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Geochemistry: add NearestNodeNumber postprocessor #15749

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WilkAndy opened this issue Aug 11, 2020 · 1 comment
Closed

Geochemistry: add NearestNodeNumber postprocessor #15749

WilkAndy opened this issue Aug 11, 2020 · 1 comment
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C: Modules P: normal A defect affecting operation with a low possibility of significantly affects. T: task An enhancement to the software.

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@WilkAndy
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WilkAndy commented Aug 11, 2020

Reason

Given a point, this postprocessor returns the ID of the nearest node to the point. This can be used by the GeochemistryConsoleOutput object. Currently GeochemistryConsoleOutput accepts a point input, but i think it's better if it accepts a NearestNodeNumber postprocessor input that will give it the node number to output info from. Then the GeochemistryConsoleOutput can more easily query the Reactor classes for the desired output

Design

Create NearestNodeNumber. Ensure it works for multiple procs and threads and adaptivity

Impact

Cleaner interface in GeochemistryConsoleOutput and hence all the Reactor classes

@WilkAndy WilkAndy added P: normal A defect affecting operation with a low possibility of significantly affects. T: task An enhancement to the software. labels Aug 11, 2020
WilkAndy added a commit to WilkAndy/moose that referenced this issue Aug 11, 2020
WilkAndy added a commit to WilkAndy/moose that referenced this issue Oct 9, 2020
WilkAndy added a commit to WilkAndy/moose that referenced this issue Nov 6, 2020
WilkAndy added a commit to WilkAndy/moose that referenced this issue Nov 6, 2020
…, the newest message is down the bottom.

ModelGeochemicalDatabase records swap matrix in order to translate bulk compositions back to original basis.  This swap matrix is updated every time a swap is performed by the GeochemistrySpeciesSwapper.  GeochemicalSystem has a method for getting the bulk in the original basis.

ModelGeochemicalDatabase has boolean vectors (basis_species_transported, eqm_species_transported and kin_species_transported) that define whether the species is involved in the transport side of reactive-transport.  GeochemistrySpeciesSwapper swaps these appropriate upon swapping

GeochemicalSystem has methods for computing the bulk-composition mole number of transporting species, both in the current basis and the original basis, based on the current values of molalities

Refs idaholab#15693

GeochemicalSolver now does not get instantiated with a GeochemicalSystem or a ModelGeochemicalDatabase.  Instead all of its methods have the GeochemicalSystem as an argument.  This is so a spatially-varying simulation can have just one GeochemicalSolver that solves the systems at all nodes.  Refs idaholab#15693

PertinentGeochemicalSystem now offers the method getIndexOfOriginalBasisSpecies that will be used when retrieving certain information expressed in the original basis

GeochemicalSystem now has a copy-assignment operator that is used in the threadJoin of the Reactors

GeochemicalModelDefinition now provides a const reference to the underlying PertinentGeochemicalSystem.  This is used in the GeochemistryAux to get various things about the original basis species

GeochemicalSystem.h GeochemistryActivityCoefficients.h GeochemistryActivityCoefficientsDebyeHuckel.h GeochemistryIonicStrength.h GeochemistryKineticRateCalculator.h GeochemistrySpeciesSwapper.h PertinentGeochemicalSystem.h now have comparitors in them for testing equality

NearestNodeNumber postprocessor added.  Refs idaholab#15749

NearestNodeNumber postprocessor and userobject added.  Refs  idaholab#15749

asdf

GeochemistryConsoleOutput now uses the NearestNodeNumber UserObject instead of a point

tests updated to reflect that GeochemistryConsoleOutput now uses NearestNodeNumber UserObject

doc updated regarding GeochemistryConsoleOutput using NearestNodeNumber UserObject

Actions and Reactor UserObjects now do not have getters regarding the point used for output purposes - only the node id is now used.  Also, some enhancements getting ready for spatial dependence

