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8
doc/Section_commands.html
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@ -287,7 +287,7 @@ can be enclosed in triple quotes, in which case “&” characters a
needed. For example:</p> needed. For example:</p>
<div class="highlight-python"><div class="highlight"><pre>print &quot;Volume = $v&quot; <div class="highlight-python"><div class="highlight"><pre>print &quot;Volume = $v&quot;
print &#39;Volume = $v&#39; print &#39;Volume = $v&#39;
if &quot;$*steps* &gt; 1000&quot; then quit if &quot;${steps} &gt; 1000&quot; then quit
variable a string &quot;red green blue &amp; variable a string &quot;red green blue &amp;
purple orange cyan&quot; purple orange cyan&quot;
print &quot;&quot;&quot; print &quot;&quot;&quot;
@ -891,10 +891,10 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a></td> <td><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a></td>
<td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a></td> <td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a></td>
<td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td> <td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td>
<td><code class="xref doc docutils literal"><span class="pre">sna/atom</span></code></td> <td><a class="reference internal" href="compute_sna_atom.html"><em>sna/atom</em></a></td>
</tr> </tr>
<tr class="row-odd"><td><code class="xref doc docutils literal"><span class="pre">snad/atom</span></code></td> <tr class="row-odd"><td><a class="reference internal" href="compute_sna_atom.html"><em>snad/atom</em></a></td>
<td><code class="xref doc docutils literal"><span class="pre">snav/atom</span></code></td> <td><a class="reference internal" href="compute_sna_atom.html"><em>snav/atom</em></a></td>
<td><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a></td> <td><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a></td>
<td><a class="reference internal" href="compute_temp.html"><em>temp (c)</em></a></td> <td><a class="reference internal" href="compute_temp.html"><em>temp (c)</em></a></td>
<td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td> <td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td>

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doc/Section_commands.txt
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@ -164,7 +164,7 @@ needed. For example:
print "Volume = $v" print "Volume = $v"
print 'Volume = $v' print 'Volume = $v'
if "${steps} > 1000" then quit if "$\{steps\} > 1000" then quit
variable a string "red green blue & variable a string "red green blue &
purple orange cyan" purple orange cyan"
print """ print """
@ -697,9 +697,9 @@ KOKKOS, o = USER-OMP, t = OPT.
"reduce"_compute_reduce.html, "reduce"_compute_reduce.html,
"reduce/region"_compute_reduce.html, "reduce/region"_compute_reduce.html,
"slice"_compute_slice.html, "slice"_compute_slice.html,
"sna/atom"_compute_sna.html, "sna/atom"_compute_sna_atom.html,
"snad/atom"_compute_sna.html, "snad/atom"_compute_sna_atom.html,
"snav/atom"_compute_sna.html, "snav/atom"_compute_sna_atom.html,
"stress/atom"_compute_stress_atom.html, "stress/atom"_compute_stress_atom.html,
"temp (c)"_compute_temp.html, "temp (c)"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html, "temp/asphere"_compute_temp_asphere.html,

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doc/Section_python.html
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@ -337,8 +337,8 @@ described above.</p>
<p>If you set the paths to these files as environment variables, you only <p>If you set the paths to these files as environment variables, you only
have to do it once. For the csh or tcsh shells, add something like have to do it once. For the csh or tcsh shells, add something like
this to your ~/.cshrc file, one line for each of the two files:</p> this to your ~/.cshrc file, one line for each of the two files:</p>
<div class="highlight-python"><div class="highlight"><pre>setenv PYTHONPATH $*PYTHONPATH*:/home/sjplimp/lammps/python <div class="highlight-python"><div class="highlight"><pre>setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
setenv LD_LIBRARY_PATH $*LD_LIBRARY_PATH*:/home/sjplimp/lammps/src setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
</pre></div> </pre></div>
</div> </div>
<p>If you use the python/install.py script, you need to invoke it every <p>If you use the python/install.py script, you need to invoke it every

