forked from lijiext/lammps
Merge pull request #744 from akohlmey/doc-update
Documentation build updates
This commit is contained in:
Steve Plimpton
GitHub
commit
1b51efd6b8
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@ -20,6 +20,7 @@ ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
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HAS_VIRTUALENV = YES
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endif
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SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
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SOURCES=$(wildcard src/*.txt)
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OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
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@ -55,7 +56,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
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@(\
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. $(VENV)/bin/activate ;\
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cp -r src/* $(RSTDIR)/ ;\
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sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
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sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
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echo "############################################" ;\
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doc_anchor_check src/*.txt ;\
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echo "############################################" ;\
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@ -91,7 +92,7 @@ epub: $(OBJECTS)
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@(\
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. $(VENV)/bin/activate ;\
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cp -r src/* $(RSTDIR)/ ;\
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sphinx-build -j 8 -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
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sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
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deactivate ;\
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)
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@mv epub/LAMMPS.epub .
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@ -159,7 +160,7 @@ $(VENV):
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@( \
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virtualenv -p $(PYTHON) $(VENV); \
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. $(VENV)/bin/activate; \
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pip install Sphinx==1.5.6; \
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pip install Sphinx; \
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pip install sphinxcontrib-images; \
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deactivate;\
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)
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@ -454,7 +454,7 @@ NOTE: By default, for 2d systems, granular particles are still modeled
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as 3d spheres, not 2d discs (circles), meaning their moment of inertia
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will be the same as in 3d. If you wish to model granular particles in
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2d as 2d discs, see the note on this topic in "Section
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6.2"_Section_howto.html#howto_2, where 2d simulations are disussed.
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6.2"_Section_howto.html#howto_2, where 2d simulations are discussed.
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:line
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@ -243,7 +243,7 @@ COLLOID package :link(COLLOID),h4
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[Contents:]
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Coarse-grained finite-size colloidal particles. Pair stayle and fix
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Coarse-grained finite-size colloidal particles. Pair styles and fix
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wall styles for colloidal interactions. Includes the Fast Lubrication
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Dynamics (FLD) method for hydrodynamic interactions, which is a
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simplified approximation to Stokesian dynamics.
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@ -734,7 +734,7 @@ make lib-latte args="-b -m gfortran" # download and build in lib/latte and
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Note that 3 symbolic (soft) links, "includelink" and "liblink" and
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"filelink", are created in lib/latte to point into the LATTE home dir.
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When LAMMPS builds in src it will use these links. You should
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also check that the Makefile.lammps file you create is apporpriate
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also check that the Makefile.lammps file you create is appropriate
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for the compiler you use on your system to build LATTE.
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You can then install/un-install the package and build LAMMPS in the
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@ -984,7 +984,7 @@ MSCG package :link(mscg),h4
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[Contents:]
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A "fix mscg"_fix_mscg.html command which can parameterize a
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Mulit-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
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Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
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library"_mscg_home.
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:link(mscg_home,https://github.com/uchicago-voth/MSCG-release)
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@ -1781,7 +1781,7 @@ coarse-grained DPD-based models for energetic, reactive molecular
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crystalline materials. It includes many pair styles specific to these
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systems, including for reactive DPD, where each particle has internal
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state for multiple species and a coupled set of chemical reaction ODEs
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are integrated each timestep. Highly accurate time intergrators for
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are integrated each timestep. Highly accurate time integrators for
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isothermal, isoenergetic, isobaric and isenthalpic conditions are
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included. These enable long timesteps via the Shardlow splitting
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algorithm.
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@ -2231,7 +2231,7 @@ Several extensions of the the dissipative particle dynamics (DPD)
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method. Specifically, energy-conserving DPD (eDPD) that can model
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non-isothermal processes, many-body DPD (mDPD) for simulating
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vapor-liquid coexistence, and transport DPD (tDPD) for modeling
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advection-diffuion-reaction systems. The equations of motion of these
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advection-diffusion-reaction systems. The equations of motion of these
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DPD extensions are integrated through a modified velocity-Verlet (MVV)
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algorithm.
