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rLAMMPS lammps
fix_gld.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 authors: Stephen Bond (SNL) and
Andrew Baczewski (Michigan State/SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <string.h>
#include "fix_gld.h"
#include "math_extra.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
#include "group.h"
#define GLD_UNIFORM_DISTRO
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
/* ----------------------------------------------------------------------
Parses parameters passed to the method, allocates some memory
------------------------------------------------------------------------- */
FixGLD
::
FixGLD
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
Fix
(
lmp
,
narg
,
arg
),
step_respa
(
NULL
),
prony_c
(
NULL
),
prony_tau
(
NULL
),
s_gld
(
NULL
),
random
(
NULL
)
{
int
narg_min
=
8
;
// Check to make sure we have the minimal number of inputs
if
(
narg
<
narg_min
)
error
->
all
(
FLERR
,
"Illegal fix gld command"
);
time_integrate
=
1
;
restart_peratom
=
1
;
// Parse the first set of required input arguments
// 0 = Fix ID (e.g., 1)
// 1 = Group ID (e.g., all)
// 2 = gld (name of this fix)
// 3 = t_start (Starting target temperature)
t_start
=
force
->
numeric
(
FLERR
,
arg
[
3
]);
// 4 = t_stop (Stopping target temperature)
t_stop
=
force
->
numeric
(
FLERR
,
arg
[
4
]);
// 5 = prony_terms (number of terms in Prony series)
prony_terms
=
force
->
inumeric
(
FLERR
,
arg
[
5
]);
// 6 = seed (random seed)
int
seed
=
force
->
inumeric
(
FLERR
,
arg
[
6
]);
// 7 = series type
if
(
strcmp
(
arg
[
7
],
"pprony"
)
==
0
)
{
series_type
=
1
;
// series type 1 is 'positive Prony series'
}
else
{
error
->
all
(
FLERR
,
"Fix gld series type must be pprony for now"
);
}
// Error checking for the first set of required input arguments
if
(
seed
<=
0
)
error
->
all
(
FLERR
,
"Illegal fix gld command"
);
if
(
prony_terms
<=
0
)
error
->
all
(
FLERR
,
"Fix gld prony terms must be > 0"
);
if
(
t_start
<
0
)
error
->
all
(
FLERR
,
"Fix gld start temperature must be >= 0"
);
if
(
t_stop
<
0
)
error
->
all
(
FLERR
,
"Fix gld stop temperature must be >= 0"
);
if
(
narg
-
narg_min
<
2
*
(
prony_terms
)
)
error
->
all
(
FLERR
,
"Fix gld needs more prony series coefficients"
);
// allocate memory for Prony series force coefficients
memory
->
create
(
prony_c
,
prony_terms
,
"gld:prony_c"
);
// allocate memory for Prony series timescale coefficients
memory
->
create
(
prony_tau
,
prony_terms
,
"gld:prony_tau"
);
// allocate memory for Prony series extended variables
s_gld
=
NULL
;
grow_arrays
(
atom
->
nmax
);
// add callbacks to enable restarts
atom
->
add_callback
(
0
);
atom
->
add_callback
(
1
);
// read in the Prony series coefficients
int
iarg
=
narg_min
;
int
icoeff
=
0
;
while
(
iarg
<
narg
&&
icoeff
<
prony_terms
)
{
double
pc
=
force
->
numeric
(
FLERR
,
arg
[
iarg
]);
double
ptau
=
force
->
numeric
(
FLERR
,
arg
[
iarg
+
1
]);
if
(
pc
<
0
)
error
->
all
(
FLERR
,
"Fix gld c coefficients must be >= 0"
);
if
(
ptau
<=
0
)
error
->
