Coverage for pySDC/projects/Monodomain/run_scripts/run_MonodomainODE_cli.py: 100%

1import argparse 

2from pySDC.projects.Monodomain.run_scripts.run_MonodomainODE import setup_and_run 

3 

4 

5def list_of_ints(arg): 

6 arg = arg.replace(' ', '') 

7 arg = arg.replace('_', '-') 

8 arg = arg.split(',') 

9 return list(map(int, arg)) 

10 

11 

12# This is to run the MonodomainODE example from the command line 

13# Pretty much all the parameters can be defined from the command line 

14 

15# For the refinements, it is possible to set negative values, which yield a mesh coarser than the baseline. 

16# To do so in the command line use an underscore _ insteaf of a minus sign -. 

17# For example, to solve a 3 level example with meshes refinements 1, 0 and -1, use the option --refinements 1,0,_1 

18 

19 

20def main(): 

21 parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) 

22 # define sweeper parameters 

23 parser.add_argument("--integrator", default="IMEXEXP_EXPRK", type=str, help="sweeper name") 

24 parser.add_argument( 

25 "--num_nodes", 

26 default="4", 

27 type=list_of_ints, 

28 help="list of ints (as '5,3', i.e. no brackets): number of collocation nodes per level", 

29 ) 

30 parser.add_argument("--num_sweeps", default="1", type=list_of_ints, help="list of ints: number of sweeps per level") 

31 parser.add_argument( 

32 "--skip_res", 

33 default=False, 

34 action=argparse.BooleanOptionalAction, 

35 help="compute residual only when really needed", 

36 ) 

37 # set step parameters 

38 parser.add_argument("--max_iter", default=100, type=int, help="maximal number of iterations") 

39 # set level parameters 

40 parser.add_argument("--dt", default=0.05, type=float, help="step size") 

41 parser.add_argument("--restol", default=5e-8, type=float, help="residual tolerance") 

42 # problem args 

43 parser.add_argument( 

44 "--domain_name", default="cuboid_2D_small", type=str, help="cuboid_2D, cuboid_3D, truncated_ellipsoid,..." 

45 ) 

46 parser.add_argument( 

47 "--refinements", 

48 default="0", 

49 type=list_of_ints, 

50 help="list of ints: number of refinements per level, with respect to a baseline mesh (negative values yield coarser meshes). For negative values use _ instead of -.", 

51 ) 

52 parser.add_argument( 

53 "--order", default="4", type=list_of_ints, help="list of ints: order of FEM or FD discretization" 

54 ) 

55 parser.add_argument("--ionic_model_name", default="TTP", type=str, help="ionic_model: HH, CRN, TTP") 

56 parser.add_argument( 

57 "--read_init_val", default=False, action=argparse.BooleanOptionalAction, help="read the initial value from file" 

58 ) 

59 parser.add_argument("--init_time", default=0.0, type=float, help="duration of stimulus. -1 means default") 

60 parser.add_argument( 

61 "--enable_output", 

62 default=False, 

63 action=argparse.BooleanOptionalAction, 

64 help="activate or deactivate xdmf output: True or False", 

65 ) 

66 parser.add_argument( 

67 "--write_as_reference_solution", 

68 default=False, 

69 action=argparse.BooleanOptionalAction, 

70 help="write as reference solution: True or False", 

71 ) 

72 parser.add_argument( 

73 "--write_all_variables", 

74 default=False, 

75 action=argparse.BooleanOptionalAction, 

76 help="when write_as_reference_solution=True, write write all variables (True) or only potential V (False)", 

77 ) 

78 parser.add_argument("--end_time", default=1.0, type=float, help="end time. If negative, a default one is used") 

79 parser.add_argument("--output_file_name", default="monodomain", type=str, help="output file name") 

80 parser.add_argument("--ref_sol", default="ref_sol", type=str, help="reference solution file name") 

81 parser.add_argument("--output_root", default="results_tmp/", type=str, help="output root folder") 

82 parser.add_argument( 

83 "--finter", 

84 default=False, 

85 action=argparse.BooleanOptionalAction, 

86 help="in prolong, re-evaluate f (false) or interpolate (true)", 

87 ) 

88 # controller args 

89 parser.add_argument( 

90 "--truly_time_parallel", 

91 default=False, 

92 action=argparse.BooleanOptionalAction, 

93 help="truly time parallel or emulated", 

94 ) 

95 parser.add_argument("--n_time_ranks", default=1, type=int, help="number of time ranks") 

96 

97 parser.add_argument( 

98 "--write_database", 

99 default=True, 

100 action=argparse.BooleanOptionalAction, 

101 help="save some simulation results in a database", 

102 ) 

103 

104 args = parser.parse_args() 

105 

106 error_L2, rel_error_L2, avg_niters, times, niters, residuals = setup_and_run( 

107 args.integrator, 

108 args.num_nodes, 

109 args.skip_res, 

110 args.num_sweeps, 

111 args.max_iter, 

112 args.dt, 

113 args.restol, 

114 args.domain_name, 

115 args.refinements, 

116 args.order, 

117 args.ionic_model_name, 

118 args.read_init_val, 

119 args.init_time, 

120 args.enable_output, 

121 args.write_as_reference_solution, 

122 args.write_all_variables, 

123 args.output_root, 

124 args.output_file_name, 

125 args.ref_sol, 

126 args.end_time, 

127 args.truly_time_parallel, 

128 args.n_time_ranks, 

129 args.finter, 

130 args.write_database, 

131 ) 

132 

133 

134if __name__ == "__main__": 

135 main()