mirror of https://github.com/lammps/lammps.git
Adding molecule capability to fix GCMC.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9060 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
pscrozi
parent
b1c7c64624
commit
d4b7bd9ec4
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@ -25,7 +25,7 @@
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<LI>M = number of MC displacements to attempt every N steps
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<LI>type = atom type of exchanged particles
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<LI>type = atom type or molecule ID of exchanged gas
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<LI>seed = random # seed (positive integer)
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@ -42,49 +42,61 @@
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<PRE> <I>molecule</I> value = <I>no</I> or <I>yes</I>
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<I>region</I> value = region-ID
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region-ID = ID of region to use as an exchange/move volume
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<I>maxangle</I> value = maximum molecular rotation angle (degrees)
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 2 all gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
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fix 3 all gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes
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fix 4 all gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
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<PRE>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
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fix 3 Kr gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes maxrot 180
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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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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
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particles 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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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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<A HREF = "#Frenkel">(Frenkel)</A>. If used with the <A HREF = "fix_nh.html">fix nvt</A> command,
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simulations in the grand canonical enemble (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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</P>
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<P>Perform up to X exchanges of particles of the given type between the
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simulation domain and the imaginary reservoir every N timesteps. Also
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perform M Monte Carlo displacements of particles of the given type
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within the simulation domain. M should typically be chosen to be
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approximately equal to the expected number of particles of the given
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type within the domain, which will result in roughly one MC
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translation per particle per MC cycle.
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<P>Perform up to X exchanges of gas atoms or molecules of the given type
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between the simulation domain and the imaginary reservoir every N
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timesteps. Also perform M Monte Carlo displacements or rotations
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(for molecules) of gas of the given type within the simulation domain.
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M should typically be chosen to be approximately equal to the expected
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number of gas atoms or molecules of the given type within the domain,
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which will result in roughly one MC translation per atom or molecule
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per MC cycle.
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</P>
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<P>This fix cannot be used to perform MC displacements of particles other
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than the exchanged type. All particles in the simulation domain can be
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moved using regular time integration displacements, e.g. via
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<A HREF = "fix_nvt.html">fix_nvt</A>, resulting in a hybrid GCMC+MD simulation.
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<P>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 either
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molecular or atomic gasses, deletions and insertions are each attempted
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with 50% probability.
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</P>
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<P>This command may optionally use the <I>region</I> 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 <A HREF = "region.html">region</A> command. It must be
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defined with side = <I>in</I>. Insertion attempts occur only within the
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specified region. Move and deletion attempt candidates are selected
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from particles within the region. If no candidate can be found within
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the specified region after randomly selecting candidates 1000 times,
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the move or deletion attempt is considered a failure. Moves must start
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within the specified region, but may move the particle slightly
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outside of the region.
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<P>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, translations,
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and rotations can be performed on any atom/molecule in the fix group.
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All atoms in the simulation domain can be moved using regular time
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integration displacements, e.g. via <A HREF = "fix_nvt.html">fix_nvt</A>, resulting
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in a hybrid GCMC+MD simulation. A smaller-than-usual timestep size
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may be needed when running such a hybrid simulation, especially if
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the inserted molecules are not well equilibrated.
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</P>
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<P>This command may optionally use the <I>region</I> 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 <A HREF = "region.html">region</A> command. It must be
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defined with side = <I>in</I>. Insertion attempts occur only within the
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specified region. Move and deletion attempt candidates are selected
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from gas atoms or molecules within the region. If no candidate can be
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found within the specified region after randomly selecting candidates
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1000 times, the move or deletion attempt is considered a failure. Moves
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must start within the specified region, but may move the atom or molecule
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slightly outside of the region.
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</P>
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<P>If used with <A HREF = "fix_nvt.html">fix_nvt</A>, 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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@ -95,17 +107,16 @@ will not be in thermal equilibrium with the simulation domain.
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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 displacements
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per timestep that a particle can move beyond the neighbor list skin
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per timestep that atoms can move beyond the neighbor list skin
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distance. See the <A HREF = "neighbor.html">neighbor</A> command for details.
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</P>
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<P>When a particle is to be inserted, its coordinates are chosen as a
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random position within the current simulation domain, and its velocity
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is randomly chosen from the specified temperature distribution given
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by T.
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</P>
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<P>Exchanged particles have the specified atom type and are assigned to
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two groups: the default group "all" and the group specified in the fix
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gcmc command (which can also be "all").
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<P>When an atom or molecule is to be inserted, its center-of-mass
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coordinates are chosen as a random position within the current
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simulation domain, and new atom velocities are randomly chosen
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from the specified temperature distribution given by T. 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. A random initial rotation is used in the
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case of molecule insertions.
