Having problemas with surface creation (fwd)

I’ve already sent this question to avogadro-discuss but received no
answer, maybe this is the proper list.

best regards
Kenneth

---------- Forwarded message ----------
Date: Fri, 30 Jul 2010 17:28:44 -0300 (UYT)
From: Kenneth Irving ken@mail.fq.edu.uy
To: avogadro-discuss@lists.sourceforge.net
Subject: Having problemas with surface creation

First of All let me say I find Avogadro an excellent program. I’ve been using
it lately and it’s been of great help to create Gaussian09 input files and
after displaying Gaussian09 results. Not many molecular modeling programs
available for Linux platform, and Avogadro is one of the best I’ve ever used.

Didn’t have problems with Gaussian09 .fchk files, until reacently when I tried
to create density and ESP surfaces and Avogadro just cancels execution.

Running it from a shell I get error output which I include below.

Hope someone can tell me what can be the problem. With some .fchk files I have
no problems, with others, I get this error:

QStackedLayout::setCurrentWidget: Widget 0x9524f58 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
*** glibc detected *** avogadro: free(): invalid next size (fast): 0x09d730b0


======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6[0x17b0d1]
/lib/tls/i686/cmov/libc.so.6[0x17c7d2]
/lib/tls/i686/cmov/libc.so.6(cfree+0x6d)[0x17f8ad]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d6f7ca]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d72152]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d721a1]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d7334a]
/usr/lib/libQtCore.so.4(_ZN12QtConcurrent16ThreadEngineBase3runEv+0x38)[0x68c6c8]
/usr/lib/libQtCore.so.4[0x68f8d7]
/usr/lib/libQtCore.so.4[0x699e32]
/lib/tls/i686/cmov/libpthread.so.0[0x25a80e]
/lib/tls/i686/cmov/libc.so.6(clone+0x5e)[0x1dca0e]
======= Memory map: ========
00110000-0024e000 r-xp 00000000 08:01 307002 /lib/tls/i686/cmov/libc-2.10.1.so
0024e000-0024f000 —p 0013e000 08:01 307002 /lib/tls/i686/cmov/libc-2.10.1.so
0024f000-00251000 r–p 0013e000 08:01 307002 /lib/tls/i686/cmov/libc-2.10.1.so
00251000-00252000 rw-p 00140000 08:01 307002 /lib/tls/i686/cmov/libc-2.10.1.so
00252000-00255000 rw-p 00000000 00:00 0
00255000-0026a000 r-xp 00000000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026a000-0026b000 r–p 00014000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026b000-0026c000 rw-p 00015000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026c000-0026e000 rw-p 00000000 00:00 0
0026e000-00292000 r-xp 00000000 08:01 308164 /lib/tls/i686/cmov/libm-2.10.1.so
00292000-00293000 r–p 00023000 08:01 308164 /lib/tls/i686/cmov/libm-2.10.1.so
00293000-00294000 rw-p 00024000 08:01 308164 /lib/tls/i686/cmov/libm-2.10.1.so
00294000-002b0000 r-xp 00000000 08:01 289753 /lib/libgcc_s.so.1
002b0000-002b1000 r–p 0001b000 08:01 289753 /lib/libgcc_s.so.1
002b1000-002b2000 rw-p 0001c000 08:01 289753 /lib/libgcc_s.so.1
002b2000-002b4000 r-xp 00000000 08:01 307008 /lib/tls/i686/cmov/libdl-2.10.1.so
002b4000-002b5000 r–p 00001000 08:01 307008 /lib/tls/i686/cmov/libdl-2.10.1.so
002b5000-002b6000 rw-p 00002000 08:01 307008 /lib/tls/i686/cmov/libdl-2.10.1.so
002b6000-002ca000 r-xp 00000000 08:01 289903 /lib/libz.so.1.2.3.3
002ca000-002cb000 r–p 00013000 08:01 289903 /lib/libz.so.1.2.3.3
002cb000-002cc000 rw-p 00014000 08:01 289903 /lib/libz.so.1.2.3.3
002cc000-002ce000 r-xp 00000000 08:16 48753 /usr/lib/libXdamage.so.1.1.0
002ce000-002cf000 rw-p 00001000 08:16 48753 /usr/lib/libXdamage.so.1.1.0
002cf000-002e7000 r-xp 00000000 08:16 48615 /usr/lib/libaudio.so.2.4
002e7000-002e8000 r–p 00017000 08:16 48615 /usr/lib/libaudio.so.2.4
002e8000-002e9000 rw-p 00018000 08:16 48615 /usr/lib/libaudio.so.2.4
002e9000-002f0000 r-xp 00000000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f0000-002f1000 r–p 00006000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f1000-002f2000 rw-p 00007000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f2000-002fa000 r-xp 00000000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fa000-002fb000 r–p 00007000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fb000-002fc000 rw-p 00008000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fc000-00300000 r-xp 00000000 08:16 51231 /usr/lib/libgthread-2.0.so.0.2200.3
00300000-00301000 r–p 00003000 08:16 51231 /usr/lib/libgthread-2.0.so.0.2200.3
