HPC Q-Chem Skill

Treat Q-Chem as a staged quantum-chemistry workflow built around a valid input deck with modular section structure.

Quick Start

Typical Workflow

1. Write input file ($rem, $molecule sections) —see references/01-input-file-structure.md
2. Select method and basis set —see references/02-method-selection.md
3. Choose job type (SP, Opt, Freq) —see references/03-job-types.md
4. Handle SCF convergence if needed —see references/04-scf-convergence.md
5. Set up geometry, charge, and multiplicity —see references/05-geometries-charges.md
6. Configure restart for multi-step workflows —see references/06-restart-workflows.md
7. Add solvent model if needed —see references/07-solvent-models.md
8. Submit to HPC cluster —see references/08-cluster-execution.md
9. Handle errors —see references/error-recovery.md

Skill Map

User Requirements
├─ Input Deck Authoring
│ ├─ $rem section (job control keywords) →01-input-file-structure.md
│ ├─ $molecule section (charge/mult/geometry) →01-input-file-structure.md
│ ├─ $basis section (custom basis) →01-input-file-structure.md
│ └─ Method selection (HF, DFT, MP2, CCSD(T)) →02-method-selection.md
├─ Job Types
│ ├─ Single Point (SP) →03-job-types.md
│ ├─ Geometry Optimization (Opt) →03-job-types.md
│ ├─ Frequency (Freq) →03-job-types.md
│ ├─ Excited States (TDDFT, CIS) →03-job-types.md
│ └─ Properties (NMR, dipole) →03-job-types.md
├─ SCF & Convergence
│ ├─ SCF convergence strategies →04-scf-convergence.md
│ └─ Guess methods (SAD, Core, Read) →04-scf-convergence.md
├─ Solvent Effects
│ └─ PCM, SM8, SMD models →07-solvent-models.md
├─ Restart & Workflows
│ ├─ Reading previous job →06-restart-workflows.md
│ └─ Multi-job batch files →06-restart-workflows.md
│ └─ Plot files and Fchk →06-restart-workflows.md
└─ HPC Cluster Execution
   ├─ SLURM/PBS job scripts →08-cluster-execution.md
   ├─ MPI and OpenMP parallelization →08-cluster-execution.md
   └─ Scratch directory management →08-cluster-execution.md

Reference Documents

Document	Content
references/01-input-file-structure.md	Input file anatomy: $comment, $molecule, $rem, $basis sections
references/02-method-selection.md	HF, DFT functionals (B3LYP, ωB97X-D, M06-2X), basis sets, MP2, CCSD(T)
references/03-job-types.md	SP, Opt, Freq, TDDFT, CIS, property calculations
references/04-scf-convergence.md	SCF guess methods, DIIS, GDM, level-shifting, stability checks
references/05-geometries-charges.md	Charge/mult format, Cartesian/Z-matrix, symmetry
references/06-restart-workflows.md	Reading MOs, batch jobs, plot files
references/07-solvent-models.md	PCM, SM8, SMD; solvent selection
references/08-cluster-execution.md	SLURM/PBS scripts, MPI/OpenMP, scratch directory
references/error-recovery.md	Input, SCF, optimization, frequency, runtime errors; recovery workflow

Key Decision Points

Question	Guide	Summary
Single point, opt, or freq?	03-job-types.md	SP, Opt, Freq job types
Which method and basis?	02-method-selection.md	HF, DFT, MP2, CCSD(T) with appropriate basis
SCF convergence issues?	04-scf-convergence.md	SCF_GUESS, MAX_SCF_CYCLES, or GDM
Solvent effects needed?	07-solvent-models.md	SOLVENT_MODEL = PCM or SMD
Need to restart?	06-restart-workflows.md	Read MOs or batch jobs

Guardrails

• Do not invent Q-Chem $rem keywords —consult 01-input-file-structure.md
• Do not treat charge and multiplicity as cosmetic metadata —they must match the electron count.
• Do not run restart-sensitive workflows without proper file handling —see 06-restart-workflows.md
• Do not copy $rem sections from unrelated systems without checking method, basis, and job intent.
• Do not run Freq on a non-optimized geometry.
• Do not mix incompatible job types (e.g., Opt with TDDFT requires specific settings).

Outputs

Always report:

• job type (SP, Opt, Freq, TDDFT, etc.)
• method and basis selection
• charge and multiplicity
• restart policy if applicable
• expected key outputs (.out, .fchk, plot files) and next stage

Template Files

Template files in assets/templates/ are ready-to-use starting scaffolds that can be copied and modified:

Template	Type	Use Case	Reference
assets/templates/sp_water.in	Input (.in)	Single point energy of water	01-input-file-structure.md, 02-method-selection.md
assets/templates/opt_freq_water.in	Input (.in)	Geometry optimization + frequency	03-job-types.md, 06-restart-workflows.md
assets/templates/qchem-slurm.sh	Batch script	SLURM submission for Q-Chem	08-cluster-execution.md

Error Recovery

Consult references/error-recovery.md for structured diagnosis of:

• Input file errors ($rem, $molecule, $basis)
• SCF convergence failures
• Optimization failures
• Frequency calculation errors
• Restart and file issues
• Runtime errors (memory, scratch, segmentation)