Add ztUSO0doTz_aneurysm1

.gitattributes

@@ -7570,3 +7570,8 @@ cfd_data/yUJN2uVA3D_aneurysm2/wall_mesh_registration.pt filter=lfs diff=lfs merg
 cfd_data/ziSACL5Z7M_aneurysm1/blood_data.pt filter=lfs diff=lfs merge=lfs -text
 cfd_data/ziSACL5Z7M_aneurysm1/wall_data.pt filter=lfs diff=lfs merge=lfs -text
 cfd_data/ziSACL5Z7M_aneurysm1/wall_mesh_registration.pt filter=lfs diff=lfs merge=lfs -text
+cfd_data/ztUSO0doTz_aneurysm1/blood_data.pt filter=lfs diff=lfs merge=lfs -text
+cfd_data/ztUSO0doTz_aneurysm1/mesh.msh filter=lfs diff=lfs merge=lfs -text
+cfd_data/ztUSO0doTz_aneurysm1/mesh.vtu filter=lfs diff=lfs merge=lfs -text
+cfd_data/ztUSO0doTz_aneurysm1/wall_data.pt filter=lfs diff=lfs merge=lfs -text
+cfd_data/ztUSO0doTz_aneurysm1/wall_mesh_registration.pt filter=lfs diff=lfs merge=lfs -text

cfd_data/ztUSO0doTz_aneurysm1/blood_data.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b09d838bae137d903821341f9b44d6f4e5420fca812e3c4892434f51d82ba058
+size 3147077154

cfd_data/ztUSO0doTz_aneurysm1/flowsplit_ratio.txt

@@ -0,0 +1 @@
+0.5532686246359912 0.4467313753640088

cfd_data/ztUSO0doTz_aneurysm1/ghd_fusion_params.json

@@ -0,0 +1,11 @@
+{
+  "flaw_opening_min_size": 5,
+  "init_step": 1,
+  "max_cl_length": null,
+  "ring_downsample_ratio": 1,
+  "smooth_n_rings": 5,
+  "smooth_n_iter": 10,
+  "extrude_outlets": true,
+  "extrude_inlet": true,
+  "min_torsion": true
+}

cfd_data/ztUSO0doTz_aneurysm1/jnl_transient

@@ -0,0 +1,31 @@
+/file/read-case mesh.msh
+/mesh/scale 0.001 0.001 0.001
+/define/models/unsteady-2nd-order? yes
+/define/models/viscous/laminar yes
+/define/materials/change-create air blood yes constant 1050 no no yes carreau shear-rate-dependent 3.313 0.3568 0.056 0.00345 no no no yes
+/define/boundary-conditions/zone-type 4 velocity-inlet
+/define/boundary-conditions/zone-type 5 outflow
+/define/boundary-conditions/zone-type 6 outflow
+(define in-file (open-input-file "flowsplit_ratio.txt"))
+(define out1 (read in-file))
+(define out2 (read in-file))
+(close-input-port in-file)
+
+(define cmd1 (string-append "/define/boundary-conditions/outflow 5 " (number->string out1)))
+(define cmd2 (string-append "/define/boundary-conditions/outflow 6 " (number->string out2)))
+
+(ti-menu-load-string cmd1)
+(ti-menu-load-string cmd2)
+/define/user-defined/compiled-functions compile libudf yes parabolic_vinlet_udf_full.c "" ""
+/define/user-defined/compiled-functions load libudf
+/define/boundary-conditions/set/velocity-inlet surface4 () vmag yes yes udf inlet_x_velocity_transient::libudf quit
+/solve/set/p-v-coupling 24
+/solve/set/p-v-controls 2000000 0.5 0.5
+/solve/monitors/residual/convergence-criteria 0.0001 0.0001 0.0001 0.0001
+/solve/initialize/hyb-initialization
+/file/transient-export/ensight-gold-transient ensight_files () * () absolute-pressure dynamic-pressure x-velocity y-velocity z-velocity wall-shear x-wall-shear y-wall-shear z-wall-shear dx-velocity-dx dy-velocity-dy dz-velocity-dz dx-velocity-dy dy-velocity-dx dx-velocity-dz dz-velocity-dx dy-velocity-dz dz-velocity-dy dp-dx dp-dy dp-dz dp-dt viscosity-lam x-coordinate y-coordinate z-coordinate quit no yes export-1 time-step 10 yes
+/file/autosave/data-frequency 1600
+/solve/set/time-step 0.001
+/solve/dual-time-iterate 1600 100
+exit
+yes

