{ "cells": [ { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "import ivp\n", "import solveMatrix\n", "import os\n", "import cModel\n", "import sys\n", "import json\n", "from contextlib import contextmanager\n", "import numpy as np\n", "import time\n", "import scipy.interpolate\n", "import shutil\n", "import importlib\n", "from scipy.optimize import least_squares\n", "importlib.reload(solveMatrix)\n", "\n", "import runSolver\n", "importlib.reload(runSolver)\n", "\n", "def updateSetup(job):\n", " setupFileSrc = job['setupFile']\n", " setupFile = os.path.join(job['jobDir'], 'setupInput.json')\n", " with open(setupFileSrc, 'r') as f:\n", " setup = json.load(f)\n", " try:\n", " setup.update(job['setupUpdates'])\n", " except KeyError:\n", " pass\n", " with open(setupFile, 'w+') as f:\n", " f.write(json.dumps(setup))\n", " return setupFile\n", "\n", "\n", "def generate_noisy_data(full_sol, noise_std=20.5):\n", " full_sol = np.asarray(full_sol) # Ensure input is a NumPy array\n", " random_state = np.random.RandomState(seed=None)\n", " \n", " # Create highly volatile noise\n", " noise = random_state.normal(loc=0, scale=noise_std, size=full_sol.shape) ** 2 # Squared to amplify large deviations\n", " noise2 = np.random.laplace(loc=0, scale=noise_std * 10, size=full_sol.shape) # Increased scale for even more extreme spikes\n", " \n", " # Introduce highly chaotic scaling factors\n", " random_scaling = random_state.uniform(-200, 400, size=full_sol.shape) # Further extended range for more variation\n", " random_exponent = random_state.uniform(4, 12, size=full_sol.shape) # Increased exponentiation for more instability\n", " \n", " # Apply extreme, chaotic transformations\n", " noisy_data = np.zeros_like(full_sol)\n", " for i in range(len(full_sol)):\n", " perturbation = random_scaling[i] * (abs(noise[i]) ** random_exponent[i]) - noise2[i] * np.sin(full_sol[i])\n", " noisy_data[i] = (1 + np.tanh(perturbation)) * full_sol[i] * np.cosh(noise[i])\n", " \n", " # Introduce frequent large perturbations to increase instability\n", " if random_state.rand() < 0.75: # 30% chance of a drastic shift\n", " noisy_data[i] *= random_state.uniform(2, 5)\n", " \n", " return noisy_data\n", "\n", "\n", "def calculate_residuals(full_sol, noisy_data):\n", " \"\"\"\n", " Calculates residuals based on the solution and noisy data.\n", " \"\"\"\n", " residuals = np.ravel((noisy_data - full_sol))\n", " #print(residuals)\n", " return residuals\n", "\n", "\n", "# Updated cost function\n", "def cost_function(params,parnames,noisy_data,model,startPoint,setup,jobDir):\n", " \"\"\"\n", " Cost function that calculates residuals based on the model.\n", " \"\"\" \n", " #print(params)\n", " model.setValues(parnames,params)\n", " clean_dir(jobDir)\n", " t,sol,se,qt,sOut,full_t,full_sol=runSolver.solve(model,setup,startPoint,jobDir)\n", " residuals = calculate_residuals(np.array(full_sol), noisy_data)\n", " return residuals\n", "\n", "\n", "def create_name_value_dict(original_dict):\n", " return {\n", " val['name']: val['value']\n", " for key, val in original_dict.items()\n", " if isinstance(val, dict) and 'name' in val and 'value' in val\n", " }\n", " \n", " # Create parameter dictionary\n", "def clean_dir(jobDir):\n", " \n", " shutil.rmtree(jobDir)\n", " os.mkdir(jobDir)\n" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Using solution from None\n", "t0=0\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.019 s\n", "Completed step _step000\n", "Completed run\n" ] } ], "source": [ "#PRENOS ZAČETNIH PODATKOV \n", "##############################################################################################################################################\n", "\n", "fh = os.path.expanduser(\"~\")\n", "jobDir = os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_ociscen',\"rezultati\")\n", "setup_file = os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_ociscen', 'setup', 'setupMinute.json')\n", "model_file = os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_ociscen', 'models', 'cDiazepam.json')\n", "parameter_file1 = os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_ociscen', 'models', 'cDiazepam_parameters.json')\n", "\n", "\n", "# Prvi model s prvim parameter file\n", "model1 = cModel.model()\n", "model1.parse(model_file, parameter_file1)\n", "setup1 = runSolver.parseSetup(setup_file)\n", "name_value_dict1 = create_name_value_dict(model1.parSetup['parameters'])\n", "\n", "\n", "# Lahko zdaj uporabiš name_value_dict1 in name_value_dict2 ločeno\n", "\n", "\n", " # Excluded parameters\n", "excluded_params1 = {'venousInput',\"heartPC\",\"kidneyPC\",\"remainderPC\",\"skinPC\",\"splanchnicPC\",\"stomachPC\",\"testesPC\",\"one\",\"venousVolume\",\"heartVolume\",\"brainVolume\",\"adiposeVolume\",\"remainderFlow\"}\n", "\n", " # Create initial guesses without excluded parameters\n", "initial_guesses = np.array(\n", " [val for par, val in name_value_dict1.items() if par not in excluded_params1],\n", " dtype=np.float64\n", " )\n", "\n", " # Create list of parameter names without excluded\n", "param_names = [par for par in name_value_dict1.keys() if par not in excluded_params1]\n", "initial_pars = np.array([x for x in initial_guesses])\n", "#initial_pars[3]*=1.1\n", "clean_dir(jobDir)\n", "#print(\"kolicnik\")\n", "#print(initial_guesses/initial_pars)\n", "#print(param_names)\n", "\n", "\n", "\n", "# TO NAREDI REŠITVE Z ZAČETNIMI PARAMETRI\n", "start_point= runSolver.findStartPoint(\"NONE\",setup1)\n", "model1.setValues(param_names,initial_pars)\n", "t,sol,se,qt,sOut,full_t,full_sol = runSolver.solve(model1,setup1,start_point,jobDir)\n", "clean_dir(jobDir)\n", "\n", "\n", "# Step 4: Create a new dictionary for the optimized parameters\n", "# Map the optimized parameters