Molpro Automation Skill

Use the extended reference library only when needed for one of the following:

• determining exact Molpro input syntax
• selecting the correct Molpro module or keyword
• checking method-specific prerequisites
• handling advanced workflows such as CASSCF, MRCI, NEVPT2, SOC, EOM-CCSD, DFT, density fitting, gradients, frequencies, or relativistic corrections
• diagnosing failures that appear related to Molpro program structure, variables, file handling, parallel execution, or method limitations

When using reference files:

1. Prefer the smallest relevant subset.
2. Consult references/Index.md first when the relevant module is unclear.
3. Prefer task-local references over broad manual pages.
4. Reuse already extracted rules instead of rereading the same reference files.

Operating contract

Always follow this sequence:

1. Identify the task type:

   • sp
   • opt
   • freq
   • opt+freq
   • casscf
   • mrci
   • custom only if explicitly requested

2. Normalize the minimum required inputs:

   • molecule specification
   • charge
   • multiplicity or spin state
   • basis
   • method
   • target properties
   • working directory
   • resource limits if provided

3. Prepare the first candidate. Do not hand-write large Molpro inputs in the conversation unless the user explicitly asked for the text only.

4. Run Molpro using scripts/run_molpro.py. Example: python run_molpro.py /home/user/calc/water.inp

5. Parse results of scripts/run_molpro.py.

6. Decide based on parser result:

   • If terminated = normal, report results and save structured outputs.
   • If terminated = error, classify the failure from parser result.
   • If the failure is repairable and retry count is below limit, repair the failure in a new input file, then rerun.
   • If not repairable or retry limit reached, stop and provide the best diagnosis.

Success criteria

A Molpro run is considered successful only when all conditions are met:

• parser returns terminated = normal
• target quantities requested by the task are present
• no unresolved fatal condition remains
• for opt, geometry optimization reached convergence
• for freq, frequencies were actually produced
• for opt+freq, both optimization and frequency stages completed

Do not assume success from file existence alone.

Retry policy

Default maximum retries: 3

Allowed conservative repair actions:

• fix malformed input structure
• add or correct missing charge / spin / wavefunction metadata
• switch to a safer initial template for the same requested task
• reduce unnecessary complexity in the first pass
• split opt+freq into two stages if combined flow is fragile
• preserve the user’s requested chemistry intent

Disallowed automatic repair actions unless explicitly requested:

• silently changing the target electronic structure method to a chemically different one
• silently changing charge or multiplicity
• silently dropping the requested property
• fabricating numerical results

Failure handling

When a run fails:

1. Parse and classify the failure.
2. Check whether the cause is input syntax, missing metadata, convergence, resource, filesystem, or executable access.
3. Apply only the smallest valid repair.
4. Record each retry in a machine-readable log.
5. Stop after max retries and report:
   • failure class
   • attempted repairs
   • current best input
   • most likely next manual action

Performance rules

• Keep conversation output compact.
• Prefer structured JSON artifacts over long prose during execution.
• Do not load references/* unless needed.
• Do not preload the entire extended reference library.
• Do not read large output files repeatedly; parse once into JSON and reuse.
• Do not rerun a successful step unless an upstream assumption changed.
• For opt+freq, cache the optimized geometry and reuse it.

Reporting format

At the end of a successful run, provide:

• task type
• status
• final input file path
• final output file path
• retries used
• key numerical results
• concise note on any assumptions

At the end of an unsuccessful run, provide:

• task type
• status
• retries used
• failure class
• attempted repairs
• best diagnostic summary
• files available for manual inspection

Start procedure

When invoked:

1. Read user request.
2. Infer the smallest valid Molpro job type.
3. Use scripts/run_molpro.py.
4. Run Molpro.
5. Parse output.
6. Repair only if allowed.
7. Return concise structured summary.

Extended reference library

The following reference files are grouped by topic for easier routing.
Load only the smallest relevant subset for the current task.
Do not read the whole library unless explicitly required.

1. Manual navigation and getting started

Use for onboarding, manual lookup, examples, and general orientation.

• references/How_to_read_this_manual.md
• references/Introduction_to_Molpro.md
• references/Quickstart.md
• references/Introductory_examples.md
• references/Index.md
• references/References.md
• references/Recent_changes.md
• references/License_information.md
• references/Molpro_on_the_www.md

2. Input language, execution, and program control

Use for input syntax, variables, job structure, file handling, runtime control, and execution issues.

• references/Installation_guide.md
• references/Definition_of_Molpro_input_language.md
• references/General_program_structure.md
• references/Program_control.md
• references/Variables.md
• references/File_handling.md
• references/Running_Molpro.md
• references/Running_Molpro_on_parallel_computers.md
• references/General_hints_-_frequently_asked_questions.md
• references/SMILES.md

3. Molecular structure, optimization, gradients, and numerical procedures

Use for geometry definitions, optimization, gradients, frequencies, and related numerical procedures.

• references/Molecular_geometry.md
• references/Region.md
• references/Minimization_of_functions.md
• references/Integration.md
• references/Energy_gradients.md
• references/Geometry_optimization_OPTG.md
• references/Harmonic_vibrational_frequencies_FREQUENCIES.md

4. Basis sets, auxiliary approximations, effective potentials, and relativistic treatment

Use for basis specification, extrapolation, ECP/CPP, density fitting, F12, and relativistic options.

