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24
doc/Section_howto.html
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@ -363,8 +363,8 @@ commands like <a class="reference internal" href="pair_coeff.html"><em>pair_coef
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>. See <a class="reference internal" href="Section_tools.html"><em>Section_tools</em></a> <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>. See <a class="reference internal" href="Section_tools.html"><em>Section_tools</em></a>
for additional tools that can use CHARMM or AMBER to assign force for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.</p> field coefficients and convert their output into LAMMPS input.</p>
<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force <p>See <a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field. See <a class="reference internal" href="special_bonds.html#cornell"><span>(Cornell)</span></a> for a description of the AMBER force field. See <a class="reference internal" href="#cornell"><span>(Cornell)</span></a> for a description of the AMBER force
field.</p> field.</p>
<p>These style choices compute force field formulas that are consistent <p>These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command&#8217;s with common options in CHARMM or AMBER. See each command&#8217;s
@ -389,7 +389,7 @@ atoms involved in the bond, angle, or torsion terms. DREIDING has an
<a class="reference internal" href="pair_hbond_dreiding.html"><em>explicit hydrogen bond term</em></a> to describe <a class="reference internal" href="pair_hbond_dreiding.html"><em>explicit hydrogen bond term</em></a> to describe
interactions involving a hydrogen atom on very electronegative atoms interactions involving a hydrogen atom on very electronegative atoms
(N, O, F).</p> (N, O, F).</p>
<p>See <a class="reference internal" href="special_bonds.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p> <p>See <a class="reference internal" href="#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>These style choices compute force field formulas that are consistent <p>These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command&#8217;s with the DREIDING force field. See each command&#8217;s
documentation for the formula it computes.</p> documentation for the formula it computes.</p>
@ -587,7 +587,7 @@ computations between frozen atoms by using this command:</p>
<div class="section" id="tip3p-water-model"> <div class="section" id="tip3p-water-model">
<span id="howto-7"></span><h2>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline"></a></h2> <span id="howto-7"></span><h2>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline"></a></h2>
<p>The TIP3P water model as implemented in CHARMM <p>The TIP3P water model as implemented in CHARMM
<a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with <a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms. charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of the two O-H bonds and the H-O-H angle rigid. A bond style of
@ -598,7 +598,7 @@ atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
cutoff. The K values can be used if a flexible TIP3P model (without cutoff. The K values can be used if a flexible TIP3P model (without
fix shake) is desired. If the LJ epsilon and sigma for HH and OH are fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
set to 0.0, it corresponds to the original 1983 TIP3P model set to 0.0, it corresponds to the original 1983 TIP3P model
<a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>.</p> <a class="reference internal" href="#jorgensen"><span>(Jorgensen)</span></a>.</p>
<div class="line-block"> <div class="line-block">
<div class="line">O mass = 15.9994</div> <div class="line">O mass = 15.9994</div>
<div class="line">H mass = 1.008</div> <div class="line">H mass = 1.008</div>
@ -617,7 +617,7 @@ set to 0.0, it corresponds to the original 1983 TIP3P model
<div class="line"><br /></div> <div class="line"><br /></div>
</div> </div>
<p>These are the parameters to use for TIP3P with a long-range Coulombic <p>These are the parameters to use for TIP3P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS), see <a class="reference internal" href="pair_dipole.html#price"><span>(Price)</span></a> for solver (e.g. Ewald or PPPM in LAMMPS), see <a class="reference internal" href="#price"><span>(Price)</span></a> for
details:</p> details:</p>
<div class="line-block"> <div class="line-block">
<div class="line">O mass = 15.9994</div> <div class="line">O mass = 15.9994</div>
@ -656,7 +656,7 @@ for a cutoff model:</p>
using the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command.</p> using the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command.</p>
<p>These are the additional parameters (in real units) to set for O and H <p>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff atoms and the water molecule to run a rigid TIP4P model with a cutoff
<a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>. Note that the OM distance is specified in <a class="reference internal" href="#jorgensen"><span>(Jorgensen)</span></a>. Note that the OM distance is specified in
the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command, not as part of the pair the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command, not as part of the pair
coefficients.</p> coefficients.</p>
<div class="line-block"> <div class="line-block">
@ -766,7 +766,7 @@ the partial charge assignemnts change:</p>
<div class="line">H charge = 0.4238</div> <div class="line">H charge = 0.4238</div>
<div class="line"><br /></div> <div class="line"><br /></div>
</div> </div>
<p>See the <a class="reference internal" href="fix_temp_berendsen.html#berendsen"><span>(Berendsen)</span></a> reference for more details on both <p>See the <a class="reference internal" href="#berendsen"><span>(Berendsen)</span></a> reference for more details on both
the SPC and SPC/E models.</p> the SPC and SPC/E models.</p>
<p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p> <p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p>
<hr class="docutils" /> <hr class="docutils" />
@ -788,7 +788,7 @@ the fix is invoked, and can make library calls to the other code,
which has been linked to LAMMPS as a library. This is the way the which has been linked to LAMMPS as a library. This is the way the
<a class="reference external" href="http://www.rpi.edu/~anderk5/lab">POEMS</a> package that performs constrained rigid-body motion on <a class="reference external" href="http://www.rpi.edu/~anderk5/lab">POEMS</a> package that performs constrained rigid-body motion on
groups of atoms is hooked to LAMMPS. See the groups of atoms is hooked to LAMMPS. See the
<a class="reference internal" href="fix_poems.html"><em>fix_poems</em></a> command for more details. See <a class="reference internal" href="Section_modify.html"><em>this section</em></a> of the documentation for info on how to add <a class="reference internal" href="fix_poems.html"><em>fix poems</em></a> command for more details. See <a class="reference internal" href="Section_modify.html"><em>this section</em></a> of the documentation for info on how to add
a new fix to LAMMPS.</p> a new fix to LAMMPS.</p>
<p>(2) Define a new LAMMPS command that calls the other code. This is <p>(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the conceptually similar to method (1), but in this case LAMMPS and the
@ -1893,7 +1893,7 @@ the deformation must be chosen judiciously, and care must be taken to
fully equilibrate the deformed cell before sampling the stress fully equilibrate the deformed cell before sampling the stress
tensor. Another approach is to sample the triclinic cell fluctuations tensor. Another approach is to sample the triclinic cell fluctuations
that occur in an NPT simulation. This method can also be slow to that occur in an NPT simulation. This method can also be slow to
converge and requires careful post-processing <a class="reference internal" href="pair_sdk.html#shinoda"><span>(Shinoda)</span></a></p> converge and requires careful post-processing <a class="reference internal" href="#shinoda"><span>(Shinoda)</span></a></p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
<div class="section" id="library-interface-to-lammps"> <div class="section" id="library-interface-to-lammps">
@ -2516,7 +2516,7 @@ well.</p>
</div> </div>
<div class="section" id="adiabatic-core-shell-model"> <div class="section" id="adiabatic-core-shell-model">
<span id="howto-26"></span><h2>6.26. Adiabatic core/shell model<a class="headerlink" href="#adiabatic-core-shell-model" title="Permalink to this headline"></a></h2> <span id="howto-26"></span><h2>6.26. Adiabatic core/shell model<a class="headerlink" href="#adiabatic-core-shell-model" title="Permalink to this headline"></a></h2>
<p>The adiabatic core-shell model by <a class="reference internal" href="pair_cs.html#mitchellfinchham"><span>Mitchell and Finchham</span></a> is a simple method for adding <p>The adiabatic core-shell model by <a class="reference internal" href="#mitchellfinchham"><span>Mitchell and Finchham</span></a> is a simple method for adding
polarizability to a system. In order to mimic the electron shell of polarizability to a system. In order to mimic the electron shell of
an ion, a satellite particle is attached to it. This way the ions are an ion, a satellite particle is attached to it. This way the ions are
split into a core and a shell where the latter is meant to react to split into a core and a shell where the latter is meant to react to
@ -2725,7 +2725,7 @@ fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
model, representes induced dipoles by a pair of charges (the core atom model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems model has a number of features aimed at its use in molecular systems
(<a class="reference internal" href="tutorial_drude.html#lamoureux"><span>Lamoureux and Roux</span></a>):</p> (<a class="reference internal" href="#lamoureux"><span>Lamoureux and Roux</span></a>):</p>
<ul class="simple"> <ul class="simple">
<li>Thermostating of the additional degrees of freedom associated with the <li>Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced induced dipoles at very low temperature, in terms of the reduced

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@ -650,7 +650,7 @@ the fix is invoked, and can make library calls to the other code,
which has been linked to LAMMPS as a library. This is the way the which has been linked to LAMMPS as a library. This is the way the
"POEMS"_poems package that performs constrained rigid-body motion on "POEMS"_poems package that performs constrained rigid-body motion on
groups of atoms is hooked to LAMMPS. See the groups of atoms is hooked to LAMMPS. See the
"fix_poems"_fix_poems.html command for more details. See "this "fix poems"_fix_poems.html command for more details. See "this
section"_Section_modify.html of the documentation for info on how to add section"_Section_modify.html of the documentation for info on how to add
a new fix to LAMMPS. a new fix to LAMMPS.

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doc/Section_packages.html
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@ -494,7 +494,7 @@ name links to a sub-section below with more details.</p>
<td>python</td> <td>python</td>
<td>lib/python</td> <td>lib/python</td>
</tr> </tr>
<tr class="row-even"><td><a class="reference internal" href="Section_tools.html#reax"><span>REAX</span></a></td> <tr class="row-even"><td><a class="reference internal" href="#reax"><span>REAX</span></a></td>
<td>ReaxFF potential</td> <td>ReaxFF potential</td>
<td>Aidan Thompson (Sandia)</td> <td>Aidan Thompson (Sandia)</td>
<td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td> <td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td>
@ -1283,7 +1283,7 @@ make machine
</pre></div> </pre></div>
</div> </div>
<p>Supporting info: src/POEMS/README, lib/poems/README, <p>Supporting info: src/POEMS/README, lib/poems/README,
<a class="reference internal" href="fix_poems.html"><em>fix_poems</em></a>, examples/rigid</p> <a class="reference internal" href="fix_poems.html"><em>fix poems</em></a>, examples/rigid</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
<div class="section" id="python-package"> <div class="section" id="python-package">
@ -1863,7 +1863,7 @@ make machine
<tr class="row-odd"><td><a class="reference internal" href="#user-qtb"><span>USER-QTB</span></a></td> <tr class="row-odd"><td><a class="reference internal" href="#user-qtb"><span>USER-QTB</span></a></td>
<td>quantum nuclear effects</td> <td>quantum nuclear effects</td>
<td>Yuan Shen (Stanford)</td> <td>Yuan Shen (Stanford)</td>
<td><a class="reference internal" href="fix_qtb.html"><em>fix qtb</em></a> <a class="reference internal" href="fix_qbmsst.html"><em>fix_qbmsst</em></a></td> <td><a class="reference internal" href="fix_qtb.html"><em>fix qtb</em></a> <a class="reference internal" href="fix_qbmsst.html"><em>fix qbmsst</em></a></td>
<td>qtb</td> <td>qtb</td>
<td><ul class="first last simple"> <td><ul class="first last simple">
<li></li> <li></li>
@ -2227,8 +2227,8 @@ make machine
</div> </div>
<p>Supporting info: /src/USER-DPD/README, <a class="reference internal" href="compute_dpd.html"><em>compute dpd</em></a> <p>Supporting info: /src/USER-DPD/README, <a class="reference internal" href="compute_dpd.html"><em>compute dpd</em></a>
<a class="reference internal" href="compute_dpd_atom.html"><em>compute dpd/atom</em></a> <a class="reference internal" href="compute_dpd_atom.html"><em>compute dpd/atom</em></a>
<a class="reference internal" href="fix_eos_table.html"><em>fix_eos/cv</em></a> <a class="reference internal" href="fix_eos_table.html"><em>fix_eos/table</em></a> <a class="reference internal" href="fix_eos_table.html"><em>fix eos/cv</em></a> <a class="reference internal" href="fix_eos_table.html"><em>fix eos/table</em></a>
<a class="reference internal" href="fix_shardlow.html"><em>fix_shardlow</em></a> <a class="reference internal" href="fix_shardlow.html"><em>fix shardlow</em></a>
<a class="reference internal" href="pair_dpd_conservative.html"><em>pair_dpd/conservative</em></a> <a class="reference internal" href="pair_dpd_conservative.html"><em>pair_dpd/conservative</em></a>
<a class="reference internal" href="pair_dpd_fdt.html"><em>pair_dpd/fdt</em></a> <a class="reference internal" href="pair_dpd_fdt.html"><em>pair_dpd/fdt</em></a>
<a class="reference internal" href="pair_dpd_fdt.html"><em>pair_dpd/fdt/energy</em></a>, examples/USER/dpd</p> <a class="reference internal" href="pair_dpd_fdt.html"><em>pair_dpd/fdt/energy</em></a>, examples/USER/dpd</p>

