Release Notes

Version 0.98.0

  • Main Chemistream GUI improvements
    • Improved behavior when compute session setup fails, remote instances now terminate automatically thereby saving money

    • Further improvements in CI/CD pipelines for GUI and compute images

    • Better startup logic and error catching when loading license file and user settings

    • Improved UI design including improved error messaging and links to troubleshooting help page

    • Robust checking for internet connection before attempting remote compute session

    • Reorganizing compute session window and adding an ‘Instance type’ column

  • Initial unit testing framework in place for main GUI

  • Fixed bug for managing remote ssh keys on AWS

  • Locking all dependencies for GUI and workflow images

  • Improved re-connection behavior for remote compute sessions

  • More robust compute session startup procedure, including purging old ssh key files

  • Remote storage interface in workflows now connect to individual S3 accounts on AWS

  • Updated demos/tutorials including new demos for NWChem and integrated charge analysis, ALFABET, reinforcement learning and BDE training data generation

  • Improved error catching for storage interface in all workflows

  • Single license file for application and compute images

  • New off-lattice deposition model implemented in SPPARKS source

  • Reinforement learning (RL) workflow added. Includes user defined initial molecule, UI settings for hyperparameter scans and RLMolecule setup and molecule rendering for top rewards found

  • Embedded tensorboard supported in RL workflows

  • Improved documentation for RL workflow, descriptions of all menu settings added

  • Improving handling of ports for tensorboard for local and remote compute sessions

  • Simplifying dependencies in all compute images, reducing their size

  • Updating SPPARKS version to include a recent bug fix branch

  • Including license agreements for all underlying compute applications in and source code where required

Version 0.90.0

  • Main GUI setup table now includes a dynamic cost estimator

  • Improved clarity for all workflows implemented with a design of enabling disabled buttons/menus in all custom JupyterLab notebooks

  • Simplified build dependencies for the images and main GUI

  • updated to ipywidgets to 7.7.1, Jupyterlab 3.4.7 and Python 3.10

  • SPPARKS image updated to version 19Sep22

  • SPPARKS-ALD workflow has additional simulation parameters exposed including separate controls for:
    • species A,B pressure

    • species A,B deposition/desorption time

    • species A,B energy of surface reaction energies

    • number of adsorption/desorption cycles

  • Makalii updates to improve setup stability

  • Waihona storage interface to AWS S3/Azure Blob storage has improved clarity and stability with dynamic dropdown menus for up(down)load location in cloud compute sessions

  • AI/ML images include setup for GPU instance (g3.4xlarge) at AWS

  • Updated NREL AI/ML libraries NFP(0.3.12), GraphEnv(0.2.0) and RLMolecule(0.0.6) for the latest versions of TensorFlow(2.11.0) and Ray(2.10.0)

  • Compute session docker images now include explicit memory allocation for /dev/shm in order to improve AI/ML library Ray performance

  • Chemistream tools modules have been split up for reduced image sizes and faster startup

  • Migrated from conda to mamba for faster development and testing

  • Source code for main Chemistream GUI and compute images has been migrated from GitHub to GitLab

  • User issue tracking, development and modern CI/CD build pipelines for the main GUI and compute images now implemented in private GitLab project

  • New and improved product website (chemistream.io)

  • Improved NWChem workflows for:
    • bond dissociation energy (BDE) calculations at scale ie accepting a CSV of SMILES strings

    • parsing of DDEC6 analysis files to seamlessly tabulate bond connectivity, bond-orders, partial charges and generate RDKit mol-object for additional analysis

    • using the NREL OPV molecule database to setup NWChem simulations for further analysis including DDEC6 bond/partial-charge analysis

  • Bug fixes and improved robustness across all workflows

  • Improved stability for embedded JSME drawing widget

  • Prototype Chemistream embedded window for cloud resource management implemented

  • NWChem setup menu now as a toggle for turning pre-opt HF/2-21G step on/off

  • For local compute sessions, Chemistream performs a docker system clean on termination

  • Simplified prototype for pricing models (still under development in cooperation with beta-testers) See Pricing Models for current details.

Version 0.80.0

  • Improved ‘pre-optimization/embedding’ for molecules in DFT workflows (implemented with customized RDKit code).

  • Improvements to Dalton & NWChem DFT workflows to accept CSV files with lists of SMILES strings.

  • Improvements to Dalton & NWChem DFT workflows to improve the geometry optimization for organic molecules. There is now an explicit HF/3-21G calculation for both codes before proceeding to a user-requested functional and basis set to further refine geometry optimization.

  • Adding parsing of polarizability and dipole moments for all DFT workflows.

  • Enabled including solvent models in Dalton and NWChem DFT workflows.

  • Adding menu choices to simplify control of level of accuracy during geometry optimization for NWChem workflows.

  • Adding viz for HOMO/LUMO molecular orbitals for NWChem DFT workflows.

  • Adding final molecular configuration output to mol2 files for DFT workflows.

  • Integrating bonding and partial-charge analysis (using DDEC6) into NWChem DFT workflows.

  • Toggle between default input template and user defined inputs for DFT workflows

  • Formatting improvements for all workflows including - file manager window default width - instructions for starting terminals and better menu formatting

  • Better startup instructions for user settings including a prototype UI for interacting with S3 storage at AWS. This permanent storage will be used for downloading workflows, checkpointing calculations and saving user-generated results.

  • Reworking user account setup
    • AWS security group settings configured automatically

    • AWS ssh-key pairs managed automatically

    • default, reserved user settings account (‘techx’) can be used for connecting to common remote compute resources (prototype of collaborative platform mode)

    • new UI dialog for loading a user’s custom settings file

    • Automated AWS user-accounts through new Chemistream Tech-X website

  • Improving AWS billing by using internally generated institution and user accounts at AWS by utilizing their organizational tools.

  • Improved viz speed for ALD SPPARKS workflow.

  • Improved model selection and setup for ALD SPPARKS workflow.

  • Adding internet download/upload speed check in launchpad startup window.

  • Improved stability for Mac/Windows installers (including working with conda constructor developers).

  • Improved behavior for re-connecting to remote compute sessions when internet connections are changed or temporarily drop-out.

  • Adding embedded Tensorboard capability for AI/ML workflows.

  • Reworking AI/ML image dependencies to include the ‘Ray’ project. This is part of NREL’s refactoring of RL capability with the GraphEnv project. A new image is now available through Chemistream utilizing the GraphEnv NREL library.

Version 0.60.0

  • Updating LAMMPS image to version 29Oct2020 and the corresponding LAMMPS-AWESEMMD

  • New prototypes for NWChem workflow menus in NWChem NEXT examples

  • Prototype of new launchpad PySide2 application for starting cloud resources in place.

  • New quantum chemistry code DALTON image available

  • Major revision to Chemistream starting application:
    • JupyterLab local manager session is deprecated

    • Startup GUI now manages license file installation and cloud startup functions

    • Multiple remote compute sessions can now be managed through startup GUI

    • Improved error handling throughout the startup process

  • Reworking of compute session workflows for ALFABET, NWChem and Dalton to use ipywidgets for all functions

  • Improving startup user instructions for all remote workflows

  • New streamlined workflows for Dalton and NWChem for
    • scaling studies

    • parsing HOMO/LUMO values

    • series of runs given input SMILES strings

    • calculating hyperpolarizabilities

  • Implemented multi-stage builds for Docker images resulting in a further 50% size reduction

  • Updating panel and panel-chemistry dependencies resulting in faster app/image installs

  • Updating to JupyterLab=3.3.0

  • Using jupyterlab_scenes module to enable auto-execution for turnkey workflows

Version 0.20.0

  • Reworked Chemistream application build system so pyinstaller no longer used, thereby resulting in smaller installers

  • Streamlined startup page on JupyterLab: Manager tab

  • Adding menu selection for new RLMolecule (from NREL) image

  • Adding menu selection for new SPPARKS image with proprietary ALD model pre-compiled

  • Adding menu selection for new NWChem image with the DDEC6 and Molden packages added

  • Maintaining separate local ports for remote cloud compute session and local compute session

  • Fixing temporary directory scratch space for NWChem sims

  • Improved docker desktop setup for ‘local’ compute session across platforms

  • Improved checks for installed docker and docker engine start for ‘local’ compute session

  • Updating LAMMPS and SPPARKS examples for better results parsing

  • Improved visualization for SPPARKS diffusion 3d example

  • Reworking of dependencies in Chemistream installer. The installer depends on Makalii and Jupyterlab only. All compute modules and codes are moved to Docker images available from Tech-X repo. All installers are nearly half as large.

  • Installer setup and configuration now ~2-3x faster due to simplified dependencies.

  • All Tech-X Docker images have been reworked for fewer dependencies and are smaller

  • JSME editor is now embedded in Jupyterlab notebooks, available through the Chemistream RDKitBase class

Version 0.12.1

  • Updating to conda Python 3.8

  • Updating to JupyterLab > 3

  • Updating ipywidgets to latest version that simplifies and speeds up installation

  • Updating pyinstaller and constructor packages to latest version (these can use conda python)

  • Adding menu selection for new GROMACS image

  • Using development version of NGLView that simplifies and speeds up installation

  • Removing STREAMM dependency from Chemistream module as this is only used in remote compute sessions. This has decreased the size of installers on all platforms

  • Adding ability to start a ‘local’ compute session so users can test workflows without need for configuring cloud accounts. This is valid on MacOS, Linux and Windows

  • Improving stability of setup of compute session

  • New example modules for BDE training model

  • Bug fixes for storage (Waihona) interface methods

Version 0.9.12

  • Removing py3Dmol dependencies and methods from ChemVis module

  • Adding NGLView dependencies and migrating from py3Dmol

  • New methods for NGLView added to ChemVis module

  • Adding example directories for rDock and QMCPack

Version 0.9.10

  • Upgrading to JupyterLab v 2.1.0

  • Examples for remote storage (eg AWS S3 and Azure Blob)

  • Adding RDKit dependency for a base class RDKitBase that is used by several examples’ derived classes.

  • Adding example for downloading OPV database info and analyzing with RDKit

  • Adding extra setup python files to tailor installs for app/cloud and (un)licensed versions

  • Freezing Miniconda version to version Miniconda3-py37_4.8.3-platform-x86_64.sh”

Version 0.9.8

  • Examples for machine learning, image recognition for ‘Digits’ and ‘Fashion’

  • Example for neural net prediction of bond dissociation energies using Alfabet

  • Example for complex P3HT workflow

Version 0.9.1

  • Cloud management for Amazon and AWS

  • Initial development of Jupyterlab framework using ipywidgets

  • Examples for scaling with NWChem, LAMMPS and SPPARKS

  • Cloud images all enabled with generation of multi-node HPC cluster

  • Cloud images all enabled with creation of NFS shared directory