From f62d15de78d77e52f43ab5f536ae9ffe0ba40c59 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 3 Dec 2009 17:57:33 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3482 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 12 +-- doc/Section_commands.txt | 4 +- doc/fix.html | 4 +- doc/fix.txt | 4 +- doc/fix_coord_original.html | 5 +- doc/fix_coord_original.txt | 5 +- doc/fix_gravity.html | 17 ++- doc/fix_gravity.txt | 15 ++- doc/fix_move.html | 206 ++++++++++++++++++++++++++++++++++++ doc/fix_move.txt | 195 ++++++++++++++++++++++++++++++++++ doc/fix_wall_gran.html | 23 ++-- doc/fix_wall_gran.txt | 21 ++-- doc/variable.html | 23 ++-- doc/variable.txt | 23 ++-- 14 files changed, 495 insertions(+), 62 deletions(-) create mode 100644 doc/fix_move.html create mode 100644 doc/fix_move.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 9b933e20a4..82527f4a03 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -323,12 +323,12 @@ of each style or click on the style itself for a full description: addforceaveforceave/atomave/spatialave/timebond/breakbond/createbond/swap box/relaxcomcoord/originaldeformdepositdragdt/resetefield enforce2devaporatefreezegravitygyrationheatindentlangevin -lineforcemsdmomentumnphnptnpt/aspherenpt/spherenve -nve/aspherenve/limitnve/noforcenve/spherenvtnvt/aspherenvt/sllodnvt/sphere -orient/fccplaneforcepoemspourpress/berendsenprintrdfreax/bonds -recenterrigidsetforceshakespringspring/rgspring/selftemp/berendsen -temp/rescalethermal/conductivitytmdttmviscosityviscouswall/colloidwall/gran -wall/lj126wall/lj93wall/reflectwiggle +lineforcemsdmomentummovenphnptnpt/aspherenpt/sphere +nvenve/aspherenve/limitnve/noforcenve/spherenvtnvt/aspherenvt/sllod +nvt/sphereorient/fccplaneforcepoemspourpress/berendsenprintrdf +reax/bondsrecenterrigidsetforceshakespringspring/rgspring/self +temp/berendsentemp/rescalethermal/conductivitytmdttmviscosityviscouswall/colloid +wall/granwall/lj126wall/lj93wall/reflect

These are fix styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 0e1be8d521..24cf75f6ce 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -406,6 +406,7 @@ of each style or click on the style itself for a full description: "lineforce"_fix_lineforce.html, "msd"_fix_msd.html, "momentum"_fix_momentum.html, +"move"_fix_move.html, "nph"_fix_nph.html, "npt"_fix_npt.html, "npt/asphere"_fix_npt_asphere.html, @@ -445,8 +446,7 @@ of each style or click on the style itself for a full description: "wall/gran"_fix_wall_gran.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) +"wall/reflect"_fix_wall_reflect.html :tb(c=8,ea=c) These are fix styles contributed by users, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#2_3. diff --git a/doc/fix.html b/doc/fix.html index ed409c6e71..79e34a3f9f 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -130,6 +130,7 @@ list of fix styles available in LAMMPS:

  • lineforce - constrain atoms to move in a line
  • msd - compute mean-squared displacement (i.e. diffusion coefficient)
  • momentum - zero the linear and/or angular momentum of a group of atoms +
  • move - move atoms in a prescribed fashion
  • nph - constant NPH time integration via Nose/Hoover
  • npt - constant NPT time integration via Nose/Hoover
  • npt/asphere - NPT for aspherical particles @@ -168,8 +169,7 @@ list of fix styles available in LAMMPS:
  • wall/gran - frictional wall(s) for granular simulations
  • wall/lj126 - Lennard-Jones 12-6 wall
  • wall/lj93 - Lennard-Jones 9-3 wall -
  • wall/reflect - reflecting wall(s) -
  • wiggle - oscillate walls and frozen atoms +
  • wall/reflect - reflecting wall(s)

