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[lammps-users] Question on: The results about coul interaction energy obtained by Lammps and MS are very different
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[lammps-users] Question on: The results about coul interaction energy obtained by Lammps and MS are very different


From: "sunny" <254958987@...1204...>
Date: Wed, 19 Jul 2017 15:16:34 +0800

Dear All,
I want to simulate molecular diffusion properties in zeolites with lammps. I created .car and .mdf file of the structure with Material Studio and then I used them to create data file with msi2lmp and pcff. But I found the coul interaction energy obtained by Lammps and MS are very different. E-coul obtained by lammps is positive but MS is negative. A simple example about CHA zeolite is given as follows,just do minimization.The data and in files are in the attachment. Thank you very much!

Lammps results:
LAMMPS (31 Mar 2017)
units        real
atom_style   full
pair_style   lj/class2/coul/long 12
bond_style   class2
angle_style  class2
dihedral_style class2
improper_style class2
kspace_style ewald 0.0001
pair_modify  mix arithmetic

read_data    CHA-36T.data
  triclinic box = (-6.96522 2.09529 -5.05796) to (6.75128 13.9755 9.80515) with tilt (-6.85539 0.000726348 -0.00035957)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  108 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  6 = max dihedrals/atom
  scanning impropers ...
  4 = max impropers/atom
  reading bonds ...
  144 bonds
  reading angles ...
  288 angles
  reading dihedrals ...
  432 dihedrals
  reading impropers ...
  144 impropers
  4 = max # of 1-2 neighbors
  6 = max # of 1-3 neighbors
  16 = max # of 1-4 neighbors
  20 = max # of special neighbors
neighbor     0.5 bin
neigh_modify delay 10

thermo_style multi
minimize 0.0001 0.005 100 500
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.188538
  estimated absolute RMS force accuracy = 0.0387266
  estimated relative force accuracy = 0.000116624
  KSpace vectors: actual max1d max3d = 28 2 62
                  kxmax kymax kzmax  = 2 2 2
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12.5
  ghost atom cutoff = 12.5
  binsize = 6.25, bins = 4 2 3
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton/tri
      stencil: half/bin/3d/newton/tri
      bin: standard
WARNING: Inconsistent image flags (../domain.cpp:785)
Per MPI rank memory allocation (min/avg/max) = 17.15 | 17.15 | 17.15 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =      2977.5571 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =      2977.5571 E_bond   =         3.2879 E_angle  =       195.1358 
E_dihed  =       -23.1013 E_impro  =         1.1617 E_vdwl   =       -50.4755 
E_coul   =      3373.9913 E_long   =      -522.4428 Press    =     31153.9109 
---------------- Step        8 ----- CPU =      0.0272 (sec) ----------------
TotEng   =      2943.1443 KinEng   =         0.0000 Temp     =         0.0000 
PotEng   =      2943.1443 E_bond   =         3.8698 E_angle  =       182.1567 
E_dihed  =       -43.8653 E_impro  =         1.5510 E_vdwl   =       -49.1766 
E_coul   =      3371.1048 E_long   =      -522.4960 Press    =     30627.9005 
Loop time of 0.027262 on 1 procs for 8 steps with 108 atoms

99.0% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
         2977.55711384       2943.3268794      2943.14432948
  Force two-norm initial, final = 128.004 17.3911
  Force max component initial, final = 16.8661 2.50815
  Final line search alpha, max atom move = 0.0368907 0.0925273
  Iterations, force evaluations = 8 16

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.01663    | 0.01663    | 0.01663    |   0.0 | 61.00
Bond    | 0.0073097  | 0.0073097  | 0.0073097  |   0.0 | 26.81
Kspace  | 0.0010347  | 0.0010347  | 0.0010347  |   0.0 |  3.80
Neigh   | 0.0018408  | 0.0018408  | 0.0018408  |   0.0 |  6.75
Comm    | 0.00029492 | 0.00029492 | 0.00029492 |   0.0 |  1.08
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.0001521  |            |       |  0.56

Nlocal:    108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    2718 ave 2718 max 2718 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    19827 ave 19827 max 19827 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 19827
Ave neighs/atom = 183.583
Ave special neighs/atom = 16
Neighbor list builds = 1
Dangerous builds = 0

write_data  CHA-ethene-cvff.dataM
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.188538
  estimated absolute RMS force accuracy = 0.0387266
  estimated relative force accuracy = 0.000116624
  KSpace vectors: actual max1d max3d = 28 2 62
                  kxmax kymax kzmax  = 2 2 2
Total wall time: 0:00:00

