MCDS Homepage: http://faculty.washington.edu/trawets/mcds/
File Last Updated: October 18, 2012 (RD Stewart)

HOW TO EXECUTE THE MCDS PROGRAM:

The MCDS program can be executed from the MS Windows command prompt or by double clicking on the MCDS executable.  The command prompt can be accessed from the start menu by typing command.com from the run menu-item.  Alternatively, the command prompt can (usually) be accessed from the Program Accessories menu item.  Refer to your MS Windows documentation for more detailed information on how to access and use the command prompt.

To execute the MCDS program from the command prompt, type

       mcds {name of input file}

and then press enter. A sample input file (mcds.inp) is provided in the same folder as the MCDS executable (mcds.exe).  To execute this program with the mcds.inp file, type

       mcds mcds.inp

The program will automatically generate an output file called mcds.out.  Both the mcds.inp and mcds.out files are ASCII text files.  It is recommended that you open and edit these files using a program such as the NotePad application that comes with MS Windows.  Some additional sample input and output files can be found in the .\sample folder


OVERALL FORMAT AND PROGRAM EXPECTATIONS

  CELL: DNA={R8} NDIA={R8} CDIA={R8} WEM={R8}
  SIMCON: seed={I} nocs={I} 
  RADX: FN={C240} PAR={C5} KE={R8} MeV/A={R8} AD={R8} 
  EVO2: pO2={R8} mmHg={R8} m0={R8} k={R8} q={R8} r={R8}
  MCDS: fbl={r8}
  DMSO: CONC={R8} FNSD={R8} CHMX={R8}

  {I4} = integer
  {R8} = double precision real number
{C240} = alphanumeric filename <= 240 characters in length
  {C5} = alphanumeric particle type (e.g., 56Fe)

NOTE: any information to the right of an exclamation mark (!) is treated as a comment and ignored by the MCDS.


DESCRIPTION OF MCDS INPUT FILE PARAMETERS

CELL: Cell Characterisics and Parameters
  DNA = DNA content of cell nucleus (in Gbp)
 NDIA = diameter of cell nucleus (in um) -- used to compute microdosimetric quantities
 CDIA = diameter of cell (in um) -- must be greater than or equal to NDIA (default CDIA=NDIA)
  WEM = Water-equivalent distance particle must travel to cell surface (mg/cm^2)

SIMCON: "simulation control" parameters
  seed = seed for random number generator (default = 987654321)
  nocs = number of MC simulations (ea. simulation represent damage to one cell)

RADX:   "radiation exposure" parameters
    FN = {name of a secondary input file specifying a polyenergetic
          and/or mixed radiation field}
   PAR = particle type (e.g., e, p, 1H, 2H, 4He, 12C, 56Fe, ...}
    KE = kinetic energy of particle (MeV)
 MeV/A = kinetic energy specified as MeV per nucleon (often used for massive ions)
    AD = absorbed dose (Gy)

 NOTE: If a filename is specified, the information associated with the PAR and KE keywords will be ignored

EVO2: Environmental O2 Concentration ("oxygen effect")
   pO2 = % oxygen concentration (0 to 100%)
  mmHg = alternate method to specify the oxygen concentration (760 mmHg= 100%)
    m0 = approximate max OER for SSB induction (m0*m0 = approx. max OER for DSB induction)
     k = concentration at which half the maximum OER occurs
     q = 1st parameter related to ad hoc correction for radiation quality
     r = 1st parameter related to ad hoc correction for radiation quality

EMSO: Parameters related to simulating the effects of DMSO
  CONC = DMSO concentration (mol dm^-3)
  FNSD = fraction of non-scavengeable DNA damage
  CHMX = concentration at half-level (mol dm^-3)

MCDS: Other adjustable damage simulation parameters
  fbl = fraction of total base damage that is an abasic site (site of base loss)


****** EXAMPLE 1 (minimal input file -- run with default parameters)
  !Perform 999 simulation (1 MeV electron; 100% O2, no DMSO)
  SIMCON: nocs=999
  RADX: PAR=e KE=1


****** EXAMPLE 2 (full input file -- monoenergetic proton)
  CELL:   DNA=1 ndia=5 CDIA=10 WEM=1
  SIMCON: seed=123456789 nocs=1999
  RADX:   PAR=p KE=0.1
  EVO2:   pO2=21 m0=2.0 k=0.25 q=1000 r=2
  MCDS:   fbl=0.25
  DMSO:   CONC=1 FNSD=0.75 CHMX=0.2

NOTE: By setting DNA=1, results are effectively reported in units of clusters per Gy per Gbp.

****** EXAMPLE 3 (read spectrum from secondary file "xray55kVp.dat")
  CELL: DNA=1 
  SIMCON: seed=123456789 nocs=1999
  RADX: fn=xray55kVp.dat
  EVO2: mmHg=1   !equv. to setting pO2 = 0.1316
  MCDS: fbl=0.25
  DMSO: CONC=1 FNSD=0.75 CHMX=0.2