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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14590 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2016-02-15 15:28:30 +00:00
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38
doc/Section_commands.html
View File

@ -607,12 +607,12 @@ This is indicated by additional letters in parenthesis: c = USER-CUDA,
g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="12%" />
<col width="11%" />
<col width="15%" />
<col width="11%" />
<col width="11%" />
<col width="10%" />
<col width="13%" />
<col width="11%" />
<col width="15%" />
<col width="12%" />
</colgroup>
@ -696,61 +696,61 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="fix_qeq.html"><em>qeq/point</em></a></td>
<td><a class="reference internal" href="fix_qeq.html"><em>qeq/shielded</em></a></td>
<td><a class="reference internal" href="fix_qeq.html"><em>qeq/slater</em></a></td>
<td><a class="reference internal" href="fix_reax_bonds.html"><em>reax/bonds</em></a></td>
<td><a class="reference internal" href="fix_shake.html"><em>rattle</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_recenter.html"><em>recenter</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="fix_reax_bonds.html"><em>reax/bonds</em></a></td>
<td><a class="reference internal" href="fix_recenter.html"><em>recenter</em></a></td>
<td><a class="reference internal" href="fix_restrain.html"><em>restrain</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/nph (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/npt (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/nve (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/nvt (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nph</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="fix_rigid.html"><em>rigid/small (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nph</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/npt</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nve</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nvt</em></a></td>
<td><a class="reference internal" href="fix_setforce.html"><em>setforce (ck)</em></a></td>
<td><a class="reference internal" href="fix_shake.html"><em>shake (c)</em></a></td>
<td><a class="reference internal" href="fix_spring.html"><em>spring</em></a></td>
<td><a class="reference internal" href="fix_spring_rg.html"><em>spring/rg</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_spring_self.html"><em>spring/self</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="fix_spring_rg.html"><em>spring/rg</em></a></td>
<td><a class="reference internal" href="fix_spring_self.html"><em>spring/self</em></a></td>
<td><a class="reference internal" href="fix_srd.html"><em>srd</em></a></td>
<td><a class="reference internal" href="fix_store_force.html"><em>store/force</em></a></td>
<td><a class="reference internal" href="fix_store_state.html"><em>store/state</em></a></td>
<td><a class="reference internal" href="fix_temp_berendsen.html"><em>temp/berendsen (c)</em></a></td>
<td><a class="reference internal" href="fix_temp_csvr.html"><em>temp/csld</em></a></td>
<td><a class="reference internal" href="fix_temp_csvr.html"><em>temp/csvr</em></a></td>
<td><a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale (c)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_tfmc.html"><em>tfmc</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale (c)</em></a></td>
<td><a class="reference internal" href="fix_tfmc.html"><em>tfmc</em></a></td>
<td><a class="reference internal" href="fix_thermal_conductivity.html"><em>thermal/conductivity</em></a></td>
<td><a class="reference internal" href="fix_tmd.html"><em>tmd</em></a></td>
<td><a class="reference internal" href="fix_ttm.html"><em>ttm</em></a></td>
<td><a class="reference internal" href="fix_tune_kspace.html"><em>tune/kspace</em></a></td>
<td><a class="reference internal" href="fix_vector.html"><em>vector</em></a></td>
<td><a class="reference internal" href="fix_viscosity.html"><em>viscosity</em></a></td>
<td><a class="reference internal" href="fix_viscous.html"><em>viscous (c)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_wall.html"><em>wall/colloid</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="fix_viscous.html"><em>viscous (c)</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/colloid</em></a></td>
<td><a class="reference internal" href="fix_wall_gran.html"><em>wall/gran</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/harmonic</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/lj1043</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/lj126</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/lj93</em></a></td>
<td><a class="reference internal" href="fix_wall_piston.html"><em>wall/piston</em></a></td>
<td><a class="reference internal" href="fix_wall_reflect.html"><em>wall/reflect (k)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_wall_region.html"><em>wall/region</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="fix_wall_reflect.html"><em>wall/reflect (k)</em></a></td>
<td><a class="reference internal" href="fix_wall_region.html"><em>wall/region</em></a></td>
<td><a class="reference internal" href="fix_wall_srd.html"><em>wall/srd</em></a></td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>
@ -776,7 +776,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<tr class="row-even"><td><a class="reference internal" href="fix_drude.html"><em>drude</em></a></td>
<td><a class="reference internal" href="fix_drude_transform.html"><em>drude/transform/direct</em></a></td>
<td><a class="reference internal" href="fix_drude_transform.html"><em>drude/transform/reverse</em></a></td>
<td><code class="xref doc docutils literal"><span class="pre">eos/cv</span></code></td>
<td><a class="reference internal" href="fix_eos_cv.html"><em>eos/cv</em></a></td>
<td><a class="reference internal" href="fix_eos_table.html"><em>eos/table</em></a></td>
<td><a class="reference internal" href="fix_gle.html"><em>gle</em></a></td>
</tr>
@ -1448,8 +1448,8 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="25%" />
<col width="26%" />
<col width="24%" />
<col width="23%" />
<col width="27%" />
</colgroup>
@ -1464,8 +1464,8 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="kspace_style.html"><em>pppm/disp</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>pppm/disp/tip4p</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="kspace_style.html"><em>pppm/tip4p (o)</em></a></td>
<td>&nbsp;</td>
<tr class="row-odd"><td><a class="reference internal" href="kspace_style.html"><em>pppm/stagger</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>pppm/tip4p (o)</em></a></td>
<td>&nbsp;</td>
<td>&nbsp;</td>
</tr>

