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fix_langevin_eff.cpp
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rLAMMPS lammps
fix_langevin_eff.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: Andres Jaramillo-Botero
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_langevin_eff.h"
#include "math_extra.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "domain.h"
#include "region.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"
using
namespace
LAMMPS_NS
;
using
namespace
FixConst
;
enum
{
NOBIAS
,
BIAS
};
enum
{
CONSTANT
,
EQUAL
,
ATOM
};
#define SINERTIA 0.4
// moment of inertia prefactor for sphere
#define EINERTIA 0.2
// moment of inertia prefactor for ellipsoid
/* ---------------------------------------------------------------------- */
FixLangevinEff
::
FixLangevinEff
(
LAMMPS
*
lmp
,
int
narg
,
char
**
arg
)
:
FixLangevin
(
lmp
,
narg
,
arg
)
{
erforcelangevin
=
NULL
;
}
/* ---------------------------------------------------------------------- */
FixLangevinEff
::~
FixLangevinEff
()
{
memory
->
destroy
(
erforcelangevin
);
}
/* ---------------------------------------------------------------------- */
void
FixLangevinEff
::
post_force_no_tally
()
{
double
gamma1
,
gamma2
,
t_target
;
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
*
ervel
=
atom
->
ervel
;
double
*
erforce
=
atom
->
erforce
;
int
*
spin
=
atom
->
spin
;
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
mefactor
=
domain
->
dimension
/
4.0
;
double
sqrtmefactor
=
sqrt
(
mefactor
);
double
delta
=
update
->
ntimestep
-
update
->
beginstep
;
delta
/=
update
->
endstep
-
update
->
beginstep
;
// set current t_target and t_sqrt
// if variable temp, evaluate variable, wrap with clear/add
// reallocate tforce array if necessary
if
(
tstyle
==
CONSTANT
)
{
t_target
=
t_start
+
delta
*
(
t_stop
-
t_start
);
tsqrt
=
sqrt
(
t_target
);
}
else
{
modify
->
clearstep_compute
();
if
(
tstyle
==
EQUAL
)
{
t_target
=
input
->
variable
->
compute_equal
(
tvar
);
if
(
t_target
<
0.0
)
error
->
one
(
FLERR
,
"Fix langevin/eff variable returned negative temperature"
);
tsqrt
=
sqrt
(
t_target
);
}
else
{
if
(
nlocal
>
maxatom2
)
{
maxatom2
=
atom
->
nmax
;
memory
->
destroy
(
tforce
);
memory
->
create
(
tforce
,
maxatom2
,
"langevin/eff:tforce"
);
}
input
->
variable
->
compute_atom
(
tvar
,
igroup
,
tforce
,
1
,
0
);
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
if
(
tforce
[
i
]
<
0.0
)
error
->
one
(
FLERR
,
"Fix langevin/eff variable returned negative temperature"
);
}
modify
->
addstep_compute
(
update
->
ntimestep
+
1
);
}
// apply damping and thermostat to atoms in group
// for BIAS:
// calculate temperature since some computes require temp
// computed on current nlocal atoms to remove bias
// test v = 0 since some computes mask non-participating atoms via v = 0
// and added force has extra term not multiplied by v = 0
// for ZEROFLAG:
// sum random force over all atoms in group
// subtract sum/particles from each atom in group
double
fran
[
4
],
fsum
[
4
],
fsumall
[
4
];
fsum
[
0
]
=
fsum
[
1
]
=
fsum
[
2
]
=
fsum
[
3
]
=
0.0
;
double
boltz
=
force
->
boltz
;
double
dt
=
update
->
dt
;
double
mvv2e
=
force
->
mvv2e
;
double
ftm2v
=
force
->
ftm2v
;
int
particles
=
group
->
count
(
igroup
);
if
(
zeroflag
)
{
if
(
particles
==
0
)
error
->
all
(
FLERR
,