all
(
FLERR
,
"Fix gld tau coefficients must be > 0"
);
// All atom types to have the same Prony series
prony_c
[
icoeff
]
=
pc
;
prony_tau
[
icoeff
]
=
ptau
;
icoeff
+=
1
;
iarg
+=
2
;
}
// initialize Marsaglia RNG with processor-unique seed
random
=
new
RanMars
(
lmp
,
seed
+
comm
->
me
);
// initialize the extended variables
init_s_gld
();
// optional arguments
freezeflag
=
0
;
zeroflag
=
0
;
while
(
iarg
<
narg
)
{
if
(
strcmp
(
arg
[
iarg
],
"zero"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
{
error
->
all
(
FLERR
,
"Illegal fix gld command"
);
}
if
(
strcmp
(
arg
[
iarg
+
1
],
"no"
)
==
0
)
{
}
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"yes"
)
==
0
)
{
zeroflag
=
1
;
}
else
{
error
->
all
(
FLERR
,
"Illegal fix gld command"
);
}
iarg
+=
2
;
}
else
if
(
strcmp
(
arg
[
iarg
],
"frozen"
)
==
0
)
{
if
(
iarg
+
2
>
narg
)
{
error
->
all
(
FLERR
,
"Illegal fix gld command"
);
}
if
(
strcmp
(
arg
[
iarg
+
1
],
"no"
)
==
0
)
{
}
else
if
(
strcmp
(
arg
[
iarg
+
1
],
"yes"
)
==
0
)
{
freezeflag
=
1
;
for
(
int
i
=
0
;
i
<
atom
->
nlocal
;
i
++
)
{
if
(
atom
->
mask
[
i
]
&
groupbit
)
{
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
=
k
+
3
)
{
s_gld
[
i
][
k
]
=
0.0
;
s_gld
[
i
][
k
+
1
]
=
0.0
;
s_gld
[
i
][
k
+
2
]
=
0.0
;
}
}
}
}
else
{
error
->
all
(
FLERR
,
"Illegal fix gld command"
);
}
iarg
+=
2
;
}
else
error
->
all
(
FLERR
,
"Illegal fix gld command"
);
}
// Initialize the target temperature
t_target
=
t_start
;
}
/* ----------------------------------------------------------------------
Destroys memory allocated by the method
------------------------------------------------------------------------- */
FixGLD
::~
FixGLD
()
{
delete
random
;
memory
->
destroy
(
prony_c
);
memory
->
destroy
(
prony_tau
);
memory
->
destroy
(
s_gld
);
// remove callbacks to fix, so atom class stops calling it
atom
->
delete_callback
(
id
,
0
);
atom
->
delete_callback
(
id
,
1
);
}
/* ----------------------------------------------------------------------
Specifies when the fix is called during the timestep
------------------------------------------------------------------------- */
int
FixGLD
::
setmask
()
{
int
mask
=
0
;
mask
|=
INITIAL_INTEGRATE
;
mask
|=
FINAL_INTEGRATE
;
mask
|=
INITIAL_INTEGRATE_RESPA
;
mask
|=
FINAL_INTEGRATE_RESPA
;
return
mask
;
}
/* ----------------------------------------------------------------------
Initialize the method parameters before a run
------------------------------------------------------------------------- */
void
FixGLD
::
init
()
{
dtv
=
update
->
dt
;
dtf
=
0.5
*
update
->
dt
*
force
->
ftm2v
;
if
(
strstr
(
update
->
integrate_style
,
"respa"
))
step_respa
=
((
Respa
*
)
update
->
integrate
)
->
step
;
}
/* ----------------------------------------------------------------------
First half of a timestep (V^{n} -> V^{n+1/2}; X^{n} -> X^{n+1})
------------------------------------------------------------------------- */
void
FixGLD
::
initial_integrate
(
int
vflag
)
{
double
dtfm
;
double
ftm2v
=
force
->
ftm2v
;
double
fran
[
3
],
fsum
[
3
],
