Style vector imposes an acceleration in the vector direction given by (x,y,z). For 2d systems, the z component is ignored. @@ -92,15 +91,9 @@ 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. -
-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. +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.
Restrictions: none
diff --git a/doc/fix_gravity.txt b/doc/fix_gravity.txt index 9f791d740b..164d8a7540 100644 --- a/doc/fix_gravity.txt +++ b/doc/fix_gravity.txt @@ -71,9 +71,8 @@ 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 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. +is set to phi,theta when the fix is specified and evolves thereafter. +For 2d systems, {phi} and {phi_grad} are ignored. Style {vector} imposes an acceleration in the vector direction given by (x,y,z). For 2d systems, the z component is ignored. @@ -84,14 +83,8 @@ 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. - -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. - +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. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_move.html b/doc/fix_move.html index 1eb61dc08b..716cc7e562 100644 --- a/doc/fix_move.html +++ b/doc/fix_move.html @@ -87,8 +87,8 @@ notation aswhere 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), and delta is the time elapsed since the fix was +specified. 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 @@ -103,9 +103,9 @@ notation as
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 +elapsed since the fix was specified. 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. @@ -187,11 +187,9 @@ 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. +
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.
Restrictions: none
diff --git a/doc/fix_move.txt b/doc/fix_move.txt index ef0d40473e..01a4e938d0 100644 --- a/doc/fix_move.txt +++ b/doc/fix_move.txt @@ -78,8 +78,8 @@ 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), and {delta} is the time elapsed since the fix was +specified. 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 @@ -94,9 +94,9 @@ 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 +elapsed since the fix was specified. 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. @@ -178,11 +178,9 @@ 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. +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 +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_wall.html b/doc/fix_wall.html index 00a891ba5c..4d4378a13d 100644 --- a/doc/fix_wall.html +++ b/doc/fix_wall.html @@ -34,7 +34,10 @@ 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 + wiggle/sin values = amplitude period + amplitude = size of oscillation (distance units) + period = time of oscillation (time units) + wiggle/cos values = amplitude period amplitude = size of oscillation (distance units) period = time of oscillation (time units) units value = lattice or box @@ -102,42 +105,39 @@ 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. +elapsed since the fix was specified. 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/sin 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) +position = coord + A sin(omega*delta)If the wiggle/cos 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 (1 - cos(omega*delta)) +position = coord + A (1 - cos(omega*delta))-In both cases, 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. Note that the wiggle/sin -option oscillates with amplitude A around the pos0 position and the -velocity of the wall is a maximum at time 0. By contrast, for the -wiggle/cos option the wall moves up to 2A away from pos0 in one -direction and the velocity of the wall is 0 at time 0. If you want -different walls to oscillate with different amplitudes or periods, -then you need to use multiple fix wall commands. +
In both cases, coord is the specified initial position of the wall, +A is the amplitude, omega is 2 PI / period, and delta is the +time elapsed since the fix was specified. 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. Note that the wiggle/sin option oscillates with +amplitude A around the pos0 position and the velocity of the wall is +a maximum at time 0. By contrast, for the wiggle/cos option the +wall moves up to 2A away from pos0 in one direction and the velocity +of the wall is 0 at time 0. If you want different walls to oscillate +with different amplitudes or periods, then you need to use multiple +fix wall commands.
The units keyword determines the meaning of the distance units used to define the position of the wall and its velocity and wiggle @@ -175,11 +175,8 @@ corresponding wall is defined. Note that an outward force on a wall will be a negative value for lo walls and a positive value for hi walls.
-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. +
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. @@ -193,7 +190,8 @@ being minimized), you MUST enable the fix_modify
Any dimension (xyz) that has a wall must be non-periodic.
-You cannot use both the vel and wiggle keywords together. +
You cannot use both the vel and either of the wiggle keywords +together.
