Alamode: A LAyered Model Development Environment

D.W. Yergeau and R.W. Dutton
Stanford University

• Introduction
• Model development in Alamode
  • Commands Overview
  • Input and output commands
    • structure
    • sstructure
  • Query commands
    • regions
    • region regionName
    • fields
    • field fieldName
  • Model definition commands
    • function
    • operator
    • equation
    • systemInRegion
    • model
  • Simulation commands
    • Universal timestepping parameters
    • TR/BDF2 timestepping parameters
    • Generalized trapezoid timestepping parameters
    • Nonlinear solution parameters
    • Linear solver parameters
• Function and Operator Reference
  • Functions
    • const
    • scaledField
    • abs
    • exp
    • sum
    • times
    • div
    • power
    • carrierConc
    • fermi
    • ssactive
    • constInjectionRate
    • constInjectionLoss
    • cstar2
    • cstar3
  • Operators
    • diffusion
    • simplerecombination
    • bimole
    • k1fg_k2h
    • segregation
    • surfacerecombination
    • quasiFermiEField
    • rhsFunction/functionTerm
• Discretizations and Numerical Algorithms
  • Spatial Discretization
  • Time integration algorithms
    • Generalized Trapezoid Family
      • Concentration form
      • Rate form
      • Remarks on Generalized Trapezoid
    • TR/BDF2
  • Nonlinear Solution Algorithms
  • Overcoming Numerical Difficulties
    • Divergence in the nonlinear solution
    • Residuals ``bottom out''
  • Threshold violations
• Examples
  • Multi-region diffusion with segregation
  • Multi-species reactive-diffusive model
• Simple 1D Structure File Format
• SUPREM Structure File Format
• References
• About this document ...