Geometry module (geometry.f90)

Module geometry

Description

Brief Description: This module handles all geometry read/write/tree generation.

LICENSE:

Full Description:

This module handles all geometry read/write/generation.

Quick access

Routines:add_matching_mesh(), add_mesh(), allocate_node_arrays(), append_units(), coord_at_xi(), define_1d_elements(), define_data_geometry(), define_elem_geometry_2d(), define_mesh_geometry_test(), define_node_geometry(), define_node_geometry_2d(), define_rad_from_file(), define_rad_from_geom(), element_connectivity_1d(), element_connectivity_2d(), evaluate_ordering(), geo_entry_exit_cap(), geo_node_offset(), get_final_integer(), get_final_real(), get_final_string(), get_four_nodes(), get_local_elem(), get_local_elem_1d(), get_local_node(), get_local_node_f(), get_parent_branch(), group_elem_parent_term(), import_node_geometry_2d(), import_ply_triangles(), line_segments_for_2d_mesh(), make_2d_vessel_from_1d(), make_data_grid(), merge_2d_from_1d_mesh(), merge_trifurcations(), mesh_2d_from_1d_crux(), mesh_2d_from_1d_generic(), mesh_rotate_about_axis(), mesh_rotate_vector_about_axis(), reallocate_node_elem_arrays(), redistribute_mesh_nodes_2d_from_1d(), set_initial_volume(), triangles_from_surface(), volume_of_mesh(), where_inlist(), write_3d_geo(), write_elem_geometry_2d(), write_geo_file(), write_node_geometry_2d(), write_surface_geo()

Needed modules

  • arrays: Brief Description: This module defines arrays.
  • precision: Brief Description: Defines the precision of real parameters.
  • mesh_utilities
  • diagnostics
  • indices
  • other_consts

Variables

Subroutines and functions

subroutine geometry/allocate_node_arrays(num_nodes)

allocate_node_arrays: allocate memory for arrays associated with 1D trees

Parameters:num_nodes [integer,in]
Called from:define_node_geometry()
Call to:enter_exit()
subroutine geometry/add_mesh(airway_meshfile)
add_mesh: Reads in an ipmesh file and adds this mesh to the terminal
branches of an existing tree geometry
Parameters:airway_meshfile [character(len=max_filename_len),in]
Call to:enter_exit(), reallocate_node_elem_arrays(), element_connectivity_1d(), evaluate_ordering()
subroutine geometry/add_matching_mesh()

add_matching_mesh:

Call to:enter_exit(), reallocate_node_elem_arrays()
subroutine geometry/append_units()

append_units: Appends terminal units at the end of a tree structure

Called from:two_unit_test()
Call to:enter_exit()
subroutine geometry/define_1d_elements(elemfile)

define_1d_elements: Reads in an 1D element ipelem file to define a geometry

Parameters:elemfile [character(len=max_filename_len),in]
Call to:enter_exit(), get_final_integer(), get_local_node(), element_connectivity_1d(), evaluate_ordering()
subroutine geometry/define_elem_geometry_2d(elemfile, sf_option)

Reads in 2D ipelem file.

Parameters:
  • elemfile [character(len=*)]
  • sf_option [character(len=4)]
Call to:

enter_exit(), get_final_integer(), get_four_nodes(), element_connectivity_2d(), line_segments_for_2d_mesh()
subroutine geometry/define_mesh_geometry_test()

define_mesh_geometry_test:

Call to:enter_exit(), element_connectivity_1d(), evaluate_ordering()
subroutine geometry/define_node_geometry(nodefile)

define_node_geometry: Reads in an ipnode file to define a tree geometry

Parameters:nodefile [character(len=max_filename_len),in] :: Input nodefile
Call to:enter_exit(), get_final_integer(), allocate_node_arrays(), get_final_real()
subroutine geometry/define_node_geometry_2d(nodefile)

define_node_geometry_2d: Reads in an ipnode file to define surface nodes

Parameters:nodefile [character(len=*),in]
Call to:enter_exit(), get_final_integer(), get_final_real()
subroutine geometry/define_data_geometry(datafile)

define_data_geometry: reads data points from a file

Parameters:datafile [character(len=*)]
Call to:enter_exit()
subroutine geometry/import_node_geometry_2d(nodefile)

define_node_geometry_2d: Reads in an exnode file to define surface nodes DEC$ ATTRIBUTES DLLEXPORT,ALIAS:”SO_DEFINE_NODE_GEOMETRY_2D” :: DEFINE_NODE_GEOMETRY_2D

Parameters:nodefile [character(len=*),in]
Call to:enter_exit(), get_final_integer()
subroutine geometry/import_ply_triangles(ply_file)
import_ply_triangles: Reads in vtk ply file with list of vertex coordinates
and triangles. Used instead of internal triangle mesh creation for tree growing Writes over any existing triangle mesh.
Parameters:ply_file [character(len=*),in]
Call to:enter_exit()
subroutine geometry/triangles_from_surface(surface_elems)
triangles_from_surface: generates a linear surface mesh of triangles
from an existing high order surface mesh.
Parameters:surface_elems (*) [integer,in]
Called from:make_data_grid(), grow_tree()
Call to:enter_exit(), coord_at_xi()
subroutine geometry/group_elem_parent_term(parent_list, ne_parent)
group_elem_parent_term: group the terminal elements that sit distal to
a given parent element (ne_parent)
Parameters:
  • parent_list (*) [integer] :: will contain terminal elements below ne_parent on exit
  • ne_parent [integer,in] :: the parent element number
Use :

mesh_utilities (group_elem_by_parent())
Called from:

grow_tree()
Call to:

enter_exit(), group_elem_by_parent()
subroutine geometry/make_data_grid(surface_elems, offset, spacing, filename, groupname)
make_data_grid: makes a regularly-spaced 3D grid of data points to
fill a bounding surface
Parameters:
  • surface_elems (*) [integer,in]
  • offset [real,in]
  • spacing [real,in]
  • filename [character(len=*),in]
  • groupname [character(len=*),in]
Call to:

enter_exit(), get_local_elem_2d(), triangles_from_surface(), volume_internal_to_surface(), point_internal_to_surface()
subroutine geometry/make_2d_vessel_from_1d(elem_list)
make_2d_vessel_from_1d: create a surface mesh that aligns with the
centrelines of a 1D tree, and located at distance ‘radius’ from the centre. a template for a set of 5 nodes (that together define a bifurcation) is scaled, rotated, translated to align with the 1d mesh and its radii.
Parameters:elem_list (*) [integer,in] :: the global stem element number for the 2d mesh
Call to:enter_exit(), mesh_2d_from_1d_generic(), get_local_elem_1d(), mesh_rotate_about_axis(), mesh_rotate_vector_about_axis(), bifurcation_element(), stem_element(), which_child(), distance_between_points(), mesh_2d_from_1d_crux(), angle_btwn_points(), unit_vector(), angle_btwn_vectors(), element_connectivity_2d(), line_segments_for_2d_mesh(), redistribute_mesh_nodes_2d_from_1d(), merge_2d_from_1d_mesh(), merge_trifurcations()
subroutine geometry/mesh_2d_from_1d_generic(template_coords)
mesh_2d_from_1d_generic: provide the coordinates of the templated nodes
for a surface mesh creation about a 1d tree mesh
Parameters:template_coords (,,*,*) [real] :: side node
Called from:make_2d_vessel_from_1d()
Call to:enter_exit()
subroutine geometry/mesh_rotate_about_axis(ne, angle_z, rx, ry, txyz, template_coords)
mesh_rotate_about_axis: calculates the rotation matrices and z-angle for
rotation of a vector about an arbitrary axis defined by the direction of element ne.
Parameters:
  • ne [integer,in]
  • angle_z [real]
  • rx (,) [real] :: x-x = 1
  • ry (,) [real] :: x-x = 1
  • txyz (*) [real]
  • template_coords (,,*,*) [real,in] :: direction to the ‘side’ node
Called from:

make_2d_vessel_from_1d()
Call to:

enter_exit(), make_plane_from_3points(), unit_vector(), scalar_product_3()
subroutine geometry/mesh_rotate_vector_about_axis(n, template_vrsns, angle, length, radius, radius_weighted, rx, ry, txyz, template_coords, new_coords_derivs)
mesh_rotate_vector_about_axis: rotates a vector (starting at (0,0,0))
about an arbitrary axis. Rotation matrices are in Rx and Ry.
Parameters:
  • angle [real,in] :: is the amount to rotate about z-axis.
  • n [integer,in] :: each node in ring, plus crux if at bifurcation
  • template_vrsns (*) [integer,in]
  • length [real,in]
  • radius [real,in]
  • radius_weighted [real,in]
  • rx (3,3) [real,in]
  • ry (3,3) [real,in]
  • txyz (3) [real,in]
  • template_coords (,,*,*) [real,in]
  • new_coords_derivs (,,*,*) [real]
Called from:

make_2d_vessel_from_1d()
Call to:

enter_exit()
subroutine geometry/mesh_2d_from_1d_crux(np0, ne_1, ne_2, distance, new_coords_derivs)
mesh_2d_from_1d_crux: adjusts the location of the crux node for deriving
a 2d surface mesh over a 1d tree mesh.
Parameters:
  • np0 [integer,in]
  • ne_1 [integer,in]
  • ne_2 [integer,in]
  • distance [real]
  • new_coords_derivs (,,*,*) [real]
Called from:

make_2d_vessel_from_1d()
Call to:

enter_exit(), cross_product(), unit_vector(), scalar_product_3(), mesh_a_x_eq_b()
subroutine geometry/merge_2d_from_1d_mesh()
merge_2d_from_1d_mesh: used for deriving a 2d surface mesh over a 1d
tree mesh. merges the elements in the ‘rings’ that are adjacent to the bifurcations in the +Xi2 direction
Called from:make_2d_vessel_from_1d()
Call to:enter_exit()
subroutine geometry/merge_trifurcations(short_elements)
merge_trifurcations: used when deriving a 2d surface mesh from a 1d tree
mesh. merges short 2d elements with neighbouring elements, and removes. this is required for two bifurcations that occur with a very short distance between them. i.e. when approximately a trifurcation.
Parameters:short_elements (*) [integer,in]
Called from:make_2d_vessel_from_1d()
Call to:enter_exit()
subroutine geometry/define_rad_from_file(fieldfile[, radius_type_in])
define_rad_from_file: reads in a radius field associated with an
airway tree and assigns radius information to each element, also calculates volume of each element
Parameters:fieldfile [character(len=max_filename_len),in]
Options:radius_type_in [character(len=max_string_len)]
Call to:enter_exit(), get_final_integer(), get_local_node(), get_final_real(), get_local_elem_1d()
subroutine geometry/define_rad_from_geom(order_system, control_param, start_from, user_rad[, group_type_in[, group_option_in]])
define_rad_from_geom: Defines vessel or airway radius based on
their geometric structure. For ‘order_system’ == ‘strah’ or ‘horsf’, uses a user-defined maximum radius and branching ratio; for == ‘fit’, uses pre- defined radii (read in) and a calculated branching ratio for each path so that the order 1 branches have radius = USER_RAD.
Parameters:
  • order_system [character(len=*),in]
  • control_param [real,in]
  • start_from [character(len=*),in]
  • user_rad [real,in] :: radius of largest branch when order_system
Options:
  • group_type_in [character(len=*)]
  • group_option_in [character(len=*)]
Call to:

enter_exit()
subroutine geometry/element_connectivity_1d()
element_connectivity_1d: Calculates element connectivity in 1D and
stores in array elem_cnct
Called from:add_mesh(), define_1d_elements(), define_mesh_geometry_test(), grow_tree()
Call to:enter_exit()
subroutine geometry/element_connectivity_2d()
element_connectivity_2d: Calculates element connectivity in 2D and
stores in array elem_cnct_2d
Called from:define_elem_geometry_2d(), make_2d_vessel_from_1d()
Call to:enter_exit(), inlist()
subroutine geometry/line_segments_for_2d_mesh(sf_option)

line_segments_for_2d_mesh: set up the line segment arrays for a 2d mesh

Parameters:sf_option [character(len=4),in]
Called from:define_elem_geometry_2d(), make_2d_vessel_from_1d()
Call to:enter_exit(), inlist(), calc_scale_factors_2d()
subroutine geometry/evaluate_ordering()
evaluate_ordering: calculates generations, Horsfield orders,
Strahler orders for a given tree
Called from:add_mesh(), define_1d_elements(), define_mesh_geometry_test(), grow_tree()
Call to:enter_exit()
subroutine geometry/set_initial_volume(gdirn, cov, total_volume, rmax, rmin)
set_initial_volume: assigns a volume to terminal units appended on a
tree structure based on an assumption of a linear gradient in the gravitational direction with max, min, and COV values defined.
Parameters:
  • gdirn [integer,in]
  • cov [real,in]
  • total_volume [real,in]
  • rmax [real,in]
  • rmin [real,in]
Called from:

evaluate_vent()
Call to:

enter_exit(), volume_of_mesh()
subroutine geometry/volume_of_mesh(volume_model, volume_tree)
volume_of_mesh: calculates the volume of an airway mesh including
conducting and respiratory airways
Parameters:
  • volume_model [real]
  • volume_tree [real]
Called from:

solve_gasmix(), airway_mesh_deform(), set_initial_volume(), evaluate_vent(), evaluate_vent_step(), evaluate_uniform_flow()
Call to:

enter_exit()
subroutine geometry/write_geo_file(type_bn, filename)
write_geo_file: converts a surface mesh (created using make_2d_vessel_from_1d)

into a gmsh formatted mesh and writes to file. options on ‘type’: 1== single layered surface mesh of the vessel wall

2== double-layered thick-walled volume mesh of vessel wall 3== volume mesh of vessel lumen
Parameters:
  • type_bn [integer,in]
  • filename [character(len=*),in]
Call to:

enter_exit(), write_surface_geo(), geo_node_offset(), geo_entry_exit_cap(), write_3d_geo()
function geometry/get_final_real(string_bn)
Return:get_final_real [real] :: return the real value
Parameters:string_bn [character(len=*),in]
Called from:define_node_geometry(), define_node_geometry_2d(), define_rad_from_file(), import_exelemfield()
subroutine geometry/get_final_string(string_bn, rtemp)
get_final_string: gets the last set of characters surrounded
by whitespace in a string
Parameters:
  • string_bn [character(len=*),in]
  • rtemp [real,out] :: apply sign to number
Call to:

enter_exit()
subroutine geometry/get_local_node(np_global, np_local)

get_local_node: gets the local node number for a given global node

Parameters:
  • np_global [integer,in]
  • np_local [integer,out]
Called from:

define_1d_elements(), define_rad_from_file()
Call to:

enter_exit()
function geometry/get_parent_branch(ne)

gets the elements number of the first proximal element that is a different generation number to the current elements