    There are also additional fix styles submitted by users which are included in the LAMMPS distribution. The list of these with links to diff --git a/doc/fix.txt b/doc/fix.txt index 89540b1286..0c089348f8 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -129,6 +129,7 @@ list of fix styles available in LAMMPS: (i.e. diffusion coefficient) "momentum"_fix_momentum.html - zero the linear and/or angular momentum \ of a group of atoms +"move"_fix_move.html - move atoms in a prescribed fashion "nph"_fix_nph.html - constant NPH time integration via Nose/Hoover "npt"_fix_npt.html - constant NPT time integration via Nose/Hoover "npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles @@ -177,8 +178,7 @@ list of fix styles available in LAMMPS: "wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations "wall/lj126"_fix_wall_lj126.html - Lennard-Jones 12-6 wall "wall/lj93"_fix_wall_lj93.html - Lennard-Jones 9-3 wall -"wall/reflect"_fix_wall_reflect.html - reflecting wall(s) -"wiggle"_fix_wiggle.html - oscillate walls and frozen atoms :ul +"wall/reflect"_fix_wall_reflect.html - reflecting wall(s) :ul There are also additional fix styles submitted by users which are included in the LAMMPS distribution. The list of these with links to diff --git a/doc/fix_coord_original.html b/doc/fix_coord_original.html index 7538a9b3cd..d3c32599b7 100644 --- a/doc/fix_coord_original.html +++ b/doc/fix_coord_original.html @@ -59,8 +59,9 @@ fix.

    This fix produces a per-atom vector which can be accessed by various output commands. The length of the vector -for each atom is 3, and the components store the x,y,z coords of each -atom. The per-atom values be accessed on any timestep. +for each atom is 3, and the components store the original unwrapped +x,y,z coords of each atom. The per-atom values be accessed on any +timestep.

    No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy diff --git a/doc/fix_coord_original.txt b/doc/fix_coord_original.txt index d4f3158045..e1d206465d 100644 --- a/doc/fix_coord_original.txt +++ b/doc/fix_coord_original.txt @@ -56,8 +56,9 @@ fix. This fix produces a per-atom vector which can be accessed by various "output commands"_Section_howto.html#4_15. The length of the vector -for each atom is 3, and the components store the x,y,z coords of each -atom. The per-atom values be accessed on any timestep. +for each atom is 3, and the components store the original unwrapped +x,y,z coords of each atom. The per-atom values be accessed on any +timestep. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/fix_gravity.html b/doc/fix_gravity.html index 28865d7ada..a964083388 100644 --- a/doc/fix_gravity.html +++ b/doc/fix_gravity.html @@ -79,8 +79,9 @@ the gradient arguments are in full rotations per time unit. E.g. a timestep of 0.001 and a gradient of 0.1 means the acceleration vector would rotate thru 360 degrees every 10,000 timesteps. For the time-dependent case, the initial direction of the acceleration vector -is phi,theta at the time the fix is specified. For 2d systems, phi -and phi_grad are ignored. +is phi,theta at the beginning of the simulation. For 2d systems, +phi and phi_grad are ignored. See the note below about making the +acceleration vector rotate continuously across multiple runs.

    Style vector imposes an acceleration in the vector direction given by (x,y,z). For 2d systems, the z component is ignored. @@ -91,9 +92,15 @@ by (x,y,z). For 2d systems, the z component is ignored. files. None of the fix_modify options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various output -commands. No parameter of this fix can be -used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. +commands. +

    +

    This fix can change the direction of the gravity vector, due to the +time-dependent gradient keyword, continuously over multiple runs, +using the start and stop keywords of the run command. +If you do not do this, the direction of the gravity vector will be +reset to its initial value at the beginning of each run. +

    +

    This fix is not invoked during energy minimization.