• references/Basis_input.md
• references/Basis_set_extrapolation.md
• references/Effective_core_potentials.md
• references/Core_polarization_potentials.md
• references/Density_fitting.md
• references/Explicitly_correlated_methods.md
• references/Relativistic_corrections.md

5. SCF, DFT, TDDFT, and response-type methods

Use for Hartree–Fock, DFT, TDDFT/TDKS, and related response frameworks.

• references/The_SCF_program.md
• references/Density_functional_descriptions.md
• references/The_density_functional_program.md
• references/Time-dependent_density_functional_theory.md
• references/The_TDHF_and_TDKS_programs.md
• references/Kohn-Sham_random-phase_approximation.md

6. Single-reference correlation and coupled-cluster family

Use for MP2, CCSD, open-shell CC, EOM-CCSD, CC2, MRCC interface, and local single-reference excited-state methods.

• references/Møller_Plesset_perturbation_theory.md
• references/The_closed_shell_CCSD_program.md
• references/Open-shell_coupled_cluster_theories.md
• references/Excited_states_with_equation-of-motion_CCSD_EOM-CCSD.md
• references/The_closed-shell_density_fitting_CC2_program_for_ground_and_excited_states.md
• references/The_MRCC_program_of_M._Kallay_MRCC.md
• references/Local_methods_for_excited_states.md
• references/PAO-based_local_correlation_treatments.md

7. Multireference, active-space, CI, and valence-bond methods

Use for CASSCF/MCSCF, MRCI, NEVPT2, MR perturbation theory, MRCC-like treatments, active-space construction, and orbital preparation.

• references/Automated_construction_of_atomic_valence_active_spaces.md
• references/The_MCSCF_program_MULTI.md
• references/The_MRCI_program.md
• references/The_NEVPT2_program.md
• references/Internally_contracted_multireference_coupled-cluster_theory.md
• references/Multireference_Rayleigh_Schrödinger_perturbation_theory.md
• references/Multireference_local_correlation_methods_PNO-CASPT2.md
• references/The_full_CI_program.md
• references/The_VB_program_CASVB.md
• references/Orbital_localization.md
• references/Orbital_merging.md
• references/Intrinsic_basis_bonding_analysis_IAO-IBO.md

8. Excited-state dynamics, nonadiabatic effects, spin–orbit, and PES workflows

Use for nonadiabatic couplings, SOC, quasi-diabatic workflows, surface generation, and dynamics-oriented tasks.

• references/Ab_initio_multiple_spawning_dynamics.md
• references/Non_adiabatic_coupling_matrix_elements.md
• references/Spin-orbit-coupling.md
• references/Quasi-diabatization.md
• references/PES_generators.md
• references/PES_transformations.md

9. Vibrational spectroscopy, Franck–Condon, tunneling, and rovibrational analysis

Use for post-optimization vibrational analysis and spectroscopy-related workflows.

• references/Franck-Condon_calculations.md
• references/Instantons.md
• references/Processing_of_rovibrational_line_lists_DAT2GR.md
• references/Vibrational_perturbation_theory_VPT2.md
• references/Vibrational_SCF_programs.md
• references/Vibration_correlation_programs.md

10. Environment, embedding, intermolecular methods, and external interfaces

Use for solvent/environment models, embedding, QM/MM, intermolecular energy decomposition, and specialized coupled electron–nuclear treatments.

• references/Intermolecular_interaction_energies.md
• references/Symmetry-adapted_intermolecular_perturbation_theory.md
• references/The_COSMO_model.md
• references/Projection-based_WF-in-DFT_embedding.md
• references/QM-MM_interfaces.md
• references/Nuclear-electronic_orbital_method.md

11. Properties, densities, analysis, plotting, and post-processing

Use for expectation values, magnetic properties, cube export, analysis utilities, tables/plots, and database-style post-processing.

• references/Properties_and_expectation_values.md
• references/Chemical_shieldings,_magnetizability,_and_rotational_g-tensor.md
• references/Dump_density_or_orbital_values_CUBE.md
• references/Post-processing_of_output_and_databases.md
• references/Tables_and_plotting.md
• references/Matrix_operations.md
• references/Physical_constants.md

Task-specific guidance

Single-point (sp)

Use the simplest valid input that preserves the requested method and basis. Return:

• final energy
• method
• basis
• charge / multiplicity
• key warnings if any

Geometry optimization (opt)

Prefer a dedicated optimization job. Return:

• optimized energy
• optimized geometry
• convergence status
• key warnings

Frequency (freq)

Frequency should normally be run on an optimized structure. If the structure has not yet been optimized in the current workflow, prefer:

1. optimize first
2. run frequency second

Optimization + frequency (opt+freq)

Prefer two-step execution:

1. optimize
2. frequency on optimized geometry

Multireference workflows (casscf, mrci)

Use only when the user clearly requests them or the project rules require them. Before execution, ensure:

• active space or state-averaging requirements are explicit
• wavefunction metadata is explicit enough If not explicit, make a conservative best effort and clearly record assumptions.