Started a long running operation: loading a cartridge Call for loading a cartridge finished successfully Z = 0: The original displacements in the overlap zones have mean 56.94 maximum 229.68 pixels. After shifting pieces into register, the displacements have mean 20.50 maximum 93.33 pixels. Item 1: Stage: -0.00 0.02 -0 Label: 1 Note: Sec 0 - LMM-Car2-Alisson-g4.st 434.97 seconds elapsed time 434.969 Started a long running operation: loading a cartridge Call for loading a cartridge finished successfully Z = 0: The original displacements in the overlap zones have mean 30.30 maximum 211.08 pixels. After shifting pieces into register, the displacements have mean 18.04 maximum 115.32 pixels. Item 2: Stage: -0.01 0.03 -0 Label: 2 Note: Sec 0 - LMM-Car3-Alisson-g1.st 965.06 seconds elapsed time 965.062 Started a long running operation: loading a cartridge Call for loading a cartridge finished successfully Z = 0: The original displacements in the overlap zones have mean 99.36 maximum 291.28 pixels. After shifting pieces into register, the displacements have mean 63.00 maximum 183.53 pixels. Item 3: Stage: -0.00 0.09 -0 Label: 3 Note: Sec 0 - LMM-Car4-YGA-g1.st 1494.75 seconds elapsed time 1494.75 Started a long running operation: loading a cartridge Call for loading a cartridge finished successfully Z = 0: The original displacements in the overlap zones have mean 83.62 maximum 234.05 pixels. After shifting pieces into register, the displacements have mean 46.33 maximum 236.94 pixels. Item 4: Stage: -0.00 -0.01 -0 Label: 4 Note: Sec 0 - LMM-Car5-VIT-g4.st 2026.66 seconds elapsed time 2026.656 Started a long running operation: loading a cartridge Call for loading a cartridge finished successfully Z = 0: The original displacements in the overlap zones have mean 142.36 maximum 353.21 pixels. After shifting pieces into register, the displacements have mean 64.72 maximum 156.10 pixels. Item 5: Stage: -0.00 -0.06 -0 Label: 5 Note: Sec 0 - LMM-Car6-VIT-g1.st 2558.61 seconds elapsed time 2558.609 Started a long running operation: loading a cartridge Call for loading a cartridge finished successfully Z = 0: The original displacements in the overlap zones have mean 43.95 maximum 211.08 pixels. After shifting pieces into register, the displacements have mean 21.12 maximum 86.92 pixels. Item 6: Stage: -0.01 0.03 -0 Label: 6 Note: Sec 0 - LMM-Car7-B4-g3.st 3090.53 seconds elapsed time 3090.531 Started a long running operation: loading a cartridge Call for loading a cartridge finished successfully Z = 0: The original displacements in the overlap zones have mean 99.02 maximum 394.93 pixels. After shifting pieces into register, the displacements have mean 47.37 maximum 148.72 pixels. Item 7: Stage: -0.00 -0.01 -0 Label: 7 Note: Sec 0 - LMM-Car8-LB-g4.st 3625.56 seconds elapsed time 3625.562 Started a long running operation: loading a cartridge Call for loading a cartridge finished successfully Z = 0: The original displacements in the overlap zones have mean 170.77 maximum 418.73 pixels. After shifting pieces into register, the displacements have mean 80.45 maximum 185.37 pixels. Item 8: Stage: -0.00 -0.05 -0 Label: 8 Note: Sec 0 - LMM-Car9-Carli-g4.st 4161.31 seconds elapsed time 4161.312 Started a long running operation: loading a cartridge Call for loading a cartridge finished successfully Z = 0: The original displacements in the overlap zones have mean 51.80 maximum 211.63 pixels. After shifting pieces into register, the displacements have mean 32.92 maximum 85.61 pixels. Item 9: Stage: 0.00 0.00 -0 Label: 9 Note: Sec 0 - LMM-Car10-Trent-g1.st 4698.64 seconds elapsed time 4698.64 Started a long running operation: loading a cartridge Call for loading a cartridge finished successfully Z = 0: The original displacements in the overlap zones have mean 37.47 maximum 211.08 pixels. After shifting pieces into register, the displacements have mean 33.27 maximum 91.95 pixels. Item 10: Stage: -0.00 0.06 -0 Label: 10 Note: Sec 0 - LMM-Car11-Virgil-g1.st 5236.58 seconds