cfd_data/ztUSO0doTz_aneurysm1/mesh.msh

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4a8ba31884282f60a8117b44efce12817b78b532f27c2ab1ae146ad503a9266c
+size 234191201

cfd_data/ztUSO0doTz_aneurysm1/mesh.vtu

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a7b2515614ec0c62d9341c0748368eb8c343efa545b83528c2e7a7f6354b2952
+size 51208788

cfd_data/ztUSO0doTz_aneurysm1/parabolic_vinlet_udf_full.c

@@ -0,0 +1,200 @@
+/*
+vprofile_transient_parabolic.c
+UDF for specifying steady-state velocity profile boundary condition
+
+AUTHOR	Wenhao Ding
+DATE	22.03.2024
+
+Instruction:
+define VINREF, the maximum velocity at the center
+define FIXED_TIME_STEP and make sure MAX_PCD_SIZE is larger than int(total_time/FIXED_TIME_STEP)
+define filename (txt for the waveform, this txt file must be in the same directory as this script)
+*/
+
+#include "udf.h"
+#include <math.h>
+#include <stdio.h>
+
+#define PI 3.14159265358979323846
+#define VINREF	1.3158	/* ref inlet v  */
+#define VIN	0	/* ref inlet v  */
+#define MAX_PCD_SIZE 400001  /* Least PCD number the waveform file has cannot exceed point number in txt 574578 41160*/
+#define MAX_LOG_SIZE 600
+#define FIXED_TIME_STEP 0.00001  /* Fixed time step during transient simulation*/
+#define MAX_POINTS 6000 /* Maximum point number on the inlet*/
+#define ND_ND 3
+/* static double* Q_array[MAX_PCD_SIZE]; */
+
+
+typedef struct {
+    double x;
+    double y;
+    double z;
+} Vector3D;
+
+double dot_product(Vector3D v1, Vector3D v2) {
+    return v1.x * v2.x + v1.y * v2.y + v1.z * v2.z;
+}
+
+Vector3D cross_product(Vector3D v1, Vector3D v2) {
+    Vector3D cross_v;
+
+    cross_v.x = v1.y * v2.z - v1.z * v2.y;
+    cross_v.y = v1.z * v2.x - v1.x * v2.z;
+    cross_v.z = v1.x * v2.y - v1.y * v2.x;
+
+    return cross_v;
+}
+
+double get_norm(Vector3D result) {
+    return sqrt(pow(result.x, 2) + pow(result.y, 2) + pow(result.z, 2));
+}
+
+double getDegAngle(Vector3D v1, Vector3D v2) {
+    Vector3D v_cross = cross_product(v1, v2);
+    double radian_angle = atan2(get_norm(v_cross), dot_product(v1, v2));
+    if (v_cross.z < 0) {
+        radian_angle = 2 * PI - radian_angle;
+    }
+    return radian_angle;
+}
+
+
+
+DEFINE_PROFILE(inlet_x_velocity_transient, thread, position)
+{   
+    /*Domain* d;*/
+    /*d = Get_Domain(1);*/
+    /*Thread* tr = Lookup_Thread(d, 5);*/
+    real x[ND_ND]; /* ND_ND=3 for 3D */
+    real curr_x, curr_y, curr_z;
+    face_t f;
+    /* real current_time;  */
+    FILE* rfile; /* declare a FILE pointer */
+    rfile = fopen("udf_waveform_5cycles.txt", "r+");
+    double Q_array[MAX_PCD_SIZE];
+    int i = 0;
+    for (i = 0; i < MAX_PCD_SIZE; i++) {
+        fscanf(rfile, "%lf", &Q_array[i]); /* that supposes one value per line */
+    }fclose(rfile);
+    /* load from csv file */
+    double centroids[MAX_POINTS][ND_ND];
+    int num_points_inlet = 0;
+    FILE* file;
+    char line[256];
+    file = fopen("inlet_centroids.csv", "r");
+    if (file == NULL)
+    {
+        Message("Error: Cannot open file %s\n", "inlet_centroids.csv");
+        return;
+    }
+    fgets(line, sizeof(line), file);
+    num_points_inlet = 0;
+    while (fgets(line, sizeof(line), file) && num_points_inlet < MAX_POINTS)
+    {
+        sscanf(line, "%lf,%lf,%lf", &centroids[num_points_inlet][0], &centroids[num_points_inlet][1], &centroids[num_points_inlet][2]);
+        num_points_inlet++;
+    }
+    fclose(file);
+    /* record average coordinates on the inlet (center) */
+    double center_x = 0.0, center_y = 0.0, center_z = 0.0;
+    for (i = 0; i < num_points_inlet; i++)
+    {
+        center_x += centroids[i][0];
