Usage Guide =========== This comprehensive guide covers all features and commands of ComChemKit with detailed examples and explanations. Quick Start ----------- **Basic Usage:** .. code-block:: bash # Extract data from all .log files in current directory cck # Process with custom settings cck -t 300 -c 2 -f csv -q # Get help cck --help Command Overview ---------------- ComChemKit supports the following commands: +------------------+--------------------------------------------------+ | Command | Description | +==================+==================================================+ | ``extract`` | Extract thermodynamic data (default) | +------------------+--------------------------------------------------+ | ``done`` | Check and organize completed jobs | +------------------+--------------------------------------------------+ | ``errors`` | Check and organize failed jobs | +------------------+--------------------------------------------------+ | ``pcm`` | Check PCM convergence failures | +------------------+--------------------------------------------------+ | ``imode`` | Check jobs with imaginary frequencies | +------------------+--------------------------------------------------+ | ``check`` | Run all job checks | +------------------+--------------------------------------------------+ | ``thermo`` | Calculate thermochemical properties (OpenThermo) | +------------------+--------------------------------------------------+ | ``high-kj`` | Calculate high-level energies (kJ/mol) | +------------------+--------------------------------------------------+ | ``high-au`` | Calculate high-level energies (atomic units) | +------------------+--------------------------------------------------+ | ``xyz`` | Extract coordinates to XYZ format | +------------------+--------------------------------------------------+ | ``ci`` | Create Gaussian input files from XYZ | +------------------+--------------------------------------------------+ | ``interactive`` | Launch interactive mode (Windows) | +------------------+--------------------------------------------------+ Core Commands ============= 1. Extract (Default Command) ----------------------------- **Purpose:** Extract thermodynamic data from Gaussian log files. **Basic Usage:** .. code-block:: bash # Process all .log files in current directory cck # Process .out files instead cck -e out **Output Formats:** **Text Format (Default):** .. code-block:: bash cck **CSV Format:** .. code-block:: bash cck -f csv **Sample Output:** .. code-block:: Found 150 .log files Using 4 threads (requested: half) Processed 75/150 files (50%) Processed 150/150 files (100%) Results written to project_directory.results Total execution time: 12.347 seconds Memory usage: 256.7 MB / 4.0 GB **Output Columns Explanation:** +------------------+--------------------------------------------------+ | Column | Description | +==================+==================================================+ | Output name | Name of the Gaussian output file | +------------------+--------------------------------------------------+ | ETG kJ/mol | Gibbs free energy with phase correction | +------------------+--------------------------------------------------+ | Low FC | Lowest vibrational frequency | +------------------+--------------------------------------------------+ | ETG a.u | Gibbs free energy in atomic units | +------------------+--------------------------------------------------+ | Nuclear E au | Nuclear repulsion energy | +------------------+--------------------------------------------------+ | SCFE | SCF energy in atomic units | +------------------+--------------------------------------------------+ | ZPE | Zero-point energy | +------------------+--------------------------------------------------+ | Status | Job status (DONE/UNDONE) | +------------------+--------------------------------------------------+ | PCorr | Phase correction applied (YES/NO) | +------------------+--------------------------------------------------+ | Round | Number of Gaussian calculation rounds | +------------------+--------------------------------------------------+ **Advanced Options:** .. code-block:: bash # Custom temperature and concentration cck -t 310.15 -c 5 # Sort by different column (2=ETG kJ/mol, 3=Low FC, 6=SCFE) cck -col 6 # Quiet mode (minimal output) cck -q # Use specific number of threads cck -nt 8 # Process files larger than default 100MB limit cck --max-file-size 500 **Temperature and Phase Correction:** .. code-block:: bash # Use temperature from input files (default) cck # Override with custom temperature cck -t 298.15 # Custom concentration for phase correction cck -c 2 # 2M concentration **Understanding Phase Correction:** Phase