"Cannot zero Langevin force of 0 atoms/electrons"
);
}
// find number of electrons in group
int
dof
,
fix_dof
;
dof
=
domain
->
dimension
*
particles
;
fix_dof
=
0
;
for
(
int
i
=
0
;
i
<
modify
->
nfix
;
i
++
)
fix_dof
+=
modify
->
fix
[
i
]
->
dof
(
igroup
);
// extra_dof = domain->dimension
dof
-=
domain
->
dimension
+
fix_dof
;
int
one
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
if
(
fabs
(
spin
[
i
])
==
1
)
one
++
;
}
int
nelectrons
,
dofelectrons
,
dofnuclei
;
MPI_Allreduce
(
&
one
,
&
nelectrons
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
dofelectrons
=
domain
->
dimension
*
nelectrons
;
dofnuclei
=
dof
-
dofelectrons
;
// thermal partitioning factor between nuclei and electrons
// extra dof from electron size
double
gfactor3
=
(
double
)
(
dof
+
nelectrons
)
/
dofnuclei
;
if
(
which
==
NOBIAS
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
if
(
tstyle
==
ATOM
)
tsqrt
=
sqrt
(
tforce
[
i
]);
gamma1
=
gfactor1
[
type
[
i
]]
*
gfactor3
;
gamma2
=
gfactor2
[
type
[
i
]]
*
tsqrt
;
fran
[
0
]
=
gamma2
*
(
random
->
uniform
()
-
0.5
);
fran
[
1
]
=
gamma2
*
(
random
->
uniform
()
-
0.5
);
fran
[
2
]
=
gamma2
*
(
random
->
uniform
()
-
0.5
);
f
[
i
][
0
]
+=
gamma1
*
v
[
i
][
0
]
+
fran
[
0
];
f
[
i
][
1
]
+=
gamma1
*
v
[
i
][
1
]
+
fran
[
1
];
f
[
i
][
2
]
+=
gamma1
*
v
[
i
][
2
]
+
fran
[
2
];
fsum
[
0
]
+=
fran
[
0
];
fsum
[
1
]
+=
fran
[
1
];
fsum
[
2
]
+=
fran
[
2
];
if
(
fabs
(
spin
[
i
])
==
1
)
{
fran
[
3
]
=
sqrtmefactor
*
gamma2
*
(
random
->
uniform
()
-
0.5
);
erforce
[
i
]
+=
mefactor
*
gamma1
*
ervel
[
i
]
+
fran
[
3
];
fsum
[
3
]
+=
fran
[
3
];
}
}
}
}
else
if
(
which
==
BIAS
)
{
temperature
->
compute_scalar
();
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
if
(
tstyle
==
ATOM
)
tsqrt
=
sqrt
(
tforce
[
i
]);
gamma1
=
gfactor1
[
type
[
i
]]
*
gfactor3
;
gamma2
=
gfactor2
[
type
[
i
]]
*
tsqrt
;
temperature
->
remove_bias
(
i
,
v
[
i
]);
fran
[
0
]
=
gamma2
*
(
random
->
uniform
()
-
0.5
);
fran
[
1
]
=
gamma2
*
(
random
->
uniform
()
-
0.5
);
fran
[
2
]
=
gamma2
*
(
random
->
uniform
()
-
0.5
);
if
(
v
[
i
][
0
]
!=
0.0
)
f
[
i
][
0
]
+=
gamma1
*
v
[
i
][
0
]
+
fran
[
0
];
if
(
v
[
i
][
1
]
!=
0.0
)
f
[
i
][
1
]
+=
gamma1
*
v
[
i
][
1
]
+
fran
[
1
];
if
(
v
[
i
][
2
]
!=
0.0
)
f
[
i
][
2
]
+=
gamma1
*
v
[
i
][
2
]
+
fran
[
2
];
fsum
[
0
]
+=
fran
[
0
];
fsum
[
1
]
+=
fran
[
1
];
fsum
[
2
]
+=
fran
[
2
];
if
(
fabs
(
spin
[
i
])
==
1
)
{
fran
[
3
]
=
sqrtmefactor
*
gamma2
*
(
random
->
uniform
()
-
0.5
);
if
(
ervel
[
i
]
!=
0.0
)
erforce
[
i
]
+=
mefactor
*
gamma1
*
ervel
[
i
]
+
fran
[
3
];
fsum
[
3
]
+=
fran
[
3
];
}
temperature
->
restore_bias
(
i
,
v
[
i
]);
}
}
}
// set total force to zero
if
(
zeroflag
)
{
MPI_Allreduce
(
fsum
,
fsumall
,
3
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
fsumall
[
0
]
/=
particles
;
fsumall
[
1
]
/=
particles
;
fsumall
[
2
]
/=
particles
;
fsumall
[
3
]
/=
nelectrons
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
f
[
i
][
0
]
-=
fsumall
[
0
];
f
[
i
][
1
]
-=
fsumall
[
1
];
f
[
i
][
2
]
-=
fsumall
[
2
];
if
(
fabs
(
spin
[
i
])
==
1
)
erforce
[
i
]
-=
fsumall
[
3
];
}
}
}
}
/* ---------------------------------------------------------------------- */
void
FixLangevinEff
::
post_force_tally
()
{
double
gamma1
,
gamma2
,
t_target
;
// reallocate flangevin and erforcelangevin if necessary
