forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13461 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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parent
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29746678ff
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@ -9,15 +9,15 @@
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<HR>
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<H3>fix atom_swap command
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<H3>fix atom/swap command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID atom_swap N X seed T keyword values ...
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<PRE>fix ID group-ID atom/swap N X seed T keyword values ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>atom_swap = style name of this fix command
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<LI>atom/swap = style name of this fix command
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<LI>N = invoke this fix every N steps
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@ -47,66 +47,72 @@
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<P><B>Examples:</B>
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</P>
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<PRE>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
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fix atom_swap_fix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
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fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
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fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 delta_mu 4.3 -5.0
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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 Monte Carlo swaps of atoms of one given atom type with atoms
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of the other given atom types. The specified T is used in the Metropolis criterion
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dictating swap probabilities.
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<P>This fix performs Monte Carlo swaps of atoms of one given atom type
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with atoms of the other given atom types. The specified T is used in
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the Metropolis criterion dictating swap probabilities.
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</P>
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<P>Perform X swaps of atoms of one type with atoms of another type according to a
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Monte Carlo probability. Swap candidates must be in the fix group, must be in
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the region (if specified), and must be of one of the listed types. Swaps are
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attempted between candidates that are chosen randomly with equal probability
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among the candidate atoms. Swaps are not attempted between atoms of the same
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type since nothing would happen.
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<P>Perform X swaps of atoms of one type with atoms of another type
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according to a Monte Carlo probability. Swap candidates must be in the
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fix group, must be in the region (if specified), and must be of one of
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the listed types. Swaps are attempted between candidates that are
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chosen randomly with equal probability among the candidate
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atoms. Swaps are not attempted between atoms of the same type since
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nothing would happen.
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</P>
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<P>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 MC+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 swapped atoms are not well equilibrated.
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in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
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be needed when running such a hybrid simulation, especially if the
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swapped atoms are not well equilibrated.
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</P>
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<P>The <I>types</I> keyword is required. At least two atom types must be specified.
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<P>The <I>types</I> keyword is required. At least two atom types must be
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specified.
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</P>
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<P>The <I>ke</I> keyword can be set to <I>no</I> to turn off kinetic energy conservation
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for swaps. The default is <I>yes</I>, which means that swapped atoms have their
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velocities scaled by the ratio of the masses of the swapped atom types. This
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ensures that the kinetic energy of each atom is the same after the swap as it
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was before the swap, even though the atom masses have changed.
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<P>The <I>ke</I> keyword can be set to <I>no</I> to turn off kinetic energy
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conservation for swaps. The default is <I>yes</I>, which means that swapped
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atoms have their velocities scaled by the ratio of the masses of the
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swapped atom types. This ensures that the kinetic energy of each atom
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is the same after the swap as it was before the swap, even though the
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atom masses have changed.
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</P>
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<P>The <I>semi-grand</I> keyword can be set to <I>yes</I> to switch to the semi-grand
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canonical ensemble as discussed in <A HREF = "#Sadigh">(Sadigh)</A>. This means that the
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total number of each particle type does not need to be conserved. The default
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is <I>no</I>, which means that the only kind of swap allowed exchanges an atom of
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one type with an atom of a different given type. In other words, the relative
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mole fractions of the swapped atoms remains constant. Whereas in the
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semi-grand canonical ensemble, the composition of the system can change. Note
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that when using <I>semi-grand</I>, all atoms in the fix group are eligible for
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attempted conversion to one of the given types, even if its current type is
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not one of the given types. An attempt is made to switch the selected atom to
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one of the listed <I>types</I> with equal probability. Acceptance of each attempt
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depends upon the Metropolis criterion.
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<P>The <I>semi-grand</I> keyword can be set to <I>yes</I> to switch to the
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semi-grand canonical ensemble as discussed in <A HREF = "#Sadigh">(Sadigh)</A>. This
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means that the total number of each particle type does not need to be
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conserved. The default is <I>no</I>, which means that the only kind of swap
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allowed exchanges an atom of one type with an atom of a different
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given type. In other words, the relative mole fractions of the swapped
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atoms remains constant. Whereas in the semi-grand canonical ensemble,
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the composition of the system can change. Note that when using
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<I>semi-grand</I>, all atoms in the fix group are eligible for attempted
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conversion to one of the given types, even if its current type is not
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one of the given types. An attempt is made to switch the selected atom
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to one of the listed <I>types</I> with equal probability. Acceptance of
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each attempt depends upon the Metropolis criterion.
