implemented json input

+ few addidtional changes:
SRCREC is now the switch to either read from .dat file =1 or use plane wave =2
reduced some arrays (currently unused) to variables

par/in_and_out/ifos3d_inv_all_parameters.json

+{
+"MODELING PARAMETERS" : "comment",
+
+"Domain Decomposition" : "comment",
+			"NPROCX" : "2",
+			"NPROCY" : "2",
+			"NPROCZ" : "2",
+
+"3-D Grid" : "comment",
+			"NX" : "160",
+			"NY" : "160",
+			"NZ" : "184",
+			"DX" : "0.8",
+			"DY" : "0.8",
+			"DZ" : "0.8",
+
+"FD order" : "comment",
+			"FDORDER" : "4",
+			"FDCOEFF" : "2",
+
+"Time Stepping" : "comment",
+			"TIME" : "0.06",
+			"DT" : "5.0e-05",
+
+"Source" : "comment",
+			"SOURCE_SHAPE" : "4",
+			"SOURCE_TYPE" : "4",
+			"ALPHA" : "45.0",
+			"BETA" : "45.0",
+			"PLANE_WAVE_DEPTH" : "0.0",
+			"PHI" : "0.0",
+			"TS" : "0.0033",
+			"SIGNAL_FILE" : "./STF/stf.su",
+			"SRCREC" : "1",
+			"SOURCE_FILE" : "./sources/sources_toy.dat",
+			"RUN_MULTIPLE_SHOTS" : "1",
+
+"Model" : "comment",
+			"READMOD" : "0",
+			"MFILE" : "model/toy",
+			
+
+"Q-approximation" : "comment",
+			"L" : "0",
+			"FL1" : "1000.0", 
+			"TAU" : "0.000001",
+
+"Free Surface" : "comment",
+			"FREE_SURF" : "0",
+			
+
+"Absorbing Boundary" : "comment",
+			"ABS_TYPE" : "1",			
+			"FW" : "10",
+			"DAMPING" : "8.0",
+			"VPPML" : "6200.0",
+			"FPML" : "200.00",
+			"BOUNDARY" : "0",
+
+"Snapshots" : "comment",
+			"SNAP" : "0",
+			"TSNAP1" : "0.01",
+			"TSNAP2" : "0.24",
+			"TSNAPINC" : "0.0075",
+			"IDX, IDY, IDZ" : "1,1,1",
+			"SNAP_FORMAT" : "4",
+			"SNAP_FILE" : "./snap/back",
+			"SNAP_PLANE" : "1",
+
+"Receiver" : "comment",
+			"SEISMO" : "1",
+			"READREC" : "0",
+			"REC_FILE" : "./receiver/receiver.dat",
+			"REFRECX, REFRECY, REFRECZ" : "0.0 , 0.0, 0.0",
+			"XREC1, YREC1, ZREC1" : "90.0 , 90.0, 90.0",
+			"XREC2, YREC2, ZREC2" : "90.0 , 90.0, 90.0",
+			"NGEOPH" : "1",
+
+"Receiver array" : "comment",
+			"REC_ARRAY" : "1",
+			"REC_ARRAY_DEPTH" : "24.0",
+			"REC_ARRAY_DIST" : "30.0",
+			"DRX" : "10",
+			"DRY" : "10",
+			
+
+"Seismograms" : "comment",
+			"NDT" : "1",
+			"NDTSHIFT" : "0",
+			"SEIS_FORMAT" : "1",
+			"SEIS_FILE" : "su/IFOS",
+
+
+"Method" : "comment",
+			"METHOD" : "0",
+			
+"INVERSION PARAMETERS" : "comment",
+
+"In- and Output Files" : "comment",
+			"GRAD_FILE" : "./grad/toy_grad",
+			"MOD_OUT_FILE" : "./model/toy",
+			"SEIS_OBS_FILE" : "./su_obs/obs_toy",
+			"EXTOBS" : "0",
+			"INV_FILE" : "./in_and_out/workflow_toy.dat",
+			"HESS_FILE" : "./hess/toy_hess",
+
+"General" : "comment",
+			"ITMIN, ITMAX" : "1 , 80",
+			"FILT" : "1",
+			"NFMAX" : "5",
+			"TAST" : "100",
+			"VP0, VS0, RHO0" : "6200.0, 3600.0, 2800.0",
+			"WEIGHT_VP,WEIGHT_VS,WEIGHT_RHO" : "1.0, 1.0, 0.0",
+
+"Steplength estimation" : "comment",
+			"NSHOTS_STEP" : "4",
+			"TESTSTEP" : "0.02",