00301000-00302000 rw-p 00004000 08:16 51231 /usr/lib/libgthread-2.0.so.0.2200.3
00302000-00304000 r-xp 00000000 08:16 48744 /usr/lib/libXau.so.6.0.0
00304000-00305000 r–p 00001000 08:16 48744 /usr/lib/libXau.so.6.0.0
00305000-00306000 rw-p 00002000 08:16 48744 /usr/lib/libXau.so.6.0.0
00306000-00308000 r-xp 00000000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
00308000-00309000 r–p 00001000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
00309000-0030a000 rw-p 00002000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
0030a000-00390000 r-xp 00000000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00390000-00391000 —p 00086000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00391000-00392000 r–p 00086000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00392000-00396000 rw-p 00087000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00396000-004c0000 r-xp 00000000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c0000-004c1000 —p 0012a000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c1000-004c2000 r–p 0012a000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c2000-004c4000 rw-p 0012b000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c4000-004c5000 rw-p 00000000 00:00 0
004c5000-00535000 r-xp 00000000 08:16 51020 /usr/lib/libfreetype.so.6.3.20
00535000-00539000 r–p 0006f000 08:16 51020 /usr/lib/libfreetype.so.6.3.20
00539000-0053a000 rw-p 00073000 08:16 51020 /usr/lib/libfreetype.so.6.3.20
0053a000-00551000 r-xp 00000000 08:16 48707 /usr/lib/libICE.so.6.3.0
00551000-00552000 r–p 00016000 08:16 48707 /usr/lib/libICE.so.6.3.0
00552000-00553000 rw-p 00017000 08:16 48707 /usr/lib/libICE.so.6.3.0
00553000-00555000 rw-p 00000000 00:00 0
00555000-00580000 r-xp 00000000 08:16 49042 /usr/lib/libfontconfig.so.1.3.0
00580000-00581000 r–p 0002a000 08:16 49042 /usr/lib/libfontconfig.so.1.3.0
00581000-00582000 rw-p 0002b000 08:16 49042 /usr/lib/libfontconfig.so.1.3.0
00582000-00585000 r-xp 00000000 08:01 289896 /lib/libuuid.so.1.3.0
00585000-00586000 r–p 00002000 08:01 289896 /lib/libuuid.so.1.3.0
00586000-00587000 rw-p 00003000 08:01 289896 /lib/libuuid.so.1.3.0
00587000-00588000 rwxp 00000000 00:00 0
00589000-005a4000 r-xp 00000000 08:01 289965 /lib/ld-2.10.1.so
005a4000-005a5000 r–p 0001a000 08:01 289965 /lib/ld-2.10.1.so
005a5000-005a6000 rw-p 0001b000 08:01 289965 /lib/ld-2.10.1.so
005a6000-005c2000 r-xp 00000000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c2000-005c3000 r–p 0001c000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c3000-005c4000 rw-p 0001d000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c4000-005cb000 r-xp 00000000 08:01 308181 /lib/tls/i686/cmov/librt-2.10.1.so
005cb000-005cc000 r–p 00006000 08:01 308181 /lib/tls/i686/cmov/librt-2.10.1.so
005cc000-005cd000 rw-p 00007000 08:01 308181 /lib/tls/i686/cmov/librt-2.10.1.so
005cd000-005fc000 r-xp 00000000 08:01 289856 /lib/libpcre.so.3.12.1
005fc000-005fd000 r–p 0002e000 08:01 289856 /lib/libpcre.so.3.12.1
005fd000-005fe000 rw-p 0002f000 08:01 289856 /lib/libpcre.so.3.12.1
005fe000-00602000 r-xp 00000000 08:16 48755 /usr/lib/libXdmcp.so.6.0.0
00602000-00603000 rw-p 00003000 08:16 48755 /usr/lib/libXdmcp.so.6.0.0
00603000-0060c000 r-xp 00000000 08:16 48765 /usr/lib/libXi.so.6.0.0
0060c000-0060d000 r–p 00008000 08:16 48765 /usr/lib/libXi.so.6.0.0
0060d000-0060e000 rw-p 00009000 08:16 48765 /usr/lib/libXi.so.6.0.0
00610000-0061e000 r-xp 00000000 08:16 48757 /usr/lib/libXext.so.6.4.0
0061e000-0061f000 r–p 0000d000 08:16 48757 /usr/lib/libXext.so.6.4.0
0061f000-00620000 rw-p 0000e000 08:16 48757 /usr/lib/libXext.so.6.4.0Aborted

Best regards

Kenneth

Hi Kenneth,

Can you attach one of the problematic files?

Thanks,

Dave

On Mon, Aug 2, 2010 at 11:43 AM, Kenneth Irving ken@fq.edu.uy wrote:

I’ve already sent this question to avogadro-discuss but received no
answer, maybe this is the proper list.

best regards
Kenneth

---------- Forwarded message ----------
Date: Fri, 30 Jul 2010 17:28:44 -0300 (UYT)
From: Kenneth Irving ken@mail.fq.edu.uy
To: avogadro-discuss@lists.sourceforge.net
Subject: Having problemas with surface creation

First of All let me say I find Avogadro an excellent program. I’ve been using
it lately and it’s been of great help to create Gaussian09 input files and
after displaying Gaussian09 results. Not many molecular modeling programs
available for Linux platform, and Avogadro is one of the best I’ve ever used.

