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Re: [lammps-users] Bond style hydrid using harmonic and table
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Re: [lammps-users] Bond style hydrid using harmonic and table


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 1 Aug 2017 13:02:48 -0400



On Tue, Aug 1, 2017 at 12:10 PM, George Ray <uraykol12@...24...> wrote:
Hello everyone,

I am trying to run a  bead-spring model in Lammps 14May-2016 version at 300K. There is harmonic potential between bonds, angles and dihedrals. Also, between each beads there is a lj12/6 non-bonded potential. I define additional bonds using "fix bond/create" (Reference - http://lammps.sandia.gov/threads/msg59117.html) and "special_bonds extra" and use "bond_style hybrid" to reproduce the harmonic and l/j interactions between beads.

​there is no reason to use either fix bond/create or bond_style hybrid in your simulation. the e-mail you quote is irrelevant to your system.

you already have a suitable bond topology, so there is no need to create *additional* bonds.
also, with your special_bonds setting of 1.0 1.0 1.0, you do​ include the 1-2 LJ interactions as specified by your pair style, so there is no need to specify them again with the bond style.
furthermore, bond style hybrid does an "either or" setup and not "one plus the other",  thus your tabulated potential will wipe out the harmonic interaction, which is definitely not what you want for a spring-bead polymer.
 


However when I am running NVT, I see that the temperature and the Ebond energy is not rising from 0. The visualized trajectory shows a chain not moving at all.

​that is because your minimization is not working as expected due to the symmetry of your system. you need to carefully evaluate your bond topology, it may not be what you expect. you can see what happens by replacing fix nvt by fix nve. after a few steps, the symmetry is broken due to the assign​ment of random velocities and then all the stored potential energy is quickly released, which would overload the nose-hoover thermostat.

the remedy for this is simple. insert a smaller randomization of positions *before* the minimization, e.g. with:


displace_atoms all random 0.01 0.01 0.01 443322

​this will then break the symmetry and minimize can relax your system to a local potential energy minimum and after that, the nose-hoover thermostat can handle your system well.

axel.​



I am attaching the input script and log file here along with the data file. Can someone please help and tell me where I am going wrong? Is the sytax for bond_style hybrid or special_bonds or bonds/create wrong? Or is it something else? Please do provide your feedback. Thank you so much

INPUT SCRIPT

dimension    3
boundary    s s s
units        real
atom_style    full
newton        on

read_data    data.chain


neighbor 2.0 nsq
neigh_modify every 10 delay 10 check yes

fix 1 all bond/create 1 1 1 6.5 1

##POTENTIAL SPECIFICATION

pair_style lj/cut 12.0
pair_modify shift yes
pair_coeff 1 1 0 4.42

special_bonds lj/coul 1.0 1.0 1.0 extra 1

bond_style hybrid harmonic table spline 51
bond_coeff 1 harmonic 90.283 5.6393
bond_coeff 1 table ljvalues.table INTRABEAD

angle_style harmonic
angle_coeff 1 366068.3768 163.272

dihedral_style harmonic
dihedral_coeff 1 37442.11445 1 1



min_style    cg
min_modify    line quadratic
minimize    1.0e-20 1.0e-15 100000000 1000000000



dump 1 all custom 500 releasedall_equilibrate.lammpstrj id type x y z


velocity all create 300.0 53244 dist gaussian mom no rot no units box


thermo_style    custom step cpu temp pe ke ebond eangle edihed etotal
thermo        1000
thermo_modify flush yes
reset_timestep 0
timestep    0.25



fix 3 all nvt temp 300.0 300.0 10
run 50000

write_restart equil.restart2










LOG FILE




LAMMPS (14 May 2016)
dimension    3
boundary    s s s
units        real
atom_style    full
newton        on

read_data    data.chain
  orthogonal box = (-5.5 -5 -5) to (23.5 5 5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  4 atoms
  scanning bonds ...
  1 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  scanning dihedrals ...
  1 = max dihedrals/atom
  reading bonds ...
  3 bonds
  reading angles ...
  2 angles
  reading dihedrals ...
  1 dihedrals
  2 = max # of 1-2 neighbors
  1 = max # of 1-3 neighbors
  2 = max # of 1-4 neighbors
  3 = max # of special neighbors
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:925)