    Restrictions: none

    diff --git a/doc/fix_gravity.txt b/doc/fix_gravity.txt index 86cff8cc07..9f791d740b 100644 --- a/doc/fix_gravity.txt +++ b/doc/fix_gravity.txt @@ -71,8 +71,9 @@ the gradient arguments are in full rotations per time unit. E.g. a timestep of 0.001 and a gradient of 0.1 means the acceleration vector would rotate thru 360 degrees every 10,000 timesteps. For the time-dependent case, the initial direction of the acceleration vector -is phi,theta at the time the fix is specified. For 2d systems, {phi} -and {phi_grad} are ignored. +is phi,theta at the beginning of the simulation. For 2d systems, +{phi} and {phi_grad} are ignored. See the note below about making the +acceleration vector rotate continuously across multiple runs. Style {vector} imposes an acceleration in the vector direction given by (x,y,z). For 2d systems, the z component is ignored. @@ -83,8 +84,14 @@ No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output -commands"_Section_howto.html#4_15. No parameter of this fix can be -used with the {start/stop} keywords of the "run"_run.html command. +commands"_Section_howto.html#4_15. + +This fix can change the direction of the gravity vector, due to the +time-dependent {gradient} keyword, continuously over multiple runs, +using the {start} and {stop} keywords of the "run"_run.html command. +If you do not do this, the direction of the gravity vector will be +reset to its initial value at the beginning of each run. + This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_move.html b/doc/fix_move.html new file mode 100644 index 0000000000..1eb61dc08b --- /dev/null +++ b/doc/fix_move.html @@ -0,0 +1,206 @@ + +
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    fix move command +

    +

    Syntax: +

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

    Examples: +

    +
    fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
+fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
+fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL 
+
    +

    Description: +

    +

    Perform updates of position and velocity for atoms in the group each +timestep using the specified settings or formulas, without regard to +forces on the atoms. This can be useful for boundary or other atoms, +whose movement can influence nearby atoms. +

    +

    IMPORTANT NOTE: The atoms affected by this fix should not normally be +time integrated by other fixes (e.g. fix nve, fix +nvt), since that will change their positions and +velocities twice. +

    +

    IMPORTANT NOTE: As atoms move due to this fix, they will pass thru +periodic boundaries and be remapped to the other side of the +simulation box, just as they would during normal time integration +(e.g. via the fix nve command). It is up to you to +decide whether periodic boundaries are appropriate with the kind of +atom motion you are prescribing with this fix. +

    +

    IMPORTANT NOTE: As dicsussed below, atoms are moved relative to their +initial position at the time the fix is specified. These initial +coordinates are stored by the fix in "unwrapped" form, by using the +image flags associated with each atom. See the dump +custom command for a discussion of "unwrapped" coordinates. +See the Atoms section of the read_data command for a +discussion of image flags and how they are set for each atom. You can +reset the image flags (e.g. to 0) before invoking this fix by using +the set image command. +

    +
    + +

    The linear style moves atoms at a constant velocity, so that their +position X = (x,y,z) as a function of time is given in vector +notation as +

    +
    X(t) = X0 + V * delta 
+
    +

    where X0 = (x0,y0,z0) is their position at the time the fix is +specified, V is the specified velocity vector with components +(Vx,Vy,Vz), and delta is the time elapsed since the beginning of the +simulation. This style also sets the velocity of each atom to V = +(Vx,Vy,Vz). If any of the velocity components is specified as NULL, +then the position and velocity of that component is time integrated +the same as the fix nve command would perform, using +the corresponding force component on the atom. +

    +

    The wiggle style moves atoms in an oscillatory fashion, so that +their position X = (x,y,z) as a function of time is given in vector +notation as +

    +
    X(t) = X0 + A sin(omega*delta) 
+
    +

    where X0 = (x0,y0,z0) is their position at the time the fix is +specified, A is the specified amplitude vector with components +(Ax,Ay,Az), omega is 2 PI / period, and delta is the time +elapsed since the beginning of the simulation. This style also sets +the velocity of each atom to the time derivative of this expression. +If any of the amplitude components is specified as NULL, then the +position and velocity of that component is time integrated the same as +the fix nve command would perform, using the +corresponding force component on the atom. +

    +

    The rotate style rotates atoms around a rotation axis R = +(Rx,Ry,Rz) that goes thru a point P = (Px,Py,Pz). The period of +the rotation is also specified. This style also sets the velocity of +each atom to (omega cross Rperp) where omega is its angular velocity +around the rotation axis and Rperp is a perpendicular vector from the +rotation axis to the atom. If the defined +atom_style assigns an angular velocity to each atom, +then each atom's angular velocity is also set to omega. +

