forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13078 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
06b956da10
commit
ff40107a01
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@ -1617,15 +1617,15 @@ pressure</A> command calculates pressure.
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<LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
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<LI><A HREF = "compute_temp_region.html">compute temp/region</A>
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</UL>
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<P>All but the first 3 calculate velocity biases (i.e. advection
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<P>All but the first 3 calculate velocity biases directly (e.g. advection
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velocities) that are removed when computing the thermal temperature.
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<A HREF = "compute_temp_sphere.html">Compute temp/sphere</A> and <A HREF = "compute_temp_asphere.html">compute
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temp/asphere</A> compute kinetic energy for
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finite-size particles that includes rotational degrees of freedom.
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They both allow, as an extra argument, which is another temperature
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compute that subtracts a velocity bias. This allows the translational
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velocity of spherical or aspherical particles to be adjusted in
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prescribed ways.
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They both allow for velocity biases indirectly, via an optional extra
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argument, another temperature compute that subtracts a velocity bias.
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This allows the translational velocity of spherical or aspherical
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particles to be adjusted in prescribed ways.
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</P>
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<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>, or in one
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case by a pair style. Several thermostatting fixes are available:
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@ -1658,15 +1658,21 @@ to the per-particle thermostatting of <A HREF = "fix_langevin.html">fix
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langevin</A>.
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</P>
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<P>Any of the thermostatting fixes can use temperature computes that
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remove bias for two purposes: (a) computing the current temperature to
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compare to the requested target temperature, and (b) adjusting only
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the thermal temperature component of the particle's velocities. See
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the doc pages for the individual fixes and for the
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remove bias which has two effects. First, the current calculated
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temperature, which is compared to the requested target temperature, is
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caluclated with the velocity bias removed. Second, the thermostat
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adjusts only the thermal temperature component of the particle's
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velocities, which are the velocities with the bias removed. The
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removed bias is then added back to the adjusted velocities. See the
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doc pages for the individual fixes and for the
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<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
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a temperature compute to a thermostatting fix. For example, you can
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apply a thermostat to only the x and z components of velocity by using
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it in conjunction with <A HREF = "compute_temp_partial.html">compute
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temp/partial</A>.
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temp/partial</A>. Of you could thermostat only
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the thermal temperature of a streaming flow of particles without
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affecting the streaming velocity, by using <A HREF = "compute_temp_profile.html">compute
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temp/profile</A>.
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</P>
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<P>IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
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they update the velocities and positions of particles due to forces
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@ -1604,15 +1604,15 @@ pressure"_compute_pressure.html command calculates pressure.
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"compute temp/ramp"_compute_temp_ramp.html
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"compute temp/region"_compute_temp_region.html :ul
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All but the first 3 calculate velocity biases (i.e. advection
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All but the first 3 calculate velocity biases directly (e.g. advection
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velocities) that are removed when computing the thermal temperature.
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"Compute temp/sphere"_compute_temp_sphere.html and "compute
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temp/asphere"_compute_temp_asphere.html compute kinetic energy for
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finite-size particles that includes rotational degrees of freedom.
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They both allow, as an extra argument, which is another temperature
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compute that subtracts a velocity bias. This allows the translational
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velocity of spherical or aspherical particles to be adjusted in
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prescribed ways.
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They both allow for velocity biases indirectly, via an optional extra
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argument, another temperature compute that subtracts a velocity bias.
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This allows the translational velocity of spherical or aspherical
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particles to be adjusted in prescribed ways.
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Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one
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case by a pair style. Several thermostatting fixes are available:
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@ -1645,15 +1645,21 @@ to the per-particle thermostatting of "fix
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langevin"_fix_langevin.html.
