Avogadro::MoleQueue::InputGenerator#

class InputGenerator : public QObject#

The InputGenerator class provides an interface to input generator scripts.

The QuantumInput extension provides a scriptable method for users to add custom input generators to Avogadro. By writing an executable that implements the interface defined below, new input generators can be created faster and easier than writing full Avogadro extensions.

Script Entry Points#

The script must handle the following command-line arguments:

--debug Enable extra debugging output. Used with other commands. It is not required that the script support extra debugging, but it should not crash when this option is passed.
--print-options Print the available options supported by the script, e.g. simulation parameters, etc. See below for more details.
--generate-input Read an option block from stdin and print input files to stdout. See below for more details.
--display-name Print a user-friendly name for the input generator. This is used in the GUI for menu entries, window titles, etc.

Specifying parameters with <tt>–print-options</tt>#

The format of the --print-options output must be a JSON object of the following form:

{
  "userOptions": {
    ...
  },
  "highlightStyles": [
    {
      "style": "Descriptive name",
      "rules": [
        {
          "patterns": [ ... ],
          "format": { ... }
        },
        ...
      ],
    },
    ...
  ],
  "inputMoleculeFormat": "cjson"
}

The userOptions block contains a JSON object keyed with option names (e.g. “First option name”), which are used in the GUI to label simulation parameter settings. Various parameter types are supported:

Fixed Mutually-Exclusive Parameter Lists#

Parameters that have a fixed number of mutually-exclusive string values will be presented using a QComboBox. Such a parameter can be specified in the userOptions block as:

{
  "userOptions": {
    "Parameter Name": {
      "type": "stringList",
      "values": ["Option 1", "Option 2", "Option 3"],
      "default": 0
    }
  }
}

Here, Parameter Name is the label that will be displayed in the GUI as a label next to the combo box. The array of strings in values will be used as the available entries in the combo box in the order they are written. default is a zero-based index into the values array and indicates which value should be initially selected by default.

Short Free-Form Text Parameters#

A short text string can be requested (e.g. for the “title” of an optimization) via:

{
  "userOptions": {
    "Parameter Name": {
      "type": "string",
      "default": "blah blah blah"
    }
  }
}

This will add a QLineEdit to the GUI, initialized with the text specified by default.

Existing files#

An input generator can ask for the absolute path to an existing file using the following option block:

{
  "userOptions": {
    "Parameter Name": {
      "type": "filePath",
      "default": "/path/to/some/file"
    }
  }
}

This will add an Avogadro::QtGui::FileBrowseWidget to the GUI, initialized to the file pointed to by default.

Clamped Integer Values#

Scripts may request integer values from a specified range by adding a user-option of the following form:

{
  "userOptions": {
    "Parameter Name": {
      "type": "integer",
      "minimum": -5,
      "maximum": 5,
      "default": 0,
      "prefix": "some text ",
      "suffix": " units"
    }
  }
}

This block will result in a QSpinBox, configured as follows:

minimum and maximum indicate the valid range of integers for the parameter.
default is the integer value that will be shown initially.
(optional) prefix and suffix are used to insert text before or after the integer value in the spin box. This is handy for specifying units. Note that any prefix or suffix will be stripped out of the corresponding entry in the call to --generate-input, and just the raw integer value will be sent.

Boolean Parameters#

If a simple on/off value is needed, a boolean type option can be requested:

{
  "userOptions": {
    "Parameter Name": {
      "type": "boolean",
      "default": true,
    }
  }
}

This will result in a QCheckBox in the dynamically generated GUI, with the initial check state shown in default.

Special Parameters#

Some parameters are common to most calculation codes. If the following parameter names are found, they will be handled specially while creating the GUI. It is recommended to use the names below for these options to provide a consistent interface and ensure that MoleQueue job staging uses correct values where appropriate.

Syntax Highlighting#

Rules for syntax highlighting can be specified as a collection of regular expressions or wildcard patterns and text format specifications in the “highlightRules” array. The highlightRules format is:

"highlightStyles": [
  {
    "style": "Style 1",
    "rules": [ (list of highlight rules, see below) ],
  },
  {
    "style": "Style 2",
    "rules": [ (list of highlight rules, see below) ],
  },
  ...
],

The style name is unique to the style object, and used to associate a set of highlighting rules with particular output files. See the --generate-input documentation for more details.