    +

    The variable style allows the position and velocity components of +each atom to be set by formulas specified via the +variable command. Each of the 6 variables is +specified as an argument to the fix as v_name, where name is the +name of the variable that appears elsewhere in the input script. +

    +

    Each variable must be of either the equal or atom style. +Equal-style variables compute a single numeric quantity, that can be +a function of the timestep as well as of other simulation values. +Atom-style variables compute a numeric quantity for each atom, that +can be a function per-atom quantities, such as the atom's position, as +well as of the timestep and other simulation values. See the +variable command for details. +

    +

    The first 3 variables (v_dx,v_dy,v_dz) specified for the variable +style are used to calculate a displacement from the atom's original +position at the time the fix was specified. The second 3 variables +(v_vx,v_vy,v_vz) specified are used to compute a velocity for each +atom. +

    +

    Any of the 6 variables can be specified as NULL. If both the +displacement and velocity variables for a particular x,y,z component +are specified as NULL, then the position and velocity of that +component is time integrated the same as the fix nve +command would perform, using the corresponding force component on the +atom. If only the velocity variable for a component is specified as +NULL, then the displacement variable will be used to set the position +of the atom, and its velocity component will not be changed. If only +the displacement variable for a component is specified as NULL, then +the velocity variable will be used to set the velocity of the atom, +and the position of the atom will be time integrated using that +velocity. +

    +

    The units keyword determines the meaning of the distance units used +to define the linear velocity and wiggle amplitude and rotate +origin. This setting is ignored for the variable style. A box +value selects standard units as defined by the units +command, e.g. velocity in Angstroms/fmsec and amplitude and position +in Angstroms for units = real. A lattice value means the velocity +units are in lattice spacings per time and the amplitude and position +are in lattice spacings. The lattice command must have +been previously used to define the lattice spacing. Each of these 3 +quantities may be dependent on the x,y,z dimension, since the lattice +spacings can be different in x,y,z. +

    +

    For rRESPA time integration, this fix adjusts the +position and velocity of atoms on the outermost rRESPA level. +

    +
    + +

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

    +

    This fix writes the original coordinates of moving atoms to binary +restart files, so that the motion can be continuous in a +restarted simulation. See the read_restart +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. +

    +

    None of the fix_modify options are relevant to this +fix. +

    +

    This fix produces a per-atom vector which can be accessed by various +output commands. The length of the vector +for each atom is 3, and the components store the original unwrapped +x,y,z coords of each atom. The per-atom values be accessed on any +timestep. +

    +

    This fix can move atoms continously over multiple runs, using the +start and stop keywords of the run command. See the +run command for details of how to do this. +

