Version Information

2024/03/25 Version 2.9.2

  • New features

    • added chatbot functionality utilizing ChatGPT for questions about how to use NanoLabo

    • added interface for “SevenNet”, a multi-GPU compatible GNN versatile force field

    • added tool bar button show/hide settings

    • QE: added algorithm settings for image import in NEB

    • LAMMPS: added LG-vdW setting option in ReaxFF configuration

    • LAMMPS: support for deformation in 2D and 1D directions of cell shape

    • added editing interface in SSH server settings to allow reordering of configurations etc.

    • added functionality to copy existing settings when creating new configurations in SSH server settings

    • NeuralMD: new features corresponding to Ver.1.9.2

      • SLHMC: support for deformation in 2D and 1D directions of cell shape

  • Change / fix

    • QE: change default Occupations of isolated atomic systems from Fixed to Smearing

    • SLHMC: exclude data from plotting if SCF calculation did not converge

    • LAMMPS: compatibility with the latest version of the Open Catalyst Project

    • LAMMPS: compatibility with the latest version of MatGL

    • LAMMPS: fix for the issue where element name Pm is not recognized correctly when using GNN force fields

    • hide temporary files of Word/Excel/PowerPoint in explorer

    • (Mac) fix for the issue where zoom shortcut keys are not functional in the built-in web browser

    • update the build-in web browser library JxBrowser (7.34→7.37.1)

    • revise FOCUS supercomputer preset settings in SSH server configuration to the latest version

    • for remote execution, support cases where long job IDs are truncated at the end in the output of the qstat command in PBS

  • Tune-ups, bug fixes, etc.

2023/11/15 Version 2.9.1

  • New features

    • added collaboration feature with Matlantis™(using Jupyter Interface)

    • LAMMPS: support for MatGL version of M3GNet force field (the successor to the original M3GNet)

    • LAMMPS: support for CHGNet graph neural network force field

    • LAMMPS: added charge setting feature for external electric fields (within the Force-Field screen)

    • LAMMPS: added feature to import M3GNet/CHGNet models

    • LAMMPS: enhancement of the Scheme screen functionality

      • added Undo/Redo function (+ shortcut keys)

      • added detailed settings of autocorrelation function for thermal conductivity and viscosity coefficient calculations

    • enhancement of the built-in web browser features

      • added zoom feature

      • added in-page search toolbar button

      • added right-click menu

      • added function to search selected text in Materials Finder

    • enhancement of Jupyter Interface features

      • added behavior setting for drag & drop (option to pass the file directly to JupyterLab)

      • added in-page search function

    • support for copying screenshot to clipboard / drag & dropping screenshot

    • added option to display Materials Project and PubChem web pages in the built-in browser

    • added ability to import and use any molecule for modeler’s molecule adsorption function

    • added pseudopotential file import feature

    • added enable/disable setting for proxy server

    • added XYZ, CIF, and POSCAR to Save Movie output formats

    • added MD5 check for binaries transferred during remote job submission

    • added version check feature for NanoLabo Tool

  • Change / fix

    • QE: fixed an issue with the simulation time display panel (progress display) on the Result screen during first principle MD calculations

    • QE: fixed an issue when switching NEB image displays

    • QE: improved the pseudopotential file download function

    • QE: changed the initial Isovalue for visualizing 3D change density distribution

    • LAMMPS: updated version to 2Aug2023

    • LAMMPS: fixed an issue where Option reset during Scheme editing

    • LAMMPS: for M3GNet, the import of dftd3 is now omitted if DFT-D3 correction is not used

    • LAMMPS: implemented a workaround to avoid parameter assigning error on some systems with undefined OPLS-AA parameters by using alternative parameters

    • NeuralMD: updated to Ver.1.9.1

    • separated external Jar libraries to improve NanoLabo’s startup speed

    • the built-in browser now inherits the system locale (improvements in displaying Japanese fonts, etc.)

    • improved behavior when multiple instances of NanoLabo are launched

    • adjusted environment variables related to OpenMP parallel for local calculations

  • Tune-ups, bug fixes, etc.