MS results:
Forcite
-------
Task             : Geometry Optimization
Version          : 7.0
Build date       : Feb  2 2014
Host             : DESKTOP-UJDQA16
Threads          : Parallel 4
Operating system : Windows
Task started     : Wed Jul 19 09:09:45 2017

---- Geometry optimization parameters ----

Algorithm                       : Smart
Convergence tolerance:
  Energy                        : 0.0001 kcal/mol
  Force                         : 0.005 kcal/mol/A
  Stress                        : 0.005 GPa
  Displacement                  : 5e-005 A
Maximum number of iterations    : 500
External pressure               : 0 GPa
Motion groups rigid             : NO
Optimize cell                   : NO

---- Energy parameters ----

Forcefield                      : pcff (Version 3.1)
Charges                         : Forcefield assigned
Electrostatic terms:
  Summation method              : Ewald
  Accuracy                      : 0.0001 kcal/mol
  Buffer width                  : 0.5 A

van der Waals terms:
  Summation method              : Ewald
  Accuracy                      : 0.0001 kcal/mol
  Repulsive cutoff              : 12 A
  Buffer width                  : 0.5 A


---- Initial structure ----

Total enthalpy                  : -2022.894074 kcal/mol
  External pressure term        : 0.000000 kcal/mol

Total energy                    :       -2022.894074 kcal/mol

Contributions to total energy (kcal/mol):
  Valence energy (diag. terms)  :         195.078
    Bond                        :           3.287
    Angle                       :         203.428
    Torsion                     :         -11.637
    Inversion                   :           0.000
  Valence energy (cross terms)  :         -18.598
    Stretch-Stretch             :           2.271
    Stretch-Bend-Stretch        :         -10.566
    Stretch-Torsion-Stretch     :           0.000
    Separated-Stretch-Stretch   :           0.000
    Torsion-Stretch             :           0.000
    Bend-Bend                   :           1.162
    Torsion-Bend-Bend           :         -11.464
    Bend-Torsion-Bend           :           0.000
  Non-bond energy               :       -2199.374
    van der Waals               :         -52.619
    Electrostatic               :       -2146.754
 
rms force  : 8.140E+000 kcal/mol/A     
max force  : 1.947E+001 kcal/mol/A
       
Cell parameters:    a:  13.716476 A    b:  13.716318 A    c:  14.863095 A   
                alpha:  90.003 deg  beta:  89.997 deg gamma: 119.987 deg

---- Final structure ----

Total enthalpy                  : -2057.293217 kcal/mol
  External pressure term        : 0.000000 kcal/mol

Total energy                    :       -2057.293217 kcal/mol

Contributions to total energy (kcal/mol):
  Valence energy (diag. terms)  :         141.930
    Bond                        :           0.601
    Angle                       :         186.619
    Torsion                     :         -45.291
    Inversion                   :           0.000
  Valence energy (cross terms)  :           0.611
    Stretch-Stretch             :           0.369
    Stretch-Bend-Stretch        :          -4.791
    Stretch-Torsion-Stretch     :           0.000
    Separated-Stretch-Stretch   :           0.000
    Torsion-Stretch             :           0.000
    Bend-Bend                   :           1.522
    Torsion-Bend-Bend           :           3.511
    Bend-Torsion-Bend           :           0.000
  Non-bond energy               :       -2199.834
    van der Waals               :         -51.634
    Electrostatic               :       -2148.200
 
rms force  : 9.335E-004 kcal/mol/A     
max force  : 2.902E-003 kcal/mol/A
       
Cell parameters:    a:  13.716476 A    b:  13.716318 A    c:  14.863095 A   
                alpha:  90.003 deg  beta:  89.997 deg gamma: 119.987 deg



Task terminated               : Wed Jul 19 09:09:47 2017
Total CPU time used by Forcite: 2 seconds (1.63s)

Termination status : Normal


I definitely need help on this from lammps users.
Guang Yang
Sinopec,China

Attachment: CHA-36T.data
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Attachment: run_minimization.in
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