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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14055 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp 2015-09-24 20:02:03 +00:00
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2
doc/doc2/accelerate_kokkos.html
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@ -94,7 +94,7 @@ following kinds of hardware:
<LI>GPU: on the GPUs of a node with additional OpenMP threading on the CPUs
</UL>
<P>Kokkos support within LAMMPS must be built with a C++11 compatible
compiler. For example, gcc 4.7.2 or later.
compiler. If using gcc, version 4.8.1 or later is required.
</P>
<P>Note that Intel Xeon Phi coprocessors are supported in "native" mode,
not "offload" mode like the USER-INTEL package supports.

8
doc/doc2/compute_temp_region.html
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@ -68,9 +68,11 @@ remaining thermal velocity will be performed, and the bias will be
added back in. Thermostatting fixes that work in this way include
<A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>. This means any of the thermostatting
fixes can operate on a geometric region of atoms, as defined by this
compute.
langevin</A>. This means that when this compute
is used to calculate the temperature for any of the thermostatting
fixes via the <A HREF = "fix_modify.html">fix modify temp</A> command, the thermostat
will operate only on atoms that are currently in the geometric
region.
</P>
<P>Unlike other compute styles that calculate temperature, this compute
does not subtract out degrees-of-freedom due to fixes that constrain

54
doc/doc2/fix_atom_swap.html
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@ -29,10 +29,10 @@
<LI>one or more keyword/value pairs may be appended to args
<LI>keyword = <I>types</I> or <I>delta_mu</I> or <I>ke</I> or <I>semi-grand</I> or <I>region</I>
<LI>keyword = <I>types</I> or <I>mu</I> or <I>ke</I> or <I>semi-grand</I> or <I>region</I>
<PRE> <I>types</I> values = two or more atom types
<I>delta_mu</I> values = number_of_types-1 relative chemical potentials (energy units)
<I>mu</I> values = chemical potential of swap types (energy units)
<I>ke</I> value = <I>no</I> or <I>yes</I>
<I>no</I> = no conservation of kinetic energy after atom swaps
<I>yes</I> = kinetic energy is conserved after atom swaps
@ -48,7 +48,7 @@
</P>
<PRE>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 delta_mu 4.3 -5.0
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 4.3 -5.0
</PRE>
<P><B>Description:</B>
</P>
@ -88,25 +88,20 @@ allowed exchanges an atom of one type with an atom of a different
given type. In other words, the relative mole fractions of the swapped
atoms remains constant. Whereas in the semi-grand canonical ensemble,
the composition of the system can change. Note that when using
<I>semi-grand</I>, all atoms in the fix group are eligible for attempted
conversion to one of the given types, even if its current type is not
one of the given types. An attempt is made to switch the selected atom
to one of the listed <I>types</I> with equal probability. Acceptance of
each attempt depends upon the Metropolis criterion.
<I>semi-grand</I>, atoms in the fix group whose type is not listed
in the <I>types</I> keyword are ineligible for attempted
conversion. An attempt is made to switch
the selected atom (if eligible) to one of the other listed types
with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
</P>
<P>The <I>delta_mu</I> keyword allows users to specify non-zero chemical
potentials for each of the atom types. All chemical potentials are
relative to the first 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 desirable to actively control the
composition of the system. When given, 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 <I>semi-grand</I>, even for atom types not listed following the
<I>types</I> keyword. This is because when using <I>semi-grand</I>, it is
possible that any of the atom types in the system could be part of the
fix group and therefore are eligible for swapping to one of the listed
atom types.
<P>The <I>mu</I> keyword allows users to specify chemical
potentials. This is required and allowed only when using <I>semi-grand</I>.
All chemical potentials are absolute, so there is one for
each swap type listed following the <I>types</I> keyword.
In semi-grand canonical ensemble simulations the chemical composition
of the system is controlled by the difference in these values. So
shifting all values by a constant amount will have no effect
on the simulation.
</P>
<P>This command may optionally use the <I>region</I> keyword to define swap
volume. The specified region must have been previously defined with a
@ -120,10 +115,17 @@ LAMMPS will warn you if any of the atoms eligible for swapping have a
non-zero molecule ID, but does not check for this at the time of
swapping.
</P>
<P>This fix checks to ensure all atoms of the given types have the same
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.
<P>If not using <I>semi-grand</I> this fix checks to ensure all atoms of the
given types have the same 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. Conversely, when using <I>semi-grand</I>, it is assumed that all the atom
types involved in switches have the same charge. Otherwise, charge
would not be conserved. As a consequence, no checks on atomic charges are
performed, and successful switches update the atom type but not the
atom charge. While it is possible to use <I>semi-grand</I> with groups of
atoms that have different charges, these charges will not be changed when the
atom types change.
</P>
<P>Since this fix computes total potential energies before and after
proposed swaps, so even complicated potential energy calculations are
@ -186,7 +188,7 @@ LAMMPS</A> section for more info.
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are ke = yes, semi-grand = no, delta_mu = 0.0 for
<P>The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
all atom types.
</P>
<HR>

