forked from lijiext/lammps
refactoring of code and doc files
This commit is contained in:
Steve Plimpton
parent
aa70f8cc6b
commit
d3348371e1
|
|
@ -21,13 +21,9 @@ Syntax
|
|||
|
||||
.. parsed-literal::
|
||||
|
||||
*xlo*\ ,\ *ylo*\ ,\ *zlo* arg = EDGE or constant or variable
|
||||
arg = EDGE or constant or variable
|
||||
EDGE = current lo edge of simulation box
|
||||
constant = number like 0.0 or -30.0 (distance units)
|
||||
variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
|
||||
*xhi*\ ,\ *yhi*\ ,\ *zhi* arg = EDGE or constant or variable
|
||||
EDGE = current hi edge of simulation box
|
||||
constant = number like 50.0 or 100.3 (distance units)
|
||||
constant = number like 0.0 or 30.0 (distance units)
|
||||
variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle
|
||||
|
||||
* zero or more keyword/value pairs may be appended
|
||||
|
|
@ -62,11 +58,12 @@ by a distance delta (e.g. due to :doc:`fix nve <fix_nve>`), then it is
|
|||
put back inside the face by the same delta, and the sign of the
|
||||
corresponding component of its velocity is flipped.
|
||||
|
||||
When used in conjunction with :doc:`fix nve <fix_nve>` and :doc:`run\_style verlet <run_style>`, the resultant time-integration algorithm is
|
||||
equivalent to the primitive splitting algorithm (PSA) described by
|
||||
:ref:`Bond <Bond1>`. Because each reflection event divides
|
||||
the corresponding timestep asymmetrically, energy conservation is only
|
||||
satisfied to O(dt), rather than to O(dt\^2) as it would be for
|
||||
When used in conjunction with :doc:`fix nve <fix_nve>` and
|
||||
:doc:`run\_style verlet <run_style>`, the resultant time-integration
|
||||
algorithm is equivalent to the primitive splitting algorithm (PSA)
|
||||
described by :ref:`Bond <Bond1>`. Because each reflection event
|
||||
divides the corresponding timestep asymmetrically, energy conservation
|
||||
is only satisfied to O(dt), rather than to O(dt\^2) as it would be for
|
||||
velocity-Verlet integration without reflective walls.
|
||||
|
||||
Up to 6 walls or faces can be specified in a single command: *xlo*\ ,
|
||||
|
|
@ -156,17 +153,19 @@ perturbation on the particles:
|
|||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>`
|
||||
doc page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
LAMMPS was built with those packages. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
by including their suffix, or you can use the :doc:`-suffix
|
||||
command-line switch <Run_options>` when you invoke LAMMPS, or you can
|
||||
use the :doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
|
@ -177,11 +176,13 @@ instructions on how to use the accelerated styles effectively.
|
|||
|
||||
**Restart, fix\_modify, output, run start/stop, minimize info:**
|
||||
|
||||
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix\_modify <fix_modify>` options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various :doc:`output commands <Howto_output>`.
|
||||
No information about this fix is written to :doc:`binary restart files
|
||||
<restart>`. None of the :doc:`fix\_modify <fix_modify>` options are
|
||||
relevant to this fix. No global or per-atom quantities are stored by
|
||||
this fix for access by various :doc:`output commands <Howto_output>`.
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
|
||||
the :doc:`run <run>` command. This fix is not invoked during
|
||||
:doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
|
@ -192,17 +193,18 @@ Any dimension (xyz) that has a reflecting wall must be non-periodic.
|
|||
A reflecting wall should not be used with rigid bodies such as those
|
||||
defined by a "fix rigid" command. This is because the wall/reflect
|
||||
displaces atoms directly rather than exerts a force on them. For
|
||||
rigid bodies, use a soft wall instead, such as :doc:`fix wall/lj93 <fix_wall>`. LAMMPS will flag the use of a rigid
|
||||
fix with fix wall/reflect with a warning, but will not generate an
|
||||
error.
|
||||
rigid bodies, use a soft wall instead, such as :doc:`fix wall/lj93
|
||||
<fix_wall>`. LAMMPS will flag the use of a rigid fix with fix
|
||||
wall/reflect with a warning, but will not generate an error.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix wall/lj93 <fix_wall>`, :doc:`fix oneway <fix_oneway>`
|
||||
|
||||
**Default:** none
|
||||
**Default:**
|
||||
|
||||
The default for the units keyword is lattice.