+
+"Gradient preconditioning" : "comment",
+			"DAMPTYPE" : "2",
+
+"Hessian" : "comment",
+			"HESS" : "0",
+			"READ_HESS" : "0",
+			"REC_HESS" : "1", 
+			"WATER_HESS_VP, WATER_HESS_VS, WATER_HESS_RHO" : "0.0192, 0.0192, 1.0e-14",
+ 
+"L-BFGS" : "comment",
+			"LBFGS" : "0",
+			"NUMPAR" : "2",
+			"BFGSNUM" : "5"
+}

par/in_and_out/ifos3d_inv_all_parameters_commented.json

+{
+"MODELING PARAMETERS" : "comment",
+
+"Note that z denotes the vertical direction !" : "comment",
+
+"Domain Decomposition" : "comment",
+			"NPROCX" : "2",
+			"NPROCY" : "2",
+			"NPROCZ" : "2",
+
+"3-D Grid" : "comment",
+			"NX" : "160",
+			"NY" : "160",
+			"NZ" : "184",
+			"DX" : "0.8",
+			"DY" : "0.8",
+			"DZ" : "0.8",
+			"Caution: first gridpoint is not at {0.0,0.0,0.0} but at {dx,dy,dz}!" : "comment",
+
+"FD order" : "comment",
+			"FDORDER" : "4",
+			"possible values are 2, 4, 6, 8, 10, 12" : "comment",
+			"fd_coefficients_(Taylor=1;Holberg=2)" : "comment",
+			"FDCOEFF" : "2",
+
+"Time Stepping" : "comment",
+			"time_of_wave_propagation_(in_sec)" : "comment",
+			"TIME" : "0.06",
+			"timestep_(in_seconds)" : "comment",
+			"DT" : "5.0e-05",
+
+"Source" : "comment",
+			"Shape_of_source-signal:" : "comment",
+			"SOURCE_SHAPE" : "4",
+			"SOURCE_SHAPE values: ricker=1;fumue=2;from_SIGNAL_FILE=3;SIN**3=4;deltapulse=5" : "comment",
+			"External signal input instead of SOURCE_SHAPE" : "comment",
+			"SIGNAL_FILE" : "./STF/stf.su",
+			"SOURCE_TYPE" : "4",
+			"SOURCE_TYPE values (point_source): explosive=1;force_in_x=2;force_in_y=3;force_in_z=4;custom=5" : "comment",
+			"If SOURCE_TYPE <5 the following two lines are ignored" : "comment",
+			"ALPHA" : "45.0",
+			"BETA" : "45.0",
+			"ALPHA=force_angle_between_x_y_(in_degree) (BETA between x_z)" : "comment",
+			"read_source_positions_from_SOURCE_FILE_(yes=1;Plane wave=2) " : "comment",
+			"SRCREC" : "1",
+			"SOURCE_FILE" : "./sources/sources_toy.dat",
+			"run_multiple_shots_defined_in_SOURCE_FILE_(yes=1)" : "comment",
+			"RUN_MULTIPLE_SHOTS" : "1",
+			
+			"Following lines can be ignored if SRCREC!=2" : "comment",
+			"Plane wave (PW) excitation,if PLANE_WAVE_DEPTH>0, SRCREC is treated as 0" : "comment",
+			"depth_of_PW_excitation_(no<=0)_(in_meter)" : "comment",
+			"PLANE_WAVE_DEPTH" : "0.0",
+			"dip_of_PW_from_vertical_(in_degrees)" : "comment",
+			"PHI" : "0.0",
+			"duration_of_source-signal_PW_(in_seconds)" : "comment",
+			"TS" : "0.0033",
+
+"Model" : "comment",
+			"read_model_from_MFILE(yes=1)" : "comment",
+			"READMOD" : "0",
+			"MFILE" : "model/toy",
+			
+
+"Q-approximation" : "comment",
+			"Number_of_relaxation_mechanisms" : "comment",
+			"L" : "0",
+			"L_Relaxation_frequencies" : "comment",
+			"FL1" : "1000.0", 
+			"Tau_value_for_entire_model" : "comment",
+			"TAU" : "0.000001",
+
+"Free Surface" : "comment",