fsumall
[
3
];
bigint
count
;
int
icoeff
;
// update v and x of atoms in group
double
**
x
=
atom
->
x
;
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
*
rmass
=
atom
->
rmass
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
igroup
==
atom
->
firstgroup
)
nlocal
=
atom
->
nfirst
;
// set kT to the temperature in mvvv units
double
kT
=
(
force
->
boltz
)
*
t_target
/
(
force
->
mvv2e
);
// zero an accumulator for the total random force
fsum
[
0
]
=
fsum
[
1
]
=
fsum
[
2
]
=
0.0
;
if
(
rmass
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
rmass
[
i
];
// Advance V by dt/2
v
[
i
][
0
]
+=
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
+=
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
+=
dtfm
*
f
[
i
][
2
];
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
=
k
+
3
)
{
v
[
i
][
0
]
+=
dtfm
*
s_gld
[
i
][
k
];
v
[
i
][
1
]
+=
dtfm
*
s_gld
[
i
][
k
+
1
];
v
[
i
][
2
]
+=
dtfm
*
s_gld
[
i
][
k
+
2
];
}
// Advance X by dt
x
[
i
][
0
]
+=
dtv
*
v
[
i
][
0
];
x
[
i
][
1
]
+=
dtv
*
v
[
i
][
1
];
x
[
i
][
2
]
+=
dtv
*
v
[
i
][
2
];
// Advance S by dt
icoeff
=
0
;
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
=
k
+
3
)
{
double
theta
=
exp
(
-
dtv
/
prony_tau
[
icoeff
]);
double
ck
=
prony_c
[
icoeff
];
double
vmult
=
(
theta
-
1.
)
*
ck
/
ftm2v
;
double
rmult
=
sqrt
(
2.0
*
kT
*
ck
/
dtv
)
*
(
1.
-
theta
)
/
ftm2v
;
// random force
#ifdef GLD_GAUSSIAN_DISTRO
fran
[
0
]
=
rmult
*
random
->
gaussian
();
fran
[
1
]
=
rmult
*
random
->
gaussian
();
fran
[
2
]
=
rmult
*
random
->
gaussian
();
#endif
#ifdef GLD_UNIFORM_DISTRO
rmult
*=
sqrt
(
12.0
);
// correct variance of uniform distribution
fran
[
0
]
=
rmult
*
(
random
->
uniform
()
-
0.5
);
fran
[
1
]
=
rmult
*
(
random
->
uniform
()
-
0.5
);
fran
[
2
]
=
rmult
*
(
random
->
uniform
()
-
0.5
);
#endif
// sum of random forces
fsum
[
0
]
+=
fran
[
0
];
fsum
[
1
]
+=
fran
[
1
];
fsum
[
2
]
+=
fran
[
2
];
s_gld
[
i
][
k
]
*=
theta
;
s_gld
[
i
][
k
+
1
]
*=
theta
;
s_gld
[
i
][
k
+
2
]
*=
theta
;
s_gld
[
i
][
k
]
+=
vmult
*
v
[
i
][
0
];
s_gld
[
i
][
k
+
1
]
+=
vmult
*
v
[
i
][
1
];
s_gld
[
i
][
k
+
2
]
+=
vmult
*
v
[
i
][
2
];
s_gld
[
i
][
k
]
+=
fran
[
0
];
s_gld
[
i
][
k
+
1
]
+=
fran
[
1
];
s_gld
[
i
][
k
+
2
]
+=
fran
[
2
];
icoeff
+=
1
;
}
}
}
else
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
mass
[
type
[
i
]];
// Advance V by dt/2
v
[
i
][
0
]
+=
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
+=
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
+=
dtfm
*
f
[
i
][
2
];
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
=
k
+
3
)
{
v
[
i
][
0
]
+=
dtfm
*
s_gld
[
i
][
k
];
v
[
i
][
1
]
+=
dtfm
*
s_gld
[
i
][
k
+
1
];
v
[
i
][
2
]
+=
dtfm
*
s_gld
[
i
][
k
+
2
];
}
// Advance X by dt
x
[
i
][
0
]
+=
dtv
*
v
[
i
][
0
];
x
[
i
][
1
]
+=
dtv
*
v
[
i
][
1
];
x
[
i
][
2
]
+=
dtv
*
v
[
i
][
2
];
// Advance S by dt
icoeff
=
0
;
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
=
k
+
3
)
{
double
theta
=
exp
(
-
dtv
/
prony_tau
[
icoeff
]);
double
ck
=
prony_c
[
icoeff
];
double
vmult
=
(
theta
-
1.
