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0bjVkRg2pM_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
+}

0bjVkRg2pM_aneurysm1/jnl_transient

@@ -0,0 +1,24 @@
+/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 pressure-outlet
+/define/user-defined/use-built-in-compiler? yes
+/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/compute-defaults velocity-inlet surface4
+/solve/initialize/initialize-flow
+/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 10
+/solve/set/time-step 0.001
+/solve/dual-time-iterate 1600 100
+/file/write-case mesh_new.cas yes
+/file/write-data mesh_new.dat yes
+exit
+yes

0bjVkRg2pM_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)
+}

0bjVkRg2pM_aneurysm1/regularization.json

@@ -0,0 +1,187 @@
+{
+  "input": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/ImperialNHS_fix/0bjVkRg2pM_aneurysm1/geomagic_processed.obj",
+  "tolerance": 0.25,
+  "mode": "dome_normalized",
+  "dome_sac_mm": 8.39741744541938,
+  "stopping": "relaxed",
+  "assessment": {
+    "needs_regularization": true,
+    "worst_target_excess_sd": 1.9250131827234862,
+    "tolerance_sd": 0.25,
+    "signed_excess_sd": {
+      "0.3": 1.7083360249963617,
+      "0.38": 1.8622068143385462,
+      "0.47": 1.9250131827234862,
+      "0.58": 1.850666677370994,
+      "0.72": 1.7426554428198795,
+      "0.9": 1.6096592485956958,
+      "1.1": 1.4809921329366942
+    },
+    "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
+    ],
+    "measured_at_edge": 0.13602009439404106,
+    "edge_after_measurement_remesh": 0.11195124294675476,
+    "remesher": "auto",
+    "n_seeds": 4000,
+    "elapsed_s": 53.0,
+    "sac_span_mm": 8.39741744541938,
+    "alpha": 0.7323680214748285,
+    "stopping": "relaxed",
+    "reference_sac_mm": 6.15,
+    "target_scales_used": [
+      0.3,
+      0.38,
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1
+    ],
+    "target_scales_dropped": {
+      "1.35": "1.843 mm real: above the 1.60 mm calibre ceiling",
+      "1.65": "2.253 mm real: above the 1.60 mm calibre ceiling"
+    },
+    "scales_in_real_mm": {
+      "0.3": 0.40963011928875026,
+      "0.38": 0.5188648177657503,
+      "0.47": 0.6417538535523754,
+      "0.58": 0.7919515639582504,
+      "0.72": 0.9831122862930005,
+      "0.9": 1.228890357866251,
+      "1.1": 1.501977104058751
+    }
+  },
+  "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
+    ],
+    "guard_scale": null,
+    "rounds": 25,
+    "total_sigma_mm": 0.39999999999999997,
+    "target_edge": 0.13602009439404106,
+    "export_edge": 0.09667257883467736,
+    "metrics_measured_at_edge": 0.13602009439404106,
+    "n_vertices_in": 49780,
+    "n_vertices_out": 36007,
+    "n_seeds_used": 4000,
+    "elapsed_s": 1553.56,
+    "edge_out": 0.0764943650945228,
+    "quality_out": 0.9824337594895282,
+    "smoothing_displacement_mm": 0.25766934967331173,
+    "surface_deviation_vs_original_max_mm": 0.26397545917042087,
+    "surface_deviation_vs_original_mean_mm": 0.024390649658802395,
+    "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
+    },
+    "signed_excess_before": {
+      "0.3": 1.7083360249963617,
+      "0.38": 1.8622068143385462,
+      "0.47": 1.9250131827234862,
+      "0.58": 1.850666677370994,
+      "0.72": 1.7426554428198795,
+      "0.9": 1.6096592485956958,
+      "1.1": 1.4809921329366942
+    },
+    "signed_excess_after": {
+      "0.3": -1.2849885342544964,
+      "0.38": -0.633000560821949,
+      "0.47": 0.010993469178017419,
+      "0.58": 0.44962390383689727,
+      "0.72": 0.757708666272952,
+      "0.9": 0.9583816541393957,
+      "1.1": 1.0641958129553086
+    },
+    "below_band_after": {
+      "0.3": 0.9206798574260945,
+      "0.38": 0.28886742870641396,
+      "0.47": 0.0,
+      "0.58": 0.0,
+      "0.72": 0.0,
+      "0.9": 0.0,
+      "1.1": 0.0
+    },
+    "input_inspection": {
+      "n_vertices": 49780,
+      "n_faces": 99320,
+      "bbox_diagonal": 20.534229166503618,
+      "watertight": false,
+      "n_components": 1,
+      "n_degenerate_faces": 0,
+      "edge_mean": 0.06604746105644796,
+      "edge_cv": 0.1622334486933629,
+      "n_boundary_vertices": 242,
+      "warnings": []
+    },
+    "reference_cases": 323,
+    "sac_span_mm": 8.39741744541938,
+    "alpha": 0.7323680214748285,
+    "stopping": "relaxed",
+    "reference_sac_mm": 6.15,
+    "target_scales_used": [
+      0.3,
+      0.38,
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1
+    ],
+    "target_scales_dropped": {
+      "1.35": "1.843 mm real: above the 1.60 mm calibre ceiling",
+      "1.65": "2.253 mm real: above the 1.60 mm calibre ceiling"
+    },
+    "scales_in_real_mm": {
+      "0.3": 0.40963011928875026,
+      "0.38": 0.5188648177657503,
+      "0.47": 0.6417538535523754,
+      "0.58": 0.7919515639582504,
+      "0.72": 0.9831122862930005,
+      "0.9": 1.228890357866251,
+      "1.1": 1.501977104058751
+    },
+    "surface_deviation_vs_original_max_mm_real": 0.36044099609760705,
+    "surface_deviation_vs_original_mean_mm_real": 0.0333038157642178,
+    "smoothing_displacement_mm_real": 0.3518304214791113,
+    "total_sigma_mm_real": 0.5461734923850002,
+    "edge_out_real": 0.10444798632862196
+  },
+  "cap_shift_mm": [
+    0.03219756896694232,
+    0.0178458257340387
+  ],
+  "action": "regularized",
+  "surface_used": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/ImperialNHS_fix/0bjVkRg2pM_aneurysm1/ghd_surface_regularized.vtp",
+  "reason": "roughness above reference (worst target excess +1.93 SD); regularizer status stalled_at_overshoot_limit"
+}