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@ -839,7 +839,7 @@ make machine :pre
Make.py -p ^meam -a machine :pre Make.py -p ^meam -a machine :pre
Supporting info: src/POEMS/README, lib/poems/README, Supporting info: src/POEMS/README, lib/poems/README,
"fix_poems"_fix_poems.html, examples/rigid "fix poems"_fix_poems.html, examples/rigid
:line :line
@ -1183,7 +1183,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, - "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, -
"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, - "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
"USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix_qbmsst"_fix_qbmsst.html, qtb, -, - "USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, -
"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_style quip"_pair_quip.html, USER/quip, -, lib/quip "USER-QUIP"_#USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_style quip"_pair_quip.html, USER/quip, -, lib/quip
"USER-REAXC"_#USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, - "USER-REAXC"_#USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
"USER-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, - "USER-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, -
@ -1481,8 +1481,8 @@ Make.py -p ^atc -a machine :pre
Supporting info: /src/USER-DPD/README, "compute dpd"_compute_dpd.html Supporting info: /src/USER-DPD/README, "compute dpd"_compute_dpd.html
"compute dpd/atom"_compute_dpd_atom.html "compute dpd/atom"_compute_dpd_atom.html
"fix_eos/cv"_fix_eos_table.html "fix_eos/table"_fix_eos_table.html "fix eos/cv"_fix_eos_table.html "fix eos/table"_fix_eos_table.html
"fix_shardlow"_fix_shardlow.html "fix shardlow"_fix_shardlow.html
"pair_dpd/conservative"_pair_dpd_conservative.html "pair_dpd/conservative"_pair_dpd_conservative.html
"pair_dpd/fdt"_pair_dpd_fdt.html "pair_dpd/fdt"_pair_dpd_fdt.html
"pair_dpd/fdt/energy"_pair_dpd_fdt.html, examples/USER/dpd "pair_dpd/fdt/energy"_pair_dpd_fdt.html, examples/USER/dpd

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@ -737,7 +737,7 @@ the fix is invoked, and can make library calls to the other code,
which has been linked to LAMMPS as a library. This is the way the which has been linked to LAMMPS as a library. This is the way the
`POEMS <poems_>`_ package that performs constrained rigid-body motion on `POEMS <poems_>`_ package that performs constrained rigid-body motion on
groups of atoms is hooked to LAMMPS. See the groups of atoms is hooked to LAMMPS. See the
:doc:`fix_poems <fix_poems>` command for more details. See :doc:`this section <Section_modify>` of the documentation for info on how to add :doc:`fix poems <fix_poems>` command for more details. See :doc:`this section <Section_modify>` of the documentation for info on how to add
a new fix to LAMMPS. a new fix to LAMMPS.
.. _poems: http://www.rpi.edu/~anderk5/lab .. _poems: http://www.rpi.edu/~anderk5/lab

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@ -1097,7 +1097,7 @@ To un-install via make or Make.py:
Make.py -p ^meam -a machine Make.py -p ^meam -a machine
Supporting info: src/POEMS/README, lib/poems/README, Supporting info: src/POEMS/README, lib/poems/README,
:doc:`fix_poems <fix_poems>`, examples/rigid :doc:`fix poems <fix_poems>`, examples/rigid
---------- ----------
@ -1588,7 +1588,7 @@ The current list of user-contributed packages is as follows:
+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| :ref:`USER-QMMM <USER-QMMM>` | QM/MM coupling | Axel Kohlmeyer (Temple U) | :doc:`fix qmmm <fix_qmmm>` | USER/qmmm | - | lib/qmmm | | :ref:`USER-QMMM <USER-QMMM>` | QM/MM coupling | Axel Kohlmeyer (Temple U) | :doc:`fix qmmm <fix_qmmm>` | USER/qmmm | - | lib/qmmm |
+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| :ref:`USER-QTB <USER-QTB>` | quantum nuclear effects | Yuan Shen (Stanford) | :doc:`fix qtb <fix_qtb>` :doc:`fix_qbmsst <fix_qbmsst>` | qtb | - | - | | :ref:`USER-QTB <USER-QTB>` | quantum nuclear effects | Yuan Shen (Stanford) | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | - | - |
+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| :ref:`USER-QUIP <USER-QUIP>` | QUIP/libatoms interface | Albert Bartok-Partay (U Cambridge) | :doc:`pair_style quip <pair_quip>` | USER/quip | - | lib/quip | | :ref:`USER-QUIP <USER-QUIP>` | QUIP/libatoms interface | Albert Bartok-Partay (U Cambridge) | :doc:`pair_style quip <pair_quip>` | USER/quip | - | lib/quip |
+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
@ -1995,8 +1995,8 @@ To un-install via make or Make.py:
Supporting info: /src/USER-DPD/README, :doc:`compute dpd <compute_dpd>` Supporting info: /src/USER-DPD/README, :doc:`compute dpd <compute_dpd>`
:doc:`compute dpd/atom <compute_dpd_atom>` :doc:`compute dpd/atom <compute_dpd_atom>`
:doc:`fix_eos/cv <fix_eos_table>` :doc:`fix_eos/table <fix_eos_table>` :doc:`fix eos/cv <fix_eos_table>` :doc:`fix eos/table <fix_eos_table>`
:doc:`fix_shardlow <fix_shardlow>` :doc:`fix shardlow <fix_shardlow>`
:doc:`pair_dpd/conservative <pair_dpd_conservative>` :doc:`pair_dpd/conservative <pair_dpd_conservative>`
:doc:`pair_dpd/fdt <pair_dpd_fdt>` :doc:`pair_dpd/fdt <pair_dpd_fdt>`
:doc:`pair_dpd/fdt/energy <pair_dpd_fdt>`, examples/USER/dpd :doc:`pair_dpd/fdt/energy <pair_dpd_fdt>`, examples/USER/dpd

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doc/_sources/comm_style.txt
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@ -50,7 +50,7 @@ commands. For both the *brick* and *tiled* styles, the initial
decomposition will be the same, as described by decomposition will be the same, as described by
:doc:`create_box <create_box>` and :doc:`processors <processors>` :doc:`create_box <create_box>` and :doc:`processors <processors>`
commands. The decomposition can be changed via the commands. The decomposition can be changed via the
:doc:`balance <balance>` or :doc:`fix_balance <fix_balance>` commands. :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
Restrictions Restrictions
"""""""""""" """"""""""""

2
doc/_sources/compute_ti.txt
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@ -106,7 +106,7 @@ long-range tail correction to the energy via the *tail* keyword.
For each term you can specify a different (or the same) scale factor For each term you can specify a different (or the same) scale factor
by the two variables that you list. Again, these will typically by the two variables that you list. Again, these will typically
correspond toe the scale factors applied to these various potentials correspond toe the scale factors applied to these various potentials
and the K-Space contribution via the :doc:`fix_adapt <fix_adapt>` and the K-Space contribution via the :doc:`fix adapt <fix_adapt>`
command. command.
More details about the exact functional forms for the computation of More details about the exact functional forms for the computation of

2
doc/_sources/displace_atoms.txt
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@ -150,7 +150,7 @@ Related commands
"""""""""""""""" """"""""""""""""
:doc:`lattice <lattice>`, :doc:`change_box <change_box>`, :doc:`lattice <lattice>`, :doc:`change_box <change_box>`,
:doc:`fix_move <fix_move>` :doc:`fix move <fix_move>`
Default Default
""""""" """""""

6
doc/_sources/fix_adapt_fep.txt
View File

@ -62,7 +62,7 @@ Description
Change or adapt one or more specific simulation attributes or settings Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs. over time as a simulation runs.
This is an enhanced version of the :doc:`fix_adapt <fix_adapt>` command This is an enhanced version of the :doc:`fix adapt <fix_adapt>` command
with two differences, with two differences,
* It is possible to modify the charges of chosen atom types only, * It is possible to modify the charges of chosen atom types only,
@ -70,7 +70,7 @@ with two differences,
* There is a new option *after* for better compatibility with "fix * There is a new option *after* for better compatibility with "fix
ave/time". ave/time".
This version is suited for free energy calculations using This version is suited for free energy calculations using
:doc:`compute_ti <compute_ti>` or :doc:`compute_fep <compute_fep>`. :doc:`compute ti <compute_ti>` or :doc:`compute fep <compute_fep>`.
If *N* is specified as 0, the specified attributes are only changed If *N* is specified as 0, the specified attributes are only changed
once, before the simulation begins. This is all that is needed if the once, before the simulation begins. This is all that is needed if the
@ -281,7 +281,7 @@ Restrictions
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`compute fep <compute_fep>`, :doc:`fix_adapt <fix_adapt>`, :doc:`compute ti <compute_ti>` :doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`
Default Default
""""""" """""""

8
doc/_sources/fix_atom_swap.txt
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@ -58,7 +58,7 @@ atoms. Swaps are not attempted between atoms of the same type since
nothing would happen. nothing would happen.
All atoms in the simulation domain can be moved using regular time All atoms in the simulation domain can be moved using regular time
integration displacements, e.g. via :doc:`fix_nvt <fix_nvt>`, resulting integration displacements, e.g. via :doc:`fix nvt <fix_nh>`, resulting
in a hybrid MC+MD simulation. A smaller-than-usual timestep size may in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
be needed when running such a hybrid simulation, especially if the be needed when running such a hybrid simulation, especially if the
swapped atoms are not well equilibrated. swapped atoms are not well equilibrated.
@ -176,9 +176,9 @@ built with that package. See the :ref:`Making LAMMPS <start_3>` section for mor
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`fix_nvt <fix_nvt>`, :doc:`neighbor <neighbor>`, :doc:`fix nvt <fix_nh>`, :doc:`neighbor <neighbor>`,
:doc:`fix_deposit <fix_deposit>`, :doc:`fix_evaporate <fix_evaporate>`, :doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
:doc:`delete_atoms <delete_atoms>`, :doc:`fix_gcmc <fix_gcmc>` :doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`
Default Default
""""""" """""""

