All but the first 3 calculate velocity biases (i.e. advection +
All but the first 3 calculate velocity biases directly (e.g. advection velocities) that are removed when computing the thermal temperature. Compute temp/sphere and compute temp/asphere compute kinetic energy for finite-size particles that includes rotational degrees of freedom. -They both allow, as an extra argument, which is another temperature -compute that subtracts a velocity bias. This allows the translational -velocity of spherical or aspherical particles to be adjusted in -prescribed ways. +They both allow for velocity biases indirectly, via an optional extra +argument, another temperature compute that subtracts a velocity bias. +This allows the translational velocity of spherical or aspherical +particles to be adjusted in prescribed ways.
Thermostatting in LAMMPS is performed by fixes, or in one case by a pair style. Several thermostatting fixes are available: @@ -1658,15 +1658,21 @@ to the per-particle thermostatting of fix langevin.
Any of the thermostatting fixes can use temperature computes that -remove bias for two purposes: (a) computing the current temperature to -compare to the requested target temperature, and (b) adjusting only -the thermal temperature component of the particle's velocities. See -the doc pages for the individual fixes and for the +remove bias which has two effects. First, the current calculated +temperature, which is compared to the requested target temperature, is +caluclated with the velocity bias removed. Second, the thermostat +adjusts only the thermal temperature component of the particle's +velocities, which are the velocities with the bias removed. The +removed bias is then added back to the adjusted velocities. See the +doc pages for the individual fixes and for the fix_modify command for instructions on how to assign a temperature compute to a thermostatting fix. For example, you can apply a thermostat to only the x and z components of velocity by using it in conjunction with compute -temp/partial. +temp/partial. Of you could thermostat only +the thermal temperature of a streaming flow of particles without +affecting the streaming velocity, by using compute +temp/profile.
IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning they update the velocities and positions of particles due to forces diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 99b0bba89d..13274c2fe5 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -1604,15 +1604,15 @@ pressure"_compute_pressure.html command calculates pressure. "compute temp/ramp"_compute_temp_ramp.html "compute temp/region"_compute_temp_region.html :ul -All but the first 3 calculate velocity biases (i.e. advection +All but the first 3 calculate velocity biases directly (e.g. advection velocities) that are removed when computing the thermal temperature. "Compute temp/sphere"_compute_temp_sphere.html and "compute temp/asphere"_compute_temp_asphere.html compute kinetic energy for finite-size particles that includes rotational degrees of freedom. -They both allow, as an extra argument, which is another temperature -compute that subtracts a velocity bias. This allows the translational -velocity of spherical or aspherical particles to be adjusted in -prescribed ways. +They both allow for velocity biases indirectly, via an optional extra +argument, another temperature compute that subtracts a velocity bias. +This allows the translational velocity of spherical or aspherical +particles to be adjusted in prescribed ways. Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one case by a pair style. Several thermostatting fixes are available: @@ -1645,15 +1645,21 @@ to the per-particle thermostatting of "fix langevin"_fix_langevin.html. Any of the thermostatting fixes can use temperature computes that -remove bias for two purposes: (a) computing the current temperature to -compare to the requested target temperature, and (b) adjusting only -the thermal temperature component of the particle's velocities. See -the doc pages for the individual fixes and for the +remove bias which has two effects. First, the current calculated +temperature, which is compared to the requested target temperature, is +caluclated with the velocity bias removed. Second, the thermostat +adjusts only the thermal temperature component of the particle's +velocities, which are the velocities with the bias removed. The +removed bias is then added back to the adjusted velocities. See the +doc pages for the individual fixes and for the "fix_modify"_fix_modify.html command for instructions on how to assign a temperature compute to a thermostatting fix. For example, you can apply a thermostat to only the x and z components of velocity by using it in conjunction with "compute -temp/partial"_compute_temp_partial.html. +temp/partial"_compute_temp_partial.html. Of you could thermostat only +the thermal temperature of a streaming flow of particles without +affecting the streaming velocity, by using "compute +temp/profile"_compute_temp_profile.html. IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning they update the velocities and positions of particles due to forces diff --git a/doc/velocity.html b/doc/velocity.html index 53513fbe4e..5e06774da6 100644 --- a/doc/velocity.html +++ b/doc/velocity.html @@ -38,13 +38,14 @@
dist value = uniform or gaussian
sum value = no or yes
mom value = no or yes
rot value = no or yes
- temp value = temperature ID
+ temp value = temperature compute ID
+ bias value = no or yes
loop value = all or local or geom
rigid value = fix-ID
fix-ID = ID of rigid body fix
@@ -124,42 +125,69 @@ simulation is 2d; see the dimension command.
-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 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 that calculates temperature in a
+desired way, e.g. by first subtracting out a velocity bias, as
+discussed in Section howto 16 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
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 command for details. If the computed
+temp 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 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 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 or
+compute temp/profile command, and the
+bias keyword set to a yes value.
+
-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
@@ -183,23 +211,23 @@ 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.
-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 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 command
(e.g. Angstroms/fmsec for real units). If units = lattice, velocities
@@ -207,14 +235,16 @@ are in units of lattice spacings per time (e.g. spacings/fmsec) and
coordinates are in lattice spacings. The lattice
command must have been previously used to define the lattice spacing.
+
+
Restrictions:
-Assigning a temperature via the create option to a system with
-rigid bodies or SHAKE constraints
-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 or SHAKE constraints 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
@@ -228,12 +258,13 @@ velocity all scale 300.0 # now it should be
Related commands:
-fix rigid, fix shake, lattice +
fix rigid, fix shake, +lattice
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.