diff --git a/doc/fix_append_atoms.html b/doc/fix_append_atoms.html new file mode 100644 index 0000000000000000000000000000000000000000..5c591dc8ac590c6408cb0a2fccb5c2faa74f313d --- /dev/null +++ b/doc/fix_append_atoms.html @@ -0,0 +1,108 @@ +<HTML> +<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> +</CENTER> + + + + + + +<HR> + +<H3>fix append_atoms command +</H3> +<P><B>Syntax:</B> +</P> +<PRE>fix ID group-ID append_atoms face arg ... keyword value ... +</PRE> +<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command + +<LI>append_atoms = style name of this fix command + +<LI>one face/arg pairs must be appended + +<LI>face = <I>zhi</I> + +<LI>zero or more keyword/value pairs may be appended + +<LI>keyword = <I>size</I> or <I>freq</I> or <I>temp</I> or <I>random</I> or <I>units</I> + +<PRE> <I>size</I> args = Lz + Lz = z size of lattice region appended in a single event(distance units) + <I>freq</I> args = freq + freq = the number of timesteps between append events + <I>temp</I> args = target damp seed extent + target = target velocity for region immediately ahead of the piston + damp = damping parameter (time units) + seed = random number seed for langevin kicks + extent = extent of thermostated region (distance units) + <I>random</I> args = xmax ymax zmax seed + <I>xmax</I>, <I>ymax</I>, <I>zmax</I> = maximum displacement in particular direction (distance units) + <I>seed</I> = random number seed for random displacement + <I>units</I> value = <I>lattice</I> or <I>box</I> + <I>lattice</I> = the wall position is defined in lattice units + <I>box</I> = the wall position is defined in simulation box units +</PRE> + +</UL> +<P><B>Examples:</B> +</P> +<PRE>fix 1 all append_atoms zhi size 5.0 freq 295 units lattice +fix 4 all append_atoms zhi size 15.0 freq 5 units box +fix A all append_atoms zhi size 1.0 freq 1000 units lattice +</PRE> +<P><B>Description:</B> +</P> +<P>This fix creates atoms on a lattice, appended on the zhi edge of the system box. +This can be useful when a shock or wave is propagating from zlo. This allows +the system to grow with time to accommodate an expanding wave. A simulation +box must already exist, which is typically created via the +<A HREF = "create_box.html">create_box</A> command. Before using this command, a +lattice must also be defined using the <A HREF = "lattice.html">lattice</A> command. +</P> +<P>This fix will automatically freeze atoms on the zhi edge of the system, so that +overlaps are avoided when new atoms are appended. +</P> +<P>The <I>size</I> keyword defines the size in z of the chunk of material to be added. +</P> +<P>The <I>random</I> keyword will give the atoms random displacements around their +lattice points to simulate some initial temperature. +</P> +<P>The <I>temp</I> keyword will cause a region to be thermostated with a Langevin +thermostat on the zhi boundary. The size of the region is measured from zhi and +is set with the <I>extent</I> argument. +</P> +<P>The <I>units</I> keyword determines the meaning of the distance units used +to define a wall position, but only when a numeric constant is used. +A <I>box</I> value selects standard distance units as defined by the +<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal. +A <I>lattice</I> value means the distance units are in lattice spacings. +The <A HREF = "lattice.html">lattice</A> command must have been previously used to +define the lattice spacings. +</P> +<HR> + +<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B> +</P> +<P>No information about this fix is written to <A HREF = "restart.html">binary restart +files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various <A HREF = "Section_howto.html#4_15">output +commands</A>. No parameter of this fix can be +used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command. +This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>. +</P> +<P><B>Restrictions:</B> +</P> +<P>The zhi boundary on which atoms are added with append_atoms must be shrink-wrapped. +The zlo boundary may be any boundary type other than periodic. +</P> +<P><B>Related commands:</B> +</P> +<P><A HREF = "fix_wall_piston.html">fix wall/piston</A> command +</P> +<P><B>Default:</B> <I>size</I> = 0.0, <I>freq</I> = 0, <I>units</I> = lattice. +</P> +<HR> + +</HTML> diff --git a/doc/fix_append_atoms.txt b/doc/fix_append_atoms.txt new file mode 100644 index 0000000000000000000000000000000000000000..2e233c2cd82fb925cf0a152d070c9e6479c16c02 --- /dev/null +++ b/doc/fix_append_atoms.txt @@ -0,0 +1,96 @@ +"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 append_atoms command :h3 + +[Syntax:] + +fix ID group-ID append_atoms face arg ... keyword value ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +append_atoms = style name of this fix command :l +one face/arg pairs must be appended :l +face = {zhi} :l +zero or more keyword/value pairs may be appended :l +keyword = {size} or {freq} or {temp} or {random} or {units} :l + {size} args = Lz + Lz = z size of lattice region appended in a single event(distance units) + {freq} args = freq + freq = the number of timesteps between append events + {temp} args = target damp seed extent + target = target velocity for region immediately ahead of the piston + damp = damping parameter (time units) + seed = random number seed for langevin kicks + extent = extent of thermostated region (distance units) + {random} args = xmax ymax zmax seed + {xmax}, {ymax}, {zmax} = maximum displacement in particular direction (distance units) + {seed} = random number seed for random displacement + {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 1 all append_atoms zhi size 5.0 freq 295 units lattice +fix 4 all append_atoms zhi size 15.0 freq 5 units box +fix A all append_atoms zhi size 1.0 freq 1000 units lattice :pre + +[Description:] + +This fix creates atoms on a lattice, appended on the zhi edge of the system box. +This can be useful when a shock or wave is propagating from zlo. This allows +the system to grow with time to accommodate an expanding wave. A simulation +box must already exist, which is typically created via the +"create_box"_create_box.html command. Before using this command, a +lattice must also be defined using the "lattice"_lattice.html command. + +This fix will automatically freeze atoms on the zhi edge of the system, so that +overlaps are avoided when new atoms are appended. + +The {size} keyword defines the size in z of the chunk of material to be added. + +The {random} keyword will give the atoms random displacements around their +lattice points to simulate some initial temperature. + +The {temp} keyword will cause a region to be thermostated with a Langevin +thermostat on the zhi boundary. The size of the region is measured from zhi and +is set with the {extent} argument. + +The {units} keyword determines the meaning of the distance units used +to define a wall position, but only when a numeric constant is used. +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 + +[Restart, fix_modify, output, run start/stop, minimize info:] + +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 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. +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] + +The zhi boundary on which atoms are added with append_atoms must be shrink-wrapped. +The zlo boundary may be any boundary type other than periodic. + +[Related commands:] + +"fix wall/piston"_fix_wall_piston.html command + +[Default:] {size} = 0.0, {freq} = 0, {units} = lattice. + +:line diff --git a/doc/fix_nphug.html b/doc/fix_nphug.html index 5d4b56cbce004bcc3f14b20a93a04f87b018ee11..7a85d2da99dae0de48ae608c506ccd033cee4c8a 100644 --- a/doc/fix_nphug.html +++ b/doc/fix_nphug.html @@ -153,10 +153,10 @@ operation of the fix continues in an uninterrupted fashion. </P> <P>The <A HREF = "fix_modify.html">fix_modify</A> <I>e0</I>, <I>v0</I> and <I>p0</I> keywords can be used to define the values of E0, V0, and P0. Note the -the values for <I>e0</I> and <I>p0</I> are extensive, and so must correspond +the values for <I>e0</I> and <I>v0</I> are extensive, and so must correspond to the total energy and volume of the entire system, not energy and volume per atom. If any of these quantities are not specified, then the -instanteous value in the system at the start of the simulation is used. +instantaneous value in the system at the start of the simulation is used. </P> <P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are supported by these fixes. You can use them to assign a diff --git a/doc/fix_nphug.txt b/doc/fix_nphug.txt index 6ac59d1e1605aa346b6de23ae36841036ebc7bb4..aa880ac01d69b662df07e3a47d2c482db6aca1f3 100644 --- a/doc/fix_nphug.txt +++ b/doc/fix_nphug.txt @@ -148,10 +148,10 @@ operation of the fix continues in an uninterrupted fashion. The "fix_modify"_fix_modify.html {e0}, {v0} and {p0} keywords can be used to define the values of E0, V0, and P0. Note the -the values for {e0} and {p0} are extensive, and so must correspond +the values for {e0} and {v0} are extensive, and so must correspond to the total energy and volume of the entire system, not energy and volume per atom. If any of these quantities are not specified, then the -instanteous value in the system at the start of the simulation is used. +instantaneous value in the system at the start of the