Python API reference¶
The signatures below are generated from the Python docstrings for the source revision used to build this manual. A development checkout can differ from the published release docs; compare the installed version and source identity before copying an option from a newer guide.
Choose the right API layer¶
Goal |
API or guide |
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Run a molecular job and write its output bundle |
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Run a crystal or slab calculation |
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Obtain a low-level SCF result for a custom workflow |
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Use ASE structures, forces and optimizers |
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Solve a supplied Hermitian eigenproblem |
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Fit selected molecular semiempirical parameters |
Parameter-opt, experimental and limited to its documented scope |
A symbol’s presence in this index is not a capability guarantee for every method, boundary condition, derivative or solver combination. Consult the linked guide’s route table before combining options. The methods and status page distinguishes supported production routes from previews and experimental work.
Units, results and output¶
Native Atom coordinates are in bohr; XYZ readers accept angstrom. Native
SCF energies such as RHFResult.energy are in hartree. The ASE adapter follows
ASE conventions instead: positions in angstrom, energies in eV and forces in
eV/angstrom. Check the specific function’s documented units before exchanging
arrays between these interfaces.
Low-level drivers return result objects. Check their convergence fields before using energies, and use the output helpers explicitly when composing your own workflow. High-level job runners coordinate output files, but a written QVF archive or manifest alone does not certify convergence or the chosen electronic state. See output files for filenames, optional exports and provenance, and SCF convergence for interpreting the result.
Molecular¶
Parse an XYZ file (positions in Ångström). |
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Restricted Hartree-Fock SCF on a closed-shell molecule. |
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Unrestricted Hartree-Fock SCF on an open-shell molecule. |
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Restricted Kohn-Sham SCF on a closed-shell molecule. |
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Unrestricted Kohn-Sham SCF on an open-shell molecule. |
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Python-friendly CCSD option struct with aux-basis autodetection. |
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Run closed-shell CCSD (and optionally CCSD(T)). |
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Return the published element-based frozen-core orbital count. |
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Controls for the dense ground-state CC3 iteration. |
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Result of a dense ground-state CC3 calculation. |
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One CC3 T1/T2 iteration. |
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Solve ground-state CC3 for a canonical closed-shell reference. |
Input / output workflow¶
High-level “run a job” driver plus external-format writers.
Run a vibe-qc SCF job and write the standard output files. |
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Run a QCSchema atomic input and optionally write an atomic result JSON. |
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Read a QCSchema JSON document from disk. |
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Write a QCSchema molecule, atomic input, or atomic result to JSON. |
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Construct a native molecule from QCSchema molecule data. |
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Return a QCSchema molecule with the native atom order and Bohr positions. |
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Write geometry, basis, and molecular orbitals to a Molden-format file. |
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Write a vibe-qc |
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Write a sequence of |
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Write a geometry-optimization history as a multi-XYZ trajectory with per-step energies on the comment line. |
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Generate a list of |
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Return a multi-line SCF report with a convergence summary. |
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Emit the SCF trace through the |
The trajectory trio above (Phase M2) writes the multi-XYZ format that moltui, ASE, OVITO, Avogadro, and PyMOL all read directly:
:func:
vibeqc.write_xyz_trajectory, generic multi-frame writer.:func:
vibeqc.write_opt_trajectory, geometry-optimization history with auto-formatted comment lines ("step N E = … |grad| = …"). Default extension.optby ORCA-style convention; on-disk format is identical to a plain multi-XYZ.:func:
vibeqc.normal_mode_trajectory, discretise one vibrational mode inton_framesdisplaced geometries for an animated normal-mode movie. Pair with :func:~vibeqc.write_xyz_trajectory.
IAO population analysis¶
See IAO charges and IAO-Wiberg bonds for conventions, validation and supported determinants.