Didn’t have problems with Gaussian09 .fchk files, until reacently when I tried
to create density and ESP surfaces and Avogadro just cancels execution.

Running it from a shell I get error output which I include below.

Hope someone can tell me what can be the problem. With some .fchk files I have
no problems, with others, I get this error:

QStackedLayout::setCurrentWidget: Widget 0x9524f58 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
*** glibc detected *** avogadro: free(): invalid next size (fast): 0x09d730b0


======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6[0x17b0d1]
/lib/tls/i686/cmov/libc.so.6[0x17c7d2]
/lib/tls/i686/cmov/libc.so.6(cfree+0x6d)[0x17f8ad]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d6f7ca]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d72152]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d721a1]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d7334a]
/usr/lib/libQtCore.so.4(_ZN12QtConcurrent16ThreadEngineBase3runEv+0x38)[0x68c6c8]
/usr/lib/libQtCore.so.4[0x68f8d7]
/usr/lib/libQtCore.so.4[0x699e32]
/lib/tls/i686/cmov/libpthread.so.0[0x25a80e]
/lib/tls/i686/cmov/libc.so.6(clone+0x5e)[0x1dca0e]
======= Memory map: ========
00110000-0024e000 r-xp 00000000 08:01 307002 /lib/tls/i686/cmov/libc-2.10.1.so
0024e000-0024f000 —p 0013e000 08:01 307002 /lib/tls/i686/cmov/libc-2.10.1.so
0024f000-00251000 r–p 0013e000 08:01 307002 /lib/tls/i686/cmov/libc-2.10.1.so
00251000-00252000 rw-p 00140000 08:01 307002 /lib/tls/i686/cmov/libc-2.10.1.so
00252000-00255000 rw-p 00000000 00:00 0
00255000-0026a000 r-xp 00000000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026a000-0026b000 r–p 00014000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026b000-0026c000 rw-p 00015000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026c000-0026e000 rw-p 00000000 00:00 0
0026e000-00292000 r-xp 00000000 08:01 308164 /lib/tls/i686/cmov/libm-2.10.1.so
00292000-00293000 r–p 00023000 08:01 308164 /lib/tls/i686/cmov/libm-2.10.1.so
00293000-00294000 rw-p 00024000 08:01 308164 /lib/tls/i686/cmov/libm-2.10.1.so
00294000-002b0000 r-xp 00000000 08:01 289753 /lib/libgcc_s.so.1
002b0000-002b1000 r–p 0001b000 08:01 289753 /lib/libgcc_s.so.1
002b1000-002b2000 rw-p 0001c000 08:01 289753 /lib/libgcc_s.so.1
002b2000-002b4000 r-xp 00000000 08:01 307008 /lib/tls/i686/cmov/libdl-2.10.1.so
002b4000-002b5000 r–p 00001000 08:01 307008 /lib/tls/i686/cmov/libdl-2.10.1.so
002b5000-002b6000 rw-p 00002000 08:01 307008 /lib/tls/i686/cmov/libdl-2.10.1.so
002b6000-002ca000 r-xp 00000000 08:01 289903 /lib/libz.so.1.2.3.3
002ca000-002cb000 r–p 00013000 08:01 289903 /lib/libz.so.1.2.3.3
002cb000-002cc000 rw-p 00014000 08:01 289903 /lib/libz.so.1.2.3.3
002cc000-002ce000 r-xp 00000000 08:16 48753 /usr/lib/libXdamage.so.1.1.0
002ce000-002cf000 rw-p 00001000 08:16 48753 /usr/lib/libXdamage.so.1.1.0
002cf000-002e7000 r-xp 00000000 08:16 48615 /usr/lib/libaudio.so.2.4
002e7000-002e8000 r–p 00017000 08:16 48615 /usr/lib/libaudio.so.2.4
002e8000-002e9000 rw-p 00018000 08:16 48615 /usr/lib/libaudio.so.2.4
002e9000-002f0000 r-xp 00000000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f0000-002f1000 r–p 00006000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f1000-002f2000 rw-p 00007000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f2000-002fa000 r-xp 00000000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fa000-002fb000 r–p 00007000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fb000-002fc000 rw-p 00008000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fc000-00300000 r-xp 00000000 08:16 51231 /usr/lib/libgthread-2.0.so.0.2200.3
00300000-00301000 r–p 00003000 08:16 51231 /usr/lib/libgthread-2.0.so.0.2200.3
00301000-00302000 rw-p 00004000 08:16 51231 /usr/lib/libgthread-2.0.so.0.2200.3
00302000-00304000 r-xp 00000000 08:16 48744 /usr/lib/libXau.so.6.0.0
00304000-00305000 r–p 00001000 08:16 48744 /usr/lib/libXau.so.6.0.0
00305000-00306000 rw-p 00002000 08:16 48744 /usr/lib/libXau.so.6.0.0
00306000-00308000 r-xp 00000000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
00308000-00309000 r–p 00001000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
00309000-0030a000 rw-p 00002000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
0030a000-00390000 r-xp 00000000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00390000-00391000 —p 00086000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00391000-00392000 r–p 00086000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00392000-00396000 rw-p 00087000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00396000-004c0000 r-xp 00000000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c0000-004c1000 —p 0012a000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c1000-004c2000 r–p 0012a000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c2000-004c4000 rw-p 0012b000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c4000-004c5000 rw-p 00000000 00:00 0
004c5000-00535000 r-xp 00000000 08:16 51020 /usr/lib/libfreetype.so.6.3.20
00535000-00539000 r–p 0006f000 08:16 51020 /usr/lib/libfreetype.so.6.3.20
00539000-0053a000 rw-p 00073000 08:16 51020 /usr/lib/libfreetype.so.6.3.20
0053a000-00551000 r-xp 00000000 08:16 48707 /usr/lib/libICE.so.6.3.0
00551000-00552000 r–p 00016000 08:16 48707 /usr/lib/libICE.so.6.3.0
00552000-00553000 rw-p 00017000 08:16 48707 /usr/lib/libICE.so.6.3.0
00553000-00555000 rw-p 00000000 00:00 0
00555000-00580000 r-xp 00000000 08:16 49042 /usr/lib/libfontconfig.so.1.3.0
00580000-00581000 r–p 0002a000 08:16 49042 /usr/lib/libfontconfig.so.1.3.0
00581000-00582000 rw-p 0002b000 08:16 49042 /usr/lib/libfontconfig.so.1.3.0
00582000-00585000 r-xp 00000000 08:01 289896 /lib/libuuid.so.1.3.0
00585000-00586000 r–p 00002000 08:01 289896 /lib/libuuid.so.1.3.0
00586000-00587000 rw-p 00003000 08:01 289896 /lib/libuuid.so.1.3.0
00587000-00588000 rwxp 00000000 00:00 0
00589000-005a4000 r-xp 00000000 08:01 289965 /lib/ld-2.10.1.so
005a4000-005a5000 r–p 0001a000 08:01 289965 /lib/ld-2.10.1.so
005a5000-005a6000 rw-p 0001b000 08:01 289965 /lib/ld-2.10.1.so
005a6000-005c2000 r-xp 00000000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c2000-005c3000 r–p 0001c000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c3000-005c4000 rw-p 0001d000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c4000-005cb000 r-xp 00000000 08:01 308181 /lib/tls/i686/cmov/librt-2.10.1.so
005cb000-005cc000 r–p 00006000 08:01 308181 /lib/tls/i686/cmov/librt-2.10.1.so
005cc000-005cd000 rw-p 00007000 08:01 308181 /lib/tls/i686/cmov/librt-2.10.1.so
005cd000-005fc000 r-xp 00000000 08:01 289856 /lib/libpcre.so.3.12.1
005fc000-005fd000 r–p 0002e000 08:01 289856 /lib/libpcre.so.3.12.1
005fd000-005fe000 rw-p 0002f000 08:01 289856 /lib/libpcre.so.3.12.1
005fe000-00602000 r-xp 00000000 08:16 48755 /usr/lib/libXdmcp.so.6.0.0
00602000-00603000 rw-p 00003000 08:16 48755 /usr/lib/libXdmcp.so.6.0.0
00603000-0060c000 r-xp 00000000 08:16 48765 /usr/lib/libXi.so.6.0.0
0060c000-0060d000 r–p 00008000 08:16 48765 /usr/lib/libXi.so.6.0.0
0060d000-0060e000 rw-p 00009000 08:16 48765 /usr/lib/libXi.so.6.0.0
00610000-0061e000 r-xp 00000000 08:16 48757 /usr/lib/libXext.so.6.4.0
0061e000-0061f000 r–p 0000d000 08:16 48757 /usr/lib/libXext.so.6.4.0
0061f000-00620000 rw-p 0000e000 08:16 48757 /usr/lib/libXext.so.6.4.0Aborted

