examples/etching_begin.rb
elements
atom H, valence: 1
atom C, valence: 4
dimensions
temperature 'K'
concentration 'mol/cm3'
energy 'kcal/mol'
rate '1/s'
time 's'
gas
spec :hydrogen
atoms h: H
spec :methane
atoms c: C
concentration hydrogen(h: *), 1e-9
concentration methane(c: *), 1e-10
temperature 1200
surface
lattice :d, class: Diamond
spec :bridge
atoms ct: C%d, cl: bridge(:ct), cr: bridge(:ct)
bond :ct, :cl, face: 110, dir: :cross
bond :ct, :cr, face: 110, dir: :cross
spec :methyl_on_bridge
aliases basis: bridge
atoms cm: methane(:c), cb: basis(:ct), cl: basis(:cl), cr: basis(:cr)
bond :cm, :cb
spec :high_bridge
atoms ch: methane(:c), ct: bridge(:ct)
dbond :ch, :ct
spec :dimer
atoms cl: bridge(:ct), cr: bridge(:ct)
bond :cl, :cr, face: 100, dir: :front
spec :methyl_on_dimer
aliases mb: methyl_on_bridge
atoms cl: bridge(:ct), cr: mb(:cb), cm: mb(:cm)
bond :cl, :cr, face: 100, dir: :front
spec :methyl_on_dimer_with_bridge
aliases mb: methyl_on_bridge
atoms cl: bridge(:cr), cr: mb(:cb), cm: mb(:cm)
bond :cl, :cr, face: 100, dir: :front
spec :methyl_on_111
atoms cm: C, cb: bridge(:cr)
bond :cm, :cb
spec :bridge_with_dimer
atoms ct: C%d, cl: bridge(:ct), cr: dimer(:cr)
bond :ct, :cl, face: 110, dir: :cross
bond :ct, :cr, face: 110, dir: :cross
spec :three_bridges
atoms ctl: C%d, cl: bridge(:ct), cc: bridge(:cr)
bond :ctl, :cl, face: 110, dir: :cross
bond :ctl, :cc, face: 110, dir: :cross
spec :cross_bridge_on_bridges
atoms ct: C, cl: bridge(:ct), cr: bridge(:ct)
bond :ct, :cl
bond :ct, :cr
position :cl, :cr, face: 100, dir: :cross
spec :cross_bridge_on_dimers
aliases mod: methyl_on_dimer
atoms ct: mod(:cm), cl: mod(:cr), cr: dimer(:cr)
bond :ct, :cr
position :cl, :cr, face: 100, dir: :cross
spec :dimer_after_down_111
atoms cl: bridge(:cr), cr: C%d, crs: bridge(:ct), cls: bridge(:ct)
bond :cl, :cr, face: 100, dir: :front
bond :cr, :crs, face: 110, dir: :cross
bond :cr, :cls, face: 110, dir: :cross
spec :dimer_after_gap_b
atoms cls: bridge(:cr), crs: bridge(:cr), cr: C%d, cl: bridge(:ct)
bond :cls, :cr, face: 110, dir: :front
bond :crs, :cr, face: 110, dir: :front
bond :cr, :cl, face: 100, dir: :front
spec :dimer_after_gap_111
atoms cls: bridge(:cr), crs: bridge(:cr), cr: C%d, cl: bridge(:cr)
bond :cls, :cr, face: 110, dir: :front
bond :crs, :cr, face: 110, dir: :front
bond :cr, :cl, face: 100, dir: :front
size x: 100, y: 100, z: 5
temperature 1200
events
reaction 'hydrogen abstraction from gap'
aliases one: bridge, two: bridge
equation one(cr: H) + two(cr: H) = one(cr: *) + two(cr: *) + hydrogen
position one(:cr), two(:cr), face: 100, dir: :front
activation 35
forward_rate 3e5
reaction 'methyl adsorption to face 111'
equation bridge(cr: *) + methane(c: *) = methyl_on_111
forward_rate 1.2e9, 'cm3/(mol * s)'
reaction 'adsorption methyl to dimer'
equation dimer(cr: *) + methane(c: *) = methyl_on_dimer
enthalpy -73.6
forward_rate 1e13, 'cm3/(mol * s)'
reaction 'high bridge stand to dimer'
equation high_bridge(ch: i) + dimer(cr: *, cl: i) = bridge_with_dimer(cl: *)
activation 14.9
forward_rate 2.2e9
reverse_rate 4.2e8
reaction 'desorption methyl from 111'
equation methyl_on_111 + hydrogen(h: *) = bridge(cr: *) + methane
forward_rate 5.4e13, 'cm3/(mol * s)'
reaction 'desorption methyl from bridge'
equation methyl_on_bridge + hydrogen(h: *) = bridge(ct: *, ct: i) + methane
forward_rate 1.7e14, 'cm3/(mol * s)'
reaction 'desorption methyl from dimer'
equation methyl_on_dimer + hydrogen(h: *) = dimer(cr: *) + methane
enthalpy -73.6
forward_rate 5.3e12, 'cm3/(mol * s)'
environment :dimers_row
targets :one_atom, :two_atom
aliases left: dimer, right: dimer
where :end_row, 'at end of dimers row'
position one_atom, left(:cl), face: 100, dir: :cross
position two_atom, left(:cr), face: 100, dir: :cross
where :mid_row, 'in middle of dimers row'
use :end_row
position one_atom, right(:cl), face: 100, dir: :cross
position two_atom, right(:cr), face: 100, dir: :cross
reaction 'dimer formation'
aliases one: bridge, two: bridge
equation one(ct: *) + two(ct: *) = dimer
incoherent one(:ct), two(:ct)
refinement 'not in dimers row'
enthalpy -36
activation 0.8
lateral :dimers_row, one_atom: one(:ct), two_atom: two(:ct)
there :end_row
enthalpy -39
forward_activation 0.75
reverse_activation 0.85
there :mid_row
enthalpy -43
forward_activation 0.7
reverse_activation 0.9
forward_rate 8.9e11
reverse_rate 2.2e6
reaction 'dimer formation near bridge'
aliases one: bridge, two: bridge
equation one(ct: *, ct: i) + two(cr: *) = bridge_with_dimer
enthalpy -29.4
activation 4
forward_rate 7.5e8
reverse_rate 1.2e8
reaction 'high bridge stand to bridge at new level'
aliases source: bridge, product: bridge
equation high_bridge + source(ct: *, ct: i) = product(cr: *, ct: i)