GeochemistyQuantityAux can now extract transported_moles_in_original_basis - useful for reactive transport

spatially-dependent Reactor classes added.  Refs idaholab#15693

doco added for spatial dependent sims.  Fixes idaholab#15693

overall kinetic mole_additions now allowed in GeochemicalSolver::solveSystem.  This is because these species may be transported in reactive transport and should not be added as basis species, but as kinetic species

mole_additions input to the solver can now include additions of kinetic species so that an external agent can pump kinetic species into the system.

transported mole numbers do not include kinetic species - including them was a mistake because that would mean transport short-circuits any kinetic rates, oh dear.  transporting kinetic species is easy now - just evaluate the kinetic moles and transport them

reorder temperature-setting before flushing in GeochemistryTimeDependentReactor.  This makes it easier to flush with different-temperature fluids.  Also, changes in kinetic-nonminerals in flush.  I think the previous implementation was incorrect, but the Bethke book doesn't actually specify what's supposed to happen for flushing kinetic-nonminerals.  This current implementation makes more sense to me than the previous one

2D GeoTES example added

heat-exchanger mode added to GeochemistryTimeDependentReactor, as well as some refactoring of its code.  Fixes idaholab#15768

Actions now have inputs that allow the UserObjects to be block or boundary restrictable.  Fixes idaholab#15769

Actions also have a flag that allows a usual moose solve involving Variables and Kernels to proceed.  It defaults to False.  Fixes idaholab#15770

PorousFlow DiracKernels now have a coupledVar that multiplies their fluxes.  Fixes idaholab#15771

PertinentGeochemicalSystem has a method originalBasisNames so that GeochemistryConsoleOutput can output the bulk composition in the original basis, which i feel might be useful.

Also:

RobPod weber-tensleep geotes example

moved geotes_2D example to combined and golded some tests

computational_efficiencies.md started

Start of Forge simulation

GeochemistrySpatialReactor bug with intel compilers fixed - cannot use size of map while inserting into map

forge equilibrium system

ability to use all relevant minerals in geochemical models.  Refs idaholab#15798

kinetic.i changed

forge water chemistry by Stuart suggestions

forge input files and doco

better mesh creation in weber_Tensleep example

forge porous_flow input file test and doco and pics

forge aquifer geochemistry input file and tests

compute efficiencies completed

Ability for GeochemistrySpatialReactor to adaptively change the timestep node-by-node in the case of solver failures.  Refs idaholab#15816

remarks on compute efficiencies of fieldsplit method

Reorganize the initialization list in GeochemistrySpatialReactor so that the swaps are implemented in the correct order, ooops

Slightly modify the input Quartz mole number in weber-tensleep so that the porosity is 0.1 not 0.099947
3D pics added to weber-tensleep example

utilize NodalVoidVolume UserObject in examples, now that it is merged.

trying to eliminate CIVET errors
WilkAndy added a commit to WilkAndy/moose that referenced this issue Nov 6, 2020
…, the newest message is down the bottom.

ModelGeochemicalDatabase records swap matrix in order to translate bulk compositions back to original basis.  This swap matrix is updated every time a swap is performed by the GeochemistrySpeciesSwapper.  GeochemicalSystem has a method for getting the bulk in the original basis.

ModelGeochemicalDatabase has boolean vectors (basis_species_transported, eqm_species_transported and kin_species_transported) that define whether the species is involved in the transport side of reactive-transport.  GeochemistrySpeciesSwapper swaps these appropriate upon swapping

GeochemicalSystem has methods for computing the bulk-composition mole number of transporting species, both in the current basis and the original basis, based on the current values of molalities

Refs idaholab#15693

GeochemicalSolver now does not get instantiated with a GeochemicalSystem or a ModelGeochemicalDatabase.  Instead all of its methods have the GeochemicalSystem as an argument.  This is so a spatially-varying simulation can have just one GeochemicalSolver that solves the systems at all nodes.  Refs idaholab#15693

PertinentGeochemicalSystem now offers the method getIndexOfOriginalBasisSpecies that will be used when retrieving certain information expressed in the original basis

