Free trial
Toggle navigation
Applications
Products
Support
About us
Search
Search
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. Case sensitivity
3.1.4. Global settings
3.1.5. 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
3.7.1.1. Atom labeling
3.7.2. Atom
3.7.3. Bond
3.7.4. RDKit interface
3.7.5. ASE interface
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. AMS driver
4.1.1.1. Preparing input
4.1.1.2. Preparing runscript
4.1.1.3. Molecule handling
4.1.1.4. AMSJob API
4.1.1.5. AMSResults API
4.1.2. ADF
4.1.2.1. Preparing input
4.1.2.2. Preparing runscript
4.1.2.3. API
4.1.3. ReaxFF
4.1.4. Analysis tools: Densf, FCF
4.1.5. KF files
4.1.6. COSMO-RS
4.1.6.1. Settings
4.1.6.2. Settings with multiple compound
4.1.6.3. ADFJob and CRSJob
4.1.6.4. COSMO-RS Parameters
4.1.6.5. Data analyses and plotting
4.1.6.6. API
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
4.2.4.1. Settings
4.2.4.2. Molecule parsing
4.2.4.3. Loading jobs
4.2.4.4. Molecule loading
4.2.4.5. API
4.2.5. ORCA
4.2.5.1. API
4.2.6. MOPAC (standalone program)
4.2.6.1. Preparing input
4.2.6.2. API
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 and COSMO-RS workflow
5.3.2. ADF fragment job
5.3.3. NBO with ADF
5.3.4. Numerical gradients
5.3.5. Numerical Hessian
5.3.6. ReaxFF molecule gun
5.3.7. Global Minimum Search
5.3.8. Vibrational analysis with ASE
5.3.8.1. Example
5.3.8.2. API
6. Citations
PLAMS
Documentation
/
PLAMS
/
¶
Python Library for Automating Molecular Simulations
¶
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. Case sensitivity
3.1.4. Global settings
3.1.5. 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 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
3.7.4. RDKit interface
3.7.5. ASE interface
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. AMS driver
4.1.2. ADF
4.1.3. ReaxFF
4.1.4. Analysis tools: Densf, FCF
4.1.5. KF files
4.1.6. COSMO-RS
4.2. Other programs
4.2.1. Dirac
4.2.2. Crystal
4.2.3. DFTB+
4.2.4. CP2K
4.2.5. ORCA
4.2.6. MOPAC (standalone program)
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 and COSMO-RS workflow
5.3.2. ADF fragment job
5.3.3. NBO with ADF
5.3.4. Numerical gradients
5.3.5. Numerical Hessian
5.3.6. ReaxFF molecule gun
5.3.7. Global Minimum Search
5.3.8. Vibrational analysis with ASE
6. Citations