Changes between Version 318 and Version 319 of doc/app/runtime_parameters

Timestamp:

Feb 12, 2020 1:04:39 PM (5 years ago)

Author:

scharf

Comment:

--

doc/app/runtime_parameters

@@ -91 +91 @@
 ||e  ||SGS turbulence kinetic energy||m^2^/s^2^ || ||
 ||lwp* ||liquid water path ||kg/m^2^ ||only horizontal cross section is allowed, requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' ||
-||nr ||rain drop number density ||1/m^3^ ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' and [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' and [[../inipar#precipitation|precipitation]] = ''.T.''||
+||nr ||rain drop number density ||1/m^3^ ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' and [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' and [[../initialization_parameters#precipitation|precipitation]] = ''.T.''||
 ||ol* ||Obukhov length in the constant flux layer ||m ||only horizontal cross section is allowed ||
 ||p ||perturbation pressure ||N/m^2^, Pa || ||
 ||pc ||particle/droplet concentration ||#/gridbox || ||
 ||pr ||mean particle/droplet radius ||m || ||
-||pra* ||precipitation amount ||mm ||only horizontal cross section is allowed, requires [[../inipar#precipitation|precipitation]] = ''.T.'', time interval on which amount refers to is defined by [#precipitation_amount_interval precipitation_amount_interval] ||
-||prr* ||precipitation rate ||mm/s ||only horizontal cross section is allowed, requires [[../bcmpar#cloud_scheme|cloud_scheme]] = ''kessler'' and [[../inipar#precipitation|precipitation]] = ''.T.'' ||
-||prr ||precipitation rate ||kg/kg m/s ||requires [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' and [[../inipar#precipitation|precipitation]] = ''.T.''||
-||q ||water vapor mixing ratio (or total water mixing ratio if cloud physics is switched on) ||kg/kg ||requires [[../inipar#humidity|humidity]] = ''.T.'' ||
+||pra* ||precipitation amount ||mm ||only horizontal cross section is allowed, requires [[../initialization_parameters#precipitation|precipitation]] = ''.T.'', time interval on which amount refers to is defined by [#precipitation_amount_interval precipitation_amount_interval] ||
+||prr* ||precipitation rate ||mm/s ||only horizontal cross section is allowed, requires [[../bcmpar#cloud_scheme|cloud_scheme]] = ''kessler'' and [[../initialization_parameters#precipitation|precipitation]] = ''.T.'' ||
+||prr ||precipitation rate ||kg/kg m/s ||requires [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' and [[../initialization_parameters#precipitation|precipitation]] = ''.T.''||
+||q ||water vapor mixing ratio (or total water mixing ratio if cloud physics is switched on) ||kg/kg ||requires [[../initialization_parameters#humidity|humidity]] = ''.T.'' ||
 ||qc ||cloud water mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' and [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' ||
-||ql ||liquid water mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' or [[../inipar#cloud_droplets|cloud_droplets]] = ''.T.'' ||
-||ql_c ||change in liquid water mixing ratio due to condensation/evaporation during last time step ||kg/kg ||requires [[../inipar#cloud_droplets|cloud_droplets]] = ''.T.'' ||
-||ql_v ||volume of liquid water ||m^3^/gridbox ||requires [[../inipar#cloud_droplets|cloud_droplets]] = ''.T.'' ||
-||ql_vp ||weighting factor || ||requires [[../inipar#cloud_droplets|cloud_droplets]] = ''.T.'' ||
-||qr ||rain water mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' and [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' and [[../inipar#precipitation|precipitation]] = ''.T.''||
-||qsws* ||surface latent heatflux ||kg/kg m/s or W/m^2^ ||only horizontal cross section is allowed (see [[#section_xy|section_xy]]), requires [[../inipar#humidity|humidity]] = ''.T.'' ||
+||ql ||liquid water mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' or [[../initialization_parameters#cloud_droplets|cloud_droplets]] = ''.T.'' ||
+||ql_c ||change in liquid water mixing ratio due to condensation/evaporation during last time step ||kg/kg ||requires [[../initialization_parameters#cloud_droplets|cloud_droplets]] = ''.T.'' ||
+||ql_v ||volume of liquid water ||m^3^/gridbox ||requires [[../initialization_parameters#cloud_droplets|cloud_droplets]] = ''.T.'' ||
+||ql_vp ||weighting factor || ||requires [[../initialization_parameters#cloud_droplets|cloud_droplets]] = ''.T.'' ||
+||qr ||rain water mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' and [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' and [[../initialization_parameters#precipitation|precipitation]] = ''.T.''||
+||qsws* ||surface latent heatflux ||kg/kg m/s or W/m^2^ ||only horizontal cross section is allowed (see [[#section_xy|section_xy]]), requires [[../initialization_parameters#humidity|humidity]] = ''.T.'' ||
 ||qv ||water vapor mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' ||
-||rho ||density ||kg/m^3^ ||requires [[../inipar#ocean|ocean]] = ''.T.'' ||
-||s ||concentration of the scalar ||kg m^-3^ or ppm ||requires [[../inipar#passive_scalar|passive_scalar]] = ''.T.'' ||
-||sa ||salinity ||psu ||requires [[../inipar#ocean|ocean]] = ''.T.'' ||
+||rho ||density ||kg/m^3^ ||requires [[../initialization_parameters#ocean|ocean]] = ''.T.'' ||
