Update of the example inputs structure.

example_inputs/input_BHW.yaml

@@ -10,12 +10,12 @@ grid:
 time: # Unit is reference ion cyclotron period unless specified
   #  Choose three among dt_diag, dt_rk4, Nt_diag, Nt_rk4, Tsim (rk4_per_diag can replace one of [dt_diag, dt_rk4])
 
-  dt_rk4: null      # Time step for RK4 scheme
-  dt_diag: null     # Time step for diagnostics
-  rk4_per_diag: 64  # Number of RK4 steps between two saving of outputs
-  Tsim: 100.        # Total simulation time (overriden for HW schemes unless HW_duration=0)
-  Nt_rk4: null      # Number of total RK4 steps
-  Nt_diag: 2048     # Number of total diagnostic time steps
+  dt_rk4:       null # Time step for RK4 scheme
+  dt_diag:      null # Time step for diagnostics
+  rk4_per_diag: 64   # Number of RK4 steps between two saving of outputs
+  Tsim:         100. # Total simulation time (overriden for HW schemes unless HW_duration=0)
+  Nt_rk4:       null # Number of total RK4 steps
+  Nt_diag:      2048 # Number of total diagnostic time steps
 
 pde:
   eq: "BHW" # Choice between "SOL", "HW", "mHW" ,"BHW"
@@ -43,10 +43,10 @@ initial_condition:
   load_init_path: "/path/to/sim_folder" # Path to simulation folder for restart
 
   # 2D Gaussian initialization
-  init_gauss_ampl_n:   [0. ,] # Peak amplitude of the Gaussian in density
-  init_gauss_ampl_phi: [0. ,] # Peak amplitude of the Gaussian in potential
-  init_gauss_sigma_x:  [0. ,] # Std of the Gaussian in density
-  init_gauss_sigma_y:  [0. ,] # Std of the Gaussian in potential
+  init_gauss_ampl_n:   [0.,] # Peak amplitude of the Gaussian in density
+  init_gauss_ampl_phi: [0.,] # Peak amplitude of the Gaussian in potential
+  init_gauss_sigma_x:  [0.,] # Std of the Gaussian in x
+  init_gauss_sigma_y:  [0.,] # Std of the Gaussian in y
   init_gauss_x0:       [0.,] # Center position of the Gaussian in x
   init_gauss_y0:       [0.,] # Center position of the Gaussian in y
 
@@ -57,21 +57,21 @@ initial_condition:
   # Harmonic initial perturbation
   init_harm_kx:       [0, ] # Harmonic in x of the perturbation
   init_harm_ky:       [0, ] # Harmonic in y of the perturbation
-  init_harm_ampl_n:   [0.e-0, ] # Amplitude of the perturbation in density
-  init_harm_ampl_phi: [0.e-2, ] # Amplitude of the perturbation in potential
+  init_harm_ampl_n:   [0.,] # Amplitude of the perturbation in density
+  init_harm_ampl_phi: [0.,] # Amplitude of the perturbation in potential
 
   # Random initial perturbation
   init_rand_ampl_n: 0. # Amplitude of the random perturbation in density
   init_rand_ampl_phi: 1.e-3 # Amplitude of the random perturbation in potential
 
 source:
   # Gaussian source (set sigma=0 for uniform source along a direction)
-  source_gauss_ampl_n:   [0.   ,] # Peak amplitude of the Gaussian in density
-  source_gauss_ampl_phi: [0.   ,] # Peak amplitude of the Gaussian in potential
-  source_gauss_sigma_x:  [0.   ,] # Std of the Gaussian in density
-  source_gauss_sigma_y:  [0.   ,] # Std of the Gaussian in potential
-  source_gauss_x0:       [0.   ,] # Center position of the Gaussian in x
-  source_gauss_y0:       [0.   ,] # Center position of the Gaussian in y
+  source_gauss_ampl_n:   [0.,] # Peak amplitude of the Gaussian in density
+  source_gauss_ampl_phi: [0.,] # Peak amplitude of the Gaussian in potential
+  source_gauss_sigma_x:  [0.,] # Std of the Gaussian in x
+  source_gauss_sigma_y:  [0.,] # Std of the Gaussian in y
+  source_gauss_x0:       [0.,] # Center position of the Gaussian in x
+  source_gauss_y0:       [0.,] # Center position of the Gaussian in y
 
   source_balance_par_loss: false # Balance parallel losses (maintain constant density background)
 