GeochemicalSystem now has a copy-assignment operator that is used in the threadJoin of the Reactors

GeochemicalModelDefinition now provides a const reference to the underlying PertinentGeochemicalSystem.  This is used in the GeochemistryAux to get various things about the original basis species

GeochemicalSystem.h GeochemistryActivityCoefficients.h GeochemistryActivityCoefficientsDebyeHuckel.h GeochemistryIonicStrength.h GeochemistryKineticRateCalculator.h GeochemistrySpeciesSwapper.h PertinentGeochemicalSystem.h now have comparitors in them for testing equality

NearestNodeNumber postprocessor added.  Refs idaholab#15749

NearestNodeNumber postprocessor and userobject added.  Refs  idaholab#15749

asdf

GeochemistryConsoleOutput now uses the NearestNodeNumber UserObject instead of a point

tests updated to reflect that GeochemistryConsoleOutput now uses NearestNodeNumber UserObject

doc updated regarding GeochemistryConsoleOutput using NearestNodeNumber UserObject

Actions and Reactor UserObjects now do not have getters regarding the point used for output purposes - only the node id is now used.  Also, some enhancements getting ready for spatial dependence

GeochemistyQuantityAux can now extract transported_moles_in_original_basis - useful for reactive transport

spatially-dependent Reactor classes added.  Refs idaholab#15693

doco added for spatial dependent sims.  Fixes idaholab#15693

overall kinetic mole_additions now allowed in GeochemicalSolver::solveSystem.  This is because these species may be transported in reactive transport and should not be added as basis species, but as kinetic species

mole_additions input to the solver can now include additions of kinetic species so that an external agent can pump kinetic species into the system.

transported mole numbers do not include kinetic species - including them was a mistake because that would mean transport short-circuits any kinetic rates, oh dear.  transporting kinetic species is easy now - just evaluate the kinetic moles and transport them

reorder temperature-setting before flushing in GeochemistryTimeDependentReactor.  This makes it easier to flush with different-temperature fluids.  Also, changes in kinetic-nonminerals in flush.  I think the previous implementation was incorrect, but the Bethke book doesn't actually specify what's supposed to happen for flushing kinetic-nonminerals.  This current implementation makes more sense to me than the previous one

2D GeoTES example added

heat-exchanger mode added to GeochemistryTimeDependentReactor, as well as some refactoring of its code.  Fixes idaholab#15768

Actions now have inputs that allow the UserObjects to be block or boundary restrictable.  Fixes idaholab#15769

Actions also have a flag that allows a usual moose solve involving Variables and Kernels to proceed.  It defaults to False.  Fixes idaholab#15770

PorousFlow DiracKernels now have a coupledVar that multiplies their fluxes.  Fixes idaholab#15771

PertinentGeochemicalSystem has a method originalBasisNames so that GeochemistryConsoleOutput can output the bulk composition in the original basis, which i feel might be useful.

Also:

RobPod weber-tensleep geotes example

moved geotes_2D example to combined and golded some tests

computational_efficiencies.md started

Start of Forge simulation

GeochemistrySpatialReactor bug with intel compilers fixed - cannot use size of map while inserting into map

forge equilibrium system

ability to use all relevant minerals in geochemical models.  Refs idaholab#15798

kinetic.i changed

forge water chemistry by Stuart suggestions

forge input files and doco

better mesh creation in weber_Tensleep example

forge porous_flow input file test and doco and pics

forge aquifer geochemistry input file and tests

compute efficiencies completed

Ability for GeochemistrySpatialReactor to adaptively change the timestep node-by-node in the case of solver failures.  Refs idaholab#15816

remarks on compute efficiencies of fieldsplit method

Reorganize the initialization list in GeochemistrySpatialReactor so that the swaps are implemented in the correct order, ooops

Slightly modify the input Quartz mole number in weber-tensleep so that the porosity is 0.1 not 0.099947
3D pics added to weber-tensleep example

utilize NodalVoidVolume UserObject in examples, now that it is merged.

trying to eliminate CIVET errors

removed png files
loganharbour pushed a commit to loganharbour/moose that referenced this issue Nov 10, 2020
…, the newest message is down the bottom.

