From a66aa5e0f65163397117e1eea74fd40d44a6d2dc Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 18 Nov 2009 00:30:50 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3426 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.txt | 6 +- doc/fix_wall.html | 175 ++++++++++++++++++++++++++++++++++++++ doc/fix_wall.txt | 164 +++++++++++++++++++++++++++++++++++ doc/fix_wall_colloid.html | 94 -------------------- doc/fix_wall_colloid.txt | 89 ------------------- doc/fix_wall_lj126.html | 113 ------------------------ doc/fix_wall_lj126.txt | 98 --------------------- doc/fix_wall_lj93.html | 114 ------------------------- doc/fix_wall_lj93.txt | 99 --------------------- 9 files changed, 342 insertions(+), 610 deletions(-) create mode 100644 doc/fix_wall.html create mode 100644 doc/fix_wall.txt delete mode 100644 doc/fix_wall_colloid.html delete mode 100644 doc/fix_wall_colloid.txt delete mode 100644 doc/fix_wall_lj126.html delete mode 100644 doc/fix_wall_lj126.txt delete mode 100644 doc/fix_wall_lj93.html delete mode 100644 doc/fix_wall_lj93.txt diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 7a81bfffe3..7e06879668 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -441,10 +441,10 @@ of each style or click on the style itself for a full description: "ttm"_fix_ttm.html, "viscosity"_fix_viscosity.html, "viscous"_fix_viscous.html, -"wall/colloid"_fix_wall_colloid.html, +"wall/colloid"_fix_wall.html, "wall/gran"_fix_wall_gran.html, -"wall/lj126"_fix_wall_lj126.html, -"wall/lj93"_fix_wall_lj93.html, +"wall/lj126"_fix_wall.html, +"wall/lj93"_fix_wall.html, "wall/reflect"_fix_wall_reflect.html, "wiggle"_fix_wiggle.html :tb(c=8,ea=c) diff --git a/doc/fix_wall.html b/doc/fix_wall.html new file mode 100644 index 0000000000..7b05bd158c --- /dev/null +++ b/doc/fix_wall.html @@ -0,0 +1,175 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

fix wall/lj93 command +

+

fix wall/lj126 command +

+

fix wall/colloid command +

+

Syntax: +

+
fix ID group-ID style keyword values ... 
+
+ +

Examples: +

+
fix wallhi all wall/lj93 xhi 10.0 1.0 1.0 2.5
+fix wallhi all wall/lj126 xhi 10.0 1.0 1.0 2.5 vel 1.0
+fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 
+
+

Description: +

+

Bound the simulation domain on one or more of its faces with a flat +wall that interacts with the atoms in the group by generating a force +on the atom in a direction perpendicular to the wall. The energy E of +wall-particle interactions depends on the style. +

+

For style wall/lj93, the energy is given by the 9/3 potential: +

+
+
+

For style wall/lj126, the energy is given by the 12/6 potential: +

+
+
+

For style wall/colloid, the energy is given by an integrated form of +the pair_style colloid potential: +

+
+
+

In all cases, r is the distance from the particle to the wall +coord, and Rc is the cutoff distance at which the particle and +wall no longer interact, as specified in the command. The energy of +the wall potential is shifted so that the energy of the wall-particle +interaction is 0.0 at the cutoff distance. +

+

For the wall/lj93 and wall/lj126 styles, epsilon and sigma are +the usual Lennard-Jones parameters, which determine the strength and +size of the particle as it interacts with the wall. Note that this +sigma may be different than any sigma values defined for a pair +style that computes particle-particle interactions. +

+

The wall/lj93 interaction is derived by integrating over a 3d +half-lattice of Lennard-Jones 12/6 particles. The wall/lj126 +interaction is effectively a harder, more repulsive wall interaction. +

+

For the wall/colloid style, epsilon is effectively a Hamaker +constant for the colloid-wall interaction, R is the radius of the +colloid particle, D is the distance from the surface of the colloid +particle to the wall (r-R), and sigma is the size of the constituent +LJ particle inside the colloid particle. Note that the cutoff +distance Rc in this case is the distance from the colloid particle +center to the wall. +

+

The wall/colloid interaction is derived by integrating over +constituent LJ particles of size sigma within the colloid particle +and a 3d half-lattice of Lennard-Jones 12/6 particles with the same +sigma in the wall. +

