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6
doc/Manual.txt
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@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree::
:maxdepth: 2
:numbered:
:numbered: // comment
Section_intro
Section_start
@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables
==================
* :ref:`genindex`
* :ref:`search`
* :ref:`genindex` // comment
* :ref:`search` // comment
END_RST -->

2
doc/fix.txt
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@ -172,7 +172,7 @@ in the fix section of "this page"_Section_commands.html#cmd_5.
"append/atoms"_fix_append_atoms.html - append atoms to a running simulation
"aveforce"_fix_aveforce.html - add an averaged force to each atom
"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
"ave/correlate"_fix_correlate_atom.html - compute/output time correlations
"ave/correlate"_fix_ave_correlate.html - compute/output time correlations
"ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
"ave/spatial"_fix_ave_spatial.html - compute/output time-averaged per-atom quantities by layer
"ave/time"_fix_ave_time.html - compute/output global time-averaged quantities

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doc/pair_hybrid.txt
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@ -185,15 +185,14 @@ potentials.
:line
Different force fields (e.g. CHARMM vs AMBER) may have different rules
for applying these factors to modulate the strength of pairwise
for applying weightings that change the strength of pairwise
interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology. Specific
"special_bonds"_special_bonds.html settings can be assigned to
different pair hybrid sub-styles via the "pair_modify
special"_pair_modify.html special command, using its {pair} keyword
and optional {special} argument. This allows multiple force fields to
be used to a model a hybrid system. See the
"special_bonds"_special_bonds.html doc page for details.
neighbors in the molecular bond topology, as normally set by the
"special_bonds"_special_bonds.html command. Different weights can be
assigned to different pair hybrid sub-styles via the "pair_modify
special"_pair_modify.html command. This allows multiple force fields
to be used in a model of a hybrid system. See the
"pair_modify"_pair_modify.html doc page for details.
The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the "compute