@@ -82,3 +82,4 @@ callbacks:
 
 inline_operations:
   fft_filter: true # 2/3 rule for dealiasing
+  compute_time_derivatives: false # Compute time derivatives inline

example_inputs/input_HW.yaml

@@ -10,12 +10,12 @@ grid:
 time: # Unit is reference ion cyclotron period unless specified
   #  Choose three among dt_diag, dt_rk4, Nt_diag, Nt_rk4, Tsim (rk4_per_diag can replace one of [dt_diag, dt_rk4])
 
-  dt_rk4: null      # Time step for RK4 scheme
-  dt_diag: null     # Time step for diagnostics
-  rk4_per_diag: 64  # Number of RK4 steps between two saving of outputs
-  Tsim: 100.        # Total simulation time (overriden for HW schemes unless HW_duration=0)
-  Nt_rk4: null      # Number of total RK4 steps
-  Nt_diag: 2048     # Number of total diagnostic time steps
+  dt_rk4:       null # Time step for RK4 scheme
+  dt_diag:      null # Time step for diagnostics
+  rk4_per_diag: 64   # Number of RK4 steps between two saving of outputs
+  Tsim:         100. # Total simulation time (overriden for HW schemes unless HW_duration=0)
+  Nt_rk4:       null # Number of total RK4 steps
+  Nt_diag:      2048 # Number of total diagnostic time steps
 
 pde:
   eq: "HW" # Choice between "SOL", "HW", "mHW" ,"BHW"
@@ -43,10 +43,10 @@ initial_condition:
   load_init_path: "/path/to/sim_folder" # Path to simulation folder for restart
 
   # 2D Gaussian initialization
-  init_gauss_ampl_n:   [0. ,] # Peak amplitude of the Gaussian in density
-  init_gauss_ampl_phi: [0. ,] # Peak amplitude of the Gaussian in potential
-  init_gauss_sigma_x:  [0. ,] # Std of the Gaussian in density
-  init_gauss_sigma_y:  [0. ,] # Std of the Gaussian in potential
+  init_gauss_ampl_n:   [0.,] # Peak amplitude of the Gaussian in density
+  init_gauss_ampl_phi: [0.,] # Peak amplitude of the Gaussian in potential
+  init_gauss_sigma_x:  [0.,] # Std of the Gaussian in x
+  init_gauss_sigma_y:  [0.,] # Std of the Gaussian in y
   init_gauss_x0:       [0.,] # Center position of the Gaussian in x
   init_gauss_y0:       [0.,] # Center position of the Gaussian in y
 
@@ -55,23 +55,23 @@ initial_condition:
   init_uni_ampl_phi: 0. # Background potential amplitude
 
   # Harmonic initial perturbation
-  init_harm_kx:       [0, ] # Harmonic in x of the perturbation
-  init_harm_ky:       [0, ] # Harmonic in y of the perturbation
-  init_harm_ampl_n:   [0.e-0, ] # Amplitude of the perturbation in density
-  init_harm_ampl_phi: [0.e-2, ] # Amplitude of the perturbation in potential
+  init_harm_kx:       [0 ,] # Harmonic in x of the perturbation
+  init_harm_ky:       [0 ,] # Harmonic in y of the perturbation
+  init_harm_ampl_n:   [0.,] # Amplitude of the perturbation in density
+  init_harm_ampl_phi: [0.,] # Amplitude of the perturbation in potential
 
   # Random initial perturbation
   init_rand_ampl_n: 0. # Amplitude of the random perturbation in density
   init_rand_ampl_phi: 1.e-3 # Amplitude of the random perturbation in potential
 
 source:
   # Gaussian source (set sigma=0 for uniform source along a direction)
-  source_gauss_ampl_n:   [0.   ,] # Peak amplitude of the Gaussian in density
-  source_gauss_ampl_phi: [0.   ,] # Peak amplitude of the Gaussian in potential
-  source_gauss_sigma_x:  [0.   ,] # Std of the Gaussian in density
-  source_gauss_sigma_y:  [0.   ,] # Std of the Gaussian in potential
-  source_gauss_x0:       [0.   ,] # Center position of the Gaussian in x
-  source_gauss_y0:       [0.   ,] # Center position of the Gaussian in y
+  source_gauss_ampl_n:   [0.,] # Peak amplitude of the Gaussian in density
+  source_gauss_ampl_phi: [0.,] # Peak amplitude of the Gaussian in potential
+  source_gauss_sigma_x:  [0.,] # Std of the Gaussian in x
+  source_gauss_sigma_y:  [0.,] # Std of the Gaussian in y
+  source_gauss_x0:       [0.,] # Center position of the Gaussian in x
+  source_gauss_y0:       [0.,] # Center position of the Gaussian in y
 
   source_balance_par_loss: false # Balance parallel losses (maintain constant density background)
 