4
doc/Section_commands.txt
View File

@ -552,6 +552,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"qeq/point"_fix_qeq.html,
"qeq/shielded"_fix_qeq.html,
"qeq/slater"_fix_qeq.html,
"rattle"_fix_shake.html,
"reax/bonds"_fix_reax_bonds.html,
"recenter"_fix_recenter.html,
"restrain"_fix_restrain.html,
@ -609,7 +610,7 @@ package"_Section_start.html#start_3.
"drude"_fix_drude.html,
"drude/transform/direct"_fix_drude_transform.html,
"drude/transform/reverse"_fix_drude_transform.html,
"eos/cv"_fix_eos_vs.html,
"eos/cv"_fix_eos_cv.html,
"eos/table"_fix_eos_table.html,
"gle"_fix_gle.html,
"imd"_fix_imd.html,
@ -1095,4 +1096,5 @@ KOKKOS, o = USER-OMP, t = OPT.
"pppm/cg (o)"_kspace_style.html,
"pppm/disp"_kspace_style.html,
"pppm/disp/tip4p"_kspace_style.html,
"pppm/stagger"_kspace_style.html,
"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)

31
doc/Section_python.html
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@ -281,8 +281,10 @@ examples of Python code you can write for both pure Python operations
and callbacks to LAMMPS.</p>
<p>To run pure Python code from LAMMPS, you only need to build LAMMPS
with the PYTHON package installed:</p>
<p>make yes-python
make machine</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-python
make machine
</pre></div>
</div>
<p>Note that this will link LAMMPS with the Python library on your
system, which typically requires several auxiliary system libraries to
also be linked. The list of these libraries and the paths to find
@ -303,7 +305,7 @@ file and the shared library.</p>
<a class="reference internal" href="Section_start.html#start-5"><span>Section_start 5</span></a>. A shared library is one
that is dynamically loadable, which is what Python requires to wrap
LAMMPS. On Linux this is a library file that ends in &#8221;.so&#8221;, not &#8221;.a&#8221;.</p>
<p>&gt;From the src directory, type</p>
<p>From the src directory, type</p>
<div class="highlight-python"><div class="highlight"><pre>make foo mode=shlib
</pre></div>
</div>
@ -313,10 +315,14 @@ well as a soft link liblammps.so, which is what the Python wrapper will
load by default. Note that if you are building multiple machine
versions of the shared library, the soft link is always set to the
most recently built version.</p>
<p>If this fails, see <a class="reference internal" href="Section_start.html#start-5"><span>Section_start 5</span></a> for
more details, especially if your LAMMPS build uses auxiliary libraries
like MPI or FFTW which may not be built as shared libraries on your
system.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you are building LAMMPS with an MPI or FFT library or other
auxiliary libraries (used by various packages), then all of these
extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
<a class="reference internal" href="Section_start.html#start-5"><span>Section_start 5</span></a> for more details.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="installing-the-python-wrapper-into-python">
@ -715,17 +721,6 @@ lmp = lammps(name=&quot;g++&quot;,cmdargs=list) # add LAMMPS command-line arg
</pre></div>
</div>
<hr class="docutils" />
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Currently, the creation of a LAMMPS object from within lammps.py
does not take an MPI communicator as an argument. There should be a
way to do this, so that the LAMMPS instance runs on a subset of
processors if desired, but I don&#8217;t know how to do it from Pypar. So
for now, it runs with MPI_COMM_WORLD, which is all the processors. If
someone figures out how to do this with one or more of the Python
wrappers for MPI, like Pypar, please let us know and we will amend
these doc pages.</p>
</div>
<p>The lines</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">lammps</span> <span class="kn">import</span> <span class="n">lammps</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>

