broken parmetis link fix

.gitignore

@@ -8,12 +8,10 @@ build*/
 Code/build/*
 Code/build_clang/*
 install/*
-results/*
 dependencies/build/*
 deploy/.jobscripts
 deploy/machines_user.json
 deploy/machines_user.yml
-personal/*
 CMakeFiles/*
 CMakeCache.txt
 Code/client/displayClient
@@ -42,3 +40,11 @@ Tools/GenerateStl
 _skbuild
 dist
 .vagrant
+
+
+hemelb-experiments/*
+results/*
+personal/*
+hemelb-scripts/*
+papers/*
+outputs/*

Code/tests/pythontests/poiseuilleflowtest.py

@@ -94,4 +94,4 @@ def test_velocity_profile(self):
 
     def test_shear_stress_profile(self):
         pass
-
+

README.md

@@ -29,4 +29,4 @@ Key publications:
   complex domains", Phys. Rev. E (2014).
   https://doi.org/10.1103/PhysRevE.89.023303
 
-Please see the [doc] folder for more details.
+Documentation available at the [doc](/doc/) folder.

dependencies/ParMETIS/build.cmake

@@ -4,16 +4,16 @@
 # license in the file LICENSE.
 include_guard()
 
-find_file(ParMETIS_TARBALL parmetis-4.0.2.tar.gz 
+find_file(ParMETIS_TARBALL parmetis-4.0.2.tar.gz
   DOC "Path to download ParMETIS (can be url http://)"
   PATHS ${HEMELB_DEPENDENCIES_PATH}/distributions
   )
 if(NOT ParMETIS_TARBALL)
   message("No ParMETIS source found, will download.")
-  set(ParMETIS_TARBALL http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.2.tar.gz 
+  set(ParMETIS_TARBALL https://karypis.github.io/glaros/files/sw/parmetis/parmetis-4.0.2.tar.gz
     CACHE STRING "Path to download ParMETIS (can be local file://)" FORCE)
 endif()
-  
+
 set(ParMETIS_CC ${MPI_C_COMPILER} CACHE STRING "MPI Compiler to use for ParMETIS, leave blank to let ParMETIS guess")
 set(ParMETIS_CXX ${MPI_CXX_COMPILER} CACHE STRING "MPI Compiler to use for ParMETIS, leave blank to let ParMETIS guess")
 if(ParMETIS_CC)

doc/README.md

@@ -2,22 +2,14 @@
 
 A typical workflow with HemeLB consists of four steps:
 
-1. A preprocessing step where you create a mesh or geometry file (we
-   use extension .gmy) from a representation of the surface of your
-   domain. For this, you need to use the application in the
-   [geometry-tool](../geometry-tool)
-   directory. [Documentation](user/geometry-tool.md)
+1. A preprocessing step where you create a mesh or geometry file (we use extension .gmy) from a representation of the surface of your domain (.stl file). For this, you need to use the application in the [geometry-tool](../geometry-tool) directory. Please refer to the [Documentation](user/geometry-tool.md). 
 
-2. Setting options in the configuration XML file, such as timestep and
-   output data and
-   frequency. [Documentation](user/XmlConfiguration.md)
+2. Setting options in the configuration XML file, such as timestep and output data and frequency. Please refer to the [Documentation](user/XmlConfiguration.md).
 
-3. Compiling and running the
-   [main application](user/main-application.md).
+3. Compiling and running the [main application](user/main-application.md).
 
-4. Post processing the results, using the Python packages in the
-   [python-tools](../python-tools) directory. [Documentation](user/python-tools.md)
+4. Post processing the results, using the Python packages in the [python-tools](../python-tools) directory. Please refer to the [Documentation](user/python-tools.md).
 