+||s ||concentration of the scalar ||kg m^-3^ or ppm ||requires [[../initialization_parameters#passive_scalar|passive_scalar]] = ''.T.'' ||
+||sa ||salinity ||psu ||requires [[../initialization_parameters#ocean|ocean]] = ''.T.'' ||
 ||shf* ||surface sensible heatflux ||K m/s or W/m^2^ ||only horizontal cross section is allowed ||
-||ssws* ||surface scalarflux ||kg m^-2^ s^-1^ or ppm m s^-1^ ||only horizontal cross section is allowed (see [[#section_xy|section_xy]]), requires [[../inipar#passive_scalar|passive_scalar]] = ''.T.'' ||
+||ssws* ||surface scalarflux ||kg m^-2^ s^-1^ or ppm m s^-1^ ||only horizontal cross section is allowed (see [[#section_xy|section_xy]]), requires [[../initialization_parameters#passive_scalar|passive_scalar]] = ''.T.'' ||
 ||t* ||(near surface) characteristic temperature ||K ||only horizontal cross section is allowed ||
 ||theta ||potential temperature ||K || ||
 ||thetal ||liquid water potential temperature ||K ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.''||
-||thetav ||virtual potential temperature ||K ||requires [[../inipar#humidity|humidity]] = ''.T.'' ||
+||thetav ||virtual potential temperature ||K ||requires [[../initialization_parameters#humidity|humidity]] = ''.T.'' ||
 ||theta_2m* ||2-m air potential temperature (estimated from logarithmic interpolation if the 2m level is below the first prognostic grid point, else interpolated between two vertical  levels)||K ||only horizontal cross section is allowed ||
 ||ti ||turbulence intensity (absolute value of the rotation vector)||1/s || ||
@@ -124 +124 @@
 ||v ||v-component of the velocity ||m/s || ||
 ||w ||w-component of the velocity ||m/s || ||
-||wq ||product of w and q, output of wq_av can be used to calculate the resolved turbulent water flux according to the temporal eddy covariance method by substracting the advective water flux (product of w_av and q_av) from wq_av. ||m/s ||requires [[../inipar#humidity|humidity]] = ''.T.'' ||
+||wq ||product of w and q, output of wq_av can be used to calculate the resolved turbulent water flux according to the temporal eddy covariance method by substracting the advective water flux (product of w_av and q_av) from wq_av. ||m/s ||requires [[../initialization_parameters#humidity|humidity]] = ''.T.'' ||
 ||wspeed_10m* ||10-m wind speed (estimated from logarithmic interpolation if the 10m level is below the first prognostic grid point, else interpolated between two vertical levels)||m/s ||only horizontal cross section is allowed ||
 ||wtheta ||product of w and theta, refer to wq ||K m/s || ||
@@ -194 +194 @@
 The parameter [#skip_time_data_output skip_time_data_output] can be used to shift data output activities for a given time interval. Individual intervals can be set using [#skip_time_do3d skip_time_do3d], [#skip_time_do2d_xy skip_time_do2d_xy], [#skip_time_do2d_xz skip_time_do2d_xz], [#skip_time_do2d_yz skip_time_do2d_yz], and [#skip_time_data_output_av skip_time_data_output_av].\\\\
 With the parameter [[#nz_do3d|nz_do3d]] the output can be limited in the vertical direction up to a certain grid point.\\\\
-Cross sections extend through the total model domain. In the two horizontal directions all grid points with 0 <= i <= [[../inipar#nx|nx]]+1 and 0 <= j <= [[../inipar#ny|ny]]+1 are output so that in case of cyclic boundary conditions the complete total domain is represented. The location(s) of the cross sections can be defined with parameters [#section_xy section_xy], [#section_xz section_xz], and [#section_yz section_yz]. Assigning '''section_...''' = ''-1'' causes the output data to be averaged along the direction normal to the respective section.\\\\
+Cross sections extend through the total model domain. In the two horizontal directions all grid points with 0 <= i <= [[../initialization_parameters#nx|nx]]+1 and 0 <= j <= [[../initialization_parameters#ny|ny]]+1 are output so that in case of cyclic boundary conditions the complete total domain is represented. The location(s) of the cross sections can be defined with parameters [#section_xy section_xy], [#section_xz section_xz], and [#section_yz section_yz]. Assigning '''section_...''' = ''-1'' causes the output data to be averaged along the direction normal to the respective section.\\\\
 '''Output of user-defined quantities:'''\\\\
 Besides the standard quantities from the above list, the user can output any other quantities. These have to be defined and calculated within the user-defined code (see [[../userint/output|User-defined output quantities]]). They can be selected for output with the user-parameter [[../userpar#data_output_user|data_output_user]] for which the same rules apply as for '''data_output'''. Output of the user-defined quantities (time interval, averaging, selection of cross sections, etc.) is controlled by the parameters listed above and data are written to the same file(s) as the standard quantities.\\\\
@@ -219 +219 @@
 ||='''Quantity name''' =||='''Meaning''' =||='''Unit''' =||='''Remarks''' =||
 ||e  ||SGS turbulence kinetic energy|| m^2^/s^2^ || ||
-||nr ||rain drop number density ||1/m^3^ ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' and [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' and [[../inipar#precipitation|precipitation]] = ''.T.''||