correction converts gas-phase energies to solution-phase: - **Gas phase (1 atm)** → **Solution (1M standard state)** - Applied automatically for SCRF calculations - Critical for accurate free energy comparisons 2. Job Status Commands ----------------------- **Purpose:** Check and organize Gaussian jobs by completion status. **Check Completed Jobs:** .. code-block:: bash # Move completed jobs to {dirname}-done/ cck done # Custom directory suffix cck done --dir-suffix completed **Check Failed Jobs:** .. code-block:: bash # Move failed jobs to errorJobs/ cck errors # Show detailed error messages cck errors --show-details # Custom target directory cck errors --target-dir failed_calculations **Check PCM Failures:** .. code-block:: bash # Move PCM convergence failures to PCMMkU/ cck pcm **Check Imaginary Frequencies:** .. code-block:: bash # Move jobs with imaginary frequencies to imaginary_freqs/ cck imode **Run All Checks:** .. code-block:: bash # Execute all job checks in sequence cck check **Workflow Example:** .. code-block:: bash # 1. Run calculations # (submit your Gaussian jobs) # 2. Check completion status cck done # 3. Check for failures cck errors # 4. Check PCM issues cck pcm # 5. Check vibrational analysis cck imode 3. High-Level Energy Calculations ---------------------------------- **Purpose:** Calculate energies using high-level electronic energies combined with low-level thermal corrections. **Directory Structure:** .. code-block:: project/ ├── low_level/ # Opt + Freq calculations │ ├── molecule1.log │ └── molecule2.log └── high_level/ # Single point calculations ├── molecule1.log └── molecule2.log **Basic Usage:** .. code-block:: bash # Navigate to high-level directory cd high_level # Calculate energies in kJ/mol cck high-kj # Calculate detailed energies in atomic units cck high-au **Energy Combination Process:** 1. **High-level electronic energy** from current directory 2. **Thermal corrections** from parent directory (../) 3. **Combined result**: E_high + (E_low_thermal - E_low_electronic) **Output Formats:** **high-kj (kJ/mol):** .. code-block:: Name G kJ/mol Status molecule1 -1234.56 DONE molecule2 -2345.67 DONE **high-au (Atomic Units - Detailed):** .. code-block:: Name E high E low ZPE TC TS H G mol1 -456.78 -450.12 0.123 0.456 0.789 -455.67 -456.46 **Advanced Options:** .. code-block:: bash # Custom temperature cck high-kj -t 310.15 # Custom concentration (accepts -c, -C, --cm, --conc) cck high-kj -c 2 # Sort by different column cck high-kj -col 4 # CSV output cck high-kj -f csv 4. Coordinate Extraction ------------------------- **Purpose:** Extract final Cartesian coordinates from Gaussian log files and organize them. **Basic Usage:** .. code-block:: bash # Extract coordinates from all log files cck xyz # Extract from specific files cck xyz -f molecule1.log molecule2.log **Output Organization:** .. code-block:: current_directory/ ├── molecule1.log ├── molecule2.log └── current_directory_final_coord/ ├── molecule1.xyz └── molecule2.xyz **Directory Structure:** - **Completed jobs** → ``{dirname}_final_coord/`` - **Incomplete jobs** → ``{dirname}_running_coord/`` **XYZ File Format:** .. code-block:: 12 molecule1.log Final coordinates C 0.000000 0.000000 0.000000 H 1.089000 0.000000 0.000000 H -0.363000 1.032000 0.000000 ... **Advanced Usage:** .. code-block:: bash # Process .out files cck xyz -e out # Use multiple threads cck xyz -nt 8 # Quiet mode cck xyz -q 5. Create Input Files (ci) --------------------------- **Purpose:** Generate Gaussian input files from XYZ coordinate files. **Supported Calculation Types:** +------------------+--------------------------------------------------+ | Type | Description | +==================+==================================================+ | ``sp`` | Single point energy (default) | +------------------+--------------------------------------------------+ | ``opt_freq`` | Geometry optimization + frequency | +------------------+--------------------------------------------------+ | ``ts_freq`` | Transition state search + frequency | +------------------+--------------------------------------------------+ | ``oss_ts_freq`` | Open-shell singlet TS + frequency | +------------------+--------------------------------------------------+ | ``modre_ts_freq``| Modredundant TS + frequency | +------------------+--------------------------------------------------+ | ``oss_check_sp`` | Open-shell singlet stability check | +------------------+--------------------------------------------------+ | ``high_sp`` | High-level single point | +------------------+--------------------------------------------------+ | ``irc_forward`` | IRC calculation (forward