 
-[Developer documentation](dev)
+[Developer documentation](/doc/dev/)
 

doc/user/CMakeOptions.md

@@ -75,7 +75,7 @@ by setting these options.
   `HEMELB_INLET_BOUNDARY` and `HEMELB_OUTLET_BOUNDARY` respectively from
   NASHZEROTHORDERPRESSUREIOLET (default), LADDIOLET. It is *very
   important* that you also select `HEMELB_WALL_INLET_BOUNDARY` and
-  `HEMELB_WALL_INLET_BOUNDARY` to match the combination of your
+  `HEMELB_WALL_OUTLET_BOUNDARY` to match the combination of your
   selected wall and in/outlet boundaries. (Options are:
   NASHZEROTHORDERPRESSURESBB, NASHZEROTHORDERPRESSUREBFL, LADDIOLETSBB,
   LADDIOLETBFL)

doc/user/XmlConfiguration.md

@@ -1,22 +1,15 @@
 # The HemeLB XML configuration file
 
-This file is the main input file for a HemeLB simulation. If you use
-the geometry tool to generate a .gmy file, it will also create a
-minimal XML file that contains the required geometry-related data,
-however it is currently (2023) not suitable to run immediately and
-must be manually edited. Here we describe the file.
+This file is the main input file for a HemeLB simulation. If you use the geometry tool to generate a .gmy file, it will also create a minimal XML file that contains the required geometry-related data, however, it is currently (2025) not suitable to run immediately, and must be manually edited. Here we describe the file.
 
-All parameters that correspond to a property of the modelled system
-should be given as follows:
+All parameters that correspond to a property of the modelled system should be given as follows:
 
     <$NAME value="$VALUE" unit="$UNITS" />
 where:
  * `$NAME` is a descriptive (considering the context of containing
    elements) name for the physical quantity;
- * `$UNITS` is a string specifying the units in which the value is
-   given; and,
- * `$VALUE` is a string which can be converted to the C++ type of the
-   quantity (`T`) by `operator>>(stream&, T&)`. For example:
+ * `$UNITS` is a string specifying the units in which the value is given; and,
+ * `$VALUE` is a string which can be converted to the C++ type of the quantity (`T`) by `operator>>(stream&, T&)`. For example:
 ```xml
 <step_length value="0.0001" units="s" />
 ```
@@ -28,12 +21,10 @@ or:
    a `util::Vector3D<float>`).
 
 At the top level there must be the root element: `<hemelbsettings
-version="int">`. It MUST have a version attribute, an integer. This is
-currently 5.
+version="int">`. It MUST have a version attribute, an integer. This is currently **5**.
 
 ## Simulation
-The `<simulation>` is required and specifies some global properties of
-the simulation, mainly time-related.
+The `<simulation>` is required and specifies some global properties of the simulation, mainly time-related.
 
 It's child elements are:
 * Required: `<stresstype value="int">` - the type of stresses to calculate. Must correspond to the `enum hemelb::lb::StressTypes`
@@ -55,25 +46,15 @@ It's child elements are:
 
 ## Geometry
 The `<geometry>` element is required. It has one, required, child element:
-* `<datafile path="relative path to geometry file" />` - the path
-  (relative to the XML file) of the GMY file.
+* `<datafile path="relative path to geometry file" />` - the path (relative to the XML file) of the GMY file.
 