+

If the vel keyword is specified, the position of all walls will move +during the simulation in a perpendicular direction, based on their +initial position (coord), the specified velocity (vel), and the time +elapsed since the beginning of the simulation. See the note below +about making a wall move continuously across multiple runs. A +positive velocity means each wall moves inward, towards the center of +the box. I.e. an xlo wall will move in the +x direction; an xhi +wall will move in the -x direction. A negative velocity means each +wall moves outward, away from the center of the box. If you want +different walls to move with different velocities, then you need to +use multiple fix wall commands. +

+

If the wiggle keyword is specified, the position of all walls will +oscillate sinusoidally during the simulation in the perpendicular +direction, according to the equation: +

+
position = pos0 + A sin (omega * delta) 
+
+

where pos0 is the position at the time the beginning of the +simulation, A is the amplitude, omega is 2 PI / period, and +delta is the time elapsed since the beginning of the simulation. +See the note below about making a wall oscillate continuously across +multiple runs. A positive amplitude means each wall initially moves +inward, towards the center of the box. I.e. an xlo wall will move +initially in the +x direction; an xhi wall will move in the -x +direction. A negative velocity means each wall moves initially +outward, away from the center of the box. If you want different walls +to oscillate with different amplitudes or periods, then you need to +use multiple fix wall commands. +

+

Restart, fix_modify, output, run start/stop, minimize info: +

+

No information about this fix is written to binary restart +files. +

+

The fix_modify energy option is supported by this +fix to add the energy of interaction between atoms and each wall to +the system's potential energy as part of thermodynamic +output. +

+

This fix computes a scalar energy and a 3-vector of forces (on the +walls), which can be accessed by various output +commands. The scalar and vector values +calculated by this fix are "extensive", meaning they scale with the +number of atoms in the simulation. Note that if you define multiple +walls, then the energy and force will be summed over all the walls. +If you want the energy/force on a per-wall basis, you need to use +multiple fix wall commands. +

+

This fix can change the position of each wall, due to the vel or +wiggle keywords, continuously over multiple runs, using the start +and stop keywords of the run command. If you do not do +this, the wall position will be reset to coord at the beginning of +each run. +

+

The forces due to this fix are imposed during an energy minimization, +invoked by the minimize command. +

+

IMPORTANT NOTE: If you want the atom/wall interaction energy to be +included in the total potential energy of the system (the quantity +being minimized), you MUST enable the fix_modify +energy option for this fix. +