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -1,98 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
fix wall/stochastic command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID wall/reflect/stochastic reflectionstyle seed face pos temp velx vely velz accomx accomy accomz ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
wall/reflect/stochastic = style name of this fix command :l
|
||||
one or more face/arg pairs may be appended :l
|
||||
reflectionstyle = diffusive or maxwell or cercignanilampis :l
|
||||
seed = random seed for stochastic wall (must be less than 900000000) :l
|
||||
face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
|
||||
{xlo},{ylo},{zlo} pos = EDGE or constant
|
||||
EDGE = current lo edge of simulation box
|
||||
constant = number like 0.0 or -30.0 (distance units)
|
||||
temp = wall temperature
|
||||
velx, vely, velz = wall velocity along x, y, z directions
|
||||
accomx, accomy, accomz = accommodation coefficients along x, y, z directions (only for maxwell and cercignanilampis reflection style)
|
||||
{xhi},{yhi},{zhi} pos = EDGE or constant or variable
|
||||
EDGE = current hi edge of simulation box
|
||||
constant = number like 50.0 or 100.3 (distance units)
|
||||
temp = wall temperature
|
||||
velx, vely, velz = wall velocity along x, y, z directions
|
||||
accomx, accomy, accomz = accommodation coefficients along x, y, z directions (only for maxwell and cercignanilampis style) :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {units} :l
|
||||
{units} value = {lattice} or {box}
|
||||
{lattice} = the wall position is defined in lattice units
|
||||
{box} = the wall position is defined in simulation box units :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix zwalls all wall/reflect/stochastic diffusive 23424 zlo EDGE 300 0.1 0.1 0 zhi EDGE 200 0.1 0.1 0
|
||||
fix ywalls all wall/reflect/stochastic maxwell 345533 ylo 5.0 300 0.1 0.0 0.0 0.8 yhi 10.0 300 0.1 0.0 0.0 0.8
|
||||
fix xwalls all wall/reflect/stochastic cercignanilampis 2308 xlo 0.0 300 0.0 0.1 0.9 0.8 0.7 xhi EDGE 300 0.0 0.1 0 0.9 0.8 0.7 units box :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This fix models the stochastic and inelastic collisions between fluid atoms and a solid boundary. The solid surface with finite temperature and moving speed can exchange energy with the fluid atoms. Different from the command fix wall/reflect which is equivalent to the mirror reflection, the post collision velocity of the fluid atoms in the stochastic wall model is random. The randomness can come from many sources: thermal motion of solid atoms, the surface roughness, etc... Three stochastic wall models are implemented.
|
||||
|
||||
Diffusive wall (reflectionstyle = diffusive): all the gas atoms are
|
||||
reflected diffusively. Their velocity distribution corresponds to the
|
||||
equilibrium distribution at the wall temperature.
|
||||
|
||||
Maxwell model (reflectionstyle = maxwell): the reflection is partially
|
||||
diffusive and partially specular. The accommodation coefficient is the
|
||||
portion of the diffusive reflection "Maxwell"_#Maxwell.
|
||||
|
||||
Cercignani/Lampis model: 3 accommodations coefficients are used, two
|
||||
velocity accommodation coefficients and one normal kinetic energy
|
||||
accommodation "CL"_#CL, "To"_#To. The code will recognize automatically
|
||||
the normal direction of the wall and the other two tangential
|
||||
directions. For example, if accomx = 0.5, accomy = 0.2, accomz = 0.3 and
|
||||
the wall is normal to direction y, accomx and accomz are the tangential
|
||||
velocity accommodation coefficients and accomy is the normal kinetic
|
||||
energy accommodation coefficients.