A full atom partition, or an explicit reason it is unavailable. |
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Analyze a converged molecular RHF/RKS/UHF/UKS result, without localization. |
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Analyze unit-occupied, S-orthonormal MO columns in the supplied AO order. |
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Spin-resolved Wiberg indices in labeled orthonormal IAO bases. |
Integrals, basis, XC¶
RHF analytic nuclear gradient (Ha/bohr, per atom). |
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UHF analytic nuclear gradient (Ha/bohr, per atom). |
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RKS analytic nuclear gradient (Ha/bohr, per atom). |
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UKS analytic nuclear gradient (Ha/bohr, per atom). |
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Register a user-defined XC functional alias at runtime. |
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Register a differentiable full-grid XC provider. |
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Return a verified local model, downloading it atomically if needed. |
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Return the immutable source and integrity record stored with the model. |
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str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str |
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str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str |
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str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str |
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The SKALA constants identify the immutable checkpoint selected by
functional="skala-1.1". Model download is lazy: importing the module or
calling skala_model_provenance() does not import PyTorch or access the
network. See the SKALA-1.1 user guide for the grid,
cache, route, and reproducibility contracts.
Periodic¶
Build a legacy |
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Γ-only closed-shell RHF for a periodic system (molecular-limit regime). |
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Native multi-k RHF with optional result/QVF READ source. |
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Multi-k closed-shell periodic Kohn-Sham SCF (DIRECT_TRUNCATED). |
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Per-atom radial x Lebedev quadrature grid. |
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Mura-Knowles radial scale |
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Return the Lebedev orders scipy.integrate.lebedev_rule supports. |
The AtomicRadialGrid family (per-atom Mura-Knowles radial ×
Lebedev-Laikov angular quadrature) is the M3b-aug-A
infrastructure for GAPW augmentation, wired into the SCF via
run_periodic_job’s GAPW dispatch (per-atom augmentation
correction for all-electron accuracy). See
gapw.md for the user-facing surface
and vibeqc.periodic_gapw_atomic_grid for the module-level entry.
Crystal / symmetry¶
Metadata describing a periodic-structure symmetrisation. |
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Return value of |
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Result bundle for GS3 standardise-then-compress helpers. |
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Return spglib's space-group analysis without mutating |
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Standardise and idealise a 3D periodic structure via spglib. |
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Standardise |
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Standardise |
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Standardise |
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Parse a CIF file into a |
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Parse a VASP 5 POSCAR/CONTCAR file into a |
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Write a Crystal to VASP 5 POSCAR (Direct coordinates, Å lattice). |
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Properties¶
Mulliken atomic partial charges q_A = Z_A - S_{mu in A} (P.S)_mumu. |
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Löwdin (symmetric-orthogonalization) atomic partial charges. |
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Mayer bond-order matrix, shape (n_atoms, n_atoms). |
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Electric dipole moment of a converged SCF calculation. |
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Dipole moment components in atomic units (e.bohr), plus Debye. |
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Center of mass (bohr). |
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Live progress, runtime manifest, and perf log¶
Observability surface: defeats output buffering on long runs,
pins the runtime environment alongside every job,
writes a post-mortem perf breakdown when opted in,
exposes a verbosity knob plus a stdlib logging
adapter, writes a machine-readable NDJSON convergence
log, writes a crash dump on SCF failure, and records
the external-program validation boundary in the .system manifest.
run_job accepts verbose: int = None (PySCF-convention
0..9; None reads $VIBEQC_VERBOSE, default 4) and
use_logging: bool = False (route emits through
logging.getLogger("vibeqc.run_job"), banners + milestones
land at INFO, per-iter SCF rows at DEBUG, warnings at
WARNING). The same verbose= kwarg is threaded through
every periodic SCF entry point (run_rhf_periodic_gamma_ewald3d,
run_rks_periodic_multi_k_ewald3d, …) so direct callers of
the lower-level drivers can dial verbosity without going
through run_job. See
docs/user_guide/output_files.md § “Verbosity”
for the level table.
Per-stage progress emitter for long-running calculations. |
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Normalize the |
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Collect the runtime environment as a nested dict. |
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Write the per-job system manifest next to |
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Accumulator for per-phase wall/CPU timings, per-iteration SCF rows, and memory snapshots over the course of a calculation. |
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Context manager that times its body and pushes the wall + CPU delta into the currently active |
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Activate a fresh |
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The currently active |
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Render |
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One-record-per-line NDJSON writer with line-flushed I/O. |
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Activate a fresh |
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The currently active |
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A short hex digest summarizing a job's identifying inputs. |
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Write |
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Parse a |
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Return a one-line |
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Register a crash-dump stem for the duration of the block. |
ProgressLogger is wired into every periodic SCF entry point (and
into run_job); system_info() / write_system_manifest() are
the public hooks for users driving the SCF drivers directly without
run_job. perf_log() is the context-manager entry point for
post-mortem perf logging, paired with PerfScope for instrumenting
custom code. structured_log() is the v0.6 NDJSON entry point,
one JSON record per SCF transition, format-stable, jq-friendly.
dump_on_failure() / load_dump() are the v0.6 crash-dump pair:
a snapshot on disk when an SCF fails ungracefully, round-trippable
via load_dump() for bit-for-bit failure reproduction. See
docs/user_guide/output_files.md
for the user-facing walkthrough.
