forked from lijiext/lammps
correct and improve typesetting for various sub-sub-subsections in "Getting started"
This commit is contained in:
Axel Kohlmeyer
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cf6f504977
commit
555a02786d
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@ -79,7 +79,7 @@ This section has the following sub-sections:
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:line
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[{Read this first:}] :link(start_2_1)
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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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section about options available for downloading and installing
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@ -148,9 +148,9 @@ include it in the LAMMPS distribution.
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:line
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[{Steps to build a LAMMPS executable:}] :link(start_2_2)
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Steps to build a LAMMPS executable :h5,link(start_2_2)
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[Step 0]
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Step 0 :h6
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The src directory contains the C++ source and header files for LAMMPS.
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It also contains a top-level Makefile and a MAKE sub-directory with
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@ -172,10 +172,12 @@ a list of available choices from src/MAKE and all of its
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sub-directories. If one of those has the options you want or is the
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machine you want, you can type a command like:
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make mpi
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make mpi :pre
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or
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make serial_icc
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make serial :pre
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or
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gmake mac :pre
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Note that the corresponding Makefile.machine can exist in src/MAKE or
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@ -189,14 +191,14 @@ Note that on a multi-processor or multi-core platform you can launch a
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parallel make, by using the "-j" switch with the make command, which
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will build LAMMPS more quickly.
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If you get no errors and an executable like lmp_mpi or lmp_g++_serial
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or lmp_mac is produced, then you're done; it's your lucky day.
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If you get no errors and an executable like [lmp_mpi] or [lmp_serial]
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or [lmp_mac] is produced, then you're done; it's your lucky day.
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Note that by default only a few of LAMMPS optional packages are
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installed. To build LAMMPS with optional packages, see "this
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section"_#start_3 below.
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[Step 1]
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Step 1 :h6
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If Step 0 did not work, you will need to create a low-level Makefile
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for your machine, like Makefile.foo. You should make a copy of an
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@ -207,13 +209,13 @@ the first line, the "compiler/linker settings" section, and the
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file in src/MAKE/MINE and it will not be altered by any future LAMMPS
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updates.
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[Step 2]
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Step 2 :h6
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Change the first line of Makefile.foo to list the word "foo" after the
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"#", and whatever other options it will set. This is the line you
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will see if you just type "make".
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[Step 3]
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Step 3 :h6
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The "compiler/linker settings" section lists compiler and linker
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settings for your C++ compiler, including optimization flags. You can
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@ -242,7 +244,7 @@ first time on a new platform, a long list of *.d files will be printed
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out rapidly. This is not an error; it is the Makefile doing its
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normal creation of dependencies.
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[Step 4]
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Step 4 :h6
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The "system-specific settings" section has several parts. Note that
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if you change any -D setting in this section, you should do a full
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@ -349,7 +351,7 @@ platforms. The -DPACK_ARRAY setting is the default. See the
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"kspace_style"_kspace_style.html command for info about PPPM. See
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Step 6 below for info about building LAMMPS with an FFT library.
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[Step 5]
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Step 5 :h6
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The 3 MPI variables are used to specify an MPI library to build LAMMPS
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with. Note that you do not need to set these if you use the MPI
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@ -405,7 +407,7 @@ Note that the ANSI-standard function clock() rolls over after an hour
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or so, and is therefore insufficient for timing long LAMMPS
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simulations.
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[Step 6]
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Step 6 :h6
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The 3 FFT variables allow you to specify an FFT library which LAMMPS
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uses (for performing 1d FFTs) when running the particle-particle
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@ -458,7 +460,7 @@ accuracy for reduced memory use and parallel communication costs for
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transposing 3d FFT data. Note that single precision FFTs have only
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been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
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[Step 7]
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Step 7 :h6
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The 3 JPG variables allow you to specify a JPEG and/or PNG library
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which LAMMPS uses when writing out JPEG or PNG files via the "dump
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@ -481,13 +483,13 @@ find it.
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As before, if these header and library files are in the usual place on
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your machine, you may not need to set these variables.
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[Step 8]
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Step 8 :h6
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Note that by default only a few of LAMMPS optional packages are
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installed. To build LAMMPS with optional packages, see "this
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section"_#start_3 below, before proceeding to Step 9.