5y61ssrDxn_aneurysm1/flowsplit_ratio.txt

@@ -0,0 +1 @@
+0.9294091852096452 0.0705908147903548

5y61ssrDxn_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
+}

5y61ssrDxn_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

5y61ssrDxn_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)
+}

5y61ssrDxn_aneurysm1/regularization.json

@@ -0,0 +1,195 @@
+{
+  "input": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/ImperialNHS_fix/5y61ssrDxn_aneurysm1/geomagic_processed.obj",
+  "tolerance": -1.0,
+  "mode": "dome_normalized",
+  "dome_sac_mm": 4.583339502637903,
+  "stopping": "relaxed",
+  "snap_levels": [
+    -1.0,
+    -0.5,
+    -0.25,
+    0.0,
+    0.25
+  ],
+  "assessment": {
+    "needs_regularization": true,
+    "worst_target_excess_sd": -0.873035365261764,
+    "tolerance_sd": -1.0,
+    "signed_excess_sd": {
+      "0.47": -1.2039217772062059,
+      "0.58": -1.0839319812643895,
+      "0.72": -0.9666678991453571,
+      "0.9": -0.8906791145260463,
+      "1.1": -0.873035365261764,
+      "1.35": -0.8906862845569088,
+      "1.65": -0.9310212585328028
+    },
+    "verdict": "rougher_than_reference",
+    "guard_scale": null,
+    "guard_below_band": null,
+    "target_scales": [
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1,
+      1.35,
+      1.65
+    ],
+    "measured_at_edge": 0.13602009439404106,
+    "edge_after_measurement_remesh": 0.11307766443143615,
+    "remesher": "auto",
+    "n_seeds": 4000,
+    "elapsed_s": 222.71,
+    "sac_span_mm": 4.583339502637903,
+    "alpha": 1.3418163756929677,
+    "stopping": "relaxed",
+    "reference_sac_mm": 6.15,
+    "target_scales_used": [
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1,
+      1.35,
+      1.65
+    ],
+    "target_scales_dropped": {
+      "0.3": "0.224 mm real: below the 0.30 mm resolution floor",
+      "0.38": "0.283 mm real: below the 0.30 mm resolution floor"
+    },
+    "scales_in_real_mm": {
+      "0.47": 0.3502714741853356,
+      "0.58": 0.43224990431381843,
+      "0.72": 0.5365860881137057,
+      "0.9": 0.6707326101421321,
+      "1.1": 0.8197843012848282,
+      "1.35": 1.0060989152131983,
+      "1.65": 1.229676451927242
+    }
+  },
+  "forward": {
+    "status": "converged",
+    "converged": true,
+    "guard_scale_below_reference_at_input": false,
+    "smoother": "mcf",
+    "remesher": "auto",
+    "sigma_step_mm": 0.08,
+    "tolerance_sd": -1.0,
+    "time_budget_s": null,
+    "overshoot_limit_sd": -3.0,
+    "guard_tolerance_sd": 1000000.0,
+    "target_scales": [
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1,
+      1.35,
+      1.65
+    ],
+    "guard_scale": null,
+    "rounds": 8,
+    "total_sigma_mm": 0.22627416997969524,
+    "target_edge": 0.13602009439404106,
+    "export_edge": 0.17711976159147175,
+    "metrics_measured_at_edge": 0.13602009439404106,
+    "n_vertices_in": 52397,
+    "n_vertices_out": 39625,
+    "n_seeds_used": 4000,
+    "elapsed_s": 494.99,
+    "edge_out": 0.1404887728035712,
