Merge pull request #45 from SciML/repeat

Remove repeat times

Author: ChrisRackauckas

src/nbody_simulation_result.jl

@@ -297,7 +297,7 @@ end
 # this should be a method for integrators designed for the SecondOrderODEProblem (It is worth somehow to sort them from other algorithms)
 function calculate_simulation(s::NBodySimulation, alg_type::Union{VelocityVerlet,DPRKN6,Yoshida6}, args...; kwargs...)
     cb = obtain_callbacks_for_so_ode_problem(s)
-    solution = solve(SecondOrderODEProblem(s), alg_type, args...; callback=cb, kwargs...)
+    solution = solve(SecondOrderODEProblem(s), alg_type, args...; callback=cb, save_everystep = isempty(cb), kwargs...)
     return SimulationResult(solution, s)
 end
 
@@ -331,7 +331,7 @@ function get_andersen_thermostating_callback(s::NBodySimulation)
             end
         end
     end
-    cb = DiscreteCallback(condition, affect!)
+    cb = DiscreteCallback(condition, affect!, save_positions = (false,true))
 end
 
 function apply_andersen_rescaling_velocity(integrator, i, kb, system::PotentialNBodySystem, p::AndersenThermostat)
@@ -382,11 +382,11 @@ end
     positions = get_position(sr, time)
     seriestype --> :scatter
     markersize --> 5
-    
+
     for i in 1:n
         @series begin
             label --> "Body no. $i"
-            
+
             if all(positions[3,:] .- positions[3,1] .< 1e-15)
                 ([positions[1,i]], [positions[2,i]])
             else

test/thermostat_test.jl

@@ -1,4 +1,4 @@
-@testset "Testing thermostats on liquid argon " begin 
+@testset "Testing thermostats on liquid argon " begin
     T = 120.0 # °K
     T0 = 90 # °K
     kb = 8.3144598e-3 # kJ/(K*mol)
@@ -8,9 +8,9 @@
     m = 39.95# Da
     N = 125
     L = (m * N / ρ)^(1 / 3)#10.229σ
-    R = 0.5 * L   
+    R = 0.5 * L
     v_dev = sqrt(kb * T / m)
-    @testset "Andersen thermostat" begin 
+    @testset "Andersen thermostat" begin
         bodies = generate_bodies_in_cell_nodes(N, m, v_dev, L)
 
         τ = 0.5e-3 # ps or 1e-12 s
@@ -22,15 +22,16 @@
         thermostat = AndersenThermostat(T0, 0.1/τ)
         simulation = NBodySimulation(lj_system, (t1, t2), PeriodicBoundaryConditions(L), thermostat, kb);
         result = run_simulation(simulation, VelocityVerlet(), dt=τ)
-    
 
-        T1 = temperature(result, t1) 
+
+        T1 = temperature(result, t1)
         T2 = temperature(result, t2)
         ε = 0.5
         @test abs(T2 - T0) / T0 ≈ 0.0 atol = ε
+        @test result.solution.t == unique(result.solution.t)
     end
 
-    @testset "Berendsen thermostat" begin 
+    @testset "Berendsen thermostat" begin
         bodies = generate_bodies_in_cell_nodes(N, m, v_dev, L)
 
         τ = 0.5e-3
@@ -43,13 +44,13 @@
         pbc = CubicPeriodicBoundaryConditions(L)
         simulation = NBodySimulation(lj_system, (t1, t2), pbc, thermostat, kb);
         result = run_simulation(simulation, VelocityVerlet(), dt=τ)
-     
+
         T2 = temperature(result, t2)
         ε = 0.1
         @test abs(T2 - T0) / T ≈ 0.0 atol = ε
     end
 
-    @testset "Nose-Hoover thermostat" begin 
+    @testset "Nose-Hoover thermostat" begin
         bodies = generate_bodies_in_cell_nodes(N, m, v_dev, L)
 
         τ = 0.5e-3
@@ -62,13 +63,13 @@
         pbc = CubicPeriodicBoundaryConditions(L)
         simulation = NBodySimulation(lj_system, (t1, t2), pbc, thermostat, kb);
         result = run_simulation(simulation, VelocityVerlet(), dt=τ)
-     
+
         T2 = temperature(result, t2)
         ε = 0.5
         @test abs(T2 - T0) / T0 ≈ 0.0 atol = ε
     end
 
-    @testset "Langevin thermostat" begin 
+    @testset "Langevin thermostat" begin
         bodies = generate_bodies_in_cell_nodes(N, m, v_dev, L)
 
         τ = 0.5e-3
@@ -81,9 +82,9 @@
         pbc = CubicPeriodicBoundaryConditions(L)
         simulation = NBodySimulation(lj_system, (t1, t2), pbc, thermostat, kb);
         result = run_simulation(simulation, EM(),  dt=τ)
-     
+
         T2 = temperature(result, t2)
         ε = 0.5
         @test abs(T2 - T0) / T0 ≈ 0.0 atol = ε
     end
-end
+end