back to the correct order in the original parameter dictionary\n", "optimized_params_dict1 = {par: initial_guesses[i] for i, par in enumerate(param_names)}\n", "\n", "# Step 5: Include the excluded parameters with their original values\n", "for par in excluded_params1:\n", " optimized_params_dict1[par] = name_value_dict1[par]\n", "\n", "# Step 6: Ensure that everything stays in order in the final dictionary\n", "# This will maintain the order of parameters as they appear in the original `name_value_dict2`\n", "final_dict1 = {par: optimized_params_dict1.get(par, name_value_dict1[par]) for par in name_value_dict1}\n", "\n", "\n", "#################################################################################################################333\n" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.028 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.38\n", "Done simultaneous LSODA SE\n", "Time: 0.027 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.026 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.025 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step 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t=0.48\n", "Done simultaneous LSODA SE\n", "Time: 0.027 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.026 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.027 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.027 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.045 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.01\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done 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"Time: 0.029 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.31\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.028 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.079 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.41\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 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"sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.09\n", "Done simultaneous LSODA SE\n", "Time: 0.041 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.45\n", "Done simultaneous LSODA SE\n", "Time: 0.043 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.041 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.98\n", "Done simultaneous LSODA SE\n", "Time: 0.040 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.040 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.044 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.08\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.47\n", "Done simultaneous LSODA SE\n", "Time: 0.042 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.041 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.041 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.96\n", "Done simultaneous LSODA SE\n", "Time: 0.043 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.152 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.18\n", "Done simultaneous LSODA SE\n", "Time: 0.120 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.06\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.069 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.029 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.87\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.43\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.029 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.21\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.07\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.01\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.083 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.78\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.053 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.29\n", "Done simultaneous LSODA SE\n", "Time: 0.050 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.10\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.029 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.01\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.60\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.30\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.028 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.089 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.13\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.041 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.040 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.04\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.029 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.93\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.52\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.064 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.27\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.029 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.11\n", "Done simultaneous LSODA SE\n", "Time: 0.081 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.02\n", "Done simultaneous LSODA SE\n", "Time: 0.053 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.050 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.047 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.71\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.39\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.20\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.029 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.08\n", "Done simultaneous LSODA SE\n", "Time: 0.045 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.01\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.029 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.112 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.34\n", "Done simultaneous LSODA SE\n", "Time: 0.061 