Best regards

Kenneth


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Kenneth,

I’ve put the problematic file on:

http://xtalopt.openmolecules.net/tmp/5h2o.fchk

It seems to just be missing the density information altogether (There
should be a section with the scf density matrix – identified by
"Total SCF Density" – but its not present in this file). I’m by no
means a gaussian expert, but there should be an option to tell
gaussian to print this.

Marcus – I suppose the surface generator should check if the density
matrix is present and fail gracefully if not? Unless you have a better
idea, I’ll try to add this in at some point soon.

Dave

On Mon, Aug 2, 2010 at 1:31 PM, Kenneth Irving ken@fq.edu.uy wrote:

Sure, thanks, sending one. This complex, without the water molecule, works
fine. But with the water molecule, if I try to calculate density surface, it
breaks down. With Van der Waals surface mapped with ESP colors or molecular
orbitals also works fine. The moment I ask any surface that involves
density, it cancels execution.

best regards

Kenneth

On Mon, 2 Aug 2010, David Lonie wrote:

Hi Kenneth,

Can you attach one of the problematic files?

Thanks,

Dave

On Mon, Aug 2, 2010 at 11:43 AM, Kenneth Irving ken@fq.edu.uy wrote:

I’ve already sent this question to avogadro-discuss but received no
answer, maybe this is the proper list.

best regards
Kenneth

---------- Forwarded message ----------
Date: Fri, 30 Jul 2010 17:28:44 -0300 (UYT)
From: Kenneth Irving ken@mail.fq.edu.uy
To: avogadro-discuss@lists.sourceforge.net
Subject: Having problemas with surface creation

First of All let me say I find Avogadro an excellent program. I’ve been
using
it lately and it’s been of great help to create Gaussian09 input files
and
after displaying Gaussian09 results. Not many molecular modeling programs
available for Linux platform, and Avogadro is one of the best I’ve ever
used.