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[Step 9]
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Step 9 :h6
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That's it. Once you have a correct Makefile.foo, and you have
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pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
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@ -506,7 +508,7 @@ You should get the executable lmp_foo when the build is complete.
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:line
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[{Errors that can occur when making LAMMPS:}] :link(start_2_3)
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Errors that can occur when making LAMMPS: h5 :link(start_2_3)
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NOTE: If an error occurs when building LAMMPS, the compiler or linker
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will state very explicitly what the problem is. The error message
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@ -543,22 +545,22 @@ above in Step 4.
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:line
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[{Additional build tips:}] :link(start_2_4)
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Additional build tips :h5,link(start_2_4)
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(1) Building LAMMPS for multiple platforms.
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Building LAMMPS for multiple platforms. :h6
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You can make LAMMPS for multiple platforms from the same src
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directory. Each target creates its own object sub-directory called
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Obj_target where it stores the system-specific *.o files.
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(2) Cleaning up.
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Cleaning up. :h6
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Typing "make clean-all" or "make clean-machine" will delete *.o object
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files created when LAMMPS is built, for either all builds or for a
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particular machine.
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(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
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-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
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Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
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-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
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As explained above, any of these 3 settings can be specified on the
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LMP_INC line in your low-level src/MAKE/Makefile.foo.
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@ -608,14 +610,14 @@ neighbor lists and would run very slowly in terms of CPU secs/timestep.
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:line
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Building for a Mac :h5 :link(start_2_5)
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Building for a Mac :h5,link(start_2_5)
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OS X is BSD Unix, so it should just work. See the
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src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
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:line
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Building for Windows :h5 :link(start_2_6)
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Building for Windows :h5,link(start_2_6)
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If you want to build a Windows version of LAMMPS, you can build it
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yourself, but it may require some effort. LAMMPS expects a Unix-like
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@ -664,7 +666,7 @@ Makefile.machine to add settings needed by some packages.
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:line
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[{Package basics:}] :link(start_3_1)
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Package basics: :h5,link(start_3_1)
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The source code for LAMMPS is structured as a set of core files which
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are always included, plus optional packages. Packages are groups of
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@ -718,7 +720,7 @@ files or either a standard or user-contributed package are given in
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:line
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[{Including/excluding packages:}] :link(start_3_2)
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Including/excluding packages :h5,link(start_3_2)
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To use (or not use) a package you must include it (or exclude it)
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before building LAMMPS. From the src directory, this is typically as
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@ -792,7 +794,7 @@ package-related make options.
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:line
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[{Packages that require extra libraries:}] :link(start_3_3)
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Packages that require extra libraries :h5,link(start_3_3)
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A few of the standard and user packages require additional auxiliary
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libraries. Many of them are provided with LAMMPS, in which case they
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@ -877,7 +879,7 @@ the LAMMPS build will typically fail.
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:line
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[{Packages that require Makefile.machine settings}] :link(start_3_4)
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Packages that require Makefile.machine settings :h5,link(start_3_4)
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A few packages require specific settings in Makefile.machine, to
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either build or use the package effectively. These are the
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@ -1037,7 +1039,7 @@ then be called from another application or a scripting language. See
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LAMMPS to other codes. See "this section"_Section_python.html for
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more info on wrapping and running LAMMPS from Python.
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[Static library:] :h5
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Static library :h5
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To build LAMMPS as a static library (*.a file on Linux), type
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@ -1051,7 +1053,7 @@ will create the file liblammps_foo.a which another application can
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link to. It will also create a soft link liblammps.a, which will
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point to the most recently built static library.
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[Shared library:] :h5
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Shared library :h5
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To build LAMMPS as a shared library (*.so file on Linux), which can be
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dynamically loaded, e.g. from Python, type
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@ -1123,7 +1125,7 @@ For the csh or tcsh shells, you would add something like this to your
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setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
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[Calling the LAMMPS library:] :h5
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Calling the LAMMPS library :h5
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Either flavor of library (static or shared) allows one or more LAMMPS
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objects to be instantiated from the calling program.
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