[docs] Add YAML format tutorial from cantera-website

doc/doxygen/yaml.md

@@ -17,6 +17,9 @@ information on thermodynamics, kinetics, and transport in a single file.
 -   \subpage sec-yaml-reactions
     -   \subpage sec-yaml-reaction-models
 
+For an introductory tutorial of the YAML data language, refer to the
+@ref sec-yaml-format-tutorial.
+
 %Cantera provides the following conversion utilities to obtain YAML input from other
 input file formats:
 

doc/doxygen/yaml/yamlformat.md

@@ -0,0 +1,323 @@
+# YAML Format Tutorial  {#sec-yaml-format-tutorial}
+
+Here we describe the syntax and structure of %Cantera YAML files, how
+dimensional values in %Cantera YAML files are handled, and how to
+understand some of the error messages that may be encountered when
+reading these input files.
+
+## Syntax
+
+%Cantera YAML files use a subset of the [YAML 1.2](https://yaml.org/spec/1.2/spec.html)
+specification. %Cantera YAML files consist of individual values, which may be strings,
+numbers or booleans, that are then composed as elements of nested mappings and
+sequences.
+
+## Strings
+
+Strings may be generally written without quotes, but may be enclosed in
+single quotes or double quotes if needed in order to avoid certain
+parsing ambiguities.
+
+``` yaml
+A string
+Another 'string'
+"A string: that requires quotes"
+```
+
+## Numbers
+
+Numbers can be written as integers, decimal values, or using E-notation
+
+``` yaml
+3
+3.14
+6.022e23
+```
+
+## Booleans
+
+Boolean values in YAML are written as the words `true` or `false`.
+
+## Sequences
+
+A sequence of multiple items is specified by separating the items by
+commas and enclosing them in square brackets. The individual items can
+have any type \--strings, integers, floating-point numbers, mappings, or
+sequences.
+
+``` yaml
+elements: [O, H, C, N, Ar]
+temperature-ranges: [200.0, 1000.0, 3500.0]
+```
+
+The syntax above, using square brackets to define a list, is called
+**flow style** in YAML. Sequences can also be written in **block style**,
+using one line for each item in the sequence, with each line starting with a dash:
+
+``` yaml
+elements:
+- O
+- H
+- C
+- N
+- Ar
+```
+
+Sequences can also be nested. The following examples are all equivalent:
+
+``` yaml
+data: [[1, 2], [3, 4]]
+
+data:
+-
+  - 1
+  - 2
+-
+  - 3
+  - 4
+
+data:
+- - 1
+  - 2
+- - 3
+  - 4
+```
+
+## Mappings
+
+A mapping is a container consisting of key\--value pairs. The keys in a
+mapping must be unique. Like sequences, there are two ways to write a
+mapping. In the **flow style**, the mapping is enclosed in curly
+brackets, colons (followed by spaces) are used to separate keys and
+values, and key\--value pairs are separated by commas:
+
+``` yaml
+composition: {H: 2, C: 1, O: 1}
+```
+
+In the **block style**, each key is written on a new line, followed by a
+colon. The value can be placed either on the same line, or on the
+following line, indented one level:
+
+``` yaml
+composition:
+  H: 2
+  C:
+    1
+  O: 1
+```
+
+All keys in %Cantera YAML files are treated as strings. A %Cantera YAML
+file is itself a mapping, usually in the **block style**. We refer to
+the keys in this top-level mapping as the **sections** of the input
+file.
+
+## Sequences of Mappings
+
+A common structure in %Cantera input files is a nested sequence of
+mappings. This can be written in the **block style** as:
+
+``` yaml
+- equation: O2 + CO <=> O + CO2
+  rate-constant: {A: 2.5e+12, b: 0, Ea: 47800}
+- equation: O2 + CH2O <=> HO2 + HCO
+  rate-constant: {A: 1.0e+14, b: 0, Ea: 40000}
+- equation: H + O2 + M <=> HO2 + M
+  type: three-body
+  rate-constant: {A: 2.8e+18, b: -0.86, Ea: 0}
+  efficiencies: {AR: 0, C2H6: 1.5, CO: 0.75, CO2: 1.5, H2O: 0, N2: 0, O2: 0}
+```
+
+The keys in each mapping need not be the same. In this example, each of
+the three mappings in the sequence has `equation` and `rate-constant`
+keys, while only the third entry has `type` and `efficiencies` keys.
+
+## Comments
+
+The character `#` is the comment character. Everything to the right of
+this character on a line is ignored:
+
+``` yaml
+# set the default units
+units:
+  length: cm  # use centimeters for length
+  quantity: mol  # use moles for quantity
+```
+
+## Dimensional Values
+
+Many fields have numerical values that represent dimensional
+quantities\-\--a pressure, or a density, for example. If these are
+entered without specifying the units, the default units (set by the
+`units` directive) will be used. However, it is also possible to specify
+the units for each individual dimensional quantity, unless stated
+otherwise. All that is required is to write the units after the value,
+separated by a space:
+
+``` yaml
+pressure: 1.0e5  # default is Pascals
+pressure: 1.0 bar  # this is equivalent
+density: 4.0 g/cm^3
+density: 4000.0  # kg/m^3
+```
+
+Compound unit strings may be used, as long as a few rules are followed:
+
+1.  Units in the denominator follow `/`.
+2.  Units in the numerator follow `*`, except for the first one.
+3.  Numerical exponents follow the unit string with a `^` character.
+
+Examples of compound units:
+
+``` yaml
+A: 1.0e20 cm^6/mol^2/s  # OK
+h: 6.626e-34 J*s  # OK
+density: 3.0 g*cm^-3  # OK
+A: 1.0e20 cm6/mol/s  # error (missing '^')
+A: 1.0e20 cm^6/mol^2-s  # error ('s' should be in denominator)
+density: 3.0g/cm^3  # error (missing space between value and units)
+```
+
+See the [Units
+API](%7B%7B%%20ct_docs%20sphinx/html/yaml/general.html#units%20%%7D%7D)
+documentation for additional details, including the full set of
+supported units.
+
+## Default units