The general form of a highlight rule is:

{
  "patterns": [
    { "regexp": "^Some regexp?$" },
    { "wildcard": "A * wildcard expression" },
    { "string": "An exact string to match.",
      "caseSensitive": false
    },
    ...
  ],
  "format": {
    "preset": "<preset name>"
  }
}

or,

{
  "patterns": [
    ...
  ],
  "format": {
    "foreground": [ 255, 128,  64 ],
    "background": [   0, 128, 128 ],
    "attributes": ["bold", "italic", "underline"],
    "family": "serif"
  }
}

The patterns array contains a collection of fixed strings, wildcard expressions, and regular expressions (using the QRegularExpression syntax flavor, see the QRegularExpression documentation) that are used to identify strings that should be formatted. There must be one of the following members present in each pattern object:

regexp A QRegularExpresion-style regular expression. If no capture groups (“(…)”) are defined, the entire match is formatted. If one or more capture groups, only the captured texts will be marked.
wildcard A wildcard expression
string An exact string to match.

Any pattern object may also set a boolean caseSensitive member to indicate whether the match should consider character case. If omitted, a case-sensitive match is assumed.

The preferred form of the format member is simply a specification of a preset format. This allows for consistent color schemes across input generators. The recognized presets are:

"title": A human readable title string.
"keyword": directives defined by the target input format specification to have special meaning, such as tags indicating where coordinates are to be found.
"property": A property of the simulation, such as level of theory, basis set, minimization method, etc.
"literal": A numeric literal (i.e. a raw number, such as a coordinate).
"comment": Sections of the input that are ignored by the simulation code.

If advanced formatting is desired, the second form of the format member allows fine-tuning of the font properties:

foreground color as an RGB tuple, ranged 0-255
background color as an RGB tuple, ranged 0-255
attributes array of font attributes, valid strings are "bold", "italic", or "underline"
family of font. Valid values are "serif", "sans", or "mono"

Any of the font property members may be omitted and default QTextCharFormat settings will be substituted.

The input generator extension will apply the entries in the highlightRules object to the text in the order they appear. Thus, later rules will override the formatting of earlier rules should a conflict arise.

Requesting Full Structure of Current Molecule#

The inputMoleculeFormat is optional, and can be used to request a representation of the current molecule’s geometry when --generate-input is called. The corresponding value indicates the format of the molecule that the script expects. If this value is omitted, no representation of the structure will be provided.

Handling User Selections: <tt>–generate-input</tt>#

When --generate-input is passed, the information needed to generate the input file will be written to the script’s standard input channel as JSON string of the following form:

{
  "cjson": {...},
  "options": {
    "First option name": "Value 2",
    "Second option name": "Value 1",
    ...
  }
}

The cjson entry will contain a Chemical JSON representation of the molecule if inputMoleculeFormat is set to “cjson” in the --print-options output. Similarly, a cml entry and CML string will exist if a Chemical Markup Language representation was requested. It will be omitted entirely if inputMoleculeFormat is not set. The options block contains key/value pairs for each of the options specified in the userOptions block of the --print-options output.

If the script is called with --generate-input, it must write a JSON string to standard output with the following format:

{
  "files": [
    {
      "filename": "file1.ext",
      "contents": "...",
      "highlightStyles": [ ... ]
    },
    {
      "filename": "file2.ext",
      "filePath": "/path/to/file/on/local/filesystem"
    },
    ...
  ],
  "warnings": ["First warning.", "Second warning.", ... ],
  "mainFile": "file2.ext"
}

The files block is an array of objects, which define the actual input files. The filename member provides the name of the file, and either contents or filePath provide the text that goes into the file. The contents string will be used as the file contents, and filePath should contain an absolute path to a file on the filesystem to read and use as the input file contents. The optional highlightStyles member is an array of strings describing any highlight styles to apply to the file (see --print-options documentation). Each string in this array must match a style description in a highlighting rule in the --print-options output. Zero or more highlighting styles may be applied to any file. The order of the files in the GUI will match the order of the files in the array, and the first file will be displayed first.