|
||||
|
||||
The {units} keyword determines the distance units used to define a wall
|
||||
position. A {box} value selects standard distance units as defined by
|
||||
the "units"_units.html command, e.g. Angstroms for units = real or
|
||||
metal. A {lattice} value means the distance units are in lattice
|
||||
spacings. The "lattice"_lattice.html command must have been previously
|
||||
used to define the lattice spacings.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Due to the similarities, this fix has the same limitation as the the
|
||||
wall/reflect. Any dimension (xyz) that has a wall must be non-periodic. It
|
||||
should not be used with rigid bodies such as those defined by a "fix rigid"
|
||||
command. Furthermore, the wall velocity must lie on the same plane as the wall. Package USER-MISC is required to use this fix.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix wall/reflect"_fix_wall_reflect.html,
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Maxwell)
|
||||
[(Maxwell)] J.C. Maxwell, Philos. Tans. Royal Soc. London, 157: 49-88 (1867).
|
||||
|
||||
:link(CL)
|
||||
[(Cercignani)] C. Cercignani and M. Lampis. Trans. Theory Stat. Phys. 1, 2, 101 (1971).
|
||||
|
||||
:link(To)
|
||||
[(To)] Q.D. To, V.H. Vu, G. Lauriat, and C. Leonard. J. Math. Phys. 56, 103101 (2015).
|
||||
|
|
@ -0,0 +1,126 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
fix wall/reflect/stochastic command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID wall/reflect/stochastic rstyle seed face args ... keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
wall/reflect/stochastic = style name of this fix command :l
|
||||
rstyle = diffusive or maxwell or ccl :l
|
||||
seed = random seed for stochasticity (positive integer) :l
|
||||
one or more face/args pairs may be appended :l
|
||||
face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
|
||||
args = pos temp velx vely velz accomx accomy accomz
|
||||
pos = EDGE or constant
|
||||
EDGE = current lo or hi edge of simulation box
|
||||
constant = number like 0.0 or 30.0 (distance units)
|
||||
temp = wall temperature (temperature units)
|
||||
velx,vely,velz = wall velocity in x,y,z directions (velocity units)
|
||||
accomx,accomy,accomz = accommodation coeffs in x,y,z directions (unitless)
|
||||
not specified for rstyle = diffusive
|
||||
single accom coeff specified for rstyle maxwell
|
||||
all 3 coeffs specified for rstyle cll :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {units} :l
|
||||
{units} value = {lattice} or {box}
|
||||
{lattice} = the wall position is defined in lattice units
|
||||
{box} = the wall position is defined in simulation box units :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix zwalls all wall/reflect/stochastic diffusive 23424 zlo EDGE 300 0.1 0.1 0 zhi EDGE 200 0.1 0.1 0
|
||||
fix ywalls all wall/reflect/stochastic maxwell 345533 ylo 5.0 300 0.1 0.0 0.0 0.8 yhi 10.0 300 0.1 0.0 0.0 0.8
|
||||
fix xwalls all wall/reflect/stochastic cercignanilampis 2308 xlo 0.0 300 0.0 0.1 0.9 0.8 0.7 xhi EDGE 300 0.0 0.1 0 0.9 0.8 0.7 units box :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Bound the simulation with one or more walls which reflect particles
|
||||
in the specified group when they attempt to move through them.
|
||||
|
||||
Reflection means that if an atom moves outside the wall on a timestep
|
||||
(e.g. due to the "fix nve"_fix_nve.html command), then it is put back
|
||||
inside the wall with a changed velocity.
|
||||
|
||||
This fix models treats the wall as a moving solid boundary with a
|
||||
finite temperature, which can exchange energy with particles that
|
||||
collide with it. This is different than the simpler "fix
|
||||
wall/reflect"_fix_wall_reflect.html command which models mirror
|
||||
reflection. For this fix, the post collision velocity of each
|
||||
particle is treated stochastically. The randomness can come from many
|
||||
sources: thermal motion of the wall atoms, surface roughness, etc.