2
doc/_sources/fix_deposit.txt
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@ -275,7 +275,7 @@ defined by the :doc:`region <region>` command.
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`fix_pour <fix_pour>`, :doc:`region <region>` :doc:`fix pour <fix_pour>`, :doc:`region <region>`
Default Default
""""""" """""""

10
doc/_sources/fix_gcmc.txt
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@ -100,7 +100,7 @@ molecules other than the exchanged type, but MC deletions,
translations, and rotations can be performed on any atom/molecule in translations, and rotations can be performed on any atom/molecule in
the fix group. All atoms in the simulation cell can be moved using the fix group. All atoms in the simulation cell can be moved using
regular time integration translations, e.g. via regular time integration translations, e.g. via
:doc:`fix_nvt <fix_nvt>`, resulting in a hybrid GCMC+MD simulation. A :doc:`fix nvt <fix_nh>`, resulting in a hybrid GCMC+MD simulation. A
smaller-than-usual timestep size may be needed when running such a smaller-than-usual timestep size may be needed when running such a
hybrid simulation, especially if the inserted molecules are not well hybrid simulation, especially if the inserted molecules are not well
equilibrated. equilibrated.
@ -120,9 +120,9 @@ or deletion. If an attempted move places the atom or molecule center-of-mass out
the specified region, a new attempted move is generated. This process is repeated the specified region, a new attempted move is generated. This process is repeated
until the atom or molecule center-of-mass is inside the specified region. until the atom or molecule center-of-mass is inside the specified region.
If used with :doc:`fix_nvt <fix_nvt>`, the temperature of the imaginary If used with :doc:`fix nvt <fix_nh>`, the temperature of the imaginary
reservoir, T, should be set to be equivalent to the target temperature reservoir, T, should be set to be equivalent to the target temperature
used in :doc:`fix_nvt <fix_nvt>`. Otherwise, the imaginary reservoir used in fix nvt. Otherwise, the imaginary reservoir
will not be in thermal equilibrium with the simulation cell. Also, will not be in thermal equilibrium with the simulation cell. Also,
it is important that the temperature used by fix nvt be dynamic, it is important that the temperature used by fix nvt be dynamic,
which can be achieved as follows: which can be achieved as follows:
@ -259,7 +259,7 @@ Use the *charge* option to insert atoms with a user-specified point
charge. Note that doing so will cause the system to become non-neutral. charge. Note that doing so will cause the system to become non-neutral.
LAMMPS issues a warning when using long-range electrostatics (kspace) LAMMPS issues a warning when using long-range electrostatics (kspace)
with non-neutral systems. See the with non-neutral systems. See the
:doc:`compute_group_group <compute_group_group>` documentation for more :doc:`compute group/group <compute_group_group>` documentation for more
details about simulating non-neutral systems with kspace on. details about simulating non-neutral systems with kspace on.
Use of this fix typically will cause the number of atoms to fluctuate, Use of this fix typically will cause the number of atoms to fluctuate,
@ -343,7 +343,7 @@ Related commands
"""""""""""""""" """"""""""""""""
:doc:`fix atom/swap <fix_atom_swap>`, :doc:`fix atom/swap <fix_atom_swap>`,
:doc:`fix nvt <fix_nvt>`, :doc:`neighbor <neighbor>`, :doc:`fix nvt <fix_nh>`, :doc:`neighbor <neighbor>`,
:doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`, :doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
:doc:`delete_atoms <delete_atoms>` :doc:`delete_atoms <delete_atoms>`

6
doc/_sources/fix_gle.txt
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@ -88,7 +88,7 @@ Note also that the Generalized Langevin Dynamics scheme that is
implemented by the :doc:`fix gld <fix_gld>` scheme is closely related implemented by the :doc:`fix gld <fix_gld>` scheme is closely related
to the present one. In fact, it should be always possible to cast the to the present one. In fact, it should be always possible to cast the
Prony series form of the memory kernel used by GLD into an appropriate Prony series form of the memory kernel used by GLD into an appropriate
input matrix for :doc:`fix_gle <fix_gle>`. While the GLE scheme is more input matrix for :doc:`fix gle <fix_gle>`. While the GLE scheme is more
general, the form used by :doc:`fix gld <fix_gld>` can be more directly general, the form used by :doc:`fix gld <fix_gld>` can be more directly
related to the representation of an implicit solvent environment. related to the representation of an implicit solvent environment.
@ -130,7 +130,7 @@ ensemble will not be correct otherwise.
In order to perform constant-pressure simulations please use In order to perform constant-pressure simulations please use
:doc:`fix press/berendsen <fix_press_berendsen>`, rather than :doc:`fix press/berendsen <fix_press_berendsen>`, rather than
:doc:`fix_npt <fix_npt>`, to avoid duplicate integration of the :doc:`fix npt <fix_nh>`, to avoid duplicate integration of the
equations of motion. equations of motion.
This fix is part of the USER-MISC package. It is only enabled if LAMMPS This fix is part of the USER-MISC package. It is only enabled if LAMMPS
@ -139,7 +139,7 @@ was built with that package. See the :ref:`Making LAMMPS <start_3>` section for
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix viscous <fix_viscous>`, :doc:`fix nvt <fix_nh>`, :doc:`pair_style dpd/tstat <pair_dpd>`, :doc:`fix_gld <fix_gld>` :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix viscous <fix_viscous>`, :doc:`fix nvt <fix_nh>`, :doc:`pair_style dpd/tstat <pair_dpd>`, :doc:`fix gld <fix_gld>`
---------- ----------

4
doc/_sources/fix_lb_rigid_pc_sphere.txt
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@ -81,7 +81,7 @@ central atoms interact with one another.
Apart from the features described above, this fix is very similar to Apart from the features described above, this fix is very similar to
the rigid fix (although it includes fewer optional arguments, and the rigid fix (although it includes fewer optional arguments, and
assumes the constituent atoms are point particles); see assumes the constituent atoms are point particles); see
:doc:`fix_rigid <fix_rigid>` for a complete documentation. :doc:`fix rigid <fix_rigid>` for a complete documentation.
Restart, fix_modify, output, run start/stop, minimize info Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """"""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -89,7 +89,7 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about the *rigid* and *rigid/nve* fixes are written to No information about the *rigid* and *rigid/nve* fixes are written to
:doc:`binary restart files <restart>`. :doc:`binary restart files <restart>`.
Similar to the :doc:`fix_rigid <fix_rigid>` command: &quot; The rigid Similar to the :doc:`fix rigid <fix_rigid>` command: &quot; The rigid
fix computes a global scalar which can be accessed by various :ref:`output commands <howto_15>`. The scalar value calculated by fix computes a global scalar which can be accessed by various :ref:`output commands <howto_15>`. The scalar value calculated by
these fixes is "intensive". The scalar is the current temperature of these fixes is "intensive". The scalar is the current temperature of
the collection of rigid bodies. This is averaged over all rigid the collection of rigid bodies. This is averaged over all rigid

4
doc/_sources/fix_nphug.txt
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@ -217,7 +217,7 @@ The scalar is the cumulative energy change due to the fix.
The vector stores three quantities unique to this fix (Delta, Us, and up), The vector stores three quantities unique to this fix (Delta, Us, and up),
followed by all the internal Nose/Hoover thermostat and barostat followed by all the internal Nose/Hoover thermostat and barostat
variables defined for :doc:`fix_style npt <fix_nh>`. Delta is the deviation variables defined for :doc:`fix npt <fix_nh>`. Delta is the deviation
of the temperature from the target temperature, given by the above equation. of the temperature from the target temperature, given by the above equation.
Us and up are the shock and particle velocity corresponding to a steady Us and up are the shock and particle velocity corresponding to a steady
shock calculated from the RH conditions. They have units of distance/time. shock calculated from the RH conditions. They have units of distance/time.
@ -229,7 +229,7 @@ Restrictions
This fix style is part of the SHOCK package. It is only enabled if This fix style is part of the SHOCK package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info. LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
All the usual restrictions for :doc:`fix_style npt <fix_nh>` apply, All the usual restrictions for :doc:`fix npt <fix_nh>` apply,
plus the additional ones mentioned above. plus the additional ones mentioned above.
Related commands Related commands

2
doc/_sources/fix_pour.txt
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@ -262,7 +262,7 @@ defined by the :doc:`region <region>` command.
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`fix_deposit <fix_deposit>`, :doc:`fix_gravity <fix_gravity>`, :doc:`fix deposit <fix_deposit>`, :doc:`fix gravity <fix_gravity>`,
:doc:`region <region>` :doc:`region <region>`
Default Default

2
doc/_sources/fix_rigid.txt
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@ -176,7 +176,7 @@ differences may accumulate to produce divergent trajectories.
.. note:: .. note::
You should not update the atoms in rigid bodies via other You should not update the atoms in rigid bodies via other
time-integration fixes (e.g. :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nvt>`, :doc:`fix npt <fix_npt>`), or you will be integrating time-integration fixes (e.g. :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`), or you will be integrating
their motion more than once each timestep. When performing a hybrid their motion more than once each timestep. When performing a hybrid
simulation with some atoms in rigid bodies, and some not, a separate simulation with some atoms in rigid bodies, and some not, a separate
time integration fix like :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>` should be used for the non-rigid particles. time integration fix like :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>` should be used for the non-rigid particles.