Didn’t have problems with Gaussian09 .fchk files, until reacently when I
tried
to create density and ESP surfaces and Avogadro just cancels execution.

Running it from a shell I get error output which I include below.

Hope someone can tell me what can be the problem. With some .fchk files I
have
no problems, with others, I get this error:

QStackedLayout::setCurrentWidget: Widget 0x9524f58 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
*** glibc detected *** avogadro: free(): invalid next size (fast):
0x09d730b0


======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6[0x17b0d1]
/lib/tls/i686/cmov/libc.so.6[0x17c7d2]
/lib/tls/i686/cmov/libc.so.6(cfree+0x6d)[0x17f8ad]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d6f7ca]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d72152]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d721a1]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d7334a]

/usr/lib/libQtCore.so.4(_ZN12QtConcurrent16ThreadEngineBase3runEv+0x38)[0x68c6c8]
/usr/lib/libQtCore.so.4[0x68f8d7]
/usr/lib/libQtCore.so.4[0x699e32]
/lib/tls/i686/cmov/libpthread.so.0[0x25a80e]
/lib/tls/i686/cmov/libc.so.6(clone+0x5e)[0x1dca0e]
======= Memory map: ========
00110000-0024e000 r-xp 00000000 08:01 307002
/lib/tls/i686/cmov/libc-2.10.1.so
0024e000-0024f000 —p 0013e000 08:01 307002
/lib/tls/i686/cmov/libc-2.10.1.so
0024f000-00251000 r–p 0013e000 08:01 307002
/lib/tls/i686/cmov/libc-2.10.1.so
00251000-00252000 rw-p 00140000 08:01 307002
/lib/tls/i686/cmov/libc-2.10.1.so
00252000-00255000 rw-p 00000000 00:00 0
00255000-0026a000 r-xp 00000000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026a000-0026b000 r–p 00014000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026b000-0026c000 rw-p 00015000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026c000-0026e000 rw-p 00000000 00:00 0
0026e000-00292000 r-xp 00000000 08:01 308164
/lib/tls/i686/cmov/libm-2.10.1.so
00292000-00293000 r–p 00023000 08:01 308164
/lib/tls/i686/cmov/libm-2.10.1.so
00293000-00294000 rw-p 00024000 08:01 308164
/lib/tls/i686/cmov/libm-2.10.1.so
00294000-002b0000 r-xp 00000000 08:01 289753 /lib/libgcc_s.so.1
002b0000-002b1000 r–p 0001b000 08:01 289753 /lib/libgcc_s.so.1
002b1000-002b2000 rw-p 0001c000 08:01 289753 /lib/libgcc_s.so.1
002b2000-002b4000 r-xp 00000000 08:01 307008
/lib/tls/i686/cmov/libdl-2.10.1.so
002b4000-002b5000 r–p 00001000 08:01 307008
/lib/tls/i686/cmov/libdl-2.10.1.so
002b5000-002b6000 rw-p 00002000 08:01 307008
/lib/tls/i686/cmov/libdl-2.10.1.so
002b6000-002ca000 r-xp 00000000 08:01 289903 /lib/libz.so.1.2.3.3
002ca000-002cb000 r–p 00013000 08:01 289903 /lib/libz.so.1.2.3.3
002cb000-002cc000 rw-p 00014000 08:01 289903 /lib/libz.so.1.2.3.3
002cc000-002ce000 r-xp 00000000 08:16 48753 /usr/lib/libXdamage.so.1.1.0
002ce000-002cf000 rw-p 00001000 08:16 48753 /usr/lib/libXdamage.so.1.1.0
002cf000-002e7000 r-xp 00000000 08:16 48615 /usr/lib/libaudio.so.2.4
002e7000-002e8000 r–p 00017000 08:16 48615 /usr/lib/libaudio.so.2.4
002e8000-002e9000 rw-p 00018000 08:16 48615 /usr/lib/libaudio.so.2.4
002e9000-002f0000 r-xp 00000000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f0000-002f1000 r–p 00006000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f1000-002f2000 rw-p 00007000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f2000-002fa000 r-xp 00000000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fa000-002fb000 r–p 00007000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fb000-002fc000 rw-p 00008000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fc000-00300000 r-xp 00000000 08:16 51231
/usr/lib/libgthread-2.0.so.0.2200.3
00300000-00301000 r–p 00003000 08:16 51231
/usr/lib/libgthread-2.0.so.0.2200.3
00301000-00302000 rw-p 00004000 08:16 51231
/usr/lib/libgthread-2.0.so.0.2200.3
00302000-00304000 r-xp 00000000 08:16 48744 /usr/lib/libXau.so.6.0.0
00304000-00305000 r–p 00001000 08:16 48744 /usr/lib/libXau.so.6.0.0
00305000-00306000 rw-p 00002000 08:16 48744 /usr/lib/libXau.so.6.0.0
00306000-00308000 r-xp 00000000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
00308000-00309000 r–p 00001000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
00309000-0030a000 rw-p 00002000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
0030a000-00390000 r-xp 00000000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00390000-00391000 —p 00086000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00391000-00392000 r–p 00086000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00392000-00396000 rw-p 00087000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00396000-004c0000 r-xp 00000000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c0000-004c1000 —p 0012a000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c1000-004c2000 r–p 0012a000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c2000-004c4000 rw-p 0012b000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c4000-004c5000 rw-p 00000000 00:00 0
004c5000-00535000 r-xp 00000000 08:16 51020
/usr/lib/libfreetype.so.6.3.20
00535000-00539000 r–p 0006f000 08:16 51020
/usr/lib/libfreetype.so.6.3.20
00539000-0053a000 rw-p 00073000 08:16 51020
/usr/lib/libfreetype.so.6.3.20
0053a000-00551000 r-xp 00000000 08:16 48707 /usr/lib/libICE.so.6.3.0
00551000-00552000 r–p 00016000 08:16 48707 /usr/lib/libICE.so.6.3.0
00552000-00553000 rw-p 00017000 08:16 48707 /usr/lib/libICE.so.6.3.0
00553000-00555000 rw-p 00000000 00:00 0
00555000-00580000 r-xp 00000000 08:16 49042
/usr/lib/libfontconfig.so.1.3.0
00580000-00581000 r–p 0002a000 08:16 49042
/usr/lib/libfontconfig.so.1.3.0
00581000-00582000 rw-p 0002b000 08:16 49042
/usr/lib/libfontconfig.so.1.3.0
00582000-00585000 r-xp 00000000 08:01 289896 /lib/libuuid.so.1.3.0
00585000-00586000 r–p 00002000 08:01 289896 /lib/libuuid.so.1.3.0
00586000-00587000 rw-p 00003000 08:01 289896 /lib/libuuid.so.1.3.0
00587000-00588000 rwxp 00000000 00:00 0
00589000-005a4000 r-xp 00000000 08:01 289965 /lib/ld-2.10.1.so
005a4000-005a5000 r–p 0001a000 08:01 289965 /lib/ld-2.10.1.so
005a5000-005a6000 rw-p 0001b000 08:01 289965 /lib/ld-2.10.1.so
005a6000-005c2000 r-xp 00000000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c2000-005c3000 r–p 0001c000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c3000-005c4000 rw-p 0001d000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c4000-005cb000 r-xp 00000000 08:01 308181
/lib/tls/i686/cmov/librt-2.10.1.so
005cb000-005cc000 r–p 00006000 08:01 308181
/lib/tls/i686/cmov/librt-2.10.1.so
005cc000-005cd000 rw-p 00007000 08:01 308181
/lib/tls/i686/cmov/librt-2.10.1.so
005cd000-005fc000 r-xp 00000000 08:01 289856 /lib/libpcre.so.3.12.1
005fc000-005fd000 r–p 0002e000 08:01 289856 /lib/libpcre.so.3.12.1
005fd000-005fe000 rw-p 0002f000 08:01 289856 /lib/libpcre.so.3.12.1
005fe000-00602000 r-xp 00000000 08:16 48755 /usr/lib/libXdmcp.so.6.0.0
00602000-00603000 rw-p 00003000 08:16 48755 /usr/lib/libXdmcp.so.6.0.0
00603000-0060c000 r-xp 00000000 08:16 48765 /usr/lib/libXi.so.6.0.0
0060c000-0060d000 r–p 00008000 08:16 48765 /usr/lib/libXi.so.6.0.0
0060d000-0060e000 rw-p 00009000 08:16 48765 /usr/lib/libXi.so.6.0.0
00610000-0061e000 r-xp 00000000 08:16 48757
/usr/lib/libXext.so.6.4.0
0061e000-0061f000 r–p 0000d000 08:16 48757
/usr/lib/libXext.so.6.4.0
0061f000-00620000 rw-p 0000e000 08:16 48757
/usr/lib/libXext.so.6.4.0Aborted

