
****
gfunc5
,
****
gfunc6
;
double
dtheta
,
rdtheta
;
/*Grids4 variables */
double
**
FsigBO
,
**
FsigBO1
,
**
FsigBO2
,
**
FsigBO3
;
double
**
FsigBO4
,
**
FsigBO5
,
**
FsigBO6
;
double
dBO
,
rdBO
;
/* End of BOP variables */
double
**
rcmin
,
**
rcmax
,
**
rcmaxp
;
struct
B_PI
{
double
dAA
[
3
];
double
dBB
[
3
];
double
dPiB
[
3
];
int
temp
;
int
i
;
int
j
;
};
B_PI
*
bt_pi
;
struct
B_SG
{
double
dAA
[
3
];
double
dBB
[
3
];
double
dCC
[
3
];
double
dDD
[
3
];
double
dEE
[
3
];
double
dEE1
[
3
];
double
dFF
[
3
];
double
dAAC
[
3
];
double
dBBC
[
3
];
double
dCCC
[
3
];
double
dDDC
[
3
];
double
dEEC
[
3
];
double
dFFC
[
3
];
double
dGGC
[
3
];
double
dUT
[
3
];
double
dSigB1
[
3
];
double
dSigB
[
3
];
int
temp
;
int
i
;
int
j
;
};
B_SG
*
bt_sg
;
void
setPbetaS
();
void
setPbetaP
();
void
setPrepul
();
void
setSign
();
void
gneigh
();
void
theta
();
void
theta_mod
();
double
sigmaBo
(
int
,
int
);
double
PiBo
(
int
,
int
);
void
memory_theta_create
();
void
memory_theta_destroy
();
void
memory_theta_grow
();
double
cutoff
(
double
,
double
,
int
,
double
);
/*
double betaSfunc(int, double);
double dBetaSfunc(int, double, double, double);
double betaPfunc(int, double);
double dBetaPfunc(int, double, double, double);
double repulfunc(int, double);
double dRepulfunc(int, double, double, double);
*/
void
read_table
(
char
*
);
void
allocate
();
void
create_pi
(
int
);
void
create_sigma
(
int
);
void
destroy_pi
();
void
destroy_sigma
();
void
grow_pi
(
int
,
int
);
void
grow_sigma
(
int
,
int
);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair style BOP requires atom IDs
This is a requirement to use the BOP potential.
E: Pair style BOP requires newton pair on
See the newton command. This is a restriction to use the BOP
potential.
E: Pair style bop requires comm ghost cutoff at least 3x larger than %g
Use the communicate ghost command to set this. See the pair bop
doc page for more details.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Too many atom pairs for pair bop
The number of atomic pairs exceeds the expected number. Check your
atomic structure to ensure that it is realistic.
E: Too many atom triplets for pair bop
The number of three atom groups for angle determinations exceeds the
expected number. Check your atomic structure to ensure that it is
realistic.
E: Cannot open BOP potential file %s
The specified BOP potential file cannot be opened. Check that the
path and name are correct.
E: Incorrect table format check for element types
Self-explanatory.
*/
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