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@ -2495,7 +2495,7 @@ make machine :pre
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NOTE: The LAMMPS executable these steps produce is not yet functional
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for a QM/MM simulation. You must also build Quantum ESPRESSO and
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create a new executable which links LAMMPS and Quanutm ESPRESSO
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create a new executable which links LAMMPS and Quantum ESPRESSO
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together. These are steps 3 and 4 described in the lib/qmmm/README
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file.
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@ -2554,7 +2554,7 @@ developed by the Cambridge University group.
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:link(quip,https://github.com/libAtoms/QUIP)
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To use this package you must have the QUIP libAatoms library available
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To use this package you must have the QUIP libAtoms library available
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on your system.
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[Author:] Albert Bartok (Cambridge University)
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@ -2809,7 +2809,7 @@ USER-VTK package :link(USER-VTK),h4
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A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
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"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
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other visuzlization packages.
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other visualization packages.
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:link(vtk,http://www.vtk.org)
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:link(paraview,http://www.paraview.org)
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@ -79,7 +79,7 @@ This section has the following sub-sections:
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Read this first :h5,link(start_2_1)
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If you want to avoid building LAMMPS yourself, read the preceeding
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If you want to avoid building LAMMPS yourself, read the preceding
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section about options available for downloading and installing
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executables. Details are discussed on the "download"_download page.
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@ -252,7 +252,7 @@ re-compile, after typing "make clean" (which will describe different
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clean options).
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The LMP_INC variable is used to include options that turn on ifdefs
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within the LAMMPS code. The options that are currently recogized are:
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within the LAMMPS code. The options that are currently recognized are:
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-DLAMMPS_GZIP
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-DLAMMPS_JPEG
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@ -363,7 +363,7 @@ installed on your platform. If MPI is installed on your system in the
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usual place (under /usr/local), you also may not need to specify these
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3 variables, assuming /usr/local is in your path. On some large
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parallel machines which use "modules" for their compile/link
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environements, you may simply need to include the correct module in
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environments, you may simply need to include the correct module in
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your build environment, before building LAMMPS. Or the parallel
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machine may have a vendor-provided MPI which the compiler has no
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trouble finding.
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@ -431,7 +431,7 @@ use the KISS library described above.
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You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
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so the compiler and linker can find the needed FFT header and library
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files. Note that on some large parallel machines which use "modules"
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for their compile/link environements, you may simply need to include
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for their compile/link environments, you may simply need to include
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the correct module in your build environment. Or the parallel machine
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may have a vendor-provided FFT library which the compiler has no
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trouble finding. See the src/MAKE/OPTIONS/Makefile.fftw file for an
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@ -470,7 +470,7 @@ precision.
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The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
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use single-precision FFTs with PPPM, which can speed-up long-range
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calulations, particularly in parallel or on GPUs. Fourier transform
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calculations, particularly in parallel or on GPUs. Fourier transform
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and related PPPM operations are somewhat insensitive to floating point
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truncation errors and thus do not always need to be performed in
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double precision. Using the -DFFT_SINGLE setting trades off a little
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@ -483,7 +483,7 @@ with support for single-precision, as explained above. For FFTW3 you
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also need to include -lfftw3f with the FFT_LIB setting, in addition to
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-lfftw3. For FFTW2, you also need to specify -DFFT_SIZE with the
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FFT_INC setting and -lsfftw with the FFT_LIB setting (in place of
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-lfftw). Similarly, if FFTW2 has been preinstalled with an explicit
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-lfftw). Similarly, if FFTW2 has been pre-installed with an explicit
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double-precision library (libdfftw.a and not the default libfftw.a),
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then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify
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-ldfftw to use double-precision FFTs.
