forked from lijiext/lammps
376 lines
17 KiB
Plaintext
376 lines
17 KiB
Plaintext
.. index:: fix gcmc
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fix gcmc 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 gcmc N X M type seed T mu displace keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* gcmc = style name of this fix command
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* N = invoke this fix every N steps
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* X = average number of GCMC exchanges to attempt every N steps
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* M = average number of MC moves to attempt every N steps
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* type = atom type for inserted atoms (must be 0 if mol keyword used)
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* seed = random # seed (positive integer)
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* T = temperature of the ideal gas reservoir (temperature units)
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* mu = chemical potential of the ideal gas reservoir (energy units)
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* translate = maximum Monte Carlo translation distance (length units)
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* zero or more keyword/value pairs may be appended to args
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.. parsed-literal::
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keyword = *mol*\ , *region*\ , *maxangle*\ , *pressure*\ , *fugacity_coeff*\ , *full_energy*\ , *charge*\ , *group*\ , *grouptype*\ , *intra_energy*\ , or *tfac_insert*
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*mol* value = template-ID
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template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
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*shake* value = fix-ID
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fix-ID = ID of :doc:`fix shake <fix_shake>` command
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*region* value = region-ID
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region-ID = ID of region where MC moves are allowed
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*maxangle* value = maximum molecular rotation angle (degrees)
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*pressure* value = pressure of the gas reservoir (pressure units)
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*fugacity_coeff* value = fugacity coefficient of the gas reservoir (unitless)
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*full_energy* = compute the entire system energy when performing MC moves
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*charge* value = charge of inserted atoms (charge units)
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*group* value = group-ID
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group-ID = group-ID for inserted atoms (string)
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*grouptype* values = type group-ID
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type = atom type (int)
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group-ID = group-ID for inserted atoms (string)
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*intra_energy* value = intramolecular energy (energy units)
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*tfac_insert* value = scale up/down temperature of inserted atoms (unitless)
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Examples
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""""""""
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.. parsed-literal::
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fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
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fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
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fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
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Description
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"""""""""""
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This fix performs grand canonical Monte Carlo (GCMC) exchanges of
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atoms or molecules of the given type with an imaginary ideal gas reservoir at
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the specified T and chemical potential (mu) as discussed in
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:ref:`(Frenkel) <Frenkel>`. If used with the :doc:`fix nvt <fix_nh>` command,
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simulations in the grand canonical ensemble (muVT, constant chemical
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potential, constant volume, and constant temperature) can be
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performed. Specific uses include computing isotherms in microporous
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materials, or computing vapor-liquid coexistence curves.
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Every N timesteps the fix attempts a number of GCMC exchanges (insertions
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or deletions) of gas atoms or molecules of
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the given type between the simulation cell and the imaginary
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reservoir. It also attempts a number of Monte Carlo
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moves (translations and molecule rotations) of gas of the given type
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within the simulation cell or region. The average number of
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attempted GCMC exchanges is X. The average number of attempted MC moves is M.
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M should typically be chosen to be
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approximately equal to the expected number of gas atoms or molecules
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of the given type within the simulation cell or region,
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which will result in roughly one
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MC translation per atom or molecule per MC cycle.
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For MC moves of molecular gasses, rotations and translations are each
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attempted with 50% probability. For MC moves of atomic gasses,
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translations are attempted 100% of the time. For MC exchanges of
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either molecular or atomic gasses, deletions and insertions are each
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attempted with 50% probability.
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All inserted particles are always assigned to two groups: the default group
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"all" and the group specified in the fix gcmc command (which can also
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be "all"). In addition, particles are also added to any groups specified
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by the *group* and *grouptype* keywords.
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If inserted particles are individual atoms, they are
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assigned the atom type given by the type argument. If they are molecules,
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the type argument has no effect and must be set to zero. Instead,
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the type of each atom in the inserted molecule is specified
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in the file read by the :doc:`molecule <molecule>` command.
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This fix cannot be used to perform MC insertions of gas atoms or
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molecules other than the exchanged type, but MC deletions,
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translations, and rotations can be performed on any atom/molecule in
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the fix group. All atoms in the simulation cell can be moved using
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regular time integration translations, e.g. via
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:doc:`fix nvt <fix_nh>`, resulting in a hybrid GCMC+MD simulation. A
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smaller-than-usual timestep size may be needed when running such a
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hybrid simulation, especially if the inserted molecules are not well
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equilibrated.
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This command may optionally use the *region* keyword to define an
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exchange and move volume. The specified region must have been
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previously defined with a :doc:`region <region>` command. It must be
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defined with side = *in*\ . Insertion attempts occur only within the
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specified region. For non-rectangular regions, random trial
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points are generated within the rectangular bounding box until a point is found
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that lies inside the region. If no valid point is generated after 1000 trials,
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no insertion is performed, but it is counted as an attempted insertion.