+||nr ||rain drop number density ||1/m^3^ ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' and [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' and [[../initialization_parameters#precipitation|precipitation]] = ''.T.''||
 ||p ||perturpation pressure ||N/m^2^, Pa || ||
 ||pc ||particle/droplet concentration ||#/gridbox || ||
 ||pr ||mean particle/droplet radius ||m || ||
-||q ||water vapor mixing ratio (or total water mixing ratio if cloud physics is switched on) ||kg/kg ||requires [[../inipar#humidity|humidity]] = ''.T.'' ||
+||q ||water vapor mixing ratio (or total water mixing ratio if cloud physics is switched on) ||kg/kg ||requires [[../initialization_parameters#humidity|humidity]] = ''.T.'' ||
 ||qc ||cloud water mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' and [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' ||
-||ql ||liquid water mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' or [[../inipar#cloud_droplets|cloud_droplets]] = ''.T.'' ||
-||ql_c ||change in liquid water mixing ratio due to condensation/evaporation during last time step ||kg/kg ||requires [[../inipar#cloud_droplets|cloud_droplets]] = ''.T.'' ||
-||ql_v ||volume of liquid water ||m^3^/gridbox ||requires [[../inipar#cloud_droplets|cloud_droplets]] = ''.T.'' ||
-||ql_vp ||weighting factor || ||requires [[../inipar#cloud_droplets|cloud_droplets]] = ''.T.'' ||
+||ql ||liquid water mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' or [[../initialization_parameters#cloud_droplets|cloud_droplets]] = ''.T.'' ||
+||ql_c ||change in liquid water mixing ratio due to condensation/evaporation during last time step ||kg/kg ||requires [[../initialization_parameters#cloud_droplets|cloud_droplets]] = ''.T.'' ||
+||ql_v ||volume of liquid water ||m^3^/gridbox ||requires [[../initialization_parameters#cloud_droplets|cloud_droplets]] = ''.T.'' ||
+||ql_vp ||weighting factor || ||requires [[../initialization_parameters#cloud_droplets|cloud_droplets]] = ''.T.'' ||
 ||qv ||water vapor mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' ||
-||qr ||rain water mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' and [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' and [[../inipar#precipitation|precipitation]] = ''.T.''||
-||rho ||density ||kg/m^3^ ||requires [[../inipar#ocean|ocean]] = ''.T.'' ||
-||s ||concentration of the scalar ||kg m^-3^ or ppm ||requires [[../inipar#passive_scalar|passive_scalar]] = ''.T.'' ||
-||sa ||salinity ||psu ||requires [[../inipar#ocean|ocean]] = ''.T.'' ||
+||qr ||rain water mixing ratio ||kg/kg ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.'' and [[../bcmpar#cloud_scheme|cloud_scheme]] = ''seifert_beheng'' and [[../initialization_parameters#precipitation|precipitation]] = ''.T.''||
+||rho ||density ||kg/m^3^ ||requires [[../initialization_parameters#ocean|ocean]] = ''.T.'' ||
+||s ||concentration of the scalar ||kg m^-3^ or ppm ||requires [[../initialization_parameters#passive_scalar|passive_scalar]] = ''.T.'' ||
+||sa ||salinity ||psu ||requires [[../initialization_parameters#ocean|ocean]] = ''.T.'' ||
 ||theta ||potential temperature ||K || ||
 ||thetal ||liquid water potential temperature ||K ||requires [[../bcmpar#bulk_cloud_model|bulk_cloud_model]] = ''.T.''||
-||thetav ||virtual potential temperature ||K ||requires [[../inipar#humidity|humidity]] = ''.T.'' ||
+||thetav ||virtual potential temperature ||K ||requires [[../initialization_parameters#humidity|humidity]] = ''.T.'' ||
 ||ti ||turbulence intensity (absolute value of the rotation vector)||1/s || ||
 ||u ||u-component of the velocity ||m/s || ||
@@ -271 +271 @@
 Quantities for which vertical profiles (horizontally averaged) are to be output.\\\\
 By default vertical profile data is output to the local file [[../iofiles#DATA_1D_PR_NETCDF|DATA_1D_PR_NETCDF]]. The file's format is netCDF. Further details about processing netCDF data are given in chapter [../netcdf netCDF data output].\\\\
-For horizontally averaged vertical profiles always '''all''' vertical grid points (0 <= k <= [[../inipar#nz|nz]]+1) are output to file. Vertical profile data refers to the total domain but profiles for subdomains can also be output (see [../inipar/#statistic_regions statistic_regions]).\\\\
+For horizontally averaged vertical profiles always '''all''' vertical grid points (0 <= k <= [[../initialization_parameters#nz|nz]]+1) are output to file. Vertical profile data refers to the total domain but profiles for subdomains can also be output (see [../initialization_parameters/#statistic_regions statistic_regions]).\\\\
 The temporal interval of the output times of profiles is assigned via the parameter [#dt_dopr dt_dopr].\\\\
 Profiles can also be temporally averaged (see [#averaging_interval_pr averaging_interval_pr]).\\\\
-The following list shows the values which can be assigned to '''data_output_pr'''. The profile data is either defined on u-v-levels (variables marked in [[span(red,style=color: red)]]) or on w-levels ([[span(green,style=color: green)]]). According to this, the z-coordinates of the individual profiles vary. Beyond that, with a constant flux layer switched on ([[../inipar#constant_flux_layer|constant_flux_layer]]) the lowest output level is z = zu(1) instead of z = zw(0) for profiles w"u", w"v", wu and wv. Turbulence quantities such as w*u* or u*2 are calculated from turbulent fluctuations that are defined as deviations from the instantaneous horizontal average.\\\\