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.052 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.02\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.030 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.80\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.031 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.15\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.01\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.032 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.044 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.71\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.041 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.20\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.087 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.126 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.035 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.20\n", "Done simultaneous LSODA SE\n", "Time: 0.042 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.040 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.81\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.033 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.06\n", "Done simultaneous LSODA SE\n", "Time: 0.041 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.48\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.01\n", "Done simultaneous LSODA SE\n", "Time: 0.043 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.56\n", "Done simultaneous LSODA SE\n", "Time: 0.034 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.08\n", "Done simultaneous LSODA SE\n", "Time: 0.056 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.036 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.71\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.116 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.041 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.81\n", "Done simultaneous LSODA SE\n", "Time: 0.055 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.82\n", "Done simultaneous LSODA SE\n", "Time: 0.041 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.052 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.84\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.040 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.85\n", "Done simultaneous LSODA SE\n", "Time: 0.042 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.040 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.048 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.86\n", "Done simultaneous LSODA SE\n", "Time: 0.042 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.040 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.038 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.88\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.037 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.89\n", "Done simultaneous LSODA SE\n", "Time: 0.041 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.039 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.041 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.042 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.040 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.042 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.053 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.01\n", "Done simultaneous LSODA SE\n", "Time: 0.076 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.129 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.84\n", "Done simultaneous LSODA SE\n", "Time: 0.079 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.094 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.065 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.16\n", "Done simultaneous LSODA SE\n", "Time: 0.071 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.043 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.045 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.047 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.045 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.33\n", "Done simultaneous LSODA SE\n", "Time: 0.044 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.045 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.085 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.01\n", "Done simultaneous LSODA SE\n", "Time: 0.060 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.104 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.61\n", "Done simultaneous LSODA SE\n", "Time: 0.131 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.056 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.080 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.07\n", "Done simultaneous LSODA SE\n", "Time: 0.073 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.057 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.85\n", "Done simultaneous LSODA SE\n", "Time: 0.140 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.092 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.056 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.18\n", "Done simultaneous LSODA SE\n", "Time: 0.050 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.047 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.050 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.056 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.053 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.35\n", "Done simultaneous LSODA SE\n", "Time: 0.052 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.182 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.27\n", "Done simultaneous LSODA SE\n", "Time: 0.088 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.124 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.04\n", "Done simultaneous LSODA SE\n", "Time: 0.093 