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  <compounddef id="namespaceisomip__tracer" kind="namespace" language="Fortran">
    <compoundname>isomip_tracer</compoundname>
    <innerclass refid="structisomip__tracer_1_1isomip__tracer__cs" prot="public">isomip_tracer::isomip_tracer_cs</innerclass>
      <sectiondef kind="var">
      <memberdef kind="variable" id="namespaceisomip__tracer_1a45a3a4465d55afd6310d5a3412b2c9c5" prot="private" static="no" mutable="no">
        <type>integer, parameter</type>
        <definition>integer, parameter isomip_tracer::ntr</definition>
        <argsstring></argsstring>
        <name>ntr</name>
        <initializer>= 1</initializer>
        <briefdescription>
<para>ntr is the number of tracers in this module. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" line="42" column="1" bodyfile="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" bodystart="42" bodyend="42"/>
        <referencedby refid="namespaceisomip__tracer_1aa268e488bb883f99ebc9cb321d442696" compoundref="ISOMIP__tracer_8F90" startline="150" endline="243">initialize_isomip_tracer</referencedby>
        <referencedby refid="namespaceisomip__tracer_1a7f06ffe89c033074c6b9bd7f375f6dd5" compoundref="ISOMIP__tracer_8F90" startline="250" endline="322">isomip_tracer_column_physics</referencedby>
        <referencedby refid="namespaceisomip__tracer_1ac2571b7b6e4dce0d5936a483159ec379" compoundref="ISOMIP__tracer_8F90" startline="329" endline="355">isomip_tracer_surface_state</referencedby>
        <referencedby refid="namespaceisomip__tracer_1a7d66fe5ba12076654324a7e7d8ab2e4f" compoundref="ISOMIP__tracer_8F90" startline="69" endline="143">register_isomip_tracer</referencedby>
      </memberdef>
      </sectiondef>
      <sectiondef kind="func">
      <memberdef kind="function" id="namespaceisomip__tracer_1a7d66fe5ba12076654324a7e7d8ab2e4f" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>logical function, public</type>
        <definition>logical function, public isomip_tracer::register_isomip_tracer</definition>
        <argsstring>(HI, GV, param_file, CS, tr_Reg, restart_CS)</argsstring>
        <name>register_isomip_tracer</name>
        <param>
          <type>HI</type>
          <defname>HI</defname>
        </param>
        <param>
          <type>GV</type>
          <defname>GV</defname>
        </param>
        <param>
          <type>param_file</type>
          <defname>param_file</defname>
        </param>
        <param>
          <type>CS</type>
          <defname>CS</defname>
        </param>
        <param>
          <type>tr_Reg</type>
          <defname>tr_Reg</defname>
        </param>
        <param>
          <type>restart_CS</type>
          <defname>restart_CS</defname>
        </param>
        <briefdescription>
<para>This subroutine is used to register tracer fields. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername direction="in">hi</parametername>
</parameternamelist>
<parameterdescription>
<para>A horizontal index type structure. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">gv</parametername>
</parameternamelist>
<parameterdescription>
<para>The ocean&apos;s vertical grid structure. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">param_file</parametername>
</parameternamelist>
<parameterdescription>
<para>A structure indicating the open file to parse for model parameter values. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>cs</parametername>
</parameternamelist>
<parameterdescription>
<para>A pointer that is set to point to the control structure for this module (in/out). </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>tr_reg</parametername>
</parameternamelist>
<parameterdescription>
<para>A pointer to the tracer registry. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>restart_cs</parametername>
</parameternamelist>
<parameterdescription>
<para>A pointer to the restart control structure. </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" line="68" column="1" bodyfile="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" bodystart="69" bodyend="143"/>
        <references refid="namespaceatmos__ocean__fluxes__mod_1a1bd0443a803dd443bd7a4f24dae28e13" compoundref="atmos__ocean__fluxes_8F90" startline="18" endline="36">atmos_ocean_fluxes_mod::aof_set_coupler_flux</references>
        <references refid="namespacemom__error__handler_1a460cfb79a06c29fc249952c2a3710d67" compoundref="MOM__error__handler_8F90" startline="72" endline="92">mom_error_handler::mom_error</references>
        <references refid="namespaceisomip__tracer_1a45a3a4465d55afd6310d5a3412b2c9c5" compoundref="ISOMIP__tracer_8F90" startline="42" endline="42">ntr</references>
        <references refid="namespacemom__tracer__registry_1a97a70989bd0318f51d90c2fc6f87c6f5" compoundref="MOM__tracer__registry_8F90" startline="158" endline="325">mom_tracer_registry::register_tracer</references>
        <references refid="namespacemom__io_1a09be50ad112d6bc134d06d82fcbe1fdc" compoundref="MOM__io_8F90" startline="600" endline="632">mom_io::var_desc</references>
      </memberdef>
      <memberdef kind="function" id="namespaceisomip__tracer_1aa268e488bb883f99ebc9cb321d442696" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>subroutine, public</type>
        <definition>subroutine, public isomip_tracer::initialize_isomip_tracer</definition>
        <argsstring>(restart, day, G, GV, h, diag, OBC, CS, ALE_sponge_CSp)</argsstring>
        <name>initialize_isomip_tracer</name>
        <param>
          <type>restart</type>
          <defname>restart</defname>
        </param>
        <param>
          <type>day</type>
          <defname>day</defname>
        </param>
        <param>
          <type>G</type>