)
*
ck
/
ftm2v
;
double
rmult
=
sqrt
(
2.0
*
kT
*
ck
/
dtv
)
*
(
1.
-
theta
)
/
ftm2v
;
// random force
#ifdef GLD_GAUSSIAN_DISTRO
fran
[
0
]
=
rmult
*
random
->
gaussian
();
fran
[
1
]
=
rmult
*
random
->
gaussian
();
fran
[
2
]
=
rmult
*
random
->
gaussian
();
#endif
#ifdef GLD_UNIFORM_DISTRO
rmult
*=
sqrt
(
12.0
);
// correct variance of uniform distribution
fran
[
0
]
=
rmult
*
(
random
->
uniform
()
-
0.5
);
fran
[
1
]
=
rmult
*
(
random
->
uniform
()
-
0.5
);
fran
[
2
]
=
rmult
*
(
random
->
uniform
()
-
0.5
);
#endif
// sum of random forces
fsum
[
0
]
+=
fran
[
0
];
fsum
[
1
]
+=
fran
[
1
];
fsum
[
2
]
+=
fran
[
2
];
s_gld
[
i
][
k
]
*=
theta
;
s_gld
[
i
][
k
+
1
]
*=
theta
;
s_gld
[
i
][
k
+
2
]
*=
theta
;
s_gld
[
i
][
k
]
+=
vmult
*
v
[
i
][
0
];
s_gld
[
i
][
k
+
1
]
+=
vmult
*
v
[
i
][
1
];
s_gld
[
i
][
k
+
2
]
+=
vmult
*
v
[
i
][
2
];
s_gld
[
i
][
k
]
+=
fran
[
0
];
s_gld
[
i
][
k
+
1
]
+=
fran
[
1
];
s_gld
[
i
][
k
+
2
]
+=
fran
[
2
];
icoeff
+=
1
;
}
}
}
// correct the random force, if zeroflag is set
if
(
zeroflag
)
{
count
=
group
->
count
(
igroup
);
if
(
count
==
0
)
error
->
all
(
FLERR
,
"Cannot zero gld force for zero atoms"
);
MPI_Allreduce
(
fsum
,
fsumall
,
3
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
fsumall
[
0
]
/=
(
count
*
prony_terms
);
fsumall
[
1
]
/=
(
count
*
prony_terms
);
fsumall
[
2
]
/=
(
count
*
prony_terms
);
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
=
k
+
3
)
{
s_gld
[
i
][
k
]
-=
fsumall
[
0
];
s_gld
[
i
][
k
+
1
]
-=
fsumall
[
1
];
s_gld
[
i
][
k
+
2
]
-=
fsumall
[
2
];
}
}
}
}
}
/* ----------------------------------------------------------------------
Second half of a timestep (V^{n+1/2} -> V^{n+1})
------------------------------------------------------------------------- */
void
FixGLD
::
final_integrate
()
{
double
dtfm
;
// update v of atoms in group
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
*
rmass
=
atom
->
rmass
;
double
*
mass
=
atom
->
mass
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
if
(
igroup
==
atom
->
firstgroup
)
nlocal
=
atom
->
nfirst
;
if
(
rmass
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
rmass
[
i
];
v
[
i
][
0
]
+=
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
+=
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
+=
dtfm
*
f
[
i
][
2
];
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
=
k
+
3
)
{
v
[
i
][
0
]
+=
dtfm
*
s_gld
[
i
][
k
];
v
[
i
][
1
]
+=
dtfm
*
s_gld
[
i
][
k
+
1
];
v
[
i
][
2
]
+=
dtfm
*
s_gld
[
i
][
k
+
2
];
}
}
}
else
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
dtfm
=
dtf
/
mass
[
type
[
i
]];
v
[
i
][
0
]
+=
dtfm
*
f
[
i
][
0
];
v
[
i
][
1
]
+=
dtfm
*
f
[
i
][
1
];
v
[
i
][
2
]
+=
dtfm
*
f
[
i
][
2
];
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
=
k
+
3
)
{
v
[
i
][
0
]
+=
dtfm
*
s_gld
[
i
][
k
];
v
[
i
][
1
]
+=
dtfm
*
s_gld
[
i
][
k
+
1
];
v
[
i
][
2
]
+=
dtfm
*
s_gld
[
i
][
k
+
2
];
}
}
}
// Change the temperature for the next step
double
delta
=
update
->
ntimestep