+    "quality_out": 0.9824560760710367,
+    "smoothing_displacement_mm": 0.0636584156125501,
+    "surface_deviation_vs_original_max_mm": 0.0650820115793598,
+    "surface_deviation_vs_original_mean_mm": 0.004618744061175878,
+    "patch_truncation_fraction": {
+      "0.47": 0.0,
+      "0.58": 0.0,
+      "0.72": 0.0,
+      "0.9": 0.0,
+      "1.1": 0.0,
+      "1.35": 0.0,
+      "1.65": 0.0
+    },
+    "signed_excess_before": {
+      "0.47": -1.2039217772062059,
+      "0.58": -1.0839319812643895,
+      "0.72": -0.9666678991453571,
+      "0.9": -0.8906791145260463,
+      "1.1": -0.873035365261764,
+      "1.35": -0.8906862845569088,
+      "1.65": -0.9310212585328028
+    },
+    "signed_excess_after": {
+      "0.47": -2.5582280824811665,
+      "0.58": -1.9551921747443906,
+      "0.72": -1.495175559719543,
+      "0.9": -1.2065245156853472,
+      "1.1": -1.0727885656602327,
+      "1.35": -1.013828714327316,
+      "1.65": -1.0074577602266206
+    },
+    "below_band_after": {
+      "0.47": 0.9061867843022319,
+      "0.58": 0.622265966990767,
+      "0.72": 0.42680971434422216,
+      "0.9": 0.3414645781035057,
+      "1.1": 0.35518279518603063,
+      "1.35": 0.42962041480392643,
+      "1.65": 0.5280144560822401
+    },
+    "input_inspection": {
+      "n_vertices": 52397,
+      "n_faces": 104418,
+      "bbox_diagonal": 38.82508287977771,
+      "watertight": false,
+      "n_components": 1,
+      "n_degenerate_faces": 0,
+      "edge_mean": 0.12248360361423062,
+      "edge_cv": 0.14967390606913206,
+      "n_boundary_vertices": 378,
+      "warnings": []
+    },
+    "reference_cases": 323,
+    "sac_span_mm": 4.583339502637903,
+    "alpha": 1.3418163756929677,
+    "stopping": "relaxed",
+    "reference_sac_mm": 6.15,
+    "target_scales_used": [
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1,
+      1.35,
+      1.65
+    ],
+    "target_scales_dropped": {
+      "0.3": "0.224 mm real: below the 0.30 mm resolution floor",
+      "0.38": "0.283 mm real: below the 0.30 mm resolution floor"
+    },
+    "scales_in_real_mm": {
+      "0.47": 0.3502714741853356,
+      "0.58": 0.43224990431381843,
+      "0.72": 0.5365860881137057,
+      "0.9": 0.6707326101421321,
+      "1.1": 0.8197843012848282,
+      "1.35": 1.0060989152131983,
+      "1.65": 1.229676451927242
+    },
+    "surface_deviation_vs_original_max_mm_real": 0.04850291944436052,
+    "surface_deviation_vs_original_mean_mm_real": 0.0034421580663677423,
+    "smoothing_displacement_mm_real": 0.04744197251257598,
+    "total_sigma_mm_real": 0.16863273848691718,
+    "edge_out_real": 0.10470044586467143
+  },
+  "cap_shift_mm": [
+    0.11307825938419881,
+    0.025907809801701525,
+    0.07275925079758963
+  ],
+  "action": "regularized",
+  "surface_used": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/ImperialNHS_fix/5y61ssrDxn_aneurysm1/ghd_surface_regularized.vtp",
+  "reason": "roughness above reference (worst target excess -0.87 SD); regularizer status converged"
+}

