Advance / NanoLabo
An integrated GUI capable of graphically operating various calculation solvers, including
Quantum ESPRESSO*1, LAMMPS*2, and our product, Advance/PHASE. This interface simplifies
setting modeling and calculation conditions by automatically searching for information in
major materials databases such as the Materials Project*3. The results from these solvers aredisplayed graphically and instantaneously.

Features- Iconic display of crystal structures (as shown on the right).
- Material database search via chemical formula input.
- Modeling for crystals, surfaces, interfaces, and molecules.
- Support for open-source calculation engines.
- Various visualization functions, including band structure,vibrational modes, reaction path afterimage display,
kinematic animations, and more.

Functions
Modeling

Functions
Material
database
CrystalSystemCalculation
Materials Project*

3

PubChem*

4

Advance/PHASE
Quantum ESPRESSO*1
LAMMPS*2, ThreeBodyTB*5

Cell Translation
Supercell
Impurity Substitution

Surface &Interface
SystemMolecularSystem

ComputationalEngine
Calculation
FunctionsSCF Calculations, Structural Optimization
Hybrid Functionals, vdW Corrections

Lattice DefectBand Structure, Density of States (PDOS

Space Group Determination

Calculator)

Primitive Cell Transformation

Charge Density Visualization, etc.

Standard Cell Transformation

First-principles MD, Classical MD

Arbitrary Orientation of Surface

Thermal Conductivity, Viscosity

Molecular Adsorption to Surface

Coefficients, Diffusion Coefficients

Mismatched Interface [Pro only]

TD-DFT, XAFS/EELS

Organic Molecule Illustration

Phonon (Band Structure, Density of States)

Solvent Molecule Filling
Polymer Modeling [Pro only]

NEB Method, Work Function (ESM Method)

Computation
ControlResources

Job Scheduler
NanoLabo-API for Python*6
Local Machine
Compute Server (SSH Connection)
Cloud

Operating EnvironmentOS

Machine Spec(Recommended)

Online Manual-Windows 10/11 (64 bit)
AlmaLinux 8 (64 bit)
macOS 13 or higher (Intel/ARM64)
CPU: Intel Core i7 or higher
Memory: 10 GB or more

*1 Quantum ESPRESSO is a general-purpose open-source application for first-principles calculation, distributed under the GPL license. (https://www.quantumespresso.org)*2 LAMMPS is a general-purpose open-source application for classical molecular dynamics simulation, distributed under the GPL license.
(https://lammps.sandia.gov)*3 The Materials Project is a database for materials informatics developed at Lawrence Berkeley National Laboratory. (https://materialsproject.org)*4 PubChem is a database for biochemistry developed at the National Center for Biotechnology Information. (https://pubchem.ncbi.nlm.nih.gov)*5 ThreeBodyTB is an open-source application developed by NIST, designed for general-purpose tight binding methods. (https://pages.nist.gov/ThreeBodyTB.jl/)*6 API specifications are available in the Advance/NanoLabo online manual. (https://nanolabo-doc.readthedocs.io/en/latest/python.html)

Modeling
1. Material database✓✓

Enter a chemical formula, molecular structure (SMILES),or molecule name into the search field to retrieve thecorresponding crystal or molecular structure.
Connect to the following databases via the Internet- Crystal structure： Materials Project- Molecular structure： PubChem

2. Crystal System
Spinel Transformation

2. 結晶系
Standard Cell

セル変換 (スピネル)
Standard Cell

Impurity Substitution (P doping in Si)
Primitive Cell
Primitive Cell

不純物置換 (Si への P ドーピング)

3. Surface & Interface System
Surface model (Ni3Al [556]surface)

Interface model (Al2O3/GaN interface)

表面モデル (Ni3Al [556]表面)

界面モデル (Al2O3/GaN 界面)

Using our original SlabGenom algorithm, arbitrary
surface conditions can be generated.

Lattice matching is achieved using the continuous
fractional algorithm, which automatically optimizes theinterplanar distances influenced by the classicalmolecular force field.

3. 表面・界面系

4. Molecular System
Polymer models

interface generation with metal slabs)
4.(Enables分子系

Solvent molecular filling(NaCl aqueous solution filling around a Pt slab)

溶媒分子充填 (Pt スラブ周囲への NaCl aq 充填)

高分子モデル (金属スラブとの界面も生成可能)

With our original packing algorithm, arbitrary
solvent molecules and ions can be denselyplaced.

Calculation✓✓✓

Quantum ESPRESSO

Automatically generates appropriate input files directly from the crystal structure.
Allows users to perform various calculations without the need for complex setting of conditions.
Supports SCF calculations, structural optimization, band structure, density of states, ab initio MD,
TD-DFT, phonon, and NEB methods.
Visualizes the progress and results of calculations, with various types of post-processing
available.

Quantum ESPRESSO✓Input interface for Quantum ESPRESSOBand structure plotting

Visualization of the NEB ReactionPathway Afterimage

Quantum ESPRESSO 用入力画面

LAMMPS

Supports Lennard-Jones, Charge, OPLS-AA, ReaxFF, Tersoff, EAM, MEAM, and Neural Network force fields*1.
Allows setting multi-step calculation schemes (e.g., 100 ps motion in NVT ensemble, then switching toNPT ensemble).
Displays animations of dynamics during calculations, with the option to save in MP4 format.
External electric field, external force and translational movement for a given atom, and cell deformation.
Visual definition of atomic groups.

✓✓LAMMPS✓✓Multi-Step Calculation SchemeSettings

List of Calculation Items

Animation Display

計算項目の一覧表示
多段階計算スキーム設定画面*1 To utilize the Neural Network force field, our products, Advance/NeuralMD and the open-source Graph Neural Network force
field, are available (for details, see the following page).

Computational Resources
Perform calculations on a
local machine
Submit jobs to a computing
serverUsing Cloud Services- Calculation management via built-in job scheduler- Support for PBS, SLURM and PJM in the Linux version- Execution of calculations on a Linux server via SSH connection- Job management using PBS, SLURM, or PJM- Science Cloud GPU*2- bare-metal cloud environment provided by HPC Systems. (https://global.hpc.co.jp/)- Submit jobs to the cloud from a local machine with NanoLabo installed.
- Mat3ra*2- SaaS cloud environment provided by Exabyte Inc. (https://www.mat3ra.com)- NanoLabo is compatible with remote desktop on various platforms*2 Additional charges are incurred for using cloud services.
※2 クラウドサービスのご利用には、別途料金が発生します。

Graph Neural Network Potential
General-purpose Graph Neural Network force fields, compatible with a wide range of elements in theperiodic table, are available. Specifically, Open Catalyst, M3GNet, and CHGNet are offered as opensource software options*1. All of these come with pre-trained models, eliminating the need for users tooptimize the neural network themselves. This offers the advantage of enabling immediate molecular
dynamics simulations for various systems. In addition, it is possible to load fine-tuned Graph Neural
Network force field models or to operate Neural Network force fields created using our product,Advance/NeuralMD.
*1 Open Catalyst (https://github.com/Open-Catalyst-Project/ocp), M3GNet (https://github.com/materialsvirtuallab/matgl) andCHGNet (https://github.com/CederGroupHub/chgnet) are all implemented in Python, and they are designed to call these Python modules fromLAMMPS to perform structure optimization calculations and molecular dynamics calculations.

Jupyter Interface for NanoLabo
This service enables the display and operation ofJupyter Lab*2 on the Advance/NanoLabo screen. It
outputs Python code to create an Atoms object of ASE*3
by transferring the structure file, modeled inAdvance/NanoLabo, to the server where Jupyter Lab isrunning. It is also feasible to integrate with Matlantis(https://matlantis.com), a general-purpose atomiclevel simulation cloud service provided by Preferred
Computational Chemistry Co., Ltd.
*2 Jupyter Lab (https://jupyter.org) is a web-based integrated development
environment; however, here we primarily envision its operation as a
Notebook with Python as the kernel.
*3 The Atomic Simulation Environment (ASE) is extensively used as a Python
module for performing first-principles and molecular dynamics
calculations.

Licensing
License TypeOS
License Type
ライセンス形態
Windows

Node Lock (Remote Desktop available)

Linux

FloatingmacOS

Node Lock (Remote Desktop available)

License Priceライセンス価格
ProductAnnual

Annual(Business /(Academic)

National Institute)

Permanent

Permanent(Business /( Academic)

National Institute)

Advance/NanoLabo

500,000JPY*5250,000JPY*51,500,000JPY*5750,000JPY*5Advance/NanoLabo Pro*4900,000JPY*5450,000JPY*52,700,000JPY*51,350,000JPY*5Jupyter Interface

400,000JPY

200,000JPY

1,200,000JPY

600,000JPY*4 Advance/NanoLabo Pro includes mismatched interface and polymer modeling functions.
*5 The license price is discounted when purchasing three or more units simultaneously.
For more details, please contact our sales representative.

Trial licenses
Free trial licenses are available for one month per individual.

CasesCalculation of Molecular Dynamics inWater/Methanol Mixtures

Work Function Calculation ofK/Cu(001)System by ESM Method

A model of a water/methanol mixture with a 1:1
volume ratio is developed, and molecular dynamics
simulations are conducted using the NPT ensemble
under standard temperature and pressure conditions(300K, 1bar). The OPLS-AA force field is utilized formolecular interactions.

Using the Effective Screening Medium (ESM)
method, the work functions of a Cu(001) surface
with adsorbed potassium are calculated. This
allows for the simulation of changes in the work
function depending on the coverage ratio.

Water/methanol mixture

Change in density of
mixed solution

水／メタノール混合溶液

Potential

混合溶液の密度変化
Fermi energy

KCu(001)

Solution

Density(calculated)

Density(experimental)

Water

1.00 g/cm3

1.00 g/cm3 *1

Methanol

0.75 g/cm30.79 g/cm3 *1

Water/methanol

0.89 g/cm3

0.93 g/cm3 *2*1 S. Kim, et al: Nucleic Acids Res. 2019; 47(D1):D1102-1109.
*2 The Chemical Society of Japan (ed.): "Handbook of Chemistry,
5th Edition, Basic Edition II", Maruzen (2004) (in Japanese)

Analysis of Diffusion Pathways of Al Adatoms Using the NEB Method※1 S. Kim, et al: Nucleic Acids Res. 2019; 47(D1):D1102-1109.
Utilizing the Nudged Elastic Band (NEB) method, the diffusion
process of adatoms on an Al(001) surface※2 日本化学会(編): "改訂 5 版 化学便覧 基礎編 II", 丸善 (2004)
is analyzed. The activation energy is determined by calculating
the two primary diffusion mechanisms:
NEB法による
Al アドアトムの拡散経路解析
Hoppingand Exchange.

Hopping diffusion

Exchange diffusion

Ea = 0.46 eV
Hopping 拡散

Ea = 0.14 eV
Exchange 拡散

Ea = 0.46 eV

Ea = 0.14 eV

AdvanceSoft Corporation
Please contact us first if you require additional information. Demonstrations canalso be arranged.
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E-mail: office@advancesoft.jp

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