Remove cfd_data_fix (merged into cfd_data) and the mesh folders angioflow_fix, angioflow_fix_batch2

angioflow_fix/VbMgxonVZy_aneurysm1/branch_ranking.npy

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:edf57b3e7cc4d837db7a3b400e84ffa2cc07b6adc347edef9feabbc11c5183cb
-size 144

angioflow_fix/VbMgxonVZy_aneurysm1/forward_fusion_info.npz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:f5c1f2cd68fa72bb3ba657ce86e51a0c2bc8df4005281416615a8a4e02f1bd59
-size 5554

angioflow_fix/VbMgxonVZy_aneurysm1/fusion_info_extruded.npz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:e20696b9f621588c936e468f164ee212d66c9da51d7c2a95b8ce3981e44552ed
-size 7282

angioflow_fix/VbMgxonVZy_aneurysm1/geomagic_processed.obj

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:6a4603360e8329936133cc93779cddc54993cdd3b776a5c55027f9c7dee1ef2a
-size 16479320

angioflow_fix/VbMgxonVZy_aneurysm1/ghd_forward_fusion_info.npz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:9107323e092d31c4e7cfc674e7b966f5d2056f6396eb8643d41ee407e8b1c8f3
-size 6370

angioflow_fix/VbMgxonVZy_aneurysm1/ghd_fusion_params.json

@@ -1,11 +0,0 @@
-{
-  "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
-}

angioflow_fix/VbMgxonVZy_aneurysm1/jnl_transient

@@ -1,24 +0,0 @@
-/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

angioflow_fix/VbMgxonVZy_aneurysm1/mesh.msh

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:f7f7bb32fd0ba5f78f4510fad758d7555053aa2b3c46475e0bf4d1062c9ff39a
-size 230451899

angioflow_fix/VbMgxonVZy_aneurysm1/mesh.vtu

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a8ea7e9f79cac5fb49b75d18277f62ffb0165fc3d2fbcf5c6fa81fc81fa7118e
-size 50633572

