diff --git a/doc/src/Bibliography.rst b/doc/src/Bibliography.rst index cc7a448bc1..27d5d3eef4 100644 --- a/doc/src/Bibliography.rst +++ b/doc/src/Bibliography.rst @@ -368,7 +368,7 @@ Bibliography Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002. **(GLE4MD)** - `http://gle4md.org/ `_ + `https://gle4md.org/ `_ **(Gao)** Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504. @@ -461,7 +461,7 @@ Bibliography Hunt, Mol Simul, 42, 347 (2016). **(IPI)** - `http://epfl-cosmo.github.io/gle4md/index.html?page=ipi `_ + `https://ipi-code.org/ ` **(IPI-CPC)** Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014). @@ -875,7 +875,7 @@ Bibliography G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) **(Paquay)** - Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 `_. + Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 `_. **(Park)** Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004) diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index 66e12a0d69..1644c7ea86 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -140,7 +140,7 @@ of the LAMMPS project on GitHub. The unit testing facility is integrated into the CMake build process of the LAMMPS source code distribution itself. It can be enabled by setting ``-D ENABLE_TESTING=on`` during the CMake configuration step. -It requires the `YAML `_ library and development +It requires the `YAML `_ library and development headers (if those are not found locally a recent version will be downloaded and compiled along with LAMMPS and the test program) to compile and will download and compile a specific recent version of the diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 0f5f5f8064..2535b9010f 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -314,7 +314,7 @@ detailed information is available at: In addition to installing the KIM API, it is also necessary to install the library of KIM models (interatomic potentials). -See `Obtaining KIM Models `_ to +See `Obtaining KIM Models `_ to learn how to install a pre-build binary of the OpenKIM Repository of Models. See the list of all KIM models here: https://openkim.org/browse/models @@ -432,7 +432,7 @@ Enabling the extra unit tests have some requirements, ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``, ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and ``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models. - See `Obtaining KIM Models `_ + See `Obtaining KIM Models `_ to learn how to install a pre-built binary of the OpenKIM Repository of Models or see `Installing KIM Models `_ @@ -1053,7 +1053,7 @@ VORONOI package ----------------------------- To build with this package, you must download and build the -`Voro++ library `_ or install a +`Voro++ library `_ or install a binary package provided by your operating system. .. tabs:: diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst index d91ac94be5..1ef0a80549 100644 --- a/doc/src/Build_manual.rst +++ b/doc/src/Build_manual.rst @@ -176,7 +176,7 @@ math expressions transparently into embedded images. For converting the generated ePUB file to a MOBI format file (for e-book readers, like Kindle, that cannot read ePUB), you also need to have the ``ebook-convert`` tool from the "calibre" software -installed. `http://calibre-ebook.com/ `_ +installed. `https://calibre-ebook.com/ `_ Typing ``make mobi`` will first create the ePUB file and then convert it. On the Kindle readers in particular, you also have support for PDF files, so you could download and view the PDF version as an alternative. diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index 7e627a052f..2d83908bb1 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -111,26 +111,25 @@ LAMMPS can use them if they are available on your system. files in its default search path. You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link. -The `KISS FFT library `_ is included in the LAMMPS -distribution. It is portable across all platforms. Depending on the size -of the FFTs and the number of processors used, the other libraries listed -here can be faster. +The `KISS FFT library `_ is +included in the LAMMPS distribution. It is portable across all +platforms. Depending on the size of the FFTs and the number of +processors used, the other libraries listed here can be faster. However, note that long-range Coulombics are only a portion of the -per-timestep CPU cost, FFTs are only a portion of long-range -Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel -communication can be costly). A breakdown of these timings is printed -to the screen at the end of a run when using the -:doc:`kspace_style pppm ` command. The -:doc:`Screen and logfile output ` -page gives more details. A more detailed (and time consuming) -report of the FFT performance is generated with the +per-timestep CPU cost, FFTs are only a portion of long-range Coulombics, +and 1d FFTs are only a portion of the FFT cost (parallel communication +can be costly). A breakdown of these timings is printed to the screen +at the end of a run when using the :doc:`kspace_style pppm +` command. The :doc:`Screen and logfile output +` page gives more details. A more detailed (and time +consuming) report of the FFT performance is generated with the :doc:`kspace_modify fftbench yes ` command. FFTW is a fast, portable FFT library that should also work on any -platform and can be faster than the KISS FFT library. You can -download it from `www.fftw.org `_. LAMMPS requires -version 3.X; the legacy version 2.1.X is no longer supported. +platform and can be faster than the KISS FFT library. You can download +it from `www.fftw.org `_. LAMMPS requires version +3.X; the legacy version 2.1.X is no longer supported. Building FFTW for your box should be as simple as ``./configure; make; make install``. The install command typically requires root privileges diff --git a/doc/src/Errors_debug.rst b/doc/src/Errors_debug.rst index 786a21ecae..787f3f6b34 100644 --- a/doc/src/Errors_debug.rst +++ b/doc/src/Errors_debug.rst @@ -75,7 +75,7 @@ Using the GDB debugger to get a stack trace There are two options to use the GDB debugger for identifying the origin of the segmentation fault or similar crash. The GDB debugger has many more features and options, as can be seen for example its `online -documentation `_. +documentation `_. Run LAMMPS from within the debugger ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/doc/src/Howto_amoeba.rst