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ChrisRackauckasChrisRackauckas
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Merge pull request #91 from SciML/fix-remaining-typos
Fix remaining spelling errors (comprehensive)
2 parents 6f96ef4 + fd7c74d commit 44277f9

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‎docs/src/index.md‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -259,8 +259,8 @@ In NBodySImulator the [SPC/Fw water model](http://www.sklogwiki.org/SklogWiki/in
259259
bodies = generate_bodies_in_cell_nodes(N, mH2O, v, L)
260260
jl_parameters = LennardJonesParameters(ϵOO, σOO, R)
261261
e_parameters = ElectrostaticParameters(k, Rel)
262-
spc_paramters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
263-
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters, spc_paramters);
262+
spc_parameters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
263+
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters, spc_parameters);
264264
```
265265
For each water molecule here, `rOH` is the equilibrium distance between a hydrogen atom and the oxygen atom, `∠HOH` denotes the equilibrium angle made of those two bonds, `k_bond` and `k_angle` are the elastic coefficients for the corresponding harmonic potentials.
266266
Further, one can pass the water system into the `NBodySimulation` constructor as a usual system of N-bodies.

‎examples/water_for_visualization.jl‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -27,9 +27,9 @@ const k = 138.935458 #
2727
bodies = generate_bodies_in_cell_nodes(N, mH2O, v_dev, L)
2828
jl_parameters = LennardJonesParameters(ϵOO, σOO, R)
2929
e_parameters = ElectrostaticParameters(k, Rel)
30-
spc_paramters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
30+
spc_parameters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
3131
pbc = CubicPeriodicBoundaryConditions(L)
32-
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters, spc_paramters);
32+
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters, spc_parameters);
3333
simulation = NBodySimulation(water, (t1, t2), pbc, kb);
3434
result = @time run_simulation(simulation, VelocityVerlet(), dt = τ)
3535

‎examples/water_spc_fw.jl‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -46,9 +46,9 @@ const k = 9e9 #
4646
bodies = load_water_molecules_from_pdb("C:/Users/Michael/Desktop/GSoC/pdbs/output_4.pdb")
4747
jl_parameters = LennardJonesParameters(ϵOO, σOO, R)
4848
e_parameters = ElectrostaticParameters(k, Rel)
49-
spc_paramters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
49+
spc_parameters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
5050
pbc = CubicPeriodicBoundaryConditions(L)
51-
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters, spc_paramters);
51+
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters, spc_parameters);
5252
#thermostat = BerendsenThermostat(T0, 200τ)
5353
simulation = NBodySimulation(water, (t1, t2), pbc, kb);
5454
#result = run_simulation(simulation, Tsit5())

‎examples/water_spc_fw_omm_units.jl‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -28,9 +28,9 @@ const k = 138.935458 #
2828
bodies = generate_bodies_in_cell_nodes(N, mH2O, v_dev, L)
2929
jl_parameters = LennardJonesParameters(ϵOO, σOO, R)
3030
e_parameters = ElectrostaticParameters(k, Rel)
31-
spc_paramters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
31+
spc_parameters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
3232
pbc = CubicPeriodicBoundaryConditions(L)
33-
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters, spc_paramters);
33+
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters, spc_parameters);
3434
#thermostat = BerendsenThermostat(T0, 200τ)
3535
#thermostat = NoseHooverThermostat(T0, 200τ)
3636
#thermostat = AndersenThermostat(90, 0.01/τ)

‎examples/water_spc_fw_sde.jl‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -28,9 +28,9 @@ const k = 138.935458 #
2828
bodies = generate_bodies_in_cell_nodes(N, mH2O, v_dev, L)
2929
jl_parameters = LennardJonesParameters(ϵOO, σOO, R)
3030