Best regards

Kenneth


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Plug-In Development Kit to bring their C/C++ apps to Palm for a share
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Ops! seems your are right, don’t know what happend with this file, why
this section is missing. Thanks!

best regards

Kenneth

On Mon, 2 Aug 2010, David Lonie wrote:

Kenneth,

I’ve put the problematic file on:

http://xtalopt.openmolecules.net/tmp/5h2o.fchk

It seems to just be missing the density information altogether (There
should be a section with the scf density matrix – identified by
"Total SCF Density" – but its not present in this file). I’m by no
means a gaussian expert, but there should be an option to tell
gaussian to print this.

Marcus – I suppose the surface generator should check if the density
matrix is present and fail gracefully if not? Unless you have a better
idea, I’ll try to add this in at some point soon.

Dave

On Mon, Aug 2, 2010 at 1:31 PM, Kenneth Irving ken@fq.edu.uy wrote:

Sure, thanks, sending one. This complex, without the water molecule, works
fine. But with the water molecule, if I try to calculate density surface, it
breaks down. With Van der Waals surface mapped with ESP colors or molecular
orbitals also works fine. The moment I ask any surface that involves
density, it cancels execution.

best regards

Kenneth

On Mon, 2 Aug 2010, David Lonie wrote:

Hi Kenneth,

Can you attach one of the problematic files?