@@ -82,3 +82,4 @@ callbacks:
 
 inline_operations:
   fft_filter: true # 2/3 rule for dealiasing
+  compute_time_derivatives: false # Compute time derivatives inline

example_inputs/input_SOL_driftwave.yaml

@@ -10,12 +10,12 @@ grid:
 time: # Unit is reference ion cyclotron period unless specified
   #  Choose three among dt_diag, dt_rk4, Nt_diag, Nt_rk4, Tsim (rk4_per_diag can replace one of [dt_diag, dt_rk4])
 
-  dt_rk4: 1         # Time step for RK4 scheme
-  dt_diag: null     # Time step for diagnostics
-  rk4_per_diag: 32  # Number of RK4 steps between two saving of outputs
-  Tsim: null        # Total simulation time (overriden for HW schemes unless HW_duration=0)
-  Nt_rk4: null      # Number of total RK4 steps
-  Nt_diag: 2048     # Number of total diagnostic time steps
+  dt_rk4:       1    # Time step for RK4 scheme
+  dt_diag:      null # Time step for diagnostics
+  rk4_per_diag: 32   # Number of RK4 steps between two saving of outputs
+  Tsim:         null # Total simulation time (overriden for HW schemes unless HW_duration=0)
+  Nt_rk4:       null # Number of total RK4 steps
+  Nt_diag:      2048 # Number of total diagnostic time steps
 
 pde:
   eq: "SOL" # Choice between "SOL", "HW", "mHW" ,"BHW"
@@ -43,10 +43,10 @@ initial_condition:
   load_init_path: "/path/to/sim_folder" # Path to simulation folder for restart
 
   # 2D Gaussian initialization
-  init_gauss_ampl_n:   [4. ,] # Peak amplitude of the Gaussian in density
-  init_gauss_ampl_phi: [0. ,] # Peak amplitude of the Gaussian in potential
-  init_gauss_sigma_x:  [8. ,] # Std of the Gaussian in density
-  init_gauss_sigma_y:  [0. ,] # Std of the Gaussian in potential
+  init_gauss_ampl_n:   [4.,] # Peak amplitude of the Gaussian in density
+  init_gauss_ampl_phi: [0.,] # Peak amplitude of the Gaussian in potential
+  init_gauss_sigma_x:  [8.,] # Std of the Gaussian in x
+  init_gauss_sigma_y:  [0.,] # Std of the Gaussian in y
   init_gauss_x0:       [0.,] # Center position of the Gaussian in x
   init_gauss_y0:       [0.,] # Center position of the Gaussian in y
 
@@ -55,10 +55,10 @@ initial_condition:
   init_uni_ampl_phi: 0. # Background potential amplitude
 
   # Harmonic initial perturbation
-  init_harm_kx:       [0    , ] # Harmonic in x of the perturbation
-  init_harm_ky:       [12   , ] # Harmonic in y of the perturbation
-  init_harm_ampl_n:   [0.e-0, ] # Amplitude of the perturbation in density
-  init_harm_ampl_phi: [1.e-4, ] # Amplitude of the perturbation in potential
+  init_harm_kx:       [0    ,] # Harmonic in x of the perturbation
+  init_harm_ky:       [12   ,] # Harmonic in y of the perturbation
+  init_harm_ampl_n:   [0.   ,] # Amplitude of the perturbation in density
+  init_harm_ampl_phi: [1.e-4,] # Amplitude of the perturbation in potential
 
   # Random initial perturbation
   init_rand_ampl_n: 0. # Amplitude of the random perturbation in density
@@ -68,8 +68,8 @@ source:
   # Gaussian source (set sigma=0 for uniform source along a direction)
   source_gauss_ampl_n:   [1.e-3,] # Peak amplitude of the Gaussian in density
   source_gauss_ampl_phi: [0.   ,] # Peak amplitude of the Gaussian in potential
-  source_gauss_sigma_x:  [8.   ,] # Std of the Gaussian in density
-  source_gauss_sigma_y:  [0.   ,] # Std of the Gaussian in potential
+  source_gauss_sigma_x:  [8.   ,] # Std of the Gaussian in x
+  source_gauss_sigma_y:  [0.   ,] # Std of the Gaussian in y
   source_gauss_x0:       [0.   ,] # Center position of the Gaussian in x
   source_gauss_y0:       [0.   ,] # Center position of the Gaussian in y
 