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doc/Section_python.txt
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@ -221,8 +221,8 @@ If you set the paths to these files as environment variables, you only
have to do it once. For the csh or tcsh shells, add something like have to do it once. For the csh or tcsh shells, add something like
this to your ~/.cshrc file, one line for each of the two files: this to your ~/.cshrc file, one line for each of the two files:
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src :pre setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
If you use the python/install.py script, you need to invoke it every If you use the python/install.py script, you need to invoke it every
time you rebuild LAMMPS (as a shared library) or make changes to the time you rebuild LAMMPS (as a shared library) or make changes to the

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doc/Section_start.html
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@ -1169,13 +1169,13 @@ current version of the shared library is always available to programs
that use it.</p> that use it.</p>
<p>For the csh or tcsh shells, you would add something like this to your <p>For the csh or tcsh shells, you would add something like this to your
~/.cshrc file:</p> ~/.cshrc file:</p>
<div class="highlight-python"><div class="highlight"><pre>setenv LD_LIBRARY_PATH $*LD_LIBRARY_PATH*:/home/sjplimp/lammps/src <div class="highlight-python"><div class="highlight"><pre>setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
</pre></div> </pre></div>
</div> </div>
</div> </div>
<div class="section" id="calling-the-lammps-library"> <div class="section" id="calling-the-lammps-library">
<h3>2.5.4. <strong>Calling the LAMMPS library:</strong><a class="headerlink" href="#calling-the-lammps-library" title="Permalink to this headline"></a></h3> <h3>2.5.4. <strong>Calling the LAMMPS library:</strong><a class="headerlink" href="#calling-the-lammps-library" title="Permalink to this headline"></a></h3>
<p>Either flavor of library (static or shared0 allows one or more LAMMPS <p>Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program.</p> objects to be instantiated from the calling program.</p>
<p>When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS <p>When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
namespace; you can safely use any of its classes and methods from namespace; you can safely use any of its classes and methods from

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doc/Section_start.txt
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@ -1130,11 +1130,11 @@ that use it.
For the csh or tcsh shells, you would add something like this to your For the csh or tcsh shells, you would add something like this to your
~/.cshrc file: ~/.cshrc file:
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src :pre setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
[Calling the LAMMPS library:] :h5 [Calling the LAMMPS library:] :h5
Either flavor of library (static or shared0 allows one or more LAMMPS Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program. objects to be instantiated from the calling program.
When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS

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doc/compute.html
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@ -322,9 +322,9 @@ are given in the compute section of <a class="reference internal" href="Section_
<li><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a> - combine per-atom quantities into a single global value</li> <li><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a> - combine per-atom quantities into a single global value</li>
<li><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a> - same as compute reduce, within a region</li> <li><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a> - same as compute reduce, within a region</li>
<li><a class="reference internal" href="compute_slice.html"><em>slice</em></a> - extract values from global vector or array</li> <li><a class="reference internal" href="compute_slice.html"><em>slice</em></a> - extract values from global vector or array</li>
<li><code class="xref doc docutils literal"><span class="pre">sna/atom</span></code> - calculate bispectrum coefficients for each atom</li> <li><a class="reference internal" href="compute_sna_atom.html"><em>sna/atom</em></a> - calculate bispectrum coefficients for each atom</li>
<li><code class="xref doc docutils literal"><span class="pre">snad/atom</span></code> - derivative of bispectrum coefficients for each atom</li> <li><a class="reference internal" href="compute_sna_atom.html"><em>snad/atom</em></a> - derivative of bispectrum coefficients for each atom</li>
<li><code class="xref doc docutils literal"><span class="pre">snav/atom</span></code> - virial contribution from bispectrum coefficients for each atom</li> <li><a class="reference internal" href="compute_sna_atom.html"><em>snav/atom</em></a> - virial contribution from bispectrum coefficients for each atom</li>
<li><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a> - stress tensor for each atom</li> <li><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a> - stress tensor for each atom</li>
<li><a class="reference internal" href="compute_temp.html"><em>temp</em></a> - temperature of group of atoms</li> <li><a class="reference internal" href="compute_temp.html"><em>temp</em></a> - temperature of group of atoms</li>
<li><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a> - temperature of aspherical particles</li> <li><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a> - temperature of aspherical particles</li>