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</P>
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<P>The <I>delta_mu</I> keyword allows users to specify non-zero chemical potentials
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for each of the atom types. All chemical potentials are relative to the first
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atom type, so no value is given for the first atom type. These parameters are
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useful for semi-grand canonical ensemble simulations where it may be
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desirable to actively control the composition of the system. When given,
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there must be ntypes-1 values given, where ntypes is the number of atom
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types in the simulated system. Note that a value for delta_mu is required for
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all atom types when using <I>semi-grand</I>, even for atom types not listed
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following the <I>types</I> keyword. This is because when using <I>semi-grand</I>, it is
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possible that any of the atom types in the system could be part of the fix
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group and therefore are eligible for swapping to one of the listed atom types.
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<P>The <I>delta_mu</I> keyword allows users to specify non-zero chemical
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potentials for each of the atom types. All chemical potentials are
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relative to the first atom type, so no value is given for the first
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atom type. These parameters are useful for semi-grand canonical
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ensemble simulations where it may be desirable to actively control the
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composition of the system. When given, there must be ntypes-1 values
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given, where ntypes is the number of atom types in the simulated
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system. Note that a value for delta_mu is required for all atom types
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when using <I>semi-grand</I>, even for atom types not listed following the
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<I>types</I> keyword. This is because when using <I>semi-grand</I>, it is
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possible that any of the atom types in the system could be part of the
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fix group and therefore are eligible for swapping to one of the listed
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atom types.
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</P>
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<P>This command may optionally use the <I>region</I> keyword to define
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swap 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>. Swap attempts occur only between atoms that
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are both within the specified region. Swaps are not otherwise attempted.
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<P>This command may optionally use the <I>region</I> keyword to define swap
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volume. The specified region must have been previously defined with a
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<A HREF = "region.html">region</A> command. It must be defined with side = <I>in</I>.
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Swap attempts occur only between atoms that are both within the
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specified region. Swaps are not otherwise attempted.
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</P>
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<P>You should ensure you do not swap atoms belonging to a molecule, or
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LAMMPS will soon generate an error when it tries to find those atoms.
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@ -116,8 +122,8 @@ swapping.
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</P>
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<P>This fix checks to ensure all atoms of the given types have the same
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atomic charge. LAMMPS doesn't enforce this in general, but it is
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needed for this fix to simplify the swapping procedure. Successful swaps
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will swap the atom type and charge of the swapped atoms.
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needed for this fix to simplify the swapping procedure. Successful
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swaps will swap the atom type and charge of the swapped atoms.
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</P>
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<P>Since this fix computes total potential energies before and after
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proposed swaps, so even complicated potential energy calculations are
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@ -6,14 +6,14 @@
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:line
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fix atom_swap command :h3
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fix atom/swap command :h3
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[Syntax:]
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fix ID group-ID atom_swap N X seed T keyword values ... :pre
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fix ID group-ID atom/swap N X seed T keyword values ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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atom_swap = style name of this fix command :l
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atom/swap = 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 swaps to attempt every N steps :l
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seed = random # seed (positive integer) :l
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@ -35,66 +35,72 @@ keyword = {types} or {delta_mu} or {ke} or {semi-grand} or {region} :l
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[Examples:]
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fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
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fix atom_swap_fix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
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fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
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fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 delta_mu 4.3 -5.0 :pre
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[Description:]
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This fix performs Monte Carlo swaps of atoms of one given atom type with atoms
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of the other given atom types. The specified T is used in the Metropolis criterion
|
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dictating swap probabilities.
|
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This fix performs Monte Carlo swaps of atoms of one given atom type
|
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with atoms of the other given atom types. The specified T is used in
|
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the Metropolis criterion dictating swap probabilities.
|
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Perform X swaps of atoms of one type with atoms of another type according to a
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Monte Carlo probability. Swap candidates must be in the fix group, must be in
|
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the region (if specified), and must be of one of the listed types. Swaps are
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attempted between candidates that are chosen randomly with equal probability
|
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among the candidate atoms. Swaps are not attempted between atoms of the same
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type since nothing would happen.
|
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Perform X swaps of atoms of one type with atoms of another type
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according to a Monte Carlo probability. Swap candidates must be in the
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fix group, must be in the region (if specified), and must be of one of
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the listed types. Swaps are attempted between candidates that are
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chosen randomly with equal probability among the candidate
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atoms. Swaps are not attempted between atoms of the same type since
|
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nothing would happen.
|
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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 "fix_nvt"_fix_nvt.html, resulting
|
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in a hybrid MC+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 swapped atoms are not well equilibrated.
|
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in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
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be needed when running such a hybrid simulation, especially if the
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swapped atoms are not well equilibrated.
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The {types} keyword is required. At least two atom types must be specified.
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The {types} keyword is required. At least two atom types must be
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specified.
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The {ke} keyword can be set to {no} to turn off kinetic energy conservation
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for swaps. The default is {yes}, which means that swapped atoms have their
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velocities scaled by the ratio of the masses of the swapped atom types. This
|
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ensures that the kinetic energy of each atom is the same after the swap as it
|
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was before the swap, even though the atom masses have changed.
