update readme

README.md

@@ -31,6 +31,24 @@ The code is only tested on Linux. To run the code:
     # Unit test
     ./tests/unit_tests "isosurface-inflator-periodic"
 
+The inflator code is used to map a vector of shape parameters to a periodic mesh of the microstructure cell, and compute the shape velocity of the shape parameters needed in the optimizations. The inflator code is called using terminal commands during the optimizations, since the cmake setup of CGAL (which is used by the inflator) may break the cmake of PolyFEM.
+
+Usage
+-------------
+
+To run a shape optimization and obtain the microstructure cell shape that corresponds to a specific target stress:
+
+    cd scripts/
+    python optimize.py 5000 \
+    ../inflator/data/patterns/2D/topologies/0105.obj \
+    --no_tile --strain 0.25 --n_samples 4
+
+where `5000` is the desired stress, the optimization will sample 4 strains from `10%` to `25%` and optimize the stress on those samples to match the desired stress.
+
+All 105 topologies used in the paper are in folder `inflator/data/patterns/2D/topologies/0105.obj`, one can provide a new `.obj` edge mesh to run the optimization on a custom cell topology. The edge mesh has to fit into the unit cube and be periodic in both directions.
+
+The above command creates a folder `result/0105_0.3_5000.0` and set up the JSON files needed to run PolyFEM.
+
 Documentation
 -------------
 

scripts/optimize.py

@@ -5,8 +5,6 @@
 marching_cube_res = 64
 internal_res = 1e-3
 
-perturbed_angle = 0
-
 def homogenized_yy_stress_error_obj(target_stress, n_shape_params):
     return {
         "type": "soft_constraint",
@@ -251,8 +249,8 @@ def load_opt_json(path):
     parser.add_argument('--barrier', type=float, default=-1)
 
     parser.add_argument('--threads', type=int, default=16)
-    parser.add_argument('--tile', action='store_true')
-    parser.add_argument('--penalize_expansion', action='store_true')
+    parser.add_argument('--no_tile', action='store_true')
+    parser.add_argument('--no_penalize_expansion', action='store_true')
     args = parser.parse_args()
 
     if not os.path.isabs(args.wire_path):
@@ -261,19 +259,32 @@ def load_opt_json(path):
         args.iso_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), args.iso_path)
     if not os.path.isabs(args.exe_path):
         args.exe_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), args.exe_path)
+    if not os.path.isabs(args.params):
+        args.params = os.path.join(os.path.dirname(os.path.realpath(__file__)), args.params)
 
     target_stress = args.stress
     strain_sample = np.linspace(0.1, args.strain, args.n_samples)
+
+    print("Optimize stress at strains", strain_sample, "to reach target stress", target_stress)
 
     wire_path = args.wire_path
     symmetry = args.symmetry
-    tile = args.tile # optimize on 2x2 tiles
-    penalize_expansion = args.penalize_expansion
+    tile = not args.no_tile # optimize on 2x2 tiles
+    penalize_expansion = not args.no_penalize_expansion
+
+    if tile:
+        print("Tile the cell to 2x2 in simulations")
+
+    if not os.path.exists(wire_path):
+        raise Exception("wire_path \"{}\" does not exist".format(wire_path))
+    if not os.path.exists(args.iso_path):
+        raise Exception("inflator executable \"{}\" does not exist".format(args.iso_path))
+    if not os.path.exists(args.exe_path):
+        raise Exception("inflator executable \"{}\" does not exist".format(args.exe_path))
 
     shape_param = []
     scaling_param = [1]
     t = subprocess.check_output(args.iso_path + " 2D_" + symmetry + " --defaultThickness 0.05 " + wire_path + " out.msh", shell=True)
-    print(t)
     t1 = t.decode('utf-8').split('\n')[1].split("\t")
     for token in t1:
         try:
@@ -283,12 +294,18 @@ def load_opt_json(path):
 
     # generate initial shape parameters
     if os.path.exists(args.params):
-        params = np.loadtxt(args.params)
+        print("Initial guess for shape parameters provided!")
+        with open(args.params, 'r') as file:
+            lines = file.readlines()
+            params = lines[-1]
+            params = params[params.find(":")+1:-1]
+            params = params.split(' ')
+            params = np.array([float(e) for e in params if e], dtype=float)
         shape_param = params[1:].tolist()
         scaling_param = params[:1].tolist()
 
-    print("scale paramemters:", scaling_param)
-    print("shape paramemters:", shape_param)
+    print("Cell width:", scaling_param[0], "; cell height: 1.0")
+    print("Inflator params:", shape_param)
 
     t2 = t.decode('utf-8').split('\n')[2].split("\t")
     n_shape_param = []
@@ -298,11 +315,13 @@ def load_opt_json(path):
         except ValueError:
             pass
 
-    print(n_shape_param)
     n_positional_params = n_shape_param[0]
     n_thickness_params = n_shape_param[1]
     n_blending_params = n_shape_param[2]
     n_scaling_params = 1
+    print("Number of node positional params:", n_positional_params)
+    print("Number of beam thickness params:", n_thickness_params)
+    print("Number of blending params:", n_blending_params)
 
     E = args.E
     nu = args.nu
@@ -315,9 +334,10 @@ def load_opt_json(path):
         folder = os.path.join(folder, "no_contact")
     folder = os.path.join(folder, os.path.splitext(os.path.split(wire_path)[1])[0] + "_" + str(strain_sample[-1]) + "_" + str(target_stress))
     if os.path.exists(os.path.join(folder, "optimized-params.txt")):
-        print("Already succeeded!")
+        print("The optimized result already exists! Exit...")
         exit()
     elif os.path.exists(folder):
+        print("Clean existing folder " + folder)
         os.system("rm -r " + folder)
     Path(folder).mkdir(parents=True)
 
@@ -346,7 +366,7 @@ def load_opt_json(path):
         outfile.write(json.dumps(opt_json, indent=4))
 
     os.chdir(folder)
-    print("run " + folder)
+    print("Run optimization and save results to \"" + folder + "\" ...")
     with open("log",'w') as outfile:
         subprocess.run([args.exe_path, 
                         "--max_threads", str(args.threads),