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doc/compute.txt
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@ -218,9 +218,9 @@ page"_Section_commands.html#cmd_5.
"reduce"_compute_reduce.html - combine per-atom quantities into a single global value "reduce"_compute_reduce.html - combine per-atom quantities into a single global value
"reduce/region"_compute_reduce.html - same as compute reduce, within a region "reduce/region"_compute_reduce.html - same as compute reduce, within a region
"slice"_compute_slice.html - extract values from global vector or array "slice"_compute_slice.html - extract values from global vector or array
"sna/atom"_compute_sna.html - calculate bispectrum coefficients for each atom "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
"snad/atom"_compute_sna.html - derivative of bispectrum coefficients for each atom "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
"snav/atom"_compute_sna.html - virial contribution from bispectrum coefficients for each atom "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
"stress/atom"_compute_stress_atom.html - stress tensor for each atom "stress/atom"_compute_stress_atom.html - stress tensor for each atom
"temp"_compute_temp.html - temperature of group of atoms "temp"_compute_temp.html - temperature of group of atoms
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles

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doc/fix_restrain.html
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@ -206,11 +206,11 @@ as the following may be useful:</p>
velocity all create 600.0 8675309 mom yes rot yes dist gaussian velocity all create 600.0 8675309 mom yes rot yes dist gaussian
fix NVE all nve fix NVE all nve
fix TFIX all langevin 600.0 0.0 100 24601 fix TFIX all langevin 600.0 0.0 100 24601
fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $*angle1* dihedral 3 1 2 9 0.0 5000.0 $*angle2* fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 ${angle1} dihedral 3 1 2 9 0.0 5000.0 ${angle2}
fix_modify REST energy yes fix_modify REST energy yes
run 10000 run 10000
fix TFIX all langevin 0.0 0.0 100 24601 fix TFIX all langevin 0.0 0.0 100 24601
fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $*angle1* dihedral 3 1 2 9 5000.0 5000.0 $*angle2* fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 ${angle1} dihedral 3 1 2 9 5000.0 5000.0 ${angle2}
fix_modify REST energy yes fix_modify REST energy yes
run 10000 run 10000
# sanity check for convergence # sanity check for convergence

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doc/fix_restrain.txt
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@ -85,11 +85,11 @@ as the following may be useful:
velocity all create 600.0 8675309 mom yes rot yes dist gaussian velocity all create 600.0 8675309 mom yes rot yes dist gaussian
fix NVE all nve fix NVE all nve
fix TFIX all langevin 600.0 0.0 100 24601 fix TFIX all langevin 600.0 0.0 100 24601
fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 ${angle1} dihedral 3 1 2 9 0.0 5000.0 ${angle2} fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $\{angle1\} dihedral 3 1 2 9 0.0 5000.0 $\{angle2\}
fix_modify REST energy yes fix_modify REST energy yes
run 10000 run 10000
fix TFIX all langevin 0.0 0.0 100 24601 fix TFIX all langevin 0.0 0.0 100 24601
fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 ${angle1} dihedral 3 1 2 9 5000.0 5000.0 ${angle2} fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $\{angle1\} dihedral 3 1 2 9 5000.0 5000.0 $\{angle2\}
fix_modify REST energy yes fix_modify REST energy yes
run 10000 run 10000
# sanity check for convergence # sanity check for convergence