The warnings

member provides an array of strings that describe non-fatal warnings to be shown to the users. This is useful for describing the resolution of conflicting options, e.g. “Ignoring basis set for

semi-empirical calculation.”. This member is optional and should be omitted if no warnings are present.

The mainFile member points to the primary input file for a calculation. This is the file that will be used as a command line argument when executing the simulation code (if applicable), and used by MoleQueue to set the $$inputFileName$$ and $$inputFileBaseName$$ input template keywords. This is optional; if present, the filename must exist in the files array. If absent and only one file is specified in files, the single input file will be used. Otherwise, the main file will be left unspecified.

Automatic Generation of Geometry#

The generation of molecular geometry descriptions may be skipped in the script and deferred to the InputGenerator class by use of a special keyword. The “contents” string may contain a keyword of the form

$$coords:[coordSpec]$$

where [coordSpec] is a sequence of characters. The characters in [coordSpec] indicate the information needed about each atom in the coordinate block. See the CoordinateBlockGenerator documentation for a list of recognized characters.

Other keywords that can be used in the input files are:

$$atomCount$$: Number of atoms in the molecule.
$$bondCount$$: Number of bonds in the molecule.

Error Handling#

In general, these scripts should be written robustly so that they will not fail under normal circumstances. However, if for some reason an error occurs that must be reported to the user, simply write the error message to standard output as plain text (i.e. not JSON), and it will be shown to the user.

Debugging#

Debugging may be enabled by defining AVO_QM_INPUT_DEBUG in the process’s environment. This will cause the debug option to be passed in all calls to generator scripts, and will print extra information to the qDebug() stream from within avogadro. The script is free to handle the debug flag as the author wishes.

Note

Currently valid options for inputMoleculeFormat are “cjson” for Chemical JSON or “cml” for Chemical Markup Language.

Public Functions

explicit InputGenerator(const QString &scriptFilePath_, QObject *parent_ = nullptr)#

Constructor

Parameters:: scriptFilePath_ – Absolute path to generator script.

explicit InputGenerator(QObject *parent_ = nullptr)#

~InputGenerator() override = default#

bool debug() const#

Returns:: True if debugging is enabled.

inline bool isValid() const#

Returns:: True if the generator is configured with a valid script.

QJsonObject options() const#: Query the script for the available options (generate-options) and return the output as a JSON object.

Note

The results will be cached the first time this function is called and reused in subsequent calls.

Note

If an error occurs, the error string will be set. Call hasErrors() to check for success, and errorString() or errorList() to get a user-friendly description of the error.

QString displayName() const#: Query the script for a user-friendly name (display-name).

Note

The results will be cached the first time this function is called and reused in subsequent calls.

Note

If an error occurs, the error string will be set. Call hasErrors() to check for success, and errorString() or errorList() to get a user-friendly description of the error.

QString scriptFilePath() const#

Returns:: The path to the generator file.

void setScriptFilePath(const QString &scriptFile)#: Set the path to the input generator script file. This will reset any cached data held by this class.

void reset()#: Clear any cached data and return to an uninitialized state.

bool generateInput(const QJsonObject &options_, const Core::Molecule &mol)#

Request input files from the script using the supplied options object and molecule. See the class documentation for details on the options_ object format.

If the files are generated successfully, use the functions numberOfInputFiles(), fileNames(), and fileContents() to retrieve them.

Note

If an error occurs, the error string will be set. Call hasErrors() to check for success, and errorString() or errorList() to get a user-friendly description of the error.

Returns:: true on success and false on failure.

int numberOfInputFiles() const#

Note

This function is only valid after a successful call to generateInput().

Returns:: The number of input files stored by generateInput().

QStringList fileNames() const#

Note

This function is only valid after a successful call to generateInput().

Returns:: A list of filenames created by generateInput().

QString mainFileName() const#

Note

This function is only valid after a successful call to generateInput().

Returns:: The “main” input file of the collection. This is the input file used by MoleQueue to determine the $$inputFileName$$ and $$inputFileBaseName$$ keywords.

QString fileContents(const QString &fileName) const#