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.96\n", "Done simultaneous LSODA SE\n", "Time: 0.085 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.078 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.59\n", "Done simultaneous LSODA SE\n", "Time: 0.199 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.171 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.25\n", "Done simultaneous LSODA SE\n", "Time: 0.175 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.172 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.04\n", "Done simultaneous LSODA SE\n", "Time: 0.154 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.89\n", "Done simultaneous LSODA SE\n", "Time: 0.183 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.157 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.51\n", "Done simultaneous LSODA SE\n", "Time: 0.159 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.066 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.15\n", "Done simultaneous LSODA SE\n", "Time: 0.064 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.063 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.099 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.72\n", "Done simultaneous LSODA SE\n", "Time: 0.194 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.170 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.34\n", "Done simultaneous LSODA SE\n", "Time: 0.205 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.099 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.07\n", "Done simultaneous LSODA SE\n", "Time: 0.086 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.096 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.104 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.64\n", "Done simultaneous LSODA SE\n", "Time: 0.094 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.115 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.33\n", "Done simultaneous LSODA SE\n", "Time: 0.088 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.456 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.01\n", "Done simultaneous LSODA SE\n", "Time: 0.267 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.32\n", "Done simultaneous LSODA SE\n", "Time: 0.187 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.77\n", "Done simultaneous LSODA SE\n", "Time: 0.242 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.150 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.02\n", "Done simultaneous LSODA SE\n", "Time: 0.268 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.35\n", "Done simultaneous LSODA SE\n", "Time: 0.231 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.87\n", "Done simultaneous LSODA SE\n", "Time: 0.139 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.178 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.04\n", "Done simultaneous LSODA SE\n", "Time: 0.181 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.51\n", "Done simultaneous LSODA SE\n", "Time: 0.103 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.76\n", "Done simultaneous LSODA SE\n", "Time: 0.187 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.96\n", "Done simultaneous LSODA SE\n", "Time: 0.253 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.351 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.03\n", "Done simultaneous LSODA SE\n", "Time: 0.369 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.11\n", "Done simultaneous LSODA SE\n", "Time: 0.275 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.37\n", "Done simultaneous LSODA SE\n", "Time: 0.343 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.61\n", "Done simultaneous LSODA SE\n", "Time: 0.253 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.75\n", "Done simultaneous LSODA SE\n", "Time: 0.324 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.95\n", "Done simultaneous LSODA SE\n", "Time: 0.251 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.248 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.01\n", "Done simultaneous LSODA SE\n", "Time: 0.113 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.04\n", "Done simultaneous LSODA SE\n", "Time: 0.114 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.20\n", "Done simultaneous LSODA SE\n", "Time: 0.147 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.51\n", "Done simultaneous LSODA SE\n", "Time: 0.189 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.62\n", "Done simultaneous LSODA SE\n", "Time: 0.191 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.78\n", "Done simultaneous LSODA SE\n", "Time: 0.165 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.095 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.01\n", "Done simultaneous LSODA SE\n", "Time: 0.204 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.62\n", "Done simultaneous LSODA SE\n", "Time: 0.227 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.65\n", "Done simultaneous LSODA SE\n", "Time: 0.232 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.183 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.243 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.12\n", "Done simultaneous LSODA SE\n", "Time: 0.166 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.57\n", "Done simultaneous LSODA SE\n", "Time: 0.424 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.70\n", "Done simultaneous LSODA SE\n", "Time: 0.483 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.218 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.177 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.24\n", "Done simultaneous LSODA SE\n", "Time: 0.246 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.69\n", "Done simultaneous LSODA SE\n", "Time: 0.225 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.196 