@@ -82,3 +82,4 @@ callbacks:
 
 inline_operations:
   fft_filter: true # 2/3 rule for dealiasing
+  compute_time_derivatives: false # Compute time derivatives inline

example_inputs/input_SOL_interchange.yaml

@@ -10,12 +10,12 @@ grid:
 time: # Unit is reference ion cyclotron period unless specified
   #  Choose three among dt_diag, dt_rk4, Nt_diag, Nt_rk4, Tsim (rk4_per_diag can replace one of [dt_diag, dt_rk4])
 
-  dt_rk4: 1         # Time step for RK4 scheme
-  dt_diag: null     # Time step for diagnostics
-  rk4_per_diag: 32  # Number of RK4 steps between two saving of outputs
-  Tsim: null        # Total simulation time (overriden for HW schemes unless HW_duration=0)
-  Nt_rk4: null      # Number of total RK4 steps
-  Nt_diag: 2048     # Number of total diagnostic time steps
+  dt_rk4:       1    # Time step for RK4 scheme
+  dt_diag:      null # Time step for diagnostics
+  rk4_per_diag: 32   # Number of RK4 steps between two saving of outputs
+  Tsim:         null # Total simulation time (overriden for HW schemes unless HW_duration=0)
+  Nt_rk4:       null # Number of total RK4 steps
+  Nt_diag:      2048 # Number of total diagnostic time steps
 
 pde:
   eq: "SOL" # Choice between "SOL", "HW", "mHW" ,"BHW"
@@ -43,10 +43,10 @@ initial_condition:
   load_init_path: "/path/to/sim_folder" # Path to simulation folder for restart
 
   # 2D Gaussian initialization
-  init_gauss_ampl_n:   [4. ,] # Peak amplitude of the Gaussian in density
-  init_gauss_ampl_phi: [0. ,] # Peak amplitude of the Gaussian in potential
-  init_gauss_sigma_x:  [8. ,] # Std of the Gaussian in density
-  init_gauss_sigma_y:  [0. ,] # Std of the Gaussian in potential
+  init_gauss_ampl_n:   [4.,] # Peak amplitude of the Gaussian in density
+  init_gauss_ampl_phi: [0.,] # Peak amplitude of the Gaussian in potential
+  init_gauss_sigma_x:  [8.,] # Std of the Gaussian in x
+  init_gauss_sigma_y:  [0.,] # Std of the Gaussian in y
   init_gauss_x0:       [0.,] # Center position of the Gaussian in x
   init_gauss_y0:       [0.,] # Center position of the Gaussian in y
 
@@ -55,10 +55,10 @@ initial_condition:
   init_uni_ampl_phi: 0. # Background potential amplitude
 
   # Harmonic initial perturbation
-  init_harm_kx:       [0    , ] # Harmonic in x of the perturbation
-  init_harm_ky:       [12   , ] # Harmonic in y of the perturbation
-  init_harm_ampl_n:   [0.e-0, ] # Amplitude of the perturbation in density
-  init_harm_ampl_phi: [1.e-4, ] # Amplitude of the perturbation in potential
+  init_harm_kx:       [0    ,] # Harmonic in x of the perturbation
+  init_harm_ky:       [12   ,] # Harmonic in y of the perturbation
+  init_harm_ampl_n:   [0.   ,] # Amplitude of the perturbation in density
+  init_harm_ampl_phi: [1.e-4,] # Amplitude of the perturbation in potential
 
   # Random initial perturbation
   init_rand_ampl_n: 0. # Amplitude of the random perturbation in density
@@ -68,8 +68,8 @@ source:
   # Gaussian source (set sigma=0 for uniform source along a direction)
   source_gauss_ampl_n:   [1.e-3,] # Peak amplitude of the Gaussian in density
   source_gauss_ampl_phi: [0.   ,] # Peak amplitude of the Gaussian in potential
-  source_gauss_sigma_x:  [8.   ,] # Std of the Gaussian in density
-  source_gauss_sigma_y:  [0.   ,] # Std of the Gaussian in potential
+  source_gauss_sigma_x:  [8.   ,] # Std of the Gaussian in x
+  source_gauss_sigma_y:  [0.   ,] # Std of the Gaussian in y
   source_gauss_x0:       [0.   ,] # Center position of the Gaussian in x
   source_gauss_y0:       [0.   ,] # Center position of the Gaussian in y
 