4
doc/_sources/fix_saed_vtk.txt
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@ -47,7 +47,7 @@ Examples
Description Description
""""""""""" """""""""""
Time average computed intensities from `compute_saed <compute_saed.txt>`_ and Time average computed intensities from :doc:`compute saed <compute_saed>` and
write output to a file in the 3rd generation vtk image data format for write output to a file in the 3rd generation vtk image data format for
visualization directly in parallelized visualization software packages visualization directly in parallelized visualization software packages
like ParaView and VisIt. Note that if no time averaging is done, this like ParaView and VisIt. Note that if no time averaging is done, this
@ -65,7 +65,7 @@ The group specified within this command is ignored. However, note that
specified values may represent calculations performed by saed computes specified values may represent calculations performed by saed computes
which store their own "group" definitions. which store their own "group" definitions.
Fix saed/vtk is designed to work only with `compute_saed <compute_saed.txt>`_ Fix saed/vtk is designed to work only with :doc:`compute saed <compute_saed>`
values, e.g. values, e.g.
.. parsed-literal:: .. parsed-literal::

2
doc/_sources/fix_temp_rescale_eff.txt
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@ -72,7 +72,7 @@ Related commands
"""""""""""""""" """"""""""""""""
:doc:`fix langevin/eff <fix_langevin_eff>`, :doc:`fix nvt/eff <fix_nh_eff>`, :doc:`fix_modify <fix_modify>`, :doc:`fix langevin/eff <fix_langevin_eff>`, :doc:`fix nvt/eff <fix_nh_eff>`, :doc:`fix_modify <fix_modify>`,
:doc:`fix_temp_rescale <fix_temp_rescale>`, :doc:`fix temp rescale <fix_temp_rescale>`,
**Default:** none **Default:** none

2
doc/_sources/fix_ti_spring.txt
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@ -96,7 +96,7 @@ thermodynamic integration.
'attatched' to its equilibrium positions by the Einstein 'attatched' to its equilibrium positions by the Einstein
crystal. Check the option *zero* of `fix langevin <fix_langevin_html>`_ crystal. Check the option *zero* of `fix langevin <fix_langevin_html>`_
and :doc:`velocity <velocity>`. The use of the Nose-Hoover thermostat and :doc:`velocity <velocity>`. The use of the Nose-Hoover thermostat
(:doc:`fix nvt <fix_nvt>`) is NOT recommended due to its well documented (:doc:`fix nvt <fix_nh>`) is NOT recommended due to its well documented
issues with the canonical sampling of harmonic degrees of freedom issues with the canonical sampling of harmonic degrees of freedom
(notice that the *chain* option will NOT solve this problem). The (notice that the *chain* option will NOT solve this problem). The
Langevin thermostat (`fix langevin <fix_langevin.html">`_) works fine. Langevin thermostat (`fix langevin <fix_langevin.html">`_) works fine.

4
doc/_sources/fix_wall_gran.txt
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@ -106,7 +106,7 @@ keywords are appended. Both keywords cannot be used together.
For the *wiggle* keyword, the wall oscillates sinusoidally, similar to For the *wiggle* keyword, the wall oscillates sinusoidally, similar to
the oscillations of particles which can be specified by the the oscillations of particles which can be specified by the
:doc:`fix_move <fix_move>` command. This is useful in packing :doc:`fix move <fix_move>` command. This is useful in packing
simulations of granular particles. The arguments to the *wiggle* simulations of granular particles. The arguments to the *wiggle*
keyword specify a dimension for the motion, as well as it's keyword specify a dimension for the motion, as well as it's
*amplitude* and *period*. Note that if the dimension is in the plane *amplitude* and *period*. Note that if the dimension is in the plane
@ -165,7 +165,7 @@ Any dimension (xyz) that has a granular wall must be non-periodic.
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`fix_move <fix_move>`, :doc:`pair_style granular <pair_gran>` :doc:`fix move <fix_move>`, :doc:`pair_style granular <pair_gran>`
**Default:** none **Default:** none

2
doc/_sources/molecule.txt
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@ -496,7 +496,7 @@ Related commands
"""""""""""""""" """"""""""""""""
:doc:`fix deposit <fix_deposit>`, :doc:`fix pour <fix_pour>`, :doc:`fix deposit <fix_deposit>`, :doc:`fix pour <fix_pour>`,
:doc:`fix_gcmc <fix_gcmc>` :doc:`fix gcmc <fix_gcmc>`
Default Default
""""""" """""""

2
doc/_sources/pair_body.txt
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@ -122,7 +122,7 @@ body/particle interactions requires the use of the :doc:`atom_style body <atom_s
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`fix_rigid <fix_rigid>` :doc:`pair_coeff <pair_coeff>`, :doc:`fix rigid <fix_rigid>`
**Default:** none **Default:** none

11
doc/_sources/pair_coeff.txt
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@ -102,20 +102,23 @@ copying them into your working directory. Environment variables are
set in different ways for different shells. Here are example settings set in different ways for different shells. Here are example settings
for for
csh, tcsh:
.. parsed-literal:: .. parsed-literal::
csh, tcsh:
% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials % setenv LAMMPS_POTENTIALS /path/to/lammps/potentials
bash:
.. parsed-literal:: .. parsed-literal::
bash:
% export LAMMPS_POTENTIALS=/path/to/lammps/potentials % export LAMMPS_POTENTIALS=/path/to/lammps/potentials
Windows:
.. parsed-literal:: .. parsed-literal::
Windows: % set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials"
% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials
---------- ----------

2
doc/_sources/pair_comb.txt
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@ -194,7 +194,7 @@ Related commands
"""""""""""""""" """"""""""""""""
:doc:`pair_style <pair_style>`, :doc:`pair_coeff <pair_coeff>`, :doc:`pair_style <pair_style>`, :doc:`pair_coeff <pair_coeff>`,
:doc:`fix_qeq/comb <fix_qeq_comb>` :doc:`fix qeq/comb <fix_qeq_comb>`
**Default:** none **Default:** none

8
doc/_sources/pair_lj_soft.txt
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@ -241,8 +241,8 @@ in several water models).
NOTES: When using the core-softed Coulomb potentials with long-range NOTES: When using the core-softed Coulomb potentials with long-range
solvers (*coul/long/soft*, *lj/cut/coul/long/soft*, etc.) in a free solvers (*coul/long/soft*, *lj/cut/coul/long/soft*, etc.) in a free
energy calculation in which sites holding electrostatic charges are energy calculation in which sites holding electrostatic charges are
being created or anihilated (using :doc:`fix_adapt/fep <fix_adapt_fep>` being created or anihilated (using :doc:`fix adapt/fep <fix_adapt_fep>`
and :doc:`compute_fep <compute_fep>`) it is important to adapt both the and :doc:`compute fep <compute_fep>`) it is important to adapt both the
lambda activation parameter (from 0 to 1, or the reverse) and the lambda activation parameter (from 0 to 1, or the reverse) and the
value of the charge (from 0 to its final value, or the reverse). This value of the charge (from 0 to its final value, or the reverse). This
ensures that long-range electrostatic terms (kspace) are correct. It ensures that long-range electrostatic terms (kspace) are correct. It
@ -323,8 +323,8 @@ the :ref:`Making LAMMPS <start_3>` section for more info.
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`fix_adapt <fix_adapt>`, :doc:`pair_coeff <pair_coeff>`, :doc:`fix adapt <fix_adapt>`,
:doc:`fix_adapt/fep <fix_adapt_fep>`, :doc:`compute_fep <compute_fep>` :doc:`fix adapt/fep <fix_adapt_fep>`, :doc:`compute fep <compute_fep>`
**Default:** none **Default:** none

2
doc/comm_style.html
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@ -168,7 +168,7 @@ commands. For both the <em>brick</em> and <em>tiled</em> styles, the initial
decomposition will be the same, as described by decomposition will be the same, as described by
<a class="reference internal" href="create_box.html"><em>create_box</em></a> and <a class="reference internal" href="processors.html"><em>processors</em></a> <a class="reference internal" href="create_box.html"><em>create_box</em></a> and <a class="reference internal" href="processors.html"><em>processors</em></a>
commands. The decomposition can be changed via the commands. The decomposition can be changed via the
<a class="reference internal" href="balance.html"><em>balance</em></a> or <a class="reference internal" href="fix_balance.html"><em>fix_balance</em></a> commands.</p> <a class="reference internal" href="balance.html"><em>balance</em></a> or <a class="reference internal" href="fix_balance.html"><em>fix balance</em></a> commands.</p>
</div> </div>
<div class="section" id="restrictions"> <div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2> <h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>

2
doc/comm_style.txt
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@ -49,7 +49,7 @@ commands. For both the {brick} and {tiled} styles, the initial
decomposition will be the same, as described by decomposition will be the same, as described by
"create_box"_create_box.html and "processors"_processors.html "create_box"_create_box.html and "processors"_processors.html
commands. The decomposition can be changed via the commands. The decomposition can be changed via the
"balance"_balance.html or "fix_balance"_fix_balance.html commands. "balance"_balance.html or "fix balance"_fix_balance.html commands.
[Restrictions:] none [Restrictions:] none

2
doc/compute_ti.html
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@ -215,7 +215,7 @@ long-range tail correction to the energy via the <em>tail</em> keyword.</p>
<p>For each term you can specify a different (or the same) scale factor <p>For each term you can specify a different (or the same) scale factor
by the two variables that you list. Again, these will typically by the two variables that you list. Again, these will typically
correspond toe the scale factors applied to these various potentials correspond toe the scale factors applied to these various potentials
and the K-Space contribution via the <a class="reference internal" href="fix_adapt.html"><em>fix_adapt</em></a> and the K-Space contribution via the <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a>
command.</p> command.</p>
<p>More details about the exact functional forms for the computation of <p>More details about the exact functional forms for the computation of
du/dl can be found in the paper by <a class="reference internal" href="#eike"><span>Eike</span></a>.</p> du/dl can be found in the paper by <a class="reference internal" href="#eike"><span>Eike</span></a>.</p>

2
doc/compute_ti.txt
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@ -99,7 +99,7 @@ long-range tail correction to the energy via the {tail} keyword.
For each term you can specify a different (or the same) scale factor For each term you can specify a different (or the same) scale factor
by the two variables that you list. Again, these will typically by the two variables that you list. Again, these will typically
correspond toe the scale factors applied to these various potentials correspond toe the scale factors applied to these various potentials
and the K-Space contribution via the "fix_adapt"_fix_adapt.html and the K-Space contribution via the "fix adapt"_fix_adapt.html
command. command.
More details about the exact functional forms for the computation of More details about the exact functional forms for the computation of

2
doc/displace_atoms.html
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@ -254,7 +254,7 @@ attempted to be.</p>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="lattice.html"><em>lattice</em></a>, <a class="reference internal" href="change_box.html"><em>change_box</em></a>, <p><a class="reference internal" href="lattice.html"><em>lattice</em></a>, <a class="reference internal" href="change_box.html"><em>change_box</em></a>,
<a class="reference internal" href="fix_move.html"><em>fix_move</em></a></p> <a class="reference internal" href="fix_move.html"><em>fix move</em></a></p>
</div> </div>
<div class="section" id="default"> <div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2> <h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>

2
doc/displace_atoms.txt
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@ -132,7 +132,7 @@ You cannot rotate around any rotation vector except the z-axis for a
[Related commands:] [Related commands:]
"lattice"_lattice.html, "change_box"_change_box.html, "lattice"_lattice.html, "change_box"_change_box.html,
"fix_move"_fix_move.html "fix move"_fix_move.html
[Default:] [Default:]