+			"free_surface_(yes=1)" : "comment",
+			"FREE_SURF" : "0",
+			
+
+"Absorbing Boundary" : "comment",
+			"type_of_boundary_condition_(ABS_TYPE)_(PML=1/ABS=2)" : "comment",
+			"ABS_TYPE" : "1",
+			"width_of_absorbing_frame_(in_grid_points)_(No<=0)" : "comment",			
+			"FW" : "10",
+			"percentage_of_amplitude_decay_at_outer_edge" : "comment",
+			"DAMPING" : "8.0",
+			"parameter for PML:" : "comment",
+			"P_wave_velocity_near_the_grid_boundary(in_m/s)" : "comment",
+			"VPPML" : "6200.0",
+			"Dominant_frequency_(in_Hz)" : "comment",
+			"FPML" : "200.00",
+			"apply_periodic_boundary_condition_at_edges" : "comment",
+			"BOUNDARY" : "0",
+
+"Snapshots" : "comment",
+			"output_of_snapshots(yes>0)" : "comment",
+			"SNAP" : "0",
+			"output of particle velocities: SNAP=1" : "comment",
+			"output of pressure field: SNAP=2" : "comment",
+			"output of curl and divergence energy: SNAP=3" : "comment",
+			"output of both particle velocities and energy : SNAP=4" : "comment",
+			"first_snapshot_(in_sec)" : "comment",
+			"TSNAP1" : "0.01",
+			"last_snapshot_(in_sec)" : "comment",
+			"TSNAP2" : "0.24",
+			"increment_(in_sec)" : "comment",
+			"TSNAPINC" : "0.0075",
+			"increment_x,y,z-direction" : "comment",
+			"IDX, IDY, IDZ" : "1,1,1",
+			"data-format(ASCII(2);BINARY(3))" : "comment",
+			"SNAP_FORMAT" : "4",
+			"basic_filename" : "comment",
+			"SNAP_FILE" : "./snap/back",
+			"if SNAP !=3 the following line is ignored" : "comment",
+			"SNAP_PLANE" : "1",
+			"output of snapshots as energy wihout sign SNAP_PLANE=1" : "comment",
+			"energy with sign true for x-z-plane SNAP_PLANE=2" : "comment",
+			"energy with sign true for x-y-plane SNAP_PLANE=3" : "comment",
+			"energy with sign true for y-z-plane SNAP_PLANE=4" : "comment",
+
+"Receiver" : "comment",
+			"output_of_seismograms" : "comment",
+			"SEISMO" : "1",
+			"SEISMO=0: no seismograms" : "comment",
+			"SEISMO=1: particle-velocities" : "comment",
+			"SEISMO=2: pressure (hydrophones)" : "comment",
+			"SEISMO=3: curl and div" : "comment",
+			"SEISMO=4: everything" : "comment",
+			"Warning: "curl" is not really curl in 3D" : "comment",
+			"read_receiver_positions_from_file_(yes=1)" : "comment",
+			"READREC" : "0",
+			"REC_FILE" : "./receiver/receiver.dat",
+			"reference_point_for_receiver_coordinate_system" : "comment",
+			"REFRECX, REFRECY, REFRECZ" : "0.0 , 0.0, 0.0",
+			"if READREC=1 the following three lines are ignored" : "comment",
+			"Note that z denotes the vertical direction !" : "comment",
+			"position_of_first_receiver_(in_m)" : "comment",
+			"XREC1, YREC1, ZREC1" : "90.0 , 90.0, 90.0",
+			"position_of_last_receiver_(in_m)" : "comment",
+			"XREC2, YREC2, ZREC2" : "90.0 , 90.0, 90.0",
+			"distance_between_two_adjacent_receivers" : "comment",
+			"NGEOPH" : "1",
+
+"Receiver array" : "comment",