8jD72Wn56o_aneurysm1/flowsplit_ratio.txt

@@ -0,0 +1 @@
+0.5672649521083006 0.4327350478916994

8jD72Wn56o_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
+}

8jD72Wn56o_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

8jD72Wn56o_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)
+}

8jD72Wn56o_aneurysm1/regularization.json

@@ -0,0 +1,188 @@
+{
+  "input": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/ImperialNHS_fix/8jD72Wn56o_aneurysm1/geomagic_processed.obj",
+  "tolerance": 0.25,
+  "mode": "dome_normalized",
+  "dome_sac_mm": 7.452851802985155,
+  "stopping": "relaxed",
+  "assessment": {
+    "needs_regularization": true,
+    "worst_target_excess_sd": 0.595664184262076,
+    "tolerance_sd": 0.25,
+    "signed_excess_sd": {
+      "0.3": 0.36938812127927995,
+      "0.38": 0.3590723914645372,
+      "0.47": 0.40611088900423925,
+      "0.58": 0.465102133627508,
+      "0.72": 0.5476116242769451,
+      "0.9": 0.595664184262076,
+      "1.1": 0.5874754816002385
+    },
+    "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
+    ],
+    "measured_at_edge": 0.13602009439404106,
+    "edge_after_measurement_remesh": 0.11235428322113099,
+    "remesher": "auto",
+    "n_seeds": 4000,
+    "elapsed_s": 166.31,
+    "sac_span_mm": 7.452851802985155,
+    "alpha": 0.8251874802524167,
+    "stopping": "relaxed",
+    "reference_sac_mm": 6.15,
+    "target_scales_used": [
+      0.3,
+      0.38,
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1
+    ],
+    "target_scales_dropped": {
+      "1.35": "1.636 mm real: above the 1.60 mm calibre ceiling",
+      "1.65": "2.000 mm real: above the 1.60 mm calibre ceiling"
+    },
+    "scales_in_real_mm": {
+      "0.3": 0.36355374648708066,
+      "0.38": 0.46050141221696883,
+      "0.47": 0.569567536163093,
+      "0.58": 0.7028705765416893,
+      "0.72": 0.8725289915689936,
+      "0.9": 1.090661239461242,
+      "1.1": 1.3330304037859626
+    }
+  },
+  "forward": {
+    "status": "converged",
+    "converged": true,
+    "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
+    ],
+    "guard_scale": null,
+    "rounds": 19,
+    "total_sigma_mm": 0.3487119154832539,
+    "target_edge": 0.13602009439404106,
+    "export_edge": 0.10892474739331902,
+    "metrics_measured_at_edge": 0.13602009439404106,
+    "n_vertices_in": 49377,
+    "n_vertices_out": 37223,
+    "n_seeds_used": 4000,
+    "elapsed_s": 509.51,
+    "edge_out": 0.08638134389844261,
+    "quality_out": 0.9819217757251865,
+    "smoothing_displacement_mm": 0.15736577927885373,
+    "surface_deviation_vs_original_max_mm": 0.15756497390501487,
+    "surface_deviation_vs_original_mean_mm": 0.01249744621474062,
+    "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
+    },
+    "signed_excess_before": {
+      "0.3": 0.36938812127927995,
+      "0.38": 0.3590723914645372,
+      "0.47": 0.40611088900423925,
+      "0.58": 0.465102133627508,
+      "0.72": 0.5476116242769451,
+      "0.9": 0.595664184262076,
+      "1.1": 0.5874754816002385
+    },
+    "signed_excess_after": {
+      "0.3": -2.474751841326736,
+      "0.38": -1.9556356080985733,
+      "0.47": -1.2761575863656034,
+      "0.58": -0.6976701047517929,
+      "0.72": -0.2539807708026083,
+      "0.9": 0.05831402308979494,
+      "1.1": 0.2436135926450453
+    },
+    "below_band_after": {
+      "0.3": 1.7300814179216275,
+      "0.38": 1.046451297809277,
+      "0.47": 0.5410313851002014,
+      "0.58": 0.2033637899623517,
+      "0.72": 0.019348444551515274,
+      "0.9": 0.0,
+      "1.1": 0.0
+    },
+    "input_inspection": {
+      "n_vertices": 49377,
+      "n_faces": 98482,
+      "bbox_diagonal": 27.845990627232496,
+      "watertight": false,
+      "n_components": 1,
+      "n_degenerate_faces": 0,
+      "edge_mean": 0.07543775524790175,
+      "edge_cv": 0.1471218196676118,
+      "n_boundary_vertices": 274,
+      "warnings": []
+    },
+    "reference_cases": 323,
+    "sac_span_mm": 7.452851802985155,
+    "alpha": 0.8251874802524167,
+    "stopping": "relaxed",
+    "reference_sac_mm": 6.15,
+    "target_scales_used": [
+      0.3,
+      0.38,
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1
+    ],
+    "target_scales_dropped": {
+      "1.35": "1.636 mm real: above the 1.60 mm calibre ceiling",
+      "1.65": "2.000 mm real: above the 1.60 mm calibre ceiling"
+    },
+    "scales_in_real_mm": {
+      "0.3": 0.36355374648708066,
+      "0.38": 0.46050141221696883,
+      "0.47": 0.569567536163093,
+      "0.58": 0.7028705765416893,
+      "0.72": 0.8725289915689936,
+      "0.9": 1.090661239461242,
+      "1.1": 1.3330304037859626
+    },
+    "surface_deviation_vs_original_max_mm_real": 0.1909444552610242,
+    "surface_deviation_vs_original_mean_mm_real": 0.015144977976299124,
+    "smoothing_displacement_mm_real": 0.19070306208562093,
+    "total_sigma_mm_real": 0.422585077728744,
+    "edge_out_real": 0.10468087066955913
+  },
+  "cap_shift_mm": [
+    0.04788053007611825,
+    0.05553904274622373,
+    0.06925679845659347
+  ],
+  "action": "regularized",
+  "surface_used": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/ImperialNHS_fix/8jD72Wn56o_aneurysm1/ghd_surface_regularized.vtp",
+  "reason": "roughness above reference (worst target excess +0.60 SD); regularizer status converged"
+}