38
doc/doc2/pair_zbl.html
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@ -25,8 +25,8 @@
<P><B>Examples:</B>
</P>
<PRE>pair_style zbl 3.0 4.0
pair_coeff * * 73.0
pair_coeff 1 1 14.0
pair_coeff * * 73.0 73.0
pair_coeff 1 1 14.0 14.0
</PRE>
<P><B>Description:</B>
</P>
@ -45,17 +45,23 @@ two atoms. The switching function S(r) is identical to that used by
<A HREF = "pair_gromacs.html">pair_style lj/gromacs</A>. Here, the inner and outer
cutoff are the same for all pairs of atom types.
</P>
<P>The following coefficient must be defined for each pair of atom types
<P>The following coefficients must be defined for each pair of atom types
via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
or in the LAMMPS data file. Z can not be specified for two different
atoms types. Therefore the lists of atom types I and atom types J
must match.
or in the LAMMPS data file.
</P>
<UL><LI>Z (multiples of proton charge, e.g. 13.0 for aluminum)
<UL><LI>Z_i (atomic number for first atom type, e.g. 13.0 for aluminum)
</UL>
<P>Although Z must be defined for all atom type pairs I,J, it is only
stored for individual atom types, i.e. when I = J. Z is normally equal
to the atomic number of the atom type.
<UL><LI>Z_j (ditto for second atom type)
</UL>
<P>The values of Z_i and Z_j are normally equal to the atomic
numbers of the two atom types. Thus, the user may optionally
specify only the coefficients for each I==I pair, and rely
on the obvious mixing rule for cross interactions (see below).
Note that when I==I it is required that Z_i == Z_j. When used
with <A HREF = "pair_hybrid.html">hybrid/overlay</A> and pairs are assigned
to more than one sub-style, the mixing rule is not used and
each pair of types interacting with the ZBL sub-style must
be included in a pair_coeff command.
</P>
<P>IMPORTANT NOTE: The numerical values of the exponential decay
constants in the screening function depend on the unit of distance. In
@ -92,9 +98,15 @@ more instructions on how to use the accelerated styles effectively.
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>Mixing is not relevant for this pair style, since as explained above,
Z values are stored on a per-type basis, and both Zi and Zj are used
explicitly in the ZBL formula.
<P>For atom type pairs I,J and I != J, the Z_i and Z_j coefficients
can be mixed by taking Z_i and Z_j from the values specified for
I == I and J == J cases. When used
with <A HREF = "pair_hybrid.html">hybrid/overlay</A> and pairs are assigned
to more than one sub-style, the mixing rule is not used and
each pair of types interacting with the ZBL sub-style
must be included in a pair_coeff command.
The <A HREF = "pair_modify.html">pair_modify</A> mix option has no effect on
the mixing behavior
</P>
<P>The ZBL pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option, since the ZBL interaction is already smoothed to 0.0 at