b/doc/src/Howto_amoeba.rst index c6df8a9b5c..6b84fc9f00 100644 --- a/doc/src/Howto_amoeba.rst +++ b/doc/src/Howto_amoeba.rst @@ -281,7 +281,7 @@ Here is more information about the extended XYZ format defined and used by Tinker, and links to programs that convert standard PDB files to the extended XYZ format: -* `http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html `_ +* `https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html `_ * `https://github.com/emleddin/pdbxyz-xyzpdb `_ * `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f `_ diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index 172ba3da3a..8899f7520c 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -3,24 +3,20 @@ CHARMM, AMBER, COMPASS, and DREIDING force fields A force field has 2 parts: the formulas that define it and the coefficients used for a particular system. Here we only discuss -formulas implemented in LAMMPS that correspond to formulas commonly -used in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting +formulas implemented in LAMMPS that correspond to formulas commonly used +in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting coefficients is done either from special sections in an input data file via the :doc:`read_data ` command or in the input script with -commands like :doc:`pair_coeff ` or -:doc:`bond_coeff ` and so on. See the :doc:`Tools ` doc -page for additional tools that can use CHARMM, AMBER, or Materials -Studio generated files to assign force field coefficients and convert -their output into LAMMPS input. +commands like :doc:`pair_coeff ` or :doc:`bond_coeff +` and so on. See the :doc:`Tools ` doc page for +additional tools that can use CHARMM, AMBER, or Materials Studio +generated files to assign force field coefficients and convert their +output into LAMMPS input. -See :ref:`(MacKerell) ` for a description of the CHARMM force -field. See :ref:`(Cornell) ` for a description of the AMBER -force field. See :ref:`(Sun) ` for a description of the COMPASS -force field. - -.. _charmm: http://www.scripps.edu/brooks - -.. _amber: http://amber.scripps.edu +See :ref:`(MacKerell) ` for a description of the CHARMM +force field. See :ref:`(Cornell) ` for a description of +the AMBER force field. See :ref:`(Sun) ` for a description +of the COMPASS force field. The interaction styles listed below compute force field formulas that are consistent with common options in CHARMM or AMBER. See each @@ -41,9 +37,10 @@ command's documentation for the formula it computes. .. note:: - For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released - in March 2017. We recommend they be used instead of the older *charmm* - styles. See discussion of the differences on the :doc:`pair charmm ` and :doc:`dihedral charmm ` doc + For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in + March 2017. We recommend they be used instead of the older *charmm* + styles. See discussion of the differences on the :doc:`pair charmm + ` and :doc:`dihedral charmm ` doc pages. COMPASS is a general force field for atomistic simulation of common diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index 315bacac69..9209477986 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -10,7 +10,7 @@ changes or additions you have made to LAMMPS into the official LAMMPS distribution. It uses the process of updating this very tutorial as an example to describe the individual steps and options. You need to be familiar with git and you may want to have a look at the `git book -`_ to familiarize yourself with some of the +`_ to familiarize yourself with some of the more advanced git features used below. As of fall 2016, submitting contributions to LAMMPS via pull requests diff --git a/doc/src/Howto_manifold.rst b/doc/src/Howto_manifold.rst index 8c2cbadc42..67c9d70ea6 100644 --- a/doc/src/Howto_manifold.rst +++ b/doc/src/Howto_manifold.rst @@ -47,4 +47,4 @@ to the relevant fixes. .. _Paquay1: **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016). -preprint available at `arXiv:1411.3019 `_. +preprint available at `arXiv:1411.3019 `_. diff --git a/doc/src/Howto_spc.rst b/doc/src/Howto_spc.rst index d334b09b4a..520942547e 100644 --- a/doc/src/Howto_spc.rst +++ b/doc/src/Howto_spc.rst @@ -38,7 +38,7 @@ the partial charge assignments change: See the :ref:`(Berendsen) ` reference for more details on both the SPC and SPC/E models. -Wikipedia also has a nice article on `water models `_. +Wikipedia also has a nice article on `water models `_. ---------- diff --git a/doc/src/Howto_tip3p.rst b/doc/src/Howto_tip3p.rst index 7f7ddbdf2a..5571b3291a 100644 --- a/doc/src/Howto_tip3p.rst +++ b/doc/src/Howto_tip3p.rst @@ -49,7 +49,7 @@ details: | :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` | -Wikipedia also has a nice article on `water models `_. +Wikipedia also has a nice article on `water models `_. ---------- diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 9856b8fbe7..4e0a63adc6 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -97,7 +97,7 @@ This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. The OM distance and the LJ and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long ` command. -Wikipedia also has a nice article on `water models `_. +Wikipedia also has a nice article on `water models `_. ---------- diff --git a/doc/src/Howto_viz.rst b/doc/src/Howto_viz.rst index 7c74aab8bf..28ecbfb838 100644 --- a/doc/src/Howto_viz.rst +++ b/doc/src/Howto_viz.rst @@ -17,9 +17,10 @@ formats. See the :doc:`Tools ` page for details. A Python-based toolkit distributed by our group can read native LAMMPS dump files, including custom dump files with additional columns of -user-specified atom information, and convert them to various formats -or pipe them into visualization software directly. See the `Pizza.py WWW site `_ for details. Specifically, Pizza.py can convert -LAMMPS dump files into PDB, XYZ, `EnSight `_, and VTK formats. +user-specified atom information, and convert them to various formats or +pipe them into visualization software directly. See the `Pizza.py WWW +site `_ for details. Specifically, Pizza.py can convert LAMMPS +dump files into PDB, XYZ, `EnSight `_, and VTK formats. Pizza.py can pipe LAMMPS dump files directly into the Raster3d and RasMol visualization programs. Pizza.py has tools that do interactive 3d OpenGL visualization and one that creates SVG images of dump file diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst index 108c03c249..fc167d7e68 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -6,7 +6,7 @@ Windows system can be downloaded from this site: .. parsed-literal:: - `http://packages.lammps.org/windows.html `_ + `https://packages.lammps.org/windows.html `_ Note that each installer package has a date in its name, which corresponds to the LAMMPS version of the same date. Installers for diff --git a/doc/src/Intro_citing.rst b/doc/src/Intro_citing.rst index aaf62028ae..56955cae3a 100644 --- a/doc/src/Intro_citing.rst +++ b/doc/src/Intro_citing.rst @@ -27,7 +27,7 @@ namely https://www.lammps.org. The original publication describing the parallel algorithms used in the initial versions of LAMMPS is: - `S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). `_ + `S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). `_ DOI for the LAMMPS source code diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index 2b0409b007..9344710a16 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -95,7 +95,7 @@ commands) * metal-organic framework potentials (QuickFF, MO-FF) * implicit solvent potentials: hydrodynamic lubrication, Debye * force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options -* access to the `OpenKIM Repository `_ of potentials via :doc:`kim command ` +* access to the `OpenKIM Repository `_ of potentials via the :doc:`kim command ` * hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation * overlaid potentials: superposition of multiple pair potentials (including many-body) with optional scale factor @@ -205,7 +205,7 @@ Pre- and post-processing .. _pizza: https://lammps.github.io/pizza -.. _python: http://www.python.org +.. _python: https://www.python.org .. _special: diff --git a/doc/src/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst index 3ff0507ee5..b1d68c8594 100644 --- a/doc/src/Intro_nonfeatures.rst +++ b/doc/src/Intro_nonfeatures.rst @@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks: linear bead-spring polymer chains. The moltemplate program is 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 page `_ of the LAMMPS website + LAMMPS. The `Pre/post processing page `_ of the LAMMPS website describes a variety of third party tools for this task. Furthermore, some LAMMPS internal commands allow to reconstruct, or selectively add topology information, as well as provide the option to insert molecule diff --git a/doc/src/Intro_opensource.rst b/doc/src/Intro_opensource.rst index a1baaf5185..fba0a78189 100644 --- a/doc/src/Intro_opensource.rst +++ b/doc/src/Intro_opensource.rst @@ -23,9 +23,9 @@ applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution. .. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html -.. _gnuorg: http://www.gnu.org +.. _gnuorg: https://www.gnu.org -.. _opensource: http://www.opensource.org +.. _opensource: https://www.opensource.org Here is a more specific summary of what the GPL means for LAMMPS users: diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index f89ab00039..dea49034a3 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1071,7 +1071,7 @@ H5MD is a format for molecular simulations, built on top of HDF5. This package implements a :doc:`dump h5md ` command to output LAMMPS snapshots in this format. -.. _HDF5: http://www.hdfgroup.org/HDF5 +.. _HDF5: https://www.hdfgroup.org/solutions/hdf5 To use this package you must have the HDF5 library available on your system. @@ -1954,7 +1954,7 @@ support for new file formats can be added to LAMMPS (or VMD or other programs that use them) without having to re-compile the application itself. More information about the VMD molfile plugins can be found at -`http://www.ks.uiuc.edu/Research/vmd/plugins/molfile `_. +`https://www.ks.uiuc.edu/Research/vmd/plugins/molfile `_. **Author:** Axel Kohlmeyer (Temple U). @@ -2045,7 +2045,7 @@ NETCDF package Dump styles for writing NetCDF formatted dump files. NetCDF is a portable, binary, self-describing file format developed on top of HDF5. The file contents follow the AMBER NetCDF trajectory conventions -(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions. +(https://ambermd.org/netcdf/nctraj.xhtml), but include extensions. To use this package you must have the NetCDF library available on your system. @@ -2056,7 +2056,7 @@ tools: * `Ovito `_ (Ovito supports the AMBER convention and the extensions mentioned above) * `VMD `_ -.. _ovito: http://www.ovito.org +.. _ovito: https://www.ovito.org .. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/ @@ -2417,7 +2417,7 @@ A :doc:`fix qmmm ` command which allows LAMMPS to be used as the MM code in a QM/MM simulation. This is currently only available in combination with the `Quantum ESPRESSO `_ package. -.. _espresso: http://www.quantum-espresso.org +.. _espresso: https://www.quantum-espresso.org To use this package you must have Quantum ESPRESSO (QE) available on your system and include its coupling library in the compilation and @@ -2829,7 +2829,7 @@ collection of atoms by wrapping the `Voro++ library `_. This can be used to calculate the local volume or each atoms or its near neighbors. -.. _voro-home: http://math.lbl.gov/voro++ +.. _voro-home: https://math.lbl.gov/voro++ To use this package you must have the Voro++ library available on your system. @@ -2863,9 +2863,9 @@ A :doc:`dump vtk ` command which outputs snapshot info in the `VTK format `_, enabling visualization by `Paraview `_ or other visualization packages. -.. _vtk: http://www.vtk.org +.. _vtk: https://www.vtk.org -.. _paraview: http://www.paraview.org +.. _paraview: https://www.paraview.org To use this package you must have VTK library available on your system. @@ -2902,7 +2902,7 @@ which discuss the `QuickFF `_ methodology. .. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877 .. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173 -.. _quickff: http://molmod.github.io/QuickFF +.. _quickff: https://molmod.github.io/QuickFF .. _yaff: https://github.com/molmod/yaff **Author:** Steven Vandenbrande. diff --git a/doc/src/Python_examples.rst b/doc/src/Python_examples.rst index fe5fe812c5..f795827230 100644 --- a/doc/src/Python_examples.rst +++ b/doc/src/Python_examples.rst @@ -43,26 +43,18 @@ Note that for AtomEye, you need version 3, and there is a line in the scripts that specifies the path and name of the executable. See the AtomEye web pages for more details: -* `http://li.mit.edu/Archive/Graphics/A/ `_ -* `http://li.mit.edu/Archive/Graphics/A3/A3.html `_ +* `http://li.mit.edu/Archive/Graphics/A/ `_ +* `http://li.mit.edu/Archive/Graphics/A3/A3.html `_ -.. _atomeye: http://li.mit.edu/Archive/Graphics/A/ - -.. _atomeye3: http://li.mit.edu/Archive/Graphics/A3/A3.html - -The latter link is to AtomEye 3 which has the scripting -capability needed by these Python scripts. +The latter link is to AtomEye 3 which has the scripting capability +needed by these Python scripts. Note that for PyMol, you need to have built and installed the open-source version of PyMol in your Python, so that you can import it from a Python script. See the PyMol web pages for more details: - * `https://www.pymol.org `_ - * `https://github.com/schrodinger/pymol-open-source `_ - -.. _pymolhome: https://www.pymol.org - -.. _pymolopen: https://github.com/schrodinger/pymol-open-source + * `https://www.pymol.org `_ + * `https://github.com/schrodinger/pymol-open-source `_ The latter link is to the open-source version. diff --git a/doc/src/Python_head.rst b/doc/src/Python_head.rst index 3e84ed4506..3aab3a0d4b 100644 --- a/doc/src/Python_head.rst +++ b/doc/src/Python_head.rst @@ -18,17 +18,17 @@ together. Python_error Python_trouble -If you are not familiar with `Python `_, it is a +If you are not familiar with `Python `_, it is a powerful scripting and programming language which can do almost everything that compiled languages like C, C++, or Fortran can do in fewer lines of code. It also comes with a large collection of add-on modules for many purposes (either bundled or easily installed from Python code repositories). The major drawback is slower execution speed of the script code compared to compiled programming languages. But when -the script code is interfaced to optimized compiled code, performance can -be on par with a standalone executable, for as long as the scripting is -restricted to high-level operations. Thus Python is also convenient to -use as a "glue" language to "drive" a program through its library +the script code is interfaced to optimized compiled code, performance +can be on par with a standalone executable, for as long as the scripting +is restricted to high-level operations. Thus Python is also convenient +to use as a "glue" language to "drive" a program through its library interface, or to hook multiple pieces of software together, such as a simulation code and a visualization tool, or to run a coupled multi-scale or multi-physics model. diff --git a/doc/src/Run_windows.rst b/doc/src/Run_windows.rst index f29155a839..d36864b454 100644 --- a/doc/src/Run_windows.rst +++ b/doc/src/Run_windows.rst @@ -25,8 +25,8 @@ in parallel, follow these steps. Download and install a compatible MPI library binary package: -* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi `_ -* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi `_ +* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi `_ +* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi `_ The LAMMPS Windows installer packages will automatically adjust your path for the default location of this MPI package. After the diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index 9015bff9ef..883bc9c7e3 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -39,7 +39,7 @@ toolkit software on your system (this is only tested on Linux and unsupported on Windows): * Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/\*/information -* Go to http://www.nvidia.com/object/cuda_get.html +* Go to https://developer.nvidia.com/cuda-downloads * Install a driver and toolkit appropriate for your system (SDK is not necessary) * Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to list supported devices and properties diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index 2b53af8698..e3c3fc01f7 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -537,5 +537,5 @@ References """""""""" * Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS", in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. -* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. `_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). +* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. `_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). * Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index 3d9cbe19e0..29c55df62f 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -97,7 +97,7 @@ sub-section. A description of the multi-threading strategy used in the OPENMP package and some performance examples are -`presented here `_. +`presented here `_. Guidelines for best performance """"""""""""""""""""""""""""""" diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 25b646d036..f8c8bd7240 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -512,8 +512,8 @@ with an ``.inputrc`` file in the home directory. For application specific customization, the LAMMPS shell uses the name "lammps-shell". For more information about using and customizing an application using readline, please see the available documentation at: -`http://www.gnu.org/s/readline/#Documentation -`_ +https://www.gnu.org/software/readline/ + Additional commands ^^^^^^^^^^^^^^^^^^^ @@ -715,7 +715,7 @@ See the README.pdf file for more information. These scripts were written by Arun Subramaniyan at Purdue Univ (asubrama at purdue.edu). -.. _matlabhome: http://www.mathworks.com +.. _matlabhome: https://www.mathworks.com ---------- @@ -1046,7 +1046,7 @@ the binary file. This usually is a so-called little endian hardware SWIG interface -------------- -The `SWIG tool `_ offers a mostly automated way to +The `SWIG tool `_ offers a mostly automated way to incorporate compiled code modules into scripting languages. It processes the function prototypes in C and generates wrappers for a wide variety of scripting languages from it. Thus it can also be applied to @@ -1126,7 +1126,7 @@ data passed or returned as pointers are included in the ``lammps.i`` file. So most of the functionality of the library interface should be accessible. What works and what does not depends a bit on the individual language for which the wrappers are built and how well SWIG -supports those. The `SWIG documentation `_ +supports those. The `SWIG documentation `_ has very detailed instructions and recommendations. Usage examples diff --git a/doc/src/compute_damage_atom.rst b/doc/src/compute_damage_atom.rst index b75a3ebc57..cecce56255 100644 --- a/doc/src/compute_damage_atom.rst +++ b/doc/src/compute_damage_atom.rst @@ -24,14 +24,18 @@ Description """"""""""" Define a computation that calculates the per-atom damage for each atom -in a group. This is a quantity relevant for :doc:`Peridynamics models `. See `this document `_ -for an overview of LAMMPS commands for Peridynamics modeling. +in a group. This is a quantity relevant for :doc:`Peridynamics models +`. See `this document `_ for an +overview of LAMMPS commands for Peridynamics modeling. The "damage" of a Peridynamics particles is based on the bond breakage between the particle and its neighbors. If all the bonds are broken the particle is considered to be fully damaged. -See the `PDLAMMPS user guide `_ for a formal +.. TODO the link below is broken + +See the `PDLAMMPS user guide +`_ for a formal definition of "damage" and more details about Peridynamics as it is implemented in LAMMPS. @@ -53,8 +57,9 @@ The per-atom vector values are unitless numbers (damage) :math:`\ge 0.0`. Restrictions """""""""""" -This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +This compute is part of the PERI package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_dilatation_atom.rst b/doc/src/compute_dilatation_atom.rst index 8e3c86a4af..a1037c6358 100644 --- a/doc/src/compute_dilatation_atom.rst +++ b/doc/src/compute_dilatation_atom.rst @@ -24,12 +24,15 @@ Description """"""""""" Define a computation that calculates the per-atom dilatation for each -atom in a group. This is a quantity relevant for :doc:`Peridynamics models `. See `this document `_ +atom in a group. This is a quantity relevant for :doc:`Peridynamics +models `. See `this document `_ for an overview of LAMMPS commands for Peridynamics modeling. For small deformation, dilatation of is the measure of the volumetric strain. +.. TODO the link below is broken + The dilatation :math:`\theta` for each peridynamic particle :math:`i` is calculated as a sum over its neighbors with unbroken bonds, where the contribution of the :math:`ij` pair is a function of the change in bond length @@ -38,7 +41,8 @@ fraction of the particles and an influence function. See the `PDLAMMPS user guide `_ for a formal definition of dilatation. -This command can only be used with a subset of the Peridynamic :doc:`pair styles `: peri/lps, peri/ves and peri/eps. +This command can only be used with a subset of the Peridynamic +:doc:`pair styles `: peri/lps, peri/ves and peri/eps. The dilatation value will be 0.0 for atoms not in the specified compute group. @@ -56,9 +60,9 @@ The per-atom vector values are unitless numbers :math:`(\theta \ge 0.0)`. Restrictions """""""""""" -This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the -:doc:`Build package ` page for more info. +This compute is part of the PERI package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index 699d3f2aaa..19914997a3 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -154,25 +154,25 @@ which must be installed on your system when building LAMMPS for use with this compute. See instructions on obtaining and installing the Voro++ software in the src/VORONOI/README file. -.. _voronoi: http://math.lbl.gov/voro++/ +.. _voronoi: https://math.lbl.gov/voro++/ .. note:: - The calculation of Voronoi volumes is performed by each - processor for the atoms it owns, and includes the effect of ghost - atoms stored by the processor. This assumes that the Voronoi cells of - owned atoms are not affected by atoms beyond the ghost atom cut-off - distance. This is usually a good assumption for liquid and solid - systems, but may lead to underestimation of Voronoi volumes in low - density systems. By default, the set of ghost atoms stored by each - processor is determined by the cutoff used for - :doc:`pair_style ` interactions. The cutoff can be set - explicitly via the :doc:`comm_modify cutoff ` command. The - Voronoi cells for atoms adjacent to empty regions will extend into - those regions up to the communication cutoff in :math:`x`, :math:`y`, or - :math:`z`. In that situation, an exterior face is created at the cutoff - distance normal to the :math:`x`, :math:`y`, or :math:`z` direction. - For triclinic systems, the exterior face is parallel to the corresponding + The calculation of Voronoi volumes is performed by each processor for + the atoms it owns, and includes the effect of ghost atoms stored by + the processor. This assumes that the Voronoi cells of owned atoms + are not affected by atoms beyond the ghost atom cut-off distance. + This is usually a good assumption for liquid and solid systems, but + may lead to underestimation of Voronoi volumes in low density + systems. By default, the set of ghost atoms stored by each processor + is determined by the cutoff used for :doc:`pair_style ` + interactions. The cutoff can be set explicitly via the + :doc:`comm_modify cutoff ` command. The Voronoi cells + for atoms adjacent to empty regions will extend into those regions up + to the communication cutoff in :math:`x`, :math:`y`, or :math:`z`. + In that situation, an exterior face is created at the cutoff distance + normal to the :math:`x`, :math:`y`, or :math:`z` direction. For + triclinic systems, the exterior face is parallel to the corresponding reciprocal lattice vector. .. note:: diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 21b82de4f0..f069911096 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -480,7 +480,7 @@ style. ---------- Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files -can be read directly by `VMD `_, a +can be read directly by `VMD `_, a popular molecular viewing program. ---------- diff --git a/doc/src/dump_h5md.rst b/doc/src/dump_h5md.rst index 37fc7ad600..41d6dc7594 100644 --- a/doc/src/dump_h5md.rst +++ b/doc/src/dump_h5md.rst @@ -64,7 +64,7 @@ stored within the same file by defining several dumps. A dump that refers (via *file_from*) to an already open dump ID and that concerns another particle group must specify *create_group yes*. -.. _h5md: http://nongnu.org/h5md/ +.. _h5md: https://nongnu.org/h5md/ Each data element is written every N\*N_element steps. For *image*, no sub-interval is needed as it must be present at the same interval as @@ -113,7 +113,7 @@ the `HDF5 `_ library installed (C bindings are sufficient) on your system. The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library. -.. _HDF5-ws: http://www.hdfgroup.org/HDF5/ +.. _HDF5-ws: https://www.hdfgroup.org/solutions/hdf5/ ---------- @@ -129,4 +129,4 @@ Related commands **(de Buyl)** de Buyl, Colberg and Hofling, H5MD: A structured, efficient, and portable file format for molecular data, Comp. Phys. Comm. 185(6), 1546-1553 (2014) - -`[arXiv:1308.6382] `_. +`[arXiv:1308.6382] `_. diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index c395f6ef06..bc2373afac 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -212,7 +212,7 @@ is used. Similarly, the format of the resulting movie is chosen with the *movie* dump style. This is handled by the underlying FFmpeg converter and thus details have to be looked up in the `FFmpeg documentation -`_. Typical examples are: .avi, .mpg, +`_. Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie compression like bitrate and framerate can be set using the dump_modify command as described below. @@ -642,7 +642,7 @@ MPEG or other movie file you can use: cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi Front ends for FFmpeg exist for multiple platforms. For more - information see the `FFmpeg homepage `_ + information see the `FFmpeg homepage `_ ---------- diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 29f59ffaef..0d059581eb 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -881,7 +881,7 @@ levels that sacrifice compression for performance. 0 is the default, positive levels are 1 to 22, with 22 being the most expensive compression. Zstd promises higher compression/decompression speeds for similar compression ratios. For more details see -`http://facebook.github.io/zstd/`. +`https://facebook.github.io/zstd/`. In addition, Zstd compressed files can include a checksum of the entire contents. The Zstd enabled dump styles enable this feature by diff --git a/doc/src/dump_molfile.rst b/doc/src/dump_molfile.rst index c1f0b48fe6..f8cc06d039 100644 --- a/doc/src/dump_molfile.rst +++ b/doc/src/dump_molfile.rst @@ -34,7 +34,7 @@ Dump a snapshot of atom coordinates and selected additional quantities to one or more files every N timesteps in one of several formats. Only information for atoms in the specified group is dumped. This specific dump style uses molfile plugins that are bundled with the -`VMD `_ molecular visualization and +`VMD `_ molecular visualization and analysis program. Unless the filename contains a \* character, the output will be written diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst index 04790f4986..296b725e20 100644 --- a/doc/src/dump_netcdf.rst +++ b/doc/src/dump_netcdf.rst @@ -48,21 +48,17 @@ rank. NetCDF files can be directly visualized via the following tools: -Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and -all extensions of this dump style. - -* VMD (http://www.ks.uiuc.edu/Research/vmd/). -* AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye - contains a NetCDF reader that is not present in the standard - distribution of AtomEye. +* Ovito (https://www.ovito.org/). Ovito supports the AMBER convention and + all extensions of this dump style. +* VMD (https://www.ks.uiuc.edu/Research/vmd/). In addition to per-atom data, :doc:`thermo ` data can be included in the dump file. The data included in the dump file is identical to the data specified by :doc:`thermo_style `. -.. _netcdf-home: http://www.unidata.ucar.edu/software/netcdf/ +.. _netcdf-home: https://www.unidata.ucar.edu/software/netcdf/ -.. _pnetcdf-home: http://trac.mcs.anl.gov/projects/parallel-netcdf/ +.. _pnetcdf-home: https://trac.mcs.anl.gov/projects/parallel-netcdf/ ---------- diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst index 89437bab76..4ec872cb89 100644 --- a/doc/src/dump_vtk.rst +++ b/doc/src/dump_vtk.rst @@ -29,8 +29,9 @@ Description """"""""""" Dump a snapshot of atom quantities to one or more files every :math:`N` -timesteps in a format readable by the `VTK visualization toolkit `_ or other visualization tools that use it, -such as `ParaView `_. The time steps on which dump +timesteps in a format readable by the `VTK visualization toolkit +`_ or other visualization tools that use it, such +as `ParaView `_. The time steps on which dump output is written can also be controlled by a variable; see the :doc:`dump_modify every ` command for details. @@ -38,8 +39,8 @@ This dump style is similar to :doc:`dump_style custom ` but uses the VTK library to write data to VTK simple legacy or XML format, depending on the filename extension specified for the dump file. This can be either *\*.vtk* for the legacy format or *\*.vtp* and *\*.vtu*, -respectively, for XML format; see the -`VTK homepage `_ for a detailed +respectively, for XML format; see the `VTK homepage +`_ for a detailed description of these formats. Since this naming convention conflicts with the way binary output is usually specified (see below), the :doc:`dump_modify binary ` command allows setting of a @@ -61,14 +62,15 @@ determine the kind of output. .. warning:: - Unless the :doc:`dump_modify sort ` option - is invoked, the lines of atom information written to dump files will - be in an indeterminate order for each snapshot. This is even true - when running on a single processor, if the :doc:`atom_modify sort ` option is on, which it is by default. In this - case atoms are re-ordered periodically during a simulation, due to - spatial sorting. It is also true when running in parallel, because - data for a single snapshot is collected from multiple processors, each - of which owns a subset of the atoms. + Unless the :doc:`dump_modify sort ` option is invoked, + the lines of atom information written to dump files will be in an + indeterminate order for each snapshot. This is even true when + running on a single processor, if the :doc:`atom_modify sort + ` option is on, which it is by default. In this case + atoms are re-ordered periodically during a simulation, due to spatial + sorting. It is also true when running in parallel, because data for + a single snapshot is collected from multiple processors, each of + which owns a subset of the atoms. For the *vtk* style, sorting is off by default. See the :doc:`dump_modify ` page for details. diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst index d251eb65e9..3b46e81c2c 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -78,7 +78,7 @@ example of how this is done. This sample application performs classical MD using quantum forces computed by a density functional code `Quest `_. -.. _quest: http://dft.sandia.gov/Quest +.. _quest: https://dft.sandia.gov/Quest ---------- diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst index a42fddf7f5..03add9d354 100644 --- a/doc/src/fix_gle.rst +++ b/doc/src/fix_gle.rst @@ -159,7 +159,7 @@ Related commands .. _GLE4MD: -**(GLE4MD)** `http://gle4md.org/ `_ +**(GLE4MD)** `https://gle4md.org/ `_ .. _Ceriotti2: diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index 004bc0b614..06d8787b1b 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -51,16 +51,11 @@ from the main execution thread and potentially lower the inferred latencies for slow communication links. This feature has only been tested under linux. -There are example scripts for using this package with LAMMPS in -examples/PACKAGES/imd. Additional examples and a driver for use with the -Novint Falcon game controller as haptic device can be found at: -http://sites.google.com/site/akohlmey/software/vrpn-icms. - -The source code for this fix includes code developed by the -Theoretical and Computational Biophysics Group in the Beckman -Institute for Advanced Science and Technology at the University of -Illinois at Urbana-Champaign. We thank them for providing a software -interface that allows codes like LAMMPS to hook to `VMD `_. +The source code for this fix includes code developed by the Theoretical +and Computational Biophysics Group in the Beckman Institute for Advanced +Science and Technology at the University of Illinois at +Urbana-Champaign. We thank them for providing a software interface that +allows codes like LAMMPS to hook to `VMD `_. Upon initialization of the fix, it will open a communication port on the node with MPI task 0 and wait for an incoming connection. As soon @@ -117,40 +112,40 @@ VMD are the following: In the Mouse menu of the VMD Main window, select "Mouse -> Force -> Atom". You may alternately select "Residue", or "Fragment" to apply forces to whole residues or fragments. Your mouse can now be used to -apply forces to your simulation. Click on an atom, residue, or -fragment and drag to apply a force. Click quickly without moving the -mouse to turn the force off. You can also use a variety of 3D position -trackers to apply forces to your simulation. Game controllers or haptic -devices with force-feedback such as the Novint Falcon or Sensable -PHANTOM allow you to feel the resistance due to inertia or interactions -with neighbors that the atoms experience you are trying to move, as if -they were real objects. See the `VMD IMD Homepage `_ and the -`VRPN-ICMS Homepage `_ for more details. +apply forces to your simulation. Click on an atom, residue, or fragment +and drag to apply a force. Click quickly without moving the mouse to +turn the force off. You can also use a variety of 3D position trackers +to apply forces to your simulation. Game controllers or haptic devices +with force-feedback such as the Novint Falcon or Sensable PHANTOM allow +you to feel the resistance due to inertia or interactions with neighbors +that the atoms experience you are trying to move, as if they were real +objects. See the `VMD IMD Homepage `_ for more details. If IMD control messages are received, a line of text describing the message and its effect will be printed to the LAMMPS output screen, if screen output is active. -.. _VMD: http://www.ks.uiuc.edu/Research/vmd +.. _VMD: https://www.ks.uiuc.edu/Research/vmd -.. _imdvmd: http://www.ks.uiuc.edu/Research/vmd/imd/ - -.. _vrpnicms: http://sites.google.com/site/akohlmey/software/vrpn-icms +.. _imdvmd: https://www.ks.uiuc.edu/Research/vmd/imd/ Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used -with the *start/stop* keywords of the :doc:`run ` command. This -fix is not invoked during :doc:`energy minimization `. +No information about this fix is written to :doc:`binary restart files +`. None of the :doc:`fix_modify ` options are +relevant to this fix. No global scalar or vector or per-atom quantities +are stored by this fix for access by various :doc:`output commands +`. No parameter of this fix can be used with the +*start/stop* keywords of the :doc:`run ` command. This fix is not +invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +This fix is part of the MISC package. It is only enabled if LAMMPS was +built with that package. See the :doc:`Build package ` +page for more info. When used in combination with VMD, a topology or coordinate file has to be loaded, which matches (in number and ordering of atoms) the diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst index 6ddd6976a2..6a6ff9aa87 100644 --- a/doc/src/fix_ipi.rst +++ b/doc/src/fix_ipi.rst @@ -111,4 +111,4 @@ Related commands .. _ipihome: **(IPI)** -`http://epfl-cosmo.github.io/gle4md/index.html?page=ipi `_ +`https://ipi-code.org `_ diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst index a9bf07de60..63632ebac0 100644 --- a/doc/src/fix_nve_manifold_rattle.rst +++ b/doc/src/fix_nve_manifold_rattle.rst @@ -108,4 +108,4 @@ every = 0, tchain = 3 .. _Paquay2: **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016). -preprint available at `arXiv:1411.3019 `_. +preprint available at `arXiv:1411.3019 `_. diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst index fe889bda79..91a5f28649 100644 --- a/doc/src/fix_nvt_manifold_rattle.rst +++ b/doc/src/fix_nvt_manifold_rattle.rst @@ -82,4 +82,4 @@ Related commands .. _Paquay3: **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016). -preprint available at `arXiv:1411.3019 `_. +preprint available at `arXiv:1411.3019 `_. diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index c1885e9e9f..527498bb21 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -134,7 +134,7 @@ for other systems, *nasr* = 10 is typically sufficient. The *map_file* contains the mapping information between the lattice indices and the atom IDs, which tells the code which atom sits at which lattice point; the lattice indices start from 0. An auxiliary -code, `latgen `_, can be employed to +code, `latgen `_, can be employed to generate the compatible map file for various crystals. In case one simulates a non-periodic system, where the whole simulation diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst index a62bd5ab1e..546635520c 100644 --- a/doc/src/fix_qmmm.rst +++ b/doc/src/fix_qmmm.rst @@ -31,7 +31,7 @@ wave DFT package. Electrostatic coupling is in preparation and the interface has been written in a manner that coupling to other QM