3/initiliaze from mesh by malamast · Pull Request #613 · boutproject/hermes-3

malamast · 2026-07-08T22:03:40Z

Purpose

Added a functionality to initialize number density and pressure from grid variables with names varName_init.
You can set up 2D profiles in the grid e.g. Nd+_init from example from EFIT files (1D omp profiles and no polidal variation) and then in the input file you set:
[Nd+]
initialize_from_mesh = true # Should be in SI units with name: _init

Change Summary

I changed the isothermal component as well. I made the T variable a Field3D var instead of BoutReal so that it can be set up from grid.

Validation

I tested it with my cases for 2D and 3D.

AI Assistance

No.

Documentation

None

Review Notes

None

…er density and pressure from grid variables with names varName_init. fixed_density and isothermal: Added a functionality to read the fixed denstiy or temperature from grid variables with names varName_init

codecov · 2026-07-08T22:14:52Z

Codecov Report

❌ Patch coverage is 60.00000% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 56.92%. Comparing base (1d23bd6) to head (d362cb4).

Files with missing lines	Patch %	Lines
include/fixed_density.hxx	57.14%	2 Missing and 1 partial ⚠️
src/evolve_density.cxx	57.14%	2 Missing and 1 partial ⚠️
src/evolve_pressure.cxx	66.66%	2 Missing and 1 partial ⚠️
src/isothermal.cxx	57.14%	2 Missing and 1 partial ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #613   +/-   ##
=======================================
  Coverage   56.92%   56.92%           
=======================================
  Files          97       97           
  Lines       10092    10120   +28     
  Branches     1462     1466    +4     
=======================================
+ Hits         5745     5761   +16     
- Misses       3757     3765    +8     
- Partials      590      594    +4

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mikekryjak

Thanks @malamast, this is really useful work. I left a few comments and suggestions for typo fixes.

Can you also please add a docs section on this on the https://hermes3.readthedocs.io/en/latest/execution.html page as a new subsection called Initialising from known profiles? Let me know if you need any help with this.

mikekryjak · 2026-07-13T10:08:20Z

+    // Try to read the initial field from the mesh
+    mesh->get(N, std::string("N") + name + "_init"); // Units: [m^-3/s]
+    N /= Nnorm;                                      // Normalization
+  }


This will cause a bug when evolve_log is true as logN would not be populated, causing an issue here:

hermes-3/src/evolve_density.cxx

Lines 181 to 184 in d362cb4

if (evolve_log) {

// Evolving logN, but most calculations use N

N = exp(logN);

}

Here is where logN is calculated:

hermes-3/src/evolve_density.cxx

Lines 71 to 89 in d362cb4

if (evolve_log) {

// Evolve logarithm of density

solver->add(logN, std::string("logN") + name);

// Save the density to the restart file

// so the simulation can be restarted evolving density

// get_restart_datafile()->addOnce(N, std::string("N") + name);

if (!alloptions["hermes"]["restarting"]) {

// Set logN from N input options

initial_profile(std::string("N") + name, N);

logN = log(N);

} else {

// Ignore these settings

Options::root()[std::string("N") + name].setConditionallyUsed();

}

} else {

// Evolve the density in time

solver->add(N, std::string("N") + name);

}

I think all that's needed here is to make sure it's calculated from the grid value:

if (evolve_log && !alloptions["hermes"]["restarting"]) { logN = log(N); }

mikekryjak · 2026-07-13T10:09:07Z

+  if (initialize_from_mesh) {
+    // Try to read the initial field from the mesh
+    mesh->get(P, std::string("P") + name + "_init"); // Units: Pascal [Pa]
+    P /= Pnorm;                                      // Normalization


See comment https://github.com/boutproject/hermes-3/pull/613/changes#r3569745560. Need to calculate logP if evolve_log is true.

mikekryjak · 2026-07-13T10:22:17Z

+
+  if (initialize_from_mesh) {
+    // Try to read the initial field from the mesh
+    mesh->get(N, std::string("N") + name + "_init"); // Units: [m^-3/s]


If the variable isn't in the grid, it will be set to zero. This makes it quite annoying if you misspell the variable or forget to put it in and don't check the console dump which shows the warning.