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doc/pair_modify.txt
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@ -13,12 +13,12 @@ pair_modify command :h3
pair_modify keyword values ... :pre
one or more keyword/value pairs may be listed :ulb,l
keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or {tabinner/disp} or {tail} or {compute} :l
keyword = {pair} or {special} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or {tabinner/disp} or {tail} or {compute} :l
{pair} values = sub-style N special which w1 wt2 wt3
sub-style = sub-style of "pair hybrid"_pair_hybrid.html
N = which instance of sub-style (only if sub-style is used multiple times)
special = optional if want to override "special_bonds"_special_bonds.html settings for sub-style
which = {lj/coul} or {lj} or {coul}
{special} values = flavor w1 w2 w3
flavor = {lj/coul} or {lj} or {coul}
w1,w2,w3 = weights from 0.0 to 1.0 inclusive
{mix} value = {geometric} or {arithmetic} or {sixthpower}
{shift} value = {yes} or {no}
@ -45,15 +45,26 @@ pair_modify table 12 :pre
Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.
If used, the {pair} keyword and its optional {special} arguments must
appear first in the list of keywords. It can only be used with the
"hybrid and hybrid/overlay"_pair_hybrid.html pair styles and when used
it means that all the following parameters will only be modified for
the specified sub-style. If the {pair} keyword is not used, and the
pair style is {hybrid} or {hybrid/overlay}, all the following
parameters keywords will be applied to all sub-styles. A more detailed
explanation of the {pair} keyword syntax, including its optional
{special} argument are given below.
If used, the {pair} keyword must appear first in the list of keywords.
It can only be used with the "hybrid and
hybrid/overlay"_pair_hybrid.html pair styles. It means that all the
following parameters will only be modified for the specified
sub-style. If the sub-style is defined multiple times, then an
additional numeric argument {N} must also be specified, which is a
number from 1 to M where M is the number of times the sub-style was
listed in the "pair_style hybrid"_pair_hybrid.html command. The extra
number indicates which instance of the sub-style the remaining
keywords will be applied to. Note that if the {pair} keyword is not
used, and the pair style is {hybrid} or {hybrid/overlay}, then all the
specified keywords will be applied to all sub-styles.
If used, the {special} keyword must appear second in the list of
keywords, and must follow the {pair} keyword. Like the {pair}
keyword, it also can only be used with the "hybrid and
hybrid/overlay"_pair_hybrid.html pair styles. Its parameters are
similar to the "special_bonds"_special_bonds.html command, and it
overrides the special_bond settings for the specified sub-style. More
details are given below.
The {mix} keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
@ -197,61 +208,38 @@ pair style be defined.
:line
Use of the pair keyword :h4
Use of {special} keyword :h5
If used, the {pair} keyword and its optional {special} arguments must
appear first in the list of keywords. It can only be used with the
"hybrid and hybrid/overlay"_pair_hybrid.html pair styles and when used
it means that all the following parameters will only be modified for
the specified sub-style. If the {pair} keyword is not used, and the
pair style is {hybrid} or {hybrid/overlay}, all the following
parameters keywords will be applied to all sub-styles. A more detailed
explanation of the {pair} keyword syntax, including its optional
{special} argument are given below.
As mentioned above, the {pair} keyword can only be used with the
"hybrid and hybrid/overlay"_pair_hybrid.html pair styles, and must
come first in the list of keywords. If used, the subsequent keywords
will only be applied to the specified sub-style. If the sub-style is
defined multiple times, then an additional numeric argument {N} must
also be specified, which is a number from 1 to M where M is the number
of times the sub-style was listed in the "pair_style
hybrid"_pair_hybrid.html command. The extra number indicates which
instance of the sub-style the pair_modify keywords will be applied to.
If the optional {special} argument is used, then the settings of the
"special_bonds"_special_bonds.html command are overridden for the
specified sub-style. The {special} argument requires 4 additional
arguments: {which} and w1,w2,w3. These are analogous to arguments in
the "special_bonds"_special_bonds.html command. The {which} argument
can be {lj} to change the Lennard-Jones settings, {coul} to change the
Coulombic settings, or {lj/coul} to change both to the same values.
The w1,w2,w3 arguments are numeric weights from 0.0 to 1.0 inclusive,
for the 1-2, 1-3, and 1-4 bond topology neighbors. For example, these
commands
The {special} keyword requires 4 values similar to those specified
with the "special_bonds"_special_bonds.html command, {flavor} and
w1,w2,w3. The {flavor} argument can be {lj} to change the
Lennard-Jones settings, {coul} to change the Coulombic settings, or
{lj/coul} to change both to the same set of 3 values. The w1,w2,w3
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
1-3, and 1-4 bond topology neighbors. For example, these commands
special_bonds lj/coul 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/charmm 8.0 10.0 lj/cut/coul/cut 10.0
pair_modify pair lj/charmm/coul/charmm special lj/coul 0.0 0.0 0.0
pair_modify pair lj/cut/coul/cut special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/cut special coul 0.0 0.0 0.8333 :pre
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.8333 :pre
show how to use both the CHARMM and AMBER force fields in a single
simulation. The first pair modify command sets the special bonds to
CHARMM values (all 0.0). The latter 2 pair modify commands set the
CHARMM values (all 0.0). The last 2 pair modify commands set the
standard AMBER values for LJ and Coulombic weights.
IMPORTANT NOTE: The global settings specified by the
"special_bonds"_special_bonds.html command affect the construction of
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
exclude those pairs from the neighbor list entirely. Weights of 1.0
store the neighbor with no weight flag applied. Neither of these
neighbor effects can be changed by setting a sub-style weight to a
store the neighbor with no weighting applied. The format of the
neighbor list cannot be changed by setting a sub-style weight to a
non-zero or non-one value. Thus an error is generated if the new
sub-style value is not 0.0 (or 1.0) and the global setting is 0.0 (or
sub-style value is not 0.0 (or 1.0) when the global setting is 0.0 (or
1.0). Note that as in the example above, the global factor can simply
be set a value other than 0.0 or 1.0, then overridden by any of the
sub-styles to a value that is 0.0 or 1.0.
sub-styles with a value that is 0.0 or 1.0.
:line

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@ -0,0 +1,204 @@
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