Initial Conditions: Temperature and Salinity

The temperature and salinity sections define how the water column is initialised and — optionally — how observed profiles are used to relax the model state throughout the simulation.

Both sections share the same structure (an extended InputSetting with additional sub-blocks) and are parsed by pygotm.config.settings.TemperatureSettings and pygotm.config.settings.SalinitySettings respectively. The underlying physics is implemented in pygotm.meanflow.temperature and pygotm.meanflow.salinity.

temperature

Specifies the initial temperature profile and optional relaxation forcing.

temperature:
  method: file
  constant_value: 20.0
  file: t_prof_file.dat
  column: 1
  type: in-situ
  two_layer:
    z_s: 30.0
    t_s: 20.0
    z_b: 40.0
    t_b: 15.0
  NN: 2.56e-4
  relax:
    tau: 1.0e15
    h_s: 0.0
    tau_s: 1.0e15
    h_b: 0.0
    tau_b: 1.0e15

temperature.method

Type	string
Valid values	off, constant, file, two_layer, buoyancy
Default	"off"

Selects the source of the initial temperature profile.

off

Temperature is not initialised from external data; arrays start at zero (or the restart state if restart.load: true).

constant

All levels are set to temperature.constant_value at initialisation. No relaxation file is needed.

file

A time series of full-depth temperature profiles is read from temperature.file. The first profile in the file initialises the column. If relax.tau is finite the model state is nudged toward the observed profiles at each subsequent time step.

two_layer

A simple two-layer structure with a linear gradient between the layers. Defined by the temperature.two_layer sub-block.

buoyancy

Temperature profile is reconstructed from the specified buoyancy frequency squared temperature.NN together with the salinity profile (which must be separately specified).

temperature.constant_value

Type	float
Units	°C
Default	0.0

Temperature value used when method: constant. Ignored for all other methods.

temperature.file

Type	string (file path)
Default	""

Path to an ASCII profile file containing a time series of full-depth temperature profiles. Each profile block begins with a header line (YYYY-MM-DD HH:MM:SS   N   up_down) followed by N rows of depth_m   value pairs; the model grid spacing need not match the file spacing. Relative paths are resolved from the directory containing gotm.yaml.

Required when method: file; ignored otherwise.

See also

Profile (Depth-Series) File for the complete profile file format specification, including header syntax, depth ordering (up_down), multi-column layouts, and interpolation behaviour.

temperature.column

Type	integer
Default	1

Column index (1-based) to read from the profile file. Use this when the data file contains multiple variables (e.g., temperature in column 1, salinity in column 2).

temperature.type

Type	string
Valid values	in-situ, potential, conservative
Default	"in-situ"

Temperature measure of the data in the profile file. pyGOTM uses the GSW toolbox (gsw Python package) to convert the input values to Conservative Temperature before storing them in the model state.

in-situ

In-situ temperature \(T\) (°C). No conversion applied.

potential

Potential temperature \(\theta\) (°C). Converted to Conservative Temperature via gsw.CT_from_pt().

conservative

Conservative Temperature \(\Theta\) (°C). Stored directly.

temperature.two_layer

Sub-block used only when method: two_layer.

temperature.two_layer.z_s / z_b

Depths (m, positive) where the upper (z_s) and lower (z_b) layers end / begin respectively. A linear gradient is imposed in the transition zone [z_s, z_b]. Below z_b the temperature is uniform at t_b.

Default: 0.0; range: ≥ 0.0.

temperature.two_layer.t_s

Upper-layer temperature (°C). Applied from the surface down to z_s.

Default: 0.0; range: −2 to 40 °C.

temperature.two_layer.t_b

Lower-layer temperature (°C). Applied from z_b to the bottom.

Default: 0.0; range: −2 to 40 °C.

temperature.NN

Type	float
Units	s−2
Range	≥ 0.0
Default	0.0

Buoyancy frequency squared \(N^2\) used when method: buoyancy. The temperature profile is reconstructed from the relationship \(N^2 = -\frac{g}{\rho_0}\frac{\partial\rho}{\partial z}\).

temperature.relax

Nudging parameters that pull the model temperature toward the observed profile at every time step. Relaxation is only active when method: file.

temperature.relax.tau

Interior relaxation time scale (s). The model temperature is nudged with rate \(1/\tau\) toward the observed profile in layers deeper than h_s from the surface and h_b from the bottom.

Default: 1.0e15 (no relaxation).

temperature.relax.h_s

Surface relaxation layer thickness (m). Layers shallower than h_s below the surface use tau_s instead of tau.

Default: 0.0 (no distinct surface layer).

temperature.relax.tau_s

Relaxation time scale (s) for the surface layer (depth < h_s).

Default: 1.0e15.

temperature.relax.h_b

Bottom relaxation layer thickness (m).

Default: 0.0.

temperature.relax.tau_b

Relaxation time scale (s) for the bottom layer (depth > total depth − h_b).

Default: 1.0e15.

salinity

Identical structure to temperature. Parameters have the same meaning unless noted below.

salinity:
  method: file
  constant_value: 35.0
  file: s_prof_file.dat
  column: 1
  type: practical
  two_layer:
    z_s: 30.0
    s_s: 35.0
    z_b: 40.0
    s_b: 34.5
  NN: 2.56e-4
  relax:
    tau: 172800.0
    tau_s: 172800.0
    tau_b: 172800.0

salinity.method

Type	string
Valid values	off, constant, file, two_layer, buoyancy
Default	"off"

Same as temperature.method. The buoyancy option reconstructs salinity from a specified \(N^2\) together with the temperature profile.

When method: file, the salinity profile file uses the same format as the temperature profile file. Both can share one multi-column file (see Profile (Depth-Series) File).

salinity.constant_value

Type	float
Units	psu (practical salinity units) or g kg−1
Default	0.0

salinity.type

Type	string
Valid values	practical, absolute
Default	"practical"

Salinity measure of the input data.

practical

Practical Salinity Scale 1978 (PSS-78) values. No conversion.

absolute

Absolute Salinity \(S_A\) (g kg⁻¹). Converted to Absolute Salinity using gsw.SA_from_SP().

salinity.two_layer.s_s / s_b

Upper- and lower-layer salinities (g kg⁻¹ or psu).

Default: 0.0; range: 0 to 40 g kg⁻¹.

salinity.NN

Same as temperature.NN. Used only when salinity.method: buoyancy.