6
doc/fix_adapt_fep.html
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@ -181,7 +181,7 @@ fix 1 all adapt/fep 10 atom diameter 1 v_size
<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>
<p>Change or adapt one or more specific simulation attributes or settings <p>Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs.</p> over time as a simulation runs.</p>
<p>This is an enhanced version of the <a class="reference internal" href="fix_adapt.html"><em>fix_adapt</em></a> command <p>This is an enhanced version of the <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a> command
with two differences,</p> with two differences,</p>
<ul class="simple"> <ul class="simple">
<li>It is possible to modify the charges of chosen atom types only, <li>It is possible to modify the charges of chosen atom types only,
@ -190,7 +190,7 @@ instead of scaling all the charges in the system.</li>
ave/time&#8221;.</li> ave/time&#8221;.</li>
</ul> </ul>
<p>This version is suited for free energy calculations using <p>This version is suited for free energy calculations using
<a class="reference internal" href="compute_ti.html"><em>compute_ti</em></a> or <a class="reference internal" href="compute_fep.html"><em>compute_fep</em></a>.</p> <a class="reference internal" href="compute_ti.html"><em>compute ti</em></a> or <a class="reference internal" href="compute_fep.html"><em>compute fep</em></a>.</p>
<p>If <em>N</em> is specified as 0, the specified attributes are only changed <p>If <em>N</em> is specified as 0, the specified attributes are only changed
once, before the simulation begins. This is all that is needed if the once, before the simulation begins. This is all that is needed if the
associated variables are not time-dependent. If <em>N</em> &gt; 0, then changes associated variables are not time-dependent. If <em>N</em> &gt; 0, then changes
@ -392,7 +392,7 @@ This fix is not invoked during <a class="reference internal" href="minimize.html
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_fep.html"><em>compute fep</em></a>, <a class="reference internal" href="fix_adapt.html"><em>fix_adapt</em></a>, <a class="reference internal" href="compute_ti.html"><em>compute ti</em></a></p> <p><a class="reference internal" href="compute_fep.html"><em>compute fep</em></a>, <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a>, <a class="reference internal" href="compute_ti.html"><em>compute ti</em></a></p>
</div> </div>
<div class="section" id="default"> <div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2> <h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>

6
doc/fix_adapt_fep.txt
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@ -54,7 +54,7 @@ fix 1 all adapt/fep 10 atom diameter 1 v_size :pre
Change or adapt one or more specific simulation attributes or settings Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs. over time as a simulation runs.
This is an enhanced version of the "fix_adapt"_fix_adapt.html command This is an enhanced version of the "fix adapt"_fix_adapt.html command
with two differences, with two differences,
It is possible to modify the charges of chosen atom types only, It is possible to modify the charges of chosen atom types only,
@ -64,7 +64,7 @@ There is a new option {after} for better compatibility with "fix
ave/time". :l,ule ave/time". :l,ule
This version is suited for free energy calculations using This version is suited for free energy calculations using
"compute_ti"_compute_ti.html or "compute_fep"_compute_fep.html. "compute ti"_compute_ti.html or "compute fep"_compute_fep.html.
If {N} is specified as 0, the specified attributes are only changed If {N} is specified as 0, the specified attributes are only changed
once, before the simulation begins. This is all that is needed if the once, before the simulation begins. This is all that is needed if the
@ -251,7 +251,7 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Related commands:] [Related commands:]
"compute fep"_compute_fep.html, "fix_adapt"_fix_adapt.html, "compute "compute fep"_compute_fep.html, "fix adapt"_fix_adapt.html, "compute
ti"_compute_ti.html ti"_compute_ti.html
[Default:] [Default:]

8
doc/fix_atom_swap.html
View File

@ -175,7 +175,7 @@ chosen randomly with equal probability among the candidate
atoms. Swaps are not attempted between atoms of the same type since atoms. Swaps are not attempted between atoms of the same type since
nothing would happen.</p> nothing would happen.</p>
<p>All atoms in the simulation domain can be moved using regular time <p>All atoms in the simulation domain can be moved using regular time
integration displacements, e.g. via <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, resulting integration displacements, e.g. via <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, resulting
in a hybrid MC+MD simulation. A smaller-than-usual timestep size may in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
be needed when running such a hybrid simulation, especially if the be needed when running such a hybrid simulation, especially if the
swapped atoms are not well equilibrated.</p> swapped atoms are not well equilibrated.</p>
@ -278,9 +278,9 @@ built with that package. See the <a class="reference internal" href="Section_st
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>, <p><a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>,
<a class="reference internal" href="fix_deposit.html"><em>fix_deposit</em></a>, <a class="reference internal" href="fix_evaporate.html"><em>fix_evaporate</em></a>, <a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_evaporate.html"><em>fix evaporate</em></a>,
<a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a>, <a class="reference internal" href="fix_gcmc.html"><em>fix_gcmc</em></a></p> <a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a>, <a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a></p>
</div> </div>
<div class="section" id="default"> <div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2> <h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>

8
doc/fix_atom_swap.txt
View File

@ -53,7 +53,7 @@ atoms. Swaps are not attempted between atoms of the same type since
nothing would happen. nothing would happen.
All atoms in the simulation domain can be moved using regular time All atoms in the simulation domain can be moved using regular time
integration displacements, e.g. via "fix_nvt"_fix_nvt.html, resulting integration displacements, e.g. via "fix nvt"_fix_nh.html, resulting
in a hybrid MC+MD simulation. A smaller-than-usual timestep size may in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
be needed when running such a hybrid simulation, especially if the be needed when running such a hybrid simulation, especially if the
swapped atoms are not well equilibrated. swapped atoms are not well equilibrated.
@ -170,9 +170,9 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:] [Related commands:]
"fix_nvt"_fix_nvt.html, "neighbor"_neighbor.html, "fix nvt"_fix_nh.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, "fix_gcmc"_fix_gcmc.html "delete_atoms"_delete_atoms.html, "fix gcmc"_fix_gcmc.html
[Default:] [Default:]

2
doc/fix_deposit.html
View File

@ -371,7 +371,7 @@ defined by the <a class="reference internal" href="region.html"><em>region</em><
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="fix_pour.html"><em>fix_pour</em></a>, <a class="reference internal" href="region.html"><em>region</em></a></p> <p><a class="reference internal" href="fix_pour.html"><em>fix pour</em></a>, <a class="reference internal" href="region.html"><em>region</em></a></p>
</div> </div>
<div class="section" id="default"> <div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2> <h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>

2
doc/fix_deposit.txt
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@ -264,7 +264,7 @@ defined by the "region"_region.html command.
[Related commands:] [Related commands:]
"fix_pour"_fix_pour.html, "region"_region.html "fix pour"_fix_pour.html, "region"_region.html
[Default:] [Default:]

10
doc/fix_gcmc.html
View File

@ -215,7 +215,7 @@ molecules other than the exchanged type, but MC deletions,
translations, and rotations can be performed on any atom/molecule in translations, and rotations can be performed on any atom/molecule in
the fix group. All atoms in the simulation cell can be moved using the fix group. All atoms in the simulation cell can be moved using
regular time integration translations, e.g. via regular time integration translations, e.g. via
<code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, resulting in a hybrid GCMC+MD simulation. A <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, resulting in a hybrid GCMC+MD simulation. A
smaller-than-usual timestep size may be needed when running such a smaller-than-usual timestep size may be needed when running such a
hybrid simulation, especially if the inserted molecules are not well hybrid simulation, especially if the inserted molecules are not well
equilibrated.</p> equilibrated.</p>
@ -233,9 +233,9 @@ no move or deletion is performed, but it is counted as an attempt move
or deletion. If an attempted move places the atom or molecule center-of-mass outside or deletion. If an attempted move places the atom or molecule center-of-mass outside
the specified region, a new attempted move is generated. This process is repeated the specified region, a new attempted move is generated. This process is repeated
until the atom or molecule center-of-mass is inside the specified region.</p> until the atom or molecule center-of-mass is inside the specified region.</p>
<p>If used with <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, the temperature of the imaginary <p>If used with <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, the temperature of the imaginary
reservoir, T, should be set to be equivalent to the target temperature reservoir, T, should be set to be equivalent to the target temperature
used in <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>. Otherwise, the imaginary reservoir used in fix nvt. Otherwise, the imaginary reservoir
will not be in thermal equilibrium with the simulation cell. Also, will not be in thermal equilibrium with the simulation cell. Also,
it is important that the temperature used by fix nvt be dynamic, it is important that the temperature used by fix nvt be dynamic,
which can be achieved as follows:</p> which can be achieved as follows:</p>
@ -356,7 +356,7 @@ specify if this should be done.</p>
charge. Note that doing so will cause the system to become non-neutral. charge. Note that doing so will cause the system to become non-neutral.
LAMMPS issues a warning when using long-range electrostatics (kspace) LAMMPS issues a warning when using long-range electrostatics (kspace)
with non-neutral systems. See the with non-neutral systems. See the
<a class="reference internal" href="compute_group_group.html"><em>compute_group_group</em></a> documentation for more <a class="reference internal" href="compute_group_group.html"><em>compute group/group</em></a> documentation for more
details about simulating non-neutral systems with kspace on.</p> details about simulating non-neutral systems with kspace on.</p>
<p>Use of this fix typically will cause the number of atoms to fluctuate, <p>Use of this fix typically will cause the number of atoms to fluctuate,
therefore, you will want to use the therefore, you will want to use the
@ -425,7 +425,7 @@ referenced by the user for each subsequent fix gcmc command.</p>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="fix_atom_swap.html"><em>fix atom/swap</em></a>, <p><a class="reference internal" href="fix_atom_swap.html"><em>fix atom/swap</em></a>,
<code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">nvt</span></code>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>,
<a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_evaporate.html"><em>fix evaporate</em></a>, <a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_evaporate.html"><em>fix evaporate</em></a>,
<a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a></p> <a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a></p>
</div> </div>

10
doc/fix_gcmc.txt
View File

@ -95,7 +95,7 @@ molecules other than the exchanged type, but MC deletions,
translations, and rotations can be performed on any atom/molecule in translations, and rotations can be performed on any atom/molecule in
the fix group. All atoms in the simulation cell can be moved using the fix group. All atoms in the simulation cell can be moved using
regular time integration translations, e.g. via regular time integration translations, e.g. via
"fix_nvt"_fix_nvt.html, resulting in a hybrid GCMC+MD simulation. A "fix nvt"_fix_nh.html, resulting in a hybrid GCMC+MD simulation. A
smaller-than-usual timestep size may be needed when running such a smaller-than-usual timestep size may be needed when running such a
hybrid simulation, especially if the inserted molecules are not well hybrid simulation, especially if the inserted molecules are not well
equilibrated. equilibrated.
@ -115,9 +115,9 @@ or deletion. If an attempted move places the atom or molecule center-of-mass out
the specified region, a new attempted move is generated. This process is repeated the specified region, a new attempted move is generated. This process is repeated
until the atom or molecule center-of-mass is inside the specified region. until the atom or molecule center-of-mass is inside the specified region.
If used with "fix_nvt"_fix_nvt.html, the temperature of the imaginary If used with "fix nvt"_fix_nh.html, the temperature of the imaginary
reservoir, T, should be set to be equivalent to the target temperature reservoir, T, should be set to be equivalent to the target temperature
used in "fix_nvt"_fix_nvt.html. Otherwise, the imaginary reservoir used in fix nvt. Otherwise, the imaginary reservoir
will not be in thermal equilibrium with the simulation cell. Also, will not be in thermal equilibrium with the simulation cell. Also,
it is important that the temperature used by fix nvt be dynamic, it is important that the temperature used by fix nvt be dynamic,
which can be achieved as follows: which can be achieved as follows:
@ -253,7 +253,7 @@ Use the {charge} option to insert atoms with a user-specified point
charge. Note that doing so will cause the system to become non-neutral. charge. Note that doing so will cause the system to become non-neutral.
LAMMPS issues a warning when using long-range electrostatics (kspace) LAMMPS issues a warning when using long-range electrostatics (kspace)
with non-neutral systems. See the with non-neutral systems. See the
"compute_group_group"_compute_group_group.html documentation for more "compute group/group"_compute_group_group.html documentation for more
details about simulating non-neutral systems with kspace on. details about simulating non-neutral systems with kspace on.
Use of this fix typically will cause the number of atoms to fluctuate, Use of this fix typically will cause the number of atoms to fluctuate,
@ -334,7 +334,7 @@ referenced by the user for each subsequent fix gcmc command.
[Related commands:] [Related commands:]
"fix atom/swap"_fix_atom_swap.html, "fix atom/swap"_fix_atom_swap.html,
"fix nvt"_fix_nvt.html, "neighbor"_neighbor.html, "fix nvt"_fix_nh.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 "delete_atoms"_delete_atoms.html