22
doc/Section_python.txt
View File

@ -158,7 +158,7 @@ To run pure Python code from LAMMPS, you only need to build LAMMPS
with the PYTHON package installed:
make yes-python
make machine
make machine :pre
Note that this will link LAMMPS with the Python library on your
system, which typically requires several auxiliary system libraries to
@ -183,7 +183,7 @@ Instructions on how to build LAMMPS as a shared library are given in
that is dynamically loadable, which is what Python requires to wrap
LAMMPS. On Linux this is a library file that ends in ".so", not ".a".
>From the src directory, type
From the src directory, type
make foo mode=shlib :pre
@ -194,10 +194,11 @@ load by default. Note that if you are building multiple machine
versions of the shared library, the soft link is always set to the
most recently built version.
If this fails, see "Section_start 5"_Section_start.html#start_5 for
more details, especially if your LAMMPS build uses auxiliary libraries
like MPI or FFTW which may not be built as shared libraries on your
system.
NOTE: If you are building LAMMPS with an MPI or FFT library or other
auxiliary libraries (used by various packages), then all of these
extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
"Section_start 5"_Section_start.html#start_5 for more details.
:line
@ -610,15 +611,6 @@ lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms
:line
NOTE: Currently, the creation of a LAMMPS object from within lammps.py
does not take an MPI communicator as an argument. There should be a
way to do this, so that the LAMMPS instance runs on a subset of
processors if desired, but I don't know how to do it from Pypar. So
for now, it runs with MPI_COMM_WORLD, which is all the processors. If
someone figures out how to do this with one or more of the Python
wrappers for MPI, like Pypar, please let us know and we will amend
these doc pages.
The lines
from lammps import lammps