+

Restrictions: +

+

Any dimension (xyz) that has a wall must be non-periodic. +

+

You cannot use both the vel and wiggle keywords together. +

+

Related commands: +

+

>fix wall/reflect wall/gran +

+

Default: +

+

The option defaults are no velocity and no wiggle. +

+ diff --git a/doc/fix_wall.txt b/doc/fix_wall.txt new file mode 100644 index 0000000000..1c4728a6d6 --- /dev/null +++ b/doc/fix_wall.txt @@ -0,0 +1,164 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix wall/lj93 command :h3 +fix wall/lj126 command :h3 +fix wall/colloid command :h3 + +[Syntax:] + +fix ID group-ID style keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +style = {wall/lj93} or {wall/lj126} or {wall/colloid} :l +one or more keyword/value pairs may be appended :l +keyword = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} or {vel} or {wiggle} :l + {xlo}, {xhi}, {ylo}, {yhi}, {zlo}, {zhi} values = coord epsilon sigma cutoff + coord = position of wall (distance units) + epsilon = strength factor for wall-particle interaction (energy units) + sigma = size factor for wall-particle interaction (distance units) + cutoff = distance from wall at which wall-particle interaction is cut off (distance units) + {vel} value = v + v = velocity of wall in perpendicular direction (velocity units) + {wiggle} values = amplitude period + amplitude = size of oscillation (distance units) + period = time of oscillation (time units) :pre +:ule + +[Examples:] + +fix wallhi all wall/lj93 xhi 10.0 1.0 1.0 2.5 +fix wallhi all wall/lj126 xhi 10.0 1.0 1.0 2.5 vel 1.0 +fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 :pre + +[Description:] + +Bound the simulation domain on one or more of its faces with a flat +wall that interacts with the atoms in the group by generating a force +on the atom in a direction perpendicular to the wall. The energy of +wall-particle interactions depends on the style. + +For style {wall/lj93}, the energy E is given by the 9/3 potential: + +:c,image(Eqs/fix_wall_lj93.jpg) + +For style {wall/lj126}, the energy E is given by the 12/6 potential: + +:c,image(Eqs/pair_lj.jpg) + +For style {wall/colloid}, the energy E is given by an integrated form of +the "pair_style colloid"_pair_colloid.html potential: + +:c,image(Eqs/fix_wall_colloid.jpg) + +In all cases, {r} is the distance from the particle to the wall at +position {coord}, and Rc is the {cutoff} distance at which the +particle and wall no longer interact. The energy of the wall +potential is shifted so that the wall-particle interaction energy is +0.0 at the cutoff distance. + +For the {wall/lj93} and {wall/lj126} styles, {epsilon} and {sigma} are +the usual Lennard-Jones parameters, which determine the strength and +size of the particle as it interacts with the wall. Note that this +{epsilon} and {sigma} may be different than any {epsilon} or {sigma} +values defined for a pair style that computes particle-particle +interactions. + +The {wall/lj93} interaction is derived by integrating over a 3d +half-lattice of Lennard-Jones 12/6 particles. The {wall/lj126} +interaction is effectively a harder, more repulsive wall interaction. + +For the {wall/colloid} style, {epsilon} is effectively a Hamaker +constant for the colloid-wall interaction, {R} is the radius of the +colloid particle, {D} is the distance from the surface of the colloid +particle to the wall (r-R), and {sigma} is the size of the constituent +LJ particle inside the colloid particle. Note that the cutoff +distance Rc in this case is the distance from the colloid particle +center to the wall. + +The {wall/colloid} interaction is derived by integrating over +constituent LJ particles of size {sigma} within the colloid particle +and a 3d half-lattice of Lennard-Jones 12/6 particles of size {sigma} +in the wall. + +If the {vel} keyword is specified, the position of all walls will move +during the simulation in a perpendicular direction, based on their +initial {coord} position, the specified velocity {vel}, and the time +elapsed since the beginning of the simulation. See the note below +about making a wall move continuously across multiple runs. A +positive velocity means each wall moves inward, towards the center of +the box. I.e. an {xlo} wall will move in the +x direction and an +{xhi} wall will move in the -x direction. A negative velocity means +each wall moves outward, away from the center of the box. If you want +different walls to move with different velocities, then you need to +use multiple fix wall commands. + +If the {wiggle} keyword is specified, the position of all walls will +oscillate sinusoidally during the simulation in the perpendicular +direction, according to the equation: + +position = pos0 + A sin (omega * delta) :pre + +where {pos0} is the position at the beginning of the simulation, {A} +is the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the +time elapsed since the beginning of the simulation. See the note +below about making a wall oscillate continuously across multiple runs. +A positive amplitude means each wall initially moves inward, towards +the center of the box. I.e. an {xlo} wall will move initially in the ++x direction and an {xhi} wall will move initially in the -x +direction. A negative velocity means each wall moves initially +outward, away from the center of the box. If you want different walls +to oscillate with different amplitudes or periods, then you need to +use multiple fix wall commands. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy of interaction between atoms and each wall to +the system's potential energy as part of "thermodynamic +output"_thermo_style.html. + +This fix computes a scalar energy and a 3-vector of forces (on the +walls), which can be accessed by various "output +commands"_Section_howto.html#4_15. The scalar and vector values +calculated by this fix are "extensive", meaning they scale with the +number of atoms in the simulation. Note that if you define multiple +walls, then the energy and force will be summed over all the walls. +If you want the energy/force on a per-wall basis, you need to use +multiple fix wall commands. + +This fix can change the position of each wall, due to the {vel} or +{wiggle} keywords, continuously over multiple runs, using the {start} +and {stop} keywords of the "run"_run.html command. If you do not do +this, the wall position will be reset to {coord} at the beginning of +each run. + +The forces due to this fix are imposed during an energy minimization, +invoked by the "minimize"_minimize.html command. + +IMPORTANT NOTE: If you want the atom/wall interaction energy to be +included in the total potential energy of the system (the quantity +being minimized), you MUST enable the "fix_modify"_fix_modify.html +{energy} option for this fix. + +[Restrictions:] + +Any dimension (xyz) that has a wall must be non-periodic. + +You cannot use both the {vel} and {wiggle} keywords together. + +[Related commands:] + +"fix wall/reflect"_fix_wall_reflect.html wall/gran"_fix_wall_gran.html + +[Default:] + +The option defaults are no velocity and no wiggle. diff --git a/doc/fix_wall_colloid.html b/doc/fix_wall_colloid.html deleted file mode 100644 index 6696235e89..0000000000 --- a/doc/fix_wall_colloid.html +++ /dev/null @@ -1,94 +0,0 @@ - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
- - - - - - -
- -