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Move and deletion attempt candidates are selected
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from gas atoms or molecules within the region. If there are no candidates,
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no move or deletion is performed, but it is counted as an attempt move
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or deletion. If an attempted move places the atom or molecule center-of-mass outside
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the specified region, a new attempted move is generated. This process is repeated
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until the atom or molecule center-of-mass is inside the specified region.
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If used with :doc:`fix nvt <fix_nh>`, the temperature of the imaginary
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reservoir, T, should be set to be equivalent to the target temperature
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used in fix nvt. Otherwise, the imaginary reservoir
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will not be in thermal equilibrium with the simulation cell. Also,
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it is important that the temperature used by fix nvt be dynamic,
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which can be achieved as follows:
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.. parsed-literal::
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compute mdtemp mdatoms temp
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compute_modify mdtemp dynamic yes
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fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
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fix_modify mdnvt temp mdtemp
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Note that neighbor lists are re-built every timestep that this fix is
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invoked, so you should not set N to be too small. However, periodic
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rebuilds are necessary in order to avoid dangerous rebuilds and missed
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interactions. Specifically, avoid performing so many MC translations
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per timestep that atoms can move beyond the neighbor list skin
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distance. See the :doc:`neighbor <neighbor>` command for details.
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When an atom or molecule is to be inserted, its
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coordinates are chosen at a random position within the current
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simulation cell or region, and new atom velocities are randomly chosen from
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the specified temperature distribution given by T. The effective
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temperature for new atom velocities can be increased or decreased
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using the optional keyword *tfac_insert* (see below). Relative
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coordinates for atoms in a molecule are taken from the template
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molecule provided by the user. The center of mass of the molecule
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is placed at the insertion point. The orientation of the molecule
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is chosen at random by rotating about this point.
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Individual atoms are inserted, unless the *mol* keyword is used. It
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specifies a *template-ID* previously defined using the
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:doc:`molecule <molecule>` command, which reads a file that defines the
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molecule. The coordinates, atom types, charges, etc, as well as any
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bond/angle/etc and special neighbor information for the molecule can
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be specified in the molecule file. See the :doc:`molecule <molecule>`
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command for details. The only settings required to be in this file
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are the coordinates and types of atoms in the molecule.
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When not using the *mol* keyword, you should ensure you do not delete
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atoms that are bonded to other atoms, or LAMMPS will
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soon generate an error when it tries to find bonded neighbors. LAMMPS will
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warn you if any of the atoms eligible for deletion have a non-zero
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molecule ID, but does not check for this at the time of deletion.
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If you wish to insert molecules via the *mol* keyword, that will have
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their bonds or angles constrained via SHAKE, use the *shake* keyword,
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specifying as its value the ID of a separate :doc:`fix shake <fix_shake>` command which also appears in your input script.
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Optionally, users may specify the maximum rotation angle for
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molecular rotations using the *maxangle* keyword and specifying
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the angle in degrees. Rotations are performed by generating a random
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point on the unit sphere and a random rotation angle on the
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range [0,maxangle). The molecule is then rotated by that angle about an
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axis passing through the molecule center of mass. The axis is parallel
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to the unit vector defined by the point on the unit sphere.
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The same procedure is used for randomly rotating molecules when they
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are inserted, except that the maximum angle is 360 degrees.
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Note that fix GCMC does not use configurational bias
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MC or any other kind of sampling of intramolecular degrees of freedom.
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Inserted molecules can have different orientations, but they will all
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have the same intramolecular configuration,
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which was specified in the molecule command input.
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For atomic gasses, inserted atoms have the specified atom type, but
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deleted atoms are any atoms that have been inserted or that belong
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to the user-specified fix group. For molecular gasses, exchanged
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molecules use the same atom types as in the template molecule
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supplied by the user. In both cases, exchanged
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atoms/molecules are assigned to two groups: the default group "all"
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and the group specified in the fix gcmc command (which can also be
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"all").
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The gas reservoir pressure can be specified using the *pressure*
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keyword, in which case the user-specified chemical potential is
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ignored. For non-ideal gas reservoirs, the user may also specify the
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fugacity coefficient using the *fugacity_coeff* keyword.
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The *full_energy* option means that fix GCMC will compute the total
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potential energy of the entire simulated system. The total system
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energy before and after the proposed GCMC move is then used in the
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Metropolis criterion to determine whether or not to accept the
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proposed GCMC move. By default, this option is off, in which case
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only partial energies are computed to determine the difference in
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energy that would be caused by the proposed GCMC move.
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The *full_energy* option is needed for systems with complicated
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potential energy calculations, including the following:
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* long-range electrostatics (kspace)
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* many-body pair styles
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* hybrid pair styles
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* eam pair styles
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* triclinic systems
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* need to include potential energy contributions from other fixes
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In these cases, LAMMPS will automatically apply the *full_energy*
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keyword and issue a warning message.
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When the *mol* keyword is used, the *full_energy* option also includes
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the intramolecular energy of inserted and deleted molecules. If this
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is not desired, the *intra_energy* keyword can be used to define an
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amount of energy that is subtracted from the final energy when a molecule
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is inserted, and added to the initial energy when a molecule is
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deleted. For molecules that have a non-zero intramolecular energy, this
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will ensure roughly the same behavior whether or not the *full_energy*
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option is used.