 ## Inlets
 `<inlets>` - the element contains zero or more `<inlet>` subelements
 
-* `<inlet>` - describes the position and orientation of an inlet plane
-  as well as the boundary conditions to impose upon it. Inlets always
-  have the following two sub elements
-  * `<position value="(x,y,z)" units="m" />` - the location of a point
-    on the inlet plane (should be the centre if that makes
-    sense). Must have three attributes (x,y,z) which give the location
-    in metres in the input coordinate system
-  * `<normal value="(x,y,z)" units="dimensionless" />` - a vector
-    normal to the plane. Must have x,y,z attributes. Does not *have*
-    to be normalised but for good practice should be.
-  * `<condition type="" subtype="">` - Gives the BC. There are several
-    types available, in two classes, pressure-based and
-    velocity-based.
+* `<inlet>` - describes the position and orientation of an inlet plane as well as the boundary conditions to impose upon it. Inlets always have the following two sub elements
+  * `<position value="(x,y,z)" units="m" />` - the location of a point on the inlet plane (should be the centre if that makes sense). Must have three attributes (x,y,z) which give the location in metres in the input coordinate system
+  * `<normal value="(x,y,z)" units="dimensionless" />` - a vector normal to the plane. Must have x,y,z attributes. Does not *have* to be normalised but for good practice should be.
+  * `<condition type="" subtype="">` - Gives the BC. There are several types available, in two classes, pressure-based and velocity-based.
     * `type="pressure"`
       * `subtype="cosine"` - all subelements required
 	    * `<amplitude value="float" units="mmHg" />`
@@ -87,54 +68,41 @@ The `<geometry>` element is required. It has one, required, child element:
         * `<velocity value="velocity" units="m/s" />`
         * `<label value="multiscale_label_string" />`
     * `type="velocity"`
-      * `subtype="parabolic"` - Poiseuille flow in a cylinder, i.e. parabolic
-		* `<radius value="float" units="lattice" />` -  radius of tube (in lattice units)
-		* `<maximum value="float" units="lattice">` -  maximum velocity (in lattice units)
+      * `subtype="parabolic"` - Poiseuille flow in a cylinder, i.e. parabolic. **Note:** When using this, HemeLB must be compiled with the flag `HEMELB_INLET_BOUNDARY=LADDIOLET`. Otherwise, the simulation will result in a runtime error.
+		* `<radius value="float" units="m" />` -  radius of tube 
+		* `<maximum value="float" units="m/s">` -  maximum velocity 
 	  * `subtype="womersley"`
 		* `<womersley_velocity>` - a Womersley flow in a cylinder
 		* `<pressure_gradient_amplitude value="float" units="lattice"/>`
         * `<period value="float" units="lattice"/>`
         * `<womersley_number value="float" units="dimensionless"/>`
         * `<radius value="float" units="lattice"/>`
-    * `subtype="file"` - all subelements required
-        * `<path value="relative/path/to/velocity/data/file" />`
-        * `<radius value="float" units="lattice"/>` or `<radius value="float" units="m"/>`
+      * `subtype="file"` - all subelements required
+          * `<path value="relative/path/to/velocity/data/file" />`
+          * `<radius value="float" units="lattice"/>` or `<radius value="float" units="m"/>`
 
 ## Outlets
-As for "inlets" but with `s/inlet/outlet/`
+Similar to the parameters of "inlets" but substitute with outlet or do the command `s/inlet/outlet/`.
 
 ## Initial Conditions
 `<initialconditions>` - describe initial conditions. Child elements:
 
-* `<pressure>` - start at rest and equilibrium at the given pressure
-  field
-  * `<uniform value="float" units="mmHg">` - a uniform pressure at all
-    sites. Value must be in mmHg.
+* `<pressure>` - start at rest and equilibrium at the given pressure field
+  * `<uniform value="float" units="mmHg">` - a uniform pressure at all sites. Value must be in mmHg.
 
 * `<checkpoint file="rel/path/to/file" offset="rel/path">` - restart from a
-  checkpoint + offset file. Attribute `file` is required and gives
-  path to the checkpoint. The offset file is optional - if given it
-  must be a relative path to the file, else must have the same path with
-  the extension replaced by ".off".
+  checkpoint + offset file. Attribute `file` is required and gives path to the checkpoint. The offset file is optional - if given it must be a relative path to the file, else must have the same path with the extension replaced by `.off`.
 
