Commit 729ba2cc authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14590 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 70aa37e4

doc/Section_commands.html

+19 −19
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@@ -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>

doc/Section_commands.txt

+3 −1
Original line number Diff line number Diff line
@@ -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)

doc/Section_python.html

+13 −18
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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>

doc/Section_python.txt

+7 −15
Original line number Diff line number Diff line
@@ -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

doc/_sources/Section_commands.txt

+39 −39

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