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Any of the thermostatting fixes can use temperature computes that
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remove bias for two purposes: (a) computing the current temperature to
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compare to the requested target temperature, and (b) adjusting only
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the thermal temperature component of the particle's velocities. See
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the doc pages for the individual fixes and for the
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remove bias which has two effects. First, the current calculated
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temperature, which is compared to the requested target temperature, is
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caluclated with the velocity bias removed. Second, the thermostat
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adjusts only the thermal temperature component of the particle's
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velocities, which are the velocities with the bias removed. The
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removed bias is then added back to the adjusted velocities. See the
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doc pages for the individual fixes and for the
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"fix_modify"_fix_modify.html command for instructions on how to assign
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a temperature compute to a thermostatting fix. For example, you can
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apply a thermostat to only the x and z components of velocity by using
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it in conjunction with "compute
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temp/partial"_compute_temp_partial.html.
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temp/partial"_compute_temp_partial.html. Of you could thermostat only
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the thermal temperature of a streaming flow of particles without
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affecting the streaming velocity, by using "compute
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temp/profile"_compute_temp_profile.html.
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IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
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they update the velocities and positions of particles due to forces
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|
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@ -38,13 +38,14 @@
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</PRE>
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>dist</I> or <I>sum</I> or <I>mom</I> or <I>rot</I> or <I>temp</I> or <I>loop</I> or <I>units</I>
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<LI>keyword = <I>dist</I> or <I>sum</I> or <I>mom</I> or <I>rot</I> or <I>temp</I> or <I>bias</I> or <I>loop</I> or <I>units</I>
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<PRE> <I>dist</I> value = <I>uniform</I> or <I>gaussian</I>
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<I>sum</I> value = <I>no</I> or <I>yes</I>
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<I>mom</I> value = <I>no</I> or <I>yes</I>
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<I>rot</I> value = <I>no</I> or <I>yes</I>
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<I>temp</I> value = temperature ID
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<I>temp</I> value = temperature compute ID
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<I>bias</I> value = <I>no</I> or <I>yes</I>
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<I>loop</I> value = <I>all</I> or <I>local</I> or <I>geom</I>
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<I>rigid</I> value = fix-ID
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fix-ID = ID of rigid body fix
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@ -124,42 +125,69 @@ simulation is 2d; see the <A HREF = "dimension.html">dimension</A> command.
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</P>
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<HR>
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<P>The keyword/value option pairs are used in the following ways by the
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<P>The keyword/value options are used in the following ways by the
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various styles.
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</P>
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<P>The <I>dist</I> option is used by <I>create</I>. The ensemble of generated
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<P>The <I>dist</I> keyword is used by <I>create</I>. The ensemble of generated
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velocities can be a <I>uniform</I> distribution from some minimum to
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maximum value, scaled to produce the requested temperature. Or it can
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be a <I>gaussian</I> distribution with a mean of 0.0 and a sigma scaled to
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produce the requested temperature.
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</P>
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<P>The <I>sum</I> option is used by all styles, except <I>zero</I>. The new
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<P>The <I>sum</I> keyword is used by all styles, except <I>zero</I>. The new
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velocities will be added to the existing ones if sum = yes, or will
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replace them if sum = no.
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</P>
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<P>The <I>mom</I> and <I>rot</I> options are used by <I>create</I>. If mom = yes, the
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<P>The <I>mom</I> and <I>rot</I> keywords are used by <I>create</I>. If mom = yes, the
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linear momentum of the newly created ensemble of velocities is zeroed;
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if rot = yes, the angular momentum is zeroed.
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</P>
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<P>The <I>temp</I> option is used by <I>create</I> and <I>scale</I> to specify a
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<A HREF = "compute.html">compute</A> that calculates temperature in a desired way.