-
update
->
beginstep
;
delta
/=
update
->
endstep
-
update
->
beginstep
;
t_target
=
t_start
+
delta
*
(
t_stop
-
t_start
);
}
/* ---------------------------------------------------------------------- */
void
FixGLD
::
initial_integrate_respa
(
int
vflag
,
int
ilevel
,
int
iloop
)
{
dtv
=
step_respa
[
ilevel
];
dtf
=
0.5
*
step_respa
[
ilevel
]
*
(
force
->
ftm2v
);
// innermost level - GLD update of v and x
// all other levels - GLD update of v
if
(
ilevel
==
0
)
initial_integrate
(
vflag
);
else
final_integrate
();
}
/* ---------------------------------------------------------------------- */
void
FixGLD
::
final_integrate_respa
(
int
ilevel
,
int
iloop
)
{
dtf
=
0.5
*
step_respa
[
ilevel
]
*
(
force
->
ftm2v
);
final_integrate
();
}
/* ----------------------------------------------------------------------
Called when a change to the target temperature is requested mid-run
------------------------------------------------------------------------- */
void
FixGLD
::
reset_target
(
double
t_new
)
{
t_target
=
t_start
=
t_stop
=
t_new
;
}
/* ----------------------------------------------------------------------
Called when a change to the timestep is requested mid-run
------------------------------------------------------------------------- */
void
FixGLD
::
reset_dt
()
{
// set the time integration constants
dtv
=
update
->
dt
;
dtf
=
0.5
*
update
->
dt
*
(
force
->
ftm2v
);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double
FixGLD
::
memory_usage
()
{
double
bytes
=
atom
->
nmax
*
3
*
prony_terms
*
sizeof
(
double
);
return
bytes
;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void
FixGLD
::
grow_arrays
(
int
nmax
)
{
memory
->
grow
(
s_gld
,
nmax
,
3
*
prony_terms
,
"gld:s_gld"
);
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void
FixGLD
::
copy_arrays
(
int
i
,
int
j
,
int
delflag
)
{
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
++
)
{
s_gld
[
j
][
k
]
=
s_gld
[
i
][
k
];
}
}
/* ----------------------------------------------------------------------
Pack extended variables assoc. w/ atom i into buffer for exchange
with another processor
------------------------------------------------------------------------- */
int
FixGLD
::
pack_exchange
(
int
i
,
double
*
buf
)
{
int
m
=
0
;
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
++
)
{
buf
[
m
++
]
=
s_gld
[
i
][
k
];
}
return
m
;
}
/* ----------------------------------------------------------------------
Unpack extended variables from exchange with another processor
------------------------------------------------------------------------- */
int
FixGLD
::
unpack_exchange
(
int
nlocal
,
double
*
buf
)
{
int
m
=
0
;
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
++
)
{
s_gld
[
nlocal
][
k
]
=
buf
[
m
++
];
}
return
m
;
}
/* ----------------------------------------------------------------------
Pack extended variables assoc. w/ atom i into buffer for
writing to a restart file
------------------------------------------------------------------------- */