Parameters:ne [integer,in]
Return:get_parent_branch [integer]
subroutine geometry/geo_entry_exit_cap(element_spline, ifile, ncount_loop, ncount_spline, np_offset, nl_offset)
Parameters:
  • element_spline (,) [integer,in]
  • ifile [integer,in]
  • ncount_loop [integer]
  • ncount_spline [integer] :: first new line
  • np_offset [integer,in]
  • nl_offset [integer,in]
Called from:

write_geo_file()
Call to:

enter_exit()
subroutine geometry/geo_node_offset(node_xyz_offset)
Parameters:node_xyz_offset (,) [real]
Called from:write_geo_file()
Call to:enter_exit(), distance_between_points(), direction_point_to_point()
subroutine geometry/reallocate_node_elem_arrays(num_elems_new, num_nodes_new)
reallocate_node_elem_arrays: Reallocates the size of geometric
arrays when modifying geometries
Parameters:
  • num_elems_new [integer,in]
  • num_nodes_new [integer,in]
Use :

indices
Called from:

add_mesh(), add_matching_mesh(), grow_tree()
Call to:

enter_exit()
function geometry/get_local_node_f(ndimension, np_global)
Parameters:
  • ndimension [integer,in]
  • np_global [integer,in]
Return:

get_local_node [integer]
Called from:

get_four_nodes(), define_geometry_fit(), map_versions(), distribute_surface_node_fit(), distribute_nodes_between(), centre_a_node()
function geometry/get_final_integer(string_bn)
Return:get_final_integer [integer] :: return the integer value
Parameters:string_bn [character(len=*),in]
Called from:define_1d_elements(), define_elem_geometry_2d(), define_node_geometry(), define_node_geometry_2d(), import_node_geometry_2d(), define_rad_from_file()
subroutine geometry/get_four_nodes(ne, string_bn)
Parameters:
  • ne [integer,in]
  • string_bn [character(len=132),in]
Called from:

define_elem_geometry_2d()
Call to:

enter_exit(), get_local_node_f()
subroutine geometry/redistribute_mesh_nodes_2d_from_1d()
Called from:make_2d_vessel_from_1d()
Call to:enter_exit(), distance_from_plane_to_point(), distance_between_points(), unit_vector()
function geometry/coord_at_xi(ne, xi, basis)
Parameters:
  • ne [integer,in]
  • xi (*) [real,in] :: xi^3-2xi^2+xi
  • basis [character(len=*),in]
Return:

coord_at_xi (3) [real]
Called from:

export_cubic_lagrange_2d(), triangles_from_surface(), coord_at_xi()
Call to:

coord_at_xi()
function geometry/get_local_elem(ne_global)
Parameters:ne_global [integer,in]
Return:get_local_elem [integer]
function geometry/get_local_elem_1d(ne_global)
Parameters:ne_global [integer,in]
Return:get_local_elem_1d [integer]
Called from:make_2d_vessel_from_1d(), define_rad_from_file()
function geometry/where_inlist(item, ilist)
Parameters:
  • item [integer]
  • ilist (*) [integer]
Return:

where_inlist [integer]
subroutine geometry/write_elem_geometry_2d(elemfile)
Parameters:elemfile [character(len=*),in]
Call to:enter_exit()
subroutine geometry/write_node_geometry_2d(nodefile)
Parameters:nodefile [character(len=*),in]
Call to:enter_exit()
subroutine geometry/write_surface_geo(element_spline, elem_surfaces, ifile, ncount_point, ncount_loop, ncount_spline, np_offset)
Parameters:
  • element_spline (,) [integer]
  • elem_surfaces (,) [integer]
  • ifile [integer]
  • ncount_point [integer]
  • ncount_loop [integer]
  • ncount_spline [integer]
  • np_offset [integer]
Called from:

write_geo_file()
Call to:

enter_exit()
subroutine geometry/write_3d_geo(element_spline, elem_surfaces, ifile, ncount_point, ncount_loop, ncount_spline)
Parameters:
  • element_spline (,) [integer]
  • elem_surfaces (,) [integer]
  • ifile [integer,in]
  • ncount_point [integer] :: record the centre point number for this ‘ring’
  • ncount_loop [integer]
  • ncount_spline [integer] :: the newest line
Called from:

write_geo_file()
Call to:

enter_exit()