 ## (Extracted) Properties
 Describe what data to extract under the `<properties>` element. Child elements:
 
 * `<propertyoutput file="path.xtr" period="int"
-  timestep_mode="[multi|single]">` - specify the file (under the
-  `results/Extraction` directory) and the output period (in time
-  steps). The way that multiple timesteps of data will be handled is
-  set by the `timestep_mode` attribute. Valid values are `multi` (the
-  default if the attribute is not present) or `single`. For `multi`,
-  each subsequent timestep's data will be appended to the same
-  file. For `single`, only a single timestep will be written to each
-  file; in this case the `file` attribute must contain exactly one
-  `%d` which will be replaced with the timestep number.
+  timestep_mode="[multi|single]">` - specify the file (under the `results/Extraction` directory) and the output period (in time steps). The way that multiple timesteps of data will be handled is set by the `timestep_mode` attribute. Valid values are `multi` (the default if the attribute is not present) or `single`. 
+  For `multi`, each subsequent timestep's data will be appended to the same file. For `single`, only a single timestep will be written to each file; in this case the `file` attribute must contain exactly one `%d` which will be replaced with the timestep number.
   - `<geometry type="type">` - the type string must be one of the following:
     + `type="whole"` - all lattice points - no subelements needed
 	+ `type="surface"` - all lattice points with one or more links
-      (defined by the active velocity set) intersecting a wall (not
-      inlet/outlet) - no sublements needed
+      (defined by the active velocity set) intersecting a wall (not inlet/outlet) - no sublements needed
     + `type="plane"` - all lattice points within sqrt(3)*voxel size of the specified plane
       * Required: `<point value="(x,y,z)" units="m" />`
       * Required: `<normal value="(x,y,z)" units="dimensionless" />`
@@ -154,8 +122,7 @@ Describe what data to extract under the `<properties>` element. Child elements:
     + `type="tangentialprojectiontraction"`
     + `type="mpirank"`
 
-* `<checkpoint file="path" period="int">` - save a checkpoint file to
-  the given path at the given interval (in timesteps).
+* `<checkpoint file="path" period="int">` - save a checkpoint file to the given path at the given interval (in timesteps).
 
 ## Changes
 

doc/user/geometry-tool.md

@@ -26,22 +26,20 @@ Build dependencies:
 
 Runtime dependencies:
 - Python
-- Numpy
+- NumPy
 - PyYAML
 - VTK
 - VMTK
 - wxPython (only for the GUI)
 
 Test dependencies:
 - pytest
-- hlb (NB: this must be compiled with the same version of numpy as
-  used above)
+- hlb (Note: this must be compiled with the same version of numpy as used above)
 
 
 ## Conda install
 
-VMTK is hard to build yourself but is easily installed via Conda, so
-we present this process here.
+VMTK is hard to build yourself but is easily installed via Conda. So we present this process here.
 
 ### Virtual enviroment setup
 
@@ -57,8 +55,7 @@ conda env create --file conda-environment.yml
 ```
 
 By default this will use `gmy-tool` as the name, but you can use
-anything you wish by adding `--name PREFERED_NAME` to the command
-above.
+anything you wish by adding `--name PREFERED_NAME` to the command above.
 
 
 You then need to activate this for your shell session:
@@ -77,8 +74,7 @@ pip install '.[gui]'
 
 (If your pip version is less than 21.3, add the extra flag `--use-feature=in-tree-build`)
 
-If you don't want the GUI, you can drop the `[gui]` extra
-specification.
+If you don't want the GUI, you can drop the `[gui]` extra specification.
 
 **Note for macOS**: On macOS GUI applications have to be linked
 against some special framework. If you don't fix this up you will get
@@ -106,20 +102,15 @@ python macos-fix-gui-launcher.py
 
 ## Install with custom VMTK
 
-The hemelb-codes organisation on GitHub includes a project to build
-VMTK  for Ubuntu: https://github.com/hemelb-codes/vmtk-build/
+The hemelb-codes organisation on GitHub includes a project to build VMTK  for Ubuntu: https://github.com/hemelb-codes/vmtk-build/
 
-That will hopefully give you an idea for how to proceed. If you are
-lucky you can just download the tarball. (Some Ubuntu packages will
-have to be installed - see that repo)
+That will hopefully give you an idea for how to proceed. If you are lucky you can just download the tarball. (Some Ubuntu packages will have to be installed - see that repo)
 
 ## Test
 
 Install pytest the usual way via `pip install pytest`.
 
-The Conda VMTK package forces you to use an old version of numpy. To
-ensure that the `hlb` package in `python-tools` is built with the same
-one, you need to change to that directory, install Cython (`pip
+The Conda VMTK package forces you to use an old version of numpy. To ensure that the `hlb` package in `python-tools` is built with the same one, you need to change to that directory, install Cython (`pip
 install cython`) and then install the package with:
 
 ```
@@ -131,15 +122,14 @@ Run the tests by invoking `py.test` in this directory.
 