neighbor 2.0 nsq
neigh_modify every 10 delay 10 check yes

#neighbor    2 bin
#neigh_modify    delay 50 every 10 check yes


fix 1 all bond/create 1 1 1 6.5 1

##POTENTIAL SPECIFICATION

pair_style lj/cut 12.0
pair_modify shift yes
pair_coeff 1 1 0 4.42

special_bonds lj/coul 1.0 1.0 1.0 extra 1
  2 = max # of 1-2 neighbors
  3 = max # of special neighbors

bond_style hybrid harmonic table spline 51
bond_coeff 1 harmonic 90.283 5.6393
bond_coeff 1 table ljvalues.table INTRABEAD
WARNING: 1 of 51 force values in table are inconsistent with -dE/dr.
  Should only be flagged at inflection points (../bond_table.cpp:380)

angle_style harmonic
angle_coeff 1 366068.3768 163.272

dihedral_style harmonic
dihedral_coeff 1 37442.11445 1 1



min_style    cg
min_modify    line quadratic
minimize    1.0e-20 1.0e-15 100000000 1000000000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:925)
Memory usage per processor = 6.9135 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
       0            0            0    99830.089    99830.089 -2.7258398e+10  6.77032e-05
      21            0            0    99822.296    99822.296   -61.021985  5.89032e-05
Loop time of 7.39098e-05 on 1 procs for 21 steps with 4 atoms

47.4% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final =
         99830.0893103      99822.2955809      99822.2955809
  Force two-norm initial, final = 6.74872 3.80275e-08
  Force max component initial, final = 4.77206 2.78264e-08
  Final line search alpha, max atom move = 1 2.78264e-08
  Iterations, force evaluations = 21 32

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 9.0599e-06 | 9.0599e-06 | 9.0599e-06 |   0.0 | 12.26
Bond    | 2.0742e-05 | 2.0742e-05 | 2.0742e-05 |   0.0 | 28.06
Neigh   | 2.1458e-06 | 2.1458e-06 | 2.1458e-06 |   0.0 |  2.90
Comm    | 3.8147e-06 | 3.8147e-06 | 3.8147e-06 |   0.0 |  5.16
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 3.815e-05  |            |       | 51.61

Nlocal:    4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    5 ave 5 max 5 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 5
Ave neighs/atom = 1.25
Ave special neighs/atom = 1.5
Neighbor list builds = 1
Dangerous builds = 0



dump 1 all custom 500 releasedall_equilibrate.lammpstrj id type x y z


velocity all create 300.0 53244 dist gaussian mom no rot no units box


thermo_style    custom step cpu temp pe ke ebond eangle edihed etotal
thermo        1000
thermo_modify flush yes
reset_timestep 0
timestep    0.25