+The following list shows the values which can be assigned to '''data_output_pr'''. The profile data is either defined on u-v-levels (variables marked in [[span(red,style=color: red)]]) or on w-levels ([[span(green,style=color: green)]]). According to this, the z-coordinates of the individual profiles vary. Beyond that, with a constant flux layer switched on ([[../initialization_parameters#constant_flux_layer|constant_flux_layer]]) the lowest output level is z = zu(1) instead of z = zw(0) for profiles w"u", w"v", wu and wv. Turbulence quantities such as w*u* or u*2 are calculated from turbulent fluctuations that are defined as deviations from the instantaneous horizontal average.\\\\
 ||='''Quantity name''' =||='''Meaning''' =||='''Unit''' =||
 ||[[span(e ,style=color: red)]] ||Turbulence kinetic energy (TKE, subgrid-scale) ||m^2^/s^2^ ||
@@ -294 +294 @@
 ||[[span(rho ,style=color: red)]] ||Air Density ||kg/m^3^ ||
 ||[[span(rho_sea_water ,style=color: red)]] ||Ocean Density ||kg/m^3^ ||
-||[[span(s ,style=color: red)]] ||Scalar concentration (requires [[../inipar#passive_scalar|passive_scalar]] = ''.T.'')  ||kg m^-3^ or ppm ||
-||[[span(s*2 ,style=color: red)]] ||Variance of the passive scalar (resolved, requires [../inipar#passive_scalar passive_scalar] = .T.) ||(kg m^-3^)^2^ ||
+||[[span(s ,style=color: red)]] ||Scalar concentration (requires [[../initialization_parameters#passive_scalar|passive_scalar]] = ''.T.'')  ||kg m^-3^ or ppm ||
+||[[span(s*2 ,style=color: red)]] ||Variance of the passive scalar (resolved, requires [../initialization_parameters#passive_scalar passive_scalar] = .T.) ||(kg m^-3^)^2^ ||
 ||[[span(sa ,style=color: red)]] ||Salinity ||psu ||
 ||[[span(Sw ,style=color: green)]] ||Skewness of the w-velocity component (resolved, Sw = w^3^/(w^2^)^1.5^) ||m^3^/s^2^ / (m^2^/s^2^)^1.5^ ||
@@ -311 +311 @@
 ||[[span(thetav ,style=color: red)]] ||Virtual potential temperature ||K ||
 ||[[span(u ,style=color: red)]] ||u-component of the velocity ||m/s ||
-||[[span(u*2 ,style=color: red)]] ||Variance or horizontal momentum flux (in case of [../inipar#momentum_advec momentum_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) of the u-velocity component (resolved) ||m^2^/s^2^ ||
+||[[span(u*2 ,style=color: red)]] ||Variance or horizontal momentum flux (in case of [../initialization_parameters#momentum_advec momentum_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) of the u-velocity component (resolved) ||m^2^/s^2^ ||
 ||[[span(ug ,style=color: red)]] ||u-component of the geostrophic wind ||m/s ||
 ||[[span(v ,style=color: red)]] ||v-component of the velocity ||m/s ||
-||[[span(v*2 ,style=color: red)]] ||Variance or horizontal momentum flux (in case of [../inipar#momentum_advec momentum_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) of the v-velocity component (resolved) ||m^2^/s^2^ ||
+||[[span(v*2 ,style=color: red)]] ||Variance or horizontal momentum flux (in case of [../initialization_parameters#momentum_advec momentum_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) of the v-velocity component (resolved) ||m^2^/s^2^ ||
 ||[[span(vg ,style=color: red)]] ||v-component of the geostrophic wind ||m/s ||
 ||[[span(w ,style=color: green)]] ||w-component of the velocity ||m/s ||
-||[[span(w*2 ,style=color: green)]] ||Variance or vertical momentum flux (in case of [../inipar#momentum_advec momentum_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) of the w-velocity component (resolved) ||m^2^/s^2^ ||
+||[[span(w*2 ,style=color: green)]] ||Variance or vertical momentum flux (in case of [../initialization_parameters#momentum_advec momentum_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) of the w-velocity component (resolved) ||m^2^/s^2^ ||
 ||[[span(w*3 ,style=color: green)]] ||Third moment of the w-velocity component (resolved) ||m^3^/s^3^ ||
 ||[[span(w*e* ,style=color: green)]] ||Vertical flux of perturbation energy (resolved) ||m^3^/s^3^ ||
 ||[[span(w*p*:dz ,style=color: red)]] ||Transport of resolved-scale TKE due to pressure fluctuations (term in resolved TKE budget)||Pa m/s^2^ ||
 ||[[span(w"q" ,style=color: green)]] ||Subgrid-scale vertical water flux ||kg/kg m/s ||
-||[[span(w*q* ,style=color: green)]] ||Covariance or resolved vertical water flux (in case of [../inipar#scalar_advec scalar_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||kg/kg m/s ||
+||[[span(w*q* ,style=color: green)]] ||Covariance or resolved vertical water flux (in case of [../initialization_parameters#scalar_advec scalar_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||kg/kg m/s ||
 ||[[span(wq ,style=color: green)]] ||Total vertical water flux (w"q" + w*q*) ||kg/kg m/s ||
 ||[[span(w"qv" ,style=color: green)]] ||Subgrid-scale vertical latent heat flux ||kg/kg m/s ||
-||[[span(w*qv* ,style=color: green)]] ||Covariance or resolved vertical latent heat flux (in case of [../inipar#scalar_advec scalar_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||kg/kg m/s ||
