Commit 07cd194e authored by Steven J. Plimpton's avatar Steven J. Plimpton
Browse files

tweaks to Manual formatting

parent ccacf0d4

doc/src/Build.txt

+3 −14
Original line number Diff line number Diff line
@@ -24,17 +24,9 @@ as described on the "Install"_Install.html doc page. 
   Build_cmake

   Build_make

   Build_link



.. toctree::

   :maxdepth: 1



   Build_basics

   Build_settings

   Build_package



.. toctree::

   :maxdepth: 1



   Build_extras



END_RST -->
@@ -43,12 +35,9 @@ END_RST --> 


"Build LAMMPS with CMake"_Build_cmake.html

"Build LAMMPS with make"_Build_make.html

"Link LAMMPS as a library to another code"_Build_link.html :all(b)



Build options:



"Basic build options: serial/parallel, compilers, executable/library"_Build_basics.html

"Optional build settings"_Build_settings.html :all(b)

"Link LAMMPS as a library to another code"_Build_link.html

"Basic build options"_Build_basics.html

"Optional build settings"_Build_settings.html

"Include packages in build"_Build_package.html

"Packages with extra build options"_Build_extras.html :all(b)

doc/src/Build_basics.txt

+5 −5
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@@ -20,7 +20,7 @@ CMake and make: 


:line



Serial vs parallel build :h3,link(serial)

Serial vs parallel build :h4,link(serial)



LAMMPS can be built to run in parallel using the ubiquitous "MPI

(message-passing
@@ -118,7 +118,7 @@ please refer to its documentation. 


:line



Choice of compiler and compile/link options :h3,link(compile)

Choice of compiler and compile/link options :h4,link(compile)



The choice of compiler and compiler flags can be important for

performance.  Vendor compilers can produce faster code than
@@ -210,7 +210,7 @@ Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP) :pre 


:line



Build LAMMPS as an executable or a library :h3,link(exe)

Build LAMMPS as an executable or a library :h4,link(exe)



LAMMPS can be built as either an executable or as a static or shared

library.  The LAMMPS library can be called from another application or
@@ -271,7 +271,7 @@ should be the file /usr/local/lib/libmpich.so. 


:line



Build the LAMMPS documentation :h3,link(doc)

Build the LAMMPS documentation :h4,link(doc)



[CMake variable]:
@@ -294,7 +294,7 @@ lammps/doc dir to see other options. 


:line



Install LAMMPS after a build :h3,link(install)

Install LAMMPS after a build :h4,link(install)



After building LAMMPS, you may wish to copy the LAMMPS executable of

library, along with other LAMMPS files (library header, doc files) to

doc/src/Build_settings.txt

+7 −7
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@@ -23,7 +23,7 @@ explain how to do this for building both with CMake and make. 


:line

 

FFT library :h3,link(fft)

FFT library :h4,link(fft)



When the KSPACE package is included in a LAMMPS build, the

"kspace_style pppm"_kspace_style.html command performs 3d FFTs which
@@ -126,7 +126,7 @@ ARRAY mode. 


:line



Size of LAMMPS data types :h3,link(size)

Size of LAMMPS data types :h4,link(size)



LAMMPS has a few integer data types which can be defined as 4-byte or

8-byte integers.  The default setting of "smallbig" is almost always
@@ -189,7 +189,7 @@ in whichever lib/gpu/Makefile is used must be the same as above. 


:line



Output of JPG, PNG, and movie files :h3,link(graphics)

Output of JPG, PNG, and movie files :h4,link(graphics)



The "dump image"_dump_image.html command has options to output JPEG or

PNG image files.  Likewise the "dump movie"_dump_image.html command
@@ -245,7 +245,7 @@ crash. 


:line



Read or write compressed files :h3,link(gzip)

Read or write compressed files :h4,link(gzip)



If this option is enabled, large files can be read or written with

gzip compression by several LAMMPS commands, including
@@ -276,7 +276,7 @@ what the "COMPRESS package"_Packages_details.html#PKG-COMPRESS enables. 


:line



Memory allocation alignment :h3,link(align)

Memory allocation alignment :h4,link(align)



This setting enables the use of the posix_memalign() call instead of

malloc() when LAMMPS allocates large chunks or memory.  This can make
@@ -308,7 +308,7 @@ manages its dynamical memory. 


:line



Workaround for long long integers :h3,link(longlong)

Workaround for long long integers :h4,link(longlong)



If your system or MPI version does not recognize "long long" data

types, the following setting will be needed.  It converts "long long"
@@ -325,7 +325,7 @@ LMP_INC = -DLAMMPS_LONGLONG_TO_LONG :pre 


:line



Exception handling when using LAMMPS as a library :h3,link(exceptions)

Exception handling when using LAMMPS as a library :h4,link(exceptions)



This setting is useful when external codes drive LAMMPS as a library.

With this option enabled LAMMPS errors do not kill the caller.

doc/src/Intro_authors.txt

+1 −1
Original line number Diff line number Diff line
@@ -30,7 +30,7 @@ the packages they have written are somewhat unique to LAMMPS and the 
code would not be as general-purpose as it is without their expertise

and efforts.



Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM packages

Richard Berger (Temple U), GitHub site and Sphinx doc pages

Roy Pollock (LLNL), Ewald and PPPM solvers

Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages

Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential

doc/src/Modify.txt

+2 −12
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@@ -38,19 +38,11 @@ contribute"_Modify_contribute.html doc page. 
   Modify_compute

   Modify_fix

   Modify_command



.. toctree::

   :maxdepth: 1



   Modify_dump

   Modify_kspace

   Modify_min

   Modify_region

   Modify_body



.. toctree::

   :maxdepth: 1



   Modify_thermo

   Modify_variable
@@ -66,14 +58,12 @@ END_RST --> 
"Bond, angle, dihedral, improper styles"_Modify_bond.html

"Compute styles"_Modify_compute.html

"Fix styles"_Modify_fix.html

"Input script command styles"_Modify_command.html :all(b)



"Input script command styles"_Modify_command.html

"Dump styles"_Modify_dump.html

"Kspace styles"_Modify_kspace.html

"Minimization styles"_Modify_min.html

"Region styles"_Modify_region.html

"Body styles"_Modify_body.html :all(b)



"Body styles"_Modify_body.html

"Thermodynamic output options"_Modify_thermo.html

"Variable options"_Modify_variable.html :all(b)

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