My proposal for a computational materials science expertise unit in the physics school

Below is my response to the call for proposal for the Pelan Pelaksanaan Apex Fasa 2 (Work Plan 2014-2016) by the physics school. The proposal is basically a plan of my own ambition to explore the field of computational condensed matter physics in USM. I do not really expect any positive outcome from this. Based on previous experience the fate of the proposal will most probably be just like the others we submitted in the last few years. Despite my pessimistic anticipation, I have spent my precious time and effort to prepare a serious proposal. It implicitly been encoded with my research direction and aspiration. Research has always been one of the two prime priorities of my life. The proposal reflects from a certain view point my personal plan to excellence. As a matter of fact I don't  really care whether the proposal will be shoot down during decision making by the school or just be partially approved. It is just a symbolic move in which I am reinforcing a promise to myself, and an ambition to be achieved in the long term.



Title:Establishment of computational materials science expertise in the School of Physics, USM

Objectives:

1. To establish a strong computational materials science research team specialised in solving condensed matter physics and materials science problems using high performance computers (HPC).

2. To establish a synergistic research collaboration between the Theoretical and Computational Physics group with other experimentalists within USM to theoretically investigate, interpret and design of novel material systems via computational simulations.

Motivation:
Computational condensed matter physics (used interchangeably with computational materials science in our context) is an interdisciplinary research area which main objectives include understanding, modeling, predicting, and ultimately, theoretically engineering the physical properties of realistic materials. In this research discipline, state-of-the-arts computational techniques are the weapons employed to simulate the physics of material systems at atomistic level based on quantum-mechanical or semi-empirical prescriptions. To this end, known therories in condensed matter physics, chemistry and computer science are combined and applied numerically. Prediction of macroscopic properies of materials via such approach is made possible by the spectacular increase in computational power and novel numerical algorithms, allowing fundamental equations governing the physics at the atomic level to be solved numerically and with unprecedented accuracy. Today, based only the knowledge of a single atom, one can predict how the material formed by that atom type will look, what properties that material will have and how it will behave under certain conditions. By simply changing the arrangement of constituent atoms, or by adding atoms of a different type, the macroscopic properties of all materials can be modified. It is in this way that one can learn how to improve mechanical, optical and/or electronic properties of known materials, or one can predict properties of new materials, those which are not found in nature but are designed and synthesized in the laboratory. High performance computers (HPC) and routine visualization software are utilized to generate direct comparisons with experimental conditions.

Computational materials science has also the great advantange to compliment and guide experimental searches. This point is particularly relevant to our local solid-state laboratories, where novel materials are routinely synthesised and characterised through all sorts of experimental tools, but rarely complemented by computational simulations at atomistic level. Apart from its capability to provide theoretical insight at the microscopic level for the physical origin of a condensed matter system, computational material techniques also provide a very wide oppertunity to publish relatively easily in international journals, at a relatively low cost (because it uses only computing power of computers as its main ‘ingredient’ rather than relying on real materials and experiment hard ware facilities).

Synergistic collaboration between experimentalists and theorists is not a common practice in USM, especially in the School of Physics. There are many experimental results from the NOR lab and X-ray lab that can be complemented by molecular dynamics or other computational techniques. For example, the structural phase transition observed in phenol-amines adducts is in principle model-able using either monte carlo or molecular dynamics. The XRD spectrum or Raman spectrum on GaN or ZnO samples can be simulated by constructing supercell models with density functional theory (DFT) codes. So are those novel X-ray cyrstallographic structures of organic crystal solved routinely in the X-ray lab can be calculated using DFT or MD codes. Motivated by the existence of such a huge opportunity of existing in-house experimental resources, we propose an effort to tap the potentiality and translate it into real publication and quality research outcome: by establishing a strong computational physics expertise in the School of Physics, USM.

In practice computational materials science research requires most importantly the technical know-how to carry out the computational tasks and demands relatively cheap monetary cost (mostly for setting up computer hardware, and to a lesser degree, purchase of software). However, as far as we are aware of, this is a research field barely practiced in Malaysia despite its obvious practical advantages. This is presumably due to the lack of specialised training and experts in this area, apart from its high threshold (in terms of technical knowledge) to enter the field. We are now among the very rare species in Malaysia that are able to perform atomistic computational materials simulation using highly specialised software and HPC, e.g., cluster Linux computing system, highly parallelised codes, e.g., LAMMPS, Wien2k, Gaussian, DFTB+, quantum Monte Carlo and genetic algorithm codes. Thanks to the research experiences accumulated throughout the years on computational condensed matter systems, we (the members in theoretical and computational physics group) have now readily equipped with the technical know-how to apply these specialised computational skill to perform calculations on real materials.