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</P>
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<P>If the setting for the <I>molecule</I> keyword is <I>no</I>, then only single
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atoms are exchanged. In this case, you should ensure you do not
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@ -116,7 +127,28 @@ non-zero molecule ID, but does not check for this at the time of
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deletion.
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</P>
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<P>If the setting for the <I>molecule</I> keyword is <I>yes</I>, entire molecules
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are exchanged. This feature is not yet supported.
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are exchanged. The user must supply a model molecule in the data
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file to use as a template for exchanges, and that molecule's number
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must be given in the fix GCMC command as the "type" of the exchanged
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gas. The model molecule can then be immediately deleted using the
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<A HREF = "delete_atoms.html">delete_atoms</A> command.
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</P>
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<P>Optionally, users may specify the maximum rotation angle for
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molecular rotations using the <I>maxangle</I> keyword and specifying
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the angle in degrees. The specified angle will apply to all three
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Euler angles used internally to define the rotation matrix for
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molecular rotations. The max angle can be set to zero, but rotations
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will be pointless. Note that the default is ten degrees for each
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Euler angle.
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</P>
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<P>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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</P>
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<P>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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@ -150,10 +182,12 @@ values are the following global cummulative quantities:
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</P>
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<UL><LI>1 = displacement attempts
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<LI>2 = displacement successes
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<LI>3 = deletion attempts
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<LI>4 = deletion successes
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<LI>5 = insertion attempts
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<LI>6 = insertion successes
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<LI>3 = insertion attempts
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<LI>4 = insertion successes
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<LI>5 = deletion attempts
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<LI>6 = deletion successes
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<LI>7 = rotation attempts
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<LI>8 = rotation successes
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</UL>
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<P>The vector values calculated by this fix are "extensive".
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</P>
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@ -170,9 +204,6 @@ LAMMPS</A> section for more info.
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<P>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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</P>
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<P>You cannot currently exchange charged particles or molecules with a
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net charge.
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</P>
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<P>Only pairwise interactions, as defined by the
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<A HREF = "pair_style.html">pair_style</A> command, are included in this
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calculation. Long-range interactions due to a
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@ -183,14 +214,25 @@ this fix. For example, 3-body potentials, such as
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be used. <A HREF = "pair_eam.html">EAM</A> potentials for metals only include the
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pair potential portion of the EAM interaction, not the embedding term.
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</P>
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<P>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 with orthogonal
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simulation cells.
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</P>
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<P>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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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_nvt.html">fix_nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
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<A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_evaporate.html">fix_evaporate</A>
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<A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_evaporate.html">fix_evaporate</A>,
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<A HREF = "delete_atoms.html">delete_atoms</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are molecule = no.
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<P>The option defaults are molecule = no, maxangle = 10.
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</P>
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<HR>
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136
doc/fix_gcmc.txt
136
doc/fix_gcmc.txt
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@ -17,7 +17,7 @@ gcmc = style name of this fix command :l
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N = invoke this fix every N steps :l
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X = number of exchanges to attempt every N steps :l
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M = number of MC displacements to attempt every N steps :l
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type = atom type of exchanged particles :l
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type = atom type or molecule ID of exchanged gas :l
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seed = random # seed (positive integer) :l
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T = temperature of the ideal gas reservoir (temperature units) :l
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mu = chemical potential of the ideal gas reservoir (energy units) :l
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@ -26,49 +26,61 @@ zero or more keyword/value pairs may be appended to args :l
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keyword = {molecule} or {region} :l
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{molecule} value = {no} or {yes}
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{region} value = region-ID
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region-ID = ID of region to use as an exchange/move volume :pre
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region-ID = ID of region to use as an exchange/move volume
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{maxangle} value = maximum molecular rotation angle (degrees) :pre
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:ule
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[Examples:]
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fix 2 all gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
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fix 3 all gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes
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fix 4 all gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk :pre
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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 Kr gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes maxrot 180
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fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk :pre
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[Description:]
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This fix performs grand canonical Monte Carlo (GCMC) exchanges of
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particles of the given type with an imaginary ideal gas reservoir at
|
||||
the specified T and chemical potential (mu ) as discussed in
|
||||
atoms or molecules of the given type with an imaginary ideal gas reservoir at
|
||||
the specified T and chemical potential (mu) as discussed in
|
||||
"(Frenkel)"_#Frenkel. If used with the "fix nvt"_fix_nh.html command,
|
||||
simulations in the grand canonical enemble (muVT, constant chemical
|
||||
potential, constant volume, and constant temperature) can be
|
||||
performed. Specific uses include computing isotherms in microporous
|
||||
materials, or computing vapor-liquid coexistence curves.