78
doc/_sources/Section_commands.txt
View File

@ -455,37 +455,37 @@ with the :doc:`appropriate accelerated package <Section_accelerate>`.
This is indicated by additional letters in parenthesis: c = USER-CUDA,
g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`adapt <fix_adapt>` | :doc:`addforce (c) <fix_addforce>` | :doc:`append/atoms <fix_append_atoms>` | :doc:`atom/swap <fix_atom_swap>` | :doc:`aveforce (c) <fix_aveforce>` | :doc:`ave/atom <fix_ave_atom>` | :doc:`ave/chunk <fix_ave_chunk>` | :doc:`ave/correlate <fix_ave_correlate>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`ave/histo <fix_ave_histo>` | :doc:`ave/histo/weight <fix_ave_histo>` | :doc:`ave/spatial <fix_ave_spatial>` | :doc:`ave/time <fix_ave_time>` | :doc:`balance <fix_balance>` | :doc:`bond/break <fix_bond_break>` | :doc:`bond/create <fix_bond_create>` | :doc:`bond/swap <fix_bond_swap>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`box/relax <fix_box_relax>` | :doc:`deform (k) <fix_deform>` | :doc:`deposit <fix_deposit>` | :doc:`drag <fix_drag>` | :doc:`dt/reset <fix_dt_reset>` | :doc:`efield <fix_efield>` | :doc:`enforce2d (c) <fix_enforce2d>` | :doc:`evaporate <fix_evaporate>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`external <fix_external>` | :doc:`freeze (c) <fix_freeze>` | :doc:`gcmc <fix_gcmc>` | :doc:`gld <fix_gld>` | :doc:`gravity (co) <fix_gravity>` | :doc:`heat <fix_heat>` | :doc:`indent <fix_indent>` | :doc:`langevin (k) <fix_langevin>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`lineforce <fix_lineforce>` | :doc:`momentum <fix_momentum>` | :doc:`move <fix_move>` | :doc:`msst <fix_msst>` | :doc:`neb <fix_neb>` | :doc:`nph (ko) <fix_nh>` | :doc:`nphug (o) <fix_nphug>` | :doc:`nph/asphere (o) <fix_nph_asphere>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`nph/sphere (o) <fix_nph_sphere>` | :doc:`npt (ckio) <fix_nh>` | :doc:`npt/asphere (o) <fix_npt_asphere>` | :doc:`npt/sphere (o) <fix_npt_sphere>` | :doc:`nve (ckio) <fix_nve>` | :doc:`nve/asphere (i) <fix_nve_asphere>` | :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/body <fix_nve_body>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`nve/limit <fix_nve_limit>` | :doc:`nve/line <fix_nve_line>` | :doc:`nve/noforce <fix_nve_noforce>` | :doc:`nve/sphere (o) <fix_nve_sphere>` | :doc:`nve/tri <fix_nve_tri>` | :doc:`nvt (cko) <fix_nh>` | :doc:`nvt/asphere (o) <fix_nvt_asphere>` | :doc:`nvt/sllod (o) <fix_nvt_sllod>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`nvt/sphere (o) <fix_nvt_sphere>` | :doc:`oneway <fix_oneway>` | :doc:`orient/fcc <fix_orient_fcc>` | :doc:`planeforce <fix_planeforce>` | :doc:`poems <fix_poems>` | :doc:`pour <fix_pour>` | :doc:`press/berendsen <fix_press_berendsen>` | :doc:`print <fix_print>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`property/atom <fix_property_atom>` | :doc:`qeq/comb (o) <fix_qeq_comb>` | :doc:`qeq/dynamic <fix_qeq>` | :doc:`qeq/fire <fix_qeq>` | :doc:`qeq/point <fix_qeq>` | :doc:`qeq/shielded <fix_qeq>` | :doc:`qeq/slater <fix_qeq>` | :doc:`reax/bonds <fix_reax_bonds>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`recenter <fix_recenter>` | :doc:`restrain <fix_restrain>` | :doc:`rigid (o) <fix_rigid>` | :doc:`rigid/nph (o) <fix_rigid>` | :doc:`rigid/npt (o) <fix_rigid>` | :doc:`rigid/nve (o) <fix_rigid>` | :doc:`rigid/nvt (o) <fix_rigid>` | :doc:`rigid/small (o) <fix_rigid>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`rigid/small/nph <fix_rigid>` | :doc:`rigid/small/npt <fix_rigid>` | :doc:`rigid/small/nve <fix_rigid>` | :doc:`rigid/small/nvt <fix_rigid>` | :doc:`setforce (ck) <fix_setforce>` | :doc:`shake (c) <fix_shake>` | :doc:`spring <fix_spring>` | :doc:`spring/rg <fix_spring_rg>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`spring/self <fix_spring_self>` | :doc:`srd <fix_srd>` | :doc:`store/force <fix_store_force>` | :doc:`store/state <fix_store_state>` | :doc:`temp/berendsen (c) <fix_temp_berendsen>` | :doc:`temp/csld <fix_temp_csvr>` | :doc:`temp/csvr <fix_temp_csvr>` | :doc:`temp/rescale (c) <fix_temp_rescale>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`tfmc <fix_tfmc>` | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`tmd <fix_tmd>` | :doc:`ttm <fix_ttm>` | :doc:`tune/kspace <fix_tune_kspace>` | :doc:`vector <fix_vector>` | :doc:`viscosity <fix_viscosity>` | :doc:`viscous (c) <fix_viscous>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`wall/colloid <fix_wall>` | :doc:`wall/gran <fix_wall_gran>` | :doc:`wall/harmonic <fix_wall>` | :doc:`wall/lj1043 <fix_wall>` | :doc:`wall/lj126 <fix_wall>` | :doc:`wall/lj93 <fix_wall>` | :doc:`wall/piston <fix_wall_piston>` | :doc:`wall/reflect (k) <fix_wall_reflect>` |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
