diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst index cb31369501..0a23691181 100644 --- a/doc/src/Commands_all.rst +++ b/doc/src/Commands_all.rst @@ -1,23 +1,27 @@ -.. table_from_list:: - :columns: 3 +.. only:: html - * :doc:`General commands ` - * :doc:`Fix styles ` - * :doc:`Compute styles ` - * :doc:`Pair styles ` - * :ref:`Bond styles ` - * :ref:`Angle styles ` - * :ref:`Dihedral styles ` - * :ref:`Improper styles ` - * :doc:`KSpace styles ` - * :doc:`Dump styles ` + .. table_from_list:: + :columns: 3 + + * :doc:`General commands ` + * :doc:`Fix styles ` + * :doc:`Compute styles ` + * :doc:`Pair styles ` + * :ref:`Bond styles ` + * :ref:`Angle styles ` + * :ref:`Dihedral styles ` + * :ref:`Improper styles ` + * :doc:`KSpace styles ` + * :doc:`Dump styles ` + +.. raw:: latex + + \clearpage General commands ================ -An alphabetic list of general LAMMPS commands. Note that style -commands with many variants, can be more easily accessed via the small -table above. +An alphabetic list of general LAMMPS commands. .. table_from_list:: :columns: 5 diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index 2664b74076..a8b52912c2 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -1,21 +1,23 @@ -.. table_from_list:: - :columns: 3 - - * :doc:`General commands ` - * :doc:`Fix styles ` - * :doc:`Compute styles ` - * :doc:`Pair styles ` - * :ref:`Bond styles ` - * :ref:`Angle styles ` - * :ref:`Dihedral styles ` - * :ref:`Improper styles ` - * :doc:`KSpace styles ` - * :doc:`Dump styles ` +.. only:: html + .. table_from_list:: + :columns: 3 + + * :doc:`General commands ` + * :doc:`Fix styles ` + * :doc:`Compute styles ` + * :doc:`Pair styles ` + * :ref:`Bond styles ` + * :ref:`Angle styles ` + * :ref:`Dihedral styles ` + * :ref:`Improper styles ` + * :doc:`KSpace styles ` + * :doc:`Dump styles ` + .. _bond: -Bond_style potentials -===================== +Bonds styles +============ All LAMMPS :doc:`bond_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in @@ -60,8 +62,8 @@ OPT. .. _angle: -Angle_style potentials -====================== +Angle styles +============ All LAMMPS :doc:`angle_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in @@ -106,8 +108,8 @@ OPT. .. _dihedral: -Dihedral_style potentials -========================= +Dihedral styles +=============== All LAMMPS :doc:`dihedral_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in @@ -144,8 +146,8 @@ OPT. .. _improper: -Improper_style potentials -========================= +Improper styles +=============== All LAMMPS :doc:`improper_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in diff --git a/doc/src/Commands_category.rst b/doc/src/Commands_category.rst index 7ac747e8fc..8d4f306151 100644 --- a/doc/src/Commands_category.rst +++ b/doc/src/Commands_category.rst @@ -1,3 +1,7 @@ +.. raw:: latex + + \clearpage + Commands by category ==================== @@ -6,8 +10,8 @@ This page lists most of the LAMMPS commands, grouped by category. The alphabetically. Style options for entries like fix, compute, pair etc. have their own pages where they are listed alphabetically. -Initialization: ------------------------------- +Initialization +-------------- .. table_from_list:: :columns: 5 @@ -18,8 +22,8 @@ Initialization: * :doc:`suffix ` * :doc:`units ` -Setup simulation box: ------------------------------- +Setup simulation box +-------------------- .. table_from_list:: :columns: 4 @@ -31,8 +35,8 @@ Setup simulation box: * :doc:`lattice ` * :doc:`region ` -Setup atoms: ------------------------------- +Setup atoms +----------- .. table_from_list:: :columns: 4 @@ -55,8 +59,8 @@ Setup atoms: * :doc:`set ` * :doc:`velocity ` -Force fields: ------------------------------- +Force fields +------------ .. table_from_list:: :columns: 4 @@ -79,8 +83,8 @@ Force fields: * :doc:`pair_write ` * :doc:`special_bonds ` -Settings: ------------------------------- +Settings +-------- .. table_from_list:: :columns: 4 @@ -98,8 +102,8 @@ Settings: * :doc:`timer ` * :doc:`timestep ` -Operations within timestepping (fixes) and diagnostics (computes): ------------------------------------------------------------------------------------------- +Operations within timestepping (fixes) and diagnostics (computes) +----------------------------------------------------------------- .. table_from_list:: :columns: 4 @@ -111,8 +115,8 @@ Operations within timestepping (fixes) and diagnostics (computes): * :doc:`uncompute ` * :doc:`unfix ` -Output: ------------------------------- +Output +------ .. table_from_list:: :columns: 