|
||||
|
||||
Perform up to X exchanges of particles of the given type between the
|
||||
simulation domain and the imaginary reservoir every N timesteps. Also
|
||||
perform M Monte Carlo displacements of particles of the given type
|
||||
within the simulation domain. M should typically be chosen to be
|
||||
approximately equal to the expected number of particles of the given
|
||||
type within the domain, which will result in roughly one MC
|
||||
translation per particle per MC cycle.
|
||||
Perform up to X exchanges of gas atoms or molecules of the given type
|
||||
between the simulation domain and the imaginary reservoir every N
|
||||
timesteps. Also perform M Monte Carlo displacements or rotations
|
||||
(for molecules) of gas of the given type within the simulation domain.
|
||||
M should typically be chosen to be approximately equal to the expected
|
||||
number of gas atoms or molecules of the given type within the domain,
|
||||
which will result in roughly one MC translation per atom or molecule
|
||||
per MC cycle.
|
||||
|
||||
This fix cannot be used to perform MC displacements of particles other
|
||||
than the exchanged type. All particles in the simulation domain can be
|
||||
moved using regular time integration displacements, e.g. via
|
||||
"fix_nvt"_fix_nvt.html, resulting in a hybrid GCMC+MD simulation.
|
||||
For MC moves of molecular gasses, rotations and translations are each
|
||||
attempted with 50% probability. For MC moves of atomic gasses,
|
||||
translations are attempted 100% of the time. For MC exchanges of either
|
||||
molecular or atomic gasses, deletions and insertions are each attempted
|
||||
with 50% probability.
|
||||
|
||||
This command may optionally use the {region} keyword to define an
|
||||
exchange and move volume. The specified region must have been
|
||||
previously defined with a "region"_region.html command. It must be
|
||||
defined with side = {in}. Insertion attempts occur only within the
|
||||
specified region. Move and deletion attempt candidates are selected
|
||||
from particles within the region. If no candidate can be found within
|
||||
the specified region after randomly selecting candidates 1000 times,
|
||||
the move or deletion attempt is considered a failure. Moves must start
|
||||
within the specified region, but may move the particle slightly
|
||||
outside of the region.
|
||||
This fix cannot be used to perform MC insertions of gas atoms or
|
||||
molecules other than the exchanged type, but MC deletions, translations,
|
||||
and rotations can be performed on any atom/molecule in the fix group.
|
||||
All atoms in the simulation domain can be moved using regular time
|
||||
integration displacements, e.g. via "fix_nvt"_fix_nvt.html, resulting
|
||||
in a hybrid GCMC+MD simulation. A smaller-than-usual timestep size
|
||||
may be needed when running such a hybrid simulation, especially if
|
||||
the inserted molecules are not well equilibrated.
|
||||
|
||||
This command may optionally use the {region} keyword to define an
|
||||
exchange and move volume. The specified region must have been
|
||||
previously defined with a "region"_region.html command. It must be
|
||||
defined with side = {in}. Insertion attempts occur only within the
|
||||
specified region. Move and deletion attempt candidates are selected
|
||||
from gas atoms or molecules within the region. If no candidate can be
|
||||
found within the specified region after randomly selecting candidates
|
||||
1000 times, the move or deletion attempt is considered a failure. Moves
|
||||
must start within the specified region, but may move the atom or molecule
|
||||
slightly outside of the region.
|
||||
|
||||
If used with "fix_nvt"_fix_nvt.html, the temperature of the imaginary
|
||||
reservoir, T, should be set to be equivalent to the target temperature
|
||||
|
|
@ -79,17 +91,16 @@ Note that neighbor lists are re-built every timestep that this fix is
|
|||
invoked, so you should not set N to be too small. However, periodic
|
||||
rebuilds are necessary in order to avoid dangerous rebuilds and missed
|
||||
interactions. Specifically, avoid performing so many MC displacements
|
||||
per timestep that a particle can move beyond the neighbor list skin
|
||||
per timestep that atoms can move beyond the neighbor list skin
|
||||
distance. See the "neighbor"_neighbor.html command for details.
|
||||
|
||||
When a particle is to be inserted, its coordinates are chosen as a
|
||||
random position within the current simulation domain, and its velocity
|
||||
is randomly chosen from the specified temperature distribution given
|
||||
by T.
|
||||
|
||||
Exchanged particles have the specified atom type and are assigned to
|
||||
two groups: the default group "all" and the group specified in the fix
|
||||
gcmc command (which can also be "all").