| :doc:`wall/region <fix_wall_region>` | :doc:`wall/srd <fix_wall_srd>` | | | | | | |
+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`adapt <fix_adapt>` | :doc:`addforce (c) <fix_addforce>` | :doc:`append/atoms <fix_append_atoms>` | :doc:`atom/swap <fix_atom_swap>` | :doc:`aveforce (c) <fix_aveforce>` | :doc:`ave/atom <fix_ave_atom>` | :doc:`ave/chunk <fix_ave_chunk>` | :doc:`ave/correlate <fix_ave_correlate>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`ave/histo <fix_ave_histo>` | :doc:`ave/histo/weight <fix_ave_histo>` | :doc:`ave/spatial <fix_ave_spatial>` | :doc:`ave/time <fix_ave_time>` | :doc:`balance <fix_balance>` | :doc:`bond/break <fix_bond_break>` | :doc:`bond/create <fix_bond_create>` | :doc:`bond/swap <fix_bond_swap>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`box/relax <fix_box_relax>` | :doc:`deform (k) <fix_deform>` | :doc:`deposit <fix_deposit>` | :doc:`drag <fix_drag>` | :doc:`dt/reset <fix_dt_reset>` | :doc:`efield <fix_efield>` | :doc:`enforce2d (c) <fix_enforce2d>` | :doc:`evaporate <fix_evaporate>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`external <fix_external>` | :doc:`freeze (c) <fix_freeze>` | :doc:`gcmc <fix_gcmc>` | :doc:`gld <fix_gld>` | :doc:`gravity (co) <fix_gravity>` | :doc:`heat <fix_heat>` | :doc:`indent <fix_indent>` | :doc:`langevin (k) <fix_langevin>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`lineforce <fix_lineforce>` | :doc:`momentum <fix_momentum>` | :doc:`move <fix_move>` | :doc:`msst <fix_msst>` | :doc:`neb <fix_neb>` | :doc:`nph (ko) <fix_nh>` | :doc:`nphug (o) <fix_nphug>` | :doc:`nph/asphere (o) <fix_nph_asphere>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`nph/sphere (o) <fix_nph_sphere>` | :doc:`npt (ckio) <fix_nh>` | :doc:`npt/asphere (o) <fix_npt_asphere>` | :doc:`npt/sphere (o) <fix_npt_sphere>` | :doc:`nve (ckio) <fix_nve>` | :doc:`nve/asphere (i) <fix_nve_asphere>` | :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/body <fix_nve_body>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`nve/limit <fix_nve_limit>` | :doc:`nve/line <fix_nve_line>` | :doc:`nve/noforce <fix_nve_noforce>` | :doc:`nve/sphere (o) <fix_nve_sphere>` | :doc:`nve/tri <fix_nve_tri>` | :doc:`nvt (cko) <fix_nh>` | :doc:`nvt/asphere (o) <fix_nvt_asphere>` | :doc:`nvt/sllod (o) <fix_nvt_sllod>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`nvt/sphere (o) <fix_nvt_sphere>` | :doc:`oneway <fix_oneway>` | :doc:`orient/fcc <fix_orient_fcc>` | :doc:`planeforce <fix_planeforce>` | :doc:`poems <fix_poems>` | :doc:`pour <fix_pour>` | :doc:`press/berendsen <fix_press_berendsen>` | :doc:`print <fix_print>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`property/atom <fix_property_atom>` | :doc:`qeq/comb (o) <fix_qeq_comb>` | :doc:`qeq/dynamic <fix_qeq>` | :doc:`qeq/fire <fix_qeq>` | :doc:`qeq/point <fix_qeq>` | :doc:`qeq/shielded <fix_qeq>` | :doc:`qeq/slater <fix_qeq>` | :doc:`rattle <fix_shake>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`reax/bonds <fix_reax_bonds>` | :doc:`recenter <fix_recenter>` | :doc:`restrain <fix_restrain>` | :doc:`rigid (o) <fix_rigid>` | :doc:`rigid/nph (o) <fix_rigid>` | :doc:`rigid/npt (o) <fix_rigid>` | :doc:`rigid/nve (o) <fix_rigid>` | :doc:`rigid/nvt (o) <fix_rigid>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`rigid/small (o) <fix_rigid>` | :doc:`rigid/small/nph <fix_rigid>` | :doc:`rigid/small/npt <fix_rigid>` | :doc:`rigid/small/nve <fix_rigid>` | :doc:`rigid/small/nvt <fix_rigid>` | :doc:`setforce (ck) <fix_setforce>` | :doc:`shake (c) <fix_shake>` | :doc:`spring <fix_spring>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`spring/rg <fix_spring_rg>` | :doc:`spring/self <fix_spring_self>` | :doc:`srd <fix_srd>` | :doc:`store/force <fix_store_force>` | :doc:`store/state <fix_store_state>` | :doc:`temp/berendsen (c) <fix_temp_berendsen>` | :doc:`temp/csld <fix_temp_csvr>` | :doc:`temp/csvr <fix_temp_csvr>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`temp/rescale (c) <fix_temp_rescale>` | :doc:`tfmc <fix_tfmc>` | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`tmd <fix_tmd>` | :doc:`ttm <fix_ttm>` | :doc:`tune/kspace <fix_tune_kspace>` | :doc:`vector <fix_vector>` | :doc:`viscosity <fix_viscosity>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`viscous (c) <fix_viscous>` | :doc:`wall/colloid <fix_wall>` | :doc:`wall/gran <fix_wall_gran>` | :doc:`wall/harmonic <fix_wall>` | :doc:`wall/lj1043 <fix_wall>` | :doc:`wall/lj126 <fix_wall>` | :doc:`wall/lj93 <fix_wall>` | :doc:`wall/piston <fix_wall_piston>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`wall/reflect (k) <fix_wall_reflect>` | :doc:`wall/region <fix_wall_region>` | :doc:`wall/srd <fix_wall_srd>` | | | | | |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