direction) | +------------------+--------------------------------------------------+ | ``irc_reverse`` | IRC calculation (reverse direction) | +------------------+--------------------------------------------------+ | ``irc`` | IRC calculation (both directions) | +------------------+--------------------------------------------------+ | ``tddft`` | TD-DFT excited state calculation | +------------------+--------------------------------------------------+ **Basic Examples:** .. code-block:: bash # Single point energy calculation (default) cck ci # Geometry optimization + frequency cck ci --calc-type opt_freq # Transition state search cck ci --calc-type ts_freq **Advanced Examples:** .. code-block:: bash # Transition state with frozen bond cck ci --calc-type modre_ts_freq --freeze-atoms 1 2 # High-level single point with custom functional cck ci --calc-type high_sp --functional B3LYP --basis 6-311+G** # Solvent calculation cck ci --calc-type opt_freq --solvent water --solvent-model smd # IRC from transition state cck ci --calc-type irc --tschk-path ../ts_checkpoints # Custom settings cck ci --calc-type opt_freq --charge 1 --mult 2 **Multiple XYZ Files:** .. code-block:: bash # Process multiple files (comma-separated) cck ci file1.xyz,file2.xyz,file3.xyz # Mixed separators (space and comma) cck ci file1.xyz file2.xyz,file3.xyz # With calculation type cck ci --calc-type opt_freq file1.xyz,file2.xyz **Template System:** **Generate Templates:** .. code-block:: bash # Generate template for specific calculation type cck ci --genci-params opt_freq # Generate all available templates cck ci --genci-all-params # Generate in specific directory cck ci --genci-params opt_freq ./my_templates **Use Templates:** .. code-block:: bash # Use specific parameter file cck ci --param-file opt_freq.params # Use default parameter file cck ci --param-file **Template Workflow:** 1. **Generate Template:** .. code-block:: bash cck ci --genci-params opt_freq 2. **Edit Template (opt_freq.params):** .. code-block:: calc_type = opt_freq functional = B3LYP basis = 6-31G* solvent = chloroform charge = 1 mult = 2 extra_keywords = Int=UltraFine 3. **Use Template:** .. code-block:: bash cck ci --param-file opt_freq.params **Generated Input File Example:** .. code-block:: %chk=molecule1.chk # B3LYP/6-31G* Opt Freq molecule1 B3LYP/6-31G* Opt Freq 1 2 C 0.000000 0.000000 0.000000 H 1.089000 0.000000 0.000000 ... 6. Thermo Module (OpenThermo) ----------------------------- **Purpose:** Comprehensive thermochemical property calculations using statistical mechanics methods from quantum chemistry output files. **Supported Quantum Chemistry Programs:** - Gaussian (.log, .out) - ORCA (.out) - GAMESS-US (.log) - NWChem (.out) - CP2K (.out) - VASP (OUTCAR) - Q-Chem (.out/.log) - OpenThermo Format (.otm) **Basic Usage:** .. code-block:: bash # Single file thermochemistry calculation cck thermo molecule.log # Custom temperature and pressure cck thermo molecule.log -T 298.15 -P 1.0 # Head-Gordon's low-frequency treatment with Q-Chem preset cck thermo molecule.log -lowvibmeth headgordon -bav qchem -prtlevel 2 **Batch Processing (Parallel):** .. code-block:: bash # Process multiple files with auto-detected threads cck thermo files.list # Specify thread count cck thermo files.list -nt 8 # OpenMP parallelization for scan loops cck thermo molecule.log -T 200 400 25 -omp-threads 4 **Temperature/Pressure Scanning:** .. code-block:: bash # Temperature scan cck thermo molecule.log -T 200 400 25 # Combined scan (creates .UHG and .SCq files) cck thermo molecule.log -T 273 373 50 -P 0.5 2.0 0.5 **Command-Line Options:** +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | Option | Description | Values | Default | +===============================+===================================+===========================================+=========+ | ``-T `` or ``-T <...>`` | Temperature (K) | number or range | 298.15 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-P

`` or ``-P <...>`` | Pressure (atm) | number or range | 1.0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-sclZPE `` | ZPE frequency scaling | decimal | 1.0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-sclheat `` | Thermal energy scaling | decimal | 1.0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-sclS `` | Entropy scaling | decimal | 1.0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-sclCV `` | Heat capacity scaling | decimal | 1.0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-lowvibmeth `` | Low-frequency treatment | 0/Harmonic, 1/Truhlar, ... 