ModelGeochemicalDatabase records swap matrix in order to translate bulk compositions back to original basis.  This swap matrix is updated every time a swap is performed by the GeochemistrySpeciesSwapper.  GeochemicalSystem has a method for getting the bulk in the original basis.

ModelGeochemicalDatabase has boolean vectors (basis_species_transported, eqm_species_transported and kin_species_transported) that define whether the species is involved in the transport side of reactive-transport.  GeochemistrySpeciesSwapper swaps these appropriate upon swapping

GeochemicalSystem has methods for computing the bulk-composition mole number of transporting species, both in the current basis and the original basis, based on the current values of molalities

Refs idaholab#15693

GeochemicalSolver now does not get instantiated with a GeochemicalSystem or a ModelGeochemicalDatabase.  Instead all of its methods have the GeochemicalSystem as an argument.  This is so a spatially-varying simulation can have just one GeochemicalSolver that solves the systems at all nodes.  Refs idaholab#15693

PertinentGeochemicalSystem now offers the method getIndexOfOriginalBasisSpecies that will be used when retrieving certain information expressed in the original basis

GeochemicalSystem now has a copy-assignment operator that is used in the threadJoin of the Reactors

GeochemicalModelDefinition now provides a const reference to the underlying PertinentGeochemicalSystem.  This is used in the GeochemistryAux to get various things about the original basis species

GeochemicalSystem.h GeochemistryActivityCoefficients.h GeochemistryActivityCoefficientsDebyeHuckel.h GeochemistryIonicStrength.h GeochemistryKineticRateCalculator.h GeochemistrySpeciesSwapper.h PertinentGeochemicalSystem.h now have comparitors in them for testing equality

NearestNodeNumber postprocessor added.  Refs idaholab#15749

NearestNodeNumber postprocessor and userobject added.  Refs  idaholab#15749

asdf

GeochemistryConsoleOutput now uses the NearestNodeNumber UserObject instead of a point

tests updated to reflect that GeochemistryConsoleOutput now uses NearestNodeNumber UserObject

doc updated regarding GeochemistryConsoleOutput using NearestNodeNumber UserObject

Actions and Reactor UserObjects now do not have getters regarding the point used for output purposes - only the node id is now used.  Also, some enhancements getting ready for spatial dependence

GeochemistyQuantityAux can now extract transported_moles_in_original_basis - useful for reactive transport

spatially-dependent Reactor classes added.  Refs idaholab#15693

doco added for spatial dependent sims.  Fixes idaholab#15693

overall kinetic mole_additions now allowed in GeochemicalSolver::solveSystem.  This is because these species may be transported in reactive transport and should not be added as basis species, but as kinetic species

mole_additions input to the solver can now include additions of kinetic species so that an external agent can pump kinetic species into the system.

transported mole numbers do not include kinetic species - including them was a mistake because that would mean transport short-circuits any kinetic rates, oh dear.  transporting kinetic species is easy now - just evaluate the kinetic moles and transport them

reorder temperature-setting before flushing in GeochemistryTimeDependentReactor.  This makes it easier to flush with different-temperature fluids.  Also, changes in kinetic-nonminerals in flush.  I think the previous implementation was incorrect, but the Bethke book doesn't actually specify what's supposed to happen for flushing kinetic-nonminerals.  This current implementation makes more sense to me than the previous one

2D GeoTES example added

heat-exchanger mode added to GeochemistryTimeDependentReactor, as well as some refactoring of its code.  Fixes idaholab#15768

Actions now have inputs that allow the UserObjects to be block or boundary restrictable.  Fixes idaholab#15769

Actions also have a flag that allows a usual moose solve involving Variables and Kernels to proceed.  It defaults to False.  Fixes idaholab#15770

PorousFlow DiracKernels now have a coupledVar that multiplies their fluxes.  Fixes idaholab#15771

PertinentGeochemicalSystem has a method originalBasisNames so that GeochemistryConsoleOutput can output the bulk composition in the original basis, which i feel might be useful.

