output at the first timestep

The output at time t = 0 is truly the solution at that time, but noticed that current formulation has outputs at t = t* - dt, where t* is the intended time of output (see #46) -- this is because the clock and thickness are updated *before* the outputting is performed

src/OutputParams/OutputParams.jl

@@ -9,6 +9,7 @@ struct OutputParams{T <: Real, R <: Real, O}
     output_path::String #folder in which to save
     dump_vel::Bool     #toggle on dumping the velocity after the final timestep
     zip_format::String     #specify whether or not to zip the output, and the format
+    output_start::Bool  #flag to specify whether to output the initial state or not 
 end
 
 #output constructor
@@ -19,7 +20,8 @@ function OutputParams(;
     prefix = "outfile", 
     output_path = "./",
     dump_vel = false,
-    zip_format = "none")
+    zip_format = "none",
+    output_start = false)
 
     #default the n_iter_out to -1 (this is updated in simulation once we know timestep from timestepping_params)
     n_iter_out = -1
@@ -47,7 +49,7 @@ function OutputParams(;
         zip_format = "none"
     end
 
-    return OutputParams(outputs, output_freq, n_iter_out, output_format, prefix, output_path, dump_vel, zip_format)
+    return OutputParams(outputs, output_freq, n_iter_out, output_format, prefix, output_path, dump_vel, zip_format, output_start)
 end
 
 include("output_writing.jl")

src/OutputParams/output_writing.jl

@@ -22,6 +22,8 @@ function write_output(simulation)
         fname = string(fname, ".mat")
         matwrite(fname, output_dict)
     end
+
+    println("outputting at timestep number $(simulation.clock.n_iter)")
 end
 
 """

src/Simulations/run_simulation.jl

@@ -4,8 +4,12 @@
 Perform one timestep of the simulation
 """
 function timestep!(simulation)
-    @unpack model,timestepping_params = simulation
+    @unpack model,timestepping_params, output_params = simulation
     update_state!(model)
+    #write solution if at the first timestep (hack for https://github.com/RJArthern/WAVI.jl/issues/46 until synchronicity is fixed)
+    if (output_params.output_start) && (simulation.clock.n_iter == 0)
+        write_output(simulation)
+    end
     if timestepping_params.step_thickness
         update_thickness!(simulation)
     end
@@ -58,7 +62,7 @@ function run_simulation!(simulation)
     chkpt_tag = "A"
     for i = (simulation.clock.n_iter+1):timestepping_params.n_iter_total
         timestep!(simulation)
-
+        
         #check if we have hit a temporary checkpoint
         if mod(i,timestepping_params.n_iter_chkpt) == 0
             #output a temporary checkpoint
@@ -80,9 +84,6 @@ function run_simulation!(simulation)
         #check if we have hit an output timestep
         if mod(i,simulation.output_params.n_iter_out) == 0
             write_output(simulation)
-            println(simulation.clock.n_iter)
-            println("outputting at timestep number $(simulation.clock.n_iter)")
-
         end
 
         #check the dump velocity flag at the final timestep