elapsed time 5236.578 Started a long running operation: loading a cartridge Call for loading a cartridge finished successfully Z = 0: The original displacements in the overlap zones have mean 70.57 maximum 418.94 pixels. After shifting pieces into register, the displacements have mean 36.32 maximum 158.82 pixels. Item 11: Stage: -0.00 -0.02 -0 Label: 11 Note: Sec 0 - LMM-Car12-Virgil-g3.st 5775.42 seconds elapsed time 5775.422 Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is DOWN Now Screen is UP! Screen is UP Now screen is DOWN! Screen is DOWN Now Screen is UP! Screen is UP Now screen is DOWN! WARNING: Column valves closed or beam off while acquiring image. WARNING: Column valves closed or beam off while acquiring image. Screen is UP Now screen is DOWN! Screen is DOWN Now Screen is UP! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is DOWN Now Screen is UP! Drawn line is 864.0 pixels, 15.07 um at -0.4 degrees Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! WARNING: Column valves closed or beam off while acquiring image. Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Dose rate calculated to be 3.39 electrons/square Angstrom/sec for spot 8, IA 2.15um 22.28 electrons/unbinned pixel/sec Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! CallFunction MyFuncs::Z_byV2 3 -230 ===> Running Z_byV2 ... Absolute focus = -0.10779 Measured defocus = 38.83 microns drift = 0.27 nm/sec Last defocus in autofocus: 38.83 um Z has moved --> -38.826351 micron Measured defocus = -0.82 microns drift = 0.24 nm/sec Last defocus in autofocus: -0.82 um Z has moved --> 0.824373 micron Measured defocus = 0.29 microns drift = 0.40 nm/sec Last defocus in autofocus: 0.29 um Z has moved --> -0.290678 micron Absolute focus = -0.10779 Screen is UP Now screen is DOWN! Refine ZLP: additional offset = 0.9 eV; total offset = -0.3 eV Refine ZLP: additional offset = -0.8 eV; total offset = -1.1 eV Screen is UP Now screen is DOWN! CallFunction MyFuncs::Z_byV2 3 -230 ===> Running Z_byV2 ... Absolute focus = -0.10779 Measured defocus = 1.47 microns drift = 1.13 nm/sec Last defocus in autofocus: 1.47 um Z has moved --> -1.471495 micron Measured defocus = 0.56 microns drift = 1.68 nm/sec Last defocus in autofocus: 0.56 um Z has moved --> -0.56381 micron Measured defocus = -0.58 microns drift = 1.16 nm/sec Last defocus in autofocus: -0.58 um Z has moved --> 0.583834 micron Absolute focus = -0.10779 Screen is UP Now screen is DOWN! CallFunction MyFuncs::Z_byV2 3 -230 ===> Running Z_byV2 ... Absolute focus = -0.10779 Measured defocus = -11.67 microns drift = 0.72 nm/sec Last defocus in autofocus: -11.67 um Z has moved --> 11.666689 micron Measured defocus = -2.13 microns drift = 0.48 nm/sec Last defocus in autofocus: -2.13 um Z has moved --> 2.126223 micron Measured defocus = -0.60 microns drift = 0.41 nm/sec Last defocus in autofocus: -0.60 um Z has moved --> 0.59778 micron Absolute focus = -0.10779 Screen is UP Now screen is DOWN! Screen is UP Now screen is DOWN! CallFunction MyFuncs::Z_byV2 3 -230 ===> Running Z_byV2 ... Absolute focus = -0.10779 Measured defocus = 2.63 microns drift = 0.54 nm/sec Last defocus in autofocus: 2.63 um Z has moved --> -2.625425 micron Measured defocus = 0.14 microns drift = 0.62 nm/sec Last defocus in autofocus: 0.14 um Z has moved --> -0.136259 micron Measured defocus = -0.98 microns drift = 0.36 nm/sec Last defocus in autofocus: -0.98 um Z has moved --> 0.975435 micron Absolute focus = -0.10779 CallFunction MyFuncs::Z_byV2 3 -230 ===> Running Z_byV2 ... Absolute focus = -0.10779 Measured defocus = 141.89 microns drift = 1.10 nm/sec Last defocus in autofocus: 141.89 um Z has moved --> -141.890137 micron Measured defocus = -3.76 microns drift = 0.66 nm/sec Last defocus in autofocus: -3.76 um Z has moved --> 3.756716 micron Measured defocus = -1.10 microns drift = 1.07 nm/sec Last defocus in autofocus: -1.10 um Z has moved --> 1.095766 micron Absolute focus = -0.10779 CallFunction MyFuncs::Z_byV2 3 -230 ===> Running Z_byV2 ... Absolute