@@ -82,3 +82,4 @@ callbacks:
 
 inline_operations:
   fft_filter: true # 2/3 rule for dealiasing
+  compute_time_derivatives: false # Compute time derivatives inline

example_inputs/input_SOL_interchange_driftwave.yaml

@@ -10,12 +10,12 @@ grid:
 time: # Unit is reference ion cyclotron period unless specified
   #  Choose three among dt_diag, dt_rk4, Nt_diag, Nt_rk4, Tsim (rk4_per_diag can replace one of [dt_diag, dt_rk4])
 
-  dt_rk4: 1         # Time step for RK4 scheme
-  dt_diag: null     # Time step for diagnostics
-  rk4_per_diag: 32  # Number of RK4 steps between two saving of outputs
-  Tsim: null        # Total simulation time (overriden for HW schemes unless HW_duration=0)
-  Nt_rk4: null      # Number of total RK4 steps
-  Nt_diag: 2048     # Number of total diagnostic time steps
+  dt_rk4:       1    # Time step for RK4 scheme
+  dt_diag:      null # Time step for diagnostics
+  rk4_per_diag: 32   # Number of RK4 steps between two saving of outputs
+  Tsim:         null # Total simulation time (overriden for HW schemes unless HW_duration=0)
+  Nt_rk4:       null # Number of total RK4 steps
+  Nt_diag:      2048 # Number of total diagnostic time steps
 
 pde:
   eq: "SOL" # Choice between "SOL", "HW", "mHW" ,"BHW"
@@ -43,10 +43,10 @@ initial_condition:
   load_init_path: "/path/to/sim_folder" # Path to simulation folder for restart
 
   # 2D Gaussian initialization
-  init_gauss_ampl_n:   [4. ,] # Peak amplitude of the Gaussian in density
-  init_gauss_ampl_phi: [0. ,] # Peak amplitude of the Gaussian in potential
-  init_gauss_sigma_x:  [8. ,] # Std of the Gaussian in density
-  init_gauss_sigma_y:  [0. ,] # Std of the Gaussian in potential
+  init_gauss_ampl_n:   [4.,] # Peak amplitude of the Gaussian in density
+  init_gauss_ampl_phi: [0.,] # Peak amplitude of the Gaussian in potential
+  init_gauss_sigma_x:  [8.,] # Std of the Gaussian in x
+  init_gauss_sigma_y:  [0.,] # Std of the Gaussian in y
   init_gauss_x0:       [0.,] # Center position of the Gaussian in x
   init_gauss_y0:       [0.,] # Center position of the Gaussian in y
 
@@ -55,10 +55,10 @@ initial_condition:
   init_uni_ampl_phi: 0. # Background potential amplitude
 
   # Harmonic initial perturbation
-  init_harm_kx:       [0    , ] # Harmonic in x of the perturbation
-  init_harm_ky:       [12   , ] # Harmonic in y of the perturbation
-  init_harm_ampl_n:   [0.e-0, ] # Amplitude of the perturbation in density
-  init_harm_ampl_phi: [1.e-4, ] # Amplitude of the perturbation in potential
+  init_harm_kx:       [0    ,] # Harmonic in x of the perturbation
+  init_harm_ky:       [12   ,] # Harmonic in y of the perturbation
+  init_harm_ampl_n:   [0.   ,] # Amplitude of the perturbation in density
+  init_harm_ampl_phi: [1.e-4,] # Amplitude of the perturbation in potential
 
   # Random initial perturbation
   init_rand_ampl_n: 0. # Amplitude of the random perturbation in density
@@ -68,8 +68,8 @@ source:
   # Gaussian source (set sigma=0 for uniform source along a direction)
   source_gauss_ampl_n:   [1.e-3,] # Peak amplitude of the Gaussian in density
   source_gauss_ampl_phi: [0.   ,] # Peak amplitude of the Gaussian in potential
-  source_gauss_sigma_x:  [8.   ,] # Std of the Gaussian in density
-  source_gauss_sigma_y:  [0.   ,] # Std of the Gaussian in potential
+  source_gauss_sigma_x:  [8.   ,] # Std of the Gaussian in x
+  source_gauss_sigma_y:  [0.   ,] # Std of the Gaussian in y
   source_gauss_x0:       [0.   ,] # Center position of the Gaussian in x
   source_gauss_y0:       [0.   ,] # Center position of the Gaussian in y
 
@@ -82,3 +82,4 @@ callbacks:
 
 inline_operations:
   fft_filter: true # 2/3 rule for dealiasing
+  compute_time_derivatives: false # Compute time derivatives inline