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doc/pair_hybrid.html
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@ -310,9 +310,40 @@ for applying weightings that change the strength of pairwise
interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4 interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology, as normally set by the neighbors in the molecular bond topology, as normally set by the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. Different weights can be <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. Different weights can be
assigned to different pair hybrid sub-styles via the <a class="reference internal" href="pair_modify.html"><em>pair_modify special</em></a> command. This allows multiple force fields assigned to different pair hybrid sub-styles via the <a class="reference internal" href="pair_modify.html"><em>pair_modify special</em></a> command. This allows multiple force fields
to be used in a model of a hybrid system. See the to be used in a model of a hybrid system, however, there is no consistent
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> doc page for details.</p> approach to determine parameters automatically for the interactions
between the two force fields, this is only recommended when particles
described by the different force fields do not mix.</p>
<p>Here is an example for mixing CHARMM and AMBER: The global <em>amber</em>
setting sets the 1-4 interactions to non-zero scaling factors and
then overrides them with 0.0 only for CHARMM:</p>
<div class="highlight-python"><div class="highlight"><pre>special_bonds amber
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
</pre></div>
</div>
<p>The this input achieves the same effect:</p>
<div class="highlight-python"><div class="highlight"><pre>special_bonds 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
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 0.83333333
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
</pre></div>
</div>
<p>Here is an example for mixing Tersoff with OPLS/AA based on
a data file that defines bonds for all atoms where for the
Tersoff part of the system the force constants for the bonded
interactions have been set to 0. Note the global settings are
effectively <em>lj/coul 0.0 0.0 0.5</em> as required for OPLS/AA:</p>
<div class="highlight-python"><div class="highlight"><pre>special_bonds lj/coul 1e-20 1e-20 0.5
pair_hybrid tersoff lj/cut/coul/long 12.0
pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
</pre></div>
</div>
<p>See the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> doc page for details on
the specific syntax, requirements and restrictions.</p>
<hr class="docutils" />
<p>The potential energy contribution to the overall system due to an <p>The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a> command.</p> individual sub-style can be accessed and output via the <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a> command.</p>
<hr class="docutils" /> <hr class="docutils" />

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doc/pair_hybrid.txt
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@ -190,9 +190,42 @@ interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology, as normally set by the neighbors in the molecular bond topology, as normally set by the
"special_bonds"_special_bonds.html command. Different weights can be "special_bonds"_special_bonds.html command. Different weights can be
assigned to different pair hybrid sub-styles via the "pair_modify assigned to different pair hybrid sub-styles via the "pair_modify
special"_pair_modify.html command. This allows multiple force fields special"_pair_modify.html command. This allows multiple force fields
to be used in a model of a hybrid system. See the to be used in a model of a hybrid system, however, there is no consistent
"pair_modify"_pair_modify.html doc page for details. approach to determine parameters automatically for the interactions
between the two force fields, this is only recommended when particles
described by the different force fields do not mix.
Here is an example for mixing CHARMM and AMBER: The global {amber}
setting sets the 1-4 interactions to non-zero scaling factors and
then overrides them with 0.0 only for CHARMM:
special_bonds amber
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 :pre
The this input achieves the same effect:
special_bonds 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
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 0.83333333
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 :pre
Here is an example for mixing Tersoff with OPLS/AA based on
a data file that defines bonds for all atoms where for the
Tersoff part of the system the force constants for the bonded
interactions have been set to 0. Note the global settings are
effectively {lj/coul 0.0 0.0 0.5} as required for OPLS/AA:
special_bonds lj/coul 1e-20 1e-20 0.5
pair_hybrid tersoff lj/cut/coul/long 12.0
pair_modify pair tersoff special lj/coul 1.0 1.0 1.0 :pre
See the "pair_modify"_pair_modify.html doc page for details on
the specific syntax, requirements and restrictions.
:line
The potential energy contribution to the overall system due to an The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the "compute individual sub-style can be accessed and output via the "compute

