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v1.0.0-rc.145 (#55)
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Browse Source 
This is an UNSTABLE release. The release has significant modifications for HDF5 writing logic - in case of troubles go back to 1.0.0-rc.144.

* **Default HDF5 writing mode is with VDS, not soft-links** - this improves DIALS compatibility and makes format more future-proof, NXmx legacy format might be phased-out in the future.
* XDS plugin: Improve performance of VDS reading.
* jfjoch_writer: Significant improvement on how file systems I/O are handled through a dedicated pass-through VFD.
* jfjoch_writer: Clean-up of HDF5 routines to better handle issues.

Reviewed-on: #55
This commit was merged in pull request #55.
This commit is contained in:
leonarski_f
2026-05-06 21:50:02 +02:00
parent 7d34e8a049
commit caef26873e
152 changed files with 1995 additions and 276 deletions
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tests/XtalOptimizerTest.cpp
+11 -1
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@@ -32,6 +32,7 @@ TEST_CASE("XtalOptimizer") {
}
XtalOptimizerData xtal_opt{};
xtal_opt.max_time = 30.0;
xtal_opt.latt = CrystalLattice(40.2,39.4,80.2, 90,91, 89);
xtal_opt.geom.BeamX_pxl(1010).BeamY_pxl(995).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
@@ -90,6 +91,7 @@ TEST_CASE("XtalOptimizer_NoBeamCenter") {
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
xtal_opt.refine_beam_center = false;
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
@@ -140,6 +142,7 @@ TEST_CASE("XtalOptimizer_orthorombic") {
xtal_opt.latt = CrystalLattice(40.2,49.6,80.3, 90,91, 89);
xtal_opt.geom.BeamX_pxl(1005).BeamY_pxl(997).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.max_time = 30.0;
xtal_opt.crystal_system = gemmi::CrystalSystem::Orthorhombic;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
@@ -192,7 +195,7 @@ TEST_CASE("XtalOptimizer_triclinic") {
xtal_opt.geom.BeamX_pxl(997).BeamY_pxl(1005).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Triclinic;
xtal_opt.max_time = 1.0;
xtal_opt.max_time = 36.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
auto end = std::chrono::high_resolution_clock::now();
@@ -245,6 +248,7 @@ TEST_CASE("XtalOptimizer_tetragonal") {
xtal_opt.geom.BeamX_pxl(1010).BeamY_pxl(995).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Tetragonal;
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
auto end = std::chrono::high_resolution_clock::now();
@@ -296,6 +300,7 @@ TEST_CASE("XtalOptimizer_hexagonal") {
xtal_opt.geom.BeamX_pxl(1007).BeamY_pxl(990).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Hexagonal;
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
auto end = std::chrono::high_resolution_clock::now();
@@ -349,6 +354,7 @@ TEST_CASE("XtalOptimizer_hexagonal_unconstrained") {
xtal_opt.geom.BeamX_pxl(1002).BeamY_pxl(998).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Triclinic;
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
auto end = std::chrono::high_resolution_clock::now();
@@ -407,6 +413,7 @@ TEST_CASE("XtalOptimizer_cubic") {
xtal_opt.geom.BeamX_pxl(1007).BeamY_pxl(990).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Cubic;
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
auto end = std::chrono::high_resolution_clock::now();
@@ -460,6 +467,7 @@ TEST_CASE("XtalOptimizer_monoclinic") {
xtal_opt.geom.BeamX_pxl(1007).BeamY_pxl(990).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
auto end = std::chrono::high_resolution_clock::now();
@@ -606,6 +614,7 @@ TEST_CASE("XtalOptimizer_rotation") {
xtal_opt.refine_beam_center = true;
xtal_opt.refine_distance_mm = true;
xtal_opt.refine_detector_angles = false;
xtal_opt.max_time = 30.0;
auto t0 = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
@@ -693,6 +702,7 @@ TEST_CASE("XtalOptimizer_refine_rotation_axis") {
xtal_opt.refine_distance_mm = false;
xtal_opt.refine_detector_angles = false;
xtal_opt.refine_rotation_axis = true;
xtal_opt.max_time = 30.0;
auto t0 = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));