+			"parameters for horizontal plane of receivers" : "comment",
+			"number_of_planes_(no<=0)" : "comment",
+			"REC_ARRAY" : "1",
+			"depth_of_first_(upper)_plane_(in_m)" : "comment",
+			"REC_ARRAY_DEPTH" : "24.0",
+			"vertical_distance_between_planes_(in_m)" : "comment",
+			"REC_ARRAY_DIST" : "30.0",
+			"distance_between_receivers_in_x/y-direction" : "comment",
+			"DRX" : "10",
+			"DRY" : "10",
+			
+
+"Seismograms" : "comment",
+			"samplingrate_and_timelag_(in_timesteps!)" : "comment",
+			"NDT" : "1",
+			"NDTSHIFT" : "0",
+			"write every (ndt)th sample, leaving ndtshift samples at the beginning out" : "comment",
+			"default: ndt=1 and ndtshift=0. (ndt=0 is set to ndt=1, ndt<0 are set to -ndt.)" : "comment",
+			"data-format" : "comment",
+			"SEIS_FORMAT" : "1",
+			"0: SEG-Y (ASCII-text/native 4-byte-floats (IEEE on PC)/little endian on PC)" : "comment",
+			"1: SU (native 4-byte-floats (IEEE on PC)/little endian on PC)" : "comment",
+			"2: TEXTUAL (native ASCII)" : "comment",
+			"3: BINARY (IEEE-4-byte-floats on PC/little endian on PC)" : "comment",
+			"4: SEG-Y (ASCII-text/native 4-byte-floats (IEEE on PC)/little endian on PC)" : "comment",
+			"5: SEG-Y (ASCII-text/IBM-4-byte-floats on PC/big endian on PC) " : "comment",
+			"basic_filename" : "comment",
+			"SEIS_FILE" : "su/IFOS",
+
+
+"Method" : "comment",
+			"METHOD" : "0",
+			"0: only forward simulation" : "comment",
+			"1: conjugate_gradient_FWI" : "comment",
+			
+"INVERSION PARAMETERS" : "comment",
+
+"In- and Output Files" : "comment",
+			"gradient_filename" : "comment",
+			"GRAD_FILE" : "./grad/toy_grad",
+			"model_output_filename" : "comment",
+			"MOD_OUT_FILE" : "./model/toy",
+			"observed_data_fileneame" : "comment",
+			"SEIS_OBS_FILE" : "./su_obs/obs_toy",
+			"external_or_internal_observed_data" : "comment",
+			"EXTOBS" : "0",
+			"inversion_parameter_file" : "comment",
+			"INV_FILE" : "./in_and_out/workflow_toy.dat",
+			"hessian_file" : "comment",
+			"HESS_FILE" : "./hess/toy_hess",
+
+"General" : "comment",
+			"minimum/maximum_iteration_number >0" : "comment",
+			"ITMIN, ITMAX" : "1 , 80",
+			"filtering_(yes=1/no=0)" : "comment",
+			"FILT" : "1",
+			"maximum_number_frequencies_per_iteration" : "comment",
+			"NFMAX" : "5",
+			"number_of_timestep_per_period_used_for_inversion" : "comment",
+			"TAST" : "100",
+			"average_model_parameter" : "comment",
+			"VP0, VS0, RHO0" : "6200.0, 3600.0, 2800.0",
+			"velocities  in m/s, density in kg/m³" : "comment",
+			"parameter_class_weighting_factors_for_vp/vs/rho_" : "comment",
+			"WEIGHT_VP,WEIGHT_VS,WEIGHT_RHO" : "1.0, 1.0, 0.0",
+			"choose from 1.0 (full update) to 0.0 (no update)" : "comment",
+
+"Steplength estimation" : "comment",
+			"number_of_shots_used_for_steplength_estimation" : "comment",
+			"NSHOTS_STEP" : "4",