Thanks,

Dave

On Mon, Aug 2, 2010 at 11:43 AM, Kenneth Irving ken@fq.edu.uy wrote:

I’ve already sent this question to avogadro-discuss but received no
answer, maybe this is the proper list.

best regards
Kenneth

---------- Forwarded message ----------
Date: Fri, 30 Jul 2010 17:28:44 -0300 (UYT)
From: Kenneth Irving ken@mail.fq.edu.uy
To: avogadro-discuss@lists.sourceforge.net
Subject: Having problemas with surface creation

First of All let me say I find Avogadro an excellent program. I’ve been
using
it lately and it’s been of great help to create Gaussian09 input files
and
after displaying Gaussian09 results. Not many molecular modeling programs
available for Linux platform, and Avogadro is one of the best I’ve ever
used.

Didn’t have problems with Gaussian09 .fchk files, until reacently when I
tried
to create density and ESP surfaces and Avogadro just cancels execution.

Running it from a shell I get error output which I include below.

Hope someone can tell me what can be the problem. With some .fchk files I
have
no problems, with others, I get this error:

QStackedLayout::setCurrentWidget: Widget 0x9524f58 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
*** glibc detected *** avogadro: free(): invalid next size (fast):
0x09d730b0


======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6[0x17b0d1]
/lib/tls/i686/cmov/libc.so.6[0x17c7d2]
/lib/tls/i686/cmov/libc.so.6(cfree+0x6d)[0x17f8ad]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d6f7ca]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d72152]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d721a1]
/usr/lib/avogadro/1_0/extensions/surfaceextension.so[0x1d7334a]

