Make RBC cell insert seed required

Code/configuration/SimConfigReader.cc

@@ -7,7 +7,6 @@
 
 #include <algorithm>
 #include <array>
-#include <chrono>
 #include <concepts>
 #include <memory>
 #include <optional>
@@ -577,34 +576,10 @@ namespace hemelb::configuration {
         }
 
         // Optional element(s) <insertcell>
-        PrngSeedType horrible_hack_seed = 0;
         for (auto insertEl: ioletEl.Children("insertcell")) {
             CellInserterConfig inserterConf;
-            auto maybeSeed = insertEl.GetChildOrNull("seed").transform(
-                    [](Element const& _) { return _.GetAttributeOrThrow<PrngSeedType>("value"); }
-            );
-            if (maybeSeed) {
-                inserterConf.seed = *maybeSeed;
-            } else {
-                // We need to seed each of the RBCInserterWithPerturbation objects consistently across MPI processes
-                if (horrible_hack_seed == 0) {
-                    PrngSeedType seed = std::chrono::system_clock::now().time_since_epoch().count();
-                    auto comm_world = hemelb::net::MpiCommunicator::World();
-                    comm_world.Broadcast(seed, 0);
-                    std::stringstream message;
-                    message << "RBC insertion random seed: " << std::hex << std::showbase << seed;
-                    log::Logger::Log<log::Info, log::Singleton>(message.str());
-                    horrible_hack_seed = seed;
-                } else {
-                    horrible_hack_seed += 1;
-                }
-                inserterConf.seed = horrible_hack_seed;
-            }
+            inserterConf.seed = insertEl.GetChildOrThrow("seed").GetAttributeOrThrow<PrngSeedType>("value");
             inserterConf.template_name = insertEl.GetAttributeOrThrow("template");
-//                    if (templateCells.count(templateName) == 0)
-//                    {
-//                        throw Exception() << "Template cell name does not match a known template cell";
-//                    }
 
             // Rotate cell to align z axis with given position, and then z axis with flow
             // If phi == 0, then cell symmetry axis is aligned with the flow

Code/tests/redblood/CellInserterTests.cc

@@ -27,27 +27,26 @@ namespace hemelb::tests
 
         auto getDocument = [&](LatticeDistance radius = 1e0, int numInserters = 0) {
             std::ostringstream sstr;
-            sstr << "<hemelbsettings>"
-                    "<inlets><inlet>"
-                    "  <condition type=\"pressure\" subtype=\"file\">"
-                    "  <path value=\"ignored.dat\" />"
-                    "  </condition>"
-                    "  <normal units=\"dimensionless\" value=\"(0.0,1.0,1.0)\" />"
-                    "  <position units=\"m\" value=\"(0.1,0.2,0.3)\" />"
-                    "  <flowextension>"
-                    "    <length units=\"m\" value=\"0.5\" />"
-                    "    <radius units=\"m\" value=\"" << radius << "\" />"
-                                                                    "    <fadelength units=\"m\" value=\"0.4\" />"
-                                                                    "  </flowextension>";
+            sstr << "<hemelbsettings>\n<inlets>\n<inlet>\n"
+                    "  <condition type=\"pressure\" subtype=\"file\">\n"
+                    "  <path value=\"ignored.dat\" />\n"
+                    "  </condition>\n"
+                    "  <normal units=\"dimensionless\" value=\"(0.0,1.0,1.0)\" />\n"
+                    "  <position units=\"m\" value=\"(0.1,0.2,0.3)\" />\n"
+                    "  <flowextension>\n"
+                    "    <length units=\"m\" value=\"0.5\" />\n"
+                    "    <radius units=\"m\" value=\"" << radius << "\" />\n"
+                    "    <fadelength units=\"m\" value=\"0.4\" />\n"
+                    "  </flowextension>\n";
             for (int i = 0; i < numInserters; ++i)
             {
-                sstr << "  <insertcell template=\"joe\">"
-                        "    <every units=\"s\" value=\"" << every << "\"/>"
-                                                                      "    <offset units=\"s\" value=\"" << offset << "\"/>"
-                                                                                                                      "  </insertcell>";
+                sstr << "  <insertcell template=\"joe\">\n"
+                     << "    <every units=\"s\" value=\"" << every << "\"/>\n"
+                     << "    <offset units=\"s\" value=\"" << offset << "\"/>\n"
+                     << "    <seed value=\"854" << i << "\" />\n"
+                     << "  </insertcell>\n";
             }
-            sstr << "</inlet></inlets>"
-                    "</hemelbsettings>";
+            sstr << "</inlet>\n</inlets>\n</hemelbsettings>\n";
             Document doc;
             doc.LoadString(sstr.str().c_str());
             return doc;