focus = -0.10779 Measured defocus = 1.97 microns drift = 0.57 nm/sec Last defocus in autofocus: 1.97 um Z has moved --> -1.968748 micron Measured defocus = -1.02 microns drift = 0.16 nm/sec Last defocus in autofocus: -1.02 um Z has moved --> 1.02463 micron Measured defocus = -0.54 microns drift = 0.37 nm/sec Last defocus in autofocus: -0.54 um Z has moved --> 0.536898 micron Absolute focus = -0.10779 Screen is UP Now screen is DOWN! Screen is DOWN Now Screen is UP! Measured defocus = -0.14 microns drift = 0.01 nm/sec Changing defocus to -0.90 to get an acceptable number of CTF rings Ctffind: defocus: -1.202, astig: 0.377 um, angle: -58.3, score 0.7844, fit to 3.8 A Objective stigmator was adjusted by -0.0018 -0.0100 Changing defocus to -0.90 to get an acceptable number of CTF rings Ctffind: defocus: -1.218, astig: 0.022 um, angle: -49.0, score 0.7107, fit to 4.3 A Objective stigmator was adjusted by -0.0003 -0.0005 Changing defocus to -0.90 to get an acceptable number of CTF rings Ctffind: defocus: -1.217, astig: 0.008 um, angle: -88.8, score 0.7760, fit to 3.9 A Objective stigmator was adjusted by 0.0002 -0.0001 Changing defocus to -1.40 to get an acceptable number of CTF rings Ctffind: defocus: -1.730, astig: 0.000 um, angle: 51.7, score 0.7635, fit to 4.1 A Ctffind: defocus: -1.389, astig: 0.348 um, angle: -29.9, score 0.7911, fit to 3.8 A Ctffind: defocus: -1.419, astig: 0.324 um, angle: -28.6, score 0.7861, fit to 4.0 A Ctffind: defocus: -1.420, astig: 0.324 um, angle: 61.1, score 0.7723, fit to 4.0 A Ctffind: defocus: -1.405, astig: 0.340 um, angle: 63.6, score 0.7855, fit to 4.0 A Beam tilt was adjusted by 0.18 -0.09 milliradians Changing defocus to -1.40 to get an acceptable number of CTF rings Ctffind: defocus: -1.737, astig: 0.004 um, angle: 32.0, score 0.7881, fit to 4.0 A Ctffind: defocus: -1.404, astig: 0.334 um, angle: -29.2, score 0.7957, fit to 3.8 A Ctffind: defocus: -1.399, astig: 0.337 um, angle: -29.3, score 0.7873, fit to 3.8 A Ctffind: defocus: -1.407, astig: 0.332 um, angle: 62.5, score 0.7894, fit to 3.7 A Ctffind: defocus: -1.406, astig: 0.334 um, angle: 62.4, score 0.7916, fit to 4.1 A Beam tilt was adjusted by -0.03 -0.00 milliradians Screen is UP Now screen is DOWN! Beam tilt 6.746 0.748 Screen is UP Now screen is DOWN! Dose rate calculated to be 3.40 electrons/square Angstrom/sec for spot 8, IA 2.15um 22.35 electrons/unbinned pixel/sec 4 frames were saved to X:\Luke_20200318\YGA-g1_00000_-0.0.tif Disparity in stage position after aligning to center of map frame: 12.57 1.00 Disparity in stage position after aligning to target position: 12.74 0.57 (2nd move error -0.20 -0.35) Finished aligning to item in 2 rounds CallFunction MyFuncs::Z_byV2 3 -230 ===> Running Z_byV2 ... Absolute focus = -0.10731 Measured defocus = 151.96 microns drift = 0.40 nm/sec Last defocus in autofocus: 151.96 um Z has moved --> -151.962982 micron Measured defocus = -2.31 microns drift = 0.18 nm/sec Last defocus in autofocus: -2.31 um Z has moved --> 2.30707 micron Measured defocus = -1.06 microns drift = 1.13 nm/sec Last defocus in autofocus: -1.06 um Z has moved --> 1.055606 micron Absolute focus = -0.10731 Full View shift offset is set to -0.175, -0.314 image shift units Taking a new View image - if feature is not centered, shift to center it and press "Set" again Skipping first round alignment to center of map frame Disparity in stage position after aligning to target position: 11.94 1.04 (2nd move error -1.08 0.09) Finished aligning to item in 1 rounds Stage position error of 11.94, 1.04 assigned to this map from last realign to nearby item Stage position error of 11.94, 1.04 assigned to this map from last realign to nearby item Stage position error of 11.94, 1.04 assigned to this map from last realign to nearby item Stage position error of 11.94, 1.04 assigned to this map from last realign to nearby item Refining eucentricity: Fit to 8 positions gives tilt axis Z displacement of -2.88 microns and lateral displacement of 0.52 microns