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[ESPResSo-users] Using Virtual sites in the center of mass of a molecule

From: Hender Lopez
Subject: [ESPResSo-users] Using Virtual sites in the center of mass of a molecule
Date: Fri, 22 Nov 2013 14:44:34 +0000

Dear all,

I have been trying to use virtual particles in the center of mass
(COM) of the a molecule (section 4.4.1 in the manual) and it seems
that it has some bugs. First, it only works if you use 1 molecule.
Although in this case you have to be careful because all the particles
id have to be consecutive.  Secondly, even with only one molecule I
haven't be able to run a sim in parallel. Does any body have any idea
of how to fix this? Attached you will find a script that illustrates
what I ask. It defines two molecules each with 3 particles. In each of
the molecules there is a virtual particle. After the definitions, the
script prints the position of the COM and the virtual particles (they
should be the same and they effectively are). But when the update of
the system is done (by calling integrate 0) the position of the
virtual particle of molecule 2 crashes (-NaN -NaN -NaN).  If you run
the program in parallel in gives the following error:

[nanopart:18254] *** Process received signal ***
[nanopart:18254] Signal: Segmentation fault (11)
[nanopart:18254] Signal code: Address not mapped (1)
[nanopart:18254] Failing at address: 0x18
[nanopart:18254] [ 0] /lib/x86_64-linux-gnu/
[nanopart:18254] [ 1]
/home/hender/espresso-3.2.0/Espresso(calc_mol_pos+0x78) [0x456cd8]
[nanopart:18254] [ 2]
[nanopart:18254] [ 3]
[nanopart:18254] [ 4]
/home/hender/espresso-3.2.0/Espresso(updatePartCfg+0x121) [0x4366c1]
[nanopart:18254] [ 5]
/home/hender/espresso-3.2.0/Espresso(centermass+0x22) [0x440592]
[nanopart:18254] [ 6]
[nanopart:18254] [ 7]
/usr/lib/ [0x7fd14d18e12c]
[nanopart:18254] [ 8] /usr/lib/ [0x7fd14d18f757]
[nanopart:18254] [ 9] /usr/lib/ [0x7fd14d190463]
[nanopart:18254] [10] /usr/lib/ [0x7fd14d20bff6]
[nanopart:18254] [11] /usr/lib/ [0x7fd14d1901b3]
[nanopart:18254] [12] /usr/lib/ [0x7fd14d18fe46]
[nanopart:18254] [13] /usr/lib/
[nanopart:18254] [14] /usr/lib/ [0x7fd14d1fdcc6]
[nanopart:18254] [15] /home/hender/espresso-3.2.0/Espresso(main+0x4a) [0x413baa]
[nanopart:18254] [16]
[nanopart:18254] [17] /home/hender/espresso-3.2.0/Espresso() [0x413bd5]
[nanopart:18254] *** End of error message ***

Thanks in advance.


Attachment: test_virtual.tcl
Description: Tcl script

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