    +

    This fix is not invoked during energy minimization. +

    +

    Restrictions: none +

    +

    Related commands: +

    +

    fix nve +

    +

    Default: none +

    +

    The option default is units = lattice. +

    + diff --git a/doc/fix_move.txt b/doc/fix_move.txt new file mode 100644 index 0000000000..ef0d40473e --- /dev/null +++ b/doc/fix_move.txt @@ -0,0 +1,195 @@ +"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 move command :h3 + +[Syntax:] + +fix ID group-ID move style args keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +move = style name of this fix command :l +style = {linear} or {wiggle} or {rotate} or {variable} :l + {linear} args = Vx Vy Vz + Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL + {wiggle} args = Ax Ay Az period + Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL + period = period of oscillation (time units) + {rotate} args = Px Py Pz Rx Ry Rz period + Px,Py,Pz = origin point of axis of rotation (distance units) + Rx,Ry,Rz = axis of rotation vector + period = period of rotation (time units) + {variable} args = v_dx v_dy v_dz v_vx v_vy v_vz + v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL + v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL :pre + +zero or more keyword/value pairs may be appended :l +keyword = {units} :l + {units} value = {box} or {lattice} :pre +:ule + +[Examples:] + +fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box +fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0 +fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL :pre + +[Description:] + +Perform updates of position and velocity for atoms in the group each +timestep using the specified settings or formulas, without regard to +forces on the atoms. This can be useful for boundary or other atoms, +whose movement can influence nearby atoms. + +IMPORTANT NOTE: The atoms affected by this fix should not normally be +time integrated by other fixes (e.g. "fix nve"_fix_nve.html, "fix +nvt"_fix_nvt.html), since that will change their positions and +velocities twice. + +IMPORTANT NOTE: As atoms move due to this fix, they will pass thru +periodic boundaries and be remapped to the other side of the +simulation box, just as they would during normal time integration +(e.g. via the "fix nve"_fix_nve.html command). It is up to you to +decide whether periodic boundaries are appropriate with the kind of +atom motion you are prescribing with this fix. + +IMPORTANT NOTE: As dicsussed below, atoms are moved relative to their +initial position at the time the fix is specified. These initial +coordinates are stored by the fix in "unwrapped" form, by using the +image flags associated with each atom. See the "dump +custom"_dump.html command for a discussion of "unwrapped" coordinates. +See the Atoms section of the "read_data"_read_data.html command for a +discussion of image flags and how they are set for each atom. You can +reset the image flags (e.g. to 0) before invoking this fix by using +the "set image"_set.html command. + +:line + +The {linear} style moves atoms at a constant velocity, so that their +position {X} = (x,y,z) as a function of time is given in vector +notation as + +X(t) = X0 + V * delta :pre + +where {X0} = (x0,y0,z0) is their position at the time the fix is +specified, {V} is the specified velocity vector with components +(Vx,Vy,Vz), and {delta} is the time elapsed since the beginning of the +simulation. This style also sets the velocity of each atom to V = +(Vx,Vy,Vz). If any of the velocity components is specified as NULL, +then the position and velocity of that component is time integrated +the same as the "fix nve"_fix_nve.html command would perform, using +the corresponding force component on the atom. + +The {wiggle} style moves atoms in an oscillatory fashion, so that +their position {X} = (x,y,z) as a function of time is given in vector +notation as + +X(t) = X0 + A sin(omega*delta) :pre + +where {X0} = (x0,y0,z0) is their position at the time the fix is +specified, {A} is the specified amplitude vector with components +(Ax,Ay,Az), {omega} is 2 PI / {period}, and {delta} is the time +elapsed since the beginning of the simulation. This style also sets +the velocity of each atom to the time derivative of this expression. +If any of the amplitude components is specified as NULL, then the +position and velocity of that component is time integrated the same as +the "fix nve"_fix_nve.html command would