def modelOutputSlow(self,params): filename,namesList = self.filename,self.namesList endTime,nSteps = self.endTime,self.nSteps # use BNG to integrate the model writeBNGL.writeBNGLsimulate(filename,namesList,params,endTime,nSteps) os.system(BNGpath+"Perl2/BNG2.pl "+filename+"_simulate.bngl > " \ +filename+"_simulate_messages.txt") # read in output of model output = self._readModelOutput(filename+"_simulate.cdat") self.recentOutput = output return output
def modelOutputSlow(self, params): filename, namesList = self.filename, self.namesList endTime, nSteps = self.endTime, self.nSteps # use BNG to integrate the model writeBNGL.writeBNGLsimulate(filename, namesList, params, endTime, nSteps) os.system(BNGpath+"Perl2/BNG2.pl "+filename+"_simulate.bngl > " \ +filename+"_simulate_messages.txt") # read in output of model output = self._readModelOutput(filename + "_simulate.cdat") self.recentOutput = output return output
def modelOutput(self,params): """ Returns model output as array: output[0] = time series for species 1, output[1] = time series for species 2, ... """ netFile,namesList = self.filename,self.namesList endTime,nSteps = self.endTime,self.nSteps # use BNG to integrate the model writeBNGL.writeModifiedNet(netFile,namesList,params,"_modified") writeBNGL.writeBNGLsimulate(netFile+"_modified",endTime,nSteps) self._runBNGLfile(netFile+"_modified_simulate") # or use (slow) #writeBNGL.writeBNGLsimulateSlow(filename,namesList,params,endTime,nSteps) #os.system(BNGpath+"Perl2/BNG2.pl "+filename+"_simulate.bngl > " \ # +filename+"_simulate_messages.txt") # read in output of model output = self._readModelOutput(netFile+"_modified_simulate.cdat") self.recentOutput = output return output
def modelOutput(self, params): """ Returns model output as array: output[0] = time series for species 1, output[1] = time series for species 2, ... """ netFile, namesList = self.filename, self.namesList endTime, nSteps = self.endTime, self.nSteps # use BNG to integrate the model writeBNGL.writeModifiedNet(netFile, namesList, params, "_modified") writeBNGL.writeBNGLsimulate(netFile + "_modified", endTime, nSteps) self._runBNGLfile(netFile + "_modified_simulate") # or use (slow) #writeBNGL.writeBNGLsimulateSlow(filename,namesList,params,endTime,nSteps) #os.system(BNGpath+"Perl2/BNG2.pl "+filename+"_simulate.bngl > " \ # +filename+"_simulate_messages.txt") # read in output of model output = self._readModelOutput(netFile + "_modified_simulate.cdat") self.recentOutput = output return output