Saturday, 21 April 2018

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Workshop Info

The HPC school of 2018 is the continuation of the last HPC schools. This year the School will be focused on technical skills for the HPC users, in particular introduction to tools in HPC for molecular dynamics simulation using LAMPPS ( 2018 regional school for HPC will be held in Bandung at Research Center for Informatics, Indonesian Institute of Science. The school is scheduled in 22-26 October 2018 (tentative).


The workshop consists of both lecture and hands-on sessions with the lecturers from ICTP, Sandia, ITB and LIPI.

    Dr. Axel Kohlmeyer * (under confirmation) , Institute for Computational Molecular Science (035-07) College of Science and Technology Temple University, Philadelphia, PA 19122


We invite young scientists and engineers, post-graduate students from all South-East Asian countries who (already or plan to) work with Molecular Dynamics. The school will be conducted in English and hence participants should have an adequate working knowledge of this language. The participants are also required to already be familiar basic knowledge of Molecular Dynamics.The number of participants is limited to around 24 persons from local, and 6-10 persons from regional region. There is no registration fee for all participants. All participants will be provided with lunch and snacks during the workshop.


Registration can be made through Registration tab in this webpage no later than 1 October 2018. Moreover, to show your interest to join the School please fill out this questionnaire: The selection for participants for the School will be based the answers in the registration form.


    Disseminating Unit (c.p. Indra Sakti/Ana Harlina/Rifki Sadikin)
    Research Center for Informatics
    Indonesian Institute of Sciences
    Phone (Office) : +62-22-2504711; +62-21-87917216 (ext 112)
    Fax: + 62-22-2504712;

Tentative Program

Day 1
Monday, October 22, 2018
08:30 Registration of participants attending LAMPPS user workshop.
09:00 Welcome and Agenda
09:10 Lecture: Overview of Molecular Dynamics with LAMMPS.
MD Simulation basics: Time Integration, Thermostats/Barostats, Rigid Bodies and Constraints, Basic Program features
10:30 Coffee Break
11:00 Lecture: LAMMPS input and output files.
- basic script syntax and rules, - standard thermodynamic output - dump files and internal visualization12:30 Lunch
13:30 Hands-on:
- Running simple LAMMPS examples
- Controlling thermodynamic output
- Using the internal visualization
- Debugging LAMMPS input scripts
15:00 Coffee Break
15:30 Hands-on:
- Building atomic topologies and input files from scratch
- Restarting/continuing simulations
- Using thermostats and integrators
17:00 Adjourn

Day 2
Tuesday, October 23, 2018

09:00 Lecture: Force fields for Molecular dynamics
- Pairwise additive interactions
- Bonded interactions, Exclusions
- Manybody force fields
- Reactive force fields and beyond
- Hybrid force fields
- Syntax specifying advanced force field input
- Data file and molecule file formats
10:30 Coffee Break
11:00 Lecture: Introduction to VMD for Visualization and Analysis.
12:30 Lunch
13:30 Hands-on: Using VMD with LAMMPS
15:00 Coffee Break
15:30 Hands-on: Simulation of Molecular Systems with LAMMPS
- Using molecule templates
- Creating simple data files generated with custom scripts
- Creating data files with converter tools
- Creating topologies and data files with VMD
- Including long-range electrostatics
17:00 Adjourn

Day 3
Wednesday, October 24, 2018

09:00 Lecture: Computing static and thermodynamic properties
of materials from Molecular Mechanics and MD simulations
10:30 Coffee Break
11:00 Lecture: Using Computes, Variables and Fixes in LAMMPS
for computing properties and monitoring simulation progress
12:30 Lunch
13:30 Hands-on: Computing properties with LAMMPS part 1
- using computes and variables to generate custom output
- using time and spatial averaging, histograms
15:00 Coffee break
15:30 Hands-on: Computing properties with LAMMPS part 2
- using loops and other complex script commands
- advanced computation with complex scripts:
elastic properties, thermal conductivity
17:00 Adjourn

Day 4
Thursday, October 25, 2018
09:00 Lecture: Current status and Future of LAMMPS
- Overview of capabilities currently available in LAMMPS
- Recently added and planned features
- Coupling of LAMMPS to other programs and library interface
- Python wrapper and python package
10:30 Coffee Break
11:00 Lecture: LAMMPS Development
- Compiling LAMMPS and available compilation settings
- Including optional features via packages and support libraries
- Overview of the internal structure of LAMMPS
- Flow of control during a run/minimization
- Modifying and extending LAMMPS with custom styles
- LAMMPS on accelerators and in hybrid parallel mode
12:30 Lunch
13:30 Hands-on:
- Compiling LAMMPS with different settings
- Compiling LAMMPS on different platforms
- Compiling LAMMPS with different features from packages
- Writing custom styles for LAMMPS
15:00 Coffee break
15:30 Hands-on:
- Compiling and running LAMMPS with accelerators and in hybrid mode:
- Using the library interface to LAMMPS via the Python script wrapper
in serial and parallel
17:00 Adjourn

Day 5
Friday, 26 October, 2016

09:00 LAMMPS experience (ITB)
10:00 Coffee break
10:30 LAMMPS experience (LIPI)
12:30 Lunch
13:30 Discussion on Regional MD User/Developer Group
15:00 Coffee break
15:30 Conclusion / Closing Ceremony
17:00 Adjourn

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