These are additional fix styles in USER packages, which can be used if
:ref:`LAMMPS is built with the appropriate package <start_3>`.
@ -493,7 +493,7 @@ These are additional fix styles in USER packages, which can be used if
+--------------------------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------------------------------------+----------------------------------------------------+------------------------------------------------------+------------------------------------------------------+
| :doc:`adapt/fep <fix_adapt_fep>` | :doc:`addtorque <fix_addtorque>` | :doc:`atc <fix_atc>` | :doc:`ave/correlate/long <fix_ave_correlate_long>` | :doc:`ave/spatial/sphere <fix_ave_spatial_sphere>` | :doc:`colvars <fix_colvars>` |
+--------------------------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------------------------------------+----------------------------------------------------+------------------------------------------------------+------------------------------------------------------+
| :doc:`drude <fix_drude>` | :doc:`drude/transform/direct <fix_drude_transform>` | :doc:`drude/transform/reverse <fix_drude_transform>` | :doc:`eos/cv <fix_eos_vs>` | :doc:`eos/table <fix_eos_table>` | :doc:`gle <fix_gle>` |
| :doc:`drude <fix_drude>` | :doc:`drude/transform/direct <fix_drude_transform>` | :doc:`drude/transform/reverse <fix_drude_transform>` | :doc:`eos/cv <fix_eos_cv>` | :doc:`eos/table <fix_eos_table>` | :doc:`gle <fix_gle>` |
+--------------------------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------------------------------------+----------------------------------------------------+------------------------------------------------------+------------------------------------------------------+
| :doc:`imd <fix_imd>` | :doc:`ipi <fix_ipi>` | :doc:`langevin/drude <fix_langevin_drude>` | :doc:`langevin/eff <fix_langevin_eff>` | :doc:`lb/fluid <fix_lb_fluid>` | :doc:`lb/momentum <fix_lb_momentum>` |
+--------------------------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------------------------------------+----------------------------------------------------+------------------------------------------------------+------------------------------------------------------+
@ -800,13 +800,13 @@ LAMMPS is built with the :doc:`appropriate accelerated package <Section_accelera
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
+--------------------------------------+-----------------------------------+---------------------------------+---------------------------------------+
| :doc:`ewald (o) <kspace_style>` | :doc:`ewald/disp <kspace_style>` | :doc:`msm (o) <kspace_style>` | :doc:`msm/cg (o) <kspace_style>` |
+--------------------------------------+-----------------------------------+---------------------------------+---------------------------------------+
| :doc:`pppm (cgo) <kspace_style>` | :doc:`pppm/cg (o) <kspace_style>` | :doc:`pppm/disp <kspace_style>` | :doc:`pppm/disp/tip4p <kspace_style>` |
+--------------------------------------+-----------------------------------+---------------------------------+---------------------------------------+
| :doc:`pppm/tip4p (o) <kspace_style>` | | | |
+--------------------------------------+-----------------------------------+---------------------------------+---------------------------------------+
+------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
| :doc:`ewald (o) <kspace_style>` | :doc:`ewald/disp <kspace_style>` | :doc:`msm (o) <kspace_style>` | :doc:`msm/cg (o) <kspace_style>` |
+------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
| :doc:`pppm (cgo) <kspace_style>` | :doc:`pppm/cg (o) <kspace_style>` | :doc:`pppm/disp <kspace_style>` | :doc:`pppm/disp/tip4p <kspace_style>` |
+------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
| :doc:`pppm/stagger <kspace_style>` | :doc:`pppm/tip4p (o) <kspace_style>` | | |
+------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
.. _lws: http://lammps.sandia.gov