if
(
atom
->
nlocal
>
maxatom1
)
{
memory
->
destroy
(
flangevin
);
memory
->
destroy
(
erforcelangevin
);
maxatom1
=
atom
->
nmax
;
memory
->
create
(
flangevin
,
maxatom1
,
3
,
"langevin/eff:flangevin"
);
memory
->
create
(
erforcelangevin
,
maxatom1
,
"langevin/eff:erforcelangevin"
);
}
double
**
v
=
atom
->
v
;
double
**
f
=
atom
->
f
;
double
*
erforce
=
atom
->
erforce
;
double
*
ervel
=
atom
->
ervel
;
int
*
spin
=
atom
->
spin
;
double
mefactor
=
domain
->
dimension
/
4.0
;
double
sqrtmefactor
=
sqrt
(
mefactor
);
int
*
type
=
atom
->
type
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
double
delta
=
update
->
ntimestep
-
update
->
beginstep
;
delta
/=
update
->
endstep
-
update
->
beginstep
;
// set current t_target and t_sqrt
// if variable temp, evaluate variable, wrap with clear/add
// reallocate tforce array if necessary
if
(
tstyle
==
CONSTANT
)
{
t_target
=
t_start
+
delta
*
(
t_stop
-
t_start
);
tsqrt
=
sqrt
(
t_target
);
}
else
{
modify
->
clearstep_compute
();
if
(
tstyle
==
EQUAL
)
{
t_target
=
input
->
variable
->
compute_equal
(
tvar
);
if
(
t_target
<
0.0
)
error
->
one
(
FLERR
,
"Fix langevin/eff variable returned negative temperature"
);
tsqrt
=
sqrt
(
t_target
);
}
else
{
if
(
nlocal
>
maxatom2
)
{
maxatom2
=
atom
->
nmax
;
memory
->
destroy
(
tforce
);
memory
->
create
(
tforce
,
maxatom2
,
"langevin/eff:tforce"
);
}
input
->
variable
->
compute_atom
(
tvar
,
igroup
,
tforce
,
1
,
0
);
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
if
(
tforce
[
i
]
<
0.0
)
error
->
one
(
FLERR
,
"Fix langevin/eff variable returned negative temperature"
);
}
modify
->
addstep_compute
(
update
->
ntimestep
+
1
);
}
// apply damping and thermostat to appropriate atoms
// for BIAS:
// calculate temperature since some computes require temp
// computed on current nlocal atoms to remove bias
// test v = 0 since some computes mask non-participating atoms via v = 0
// and added force has extra term not multiplied by v = 0
double
boltz
=
force
->
boltz
;
double
dt
=
update
->
dt
;
double
mvv2e
=
force
->
mvv2e
;
double
ftm2v
=
force
->
ftm2v
;
int
particles
=
group
->
count
(
igroup
);
if
(
zeroflag
)
{
if
(
particles
==
0
)
error
->
all
(
FLERR
,
"Cannot zero Langevin force of 0 atoms/electrons"
);
}
// find number of electrons in group
int
dof
,
fix_dof
;
dof
=
domain
->
dimension
*
particles
;
fix_dof
=
0
;
for
(
int
i
=
0
;
i
<
modify
->
nfix
;
i
++
)
fix_dof
+=
modify
->
fix
[
i
]
->
dof
(
igroup
);
// extra_dof = domain->dimension
dof
-=
domain
->
dimension
+
fix_dof
;
int
one
=
0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
if
(
fabs
(
spin
[
i
])
==
1
)
one
++
;
}
int
nelectrons
,
dofelectrons
,
dofnuclei
;
MPI_Allreduce
(
&
one
,
&
nelectrons
,
1
,
MPI_INT
,
MPI_SUM
,
world
);
dofelectrons
=
domain
->
dimension
*
nelectrons
;
dofnuclei
=
dof
-
dofelectrons
;
// thermal partitioning factor between nuclei and electrons
// extra dof from electron size
double
gfactor3
=
(
double
)
(
dof
+
nelectrons
)
/
dofnuclei
;
if
(
which
==
NOBIAS
)
{
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
if
(
tstyle
==
ATOM
)
tsqrt
=
sqrt
(
tforce
[
i
]);
gamma1
=
gfactor1
[
type
[
i
]]
*
gfactor3
;
gamma2
=
gfactor2
[
type
[
i
]]
*
tsqrt
;
flangevin
[
i
][
0
]
=
gamma1
*
v
[
i
][
0
]
+
gamma2
*
(
random
->
uniform
()
-
0.5
);
flangevin
[
i
][
1
]