|
||||
Three stochastic reflection models are currently implemented.
|
||||
|
||||
For rstyle {diffusive}, particles are reflected diffusively. Their
|
||||
velocity distribution corresponds to an equilibrium distribution of
|
||||
particles at the wall temperature. No accomondation coeffs are
|
||||
specified.
|
||||
|
||||
For rstyle {maxwell}, particle reflection is Maxwellian which means
|
||||
partially diffusive and partially specular ("Maxwell"_#Maxwell). A
|
||||
single accommodation coeff is specified which must be between 0.0 and
|
||||
1.0 inclusive. It determines the fraction of the collision which is
|
||||
diffusive versus specular. An accomodation coeff of 1.0 is fully
|
||||
diffusive; a coeff of 0.0 is fully specular.
|
||||
|
||||
For rstyle {cll}, particle collisons are computed by the
|
||||
Cercignani/Lampis model. See "CL"_#CL and "To"_#To for details.
|
||||
Three accommodations coefficient are specified. Each must be between
|
||||
0.0 and 1.0 inclusive. Two are velocity accommodation coefficients;
|
||||
one is a normal kinetic energy accommodation. The normal coeff is the
|
||||
one corresponding to the normal of the wall itself. For example if
|
||||
the wall is {ylo} or {yhi}, {accomx} and {accomz} are the tangential
|
||||
velocity accommodation coefficients, and {accomy} is the normal
|
||||
kinetic energy accommodation coefficient.
|
||||
|
||||
The optional {units} keyword determines the distance units used to
|
||||
define a wall position. A {box} value selects standard distance units
|
||||
as defined by the "units"_units.html command, e.g. Angstroms for units
|
||||
= real or metal. A {lattice} value means the distance units are in
|
||||
lattice spacings. The "lattice"_lattice.html command must have been
|
||||
previously used to define the lattice spacings.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix has the same limitations as the "fix
|
||||
wall/reflect"_fix_wall_reflect.html command. Any dimension (xyz) that
|
||||
has a wall must be non-periodic. It should not be used with rigid
|
||||
bodies such as those defined by the "fix rigid"_fix_rigid.html
|
||||
command. The wall velocity must lie on the same plane as the wall
|
||||
itself.
|
||||
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix wall/reflect"_fix_wall_reflect.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The default for the units keyword is lattice.
|
||||
|
||||
:line
|
||||
|
||||
:link(Maxwell)
|
||||
[(Maxwell)] J.C. Maxwell, Philos. Tans. Royal Soc. London, 157: 49-88
|
||||
(1867).
|
||||
|
||||
:link(CL)
|
||||
[(Cercignani)] C. Cercignani and M. Lampis. Trans. Theory
|
||||
Stat. Phys. 1, 2, 101 (1971).
|
||||
|
||||
:link(To)
