loading system configuration loading override configuration from /home/nexmap/pkwi/McCode/tools/Python/mctest/../mccodelib/mcstas-test/McStas-2.x_CPU_MPICC/mccode_config.json INFO: Using directory: "1" INFO: Using existing c-file: ./Union_single_crystal_validation.c INFO: Using existing binary: ./Union_single_crystal_validation.out INFO: === Simulation 'Union_single_crystal_validation' (/home/nexmap/pkwi/TESTS/2022-08-01/McStas-2.x_CPU_MPICC_5e7/Union_single_crystal_validation/Union_single_crystal_validation.instr): running on 16 nodes (master is 'elearn1.fysik.dtu.dk', MPI version 3.1). Opening input file '/home/nexmap/pkwi/McStas/mcstas/2.x-dev/tools/Python/mcrun/../mccodelib/../../../data/YBaCuO.lau' (Table_Read_Offset) Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize [Union_single_crystal_validation] Initialize Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' [Union_single_crystal_validation] Initialize Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize Single_crystal_process: Single_crystal_test_process: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: Single_crystal_test_process: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau [Union_single_crystal_validation] Initialize --------------------------------------------------------------------- global_process_list.num_elements: 2 name of process [0]: Incoherent_process component index [0]: 1 name of process [1]: Single_crystal_test_process component index [1]: 2 --------------------------------------------------------------------- global_material_list.num_elements: 1 name of material [0]: test_material component index [0]: 3 my_absoprtion [0]: 8.550000 number of processes [0]: 2 --------------------------------------------------------------------- global_geometry_list.num_elements: 1 name of geometry [0]: cylinder_sample_union component index [0]: 7 Volume.name [0]: cylinder_sample_union Volume.p_physics.is_vacuum [0]: 0 Volume.p_physics.my_absorption [0]: 8.550000 Volume.p_physics.number of processes [0]: 2 Volume.geometry.shape [0]: cylinder Volume.geometry.center.x [0]: 0.000000 Volume.geometry.center.y [0]: 0.000000 Volume.geometry.center.z [0]: 5.100000 Volume.geometry.rotation_matrix[0] [0]: [1.000000 0.000000 0.000000] Volume.geometry.rotation_matrix[1] [0]: [0.000000 1.000000 0.000000] Volume.geometry.rotation_matrix[2] [0]: [0.000000 0.000000 1.000000] Volume.geometry.geometry_parameters.cyl_radius [0]: 0.010000 Volume.geometry.geometry_parameters.height [0]: 0.010000 Volume.geometry.focus_data_array.elements[0].Aim [0]: [0.000000 0.000000 1.000000] --------------------------------------------------------------------- number_of_volumes = 2 number_of_masks = 0 number_of_masked_volumes = 0 ---- Overview of the lists generated for each volume ---- List overview for surrounding vacuum LIST: Children for Volume 0 = [1] LIST: Direct_children for Volume 0 = [1] LIST: Intersect_check_list for Volume 0 = [1] LIST: Mask_intersect_list for Volume 0 = [] LIST: Destinations_list for Volume 0 = [] LIST: Reduced_destinations_list for Volume 0 = [] LIST: Next_volume_list for Volume 0 = [1] LIST: mask_list for Volume 0 = [] LIST: masked_by_list for Volume 0 = [] LIST: masked_by_mask_index_list for Volume 0 = [] mask_mode for Volume 0 = 0 List overview for cylinder_sample_union with cylinder shape made of test_material LIST: Children for Volume 1 = [] LIST: Direct_children for Volume 1 = [] LIST: Intersect_check_list for Volume 1 = [] LIST: Mask_intersect_list for Volume 1 = [] LIST: Destinations_list for Volume 1 = [0] LIST: Reduced_destinations_list for Volume 1 = [] LIST: Next_volume_list for Volume 1 = [0] Is_vacuum for Volume 1 = 0 is_mask_volume for Volume 1 = 0 is_masked_volume for Volume 1 = 0 is_exit_volume for Volume 1 = 0 LIST: mask_list for Volume 1 = [] LIST: masked_by_list for Volume 1 = [] LIST: masked_by_mask_index_list for Volume 1 = [] mask_mode for Volume 1 = 0 Union_master component test_sample initialized sucessfully Opening input file '/home/nexmap/pkwi/McStas/mcstas/2.x-dev/tools/Python/mcrun/../mccodelib/../../../data/YBaCuO.lau' (Table_Read_Offset) Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Single_crystal: YBaCuO.lau structure a=[3.8186,0,0] b=[0,3.8843,0] c=[0,0,11.6777] V0=173.211 Single_crystal: sample: Read 62 reflections from file 'YBaCuO.lau' Single_crystal: sample: Vc=173.211 [Angs] sigma_abs=14.82 [barn] sigma_inc=2.105 [barn] reflections=YBaCuO.lau Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 711159 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 710794 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 711387 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 711197 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 710264 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 711673 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 712078 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Warning: 710914 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 710863 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Save [Union_single_crystal_validation] Detector: Union_logger_2DQ_crystal_I=4.29504e+08 Union_logger_2DQ_crystal_ERR=66768.2 Union_logger_2DQ_crystal_N=8.14424e+07 "Union_logger_2DQ_crystal.dat" Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 710123 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Warning: 711384 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 710117 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Detector: Union_logger_2DQ_incoherent_I=8.35229e+06 Union_logger_2DQ_incoherent_ERR=2280.97 Union_logger_2DQ_incoherent_N=2.84731e+07 "Union_logger_2DQ_incoherent.dat" Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 711265 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 710687 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Warning: 710913 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Detector: det_I=1.44357e+07 det_ERR=8194.51 det_N=2.32716e+07 "psd.dat" Detector: Banana_monitor_I=978423 Banana_monitor_ERR=2575.17 Banana_monitor_N=558108 "banana.dat" Detector: PSDlin_transmission_scattered_I=790836 PSDlin_transmission_scattered_ERR=2323.99 PSDlin_transmission_scattered_N=140212 "Output_transmission_lin_scattered.psd" Detector: PSDlin_transmission_transmitted_I=2.28084e+08 PSDlin_transmission_transmitted_ERR=47884.3 PSDlin_transmission_transmitted_N=2.26883e+07 "Output_transmission_lin_transmitted.psd" Finally [Union_single_crystal_validation: 1]. Time: 10 [s] Warning: 710863 events were removed in Component[14] PSDlin_transmission_scattered=PSDlin_monitor() (negative time, miss next components, rounding errors, Nan, Inf). INFO: Placing instr file copy /home/nexmap/pkwi/TESTS/2022-08-01/McStas-2.x_CPU_MPICC_5e7/Union_single_crystal_validation/Union_single_crystal_validation.instr in dataset 1