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Bugfix: fixes GBDiffusion post MaterialManager update and adds a test case #147

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sanathkeshav merged 2 commits into from
Jul 10, 2026
Merged

Bugfix: fixes GBDiffusion post MaterialManager update and adds a test case #147

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3498498
fixes GBDiffusion post MaterialManager update and adds a test case
sanathkeshav Jul 10, 2026
536fb8e
add changelog entry
sanathkeshav Jul 10, 2026
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -199,10 +199,12 @@ test/input_files/**/*.json

# Test microstructure files
!sphere32.h5
!diamond_GB.h5

# Test input files
!test_LinearElastic.json
!test_LinearThermal.json
!test_GBDiffusion.json
!test_PseudoPlastic.json
!test_J2Plasticity.json
!test_MixedBCs.json
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -2,6 +2,7 @@

## latest

- Bugfix: fixes GBDiffusion post MaterialManager update and adds a test case [#147](https://github.com/DataAnalyticsEngineering/FANS/pull/147)
- Bugfix: mem-leak while reading microstructure and added wider CMake support [#140](https://github.com/DataAnalyticsEngineering/FANS/pull/140)
- Added MPI communicator abstraction [#139](https://github.com/DataAnalyticsEngineering/FANS/pull/139)

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2 changes: 2 additions & 0 deletions include/MaterialManager.h
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Expand Up @@ -260,6 +260,8 @@ class MaterialManager {
temp_reader.method = base_reader.method;
temp_reader.l_e = base_reader.l_e;
temp_reader.dims = base_reader.dims;
std::snprintf(temp_reader.ms_filename, sizeof(temp_reader.ms_filename), "%s", base_reader.ms_filename);
std::snprintf(temp_reader.ms_datasetname, sizeof(temp_reader.ms_datasetname), "%s", base_reader.ms_datasetname);

// Override material properties and n_mat for this specific material group
temp_reader.materialProperties = mat_group["material_properties"];
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10 changes: 5 additions & 5 deletions include/material_models/GBDiffusion.h
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Expand Up @@ -24,9 +24,9 @@
* - Provides visualization of grain boundary normals in post-processing
*
* Required material parameters in JSON format:
* - GB_unformity: Boolean flag for uniform GB properties
* - GB_uniformity: Boolean flag for uniform GB properties
*
* When GB_unformity is true (uniform properties):
* When GB_uniformity is true (uniform properties):
* {
* "GB_unformity": true,
* "D_bulk": 1.0, // Isotropic diffusion coefficient for all crystals
Expand Down Expand Up @@ -69,13 +69,13 @@ class GBDiffusion : public ThermalModel, public LinearModel<1, 3> {
GBnormals[(tag) * 3 + 1] = normal[1].get<double>();
GBnormals[(tag) * 3 + 2] = normal[2].get<double>();
}
GB_unformity = reader.materialProperties["GB_unformity"].get<bool>();
GB_uniformity = reader.materialProperties["GB_uniformity"].get<bool>();

D_bulk.resize(n_mat, 0.0);
D_par.resize(n_mat, 0.0);
D_perp.resize(n_mat, 0.0);

if (GB_unformity) {
if (GB_uniformity) {
double bulk_val = reader.materialProperties["D_bulk"].get<double>();
double par_val = reader.materialProperties["D_par"].get<double>();
double perp_val = reader.materialProperties["D_perp"].get<double>();
Expand Down Expand Up @@ -187,7 +187,7 @@ class GBDiffusion : public ThermalModel, public LinearModel<1, 3> {
private:
int num_crystals = 0;
int num_GB = 0;
bool GB_unformity;
bool GB_uniformity;