int
FixGLD
::
pack_restart
(
int
i
,
double
*
buf
)
{
int
m
=
0
;
buf
[
m
++
]
=
3
*
prony_terms
+
1
;
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
=
k
+
3
)
{
buf
[
m
++
]
=
s_gld
[
i
][
k
];
buf
[
m
++
]
=
s_gld
[
i
][
k
+
1
];
buf
[
m
++
]
=
s_gld
[
i
][
k
+
2
];
}
return
m
;
}
/* ----------------------------------------------------------------------
Unpack extended variables to restart the fix from a restart file
------------------------------------------------------------------------- */
void
FixGLD
::
unpack_restart
(
int
nlocal
,
int
nth
)
{
double
**
extra
=
atom
->
extra
;
// skip to the nth set of extended variables
int
m
=
0
;
for
(
int
i
=
0
;
i
<
nth
;
i
++
)
m
+=
static_cast
<
int
>
(
extra
[
nlocal
][
m
]);
m
++
;
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
=
k
+
3
)
{
s_gld
[
nlocal
][
k
]
=
extra
[
nlocal
][
m
++
];
s_gld
[
nlocal
][
k
+
1
]
=
extra
[
nlocal
][
m
++
];
s_gld
[
nlocal
][
k
+
2
]
=
extra
[
nlocal
][
m
++
];
}
}
/* ----------------------------------------------------------------------
Returns the number of items in atomic restart data associated with
local atom nlocal. Used in determining the total extra data stored by
fixes on a given processor.
------------------------------------------------------------------------- */
int
FixGLD
::
size_restart
(
int
nlocal
)
{
return
3
*
prony_terms
+
1
;
}
/* ----------------------------------------------------------------------
Returns the maximum number of items in atomic restart data
Called in Modify::restart for peratom restart.
------------------------------------------------------------------------- */
int
FixGLD
::
maxsize_restart
()
{
return
3
*
prony_terms
+
1
;
}
/* ----------------------------------------------------------------------
Initializes the extended variables to equilibrium distribution
at t_start.
------------------------------------------------------------------------- */
void
FixGLD
::
init_s_gld
()
{
int
icoeff
;
double
eq_sdev
=
0.0
;
// set kT to the temperature in mvvv units
double
kT
=
(
force
->
boltz
)
*
t_start
/
(
force
->
mvv2e
);
#ifdef GLD_GAUSSIAN_DISTRO
double
scale
=
sqrt
(
kT
)
/
(
force
->
ftm2v
);
#endif
#ifdef GLD_UNIFORM_DISTRO
double
scale
=
sqrt
(
12.0
*
kT
)
/
(
force
->
ftm2v
);
#endif
for
(
int
i
=
0
;
i
<
atom
->
nlocal
;
i
++
)
{
if
(
atom
->
mask
[
i
]
&
groupbit
)
{
icoeff
=
0
;
for
(
int
k
=
0
;
k
<
3
*
prony_terms
;
k
=
k
+
3
)
{
eq_sdev
=
scale
*
sqrt
(
prony_c
[
icoeff
]
/
prony_tau
[
icoeff
]);
#ifdef GLD_GAUSSIAN_DISTRO
s_gld
[
i
][
k
]
=
eq_sdev
*
random
->
gaussian
();
s_gld
[
i
][
k
+
1
]
=
eq_sdev
*
random
->
gaussian
();
s_gld
[
i
][
k
+
2
]
=
eq_sdev
*
random
->
gaussian
();
#endif
#ifdef GLD_UNIFORM_DISTRO
s_gld
[
i
][
k
]
=
eq_sdev
*
(
random
->
uniform
()
-
0.5
);
s_gld
[
i
][
k
+
1
]
=
eq_sdev
*
(
random
->
uniform
()
-
0.5
);
s_gld
[
i
][
k
+
2
]
=
eq_sdev
*
(
random
->
uniform
()
-
0.5
);
#endif
icoeff
+=
1
;
}
}
}
return
;
}
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