My LLM suggests that this can be overcome because get() gives a return status you can use:

std::string variable = std::string("N") + name + "_init" if (mesh->get(N, variable) != 0) { throw BoutException("Could not load '{}' from the mesh", variable); }

You can see the return status for mesh->get() defined here - if the value isn't found, it will be set to default and it will return 1:
https://github.com/boutproject/BOUT-dev/blob/9eb94c7c9d9539c1e4e60ec84377a48d5ab50b22/src/mesh/mesh.cxx#L231-L236

This needs to be applied to every place a variable is read from the grid.

mikekryjak · 2026-07-13T10:22:50Z

+
+    if (initialize_from_mesh) {
+      // Try to read the initial field from the mesh
+      mesh->get(N, std::string("N") + name + "_init"); // Units: [m^-3/s]


See https://github.com/boutproject/hermes-3/pull/613/changes#r3569831967

mikekryjak · 2026-07-13T10:23:17Z

+
+  if (initialize_from_mesh) {
+    // Try to read the initial field from the mesh
+    mesh->get(P, std::string("P") + name + "_init"); // Units: Pascal [Pa]


See https://github.com/boutproject/hermes-3/pull/613/changes#r3569831967

mikekryjak · 2026-07-13T10:28:01Z

+  // Initilize the Field3D N from 2D profiles stored in the mesh file.
+  initialize_from_mesh =
+      n_options["initialize_from_mesh"]
+          .doc("Initilize field from 2D profiles stored in the mesh file?")


Suggested change

.doc("Initilize field from 2D profiles stored in the mesh file?")

.doc("Initialize field from 2D profiles stored in the mesh file?")

mikekryjak · 2026-07-13T10:28:19Z

+  // Initilize the Field3D P from 2D profiles stored in the mesh file.
+  initialize_from_mesh =
+      p_options["initialize_from_mesh"]
+          .doc("Initilize field from 2D profiles stored in the mesh file?")


Suggested change

.doc("Initilize field from 2D profiles stored in the mesh file?")

.doc("Initialize field from 2D profiles stored in the mesh file?")

mikekryjak · 2026-07-13T10:28:33Z

+  // Initilize the Field3D T from 2D profiles stored in the mesh file.
+  initialize_from_mesh =
+      options["initialize_from_mesh"]
+          .doc("Initilize field from 2D profiles stored in the mesh file?")


Suggested change

.doc("Initilize field from 2D profiles stored in the mesh file?")

.doc("Initialize field from 2D profiles stored in the mesh file?")

mikekryjak · 2026-07-13T10:29:50Z

+
+    if (initialize_from_mesh) {
+      // Try to read the initial field from the mesh
+      mesh->get(N, std::string("N") + name + "_init"); // Units: [m^-3/s]


Suggested change

mesh->get(N, std::string("N") + name + "_init"); // Units: [m^-3/s]

mesh->get(N, std::string("N") + name + "_init"); // Units: [m^-3]

mikekryjak · 2026-07-13T10:30:02Z

+
+  if (initialize_from_mesh) {
+    // Try to read the initial field from the mesh
+    mesh->get(N, std::string("N") + name + "_init"); // Units: [m^-3/s]


Suggested change

mesh->get(N, std::string("N") + name + "_init"); // Units: [m^-3/s]

mesh->get(N, std::string("N") + name + "_init"); // Units: [m^-3]

malamast added 2 commits July 8, 2026 14:48

evolve_density and pressure: Added a functionality to initialize numb…

49aebe1

…er density and pressure from grid variables with names varName_init. fixed_density and isothermal: Added a functionality to read the fixed denstiy or temperature from grid variables with names varName_init

Apply clang-format

d362cb4

malamast requested review from bendudson and mikekryjak July 8, 2026 22:03

mikekryjak requested changes Jul 13, 2026

View reviewed changes

mikekryjak mentioned this pull request Jul 16, 2026

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3/initiliaze from mesh#613

3/initiliaze from mesh#613
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	if (evolve_log) {
	// Evolving logN, but most calculations use N
	N = exp(logN);
	}

	if (evolve_log) {
	// Evolve logarithm of density
	solver->add(logN, std::string("logN") + name);
	// Save the density to the restart file
	// so the simulation can be restarted evolving density
	// get_restart_datafile()->addOnce(N, std::string("N") + name);

	if (!alloptions["hermes"]["restarting"]) {
	// Set logN from N input options
	initial_profile(std::string("N") + name, N);
	logN = log(N);
	} else {
	// Ignore these settings
	Options::root()[std::string("N") + name].setConditionallyUsed();
	}
	} else {
	// Evolve the density in time
	solver->add(N, std::string("N") + name);
	}

	.doc("Initilize field from 2D profiles stored in the mesh file?")
	.doc("Initialize field from 2D profiles stored in the mesh file?")

	mesh->get(N, std::string("N") + name + "_init"); // Units: [m^-3/s]
	mesh->get(N, std::string("N") + name + "_init"); // Units: [m^-3]

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malamast commented Jul 8, 2026

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