vector<double> D_bulk;
vector<double> D_par;
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56 changes: 27 additions & 29 deletions include/solver.h
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Expand Up @@ -592,14 +592,15 @@ void Solver<howmany, n_str>::postprocess(Reader &reader, int load_idx, int time_
/* ====================================================================== *
* u_total = g0·X + ũ (vector or scalar, decided at compile time)
* ====================================================================== */
const double dx = reader.l_e[0];
const double dy = reader.l_e[1];
const double dz = reader.l_e[2];
const double Lx2 = reader.L[0] / 2.0;
const double Ly2 = reader.L[1] / 2.0;
const double Lz2 = reader.L[2] / 2.0;
constexpr double rs2 = 0.7071067811865475; // 1.0 / std::sqrt(2.0)
VectorXd u_total(local_n0 * n_y * n_z * howmany);
const vector<double> &ml = matmanager->models[0]->macroscale_loading;
const double dx = reader.l_e[0];
const double dy = reader.l_e[1];
const double dz = reader.l_e[2];
const double Lx2 = reader.L[0] / 2.0;
const double Ly2 = reader.L[1] / 2.0;
const double Lz2 = reader.L[2] / 2.0;
constexpr double rs2 = 0.7071067811865475; // 1.0 / std::sqrt(2.0)
VectorXd u_total(local_n0 * n_y * n_z * howmany);
/* ---------- single sweep ------------------------------------------------- */
ptrdiff_t n = 0;
for (ptrdiff_t ix = 0; ix < local_n0; ++ix) {
Expand All @@ -610,13 +611,13 @@ void Solver<howmany, n_str>::postprocess(Reader &reader, int load_idx, int time_
const double z = iz * dz - Lz2;
if (howmany == 3) { /* ===== mechanics (vector) ===== */
if constexpr (n_str == 6) {
/* Small strain: strain_average contains 6 Voigt components */
const double g11 = strain_average[0];
const double g22 = strain_average[1];
const double g33 = strain_average[2];
const double g12 = strain_average[3] * rs2;
const double g13 = strain_average[4] * rs2;
const double g23 = strain_average[5] * rs2;
/* Small strain: ml holds 6 Mandel components of the mean strain */
const double g11 = ml[0];
const double g22 = ml[1];
const double g33 = ml[2];
const double g12 = ml[3] * rs2;
const double g13 = ml[4] * rs2;
const double g23 = ml[5] * rs2;
const double ux = g11 * x + g12 * y + g13 * z;
const double uy = g12 * x + g22 * y + g23 * z;
const double uz = g13 * x + g23 * y + g33 * z;
Expand All @@ -625,16 +626,16 @@ void Solver<howmany, n_str>::postprocess(Reader &reader, int load_idx, int time_
u_total[b + 1] = v_u[b + 1] + uy;
u_total[b + 2] = v_u[b + 2] + uz;
} else if constexpr (n_str == 9) {
/* Large strain: strain_average contains 9 components of F */
const double F11 = strain_average[0];
const double F12 = strain_average[1];
const double F13 = strain_average[2];
const double F21 = strain_average[3];
const double F22 = strain_average[4];
const double F23 = strain_average[5];
const double F31 = strain_average[6];
const double F32 = strain_average[7];
const double F33 = strain_average[8];
/* Large strain: ml holds 9 components of the mean deformation gradient F */
const double F11 = ml[0];
const double F12 = ml[1];
const double F13 = ml[2];
const double F21 = ml[3];
const double F22 = ml[4];
const double F23 = ml[5];
const double F31 = ml[6];
const double F32 = ml[7];
const double F33 = ml[8];
// u = (F - I) * X
const double ux = (F11 - 1.0) * x + F12 * y + F13 * z;
const double uy = F21 * x + (F22 - 1.0) * y + F23 * z;
Expand All @@ -645,10 +646,7 @@ void Solver<howmany, n_str>::postprocess(Reader &reader, int load_idx, int time_
u_total[b + 2] = v_u[b + 2] + uz;
}
} else { /* ===== scalar (howmany==1) ==== */
const double g1 = strain_average[0];
const double g2 = strain_average[1];
const double g3 = strain_average[2];
u_total[n] = v_u[n] + (g1 * x + g2 * y + g3 * z);
u_total[n] = v_u[n] + (ml[0] * x + ml[1] * y + ml[2] * z);
}
}
}
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1 change: 1 addition & 0 deletions test/CMakeLists.txt
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Expand Up @@ -16,6 +16,7 @@ set(FANS_TEST_CASES
J2Plasticity
LinearElastic
LinearThermal
GBDiffusion
PseudoPlastic
MixedBCs
CompressibleNeoHookean
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33 changes: 33 additions & 0 deletions test/input_files/test_GBDiffusion.json
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@@ -0,0 +1,33 @@
{
"microstructure": {
"filepath": "microstructures/diamond_GB.h5",
"datasetname": "/dset_0/eroded_image",
"L": [1.0, 1.0, 1.0]
},
"problem_type": "thermal",
"strain_type": "small",
"materials": [
{
"phases": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],
"matmodel": "GBDiffusion",
"material_properties": {
"GB_uniformity": true,
"D_bulk": 1.0,
"D_perp": 0.1,
"D_par": 10.0
}
}
],
"method": "cg",
"error_parameters": {
"measure": "Linfinity",
"type": "absolute",
"tolerance": 1e-10
},
"n_it": 1000,
"macroscale_loading": [
[[0.01, 0.02, -0.01]]
],
"results": ["homogenized_tangent", "stress_average", "strain_average", "absolute_error",
"microstructure", "displacement", "displacement_fluctuation", "stress", "strain"]
}
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1 change: 1 addition & 0 deletions test/pytest/conftest.py
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Expand Up @@ -16,6 +16,7 @@ def pytest_addoption(parser):
"test_J2Plasticity",
"test_LinearElastic",
"test_LinearThermal",
"test_GBDiffusion",
"test_PseudoPlastic",
"test_MixedBCs",
"test_CompressibleNeoHookean",
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1 change: 1 addition & 0 deletions test/run_tests.sh
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Expand Up @@ -22,6 +22,7 @@ FANS_TEST_CASES=(
"J2Plasticity"
"LinearElastic"
"LinearThermal"
"GBDiffusion"
"PseudoPlastic"
"MixedBCs"
"CompressibleNeoHookean"
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