2005 Summer School on Computational Materials Science
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Additional explanation on INPUT/OUTPUT and plotting
for Anton Van der Ven's Computer Lab


A) Kinetic Monte Carlo for Diffusion Coefficient (tracer-D and D-jump)
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output files:   diff.0
input file for Diffusion Coefficient MC (line by line meaning):   conditions.diff
1. # of MC passes
2. # equilibriation steps
3. initial concentration, c
4. min. c
5. max. c
6. increment (step-size) of c
7. initial Temperature (T)
8. min. T
9. max. T
10. increment of T
11. # of runs to avg. to get Diffusion coefficient (could be parallelized)


output:    diff.0
col 1:   concentration, c
col 2:   tracer diffusion coefficient, D*
col 3:   jump diffusion coefficient, DJ


What to plot?  Same quantities plotted in lab overview (PPT).
You may plot using 'gnuplot':
    > gnuplot
    > set semilog y
    > plot  'diff.0'  u 1:3, 'diff.0' u 1:2      (D-jump and D*)
 
B) Kinetic Monte Carlo  Grand Canonical Thermodynamic Quantity (Theta)
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input file for Grand Canonical MC (line by line meaning):   conditions
1. # of MC passes
2. # equilibriation steps
3. initial chemical potential (mu)
4. min. mu
5. max. mu
6. increment (step-size) of mu
7. initial Temperature (T)
8. min. T
9. max. T
10. increment of T
11.  ----empty-----

output files:   chem.0    and    susc.0

output:    chem.0
col 1:   mu
col 2:   concentration, c
col 3:   E-GC = <E - mu*c>  grand canonical energy (can be calculated by avg.)
col 4:   E-GC - <mu*c>      approx. estimate of energy (cannot be calculated directly) 
col 5:   flip frequency

output:    susc.0
col 1:   mu
col 2:   c
col 3:   thermodynamic quantity (theta) to get Diffusion Coefficient 
col 4:   Specific Heat, C_v     transition identified by dE/dT
col 5:   <(delta-c)^2>/kT        fluctuations in concentrations


What to plot?  Same quantities plotted in lab overview (PPT).
You may plot using 'gnuplot':
    > gnuplot
    > plot  'chem.0'  u 2:4    (Formation Enthalpy vs. c, 'GS hull') 
    > plot  'chem.0'  u 1:2    (mu vs. c)
    > plot 'susc.0'  u 2:3     (theta vs. c)
    > set semilog y
    > replot                   (ln(theta) vs c, you can see ordered and 2-phase regions)