68
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@ -133,15 +133,15 @@
</div> </div>
<ul class="simple"> <ul class="simple">
<li>one or more keyword/value pairs may be listed</li> <li>one or more keyword/value pairs may be listed</li>
<li>keyword = <em>pair</em> or <em>special</em> or <em>shift</em> or <em>mix</em> or <em>table</em> or <em>table/disp</em> or <em>tabinner</em> or <em>tabinner/disp</em> or <em>tail</em> or <em>compute</em></li> <li>keyword = <em>pair</em> or <em>shift</em> or <em>mix</em> or <em>table</em> or <em>table/disp</em> or <em>tabinner</em> or <em>tabinner/disp</em> or <em>tail</em> or <em>compute</em></li>
</ul> </ul>
<pre class="literal-block"> <pre class="literal-block">
<em>pair</em> values = sub-style N special which w1 wt2 wt3 <em>pair</em> values = sub-style N <em>special</em> which wt1 wt2 wt3
sub-style = sub-style of <a class="reference internal" href="pair_hybrid.html"><em>pair hybrid</em></a> sub-style = sub-style of <a class="reference internal" href="pair_hybrid.html"><em>pair hybrid</em></a>
N = which instance of sub-style (only if sub-style is used multiple times) N = which instance of sub-style (only if sub-style is used multiple times)
<em>special</em> values = flavor w1 w2 w3 <em>special</em> which wt1 wt2 wt3 = override <em>special_bonds</em> settings (optional)
flavor = <em>lj/coul</em> or <em>lj</em> or <em>coul</em> which = <em>lj/coul</em> or <em>lj</em> or <em>coul</em>
w1,w2,w3 = weights from 0.0 to 1.0 inclusive w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
<em>mix</em> value = <em>geometric</em> or <em>arithmetic</em> or <em>sixthpower</em> <em>mix</em> value = <em>geometric</em> or <em>arithmetic</em> or <em>sixthpower</em>
<em>shift</em> value = <em>yes</em> or <em>no</em> <em>shift</em> value = <em>yes</em> or <em>no</em>
<em>table</em> value = N <em>table</em> value = N
@ -158,11 +158,11 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2> <h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_modify shift yes mix geometric <p>pair_modify shift yes mix geometric
pair_modify tail yes pair_modify tail yes
pair_modify table 12 pair_modify table 12
</pre></div> pair_modify pair lj/cut compute no
</div> pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0:pre</p>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2> <h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
@ -179,12 +179,10 @@ number indicates which instance of the sub-style the remaining
keywords will be applied to. Note that if the <em>pair</em> keyword is not keywords will be applied to. Note that if the <em>pair</em> keyword is not
used, and the pair style is <em>hybrid</em> or <em>hybrid/overlay</em>, then all the used, and the pair style is <em>hybrid</em> or <em>hybrid/overlay</em>, then all the
specified keywords will be applied to all sub-styles.</p> specified keywords will be applied to all sub-styles.</p>
<p>If used, the <em>special</em> keyword must appear second in the list of <p>The <em>special</em> keyword can only be used in conjunction with the <em>pair</em>
keywords, and must follow the <em>pair</em> keyword. Like the <em>pair</em> keyword and must directly follow it. It allows to override the
keyword, it also can only be used with the <a class="reference internal" href="pair_hybrid.html"><em>hybrid and hybrid/overlay</em></a> pair styles. Its parameters are <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> settings for the specified sub-style.
similar to the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command, and it More details are given below.</p>
overrides the special_bond settings for the specified sub-style. More
details are given below.</p>
<p>The <em>mix</em> keyword affects pair coefficients for interactions between <p>The <em>mix</em> keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not atoms of type I and J, when I != J and the coefficients are not
explicitly set in the input script. Note that coefficients for I = J explicitly set in the input script. Note that coefficients for I = J
@ -228,7 +226,7 @@ see the doc page for individual styles to see which potentials support
these options. If N is non-zero, a table of length 2^N is these options. If N is non-zero, a table of length 2^N is
pre-computed for forces and energies, which can shrink their pre-computed for forces and energies, which can shrink their
computational cost by up to a factor of 2. The table is indexed via a computational cost by up to a factor of 2. The table is indexed via a
bit-mapping technique <a class="reference internal" href="pair_table.html#wolff"><span>(Wolff)</span></a> and a linear interpolation is bit-mapping technique <a class="reference internal" href="#wolff"><span>(Wolff)</span></a> and a linear interpolation is
performed between adjacent table values. In our experiments with performed between adjacent table values. In our experiments with
different table styles (lookup, linear, spline), this method typically different table styles (lookup, linear, spline), this method typically
gave the best performance in terms of speed and accuracy.</p> gave the best performance in terms of speed and accuracy.</p>
@ -319,37 +317,29 @@ pair style be defined.</p>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="use-of-special-keyword"> <div class="section" id="use-of-special-keyword">
<h3>Use of <em>special</em> keyword<a class="headerlink" href="#use-of-special-keyword" title="Permalink to this headline"></a></h3> <h3>Use of <em>special</em> keyword<a class="headerlink" href="#use-of-special-keyword" title="Permalink to this headline"></a></h3>
<p>The <em>special</em> keyword requires 4 values similar to those specified <p>The <em>special</em> keyword allows to override the 1-2, 1-3, and 1-4
with the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command, <em>flavor</em> and exclusion settings for individual sub-styles of a
w1,w2,w3. The <em>flavor</em> argument can be <em>lj</em> to change the <a class="reference internal" href="pair_hybrid.html"><em>hybrid pair style</em></a>. It requires 4 arguments similar
Lennard-Jones settings, <em>coul</em> to change the Coulombic settings, or to the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command, <em>which</em> and
<em>lj/coul</em> to change both to the same set of 3 values. The w1,w2,w3 wt1,wt2,wt3. The <em>which</em> argument can be <em>lj</em> to change the
Lennard-Jones settings, <em>coul</em> to change the Coulombic settings,
or <em>lj/coul</em> to change both to the same set of 3 values. The wt1,wt2,wt3
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2, 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</p> 1-3, and 1-4 bond topology neighbors, respectively. The <em>special</em>
<div class="highlight-python"><div class="highlight"><pre>special_bonds lj/coul 0.0 0.0 0.1 keyword can only be used in conjunction with the <em>pair</em> keyword
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0 and has to directly follow it.</p>
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></div>
</div>
<p>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 last 2 pair modify commands set the
standard AMBER values for LJ and Coulombic weights.</p>
<div class="admonition warning"> <div class="admonition warning">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Warning</p>
<p class="last">The global settings specified by the <p class="last">The global settings specified by the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command affect the construction of <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command affect the construction of
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors) 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 exclude those pairs from the neighbor list entirely. Weights of 1.0
store the neighbor with no weighting applied. The format of the store the neighbor with no weighting applied. Thus only global values
neighbor list cannot be changed by setting a sub-style weight to a different from exactly 0.0 or 1.0 can be overridden and an error
non-zero or non-one value. Thus an error is generated if the new is generated if the requested setting is not compatible with the
sub-style value is not 0.0 (or 1.0) when the global setting is 0.0 (or global setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for
1.0). Note that as in the example above, the global factor can simply 1.0 is usually a sufficient workaround in this case without causing
be set a value other than 0.0 or 1.0, then overridden by any of the a significant error.</p>
sub-styles with a value that is 0.0 or 1.0.</p>
</div> </div>
</div> </div>
</div> </div>

