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Re: [lammps-users] error in gcmc result
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Re: [lammps-users] error in gcmc result


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 16 May 2018 10:36:22 -0400



On Wed, May 16, 2018 at 10:26 AM, SATYARANJAN BISWAL <gurubio786@...24...> wrote:
Dear Axel and users,
I am trying to run the GCMC simulation of a rigid and fixed mof structure to adsrob CO2 molecules. In simulation, the UFF/DREIDING inter-atomic parameters  are used for MOF along with a three-site model parameter for CO2 (TraPPE).  which pair coefficients carried data of UFF data. I just used the TraPPE parameters given  in example/gcmc/CO2.txt. 

I am using the lammps-23oct2017 version.


​there are several principal issues here.​
- your system is *tiny*. doing gcmc insertion moves are likely to cause high energy differences and thus will be not very probable.
- your initial energy/pressure is *gigantic*. so either your initial structure is bad or your force field parameters or both.
- it is rather pointless to try gcmc with a system that doesn't look like it is properly relaxed.
- you are mix and matching force field parameters. that is a bad idea.
- it is not very relevant here, but there have been plenty of improvements and fixes to the gcmc facility in LAMMPS, so you should upgrade your version to the latest release.

but in result file atom value not changing with respect to steps and other parameter changing but in gcmc atom no varry is very important.can any one suggest why it happening.when i changed it by pair style lj/cut instead of  pair_style lj/cut/coul/long 12.500 ,it gave good result atom no got change.so,where is the problem in force-field parameter or any other place.


kindly suggest me about  the problem how to figure out and valuable advice.

​you need help and training from an experienced collaborator. the issues ​you are seeing are due to lack of proper understanding of the fundamentals of managing MD simulations. a mailing list is not a classroom and thus you cannot expect to get the support that you need only from this list. we may help you with technical issues, and throw in the occasional advanced technique suggestion, but we cannot teach you how to do your research as such.


​axel.​

 

Thank you very much.

Regards,
satyaranjan







LAMMPS (23 Oct 2017)
Reading data file ...
  orthogonal box = (-17.1959 -17.1959 -17.1959) to (37.7508 37.7508 37.7508)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  675 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:   0          0          0
  special bond factors coul: 0          0          0
  0 = max # of 1-2 neighbors
  0 = max # of 1-3 neighbors
  0 = max # of 1-4 neighbors
  1 = max # of special neighbors
Read molecule gas:
  3 atoms with 6 types
  0 bonds with 0 types
  0 angles with 0 types
  0 dihedrals with 0 types
  0 impropers with 0 types
3 atoms in group gas
672 atoms in group sol
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.115288
  estimated absolute RMS force accuracy = 0.437615
  estimated relative force accuracy = 0.00131786
  KSpace vectors: actual max1d max3d = 61 3 171
                  kxmax kymax kzmax  = 3 3 3
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
0 atoms in group FixGCMC:gcmc_exclusion_group:2
0 atoms in group FixGCMC:rotation_gas_atoms:2
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14.5
  ghost atom cutoff = 14.5
  binsize = 7.25, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/multi/newton
      stencil: half/multi/3d/newton
      bin: standard
Setting up Verlet run ...
  Unit style    : real
  Current step  : 0
  Time step     : 1
Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.65 | 12.65 Mbytes
Step Atoms Volume Press TotEng Enthalpy Density
       0      675    165892.04    2783183.7    1660098.4    8393636.5   0.09676333
      10      675    165892.04    2783181.6    1660095.9    8393628.7   0.09676333
      20      675    165892.04    2783179.9    1660093.8    8393622.7   0.09676333
      30      675    165892.04      2783180      1660094    8393623.1   0.09676333


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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.