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fix_latte.cpp
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Thu, Jun 6, 20:24
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rLAMMPS lammps
fix_latte.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.
------------------------------------------------------------------------- */
// NOTES on possible future issues:
// LATTE compute and return 6-value virial tensor
// can LATTE compute per-atom energy and per-atom virial
// for minimize, what about charge DOFs
// implement charge DOF integration
// pass neighbor list to LATTE: half or full
// will we ever auto-adjust the timestep in reset_dt()
// could pass an input file to LATTE, specified in LAMMPS input script
// what units options can LAMMPS be using
// should LATTE take triclinic box from LAMMPS
// does Coulomb potential = pe[i]/q[i], is it 0 when q = 0
// how will this work for serial/parallel LAMMPS with serial/parallel LATTE
// INPORTANT NOTE: ADD checks for metal units !!!!!!!!!!!!!
#include <stdio.h>
#include <string.h>
#include "fix_latte.h"
#include "atom.h"
#include "comm.h"
#include "update.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "modify.h"
#include "compute.h"
#include "memory.h"
#include "error.h"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
extern
"C"
{
void
latte
(
int
*
,
int
*
,
double
*
,
int
*
,
int
*
,
double
*
,
double
*
,
double
*
,
double
*
,
double
*
,
double
*
,
double
*
,
int
*
,
double
*
,
double
*
,
double
*
,
double
*
);
}
#define INVOKED_PERATOM 8
/* ---------------------------------------------------------------------- */
FixLatte
::
FixLatte
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
)
{
if
(
narg
!=
4
)
error
->
all
(
FLERR
,
"Illegal fix latte command"
);
if
(
comm
->
nprocs
!=
1
)
error
->
all
(
FLERR
,
"Fix latte currently runs only in serial"
);
scalar_flag
=
1
;
global_freq
=
1
;
extscalar
=
1
;
virial_flag
=
1
;
// store ID of compute pe/atom used to generate Coulomb potential for LATTE
// NULL means LATTE will compute Coulombic potential
coulomb
=
0
;
id_pe
=
NULL
;
if
(
strcmp
(
arg
[
3
],
"NULL"
)
!=
0
)
{
coulomb
=
1
;
int
n
=
strlen
(
arg
[
3
])
+
1
;
id_pe
=
new
char
[
n
];
strcpy
(
id_pe
,
arg
[
3
]);
int
ipe
=
modify
->
find_compute
(
id_pe
);
if
(
ipe
<
0
)
error
->
all
(
FLERR
,
"Could not find fix latte compute ID"
);
if
(
modify
->
compute
[
ipe
]
->
peatomflag
==
0
)
error
->
all
(
FLERR
,
"Fix latte compute ID does not compute pe/atom"
);
}
// initializations
nmax
=
0
;
qpotential
=
NULL
;
flatte
=
NULL
;
latte_energy
=
0.0
;
}
/* ---------------------------------------------------------------------- */
FixLatte
::~
FixLatte
()
{
delete
[]
id_pe
;
memory
->
destroy
(
qpotential
);
memory
->
destroy
(
flatte
);
}
/* ---------------------------------------------------------------------- */
int
FixLatte
::
setmask
()
{
int
mask
=
0
;
//mask |= INITIAL_INTEGRATE;
//mask |= FINAL_INTEGRATE;
mask
|=
PRE_REVERSE
;
mask
|=
POST_FORCE
;
mask
|=
MIN_POST_FORCE
;
mask
|=
THERMO_ENERGY
;
return
mask
;
}
/* ---------------------------------------------------------------------- */
void
FixLatte
::
init
()
{
// error checks
if
(
domain
->
dimension
==
2
)
error
->
all
(
FLERR
,
"Fix latte requires 3d problem"
);
if
(
coulomb
)
{
if
(
atom
->
q_flag
==
0
||
force
->
pair
==
NULL
||
force
->
kspace
==
NULL
)
error
->
all
(
FLERR
,
"Fix latte cannot compute Coulombic potential"
);
int
ipe
=
modify
->
find_compute
(
id_pe
);
if
(
ipe
<
0
)
error
->
all
(
FLERR
,
"Could not find fix latte compute ID"
);
c_pe
=
modify
->
compute
[
ipe
];
}
// must be fully periodic or fully non-periodic
if
(
domain
->
nonperiodic
==
0
)
pbcflag
=
1
;
else
if
(
!
domain
->
xperiodic
&&
!
domain
->
yperiodic
&&
!
domain
->
zperiodic
)
pbcflag
=
0
;
else
error
->
all
(
FLERR
,
"Fix latte requires 3d simulation"
);
// create qpotential & flatte if needed
// for now, assume nlocal will never change
if
(
coulomb
&&
qpotential
==
NULL
)
{
memory
->
create
(
qpotential
,
atom
->
nlocal
,
"latte:qpotential"
);
memory
->
create
(
flatte
,
atom
->
nlocal
,
3
,
"latte:flatte"
);
}
/*
// warn if any integrate fix comes after this one
// is it actually necessary for q(n) update to come after x,v update ??
int after = 0;
int flag = 0;
for (int i = 0; i < modify->nfix; i++) {
if (strcmp(id,modify->fix[i]->id) == 0) after = 1;
else if ((modify->fmask[i] & INITIAL_INTEGRATE) && after) flag = 1;
}
if (flag && comm->me == 0)
error->warning(FLERR,"Fix latte should come after all other "
"integration fixes");
*/
/*
// need a full neighbor list
// could we use a half list?