+			"initial_test_steplength" : "comment",
+			"TESTSTEP" : "0.02",
+
+"Gradient preconditioning" : "comment",
+			"Type_of_preconditioning" : "comment",
+			"DAMPTYPE" : "2",
+			"0: no damping; 1: Circular taper around receivers;" : "comment",
+			"2: Cicular taper around sources and receivers; 3: Tapering of source and receiver planes" : "comment",
+
+"Hessian" : "comment",
+			"Apply_Hessian_(yes=1/no=0)" : "comment",
+			"HESS" : "0",
+			"Read_Hessian_from_file" : "comment",
+			"READ_HESS" : "0",
+			"Part_of_receivers_used_for_Hessian" : "comment",
+			"REC_HESS" : "1", 
+			"(Each REC_HESS Receiver is used to calculate the Hessian, not yet implemented)" : "comment",
+			"Water_level_Hessian_for_vp/vs/rho" : "comment",
+			"WATER_HESS_VP, WATER_HESS_VS, WATER_HESS_RHO" : "0.0192, 0.0192, 1.0e-14",
+ 
+"L-BFGS" : "comment",
+			"Apply_L_BFGS" : "comment",
+			"LBFGS" : "0",
+			"Number_of_inverted_parameters" : "comment",
+			"NUMPAR" : "2",
+			"Number_iterations_used_for_LBFGS" : "comment",
+			"BFGSNUM" : "5"
+}

par/in_and_out/ifos3d_toy.json

+{
+"MODELING PARAMETERS" : "comment",
+
+"Domain Decomposition" : "comment",
+			"NPROCX" : "2",
+			"NPROCY" : "2",
+			"NPROCZ" : "2",
+
+"3-D Grid" : "comment",
+			"NX" : "160",
+			"NY" : "160",
+			"NZ" : "184",
+			"DX" : "0.8",
+			"DY" : "0.8",
+			"DZ" : "0.8",
+
+"FD order" : "comment",
+			"FDORDER" : "4",
+			"FDCOEFF" : "2",
+
+"Time Stepping" : "comment",
+			"TIME" : "0.06",
+			"DT" : "5.0e-05",
+
+"Source" : "comment",
+			"SOURCE_SHAPE" : "4",
+			"SOURCE_TYPE" : "4",
+			"SIGNAL_FILE" : "./STF/stf.su",
+			"SRCREC" : "1",
+			"SOURCE_FILE" : "./sources/sources_toy.dat",
+			"RUN_MULTIPLE_SHOTS" : "1",
+
+"Model" : "comment",
+			"READMOD" : "0",
+			"MFILE" : "model/toy",
+			
+
+"Q-approximation" : "comment",
+			"L" : "0",
+			"FL1" : "1000.0", 
+			"TAU" : "0.000001",
+
+"Free Surface" : "comment",
+			"FREE_SURF" : "0",
+			
+
+"Absorbing Boundary" : "comment",
+			"ABS_TYPE" : "1",			
+			"FW" : "10",
+			"VPPML" : "6200.0",
+			"FPML" : "200.00",
+			"BOUNDARY" : "0",
+
+"Snapshots" : "comment",
+			"SNAP" : "0",
+			"TSNAP1" : "0.01",
+			"TSNAP2" : "0.24",
+			"TSNAPINC" : "0.0075",
+			"IDX, IDY, IDZ" : "1,1,1",
+			"SNAP_FORMAT" : "4",
+			"SNAP_FILE" : "./snap/back",
+			"SNAP_PLANE" : "1",
+
+"Receiver" : "comment",
+			"SEISMO" : "1",
+			"READREC" : "0",
+			"REC_FILE" : "./receiver/receiver.dat",
+			"REFRECX, REFRECY, REFRECZ" : "0.0 , 0.0, 0.0",
+			"XREC1, YREC1, ZREC1" : "90.0 , 90.0, 90.0",
+			"XREC2, YREC2, ZREC2" : "90.0 , 90.0, 90.0",
+			"NGEOPH" : "1",
+
+"Receiver array" : "comment",
+			"REC_ARRAY" : "1",
+			"REC_ARRAY_DEPTH" : "24.0",
+			"REC_ARRAY_DIST" : "30.0",
+			"DRX" : "10",
+			"DRY" : "10",
+			
+
+"Seismograms" : "comment",
+			"NDT" : "1",
+			"NDTSHIFT" : "0",