Having established the potential, practical advantages of and our readiness in this research front, we propose to the School of Physics to strategically create an expert team for computational condensed matter physics. The team can be formally considered as a subgroup under the theoretical physics and computational physics research group. The subgroup will team up with experimentalists from all the research labs in USM, especially those from the School of Physics, to form a synergic research collaboration in which experimental investigations of novel materials are coupled with state-of-the-arts computational physics techniques. For the sake of reference, we shall refer to this subgroup as the computational materials science expertise unit, or just the expertise unit, hereafter. The proposed expertise unit will develop all the necessary expertise, in particular first-principles calculation and molecular dynamics methods, to compliment the research investigations carried out in our experimentalist colleagues' lab.

Current status:
Leader
Computational condensed matter physics research in the School of Physics, USM, is first pioneered by Dr. Yoon Tiem Leong, in closed collaboration with experts in the field from MMU Melaka, National Taiwan National University and Academy Sciences of Moldova.

Publications (already published)
1. Thong Leng Lim, Mihail Nazarov, Tiem Leong Yoon, Lay Chen Low, M. N. Ahmad Fauzi, X-ray diffraction experiments, luminescence measurements and first-principles GGA+U calculations on YTaO4, Computational Materials Science 77 (2013) 13–18 (http://dx.doi.org/10.1016/j.commatsci.2013.03.042).

2. Wen Fong Goh, Sohail Aziz Khan and Tiem Leong Yoon, A molecular dynamics study of the thermodynamic properties of barium zirconate, Modelling Simul. Mater. Sci. Eng. 21 (2013) 045001 (11pp).

3. Molecular dynamics simulation of thermodynamic and thermal transport properties of strontium titanate with improved potential parameters, GOH Wen Fong, YOON Tiem Leong, Sohail Aziz KHAN, Computational Material Science 60 (2012) 123–129.

4. Surface and interface phonon polaritons of wurtzite GaN thin film grown on 6H-SiC substrate, S. S. Ng, T. L. Yoon, Z. Hassan, and H. Abu Hassan, Applied Physics Letters 94, 241912 (2009).

5. Yoon Tiem Leong, Goh Eong Sheng, Calculation of ground state energy of a “4 × 4” flux qubit Josephson junction array using diffusion quantum Monte Carlo Method, PERFIK 2012, Bukit Tinggi, Pahang, Malaysia, 21 Nov 2012 (AIP Conf. Proc. 1528, pp. 384-389; doi: http://dx.doi.org/10.1063/1.4803631).

Papers submitted for publication in peer reviewed journals:
6. Thong Leng Lim, Mihail Nazarov, Tiem Leong Yoon, Lay Chen Low, M. N. Ahmad Fauzi, Ab initio calculations and luminescence study of YNb$O_4$ (Scripta Physica, submitted)

7. Tjun Kit Min, Tiem Leong Yoon , Chuo Ann Ling, Shahrom Mahmud, Thong Leng Lim, Annealing of ZnO surfaces via molecular dynamics simulation with reactive force field (Surface Science, submitted)

Papers in preparation for publication in peer reviewed journals
8. Epitaxial growth of graphene on 6H-silicon carbide substrate by simulated annealing method (in collaboration with S. K. Lai, NCU Taiwan, in preparation).

9. Temperature Quench Molecular Dynamics Simulation of Phase Coexistence Curve of Lennard-Jones Fluid (Goh Eong Sheng, Yoon Tiem Leong, in preparation).

Current research projects:
1. Molecular dynamics simulation of epitaxial graphene growth

2. Genetic Algorithm assisted DFTB calculations on boron clusters

3. DFT calculations on new generation of phosphors

4. Molecular dynamics simulation of graphene nanoribbon melting

5. Molecular dynamics simulation of carbon nanotube melting

6. DFT calculation on ferroelectrics (Ph.D project)

7. DFT calculation of phonon vibrational modes in ternary alloy (Ph.D project, collaboration with experimentalist from NOR lab).

8. 3D FDTD Modeling of the effects of electromagnetic phenomena in the ionosphere and Earth’s magnetic field over the Sumatera-Malaysia region (Ph.D project, in collaboration with remote sensing group)

Research students
1. Ng Wei Chun, research assistant (RA) – already obtained M.Sc offer latter from USM, to register soon.

2. Min Tjun Kit, research assistant (RA) – already obtained M.Sc offer latter from USM, to register soon.

3. Siti Harwani bt Md Yusoff, current Ph.D student.

4. Lee Thong Yan, current Ph.D student.

5. Pauline Yeoh, current Ph.D student.

6. Goh Wen Fong (M.Sc, graduated).

Research Collaborators
1. Dr.  Lim Thong Leng, Faculty of Engineering and Technology, Multimedia University (Melaka), Malaysia.

2. Prof. S. K. Lai, National Central University, Taiwan.

3. Prof. Mihail Nazarov, Institute of Applied Physics, Academy Sciences of Moldova, Republic of Moldova.

4. Dr. Shahrom Mahmud, NOR lab, USM (experimentalist)

5. Dr. Ng Sha Shiong, NOR lab, USM (experimentalist)

6. Dr. Saw Kim Guan, PPJJ, USM (experimentalist)

Current computing resources
(i) Hardware
We have more than a combined number of 256 cpu cores available for HPC parallel computing. All of these hardware were build from ground zero with our own effort, and are currently maintained also by ourselves (cooling systems, LAN connections, software and hardware technical problems, etc.) with technical consultation provided by (1) Mr. Tan Choo Jun, a doctorate student from School of Computer Science, USM, and (2) Associate Prof. Dr. Chan Huah Yong of the School of Computer Science, USM. Hardware resources available to group members and members from the theoretical physics group are listed below:

1. comsics cluster (comsics.usm.my, 20 nodes x 4 intel i5 cores, Linux Rocks OS). Located in the Integrated Computater Lab, 3rd floor, Physics School building.

2. anicca cluster (anicca.usm.my, 20 nodes x 4 intel core 2 duo, Linux Rocks OS). Located in the Integrated Computater Lab, 3rd floor, Physics School building.

3. jaws workstation (Supermicro workstation, 64 x AMD 2.2 GHz Interlagos cores, CENTOS 6.3 OS). Located in the server room "Bilik Delta" in student center, 2nd floor, Physics School building.

4. chakra cluster (4 nodes x 8 intel i7 cores, 3.4 GHz, CENTOS 6.3 OS). Located in the Theory Lab, 3rd floor, Physics School building.

All these HPC hardware are capable of running MPI-enabled parallel computing. The comsics and anicca cluster are built by using PCs in the integrated computer lab, School of Physics. Formally the computers in the computer lab belongs to the School of Physics for the purpose of running Computational Physics ZCE 111 and MAT 181 courses, and occasionally, conducting workshop. The computer clusters in the computer lab are used to run various computational simulations during free period (i.e., when no classes / workshop are being conducted in the computer lab). In this sense the computers in the computer lab are being optimally ultilised for both teaching and research purposes without noticeable interference between these two modes of usage.

(ii) Software
Software installed in our HPC resources include:
Mathematica (fully licensed), Wien2k (DFT package, fully licensed), CRYSTALS (DFT package, fully licensed), VASP (DFT package, fully licensed), LAMMPS (MD package, free), DFTB+ (DFTB package, free), genetic algorithm codes, basin hoping codes (both codes are meant for finding global minimisation purposes, developed by NCU group from Taiwan).

Implementation plan
Who will be involved
1. The key player will be the existing expert in computational physics in the theoretical and computational physics group, Dr. Yoon. He will be responsible for the operation of the expertise unit, along with his graduate students, project students and research assistants.
2. Other theoretical and computational physics group members who are interested in running computational simulations or HPC calculations.
3. All researchers and experimentalists in the School of Physics or from other schools within USM (e.g. PPJJ, Materials Engineering, Chemistry School, etc.) who are interested to incorporate an intensive computational component in their researches are all welcomed. Graduate students from other research labs are encouraged to engage in collaborative project with the proposed expertise unit.

Main activities
1. Conducting high-impact researches in computational physics / computational condensed matter physics / computational materials science.

2. Creating international and national research linkages in the field, including inviting experts from the related field to the school of physics for research visit from time to time.

3. Training of our own human capital in the research field of computational condensed matter physics.

4. Providing training to current researches / students / research personnel on advanced level computing techniques and computational methods for generic purposes (such as programming in Mathematica, Fortran, GPU programming, parallel programming, visualization techniques, software and computer system maintenance, Linux, LaTeX, virtualization, etc.)

5. Acting as technical consultation and service provider entity for the physics school research community as a whole on issues related to HPC and other computationally related issues, such as setting up of parallel computing facilities, purchasing of high-performing computing facilities, installing software in Linux systems, etc.

6. Training of graduate students / academic staffs / research personnel from other research labs to run numerical programming prompted by their specific research needs.

Human resource
In order to effectively realize the ideal role of the expertise unit as proposed above, the single most important factor is to train our own experts. At the moment the only expert in the field is Dr. Yoon. But the proper functioning of the expert unit definitely necessitates more human power. To this end the School of Physics should

1. provide practical incentive and encouragement for undergraduate and graduate students to take up projects / courses provided by the expertise unit. This incentive could be in the form a guaranteed scholarship for Ph. D or M.Sc. students taking up projects in computational materials science research.

2. provide monetary incentive to graduate students from the experimental research lab to incorporate computational component in their researches.

3. tenure a new academic staff in the field of computational condensed matter physics or computational physics.

4. set up a post-doc position for computational condensed matter physics or computational physics.

5. encourage existing academic staff to incorporate more computational physics component in their research.

6. provide financial allocation to invite internationally renowned experts in the research field to visit School of Physics for an extended period or time, or even to conduct short courses.

7. The expertise unit does not request for any non-academic staff.


Computing hardware and software requirement
Rack mount computer cluster
The only hardware needed for computational condensed matter physics is computers, the more the better. As a teaching lab, the current computing facilities in the computer lab are not especially built for running really huge computational job. For a start we recommend to purchase a scalable rack-mount computer cluster system. This kind of computing facility is flexible, easy to maintain, relatively cheap and compact (less space consuming). The system comprise of a metal rack (of the size of a fridge) into which one could slot in a number of ‘blades’, where each blade is a plug-and-play motherboard having several slots of multiple-core processor. Depending on the availability of funding, the computational power of the system can be upgraded from time to time. This shall be the “primary weapon” of the expertise unit to tackle computational research problems.

Software
Software wise, many major software for computational physics are either open source (e.g. ABINIT, LAMMPS, DFTB+, CPMD, etc.) or free for academic use (e.g. Intel Fortran and its libraries). We do not expect to spend much on software as is for computer hardware.

Maintenance
1. The proposed expertise unit would be fully responsible to maintain all the computer hardware, software, and the physical spaces in which the computers are sitting. A small budget should be allocated annually for maintenance purposes, such as fixing failed components and peripherals, wiring, networking or system configuration.
2. We also propose, for the sake of a more effective maintenance of the computer clusters, the integrated computer lab be formally placed under the care / responsibility of the computational physics expertise unit.
3. Individual researchers in the unit will contribute to the maintenance cost of the computing facilities via their research grants.

Space requirement
1. All the computing facilities will be occupying the existing space as they are at the present. These include the present computer labs, theory lab, the server room "bilik Delta" in student center, 2nd floor, Physics School building.
2. In addition, we formally propose the email room located between the computer lab and theory lab be allocated exclusively for the computational physics expertise unit as its physical ‘center’.
3. The computer lab be placed under the care / responsibility of proposed expertise unit (as proposed in (2) in Maintenance).

Expected Output / Evaluation Measures
1. Based on the current publication rate, we expect to publish at least 6 international ISI journal papers per year from the computational physics expertise unit. Even more publication can be generated if the team can have a new academic staff or a post-doc.
2. We will publish at least two joined papers with our experimentalist colleagues per year.
3. We expect to graduate two Ph.D and 2 M.Sc. graduates in three years time.
4. We will establish at least two international research collaborations in the first three years.
5. We will conduct at least one workshop on various computationally-related short courses for the physics school and USM in general annually.