|
||||
When an atom or molecule is to be inserted, its center-of-mass
|
||||
coordinates are chosen as a random position within the current
|
||||
simulation domain, and new atom velocities are randomly chosen
|
||||
from the specified temperature distribution given by T. Relative
|
||||
coordinates for atoms in a molecule are taken from the template
|
||||
molecule provided by the user. A random initial rotation is used in the
|
||||
case of molecule insertions.
|
||||
|
||||
If the setting for the {molecule} keyword is {no}, then only single
|
||||
atoms are exchanged. In this case, you should ensure you do not
|
||||
|
|
@ -100,7 +111,28 @@ non-zero molecule ID, but does not check for this at the time of
|
|||
deletion.
|
||||
|
||||
If the setting for the {molecule} keyword is {yes}, entire molecules
|
||||
are exchanged. This feature is not yet supported.
|
||||
are exchanged. The user must supply a model molecule in the data
|
||||
file to use as a template for exchanges, and that molecule's number
|
||||
must be given in the fix GCMC command as the "type" of the exchanged
|
||||
gas. The model molecule can then be immediately deleted using the
|
||||
"delete_atoms"_delete_atoms.html command.
|
||||
|
||||
Optionally, users may specify the maximum rotation angle for
|
||||
molecular rotations using the {maxangle} keyword and specifying
|
||||
the angle in degrees. The specified angle will apply to all three
|
||||
Euler angles used internally to define the rotation matrix for
|
||||
molecular rotations. The max angle can be set to zero, but rotations
|
||||
will be pointless. Note that the default is ten degrees for each
|
||||
Euler angle.
|
||||
|
||||
For atomic gasses, inserted atoms have the specified atom type, but
|
||||
deleted atoms are any atoms that have been inserted or that belong
|
||||
to the user-specified fix group. For molecular gasses, exchanged
|
||||
molecules use the same atom types as in the template molecule
|
||||
supplied by the user. In both cases, exchanged
|
||||
atoms/molecules are assigned to two groups: the default group "all"
|
||||
and the group specified in the fix gcmc command (which can also be
|
||||
"all").
|
||||
|
||||
Use of this fix typically will cause the number of atoms to fluctuate,
|
||||
therefore, you will want to use the
|
||||
|
|
@ -134,10 +166,12 @@ values are the following global cummulative quantities:
|
|||
|
||||
1 = displacement attempts
|
||||
2 = displacement successes
|
||||
3 = deletion attempts
|
||||
4 = deletion successes
|
||||
5 = insertion attempts
|
||||
6 = insertion successes :ul
|
||||
3 = insertion attempts
|
||||
4 = insertion successes
|
||||
5 = deletion attempts
|
||||
6 = deletion successes
|
||||
7 = rotation attempts
|
||||
8 = rotation successes :ul
|
||||
|
||||
The vector values calculated by this fix are "extensive".
|
||||
|
||||
|
|
@ -154,9 +188,6 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
|||
Do not set "neigh_modify once yes" or else this fix will never be
|
||||
called. Reneighboring is required.
|
||||
|
||||
You cannot currently exchange charged particles or molecules with a
|
||||
net charge.
|
||||
|
||||
Only pairwise interactions, as defined by the
|
||||
"pair_style"_pair_style.html command, are included in this
|
||||
calculation. Long-range interactions due to a
|
||||
|
|
@ -167,14 +198,25 @@ this fix. For example, 3-body potentials, such as
|
|||
be used. "EAM"_pair_eam.html potentials for metals only include the
|
||||
pair potential portion of the EAM interaction, not the embedding term.
|
||||
|
||||
Can be run in parallel, but aspects of the GCMC part will not scale
|
||||
well in parallel. Only usable for 3D simulations with orthogonal
|
||||
simulation cells.
|
||||
|
||||
Note that very lengthy simulations involving insertions/deletions of
|
||||
billions of gas molecules may run out of atom or molecule IDs and
|
||||
trigger an error, so it is better to run multiple shorter-duration
|
||||
simulations. Likewise, very large molecules have not been tested
|
||||
and may turn out to be problematic.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix_nvt"_fix_nvt.html, "neighbor"_neighbor.html,
|
||||
"fix_deposit"_fix_deposit.html, "fix_evaporate"_fix_evaporate.html
|
||||
"fix_deposit"_fix_deposit.html, "fix_evaporate"_fix_evaporate.html,
|
||||
"delete_atoms"_delete_atoms.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are molecule = no.
|
||||
The option defaults are molecule = no, maxangle = 10.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue