diff --git a/doc/src/404.rst b/doc/src/404.rst new file mode 100644 index 00000000000..ae3cb5e0370 --- /dev/null +++ b/doc/src/404.rst @@ -0,0 +1,16 @@ +:orphan: + +404 - LAMMPS Document Not Found +=============================== + +.. figure:: JPG/lammps-lost-logo-library.jpg + :figwidth: 50% + :alt: LAMMPS logo cubes scattered around a maze-like library with staircases going in all directions + + *.* + + **We are sorry.** + + We have looked everywhere, but the page you asked for isn't + anywhere in this LAMMPS manual. It may be in reference to a command that + has been renamed or removed, or the link was mistyped. Please try again. diff --git a/doc/src/Build_diskspace.rst b/doc/src/Build_diskspace.rst index 80d83956cb7..cc275459a98 100644 --- a/doc/src/Build_diskspace.rst +++ b/doc/src/Build_diskspace.rst @@ -14,32 +14,44 @@ environments with restricted disk space capacity it may be needed to reduce the storage requirements. Here are some suggestions: - Create a so-called shallow repository by cloning only the last commit - instead of the full project history by using ``git clone git@github.com:lammps/lammps --depth=1 --branch=develop``. - This reduces the downloaded size to about half. With ``--depth=1`` it is not possible to check out different - versions/branches of LAMMPS, using ``--depth=1000`` will make multiple recent versions available at little - extra storage needs (the entire git history had nearly 30,000 commits in fall 2021). - -- Download a tar archive from either the `download section on the LAMMPS homepage `_ - or from the `LAMMPS releases page on GitHub `_ these will not - contain the git history at all. - -- Build LAMMPS without the debug flag (remove ``-g`` from the machine makefile or use ``-DCMAKE_BUILD_TYPE=Release``) - or use the ``strip`` command on the LAMMPS executable when no more debugging would be needed. The strip command - may also be applied to the LAMMPS shared library. The static library may be deleted entirely. - -- Delete compiled object files and libraries after copying the LAMMPS executable to a permanent location. - When using the traditional build process, one may use ``make clean-`` or ``make clean-all`` - to delete object files in the src folder. For CMake based builds, one may use ``make clean`` or just - delete the entire build folder. - -- The folders containing the documentation tree (doc), the examples (examples) are not needed to build and - run LAMMPS and can be safely deleted. Some files in the potentials folder are large and may be deleted, - if not needed. The largest of those files (occupying about 120 MBytes combined) will only be downloaded on - demand, when the corresponding package is installed. - -- When using the CMake build procedure, the compilation can be done on a (local) scratch storage that will not - count toward the quota. A local scratch file system may offer the additional benefit of speeding up creating - object files and linking with libraries compared to a networked file system. Also with CMake (and unlike with - the traditional make) it is possible to compile LAMMPS executables with different settings and packages included - from the same source tree since all the configuration information is stored in the build folder. So it is - not necessary to have multiple copies of LAMMPS. + instead of the full project history by using ``git clone + git@github.com:lammps/lammps --depth=1 --branch=develop``. This + reduces the downloaded size to about half. With ``--depth=1`` it is + not possible to check out different versions/branches of LAMMPS, using + ``--depth=1000`` will make multiple recent versions available at + little extra storage needs (the entire git history had nearly 30,000 + commits in fall 2021). + +- Download a tar archive from either the `download section on the LAMMPS + homepage `_ or from the `LAMMPS + releases page on GitHub `_ + these will not contain the git history at all. + +- Build LAMMPS without the debug flag (remove ``-g`` from the machine + makefile or use ``-DCMAKE_BUILD_TYPE=Release``) or use the ``strip`` + command on the LAMMPS executable when no more debugging would be + needed. The strip command may also be applied to the LAMMPS shared + library. The static library may be deleted entirely. + +- Delete compiled object files and libraries after copying the LAMMPS + executable to a permanent location. When using the traditional build + process, one may use ``make clean-`` or ``make clean-all`` to + delete object files in the src folder. For CMake based builds, one + may use ``make clean`` or just delete the entire build folder. + +- The folders containing the documentation tree (doc), the examples + (examples) are not needed to build and run LAMMPS and can be safely + deleted. Some files in the potentials folder are large and may be + deleted, if not needed. The largest of those files (occupying about + 120 MBytes combined) will only be downloaded on demand, when the + corresponding package is installed. + +- When using the CMake build procedure, the compilation can be done on a + (local) scratch storage that will not count toward the quota. A local + scratch file system may offer the additional benefit of speeding up + creating object files and linking with libraries compared to a + networked file system. Also with CMake (and unlike with the + traditional make) it is possible to compile LAMMPS executables with + different settings and packages included from the same source tree + since all the configuration information is stored in the build folder. + So it is not necessary to have multiple copies of the LAMMPS sources. diff --git a/doc/src/Errors_bugs.rst b/doc/src/Errors_bugs.rst index ed60999b5fd..31cbb293d89 100644 --- a/doc/src/Errors_bugs.rst +++ b/doc/src/Errors_bugs.rst @@ -4,11 +4,9 @@ Reporting bugs If you are confident that you have found a bug in LAMMPS, please follow the steps outlined below: - * Check the `New features and bug fixes - `_ section of the `LAMMPS WWW site - `_ or the - `GitHub Releases page `_ to - see if the bug has already been addressed in a patch release. + * Check the `GitHub Releases page + `_ to see if the bug has + already been addressed in a release. * Check that your issue can be reproduced with the latest development version of LAMMPS. * Check the manual carefully to verify that the unexpected behavior you diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index ea560b0c7b9..d0b631bb378 100644 --- a/doc/src/Errors_common.rst +++ b/doc/src/Errors_common.rst @@ -57,7 +57,7 @@ sometimes be confusing or need additional explanations. do, but very strictly applies the syntax as described in the documentation. If you run into errors that LAMMPS does not catch that you think it should flag, please send an email to the `developers - `_ or create a new topic on the + `_ or create a new topic on the dedicated `MatSci forum section `_. - If you get an error message about an invalid command in your input diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 596ed594265..5bdfbac9441 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -2115,7 +2115,7 @@ Please also see the page with :doc:`Warning messages `. *Fix orient/fcc found self twice* The neighbor lists used by fix orient/fcc are messed up. If this error occurs, it is likely a bug, so send an email to the - `developers `_. + `developers `_. *Fix peri neigh does not exist* Somehow a fix that the pair style defines has been deleted. diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 322b11f1abb..697d20e6793 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -18,7 +18,7 @@ files and image files. If you uncomment the :doc:`dump ` command in the input script, a text dump file will be produced, which can be animated by various -`visualization programs `_. +`visualization programs `_. If you uncomment the :doc:`dump image ` command in the input script, and assuming you have built LAMMPS with a JPG library, JPG @@ -26,8 +26,8 @@ snapshot images will be produced when the simulation runs. They can be quickly post-processed into a movie using commands described on the :doc:`dump image ` doc page. -Animations of many of the examples can be viewed on the Movies section -of the `LAMMPS website `_. +Animations of many of the examples can be viewed on the Examples gallery section +of the `LAMMPS website `_. There are two kinds of subdirectories in the examples folder. Lower case named directories contain one or a few simple, quick-to-run @@ -195,8 +195,8 @@ Here is how you can run and visualize one of the sample problems: Running the simulation produces the files *dump.indent* and *log.lammps*\ . You can visualize the dump file of snapshots with a -variety of third-party tools highlighted on the -`Visualization `_ page of the LAMMPS +variety of third-party tools highlighted on the `Visualization +`_ page of the LAMMPS website. If you uncomment the :doc:`dump image ` line(s) in the input diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index 38848d6f390..f3ffebd02ab 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -1,13 +1,11 @@ Howto discussions ***************** -These doc pages describe how to perform various tasks with LAMMPS, -both for users and developers. The -`glossary `_ website page also lists MD -terminology, with links to corresponding LAMMPS manual pages. The -example input scripts included in the ``examples`` directory of the LAMMPS -source code distribution and highlighted on the :doc:`Examples` page -also show how to set up and run various kinds of simulations. +These doc pages describe how to perform various tasks with LAMMPS, both +for users and developers. The example input scripts included in the +``examples`` directory of the LAMMPS source code distribution and +highlighted on the :doc:`Examples` page also show how to set up and run +various kinds of simulations. General howto ============= diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index d400ec03678..87795a6f2d6 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -240,7 +240,7 @@ converted into the ClassII-xe functional form. The conversion from ClassII to ClassII-xe functional form requires reparameterizing the cross-terms, which can be accomplished via the LUNAR tool, for which a link is provided on the `Pre/Post processing -`_ page. LUNAR can be used to +`_ page. LUNAR can be used to build a model from scratch in either COMPASS or PCFF (using its 'atom_typing' and 'all2lmp' modules) and then convert that model to COMPASS-xe or PCFF-xe (using its 'auto_morse_bond_update' module). To diff --git a/doc/src/Howto_bpm.rst b/doc/src/Howto_bpm.rst index 4f4227685b6..cbf20941143 100644 --- a/doc/src/Howto_bpm.rst +++ b/doc/src/Howto_bpm.rst @@ -22,7 +22,7 @@ for simulations of the fragmentation of an impacted plate and the pouring of extended, elastic bodies. See :ref:`(Clemmer) ` for more general information on the approach and the LAMMPS implementation. Example movies illustrating some of these capabilities are found at -https://www.lammps.org/movies.html#bpmpackage. +https://www.lammps.org/gallery/bpmpackage/. ---------- diff --git a/doc/src/Howto_peri.rst b/doc/src/Howto_peri.rst index 52ce4fbccff..8a4b067348d 100644 --- a/doc/src/Howto_peri.rst +++ b/doc/src/Howto_peri.rst @@ -871,15 +871,12 @@ Bugs The user is cautioned that this code is a beta release. If you are confident that you have found a bug in the peridynamic module, please report it in a `GitHub Issue ` -or send an email to the LAMMPS developers. First, check the `New -features and bug fixes `_ section of -the LAMMPS website site to see if the bug has already been reported or -fixed. If not, the most useful thing you can do for us is to isolate the -problem. Run it on the smallest number of atoms and fewest number of -processors and with the simplest input script that reproduces the -bug. In your message, describe the problem and any ideas you have as to -what is causing it or where in the code the problem might be. We'll -request your input script and data files if necessary. +or send an email to the LAMMPS developers. Run it on the smallest +number of atoms and fewest number of processors and with the simplest +input script that reproduces the bug. In your message, describe the +problem and any ideas you have as to what is causing it or where in the +code the problem might be. We'll request your input script and data +files if necessary. Modifying and Extending the Peridynamic Module ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/doc/src/Howto_rheo.rst b/doc/src/Howto_rheo.rst index 2407fd484d0..d1e87d0733b 100644 --- a/doc/src/Howto_rheo.rst +++ b/doc/src/Howto_rheo.rst @@ -17,7 +17,7 @@ into distinct classes to simplify the development of new integration schemes which can call these calculations. Additional numerical details can be found in :ref:`(Palermo) ` and :ref:`(Clemmer) `. Example movies illustrating some of these capabilities are found at -https://www.lammps.org/movies.html#rheopackage. +https://www.lammps.org/gallery/rheopackage/. Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package ` package is likely better suited for your application. It has fewer advanced diff --git a/doc/src/Howto_viz.rst b/doc/src/Howto_viz.rst index 6b504f5fdb9..d3770abf933 100644 --- a/doc/src/Howto_viz.rst +++ b/doc/src/Howto_viz.rst @@ -8,7 +8,7 @@ LAMMPS snapshots are created by the :doc:`dump ` command, which can create files in several formats. The native LAMMPS dump format is a text file (see :lammps:`dump atom` or :lammps:`dump custom`) which can be visualized by `several visualization tools -`_ for MD simulation trajectories. +`_ for MD simulation trajectories. `OVITO `_ and `VMD `_ seem to be the most popular choices among them. diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index c60322cc85b..fedb148e3f4 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -96,11 +96,12 @@ this is as follows. git checkout tagID Stable versions and what tagID to use for a particular stable version -are discussed on `this page `_. -Note that this command will print some warnings, because in order to get -back to the latest revision and to be able to update with ``git pull`` -again, you will need to do ``git checkout release`` (or -check out any other desired branch) first. +can be looked up on `GitHub releases pagee +`_. Note that this command +will print some warnings, because in order to get back to the latest +revision and to be able to update with ``git pull`` again, you will need +to do ``git checkout release`` (or check out any other desired branch) +first. Once you have updated your local files with a ``git pull`` (or ``git checkout``), you still need to re-build LAMMPS if any source files have diff --git a/doc/src/Install_tarball.rst b/doc/src/Install_tarball.rst index dcde2d848ed..8addf575c64 100644 --- a/doc/src/Install_tarball.rst +++ b/doc/src/Install_tarball.rst @@ -4,18 +4,18 @@ Download source and documentation as a tarball You can download a current LAMMPS tarball from the `download page `_ of the `LAMMPS website `_ or from GitHub (see below). -.. _download: https://www.lammps.org/download.html -.. _bug: https://www.lammps.org/bug.html +.. _download: https://www.lammps.org/download/ .. _older: https://download.lammps.org/tars/ .. _lws: https://www.lammps.org +.. _git: https://github.com/lammps/lammps/releases You have two choices of tarballs, either the most recent stable release or the most recent feature release. Stable releases occur a few times per year, and undergo more testing before release. Also, between stable releases bug fixes from the feature releases are back-ported and the tarball occasionally updated. Feature releases occur every 4 to 8 -weeks. The new contents in all feature releases are listed on the `bug -and feature page `_ of the LAMMPS homepage. +weeks. The new contents in all feature releases are listed in the +`release notes `_ of the LAMMPS GitHub page. Tarballs of older LAMMPS versions can also be downloaded from `this page `_. @@ -35,18 +35,7 @@ e.g. ``lammps-28Mar23``. ---------- -You can also download a compressed tar or zip archives from the +You can also download the same compressed tar archives from the "Assets" sections of the `LAMMPS GitHub releases site `_. -The file name will be lammps-.zip which can be unzipped -with the following command, to create a lammps- directory: - -.. code-block:: bash - unzip lammps*.zip - -This version corresponds to the selected LAMMPS feature or stable -release (as indicated by the matching git tag) and will only contain the -source code and no pre-built documentation. - -.. _git: https://github.com/lammps/lammps/releases diff --git a/doc/src/Intro_authors.rst b/doc/src/Intro_authors.rst index 7f9cba350a2..ee1a39b1ba0 100644 --- a/doc/src/Intro_authors.rst +++ b/doc/src/Intro_authors.rst @@ -8,7 +8,7 @@ send an email to all of them at this address: "developers at lammps.org". General questions about LAMMPS should be posted in the `LAMMPS forum on MatSci `_. -.. We need to keep this file in sync with https://www.lammps.org/authors.html +.. We need to keep this file in sync with https://www.lammps.org/about/developers/ .. raw:: latex @@ -90,7 +90,7 @@ Fisher Scientific. ---------- -The `Authors page `_ of the +The `Contributors page `_ of the `LAMMPS website `_ has a comprehensive list of all the individuals who have contributed code for a new feature or command or tool to LAMMPS. @@ -119,7 +119,8 @@ general-purpose as it is without their expertise and efforts. ---------- -As discussed on the `History page `_ of the website, LAMMPS +As discussed on the `History page +`_ of the website, LAMMPS originated as a cooperative project between DOE labs and industrial partners. Folks involved in the design and testing of the original version of LAMMPS were the following: diff --git a/doc/src/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst index 6fe94c2f858..137c952d71d 100644 --- a/doc/src/Intro_nonfeatures.rst +++ b/doc/src/Intro_nonfeatures.rst @@ -34,7 +34,7 @@ Here are suggestions on how to perform these tasks: `_. Also, there are several external wrappers or GUI front ends that are mentioned on the `Pre-/post-processing tools page - `_ of the LAMMPS homepage. + `_ of the LAMMPS homepage. * **Builder:** Several pre-processing tools are packaged with LAMMPS. Some of them convert input files in formats produced by other MD codes @@ -44,7 +44,7 @@ Here are suggestions on how to perform these tasks: a true molecular builder that will generate complex molecular models. See the :doc:`Tools ` page for details on tools packaged with LAMMPS. The `Pre-/post-processing tools page - `_ of the LAMMPS homepage + `_ of the LAMMPS homepage describes a variety of third party tools for this task. Furthermore, some internal LAMMPS commands allow reconstructing, or selectively adding topology information, as well as provide the option to insert molecule @@ -77,7 +77,7 @@ Here are suggestions on how to perform these tasks: into other programs. See the :doc:`Tools ` page for details on these various options. - The `Pre-/post-processing page `_ + The `Pre-/post-processing page `_ on the LAMMPS homepage lists some external packages for analysis of MD simulation data, including data produced by LAMMPS. @@ -94,8 +94,9 @@ Here are suggestions on how to perform these tasks: For high-quality, interactive visualization, there are many excellent and free tools available. See the `Visualization Tools - `_ page of the LAMMPS website for - visualization packages that can process LAMMPS output data. + `_ page of the LAMMPS + website for visualization packages that can process LAMMPS output + data. * **Plotting:** See the next bullet about Pizza.py as well as the :doc:`Python ` page for examples of plotting LAMMPS diff --git a/doc/src/Intro_overview.rst b/doc/src/Intro_overview.rst index 9511873f4c0..40a0e76e4de 100644 --- a/doc/src/Intro_overview.rst +++ b/doc/src/Intro_overview.rst @@ -23,7 +23,7 @@ acceleration. LAMMPS is written in C++ and currently requires a compiler that is at least compatible with the C++-11 standard. Earlier versions were written in F77, F90, and C++-98. See the `History page -`_ of the website for details. All +`_ of the website for details. All versions can be downloaded as source code from the `LAMMPS website `_. diff --git a/doc/src/Intro_website.rst b/doc/src/Intro_website.rst index ff0ec9e72d7..a37f3a8e86c 100644 --- a/doc/src/Intro_website.rst +++ b/doc/src/Intro_website.rst @@ -9,23 +9,21 @@ available online are listed below. * `LAMMPS source code repository on GitHub `_ * `LAMMPS plugins source code repository on GitHub `_ -* `LAMMPS forum on matsci.org `_ +* `LAMMPS forum on matsci.org `_ -* `Recent bug fixes and new features `_ -* `Download info `_ +* `Download info `_ -* `Glossary of terms relevant to LAMMPS `_ -* `LAMMPS highlights with images `_ -* `LAMMPS highlights with movies `_ -* `Workshops `_ -* `Tutorials `_ +* `LAMMPS highlights with journal covers `_ +* `LAMMPS highlights with images `_ +* `LAMMPS highlights with movies `_ +* `Workshops `_ +* `Tutorials `_ -* `Pre- and post-processing tools for LAMMPS `_ -* `Other software usable with LAMMPS `_ -* `Viz tools usable with LAMMPS `_ +* `Pre- and post-processing tools for LAMMPS `_ +* `Other software usable with LAMMPS `_ +* `Viz tools usable with LAMMPS `_ -* `Benchmark performance `_ -* `Publications that have cited LAMMPS `_ -* `Authors of LAMMPS `_ -* `History of LAMMPS development `_ -* `Funding for LAMMPS `_ +* `Publications that have cited LAMMPS `_ +* `Authors of LAMMPS `_ +* `History of LAMMPS development `_ +* `Funding for LAMMPS `_ diff --git a/doc/src/JPG/lammps-lost-logo-library.jpg b/doc/src/JPG/lammps-lost-logo-library.jpg new file mode 100644 index 00000000000..8ac42a2d3be Binary files /dev/null and b/doc/src/JPG/lammps-lost-logo-library.jpg differ diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index 1bf7ae11b78..ff7c11d43a1 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -23,7 +23,7 @@ distributed under the terms of the GNU Public License Version 2 (GPLv2). The `LAMMPS website `_ has a variety of information about the code. It includes links to an online version of this manual, an -`online forum `_ where users can post +`online forum `_ where users can post questions and discuss LAMMPS, and a `GitHub site `_ where all LAMMPS development is coordinated. diff --git a/doc/src/Manual_version.rst b/doc/src/Manual_version.rst index aec51f367b0..24bc0cae280 100644 --- a/doc/src/Manual_version.rst +++ b/doc/src/Manual_version.rst @@ -67,10 +67,9 @@ When a sufficient number of new features and updates have accumulated of automated tests, we release it as a *feature release*, which are currently made every 4 to 8 weeks. The *release* branch of the git repository is updated with every such *feature release* and a tag in the -format ``patch_1May2014`` is added. A summary of the most important -changes of these releases for the current year are posted on `this -website page `_. More detailed release -notes are `available on GitHub `_. +format ``patch_1May2014`` is added. Release notes with the most +important changes of these releases are `available on GitHub +`_. Stable Releases """"""""""""""" diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index 78d88ee69dd..f49fd86a0fa 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -37,7 +37,7 @@ an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS you are working on. Only discussions related to LAMMPS development are tolerated in that work space, so this is **NOT** for people looking for help with compiling, installing, or using LAMMPS. Please post a -message to the `LAMMPS forum `_ for +message to the `LAMMPS forum `_ for those purposes. @@ -73,7 +73,7 @@ Tutorial ` page for instructions on how to submit your changes or new files through a GitHub pull request. If you are unable or unwilling to submit via GitHub yourself, you may also send patch files or full files to the `LAMMPS developers -`_ and ask them to submit a pull +`_ and ask them to submit a pull request on GitHub on your behalf. If this is the case, create a gzipped tar file of all new or changed files or a corresponding patch file using 'diff -u' or 'diff -c' format and compress it with gzip. @@ -88,10 +88,10 @@ External contributions If you prefer to do so, you can also develop and support your add-on feature **without** having it included in the LAMMPS distribution, for example as a download from a website of your own. See the `External -LAMMPS packages and tools `_ +LAMMPS packages and tools `_ page of the LAMMPS website for examples of groups that do this. We are happy to advertise your package and website from that page. -Simply email the `developers `_ +Simply email the `developers `_ with info about your package, and we will post it there. We recommend naming external packages USER-\ so they can be easily distinguished from packages in the LAMMPS distribution which do not diff --git a/doc/src/Packages.rst b/doc/src/Packages.rst index 0fcd544e784..ddbcc35192a 100644 --- a/doc/src/Packages.rst +++ b/doc/src/Packages.rst @@ -226,7 +226,7 @@ whether an extra library is needed to build and use the package: * - :ref:`GPU ` - GPU-enabled styles - :doc:`Section gpu ` - - `Benchmarks `_ + - n/a - int * - :ref:`GRANULAR ` - granular systems @@ -251,7 +251,7 @@ whether an extra library is needed to build and use the package: * - :ref:`INTEL ` - optimized Intel CPU styles - :doc:`Speed intel ` - - `Benchmarks `_ + - n/a - no * - :ref:`INTERLAYER ` - Inter-layer pair potentials @@ -266,7 +266,7 @@ whether an extra library is needed to build and use the package: * - :ref:`KOKKOS ` - Kokkos-enabled styles - :doc:`Speed kokkos ` - - `Benchmarks `_ + - n/a - no * - :ref:`KSPACE ` - long-range Coulombic solvers @@ -401,12 +401,12 @@ whether an extra library is needed to build and use the package: * - :ref:`OPENMP ` - OpenMP-enabled styles - :doc:`Speed omp ` - - `Benchmarks `_ + - n/a - no * - :ref:`OPT ` - optimized pair styles - :doc:`Speed opt ` - - `Benchmarks `_ + - n/a - no * - :ref:`ORIENT ` - fixes for orientation depended forces diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index cbfb6257c57..8209024288e 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -272,8 +272,8 @@ including ellipsoids, granular superellipsoids, 2d lines, and 3d triangles. * `doc/PDF/pair_resquared_extra.pdf `_ * ``examples/ASPHERE`` * ``examples/ellipse`` -* https://www.lammps.org/movies.html#line -* https://www.lammps.org/movies.html#tri +* https://www.lammps.org/examples/line/ +* https://www.lammps.org/examples/tri/ ---------- @@ -392,7 +392,7 @@ models for mesoscale simulations of solids and fracture. See the * :doc:`compute nbond/atom ` * :doc:`fix nve/bpm/sphere ` * :doc:`pair_style bpm/spring ` -* https://www.lammps.org/movies.html#bpmpackage +* https://www.lammps.org/gallery/bpmpackage/ * ``examples/bpm`` ---------- @@ -478,7 +478,7 @@ simulation of biological or soft material systems. * :doc:`pair_style lj/spica/\* ` * :doc:`angle_style spica ` * ``examples/PACKAGES/cgspica`` -* https://www.lammps.org/pictures.html#cg +* https://www.lammps.org/gallery/cg/ * https://www.spica-ff.org/ ---------- @@ -909,7 +909,7 @@ tools/eff; see its README file. * ``examples/PACKAGES/eff`` * tools/eff/README * tools/eff -* https://www.lammps.org/movies.html#eff +* https://www.lammps.org/gallery/eff/ ------------------- @@ -1112,7 +1112,6 @@ This package has :ref:`specific installation instructions ` on the * :doc:`package gpu ` * :doc:`Commands ` pages (:doc:`pair `, :doc:`kspace `) for styles followed by (g) -* `Benchmarks page `_ of website ---------- @@ -1171,11 +1170,11 @@ potentials. * ``examples/granregion`` * ``examples/pour`` * bench/in.chute -* https://www.lammps.org/pictures.html#jamming -* https://www.lammps.org/movies.html#hopper -* https://www.lammps.org/movies.html#dem -* https://www.lammps.org/movies.html#brazil -* https://www.lammps.org/movies.html#granregion +* https://www.lammps.org/gallery/jamming/ +* https://www.lammps.org/gallery/hopper/ +* https://www.lammps.org/gallery/dem/ +* https://www.lammps.org/gallery/brazil/ +* https://www.lammps.org/gallery/granregion/ ---------- @@ -1283,7 +1282,6 @@ This package has :ref:`specific installation instructions ` on the :doc:` * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (i) * ``src/INTEL/TEST`` -* `Benchmarks page `_ of website ---------- @@ -1421,7 +1419,6 @@ This package has :ref:`specific installation instructions ` on the :doc: * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (k) -* `Benchmarks page `_ of website ---------- @@ -1594,7 +1591,7 @@ Waltham, MA, USA) * :doc:`fix nve/manifold/rattle ` * :doc:`fix nvt/manifold/rattle ` * ``examples/PACKAGES/manifold`` -* https://www.lammps.org/movies.html#manifold +* https://www.lammps.org/gallery/manifold/ ---------- @@ -1686,7 +1683,7 @@ or similar processes in conjunction with molecular dynamics (MD). * :doc:`fix tfmc ` * :doc:`fix widom ` * :doc:`pair_style dsmc ` -* https://www.lammps.org/movies.html#gcmc +* https://www.lammps.org/gallery/gcmc/ ---------- @@ -2353,7 +2350,6 @@ the :doc:`Build extras ` page. * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (o) -* `Benchmarks page `_ of website ---------- @@ -2387,7 +2383,6 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * :doc:`OPT package ` * :doc:`Section 4.2 -sf opt ` * Search the :doc:`pair style ` page for styles followed by (t) -* `Benchmarks page `_ of website .. _PKG-ORIENT: @@ -2436,7 +2431,7 @@ Foster (UTSA). * :doc:`compute damage/atom ` * :doc:`compute plasticity/atom ` * ``examples/peri`` -* https://www.lammps.org/movies.html#impact +* https://www.lammps.org/gallery/impact/ ---------- @@ -2809,7 +2804,7 @@ Thomas C. O'Connor (Carnegie Mellon University) * :doc:`fix rheo/viscosity ` * :doc:`pair_style rheo ` * :doc:`pair_style rheo/solid ` -* https://www.lammps.org/movies.html#rheopackage +* https://www.lammps.org/gallery/rheopackage/ * ``examples/rheo`` ---------- @@ -2836,8 +2831,8 @@ Also several computes which calculate properties of rigid bodies. * ``examples/ASPHERE`` * ``examples/rigid`` * bench/in.rhodo -* https://www.lammps.org/movies.html#box -* https://www.lammps.org/movies.html#star +* https://www.lammps.org/examples/box/ +* https://www.lammps.org/examples/star/ ---------- @@ -2957,7 +2952,7 @@ Dynamics, Ernst Mach Institute, Germany). * ``src/SPH/README`` * `doc/PDF/SPH_LAMMPS_userguide.pdf `_ * ``examples/PACKAGES/sph`` -* https://www.lammps.org/movies.html#sph +* https://www.lammps.org/gallery/sph/ .. note:: @@ -3022,9 +3017,9 @@ colloidal particles. * :doc:`fix wall/srd ` * ``examples/srd`` * ``examples/ASPHERE`` -* https://www.lammps.org/movies.html#tri -* https://www.lammps.org/movies.html#line -* https://www.lammps.org/movies.html#poly +* https://www.lammps.org/examples/tri/ +* https://www.lammps.org/examples/line/ +* https://www.lammps.org/gallery/poly/ ---------- diff --git a/doc/src/Speed.rst b/doc/src/Speed.rst index 916d98a2c21..c85711cb562 100644 --- a/doc/src/Speed.rst +++ b/doc/src/Speed.rst @@ -11,12 +11,14 @@ speed-up a simulation. The second is to use one of the several accelerator packages provided with LAMMPS that contain code optimized for certain kinds of hardware, including multicore CPUs and GPUs. -The `Benchmark page `_ of the LAMMPS -website gives performance results for the various accelerator -packages discussed on the :doc:`Accelerator packages ` -page, for several of the standard LAMMPS benchmark problems, as a -function of problem size and number of compute nodes, on different -hardware platforms. +.. + FIXME: + The `Benchmark page `_ of the LAMMPS + website gives performance results for the various accelerator + packages discussed on the :doc:`Accelerator packages ` + page, for several of the standard LAMMPS benchmark problems, as a + function of problem size and number of compute nodes, on different + hardware platforms. .. toctree:: :maxdepth: 1 diff --git a/doc/src/Speed_bench.rst b/doc/src/Speed_bench.rst index 96bcf93ba24..f85f11c08f8 100644 --- a/doc/src/Speed_bench.rst +++ b/doc/src/Speed_bench.rst @@ -1,58 +1,58 @@ Benchmarks ========== -Current LAMMPS performance is discussed on the `Benchmarks page `_ of the `LAMMPS website `_ -where timings and parallel efficiency are listed. The page has -several sections, which are briefly described below: +.. + FIXME: + Current LAMMPS performance is discussed on the `Benchmarks page `_ of the `LAMMPS website `_ + where timings and parallel efficiency are listed. The page has + several sections, which are briefly described below: -* CPU performance on 5 standard problems, strong and weak scaling -* GPU performance on same and related problems -* Comparison of cost of interatomic potentials -* Performance of huge, billion-atom problems + * CPU performance on 5 standard problems, strong and weak scaling + * GPU performance on same and related problems + * Comparison of cost of interatomic potentials + * Performance of huge, billion-atom problems -The 5 standard problems are as follow: + The 5 standard problems are as follow: -#. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 - neighbors per atom), NVE integration -#. Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ - pairwise interactions with a :math:`2^{\frac{1}{6}}` sigma cutoff (5 neighbors per - atom), NVE integration -#. EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45 - neighbors per atom), NVE integration -#. Chute = granular chute flow, frictional history potential with 1.1 - sigma cutoff (7 neighbors per atom), NVE integration -#. Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force - field with a 10 Angstrom LJ cutoff (440 neighbors per atom), - particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT - integration + #. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 + neighbors per atom), NVE integration + #. Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ + pairwise interactions with a :math:`2^{\frac{1}{6}}` sigma cutoff (5 neighbors per + atom), NVE integration + #. EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45 + neighbors per atom), NVE integration + #. Chute = granular chute flow, frictional history potential with 1.1 + sigma cutoff (7 neighbors per atom), NVE integration + #. Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force + field with a 10 Angstrom LJ cutoff (440 neighbors per atom), + particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT + integration -Input files for these 5 problems are provided in the bench directory -of the LAMMPS distribution. Each has 32,000 atoms and runs for 100 -timesteps. The size of the problem (number of atoms) can be varied -using command-line switches as described in the ``bench/README`` file. -This is an easy way to test performance and either strong or weak -scalability on your machine. + Input files for these 5 problems are provided in the bench directory + of the LAMMPS distribution. Each has 32,000 atoms and runs for 100 + timesteps. The size of the problem (number of atoms) can be varied + using command-line switches as described in the ``bench/README`` file. + This is an easy way to test performance and either strong or weak + scalability on your machine. -The bench directory includes a few ``log.*`` files that show performance -of these 5 problems on 1 or 4 cores of Linux desktop. The ``bench/FERMI`` -and ``bench/KEPLER`` directories have input files and scripts and instructions -for running the same (or similar) problems using OpenMP or GPU or Xeon -Phi acceleration options. See the ``README`` files in those directories and the -:doc:`Accelerator packages ` pages for instructions on how -to build LAMMPS and run on that kind of hardware. + The bench directory includes a few ``log.*`` files that show performance + of these 5 problems on 1 or 4 cores of Linux desktop. The ``bench/FERMI`` + and ``bench/KEPLER`` directories have input files and scripts and instructions + for running the same (or similar) problems using OpenMP or GPU or Xeon + Phi acceleration options. See the ``README`` files in those directories and the + :doc:`Accelerator packages ` pages for instructions on how + to build LAMMPS and run on that kind of hardware. -The ``bench/POTENTIALS`` directory has input files which correspond to the -table of results on the -`Potentials `_ section of -the Benchmarks web page. So you can also run those test problems on -your machine. + The ``bench/POTENTIALS`` directory has input files which correspond to the + table of results on the + `Potentials `_ section of + the Benchmarks web page. So you can also run those test problems on + your machine. -The `billion-atom `_ section -of the Benchmarks web page has performance data for very large -benchmark runs of simple Lennard-Jones (LJ) models, which use the -``bench/in.lj`` input script. - ----------- + The `billion-atom `_ section + of the Benchmarks web page has performance data for very large + benchmark runs of simple Lennard-Jones (LJ) models, which use the + ``bench/in.lj`` input script. For all the benchmarks, a useful metric is the CPU cost per atom per timestep. Since performance scales roughly linearly with problem size diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index eccc9c8d76d..c24794dfa80 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -163,9 +163,11 @@ in OpenCL mode on CPUs (which uses vectorization and multithreading) is usually resulting in inferior performance compared to using LAMMPS' native threading and vectorization support in the OPENMP and INTEL packages. -See the `Benchmark page `_ of the -LAMMPS website for performance of the GPU package on various -hardware, including the Titan HPC platform at ORNL. +.. + FIXME: + See the `Benchmark page `_ of the + LAMMPS website for performance of the GPU package on various + hardware, including the Titan HPC platform at ORNL. You should also experiment with how many MPI tasks per GPU to use to give the best performance for your problem and machine. This is also diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index 12125e5eaab..3818243dbf1 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -537,9 +537,11 @@ Generally speaking, the following rules of thumb apply: MPI ranks in order to avoid competing with the MPS daemon for CPU resources. -See the `Benchmark page `_ of the -LAMMPS website for performance of the KOKKOS package on different -hardware. +.. + FIXME: + See the `Benchmark page `_ of the + LAMMPS website for performance of the KOKKOS package on different + hardware. Advanced Kokkos options """"""""""""""""""""""" diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index afd9e3f31f8..c1b88b3ea45 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -114,11 +114,13 @@ packages. option for the KOKKOS package. Or the OpenCL, HIP, or CUDA option for the GPU package. -As mentioned above, the `Benchmark page -`_ of the LAMMPS website gives -performance results for the various accelerator packages for several of -the standard LAMMPS benchmark problems, as a function of problem size -and number of compute nodes, on different hardware platforms. +.. + FIXME: + As mentioned above, the `Benchmark page + `_ of the LAMMPS website gives + performance results for the various accelerator packages for several of + the standard LAMMPS benchmark problems, as a function of problem size + and number of compute nodes, on different hardware platforms. Here is a brief summary of what the various packages provide. Details are in the individual accelerator sections. diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index ff3f32e382c..4e447e700a8 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -6,8 +6,8 @@ molecular dynamics computations. Additional pre- and post-processing steps are often necessary to setup and analyze a simulation. A list of such tools can be found on the `LAMMPS webpage `_ at these links: -* `Pre/Post processing `_ -* `External LAMMPS packages & tools `_ +* `Pre/Post processing `_ +* `External LAMMPS packages & tools `_ * `Pizza.py toolkit `_ The last link for `Pizza.py `_ is a Python-based tool developed at diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 03fec0a65ba..296cf96cb06 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -67,8 +67,8 @@ non-granular particles and simpler wall geometries, respectively. Here are snapshots of example models using this command. Corresponding input scripts can be found in examples/granregion. Movies of these -simulations are `here on the Movies page `_ -of the LAMMPS website. +simulations are `here on the Movies page +`_ of the LAMMPS website. .. |wallgran1| image:: img/gran_funnel.png :width: 48% diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt index 2975c974222..d907e295b79 100644 --- a/doc/utils/requirements.txt +++ b/doc/utils/requirements.txt @@ -3,6 +3,7 @@ sphinxcontrib-spelling sphinxcontrib-jquery sphinx-design sphinx-sitemap +sphinx-notfound-page git+https://github.com/akohlmey/sphinx-fortran@parallel-read sphinx-tabs>=3.4.1 breathe diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html index 96ee0286bd1..e906ed83b2c 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html +++ b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html @@ -57,7 +57,7 @@ {%- elif show_source and has_source and sourcename %} {{ _('View page source') }} {%- endif %} - LAMMPS Homepage | Commands + LAMMPS Homepage | Commands {%- endif %} {%- endblock %} diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/layout.html b/doc/utils/sphinx-config/_themes/lammps_theme/layout.html index 327f42aa9a9..40920707730 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/layout.html +++ b/doc/utils/sphinx-config/_themes/lammps_theme/layout.html @@ -154,7 +154,7 @@ {%- endif %} {%- endblock %} {# LAMMPS customization #} -
Index
+
Index
{%- endblock %} diff --git a/doc/utils/sphinx-config/conf.py.in b/doc/utils/sphinx-config/conf.py.in index 534860c4703..c84ae233968 100644 --- a/doc/utils/sphinx-config/conf.py.in +++ b/doc/utils/sphinx-config/conf.py.in @@ -58,7 +58,8 @@ extensions = [ 'tab_or_note', 'breathe', 'sphinx_design', - 'sphinx_sitemap' + 'sphinx_sitemap', + 'notfound.extension' ] images_config = { @@ -306,6 +307,14 @@ html_permalinks = True # about as having a canonical URLs where it chooses a different one. html_baseurl = 'https://docs.lammps.org/' +# Settings for the sphinx-notfound-page extension. The web server delivers +# the generated 404.html page in place of *any* missing URL, including URLs +# in subdirectories, so all links on the 404 page must be absolute (rooted +# at html_baseurl) instead of relative. The page content is doc/src/404.rst. +# Do not advertise the 404 page in the sitemap. +notfound_urls_prefix = '/' +sitemap_excludes = ['404.html'] + if 'epub' in sys.argv: html_math_renderer = 'imgmath' else: diff --git a/examples/GRAPHICS/hbond-diagram.png b/examples/GRAPHICS/hbond-diagram.png new file mode 100644 index 00000000000..b042257f82d Binary files /dev/null and b/examples/GRAPHICS/hbond-diagram.png differ diff --git a/examples/GRAPHICS/hbond-diagram.tga b/examples/GRAPHICS/hbond-diagram.tga deleted file mode 100644 index aa91f6a2c6d..00000000000 Binary files a/examples/GRAPHICS/hbond-diagram.tga and /dev/null differ diff --git a/examples/GRAPHICS/in.bpm-fracture b/examples/GRAPHICS/in.bpm-fracture index ddf42897aee..46208d29695 100644 --- a/examples/GRAPHICS/in.bpm-fracture +++ b/examples/GRAPHICS/in.bpm-fracture @@ -4,13 +4,6 @@ # and fractures. The individual bonds are colored by the *force* carried by # each bond, computed on the fly with "compute bond/local force", so the # propagating stress wave and the cracks become directly visible. -# -# The relevant lines are the "compute bond/local" command and the "bond c_ID" -# value of the dump image command, together with the "dump_modify ... bmap" -# color map. This works for any /local compute that produces one value per -# bond, e.g. "compute bond/local dist" (bond length) or "engpot" (bond -# energy), and for ordinary molecular bond styles as well as BPM bonds. -# Please also note the fix graphics/labels command to draw the color scale units lj dimension 3 @@ -66,29 +59,29 @@ variable dumpfreq index 200 fix scale all graphics/labels ${dumpfreq} & colorscale viz "Bond Force" 400 50 0 size 28 & - length 900 horizontal tics 10 map bond + length 1100 horizontal tics 10 map bond & + colorscale viz "Atom Kinetic Energy" 400 130 0 size 28 & + length 900 horizontal tics 10 map atom -# compute per-bond force; the dump image command below maps it to a color +# compute per-bond force and per atom kinetic energy +# the dump image command below maps them to a color compute bforce all bond/local force +compute ke all ke/atom -dump viz all image ${dumpfreq} fracture.*.ppm type type adiam 0.4 bond c_bforce 0.3 & - size 800 800 zoom 1.9 view 80 20 box no 0.0 center s 0.7 0.5 0.45 & +dump viz all image ${dumpfreq} fracture.*.ppm c_ke type adiam 0.6 bond c_bforce 0.3 & + size 800 1000 zoom 1.7 view 80 40 box no 0.0 center s 0.45 0.5 0.4 & shiny 0.2 fsaa yes ssao yes 15267243 0.6 fix scale type 1 0 -# bmap sets the bond color map exactly like amap does for atoms. Instead of a -# plain blue-to-red ramp we build a "plasma" perceptually uniform color map (as -# popularized by matplotlib): first define custom colors map1..map5 from hex RGB -# codes, then list them as the color map stops. This is the same workflow the -# LAMMPS-GUI uses for custom color maps. Such maps keep a uniform perceived -# contrast across the range and place a bright yellow at the top end, so the -# most critical (near-breaking, highest-force) bonds stand out clearly, while -# relaxed bonds stay a muted dark purple. +# color atoms by their kinetic energy and bonds by their force dump_modify viz color map1 0x0d0887 color map2 0x7e03a8 color map3 0xcc4778 & color map4 0xf89540 color map5 0xf0f921 acolor 1 map1 & bmap 0.0 0.05 ca 0.0 5 min map1 0.01 map2 0.02 map3 & - 0.03 map4 max map5 backcolor2 silver backcolor darkgray + 0.03 map4 max map5 backcolor2 white backcolor black & + adiam 1 0.6 color map1 0.050 0.030 0.528 color map2 0.611 0.090 0.620 & + color map3 0.928 0.473 0.326 color map4 0.940 0.975 0.131 & + amap 1.0e-5 0.003 cf 0.0 4 min map1 0.333 map2 0.667 map3 max map4 # broken bonds are removed from the topology, so atoms become "lost"; allow it @@ -97,4 +90,4 @@ thermo_style custom step ke pe thermo_modify lost ignore lost/bond ignore timestep 0.1 -run 10000 +run 15000 diff --git a/examples/GRAPHICS/in.obstacle-lines b/examples/GRAPHICS/in.obstacle-lines index 6c9bd5b54cc..dc72145d740 100644 --- a/examples/GRAPHICS/in.obstacle-lines +++ b/examples/GRAPHICS/in.obstacle-lines @@ -38,7 +38,9 @@ set group upper type 3 compute mobile flow temp velocity flow create 1.0 482748 temp mobile fix 1 all nve -fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0 +fix 2 flow temp/berendsen 1.0 1.0 0.66 +#fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0 + fix_modify 2 temp mobile # Poiselle flow @@ -51,9 +53,9 @@ fix 6 flow addforce 1.0 0.0 0.0 # 2 obstacles -region void1 sphere 10 4 0 3 +region void1 cylinder z 10 4 3 -1 1 delete_atoms region void1 -region void2 sphere 20 7 0 3 +region void2 cylinder z 20 7 3 -1 1 delete_atoms region void2 fix 7 flow indent 100 sphere 10 4 0 4 @@ -66,16 +68,28 @@ timestep 0.003 thermo 1000 thermo_modify temp mobile -# select atoms to trace and assign atom type 4 so they have a different color (yellow) +# select atoms to trace and assign atom type 4 so they have a different color (yellow) region trace block 2 3 1.25 8.75 INF INF group trace region trace set group trace type 4 +compute ke all ke/atom +fix avg all ave/atom 10 10 100 c_ke +compute kemax flow reduce max f_avg +compute kemin flow reduce min f_avg +thermo 100 +thermo_style custom step temp c_kemin c_kemax # create trajectory lines by averaging positions over 10 MD steps each 10 steps apart fix lines trace graphics/lines 10 10 100 25 # visualize the trace in silver with a diameter of 0.6 which is half of that of the atoms -dump viz all image 100 obstacle-*.ppm type type size 800 600 zoom 2.5 center s 0.50 0.7 0 & - shiny 0.5 fsaa yes box no 0.025 fix lines const 1 0.6 -dump_modify viz pad 6 backcolor darkgray adiam * 1.2 fcolor lines silver +dump viz all image 100 obstacle-*.ppm type type size 800 500 zoom 3.0 & + center s 0.50 0.65 0 & + shiny 0.1 fsaa yes box no 0.025 ssao yes 12353 0.4 & + region void1 gray filled region void2 gray filled & + fix lines const 1 0.7 + +dump_modify viz pad 6 backcolor darkgray adiam * 1.3 & + amap 0 8 cf 0.0 5 min blue 0.25 purple 0.5 red 0.75 orange max gold & + fcolor lines silver & run 30000 diff --git a/examples/GRAPHICS/in.peptide-hbonds b/examples/GRAPHICS/in.peptide-hbonds index 34d0f831079..c4d672a9940 100644 --- a/examples/GRAPHICS/in.peptide-hbonds +++ b/examples/GRAPHICS/in.peptide-hbonds @@ -62,13 +62,13 @@ fix label all graphics/labels ${vizsteps} text " Hydrogen bonds donated: $(c_hb size 24 backcolor darkgray & text "Hydrogen bonds accepted: $(c_hb2:%02.0f)" 209 20 0.0 & size 24 backcolor darkgray & - image hbond-diagram.tga 190 210 0 scale 0.25 transcolor auto + image hbond-diagram.png 209 177 0 scale 0.555 # create colored arrows to go with text labels fix obj all graphics/objects ${vizsteps} arrow 5 80.0 56.0 34.6 80.0 64.0 34.6 0.3 0.2 & arrow 6 80.0 56.0 33.2 80.0 64.0 33.2 0.3 0.2 # combine the graphics into visualization -dump viz viz image ${vizsteps} hbonds-*.ppm element element size 800 800 zoom 2.1 view 80 0 bond atom 0.3& +dump viz viz image ${vizsteps} hbonds-*.png element element size 800 800 zoom 2.1 view 80 0 bond atom 0.3& fsaa yes ssao yes 12384 0.6 shiny 0.1 box no 0.1 center s 0.65 0.45 0.42 & compute hb1 const -0.4 0.3 compute hb2 const -0.4 0.3 & fix label const 1 0 fix obj type 0.0 0.0