Merge pull request #87 from keiyamamo/switch2json

switch to json format

Author: keiyamamo

turtleFSI/monolithic.py

@@ -10,7 +10,7 @@
 
 from dolfin import *
 from pathlib import Path
-import pickle
+import json
 import time
 from pprint import pprint
 
@@ -44,8 +44,8 @@
 if default_variables["restart_folder"] is not None:
     restart_folder = Path(default_variables["restart_folder"])
     restart_folder = restart_folder if "Checkpoint" in restart_folder.__str__() else restart_folder.joinpath("Checkpoint")
-    with open(restart_folder.joinpath("default_variables.pickle"), "rb") as f:
-        restart_dict = pickle.load(f)
+    with open(restart_folder.joinpath("default_variables.json"), "r") as f:
+        restart_dict = json.load(f)
     default_variables.update(restart_dict)
     default_variables["restart_folder"] = restart_folder
 
@@ -168,7 +168,6 @@
 first_step_num = counter # This is so that the solver will recompute the jacobian on the first step of the simulation
 while t <= T + dt / 10 and not stop:  # + dt / 10 is a hack to ensure that we take the final time step t == T
     t += dt
-
     # Pre solve hook
     tmp_dict = pre_solve(**vars())
     if tmp_dict is not None:

turtleFSI/problems/__init__.py

@@ -8,7 +8,7 @@
 """
 
 from dolfin import parameters, XDMFFile, MPI, assign, Mesh, refine, project, VectorElement, FiniteElement, PETScDMCollection, FunctionSpace, Function
-import pickle
+import json
 from pathlib import Path
 from xml.etree import ElementTree as ET
 import numpy as np
@@ -187,8 +187,9 @@ def checkpoint(dvp_, default_variables, checkpoint_folder, mesh, **namespace):
 
     # Dump default parameters
     if MPI.rank(MPI.comm_world) == 0:
-        with open(str(checkpoint_folder.joinpath("default_variables.pickle")), "bw") as f:
-            pickle.dump(default_variables, f)
+        with open(str(checkpoint_folder.joinpath("default_variables.json")), "w") as f:
+            default_variables["restart_folder"] = str(default_variables["restart_folder"])
+            json.dump(default_variables, f)
 
     # Dump physical fields
     fields = _get_fields(dvp_, mesh)