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@ -714,7 +714,7 @@ list various make commands that can be used to manage packages.
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If you use a command in a LAMMPS input script that is part of a
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package, you must have built LAMMPS with that package, else you will
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get an error that the style is invalid or the command is unknown.
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Every command's doc page specfies if it is part of a package. You can
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Every command's doc page specifies if it is part of a package. You can
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type
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lmp_machine -h :pre
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@ -859,7 +859,7 @@ details for each package.
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[External libraries:]
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Packages in the tables "Section 4"_Section_packages.html with an "ext"
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in the last column link to exernal libraries whose source code is not
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in the last column link to external libraries whose source code is not
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included with LAMMPS. You must first download and install the library
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before building LAMMPS with that package installed. E.g. the voronoi
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package links to the freely available "Voro++ library"_voro_home2. You
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@ -963,7 +963,7 @@ src/MAKE/Makefile.foo and perform the build in the directory
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Obj_shared_foo. This is so that each file can be compiled with the
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-fPIC flag which is required for inclusion in a shared library. The
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build will create the file liblammps_foo.so which another application
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can link to dyamically. It will also create a soft link liblammps.so,
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can link to dynamically. It will also create a soft link liblammps.so,
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which will point to the most recently built shared library. This is
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the file the Python wrapper loads by default.
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@ -1329,8 +1329,8 @@ LAMMPS is compiled with CUDA=yes.
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numa Nm :pre
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This option is only relevant when using pthreads with hwloc support.
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In this case Nm defines the number of NUMA regions (typicaly sockets)
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on a node which will be utilizied by a single MPI rank. By default Nm
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In this case Nm defines the number of NUMA regions (typically sockets)
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on a node which will be utilized by a single MPI rank. By default Nm
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= 1. If this option is used the total number of worker-threads per
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MPI rank is threads*numa. Currently it is always almost better to
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assign at least one MPI rank per NUMA region, and leave numa set to
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@ -1394,7 +1394,7 @@ replica runs on on one or a few processors. Note that with MPI
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installed on a machine (e.g. your desktop), you can run on more
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(virtual) processors than you have physical processors.
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To run multiple independent simulatoins from one input script, using
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To run multiple independent simulations from one input script, using
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multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
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of the manual. World- and universe-style "variables"_variable.html
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are useful in this context.
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@ -1673,7 +1673,7 @@ The first section provides a global loop timing summary. The {loop time}
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is the total wall time for the section. The {Performance} line is
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provided for convenience to help predicting the number of loop
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continuations required and for comparing performance with other,
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similar MD codes. The {CPU use} line provides the CPU utilzation per
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similar MD codes. The {CPU use} line provides the CPU utilization per
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MPI task; it should be close to 100% times the number of OpenMP
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threads (or 1 of no OpenMP). Lower numbers correspond to delays due
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to file I/O or insufficient thread utilization.
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@ -78,7 +78,7 @@ order of operations compared to LAMMPS without acceleration:
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Neighbor lists can be created in a different order :ulb,l
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Bins used for sorting atoms can be oriented differently :l
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The default stencil order for PPPM is 7. By default, LAMMPS will
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calculate other PPPM parameters to fit the desired acuracy with
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calculate other PPPM parameters to fit the desired accuracy with
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this order :l
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The {newton} setting applies to all atoms, not just atoms shared
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between MPI tasks :l
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@ -28,7 +28,7 @@ compute 1 all aggregate/atom 3.5 :pre
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[Description:]
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Define a computation that assigns each atom a cluster, fragement,
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Define a computation that assigns each atom a cluster, fragment,
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or aggregate ID.
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A cluster is defined as a set of atoms, each of which is within the
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@ -53,7 +53,7 @@ like micelles.
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Only atoms in the compute group are clustered and assigned cluster
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IDs. Atoms not in the compute group are assigned a cluster ID = 0.
