Change default solver to LSODA

findSim.py

@@ -1532,7 +1532,7 @@ def main():
     parser.add_argument( '-p', '--plot', type = str, nargs = '*', help='Optional: Plot specified fields as time-series', default = "" )
     parser.add_argument( '-tp', '--tweak_param_file', type = str, help='Optional: Generate file of tweakable params belonging to selected subset of model', default = "" )
     parser.add_argument( '-sf', '--scoreFunc', type = str, help='Optional: specify scoring function for comparing expt and sim. One can do this either as an expression of the form f(expt, sim, datarange), eg. (expt-sim)/datarange; or as NRMS which does a normalized root-mean-square. NRMS is highly recommended. Default: ' + defaultScoreFunc, default = defaultScoreFunc )
-    parser.add_argument( '--solver', type = str, help='Optional: Solver to use. Options are gsl, gssa and lsoda', default = "gsl" )
+    parser.add_argument( '--solver', type = str, help='Optional: Solver to use. Options are gsl, gssa and lsoda', default = "lsoda" )
     parser.add_argument( '-t', '--tabulate_output', action="store_true", help='Flag: Print table of plot values. Default is NOT to print table' )
     parser.add_argument( '-hp', '--hide_plot', action="store_true", help='Hide plot output of simulation along with expected values. Default is to show plot.' )
     parser.add_argument( '-hs', '--hide_subplots', action="store_true", help='Hide subplot output of simulation. By default the graphs include dotted lines to indicate individual quantities (e.g., states of a molecule) that are being summed to give a total response. This flag turns off just those dotted lines, while leaving the main plot intact.' )
@@ -1549,7 +1549,7 @@ def main():
         simWrap = "HillTau"
     innerMain( args.script, scoreFunc = args.scoreFunc, modelFile = args.model, mapFile = args.map, chemFile = args.chemFile, dumpFname = args.dump_subset, paramFname = args.tweak_param_file, hidePlot = args.hide_plot, hideSubplots = args.hide_subplots, bigFont = args.big_font, optimizeElec = args.optimize_elec, silent = not args.verbose, scaleParam = args.scale_param, settleTime = args.settle_time, tabulateOutput = args.tabulate_output, ignoreMissingObj = args.ignore_missing_obj, simWrap = simWrap, plots = args.plot, generate = args.generate, solver = args.solver )
 
-def innerMain( exptFile, scoreFunc = defaultScoreFunc, modelFile = "", mapFile = "", chemFile = None, dumpFname = "", paramFname = "", hidePlot = False, hideSubplots = True, bigFont = False, labelPos = None, deferPlot = False, optimizeElec=False, silent = False, scaleParam=[], settleTime = 0, settleDict = {}, tabulateOutput = False, ignoreMissingObj = False, simWrap = "", plots = None, generate = None, solver = "gsl" ):
+def innerMain( exptFile, scoreFunc = defaultScoreFunc, modelFile = "", mapFile = "", chemFile = None, dumpFname = "", paramFname = "", hidePlot = False, hideSubplots = True, bigFont = False, labelPos = None, deferPlot = False, optimizeElec=False, silent = False, scaleParam=[], settleTime = 0, settleDict = {}, tabulateOutput = False, ignoreMissingObj = False, simWrap = "", plots = None, generate = None, solver = "lsoda" ):
     ''' If *settleTime* > 0, then we need to return a dict of concs of
     all variable pools in the chem model obtained after loading in model, 
     applying all modifications, and running for specified settle time.\n

runAllParallel.py

@@ -85,7 +85,7 @@ def main():
     parser.add_argument( '-n', '--numProcesses', type = int, help='Optional: Number of processes to spawn, default = 4', default = 4 )
     parser.add_argument( '-m', '--model', type = str, help='Optional: Composite model definition file. First searched in directory "location", then in current directory.', default = "" )
     parser.add_argument( '-map', '--map', type = str, help='Model entity mapping file. This is a JSON file.', default = "" )
-    parser.add_argument( '--solver', type = str, help='Solver to use. Options gsl, gssa, lsoda. Default gsl.', default = "gsl" )
+    parser.add_argument( '--solver', type = str, help='Solver to use. Options gsl, gssa, lsoda. Default lsoda.', default = "lsoda" )
     parser.add_argument( '-s', '--scale_param', nargs=3, default=[],  help='Scale specified object.field by ratio.' )
     parser.add_argument( '-v', '--verbose', action="store_true", help="Flag: default False. When set, prints all sorts of warnings and diagnostics.")
     args = parser.parse_args()