+||[[span(w*qv* ,style=color: green)]] ||Covariance or resolved vertical latent heat flux (in case of [../initialization_parameters#scalar_advec scalar_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||kg/kg m/s ||
 ||[[span(wqv ,style=color: green)]] ||Total vertical latent heat flux (w"qv" + w*qv*) ||kg/kg m/s ||
-||[[span(w"s" ,style=color: green)]] ||Subgrid-scale vertical scalar concentration flux (requires [[../inipar#passive_scalar|passive_scalar]] = ''.T.'') ||kg m^-2^ s^-1^ or ppm m s^-1^ ||
-||[[span(w*s* ,style=color: green)]] ||Resolved vertical scalar concentration flux (requires [[../inipar#passive_scalar|passive_scalar]] = ''.T.'') ||kg m^-2^ s^-1^ or ppm m s^-1^ ||
-||[[span(ws ,style=color: green)]] ||Total vertical scalar concentration flux (w"s" + w*s*) (requires [[../inipar#passive_scalar|passive_scalar]] = ''.T.'') ||kg m^-2^ s^-1^ or ppm m s^-1^ ||
+||[[span(w"s" ,style=color: green)]] ||Subgrid-scale vertical scalar concentration flux (requires [[../initialization_parameters#passive_scalar|passive_scalar]] = ''.T.'') ||kg m^-2^ s^-1^ or ppm m s^-1^ ||
+||[[span(w*s* ,style=color: green)]] ||Resolved vertical scalar concentration flux (requires [[../initialization_parameters#passive_scalar|passive_scalar]] = ''.T.'') ||kg m^-2^ s^-1^ or ppm m s^-1^ ||
+||[[span(ws ,style=color: green)]] ||Total vertical scalar concentration flux (w"s" + w*s*) (requires [[../initialization_parameters#passive_scalar|passive_scalar]] = ''.T.'') ||kg m^-2^ s^-1^ or ppm m s^-1^ ||
 ||[[span(w"sa"  ,style=color: green)]] ||Subgrid-scale vertical salinity flux ||psu m/s ||
-||[[span(w*sa* ,style=color: green)]] ||Covariance or resolved vertical salinity flux (in case of [../inipar#scalar_advec scalar_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||psu m/s ||
+||[[span(w*sa* ,style=color: green)]] ||Covariance or resolved vertical salinity flux (in case of [../initialization_parameters#scalar_advec scalar_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||psu m/s ||
 ||[[span(wsa  ,style=color: green)]] ||Total vertical salinity flux (w"sa" + w*sa*) ||psu m/s ||
 ||[[span(w_subs ,style=color: red)]] ||large-scale vertical velocity ||m/s ||
 ||[[span(w"theta" ,style=color: green)]] ||Subgrid-scale vertical sensible heat flux ||K m/s ||
-||[[span(w*theta* ,style=color: green)]] ||Covariance or resolved vertical sensible heat flux (in case of [../inipar#scalar_advec scalar_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||K m/s ||
+||[[span(w*theta* ,style=color: green)]] ||Covariance or resolved vertical sensible heat flux (in case of [../initialization_parameters#scalar_advec scalar_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||K m/s ||
 ||[[span(wtheta ,style=color: green)]] ||Total vertical sensible heat flux (w"theta" + w*theta*) ||K m/s ||
 ||[[span(w*theta*BC ,style=color: green)]] ||Subgrid-scale vertical sensible heat flux using the Bott-Chlond scheme ||K m/s ||
@@ -345 +345 @@
 ||[[span(w*theta*2 ,style=color: green)]] ||Third moment (resolved) ||K^2^ m/s ||
 ||[[span(w"u" ,style=color: green)]] ||u-component of the subgrid-scale vertical momentum flux ||m^2^/s^2^ ||
-||[[span(w*u* ,style=color: green)]] ||Covariance or u-component of the resolved vertical momentum flux (in case of [../inipar#momentum_advec momentum_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||m^2^/s^2^ ||
+||[[span(w*u* ,style=color: green)]] ||Covariance or u-component of the resolved vertical momentum flux (in case of [../initialization_parameters#momentum_advec momentum_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||m^2^/s^2^ ||
 ||[[span(wu ,style=color: green)]] ||u-component of the total vertical momentum flux (w"u" + w*u*) ||m^2^/s^2^ ||
 ||[[span(w*u*u*:dz ,style=color: red)]] ||Transport of resolved-scale TKE due to turbulence (term in resolved TKE budget)||m^2^/s^3^ ||
 ||[[span(w"v" ,style=color: green)]] ||v-component of the subgrid-scale vertical momentum flux ||m^2^/s^2^ ||
-||[[span(w*v* ,style=color: green)]] ||Covariance or v-component of the resolved vertical momentum flux (in case of [../inipar#momentum_advec momentum_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||m^2^/s^2^ ||
+||[[span(w*v* ,style=color: green)]] ||Covariance or v-component of the resolved vertical momentum flux (in case of [../initialization_parameters#momentum_advec momentum_advec] = 'ws-scheme', see [../../tec/advection#statistical_evaluation details]) ||m^2^/s^2^ ||
 ||[[span(wv ,style=color: green)]] ||v-component of the total vertical momentum flux (w"v" + w*v*) ||m^2^/s^2^ ||
 \\
@@ -639 +639 @@
 \\\\
 Additionally, the user can add own time series quantities to the file by using the user-interface subroutines [[../userint/int#user_init|user_init.f90]] and [[../userint/int#user_statistics|user_statistics.f90]]. These routines contain a simple example (as comment lines) on how to do this.\\\\
-By default, time-series data refer to the total domain, but data can also be output for user-defined subdomains (see [../inipar/#statistic_regions statistic_regions]). However, the following time series always present the values of the total model domain (even with output for subdomains): ''umax, vmax, wmax, div_old, div_new.''