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For fragments, only bonds where [both] atoms of the bond are included
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in the compute group are assigned to fragments, so that only fragmets
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in the compute group are assigned to fragments, so that only fragments
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are detected where [all] atoms are in the compute group. Thus atoms
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may be included in the compute group, yes still have a fragment ID of 0.
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|
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@ -25,15 +25,15 @@ compute 2 all pressure/uef my_temp_uef virial :pre
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[Description:]
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|
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This command is used to compute the pressure tensor in
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This command is used to compute the pressure tensor in
|
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the reference frame of the applied flow field when
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"fix nvt/uef"_fix_nh_uef.html" or
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"fix npt/uef"_fix_nh_uef.html" is used.
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"fix nvt/uef"_fix_nh_uef.html" or
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"fix npt/uef"_fix_nh_uef.html" is used.
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It is not necessary to use this command to compute the scalar
|
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value of the pressure. A "compute pressure"_compute_pressure.html
|
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may be used for that purpose.
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The keywords and output information are documented in
|
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The keywords and output information are documented in
|
||||
"compute_pressure"_compute_pressure.html.
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[Restrictions:]
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|
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@ -46,8 +46,8 @@ This command can only be used when "fix nvt/uef"_fix_nh_uef.html
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or "fix npt/uef"_fix_nh_uef.html is active.
|
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The kinetic contribution to the pressure tensor
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will be accurate only when
|
||||
the compute specificed by {temp-ID} is a
|
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will be accurate only when
|
||||
the compute specified by {temp-ID} is a
|
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"compute temp/uef"_compute_temp_uef.html.
|
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[Related commands:]
|
||||
|
|
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|
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@ -64,10 +64,10 @@ not performed once every {N} steps by this command. Instead it is
|
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performed (typically) only a small number of times and the elapsed
|
||||
times are used to predict when the end-of-the-run will be. Both of
|
||||
these attributes can be useful when performing benchmark calculations
|
||||
for a desired length of time with minmimal overhead. For example, if
|
||||
for a desired length of time with minimal overhead. For example, if
|
||||
a run is performing 1000s of timesteps/sec, the overhead for syncing
|
||||
the timer frequently across a large number of processors may be
|
||||
non-negligble.
|
||||
non-negligible.
|
||||
|
||||
Equal-style variables evaluate to a numeric value. See the
|
||||
"variable"_variable.html command for a description. They calculate
|
||||
|
|
@ -125,7 +125,7 @@ to the screen and logfile when the halt condition is triggered. If
|
|||
{message} is set to yes, a one line message with the values that
|
||||
triggered the halt is printed. If {message} is set to no, no message
|
||||
is printed; the run simply exits. The latter may be desirable for
|
||||
post-processing tools that extract thermodyanmic information from log
|
||||
post-processing tools that extract thermodynamic information from log
|
||||
files.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@ the velocity for the force evaluation:
|
|||
|
||||
where the parameter <font size="4">λ</font> depends on the
|
||||
specific choice of DPD parameters, and needs to be tuned on a
|
||||
case-by-case basis. Specification of a {lambda} value is opttional.
|
||||
case-by-case basis. Specification of a {lambda} value is optional.
|
||||
If specified, the setting must be from 0.0 to 1.0. If not specified,
|
||||
a default value of 0.5 is used, which effectively reproduces the
|
||||
standard velocity-Verlet (VV) scheme. For more details, see
|
||||
|
|
|
|||
|
|
@ -113,9 +113,9 @@ keeping the replicas equally spaced.
|
|||
|
||||
:line
|
||||
|
||||
The keyword {perp} specifies if and how a perpendicual nudging force
|
||||
The keyword {perp} specifies if and how a perpendicular nudging force
|
||||
is computed. It adds a spring force perpendicular to the path in
|
||||
order to prevent the path from becoming too kinky. It can
|
||||
order to prevent the path from becoming too strongly kinked. It can
|
||||
significantly improve the convergence of the NEB calculation when the
|
||||
resolution is poor. I.e. when few replicas are used; see
|
||||
"(Maras)"_#Maras1 for details.
