IM6 (PFLOTRAN alquimia coupling) - #5
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bsulman
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Jun 5, 2024
bsulman
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Jun 7, 2024
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| <entry id="ELM_USE_PFLOTRAN"> | ||
| <type>logical</type> | ||
| <valid_values>TRUE,FALSE</valid_values> | ||
| <default_value>FALSE</default_value> | ||
| <group>build_component_clm</group> | ||
| <file>env_build.xml</file> | ||
| <desc>TRUE implies ELM is built with support for coupling to PFLOTRAN | ||
| through the PFLOTRAN interface. PFLOTRAN | ||
| uses the PETSc library. In order to use PFLOTRAN, CLM | ||
| must be built with PETSc support and linking to PETSc must occur | ||
| when building the ACME executable. This occurs if this variable | ||
| is set to TRUE. Note that is only available on a limited set of | ||
| machines/compilers.</desc> | ||
| </entry> |
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I'm not sure this is used for Alquimia...
bsulman
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Jul 11, 2024
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I get a message Deprecated "arg" node detected in /home/b0u/cases/Alaska_alquimia_test_AK-BEO_ICB1850CNRDCTCBC/env_batch.xml, check files /home/b0u/models/E3SM-NGEE/cime_config/machines/config_batch.xml when doing create_newcase on cades. Has the format of this xml changed?
Update cmake on cades
bsulman
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Oct 7, 2024
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| if(actual_dt<=60.0_r8) then | ||
| ! write(iulog,*),'Alquimia: Time step cut to 60 s. Attempting to solve by pausing transport and solving layer by layer' | ||
| do j=1,nlevdecomp | ||
| ! Update properties from ELM | ||
| this%chem_state%porosity = porosity(j) | ||
| this%chem_state%temperature = temperature(j) - 273.15 | ||
| this%chem_properties%volume = volume(j) | ||
| this%chem_properties%saturation = sat(j) ! Set minimum saturation to stop concentrations from blowing up at low soil moisture | ||
| call this%copy_ELM_to_Alquimia(j,water_density,& | ||
| aqueous_pressure,& | ||
| total_mobile,& | ||
| total_immobile,& | ||
| mineral_volume_fraction,& | ||
| mineral_specific_surface_area,& | ||
| surface_site_density,& | ||
| cation_exchange_capacity,& | ||
| aux_doubles,& | ||
| aux_ints) | ||
| call run_onestep(this,dt,num_cuts,ncuts) | ||
| call this%copy_Alquimia_to_ELM(j,water_density_tmp,& | ||
| aqueous_pressure_tmp,& | ||
| total_mobile_tmp,free_mobile_tmp,& | ||
| total_immobile_tmp,& | ||
| mineral_volume_fraction_tmp,& | ||
| mineral_specific_surface_area_tmp,& | ||
| surface_site_density_tmp,& | ||
| cation_exchange_capacity_tmp,& | ||
| aux_doubles_tmp,& | ||
| aux_ints_tmp) | ||
| enddo | ||
| endif |
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I think we should remove this block (the if actual_dt<60). I'm not sure it's in the right place and it's usually not necessary
fmyuan
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Apr 2, 2025
* Add vertical soil water movement to column water variables and output * Set deeper layers to 0 instead of nan and include infiltration in layer 0
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Code and configuration changes to enable coupling of E3SM to PFLOTRAN via the alquimia interface and EMI