Also:

RobPod weber-tensleep geotes example

moved geotes_2D example to combined and golded some tests

computational_efficiencies.md started

Start of Forge simulation

GeochemistrySpatialReactor bug with intel compilers fixed - cannot use size of map while inserting into map

forge equilibrium system

ability to use all relevant minerals in geochemical models.  Refs idaholab#15798

kinetic.i changed

forge water chemistry by Stuart suggestions

forge input files and doco

better mesh creation in weber_Tensleep example

forge porous_flow input file test and doco and pics

forge aquifer geochemistry input file and tests

compute efficiencies completed

Ability for GeochemistrySpatialReactor to adaptively change the timestep node-by-node in the case of solver failures.  Refs idaholab#15816

remarks on compute efficiencies of fieldsplit method

Reorganize the initialization list in GeochemistrySpatialReactor so that the swaps are implemented in the correct order, ooops

Slightly modify the input Quartz mole number in weber-tensleep so that the porosity is 0.1 not 0.099947
3D pics added to weber-tensleep example

utilize NodalVoidVolume UserObject in examples, now that it is merged.

trying to eliminate CIVET errors

removed png files
loganharbour pushed a commit to loganharbour/moose that referenced this issue Nov 10, 2020
…, the newest message is down the bottom.

ModelGeochemicalDatabase records swap matrix in order to translate bulk compositions back to original basis.  This swap matrix is updated every time a swap is performed by the GeochemistrySpeciesSwapper.  GeochemicalSystem has a method for getting the bulk in the original basis.

ModelGeochemicalDatabase has boolean vectors (basis_species_transported, eqm_species_transported and kin_species_transported) that define whether the species is involved in the transport side of reactive-transport.  GeochemistrySpeciesSwapper swaps these appropriate upon swapping

GeochemicalSystem has methods for computing the bulk-composition mole number of transporting species, both in the current basis and the original basis, based on the current values of molalities

Refs idaholab#15693

GeochemicalSolver now does not get instantiated with a GeochemicalSystem or a ModelGeochemicalDatabase.  Instead all of its methods have the GeochemicalSystem as an argument.  This is so a spatially-varying simulation can have just one GeochemicalSolver that solves the systems at all nodes.  Refs idaholab#15693

PertinentGeochemicalSystem now offers the method getIndexOfOriginalBasisSpecies that will be used when retrieving certain information expressed in the original basis

GeochemicalSystem now has a copy-assignment operator that is used in the threadJoin of the Reactors

GeochemicalModelDefinition now provides a const reference to the underlying PertinentGeochemicalSystem.  This is used in the GeochemistryAux to get various things about the original basis species

GeochemicalSystem.h GeochemistryActivityCoefficients.h GeochemistryActivityCoefficientsDebyeHuckel.h GeochemistryIonicStrength.h GeochemistryKineticRateCalculator.h GeochemistrySpeciesSwapper.h PertinentGeochemicalSystem.h now have comparitors in them for testing equality

NearestNodeNumber postprocessor added.  Refs idaholab#15749

NearestNodeNumber postprocessor and userobject added.  Refs  idaholab#15749

asdf

GeochemistryConsoleOutput now uses the NearestNodeNumber UserObject instead of a point

tests updated to reflect that GeochemistryConsoleOutput now uses NearestNodeNumber UserObject

doc updated regarding GeochemistryConsoleOutput using NearestNodeNumber UserObject

Actions and Reactor UserObjects now do not have getters regarding the point used for output purposes - only the node id is now used.  Also, some enhancements getting ready for spatial dependence