+        center_y += centroids[i][1];
+        center_z += centroids[i][2];
+    }
+
+    if (num_points_inlet > 0)
+    {
+        center_x /= num_points_inlet;
+        center_y /= num_points_inlet;
+        center_z /= num_points_inlet;
+    }
+    /*Message("Average centroid coordinates: x=%lf, y=%lf, z=%lf\n", center_x, center_y, center_z);*/
+    /* get 12 clock tick */
+    double tick_x = 0.0, tick_y = 0.0, tick_z = 0.0;
+    double tick_radius = 0.0;
+    double tick_radius_record = 0.0;
+    for (i = 0; i < num_points_inlet; i++)
+    {
+        tick_radius = sqrt(pow((centroids[i][0] - center_x), 2) + pow((centroids[i][1] - center_y), 2) + pow((centroids[i][2] - center_z), 2));
+        if (tick_radius > tick_radius_record) {
+            tick_x = x[0];
+            tick_y = x[1];
+            tick_z = x[2];
+        }
+        tick_radius_record = tick_radius;
+    }
+
+    /* start spinning and record maximum radius for every sector */
+    int num_sector = 30;
+    double angle = 0.0;
+    int id_sector = 0;
+    double current_radius = 0.0;
+    /* tick & tock vector for cross and dot production */
+    Vector3D v_tick;
+    v_tick.x = tick_x - center_x;
+    v_tick.y = tick_y - center_y;
+    v_tick.z = tick_z - center_z;
+    Vector3D v_tock;
+    double radius_list[num_sector];
+    for (i = 0; i < num_sector; ++i) {
+        radius_list[i] = 0.0;
+    }
+    /* loop and fill radius_list */
+    for (i = 0; i < num_points_inlet; i++)
+    {
+        v_tock.x = centroids[i][0] - center_x;
+        v_tock.y = centroids[i][1] - center_y;
+        v_tock.z = centroids[i][2] - center_z;
+        angle = getDegAngle(v_tick, v_tock);
+        id_sector = floor((angle + PI) / (2 * PI / num_sector));
+        if (id_sector < 0) {
+            id_sector = 0;
+        }
+        if (id_sector >= num_sector) {
+            id_sector = num_sector - 1;
+        }
+        current_radius = sqrt(pow(v_tock.x, 2) + pow(v_tock.y, 2) + pow(v_tock.z, 2));
+        if (current_radius > radius_list[id_sector]) {
+            radius_list[id_sector] = current_radius;
+        }
+    }
+
+        /* clean radius list and check (sometimes there are no nodes in the sector) */
+        for (i = 0; i < num_sector; ++i) {
+            if (radius_list[i] == 0.0) {
+                radius_list[i] = tick_radius_record;
+            }
+        }
+
+    /* assign parabolic profile */
+    begin_f_loop(f, thread)
+    {
+        F_CENTROID(x, f, thread);
+        /* current_time = CURRENT_TIME */
+        int current_time_id = (int)floor(CURRENT_TIME / FIXED_TIME_STEP);
+        double current_Q_ratio = Q_array[current_time_id];
+        curr_x = x[0]; /* x[0] is x coordinate */
+        curr_y = x[1]; /* x[1] is y coordinate */
+        curr_z = x[2]; /* x[2] is z coordinate */
+
+        v_tock.x = x[0] - center_x;
+        v_tock.y = x[1] - center_y;
+        v_tock.z = x[2] - center_z;
+        angle = getDegAngle(v_tick, v_tock);
+        id_sector = floor((angle + PI) / (2 * PI / num_sector));
+        if (id_sector < 0) {
+            id_sector = 0;
+        }
+        if (id_sector >= num_sector) {
+            id_sector = num_sector - 1;
+        }
+        current_radius = radius_list[id_sector];
+
+        /* write inlet velocity profile - need to centre the x,y,z coords and divide by Rref^2 */
+        F_PROFILE(f, thread, position) = current_Q_ratio * VINREF * (1 + VIN) * (1 - (pow((curr_x - center_x), 2) + pow((curr_y - center_y), 2) + pow((curr_z - center_z), 2)) / (current_radius * current_radius));
+    }
+    end_f_loop(f, thread)
+}

