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Re: [lammps-users] ERROR: Molecule topology/atom exceeds system topology/atom (../molecule.cpp:1398)
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Re: [lammps-users] ERROR: Molecule topology/atom exceeds system topology/atom (../molecule.cpp:1398)

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 2 Oct 2017 13:32:43 -0400

On Fri, Sep 29, 2017 at 2:40 AM, sunny <254958987@...1204...> wrote:

Dear All,
  I want to simulate the adsorption of ethene in zeolites by using fix gcmc. Now I met the error
"ERROR: Molecule topology/atom exceeds system topology/atom (../molecule.cpp:1398)
Last command: fix  mygcmc ethene gcmc 25 1000 1000 0 54341 ${temp} ${mu} ${disp} mol ethenemol                 maxangle 180 pressure ${pres} group ethene rigid myrigidnvt full_energy".

However, it worked well when I replace ethene with carbon dioxide (the molecule file of carbon dioxide used is from the the example in the lammps-31Mar17 softe package).

​the error message is pretty self-explanatory, after you understand that the data structures for storing topology information are "locked in" when the simulation box is created.
if you then add some molecules later, that require additional space in those data structures, you have to either reserve space for those using the extra/... keywords to read_data or create_box, or you can simply include one of those molecules already in your original data file. for gcmc calculations, that is most certainly the simplest approach.



I definitely need help on this from lammps users. Thanks very much!

Guang Yang

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Dr. Axel Kohlmeyer  akohlmey@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.