fix wall/colloid command -

-

Syntax: -

-
fix ID group-ID wall/colloid style coord A sigma cutoff 
-
- -

Examples: -

-
fix wallhi all wall/colloid xhi 10.0 20.0 1.0 2.5
-fix leftwall all wall/colloid zlo 0.0 10.0 1.0 0.858 
-
-

Description: -

-

Bound the simulation domain on one of its faces with a wall of -Lennard-Jones particles that interacts with finite-size colloidal -particles in the group. The energy E of wall-colloid interactions is -given by an integrated form of the pair_style -colloid potential -

-
-
-

where A is the specified Hamaker constant for the colloid-wall -interaction, r is the distance from the center of the particle to -the wall coord, R is the radius of the colloid particle, D is -the distance from the surface of the colloid particle to the wall -(r-R), sigma is the size of the constituent LJ particle integrated -over as described below, and Rc is the cutoff value specified in the -fix command and is the distance from the particle center to the wall. -

-

This colloid/wall interaction is derived by integrating over both the -constituent LJ particles in the colloid particle and a 3d half-lattice -of Lennard-Jones 12-6 particles in the wall. -

-

The wall potential is shifted so that the energy of a wall-particle -interaction is 0.0 at the cutoff distance. -

-

Restart, fix_modify, output, run start/stop, minimize info: -

-

No information about this fix is written to binary restart -files. -

-

The fix_modify energy option is supported by this -fix to add the energy of interaction between atoms and the wall to the -system's potential energy as part of thermodynamic -output. -

-

This fix computes a scalar energy and a 3-vector of forces (on the -wall), which can be accessed by various output -commands. The scalar and vector values -calculated by this fix are "extensive", meaning they scale with the -number of atoms in the simulation. -

-

No parameter of this fix can be used with the start/stop keywords of -the run command. -

-

The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

-

IMPORTANT NOTE: If you want the atom/wall interaction energy to be -included in the total potential energy of the system (the quantity -being minimized), you MUST enable the fix_modify -energy option for this fix. -

-

Restrictions: -

-

Any dimension (xyz) that has a colloid wall must be non-periodic. -

-

Related commands: -

-

fix wall/lj93, pair_style -colloid -

-

Default: none -

- diff --git a/doc/fix_wall_colloid.txt b/doc/fix_wall_colloid.txt deleted file mode 100644 index 4c4513a05e..0000000000 --- a/doc/fix_wall_colloid.txt +++ /dev/null @@ -1,89 +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,Section_commands.html#comm) - -:line - -fix wall/colloid command :h3 - -[Syntax:] - -fix ID group-ID wall/colloid style coord A sigma cutoff :pre - -ID, group-ID are documented in "fix"_fix.html command -wall/colloid = style name of this fix command -style = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} -coord = position of wall (distance units) -A = Hamaker constant for colloid-wall interactions (energy units) -sigma = size of constituent LJ particle that integration is done over (distance units) -cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :ul - -[Examples:] - -fix wallhi all wall/colloid xhi 10.0 20.0 1.0 2.5 -fix leftwall all wall/colloid zlo 0.0 10.0 1.0 0.858 :pre - -[Description:] - -Bound the simulation domain on one of its faces with a wall of -Lennard-Jones particles that interacts with finite-size colloidal -particles in the group. The energy E of wall-colloid interactions is -given by an integrated form of the "pair_style -colloid"_pair_colloid.html potential - -:c,image(Eqs/fix_wall_colloid.jpg) - -where A is the specified Hamaker constant for the colloid-wall -interaction, {r} is the distance from the center of the particle to -the wall {coord}, {R} is the radius of the colloid particle, {D} is -the distance from the surface of the colloid particle to the wall -(r-R), sigma is the size of the constituent LJ particle integrated -over as described below, and Rc is the cutoff value specified in the -fix command and is the distance from the particle center to the wall. - -This colloid/wall interaction is derived by integrating over both the -constituent LJ particles in the colloid particle and a 3d half-lattice -of Lennard-Jones 12-6 particles in the wall. - -The wall potential is shifted so that the energy of a wall-particle -interaction is 0.0 at the cutoff distance. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy of interaction between atoms and the wall to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes a scalar energy and a 3-vector of forces (on the -wall), which can be accessed by various "output -commands"_Section_howto.html#4_15. The scalar and vector values -calculated by this fix are "extensive", meaning they scale with the -number of atoms in the simulation. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -IMPORTANT NOTE: If you want the atom/wall interaction energy to be -included in the total potential energy of the system (the quantity -being minimized), you MUST enable the "fix_modify"_fix_modify.html -{energy} option for this fix. - -[Restrictions:] - -Any dimension (xyz) that has a colloid wall must be non-periodic. - -[Related commands:] - -"fix wall/lj93"_fix_wall_lj93.html, "pair_style -colloid"_pair_colloid.html - -[Default:] none diff --git a/doc/fix_wall_lj126.html b/doc/fix_wall_lj126.html deleted file mode 100644 index faa5e0dfab..0000000000 --- a/doc/fix_wall_lj126.html +++ /dev/null @@ -1,113 +0,0 @@ - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
- - - - - - -
- -