bmkieogL9h_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

bmkieogL9h_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)
+}

bmkieogL9h_aneurysm1/regularization.json

@@ -0,0 +1,188 @@
+{
+  "input": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/ImperialNHS_fix/bmkieogL9h_aneurysm1/geomagic_processed.obj",
+  "tolerance": 0.25,
+  "mode": "dome_normalized",
+  "dome_sac_mm": 7.903199282429155,
+  "stopping": "relaxed",
+  "assessment": {
+    "needs_regularization": true,
+    "worst_target_excess_sd": 0.928498674347491,
+    "tolerance_sd": 0.25,
+    "signed_excess_sd": {
+      "0.3": 0.9228527997687244,
+      "0.38": 0.8704860849584722,
+      "0.47": 0.903945489255377,
+      "0.58": 0.9195167722735331,
+      "0.72": 0.928498674347491,
+      "0.9": 0.855781395134154,
+      "1.1": 0.7468461000757843
+    },
+    "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
+    ],
+    "measured_at_edge": 0.13602009439404106,
+    "edge_after_measurement_remesh": 0.11226986146599481,
+    "remesher": "auto",
+    "n_seeds": 4000,
+    "elapsed_s": 70.97,
+    "sac_span_mm": 7.903199282429155,
+    "alpha": 0.7781658769092452,
+    "stopping": "relaxed",
+    "reference_sac_mm": 6.15,
+    "target_scales_used": [
+      0.3,
+      0.38,
+      0.47,
+      0.58,
+      0.72,
+      0.9,
+      1.1
+    ],
+    "target_scales_dropped": {
+      "1.35": "1.735 mm real: above the 1.60 mm calibre ceiling",
+      "1.65": "2.120 mm real: above the 1.60 mm calibre ceiling"
+    },
+    "scales_in_real_mm": {
+      "0.3": 0.38552191621605625,
+      "0.38": 0.48832776054033794,
+      "0.47": 0.6039843354051548,
+      "0.58": 0.7453423713510421,
+      "0.72": 0.9252525989185351,
+      "0.9": 1.1565657486481689,
+      "1.1": 1.4135803594588732
+    }
+  },
+  "forward": {
+    "status": "converged",
+    "converged": true,
+    "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,
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joCX3Lfukw_aneurysm1/flowsplit_ratio.txt

@@ -0,0 +1 @@
+0.8115248641339203 0.1884751358660796

joCX3Lfukw_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
+}

joCX3Lfukw_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