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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. Installing PLAMS
2.3. Updating PLAMS
2.4. Running PLAMS
2.5. Defaults file
2.6. The launch script
2.6.1. Working folder location
2.6.2. Passing variables
2.6.3. Importing past jobs
2.6.4. Restarting failed script
2.6.5. Multiple input scripts
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 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 scripts
3.5.4. API
3.6. Public functions
3.6.1. Logging
3.6.2. Binding decorators
3.7. Molecule
3.7.1. Molecule
3.7.2. Atom
3.7.3. Bond
3.8. Utilities
3.8.1. Periodic Table
3.8.2. Units
3.8.3. Geometry tools
4. Interfaces
4.1. Amsterdam Modeling Suite
4.1.1. Disclaimer about AMS2018
4.1.2. AMS driver
4.1.2.1. Preparing input
4.1.2.2. Preparing runscript
4.1.2.3. Molecule handling
4.1.2.4. AMSJob API
4.1.2.5. AMSResults API
4.1.3. ADF
4.1.3.1. Preparing input
4.1.3.2. Preparing runscript
4.1.3.3. API
4.1.4. ReaxFF
4.1.5. MOPAC
4.1.5.1. Preparing input
4.1.5.2. API
4.1.6. Analysis tools: Densf, FCF
4.1.7. KF files
4.1.8. Legacy: BAND, DFTB, UFF
4.2. Other programs
4.2.1. Dirac
4.2.1.1. Preparing a calculation
4.2.1.2. Results extraction
4.2.1.3. API
4.2.2. Crystal
4.2.2.1. Preparing a calculation
4.2.2.2. Molecule parsing
4.2.2.3. Results extraction
4.2.2.4. Example
4.2.2.5. API
4.2.3. DFTB+
4.2.3.1. Preparing a calculation
4.2.3.2. Results extraction
4.2.3.3. Example
4.2.3.4. API
4.2.4. CP2K
4.3. Molecule interfaces
4.3.1. RDKit
4.3.2. ASE
5. Examples
5.1. Simple examples
5.1.1. Charge transfer integrals with ADF
5.1.2. Dictionary MultiJob
5.2. Advanced examples
5.2.1. Tuning the range separation
5.3. Recipes
5.3.1. ADF fragment job
5.3.2. NBO with ADF
5.3.3. Numerical gradients
5.3.4. Numerical Hessian
5.3.5. ReaxFF molecule gun
PLAMS
Documentation
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PLAMS
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4. Interfaces
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4.3. Molecule interfaces
4.3. Molecule interfaces
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4.3.1. RDKit
¶
Coming soon.
4.3.2. ASE
¶
Coming soon.