angioflow_fix/VbMgxonVZy_aneurysm1/parabolic_vinlet_udf_full.c

@@ -1,200 +0,0 @@
-/*
-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)
-}

angioflow_fix/VbMgxonVZy_aneurysm1/reg_mesh_regularization.json

@@ -1,194 +0,0 @@
-{
-  "input": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/angioflow_fix/VbMgxonVZy_aneurysm1/ghd_smoothed_reconstruction.obj",
-  "tolerance": 0.25,
-  "mode": "dome_normalized",
-  "dome_sac_mm": 6.100635161778703,
-  "stopping": "relaxed",
-  "snap_levels": [
-    -1.0,
-    -0.5,
-    -0.25,
-    0.0,
-    0.25
-  ],
-  "assessment": {
-    "needs_regularization": true,
-    "worst_target_excess_sd": 1.4728782397338716,
-    "tolerance_sd": -1.0,
-    "signed_excess_sd": {
-      "0.38": 1.4728782397338716,
-      "0.47": 0.8569247796676103,
-      "0.58": 0.3549275633212668,
-      "0.72": 0.02365676927697215,
-      "0.9": -0.20869661304518908,
-      "1.1": -0.36555099714230327,
-      "1.35": -0.4794468203487245
-    },
-    "verdict": "rougher_than_reference",
-    "guard_scale": null,
-    "guard_below_band": null,
-    "target_scales": [
-      0.38,
-      0.47,
-      0.58,
-      0.72,
-      0.9,
-      1.1,
-      1.35
-    ],
-    "measured_at_edge": 0.13602009439404106,
-    "edge_after_measurement_remesh": 0.1122127351220293,
-    "remesher": "auto",
-    "n_seeds": 4000,
-    "elapsed_s": 87.7,
-    "sac_span_mm": 6.100635161778703,
-    "alpha": 1.0080917538768053,
-    "stopping": "relaxed",
-    "reference_sac_mm": 6.15,
-    "target_scales_used": [
-      0.38,
-      0.47,
-      0.58,
-      0.72,
-      0.9,
-      1.1,
-      1.35
-    ],
-    "target_scales_dropped": {
-      "0.3": "0.298 mm real: below the 0.30 mm resolution floor",
-      "1.65": "1.637 mm real: above the 1.60 mm calibre ceiling"
-    },
-    "scales_in_real_mm": {
-      "0.38": 0.3769498148741312,
-      "0.47": 0.4662274026074781,
-      "0.58": 0.5753444542815687,
-      "0.72": 0.7142207018667749,
-      "0.9": 0.8927758773334687,
-      "1.1": 1.0911705167409063,
-      "1.35": 1.339163816000203
-    }
-  },
-  "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": [
-      0.38,
-      0.47,
-      0.58,
-      0.72,
-      0.9,
-      1.1,
-      1.35
-    ],
-    "guard_scale": null,
-    "rounds": 2,
-    "total_sigma_mm": 0.1131370849898476,
-    "target_edge": 0.13602009439404106,
-    "export_edge": 0.1330681115117383,
-    "metrics_measured_at_edge": 0.13602009439404106,
-    "n_vertices_in": 4398,
-    "n_vertices_out": 58607,
-    "n_seeds_used": 4000,
-    "elapsed_s": 286.56,
-    "edge_out": 0.10723257815475745,
-    "quality_out": 0.9853305004334999,
-    "smoothing_displacement_mm": 0.053639460141318346,
-    "surface_deviation_vs_original_max_mm": 0.06130068761993199,
-    "surface_deviation_vs_original_mean_mm": 0.0025633040331445403,
-    "patch_truncation_fraction": {
-      "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": {
-      "0.38": 1.4728782397338716,
-      "0.47": 0.8569247796676103,
-      "0.58": 0.3549275633212668,
-      "0.72": 0.02365676927697215,
-      "0.9": -0.20869661304518908,
-      "1.1": -0.36555099714230327,
-      "1.35": -0.4794468203487245
-    },
-    "signed_excess_after": {
-      "0.38": -0.6097154149343187,
-      "0.47": -0.5904019542733746,
-      "0.58": -0.556590834128628,
-      "0.72": -0.498628276241753,
-      "0.9": -0.4889418793653347,
-      "1.1": -0.5025523668618388,
-      "1.35": -0.5415512482551077
-    },
-    "below_band_after": {
-      "0.38": 0.0,
-      "0.47": 0.0,
-      "0.58": 0.0,
-      "0.72": 0.0,
-      "0.9": 0.0,
-      "1.1": 0.01276913765366155,
-      "1.35": 0.08459766472590309
-    },
-    "input_inspection": {
-      "n_vertices": 4398,
-      "n_faces": 8704,
-      "bbox_diagonal": 33.78267662085837,
-      "watertight": false,
-      "n_components": 1,
-      "n_degenerate_faces": 0,
-      "edge_mean": 0.42592930828000103,
-      "edge_cv": 0.4979531224503949,
-      "n_boundary_vertices": 96,
-      "warnings": []
-    },
-    "reference_cases": 323,
-    "sac_span_mm": 6.100635161778703,
-    "alpha": 1.0080917538768053,
-    "stopping": "relaxed",
-    "reference_sac_mm": 6.15,
-    "target_scales_used": [
-      0.38,
-      0.47,
-      0.58,
-      0.72,
-      0.9,
-      1.1,
-      1.35
-    ],
-    "target_scales_dropped": {
-      "0.3": "0.298 mm real: below the 0.30 mm resolution floor",
-      "1.65": "1.637 mm real: above the 1.60 mm calibre ceiling"
-    },
-    "scales_in_real_mm": {
-      "0.38": 0.3769498148741312,
-      "0.47": 0.4662274026074781,
-      "0.58": 0.5753444542815687,
-      "0.72": 0.7142207018667749,
-      "0.9": 0.8927758773334687,
-      "1.1": 1.0911705167409063,
-      "1.35": 1.339163816000203
-    },
-    "surface_deviation_vs_original_max_mm_real": 0.06080863907892187,
-    "surface_deviation_vs_original_mean_mm_real": 0.0025427288967367063,
-    "smoothing_displacement_mm_real": 0.05320890676373234,
-    "total_sigma_mm_real": 0.11222895590084712,
-    "edge_out_real": 0.10637184337871482
-  },
-  "cap_shift_mm": [
-    0.08960363679677848,
-    0.1498238951631755
-  ],
-  "action": "regularized",
-  "surface_used": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/angioflow_fix/VbMgxonVZy_aneurysm1/reg_mesh.vtp",
-  "reason": "roughness above reference (worst target excess +1.47 SD); regularizer status converged"
-}

