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1. Introduction
1.1. What is PLAMS
1.2. What can be done with PLAMS
1.3. Simple example
1.4. What PLAMS is
not
1.5. About this documentation
2. Getting started
2.1. Library contents
2.2. Running PLAMS
2.3. Master script
2.3.1. Optional arguments
3. Components overview
3.1. Settings
3.1.1. Tree-like structure
3.1.2. Dot notation
3.1.3. Global settings
3.1.4. API
3.2. Jobs
3.2.1. Preparing a job
3.2.1.1. Contents of job’s settings
3.2.1.2. Default settings
3.2.2. Running a job
3.2.2.1. Name conflicts
3.2.2.2. Prerun and postrun methods
3.2.2.3. Preview mode
3.2.3. Job API
3.2.4. Single jobs
3.2.4.1. Subclassing SingleJob
3.2.5. Multijobs
3.2.5.1. Using MultiJob
3.3. Results
3.3.1. Files in the job folder
3.3.2. Synchronization of parallel job executions
3.3.2.1. Examples
3.3.3. Cleaning job folder
3.3.3.1. Cleaning for multijobs
3.3.4. API
3.4. Job runners
3.4.1. Local job runner
3.4.2. Remote job runner
3.5. Job manager
3.5.1. Rerun prevention
3.5.2. Pickling
3.5.3. Restarting crashed scripts
3.5.4. API
3.6. Public functions
3.6.1. Logging
3.6.2. Binding decorators
3.7. External binaries
3.7.1. ADF Suite
3.7.1.1. ADF, BAND and DFTB
3.7.1.2. Other tools: Densf, FCF
3.7.1.3. KF files
3.7.2. Dirac
3.7.2.1. Preparing a calculation
3.7.2.2. Results extraction
3.7.2.3. API
3.8. Molecule
3.8.1. Molecule
3.8.2. Atom
3.8.3. Bond
3.9. Utilities
3.9.1. Periodic Table
3.9.2. Units
4. PLAMS cookbook
4.1. MultiJob
PLAMS
Documentation
/
PLAMS
/
Python Library for Automating Molecular Simulations
Python Library for Automating Molecular Simulations
ΒΆ
Table of Contents
1. Introduction
1.1. What is PLAMS
1.2. What can be done with PLAMS
1.3. Simple example
1.4. What PLAMS is
not
1.5. About this documentation
2. Getting started
2.1. Library contents
2.2. Running PLAMS
2.3. Master script
2.3.1. Optional arguments
3. Components overview
3.1. Settings
3.1.1. Tree-like structure
3.1.2. Dot notation
3.1.3. Global settings
3.1.4. API
3.2. Jobs
3.2.1. Preparing a job
3.2.2. Running a job
3.2.3. Job API
3.2.4. Single jobs
3.2.5. Multijobs
3.3. Results
3.3.1. Files in the job folder
3.3.2. Synchronization of parallel job executions
3.3.3. Cleaning job folder
3.3.4. API
3.4. Job runners
3.4.1. Local job runner
3.4.2. Remote job runner
3.5. Job manager
3.5.1. Rerun prevention
3.5.2. Pickling
3.5.3. Restarting crashed scripts
3.5.4. API
3.6. Public functions
3.6.1. Logging
3.6.2. Binding decorators
3.7. External binaries
3.7.1. ADF Suite
3.7.2. Dirac
3.8. Molecule
3.8.1. Molecule
3.8.2. Atom
3.8.3. Bond
3.9. Utilities
3.9.1. Periodic Table
3.9.2. Units
4. PLAMS cookbook
4.1. MultiJob