Wrote the documentation for fix_press_langevin
This commit is contained in:
Germain Clavier
@ -181,6 +181,7 @@ OPT.
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* :doc:`pour <fix_pour>`
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* :doc:`precession/spin <fix_precession_spin>`
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* :doc:`press/berendsen <fix_press_berendsen>`
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* :doc:`press/langevin <fix_press_langevin>`
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* :doc:`print <fix_print>`
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* :doc:`propel/self <fix_propel_self>`
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* :doc:`property/atom (k) <fix_property_atom>`
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@ -333,6 +333,7 @@ accelerated styles exist.
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* :doc:`pour <fix_pour>` - pour new atoms/molecules into a granular simulation domain
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* :doc:`precession/spin <fix_precession_spin>` - apply a precession torque to each magnetic spin
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* :doc:`press/berendsen <fix_press_berendsen>` - pressure control by Berendsen barostat
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* :doc:`press/langevin <fix_press_langevin>` - pressure control by Langevin barostat
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* :doc:`print <fix_print>` - print text and variables during a simulation
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* :doc:`propel/self <fix_propel_self>` - model self-propelled particles
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* :doc:`property/atom <fix_property_atom>` - add customized per-atom values
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230
doc/src/fix_press_langevin.rst
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230
doc/src/fix_press_langevin.rst
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.. index:: fix press/langevin
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fix press/langevin command
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===========================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID press/langevin keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* press/langevin = style name of this fix command
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.. parsed-literal::
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one or more keyword value pairs may be appended
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keyword = *iso* or *aniso* or *x* or *y* or *z* or *couple* or *dilate* or *modulus* or *temp*
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*iso* or *aniso* values = Pstart Pstop Pdamp
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Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
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Pdamp = pressure damping parameter
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*x* or *y* or *z* values = Pstart Pstop Pdamp
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Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
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Pdamp = stress damping parameter
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*couple* = *none* or *xyz* or *xy* or *yz* or *xz*
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*friction* value = Friction to apply to the barostat
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*temp* values = Tstart, Tstop
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Tstart, Tstop = target temperature used for the barostat at start/end of run
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*dilate* value = *all* or *partial*
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all press/langevin iso 0.0 0.0 1000.0 temp 300 300
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fix 2 all press/langevin aniso 0.0 0.0 1000.0 temp 100 300 dilate partial
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Description
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"""""""""""
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Reset the pressure of the system by using a Langevin stochastic barostat
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:ref:`(Grønbech) <Grønbech>`, which rescales the system volume and
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(optionally) the atoms coordinates within the simulation box every
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timestep.
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The Langevin barostat couple each direction *L* with a pseudo-particle that obeys
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the Langevin equation such as:
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.. math::
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f_P = & \frac{N k_B T_{target}}{V} + \frac{1}{V d}\sum_{i=1}^{N} \vec r_i \cdot \vec f_i - P_{target} \\
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Q\ddot{L} + \alpha{}\dot{L} = & f_P + \beta(t)\\
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L^{n+1} = & L^{n} + bdt\dot{L}^{n} \frac{bdt^{2}}{2Q} \\
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\dot{L}^{n+1} = & \alpha\dot{L}^{n} + \frac{dt}{2Q}\left(a f^{n}_{P} + f^{n+1}_{P}\right) + \frac{b}{Q}\beta^{n+1} \\
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a = & \frac{1-\frac{\alpha{}dt}{2Q}}{1+\frac{\alpha{}dt}{2Q}} \\
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b = & \frac{1}{1+\frac{\alpha{}dt}{2Q}} \\
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\left< \beta(t)\beta(t') \right> = & 2\alpha k_B Tdt
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Where :math:`dt` is the timestep :math:`\dot{L}` and :math:`\ddot{L}` the first
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and second derivatives of the coupled direction with regard to time,
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:math:`\alpha` is a friction coefficient, :math:`\beta` is a random gaussian
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variable and :math:`Q` the effective mass of the coupled pseudoparticle. The
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two first terms on the righthand side of the first equation are the virial
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expression of the canonical pressure. It is to be noted that the temperature
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used to compute the pressure is not the velocity of the atom but the canonical
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target temperature directly. This temperature is specified using the *temp*
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keyword parameter and should be close to the current target temperature of the
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system.
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Regardless of what atoms are in the fix group, a global pressure is
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computed for all atoms. Similarly, when the size of the simulation
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box is changed, all atoms are re-scaled to new positions, unless the
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keyword *dilate* is specified with a value of *partial*, in which case
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only the atoms in the fix group are re-scaled. The latter can be
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useful for leaving the coordinates of atoms in a solid substrate
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unchanged and controlling the pressure of a surrounding fluid.
