change from DOS/Windows CR/LF to LF
This commit is contained in:
Axel Kohlmeyer
@ -1,227 +1,227 @@
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.. index:: fix widom
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fix widom 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 widom N M type seed T keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* widom = style name of this fix command
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* N = invoke this fix every N steps
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* M = number of Widom insertions 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 system (temperature 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*\ , *full_energy*, *charge*\ , *intra_energy*
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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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*region* value = region-ID
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region-ID = ID of region where Widom insertions are allowed
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*full_energy* = compute the entire system energy when performing Widom insertions
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*charge* value = charge of inserted atoms (charge units)
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*intra_energy* value = intramolecular energy (energy units)
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 2 gas widom 1 50000 1 19494 2.0
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fix 3 water widom 1000 100 0 29494 300.0 mol h2omol full_energy
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Description
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"""""""""""
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This fix performs Widom insertions of atoms or molecules at the given
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temperature as discussed in :ref:`(Frenkel) <Frenkel>`. Specific uses
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include computation of Henry constants of small molecules in microporous
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materials or amorphous systems.
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Every N timesteps the fix attempts M number of Widom insertions of atoms
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or molecules.
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If the *mol* keyword is used, only molecule insertions are performed.
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Conversely, if the *mol* keyword is not used, only atom insertions are
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performed.
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This command may optionally use the *region* keyword to define an
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insertion volume. The specified region must have been previously
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defined with a :doc:`region <region>` command. It must be defined with
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side = *in*\ . Insertion attempts occur only within the specified
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region. For non-rectangular regions, random trial points are generated
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within the rectangular bounding box until a point is found that lies
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inside the region. If no valid point is generated after 1000 trials, no
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insertion is performed. If an attempted insertion places the atom or
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molecule center-of-mass outside the specified region, a new attempted
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insertion is generated. This process is repeated until the atom or
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molecule center-of-mass is inside the specified region.
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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. See the :doc:`neighbor
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<neighbor>` command for details.
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When an atom or molecule is to be inserted, its coordinates are chosen
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at a random position within the current simulation cell or
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regionRelative coordinates for atoms in a molecule are taken from the
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template molecule provided by the user. The center of mass of the
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molecule is placed at the insertion point. The orientation of the
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molecule 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 :doc:`molecule
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<molecule>` command, which reads a file that defines the molecule. The
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coordinates, atom types, charges, etc., as well as any bonding and
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special neighbor information for the molecule can be specified in the
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molecule file. See the :doc:`molecule <molecule>` command for details.
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The only settings required to be in this file are the coordinates and
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types of atoms in the molecule.
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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
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<fix_shake>` command which also appears in your input script.
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Note that fix widom does not use configurational bias MC or any other
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kind of sampling of intramolecular degrees of freedom. Inserted
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molecules can have different orientations, but they will all have the
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same intramolecular configuration, which was specified in the molecule
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command input.
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For atoms, inserted particles have the specified atom type. For
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molecules, they use the same atom types as in the template molecule
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supplied by the user.
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The excess chemical potential mu_ex is defined as:
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.. math::
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\mu_{ex} = -kT \ln(<\exp(-(U_{N+1}-U_{N})/{kT})>)
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where *k* is Boltzman's constant, *T* is the user-specified temperature,
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U_N and U_{N+1} is the potential energy of the system with N and N+1
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particles.
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The *full_energy* option means that the fix calculates the total
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potential energy of the entire simulated system, instead of just the
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energy of the part that is changed. By default, this option is off, in
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which case only partial energies are computed to determine the energy
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difference due to the proposed change.
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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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* tail corrections
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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, whereas
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this energy is not included when *full_energy* is not used. If this is
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not desired, the *intra_energy* keyword can be used to define an amount
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of energy that is subtracted from the final energy when a molecule is
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inserted, and subtracted from 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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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:`restrain <fix_restrain>`, and
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:doc:`wall fixes <fix_wall>`. For that energy to be included in the
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total potential energy of the system (the quantity used when performing
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Widom insertions), you MUST enable the :doc:`fix_modify <fix_modify>`
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*energy* option for that fix. The doc pages for individual :doc:`fix
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<fix>` commands 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 :doc:`compute group/group
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<compute_group_group>` documentation for more details about simulating
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non-neutral systems with kspace on.
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**Restart, fix_modify, output, run start/stop, minimize info:**
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This fix writes the state of the fix to :doc:`binary restart files
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<restart>`. This includes information about the random number generator
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seed, the next timestep for Widom insertions etc. See the
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:doc:`read_restart <read_restart>` command for info on how to re-specify
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a fix in an input script that reads a restart file, so that the
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operation of the fix continues in an uninterrupted fashion.
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.. note::
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For this to work correctly, the timestep must **not** be changed
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after reading the restart with :doc:`reset_timestep
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<reset_timestep>`. The fix will try to detect it and stop with an
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error.
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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 3, which can be accessed by
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various :doc:`output commands <Howto_output>`. The vector values are
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the following global cumulative quantities:
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* 1 = average excess chemical potential on each timestep
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* 2 = average difference in potential energy on each timestep
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* 3 = volume of the insertion region
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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
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: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 :doc:`Build package <Build_package>`
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doc page 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 well
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in parallel. Only usable for 3D simulations.