          <defname>G</defname>
        </param>
        <param>
          <type>GV</type>
          <defname>GV</defname>
        </param>
        <param>
          <type>h</type>
          <defname>h</defname>
        </param>
        <param>
          <type>diag</type>
          <defname>diag</defname>
        </param>
        <param>
          <type>OBC</type>
          <defname>OBC</defname>
        </param>
        <param>
          <type>CS</type>
          <defname>CS</defname>
        </param>
        <param>
          <type>ALE_sponge_CSp</type>
          <defname>ALE_sponge_CSp</defname>
        </param>
        <briefdescription>
<para>Initializes the NTR tracer fields in tr(:,:,:,:) </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername direction="in">g</parametername>
</parameternamelist>
<parameterdescription>
<para>Grid structure. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">gv</parametername>
</parameternamelist>
<parameterdescription>
<para>The ocean&apos;s vertical grid structure. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">restart</parametername>
</parameternamelist>
<parameterdescription>
<para>.true. if the fields have already been read from a restart file. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">day</parametername>
</parameternamelist>
<parameterdescription>
<para>Time of the start of the run. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">h</parametername>
</parameternamelist>
<parameterdescription>
<para>Layer thickness [H ~&gt; m or kg m-2]. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">diag</parametername>
</parameternamelist>
<parameterdescription>
<para>A structure that is used to regulate diagnostic output. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>obc</parametername>
</parameternamelist>
<parameterdescription>
<para>This open boundary condition type specifies whether, where, and what open boundary conditions are used. This is not being used for now. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>cs</parametername>
</parameternamelist>
<parameterdescription>
<para>The control structure returned by a previous call to ISOMIP_register_tracer. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>ale_sponge_csp</parametername>
</parameternamelist>
<parameterdescription>
<para>A pointer to the control structure for the sponges, if they are in use. Otherwise this may be unassociated. </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" line="148" column="1" bodyfile="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" bodystart="150" bodyend="243"/>
        <references refid="namespacemom__error__handler_1a460cfb79a06c29fc249952c2a3710d67" compoundref="MOM__error__handler_8F90" startline="72" endline="92">mom_error_handler::mom_error</references>
        <references refid="namespaceisomip__tracer_1a45a3a4465d55afd6310d5a3412b2c9c5" compoundref="ISOMIP__tracer_8F90" startline="42" endline="42">ntr</references>
        <references refid="namespacemom__io_1aa583d22dfaf16e3157b2741d838f5240" compoundref="MOM__io_8F90" startline="699" endline="737">mom_io::query_vardesc</references>
      </memberdef>
      <memberdef kind="function" id="namespaceisomip__tracer_1a7f06ffe89c033074c6b9bd7f375f6dd5" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>subroutine, public</type>
        <definition>subroutine, public isomip_tracer::isomip_tracer_column_physics</definition>
        <argsstring>(h_old, h_new, ea, eb, fluxes, dt, G, GV, US, CS, evap_CFL_limit, minimum_forcing_depth)</argsstring>
        <name>isomip_tracer_column_physics</name>
        <param>
          <type>h_old</type>
          <defname>h_old</defname>
        </param>
        <param>
          <type>h_new</type>
          <defname>h_new</defname>
        </param>
        <param>
          <type>ea</type>
          <defname>ea</defname>
        </param>
        <param>
          <type>eb</type>
          <defname>eb</defname>
        </param>
        <param>
          <type>fluxes</type>
          <defname>fluxes</defname>
        </param>
        <param>
          <type>dt</type>
          <defname>dt</defname>
        </param>
        <param>
          <type>G</type>
          <defname>G</defname>
        </param>
        <param>
          <type>GV</type>
          <defname>GV</defname>
        </param>
        <param>
          <type>US</type>
          <defname>US</defname>
        </param>
        <param>
          <type>CS</type>
          <defname>CS</defname>
        </param>
        <param>
          <type>evap_CFL_limit</type>
          <defname>evap_CFL_limit</defname>
        </param>
        <param>
          <type>minimum_forcing_depth</type>
          <defname>minimum_forcing_depth</defname>
        </param>
        <briefdescription>
<para>This subroutine applies diapycnal diffusion, including the surface boundary conditions and any other column tracer physics or chemistry to the tracers from this file. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername direction="in">g</parametername>
</parameternamelist>
<parameterdescription>
<para>The ocean&apos;s grid structure </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">gv</parametername>
</parameternamelist>
<parameterdescription>
<para>The ocean&apos;s vertical grid structure </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">h_old</parametername>
</parameternamelist>
<parameterdescription>
<para>Layer thickness before entrainment [H ~&gt; m or kg m-2]. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">h_new</parametername>
</parameternamelist>
<parameterdescription>
<para>Layer thickness after entrainment [H ~&gt; m or kg m-2]. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">ea</parametername>
</parameternamelist>
