Gaussian Input

Item	Value
Format ID	gjf
Extensions	.gjf, .gif, .com, .gau, .gjc
Read	Yes
Write	Yes
Registry role	Reader, file writer, frame writer
Data level	Coordinates and QM input semantics

Gaussian input parsing and canonical rendering cover Link0, route, title, molecule specification, Link1, and additional sections. The writer can render an existing GJF frame or construct Gaussian input from another coordinate-bearing format:

Download the shared ORCA example, then run:

Python

from molop import AutoParser

frame = AutoParser("water_mp2.out", n_jobs=1)[0][-1]
rendered = frame.format_transform(
    "gjf",
    link0_commands={"nprocshared": "16", "mem": "32GB"},
    route_section="#p wb97xd/def2tzvp opt freq",
    title_card="optimization and frequency",
    coords_type="cartesian",
    chk=True,
)

rendered is a string beginning like:

Rendered prefix

Text Only

%nprocshared=16
%mem=32GB
%chk=optimization and frequency.chk
#p wb97xd/def2tzvp opt freq

Provide an explicit Gaussian route_section for cross-format conversion. The writer does not validate compatibility among methods, basis sets, tasks, and Gaussian versions.

Feature	Support	Scope	Limits
Fixture parse/render inventory	Fixture-covered	Maintained Gaussian input fixtures are parseable and renderable.	Coverage is fixture-anchored rather than a complete Gaussian grammar proof.
Route semantics	Partial	Model chemistry, job types, dispersion, solvation, population requests, and HF handling are parsed into shared semantic containers.	Functional is populated only for DFT/hybrid/double-hybrid semantics; method-specific Gaussian keywords outside tests may remain raw or unstructured.
Molecule specification	Partial	Cartesian, integer Cartesian, Z-matrix variables, free delimiters, fragments, and invalid-domain diagnostics.	Supported cases are the explicit molecule-spec grammar variants covered by tests.
Additional sections	Partial	ModRedundant, GIC, NBO, structured rendering, and mixed-section diagnostics.	Mixed GIC/ModRedundant sections intentionally fall back to unknown with diagnostics.
Link1, includes, and writer options	Partial	Link1 uses exact source spans with blank-line validation; Geom=AllCheck and checkpoint propagation during transform are supported.	@include crosses source artifacts and cannot be represented by the current single-artifact SourceSpan, so parsing rejects it with MOL.PARSE.GJF_INCLUDE_PROVENANCE_UNSUPPORTED; not every Gaussian writer option is covered.

Gaussian Input Capability Matrix

In the matrix, source fidelity means whether parsing and rendering retain original order, whitespace, line wrapping, and token representation. It is separate from preserving the same calculation meaning in structured fields.

