forked from lijiext/lammps
199 lines
8.2 KiB
Plaintext
199 lines
8.2 KiB
Plaintext
.. index:: compute temp/profile
|
|
|
|
compute temp/profile command
|
|
============================
|
|
|
|
Syntax
|
|
""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
compute ID group-ID temp/profile xflag yflag zflag binstyle args
|
|
|
|
* ID, group-ID are documented in :doc:`compute <compute>` command
|
|
* temp/profile = style name of this compute command
|
|
* xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
|
|
* binstyle = *x* or *y* or *z* or *xy* or *yz* or *xz* or *xyz*
|
|
.. parsed-literal::
|
|
|
|
*x* arg = Nx
|
|
*y* arg = Ny
|
|
*z* arg = Nz
|
|
*xy* args = Nx Ny
|
|
*yz* args = Ny Nz
|
|
*xz* args = Nx Nz
|
|
*xyz* args = Nx Ny Nz
|
|
Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
|
|
|
|
* zero or more keyword/value pairs may be appended
|
|
* keyword = *out*
|
|
.. parsed-literal::
|
|
|
|
*out* value = *tensor* or *bin*
|
|
|
|
|
|
|
|
Examples
|
|
""""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
compute myTemp flow temp/profile 1 1 1 x 10
|
|
compute myTemp flow temp/profile 1 1 1 x 10 out bin
|
|
compute myTemp flow temp/profile 0 1 1 xyz 20 20 20
|
|
|
|
Description
|
|
"""""""""""
|
|
|
|
Define a computation that calculates the temperature of a group of
|
|
atoms, after subtracting out a spatially-averaged center-of-mass
|
|
velocity field, before computing the kinetic energy. This can be
|
|
useful for thermostatting a collection of atoms undergoing a complex
|
|
flow, e.g. via a profile-unbiased thermostat (PUT) as described in
|
|
:ref:`(Evans) <Evans>`. A compute of this style can be used by any command
|
|
that computes a temperature, e.g. :doc:`thermo_modify <thermo_modify>`,
|
|
:doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
|
|
|
|
The *xflag*, *yflag*, *zflag* settings determine which components of
|
|
average velocity are subtracted out.
|
|
|
|
The *binstyle* setting and its *Nx*, *Ny*, *Nz* arguments determine
|
|
how bins are setup to perform spatial averaging. "Bins" can be 1d
|
|
slabs, 2d pencils, or 3d bricks depending on which *binstyle* is used.
|
|
The simulation box is partitioned conceptually into *Nx* by *Ny* by
|
|
*Nz* bins. Depending on the *binstyle*, you may only specify one or
|
|
two of these values; the others are effectively set to 1 (no binning
|
|
in that dimension). For non-orthogonal (triclinic) simulation boxes,
|
|
the bins are "tilted" slabs or pencils or bricks that are parallel to
|
|
the tilted faces of the box. See the :doc:`region prism <region>`
|
|
command for a discussion of the geometry of tilted boxes in LAMMPS.
|
|
|
|
When a temperature is computed, the center-of-mass velocity for the
|
|
set of atoms that are both in the compute group and in the same
|
|
spatial bin is calculated. This bias velocity is then subtracted from
|
|
the velocities of individual atoms in the bin to yield a thermal
|
|
velocity for each atom. Note that if there is only one atom in the
|
|
bin, its thermal velocity will thus be 0.0.
|
|
|
|
After the spatially-averaged velocity field has been subtracted from
|
|
each atom, the temperature is calculated by the formula KE = (dim/2 N
|
|
- dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of
|
|
atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
|
|
simulation, N = number of atoms in the group, k = Boltzmann constant,
|
|
and T = temperature. The dim*Nx*Ny*Nz term are degrees of freedom
|
|
subtracted to adjust for the removal of the center-of-mass velocity in
|
|
each of Nx*Ny*Nz bins, as discussed in the :ref:`(Evans) <Evans>` paper.
|
|
|
|
If the *out* keyword is used with a *tensor* value, which is the
|
|
default, a kinetic energy tensor, stored as a 6-element vector, is
|
|
also calculated by this compute for use in the computation of a
|
|
pressure tensor. The formula for the components of the tensor is the
|
|
same as the above formula, except that v^2 is replaced by vx*vy for
|
|
the xy component, etc. The 6 components of the vector are ordered xx,
|
|
yy, zz, xy, xz, yz.