+By default, time-series data refer to the total domain, but data can also be output for user-defined subdomains (see [../initialization_parameters/#statistic_regions statistic_regions]). However, the following time series always present the values of the total model domain (even with output for subdomains): ''umax, vmax, wmax, div_old, div_new.''
 }}}
 |----------------
@@ -817 +817 @@
    '''mask_x(2,:)''' = ''1000.''\\\\
    This example will create outputs at the specified points (at xu-grid in m, if [#mask_scale_x mask_scale_x] is not used; outputs on 
-   the x-grid are shifted by half of the grid spacing forward (e.g. x = ''75.0, 125.0, 525.0, 575.0, 625.0,'' if [[../inipar#dx|dx]]=
+   the x-grid are shifted by half of the grid spacing forward (e.g. x = ''75.0, 125.0, 525.0, 575.0, 625.0,'' if [[../initialization_parameters#dx|dx]]=
    ''50.0'')).
 If you use [#mask_scale_x mask_scale_x], '''mask_x''' has to be assigned in "grid point position along x-direction [m]/'''mask_scale_x''' " (e.g. '''mask_scale_x''' = ''10.0'' -> '''mask_x(1,:)''' = ''0., 5., 10., 50., 55., 60.'').\\\\
@@ -842 +842 @@
    '''mask_y(2,:)''' = ''1000.''\\\\
    This example will create outputs at the specified points (at yv-grid in m, if [#mask_scale_x mask_scale_x] is not used; outputs on 
-   the y-grid are shifted by half of the grid spacing forward (e.g. y = ''75.0, 125.0, 525.0, 575.0, 625.0,'' if [[../inipar#dy|dy]]=
+   the y-grid are shifted by half of the grid spacing forward (e.g. y = ''75.0, 125.0, 525.0, 575.0, 625.0,'' if [[../initialization_parameters#dy|dy]]=
    ''50.0'')).
 If you use [#mask_scale_y mask_scale_y], '''mask_y''' has to be assigned in "grid point position along y-direction [m]/'''mask_scale_y''' " (e.g. '''mask_scale_y''' = ''10.0'' -> '''mask_y(1,:)''' = ''0., 5., 10., 50., 55., 60.'').\\\\
@@ -867 +867 @@
    '''mask_z(2,:)''' = ''1000.''\\\\
    This example will create outputs at the specified points (at zw-grid in m, if [#mask_scale_x mask_scale_x] is not used; outputs on 
-   the zu-grid are shifted by half of the grid spacing downward (e.g. zu = ''25.0, 75.0, 475.0, 525.0, 575.0'', if [[../inipar#dz|dz]]= ''50.0'')).
+   the zu-grid are shifted by half of the grid spacing downward (e.g. zu = ''25.0, 75.0, 475.0, 525.0, 575.0'', if [[../initialization_parameters#dz|dz]]= ''50.0'')).
 If you use [#mask_scale_z mask_scale_z], '''mask_z''' has to be assigned in "grid point position along z-direction [m]/'''mask_scale_z''' " (e.g. '''mask_scale_z''' = ''10.0'' -> '''mask_z(1,:)''' = ''0., 5., 10., 50., 55., 60.'').\\\\
 The default results in output at every grid point along the z-direction, i.e. from 0 to nz.\\\\
@@ -931 +931 @@
 For each mask a separate '''mask_z_loop''' has to be assigned.\\\\
 The default results in output at every grid point along the z-direction, i.e. from 0 to nz.\\\\
-'''Note:''' If mask_z is also specified, mask_z_loop will be ignored. If you have assigned [../inipar#dz_stretch_level dz_stretch_level], '''mask_z_loop''' will fail above '''dz_stretch_level'''. If masked outputs are desired above '''dz_stretch_level''', you should use [#mask_z mask_z] instead.\\\\
+'''Note:''' If mask_z is also specified, mask_z_loop will be ignored. If you have assigned [../initialization_parameters#dz_stretch_level dz_stretch_level], '''mask_z_loop''' will fail above '''dz_stretch_level'''. If masked outputs are desired above '''dz_stretch_level''', you should use [#mask_z mask_z] instead.\\\\
 Further examples are given in [../maskedoutput#Examples Masked data output].
 }}}
@@ -1001 +1001 @@
 {{{#!td
 Temporal interval for which the precipitation amount (in mm) shall be calculated and output (in s).\\\\
-This parameter requires [[../inipar#precipitation|precipitation]] = ''.T.''. The interval must be smaller or equal than the output interval for 2d horizontal cross sections given by [#dt_do2d_xy dt_do2d_xy]). The output of the precipitation amount also requires setting of [#data_output data_output] = '' 'pra*'.''