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.200 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.18\n", "Done simultaneous LSODA SE\n", "Time: 0.146 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.69\n", "Done simultaneous LSODA SE\n", "Time: 0.113 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.194 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.196 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.08\n", "Done simultaneous LSODA SE\n", "Time: 0.242 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.21\n", "Done simultaneous LSODA SE\n", "Time: 0.159 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.63\n", "Done simultaneous LSODA SE\n", "Time: 0.162 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.95\n", "Done simultaneous LSODA SE\n", "Time: 0.122 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.080 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.17\n", "Done simultaneous LSODA SE\n", "Time: 0.110 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.64\n", "Done simultaneous LSODA SE\n", "Time: 0.153 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.93\n", "Done simultaneous LSODA SE\n", "Time: 0.171 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.083 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.08\n", "Done simultaneous LSODA SE\n", "Time: 0.101 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.50\n", "Done simultaneous LSODA SE\n", "Time: 0.093 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.95\n", "Done simultaneous LSODA SE\n", "Time: 0.133 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.137 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.16\n", "Done simultaneous LSODA SE\n", "Time: 0.155 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.57\n", "Done simultaneous LSODA SE\n", "Time: 0.109 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.78\n", "Done simultaneous LSODA SE\n", "Time: 0.105 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.123 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.102 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.40\n", "Done simultaneous LSODA SE\n", "Time: 0.241 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.82\n", "Done simultaneous LSODA SE\n", "Time: 0.160 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.99\n", "Done simultaneous LSODA SE\n", "Time: 0.192 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.141 s\n", "Completed step _step000\n", "Completed run\n", "{'venousInput': 300000.0, 'adiposePC': 23.1, 'brainPC': 2.2, 'heartPC': 4.3, 'kidneyPC': 5.2, 'liverPC': 9.1, 'lungPC': 5.3, 'musclePC': 2.4, 'remainderPC': 16.5, 'skinPC': 3.2, 'splanchnicPC': 4.3, 'stomachPC': 4.5, 'testesPC': 4.7, 'adiposeFlow': 2.55, 'brainFlow': 0.78, 'heartFlow': 4.2, 'kidneyFlow': 16.61, 'liverInFlow': 3.55, 'totalFlow': 80, 'muscleFlow': 16.25, 'skinFlow': 7.1, 'splanchnicFlow': 20.25, 'stomachFlow': 1.9, 'testesFlow': 1.9, 'remainderFlow': 4.91, 'adiposeVolume': 10, 'brainVolume': 1.2, 'heartVolume': 1, 'kidneyVolume': 2, 'liverVolume': 11, 'lungVolume': 1.2, 'muscleVolume': 125, 'skinVolume': 43.8, 'splanchnicVolume': 15, 'stomachVolume': 1.1, 'testesVolume': 2.5, 'remainderVolume': 15.8, 'venousVolume': 13.6, 'arterialVolume': 6.8, 'k1': 0.0105, 'one': 1}\n", "{'venousInput': 300000.0, 'adiposePC': 39.459503930348056, 'brainPC': 21.7350030614673, 'heartPC': 4.3, 'kidneyPC': 5.2, 'liverPC': -66.81790047648342, 'lungPC': 0.06380804473804387, 'musclePC': 2.543151853709495, 'remainderPC': 16.5, 'skinPC': 3.2, 'splanchnicPC': 4.3, 'stomachPC': 4.5, 'testesPC': 4.7, 'adiposeFlow': 1.8555225806396292, 'brainFlow': -0.03525587711760467, 'heartFlow': -0.023321595538575646, 'kidneyFlow': 40.39168946244715, 'liverInFlow': 5.140426181736766, 'totalFlow': 200.5628048196977, 'muscleFlow': 45.13135301105268, 'skinFlow': 10.079724428985626, 'splanchnicFlow': 105.29800422219472, 'stomachFlow': 1.6108268212416408, 'testesFlow': 1.0037721518520688, 'remainderFlow': 4.91, 'adiposeVolume': 10, 'brainVolume': 1.2, 'heartVolume': 1, 'kidneyVolume': 46.59574951502177, 'liverVolume': -8.016381080752923, 'lungVolume': 13.804510479009664, 'muscleVolume': 121.01717740493208, 'skinVolume': 25.330075390084705, 'splanchnicVolume': 85.4086471187175, 'stomachVolume': -10.421869426098299, 'testesVolume': -8.440264156191922, 'remainderVolume': 17.203625558278443, 'venousVolume': 13.6, 'arterialVolume': 53.44960231535441, 'k1': -6.623348838319975, 'one': 1}\n" ] } ], "source": [ "# Z DRUGIMI PARAMETRI\n", "##########################################################################################################################\n", "\n", "# Drugi model z drugim parameter file\n", "parameter_file2 = os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_ociscen', 'models', 'cDiazepam_parameters1.json')\n", "model2 = cModel.model()\n", "model2.parse(model_file, parameter_file2)\n", "setup2 = runSolver.parseSetup(setup_file)\n", "name_value_dict2 = create_name_value_dict(model2.parSetup['parameters'])\n", "\n", " # Excluded parameters\n", "excluded_params = {'venousInput',\"heartPC\",\"kidneyPC\",\"remainderPC\",\"skinPC\",\"splanchnicPC\",\"stomachPC\",\"testesPC\",\"one\",\"venousVolume\",\"heartVolume\",\"brainVolume\",\"adiposeVolume\",\"remainderFlow\"}\n", "\n", "\n", "# Step 1: Filter out excluded parameters for initial guesses\n", "initial_guesses2 = np.array(\n", " [val for par, val in name_value_dict2.items() if par not in excluded_params],\n", " dtype=np.float64\n", ")\n", "\n", "param_names2 = [par for par in name_value_dict2.keys() if par not in excluded_params]\n", "\n", "\n", "# Step 4: Create a new dictionary for the optimized parameters\n", "# Map the optimized parameters