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Simmate Documentation
v0.0.0 (2022.03.28)
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Simmate Documentation
GitHub
Home
Getting Started
Getting Started
Introduction
1. Installation
1. Installation
Quickstart
a) Installing Python
b) Intro to the command line
c) Create your environment
d) Explore Simmate commands
2. Initial Setup & Tour
2. Initial Setup & Tour
Quickstart
a) Configure the database
b) Exploring Apps & Data
c) Submitting a Workflow
3. Workflows
3. Workflows
Quickstart
a) Make an input structure
b) View all workflows
c) Configure QE
d) Run a workflow
(extra) Submit to a cluster
4. Toolkit
4. Toolkit
Quickstart
a) Intro to Python (& Spyder)
b) The Structure class
c) The Molecule class
d) The Composition class
e) Advanced classes
5. Database
5. Database
Quickstart
a) View data w. DBeaver
b) How tables are built
c) Workflow data
d) Third-party data
6. Use a cloud database
6. Use a cloud database
Quickstart
a) Private vs shared
b) Building a database
c) Connect to Postgres
7. Computational resources
7. Computational resources
Quickstart
a) Why use workers?
b) Running locally
c) Monitoring jobs
d) Parallel clusters
e) HPC & Clouds
8. Custom Apps
8. Custom Apps
Quickstart
a) Create an app
b) Custom workflows
c) Custom tables
Wrap up
Full Guides
Full Guides
Overview
Config
Apps
Apps
Basic Use
Creating custom apps
Website
Website
Setup & Config
Creating views
Creating components
Creating components
Overview
Frontend Elements
Frontend Elements
text_input
text_area
number_input
button
radio
molecule_input
selectbox
checkbox
search_box
plotly_figure
Backend Mix-ins
REST API
Workflows
Workflows
Naming Conventions
Accuracy Ratings
Basic Use
Parameters
Parameters
Overview
angle_tolerance
chemical_system
command
composition
compress_output
copy_previous_directory
diffusion_analysis_id
directory
directory_new
directory_old
fitness_field
input_parameters
is_restart
max_atoms
max_path_length
max_stoich_factor
max_supercell_atoms
max_structures
migrating_specie
migration_hop
migration_images
min_atoms
min_supercell_atoms
min_supercell_vector_lengths
nfirst_generation
nimages
nsteadystate
nsteps
percolation_mode
relax_bulk
relax_endpoints
run_id
search_id
selector_kwargs
selector_name
singleshot_sources
sleep_step
source
standardize_structure
steadystate_source_id
steadystate_sources
stop_conditions
structure
subworkflow_kwargs
subworkflow_name
supercell_end
supercell_start
symmetry_precision
tags
temperature_end
temperature_start
time_step
updated_settings
vacancy_mode
validator_kwargs
validator_name
workflow_base
write_summary_files
Creating basic workflows
Creating nested workflows
Creating "S3" workflows
Compute
Compute
Basic Use
HPC
Cloud
Monitoring
Advanced
Schedules
Database
Database
Basic use
Workflow data
Third-party data
Creating Data Apps
Creating New Tables
Toolkit
Toolkit
Molecules
Molecules
Overview
Single Molecule
Single Molecule
Quickstart
Loading
Exporting
Reactions
Cleaning
Common Properties
Common Analyses
SMARTS sets
Many Molecules
Many Molecules
Featurizers
Clustering
ChemSpace Mapping
Similarity & Diversity
Crystal Structures
Crystal Structures
Overview
PyMatGen Help
PyMatGen Help
Structure
Lattice
Sites
Composition
Contributing
Contributing
First time setup
Creating & submitting changes
Maintainer notes
README for AI Assistants
Apps
Apps
Overview
AFLOW
Bader (henkelman)
baderkit
BCPC
CAS Registry
Chembl
ChemSpace
COD
eMolecules
Enamine
EPPO Global Database
Evolutionary Searches
JARVIS
Lab Automation
Lab Automation
Overview
Sensors
Controllers
Devices
Materials Project
OQMD
PDB
PPDB
Quantum Espresso
RDKit
VASP
VASP
Overview
Installation
Workflows
Warren Lab
++ Experimental Apps
++ Experimental Apps
BIOVIA COMSO
CLEASE
DeepMD
OpenEye OMEGA
Schrodinger
Surflex
Updates
Updates
Overview
Upcoming Release
v0.19.0 (2026.03.22)
v0.18.0 (2025.04.20)
v0.17.0 (2024.05.20)
v0.16.0 (2024.01.27)
v0.15.0 (2024.01.04)
v0.14.0 (2023.07.06)
v0.13.0 (2023.03.06)
v0.12.0 (2022.10.23)
v0.11.0 (2022.09.10)
v0.10.0 (2022.08.29)
v0.9.0 (2022.08.17)
v0.8.0 (2022.08.11)
v0.7.0 (2022.07.19)
v0.6.0 (2022.06.25)
v0.5.0 (2022.05.30)
v0.4.0 (2022.04.24)
v0.3.0 (2022.04.19)
v0.2.0 (2022.04.15)
v0.1.4 (2022.04.12)
v0.0.0 (2022.03.28)
v0.0.0 (2022.03.28)
¶
Enhancements
initial release
adding tests and docs