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update documentation for modifying LAMMPS to reflect changes to Thermo class

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Axel Kohlmeyer
2022-03-19 18:06:56 -04:00
parent 74103b141a
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67
doc/src/Modify_thermo.rst
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Thermodynamic output options Thermodynamic output options
============================ ============================
There is one class that computes and prints thermodynamic information The ``Thermo`` class computes and prints thermodynamic information to
to the screen and log file; see the file thermo.cpp. the screen and log file; see the files ``thermo.cpp`` and ``thermo.h``.
There are two styles defined in thermo.cpp: "one" and "multi". There There are four styles defined in ``thermo.cpp``: "one", "multi", "yaml",
is also a flexible "custom" style which allows the user to explicitly and "custom". The "custom" style allows the user to explicitly list
list keywords for quantities to print when thermodynamic info is keywords for individual quantities to print when thermodynamic output is
output. See the :doc:`thermo_style <thermo_style>` command for a list generated. The others have a fixed list of keywords. See the
of defined quantities. :doc:`thermo_style <thermo_style>` command for a list of available
quantities. The formatting of the "custom" style defaults to the "one"
style, but can be adapted using :doc:`thermo_modify line <thermo_modify>`.
The thermo styles (one, multi, etc) are simply lists of keywords. The thermo styles (one, multi, etc) are defined by lists of keywords
Adding a new style thus only requires defining a new list of keywords. with associated formats for integer and floating point numbers and
Search for the word "customize" with references to "thermo style" in identified but an enumerator constant. Adding a new style thus mostly
thermo.cpp to see the two locations where code will need to be added. requires defining a new list of keywords and the associated formats and
then inserting the required output processing where the enumerators are
identified. Search for the word "CUSTOMIZATION" with references to
"thermo style" in the ``thermo.cpp`` file to see the locations where
code will need to be added. The member function ``Thermo::header()``
prints output at the very beginning of a thermodynamic output block and
can be used to print column headers or other front matter. The member
function ``Thermo::footer()`` prints output at the end of a
thermodynamic output block. The formatting of the output is done by
assembling a "line" (which may span multiple lines if the style inserts
newline characters ("\n" as in the "multi" style).
New keywords can also be added to thermo.cpp to compute new quantities New thermodynamic keywords can also be added to ``thermo.cpp`` to
for output. Search for the word "customize" with references to compute new quantities for output. Search for the word "CUSTOMIZATION"
"keyword" in thermo.cpp to see the several locations where code will with references to "keyword" in ``thermo.cpp`` to see the several
need to be added. locations where code will need to be added. Effectively, you need to
define a member function that computes the property, add an if statement
in ``Thermo::parse_fields()`` where the corresponding header string for
the keyword and the function pointer is registered by calling the
``Thermo::addfield()`` method, and add an if statement in
``Thermo::evaluate_keyword()`` which is called from the ``Variable``
class when a thermo keyword is encountered.
Note that the :doc:`thermo_style custom <thermo_style>` command already allows .. note::
for thermo output of quantities calculated by :doc:`fixes <fix>`,
:doc:`computes <compute>`, and :doc:`variables <variable>`. Thus, it may The third argument to ``Thermo::addfield()`` is a flag indicating
be simpler to compute what you wish via one of those constructs, than whether the function for the keyword computes a floating point
by adding a new keyword to the thermo command. (FLOAT), regular integer (INT), or big integer (BIGINT) value. This
information is used for formatting the thermodynamic output. Inside
the function the result must then be stored either in the ``dvalue``,
``ivalue`` or ``bivalue`` member variable, respectively.
Since the :doc:`thermo_style custom <thermo_style>` command allows to
use output of quantities calculated by :doc:`fixes <fix>`,
:doc:`computes <compute>`, and :doc:`variables <variable>`, it may often
be simpler to compute what you wish via one of those constructs, rather
than by adding a new keyword to the thermo_style command.

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doc/src/Modify_variable.rst
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Variable options Variable options
================ ================
There is one class that computes and stores :doc:`variable <variable>` The ``Variable`` class computes and stores :doc:`variable <variable>`
information in LAMMPS; see the file variable.cpp. The value information in LAMMPS; see the file ``variable.cpp``. The value
associated with a variable can be periodically printed to the screen associated with a variable can be periodically printed to the screen
via the :doc:`print <print>`, :doc:`fix print <fix_print>`, or via the :doc:`print <print>`, :doc:`fix print <fix_print>`, or
:doc:`thermo_style custom <thermo_style>` commands. Variables of style :doc:`thermo_style custom <thermo_style>` commands. Variables of style
@ -19,21 +19,22 @@ of arguments:
compute values = c_mytemp[0], c_thermo_press[3], ... compute values = c_mytemp[0], c_thermo_press[3], ...
Adding keywords for the :doc:`thermo_style custom <thermo_style>` Adding keywords for the :doc:`thermo_style custom <thermo_style>`
command (which can then be accessed by variables) is discussed on the command (which can then be accessed by variables) is discussed in the
:doc:`Modify thermo <Modify_thermo>` doc page. :doc:`Modify thermo <Modify_thermo>` documentation.
Adding a new math function of one or two arguments can be done by Adding a new math function of one or two arguments can be done by
editing one section of the Variable::evaluate() method. Search for editing one section of the ``Variable::evaluate()`` method. Search for
the word "customize" to find the appropriate location. the word "customize" to find the appropriate location.
Adding a new group function can be done by editing one section of the Adding a new group function can be done by editing one section of the
Variable::evaluate() method. Search for the word "customize" to find ``Variable::evaluate()`` method. Search for the word "customize" to
the appropriate location. You may need to add a new method to the find the appropriate location. You may need to add a new method to the
Group class as well (see the group.cpp file). Group class as well (see the ``group.cpp`` file).
Accessing a new atom-based vector can be done by editing one section Accessing a new atom-based vector can be done by editing one section
of the Variable::evaluate() method. Search for the word "customize" of the Variable::evaluate() method. Search for the word "customize"
to find the appropriate location. to find the appropriate location.
Adding new :doc:`compute styles <compute>` (whose calculated values can Adding new :doc:`compute styles <compute>` (whose calculated values can
then be accessed by variables) is discussed on the :doc:`Modify compute <Modify_compute>` doc page. then be accessed by variables) is discussed in the :doc:`Modify compute
<Modify_compute>` documentation.