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Refactor model internals to remove OS and add Steppers
The approach used before was never successful because binding time of the coefficient mapper was to slow compared to a fully coupled solution. This means that an OS approach would have to be reworked from the PDELab assembler directly. This commit removes that and adds support for the new model stepper: * Remove coefficient mapper and its use on local operators * Remove the operator map of objects within the model class * Move read/write responsibility to model state * Allow states to be independent of models. Thus, allowing several different states coexist for a given model. * Multiple domain model now needs only one file path and each sub-domain file name is deduced from the state. * Writer might write on different files on request * Clean up logger output * Update meaningful logging values on the ini file * Improved errors when a config file is incorrect * Default executable now use simple adaptive steppers * Stepper now can use all PDELab RK methods
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- dune/copasi/common/coefficient_mapper.hh 0 additions, 368 deletionsdune/copasi/common/coefficient_mapper.hh
- dune/copasi/common/enum.hh 9 additions, 8 deletionsdune/copasi/common/enum.hh
- dune/copasi/common/stepper.hh 87 additions, 24 deletionsdune/copasi/common/stepper.hh
- dune/copasi/grid/multidomain_gmsh_reader.hh 19 additions, 14 deletionsdune/copasi/grid/multidomain_gmsh_reader.hh
- dune/copasi/local_operator/diffusion_reaction/base.hh 10 additions, 78 deletionsdune/copasi/local_operator/diffusion_reaction/base.hh
- dune/copasi/local_operator/diffusion_reaction/continuous_galerkin.hh 34 additions, 57 deletions.../local_operator/diffusion_reaction/continuous_galerkin.hh
- dune/copasi/local_operator/diffusion_reaction/finite_volume.hh 35 additions, 61 deletions...copasi/local_operator/diffusion_reaction/finite_volume.hh
- dune/copasi/local_operator/diffusion_reaction/multidomain.hh 53 additions, 113 deletionsdune/copasi/local_operator/diffusion_reaction/multidomain.hh
- dune/copasi/local_operator/variadic.hh 1 addition, 33 deletionsdune/copasi/local_operator/variadic.hh
- dune/copasi/model/base.cc 3 additions, 62 deletionsdune/copasi/model/base.cc
- dune/copasi/model/base.hh 1 addition, 51 deletionsdune/copasi/model/base.hh
- dune/copasi/model/diffusion_reaction.cc 193 additions, 385 deletionsdune/copasi/model/diffusion_reaction.cc
- dune/copasi/model/diffusion_reaction.hh 101 additions, 109 deletionsdune/copasi/model/diffusion_reaction.hh
- dune/copasi/model/multidomain_diffusion_reaction.cc 186 additions, 384 deletionsdune/copasi/model/multidomain_diffusion_reaction.cc
- dune/copasi/model/multidomain_diffusion_reaction.hh 84 additions, 101 deletionsdune/copasi/model/multidomain_diffusion_reaction.hh
- dune/copasi/model/state.hh 8 additions, 2 deletionsdune/copasi/model/state.hh
- src/dune_copasi_md.cc 71 additions, 36 deletionssrc/dune_copasi_md.cc
- src/dune_copasi_sd.cc 74 additions, 38 deletionssrc/dune_copasi_sd.cc
- test/NFKappaB.mini 55 additions, 67 deletionstest/NFKappaB.mini
- test/dune_copasi_md_compare.cc 153 additions, 124 deletionstest/dune_copasi_md_compare.cc
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