diff --git a/doc/Manual.html b/doc/Manual.html index a07f57809c..149dcb1aa6 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -1,492 +1,456 @@ - - - -LAMMPS-ICMS Users Manual - - - - - - - - - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
+ + + + + + + + + LAMMPS Documentation — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+ + + - - -
- -

- -

LAMMPS-ICMS Documentation -

-

6 Nov 2015 version -

-

Version info: -

-

The LAMMPS "version" is the date when it was released, such as 1 May + +

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+ +
+ + + +
+
+
+ +

+

LAMMPS Documentation

+
+

10 Aug 2015 version

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+

Version info:

+

The LAMMPS “version” is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on this page of -the WWW site. Each dated copy of LAMMPS contains all the +feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of -the first page of the manual (this page). -

- -

LAMMPS-ICMS is an experimental variant of LAMMPS with additional -features made available for testing before they will be submitted -for inclusion into the official LAMMPS tree. The source code is -based on the official LAMMPS svn repository mirror at the Institute -for Computational Molecular Science at Temple University and generally -kept up-to-date as much as possible. Sometimes, e.g. when additional -development work is needed to adapt the upstream changes into -LAMMPS-ICMS it can take longer until synchronization; and occasionally, -e.g. in case of the rewrite of the multi-threading support, the -development will be halted except for important bugfixes until -all features of LAMMPS-ICMS fully compatible with the upstream -version or replaced by alternate implementations. -

-
  • If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current version of LAMMPS. - -
  • If you browse the HTML doc pages included in your tarball, they -describe the version you have. - -
  • The PDF file on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don't want -it to be part of every patch. - -
  • There is also a Developer.pdf file in the doc +the first page of the manual (this page).

    +
      +
    • If you browse the HTML doc pages on the LAMMPS WWW site, they always +describe the most current version of LAMMPS.
      • +
    • If you browse the HTML doc pages included in your tarball, they +describe the version you have.
      • +
    • The PDF file on the WWW site or in the tarball is updated +about once per month. This is because it is large, and we don’t want +it to be part of every patch.
      • +
    • There is also a Developer.pdf file in the doc directory, which describes the internal structure and algorithms of -LAMMPS. -
    -

    LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel -Simulator. -

    -

    LAMMPS is a classical molecular dynamics simulation code designed to +LAMMPS.

    • +
+

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel +Simulator.

+

LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL). -

-

The primary developers of LAMMPS are Steve Plimpton, Aidan +under the terms of the GNU Public License (GPL).

+

The primary developers of LAMMPS are Steve Plimpton, Aidan Thompson, and Paul Crozier who can be contacted at -sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at -http://lammps.sandia.gov has more information about the code and its -uses. -

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The LAMMPS documentation is organized into the following sections. If +sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at +http://lammps.sandia.gov has more information about the code and its +uses.

+
+

The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so -we can improve the LAMMPS documentation. -

-

Once you are familiar with LAMMPS, you may want to bookmark this -page at Section_commands.html#comm since -it gives quick access to documentation for all LAMMPS commands. -

-

PDF file of the entire manual, generated by -htmldoc -

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-
  1. -Introduction - - -
  2. Getting started - - -
  3. Commands - - -
  4. Packages - - -
  5. Accelerating LAMMPS performance - - -
  6. How-to discussions - - -
  7. Example problems - -
  8. Performance & scalability - -
  9. Additional tools - -
  10. Modifying & extending LAMMPS - - -
  11. Python interface - - -
  12. Errors - - -
  13. Future and history - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +we can improve the LAMMPS documentation.

+

Once you are familiar with LAMMPS, you may want to bookmark this page at Section_commands.html#comm since +it gives quick access to documentation for all LAMMPS commands.

+

PDF file of the entire manual, generated by +htmldoc

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+ +
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+

Indices and tables

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+ + +
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+ + +
+
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+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/Manual.html.html b/doc/Manual.html.html index c4c0509ea7..6d859f8ad0 100644 --- a/doc/Manual.html.html +++ b/doc/Manual.html.html @@ -3,7 +3,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation

-

31 Oct 2015 version +

17 Nov 2015 version

Version info:

diff --git a/doc/Manual.txt b/doc/Manual.txt index b264cd3799..48e6fc7049 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,7 +1,7 @@ LAMMPS-ICMS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS-ICMS Documentation :c,h3 -6 Nov 2015 version :c,h4 +18 Nov 2015 version :c,h4 Version info: :h4 @@ -100,7 +100,7 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 - :numbered: // comment + :numbered: Section_intro Section_start @@ -120,8 +120,8 @@ it gives quick access to documentation for all LAMMPS commands. Indices and tables ================== -* :ref:`genindex` // comment -* :ref:`search` // comment +* :ref:`genindex` +* :ref:`search` END_RST --> diff --git a/doc/Section_commands.html b/doc/Section_commands.html index dd77321061..60f2a4176e 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -839,9 +839,9 @@ KOKKOS, o = USER-OMP, t = OPT.

+ - - + angle/local @@ -884,45 +884,45 @@ KOKKOS, o = USER-OMP, t = OPT.

msd/chunk msd/nongauss omega/chunk -pair +orientorder/atom -pair/local +pair +pair/local pe (c) pe/atom plasticity/atom pressure (c) -property/atom -property/local +property/atom +property/local property/chunk rdf reduce reduce/region -slice -sna/atom +slice +sna/atom snad/atom snav/atom stress/atom temp (ck) -temp/asphere -temp/com +temp/asphere temp/chunk +temp/com temp/deform temp/partial (c) temp/profile -temp/ramp -temp/region +temp/ramp +temp/region temp/sphere ti torque/chunk vacf -vcm/chunk -voronoi/atom -  +vcm/chunk +voronoi/atom       diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 32348aab1e..098f09a3d9 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -693,6 +693,7 @@ KOKKOS, o = USER-OMP, t = OPT. "msd/chunk"_compute_msd_chunk.html, "msd/nongauss"_compute_msd_nongauss.html, "omega/chunk"_compute_omega_chunk.html, +"orientorder/atom"_compute_orientorder_atom.html, "pair"_compute_pair.html, "pair/local"_compute_pair_local.html, "pe (c)"_compute_pe.html, @@ -712,8 +713,8 @@ KOKKOS, o = USER-OMP, t = OPT. "stress/atom"_compute_stress_atom.html, "temp (ck)"_compute_temp.html, "temp/asphere"_compute_temp_asphere.html, -"temp/com"_compute_temp_com.html, "temp/chunk"_compute_temp_chunk.html, +"temp/com"_compute_temp_com.html, "temp/deform"_compute_temp_deform.html, "temp/partial (c)"_compute_temp_partial.html, "temp/profile"_compute_temp_profile.html, diff --git a/doc/compute.html b/doc/compute.html index 174e3a52e8..33a3179310 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -268,20 +268,18 @@ calculations accessed in the various ways described above.

Each compute style has its own doc page which describes its arguments and what it does. Here is an alphabetic list of compute styles available in LAMMPS. They are also given in more compact form in the -compute section of this page.

+Compute section of this page.

There are also additional compute styles (not listed here) submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the compute section of this page.

-

There are also additional accelerated compute styles (note listed -here) included in the LAMMPS distribution for faster performance on -CPUs and GPUs. The list of these with links to the individual styles -are given in the compute section of this page.