|
||||
|
|
|
|||
|
|
@ -322,9 +322,9 @@ the fix neb command.
|
|||
The forward (reverse) energy barrier is the potential energy of the
|
||||
highest replica minus the energy of the first (last) replica.
|
||||
|
||||
Supplementary informations for all replicas can be printed out to the
|
||||
screen and master log.lammps file by adding the verbose keyword. These
|
||||
informations include the following. The "path angle" (pathangle) for
|
||||
Supplementary information for all replicas can be printed out to the
|
||||
screen and master log.lammps file by adding the verbose keyword. This
|
||||
information include the following. The "path angle" (pathangle) for
|
||||
the replica i which is the angle between the 3N-length vectors (Ri-1 -
|
||||
Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
|
||||
i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
|
||||
|
|
@ -339,8 +339,8 @@ energy gradient of image i. ReplicaForce is the two-norm of the
|
|||
3N-length force vector (including nudging forces) for replica i.
|
||||
MaxAtomForce is the maximum force component of any atom in replica i.
|
||||
|
||||
When a NEB calculation does not converge properly, these suplementary
|
||||
informations can help understanding what is going wrong. For instance
|
||||
When a NEB calculation does not converge properly, the suplementary
|
||||
information can help understanding what is going wrong. For instance
|
||||
when the path angle becomes accute the definition of tangent used in
|
||||
the NEB calculation is questionable and the NEB cannot may diverge
|
||||
"(Maras)"_#Maras2.
|
||||
|
|
|
|||
|
|
@ -148,15 +148,18 @@ class RSTFormatting(Formatting):
|
|||
return "\n----------\n\n" + content.strip()
|
||||
|
||||
def image(self, content, file, link=None):
|
||||
if link and (link.lower().endswith('.jpg') or
|
||||
link.lower().endswith('.jpeg') or
|
||||
link.lower().endswith('.png') or
|
||||
link.lower().endswith('.gif')):
|
||||
converted = ".. thumbnail:: " + self.markup.unescape_rst_chars(link) + "\n"
|
||||
else:
|
||||
converted = ".. image:: " + self.markup.unescape_rst_chars(file) + "\n"
|
||||
if link:
|
||||
converted += " :target: " + self.markup.unescape_rst_chars(link) + "\n"
|
||||
# 2017-12-07: commented out to disable thumbnail processing due to dropping
|
||||
# support for obsolete sphinxcontrib.images extension
|
||||
#
|
||||
#if link and (link.lower().endswith('.jpg') or
|
||||
# link.lower().endswith('.jpeg') or
|
||||
# link.lower().endswith('.png') or
|
||||
# link.lower().endswith('.gif')):
|
||||
# converted = ".. thumbnail:: " + self.markup.unescape_rst_chars(link) + "\n"
|
||||
#else:
|
||||
converted = ".. image:: " + self.markup.unescape_rst_chars(file) + "\n"
|
||||
if link:
|
||||
converted += " :target: " + self.markup.unescape_rst_chars(link) + "\n"
|
||||
|
||||
if "c" in self.current_command_list:
|
||||
converted += " :align: center\n"
|
||||
|
|
|
|||
|
|
@ -31,8 +31,11 @@ import os
|
|||
# ones.
|
||||
extensions = [
|
||||
'sphinx.ext.mathjax',
|
||||
'sphinxcontrib.images',
|
||||
]
|
||||
# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
|
||||
# yet we can no longer use Sphinx 15.x, since that breaks with
|
||||
# newer version of the multiprocessor module.
|
||||
# 'sphinxcontrib.images',
|
||||
|
||||
images_config = {
|
||||
'default_image_width' : '25%',
|
||||
|
|
|
|||
Loading…
Reference in New Issue