6
doc/fix_gle.html
View File

@ -204,7 +204,7 @@ different numbers of processors.</p>
implemented by the <a class="reference internal" href="fix_gld.html"><em>fix gld</em></a> scheme is closely related implemented by the <a class="reference internal" href="fix_gld.html"><em>fix gld</em></a> scheme is closely related
to the present one. In fact, it should be always possible to cast the to the present one. In fact, it should be always possible to cast the
Prony series form of the memory kernel used by GLD into an appropriate Prony series form of the memory kernel used by GLD into an appropriate
input matrix for <a class="reference internal" href=""><em>fix_gle</em></a>. While the GLE scheme is more input matrix for <a class="reference internal" href=""><em>fix gle</em></a>. While the GLE scheme is more
general, the form used by <a class="reference internal" href="fix_gld.html"><em>fix gld</em></a> can be more directly general, the form used by <a class="reference internal" href="fix_gld.html"><em>fix gld</em></a> can be more directly
related to the representation of an implicit solvent environment.</p> related to the representation of an implicit solvent environment.</p>
</div> </div>
@ -239,14 +239,14 @@ thermostatted degrees of freedom are fully flexible, and the sampled
ensemble will not be correct otherwise.</p> ensemble will not be correct otherwise.</p>
<p>In order to perform constant-pressure simulations please use <p>In order to perform constant-pressure simulations please use
<a class="reference internal" href="fix_press_berendsen.html"><em>fix press/berendsen</em></a>, rather than <a class="reference internal" href="fix_press_berendsen.html"><em>fix press/berendsen</em></a>, rather than
<code class="xref doc docutils literal"><span class="pre">fix_npt</span></code>, to avoid duplicate integration of the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>, to avoid duplicate integration of the
equations of motion.</p> equations of motion.</p>
<p>This fix is part of the USER-MISC package. It is only enabled if LAMMPS <p>This fix is part of the USER-MISC package. It is only enabled if LAMMPS
was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p> was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, <a class="reference internal" href="fix_viscous.html"><em>fix viscous</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="pair_dpd.html"><em>pair_style dpd/tstat</em></a>, <a class="reference internal" href="fix_gld.html"><em>fix_gld</em></a></p> <p><a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, <a class="reference internal" href="fix_viscous.html"><em>fix viscous</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="pair_dpd.html"><em>pair_style dpd/tstat</em></a>, <a class="reference internal" href="fix_gld.html"><em>fix gld</em></a></p>
<hr class="docutils" /> <hr class="docutils" />
<p id="ceriotti"><strong>(Ceriotti)</strong> Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6, <p id="ceriotti"><strong>(Ceriotti)</strong> Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6,
1170-80 (2010)</p> 1170-80 (2010)</p>

6
doc/fix_gle.txt
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@ -88,7 +88,7 @@ Note also that the Generalized Langevin Dynamics scheme that is
implemented by the "fix gld"_fix_gld.html scheme is closely related implemented by the "fix gld"_fix_gld.html scheme is closely related
to the present one. In fact, it should be always possible to cast the to the present one. In fact, it should be always possible to cast the
Prony series form of the memory kernel used by GLD into an appropriate Prony series form of the memory kernel used by GLD into an appropriate
input matrix for "fix_gle"_fix_gle.html. While the GLE scheme is more input matrix for "fix gle"_fix_gle.html. While the GLE scheme is more
general, the form used by "fix gld"_fix_gld.html can be more directly general, the form used by "fix gld"_fix_gld.html can be more directly
related to the representation of an implicit solvent environment. related to the representation of an implicit solvent environment.
@ -128,7 +128,7 @@ ensemble will not be correct otherwise.
In order to perform constant-pressure simulations please use In order to perform constant-pressure simulations please use
"fix press/berendsen"_fix_press_berendsen.html, rather than "fix press/berendsen"_fix_press_berendsen.html, rather than
"fix_npt"_fix_npt.html, to avoid duplicate integration of the "fix npt"_fix_nh.html, to avoid duplicate integration of the
equations of motion. equations of motion.
This fix is part of the USER-MISC package. It is only enabled if LAMMPS This fix is part of the USER-MISC package. It is only enabled if LAMMPS
@ -139,7 +139,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix "fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style
dpd/tstat"_pair_dpd.html, "fix_gld"_fix_gld.html dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html
:line :line

6
doc/fix_lb_rigid_pc_sphere.html
View File

@ -176,7 +176,7 @@ fix 1 all lb/rigid/pc/sphere force 1 0 0 innerNodes ForceAtoms
created to be used in place of that fix, to integrate the equations of created to be used in place of that fix, to integrate the equations of
motion of spherical rigid bodies when a lattice-Boltzmann fluid is motion of spherical rigid bodies when a lattice-Boltzmann fluid is
present with a user-specified value of the force-coupling constant. present with a user-specified value of the force-coupling constant.
The fix uses the integration algorithm described in <a class="reference internal" href="fix_lb_viscous.html#mackay"><span>Mackay et al.</span></a> to update the positions, velocities, and orientations of The fix uses the integration algorithm described in <a class="reference internal" href="#mackay"><span>Mackay et al.</span></a> to update the positions, velocities, and orientations of
a set of spherical rigid bodies experiencing velocity dependent a set of spherical rigid bodies experiencing velocity dependent
hydrodynamic forces. The spherical bodies are assumed to rotate as hydrodynamic forces. The spherical bodies are assumed to rotate as
solid, uniform density spheres, with moments of inertia calculated solid, uniform density spheres, with moments of inertia calculated
@ -201,13 +201,13 @@ central atoms interact with one another.</p>
<p>Apart from the features described above, this fix is very similar to <p>Apart from the features described above, this fix is very similar to
the rigid fix (although it includes fewer optional arguments, and the rigid fix (although it includes fewer optional arguments, and
assumes the constituent atoms are point particles); see assumes the constituent atoms are point particles); see
<a class="reference internal" href="fix_rigid.html"><em>fix_rigid</em></a> for a complete documentation.</p> <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> for a complete documentation.</p>
</div> </div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline"></a></h2> <h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline"></a></h2>
<p>No information about the <em>rigid</em> and <em>rigid/nve</em> fixes are written to <p>No information about the <em>rigid</em> and <em>rigid/nve</em> fixes are written to
<a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</p> <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</p>
<p>Similar to the <a class="reference internal" href="fix_rigid.html"><em>fix_rigid</em></a> command: &amp;quot; The rigid <p>Similar to the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command: &amp;quot; The rigid
fix computes a global scalar which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The scalar value calculated by fix computes a global scalar which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The scalar value calculated by
these fixes is &#8220;intensive&#8221;. The scalar is the current temperature of these fixes is &#8220;intensive&#8221;. The scalar is the current temperature of
the collection of rigid bodies. This is averaged over all rigid the collection of rigid bodies. This is averaged over all rigid

4
doc/fix_lb_rigid_pc_sphere.txt
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@ -73,14 +73,14 @@ central atoms interact with one another.
Apart from the features described above, this fix is very similar to Apart from the features described above, this fix is very similar to
the rigid fix (although it includes fewer optional arguments, and the rigid fix (although it includes fewer optional arguments, and
assumes the constituent atoms are point particles); see assumes the constituent atoms are point particles); see
"fix_rigid"_fix_rigid.html for a complete documentation. "fix rigid"_fix_rigid.html for a complete documentation.
[Restart, fix_modify, output, run start/stop, minimize info:] [Restart, fix_modify, output, run start/stop, minimize info:]
No information about the {rigid} and {rigid/nve} fixes are written to No information about the {rigid} and {rigid/nve} fixes are written to
"binary restart files"_restart.html. "binary restart files"_restart.html.
Similar to the "fix_rigid"_fix_rigid.html command: &quot; The rigid Similar to the "fix rigid"_fix_rigid.html command: &quot; The rigid
fix computes a global scalar which can be accessed by various "output fix computes a global scalar which can be accessed by various "output
commands"_Section_howto.html#howto_15. The scalar value calculated by commands"_Section_howto.html#howto_15. The scalar value calculated by
these fixes is "intensive". The scalar is the current temperature of these fixes is "intensive". The scalar is the current temperature of

6
doc/fix_nphug.html
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@ -175,7 +175,7 @@ fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pch
<p>This command is a variant of the Nose-Hoover <p>This command is a variant of the Nose-Hoover
<a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> fix style. <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> fix style.
It performs time integration of the Hugoniostat equations It performs time integration of the Hugoniostat equations
of motion developed by Ravelo et al. <a class="reference internal" href="pair_lj_cubic.html#ravelo"><span>(Ravelo)</span></a>. of motion developed by Ravelo et al. <a class="reference internal" href="#ravelo"><span>(Ravelo)</span></a>.
These equations compress the system to a state with average These equations compress the system to a state with average
axial stress or pressure equal to the specified target value axial stress or pressure equal to the specified target value
and that satisfies the Rankine-Hugoniot (RH) and that satisfies the Rankine-Hugoniot (RH)
@ -302,7 +302,7 @@ these fixes is &#8220;extensive&#8221;; the vector values are &#8220;intensive&#
<p>The scalar is the cumulative energy change due to the fix.</p> <p>The scalar is the cumulative energy change due to the fix.</p>
<p>The vector stores three quantities unique to this fix (Delta, Us, and up), <p>The vector stores three quantities unique to this fix (Delta, Us, and up),
followed by all the internal Nose/Hoover thermostat and barostat followed by all the internal Nose/Hoover thermostat and barostat
variables defined for <a class="reference internal" href="fix_nh.html"><em>fix_style npt</em></a>. Delta is the deviation variables defined for <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>. Delta is the deviation
of the temperature from the target temperature, given by the above equation. of the temperature from the target temperature, given by the above equation.
Us and up are the shock and particle velocity corresponding to a steady Us and up are the shock and particle velocity corresponding to a steady
shock calculated from the RH conditions. They have units of distance/time.</p> shock calculated from the RH conditions. They have units of distance/time.</p>
@ -311,7 +311,7 @@ shock calculated from the RH conditions. They have units of distance/time.</p>
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2> <h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This fix style is part of the SHOCK package. It is only enabled if <p>This fix style is part of the SHOCK package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p> LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>All the usual restrictions for <a class="reference internal" href="fix_nh.html"><em>fix_style npt</em></a> apply, <p>All the usual restrictions for <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> apply,
plus the additional ones mentioned above.</p> plus the additional ones mentioned above.</p>
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">

