[Chimera-users] something flakey with measure buriedArea?
Scott Classen
sclassen at lbl.gov
Tue Apr 27 17:40:27 PDT 2010
I'm seeing some very odd results coming from the measure buriedArea command
if I use different values for probeRaduis and then grep for WARNINGs
I get the following results:
probeRadius # of WARNINGs
1.50 = 12
1.40 = 4
1.39 = 14
1.35 = 59
1.30 = 3
1.20 = 0
Here are some examples of the types of warnings I'm seeing:
WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
WARNING: class_arete2: warning hole in a reentrant face 1735
WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
WARNING: class_arete2: warning hole in a reentrant face 2557
WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
WARNING: class_arete2: warning hole in a reentrant face 1836
WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
WARNING: class_arete2: warning hole in a reentrant face 2090
WARNING: class_arete2: warning hole in a reentrant face 1925
WARNING: compute_SES_area: ERROR: Solide angle (-1.972093) for contact face 3142 too large or too small
Should I be concerned?
Another unusual thing is that for certain calculations I get some crazy answers. For example the following command
measure buriedArea '#0:.A,.B & #0:10.Dz<8' #0:10.D probeRadius 1.4 vertexDensity 2
outputs:
B1SES = -583.491, B2SES = 51.4762, BaveSES = -266.007
but the same command with the probeRadius changed to 1.37
measure buriedArea '#0:.A,.B & #0:10.Dz<8' #0:10.D probeRadius 1.37 vertexDensity 2
outputs:
B1SES = 53.9334, B2SES = 51.7969, BaveSES = 52.8652
Why would B1SES be so radically different for these two measurements?
Thanks,
Scott
ps When doing these calculations Chimera randomly crashes with the following mscalc crash report:
Process: mscalc [25532]
Path: /Applications/Chimera-1.5b.app/Contents/Resources/bin/mscalc
Identifier: mscalc
Version: ??? (???)
Code Type: X86-64 (Native)
Parent Process: python2.6 [25482]
Date/Time: 2010-04-27 17:23:08.864 -0700
OS Version: Mac OS X 10.6.3 (10D573)
Report Version: 6
Interval Since Last Report: 402 sec
Crashes Since Last Report: 1
Per-App Crashes Since Last Report: 1
Anonymous UUID: D0B1026B-AD5E-454C-8E35-49CCF7598339
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Application Specific Information:
abort() called
Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 libSystem.B.dylib 0x00007fff83cc7886 __kill + 10
1 libSystem.B.dylib 0x00007fff83d67eae abort + 83
2 libSystem.B.dylib 0x00007fff83c7fa75 free + 128
3 mscalc 0x00000001000218e5 MS_delete_SES_face + 920
4 mscalc 0x00000001000361f4 MS_update_ses + 919
5 mscalc 0x0000000100034f68 MS_restart_from_ses + 613
6 mscalc 0x0000000100036963 MS_update_ses + 2822
7 mscalc 0x0000000100037d94 MS_restart_from_triangulation + 591
8 mscalc 0x0000000100046c66 MS_triangulate_SES_component + 925
9 mscalc 0x00000001000066f6 MS_compute_surface + 443
10 mscalc 0x0000000100000ea2 main + 382
11 mscalc 0x0000000100000d1c start + 52
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000001 rcx: 0x00007fff5fbfd998 rdx: 0x0000000000000000
rdi: 0x00000000000063bc rsi: 0x0000000000000006 rbp: 0x00007fff5fbfd9b0 rsp: 0x00007fff5fbfd998
r8: 0x0000000000000e03 r9: 0x0000000000000000 r10: 0x00007fff83cc38ca r11: 0x0000000000000206
r12: 0x00000001001e4000 r13: 0x0000000100200000 r14: 0x0000000000000000 r15: 0x00000001004f7c70
rip: 0x00007fff83cc7886 rfl: 0x0000000000000206 cr2: 0x000000010022a000
Binary Images:
0x100000000 - 0x10004eff7 +mscalc ??? (???) <AF86E566-5546-A8C8-DE97-4A16408CB1BC> /Applications/Chimera-1.5b.app/Contents/Resources/bin/mscalc
0x7fff5fc00000 - 0x7fff5fc3bdef dyld 132.1 (???) <B633F790-4DDB-53CD-7ACF-2A3682BCEA9F> /usr/lib/dyld
0x7fff83c78000 - 0x7fff83e37ff7 libSystem.B.dylib 125.0.1 (compatibility 1.0.0) <CB9A4929-61AF-DE71-5635-133E9EC95783> /usr/lib/libSystem.B.dylib
0x7fff885a7000 - 0x7fff885abff7 libmathCommon.A.dylib 315.0.0 (compatibility 1.0.0) <95718673-FEEE-B6ED-B127-BCDBDB60D4E5> /usr/lib/system/libmathCommon.A.dylib
0x7fffffe00000 - 0x7fffffe01fff libSystem.B.dylib ??? (???) <CB9A4929-61AF-DE71-5635-133E9EC95783> /usr/lib/libSystem.B.dylib
Model: MacPro1,1, BootROM MP11.005C.B08, 4 processors, Dual-Core Intel Xeon, 2.66 GHz, 14 GB, SMC 1.7f10
Graphics: ATI Radeon X1900 XT, ATY,RadeonX1900, PCIe, 512 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x87), Broadcom BCM43xx 1.0 (5.10.91.27)
Bluetooth: Version 2.3.1f4, 2 service, 19 devices, 1 incoming serial ports
Network Service: Built-in Ethernet 2, Ethernet, en1
PCI Card: ATY,RadeonX1900, Display, Slot-1
Serial ATA Device: ST3250824AS P, 232.89 GB
Serial ATA Device: WDC WD2500JD-00HBC0, 232.89 GB
Serial ATA Device: WDC WD1002FBYS-01A6B0, 931.51 GB
Serial ATA Device: WDC WD1002FBYS-01A6B0, 931.51 GB
Parallel ATA Device: SONY DVD RW DW-D150A
USB Device: Hub, 0x05ac (Apple Inc.), 0x9131, 0xfd400000
USB Device: iPhone, 0x05ac (Apple Inc.), 0x1292, 0xfd430000
USB Device: Keyboard Hub, 0x05ac (Apple Inc.), 0x1005, 0xfd410000
USB Device: Apple Keyboard, 0x05ac (Apple Inc.), 0x021d, 0xfd412000
USB Device: Apple Cinema HD Display, 0x05ac (Apple Inc.), 0x9223, 0xfd420000
USB Device: Hub, 0x05ac (Apple Inc.), 0x9122, 0xfd300000
USB Device: Apple Cinema HD Display, 0x05ac (Apple Inc.), 0x921e, 0xfd320000
USB Device: USB Receiver, 0x046d (Logitech Inc.), 0xc525, 0x1d200000
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8206, 0x5d200000
USB Device: Back-UPS CS 500 FW:806.q5.D USB FW:q5, 0x051d (American Power Conversion), 0x0002, 0x5d100000
FireWire Device: built-in_hub, Up to 800 Mb/sec
FireWire Device: unknown_device, Unknown
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