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Inserted atoms and molecules are assigned random velocities based on the
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specified temperature T. Because the relative velocity of
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all atoms in the molecule is zero, this may result in inserted molecules
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that are systematically too cold. In addition, the intramolecular potential
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energy of the inserted molecule may cause the kinetic energy
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of the molecule to quickly increase or decrease after insertion.
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The *tfac_insert* keyword allows the user to counteract these effects
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by changing the temperature used to assign velocities to
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inserted atoms and molecules by a constant factor. For a
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particular application, some experimentation may be required
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to find a value of *tfac_insert* that results in inserted molecules that
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equilibrate quickly to the correct temperature.
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Some fixes have an associated potential energy. Examples of such fixes
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include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
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:doc:`addforce <fix_addforce>`, :doc:`langevin <fix_langevin>`,
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:doc:`restrain <fix_restrain>`, :doc:`temp/berendsen <fix_temp_berendsen>`,
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:doc:`temp/rescale <fix_temp_rescale>`, and :doc:`wall fixes <fix_wall>`.
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For that energy to be included in the total potential energy of the
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system (the quantity used when performing GCMC moves),
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you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for
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that fix. The doc pages for individual :doc:`fix <fix>` commands
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specify if this should be done.
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Use the *charge* option to insert atoms with a user-specified point
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charge. Note that doing so will cause the system to become non-neutral.
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LAMMPS issues a warning when using long-range electrostatics (kspace)
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with non-neutral systems. See the
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:doc:`compute group/group <compute_group_group>` documentation for more
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details about simulating non-neutral systems with kspace on.
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Use of this fix typically will cause the number of atoms to fluctuate,
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therefore, you will want to use the
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:doc:`compute_modify <compute_modify>` command to insure that the
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current number of atoms is used as a normalizing factor each time
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temperature is computed. Here is the necessary command:
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.. parsed-literal::
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compute_modify thermo_temp dynamic yes
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If LJ units are used, note that a value of 0.18292026 is used by this
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fix as the reduced value for Planck's constant. This value was
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derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
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epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
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mass = 39.948 amu.
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The *group* keyword assigns all inserted atoms to the :doc:`group <group>`
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of the group-ID value. The *grouptype* keyword assigns all
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inserted atoms of the specified type to the :doc:`group <group>`
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of the group-ID value.
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Restart, fix_modify, output, run start/stop, minimize info
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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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This fix writes the state of the fix to :doc:`binary restart files <restart>`. This includes information about the random
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number generator seed, the next timestep for MC exchanges, etc. See
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the :doc:`read_restart <read_restart>` command for info on how to
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re-specify a fix in an input script that reads a restart file, so that
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the operation of the fix continues in an uninterrupted fashion.
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None of the :doc:`fix_modify <fix_modify>` options are relevant to this
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fix.
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This fix computes a global vector of length 8, which can be accessed
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by various :ref:`output commands <howto_15>`. The vector
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values are the following global cumulative quantities:
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* 1 = translation attempts
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* 2 = translation successes
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* 3 = insertion attempts
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* 4 = insertion successes
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* 5 = deletion attempts
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* 6 = deletion successes
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* 7 = rotation attempts
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* 8 = rotation successes
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The vector values calculated by this fix are "extensive".
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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This fix is part of the MC package. It is only enabled if LAMMPS was
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built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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Do not set "neigh_modify once yes" or else this fix will never be
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called. Reneighboring is required.
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Can be run in parallel, but aspects of the GCMC part will not scale
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well in parallel. Only usable for 3D simulations.
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Note that very lengthy simulations involving insertions/deletions of
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billions of gas molecules may run out of atom or molecule IDs and
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trigger an error, so it is better to run multiple shorter-duration
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simulations. Likewise, very large molecules have not been tested
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and may turn out to be problematic.
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Use of multiple fix gcmc commands in the same input script can be
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problematic if using a template molecule. The issue is that the
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user-referenced template molecule in the second fix gcmc command
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may no longer exist since it might have been deleted by the first
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fix gcmc command. An existing template molecule will need to be
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referenced by the user for each subsequent fix gcmc command.
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Because molecule insertion does not work in combination with
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fix rigid, simulataneous use of fix rigid or fix rigid/small
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with this fix is not allowed.
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Related commands
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""""""""""""""""
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:doc:`fix atom/swap <fix_atom_swap>`,
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:doc:`fix nvt <fix_nh>`, :doc:`neighbor <neighbor>`,
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:doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
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:doc:`delete_atoms <delete_atoms>`
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Default
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"""""""
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The option defaults are mol = no, maxangle = 10, full_energy = no,
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except for the situations where full_energy is required, as
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listed above.
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----------
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.. _Frenkel:
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**(Frenkel)** Frenkel and Smit, Understanding Molecular Simulation,
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Academic Press, London, 2002.
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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