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Generalised surface fitting#122

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tawhai merged 28 commits intoLungNoodle:developLungNoodle/lungsim:developfrom tawhai:generalised_surface_fittingtawhai/lungsim:generalised_surface_fittingCopy head branch name to clipboardSep 1, 2022

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Commits on May 11, 2021

• reducing the dimension of 'arclength' array and removing 'parentlist' from the global parameters. 'calc_scale_factors_2d' rewritten to be more specific to the surface meshes used in the code, along…

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• new subroutine 'import_node_geometry_2d' and its bindings

  

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Commits on May 12, 2021

• surface fitting including python bindings. Includes subroutines to adjust the location of specified nodes so that they remain on the fitted surface but are spread evenly between user-specified nodes

  

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Commits on Jun 21, 2021

• subroutines to refine 1d tree, and reorder a refined tree to be sequentially numbered

  

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Commits on Jul 16, 2021

• bindings for specifying file, branch type, and refinement for add_mesh'

  

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• removed write statement in add_mesh

  

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Commits on Jul 18, 2021

• starting to move ventilation parameters out of files

  

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• setting up default parameters for ventilation model

  

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• removing the chest wall compliance from tissue compliance calculation

  

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• writing ventilation output to file

  

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Commits on Jul 20, 2021

• muscle pressure functions for passive expiration

  

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Commits on Aug 19, 2021

• in refine_1d_elements, included call to renumber_tree_in_order so that this is done automatically. we always need an ordered tree

  

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• bindings for initial_gasexchange and steadystate_gasexchange, and replaced dabs with abs in gas_exchange.f90

  

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Commits on Aug 22, 2021

• bindings and updates to make gas transfer work

  

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Commits on Sep 2, 2021

• export option for 2d cubic hermite mesh; change in method for setting up lines on a 2d mesh

  

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Commits on Aug 14, 2022

• Merge branch 'develop' into unit_ventilation

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• Merge pull request LungNoodle#127 from tawhai/unit_ventilation

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Commits on Aug 15, 2022

• Merge branch 'develop' into generalised_surface_fitting

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Commits on Aug 18, 2022

• removing WIN32 from bindings

  

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• removed changes to gas_exchange.* in bindings. removed all changes to gas_exchange in lib

  

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• removed changes to add_mesh from bindings and lib

  

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• removed refine_1d_elements and renumber_tree_in_order from bindings and lib

  

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Commits on Aug 19, 2022

• removing default arrays for defining parameters from arrays.f90 and update parameters from bindings and lib

  

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• removed DEC$ ATTRIBUTES from export_cubic_lagrange_2d

  

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• removed all changes in ventilation.f90 and bindings. removed initialise_lung_volume from geometry.f90 and bindings, and added set_initial_volume back in

  

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• removing changes to capillaryflow, wave_transmission, pressure_resistance_flow

  

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• removing DEC$ ATTRIBUTEs from surface_fitting

  

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Commits on Aug 24, 2022

• fix to line_segments_for_2d_mesh to use local node index referencing in line_versn_2d not global nodes. seg fault found as part of code review by HK. error picked up using pedantic build

  

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