angioflow_fix/VyKbIURnoD_aneurysm1/branch_ranking.npy

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:edf57b3e7cc4d837db7a3b400e84ffa2cc07b6adc347edef9feabbc11c5183cb
-size 144

angioflow_fix/VyKbIURnoD_aneurysm1/forward_fusion_info.npz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:ca3df70d6103694318c9c003ccc75f82ff5ba4318f3ee2e62c44176459924746
-size 5178

angioflow_fix/VyKbIURnoD_aneurysm1/fusion_info_extruded.npz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:14069d1388d05f8bf895cdfec3e46a1c5aafd9757a24b03bd7a235dbd82cd31f
-size 7290

angioflow_fix/VyKbIURnoD_aneurysm1/geomagic_processed.obj

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:73400b01dde66ccbdb9e0177cbf64eed83a5a3504ed7902e2ce57441ce301338
-size 19031123

angioflow_fix/VyKbIURnoD_aneurysm1/ghd_forward_fusion_info.npz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:34e2d48487a70eee7ef9adf337379c47484b120b36dfe45fb7b82edf3ffc72b0
-size 6138

angioflow_fix/VyKbIURnoD_aneurysm1/ghd_fusion_params.json

@@ -1,11 +0,0 @@
-{
-  "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
-}

angioflow_fix/VyKbIURnoD_aneurysm1/jnl_transient

@@ -1,24 +0,0 @@
-/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

angioflow_fix/VyKbIURnoD_aneurysm1/mesh.msh

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:b07fe393466bf48c0793a02ed02d32ee079145b3787ca515b9554e25090671ea
-size 211146121

angioflow_fix/VyKbIURnoD_aneurysm1/mesh.vtu

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:4d6236d62a3daa6af8cb573786c7df3683a77f0c5b9a9890a18b56a13238b23a
-size 46448740