GeochemistyQuantityAux can now extract transported_moles_in_original_basis - useful for reactive transport

spatially-dependent Reactor classes added.  Refs idaholab#15693

doco added for spatial dependent sims.  Fixes idaholab#15693

overall kinetic mole_additions now allowed in GeochemicalSolver::solveSystem.  This is because these species may be transported in reactive transport and should not be added as basis species, but as kinetic species

mole_additions input to the solver can now include additions of kinetic species so that an external agent can pump kinetic species into the system.

transported mole numbers do not include kinetic species - including them was a mistake because that would mean transport short-circuits any kinetic rates, oh dear.  transporting kinetic species is easy now - just evaluate the kinetic moles and transport them

reorder temperature-setting before flushing in GeochemistryTimeDependentReactor.  This makes it easier to flush with different-temperature fluids.  Also, changes in kinetic-nonminerals in flush.  I think the previous implementation was incorrect, but the Bethke book doesn't actually specify what's supposed to happen for flushing kinetic-nonminerals.  This current implementation makes more sense to me than the previous one

2D GeoTES example added

heat-exchanger mode added to GeochemistryTimeDependentReactor, as well as some refactoring of its code.  Fixes idaholab#15768

Actions now have inputs that allow the UserObjects to be block or boundary restrictable.  Fixes idaholab#15769

Actions also have a flag that allows a usual moose solve involving Variables and Kernels to proceed.  It defaults to False.  Fixes idaholab#15770

PorousFlow DiracKernels now have a coupledVar that multiplies their fluxes.  Fixes idaholab#15771

PertinentGeochemicalSystem has a method originalBasisNames so that GeochemistryConsoleOutput can output the bulk composition in the original basis, which i feel might be useful.

Also:

RobPod weber-tensleep geotes example

moved geotes_2D example to combined and golded some tests

computational_efficiencies.md started

Start of Forge simulation

GeochemistrySpatialReactor bug with intel compilers fixed - cannot use size of map while inserting into map

forge equilibrium system

ability to use all relevant minerals in geochemical models.  Refs idaholab#15798

kinetic.i changed

forge water chemistry by Stuart suggestions

forge input files and doco

better mesh creation in weber_Tensleep example

forge porous_flow input file test and doco and pics

forge aquifer geochemistry input file and tests

compute efficiencies completed

Ability for GeochemistrySpatialReactor to adaptively change the timestep node-by-node in the case of solver failures.  Refs idaholab#15816

remarks on compute efficiencies of fieldsplit method

Reorganize the initialization list in GeochemistrySpatialReactor so that the swaps are implemented in the correct order, ooops

Slightly modify the input Quartz mole number in weber-tensleep so that the porosity is 0.1 not 0.099947
3D pics added to weber-tensleep example

utilize NodalVoidVolume UserObject in examples, now that it is merged.

trying to eliminate CIVET errors

removed png files
@WilkAndy
Copy link
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Done by the above commits

jain651 pushed a commit to jain651/moose that referenced this issue Apr 19, 2021
…, the newest message is down the bottom.

ModelGeochemicalDatabase records swap matrix in order to translate bulk compositions back to original basis.  This swap matrix is updated every time a swap is performed by the GeochemistrySpeciesSwapper.  GeochemicalSystem has a method for getting the bulk in the original basis.

ModelGeochemicalDatabase has boolean vectors (basis_species_transported, eqm_species_transported and kin_species_transported) that define whether the species is involved in the transport side of reactive-transport.  GeochemistrySpeciesSwapper swaps these appropriate upon swapping

GeochemicalSystem has methods for computing the bulk-composition mole number of transporting species, both in the current basis and the original basis, based on the current values of molalities

Refs idaholab#15693

GeochemicalSolver now does not get instantiated with a GeochemicalSystem or a ModelGeochemicalDatabase.  Instead all of its methods have the GeochemicalSystem as an argument.  This is so a spatially-varying simulation can have just one GeochemicalSolver that solves the systems at all nodes.  Refs idaholab#15693

PertinentGeochemicalSystem now offers the method getIndexOfOriginalBasisSpecies that will be used when retrieving certain information expressed in the original basis

GeochemicalSystem now has a copy-assignment operator that is used in the threadJoin of the Reactors