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Related commands
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""""""""""""""""
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:doc:`fix gcmc <fix_gcmc>`
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:doc:`fix atom/swap <fix_atom_swap>`,
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:doc:`neighbor <neighbor>`,
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:doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
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Default
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"""""""
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The option defaults are mol = no, intra_energy = 0.0 and full_energy =
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no, except for the situations where full_energy is required, as listed
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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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.. index:: fix widom
|
||||
|
||||
fix widom command
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=================
|
||||
|
||||
Syntax
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""""""
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||||
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.. parsed-literal::
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|
||||
fix ID group-ID widom N M type seed T keyword values ...
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* widom = style name of this fix command
|
||||
* N = invoke this fix every N steps
|
||||
* M = number of Widom insertions to attempt every N steps
|
||||
* type = atom type for inserted atoms (must be 0 if mol keyword used)
|
||||
* seed = random # seed (positive integer)
|
||||
* T = temperature of the system (temperature units)
|
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* zero or more keyword/value pairs may be appended to args
|
||||
|
||||
.. parsed-literal::
|
||||
|
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keyword = *mol*\ , *region*\ , *full_energy*, *charge*\ , *intra_energy*
|
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*mol* value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
|
||||
*region* value = region-ID
|
||||
region-ID = ID of region where Widom insertions are allowed
|
||||
*full_energy* = compute the entire system energy when performing Widom insertions
|
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*charge* value = charge of inserted atoms (charge units)
|
||||
*intra_energy* value = intramolecular energy (energy units)
|
||||
|
||||
Examples
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||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 2 gas widom 1 50000 1 19494 2.0
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||||
fix 3 water widom 1000 100 0 29494 300.0 mol h2omol full_energy
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This fix performs Widom insertions of atoms or molecules at the given
|
||||
temperature as discussed in :ref:`(Frenkel) <Frenkel>`. Specific uses
|
||||
include computation of Henry constants of small molecules in microporous
|
||||
materials or amorphous systems.
|
||||
|
||||
|
||||
Every N timesteps the fix attempts M number of Widom insertions of atoms
|
||||
or molecules.
|
||||
|
||||
If the *mol* keyword is used, only molecule insertions are performed.
|
||||
Conversely, if the *mol* keyword is not used, only atom insertions are
|
||||
performed.
|
||||
|
||||
This command may optionally use the *region* keyword to define an
|
||||
insertion volume. The specified region must have been previously
|
||||
defined with a :doc:`region <region>` command. It must be defined with
|
||||
side = *in*\ . Insertion attempts occur only within the specified
|
||||
region. For non-rectangular regions, random trial points are generated
|
||||
within the rectangular bounding box until a point is found that lies
|
||||
inside the region. If no valid point is generated after 1000 trials, no
|
||||
insertion is performed. If an attempted insertion places the atom or
|
||||
molecule center-of-mass outside the specified region, a new attempted
|
||||
insertion is generated. This process is repeated until the atom or
|
||||
molecule center-of-mass is inside the specified region.
|
||||
|
||||
Note that neighbor lists are re-built every timestep that this fix is
|
||||
invoked, so you should not set N to be too small. See the :doc:`neighbor
|
||||
<neighbor>` command for details.
|
||||
|
||||
When an atom or molecule is to be inserted, its coordinates are chosen
|
||||
at a random position within the current simulation cell or
|
||||
regionRelative coordinates for atoms in a molecule are taken from the
|
||||
template molecule provided by the user. The center of mass of the
|
||||
molecule is placed at the insertion point. The orientation of the
|
||||
molecule is chosen at random by rotating about this point.
|
||||
|
||||
Individual atoms are inserted, unless the *mol* keyword is used. It
|
||||
specifies a *template-ID* previously defined using the :doc:`molecule
|
||||
<molecule>` command, which reads a file that defines the molecule. The
|
||||
coordinates, atom types, charges, etc., as well as any bonding and
|
||||
special neighbor information for the molecule can be specified in the
|
||||
molecule file. See the :doc:`molecule <molecule>` command for details.
|
||||
The only settings required to be in this file are the coordinates and
|
||||
types of atoms in the molecule.
|
||||
|
||||
If you wish to insert molecules via the *mol* keyword, that will have
|
||||
their bonds or angles constrained via SHAKE, use the *shake* keyword,
|
||||
specifying as its value the ID of a separate :doc:`fix shake
|
||||
<fix_shake>` command which also appears in your input script.
|
||||
|
||||
Note that fix widom does not use configurational bias MC or any other
|
||||
kind of sampling of intramolecular degrees of freedom. Inserted
|
||||
molecules can have different orientations, but they will all have the
|
||||
same intramolecular configuration, which was specified in the molecule
|
||||
command input.
|
||||
|
||||
For atoms, inserted particles have the specified atom type. For
|
||||
molecules, they use the same atom types as in the template molecule
|
||||
supplied by the user.