30
doc/_sources/Section_python.txt
View File

@ -158,8 +158,10 @@ and callbacks to LAMMPS.
To run pure Python code from LAMMPS, you only need to build LAMMPS
with the PYTHON package installed:
make yes-python
make machine
.. parsed-literal::
make yes-python
make machine
Note that this will link LAMMPS with the Python library on your
system, which typically requires several auxiliary system libraries to
@ -189,7 +191,7 @@ Instructions on how to build LAMMPS as a shared library are given in
that is dynamically loadable, which is what Python requires to wrap
LAMMPS. On Linux this is a library file that ends in ".so", not ".a".
>From the src directory, type
From the src directory, type
.. parsed-literal::
@ -202,10 +204,13 @@ load by default. Note that if you are building multiple machine
versions of the shared library, the soft link is always set to the
most recently built version.
If this fails, see :ref:`Section_start 5 <start_5>` for
more details, especially if your LAMMPS build uses auxiliary libraries
like MPI or FFTW which may not be built as shared libraries on your
system.
.. note::
If you are building LAMMPS with an MPI or FFT library or other
auxiliary libraries (used by various packages), then all of these
extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
:ref:`Section_start 5 <start_5>` for more details.
----------
@ -723,17 +728,6 @@ version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 20
----------
.. note::
Currently, the creation of a LAMMPS object from within lammps.py
does not take an MPI communicator as an argument. There should be a
way to do this, so that the LAMMPS instance runs on a subset of
processors if desired, but I don't know how to do it from Pypar. So
for now, it runs with MPI_COMM_WORLD, which is all the processors. If
someone figures out how to do this with one or more of the Python
wrappers for MPI, like Pypar, please let us know and we will amend
these doc pages.
The lines
.. parsed-literal::

3
doc/_sources/fix.txt
View File

@ -231,7 +231,8 @@ of :ref:`this page <cmd_5>`.
* :doc:`press/berendsen <fix_press_berendsen>` - pressure control by Berendsen barostat
* :doc:`print <fix_print>` - print text and variables during a simulation
* :doc:`property/atom <fix_property_atom>` - add customized per-atom values
* :doc:`qeq/comb <fix_qeq_comb>` - charge equilibration for COMB potential :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer :doc:`qeq/point <fix_qeq>` - charge equilibration via point method :doc:`qeq/shielded <fix_qeq>` - charge equilibration via shielded method :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method :doc:`reax/bonds <fix_reax_bonds>` - write out ReaxFF bond information :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
* :doc:`qeq/comb <fix_qeq_comb>` - charge equilibration for COMB potential :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer :doc:`qeq/point <fix_qeq>` - charge equilibration via point method :doc:`qeq/shielded <fix_qeq>` - charge equilibration via shielded method :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method :doc:`rattle <fix_shake>` - RATTLE constraints on bonds and/or angles
* :doc:`reax/bonds <fix_reax_bonds>` - write out ReaxFF bond information :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
* :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
* :doc:`rigid <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NVE integration
* :doc:`rigid/nph <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NPH integration

10
doc/_sources/fix_wall_region.txt
View File

@ -43,9 +43,13 @@ from 1, 2, or 3 faces of the block.
Regions are defined using the :doc:`region <region>` command. Note that
the region volume can be interior or exterior to the bounding surface,
which will determine in which direction the surface interacts with
particles, i.e. the direction of the surface normal. Regions can
either be primitive shapes (block, sphere, cylinder, etc) or
combinations of primitive shapes specified via the *union* or
particles, i.e. the direction of the surface normal. The surface of
the region only exerts forces on particles "inside" the region; if a
particle is "outside" the region it will generate an error, because it
has moved through the wall.
Regions can either be primitive shapes (block, sphere, cylinder, etc)
or combinations of primitive shapes specified via the *union* or
*intersect* region styles. These latter styles can be used to
construct particle containers with complex shapes. Regions can also
change over time via the :doc:`region <region>` command keywords (move)