2023/08/03 Version 2.9

  • New features

    • added interface for the versatile tight-binding method package “ThreeBodyTB”

    • NeuralMD: new features correspond to Ver.1.9

      • added setting items for the method to define one force field using the average value of multiple neural network models

      • added setting items for Super Epoch method (splits the training data into subsets and serially performs the training process using each subset)

      • changed default values of some parameters to values more suitable for inorganic crystals

    • NeuralMD: added feature to equalize SCF calculation conditions in a grand project

    • NeuralMD: in grand-project, added SLHMC as the method of generating structures”

    • NeuralMD: in grand-project, added feature to suppress automatic download of Quantum ESPRESSO calculation results executed on remote server

    • NeuralMD: in grand-project, support for restarting the calculation of training data generation by Quantum ESPRESSO

    • added capability to copy the information in the upper right corner of the calculation result graph

    • added the PDF file viewer (open in explorer, or drag & drop the file onto the screen)

  • Change / fix

    • addressed issues caused by migration to JRE17 (inaccurate screen layout, memory leak in atomic structure viewer, etc.)

    • disabled animation when displaying plots

    • improved GC performance of the Java virtual machine

    • QE: resolved an error that occurs if Γ point only and Non-Colinear spin is used

    • QE: resolved an issue where the dielectric function plots does not show when TD-DFT is executed on a remote server set to Always Offline mode

    • resolved an issue that occurs if the file owner on the remote server is “domain users”

    • NeuralMD: resolved a problem where SLHMC on Linux does not work if the login shell is dash

    • changed the library of the built-in web browser to JxBrowser (Chromium-based browser)

  • added Windows 11 to supported OS / changed supported macOS version to Ventura(13) or later

  • Tune-ups, bug fixes, etc.

2023/04/25 Version 2.8

  • New features

    • Jupyter Interface for NanoLabo (free to use until July 31, 2023)

    • (Mac) the menubar is now available for use

  • Change / fix

    • Java runtime environment updated from JRE8 to JRE17

    • LAMMPS: fixed a problem with graph display when structure optimization is used in Scheme

    • LAMMPS: fixed the setting of elements (pair_coeff) when the MEAM force field is used

    • enhanced the compatibility of CIF import/export

    • (Windows) improved behavior when pinned to the taskbar / when multiple windows are shown

    • changed the location of configuration files etc. from .nanolabo/ to .nanolabo/.system/

      • For users of previous versions, files will be moved to the new location upon the first launch after the update.

  • Tune-ups, bug fixes, etc.

2023/03/08 Version 2.7.1

  • resolved an issue where the MPI library in NanoLabo Tool2.7 does not functioning correctly on CentOS7

    • There is a problem when posting jobs to a CentOS remote server or executing locally on CentOS7. Specifically, an error related to libhwloc.so was reported during calculation execution.

    • The installer of NanoLabo itself remains unchanged. Simply download and install NanoLabo Tool2.7.1.

    • If you have already submitted jobs to a remote server, please remove the .nanobin2.7 folder from the Work Directory on the server.

2023/03/06 Version 2.7

  • New features

    • NeuralMD: new features corresponding to Ver.1.8

      • Δ-NNP method utilizing ReaxFF

    • LAMMPS: support for M3GNet, a graph neural network force field for inorganic solids

    • LAMMPS: support for the Open Catalyst 2022(GemNet-dT) force field

    • support for the PJM job management system

    • after posting remote job, results can now be retrieved even if the local project folder has been moved

    • you can post jobs even if the project is outside the .nanolabo folder or if the project name contains characters invalid on Linux

    • (Mac) released the Apple M1 support ver. (ARM ver.)

      • distributed as a separate installer from pre-existing ver. (Intel ver.). Please select the one suitable for your machine when download.

  • Change / fix

    • increased the maximum number of DOS definitions in PDOS calculator to 16

    • support for host key types other than RSA/SHA-1(ssh-rsa) when connecting to a remote server

    • reflect URL changes of Materials Project API used in materials database search

      • if you modified the configuration file to address this issue in Ver.2.6 or earlier, you can either maintain the modification or revert the change after updating to 2.7.

  • Tune-ups, bug fixes, etc.

2022/09/30 Version 2.6

  • New features

    • NeuralMD: new features corresponding to Ver.1.7

      • add cell deformation method of SLHMC which performs NNP-MD by NPH

      • output CRASH log when SLHMC terminates with an error

      • setting to utilize GPU (Linux / NeuralMD Pro edition only)

    • NeuralMD: download setting of SLHMC data (slhmc_dat) for remote execution

    • LAMMPS: generate initial velocity at a specified temperature

    • LAMMPS: display / edit input files before calculation

    • LAMMPS: reduce data points for improved display performance (can be toggled in settings)

    • LAMMPS: support NPH ensemble

    • LAMMPS: auto-fix order of atoms in input file for many-body force field (Tersoff, EAM, ReaxFF, NeuralMD)

    • LAMMPS: cell deformation setting on structure optimization

    • LAMMPS: function to insert arbitrary commands into the input file

    • LAMMPS: function to add arbitrary variables, including user-defined one, for CSV output and time series plots

    • LAMMPS: function to define atom groups via GUI

    • LAMMPS: function to apply electric field / apply external force / move at a constant speed / deform cell at a constant speed

    • LAMMPS: GPU usage for neural network force field calculation (Linux only)

    • QE: calculation of lattice dielectric function using effective charge in Phonon calculation

    • QE: support for Non-analytic term calculation in Phonon Dispersion calculation

    • QE: add Autopilot setting screen for Car-Parrinello MD

    • QE: add new pseudo-potential libraries (GBRV, SSSP) to NanoLabo Tool

    • QE: add function to specify initial charge in SCF calculation

    • Use RDkit for 3D structure generation (structure optimization by UFF) in the molecule drawing function

    • function to search for crystal structures with higher symmetry (symmetry determination with specified deviation)

    • function to test connection to remote server

    • support for OpenSSH format private key for SSH public key authentication

    • include batch file to set PATH for NanoLabo Tool (Windows only)

    • function to open folders in an external filer

  • Change / fix

    • LAMMPS: updated to the latest version (2Jun2022)

    • LAMMPS: changed input file format (more items are user-editable)

    • LAMMPS: default pseudo potential to GBRV (or SSSP if GBRV unavailable for the element)

    • reduce the number of commands when downloading files from a remote server (improved communication speed)

  • excluded CentOS 6 from supported OS

  • unified CentOS version and AlmaLinux version of calculation engines (unified NanoLabo Tool installer)

  • changed icon

  • Tune-ups, bug fixes, etc.

2022/05/20 Version 2.5

  • New features

    • LAMMPS: constraints setting on cell deformation when using NPT ensemble

    • NeuralMD: new features corresponding to Ver.1.6

      • added interface for the Self-Learning Hybrid Monte Carlo method

    • NeuralMD: setting to optimize only energy (not force) during learning

    • proxy for SSH connection

  • Change / fix

    • QE: fixed a display problem of phonon modes when using the ESM method

    • QE: fixed a bug in BAND, DOS, and NMR plots where Line Width and Line Type settings could not be changed

    • NeuralMD: fixed a bug in the Behler symmetry function where changes to G2/G3 parameters were not reflected in the calculation

    • (Linux) fixed a bug that caused grand-project calculations to fail when using the Job manager on a local machine

    • (Mac) fixed the extension filter of some file-choosing dialogs

    • fixed a bug in set_all_atoms() in nanolabo.py (“error: invalid atomsFile” would always occur)

  • Tune-ups, bug fixes, etc.

2022/02/04 Version 2.4

  • New features

    • LAMMPS: support for the Open Catalyst Project versatile force field (graph neural network)

    • added settings for memory usage, Java VM arguments (applied to NanoLabo itself)

    • NeuralMD: new features corresponding to Ver.1.5

      • queuing setting for when a license error occurs (due to simultaneous execution limits)

      • added functionality to split training data to create testing data

      • added the series of in-situ test results to the RMSE plot

      • added other setting items

    • LAMMPS: added setting for the interval of log output

    • export atomic configuration as VASP’s POSCAR format file

  • Change / fix

    • (Linux) changed the MPI library/compiler to Open MPI/oneAPI (from Intel MPI/Intel Compiler)

    • fixed an issue where failing to retrieve job status in certain environments when submitting a job to a calculation server, especially if the user name is long

  • added AlmaLinux 8 to the supported OS

  • Tune-ups, bug fixes, etc.

2021/12/10 Version 2.3

  • New features

    • NeuralMD: train(optimize) / test neural network potential

    • NeuralMD: generate atomic structures for training data by Metropolis method

      • support for opening the configuration file (sannp.metro)

    • measure bond length, bond angles and dihedral angles

    • edit lattice vectors within the modeler screen

    • non-diagonal super cell expansion

    • QE: added RPBE to exchange-correlation functional

  • Change / fix

    • QE: improved algorithm for generating intermediate images of NEB (support reactions of polyatomic molecules)

    • changed the Java runtime environment to Liberica JRE 8

    • support for the updated specification of Materials API

  • Tune-ups, bug fixes, etc.

2021/10/01 Version 2.2

  • New features

    • [Pro] QE: NMR spectrum calculation by GIPAW method

    • QE: Car-Parrinello Molecular Dynamics (CPMD) calculations

    • support for opening MDL Molfile (.mol, .sdf)

  • Change / fix

    • QE: fixed ordering of intermediate images of NEB at the initial setting

  • update Quantum ESPRESSO to version 6.7

  • Tune-ups, bug fixes, etc.

2021/06/04 Version 2.1

  • New features

    • settings for low bandwidth network

    • functionality to generate the training data for NeuralMD (Grand-project)

    • QE: 3D display of SCF calculation results (charge density, potential and spin polarization)

    • QE: setting of convergence threshold for phonon calculations

    • LAMMPS: new panel for setting atom velocities

  • Change / fix

    • suppressed the SSH session number while running remote jobs

    • QE: fixed a bug where DOS was sometimes not shown if spin is enabled

    • QE: changed the default k-point path for BAND calculations

    • edited lsf2pbs/qsub (changed the way bsub is invoked)

  • Tune-ups, bug fixes, etc.

2020/11/30 Version 2.0

  • New features

    • [Pro] Polymer Modeler

    • QE: XAFS calculation

    • support for opening LAMMPS dump file

  • Tune-ups, bug fixes, etc.

2020/07/29 Version 1.5

  • New features

    • QE: settings for exchange-correlation functional (hybrid functional / van der Waals interaction)

    • QE: PDOS Calculator

    • Suspend access during remote execution / download files from server / delete files on server

  • Tune-ups, bug fixes, etc.

2020/04/27 Version 1.4

  • New features

    • LAMMPS: Calculate and visualize thermal conductivity, viscosity coefficient, diffusion coefficient and radial distribution function

    • LAMMPS: Support for the Tersoff force field

    • QE: Added rmm to Diagonalization in SCF (set as default)

    • QE: Added Algorithm to TD-DFT

    • Flip / swap lattice vectors

    • Move atoms along coordinate axis

    • Additional operations for slab model

    • Context menu / drag operation on file tree in Result view

    • Preserve window size

  • (Linux) Fixed problem of not functioning properly over long usage periods

  • Tune-ups, bug fixes, etc.

2019/09/30 Version 1.3

  • released “Pro version” with additional functions

  • [Pro] Interface builder

  • Tune-ups, bug fixes, etc.

2019/08/05 Version 1.2.1

  • (macOS) Solved environment-dependent problem that prevented the execution of the calculation engine

  • Bug fixes, etc.

2019/06/28 Version 1.2

  • New features

    • Nudged Elastic Band (NEB) method

    • Effective Screening Medium (ESM) method

    • Cooperation with Python

  • Tune-up of atomic viewer

2019/05/09 Version 1.1.2

  • New features

    • Update check at startup

    • Lambda System

  • Fixed to use the real unit system when using ReaxFF in LAMMPS

  • Tune-ups, bug fixes, etc.

2019/01/18 Version 1.1.1

  • Bug fix (connection problem when using proxy)

2018/12/21 Version 1.1

  • macOS support

  • New features

    • Post jobs to calculation server (SSH connection)

    • Drawing a molecule

    • Molecular adsorption onto slab

    • Packing molecules

    • Automatically find Primitive Cell / Standard Cell

    • Detect space group

    • Open files with an external text editor

    • Enhancement of explorer functions

  • Bug fixes, etc.

2018/08/01 Version 1.0

  • Initial release