codes should be possible without changes to LAMMPS itself. -.. _espresso: http://www.quantum-espresso.org +.. _espresso: https://www.quantum-espresso.org The interface code for this is in the lib/qmmm directory of the LAMMPS distribution and is being made available at this early stage of diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 30f3e550c5..0852a728a4 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -314,9 +314,10 @@ pressure simulation with MSM will cause the code to run slower. ---------- -The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver library `_ which provides a variety of solver -methods which can be used with LAMMPS. The paper by :ref:`(Sutman) ` -gives an overview of ScaFaCoS. +The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver +library `_ which provides a variety of solver +methods which can be used with LAMMPS. The paper by :ref:`(Sutman) +` gives an overview of ScaFaCoS. ScaFaCoS was developed by a consortium of German research facilities with a BMBF (German Ministry of Science and Education) funded project diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst index 63045a4792..9a3ce240cd 100644 --- a/doc/src/pair_adp.rst +++ b/doc/src/pair_adp.rst @@ -54,7 +54,7 @@ command to specify them. **ADP potentials are available from:** -* The NIST WWW site at http://www.ctcms.nist.gov/potentials. +* The NIST WWW site at https://www.ctcms.nist.gov/potentials. Note that ADP potentials obtained from NIST must be converted into the extended DYNAMO *setfl* format discussed below. * The OpenKIM Project at diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index e1469ae323..768ede1320 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -110,7 +110,7 @@ These pair styles compute Lennard Jones (LJ) and Coulombic interactions with additional switching or shifting functions that ramp the energy and/or force smoothly to zero between an inner and outer cutoff. They are implementations of the widely used CHARMM force -field used in the `CHARMM `_ MD code (and +field used in the `CHARMM `_ MD code (and others). See :ref:`(MacKerell) ` for a description of the CHARMM force field. diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index af936a6bc9..a7141c3849 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -122,15 +122,11 @@ are parameterized in terms of LAMMPS :doc:`metal units `. EAM potential files list atomic masses; thus you do not need to use the :doc:`mass ` command to specify them. -There are several WWW sites that distribute and document EAM -potentials stored in DYNAMO or other formats: +There are web sites that distribute and document EAM potentials stored +in DYNAMO or other formats: -.. parsed-literal:: - - http://www.ctcms.nist.gov/potentials - http://cst-www.nrl.navy.mil/ccm6/ap - http://enpub.fulton.asu.edu/cms/potentials/main/main.htm - https://openkim.org +* https://www.ctcms.nist.gov/potentials +* https://openkim.org These potentials should be usable with LAMMPS, though the alternate formats would need to be converted to the DYNAMO format used by LAMMPS diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index ed24b481f9..cb5f223b23 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -53,7 +53,7 @@ Description The *lj/gromacs* styles compute shifted LJ and Coulombic interactions with an additional switching function S(r) that ramps the energy and force smoothly to zero between an inner and outer cutoff. It is a commonly -used potential in the `GROMACS `_ MD code and for +used potential in the `GROMACS `_ MD code and for the coarse-grained models of :ref:`(Marrink) `. .. math:: diff --git a/doc/src/pair_meam.rst b/doc/src/pair_meam.rst index 51175a071d..8227938581 100644 --- a/doc/src/pair_meam.rst +++ b/doc/src/pair_meam.rst @@ -426,6 +426,8 @@ none **(Gullet)** Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). This report may be accessed on-line via `this link `_. +.. TODO the following URL is not accessible + .. _sandreport: http://infoserve.sandia.gov/sand_doc/2003/038782.pdf .. _Lee: diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index 45b406dd61..22661d99d6 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -66,10 +66,14 @@ peridynamic viscoelastic solid (VES) model. Style *peri/eps* implements the Peridynamic state-based elastic-plastic solid (EPS) model. -The canonical papers on Peridynamics are :ref:`(Silling 2000) ` -and :ref:`(Silling 2007) `. The implementation of Peridynamics -in LAMMPS is described in :ref:`(Parks) `. Also see the `PDLAMMPS user guide `_ for -more details about its implementation. +.. TODO the following URL is not valid + +The canonical papers on Peridynamics are :ref:`(Silling 2000) +` and :ref:`(Silling 2007) `. The +implementation of Peridynamics in LAMMPS is described in :ref:`(Parks) +`. Also see the `PDLAMMPS user guide +`_ for more details +about its implementation. The peridynamic VES and EPS models in PDLAMMPS were implemented by R. Rahman and J. T. Foster at University of Texas at San Antonio. The diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst index c150561cb1..1cb6cf6f08 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -49,11 +49,12 @@ A QUIP potential is fully specified by the filename which contains the parameters of the potential in XML format, the initialization string, and the map of atomic numbers. -GAP potentials can be obtained from the Data repository section of -`http://www.libatoms.org `_, where the -appropriate initialization strings are also advised. The list of -atomic numbers must be matched to the LAMMPS atom types specified in -the LAMMPS data file or elsewhere. +GAP potentials can be obtained from the `GAP models and databases page +on the libAtoms homepage `https://libatoms.github.io +`_, where the appropriate +initialization strings are also advised. The list of atomic numbers must +be matched to the LAMMPS atom types specified in the LAMMPS data file or +elsewhere. Two examples input scripts are provided in the examples/PACKAGES/quip directory. diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index c98347914b..311727f2c6 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -397,4 +397,4 @@ Default The option defaults are box = yes, timestep = yes, replace = yes, purge = no, trim = no, add = no, scaled = no, wrapped = yes, and format = native. -.. _vmd: http://www.ks.uiuc.edu/Research/vmd +.. _vmd: https://www.ks.uiuc.edu/Research/vmd