Memory budget¶
Peak memory estimate for a calculation. |
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Raised by |
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Peak memory estimate for |
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Abort if |
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Best-effort available-RAM probe for the current process. |
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One-stop formatter for the run_job output block. |
Basis-set utilities¶
CRYSTAL-format basis-set parser and NWChem/.g94 emitter. |
Bands, DOS, plotting¶
A discretised k-path -- sequence of k-points with cumulative arc length (for the x-axis when plotting) and labeled high-symmetry points (for the x-axis tick marks). |
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Eigenvalues at every k along a path. |
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Total density of states. |
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Stitch a piecewise-linear k-path through high-symmetry points. |
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Sample a real-space Fock matrix along a k-path. |
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Non-interacting (Hcore) band structure: eigenvalues of T + V at every k-point. |
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Total DOS computed by Gaussian-broadening every eigenvalue of |
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Non-interacting DOS for a system on a Monkhorst-Pack mesh. |
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Draw a band-structure plot. |
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Draw a density-of-states plot. |
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Combined band structure + DOS panel -- the standard solid-state layout (bands on the left with shared y-axis to a horizontal DOS on the right). |
Volumetric output¶
Uniform axis-aligned grid in bohr. |
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Wrap an axis-aligned box around the molecule with |
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Write the total electron density r(r) = <D, chi⊗chi> to a Gaussian cube file. |
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Write a single molecular orbital |
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Write a stack of MOs in a single multi-value cube file. |
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Write a structure-only XSF file. |
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Write a periodic XSF file with a single 3D scalar grid. |
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Write a BXSF file (band XSF) for Fermi-surface visualization in XCrySDen. |
SCF accelerators + initial guess¶
Canonical user-facing smearing configuration. |
Wavefunction methods (non-mean-field solvers)¶
The vibeqc.solvers family: Full CI, Selected CI, DMRG,
variational 2-RDM, and the transcorrelated Hamiltonian.
One- and two-electron integrals in an orthonormal spatial-orbital basis. |
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One-shot Selected-CI solve. |
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Options for the Selected-CI solver. |
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Options for the DMRG solver. |
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One-shot v2RDM solve. |
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Options for the v2RDM solver. |
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Apply the transcorrelated similarity transformation to a Hamiltonian. |
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Options for the transcorrelated Hamiltonian builder. |
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Common result container for all non-mean-field solvers. |
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CISD options for |
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Result of a fixed-space CISD (or CIS, |
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Run fixed-space CISD on an MO-basis Hamiltonian. |
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Generate all determinants for |
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Build the full CI Hamiltonian matrix in the unrestricted determinant basis. |
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<D|H|D> for an unrestricted determinant. |
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Run vibe-qc's RHF and return the MO coefficient matrix. |
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Build a |
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Transform a Hamiltonian into a new orthonormal basis given by |
Composite methods (3c family) + double hybrids + range-separated hybrids¶
Generic double-hybrid dispatcher. |
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Result of a double-hybrid run: the SCF (hybrid-DFT) result, the post-SCF MP2 correction result, optionally a dispersion correction, and the combined total energy. |
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wB97X-D (Chai & Head-Gordon, *Phys. |
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Result of an wB97X-D run: the range-separated-hybrid SCF result, the Chai-Head-Gordon empirical dispersion correction, and the combined total energy. |
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Canonical short-range bond (SRB) correction of the 3c stack. |
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Dispersion (D3 / D4 + counterpoise + EEQ)¶
Pairwise D3(BJ) dispersion energy (and optionally gradient). |
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D4 dispersion correction (Caldeweyher et al. 2019). |
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Geometric counterpoise correction (Kruse & Grimme 2012). |
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Result of a |
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Return value of |
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Per-unit-cell dispersion energy plus optional gradient. |
Implicit solvation (CPCM / COSMO)¶
Outcome of one apparent-surface-charge solve. |
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Outcome of a CPCM-coupled SCF run. |
Geometry optimization + Hessian¶
Relax molecular geometry using analytic gradients + L-BFGS-B. |
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Container for molecular geometry optimization results. |
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Container for optimization results. |
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Knobs for |
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Output of |
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Knobs for |
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Outcome of a |
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Container for the output of |
Periodic SCF (full driver matrix)¶
The Γ-only entry points already appear under “Periodic” above. The multi-k drivers, the BIPOLE family, and the Ewald and GDF variants land here.