=
gamma1
*
v
[
i
][
1
]
+
gamma2
*
(
random
->
uniform
()
-
0.5
);
flangevin
[
i
][
2
]
=
gamma1
*
v
[
i
][
2
]
+
gamma2
*
(
random
->
uniform
()
-
0.5
);
f
[
i
][
0
]
+=
flangevin
[
i
][
0
];
f
[
i
][
1
]
+=
flangevin
[
i
][
1
];
f
[
i
][
2
]
+=
flangevin
[
i
][
2
];
if
(
fabs
(
spin
[
i
])
==
1
)
{
erforcelangevin
[
i
]
=
mefactor
*
gamma1
*
ervel
[
i
]
+
sqrtmefactor
*
gamma2
*
(
random
->
uniform
()
-
0.5
);
erforce
[
i
]
+=
erforcelangevin
[
i
];
}
}
}
}
else
if
(
which
==
BIAS
)
{
temperature
->
compute_scalar
();
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
{
if
(
mask
[
i
]
&
groupbit
)
{
if
(
tstyle
==
ATOM
)
tsqrt
=
sqrt
(
tforce
[
i
]);
gamma1
=
gfactor1
[
type
[
i
]]
*
gfactor3
;
gamma2
=
gfactor2
[
type
[
i
]]
*
tsqrt
;
temperature
->
remove_bias
(
i
,
v
[
i
]);
flangevin
[
i
][
0
]
=
gamma1
*
v
[
i
][
0
]
+
gamma2
*
(
random
->
uniform
()
-
0.5
);
flangevin
[
i
][
1
]
=
gamma1
*
v
[
i
][
1
]
+
gamma2
*
(
random
->
uniform
()
-
0.5
);
flangevin
[
i
][
2
]
=
gamma1
*
v
[
i
][
2
]
+
gamma2
*
(
random
->
uniform
()
-
0.5
);
if
(
v
[
i
][
0
]
!=
0.0
)
f
[
i
][
0
]
+=
flangevin
[
i
][
0
];
else
flangevin
[
i
][
0
]
=
0.0
;
if
(
v
[
i
][
1
]
!=
0.0
)
f
[
i
][
1
]
+=
flangevin
[
i
][
1
];
else
flangevin
[
i
][
1
]
=
0.0
;
if
(
v
[
i
][
2
]
!=
0.0
)
f
[
i
][
2
]
+=
flangevin
[
i
][
2
];
else
flangevin
[
i
][
2
]
=
0.0
;
if
(
fabs
(
spin
[
i
])
==
1
)
{
erforcelangevin
[
i
]
=
mefactor
*
gamma1
*
ervel
[
i
]
+
sqrtmefactor
*
gamma2
*
(
random
->
uniform
()
-
0.5
);
if
(
ervel
[
i
]
!=
0.0
)
erforce
[
i
]
+=
erforcelangevin
[
i
];
else
erforcelangevin
[
i
]
=
0.0
;
}
temperature
->
restore_bias
(
i
,
v
[
i
]);
}
}
}
}
/* ----------------------------------------------------------------------
tally energy transfer to thermal reservoir
------------------------------------------------------------------------- */
void
FixLangevinEff
::
end_of_step
()
{
if
(
!
tally
)
return
;
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
*
spin
=
atom
->
spin
;
energy_onestep
=
0.0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
energy_onestep
+=
flangevin
[
i
][
0
]
*
v
[
i
][
0
]
+
flangevin
[
i
][
1
]
*
v
[
i
][
1
]
+
flangevin
[
i
][
2
]
*
v
[
i
][
2
];
if
(
fabs
(
spin
[
i
])
==
1
)
energy_onestep
+=
erforcelangevin
[
i
];
}
energy
+=
energy_onestep
*
update
->
dt
;
}
/* ---------------------------------------------------------------------- */
double
FixLangevinEff
::
compute_scalar
()
{
if
(
!
tally
||
flangevin
==
NULL
||
erforcelangevin
==
NULL
)
return
0.0
;
// capture the very first energy transfer to thermal reservoir
double
**
v
=
atom
->
v
;
int
*
mask
=
atom
->
mask
;
int
nlocal
=
atom
->
nlocal
;
int
*
spin
=
atom
->
spin
;
if
(
update
->
ntimestep
==
update
->
beginstep
)
{
energy_onestep
=
0.0
;
for
(
int
i
=
0
;
i
<
nlocal
;
i
++
)
if
(
mask
[
i
]
&
groupbit
)
{
energy_onestep
+=
flangevin
[
i
][
0
]
*
v
[
i
][
0
]
+
flangevin
[
i
][
1
]
*
v
[
i
][
1
]
+
flangevin
[
i
][
2
]
*
v
[
i
][
2
];
if
(
fabs
(
spin
[
i
])
==
1
)
energy_onestep
+=
erforcelangevin
[
i
];
}
energy
=
0.5
*
energy_onestep
*
update
->
dt
;
}
double
energy_me
=
energy
-
0.5
*
energy_onestep
*
update
->
dt
;
double
energy_all
;
MPI_Allreduce
(
&
energy_me
,
&
energy_all
,
1
,
MPI_DOUBLE
,
MPI_SUM
,
world
);
return
-
energy_all
;
}
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