65
doc/pair_modify.txt
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@ -13,13 +13,13 @@ pair_modify command :h3
pair_modify keyword values ... :pre pair_modify keyword values ... :pre
one or more keyword/value pairs may be listed :ulb,l one or more keyword/value pairs may be listed :ulb,l
keyword = {pair} or {special} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or {tabinner/disp} or {tail} or {compute} :l keyword = {pair} 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 {pair} values = sub-style N {special} which wt1 wt2 wt3
sub-style = sub-style of "pair hybrid"_pair_hybrid.html sub-style = sub-style of "pair hybrid"_pair_hybrid.html
N = which instance of sub-style (only if sub-style is used multiple times) N = which instance of sub-style (only if sub-style is used multiple times)
{special} values = flavor w1 w2 w3 {special} which wt1 wt2 wt3 = override {special_bonds} settings (optional)
flavor = {lj/coul} or {lj} or {coul} which = {lj/coul} or {lj} or {coul}
w1,w2,w3 = weights from 0.0 to 1.0 inclusive w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
{mix} value = {geometric} or {arithmetic} or {sixthpower} {mix} value = {geometric} or {arithmetic} or {sixthpower}
{shift} value = {yes} or {no} {shift} value = {yes} or {no}
{table} value = N {table} value = N
@ -38,7 +38,9 @@ keyword = {pair} or {special} or {shift} or {mix} or {table} or {table/disp} or
pair_modify shift yes mix geometric pair_modify shift yes mix geometric
pair_modify tail yes pair_modify tail yes
pair_modify table 12 :pre pair_modify table 12
pair_modify pair lj/cut compute no
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0:pre
[Description:] [Description:]
@ -58,13 +60,10 @@ 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 used, and the pair style is {hybrid} or {hybrid/overlay}, then all the
specified keywords will be applied to all sub-styles. specified keywords will be applied to all sub-styles.
If used, the {special} keyword must appear second in the list of The {special} keyword can only be used in conjunction with the {pair}
keywords, and must follow the {pair} keyword. Like the {pair} keyword and must directly follow it. It allows to override the
keyword, it also can only be used with the "hybrid and "special_bonds"_special_bonds.html settings for the specified sub-style.
hybrid/overlay"_pair_hybrid.html pair styles. Its parameters are More details are given below.
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 The {mix} keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not atoms of type I and J, when I != J and the coefficients are not
@ -210,36 +209,28 @@ pair style be defined.
Use of {special} keyword :h5 Use of {special} keyword :h5
The {special} keyword requires 4 values similar to those specified The {special} keyword allows to override the 1-2, 1-3, and 1-4
with the "special_bonds"_special_bonds.html command, {flavor} and exclusion settings for individual sub-styles of a
w1,w2,w3. The {flavor} argument can be {lj} to change the "hybrid pair style"_pair_hybrid.html. It requires 4 arguments similar
Lennard-Jones settings, {coul} to change the Coulombic settings, or to the "special_bonds"_special_bonds.html command, {which} and
{lj/coul} to change both to the same set of 3 values. The w1,w2,w3 wt1,wt2,wt3. 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 set of 3 values. The wt1,wt2,wt3
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2, 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 1-3, and 1-4 bond topology neighbors, respectively. The {special}
keyword can only be used in conjunction with the {pair} keyword
special_bonds lj/coul 0.0 0.0 0.1 and has to directly follow it.
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 last 2 pair modify commands set the
standard AMBER values for LJ and Coulombic weights.
IMPORTANT NOTE: The global settings specified by the IMPORTANT NOTE: The global settings specified by the
"special_bonds"_special_bonds.html command affect the construction of "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) 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 exclude those pairs from the neighbor list entirely. Weights of 1.0
store the neighbor with no weighting applied. The format of the store the neighbor with no weighting applied. Thus only global values
neighbor list cannot be changed by setting a sub-style weight to a different from exactly 0.0 or 1.0 can be overridden and an error
non-zero or non-one value. Thus an error is generated if the new is generated if the requested setting is not compatible with the
sub-style value is not 0.0 (or 1.0) when the global setting is 0.0 (or global setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for
1.0). Note that as in the example above, the global factor can simply 1.0 is usually a sufficient workaround in this case without causing
be set a value other than 0.0 or 1.0, then overridden by any of the a significant error.
sub-styles with a value that is 0.0 or 1.0.
:line :line