e_parameters = ElectrostaticParameters(k, Rel)
31-
spc_paramters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
31+
spc_parameters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
3232
pbc = CubicPeriodicBoundaryConditions(L)
33-
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters, spc_paramters);
33+
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters, spc_parameters);
3434
thermostat = LangevinThermostat(T0, 0)
3535
simulation = NBodySimulation(water, (t1, t2), pbc, thermostat, kb);
3636
result = @time run_simulation(simulation, EM(), dt = τ)

‎src/nbody_simulation_result.jl‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -265,8 +265,8 @@ function valence_angle_harmonic_potential(rs,
265265
rba = ra - rb
266266
rbc = rc - rb
267267

268-
currenct_angle = acos(dot(rba, rbc) / (norm(rba) * norm(rbc)))
269-
e_valence += k * (currenct_angle - valence_angle)^2
268+
current_angle = acos(dot(rba, rbc) / (norm(rba) * norm(rbc)))
269+
e_valence += k * (current_angle - valence_angle)^2
270270
end
271271
return e_valence / 2
272272
end

‎test/lennard_jones_test.jl‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -90,12 +90,12 @@
9090

9191
io = IOBuffer()
9292
pdb_data = sprint(io -> NBodySimulator.write_pdb_data(io, result))
93-
splitted_data = split(pdb_data, '\n')
93+
split_data = split(pdb_data, '\n')
9494

9595
hetatm_count = 0
9696
timestep_count = 0
9797

98-
for s in splitted_data
98+
for s in split_data
9999
if length(s) >= 10 && s[1:10] == "REMARK 250"
100100
timestep_count += 1
101101
elseif length(s) >= 6 && s[1:6] == "HETATM"

‎test/water_test.jl‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@
2424

2525
jl_parameters = LennardJonesParameters(ϵOO, σOO, R)
2626
e_parameters = ElectrostaticParameters(k_el, Rel)
27-
spc_paramters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
27+
spc_parameters = SPCFwParameters(rOH, ∠HOH, k_bond, k_angle)
2828
pbc = CubicPeriodicBoundaryConditions(L)
2929

3030
@testset "Analyzing simulation result" begin
@@ -43,7 +43,7 @@
4343

4444
bodies = [p1, p2, p3]
4545
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters,
46-
spc_paramters)
46+
spc_parameters)
4747
simulation = NBodySimulation(water, (t1, t2), pbc, kb)
4848

4949
result = run_simulation(simulation, VelocityVerlet(), dt = τ)
@@ -96,7 +96,7 @@
9696

9797
bodies = [p1, p2]
9898
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters,
99-
spc_paramters)
99+
spc_parameters)
100100

101101
thermostat = BerendsenThermostat(T0, 200τ)
102102
simulation = NBodySimulation(water, (t1, t2), pbc, kb)
@@ -123,7 +123,7 @@
123123
T0 = 275
124124
bodies = generate_bodies_in_cell_nodes(N, mH2O, v_dev, L)
125125
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters,
126-
spc_paramters)
126+
spc_parameters)
127127
thermostat = LangevinThermostat(T0, 100)
128128
simulation = NBodySimulation(water, (t1, t2), pbc, thermostat, kb)
129129
result = run_simulation(simulation, EM(), dt = τ)
@@ -146,18 +146,18 @@
146146

147147
bodies = [p1, p2]
148148
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters,
149-
spc_paramters)
149+
spc_parameters)
150150
simulation = NBodySimulation(water, (t1, t2), pbc, kb)
151151
result = run_simulation(simulation, VelocityVerlet(), dt = τ)
152152

153153
io = IOBuffer()
154154
pdb_data = sprint(io -> NBodySimulator.write_pdb_data(io, result))
155-
splitted_data = split(pdb_data, '\n')
155+
split_data = split(pdb_data, '\n')
156156

157157
hetatm_count = 0
158158
timestep_count = 0
159159

160-
for s in splitted_data
160+
for s in split_data
161161
if length(s) >= 10 && s[1:10] == "REMARK 250"
162162
timestep_count += 1
163163
elseif length(s) >= 6 && s[1:6] == "HETATM"
@@ -199,7 +199,7 @@ ENDMDL")
199199

200200
bodies = NBodySimulator.extract_from_pdb(pdb_data)
201201
water = WaterSPCFw(bodies, mH, mO, qH, qO, jl_parameters, e_parameters,
202-
spc_paramters)
202+
spc_parameters)
203203
t1 = 0τ
204204
t2 = 2τ
205205
simulation = NBodySimulation(water, (t1, t2), pbc, kb)

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