enthalpy 24
# already exchanged!!
reverse_activation 36.3
reverse_rate 6.1e13
forward_activation 12.3
forward_rate 1.1e12
reaction 'methyl to high bridge'
equation methyl_on_dimer(cm: *, cm: u) = bridge(ct: *, ct: i) + high_bridge
forward_activation 15.3
reverse_activation 2.9
forward_rate 9.8e12
reverse_rate 2.7e11
reaction 'methyl to high bridge near bridge'
equation methyl_on_dimer_with_bridge(cm: *, cm: u) = bridge(cr: *) + high_bridge
forward_activation 15.3
reverse_activation 2.9
forward_rate 9.8e9
reverse_rate 2.7e8
reaction 'high bridge incorporates in crystal lattice near another bridge'
equation high_bridge(ch: i) + bridge(cr: *) = three_bridges(cl: *)
activation 3.2
forward_rate 2.9e11
reverse_rate 1.1e8
reaction 'methyl on dimer activation'
equation methyl_on_dimer(cm: H, cm: i) + hydrogen(h: *) = methyl_on_dimer(cm: *) + hydrogen
activation 37.5
forward_rate 2.8e8 * T ** 3.5, 'cm3/(mol * s)'
reaction 'methyl on dimer deactivation'
equation methyl_on_dimer(cm: *, cm: i) + hydrogen(h: *) = methyl_on_dimer(cm: H)
forward_rate 4.5e13, 'cm3/(mol * s)'
reaction 'methyl on dimer hydrogen migration'
equation methyl_on_dimer(cl: *, cm: u, cm: H) = methyl_on_dimer(cm: *, cl: H)
forward_activation 37.5
forward_rate 2.1e12
reaction 'migration down at activated dimer from methyl on bridge'
aliases source: dimer, product: dimer
equation methyl_on_bridge(cm: *, cm: u, cb: i) + source(cr: *) = product
activation 0
forward_rate 1e8
reaction 'migration down at activated dimer from high bridge HH'
aliases source: dimer, product: dimer
equation high_bridge(ch: H, ch: H) + source(cr: *) = product(cr: *, cl: H)
activation 0
forward_rate 1e8
reaction 'migration down at activated dimer from high bridge sH'
aliases source: dimer, product: dimer
equation high_bridge(ch: H, ch: *) + source(cr: *) = product(cr: *, cl: *)
activation 0
forward_rate 1e8
reaction 'migration down in gap from methyl on bridge'
equation methyl_on_bridge(cm: *, cm: *, cm: u, cb: i) + bridge(cr: *) + bridge(cr: *) = dimer_after_gap_b
activation 0
forward_rate 1e7
reaction 'migration down in gap from high bridge'
aliases source: dimer, product: dimer
equation high_bridge(ch: *, ch: i) + bridge(cr: *) + bridge(cr: *) = dimer_after_gap_b(cl: *)
activation 0
forward_rate 1e7
reaction 'migration through dimers row'
equation methyl_on_dimer(cm: *, cm: u) + dimer(cr: *) = cross_bridge_on_dimers
enthalpy 3.4
activation 16 # is different: 30
forward_rate 2.4e8
reaction 'sierpinski drop'
equation cross_bridge_on_bridges = methyl_on_bridge(cm: *, cm: u) + bridge(ct: *)
activation 14
forward_rate 4.4e9
reaction 'surface activation'
equation H + hydrogen(h: *) = * + hydrogen
activation 6.65
forward_rate 5.2e13, 'cm3/(mol * s)'
reaction 'surface deactivation'
equation * + hydrogen(h: *) = H
activation 0
forward_rate 2e13, 'cm3/(mol * s)'