angioflow_fix/VyKbIURnoD_aneurysm1/parabolic_vinlet_udf_full.c

@@ -1,200 +0,0 @@
-/*
-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)
-}

angioflow_fix/VyKbIURnoD_aneurysm1/reg_mesh_regularization.json

@@ -1,194 +0,0 @@
-{
-  "input": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/angioflow_fix/VyKbIURnoD_aneurysm1/ghd_smoothed_reconstruction.obj",
-  "tolerance": 0.25,
-  "mode": "dome_normalized",
-  "dome_sac_mm": 8.491574401105545,
-  "stopping": "relaxed",
-  "snap_levels": [
-    -1.0,
-    -0.5,
-    -0.25,
-    0.0,
-    0.25
-  ],
-  "assessment": {
-    "needs_regularization": true,
-    "worst_target_excess_sd": 2.714910970639313,
-    "tolerance_sd": -1.0,
-    "signed_excess_sd": {
-      "0.3": 2.714910970639313,
-      "0.38": 2.018037437259873,
-      "0.47": 1.4800591173270503,
-      "0.58": 1.0202181211389785,
-      "0.72": 0.6788783207714024,
-      "0.9": 0.4060114853825217,
-      "1.1": 0.21154787577521605
-    },
-    "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": 0.11225088035572318,
-    "remesher": "auto",
-    "n_seeds": 4000,
-    "elapsed_s": 34.0,
-    "sac_span_mm": 8.491574401105545,
-    "alpha": 0.7242473196960169,
-    "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": "1.864 mm real: above the 1.60 mm calibre ceiling",
-      "1.65": "2.278 mm real: above the 1.60 mm calibre ceiling"
-    },
-    "scales_in_real_mm": {
-      "0.3": 0.41422314151734363,
-      "0.38": 0.5246826459219686,
-      "0.47": 0.6489495883771716,
-      "0.58": 0.8008314069335309,
-      "0.72": 0.9941355396416247,
-      "0.9": 1.2426694245520309,
-      "1.1": 1.5188181855635934
-    }
-  },
-  "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": 3,
-    "total_sigma_mm": 0.13856406460551018,
-    "target_edge": 0.13602009439404106,
-    "export_edge": 0.09560064619987423,
-    "metrics_measured_at_edge": 0.13602009439404106,
-    "n_vertices_in": 4080,
-    "n_vertices_out": 60949,
-    "n_seeds_used": 4000,
-    "elapsed_s": 173.75,
-    "edge_out": 0.07581283365877366,
-    "quality_out": 0.9820395364749507,
-    "smoothing_displacement_mm": 0.04090644226812702,
-    "surface_deviation_vs_original_max_mm": 0.054067277155795124,
-    "surface_deviation_vs_original_mean_mm": 0.004046687348426681,
-    "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": 2.714910970639313,
-      "0.38": 2.018037437259873,
-      "0.47": 1.4800591173270503,
-      "0.58": 1.0202181211389785,
-      "0.72": 0.6788783207714024,
-      "0.9": 0.4060114853825217,
-      "1.1": 0.21154787577521605
-    },
-    "signed_excess_after": {
-      "0.3": -0.511323114215351,
-      "0.38": -0.29813799766923194,
-      "0.47": -0.051634183390755005,
-      "0.58": 0.09020605908013274,
-      "0.72": 0.16411852909519534,
-      "0.9": 0.14685599710872674,
-      "1.1": 0.07091448839711938
-    },
-    "below_band_after": {
-      "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
-    },
-    "input_inspection": {
-      "n_vertices": 4080,
-      "n_faces": 8087,
-      "bbox_diagonal": 21.115143636140687,
-      "watertight": false,
-      "n_components": 1,
-      "n_degenerate_faces": 0,
-      "edge_mean": 0.3130341720300407,
-      "edge_cv": 0.5044077678968825,
-      "n_boundary_vertices": 73,
-      "warnings": []
-    },
-    "reference_cases": 323,
-    "sac_span_mm": 8.491574401105545,
-    "alpha": 0.7242473196960169,
-    "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": "1.864 mm real: above the 1.60 mm calibre ceiling",
-      "1.65": "2.278 mm real: above the 1.60 mm calibre ceiling"
-    },
-    "scales_in_real_mm": {
-      "0.3": 0.41422314151734363,
-      "0.38": 0.5246826459219686,
-      "0.47": 0.6489495883771716,
-      "0.58": 0.8008314069335309,
-      "0.72": 0.9941355396416247,
-      "0.9": 1.2426694245520309,
-      "1.1": 1.5188181855635934
-    },
-    "surface_deviation_vs_original_max_mm_real": 0.07465305798920788,
-    "surface_deviation_vs_original_mean_mm_real": 0.005587438487345963,
-    "smoothing_displacement_mm_real": 0.05648131674867142,
-    "total_sigma_mm_real": 0.19132147380768863,
-    "edge_out_real": 0.10467810041823011
-  },
-  "cap_shift_mm": [
-    0.09705279061445618,
-    0.1622399275909303
-  ],
-  "action": "regularized",
-  "surface_used": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/angioflow_fix/VyKbIURnoD_aneurysm1/reg_mesh.vtp",
-  "reason": "roughness above reference (worst target excess +2.71 SD); regularizer status converged"
-}

angioflow_fix/W1GD4X6con_aneurysm1/branch_ranking.npy

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:edf57b3e7cc4d837db7a3b400e84ffa2cc07b6adc347edef9feabbc11c5183cb
-size 144

angioflow_fix/W1GD4X6con_aneurysm1/forward_fusion_info.npz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:0a6e8149b9fa043dda984caed5a959b94838733962b54ba3da44400f294b8c80
-size 5784

angioflow_fix/W1GD4X6con_aneurysm1/fusion_info_extruded.npz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:4f089ac98ce3652eebe815079f1212756293dd651087e7e61b907740a9283874
-size 7378

angioflow_fix/W1GD4X6con_aneurysm1/geomagic_processed.obj

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:68513a333549de1d4afbee938cdfdad7a845144a6451cd02167b1e3e7441eb59
-size 19999620

angioflow_fix/W1GD4X6con_aneurysm1/ghd_forward_fusion_info.npz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:87d3f50fdd78d9048981d63613935276655b8833d4a56319043fdb41f1f2021b
-size 6322

angioflow_fix/W1GD4X6con_aneurysm1/ghd_fusion_params.json

@@ -1,11 +0,0 @@
-{
-  "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
-}

angioflow_fix/W1GD4X6con_aneurysm1/jnl_transient

@@ -1,24 +0,0 @@
-/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