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


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 19 Jul 2017 07:24:02 -0400

On Wed, Jul 19, 2017 at 3:16 AM, sunny <254958987@...1204...> wrote:
> 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!

absolute energies have no meaning in this context, as they can be
offset by arbitrary values (see pair_modify shift yes). also, ecoul
only contains the short range contribution, for systems with
long-range coulomb support, you have to add elong. however, those
still can have a different reference energy.

if you want to compare the interactions of the two codes, you need to
compare forces at step 0, and the geometries when converged.

axel.

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