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If this option is not specified, <I>create</I> and <I>scale</I> calculate
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temperature using a compute that is defined as follows:
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<P>*line
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</P>
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<P>If specified, the <I>temp</I> keyword is used by <I>create</I> and <I>scale</I> to
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specify a <A HREF = "compute.html">compute</A> that calculates temperature in a
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desired way, e.g. by first subtracting out a velocity bias, as
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discussed in <A HREF = "Section_howto.html#howto_15">Section howto 16</A> of the doc
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pages. If this keyword is not specified, <I>create</I> and <I>scale</I>
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calculate temperature using a compute that is defined internally as
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follows:
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</P>
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<PRE>compute velocity_temp group-ID temp
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</PRE>
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<P>where group-ID is the same ID used in the velocity command. i.e. the
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group of atoms whose velocity is being altered. This compute is
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deleted when the velocity command is finished. See the <A HREF = "compute_temp.html">compute
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temp</A> command for details. If the computed
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temp</A> command for details. If the calculated
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temperature should have degrees-of-freedom removed due to fix
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constraints (e.g. SHAKE or rigid-body constraints), then the
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appropriate fix command must be specified before the velocity command
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is issued.
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</P>
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<P>The <I>bias</I> keyword with a <I>yes</I> setting is used by <I>create</I> and
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<I>scale</I>, but only if the <I>temp</I> keyword is also used to specify a
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<A HREF = "compute.html">compute</A> that calculates temperature in a desired way.
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If the temperature compute also calculates a velocity bias, the the
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bias is subtracted from atom velocities before the <I>create</I> and
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<I>scale</I> operations are performed. After the operations, the bias is
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added back to the atom velocities. See <A HREF = "Section_howto.html#howto_15">Section howto
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16</A> of the doc pages for more discussion
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of temperature computes with biases. Note that the velocity bias is
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only applied to atoms in the temperature compute specified with the
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<I>temp</I> keyword.
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</P>
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<P>As an example, assume atoms are currently streaming in a flow
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direction (which could be separately initialized with the <I>ramp</I>
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style), and you wish to initialize their thermal velocity to a desired
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temperature. In this context thermal velocity means the per-particle
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velocity that remains when the streaming velocity is subtracted. This
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can be done using the <I>create</I> style with the <I>temp</I> keyword
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specifying the ID of a <A HREF = "compute_temp_ramp.html">compute temp/ramp</A> or
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<A HREF = "compute_temp_profile.html">compute temp/profile</A> command, and the
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<I>bias</I> keyword set to a <I>yes</I> value.
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</P>
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<HR>
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<P>The <I>loop</I> option is used by <I>create</I> in the following ways.
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<P>The <I>loop</I> keyword is used by <I>create</I> in the following ways.
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</P>
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<P>If loop = all, then each processor loops over all atoms in the
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simulation to create velocities, but only stores velocities for atoms
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@ -183,23 +211,23 @@ xyz coordinates. A velocity is generated using that seed. This is a
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fast loop and the velocity assigned to a particular atom will be the
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same, independent of how many processors are used. However, the set
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of generated velocities may be more correlated than if the <I>all</I> or
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<I>local</I> options are used.
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<I>local</I> keywords are used.
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</P>
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<P>Note that the <I>loop geom</I> option will not necessarily assign identical
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velocities for two simulations run on different machines. This is
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because the computations based on xyz coordinates are sensitive to
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tiny differences in the double-precision value for a coordinate as
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stored on a particular machine.
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<P>Note that the <I>loop geom</I> keyword will not necessarily assign
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identical velocities for two simulations run on different machines.
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This is because the computations based on xyz coordinates are
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sensitive to tiny differences in the double-precision value for a
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coordinate as stored on a particular machine.
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</P>
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<HR>
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<P>The <I>rigid</I> option only has meaning when used with the <I>zero</I> style.
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<P>The <I>rigid</I> keyword only has meaning when used with the <I>zero</I> style.
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It allows specification of a fix-ID for one of the <A HREF = "fix_rigid.html">rigid-body
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fix</A> variants which defines a set of rigid bodies. The
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zeroing of linear or angular momentum is then performed for each rigid
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body defined by the fix, as described above.
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</P>
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<P>The <I>units</I> option is used by <I>set</I> and <I>ramp</I>. If units = box,
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<P>The <I>units</I> keyword is used by <I>set</I> and <I>ramp</I>. If units = box,
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the velocities and coordinates specified in the velocity command are
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in the standard units described by the <A HREF = "units.html">units</A> command
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(e.g. Angstroms/fmsec for real units). If units = lattice, velocities
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@ -207,14 +235,16 @@ are in units of lattice spacings per time (e.g. spacings/fmsec) and
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coordinates are in lattice spacings. The <A HREF = "lattice.html">lattice</A>
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command must have been previously used to define the lattice spacing.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>Assigning a temperature via the <I>create</I> option to a system with
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<A HREF = "fix_rigid.html">rigid bodies</A> or <A HREF = "fix_shake.html">SHAKE constraints</A>
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may not have the desired outcome for two reasons. First, the velocity
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command can be invoked before all of the relevant fixes are created
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and initialized and the number of adjusted degrees of freedom (DOFs)
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is known. Thus it is not possible to compute the target temperature
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<P>Assigning a temperature via the <I>create</I> style to a system with <A HREF = "fix_rigid.html">rigid
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bodies</A> or <A HREF = "fix_shake.html">SHAKE constraints</A> may not
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have the desired outcome for two reasons. First, the velocity command
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can be invoked before all of the relevant fixes are created and
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initialized and the number of adjusted degrees of freedom (DOFs) is
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known. Thus it is not possible to compute the target temperature
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correctly. Second, the assigned velocities may be partially canceled
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when constraints are first enforced, leading to a different
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temperature than desired. A workaround for this is to perform a <A HREF = "run.html">run
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@ -228,12 +258,13 @@ velocity all scale 300.0 # now it should be
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</PRE>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_rigid.html">fix rigid</A>, <A HREF = "fix_shake.html">fix shake</A>, <A HREF = "lattice.html">lattice</A>
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<P><A HREF = "fix_rigid.html">fix rigid</A>, <A HREF = "fix_shake.html">fix shake</A>,
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<A HREF = "lattice.html">lattice</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are dist = uniform, sum = no, mom = yes, rot = no,
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temp = full style on group-ID, loop = all, and units = lattice. The
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rigid option is not defined by default.
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<P>The keyword defaults are dist = uniform, sum = no, mom = yes, rot =
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no, bias = no, loop = all, and units = lattice. The temp and rigid
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keywords are not defined by default.
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</P>
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</HTML>
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|
|
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|
@ -32,12 +32,13 @@ style = {create} or {set} or {scale} or {ramp} or {zero} :l
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{angular} = zero the angular momentum :pre
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zero or more keyword/value pairs may be appended :l
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keyword = {dist} or {sum} or {mom} or {rot} or {temp} or {loop} or {units} :l
|
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keyword = {dist} or {sum} or {mom} or {rot} or {temp} or {bias} or {loop} or {units} :l
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{dist} value = {uniform} or {gaussian}
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{sum} value = {no} or {yes}
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{mom} value = {no} or {yes}
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{rot} value = {no} or {yes}
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{temp} value = temperature ID
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{temp} value = temperature compute ID
|
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{bias} value = {no} or {yes}
|
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{loop} value = {all} or {local} or {geom}
|
||||
{rigid} value = fix-ID
|
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fix-ID = ID of rigid body fix
|
||||
|
|
@ -116,42 +117,69 @@ simulation is 2d; see the "dimension"_dimension.html command.
|
|||
|
||||
:line
|
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|
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The keyword/value option pairs are used in the following ways by the
|
||||
The keyword/value options are used in the following ways by the
|
||||
various styles.
|
||||
|
||||
The {dist} option is used by {create}. The ensemble of generated
|
||||
The {dist} keyword is used by {create}. The ensemble of generated
|
||||
velocities can be a {uniform} distribution from some minimum to
|
||||
maximum value, scaled to produce the requested temperature. Or it can
|
||||
be a {gaussian} distribution with a mean of 0.0 and a sigma scaled to
|
||||
produce the requested temperature.
|
||||
|
||||
The {sum} option is used by all styles, except {zero}. The new
|
||||
The {sum} keyword is used by all styles, except {zero}. The new
|
||||
velocities will be added to the existing ones if sum = yes, or will
|
||||
replace them if sum = no.
|
||||
|
||||
The {mom} and {rot} options are used by {create}. If mom = yes, the
|
||||
The {mom} and {rot} keywords are used by {create}. If mom = yes, the
|
||||
linear momentum of the newly created ensemble of velocities is zeroed;
|
||||
if rot = yes, the angular momentum is zeroed.
|
||||
|
||||
The {temp} option is used by {create} and {scale} to specify a
|
||||
"compute"_compute.html that calculates temperature in a desired way.
|
||||
If this option is not specified, {create} and {scale} calculate
|
||||
temperature using a compute that is defined as follows:
|
||||
*line
|
||||
|
||||
If specified, the {temp} keyword is used by {create} and {scale} to
|
||||
specify a "compute"_compute.html that calculates temperature in a
|
||||
desired way, e.g. by first subtracting out a velocity bias, as
|
||||
discussed in "Section howto 16"_Section_howto.html#howto_15 of the doc
|
||||
pages. If this keyword is not specified, {create} and {scale}
|
||||
calculate temperature using a compute that is defined internally as
|
||||
follows:
|
||||
|
||||
compute velocity_temp group-ID temp :pre
|
||||
|
||||
where group-ID is the same ID used in the velocity command. i.e. the
|
||||
group of atoms whose velocity is being altered. This compute is
|
||||
deleted when the velocity command is finished. See the "compute
|
||||
temp"_compute_temp.html command for details. If the computed
|
||||
temp"_compute_temp.html command for details. If the calculated
|
||||
temperature should have degrees-of-freedom removed due to fix
|
||||
constraints (e.g. SHAKE or rigid-body constraints), then the
|
||||
appropriate fix command must be specified before the velocity command
|
||||
is issued.
|
||||
|
||||
The {bias} keyword with a {yes} setting is used by {create} and
|
||||
{scale}, but only if the {temp} keyword is also used to specify a
|
||||
"compute"_compute.html that calculates temperature in a desired way.
|
||||
If the temperature compute also calculates a velocity bias, the the
|
||||
bias is subtracted from atom velocities before the {create} and
|
||||
{scale} operations are performed. After the operations, the bias is
|
||||
added back to the atom velocities. See "Section howto
|
||||
16"_Section_howto.html#howto_15 of the doc pages for more discussion
|
||||
of temperature computes with biases. Note that the velocity bias is
|
||||
only applied to atoms in the temperature compute specified with the
|
||||
{temp} keyword.
|
||||
|
||||
As an example, assume atoms are currently streaming in a flow
|
||||
direction (which could be separately initialized with the {ramp}
|
||||
style), and you wish to initialize their thermal velocity to a desired
|
||||
temperature. In this context thermal velocity means the per-particle
|
||||
velocity that remains when the streaming velocity is subtracted. This
|
||||
can be done using the {create} style with the {temp} keyword
|
||||
specifying the ID of a "compute temp/ramp"_compute_temp_ramp.html or
|
||||
"compute temp/profile"_compute_temp_profile.html command, and the
|
||||
{bias} keyword set to a {yes} value.
|
||||
|
||||
:line
|
||||
|
||||
The {loop} option is used by {create} in the following ways.
|
||||
The {loop} keyword is used by {create} in the following ways.