4
doc/fix_nphug.txt
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@ -201,7 +201,7 @@ The scalar is the cumulative energy change due to the fix.
The vector stores three quantities unique to this fix (Delta, Us, and up), The vector stores three quantities unique to this fix (Delta, Us, and up),
followed by all the internal Nose/Hoover thermostat and barostat followed by all the internal Nose/Hoover thermostat and barostat
variables defined for "fix_style npt"_fix_nh.html. Delta is the deviation variables defined for "fix npt"_fix_nh.html. Delta is the deviation
of the temperature from the target temperature, given by the above equation. of the temperature from the target temperature, given by the above equation.
Us and up are the shock and particle velocity corresponding to a steady Us and up are the shock and particle velocity corresponding to a steady
shock calculated from the RH conditions. They have units of distance/time. shock calculated from the RH conditions. They have units of distance/time.
@ -212,7 +212,7 @@ This fix style is part of the SHOCK package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info. LAMMPS"_Section_start.html#start_3 section for more info.
All the usual restrictions for "fix_style npt"_fix_nh.html apply, All the usual restrictions for "fix npt"_fix_nh.html apply,
plus the additional ones mentioned above. plus the additional ones mentioned above.
[Related commands:] [Related commands:]

2
doc/fix_pour.html
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@ -350,7 +350,7 @@ defined by the <a class="reference internal" href="region.html"><em>region</em><
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="fix_deposit.html"><em>fix_deposit</em></a>, <a class="reference internal" href="fix_gravity.html"><em>fix_gravity</em></a>, <p><a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_gravity.html"><em>fix gravity</em></a>,
<a class="reference internal" href="region.html"><em>region</em></a></p> <a class="reference internal" href="region.html"><em>region</em></a></p>
</div> </div>
<div class="section" id="default"> <div class="section" id="default">

2
doc/fix_pour.txt
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@ -251,7 +251,7 @@ defined by the "region"_region.html command.
[Related commands:] [Related commands:]
"fix_deposit"_fix_deposit.html, "fix_gravity"_fix_gravity.html, "fix deposit"_fix_deposit.html, "fix gravity"_fix_gravity.html,
"region"_region.html "region"_region.html
[Default:] [Default:]

4
doc/fix_rigid.html
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@ -236,7 +236,7 @@ single entity.</p>
<p>Examples of large rigid bodies are a colloidal particle, or portions <p>Examples of large rigid bodies are a colloidal particle, or portions
of a biomolecule such as a protein.</p> of a biomolecule such as a protein.</p>
<p>Example of small rigid bodies are patchy nanoparticles, such as those <p>Example of small rigid bodies are patchy nanoparticles, such as those
modeled in <a class="reference internal" href="pair_gran.html#zhang"><span>this paper</span></a> by Sharon Glotzer&#8217;s group, clumps of modeled in <a class="reference internal" href="#zhang"><span>this paper</span></a> by Sharon Glotzer&#8217;s group, clumps of
granular particles, lipid molecules consiting of one or more point granular particles, lipid molecules consiting of one or more point
dipoles connected to other spheroids or ellipsoids, irregular dipoles connected to other spheroids or ellipsoids, irregular
particles built from line segments (2d) or triangles (3d), and particles built from line segments (2d) or triangles (3d), and
@ -288,7 +288,7 @@ differences may accumulate to produce divergent trajectories.</p>
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
<p class="last">You should not update the atoms in rigid bodies via other <p class="last">You should not update the atoms in rigid bodies via other
time-integration fixes (e.g. <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, <code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">nvt</span></code>, <code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">npt</span></code>), or you will be integrating time-integration fixes (e.g. <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>), or you will be integrating
their motion more than once each timestep. When performing a hybrid their motion more than once each timestep. When performing a hybrid
simulation with some atoms in rigid bodies, and some not, a separate simulation with some atoms in rigid bodies, and some not, a separate
time integration fix like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> should be used for the non-rigid particles.</p> time integration fix like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> should be used for the non-rigid particles.</p>

2
doc/fix_rigid.txt
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@ -147,7 +147,7 @@ differences may accumulate to produce divergent trajectories.
NOTE: You should not update the atoms in rigid bodies via other NOTE: You should not update the atoms in rigid bodies via other
time-integration fixes (e.g. "fix nve"_fix_nve.html, "fix time-integration fixes (e.g. "fix nve"_fix_nve.html, "fix
nvt"_fix_nvt.html, "fix npt"_fix_npt.html), or you will be integrating nvt"_fix_nh.html, "fix npt"_fix_nh.html), or you will be integrating
their motion more than once each timestep. When performing a hybrid their motion more than once each timestep. When performing a hybrid
simulation with some atoms in rigid bodies, and some not, a separate simulation with some atoms in rigid bodies, and some not, a separate
time integration fix like "fix nve"_fix_nve.html or "fix time integration fix like "fix nve"_fix_nve.html or "fix

4
doc/fix_saed_vtk.html
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@ -165,7 +165,7 @@ fix saed/vtk 1 1 1 c_2 file Ni_000.saed
</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>
<p>Time average computed intensities from <a class="reference external" href="compute_saed.txt">compute_saed</a> and <p>Time average computed intensities from <a class="reference internal" href="compute_saed.html"><em>compute saed</em></a> and
write output to a file in the 3rd generation vtk image data format for write output to a file in the 3rd generation vtk image data format for
visualization directly in parallelized visualization software packages visualization directly in parallelized visualization software packages
like ParaView and VisIt. Note that if no time averaging is done, this like ParaView and VisIt. Note that if no time averaging is done, this
@ -180,7 +180,7 @@ R_Ewald*[h k l]/norm([h k l]), where R_Ewald=1/lambda.</p>
<p>The group specified within this command is ignored. However, note that <p>The group specified within this command is ignored. However, note that
specified values may represent calculations performed by saed computes specified values may represent calculations performed by saed computes
which store their own &#8220;group&#8221; definitions.</p> which store their own &#8220;group&#8221; definitions.</p>
<p>Fix saed/vtk is designed to work only with <a class="reference external" href="compute_saed.txt">compute_saed</a> <p>Fix saed/vtk is designed to work only with <a class="reference internal" href="compute_saed.html"><em>compute saed</em></a>
values, e.g.</p> values, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>compute 3 top saed 0.0251 Al O <div class="highlight-python"><div class="highlight"><pre>compute 3 top saed 0.0251 Al O
fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed

4
doc/fix_saed_vtk.txt
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@ -42,7 +42,7 @@ fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
[Description:] [Description:]
Time average computed intensities from "compute_saed"_compute_saed.txt and Time average computed intensities from "compute saed"_compute_saed.html and
write output to a file in the 3rd generation vtk image data format for write output to a file in the 3rd generation vtk image data format for
visualization directly in parallelized visualization software packages visualization directly in parallelized visualization software packages
like ParaView and VisIt. Note that if no time averaging is done, this like ParaView and VisIt. Note that if no time averaging is done, this
@ -60,7 +60,7 @@ The group specified within this command is ignored. However, note that
specified values may represent calculations performed by saed computes specified values may represent calculations performed by saed computes
which store their own "group" definitions. which store their own "group" definitions.
Fix saed/vtk is designed to work only with "compute_saed"_compute_saed.txt Fix saed/vtk is designed to work only with "compute saed"_compute_saed.html
values, e.g. values, e.g.
compute 3 top saed 0.0251 Al O compute 3 top saed 0.0251 Al O

2
doc/fix_temp_rescale_eff.html
View File

@ -183,7 +183,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="fix_langevin_eff.html"><em>fix langevin/eff</em></a>, <a class="reference internal" href="fix_nh_eff.html"><em>fix nvt/eff</em></a>, <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a>, <p><a class="reference internal" href="fix_langevin_eff.html"><em>fix langevin/eff</em></a>, <a class="reference internal" href="fix_nh_eff.html"><em>fix nvt/eff</em></a>, <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a>,
<a class="reference internal" href="fix_temp_rescale.html"><em>fix_temp_rescale</em></a>,</p> <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp rescale</em></a>,</p>
<p><strong>Default:</strong> none</p> <p><strong>Default:</strong> none</p>
</div> </div>
</div> </div>

2
doc/fix_temp_rescale_eff.txt
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@ -71,6 +71,6 @@ LAMMPS"_Section_start.html#start_3 section for more info.
"fix langevin/eff"_fix_langevin_eff.html, "fix "fix langevin/eff"_fix_langevin_eff.html, "fix
nvt/eff"_fix_nh_eff.html, "fix_modify"_fix_modify.html, nvt/eff"_fix_nh_eff.html, "fix_modify"_fix_modify.html,
"fix_temp_rescale"_fix_temp_rescale.html, "fix temp rescale"_fix_temp_rescale.html,
[Default:] none [Default:] none

2
doc/fix_ti_spring.html
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@ -200,7 +200,7 @@ divergencies during the integration due to the fact that the atoms are
&#8216;attatched&#8217; to its equilibrium positions by the Einstein &#8216;attatched&#8217; to its equilibrium positions by the Einstein
crystal. Check the option <em>zero</em> of <a class="reference external" href="fix_langevin_html">fix langevin</a> crystal. Check the option <em>zero</em> of <a class="reference external" href="fix_langevin_html">fix langevin</a>
and <a class="reference internal" href="velocity.html"><em>velocity</em></a>. The use of the Nose-Hoover thermostat and <a class="reference internal" href="velocity.html"><em>velocity</em></a>. The use of the Nose-Hoover thermostat
(<code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">nvt</span></code>) is NOT recommended due to its well documented (<a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>) is NOT recommended due to its well documented
issues with the canonical sampling of harmonic degrees of freedom issues with the canonical sampling of harmonic degrees of freedom
(notice that the <em>chain</em> option will NOT solve this problem). The (notice that the <em>chain</em> option will NOT solve this problem). The
Langevin thermostat (<a class="reference external" href="fix_langevin.html&quot;">fix langevin</a>) works fine.</p> Langevin thermostat (<a class="reference external" href="fix_langevin.html&quot;">fix langevin</a>) works fine.</p>

2
doc/fix_ti_spring.txt
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@ -88,7 +88,7 @@ divergencies during the integration due to the fact that the atoms are
'attatched' to its equilibrium positions by the Einstein 'attatched' to its equilibrium positions by the Einstein
crystal. Check the option {zero} of "fix langevin"_fix_langevin_html crystal. Check the option {zero} of "fix langevin"_fix_langevin_html
and "velocity"_velocity.html. The use of the Nose-Hoover thermostat and "velocity"_velocity.html. The use of the Nose-Hoover thermostat
("fix nvt"_fix_nvt.html) is NOT recommended due to its well documented ("fix nvt"_fix_nh.html) is NOT recommended due to its well documented
issues with the canonical sampling of harmonic degrees of freedom issues with the canonical sampling of harmonic degrees of freedom
(notice that the {chain} option will NOT solve this problem). The (notice that the {chain} option will NOT solve this problem). The
Langevin thermostat ("fix langevin"_fix_langevin.html") works fine. Langevin thermostat ("fix langevin"_fix_langevin.html") works fine.

