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Table of contents

  • 1. Introduction
    • 1.1. Parameter Fitting: A Lennard-Jones Example
    • 1.2. General Application
  • 2. Getting Started
    • 2.1. Installation
    • 2.2. Unit Tests
    • 2.3. First Steps with ParAMS
  • 3. Components
    • 3.1. Architecture Quick Reference
    • 3.2. Collections
      • 3.2.1. Job Collection
        • 3.2.1.1. Adding Jobs
        • 3.2.1.2. Working with the Collection
        • 3.2.1.3. I/O
        • 3.2.1.4. Generating AMSJobs
        • 3.2.1.5. Running Collection Jobs
      • 3.2.2. Engine Collection
      • 3.2.3. Collections API
        • 3.2.3.1. JCEntry
        • 3.2.3.2. JobCollection
        • 3.2.3.3. Engine
        • 3.2.3.4. EngineCollection
        • 3.2.3.5. Collection Base Class
    • 3.3. Data Set
      • 3.3.1. Adding Entries
      • 3.3.2. Accessing Entries
      • 3.3.3. Removing Entries
      • 3.3.4. Adding External Reference Data
      • 3.3.5. Calculating and Adding Reference Data with AMS
      • 3.3.6. Storage and I/O
      • 3.3.7. Calculating the Loss Function Value
      • 3.3.8. Checking for Consistency with a given Job Collection
      • 3.3.9. Splitting into Subsets
      • 3.3.10. Data Set Entry API
      • 3.3.11. Data Set API
    • 3.4. Extractors and Comparators
      • 3.4.1. Supported Data Structures
      • 3.4.2. Custom Comparators
      • 3.4.3. Available Extractors
        • 3.4.3.1. Distance
        • 3.4.3.2. Angles
        • 3.4.3.3. Dihedral
        • 3.4.3.4. RMSD
        • 3.4.3.5. Energy
        • 3.4.3.6. Forces
        • 3.4.3.7. Cell Volume
        • 3.4.3.8. Lattice Parameters
        • 3.4.3.9. Hessian
        • 3.4.3.10. Stress Tensor
        • 3.4.3.11. Charges
        • 3.4.3.12. Vibrational Frequencies
        • 3.4.3.13. PES
        • 3.4.3.14. Compared PES
    • 3.5. Parameter Interfaces
      • 3.5.1. Available Parameter Interfaces
        • 3.5.1.1. xTB
        • 3.5.1.2. ReaxFF
        • 3.5.1.3. SCC-DFTB repulsive potential
        • 3.5.1.4. Lennard Jones
      • 3.5.2. Parameter Interface Basics
      • 3.5.3. Working with Parameters
      • 3.5.4. The Active Parameters Subset
      • 3.5.5. Storage
        • 3.5.5.1. Lossless Storage
      • 3.5.6. Relation to PLAMS Settings
      • 3.5.7. Parameter API
      • 3.5.8. Interface Base Class API
    • 3.6. Optimizers
      • 3.6.1. CMA-ES
        • 3.6.1.1. List of valid cmasettings
        • 3.6.1.2. References
      • 3.6.2. Scipy
      • 3.6.3. Nevergrad
      • 3.6.4. Adaptive Rate MC
      • 3.6.5. Simple Grid Optimizer
      • 3.6.6. Optimizer Base Class
        • 3.6.6.1. BaseOptimizer API
        • 3.6.6.2. MinimizeResult API
    • 3.7. Optimization
      • 3.7.1. Optimization Setup
      • 3.7.2. Optimization API
    • 3.8. Parallelization
    • 3.9. Constraints
    • 3.10. Callbacks
      • 3.10.1. Logger
      • 3.10.2. Timeout
      • 3.10.3. Target Value
      • 3.10.4. Maximum Iterations
      • 3.10.5. Early Stopping
      • 3.10.6. Stopfile
      • 3.10.7. Time per Evaluation
      • 3.10.8. Load Average
      • 3.10.9. User-Defined Callbacks
      • 3.10.10. Callback API
    • 3.11. Loss Functions
      • 3.11.1. Least Absolute Error
      • 3.11.2. Mean Absolute Error
      • 3.11.3. Root-Mean-Square Error
      • 3.11.4. Sum of Squares Error
      • 3.11.5. Loss Function API
    • 3.12. Utilities
      • 3.12.1. Optimization History
      • 3.12.2. ReaxFF Conversion
      • 3.12.3. Plotting Funcitons
    • 3.13. Experimental Features
      • 3.13.1. Active Parameter Search
      • 3.13.2. Data Set Sensitivity
  • 4. ParAMS Main Script
    • 4.1. The Configuration File
  • 5. Examples
    • 5.1. Parameterization of a Lennard-Jones Engine for Argon
      • 5.1.1. Understanding and running the example
      • 5.1.2. Evaluating the Optimization
      • 5.1.3. Modifying the example
    • 5.2. Parameterization of a Water Force Field with ReaxFF
      • 5.2.1. Complete Example Script
      • 5.2.2. Changing the Example Script
    • 5.3. Refitting HF Charges with the ACKS2 Model
      • 5.3.1. The Config File
      • 5.3.2. Preparing the YAML Files from Input
      • 5.3.3. Running the Optimization
      • 5.3.4. Comparing the new parameters
      • 5.3.5. Playing with the example
  • 6. Citations
  • 7. Changelog
  • 8. Frequently Asked Questions
ParAMS
  • Documentation/
  • ParAMS/
  • Parameterization Tools for AMS

Parameterization Tools for AMS¶

Note

This is an alpha release of the ParAMS toolkit. It is mostly feature complete, but some APIs might still change in the future. Of course it might also contain some bugs. If you are interested in trying ParAMS, feel free to get in touch with us at support@scm.com. We are happy to get you started and appreciate all kinds of feedback on ParAMS.

Table of contents

  • 1. Introduction
    • 1.1. Parameter Fitting: A Lennard-Jones Example
    • 1.2. General Application
  • 2. Getting Started
    • 2.1. Installation
    • 2.2. Unit Tests
    • 2.3. First Steps with ParAMS
  • 3. Components
    • 3.1. Architecture Quick Reference
    • 3.2. Collections
    • 3.3. Data Set
    • 3.4. Extractors and Comparators
    • 3.5. Parameter Interfaces
    • 3.6. Optimizers
    • 3.7. Optimization
    • 3.8. Parallelization
    • 3.9. Constraints
    • 3.10. Callbacks
    • 3.11. Loss Functions
    • 3.12. Utilities
    • 3.13. Experimental Features
  • 4. ParAMS Main Script
    • 4.1. The Configuration File
  • 5. Examples
    • 5.1. Parameterization of a Lennard-Jones Engine for Argon
    • 5.2. Parameterization of a Water Force Field with ReaxFF
    • 5.3. Refitting HF Charges with the ACKS2 Model
  • 6. Citations
  • 7. Changelog
  • 8. Frequently Asked Questions
Next
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