|
||||
|
||||
If loop = all, then each processor loops over all atoms in the
|
||||
simulation to create velocities, but only stores velocities for atoms
|
||||
|
|
@ -175,23 +203,23 @@ xyz coordinates. A velocity is generated using that seed. This is a
|
|||
fast loop and the velocity assigned to a particular atom will be the
|
||||
same, independent of how many processors are used. However, the set
|
||||
of generated velocities may be more correlated than if the {all} or
|
||||
{local} options are used.
|
||||
{local} keywords are used.
|
||||
|
||||
Note that the {loop geom} option will not necessarily assign identical
|
||||
velocities for two simulations run on different machines. This is
|
||||
because the computations based on xyz coordinates are sensitive to
|
||||
tiny differences in the double-precision value for a coordinate as
|
||||
stored on a particular machine.
|
||||
Note that the {loop geom} keyword will not necessarily assign
|
||||
identical velocities for two simulations run on different machines.
|
||||
This is because the computations based on xyz coordinates are
|
||||
sensitive to tiny differences in the double-precision value for a
|
||||
coordinate as stored on a particular machine.
|
||||
|
||||
:line
|
||||
|
||||
The {rigid} option only has meaning when used with the {zero} style.
|
||||
The {rigid} keyword only has meaning when used with the {zero} style.
|
||||
It allows specification of a fix-ID for one of the "rigid-body
|
||||
fix"_fix_rigid.html variants which defines a set of rigid bodies. The
|
||||
zeroing of linear or angular momentum is then performed for each rigid
|
||||
body defined by the fix, as described above.
|
||||
|
||||
The {units} option is used by {set} and {ramp}. If units = box,
|
||||
The {units} keyword is used by {set} and {ramp}. If units = box,
|
||||
the velocities and coordinates specified in the velocity command are
|
||||
in the standard units described by the "units"_units.html command
|
||||
(e.g. Angstroms/fmsec for real units). If units = lattice, velocities
|
||||
|
|
@ -199,14 +227,16 @@ are in units of lattice spacings per time (e.g. spacings/fmsec) and
|
|||
coordinates are in lattice spacings. The "lattice"_lattice.html
|
||||
command must have been previously used to define the lattice spacing.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Assigning a temperature via the {create} option to a system with
|
||||
"rigid bodies"_fix_rigid.html or "SHAKE constraints"_fix_shake.html
|
||||
may not have the desired outcome for two reasons. First, the velocity
|
||||
command can be invoked before all of the relevant fixes are created
|
||||
and initialized and the number of adjusted degrees of freedom (DOFs)
|
||||
is known. Thus it is not possible to compute the target temperature
|
||||
Assigning a temperature via the {create} style to a system with "rigid
|
||||
bodies"_fix_rigid.html or "SHAKE constraints"_fix_shake.html may not
|
||||
have the desired outcome for two reasons. First, the velocity command
|
||||
can be invoked before all of the relevant fixes are created and
|
||||
initialized and the number of adjusted degrees of freedom (DOFs) is
|
||||
known. Thus it is not possible to compute the target temperature
|
||||
correctly. Second, the assigned velocities may be partially canceled
|
||||
when constraints are first enforced, leading to a different
|
||||
temperature than desired. A workaround for this is to perform a "run
|
||||
|
|
@ -220,10 +250,11 @@ velocity all scale 300.0 # now it should be :pre
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"fix rigid"_fix_rigid.html, "fix shake"_fix_shake.html, "lattice"_lattice.html
|
||||
"fix rigid"_fix_rigid.html, "fix shake"_fix_shake.html,
|
||||
"lattice"_lattice.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are dist = uniform, sum = no, mom = yes, rot = no,
|
||||
temp = full style on group-ID, loop = all, and units = lattice. The
|
||||
rigid option is not defined by default.
|
||||
The keyword defaults are dist = uniform, sum = no, mom = yes, rot =
|
||||
no, bias = no, loop = all, and units = lattice. The temp and rigid
|
||||
keywords are not defined by default.
|
||||
|
|
|
|||
Loading…
Reference in New Issue