4
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@ -184,7 +184,7 @@ def loop(lmpptr,N,cut0):
<div class="highlight-python"><div class="highlight"><pre> for i in range(N): <div class="highlight-python"><div class="highlight"><pre> for i in range(N):
cut = cut0 + i*0.1 cut = cut0 + i*0.1
lmp.set_variable(&quot;cut&quot;,cut) # set a variable in LAMMPS lmp.set_variable(&quot;cut&quot;,cut) # set a variable in LAMMPS
lmp.command(&quot;pair_style lj/cut $*cut*&quot;) # LAMMPS commands lmp.command(&quot;pair_style lj/cut ${cut}&quot;) # LAMMPS commands
lmp.command(&quot;pair_coeff * * 1.0 1.0&quot;) lmp.command(&quot;pair_coeff * * 1.0 1.0&quot;)
lmp.command(&quot;run 100&quot;) lmp.command(&quot;run 100&quot;)
&quot;&quot;&quot; &quot;&quot;&quot;
@ -429,7 +429,7 @@ which loads and runs the following function from examples/python/funcs.py:</p>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-python"><div class="highlight"><pre><span class="n">lmp</span><span class="o">.</span><span class="n">set_variable</span><span class="p">(</span><span class="s">&quot;cut&quot;</span><span class="p">,</span><span class="n">cut</span><span class="p">)</span> <span class="c"># set a variable in LAMMPS</span> <div class="highlight-python"><div class="highlight"><pre><span class="n">lmp</span><span class="o">.</span><span class="n">set_variable</span><span class="p">(</span><span class="s">&quot;cut&quot;</span><span class="p">,</span><span class="n">cut</span><span class="p">)</span> <span class="c"># set a variable in LAMMPS</span>
<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s">&quot;pair_style lj/cut $*cut*&quot;</span><span class="p">)</span> <span class="c"># LAMMPS command</span> <span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s">&quot;pair_style lj/cut ${cut}&quot;</span><span class="p">)</span> <span class="c"># LAMMPS command</span>
<span class="c">#lmp.command(&quot;pair_style lj/cut %d&quot; % cut) # LAMMPS command option</span> <span class="c">#lmp.command(&quot;pair_style lj/cut %d&quot; % cut) # LAMMPS command option</span>
</pre></div> </pre></div>
</div> </div>