fix wall/lj126 command -

-

Syntax: -

-
fix ID group-ID wall/lj126 style coord epsilon sigma cutoff keyword values ... 
-
- -

Examples: -

-
fix wallhi all wall/lj126 xhi 10.0 1.0 1.0 1.12
-fix leftwall all wall/lj126 zlo 0.0  1.0 1.0 0.858 vel 1.0 
-
-

Description: -

-

Bound the simulation domain on one of its faces with a Lennard-Jones -wall that interacts with the atoms in the group. The energy E of -wall-particle interactions is given by the 12-6 potential -

-
-
-

where r is the distance from the particle to the wall coord, and -epsilon and sigma are the usual LJ parameters. Rc is the cutoff value -specified in the command. This interaction provides a harder, more -repulsive interaction with the wall than the softer 9-3 potential -provided by the fix wall/lj93 command. -

-

The wall potential is shifted so that the energy of a wall-particle -interaction is 0.0 at the cutoff distance. -

-

If the vel keyword is specified, the position of wall will move -during the simulation, based on its initial position (coord), the -specified velocity (vel), and the time elapsed since the beginning of -the simulation. Xlo or xhi walls move in the x direction with -whatever sign you give the v argument. Ditto for y and z walls. -See the note below about making the wall move continuously across -multiple runs. -

-

Restart, fix_modify, output, run start/stop, minimize info: -

-

No information about this fix is written to binary restart -files. -

-

The fix_modify energy option is supported by this -fix to add the energy of interaction between atoms and the wall to the -system's potential energy as part of thermodynamic -output. -

-

This fix computes a scalar energy and a 3-vector of forces (on the -wall), which can be accessed by various output -commands. The scalar and vector values -calculated by this fix are "extensive", meaning they scale with the -number of atoms in the simulation. -

-

This fix can change the position of the wall, due to the vel -keyword, continuously over multiple runs, using the start and stop -keywords of the run command. If you do not do this, the -wall position will be reset to coord at the beginning of each run. -

-

The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

-

IMPORTANT NOTE: If you want the atom/wall interaction energy to be -included in the total potential energy of the system (the quantity -being minimized), you MUST enable the fix_modify -energy option for this fix. -