cfd_data/ztUSO0doTz_aneurysm1/regularization.json

@@ -0,0 +1,206 @@
+{
+  "input": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/ImperialNHS_fix/ztUSO0doTz_aneurysm1/geomagic_processed.obj",
+  "tolerance": 0.25,
+  "mode": "dome_normalized",
+  "dome_sac_mm": 6.901136426534664,
+  "stopping": "relaxed",
+  "snap_levels": [
+    -1.0,
+    -0.5,
+    -0.25,
+    0.0,
+    0.25
+  ],
+  "assessment": {
+    "needs_regularization": true,
+    "worst_target_excess_sd": 1.4825524180316803,
+    "tolerance_sd": -1.0,
+    "signed_excess_sd": {
+      "0.3": 1.064202773750122,
+      "0.38": 1.1474416730080588,
+      "0.47": 1.2586188292634974,
+      "0.58": 1.3253231972560124,
+      "0.72": 1.4081265837491121,
+      "0.9": 1.4825524180316803,
+      "1.1": 1.4778537641830447,
+      "1.35": 1.4059503882135167
+    },
+    "verdict": "rougher_than_reference",
+    "guard_scale": null,
+    "guard_below_band": null,
+    "target_scales": [
+      0.3,
+      0.38,
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1,
+      1.35
+    ],
+    "measured_at_edge": 0.13602009439404106,
+    "edge_after_measurement_remesh": 0.11182834876280062,
+    "remesher": "auto",
+    "n_seeds": 4000,
+    "elapsed_s": 50.58,
+    "sac_span_mm": 6.901136426534664,
+    "alpha": 0.8911575746211065,
+    "stopping": "relaxed",
+    "reference_sac_mm": 6.15,
+    "target_scales_used": [
+      0.3,
+      0.38,
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1,
+      1.35
+    ],
+    "target_scales_dropped": {
+      "1.65": "1.852 mm real: above the 1.60 mm calibre ceiling"
+    },
+    "scales_in_real_mm": {
+      "0.3": 0.3366408012943738,
+      "0.38": 0.4264116816395402,
+      "0.47": 0.5274039220278522,
+      "0.58": 0.650838882502456,
+      "0.72": 0.8079379231064971,
+      "0.9": 1.0099224038831214,
+      "1.1": 1.2343496047460374,
+      "1.35": 1.5148836058246822
+    }
+  },
+  "forward": {
+    "status": "stalled_at_overshoot_limit",
+    "converged": false,
+    "guard_scale_below_reference_at_input": false,
+    "smoother": "mcf",
+    "remesher": "auto",
+    "sigma_step_mm": 0.08,
+    "tolerance_sd": 0.25,
+    "time_budget_s": null,
+    "overshoot_limit_sd": -3.0,
+    "guard_tolerance_sd": 1000000.0,
+    "target_scales": [
+      0.3,
+      0.38,
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1,
+      1.35
+    ],
+    "guard_scale": null,
+    "rounds": 10,
+    "total_sigma_mm": 0.2529822128134704,
+    "target_edge": 0.13602009439404106,
+    "export_edge": 0.11763279984998606,
+    "metrics_measured_at_edge": 0.13602009439404106,
+    "n_vertices_in": 32128,
+    "n_vertices_out": 31923,
+    "n_seeds_used": 4000,
+    "elapsed_s": 148.27,
+    "edge_out": 0.09368584887160551,
+    "quality_out": 0.982717212441033,
+    "smoothing_displacement_mm": 0.09041160137488423,
+    "surface_deviation_vs_original_max_mm": 0.09285771019041826,
+    "surface_deviation_vs_original_mean_mm": 0.011190368256327557,
+    "patch_truncation_fraction": {
+      "0.3": 0.0,
+      "0.38": 0.0,
+      "0.47": 0.0,