4
doc/fix_wall_gran.html
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@ -221,7 +221,7 @@ axis is at x = y = 0.0, and the radius of the cylinder is specified.</p>
keywords are appended. Both keywords cannot be used together.</p> keywords are appended. Both keywords cannot be used together.</p>
<p>For the <em>wiggle</em> keyword, the wall oscillates sinusoidally, similar to <p>For the <em>wiggle</em> keyword, the wall oscillates sinusoidally, similar to
the oscillations of particles which can be specified by the the oscillations of particles which can be specified by the
<a class="reference internal" href="fix_move.html"><em>fix_move</em></a> command. This is useful in packing <a class="reference internal" href="fix_move.html"><em>fix move</em></a> command. This is useful in packing
simulations of granular particles. The arguments to the <em>wiggle</em> simulations of granular particles. The arguments to the <em>wiggle</em>
keyword specify a dimension for the motion, as well as it&#8217;s keyword specify a dimension for the motion, as well as it&#8217;s
<em>amplitude</em> and <em>period</em>. Note that if the dimension is in the plane <em>amplitude</em> and <em>period</em>. Note that if the dimension is in the plane
@ -270,7 +270,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="fix_move.html"><em>fix_move</em></a>, <a class="reference internal" href="pair_gran.html"><em>pair_style granular</em></a></p> <p><a class="reference internal" href="fix_move.html"><em>fix move</em></a>, <a class="reference internal" href="pair_gran.html"><em>pair_style granular</em></a></p>
<p><strong>Default:</strong> none</p> <p><strong>Default:</strong> none</p>
</div> </div>
</div> </div>

4
doc/fix_wall_gran.txt
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@ -97,7 +97,7 @@ keywords are appended. Both keywords cannot be used together.
For the {wiggle} keyword, the wall oscillates sinusoidally, similar to For the {wiggle} keyword, the wall oscillates sinusoidally, similar to
the oscillations of particles which can be specified by the the oscillations of particles which can be specified by the
"fix_move"_fix_move.html command. This is useful in packing "fix move"_fix_move.html command. This is useful in packing
simulations of granular particles. The arguments to the {wiggle} simulations of granular particles. The arguments to the {wiggle}
keyword specify a dimension for the motion, as well as it's keyword specify a dimension for the motion, as well as it's
{amplitude} and {period}. Note that if the dimension is in the plane {amplitude} and {period}. Note that if the dimension is in the plane
@ -152,6 +152,6 @@ Any dimension (xyz) that has a granular wall must be non-periodic.
[Related commands:] [Related commands:]
"fix_move"_fix_move.html, "pair_style granular"_pair_gran.html "fix move"_fix_move.html, "pair_style granular"_pair_gran.html
[Default:] none [Default:] none

2
doc/molecule.html
View File

@ -530,7 +530,7 @@ of SHAKE clusters.</p>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_pour.html"><em>fix pour</em></a>, <p><a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_pour.html"><em>fix pour</em></a>,
<a class="reference internal" href="fix_gcmc.html"><em>fix_gcmc</em></a></p> <a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a></p>
</div> </div>
<div class="section" id="default"> <div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2> <h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>

4
doc/molecule.txt
View File

@ -1,4 +1,4 @@
<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov) :link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html) :link(ld,Manual.html)
@ -456,7 +456,7 @@ of SHAKE clusters.
[Related commands:] [Related commands:]
"fix deposit"_fix_deposit.html, "fix pour"_fix_pour.html, "fix deposit"_fix_deposit.html, "fix pour"_fix_pour.html,
"fix_gcmc"_fix_gcmc.html "fix gcmc"_fix_gcmc.html
[Default:] [Default:]

2
doc/pair_body.html
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@ -218,7 +218,7 @@ body/particle interactions requires the use of the <a class="reference internal"
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="fix_rigid.html"><em>fix_rigid</em></a></p> <p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a></p>
<p><strong>Default:</strong> none</p> <p><strong>Default:</strong> none</p>
</div> </div>
</div> </div>

2
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@ -113,6 +113,6 @@ body"_atom_style.html command.
[Related commands:] [Related commands:]
"pair_coeff"_pair_coeff.html, "fix_rigid"_fix_rigid.html "pair_coeff"_pair_coeff.html, "fix rigid"_fix_rigid.html
[Default:] none [Default:] none

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@ -213,17 +213,17 @@ then you can use those files from anywhere on your system, without
copying them into your working directory. Environment variables are copying them into your working directory. Environment variables are
set in different ways for different shells. Here are example settings set in different ways for different shells. Here are example settings
for</p> for</p>
<div class="highlight-python"><div class="highlight"><pre>csh, tcsh: <p>csh, tcsh:</p>
% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials <div class="highlight-python"><div class="highlight"><pre>% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials
</pre></div> </pre></div>
</div> </div>
<div class="highlight-python"><div class="highlight"><pre>bash: <p>bash:</p>
% export LAMMPS_POTENTIALS=/path/to/lammps/potentials <div class="highlight-python"><div class="highlight"><pre>% export LAMMPS_POTENTIALS=/path/to/lammps/potentials
</pre></div> </pre></div>
</div> </div>
<p>Windows:</p>
<pre class="literal-block"> <pre class="literal-block">
Windows: % set LAMMPS_POTENTIALS=&quot;C:Path to LAMMPSPotentials&quot;
% set LAMMPS_POTENTIALS=&quot;C:Path to LAMMPSPotentials
</pre> </pre>
<hr class="docutils" /> <hr class="docutils" />
<p>The alphabetic list of pair styles defined in LAMMPS is given on the <p>The alphabetic list of pair styles defined in LAMMPS is given on the

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@ -97,13 +97,16 @@ set in different ways for different shells. Here are example settings
for for
csh, tcsh: csh, tcsh:
% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials :pre % setenv LAMMPS_POTENTIALS /path/to/lammps/potentials :pre
bash: bash:
% export LAMMPS_POTENTIALS=/path/to/lammps/potentials :pre % export LAMMPS_POTENTIALS=/path/to/lammps/potentials :pre
Windows: Windows:
% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials :pre
% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials" :pre
:line :line

4
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@ -175,7 +175,7 @@ atoms <em>i</em> and <em>j</em>,
<em>E&lt;sup&gt;corr&lt;/sup&gt;</em> are angular correction terms.</p> <em>E&lt;sup&gt;corr&lt;/sup&gt;</em> are angular correction terms.</p>
<p>The COMB potentials (styles <em>comb</em> and <em>comb3</em>) are variable charge <p>The COMB potentials (styles <em>comb</em> and <em>comb3</em>) are variable charge
potentials. The equilibrium charge on each atom is calculated by the potentials. The equilibrium charge on each atom is calculated by the
electronegativity equalization (QEq) method. See <a class="reference internal" href="pair_smtbq.html#rick"><span>Rick</span></a> for electronegativity equalization (QEq) method. See <a class="reference internal" href="#rick"><span>Rick</span></a> for
further details. This is implemented by the <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a> command, which should normally be further details. This is implemented by the <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a> command, which should normally be
specified in the input script when running a model with the COMB specified in the input script when running a model with the COMB
potential. The <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a> command has options potential. The <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a> command has options
@ -274,7 +274,7 @@ doesn&#8217;t use &#8220;metal&#8221; units.</p>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <p><a class="reference internal" href="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
<a class="reference internal" href="fix_qeq_comb.html"><em>fix_qeq/comb</em></a></p> <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a></p>
<p><strong>Default:</strong> none</p> <p><strong>Default:</strong> none</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="comb"><strong>(COMB)</strong> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and <p id="comb"><strong>(COMB)</strong> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and

2
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@ -172,7 +172,7 @@ doesn't use "metal" units.
[Related commands:] [Related commands:]
"pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html, "pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html,
"fix_qeq/comb"_fix_qeq_comb.html "fix qeq/comb"_fix_qeq_comb.html
[Default:] none [Default:] none

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@ -340,8 +340,8 @@ in several water models).</p>
<p>NOTES: When using the core-softed Coulomb potentials with long-range <p>NOTES: When using the core-softed Coulomb potentials with long-range
solvers (<em>coul/long/soft</em>, <em>lj/cut/coul/long/soft</em>, etc.) in a free solvers (<em>coul/long/soft</em>, <em>lj/cut/coul/long/soft</em>, etc.) in a free
energy calculation in which sites holding electrostatic charges are energy calculation in which sites holding electrostatic charges are
being created or anihilated (using <a class="reference internal" href="fix_adapt_fep.html"><em>fix_adapt/fep</em></a> being created or anihilated (using <a class="reference internal" href="fix_adapt_fep.html"><em>fix adapt/fep</em></a>
and <a class="reference internal" href="compute_fep.html"><em>compute_fep</em></a>) it is important to adapt both the and <a class="reference internal" href="compute_fep.html"><em>compute fep</em></a>) it is important to adapt both the
lambda activation parameter (from 0 to 1, or the reverse) and the lambda activation parameter (from 0 to 1, or the reverse) and the
value of the charge (from 0 to its final value, or the reverse). This value of the charge (from 0 to its final value, or the reverse). This
ensures that long-range electrostatic terms (kspace) are correct. It ensures that long-range electrostatic terms (kspace) are correct. It
@ -397,8 +397,8 @@ the <a class="reference internal" href="Section_start.html#start-3"><span>Making
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="fix_adapt.html"><em>fix_adapt</em></a>, <p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a>,
<a class="reference internal" href="fix_adapt_fep.html"><em>fix_adapt/fep</em></a>, <a class="reference internal" href="compute_fep.html"><em>compute_fep</em></a></p> <a class="reference internal" href="fix_adapt_fep.html"><em>fix adapt/fep</em></a>, <a class="reference internal" href="compute_fep.html"><em>compute fep</em></a></p>
<p><strong>Default:</strong> none</p> <p><strong>Default:</strong> none</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="beutler"><strong>(Beutler)</strong> Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem <p id="beutler"><strong>(Beutler)</strong> Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem

8
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@ -191,8 +191,8 @@ in several water models).
NOTES: When using the core-softed Coulomb potentials with long-range NOTES: When using the core-softed Coulomb potentials with long-range
solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.) in a free solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.) in a free
energy calculation in which sites holding electrostatic charges are energy calculation in which sites holding electrostatic charges are
being created or anihilated (using "fix_adapt/fep"_fix_adapt_fep.html being created or anihilated (using "fix adapt/fep"_fix_adapt_fep.html
and "compute_fep"_compute_fep.html) it is important to adapt both the and "compute fep"_compute_fep.html) it is important to adapt both the
lambda activation parameter (from 0 to 1, or the reverse) and the lambda activation parameter (from 0 to 1, or the reverse) and the
value of the charge (from 0 to its final value, or the reverse). This value of the charge (from 0 to its final value, or the reverse). This
ensures that long-range electrostatic terms (kspace) are correct. It ensures that long-range electrostatic terms (kspace) are correct. It
@ -265,8 +265,8 @@ the "Making LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:] [Related commands:]
"pair_coeff"_pair_coeff.html, "fix_adapt"_fix_adapt.html, "pair_coeff"_pair_coeff.html, "fix adapt"_fix_adapt.html,
"fix_adapt/fep"_fix_adapt_fep.html, "compute_fep"_compute_fep.html "fix adapt/fep"_fix_adapt_fep.html, "compute fep"_compute_fep.html
[Default:] none [Default:] none

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