back to the correct order in the original parameter dictionary\n", "optimized_params_dict22 = {par: initial_guesses2[i] for i, par in enumerate(param_names2)}\n", "\n", "# Step 5: Include the excluded parameters with their original values\n", "for par in excluded_params1:\n", " optimized_params_dict22[par] = name_value_dict2[par]\n", "\n", "# Step 6: Ensure that everything stays in order in the final dictionary\n", "# This will maintain the order of parameters as they appear in the original `name_value_dict2`\n", "final_dict22 = {par: optimized_params_dict22.get(par, name_value_dict1[par]) for par in name_value_dict2}\n", "\n", "# Step 2: Run optimization\n", "result = least_squares(\n", " cost_function, initial_guesses2,\n", " args=(param_names2, full_sol, model2, start_point, setup2, jobDir)\n", ")\n", "\n", "# Step 3: Retrieve optimized parameters\n", "optimized_params2 = result.x\n", "\n", "# Step 4: Create a new dictionary for the optimized parameters\n", "# Map the optimized parameters back to the correct order in the original parameter dictionary\n", "optimized_params_dict2 = {par: optimized_params2[i] for i, par in enumerate(param_names2)}\n", "\n", "# Step 5: Include the excluded parameters with their original values\n", "for par in excluded_params:\n", " optimized_params_dict2[par] = name_value_dict2[par]\n", "\n", "# Step 6: Ensure that everything stays in order in the final dictionary\n", "# This will maintain the order of parameters as they appear in the original `name_value_dict2`\n", "final_optimized_dict = {par: optimized_params_dict2.get(par, name_value_dict2[par]) for par in name_value_dict2}\n", "\n", "# Now, final_optimized_dict contains the optimized values in the same order as in `name_value_dict2`\n", "print(name_value_dict2)\n", "print(final_optimized_dict)\n", "\n", "vrednosti3 = np.array(\n", " [val for par, val in final_optimized_dict.items()],\n", " dtype=np.float64\n", " )\n", "\n", "param_names3 = [par for par in final_optimized_dict.keys()]" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.028 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.19\n", "Done simultaneous LSODA SE\n", "Time: 0.176 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.71\n", "Done simultaneous LSODA SE\n", "Time: 0.107 s\n", "Completed step _step000\n", "Completed run\n", "[[ nan nan nan ... nan\n", " nan nan]\n", " [ 5.09049575e+07 -3.16258943e+06 -3.88695225e+05 ... 1.11390301e+08\n", " 2.93473760e+07 3.00000000e+07]\n", " [ 6.85202598e+07 -4.25888973e+06 -5.23990918e+05 ... 1.03977087e+08\n", " 2.87202614e+07 3.00000000e+07]\n", " ...\n", " [ 8.08537819e+06 -5.55076457e+05 -8.49485013e+04 ... 1.01302435e+07\n", " 1.08429062e+07 3.00000000e+07]\n", " [ 8.07991738e+06 -5.55040031e+05 -8.50494754e+04 ... 1.01243346e+07\n", " 1.08341421e+07 3.00000000e+07]\n", " [ 8.07450273e+06 -5.55006620e+05 -8.51509675e+04 ... 1.01184264e+07\n", " 1.08254411e+07 3.00000000e+07]]\n", "[[ nan nan nan ... nan\n", " nan nan]\n", " [ 5.09042585e+07 -3.16262698e+06 -3.88699512e+05 ... 1.11388842e+08\n", " 2.93473760e+07 3.00000000e+07]\n", " [ 6.85194922e+07 -4.25895107e+06 -5.23998023e+05 ... 1.03976033e+08\n", " 2.87202614e+07 3.00000000e+07]\n", " ...\n", " [ 8.08537832e+06 -5.55090687e+05 -8.49506105e+04 ... 1.01302432e+07\n", " 1.08429061e+07 3.00000000e+07]\n", " [ 8.07991751e+06 -5.55054260e+05 -8.50515872e+04 ... 1.01243343e+07\n", " 1.08341420e+07 3.00000000e+07]\n", " [ 8.07450287e+06 -5.55020849e+05 -8.51530818e+04 ... 1.01184261e+07\n", " 1.08254410e+07 3.00000000e+07]]\n", "[[ nan nan nan ... nan nan nan]\n", " [0.99998627 1.00001187 1.00001103 ... 0.9999869 1. 1. ]\n", " [0.9999888 1.0000144 1.00001356 ... 0.99998987 1. 1. ]\n", " ...\n", " [1.00000002 1.00002564 1.00002483 ... 0.99999997 0.99999999 1. ]\n", " [1.00000002 1.00002564 1.00002483 ... 0.99999997 0.99999999 1. ]\n", " [1.00000002 1.00002564 1.00002483 ... 0.99999997 0.99999999 1. ]]\n", "[1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1.\n", " 1. 1. 1.]\n", "[ 1.70820363e+00 9.87954685e+00 -7.34262643e+00 1.20392537e-02\n", " 1.05964661e+00 7.27655914e-01 -4.51998425e-02 -5.55276084e-03\n", " 2.43176938e+00 1.44800738e+00 2.50703506e+00 2.77731403e+00\n", " 1.41967950e+00 5.19990144e+00 8.47803590e-01 5.28301133e-01\n", " 2.32978748e+01 -7.28761916e-01 1.15037587e+01 9.68137419e-01\n", " 5.78312224e-01 5.69390981e+00 -9.47442675e+00 -3.37610566e+00\n", " 1.08883706e+00 7.86023563e+00 -6.30795127e+02]\n", "[ 1.70820363e+00 9.87954685e+00 -7.34262643e+00 1.20392537e-02\n", " 1.05964661e+00 7.27655914e-01 -4.51998425e-02 -5.55276084e-03\n", " 2.43176938e+00 1.44800738e+00 2.50703506e+00 2.77731403e+00\n", " 1.41967950e+00 5.19990144e+00 8.47803590e-01 5.28301133e-01\n", " 2.32978748e+01 -7.28761916e-01 1.15037587e+01 9.68137419e-01\n", " 5.78312224e-01 5.69390981e+00 -9.47442675e+00 -3.37610566e+00\n", " 1.08883706e+00 7.86023563e+00 -6.30795127e+02]\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/tmp/ipykernel_12189/178340154.py:15: RuntimeWarning: invalid value encountered in divide\n", " print(np.array(full_sol2)/np.array(full_sol1))\n", "/tmp/ipykernel_12189/178340154.py:16: RuntimeWarning: invalid value encountered in divide\n", " print(np.array(full_sol3)/np.array(full_sol1))\n", "/tmp/ipykernel_12189/178340154.py:17: RuntimeWarning: invalid value encountered in divide\n", " print(np.array(full_sol3)/np.array(full_sol2))\n" ] } ], "source": [ "#model2.setValues(param_names3,vrednosti3)\n", "#################################################################################################################################\n", "# PREVRBA ČE SO 3 različne rešitve\n", "clean_dir(jobDir)\n", "t,sol,se,qt,sOut,full_t,full_sol1 = runSolver.solve(model1,setup1,start_point,jobDir)\n", "clean_dir(jobDir)\n", "t,sol,se,qt,sOut,full_t,full_sol2 = runSolver.solve(model2,setup2,start_point,jobDir)\n", "\n", "\n", "model2.setValues(param_names3,vrednosti3)\n", "clean_dir(jobDir)\n", "t,sol,se,qt,sOut,full_t,full_sol3 = runSolver.solve(model2,setup2,start_point,jobDir)\n", "\n", "\n", "print(np.array(full_sol2)/np.array(full_sol1))\n", "print(np.array(full_sol3)/np.array(full_sol1))\n", "print(np.array(full_sol3)/np.array(full_sol2))\n", "\n", "\n", "print(initial_guesses2/initial_guesses)\n", "print(optimized_params2/initial_guesses2)\n", "print(optimized_params2/initial_guesses)\n", "##################################################################################################################################\n", "\n" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.025 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "Done simultaneous LSODA SE\n", "Time: 0.127 s\n", "Completed step _step000\n", "Completed run\n", "sIn (0,)\n", "t0 0 tmax 1.0\n", "Step required _step000\n", "At t=0.00\n", "Done simultaneous LSODA SE\n", "Time: 0.088 s\n", "Completed step _step000\n", "Completed run\n", "Parameters for run3 saved at: /home/jakob/Documents/Sola/IJS/PBPK_ociscen/rezultati/run3/parameters.json\n" ] } ], "source": [ "# SHRANIMO REŠITVE ZA PARAMETRE\n", "\n", "\n", "def create_or_clean_dir(directory):\n", " \"\"\"Create the directory if it doesn't exist, otherwise clean it.\"\"\"\n", " if os.path.exists(directory):\n", " shutil.rmtree(directory) # Remove the existing directory and its contents\n", " os.makedirs(directory) # Create a fresh directory\n", "\n", "def save_parameters(file_path, data):\n", " \"\"\"Save dictionary data to a JSON file.\"\"\"\n", " with open(file_path, 'w') as f:\n", " json.dump(data, f, indent=4)\n", " return file_path # Return the path for immediate use\n", "\n", "# Define unique subdirectories\n", "jobDir1 = os.path.join(jobDir, \"run1\")\n", "jobDir2 = os.path.join(jobDir, \"run2\")\n", "jobDir3 = os.path.join(jobDir, \"run3\")\n", "\n", "# Ensure directories exist and are clean\n", "create_or_clean_dir(jobDir1)\n", "create_or_clean_dir(jobDir2)\n", "create_or_clean_dir(jobDir3)\n", "\n", "# Solve and save results in respective directories\n", "t, sol, se, qt, sOut, full_t, full_sol1 = runSolver.solve(model1, setup1, start_point, jobDir1)\n", "save_parameters(os.path.join(jobDir1, \"parameters.json\"), final_dict1)\n", "\n", "t, sol, se, qt, sOut, full_t, full_sol2 = runSolver.solve(model2, setup2, start_point, jobDir2)\n", "save_parameters(os.path.join(jobDir2, \"parameters.json\"), final_dict22)\n", "\n", "model2.setValues(param_names3, vrednosti3)\n", "t, sol, se, qt, sOut, full_t, full_sol3 = runSolver.solve(model2, setup2, start_point, jobDir3)\n", "\n", "# Save parameters and immediately store the path for further use\n", "param_file3 = save_parameters(os.path.join(jobDir3, \"parameters.json\"), final_optimized_dict)\n", "\n", "# Now you can directly use param_file3 in further processing\n", "print(f\"Parameters for run3 saved at: {param_file3}\")\n", "\n", "\n", "########################################################################################################################\n", "\n" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/home/jakob/Documents/Sola/IJS/PBPK_ociscen/rezultati/run3\n" ] }, { "ename": "IsADirectoryError", "evalue": "[Errno 21] Is a directory: '/home/jakob/Documents/Sola/IJS/PBPK_ociscen/rezultati/run3'", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mIsADirectoryError\u001b[0m Traceback (most recent call last)", "Cell \u001b[0;32mIn[11], line 9\u001b[0m\n\u001b[1;32m 7\u001b[0m model3 \u001b[38;5;241m=\u001b[39m cModel\u001b[38;5;241m.\u001b[39mmodel()\n\u001b[1;32m 8\u001b[0m parameter_file3 \u001b[38;5;241m=\u001b[39m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(directory) \u001b[38;5;66;03m# Use it as a path\u001b[39;00m\n\u001b[0;32m----> 9\u001b[0m \u001b[43mmodel3\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mparse\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodel_file\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparameter_file3\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 10\u001b[0m \u001b[38;5;66;03m# Load the model using the saved parameter file\u001b[39;00m\n\u001b[1;32m 11\u001b[0m \n\u001b[1;32m 12\u001b[0m \u001b[38;5;66;03m#model3.parse(model_file, parameter_file3) # Use param_file3 here\u001b[39;00m\n\u001b[1;32m 13\u001b[0m \u001b[38;5;66;03m# Parse the setup\u001b[39;00m\n\u001b[1;32m 14\u001b[0m setup3 \u001b[38;5;241m=\u001b[39m runSolver\u001b[38;5;241m.\u001b[39mparseSetup(setup_file)\n", "File \u001b[0;32m~/Documents/Sola/IJS/PBPK_ociscen/pythonScripts/cModel.py:302\u001b[0m, in \u001b[0;36mmodel.parse\u001b[0;34m(self, setupFile, parameterFile)\u001b[0m\n\u001b[1;32m 298\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mopen\u001b[39m(setupFile,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mr\u001b[39m\u001b[38;5;124m'\u001b[39m) \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m 299\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmod\u001b[38;5;241m=\u001b[39mjson\u001b[38;5;241m.\u001b[39mload(f)\n\u001b[0;32m--> 302\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mopen\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mparameterFile\u001b[49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mr\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m 303\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mparSetup\u001b[38;5;241m=\u001b[39mjson\u001b[38;5;241m.\u001b[39mload(f)\n\u001b[1;32m 305\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmod[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcompartments\u001b[39m\u001b[38;5;124m'\u001b[39m]\u001b[38;5;241m.