/usr/lib/libQtCore.so.4(_ZN12QtConcurrent16ThreadEngineBase3runEv+0x38)[0x68c6c8]
/usr/lib/libQtCore.so.4[0x68f8d7]
/usr/lib/libQtCore.so.4[0x699e32]
/lib/tls/i686/cmov/libpthread.so.0[0x25a80e]
/lib/tls/i686/cmov/libc.so.6(clone+0x5e)[0x1dca0e]
======= Memory map: ========
00110000-0024e000 r-xp 00000000 08:01 307002
/lib/tls/i686/cmov/libc-2.10.1.so
0024e000-0024f000 —p 0013e000 08:01 307002
/lib/tls/i686/cmov/libc-2.10.1.so
0024f000-00251000 r–p 0013e000 08:01 307002
/lib/tls/i686/cmov/libc-2.10.1.so
00251000-00252000 rw-p 00140000 08:01 307002
/lib/tls/i686/cmov/libc-2.10.1.so
00252000-00255000 rw-p 00000000 00:00 0
00255000-0026a000 r-xp 00000000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026a000-0026b000 r–p 00014000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026b000-0026c000 rw-p 00015000 08:01 308178
/lib/tls/i686/cmov/libpthread-2.10.1.so
0026c000-0026e000 rw-p 00000000 00:00 0
0026e000-00292000 r-xp 00000000 08:01 308164
/lib/tls/i686/cmov/libm-2.10.1.so
00292000-00293000 r–p 00023000 08:01 308164
/lib/tls/i686/cmov/libm-2.10.1.so
00293000-00294000 rw-p 00024000 08:01 308164
/lib/tls/i686/cmov/libm-2.10.1.so
00294000-002b0000 r-xp 00000000 08:01 289753 /lib/libgcc_s.so.1
002b0000-002b1000 r–p 0001b000 08:01 289753 /lib/libgcc_s.so.1
002b1000-002b2000 rw-p 0001c000 08:01 289753 /lib/libgcc_s.so.1
002b2000-002b4000 r-xp 00000000 08:01 307008
/lib/tls/i686/cmov/libdl-2.10.1.so
002b4000-002b5000 r–p 00001000 08:01 307008
/lib/tls/i686/cmov/libdl-2.10.1.so
002b5000-002b6000 rw-p 00002000 08:01 307008
/lib/tls/i686/cmov/libdl-2.10.1.so
002b6000-002ca000 r-xp 00000000 08:01 289903 /lib/libz.so.1.2.3.3
002ca000-002cb000 r–p 00013000 08:01 289903 /lib/libz.so.1.2.3.3
002cb000-002cc000 rw-p 00014000 08:01 289903 /lib/libz.so.1.2.3.3
002cc000-002ce000 r-xp 00000000 08:16 48753 /usr/lib/libXdamage.so.1.1.0
002ce000-002cf000 rw-p 00001000 08:16 48753 /usr/lib/libXdamage.so.1.1.0
002cf000-002e7000 r-xp 00000000 08:16 48615 /usr/lib/libaudio.so.2.4
002e7000-002e8000 r–p 00017000 08:16 48615 /usr/lib/libaudio.so.2.4
002e8000-002e9000 rw-p 00018000 08:16 48615 /usr/lib/libaudio.so.2.4
002e9000-002f0000 r-xp 00000000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f0000-002f1000 r–p 00006000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f1000-002f2000 rw-p 00007000 08:16 48736 /usr/lib/libSM.so.6.0.0
002f2000-002fa000 r-xp 00000000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fa000-002fb000 r–p 00007000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fb000-002fc000 rw-p 00008000 08:16 48779 /usr/lib/libXrender.so.1.3.0
002fc000-00300000 r-xp 00000000 08:16 51231
/usr/lib/libgthread-2.0.so.0.2200.3
00300000-00301000 r–p 00003000 08:16 51231
/usr/lib/libgthread-2.0.so.0.2200.3
00301000-00302000 rw-p 00004000 08:16 51231
/usr/lib/libgthread-2.0.so.0.2200.3
00302000-00304000 r-xp 00000000 08:16 48744 /usr/lib/libXau.so.6.0.0
00304000-00305000 r–p 00001000 08:16 48744 /usr/lib/libXau.so.6.0.0
00305000-00306000 rw-p 00002000 08:16 48744 /usr/lib/libXau.so.6.0.0
00306000-00308000 r-xp 00000000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
00308000-00309000 r–p 00001000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
00309000-0030a000 rw-p 00002000 08:01 308184
/lib/tls/i686/cmov/libutil-2.10.1.so
0030a000-00390000 r-xp 00000000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00390000-00391000 —p 00086000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00391000-00392000 r–p 00086000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00392000-00396000 rw-p 00087000 08:16 52409 /usr/lib/libQtOpenGL.so.4.5.2
00396000-004c0000 r-xp 00000000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c0000-004c1000 —p 0012a000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c1000-004c2000 r–p 0012a000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c2000-004c4000 rw-p 0012b000 08:16 48738 /usr/lib/libX11.so.6.2.0
004c4000-004c5000 rw-p 00000000 00:00 0
004c5000-00535000 r-xp 00000000 08:16 51020
/usr/lib/libfreetype.so.6.3.20
00535000-00539000 r–p 0006f000 08:16 51020
/usr/lib/libfreetype.so.6.3.20
00539000-0053a000 rw-p 00073000 08:16 51020
/usr/lib/libfreetype.so.6.3.20
0053a000-00551000 r-xp 00000000 08:16 48707 /usr/lib/libICE.so.6.3.0
00551000-00552000 r–p 00016000 08:16 48707 /usr/lib/libICE.so.6.3.0
00552000-00553000 rw-p 00017000 08:16 48707 /usr/lib/libICE.so.6.3.0
00553000-00555000 rw-p 00000000 00:00 0
00555000-00580000 r-xp 00000000 08:16 49042
/usr/lib/libfontconfig.so.1.3.0
00580000-00581000 r–p 0002a000 08:16 49042
/usr/lib/libfontconfig.so.1.3.0
00581000-00582000 rw-p 0002b000 08:16 49042
/usr/lib/libfontconfig.so.1.3.0
00582000-00585000 r-xp 00000000 08:01 289896 /lib/libuuid.so.1.3.0
00585000-00586000 r–p 00002000 08:01 289896 /lib/libuuid.so.1.3.0
00586000-00587000 rw-p 00003000 08:01 289896 /lib/libuuid.so.1.3.0
00587000-00588000 rwxp 00000000 00:00 0
00589000-005a4000 r-xp 00000000 08:01 289965 /lib/ld-2.10.1.so
005a4000-005a5000 r–p 0001a000 08:01 289965 /lib/ld-2.10.1.so
005a5000-005a6000 rw-p 0001b000 08:01 289965 /lib/ld-2.10.1.so
005a6000-005c2000 r-xp 00000000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c2000-005c3000 r–p 0001c000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c3000-005c4000 rw-p 0001d000 08:16 49776 /usr/lib/libxcb.so.1.1.0
005c4000-005cb000 r-xp 00000000 08:01 308181
/lib/tls/i686/cmov/librt-2.10.1.so
005cb000-005cc000 r–p 00006000 08:01 308181
/lib/tls/i686/cmov/librt-2.10.1.so
005cc000-005cd000 rw-p 00007000 08:01 308181
/lib/tls/i686/cmov/librt-2.10.1.so
005cd000-005fc000 r-xp 00000000 08:01 289856 /lib/libpcre.so.3.12.1
005fc000-005fd000 r–p 0002e000 08:01 289856 /lib/libpcre.so.3.12.1
005fd000-005fe000 rw-p 0002f000 08:01 289856 /lib/libpcre.so.3.12.1
005fe000-00602000 r-xp 00000000 08:16 48755 /usr/lib/libXdmcp.so.6.0.0
00602000-00603000 rw-p 00003000 08:16 48755 /usr/lib/libXdmcp.so.6.0.0
00603000-0060c000 r-xp 00000000 08:16 48765 /usr/lib/libXi.so.6.0.0
0060c000-0060d000 r–p 00008000 08:16 48765 /usr/lib/libXi.so.6.0.0
0060d000-0060e000 rw-p 00009000 08:16 48765 /usr/lib/libXi.so.6.0.0
00610000-0061e000 r-xp 00000000 08:16 48757
/usr/lib/libXext.so.6.4.0
0061e000-0061f000 r–p 0000d000 08:16 48757
/usr/lib/libXext.so.6.4.0
0061f000-00620000 rw-p 0000e000 08:16 48757
/usr/lib/libXext.so.6.4.0Aborted

Best regards

Kenneth


The Palm PDK Hot Apps Program offers developers who use the
Plug-In Development Kit to bring their C/C++ apps to Palm for a share
of $1 Million in cash or HP Products. Visit us here for more details:
http://p.sf.net/sfu/dev2dev-palm


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
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