+This parameter requires [[../initialization_parameters#precipitation|precipitation]] = ''.T.''. The interval must be smaller or equal than the output interval for 2d horizontal cross sections given by [#dt_do2d_xy dt_do2d_xy]). The output of the precipitation amount also requires setting of [#data_output data_output] = '' 'pra*'.''
 }}}
 |----------------
@@ -1059 +1059 @@
 {{{#!td
 Position of cross section(s) for output of 2d (xz) vertical cross sections (grid point index j).\\\\
-If output of vertical xz cross sections is selected (see [#data_output data_output]), this parameter can be used to define the position(s) of the cross section(s). Up to 100 positions of cross sections can be selected by assigning '''section_xz''' the corresponding horizontal grid point index/indices j of the requested cross section(s). The exact position (in y-direction) of the cross section is given by j*[[../inipar#dy|dy]] or (j-0.5)*[[../inipar#dy|dy]], depending on which grid the output quantity is defined. However, in the netCDF output file, no distinction is made between the quantities and j*'''dy''' is used for all positions.\\\\
+If output of vertical xz cross sections is selected (see [#data_output data_output]), this parameter can be used to define the position(s) of the cross section(s). Up to 100 positions of cross sections can be selected by assigning '''section_xz''' the corresponding horizontal grid point index/indices j of the requested cross section(s). The exact position (in y-direction) of the cross section is given by j*[[../initialization_parameters#dy|dy]] or (j-0.5)*[[../initialization_parameters#dy|dy]], depending on which grid the output quantity is defined. However, in the netCDF output file, no distinction is made between the quantities and j*'''dy''' is used for all positions.\\\\
 Assigning '''section_xz''' = ''-1'' creates the output of vertical cross sections averaged along y. In the netCDF output file these (averaged) cross sections are given the y-coordinate -1.0.
 }}}
@@ -1074 +1074 @@
 {{{#!td
 Position of cross section(s) for output of 2d (yz) vertical cross sections (grid point index i).\\\\
-If output of vertical yz cross sections is selected (see [#data_output data_output]), this parameter can be used to define the position(s) of the cross section(s). Up to 100 positions of cross sections can be selected by assigning '''section_yz''' the corresponding horizontal grid point index/indices i of the requested cross section(s). The exact position (in x-direction) of the cross section is given by i*[[../inipar#dx|dx]] or (i-0.5)*[[../inipar#dx|dx]], depending on which grid the output quantity is defined. However, in the netCDF output file, no distinction is made between the quantities and i*'''dx''' is used for all positions.\\\\
+If output of vertical yz cross sections is selected (see [#data_output data_output]), this parameter can be used to define the position(s) of the cross section(s). Up to 100 positions of cross sections can be selected by assigning '''section_yz''' the corresponding horizontal grid point index/indices i of the requested cross section(s). The exact position (in x-direction) of the cross section is given by i*[[../initialization_parameters#dx|dx]] or (i-0.5)*[[../initialization_parameters#dx|dx]], depending on which grid the output quantity is defined. However, in the netCDF output file, no distinction is made between the quantities and i*'''dx''' is used for all positions.\\\\
 Assigning '''section_yz''' = -1 creates the output of vertical cross sections averaged along x. In the netCDF output file these (averaged) cross sections are given the x-coordinate -1.0.
 }}}
@@ -1216 +1216 @@
 }}}
 {{{#!td
-This parameter now belongs to the initialization parameters and therefore has to be set within the NAMELIST group [../inipar/#inipar inipar]. See [../inipar/#statistic_regions statistic_regions] for an explanation of this parameter. 
+This parameter now belongs to the initialization parameters and therefore has to be set within the NAMELIST group [../initialization_parameters/#initialization_parameters initialization_parameters]. See [../initialization_parameters/#statistic_regions statistic_regions] for an explanation of this parameter. 
 }}}
 |----------------
@@ -1263 +1263 @@
 Switch to impose random perturbations to the horizontal velocity field.\\\\
 With '''create_disturbances''' = .T., random perturbations can be imposed to the horizontal velocity field at certain times e.g. in order to trigger off the onset of convection, etc..\\\\
-The temporal interval between these times can be steered with [#dt_disturb dt_disturb], the vertical range of the perturbations with [#disturbance_level_b disturbance_level_b] and [#disturbance_level_t disturbance_level_t], and the perturbation amplitude with [#disturbance_amplitude disturbance_amplitude]. In case of non-cyclic lateral boundary conditions (see [[../inipar#bc_lr|bc_lr]] and [[../inipar#bc_ns|bc_ns]]), the horizontal range of the perturbations is determined by [[../inipar#inflow_disturbance_begin|inflow_disturbance_begin]] and [[../inipar#inflow_disturbance_end|inflow_disturbance_end]]. A perturbation is added to each grid point with its individual value determined by multiplying the disturbance amplitude with a uniformly distributed random number. After this, the arrays of u and v are smoothed by applying a Shuman-filter twice and made divergence-free by applying the pressure solver.\\\\
-The random number generator to be used can be chosen with [[../inipar#random_generator|random_generator]].\\\\
+The temporal interval between these times can be steered with [#dt_disturb dt_disturb], the vertical range of the perturbations with [#disturbance_level_b disturbance_level_b] and [#disturbance_level_t disturbance_level_t], and the perturbation amplitude with [#disturbance_amplitude disturbance_amplitude]. In case of non-cyclic lateral boundary conditions (see [[../initialization_parameters#bc_lr|bc_lr]] and [[../initialization_parameters#bc_ns|bc_ns]]), the horizontal range of the perturbations is determined by [[../initialization_parameters#inflow_disturbance_begin|inflow_disturbance_begin]] and [[../initialization_parameters#inflow_disturbance_end|inflow_disturbance_end]]. A perturbation is added to each grid point with its individual value determined by multiplying the disturbance amplitude with a uniformly distributed random number. After this, the arrays of u and v are smoothed by applying a Shuman-filter twice and made divergence-free by applying the pressure solver.\\\\
+The random number generator to be used can be chosen with [[../initialization_parameters#random_generator|random_generator]].\\\\
 As soon as the desired flow features have developed (e.g.  convection has started), further imposing of perturbations is not necessary and can be omitted (this does not hold for non-cyclic lateral boundaries!). This can be steered by assigning an upper limit value for the perturbation energy (the perturbation energy is defined by the deviation of the velocity from the mean flow) using the parameter [#disturbance_energy_limit disturbance_energy_limit]. As soon as the perturbation energy has exceeded this energy limit, no more random perturbations are assigned.\\\\
 Timesteps where a random perturbation has been imposed are marked in the local file [[../iofiles#RUN_CONTROL|RUN_CONTROL]] by the character "D" appended to the values of the maximum horizontal velocities. 