+
+Default units that apply to a whole input file or some portion thereof
+can be set using `units` mapping. A `units` mapping placed at the top
+level of an input file applies to the entire file. A `units` mapping
+placed as a member of another mapping applies to that mapping and any
+nested mappings or sequences, and overrides higher-level `units`
+mappings:
+
+``` yaml
+units: {length: cm, mass: kg}
+section1:
+  units: {length: m}
+  density: 4000  # interpreted as 4000 kg/m^3
+section2:
+  density: 0.1  # interpreted as 0.1 kg/cm^3
+section3:
+- units: {mass: mg}  # must be the first item in the list
+- name: species1
+  density: 5e4  # interpreted as 5e4 mg/cm^3
+```
+
+Default units may be set for `mass`, `length`, `time`, `quantity`,
+`pressure`, `energy`, and `activation-energy`.
+
+## Error Handling
+
+During processing of an input file, errors may be encountered. These
+could be syntax errors, or could be ones that are flagged as errors by
+%Cantera due to some apparent inconsistency in the data\-\--an unphysical
+value, a species that contains an undeclared element, a reaction that
+contains an undeclared species, missing species or element definitions,
+multiple definitions of elements, species, or reactions, and so on.
+
+## Syntax Errors
+
+Syntax errors are caught by the YAML parser, and must be corrected
+before proceeding further. If a syntax error is encountered, %Cantera
+will raise an exception which includes the location of the error.
+Additional information such as a traceback showing where in the code the
+input file was being read may be printed as well.
+
+For example, consider the following input file, which is intended to
+create a gas with the species and reactions of GRI-Mech 3.0, but is
+missing the colon which is needed after the `thermo` key:
+
+``` yaml
+phases:
+- name: gas
+  thermo ideal-gas
+  kinetics: gas
+  elements: [H, O]
+  species: [{gri30.yaml/species: all}]
+  reactions: [gri30.yaml/reactions]
+```
+
+When this definition is imported into an application, an error message
+like the following would be printed to the screen, and execution of the
+program or script would terminate:
+
+``` python
+Traceback (most recent call last):
+  File "<stdin>", line 1, in <module>
+  File "/some/path/cantera/base.pyx", line 25, in cantera._cantera._SolutionBase.__cinit__
+    self._init_yaml(infile, phaseid, phases, yaml)
+  File "/some/path/cantera/base.pyx", line 49, in cantera._cantera._SolutionBase._init_yaml
+    root = AnyMapFromYamlFile(stringify(infile))
+cantera._cantera.CanteraError:
+***********************************************************************
+InputFileError thrown by AnyMap::fromYamlFile:
+Error on line 4 of ./gas.yaml:
+illegal map value
+|  Line |
+|     1 | phases:
+|     2 | - name: gas
+|     3 |   thermo ideal-gas
+>     4 >   kinetics: gas
+                    ^
+|     5 |   elements: [H, O]
+|     6 |   species: [{gri30.yaml/species: all}]
+|     7 |   reactions: [gri30.yaml/reactions]
+***********************************************************************
+```
+
+The top part of the error message shows the chain of functions that were
+called before the error was encountered. For the most part, these are
+internal %Cantera functions not of direct concern here. The relevant part
+of this error message is the part between the lines of asterisks. This
+message says that the YAML parser ran into a problem on line 4 of
+`gas.yaml`. In many cases, including this one, the parser will fail
+somewhere *after* the actual problem with the input file, since it must
+continue parsing until it finds something that cannot possibly be valid
+YAML syntax. In this case, the problem from the parser's perspective is
+that the key which started on line 3 continues across a new line before
+it finds a colon that can be considered as the separator. Since a key
+can't be broken across lines like this, the parser indicates the error
+at the point where it found the colon. By looking back from the
+indicated point of the error, we can see that the problem is the missing
+colon in the previous line.
+
+## Cantera Errors
+
+Now let's consider the other class of errors, ones that %Cantera itself
+detects. Continuing the example above, suppose that the missing colon is
+corrected, and the input file processed again. Again an error message
+results, but this time it is from %Cantera:
+
+``` python
+Traceback (most recent call last):
+  File "<stdin>", line 1, in <module>
+  File "/some/path/cantera/base.pyx", line 25, in cantera._cantera._SolutionBase.__cinit__
+    self._init_yaml(infile, phaseid, phases, yaml)
+  File "/some/path/cantera/base.pyx", line 49, in cantera._cantera._SolutionBase._init_yaml
+    root = AnyMapFromYamlFile(stringify(infile))
+cantera._cantera.CanteraError:
+***********************************************************************
+CanteraError thrown by Phase::addSpecies:
+Species 'C' contains an undefined element 'C'.
+***********************************************************************
+```
+
+The problem is that the phase definition specifies that all species are
+to be imported from the `gri30` mechanism, but only the elements H and O
+are declared. The `gri30` mechanism contains species composed of the
+elements H, O, C, N, and Ar. If the definition is modified to declare
+these additional elements:
+
+``` yaml
+phases:
+- name: gas
+  thermo: ideal-gas
+  kinetics: gas
+  elements: [H, O, C, N, Ar]
+  species: [{gri30.yaml/species: all}]
+  reactions: [gri30.yaml/reactions]
+```
+
+it may be imported successfully.