|
||||
[(To)] Q.D. To, V.H. Vu, G. Lauriat, and
|
||||
C. Leonard. J. Math. Phys. 56, 103101 (2015).
|
||||
|
|
@ -29,7 +29,7 @@
|
|||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
enum{NONE=0,DIFFUSIVE=1,MAXWELL=2,CERCIGNANILAMPIS=3};
|
||||
enum{NONE,DIFFUSIVE,MAXWELL,CCL};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
|
|
@ -51,16 +51,16 @@ FixWallReflectStochastic(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
nwall = 0;
|
||||
int scaleflag = 1;
|
||||
reflectionstyle = NONE;
|
||||
rstyle = NONE;
|
||||
|
||||
if (strcmp(arg[3],"diffusive") == 0) {
|
||||
reflectionstyle = DIFFUSIVE;
|
||||
rstyle = DIFFUSIVE;
|
||||
arginc = 6;
|
||||
} else if (strcmp(arg[3],"maxwell") == 0) {
|
||||
reflectionstyle = MAXWELL;
|
||||
rstyle = MAXWELL;
|
||||
arginc = 7;
|
||||
} else if (strcmp(arg[3],"cercignanilampis") == 0) {
|
||||
reflectionstyle = CERCIGNANILAMPIS;
|
||||
} else if (strcmp(arg[3],"ccl") == 0) {
|
||||
rstyle = CCL;
|
||||
arginc = 9;
|
||||
} else error->all(FLERR,"Illegal fix wall/reflect/stochastic command");
|
||||
|
||||
|
|
@ -73,7 +73,7 @@ FixWallReflectStochastic(LAMMPS *lmp, int narg, char **arg) :
|
|||
if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) ||
|
||||
(strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) ||
|
||||
(strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) {
|
||||
if (iarg+2 > narg)
|
||||
if (iarg+arginc > narg)
|
||||
error->all(FLERR,"Illegal fix wall/reflect/stochastic command");
|
||||
|
||||
int newwall;
|
||||
|
|
@ -108,13 +108,15 @@ FixWallReflectStochastic(LAMMPS *lmp, int narg, char **arg) :
|
|||
int dim = wallwhich[nwall] / 2;
|
||||
if ((wallvel[nwall][dir] !=0) & (dir == dim))
|
||||
error->all(FLERR,"The wall velocity must be tangential");
|
||||
|
||||
if (reflectionstyle == CERCIGNANILAMPIS) {
|
||||
|
||||
// DIFFUSIVE = no accomodation coeffs
|
||||
// MAXWELL = one for all dimensions
|
||||
// CLL = one for each dimension
|
||||
|
||||
if (rstyle == CCL)
|
||||
wallaccom[nwall][dir]= force->numeric(FLERR,arg[iarg+dir+6]);
|
||||
} else if (reflectionstyle == MAXWELL) {
|
||||
// one accommodation coefficient for all directions
|
||||
else if (rstyle == MAXWELL)
|
||||
wallaccom[nwall][dir]= force->numeric(FLERR,arg[iarg+6]);
|
||||
}
|
||||
}
|
||||
|
||||
nwall++;
|
||||
|
|
@ -227,7 +229,7 @@ void FixWallReflectStochastic::wall_particle(int m, int which, double coord)
|
|||
|
||||
// only needed for Maxwell model
|
||||
|
||||
if (reflectionstyle == MAXWELL) difftest = random->uniform();
|
||||
if (rstyle == MAXWELL) difftest = random->uniform();
|
||||
|
||||
for (dir = 0; dir < 3; dir++) {
|
||||
|
||||
|
|
@ -237,14 +239,14 @@ void FixWallReflectStochastic::wall_particle(int m, int which, double coord)
|
|||
|
||||
// diffusive reflection
|
||||
|
||||
if (reflectionstyle == DIFFUSIVE) {
|
||||
if (rstyle == DIFFUSIVE) {
|
||||
if (dir != dim)
|
||||
v[i][dir] = wallvel[m][dir] + random->gaussian(0,factor);
|
||||
else v[i][dir] = sign*random->rayleigh(factor);
|
||||
|
||||
// Maxwell reflection
|
||||
|
||||
} else if (reflectionstyle == MAXWELL) {
|
||||
} else if (rstyle == MAXWELL) {
|
||||
if (difftest < wallaccom[m][dir]) {
|
||||
if (dir != dim)
|
||||
v[i][dir] = wallvel[m][dir] + random->gaussian(0,factor);
|
||||
|
|
@ -255,7 +257,7 @@ void FixWallReflectStochastic::wall_particle(int m, int which, double coord)
|
|||
|
||||
// Cercignani Lampis reflection
|
||||
|
||||
} else if (reflectionstyle == CERCIGNANILAMPIS) {
|
||||
} else if (rstyle == CCL) {
|
||||
if (dir != dim)
|
||||
v[i][dir] = wallvel[m][dir] +
|
||||
random->gaussian((1-wallaccom[m][dir]) *
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ class FixWallReflectStochastic : public FixWallReflect {
|
|||
private:
|
||||
int seedfix;
|
||||
double walltemp[6],wallvel[6][3],wallaccom[6][3];
|
||||
int reflectionstyle;
|
||||
int rstyle;
|
||||
|
||||
class RanMars *random;
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue