My research encompasses multi-scale modeling of the physics of photon absorption in third and fourth generation solar cells, physics of quantum devices and nanosensors, functional and structural nanomaterials, heterostructures, and signal/image analysis. The computational methods and software that my team and I use to that end are briefly described in this page. If you are interested in cooperation, in particular in multi-scale computational modeling of materials, or need services of that sort, please This email address is being protected from spambots. You need JavaScript enabled to view it.
High Performance Computing:
- Biovia Materials Studio (formerly Cerius2) [1]. I routinely use: Dmol3, CASTEP, DFTB, Forecite, Discover, VAMP, Gulp, Gaussian, and Amorphous modules. Materials Studio has several tools associated to each module, such as spectroscopy,...
- Quantumwise Virtual NanoLab (VNL) and Atomistic Tool Kits (ATK), powerful set of tools for simulation of nanomaterials. ATK employs the three approaches DFT, Semi-Empirical, and Classical atomistic calculations for modeling atomic systems. ATK is good for calculating electronic transport in materials and heterostructure using the Non-Equilibrium Green Function (NEGF). VNL and ATK are now part of Synopsis. I used ATK to model a wide range of physics problems in atomistic models for materials of interest, Quantum Espresso [2] was used for additional computations.
- I employed QuantumEspresso and Abinit [3] software for cases involving atoms with relativistic electrons, 3d transition metals, heavy elements,...
- ADESH [4]. This special molecular dynamics software is utilized for studying GBs and Dislocations in crystalline materials.
- I have used seldomly Discovery Studio for bio-materials [5] and NWChem [6] for studying some bio-materials.
Phenomenological Modeling:
- Finite element analysis (FEA) COMSOL Multiphysics; e.g., optics of thin film structures, phase field (for bubble formation and motion in plastic materials), stress-strain in layers and stacks, electronic transport in solar cells, states and tunneling in quantum dots, transport in quantum devices,
- Finite difference time domain (FDTD), developed programs to solve problems of point defect diffuision in crystal growth, light scattering in complex media (Maxwell Equations),...
- Developed own code for cluster formation and dissolution (solved Fokker Planck coupled with a set of Continuity Equations and Rate Equations),
- Developed own code for Monte Carlo simulation of Electron Beam Induced Current (EBIC) in solar cells and other devices, and
- Monte-Carlo Stopping and Range of Ions in Matter (SRIM): used SRIM for MeV implantation of silicon wafers with protons, impurities for δ-doping, and Si for gettering.
Photovoltaic Heterostructure Modeling:
- I use AMPS-1D [7] and AFORS-Het [8] for modeling transport, quantum efficiency, and other properties of heterostructure solar cells, and
- I use PC1D [9] as well as Griddler [10] for teaching photovoltaics.
Electric modeling of Photovoltaic Devices and Systems:
- PSPICE [11], and
- MATLAB/Simulink.
Optics Engineering of Solar Materials, Cells, and Systems:
- Own raytracing code for modeling optics problems for solar cells (e.g., enhanced absorption by textured materials, light scattering, stack of layers with rough interfaces, complex cell structure, and plasmonic nanostructures),
- Monte Carlo raytracing software SolTrace [12]. I used SolTrace for designing non-imaging optical systems and concentrated photovoltaics (CPV), and
- Monte Carlo raytracing Tonatiuh [13]. I use this software for teaching solar energy systems.
Quantitative Processing of Microscopy Images:
- Photoshop, ImageJ [14] and Developed macros for Photoshop, and for ImageJ, and
- Developed codes for image processing on Matlab and MathCAD.
CAD Tools:
- LayoutEditor [15], used for designing photolithography masks for MEMS and for nanoscale patterning,
- SolidWorks (we use it for design work and for developing objects modeled by FEA), and
- SketchUp (Google CAD program), used for generating input files for SolTrace (NREL software for optical modeling of solar systems: CPV, CSP,...).
General Math Software:
- MathCAD, MATLAB, and Mathematica,
- Statistics: SAS.
Numerical Analysis:
- Solving PDEs: Diffusion, Diffusive and Advective Processes, Fokker–Planck, Maxwell Equations...
- Solving Large Linear Equations (Diagonalization, efficient methods for Triangular matrices,...)
- Inverse Problems, Spectral Analysis, ...
- Optimization: Newton-Raphson, Conjugate gradient, Galerkin method,
- Simultaneous Non-linear Equations, and
- Very Large Linear Problems with Sparse Matrices.
Programming Languages:
- Visual Basic, Fortran, Python, I have used these languages for developing special computation and visualization programs for my research
- Basic, LabView, I have extensively used these languages for programing laboratory devices and systems,
- Perl (high-level, general-purpose, interpreted, dynamic programming language): I have extensively used Perl for automating Materials Studio modules for atomistic calculations,
- Message Passing Interface (MPI): my team and I use MPI for parallel computing on supercomputers,
- Blackboard, and Moodle, I used these Content Management Systems for my teaching and
- FrontPage, Joomla, html (markup language), and php (general-purpose scripting language) I used these platforms and languages for developing websites.
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[1] Materials Studio by BIOVIA/Accelrys Inc. High performance computing (HPC) software package for materials and quantum chemistry It includes several quantum mechanics, molecular dynamics, spectral analysis,.... modules.
[2] Quantum ESPRESSO : “opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization” is a software suite for ab-initio quantum chemistry for materials modeling and electronic-structure calculations.
[3] ABINIT : software package for computing electronic density and properties of surfaces, bulk solids, and molecules. It is based on density functional theory, plane wave basis set, and pseudopotentials.
[4] ADESH : “Atomistic DEfect Simulation Handler”, Casa Engineering, Hopewell Junction, New York, NY.
[5] Discovery Studio by BIOVIA/Accelrys Inc., HPC software package specialized in analysis of bio-molecules (proteins etc.) and other macromolecules. It includes QM-MM core calculation tools, and sequencing tools.
[6] NWChem : of the Pacific Northwest National Laboratory. It is an ab-initio computational chemistry software package designed to be scalable to allow solving large atomistic problems. It runs on parallel supercomputers and workstation clusters. It also combines quantum mechanics with molecular dynamics for solving, for instance, large bio-molecule problems.
[7] AMPS-1D : computer program for analysis of optoelectronic devices and solar cell (S. J. Fonash, Penn State University).
[8] AFORS-Het : Automat For Simulation Of Heterostructures for modelling multi-layer homo- or heterojunction solar cells (Helmholtz Zentrum Berlin).
[9] PC1D : program for 1D modeling of crystalline solar cells (Paul Basore, University of New South Wales, AU).
[10] Griddler : a finite-element simulation program developed at the Solar Energy Research Institute of Singapore. It calculates distribution of voltage, source current, recombination current, resistance parameters,… from solar cell basic material and device parameters. I also use Griddler for teaching.
[11] PSPICE : Personal Simulation Program with Integrated Circuit Emphasis, ORCAD. We used the version adapted by Luis Castaner to model and quantitatively analyze photovoltaic cells and systems.
[12] SolTrace : Monte Carlo ray-tracing tool developed at NREL to model concentrating solar power (CSP) systems and analyze their optical performance.
[13] Tonatiuh : Object-oriented Monte Carlo ray tracer for modeling sun power energy systems.
[14] ImageJ : program developed at the National Institutes of Health for image acquisition and processing.
[15] LayoutEditor : CAD software package for device design and process simulation.