perform, using the +corresponding force component on the atom. + +The {rotate} style rotates atoms around a rotation axis {R} = +(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz). The {period} of +the rotation is also specified. This style also sets the velocity of +each atom to (omega cross Rperp) where omega is its angular velocity +around the rotation axis and Rperp is a perpendicular vector from the +rotation axis to the atom. If the defined +"atom_style"_atom_style.html assigns an angular velocity to each atom, +then each atom's angular velocity is also set to omega. + +The {variable} style allows the position and velocity components of +each atom to be set by formulas specified via the +"variable"_variable.html command. Each of the 6 variables is +specified as an argument to the fix as v_name, where {name} is the +name of the variable that appears elsewhere in the input script. + +Each variable must be of either the {equal} or {atom} style. +{Equal}-style variables compute a single numeric quantity, that can be +a function of the timestep as well as of other simulation values. +{Atom}-style variables compute a numeric quantity for each atom, that +can be a function per-atom quantities, such as the atom's position, as +well as of the timestep and other simulation values. See the +"variable"_variable.html command for details. + +The first 3 variables (v_dx,v_dy,v_dz) specified for the {variable} +style are used to calculate a displacement from the atom's original +position at the time the fix was specified. The second 3 variables +(v_vx,v_vy,v_vz) specified are used to compute a velocity for each +atom. + +Any of the 6 variables can be specified as NULL. If both the +displacement and velocity variables for a particular x,y,z component +are specified as NULL, then the position and velocity of that +component is time integrated the same as the "fix nve"_fix_nve.html +command would perform, using the corresponding force component on the +atom. If only the velocity variable for a component is specified as +NULL, then the displacement variable will be used to set the position +of the atom, and its velocity component will not be changed. If only +the displacement variable for a component is specified as NULL, then +the velocity variable will be used to set the velocity of the atom, +and the position of the atom will be time integrated using that +velocity. + +The {units} keyword determines the meaning of the distance units used +to define the {linear} velocity and {wiggle} amplitude and {rotate} +origin. This setting is ignored for the {variable} style. A {box} +value selects standard units as defined by the "units"_units.html +command, e.g. velocity in Angstroms/fmsec and amplitude and position +in Angstroms for units = real. A {lattice} value means the velocity +units are in lattice spacings per time and the amplitude and position +are in lattice spacings. The "lattice"_lattice.html command must have +been previously used to define the lattice spacing. Each of these 3 +quantities may be dependent on the x,y,z dimension, since the lattice +spacings can be different in x,y,z. + +For "rRESPA time integration"_run_style.html, this fix adjusts the +position and velocity of atoms on the outermost rRESPA level. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +This fix writes the original coordinates of moving atoms to "binary +restart files"_restart.html, so that the motion can be continuous in a +restarted simulation. See the "read_restart"_read_restart.html +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. + +This fix produces a per-atom vector which can be accessed by various +"output commands"_Section_howto.html#4_15. The length of the vector +for each atom is 3, and the components store the original unwrapped +x,y,z coords of each atom. The per-atom values be accessed on any +timestep. + +This fix can move atoms continously over multiple runs, using the +{start} and {stop} keywords of the "run"_run.html command. See the +"run"_run.html command for details of how to do this. + +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] none + +[Related commands:] + +"fix nve"_fix_nve.html + +[Default:] none + +The option default is units = lattice. diff --git a/doc/fix_wall_gran.html b/doc/fix_wall_gran.html index df492c9ec0..cca9d0f17d 100644 --- a/doc/fix_wall_gran.html +++ b/doc/fix_wall_gran.html @@ -127,10 +127,11 @@ is set according to this equation: 