4 @@ -131,8 +135,8 @@ Output: * :doc:`write_dump ` * :doc:`write_restart ` -Actions: ------------------------------- +Actions +------- .. table_from_list:: :columns: 6 @@ -146,8 +150,8 @@ Actions: * :doc:`tad ` * :doc:`temper ` -Input script control: ------------------------------- +Input script control +-------------------- .. table_from_list:: :columns: 7 diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index e5ec34fc22..ba0c585014 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -1,19 +1,21 @@ -.. table_from_list:: - :columns: 3 +.. only:: html - * :doc:`General commands ` - * :doc:`Fix styles ` - * :doc:`Compute styles ` - * :doc:`Pair styles ` - * :ref:`Bond styles ` - * :ref:`Angle styles ` - * :ref:`Dihedral styles ` - * :ref:`Improper styles ` - * :doc:`KSpace styles ` - * :doc:`Dump styles ` + .. table_from_list:: + :columns: 3 + + * :doc:`General commands ` + * :doc:`Fix styles ` + * :doc:`Compute styles ` + * :doc:`Pair styles ` + * :ref:`Bond styles ` + * :ref:`Angle styles ` + * :ref:`Dihedral styles ` + * :ref:`Improper styles ` + * :doc:`KSpace styles ` + * :doc:`Dump styles ` -Compute commands -================ +Compute styles +============== An alphabetic list of all LAMMPS :doc:`compute ` commands. Some styles have accelerated versions. This is indicated by @@ -21,7 +23,7 @@ additional letters in parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: - :columns: 5 + :columns: 4 * :doc:`ackland/atom ` * :doc:`adf ` diff --git a/doc/src/Commands_dump.rst b/doc/src/Commands_dump.rst index d7c8e73b58..66505c55a7 100644 --- a/doc/src/Commands_dump.rst +++ b/doc/src/Commands_dump.rst @@ -1,19 +1,21 @@ -.. table_from_list:: - :columns: 3 +.. only:: html - * :doc:`General commands ` - * :doc:`Fix styles ` - * :doc:`Compute styles ` - * :doc:`Pair styles ` - * :ref:`Bond styles ` - * :ref:`Angle styles ` - * :ref:`Dihedral styles ` - * :ref:`Improper styles ` - * :doc:`KSpace styles ` - * :doc:`Dump styles ` + .. table_from_list:: + :columns: 3 + + * :doc:`General commands ` + * :doc:`Fix styles ` + * :doc:`Compute styles ` + * :doc:`Pair styles ` + * :ref:`Bond styles ` + * :ref:`Angle styles ` + * :ref:`Dihedral styles ` + * :ref:`Improper styles ` + * :doc:`KSpace styles ` + * :doc:`Dump styles ` -Dump commands -============= +Dump styles +=========== An alphabetic list of all LAMMPS :doc:`dump ` commands. diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 4350a98b31..ce119e32b8 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -1,19 +1,21 @@ -.. table_from_list:: - :columns: 3 +.. only:: html - * :doc:`General commands ` - * :doc:`Fix styles ` - * :doc:`Compute styles ` - * :doc:`Pair styles ` - * :ref:`Bond styles ` - * :ref:`Angle styles ` - * :ref:`Dihedral styles ` - * :ref:`Improper styles ` - * :doc:`KSpace styles ` - * :doc:`Dump styles ` + .. table_from_list:: + :columns: 3 + + * :doc:`General commands ` + * :doc:`Fix styles ` + * :doc:`Compute styles ` + * :doc:`Pair styles ` + * :ref:`Bond styles ` + * :ref:`Angle styles ` + * :ref:`Dihedral styles ` + * :ref:`Improper styles ` + * :doc:`KSpace styles ` + * :doc:`Dump styles ` -Fix commands -============ +Fix styles +========== An alphabetic list of all LAMMPS :doc:`fix ` commands. Some styles have accelerated versions. This is indicated by additional letters in @@ -21,7 +23,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: - :columns: 5 + :columns: 4 * :doc:`accelerate/cos ` * :doc:`acks2/reaxff (k) ` diff --git a/doc/src/Commands_input.rst b/doc/src/Commands_input.rst index 595b8ffa2c..dc0fb72dd9 100644 --- a/doc/src/Commands_input.rst +++ b/doc/src/Commands_input.rst @@ -10,14 +10,14 @@ for any commands that may be processed later. Commands may set an internal variable, read in a file, or run a simulation. These actions can be grouped into three categories: -a) commands that change a global setting (examples: timestep, newton, - echo, log, thermo, restart), +a) commands that change a global setting (examples: :doc:`timestep `, :doc:`newton `, + :doc:`echo `, :doc:`log `, :doc:`thermo `, :doc:`restart `), b) commands that add, modify, remove, or replace "styles" that are - executed during a "run" (examples: pair_style, fix, compute, dump, - thermo_style, pair_modify), and + executed during a "run" (examples: :doc:`pair_style `, :doc:`fix `, :doc:`compute `, :doc:`dump `, + :doc:`thermo_style `, :doc:`pair_modify `), and c) commands that execute a "run" or perform some other computation or - operation (examples: print, run, minimize, temper, write_dump, rerun, - read_data, read_restart) + operation (examples: :doc:`print `, :doc:`run `, :doc:`minimize `, :doc:`temper `, :doc:`write_dump `, :doc:`rerun `, + :doc:`read_data `, :doc:`read_restart `) Commands in category a) have default settings, which means you only need to use the command if you wish to change the defaults. @@ -61,7 +61,7 @@ between commands in the c) category. The following rules apply: ` command initializes the system by setting up the simulation box and assigning atoms to processors. If default values are not desired, the :doc:`processors ` and - :doc:`boundary ` commands need to be used before read_data + :doc:`boundary ` commands need to be used before ``read_data`` to tell LAMMPS how to map processors to the simulation box. Many input script errors are detected by LAMMPS and an ERROR or @@ -70,6 +70,6 @@ more information on what errors mean. The documentation for each command lists restrictions on how the command can be used. You can use the :ref:`-skiprun ` command line flag -to have LAMMPS skip the execution of any "run", "minimize", or similar +to have LAMMPS skip the execution of any ``run``, ``minimize``, or similar commands to check the entire input for correct syntax to avoid crashes on typos or syntax errors in long runs. diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst index 088789e321..cad493500c 100644 --- a/doc/src/Commands_kspace.rst +++ b/doc/src/Commands_kspace.rst @@ -1,19 +1,21 @@ -.. table_from_list:: - :columns: 3 +.. only:: html - * :doc:`General commands ` - * :doc:`Fix styles ` - * :doc:`Compute styles ` - * :doc:`Pair styles ` - * :ref:`Bond styles ` - * :ref:`Angle styles ` - * :ref:`Dihedral styles ` - * :ref:`Improper styles ` - * :doc:`KSpace styles ` - * :doc:`Dump styles ` + .. table_from_list:: + :columns: 3 + + * :doc:`General commands ` + * :doc:`Fix styles ` + * :doc:`Compute styles ` + * :doc:`Pair styles ` + * :ref:`Bond styles ` + * :ref:`Angle styles ` + * :ref:`Dihedral styles ` + * :ref:`Improper styles ` + * :doc:`KSpace styles ` + * :doc:`Dump styles ` -KSpace solvers -============== +KSpace styles +============= All LAMMPS :doc:`kspace_style ` solvers. Some styles have accelerated versions. This is indicated by additional letters in diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 9cf0495c8e..a9ea040c17 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -1,19 +1,21 @@ -.. table_from_list:: - :columns: 3 +.. only:: html - * :doc:`General commands ` - * :doc:`Fix styles ` - * :doc:`Compute styles ` - * :doc:`Pair styles ` - * :ref:`Bond styles ` - * :ref:`Angle styles ` - * :ref:`Dihedral styles ` - * :ref:`Improper styles ` - * :doc:`KSpace styles ` - * :doc:`Dump styles ` + .. table_from_list:: + :columns: 3 + + * :doc:`General commands ` + * :doc:`Fix styles ` + * :doc:`Compute styles ` + * :doc:`Pair styles ` + * :ref:`Bond styles ` + * :ref:`Angle styles ` + * :ref:`Dihedral styles ` + * :ref:`Improper styles ` + * :doc:`KSpace styles ` + * :doc:`Dump styles ` -Pair_style potentials -====================== +Pair styles +=========== All LAMMPS :doc:`pair_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in @@ -21,7 +23,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: - :columns: 4 + :columns: 3 * :doc:`none ` * :doc:`zero ` @@ -35,10 +37,6 @@ OPT. * * * - * - * - * - * * :doc:`adp (ko) ` * :doc:`agni (o) ` * :doc:`aip/water/2dm (t) ` diff --git a/doc/src/Commands_parse.rst b/doc/src/Commands_parse.rst index f6aa859ac2..a342441878 100644 --- a/doc/src/Commands_parse.rst +++ b/doc/src/Commands_parse.rst @@ -42,8 +42,8 @@ LAMMPS: If the $ is followed by text in curly brackets '{}', then the variable name is the text inside the curly brackets. If no curly brackets follow the $, then the variable name is the single character - immediately following the $. Thus ${myTemp} and $x refer to variables - named "myTemp" and "x", while "$xx" will be interpreted as a variable + immediately following the $. Thus ``${myTemp}`` and ``$x`` refer to variables + named "myTemp" and "x", while ``$xx`` will be interpreted as a variable named "x" followed by an "x" character. How the variable is converted to a text string depends on what style @@ -79,10 +79,10 @@ LAMMPS: Additionally, the entire "immediate" variable expression may be followed by a colon, followed by a C-style format string, - e.g. ":%f" or ":%.10g". The format string must be appropriate for + e.g. ``:%f`` or ``:%.10g``. The format string must be appropriate for a double-precision floating-point