+      "0.58": 0.0,
+      "0.72": 0.0,
+      "0.9": 0.0,
+      "1.1": 0.0,
+      "1.35": 0.0
+    },
+    "signed_excess_before": {
+      "0.3": 1.064202773750122,
+      "0.38": 1.1474416730080588,
+      "0.47": 1.2586188292634974,
+      "0.58": 1.3253231972560124,
+      "0.72": 1.4081265837491121,
+      "0.9": 1.4825524180316803,
+      "1.1": 1.4778537641830447,
+      "1.35": 1.4059503882135167
+    },
+    "signed_excess_after": {
+      "0.3": -0.9723714411471963,
+      "0.38": -0.3708530075902898,
+      "0.47": 0.2544058227560785,
+      "0.58": 0.6771240171294002,
+      "0.72": 0.9911124994475297,
+      "0.9": 1.2253384461421974,
+      "1.1": 1.3281597170036226,
+      "1.35": 1.332752704857467
+    },
+    "below_band_after": {
+      "0.3": 0.2627788973614826,
+      "0.38": 0.0,
+      "0.47": 0.0,
+      "0.58": 0.0,
+      "0.72": 0.0,
+      "0.9": 0.0,
+      "1.1": 0.0,
+      "1.35": 0.0
+    },
+    "input_inspection": {
+      "n_vertices": 32128,
+      "n_faces": 64000,
+      "bbox_diagonal": 27.523036207293455,
+      "watertight": false,
+      "n_components": 2,
+      "n_degenerate_faces": 0,
+      "edge_mean": 0.09411790269173774,
+      "edge_cv": 0.15811944577372344,
+      "n_boundary_vertices": 258,
+      "warnings": [
+        "2 disconnected components"
+      ]
+    },
+    "reference_cases": 323,
+    "sac_span_mm": 6.901136426534664,
+    "alpha": 0.8911575746211065,
+    "stopping": "relaxed",
+    "reference_sac_mm": 6.15,
+    "target_scales_used": [
+      0.3,
+      0.38,
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1,
+      1.35
+    ],
+    "target_scales_dropped": {
+      "1.65": "1.852 mm real: above the 1.60 mm calibre ceiling"
+    },
+    "scales_in_real_mm": {
+      "0.3": 0.3366408012943738,
+      "0.38": 0.4264116816395402,
+      "0.47": 0.5274039220278522,
+      "0.58": 0.650838882502456,
+      "0.72": 0.8079379231064971,
+      "0.9": 1.0099224038831214,
+      "1.1": 1.2343496047460374,
+      "1.35": 1.5148836058246822
+    },
+    "surface_deviation_vs_original_max_mm_real": 0.10419897988287714,
+    "surface_deviation_vs_original_mean_mm_real": 0.012557115121964111,
+    "smoothing_displacement_mm_real": 0.10145411311049513,
+    "total_sigma_mm_real": 0.28388044944916824,
+    "edge_out_real": 0.10512826411360296
+  },
+  "cap_shift_mm": [
+    0.034737820828662995,
+    0.041688488270283264,
+    0.06185494895383642
+  ],
+  "action": "regularized",
+  "surface_used": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/ImperialNHS_fix/ztUSO0doTz_aneurysm1/ghd_surface_regularized.vtp",
+  "reason": "roughness above reference (worst target excess +1.48 SD); regularizer status stalled_at_overshoot_limit"
+}

cfd_data/ztUSO0doTz_aneurysm1/wall_data.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4b25c3a9f421fa48bf97358d71ac7bce36c059d7001c4a990c2021971ae2b56f
+size 46517006

cfd_data/ztUSO0doTz_aneurysm1/wall_mesh_registration.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f8bd018c85bd496a1ee70ac4b93ee911c368817afdfac833b12da8f8cf089708
+size 4116841