    position = pos0 + A - A cos (omega * delta)
    -

    where pos0 is the position at the time the fix was specified, A is -the amplitude, omega is 2 PI / period, and delta is the -elapsed time since the fix was specified. The velocity of the wall is -set to the derivative of this expression. +

    where pos0 is the position at the beginning of the simulation, A +is the amplitude, omega is 2 PI / period, and delta is the +elapsed time since the beginning of the simulatoin. The velocity of +the wall is set to the derivative of this expression. See the note +below about making a wall oscillate continuously across multiple runs.

    For the shear keyword, the wall moves continuously in the specified dimension with velocity vshear. The dimension must be tangential to @@ -155,9 +156,15 @@ uninterrupted fashion.

    None of the fix_modify options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various output -commands. No parameter of this fix can be -used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. +commands. +

    +

    This fix can change the position and velocity of the wall(s), due to +the wiggle keyword, continuously over multiple runs, using the +start and stop keywords of the run command. If you do +not do this, the wall position and velocity will be reset to its +initial values at the beginning of each run. +

    +

    This fix is not invoked during energy minimization.

    Restrictions:

    @@ -169,7 +176,7 @@ LAMMPS section for more info.

    Related commands:

    -

    >fix_wiggle, pair_style granular +

    fix_wiggle, pair_style granular

    Default: none

    diff --git a/doc/fix_wall_gran.txt b/doc/fix_wall_gran.txt index 08e515452b..aadffd1a02 100644 --- a/doc/fix_wall_gran.txt +++ b/doc/fix_wall_gran.txt @@ -110,10 +110,11 @@ is set according to this equation: position = pos0 + A - A cos (omega * delta) :pre -where {pos0} is the position at the time the fix was specified, {A} is -the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the -elapsed time since the fix was specified. The velocity of the wall is -set to the derivative of this expression. +where {pos0} is the position at the beginning of the simulation, {A} +is the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the +elapsed time since the beginning of the simulatoin. The velocity of +the wall is set to the derivative of this expression. See the note +below about making a wall oscillate continuously across multiple runs. For the {shear} keyword, the wall moves continuously in the specified dimension with velocity {vshear}. The dimension must be tangential to @@ -138,8 +139,14 @@ uninterrupted fashion. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output -commands"_Section_howto.html#4_15. No parameter of this fix can be -used with the {start/stop} keywords of the "run"_run.html command. +commands"_Section_howto.html#4_15. + +This fix can change the position and velocity of the wall(s), due to +the {wiggle} 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 and velocity will be reset to its +initial values at the beginning of each run. + This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] @@ -152,6 +159,6 @@ Any dimension (xyz) that has a granular wall must be non-periodic. [Related commands:] -"fix_wiggle"_fix_wiggle.html, pair_style granular"_pair_gran.html +"fix_wiggle"_fix_wiggle.html, "pair_style granular"_pair_gran.html [Default:] none diff --git a/doc/variable.html b/doc/variable.html index 0d69c3fcfc..395ceaefce 100644 --- a/doc/variable.html +++ b/doc/variable.html @@ -267,17 +267,18 @@ can use formula elements that produce either global values or per-atom values.

    The thermo keywords allowed in a formula are those defined by the -"thermo_style custom" command. Thermo keywords that require a -compute to calculate their values such as "temp" or -"press", use computes stored and invoked by the thermo_style command. -This means that you can only use those keywords in a variable if the -style you are using with the thermo_style command (and the thermo -keywords associated with that style) also define and use the needed -compute. Note that some thermo keywords use a compute indirectly to -calculate their value (e.g. the enthalpy keyword uses temp, pe, and -pressure). If a variable is evaluated in an input script (not during -a run), then the values accessed by the thermo keyword must be -current. See the discussion below about "Variable Accuracy". +thermo_style custom command. Thermo keywords that +require a compute to calculate their values such as +"temp" or "press", use computes stored and invoked by the +thermo_style command. This means that you can +only use those keywords in a variable if the style you are using with +the thermo_style command (and the thermo keywords associated with that +style) also define and use the needed compute. Note that some thermo +keywords use a compute indirectly to calculate their value (e.g. the +enthalpy keyword uses temp, pe, and pressure). If a variable is +evaluated in an input script (not during a run), then the values +accessed by the thermo keyword must be current. See the discussion +below about "Variable Accuracy".

    Math operations are written in the usual way, where the "x" and "y" in the examples above can be another section of the formula. Operators diff --git a/doc/variable.txt b/doc/variable.txt index 2f6ce10b71..54d6e44541 100644 --- a/doc/variable.txt +++ b/doc/variable.txt @@ -263,17 +263,18 @@ can use formula elements that produce either global values or per-atom values. The thermo keywords allowed in a formula are those defined by the -"thermo_style custom" command. Thermo keywords that require a -"compute"_compute.html to calculate their values such as "temp" or -"press", use computes stored and invoked by the thermo_style command. -This means that you can only use those keywords in a variable if the -style you are using with the thermo_style command (and the thermo -keywords associated with that style) also define and use the needed -compute. Note that some thermo keywords use a compute indirectly to -calculate their value (e.g. the enthalpy keyword uses temp, pe, and -pressure). If a variable is evaluated in an input script (not during -a run), then the values accessed by the thermo keyword must be -current. See the discussion below about "Variable Accuracy". +"thermo_style custom"_thermo_style.html command. Thermo keywords that +require a "compute"_compute.html to calculate their values such as +"temp" or "press", use computes stored and invoked by the +"thermo_style"_thermo_style.html command. This means that you can +only use those keywords in a variable if the style you are using with +the thermo_style command (and the thermo keywords associated with that +style) also define and use the needed compute. Note that some thermo +keywords use a compute indirectly to calculate their value (e.g. the +enthalpy keyword uses temp, pe, and pressure). If a variable is +evaluated in an input script (not during a run), then the values +accessed by the thermo keyword must be current. See the discussion +below about "Variable Accuracy". Math operations are written in the usual way, where the "x" and "y" in the examples above can be another section of the formula. Operators