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.. note::
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Unlike the :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` commands which
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perform Nose/Hoover barostatting AND time integration, this fix does NOT
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perform time integration of the atoms but only of the barostat coupled
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coordinate. It then only modifies the box size and atom coordinates to
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effect barostatting. Thus you must use a separate time integration fix,
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like :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>` to actually update
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the positions and velocities of atoms. This fix can be used in conjunction
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with thermostatting fixes to control the temperature, such as :doc:`fix nvt
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<fix_nh>` or :doc:`fix langevin <fix_langevin>` or :doc:`fix temp/berendsen
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<fix_temp_berendsen>`.
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See the :doc:`Howto barostat <Howto_barostat>` page for a
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discussion of different ways to perform barostatting.
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----------
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The barostat is specified using one or more of the *iso*, *aniso*,
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*x*, *y*, *z*, and *couple* keywords. These keywords give you the
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ability to specify the 3 diagonal components of an external stress
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tensor, and to couple various of these components together so that the
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dimensions they represent are varied together during a
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constant-pressure simulation. Unlike the :doc:`fix npt <fix_nh>` and
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:doc:`fix nph <fix_nh>` commands, this fix cannot be used with triclinic
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(non-orthogonal) simulation boxes to control all 6 components of the
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general pressure tensor.
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The target pressures for each of the 3 diagonal components of the
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stress tensor can be specified independently via the *x*, *y*, *z*,
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keywords, which correspond to the 3 simulation box dimensions. For
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each component, the external pressure or tensor component at each
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timestep is a ramped value during the run from *Pstart* to *Pstop*\ .
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If a target pressure is specified for a component, then the
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corresponding box dimension will change during a simulation. For
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example, if the *y* keyword is used, the y-box length will change. A
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box dimension will not change if that component is not specified,
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although you have the option to change that dimension via the :doc:`fix deform <fix_deform>` command.
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For all barostat keywords, the *Pdamp* parameter determines the "mass" of the
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pseudo particle acting as a barostat. The relation is such that :math:`P_{damp}
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= \frac{1}{Q}` where Q is the mass.
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----------
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The *couple* keyword allows two or three of the diagonal components of
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the pressure tensor to be "coupled" together. The value specified
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with the keyword determines which are coupled. For example, *xz*
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means the *Pxx* and *Pzz* components of the stress tensor are coupled.
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*Xyz* means all 3 diagonal components are coupled. Coupling means two
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things: the instantaneous stress will be computed as an average of the
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corresponding diagonal components, and the coupled box dimensions will
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be changed together in lockstep, meaning coupled dimensions will be
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dilated or contracted by the same percentage every timestep. The
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*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must
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be identical. *Couple xyz* can be used for a 2d simulation; the *z*
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dimension is simply ignored.
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----------
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The *iso* and *aniso* keywords are simply shortcuts that are
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equivalent to specifying several other keywords together.
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The keyword *iso* means couple all 3 diagonal components together when
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pressure is computed (hydrostatic pressure), and dilate/contract the
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dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
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specifying these 4 keywords:
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.. parsed-literal::
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x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple xyz
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The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled
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independently using the *Pxx*, *Pyy*, and *Pzz* components of the
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stress tensor as the driving forces, and the specified scalar external
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pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
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these 4 keywords:
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.. parsed-literal::
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x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple none
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----------
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This fix computes pressure each timestep. To do
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this, the fix creates its own computes of style "pressure",
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as if this command had been issued:
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.. code-block:: LAMMPS
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compute fix-ID_press group-ID pressure fix-ID_NULL virial
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See the :doc:`compute pressure <compute_pressure>` command for details. Note
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that the IDs of the new compute is the fix-ID + underscore + "press" and the
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group for the new computes is the same as the fix group.
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Note that this is NOT the compute used by thermodynamic output (see
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the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_press*.
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This means you can change the attributes of this fix's pressure via the
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:doc:`compute_modify <compute_modify>` command or print this temperature
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or pressure during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
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It also means that changing attributes of *thermo_temp* or
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*thermo_press* will have no effect on this fix.
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`.
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The :doc:`fix_modify <fix_modify>` *press* option is
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supported by this fix. You can use it to assign a
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:doc:`compute <compute>` you have defined to this fix which will be used
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in its pressure calculations.
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No global or per-atom quantities are stored by this fix for access by
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various :doc:`output commands <Howto_output>`.
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This fix can ramp its target pressure over multiple runs, using the
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*start* and *stop* keywords of the :doc:`run <run>` command. See the
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:doc:`run <run>` command for details of how to do this.
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This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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Any dimension being adjusted by this fix must be periodic.
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Related commands
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""""""""""""""""
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:doc:`fix nve <fix_nve>`, :doc:`fix nph <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`fix langevin <fix_langevin>`,
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:doc:`fix_modify <fix_modify>`
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Default
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"""""""
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The keyword defaults are dilate = all, friction = 0.0001 in units of
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pressure for whatever :doc:`units <units>` are defined.
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----------
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.. _Grønbech:
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**(Grønbech)** Grønbech-Jensen, Farago, J Chem Phys, 141, 194108 (2014).
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