-

Restrictions: -

-

Any dimension (xyz) that has a LJ 12/6 wall must be non-periodic. -

-

Related commands: -

-

fix wall/reflect, fix -wall/lj93 -

-

Default: -

-

The option defaults are vel = 0. -

- diff --git a/doc/fix_wall_lj126.txt b/doc/fix_wall_lj126.txt deleted file mode 100644 index d7e6252ed5..0000000000 --- a/doc/fix_wall_lj126.txt +++ /dev/null @@ -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,Section_commands.html#comm) - -:line - -fix wall/lj126 command :h3 - -[Syntax:] - -fix ID group-ID wall/lj126 style coord epsilon sigma cutoff keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -wall/lj126 = style name of this fix command :l -style = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l -coord = position of wall (distance units) :l -epsilon = Lennard-Jones epsilon for wall-particle interaction (energy units) :l -sigma = Lennard-Jones sigma for wall-particle interaction (distance units) :l -cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l -one or more keyword/value pairs may be appended :l -keyword = {vel} :l - {vel} args = v - v = velocity of wall in perpendicular direction (velocity units) :pre -:ule - -[Examples:] - -fix wallhi all wall/lj126 xhi 10.0 1.0 1.0 1.12 -fix leftwall all wall/lj126 zlo 0.0 1.0 1.0 0.858 vel 1.0 :pre - -[Description:] - -Bound the simulation domain on one of its faces with a Lennard-Jones -wall that interacts with the atoms in the group. The energy E of -wall-particle interactions is given by the 12-6 potential - -:c,image(Eqs/pair_lj.jpg) - -where {r} is the distance from the particle to the wall {coord}, and -epsilon and sigma are the usual LJ parameters. Rc is the cutoff value -specified in the command. This interaction provides a harder, more -repulsive interaction with the wall than the softer 9-3 potential -provided by the "fix wall/lj93"_fix_wall_lj93.html command. - -The wall potential is shifted so that the energy of a wall-particle -interaction is 0.0 at the cutoff distance. - -If the {vel} keyword is specified, the position of wall will move -during the simulation, based on its initial position (coord), the -specified velocity (vel), and the time elapsed since the beginning of -the simulation. {Xlo} or {xhi} walls move in the x direction with -whatever sign you give the {v} argument. Ditto for {y} and {z} walls. -See the note below about making the wall move continuously across -multiple runs. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy of interaction between atoms and the wall to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes a scalar energy and a 3-vector of forces (on the -wall), which can be accessed by various "output -commands"_Section_howto.html#4_15. The scalar and vector values -calculated by this fix are "extensive", meaning they scale with the -number of atoms in the simulation. - -This fix can change the position of the wall, due to the {vel} -keyword, continuously over multiple runs, using the {start} and {stop} -keywords of the "run"_run.html command. If you do not do this, the -wall position will be reset to {coord} at the beginning of each run. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -IMPORTANT NOTE: If you want the atom/wall interaction energy to be -included in the total potential energy of the system (the quantity -being minimized), you MUST enable the "fix_modify"_fix_modify.html -{energy} option for this fix. - -[Restrictions:] - -Any dimension (xyz) that has a LJ 12/6 wall must be non-periodic. - -[Related commands:] - -"fix wall/reflect"_fix_wall_reflect.html, "fix -wall/lj93"_fix_wall_lj93.html - -[Default:] - -The option defaults are vel = 0. diff --git a/doc/fix_wall_lj93.html b/doc/fix_wall_lj93.html deleted file mode 100644 index 2357528365..0000000000 --- a/doc/fix_wall_lj93.html +++ /dev/null @@ -1,114 +0,0 @@ - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
- - - - - - -
- -

fix wall/lj93 command -

-

Syntax: -

-
fix ID group-ID wall/lj93 style coord epsilon sigma cutoff keyword values ... 
-
- -

Examples: -

-
fix wallhi all wall/lj93 xhi 10.0 1.0 1.0 2.5
-fix leftwall all wall/lj93 zlo 0.0  1.0 1.0 0.858 vel 1.0 
-
-

Description: -

-

Bound the simulation domain on one of its faces with a Lennard-Jones -wall that interacts with the atoms in the group. The energy E of -wall-particle interactions is given by the 9-3 potential -

-
-
-

where r is the distance from the particle to the wall coord, and -epsilon and sigma are the usual LJ parameters. Rc is the cutoff value -specified in the command. This interaction is derived by integrating -over a 3d half-lattice of Lennard-Jones 12-6 particles. A harder, -more repulsive wall interaction can be computed by using the fix -wall/lj126 command. -

-

The wall potential is shifted so that the energy of a wall-particle -interaction is 0.0 at the cutoff distance. -

-

If the vel keyword is specified, the position of wall will move -during the simulation, based on its initial position (coord), the -specified velocity (vel), and the time elapsed since the beginning of -the simulation. Xlo or xhi walls move in the x direction with -whatever sign you give the v argument. Ditto for y and z walls. -See the note below about making the wall move continuously across -multiple runs. -