4
doc/python.txt
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@ -58,7 +58,7 @@ def loop(lmpptr,N,cut0):
for i in range(N): for i in range(N):
cut = cut0 + i*0.1 cut = cut0 + i*0.1
lmp.set_variable("cut",cut) # set a variable in LAMMPS lmp.set_variable("cut",cut) # set a variable in LAMMPS
lmp.command("pair_style lj/cut ${cut}") # LAMMPS commands lmp.command("pair_style lj/cut $\{cut\}") # LAMMPS commands
lmp.command("pair_coeff * * 1.0 1.0") lmp.command("pair_coeff * * 1.0 1.0")
lmp.command("run 100") lmp.command("run 100")
""" :pre """ :pre
@ -326,7 +326,7 @@ def loop(N,cut0,thresh,lmpptr):
cut = cut0 + i*0.1 :pre cut = cut0 + i*0.1 :pre
lmp.set_variable("cut",cut) # set a variable in LAMMPS lmp.set_variable("cut",cut) # set a variable in LAMMPS
lmp.command("pair_style lj/cut ${cut}") # LAMMPS command lmp.command("pair_style lj/cut $\{cut\}") # LAMMPS command
#lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option :pre #lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option :pre
lmp.command("pair_coeff * * 1.0 1.0") # ditto lmp.command("pair_coeff * * 1.0 1.0") # ditto

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