Code/tests/resources/cyl_l100_r5.xml

@@ -26,6 +26,7 @@
         <fadelength units="m" value="3e-06" />
       </flowextension>
       <insertcell template="default">
+	<seed value="321" />
         <every units="s" value="1"/>
         <offset units="s" value="1.852e-6"/>
         <delta_t units="s" value="0e0"/>

Code/tests/resources/fedosov1c.xml

@@ -26,7 +26,8 @@
         <fadelength units="m" value="7e-06" />
       </flowextension>
       <insertcell template="default">
-        <every units="s" value="2e-0"/>
+	<seed value="321" />
+	<every units="s" value="2e-0"/>
         <offset units="s" value="40e-8"/>
         <delta_t units="s" value="0e0"/>
         <theta units="rad" value="0e0"/>

Code/tests/resources/large_cylinder_rbc.xml

@@ -26,6 +26,7 @@
         <fadelength units="m" value="7e-06" />
       </flowextension>
       <insertcell template="default">
+	<seed value="321" />
         <every units="s" value="2e-0"/>
         <offset units="s" value="40e-8"/>
         <delta_t units="s" value="0e0"/>

doc/user/XmlConfiguration.md

@@ -3,7 +3,7 @@
 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 (2021) not suitable to run immediately and
+however it is currently (2023) 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
@@ -27,9 +27,14 @@ or:
    (since `operator>>` has been overriden to parse such a string into
    a `util::Vector3D<float>`).
 
+Floating point values can be given in fixed point, scientific
+notation, or hexadecimal floating point. This last can exactly
+represent floating point numbers so is used by tooling to avoid loss
+of precision.
+
 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.
+currently 6.
 
 ## Simulation
 The `<simulation>` is required and specifies some global properties of
@@ -45,7 +50,14 @@ It's child elements are:
 * Optional: `<checkpoint period="int">` -
   save a checkpoint at the given interval (in timesteps) to the
   "Checkpoints" directory.
-
+* Optional: `<fluid_density value="float" units="kg/m3" />` - density
+  of the fluid, default is `DEFAULT_FLUID_DENSITY_Kg_per_m3=1000.0`.
+* Optional: `<fluid_viscosity value="float" units="Pa.s" />` - dynamic
+  viscosity of the fluid, default is `DEFAULT_FLUID_VISCOSITY_Pas =
+  0.004`.
+* Optional: `<reference_pressure value="float" units="mmHg" />` -
+  pressure from which other pressures are measured - this physical
+  pressure corresponds to a LB density of 1.0. Default is zero.
 
 ## Geometry
 The `<geometry>` element is required. It has one, required, child element:
@@ -148,11 +160,16 @@ Describe what data to extract under the `<properties>` element. Child elements:
     + `type="tangentialprojectiontraction"`
     + `type="mpirank"`
 
+## Cells
+Configure the simulation of resolved flexible particles with the IBM
+user the `<redbloodcells>` element.
+
 ## Changes
 
 ### Version 6
-Moved checkpoint 
+- Moved checkpoint.
+- Allow hexadecimal floating point
+- Basic documentation of RBC elements
 
 ### Version 5
-
 Added checkpoint element.