χ-CCM[1] entries above cover the finite-translation-group
character construction. Γ-CCM (aiccm2026dev-a) uses the separate
union-and-weight/Wigner–Seitz integral-weighting construction. Γ-CCM’s module is
vibeqc.periodic.ccm. Key entry points:
vibeqc.periodic.ccm.CCMSystem- build the cyclic clustervibeqc.periodic.ccm.scf.run_ccm_rhf/run_ccm_rhf_scalable- union-and-weight Γ-CCM HFvibeqc.periodic.ccm.dft.run_ccm_rks/run_ccm_uks- union-and-weight Γ-CCM KS-DFTvibeqc.periodic.ccm.ri.run_ccm_rhf_gdf/run_ccm_rks_gdf- neutral fitted-torus character/Bloch controls, not Γ-CCM construction identitiesvibeqc.periodic.ccm.direct.run_ccm_rhf_direct- real-Gamma evaluation of the same neutral fitted-torus controlvibeqc.periodic.ccm.ri.run_ccm_rhf_rijcosx- WSSC RIJCOSX research routevibeqc.periodic.ccm.mp2.run_ccm_mp2/vibeqc.periodic.ccm.ump2.run_ccm_ump2- union-and-weight Γ-CCM MP2/UMP2 withmethod="aiccm2026dev-a"; passing a neutralcderiselects the separately declared control insteadvibeqc.periodic.ccm.ccsd.run_ccm_ccsd- union-and-weight Γ-CCM CCSD(T) withmethod="aiccm2026dev-a"; itscderiroute is the separate neutral fitted-torus controlvibeqc.periodic.ccm.mp2.run_ccm_ri_mp2/vibeqc.periodic.ccm.ccsd.run_ccm_ri_ccsd- one-call canonical correlation on the neutral fitted-torus controlvibeqc.periodic.ccm.uccsd.run_ccm_uccsd- open-shell UCCSD(T) on the neutral fitted-torus control, not a Γ-CCM or χ-CCM construction APIProperties:
ccm_homo_lumo_gap,ccm_mulliken_charges,ccm_lowdin_charges,ccm_dipole,ccm_numerical_gradientLocalization:
localise_ccm,ccm_paoNeutral-control DLPNO:
ccm_dlpno_mp2,ccm_dlpno_ccsd,ccm_dlpno_ump2,ccm_dlpno_uccsd. These correlation APIs use the neutral fitted-torus operator and are not assigned a Γ-CCM or χ-CCM identity.Neutral reference:
ccm_eri_neutral,ccm_neutral_cderi
See the Γ-CCM reference for the construction/neutral-control API boundary and the full method inventory.