4/HeadGordon | 2 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-ravib `` | Truhlar raising threshold (cm^-1) | decimal | 100.0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-intpvib `` | Interpolation threshold (cm^-1) | decimal | 100.0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-hgEntropy <0|1>`` | Head-Gordon entropy interpolation | 0=no, 1=yes | 1 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-bav `` | Head-Gordon Bav preset | grimme, qchem, auto | auto | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-ipmode `` | Phase mode | 0=gas, 1=condensed | 0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-imagreal `` | Imaginary freq threshold (cm^-1) | decimal | 0.0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-massmod `` | Mass assignment | 1=average, 2=isotope, 3=file | 3 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-PGname `` | Point group | string or "?" | "?" | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-conc `` | Concentration (mol/L) | decimal | 0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-prtlevel <0-3>`` | Output verbosity level | 0=minimal, 1=default, 2=verbose, 3=full | 1 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-prtvib `` | Vibrational contributions | 0=no, 1=screen, -1=file | 0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-outotm `` | Output .otm file | 0=no, 1=yes | 0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-omp-threads `` | OpenMP parallelization threads | positive integer, 0=auto | 0 | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-nt `` | File processing thread count | number, half, max | half | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-memory-limit `` | Memory limit | positive integer | auto | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ | ``-E `` | Electronic energy override (a.u.) | decimal | from file | +-------------------------------+-----------------------------------+-------------------------------------------+---------+ **Calculation Methods:** **Standard RRHO (Rigid-Rotor Harmonic Oscillator)** - Traditional harmonic approximation - Suitable for most molecular systems **Quasi-RRHO Treatments:** 1. **Truhlar's Method** (``lowvibmeth = 1``) - Raises frequencies below threshold (default: 100 cm^-1) - Simple and computationally efficient 2. **Grimme's Interpolation** (``lowvibmeth = 2`` or ``grimme``) - Entropy interpolation between RRHO and free rotor - Weighting: ``w = 1 / (1 + (ν_threshold/ν)^4)`` - Better treatment of low-frequency modes 3. **Minenkov's Interpolation** (``lowvibmeth = 3`` or ``minenkov``) - Extended Grimme's method with energy interpolation - Includes both entropy and thermal energy corrections - Most comprehensive treatment for flexible molecules 4. **Head-Gordon Interpolation** (``lowvibmeth = 4`` or ``headgordon``) - Smoothed damping for entropic contributions of low vibrational modes - Supported by Q-Chem inspired free rotor references (``-bav qchem``) - Fully supports interpolating entropy (``-hgEntropy 1``) Configuration and Customization =============================== Configuration File ------------------- **Create Default Configuration:** .. code-block:: bash cck --create-config **Configuration File Location:** - **Linux/macOS:** ``~/.cck.conf`` - **Windows:** ``%USERPROFILE%\.cck.conf`` **Sample Configuration:** .. code-block:: # Default temperature for calculations default_temperature = 298.15 # Default concentration for phase correction default_concentration = 1.0 # Default output format output_format = text # Default thread count (half, max, or number) default_threads = half # File extensions to process output_extensions = .log,.out input_extensions = .com,.gjf,.gau **Configuration Options:** .. table:: Configuration Options +-------------------+--------------------------------------------------+ | Option | Description | +===================+==================================================+ | default_temperature | Default temperature (K) | +-------------------+--------------------------------------------------+ | default_concentration | Default concentration (M) | +-------------------+--------------------------------------------------+ | output_format | Default output format (text/csv) | +-------------------+--------------------------------------------------+ | default_threads | Default thread count (half/max/number) | +-------------------+--------------------------------------------------+ | output_extensions | File extensions to process | +-------------------+--------------------------------------------------+ | input_extensions | Input file extensions | +-------------------+--------------------------------------------------+ | max_file_size | Maximum file size (MB) | +-------------------+--------------------------------------------------+ | memory_limit | Memory usage limit (MB) | +-------------------+--------------------------------------------------+ Performance and Resource Management ==================================== Thread Management ----------------- **Automatic Thread Detection:** .. code-block:: bash # Use half of available cores (recommended) cck -nt half # Use all available cores cck -nt max # Use specific number cck -nt 8 **Cluster Safety:** .. code-block:: bash # Conservative settings for head nodes cck -nt 2 -q # Optimal for compute nodes cck -nt half Memory Management ----------------- **Automatic Memory Limits:** .. code-block:: bash # Check current resource usage cck --resource-info # Set custom memory limit cck --memory-limit 8192 **Memory Allocation Strategy:** - **1-4 threads:** 30% of system RAM - **5-8 threads:** 40% of system RAM - **9-16 threads:** 50% of system RAM - **17+ threads:** 60% of system RAM File Size Handling ------------------ **Large File Processing:** .. code-block:: bash # Increase file size limit (default: 100MB) cck --max-file-size 500 # Process very large files cck --max-file-size 1000 Batch Processing ---------------- **Large Directory Handling:** .. code-block:: bash # Enable batch processing cck --batch-size 50 # Auto batch size (default) cck --batch-size 0 Safety Features =============== Cluster Environment Detection ------------------------------ ComChemKit automatically detects cluster environments: - **SLURM:** ``sbatch``, ``srun`` detection - **PBS/Torque:** ``qsub``, ``qstat`` detection - **SGE:** ``qsub`` detection - **LSF:** ``bsub``, ``bjobs`` detection **Cluster-Specific Behavior:** - Conservative thread limits on head nodes - Automatic resource detection - Safe memory allocation Graceful Shutdown ----------------- **Signal Handling:** .. code-block:: bash # Program responds to SIGINT (Ctrl+C) and SIGTERM # Press Ctrl+C to gracefully stop processing **Shutdown Process:** 1. Signal received 2. Current file processing completes 3. Results written to disk 4. Clean exit with proper resource cleanup Error Handling -------------- **File Processing Errors:** - Corrupted log files are skipped with warnings - Large files (>100MB) automatically skipped by default - Memory limits prevent system overload - Thread-safe error reporting **Common Error Scenarios:** .. code-block:: bash # Handle large files cck --max-file-size 500 # Reduce memory usage cck --memory-limit 4096 -nt 2 # Check system resources cck --resource-info Advanced Workflows ================== Complete Computational Chemistry Workflow ------------------------------------------ **Step 1: Generate Input Files** .. code-block:: bash # Create optimization inputs cck ci --calc-type opt_freq # Submit jobs to queue # (use your cluster's job submission system) **Step 2: Check Job Status** .. code-block:: bash # Check completed jobs cck done # Check for failures cck errors # Check vibrational analysis cck imode **Step 3: Extract Results** .. code-block:: bash # Extract thermodynamic data cck -t 298.15 -c 1 # Extract coordinates for next step cck xyz **Step 4: High-Level Calculations** .. code-block:: bash # Navigate to high-level directory cd high_level # Calculate refined energies cck high-kj High-Throughput Processing --------------------------- **Batch Processing Setup:** .. code-block:: bash # Process large datasets cck -nt 16 --max-file-size 500 --memory-limit 16384 # Quiet mode for scripts cck -q -f csv # Resource monitoring cck --resource-info **Script Integration:** .. code-block:: bash #!/bin/bash # Process multiple directories for dir in dataset1 dataset2 dataset3; do cd $dir cck -q -f csv cd .. done Template-Based Automation ------------------------- **Create Reusable Templates:** .. code-block:: bash # Generate comprehensive template library cck ci --generate-all-templates ./templates # Customize templates for different methods # Edit template files with your preferred settings **Automated Processing:** .. code-block:: bash # Process different molecule types cck ci --param-file ./templates/opt_freq.params molecule1.xyz cck ci --param-file ./templates/ts_freq.params molecule2.xyz cck ci --param-file ./templates/high_sp.params molecule3.xyz Troubleshooting =============== Common Issues and Solutions --------------------------- **Memory Issues:** .. code-block:: bash # Reduce thread count cck -nt 2 # Set memory limit cck --memory-limit 4096 # Check system resources cck --resource-info **File Processing Issues:** .. code-block:: bash # Handle large files cck --max-file-size 500 # Process different file types cck -e out # Check file permissions ls -la *.log **Performance Issues:** .. code-block:: bash # Optimize thread usage cck -nt half # Use batch processing cck --batch-size 25 # Monitor progress cck # (remove -q for progress display) **Configuration Issues:** .. code-block:: bash # Reset configuration cck --create-config # Check configuration cck --show-config # Validate setup cck --resource-info Best Practices ============== **For Interactive Use:** .. code-block:: bash # Start with resource check cck --resource-info # Use conservative settings cck -nt 4 -q # Monitor progress cck **For Batch Processing:** .. code-block:: bash # Optimize for throughput cck -nt half --max-file-size 500 -q -f csv # Use templates for consistency cck ci --param-file template.params **For Cluster Environments:** .. code-block:: bash # Head node safety cck -nt 2 -q # Compute node optimization cck -nt max --memory-limit 16384 **Data Management:** - Use descriptive filenames - Organize by calculation type - Keep raw log files for reference - Use CSV format for data analysis - Backup important results Command Reference ================= **Global Options:** +---------------------+----------------------------------+ | Option | Description | +=====================+==================================+ | ``-h, --help`` | Show help message | +---------------------+----------------------------------+ | ``-v, --version`` | Show version information | +---------------------+----------------------------------+ | ``-q, --quiet`` | Quiet mode | +---------------------+----------------------------------+ | ``-nt, --threads`` | Thread count (number/half/max) | +---------------------+----------------------------------+ | ``-e, --ext`` | File extension (.log/.out) | +---------------------+----------------------------------+ | ``--max-file-size`` | Maximum file size (MB) | +---------------------+----------------------------------+ | ``--memory-limit`` | Memory limit (MB) | +---------------------+----------------------------------+ | ``--resource-info`` | Show system resource information | +---------------------+----------------------------------+ **Extract Command Options:** +---------------------+----------------------------------+ | Option | Description | +=====================+==================================+ | ``-t, --temp`` | Temperature (K) | +---------------------+----------------------------------+ | ``-c, --cm`` | Concentration (M) | +---------------------+----------------------------------+ | ``-col, --column`` | Sort column (2-10) | +---------------------+----------------------------------+ | ``-f, --format`` | Output format (text/csv) | +---------------------+----------------------------------+ | ``--use-input-temp``| Use temperature from files | +---------------------+----------------------------------+ **Job Checker Options:** +---------------------+----------------------------------+ | Option | Description | +=====================+==================================+ | ``--dir-suffix`` | Directory suffix for done jobs | +---------------------+----------------------------------+ | ``--target-dir`` | Custom target directory | +---------------------+----------------------------------+ | ``--show-details`` | Show detailed error messages | +---------------------+----------------------------------+ **Create Input Options:** +---------------------+----------------------------------+ | Option | Description | +=====================+==================================+ | ``--calc-type`` | Calculation type | +---------------------+----------------------------------+ | ``--functional`` | DFT functional | +---------------------+----------------------------------+ | ``--basis`` | Basis set | +---------------------+----------------------------------+ | ``--solvent`` | Solvent name | +---------------------+----------------------------------+ | ``--charge`` | Molecular charge | +---------------------+----------------------------------+ | ``--mult`` | Multiplicity | +---------------------+----------------------------------+ | ``--freeze-atoms`` | Atoms to freeze for TS | +---------------------+----------------------------------+ | ``--genci-params`` | Generate parameter template | +---------------------+----------------------------------+ | ``--param-file`` | Use parameter file | +---------------------+----------------------------------+ Getting Help ============ **Built-in Help:** .. code-block:: bash # General help cck --help # Command-specific help cck extract --help cck ci --help # Configuration help cck --config-help **Resource Information:** .. code-block:: bash # System resource check cck --resource-info # Configuration status cck --show-config **Version Information:** .. code-block:: bash cck --version This guide covers all major features and usage patterns of ComChemKit. For the most up-to-date information, always refer to the built-in help system.