\u001b[39mappend(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtotal\u001b[39m\u001b[38;5;124m'\u001b[39m)\n", "\u001b[0;31mIsADirectoryError\u001b[0m: [Errno 21] Is a directory: '/home/jakob/Documents/Sola/IJS/PBPK_ociscen/rezultati/run3'" ] } ], "source": [ "#ZGRADIMO 3 MODEL (da bo lažje pol risat)\n", "##############################################################################################################################################\n", "# param_file3 already contains the full path to \"parameters.json\"\n", "import os\n", "directory = os.path.dirname(param_file3)\n", "print(directory)\n", "model3 = cModel.model()\n", "parameter_file3 = os.path.join(directory) # Use it as a path\n", "model3.parse(model_file, parameter_file3)\n", "# Load the model using the saved parameter file\n", "\n", "#model3.parse(model_file, parameter_file3) # Use param_file3 here\n", "# Parse the setup\n", "setup3 = runSolver.parseSetup(setup_file)\n", "# Create the name-value dictionary\n", "name_value_dict3 = create_name_value_dict(model3.parSetup['parameters'])\n", "\n", "########################################################################################################3333\n", "\n", "runSolver.main([setup_file,model3,parameter_file3,jobDir])\n", "\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [ { "ename": "NameError", "evalue": "name 'os' is not defined", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", "Cell \u001b[0;32mIn[1], line 6\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;66;03m#RISANJE\u001b[39;00m\n\u001b[1;32m 2\u001b[0m \u001b[38;5;66;03m########################################################################################################################\u001b[39;00m\n\u001b[1;32m 4\u001b[0m job_configs \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m 5\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcDiazepam_IVP\u001b[39m\u001b[38;5;124m'\u001b[39m: {\n\u001b[0;32m----> 6\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mjobDir\u001b[39m\u001b[38;5;124m'\u001b[39m: \u001b[43mos\u001b[49m\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(fh, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mDocuments\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mSola\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mIJS\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mPBPK_ociscen\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrezultati\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrun1\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 7\u001b[0m },\n\u001b[1;32m 8\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcDiazepam1_IVP\u001b[39m\u001b[38;5;124m'\u001b[39m: {\n\u001b[1;32m 9\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mjobDir\u001b[39m\u001b[38;5;124m'\u001b[39m: os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(fh, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mDocuments\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mSola\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mIJS\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mPBPK_ociscen\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrezultati\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrun2\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 10\u001b[0m },\n\u001b[1;32m 11\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcDiazepamF_IVP\u001b[39m\u001b[38;5;124m'\u001b[39m: {\n\u001b[1;32m 12\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mjobDir\u001b[39m\u001b[38;5;124m'\u001b[39m: os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(fh, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mDocuments\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mSola\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mIJS\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mPBPK_ociscen\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrezultati\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrun3\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 13\u001b[0m }\n\u001b[1;32m 14\u001b[0m }\n\u001b[1;32m 18\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mmergeSolutions\u001b[39m(seq):\n\u001b[1;32m 19\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 20\u001b[0m \u001b[38;5;124;03m Merge multiple solution dictionaries into a single dictionary.\u001b[39;00m\n\u001b[1;32m 21\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n", "\u001b[0;31mNameError\u001b[0m: name 'os' is not defined" ] } ], "source": [ "#RISANJE\n", "########################################################################################################################\n", "\n", "job_configs = {\n", " 'cDiazepam_IVP': {\n", " 'jobDir': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_ociscen', 'rezultati','run1')\n", " },\n", " 'cDiazepam1_IVP': {\n", " 'jobDir': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_ociscen', 'rezultati','run2')\n", " },\n", " 'cDiazepamF_IVP': {\n", " 'jobDir': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_ociscen', 'rezultati','run3')\n", " }\n", "}\n", "\n", "\n", "\n", "def mergeSolutions(seq):\n", " \"\"\"\n", " Merge multiple solution dictionaries into a single dictionary.\n", " \"\"\"\n", " out = {}\n", " for v in ['t', 'sol', 'se', 'qt', 'sOut']: # Merge arrays from each solution\n", " out[v] = np.concatenate([x[v] for x in seq])\n", " for v in ['lut', 'lutSE', 'setup', 'model', 'parameters', 'qt', 'sOut']: # Use data from the last solution for these keys\n", " out[v] = seq[-1][v]\n", " return out # Return the merged dictionary\n", "\n", "\n" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.10.12" } }, "nbformat": 4, "nbformat_minor": 2 }