PBPK_public/pythonScripts/runSolver.py

import ivp
import os
import cModel
import sys
import json
import numpy
import time

def get(setup,par):
   defaultValues={\
      'method':'LSODA',\
      'atol':1e-4,\
      'rtol':1e-4,\
      'tmax':1,\
      'mode':'IVPSimultaneous',\
      'nt':201,
      'tUnit':'day'}
   try:
      return setup[par]
   except KeyError:
      pass
   return defaultValues[par]

def main(parFiles,jobDir):
   sys=cModel.model()
   setupFile=parFiles[1]
   parameterFile=parFiles[2]
   sys.parse(setupFile,parameterFile)
   with open(parFiles[0],'r') as f:
      setup=json.load(f)
   tmax=get(setup,'tmax')
   atol=get(setup,'atol')
   rtol=get(setup,'rtol')
   mode=get(setup,'mode')
   method=get(setup,'method')
   nt=get(setup,'nt')
   tUnit=get(setup,'tUnit')
   if tUnit=='min':
      pass
   if tUnit=='hour':
      tmax*=60
   if tUnit=='day':
      tmax*=24*60
   if tUnit=='month':
      tmax*=24*60*30
   if tUnit=='year':
      tmax*=24*60*30*365

   start_time=time.time()
   if mode=='SequentialOdeint':
      t,sol,se=ivp.solveSequentialOdeint(sys,tmax,nt)
   if mode=='SimultaneousOdeint':
      t,sol,se=ivp.solveSimultaneousOdeint(sys,tmax,nt)

   if mode=='IVP':
      t,sol,se=ivp.solveSequential(sys,tmax,atol=atol,rtol=rtol,method=method)
        
   if mode=='IVPSimultaneous':
      t,sol,se=ivp.solveSimultaneous(sys,tmax,atol=atol,rtol=rtol,method=method)

   end_time=time.time()
   print('Time: {:.3f} s'.format(end_time-start_time))
   #store
   numpy.savetxt(os.path.join(jobDir,'t.txt'),t)
   numpy.savetxt(os.path.join(jobDir,'sol.txt'),sol)
   numpy.savetxt(os.path.join(jobDir,'se.txt'),se)