3
doc/fix.html
View File

@ -337,7 +337,8 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this p
<li><a class="reference internal" href="fix_press_berendsen.html"><em>press/berendsen</em></a> - pressure control by Berendsen barostat</li>
<li><a class="reference internal" href="fix_print.html"><em>print</em></a> - print text and variables during a simulation</li>
<li><a class="reference internal" href="fix_property_atom.html"><em>property/atom</em></a> - add customized per-atom values</li>
<li><a class="reference internal" href="fix_qeq_comb.html"><em>qeq/comb</em></a> - charge equilibration for COMB potential <a class="reference internal" href="fix_qeq.html"><em>qeq/dynamic</em></a> - charge equilibration via dynamic method <a class="reference internal" href="fix_qeq.html"><em>qeq/fire</em></a> - charge equilibration via FIRE minimizer <a class="reference internal" href="fix_qeq.html"><em>qeq/point</em></a> - charge equilibration via point method <a class="reference internal" href="fix_qeq.html"><em>qeq/shielded</em></a> - charge equilibration via shielded method <a class="reference internal" href="fix_qeq.html"><em>qeq/slater</em></a> - charge equilibration via Slater method <a class="reference internal" href="fix_reax_bonds.html"><em>reax/bonds</em></a> - write out ReaxFF bond information <a class="reference internal" href="fix_recenter.html"><em>recenter</em></a> - constrain the center-of-mass position of a group of atoms</li>
<li><a class="reference internal" href="fix_qeq_comb.html"><em>qeq/comb</em></a> - charge equilibration for COMB potential <a class="reference internal" href="fix_qeq.html"><em>qeq/dynamic</em></a> - charge equilibration via dynamic method <a class="reference internal" href="fix_qeq.html"><em>qeq/fire</em></a> - charge equilibration via FIRE minimizer <a class="reference internal" href="fix_qeq.html"><em>qeq/point</em></a> - charge equilibration via point method <a class="reference internal" href="fix_qeq.html"><em>qeq/shielded</em></a> - charge equilibration via shielded method <a class="reference internal" href="fix_qeq.html"><em>qeq/slater</em></a> - charge equilibration via Slater method <a class="reference internal" href="fix_shake.html"><em>rattle</em></a> - RATTLE constraints on bonds and/or angles</li>
<li><a class="reference internal" href="fix_reax_bonds.html"><em>reax/bonds</em></a> - write out ReaxFF bond information <a class="reference internal" href="fix_recenter.html"><em>recenter</em></a> - constrain the center-of-mass position of a group of atoms</li>
<li><a class="reference internal" href="fix_restrain.html"><em>restrain</em></a> - constrain a bond, angle, dihedral</li>
<li><a class="reference internal" href="fix_rigid.html"><em>rigid</em></a> - constrain one or more clusters of atoms to move as a rigid body with NVE integration</li>
<li><a class="reference internal" href="fix_rigid.html"><em>rigid/nph</em></a> - constrain one or more clusters of atoms to move as a rigid body with NPH integration</li>

1
doc/fix.txt
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@ -234,6 +234,7 @@ of "this page"_Section_commands.html#cmd_5.
"qeq/point"_fix_qeq.html - charge equilibration via point method \
"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method \
"qeq/slater"_fix_qeq.html - charge equilibration via Slater method \
"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \
"recenter"_fix_recenter.html - constrain the center-of-mass position \
of a group of atoms

9
doc/fix_wall_region.html
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@ -163,9 +163,12 @@ from 1, 2, or 3 faces of the block.</p>
<p>Regions are defined using the <a class="reference internal" href="region.html"><em>region</em></a> command. Note that
the region volume can be interior or exterior to the bounding surface,
which will determine in which direction the surface interacts with
particles, i.e. the direction of the surface normal. Regions can
either be primitive shapes (block, sphere, cylinder, etc) or
combinations of primitive shapes specified via the <em>union</em> or
particles, i.e. the direction of the surface normal. The surface of
the region only exerts forces on particles &#8220;inside&#8221; the region; if a
particle is &#8220;outside&#8221; the region it will generate an error, because it
has moved through the wall.</p>
<p>Regions can either be primitive shapes (block, sphere, cylinder, etc)
or combinations of primitive shapes specified via the <em>union</em> or
<em>intersect</em> region styles. These latter styles can be used to
construct particle containers with complex shapes. Regions can also
change over time via the <a class="reference internal" href="region.html"><em>region</em></a> command keywords (move)

10
doc/fix_wall_region.txt
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@ -41,9 +41,13 @@ from 1, 2, or 3 faces of the block.
Regions are defined using the "region"_region.html command. Note that
the region volume can be interior or exterior to the bounding surface,
which will determine in which direction the surface interacts with
particles, i.e. the direction of the surface normal. Regions can
either be primitive shapes (block, sphere, cylinder, etc) or
combinations of primitive shapes specified via the {union} or
particles, i.e. the direction of the surface normal. The surface of
the region only exerts forces on particles "inside" the region; if a
particle is "outside" the region it will generate an error, because it
has moved through the wall.
Regions can either be primitive shapes (block, sphere, cylinder, etc)
or combinations of primitive shapes specified via the {union} or
{intersect} region styles. These latter styles can be used to
construct particle containers with complex shapes. Regions can also
change over time via the "region"_region.html command keywords (move)

2
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