|
||||
|
||||
The excess chemical potential mu_ex is defined as:
|
||||
|
||||
.. math::
|
||||
|
||||
\mu_{ex} = -kT \ln(<\exp(-(U_{N+1}-U_{N})/{kT})>)
|
||||
|
||||
where *k* is Boltzman's constant, *T* is the user-specified temperature,
|
||||
U_N and U_{N+1} is the potential energy of the system with N and N+1
|
||||
particles.
|
||||
|
||||
The *full_energy* option means that the fix calculates the total
|
||||
potential energy of the entire simulated system, instead of just the
|
||||
energy of the part that is changed. By default, this option is off, in
|
||||
which case only partial energies are computed to determine the energy
|
||||
difference due to the proposed change.
|
||||
|
||||
The *full_energy* option is needed for systems with complicated
|
||||
potential energy calculations, including the following:
|
||||
|
||||
* long-range electrostatics (kspace)
|
||||
* many-body pair styles
|
||||
* hybrid pair styles
|
||||
* eam pair styles
|
||||
* tail corrections
|
||||
* need to include potential energy contributions from other fixes
|
||||
|
||||
In these cases, LAMMPS will automatically apply the *full_energy*
|
||||
keyword and issue a warning message.
|
||||
|
||||
When the *mol* keyword is used, the *full_energy* option also includes
|
||||
the intramolecular energy of inserted and deleted molecules, whereas
|
||||
this energy is not included when *full_energy* is not used. If this is
|
||||
not desired, the *intra_energy* keyword can be used to define an amount
|
||||
of energy that is subtracted from the final energy when a molecule is
|
||||
inserted, and subtracted from the initial energy when a molecule is
|
||||
deleted. For molecules that have a non-zero intramolecular energy, this
|
||||
will ensure roughly the same behavior whether or not the *full_energy*
|
||||
option is used.
|
||||
|
||||
Some fixes have an associated potential energy. Examples of such fixes
|
||||
include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
|
||||
:doc:`addforce <fix_addforce>`, :doc:`restrain <fix_restrain>`, and
|
||||
:doc:`wall fixes <fix_wall>`. For that energy to be included in the
|
||||
total potential energy of the system (the quantity used when performing
|
||||
Widom insertions), you MUST enable the :doc:`fix_modify <fix_modify>`
|
||||
*energy* option for that fix. The doc pages for individual :doc:`fix
|
||||
<fix>` commands specify if this should be done.
|
||||
|
||||
Use the *charge* option to insert atoms with a user-specified point
|
||||
charge. Note that doing so will cause the system to become non-neutral.
|
||||
LAMMPS issues a warning when using long-range electrostatics (kspace)
|
||||
with non-neutral systems. See the :doc:`compute group/group
|
||||
<compute_group_group>` documentation for more details about simulating
|
||||
non-neutral systems with kspace on.
|
||||
|
||||
**Restart, fix_modify, output, run start/stop, minimize info:**
|
||||
|
||||
This fix writes the state of the fix to :doc:`binary restart files
|
||||
<restart>`. This includes information about the random number generator
|
||||
seed, the next timestep for Widom insertions etc. See the
|
||||
:doc:`read_restart <read_restart>` command for info on how to re-specify
|
||||
a fix in an input script that reads a restart file, so that the
|
||||
operation of the fix continues in an uninterrupted fashion.
|
||||
|
||||
.. note::
|
||||
|
||||
For this to work correctly, the timestep must **not** be changed
|
||||
after reading the restart with :doc:`reset_timestep
|
||||
<reset_timestep>`. The fix will try to detect it and stop with an
|
||||
error.
|
||||
|
||||
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
|
||||
fix.
|
||||
|
||||
This fix computes a global vector of length 3, which can be accessed by
|
||||
various :doc:`output commands <Howto_output>`. The vector values are
|
||||
the following global cumulative quantities:
|
||||
|
||||
* 1 = average excess chemical potential on each timestep
|
||||
* 2 = average difference in potential energy on each timestep
|
||||
* 3 = volume of the insertion region
|
||||
|
||||
The vector values calculated by this fix are "extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during
|
||||
:doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This fix is part of the MC package. It is only enabled if LAMMPS was
|
||||
built with that package. See the :doc:`Build package <Build_package>`
|
||||
doc page for more info.
|
||||
|
||||
Do not set "neigh_modify once yes" or else this fix will never be
|
||||
called. Reneighboring is **required**.
|
||||
|
||||
Can be run in parallel, but aspects of the GCMC part will not scale well
|
||||
in parallel. Only usable for 3D simulations.
|
||||
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix gcmc <fix_gcmc>`
|
||||
:doc:`fix atom/swap <fix_atom_swap>`,
|
||||
:doc:`neighbor <neighbor>`,
|
||||
:doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
|
||||
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The option defaults are mol = no, intra_energy = 0.0 and full_energy =
|
||||
no, except for the situations where full_energy is required, as listed
|
||||
above.
|
||||
|
||||
----------
|
||||
|
||||
.. _Frenkel:
|
||||
|
||||
**(Frenkel)** Frenkel and Smit, Understanding Molecular Simulation,
|
||||
Academic Press, London, 2002.
|
||||
|
||||
Reference in New Issue
Block a user