-

Restart, fix_modify, output, run start/stop, minimize info: -

-

No information about this fix is written to binary restart -files. -

-

The fix_modify energy option is supported by this -fix to add the energy of interaction between atoms and the wall to the -system's potential energy as part of thermodynamic -output. -

-

This fix computes a scalar energy and a 3-vector of forces (on the -wall), which can be accessed by various output -commands. The scalar and vector values -calculated by this fix are "extensive", meaning they scale with the -number of atoms in the simulation. -

-

This fix can change the position of the wall, due to the vel -keyword, continuously over multiple runs, using the start and stop -keywords of the run command. If you do not do this, the -wall position will be reset to coord at the beginning of each run. -

-

The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

-

IMPORTANT NOTE: If you want the atom/wall interaction energy to be -included in the total potential energy of the system (the quantity -being minimized), you MUST enable the fix_modify -energy option for this fix. -

-

Restrictions: -

-

Any dimension (xyz) that has a LJ 9/3 wall must be non-periodic. -

-

Related commands: -

-

fix wall/reflect, fix -wall/lj126 -

-

Default: -

-

The option defaults are vel = 0. -

- diff --git a/doc/fix_wall_lj93.txt b/doc/fix_wall_lj93.txt deleted file mode 100644 index 41ab0ef552..0000000000 --- a/doc/fix_wall_lj93.txt +++ /dev/null @@ -1,99 +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,Section_commands.html#comm) - -:line - -fix wall/lj93 command :h3 - -[Syntax:] - -fix ID group-ID wall/lj93 style coord epsilon sigma cutoff keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -wall/lj93 = style name of this fix command :l -style = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l -coord = position of wall (distance units) :l -epsilon = Lennard-Jones epsilon for wall-particle interaction (energy units) :l -sigma = Lennard-Jones sigma for wall-particle interaction (distance units) :l -cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l -one or more keyword/value pairs may be appended :l -keyword = {vel} :l - {vel} args = v - v = velocity of wall in perpendicular direction (velocity units) :pre -:ule - -[Examples:] - -fix wallhi all wall/lj93 xhi 10.0 1.0 1.0 2.5 -fix leftwall all wall/lj93 zlo 0.0 1.0 1.0 0.858 vel 1.0 :pre - -[Description:] - -Bound the simulation domain on one of its faces with a Lennard-Jones -wall that interacts with the atoms in the group. The energy E of -wall-particle interactions is given by the 9-3 potential - -:c,image(Eqs/fix_wall_lj93.jpg) - -where {r} is the distance from the particle to the wall {coord}, and -epsilon and sigma are the usual LJ parameters. Rc is the cutoff value -specified in the command. This interaction is derived by integrating -over a 3d half-lattice of Lennard-Jones 12-6 particles. A harder, -more repulsive wall interaction can be computed by using the "fix -wall/lj126"_fix_wall_lj126.html command. - -The wall potential is shifted so that the energy of a wall-particle -interaction is 0.0 at the cutoff distance. - -If the {vel} keyword is specified, the position of wall will move -during the simulation, based on its initial position (coord), the -specified velocity (vel), and the time elapsed since the beginning of -the simulation. {Xlo} or {xhi} walls move in the x direction with -whatever sign you give the {v} argument. Ditto for {y} and {z} walls. -See the note below about making the wall move continuously across -multiple runs. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy of interaction between atoms and the wall to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes a scalar energy and a 3-vector of forces (on the -wall), which can be accessed by various "output -commands"_Section_howto.html#4_15. The scalar and vector values -calculated by this fix are "extensive", meaning they scale with the -number of atoms in the simulation. - -This fix can change the position of the wall, due to the {vel} -keyword, continuously over multiple runs, using the {start} and {stop} -keywords of the "run"_run.html command. If you do not do this, the -wall position will be reset to {coord} at the beginning of each run. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -IMPORTANT NOTE: If you want the atom/wall interaction energy to be -included in the total potential energy of the system (the quantity -being minimized), you MUST enable the "fix_modify"_fix_modify.html -{energy} option for this fix. - -[Restrictions:] - -Any dimension (xyz) that has a LJ 9/3 wall must be non-periodic. - -[Related commands:] - -"fix wall/reflect"_fix_wall_reflect.html, "fix -wall/lj126"_fix_wall_lj126.html - -[Default:] - -The option defaults are vel = 0.