Run Γ-only closed-shell periodic RHF/RKS via native GDF. |
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Run closed-shell periodic HF / KS multi-k SCF via native GDF. |
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Run closed-shell periodic KS-DFT multi-k SCF via native GDF. |
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Minimise the finite-torus closed-shell RHF energy per cell. |
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Minimise the finite-torus closed-shell Kohn--Sham energy per cell. |
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Minimize the finite-torus unrestricted Hartree--Fock functional. |
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Minimize the finite-torus spin-polarized Kohn--Sham functional. |
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Run canonical closed-shell RI-MP2 on the B finite translation group. |
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Run complete-domain finite-torus restricted CCSD. |
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Run complete-domain finite-torus restricted CCSD(T). |
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Run canonical finite-torus RI-UMP2 in the exact PNO limit. |
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Run full-domain finite-torus UCCSD with the O(N^6) oracle. |
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Run full-domain finite-torus UCCSD(T) with the O(N^6) oracle. |
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Run local-PNO MP2 on the exact real representation of the B torus. |
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Run local-PNO CCSD on the real finite-torus B Hamiltonian. |
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Run local-PNO CCSD(T) on the real finite-torus B Hamiltonian. |
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Run PBC-localized, pair-natural-orbital UMP2 on the B torus. |
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Run the unrestricted local-PNO CCSD correctness pilot. |
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Run the unrestricted local-PNO CCSD(T) correctness pilot. |
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Derive all currently supported gauge-invariant SCF properties. |
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Return primitive-cell Mayer bond orders from a χ-CCM SCF result. |
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Sample the converged finite-torus Fock matrix along a k-path. |
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Localize the converged occupied space of an AICCM2026DEV-B SCF. |
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Localize the alpha and beta occupied projectors of a B-stream UHF. |
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Localized occupied orbitals on the real BvK torus. |
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Available occupied-space gauges. |
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Project occupieds from selected AOs and canonically orthogonalize. |
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Diagonalize the Hermitian MP2 model pair density. |
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Partition all unordered occupied pairs under supplied generators. |
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Validated finite-torus PAO and occupied-pair bookkeeping. |
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Analyze the space group and its exact action on a finite BvK torus. |
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Partition intrinsic-unique primitive shell pairs by point symmetry. |
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Partition intrinsic 8-fold-unique primitive shell quartets. |
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Verified symmetry metadata for one finite cyclic cluster. |
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Electron-repulsion backend for the same finite-torus functional. |
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Finite-N Hamiltonian convention attached to every B-stream result. |
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Versioned route-resolved exact-exchange assembly for one B SCF run. |
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Canonical finite-torus RI-MP2 energy per primitive cell. |
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Local-PNO MP2 result on the B finite torus, per primitive cell. |
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Local-PNO CCSD or CCSD(T) result on the B finite torus. |
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Return the reciprocal irreps of a finite cyclic cluster. |
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Construct the exact minimum-image partition of the cyclic group. |
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Wigner--Seitz representatives for translations of centre B about A. |
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Transform k-block matrices to primitive-translation blocks. |
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Internal-consistency data attached to an AICCM2026DEV_B result. |
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Gamma-point closed-shell periodic RHF with rigorous 2D slab Ewald. |
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Γ-point closed-shell periodic RHF SCF with Ewald-3D Coulomb. |
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Γ-point closed-shell periodic Kohn-Sham SCF with Ewald-3D Coulomb. |
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Γ-point open-shell UHF SCF with the EWALD_3D Coulomb dispatch. |
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Γ-point open-shell periodic Kohn-Sham SCF with Ewald-3D Coulomb. |
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Multi-k closed-shell periodic RHF SCF with EWALD_3D Coulomb. |
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Multi-k closed-shell periodic RKS SCF with EWALD_3D Coulomb. |
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Multi-k open-shell UHF SCF with EWALD_3D Coulomb. |
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Multi-k closed-shell RHF via the CRYSTAL-gauge BIPOLE scaffold. |
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Multi-k open-shell UHF via the CRYSTAL-gauge BIPOLE scaffold. |
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Multi-k closed-shell RKS via the CRYSTAL-gauge BIPOLE scaffold. |
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Multi-k open-shell UKS via the CRYSTAL-gauge BIPOLE scaffold. |
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Run a periodic SCF job and write the standard output files. |
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Result of |
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SCF result from |
Periodic gradients + stress + properties¶
Analytic Γ-only periodic RHF atomic gradient. |
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Analytic Γ-only periodic RKS atomic gradient (closed-shell DFT). |
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Force virial -- NOT the true periodic stress. |
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Classical Hirshfeld atomic partial charges from a converged SCF. |
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Output of |
ECPs + auto-population¶
Build |
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Compute the AO-basis ECP matrix V_ECP_{muν} = <chi_mu|V_ECP|chi_ν> via libecpint's built-in XML library (ecp10mdf, ecp28mdf, ecp46mdf, ecp60mdf, ecp78mdf, lanl2dz). |
QVF output¶
Write |
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Validate a QVF against the canonical SSOT schema. |
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Evaluate total electron density on a uniform grid and return a dict suitable for |
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Evaluate MO wavefunctions on a uniform grid and return a list suitable for |
Thermodynamics¶
Output of |