 ## Run GUI
 
-Ensure your environment is activated then run `hlb-gmy-gui`. There is
-basic command line help available:
+Ensure your environment is activated then run `hlb-gmy-gui`. There is basic command line help available:
 
 ```
 $ hlb-gmy-gui --help
 usage: hlb-gmy-gui [-h] [--profile PATH] [--stl PATH] [--geometry PATH]
                    [--xml PATH]
 
-Process an input STL file intosuitable input for HemeLB.
+Process an input STL file into suitable input for HemeLB.
 
 optional arguments:
   -h, --help       show this help message and exit
@@ -150,20 +140,38 @@ optional arguments:
   --xml PATH       XML output file
 ```
 
-The terminal will produced a few errors that can ignore, like:
-`vtkSTLReader (0x7fdaa773bf10): A FileName must be specified.`. (This
-is just VTK trying to display the mesh before the source file is
-specified.)
+The terminal will produce a few errors that can ignore, like: `vtkSTLReader (0x7fdaa773bf10): A FileName must be specified.` (This is just VTK trying to display the mesh before the source file is specified.) and `vtkCompositeDataPipeline (0x2fb7b9a0): UpdateInformation invoked during another request.  Returning failure to algorithm vtkSTLReader(0x2f740e60).` (This is just vtkSTLReader was called during another operation, but rendering works as the STL gets loaded and cached beforehand).
 
+## Profile (.pr2) file
 
-## Profile (.pr2) files
+The geometry tool can save inlet, outlet, and seed point data used to generate a .gmy geometry file, using this Profile file. **(Saving this is highly recommended for reproducibility)**
 
-The geometry tool can store the the data it will use to generate a
-geometry file. Saving this is highly recommended for reproducibility!
-
-It's a YAML file which can be edited manually. Floating point values
-are stored by default in hexadecimal to avoid precision loss
-(https://docs.python.org/3/library/stdtypes.html#float.hex) but can be
-set in decimal if more convenient.
+It is a YAML file which can be edited manually. Floating point values are stored by default in hexadecimal to avoid precision loss (https://docs.python.org/3/library/stdtypes.html#float.hex) but can be set in decimal if more convenient.
 
 Paths are relative to the geometry file's location.
+
+## Run CLI
+
+There is a command line version of Geometry Setup Tool, where you can use the .pr2 file to generate the geometry file. 
+Ensure your environment is activated then run `hlb-gmy-cli`. There is basic command line help available:
+
+```
+$ hlb-gmy-cli --help
+
+usage: hlb-gmy-cli [-h] [--geometry PATH] [--xml PATH] [--voxel FLOAT] PATH
+
+Generate the config file described by a profile file
+
+positional arguments:
+  PATH             The profile to use. Other options given override those in
+                   the profile file.
+
+optional arguments:
+  -h, --help       show this help message and exit
+  --geometry PATH  Config output file
+  --xml PATH       XML output file
+  --voxel FLOAT    The voxel size in metres
+
+```
+
+You need to add the path to the directory of the .pr2 file. Example command: `hlb-gmy-cli /path-to-your-profile.pr2`. *Note: The .stl file related to the .pr2 file needs to be in the same directory alongwith it.*

doc/user/main-application.md

@@ -20,10 +20,9 @@ The main HemeLB application requires:
 
 If using resolved blood cells, you also require:
 - HDF5*
-- VTK* version 9 (for RBC mode)
+- VTK*>=9 (for RBC mode)
 
-The dependencies marked with * can be built automatically by the build
-system.
+The dependencies marked with * can be built automatically by the build system.
 
 ## Download