value. The format string is used to output the result of the variable expression evaluation. If a - format string is not specified, a high-precision "%.20g" is used as + format string is not specified, a high-precision ``%.20g`` is used as the default format. This can be useful for formatting print output to a desired precision: @@ -101,8 +101,8 @@ LAMMPS: variable b2 equal 4 print "B2 = ${b$a}" - Nor can you specify an expression like "$($x-1.0)" for an immediate - variable, but you could use $(v_x-1.0), since the latter is valid + Nor can you specify an expression like ``$($x-1.0)`` for an immediate + variable, but you could use ``$(v_x-1.0)``, since the latter is valid syntax for an :doc:`equal-style variable `. See the :doc:`variable ` command for more details of how diff --git a/doc/src/Install.rst b/doc/src/Install.rst index 5ebcc4c8ed..d34e0e43e7 100644 --- a/doc/src/Install.rst +++ b/doc/src/Install.rst @@ -35,35 +35,35 @@ you **must** build LAMMPS from the source code. These are the files and subdirectories in the LAMMPS distribution: -+------------+---------------------------------------------+ -| README | Short description of the LAMMPS package | -+------------+---------------------------------------------+ -| LICENSE | GNU General Public License (GPL) | -+------------+---------------------------------------------+ -| SECURITY.md| Security policy for the LAMMPS package | -+------------+---------------------------------------------+ -| bench | benchmark inputs | -+------------+---------------------------------------------+ -| cmake | CMake build files | -+------------+---------------------------------------------+ -| doc | documentation and tools to build the manual | -+------------+---------------------------------------------+ -| examples | example input files | -+------------+---------------------------------------------+ -| fortran | Fortran module for LAMMPS library interface | -+------------+---------------------------------------------+ -| lib | additional provided or external libraries | -+------------+---------------------------------------------+ -| potentials | selected interatomic potential files | -+------------+---------------------------------------------+ -| python | Python module for LAMMPS library interface | -+------------+---------------------------------------------+ -| src | LAMMPS source files | -+------------+---------------------------------------------+ -| tools | pre- and post-processing tools | -+------------+---------------------------------------------+ -| unittest | source code and inputs for testing LAMMPS | -+------------+---------------------------------------------+ ++-----------------+---------------------------------------------+ +| ``README`` | Short description of the LAMMPS package | ++-----------------+---------------------------------------------+ +| ``LICENSE`` | GNU General Public License (GPL) | ++-----------------+---------------------------------------------+ +| ``SECURITY.md`` | Security policy for the LAMMPS package | ++-----------------+---------------------------------------------+ +| ``bench`` | benchmark inputs | ++-----------------+---------------------------------------------+ +| ``cmake`` | CMake build files | ++-----------------+---------------------------------------------+ +| ``doc`` | documentation and tools to build the manual | ++-----------------+---------------------------------------------+ +| ``examples`` | example input files | ++-----------------+---------------------------------------------+ +| ``fortran`` | Fortran module for LAMMPS library interface | ++-----------------+---------------------------------------------+ +| ``lib`` | additional provided or external libraries | ++-----------------+---------------------------------------------+ +| ``potentials`` | selected interatomic potential files | ++-----------------+---------------------------------------------+ +| ``python`` | Python module for LAMMPS library interface | ++-----------------+---------------------------------------------+ +| ``src`` | LAMMPS source files | ++-----------------+---------------------------------------------+ +| ``tools`` | pre- and post-processing tools | ++-----------------+---------------------------------------------+ +| ``unittest`` | source code and inputs for testing LAMMPS | ++-----------------+---------------------------------------------+ You will have all of these if you downloaded the LAMMPS source code. You will have only some of them if you downloaded executables, as