<parameterdescription>
<para>an array to which the amount of fluid entrained </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">eb</parametername>
</parameternamelist>
<parameterdescription>
<para>an array to which the amount of fluid entrained </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">fluxes</parametername>
</parameternamelist>
<parameterdescription>
<para>A structure containing pointers to thermodynamic and tracer forcing fields. Unused fields have NULL ptrs. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">dt</parametername>
</parameternamelist>
<parameterdescription>
<para>The amount of time covered by this call [T ~&gt; s] </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">us</parametername>
</parameternamelist>
<parameterdescription>
<para>A dimensional unit scaling type </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>cs</parametername>
</parameternamelist>
<parameterdescription>
<para>The control structure returned by a previous call to ISOMIP_register_tracer. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">evap_cfl_limit</parametername>
</parameternamelist>
<parameterdescription>
<para>Limit on the fraction of the water that can be fluxed out of the top layer in a timestep [nondim] </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">minimum_forcing_depth</parametername>
</parameternamelist>
<parameterdescription>
<para>The smallest depth over which fluxes can be applied [H ~&gt; m or kg m-2] </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" line="248" column="1" bodyfile="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" bodystart="250" bodyend="322"/>
        <references refid="namespacemom__tracer__diabatic_1ad4d3d4de0f2b84c15bccc5eb2f767df3" compoundref="MOM__tracer__diabatic_8F90" startline="230" endline="443">mom_tracer_diabatic::applytracerboundaryfluxesinout</references>
        <references refid="namespaceisomip__tracer_1a45a3a4465d55afd6310d5a3412b2c9c5" compoundref="ISOMIP__tracer_8F90" startline="42" endline="42">ntr</references>
        <references refid="namespacemom__tracer__diabatic_1ac5d57973547cc4ed3a89808d3910943e" compoundref="MOM__tracer__diabatic_8F90" startline="27" endline="222">mom_tracer_diabatic::tracer_vertdiff</references>
      </memberdef>
      <memberdef kind="function" id="namespaceisomip__tracer_1ac2571b7b6e4dce0d5936a483159ec379" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>subroutine, public</type>
        <definition>subroutine, public isomip_tracer::isomip_tracer_surface_state</definition>
        <argsstring>(sfc_state, h, G, CS)</argsstring>
        <name>isomip_tracer_surface_state</name>
        <param>
          <type>sfc_state</type>
          <defname>sfc_state</defname>
        </param>
        <param>
          <type>h</type>
          <defname>h</defname>
        </param>
        <param>
          <type>G</type>
          <defname>G</defname>
        </param>
        <param>
          <type>CS</type>
          <defname>CS</defname>
        </param>
        <briefdescription>
<para>This subroutine extracts the surface fields from this tracer package that are to be shared with the atmosphere in coupled configurations. This particular tracer package does not report anything back to the coupler. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername direction="in">g</parametername>
</parameternamelist>
<parameterdescription>
<para>The ocean&apos;s grid structure. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="inout">sfc_state</parametername>
</parameternamelist>
<parameterdescription>
<para>A structure containing fields that describe the surface state of the ocean. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">h</parametername>
</parameternamelist>
<parameterdescription>
<para>Layer thickness [H ~&gt; m or kg m-2]. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>cs</parametername>
</parameternamelist>
<parameterdescription>
<para>The control structure returned by a previous call to ISOMIP_register_tracer. </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" line="328" column="1" bodyfile="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" bodystart="329" bodyend="355"/>
        <references refid="namespaceisomip__tracer_1a45a3a4465d55afd6310d5a3412b2c9c5" compoundref="ISOMIP__tracer_8F90" startline="42" endline="42">ntr</references>
      </memberdef>
      <memberdef kind="function" id="namespaceisomip__tracer_1a104a1c0d2098aa48a52684bd1509bbc4" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>subroutine, public</type>
        <definition>subroutine, public isomip_tracer::isomip_tracer_end</definition>
        <argsstring>(CS)</argsstring>
        <name>isomip_tracer_end</name>
        <param>
          <type>CS</type>
          <defname>CS</defname>
        </param>
        <briefdescription>
<para>Deallocate any memory used by the ISOMIP tracer package. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>cs</parametername>
</parameternamelist>
<parameterdescription>
<para>The control structure returned by a previous call to ISOMIP_register_tracer. </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" line="359" column="1" bodyfile="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" bodystart="360" bodyend="367"/>
      </memberdef>
      </sectiondef>
    <briefdescription>
<para>Routines used to set up and use a set of (one for now) dynamically passive tracers in the ISOMIP configuration. </para>
    </briefdescription>
    <detaileddescription>
<para>For now, just one passive tracer is injected in the sponge layer. </para>
    </detaileddescription>
    <location file="/home/cermak/src/MOM6.devrob/src/tracer/ISOMIP_tracer.F90" line="6" column="1"/>
  </compounddef>
</doxygen>