@@ -1309 +1309 @@
 Lower limit of the vertical range for which random perturbations are to be imposed on the horizontal wind field (in m).\\\\
 This parameter must hold the condition ''zu(3)'' <= '''disturbance_level_b''' <= ''zu(nzt-2)''. Additionally, '''disturbance_level_b''' <= [#disturbance_level_t disturbance_level_t] must also hold.\\\\
-In case of ocean runs (see [[../inipar#ocean|ocean]]) the default value is '''disturbance_level_b''' = ''zu(nzt * 2 / 3)'' (negative).\\\\
+In case of ocean runs (see [[../initialization_parameters#ocean|ocean]]) the default value is '''disturbance_level_b''' = ''zu(nzt * 2 / 3)'' (negative).\\\\
 The parameter [#create_disturbances create_disturbances] describes how to impose random perturbations to the horizontal velocity field. 
 }}}
@@ -1325 +1325 @@
 Upper limit of the vertical range for which random perturbations are to be imposed on the horizontal wind field (in m).\\\\
 This parameter must hold the condition '''disturbance_level_t''' <= ''zu(nzt-2)''. Additionally, [#disturbance_level_b disturbance_level_b] <= '''disturbance_level_t''' must also hold.\\\\
-In case of ocean runs (see [[../inipar#ocean|ocean]]) the default value is '''disturbance_level_t''' = ''zu(nzt - 3)'' (negative).\\\\
+In case of ocean runs (see [[../initialization_parameters#ocean|ocean]]) the default value is '''disturbance_level_t''' = ''zu(nzt - 3)'' (negative).\\\\
 The parameter [#create_disturbances create_disturbances] describes how to impose random perturbations to the horizontal velocity field. 
 }}}
@@ -1340 +1340 @@
 {{{#!td
 Time step to be used by the 3d-model (in s).\\\\
-This parameter is described in detail with the initialization parameters (see [[../inipar#dt|dt]]). Additionally, it may be used as a run parameter and then applies to all restart runs (until it is changed again). A switch from a constant time step to a variable time step can be achieved with '''dt''' = ''-1.0.''
+This parameter is described in detail with the initialization parameters (see [[../initialization_parameters#dt|dt]]). Additionally, it may be used as a run parameter and then applies to all restart runs (until it is changed again). A switch from a constant time step to a variable time step can be achieved with '''dt''' = ''-1.0.''
 }}}
 |----------------
@@ -1463 +1463 @@
 {{{#!td
 Number of processors along x-direction of the virtual processor net.\\\\
-For parallel runs, the total number of processors to be used is given by the '''palmrun'''-option -X. By default, PALM tries to generate a 2d processor net (domain decomposition along x and y), which is more or less square-shaped. If, for example, 16 processors are assigned (-X 16), a 4 * 4 processor net is generated ('''npex''' = 4, '''npey''' = 4). This choice is optimal for square total domains ([../inipar#nx nx] = [../inipar#ny ny]) because it minimizes the number of ghost points at the lateral boundarys of the subdomains. If nx and ny differ extremely, the processor net should be manually adjusted using adequate values for '''npex''' and '''npey'''.\\\\
+For parallel runs, the total number of processors to be used is given by the '''palmrun'''-option -X. By default, PALM tries to generate a 2d processor net (domain decomposition along x and y), which is more or less square-shaped. If, for example, 16 processors are assigned (-X 16), a 4 * 4 processor net is generated ('''npex''' = 4, '''npey''' = 4). This choice is optimal for square total domains ([../initialization_parameters#nx nx] = [../initialization_parameters#ny ny]) because it minimizes the number of ghost points at the lateral boundarys of the subdomains. If nx and ny differ extremely, the processor net should be manually adjusted using adequate values for '''npex''' and '''npey'''.\\\\
 '''Important:'''\\
 The value of '''npex''' * '''npey''' must exactly match the value assigned by the '''palmrun'''-option -X. Otherwise the model run will abort with a corresponding error message.\\\\