simulation is used. The "fix_modify"_fix_modify.html {temp} and {press} options are supported by these fixes. You can use them to assign a diff --git a/doc/fix_wall_piston.html b/doc/fix_wall_piston.html new file mode 100644 index 0000000000000000000000000000000000000000..c190ac75539b4bc074024b9647fe45a565e0659d --- /dev/null +++ b/doc/fix_wall_piston.html @@ -0,0 +1,129 @@ +<HTML> +<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> +</CENTER> + + + + + + +<HR> + +<H3>fix wall/piston command +</H3> +<P><B>Syntax:</B> +</P> +<PRE>fix ID group-ID wall/piston face arg ... keyword value ... +</PRE> +<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command + +<LI>wall/piston = style name of this fix command + +<LI>one face/arg pair must be appended + +<LI>face = <I>zlo</I> + +<LI>zero or more keyword/value pairs may be appended + +<LI>keyword = <I>pos</I> or <I>vel</I> or <I>ramp</I> or <I>units</I> + +<PRE> <I>pos</I> args = z + z = z coordinate at which the piston begins (distance units) + <I>vel</I> args = vz + vz = final velocity of the piston (velocity units) + <I>ramp</I> = use a linear velocity ramp from 0 to vz + <I>temp</I> args = target damp seed extent + target = target velocity for region immediately ahead of the piston + damp = damping paramter (time units) + seed = random number seed for langevin kicks + extent = extent of thermostated region (distance units) + <I>units</I> value = <I>lattice</I> or <I>box</I> + <I>lattice</I> = the wall position is defined in lattice units + <I>box</I> = the wall position is defined in simulation box units +</PRE> + +</UL> +<P><B>Examples:</B> +</P> +<PRE>fix xwalls all wall/piston zlo +fix walls all wall/piston zlo pos 1.0 0.0 0.0 vel 0.0 0.0 10.0 units box +fix top all wall/piston zlo vel 0.0 0.0 10.0 ramp +</PRE> +<P><B>Description:</B> +</P> +<P>Bound the simulation with a moving wall which reflect particles +in the specified group and drive the system with an effective infinite-mass +piston capable of driving shock waves. +</P> +<P>A momentum mirror technique is used, which means that if an atom (or the wall) +moves such that an atom is outside the wall on a timestep +by a distance delta (e.g. due to <A HREF = "fix_nve.html">fix nve</A>), then it is +put back inside the face by the same delta, and the velocity relative to +the moving wall is flipped in z. For instance, a stationary particle hit with a +piston wall with velocity vz, will end the timestep with a velocity of 2*vz. +</P> +<P>Currently only face <I>zlo</I> may be specified. +This creates a piston moving in the positive z direction. +Particles with z coordinate less than the wall position +are reflected to a z coordinate +greater than the wall position. +If the piston velocity is vpz and the particle velocity +before reflection is vzi, the particle velocity after +reflection is -vzi + 2*vpz. +</P> +<P>The initial position of the wall can be specified by the <I>pos</I> keyword. +</P> +<P>The final velocity of the wall can be specified by the <I>vel</I> keyword +</P> +<P>The <I>ramp</I> keyword will cause the wall/piston to adjust the velocity linearly +from zero velocity to <I>vel</I> over the course of the run. If the <I>ramp</I> keyword is omitted +then the wall/piston moves at a constant velocity defined by <I>vel</I>. +</P> +<P>The <I>temp</I> keyword will cause the region immediately in front of the wall/piston +to be thermostated with a Langevin thermostat. This region moves with the piston. +The damping and kicking are measured in the reference frame of the piston. +So, a temperature of zero would mean all particles were moving at exactly the speed +of the wall/piston. +</P> +<P>The <I>units</I> keyword determines the meaning of the distance units used +to define a wall position, but only when a numeric constant is used. +</P> +<P>A <I>box</I> value selects standard distance units as defined by the +<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal. +A <I>lattice</I> value means the distance units are in lattice spacings. +The <A HREF = "lattice.html">lattice</A> command must have been previously used to +define the lattice spacings. +</P> +<HR> + +<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B> +</P> +<P>No information about this fix is written to <A HREF = "restart.html">binary restart +files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various <A HREF = "Section_howto.html#4_15">output +commands</A>. No parameter of this fix can be +used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command. +This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>. +</P> +<P><B>Restrictions:</B> +</P> +<P>The face that has the wall/piston must be boundary type 'm' (shrink-wrapped +with minimum a minimum value). The opposing face can be +any boundary type other than periodic. +</P> +<P>A wall/piston should not be used with rigid bodies such as those +defined by a "fix rigid" command. This is because the wall/piston +displaces atoms directly rather than exerting a force on them. +</P> +<P><B>Related commands:</B> +</P> +<P><A HREF = "fix_wall.html">fix wall/reflect</A> command +</P> +<P><A HREF = "fix_append_atoms.html">fix append/atoms</A> command +</P> +<P><B>Default:</B> <I>pos</I> = 0, <I>vel</I> = 0, <I>units</I> = lattice. +</P> +<HR> + +</HTML> diff --git a/doc/fix_wall_piston.txt b/doc/fix_wall_piston.txt new file mode 100644 index 0000000000000000000000000000000000000000..6da64e7059740ea103c8fac7f3a11337ccfb8102 --- /dev/null +++ b/doc/fix_wall_piston.txt @@ -0,0 +1,117 @@ +"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/piston command :h3 + +[Syntax:] + +fix ID group-ID wall/piston face arg ... keyword value ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +wall/piston = style name of this fix command :l +one face/arg pair must be appended :l +face = {zlo} :l +zero or more keyword/value pairs may be appended :l +keyword = {pos} or {vel} or {ramp} or {units} :l + {pos} args = z + z = z coordinate at which the piston begins (distance units) + {vel} args = vz + vz = final velocity of the piston (velocity units) + {ramp} = use a linear velocity ramp from 0 to vz + {temp} args = target damp seed extent + target = target velocity for region immediately ahead of the piston + damp = damping paramter (time units) + seed = random number seed for langevin kicks + extent = extent of thermostated region (distance units) + {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 xwalls all wall/piston zlo +fix walls all wall/piston zlo pos 1.0 0.0 0.0 vel 0.0 0.0 10.0 units box +fix top all wall/piston zlo vel 0.0 0.0 10.0 ramp :pre + +[Description:] + +Bound the simulation with a moving wall which reflect particles +in the specified group and drive the system with an effective infinite-mass +piston capable of driving shock waves. + +A momentum mirror technique is used, which means that if an atom (or the wall) +moves such that an atom is outside the wall on a timestep +by a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is +put back inside the face by the same delta, and the velocity relative to +the moving wall is flipped in z. For instance, a stationary particle hit with a +piston wall with velocity vz, will end the timestep with a velocity of 2*vz. + +Currently only face {zlo} may be specified. +This creates a piston moving in the positive z direction. +Particles with z coordinate less than the wall position +are reflected to a z coordinate +greater than the wall position. +If the piston velocity is vpz and the particle velocity +before reflection is vzi, the particle velocity after +reflection is -vzi + 2*vpz. + +The initial position of the wall can be specified by the {pos} keyword. + +The final velocity of the wall can be specified by the {vel} keyword + +The {ramp} keyword will cause the wall/piston to adjust the velocity linearly +from zero velocity to {vel} over the course of the run. If the {ramp} keyword is omitted +then the wall/piston moves at a constant velocity defined by {vel}. + +The {temp} keyword will cause the region immediately in front of the wall/piston +to be thermostated with a Langevin thermostat. This region moves with the piston. +The damping and kicking are measured in the reference frame of the piston. +So, a temperature of zero would mean all particles were moving at exactly the speed +of the wall/piston. + +The {units} keyword determines the meaning of the distance units used +to define a wall position, but only when a numeric constant is used. + +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 + +[Restart, fix_modify, output, run start/stop, minimize info:] + +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 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. +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] + +The face that has the wall/piston must be boundary type 'm' (shrink-wrapped +with minimum a minimum value). The opposing face can be +any boundary type other than periodic. + +A wall/piston should not be used with rigid bodies such as those +defined by a "fix rigid" command. This is because the wall/piston +displaces atoms directly rather than exerting a force on them. + +[Related commands:] + +"fix wall/reflect"_fix_wall.html command + +"fix append/atoms"_fix_append_atoms.html command + +[Default:] {pos} = 0, {vel} = 0, {units} = lattice. + +:line