+			"SEIS_FORMAT" : "1",
+			"SEIS_FILE" : "./su_obs/obs_toy",
+
+
+"Method" : "comment",
+			"METHOD" : "0",
+			
+"INVERSION PARAMETERS" : "comment",
+
+"In- and Output Files" : "comment",
+			"GRAD_FILE" : "./grad/toy_grad",
+			"MOD_OUT_FILE" : "./model/toy",
+			"SEIS_OBS_FILE" : "./su_obs/obs_toy",
+			"EXTOBS" : "0",
+			"INV_FILE" : "./in_and_out/workflow_toy.dat",
+			"HESS_FILE" : "./hess/toy_hess",
+
+"General" : "comment",
+			"ITMIN, ITMAX" : "1 , 60",
+			"FILT" : "0",
+			"NFMAX" : "5",
+			"TAST" : "100",
+			"VP0, VS0, RHO0" : "6200.0, 3600.0, 2800.0",
+			"WEIGHT" : "1.0, 1.0, 0.0",
+
+"Steplength estimation" : "comment",
+			"NSHOTS_STEP" : "4",
+			"TESTSTEP" : "0.02",
+
+"Gradient preconditioning" : "comment",
+			"DAMPTYPE" : "2",
+
+"Hessian" : "comment",
+			"HESS" : "0",
+			"READ_HESS" : "0",
+			"REC_HESS" : "1", 
+			"WATER_HESS_VP, WATER_HESS_VS, WATER_HESS_RHO" : "0.0192, 0.0192, 1.0e-14",
+ 
+"L-BFGS" : "comment",
+			"LBFGS" : "0",
+			"NUMPAR" : "2",
+			"BFGSNUM" : "5"
+}

par/in_and_out/ifos3d_toy_FW.json

+{
+"MODELING PARAMETERS" : "comment",
+
+"Domain Decomposition" : "comment",
+			"NPROCX" : "2",
+			"NPROCY" : "2",
+			"NPROCZ" : "2",
+
+"3-D Grid" : "comment",
+			"NX" : "160",
+			"NY" : "160",
+			"NZ" : "184",
+			"DX" : "0.8",
+			"DY" : "0.8",
+			"DZ" : "0.8",
+
+"FD order" : "comment",
+			"FDORDER" : "4",
+			"FDCOEFF" : "2",
+
+"Time Stepping" : "comment",
+			"TIME" : "0.06",
+			"DT" : "5.0e-05",
+
+"Source" : "comment",
+			"SOURCE_SHAPE" : "4",
+			"SOURCE_TYPE" : "4",
+			"SIGNAL_FILE" : "./STF/stf.su",
+			"SRCREC" : "1",
+			"SOURCE_FILE" : "./sources/sources_toy.dat",
+			"RUN_MULTIPLE_SHOTS" : "1",
+
+"Model" : "comment",
+			"READMOD" : "0",
+			"MFILE" : "model/toy",
+			
+
+"Q-approximation" : "comment",
+			"L" : "0",
+			"FL1" : "1000.0", 
+			"TAU" : "0.000001",
+
+"Free Surface" : "comment",
+			"FREE_SURF" : "0",
+			
+
+"Absorbing Boundary" : "comment",
+			"ABS_TYPE" : "1",			
+			"FW" : "10",
+			"VPPML" : "6200.0",
+			"FPML" : "200.00",
+			"BOUNDARY" : "0",
+
+"Snapshots" : "comment",
+			"SNAP" : "0",
+			"TSNAP1" : "0.01",
+			"TSNAP2" : "0.24",
+			"TSNAPINC" : "0.0075",
+			"IDX, IDY, IDZ" : "1,1,1",
+			"SNAP_FORMAT" : "4",
+			"SNAP_FILE" : "./snap/back",
+			"SNAP_PLANE" : "1",
+
+"Receiver" : "comment",
+			"SEISMO" : "1",
+			"READREC" : "0",
+			"REC_FILE" : "./receiver/receiver.dat",
+			"REFRECX, REFRECY, REFRECZ" : "0.0 , 0.0, 0.0",
+			"XREC1, YREC1, ZREC1" : "90.0 , 90.0, 90.0",
+			"XREC2, YREC2, ZREC2" : "90.0 , 90.0, 90.0",
+			"NGEOPH" : "1",
+
+"Receiver array" : "comment",
+			"REC_ARRAY" : "1",
+			"REC_ARRAY_DEPTH" : "24.0",
+			"REC_ARRAY_DIST" : "30.0",
+			"DRX" : "10",
+			"DRY" : "10",
+			
+
+"Seismograms" : "comment",
+			"NDT" : "1",
+			"NDTSHIFT" : "0",
+			"SEIS_FORMAT" : "1",