Start general document about file formats

doc/src/Run_formats.rst

@@ -0,0 +1,119 @@
+File formats used by LAMMPS
+===========================
+
+This page provides a general overview of the kinds of files and file
+formats that LAMMPS is reading and writing.
+
+Character Encoding
+^^^^^^^^^^^^^^^^^^
+
+For text files, LAMMPS uses `ASCII character encoding
+<https://en.wikipedia.org/wiki/ASCII>`_ which represents the digits 0 to
+9, the lower and upper case letters a to z, some common punctuation and
+other symbols and a few whitespace characters including a regular "space
+character", "line feed", "carriage return", "tabulator". These are all
+represented by bytes with a value smaller than 128 and only 95 of those
+128 values represent printable characters.  This is sufficient to represent
+most English text, but misses accented characters or umlauts or Greek
+symbols and more.
+
+Modern text often uses `UTF-8 character encoding
+<https://en.wikipedia.org/wiki/UTF-8>`_ instead. This is a way to
+represent many more different characters as defined by the Unicode
+standard.  This is compatible with ASCII, since the first 128 values are
+identical with the ASCIII encoding.  It is important to note, however,
+that there are Unicode characters that look similar or even identical to
+ASCII characters, but have a different representation.  As a general
+rule, these characters are not be correctly recognized by LAMMPS.  For
+some parts of LAMMPS' text processing, there are translation tables with
+known "lookalike" characters that will transparently substitute them
+with their ASCII equivalents.  Non-ASCII lookalike characters are often
+used by web browsers or PDF viewers to improve the readability of
+text. Thus, when using copy-n-paste to transfer text from such an
+application to your input file, you may unintentionally create text that
+is not fully in ASCII encoding and may cause errors when LAMMPS is
+trying to read it.
+
+Lines with non-printable and non-ASCII characters in text files can be
+detected for example with:
+
+.. code-block:: bash
+
+   env LC_ALL=C grep -n '[^ -~]' some_file.txt
+
+Number Formatting
+^^^^^^^^^^^^^^^^^
+
+Different countries and languages have different conventions to format
+numbers.  While in some regions commas are used for fractions and points
+to indicate thousand, million and so on, this is reversed in other
+regions.  Modern operating systems have facilities to adjust input and
+output accordingly.  The exact rules are often applied according to the
+value of the ``$LANG`` environment variable (e.g. "en_US.utf8").
+
+For the sake of simplicity of the implementation and transferability of
+results, LAMMPS does not support this and instead expects numbers being
+formatted in the generic or "C" locale.  The "C" locale has no
+punctuation for thousand, million and so on and uses a decimal point for
+fractions.  One thousand would be represented as "1000.0" and not as
+"1,000.0" nor as "1.000,0".
+
+LAMMPS also only accepts integer numbers when an integer is required,
+so using "1.0" is not accepted; you have to use "1" instead.
+
+For floating point numbers in scientific notation, the Fortran double
+precision notation "1.1d3" is not accepted either; you have to use
+"1100", "1100.0" or "1.1e3".
+
+Input file
+^^^^^^^^^^
+
+A LAMMPS input file is a text file with commands. It is read
+line-by-line and each line is processed *immediately*.  Before looking
+for commands and executing them, there is a pre-processing step where
+`${variable}` and `$(expression)` constructs are expanded or evaluated
+and lines that end in the ampersand character '&' are combined with the
+next line (similar to Fortran 90 free format source code).
+
+The LAMMPS input syntax has minimal support for conditionals and loops,
+but if more complex operations are required, it is recommended to use
+the library interface, e.g. :doc:`from Python using the LAMMPS Python
+module <Python_run>`.
+
+There is a frequent misconception about the :doc:`if command <if>`:
+this is a command for conditional execution **outside** a run or
+minimization.  To trigger actions on specific conditions **during**
+a run is a non-trivial operation that usually requires adopting one
+of the available fix commands or creating a new one.
+
+LAMMPS commands can change the internal state and thus the order of
+commands matters and reordering them can produce different results.
+
+Each line must have an "end-of-line" character (line feed or carriage
+return plus line feed).  Some text editors do not automatically insert
+one which may have the result that LAMMPS ignores the last command.
+It is thus recommended, to always have an empty line at the end of an
+input file.
+
+The specific details describing how LAMMPS input is processed and parsed
+are explained in :doc:`Commands_parse`.
+
+Data file
+^^^^^^^^^
+
+
+Molecule file
+^^^^^^^^^^^^^
+
+
+Potential file
+^^^^^^^^^^^^^^
+
+
+Restart file
+^^^^^^^^^^^^
+
+
+Dump file
+^^^^^^^^^
+

doc/src/Run_head.rst

@@ -1,10 +1,11 @@
 Run LAMMPS
 **********
 
-These pages explain how to run LAMMPS once you have :doc:`installed an executable <Install>` or :doc:`downloaded the source code <Install>`
+These pages explain how to run LAMMPS once you have :doc:`installed an
-and :doc:`built an executable <Build>`.  The :doc:`Commands <Commands>`
+executable <Install>` or :doc:`downloaded the source code <Install>` and
-doc page describes how input scripts are structured and the commands
+:doc:`built an executable <Build>`.  The :doc:`Commands <Commands>` doc
-they can contain.
+page describes how input scripts are structured and the commands they
+can contain.
 
 .. toctree::
    :maxdepth: 1
@@ -12,4 +13,5 @@ they can contain.
    Run_basics
    Run_options
    Run_output
+   Run_formats
    Run_windows

doc/utils/sphinx-config/false_positives.txt

@@ -3930,6 +3930,7 @@ username
 usleep
 usolve
 usr
+utf
 util
 utils
 utsa