// perpetual list, built whenever re-neighboring occurs
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
*/
}
/* ---------------------------------------------------------------------- */
void
FixLatte
::
init_list
(
int
id
,
NeighList
*
ptr
)
{
// list = ptr;
}
/* ---------------------------------------------------------------------- */
void
FixLatte
::
setup
(
int
vflag
)
{
post_force
(
vflag
);
}
/* ---------------------------------------------------------------------- */
void
FixLatte
::
min_setup
(
int
vflag
)
{
post_force
(
vflag
);
}
/* ----------------------------------------------------------------------
integrate electronic degrees of freedom
------------------------------------------------------------------------- */
void
FixLatte
::
initial_integrate
(
int
vflag
)
{}
/* ----------------------------------------------------------------------
store eflag, so can use it in post_force to tally per-atom energies
------------------------------------------------------------------------- */
void
FixLatte
::
pre_reverse
(
int
eflag
,
int
vflag
)
{
eflag_caller
=
eflag
;
}
/* ---------------------------------------------------------------------- */
void
FixLatte
::
post_force
(
int
vflag
)
{
int
eflag
=
eflag_caller
;
if
(
eflag
||
vflag
)
ev_setup
(
eflag
,
vflag
);
// else evflag = 0;
else
evflag
=
eflag_global
=
vflag_global
=
eflag_atom
=
vflag_atom
=
0
;
// compute Coulombic potential = pe[i]/q[i]
// invoke compute pe/atom
// wrap with clear/add and trigger pe/atom calculation every step
if
(
coulomb
)
{
modify
->
clearstep_compute
();
if
(
!
(
c_pe
->
invoked_flag
&
INVOKED_PERATOM
))
{
c_pe
->
compute_peratom
();
c_pe
->
invoked_flag
|=
INVOKED_PERATOM
;
}
modify
->
addstep_compute
(
update
->
ntimestep
+
1
);
double
*
pe
=
c_pe
->
vector_atom
;
double
*
q
=
atom
->
q
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
q
[
i
])
qpotential
[
i
]
=
pe
[
i
]
/
q
[
i
];
else
qpotential
[
i
]
=
0.0
;
}
// hardwire these unsupported flags for now
int
coulombflag
=
0
;
// pe_peratom = 0;
// virial_global = 1; // set via vflag_global at some point
// virial_peratom = 0;
neighflag
=
0
;
// set flags used by LATTE
int
flags
[
6
];
flags
[
0
]
=
pbcflag
;
// 1 for fully periodic, 0 for fully non-periodic
flags
[
1
]
=
coulombflag
;
// 1 for LAMMPS computes Coulombics, 0 for LATTE
flags
[
2
]
=
eflag_atom
;
// 1 to return per-atom energies, 0 for no
flags
[
3
]
=
vflag_global
;
// 1 to return global virial 0 for no
flags
[
4
]
=
vflag_atom
;
// 1 to return per-atom virial, 0 for no
flags
[
5
]
=
neighflag
;
// 1 to pass neighbor list to LATTE, 0 for no
// setup LATTE arguments
int
natoms
=
atom
->
nlocal
;
double
*
coords
=
&
atom
->
x
[
0
][
0
];
int
*
type
=
atom
->
type
;
int
ntypes
=
atom
->
ntypes
;
double
*
mass
=
&
atom
->
mass
[
1
];
double
*
boxlo
=
domain
->
boxlo
;
double
*
boxhi
=
domain
->
boxhi
;
double
*
forces
;
if
(
coulomb
)
forces
=
&
flatte
[
0
][
0
];
else
forces
=
&
atom
->
f
[
0
][
0
];
int
maxiter
=
-
1
;
latte
(
flags
,
&
natoms
,
coords
,
type
,
&
ntypes
,
mass
,
boxlo
,
boxhi
,
&
domain
->
xy
,
&
domain
->
xz
,
&
domain
->
yz
,
forces
,
&
maxiter
,
&
latte_energy
,
&
atom
->
v
[
0
][
0
],
&
update
->
dt
,
virial
);
// sum LATTE forces to LAMMPS (Coulombic) forces
if
(
coulomb
)
{
double
**
f
=
atom
->
f
;
int
nlocal
=
atom
->
nlocal
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
f
[
i
][
0
]
+=
flatte
[
i
][
0
];
f
[
i
][
1
]
+=
flatte
[
i
][
1
];
f
[
i
][
2
]
+=
flatte
[
i
][
2
];
}
}
}
/* ---------------------------------------------------------------------- */
void
FixLatte
::
min_post_force
(
int
vflag
)
{
post_force
(
vflag
);
}
/* ----------------------------------------------------------------------
integrate electronic degrees of freedom
------------------------------------------------------------------------- */
void
FixLatte
::
final_integrate
()
{}
/* ---------------------------------------------------------------------- */
void
FixLatte
::
reset_dt
()
{
//dtv = update->dt;
//dtf = 0.5 * update->dt * force->ftm2v;
}
/* ----------------------------------------------------------------------
DFTB energy from LATTE
------------------------------------------------------------------------- */
double
FixLatte
::
compute_scalar
()
{
return
latte_energy
;
}
/* ----------------------------------------------------------------------
memory usage of local arrays
------------------------------------------------------------------------- */
double
FixLatte
::
memory_usage
()
{
double
bytes
=
0.0
;
if
(
coulomb
)
bytes
+=
nmax
*
sizeof
(
double
);
if
(
coulomb
)
bytes
+=
nmax
*
3
*
sizeof
(
double
);
return
bytes
;
}
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