Related commands:
diff --git a/doc/fix_wall.txt b/doc/fix_wall.txt index a5bb9a6413..aae01ec73a 100644 --- a/doc/fix_wall.txt +++ b/doc/fix_wall.txt @@ -25,7 +25,10 @@ keyword = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} or {vel} or {wiggle 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 + {wiggle/sin} values = amplitude period + amplitude = size of oscillation (distance units) + period = time of oscillation (time units) + {wiggle/cos} values = amplitude period amplitude = size of oscillation (distance units) period = time of oscillation (time units) {units} value = {lattice} or {box} @@ -92,42 +95,39 @@ 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. +elapsed since the fix was specified. 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/sin} 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 +position = coord + A sin(omega*delta) :pre If the {wiggle/cos} 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 (1 - cos(omega*delta)) :pre +position = coord + A (1 - cos(omega*delta)) :pre -In both cases, {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. Note that the {wiggle/sin} -option oscillates with amplitude {A} around the pos0 position and the -velocity of the wall is a maximum at time 0. By contrast, for the -{wiggle/cos} option the wall moves up to {2A} away from pos0 in one -direction and the velocity of the wall is 0 at time 0. If you want -different walls to oscillate with different amplitudes or periods, -then you need to use multiple fix wall commands. +In both cases, {coord} is the specified initial position of the wall, +{A} is the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the +time elapsed since the fix was specified. 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. Note that the {wiggle/sin} option oscillates with +amplitude {A} around the pos0 position and the velocity of the wall is +a maximum at time 0. By contrast, for the {wiggle/cos} option the +wall moves up to {2A} away from pos0 in one direction and the velocity +of the wall is 0 at time 0. If you want different walls to oscillate +with different amplitudes or periods, then you need to use multiple +fix wall commands. The {units} keyword determines the meaning of the distance units used to define the position of the wall and its velocity and wiggle @@ -165,11 +165,8 @@ corresponding wall is defined. Note that an outward force on a wall will be a negative value for {lo} walls and a positive value for {hi} walls. -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. +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. @@ -183,7 +180,8 @@ being minimized), you MUST enable the "fix_modify"_fix_modify.html Any dimension (xyz) that has a wall must be non-periodic. -You cannot use both the {vel} and {wiggle} keywords together. +You cannot use both the {vel} and either of the {wiggle} keywords +together. [Related commands:] diff --git a/doc/fix_wall_gran.html b/doc/fix_wall_gran.html index cca9d0f17d..ef59d44127 100644 --- a/doc/fix_wall_gran.html +++ b/doc/fix_wall_gran.html @@ -125,13 +125,12 @@ is perpendicular to the wall, it is more of a shaking motion. AEach timestep, the position of a wiggled wall in the appropriate dim is set according to this equation:
-position = pos0 + A - A cos (omega * delta) +position = coord + A - A cos (omega * delta)-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. +
where coord is the specified initial position of the wall, A is +the amplitude, omega is 2 PI / period, and delta is the time +elapsed since the fix was specified. The velocity of the wall is set +to the derivative of this expression.
For the shear keyword, the wall moves continuously in the specified dimension with velocity vshear. The dimension must be tangential to @@ -156,15 +155,9 @@ 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. -
-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. +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.
Restrictions:
diff --git a/doc/fix_wall_gran.txt b/doc/fix_wall_gran.txt index aadffd1a02..d3be85abbd 100644 --- a/doc/fix_wall_gran.txt +++ b/doc/fix_wall_gran.txt @@ -108,13 +108,12 @@ is perpendicular to the wall, it is more of a shaking motion. A Each timestep, the position of a wiggled wall in the appropriate {dim} is set according to this equation: -position = pos0 + A - A cos (omega * delta) :pre +position = coord + A - A cos (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 -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. +where {coord} is the specified initial position of the wall, {A} is +the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time +elapsed since the fix was specified. The velocity of the wall is set +to the derivative of this expression. For the {shear} keyword, the wall moves continuously in the specified dimension with velocity {vshear}. The dimension must be tangential to @@ -139,14 +138,8 @@ 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. - -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. - +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. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:]