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The {ke} keyword can be set to {no} to turn off kinetic energy
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conservation for swaps. The default is {yes}, which means that swapped
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atoms have their velocities scaled by the ratio of the masses of the
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swapped atom types. This ensures that the kinetic energy of each atom
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is the same after the swap as it was before the swap, even though the
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atom masses have changed.
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The {semi-grand} keyword can be set to {yes} to switch to the semi-grand
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canonical ensemble as discussed in "(Sadigh)"_#Sadigh. This means that the
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total number of each particle type does not need to be conserved. The default
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is {no}, which means that the only kind of swap allowed exchanges an atom of
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one type with an atom of a different given type. In other words, the relative
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mole fractions of the swapped atoms remains constant. Whereas in the
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semi-grand canonical ensemble, the composition of the system can change. Note
|
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that when using {semi-grand}, all atoms in the fix group are eligible for
|
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attempted conversion to one of the given types, even if its current type is
|
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not one of the given types. An attempt is made to switch the selected atom to
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one of the listed {types} with equal probability. Acceptance of each attempt
|
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depends upon the Metropolis criterion.
|
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The {semi-grand} keyword can be set to {yes} to switch to the
|
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semi-grand canonical ensemble as discussed in "(Sadigh)"_#Sadigh. This
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means that the total number of each particle type does not need to be
|
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conserved. The default is {no}, which means that the only kind of swap
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allowed exchanges an atom of one type with an atom of a different
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given type. In other words, the relative mole fractions of the swapped
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atoms remains constant. Whereas in the semi-grand canonical ensemble,
|
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the composition of the system can change. Note that when using
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{semi-grand}, all atoms in the fix group are eligible for attempted
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conversion to one of the given types, even if its current type is not
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one of the given types. An attempt is made to switch the selected atom
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to one of the listed {types} with equal probability. Acceptance of
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each attempt depends upon the Metropolis criterion.
|
||||
|
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The {delta_mu} keyword allows users to specify non-zero chemical potentials
|
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for each of the atom types. All chemical potentials are relative to the first
|
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atom type, so no value is given for the first atom type. These parameters are
|
||||
useful for semi-grand canonical ensemble simulations where it may be
|
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desirable to actively control the composition of the system. When given,
|
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there must be ntypes-1 values given, where ntypes is the number of atom
|
||||
types in the simulated system. Note that a value for delta_mu is required for
|
||||
all atom types when using {semi-grand}, even for atom types not listed
|
||||
following the {types} keyword. This is because when using {semi-grand}, it is
|
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possible that any of the atom types in the system could be part of the fix
|
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group and therefore are eligible for swapping to one of the listed atom types.
|
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The {delta_mu} keyword allows users to specify non-zero chemical
|
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potentials for each of the atom types. All chemical potentials are
|
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relative to the first atom type, so no value is given for the first
|
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atom type. These parameters are useful for semi-grand canonical
|
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ensemble simulations where it may be desirable to actively control the
|
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composition of the system. When given, there must be ntypes-1 values
|
||||
given, where ntypes is the number of atom types in the simulated
|
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system. Note that a value for delta_mu is required for all atom types
|
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when using {semi-grand}, even for atom types not listed following the
|
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{types} keyword. This is because when using {semi-grand}, it is
|
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possible that any of the atom types in the system could be part of the
|
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fix group and therefore are eligible for swapping to one of the listed
|
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atom types.
|
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|
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This command may optionally use the {region} keyword to define
|
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swap volume. The specified region must have been
|
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previously defined with a "region"_region.html command. It must be
|
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defined with side = {in}. Swap attempts occur only between atoms that
|
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are both within the specified region. Swaps are not otherwise attempted.
|
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This command may optionally use the {region} keyword to define swap
|
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volume. The specified region must have been previously defined with a
|
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"region"_region.html command. It must be defined with side = {in}.
|
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Swap attempts occur only between atoms that are both within the
|
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specified region. Swaps are not otherwise attempted.
|
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|
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You should ensure you do not swap atoms belonging to a molecule, or
|
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LAMMPS will soon generate an error when it tries to find those atoms.
|
||||
|
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@ -104,8 +110,8 @@ swapping.
|
|||
|
||||
This fix checks to ensure all atoms of the given types have the same
|
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atomic charge. LAMMPS doesn't enforce this in general, but it is
|
||||
needed for this fix to simplify the swapping procedure. Successful swaps
|
||||
will swap the atom type and charge of the swapped atoms.
|
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needed for this fix to simplify the swapping procedure. Successful
|
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swaps will swap the atom type and charge of the swapped atoms.
|
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|
||||
Since this fix computes total potential energies before and after
|
||||
proposed swaps, so even complicated potential energy calculations are
|
||||
|
|
|
|||
Loading…
Reference in New Issue