Gaussian input capability	Parse	Structured semantics	Canonical render	Source fidelity	Current boundary
Link0 %key=value	Supported	Partial	Supported	Unsupported	Stored as ordered GJFLink0Command items; CPU and memory project to resource requests, while other keys receive no dedicated validation.
%chk / %oldchk render overrides	Not applicable	Supported	Supported	Not applicable	chk and old_chk append to a temporary Link0 copy; existing directives are neither replaced nor deduplicated.
Single-line and multiline route sections	Supported	Partial	Supported	Unsupported	Routes are normalized to text beginning with #; original wrapping, whitespace, and token case are not guaranteed.
Method / functional / basis	Partial	Partial	Supported	Not applicable	HF, DFT/hybrid/double-hybrid, selected post-HF methods, and common basis sets are recognized; unknown text remains in the route without guaranteed semantic fields.
OPT / FREQ / SP / IRC / scan tasks	Partial	Partial	Supported	Not applicable	Common job types and covered parameters enter task_requests; all Gaussian task combinations are not enumerated.
Opt(...) options	Partial	Partial	Supported	Not applicable	Covered fields include TS, CalcFC, ReadFC, ModRedundant, MaxCycles, and coordinate-system options.
Freq(...) options	Partial	Partial	Supported	Not applicable	Covered fields include anharmonic, projected, hindered rotor, VCD/ROA/Raman, temperature/pressure, and atom selectors; task compatibility is not checked.
TD, SCRF, Pop, and Geom options	Partial	Partial	Supported	Not applicable	Recognized options enter dedicated semantic containers; unknown parameters remain in the raw route.
Title card	Supported	Supported	Supported	Unsupported	Up to five lines; model validation removes specified invalid characters, and an empty title renders as the filename or title.
Charge and multiplicity	Supported	Supported	Supported	Unsupported	Single- and multi-fragment charge/multiplicity have structured models; output uses canonical whitespace.
Cartesian coordinates	Supported	Supported	Supported	Unsupported	Integer and floating-point coordinates parse; the writer uses six decimal places and does not retain original delimiters or precision.
Atom label, atom type, atomic charge, and parameters	Partial	Partial	Partial	Unsupported	Gaussian atom labels, type, charge, (...) parameters, and frozen tags are stored; all ONIOM/MM extensions are not covered.
Dummy and ghost atoms	Partial	Partial	Partial	Unsupported	Covered X and Bq forms project to the model; implicit Cartesian/internal conversion is rejected when dummy or ghost atoms are present.
Numeric Z-matrix	Supported	Supported	Supported	Unsupported	Ordinary dihedrals and trailing 0/1 alternate-angle markers are handled, with bond, angle, and reference-domain validation.
Z-matrix variables	Partial	Partial	Partial	Unsupported	Covered labeled and unlabeled variable sections are resolved to numbers during parsing; the writer does not restore variable names.
Free-format coordinate delimiters	Partial	Partial	Supported	Unsupported	Covered comma, tab, and / forms parse; output is space-delimited.
Cartesian/internal coordinate conversion	Not applicable	Supported	Partial	Not applicable	coords_type converts ordinary real-atom fragments both ways; dummy/ghost or unsafe alignment raises ValueError.
Fragment molecule specification	Partial	Supported	Supported	Unsupported	Every atom must declare contiguous Fragment=n; declared fragment charge/multiplicity counts are validated.
Geom=AllCheck / Geom=Checkpoint	Supported	Partial	Partial	Unsupported	Parsing allows missing title or molecule blocks; canonical rendering reassembles from model fields and default-title rules.
Connectivity section	Partial	Unsupported	Partial	Unsupported	Original connectivity has no dedicated field; add_gjf_connectivity=True regenerates connectivity from the recovered molecular graph.
ModRedundant	Partial	Partial	Supported	Unsupported	Covered line forms are structured; complex or unknown commands may fall back to an unknown/raw additional section.
GIC	Partial	Partial	Supported	Unsupported	Labels, options, functions, arguments, and standalone actions are parsed; complete Gaussian GIC grammar is not claimed.
$NBO ... $END	Partial	Partial	Supported	Unsupported	Header, commands, and footer are stored; individual NBO commands are not semantically validated.
Gen/GenECP, custom basis, and other extra input	Partial	Unsupported	Raw	Partial	The route recognizes Gen / GenECP; detailed basis/ECP text is usually an unknown additional section.
Mixed or unknown additional sections	Supported	Unsupported	Raw	Partial	Mixed GIC/ModRedundant content degrades to unknown with a diagnostic; raw content can render without interpretation.
--Link1-- multi-job input	Supported	Supported	Supported	Partial	Exact source spans split frames and require a blank line before the separator; the file writer uses a canonical separator.
Link1 checkpoint propagation	Not applicable	Partial	Supported	Not applicable	Batch/multiframe writing can generate %chk / %oldchk chains; filenames and output directories follow common transform parameters.
@include	Unsupported	Unsupported	Unsupported	Unsupported	Disk and memory parsers reject includes because multi-artifact provenance is not modeled; includes are not read recursively.
Build GJF from a general coordinate frame	Not applicable	Partial	Supported	Not applicable	atoms, coords, charge, and multiplicity build one Cartesian fragment; callers should supply the calculation route.
Gaussian version and keyword compatibility	Unsupported	Unsupported	Unsupported	Not applicable	qm_software_version is Any; acceptance by a specific Gaussian version is not checked.

The GJF writer is a canonical writer for constructing and normalizing Gaussian input, not a source-preserving editor. Do not use parse -> render as a lossless editing workflow when all untouched source text must remain byte-for-byte identical.