|
|
|
|
If the *out* keyword is used with a *bin* value, the count of atoms
|
|
and computed temperature for each bin are stored for output, as an
|
|
array of values, as described below. The temperature of each bin is
|
|
calculated as described above, where the bias velocity is subtracted
|
|
and only the remaining thermal velocity of atoms in the bin
|
|
contributes to the temperature. See the note below for how the
|
|
temperature is normalized by the degrees-of-freedom of atoms in the
|
|
bin.
|
|
|
|
The number of atoms contributing to the temperature is assumed to be
|
|
constant for the duration of the run; use the *dynamic* option of the
|
|
:doc:`compute_modify <compute_modify>` command if this is not the case.
|
|
|
|
The removal of the spatially-averaged velocity field by this fix is
|
|
essentially computing the temperature after a "bias" has been removed
|
|
from the velocity of the atoms. If this compute is used with a fix
|
|
command that performs thermostatting then this bias will be subtracted
|
|
from each atom, thermostatting of the remaining thermal velocity will
|
|
be performed, and the bias will be added back in. Thermostatting
|
|
fixes that work in this way include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`.
|
|
|
|
This compute subtracts out degrees-of-freedom due to fixes that
|
|
constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
|
|
:doc:`fix rigid <fix_rigid>`. This means the temperature of groups of
|
|
atoms that include these constraints will be computed correctly. If
|
|
needed, the subtracted degrees-of-freedom can be altered using the
|
|
*extra* option of the :doc:`compute_modify <compute_modify>` command.
|
|
|
|
.. note::
|
|
|
|
When using the *out* keyword with a value of *bin*, the
|
|
calculated temperature for each bin does not include the
|
|
degrees-of-freedom adjustment described in the preceeding paragraph,
|
|
for fixes that constrain molecular motion. It does include the
|
|
adjustment due to the *extra* option, which is applied to each bin.
|
|
|
|
See :ref:`this howto section <howto_16>` of the manual for
|
|
a discussion of different ways to compute temperature and perform
|
|
thermostatting. Using this compute in conjunction with a
|
|
thermostatting fix, as explained there, will effectively implement a
|
|
profile-unbiased thermostat (PUT), as described in :ref:`(Evans) <Evans>`.
|
|
|
|
**Output info:**
|
|
|
|
This compute calculates a global scalar (the temperature). Depending
|
|
on the setting of the *out* keyword, it also calculates a global
|
|
vector or array. For *out* = *tensor*, it calculates a vector of
|
|
length 6 (KE tensor), which can be accessed by indices 1-6. For *out*
|
|
= *bin* it calculates a global array which has 2 columns and N rows,
|
|
where N is the number of bins. The first column contains the number
|
|
of atoms in that bin. The second contains the temperature of that
|
|
bin, calculated as described above. The ordering of rows in the array
|
|
is as follows. Bins in x vary fastest, then y, then z. Thus for a
|
|
10x10x10 3d array of bins, there will be 1000 rows. The bin with
|
|
indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10
|
|
+ ix = 322, where the rows are numbered from 1 to 1000 and the bin
|
|
indices are numbered from 1 to 10 in each dimension.
|
|
|
|
These values can be used by any command that uses global scalar or
|
|
vector or array values from a compute as input. See :ref:`this section <howto_15>` for an overview of LAMMPS output
|
|
options.
|
|
|
|
The scalar value calculated by this compute is "intensive". The
|
|
vector values are "extensive". The array values are "intensive".
|
|
|
|
The scalar value will be in temperature :doc:`units <units>`. The
|
|
vector values will be in energy :doc:`units <units>`. The first column
|
|
of array values are counts; the values in the second column will be in
|
|
temperature :doc:`units <units>`.
|
|
|
|
Restrictions
|
|
""""""""""""
|
|
|
|
|
|
You should not use too large a velocity-binning grid, especially in
|
|
3d. In the current implementation, the binned velocity averages are
|
|
summed across all processors, so this will be inefficient if the grid
|
|
is too large, and the operation is performed every timestep, as it
|
|
will be for most thermostats.
|
|
|
|
Related commands
|
|
""""""""""""""""
|
|
|
|
:doc:`compute temp <compute_temp>`, :doc:`compute temp/ramp <compute_temp_ramp>`, :doc:`compute temp/deform <compute_temp_deform>`, :doc:`compute pressure <compute_pressure>`
|
|
|
|
Default
|
|
"""""""
|
|
|
|
The option default is out = tensor.
|
|
|
|
|
|
----------
|
|
|
|
|
|
.. _Evans:
|
|
|
|
|
|
|
|
**(Evans)** Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).
|
|
|
|
|
|
.. _lws: http://lammps.sandia.gov
|
|
.. _ld: Manual.html
|
|
.. _lc: Section_commands.html#comm
|