GeochemicalModelDefinition now provides a const reference to the underlying PertinentGeochemicalSystem.  This is used in the GeochemistryAux to get various things about the original basis species

GeochemicalSystem.h GeochemistryActivityCoefficients.h GeochemistryActivityCoefficientsDebyeHuckel.h GeochemistryIonicStrength.h GeochemistryKineticRateCalculator.h GeochemistrySpeciesSwapper.h PertinentGeochemicalSystem.h now have comparitors in them for testing equality

NearestNodeNumber postprocessor added.  Refs idaholab#15749

NearestNodeNumber postprocessor and userobject added.  Refs  idaholab#15749

asdf

GeochemistryConsoleOutput now uses the NearestNodeNumber UserObject instead of a point

tests updated to reflect that GeochemistryConsoleOutput now uses NearestNodeNumber UserObject

doc updated regarding GeochemistryConsoleOutput using NearestNodeNumber UserObject

Actions and Reactor UserObjects now do not have getters regarding the point used for output purposes - only the node id is now used.  Also, some enhancements getting ready for spatial dependence

GeochemistyQuantityAux can now extract transported_moles_in_original_basis - useful for reactive transport

spatially-dependent Reactor classes added.  Refs idaholab#15693

doco added for spatial dependent sims.  Fixes idaholab#15693

overall kinetic mole_additions now allowed in GeochemicalSolver::solveSystem.  This is because these species may be transported in reactive transport and should not be added as basis species, but as kinetic species

mole_additions input to the solver can now include additions of kinetic species so that an external agent can pump kinetic species into the system.

transported mole numbers do not include kinetic species - including them was a mistake because that would mean transport short-circuits any kinetic rates, oh dear.  transporting kinetic species is easy now - just evaluate the kinetic moles and transport them

reorder temperature-setting before flushing in GeochemistryTimeDependentReactor.  This makes it easier to flush with different-temperature fluids.  Also, changes in kinetic-nonminerals in flush.  I think the previous implementation was incorrect, but the Bethke book doesn't actually specify what's supposed to happen for flushing kinetic-nonminerals.  This current implementation makes more sense to me than the previous one

2D GeoTES example added

heat-exchanger mode added to GeochemistryTimeDependentReactor, as well as some refactoring of its code.  Fixes idaholab#15768

Actions now have inputs that allow the UserObjects to be block or boundary restrictable.  Fixes idaholab#15769

Actions also have a flag that allows a usual moose solve involving Variables and Kernels to proceed.  It defaults to False.  Fixes idaholab#15770

PorousFlow DiracKernels now have a coupledVar that multiplies their fluxes.  Fixes idaholab#15771

PertinentGeochemicalSystem has a method originalBasisNames so that GeochemistryConsoleOutput can output the bulk composition in the original basis, which i feel might be useful.

Also:

RobPod weber-tensleep geotes example

moved geotes_2D example to combined and golded some tests

computational_efficiencies.md started

Start of Forge simulation

GeochemistrySpatialReactor bug with intel compilers fixed - cannot use size of map while inserting into map

forge equilibrium system

ability to use all relevant minerals in geochemical models.  Refs idaholab#15798

kinetic.i changed

forge water chemistry by Stuart suggestions

forge input files and doco

better mesh creation in weber_Tensleep example

forge porous_flow input file test and doco and pics

forge aquifer geochemistry input file and tests

compute efficiencies completed

Ability for GeochemistrySpatialReactor to adaptively change the timestep node-by-node in the case of solver failures.  Refs idaholab#15816

remarks on compute efficiencies of fieldsplit method

Reorganize the initialization list in GeochemistrySpatialReactor so that the swaps are implemented in the correct order, ooops

Slightly modify the input Quartz mole number in weber-tensleep so that the porosity is 0.1 not 0.099947
3D pics added to weber-tensleep example

utilize NodalVoidVolume UserObject in examples, now that it is merged.

trying to eliminate CIVET errors

removed png files
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