fix 3 all nvt temp 300.0 300.0 10
run 50000
Neighbor list info ...
  2 neighbor list requests
  update every 10 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:925)
Memory usage per processor = 7.03865 Mbytes
Step CPU Temp PotEng KinEng E_bond E_angle E_dihed TotEng
       0            0          300    99822.296     2.682729   -27.060008    62407.241    37442.114    99824.978
    1000 0.0025160313            0     107827.3            0   -9.6433942    39382.416    68454.526     107827.3
    2000 0.0052881241            0    29444.587            0   -10.243009    5082.1873    24372.643    29444.587
    3000 0.0076031685            0    1551.4529            0   -10.845041    75.521725    1486.7762    1551.4529
    4000 0.0098311901            0    18.724881            0   -10.876128    1.4816518    28.119357    18.724881
    5000  0.012070179            0   -10.336999            0    -10.87704  0.057015792   0.48302578   -10.336999
    6000  0.014300108            0   -10.867145            0   -10.877602 0.0021657202 0.0082914224   -10.867145
    7000  0.016527176            0   -10.877977            0   -10.878204 8.3996325e-05 0.00014234428   -10.877977
    8000  0.019203186            0   -10.878806            0   -10.878815 6.8732991e-06 2.4435313e-06   -10.878806
    9000  0.021567106            0   -10.879425            0    -10.87943 4.3535518e-06 4.1943219e-08   -10.879425
   10000  0.023812056            0    -10.88004            0   -10.880044 4.3388128e-06 7.1914539e-10    -10.88004
   11000  0.026057005            0   -10.880655            0    -10.88066 4.3541912e-06 1.6627639e-11   -10.880655
   12000  0.028273106            0   -10.881271            0   -10.881275 4.3579973e-06            0   -10.881271
   13000  0.030480146            0   -10.881887            0   -10.881891 4.3588827e-06            0   -10.881887
   14000  0.032730103            0   -10.882503            0   -10.882507 4.3591732e-06 4.1569098e-12   -10.882503
   15000  0.034979105            0    -10.88312            0   -10.883124 4.3593469e-06 4.1569098e-12    -10.88312
   16000  0.037229061            0   -10.883737            0   -10.883741 4.3594979e-06 4.1569098e-12   -10.883737
   17000  0.039458036            0   -10.884354            0   -10.884358 4.3596444e-06            0   -10.884354
   18000  0.041685104            0   -10.884972            0   -10.884976 4.3597902e-06            0   -10.884972
   19000  0.043909073            0    -10.88559            0   -10.885594 4.3599359e-06            0    -10.88559
   20000  0.046113014            0   -10.886208            0   -10.886212 4.3600816e-06 4.1569098e-12   -10.886208
   21000  0.048349142            0   -10.886827            0   -10.886831 4.3602274e-06            0   -10.886827
   22000  0.050615072            0   -10.887446            0    -10.88745 4.3603733e-06 4.1569098e-12   -10.887446
   23000  0.053517103            0   -10.888065            0    -10.88807 4.3605193e-06 8.3138195e-12   -10.888065
   24000  0.055796146            0   -10.888685            0   -10.888689 4.3606653e-06            0   -10.888685
   25000  0.058023214            0   -10.889305            0   -10.889309 4.3608114e-06 4.1569098e-12   -10.889305
   26000  0.060265064            0   -10.889926            0    -10.88993 4.3609577e-06            0   -10.889926
   27000  0.062482119            0   -10.890546            0   -10.890551 4.3611039e-06            0   -10.890546
   28000  0.064691067            0   -10.891168            0   -10.891172 4.3612503e-06 4.1569098e-12   -10.891168
   29000  0.066916227            0   -10.891789            0   -10.891793 4.3613968e-06            0   -10.891789
   30000   0.06916523            0   -10.892411            0   -10.892415 4.3615433e-06 4.1569098e-12   -10.892411
   31000  0.071389198            0   -10.893033            0   -10.893038 4.3616899e-06            0   -10.893033
   32000    0.0735991            0   -10.893656            0    -10.89366 4.3618366e-06            0   -10.893656
   33000  0.075831175            0   -10.894279            0   -10.894283 4.3619834e-06            0   -10.894279
   34000   0.07805419            0   -10.894902            0   -10.894906 4.3621302e-06 8.3138195e-12   -10.894902
   35000  0.080314159            0   -10.895526            0    -10.89553 4.3622772e-06            0   -10.895526
   36000  0.083106041            0    -10.89615            0   -10.896154 4.3624242e-06            0    -10.89615
   37000  0.085658073            0   -10.896774            0   -10.896778 4.3625713e-06            0   -10.896774
   38000  0.087969065            0   -10.897399            0   -10.897403 4.3627185e-06            0   -10.897399
   39000  0.090229034            0   -10.898024            0   -10.898028 4.3628657e-06 4.1569098e-12   -10.898024
   40000  0.092454195            0   -10.898649            0   -10.898653 4.3630131e-06            0   -10.898649
   41000  0.094695091            0   -10.899275            0   -10.899279 4.3631605e-06            0   -10.899275
   42000  0.096913099            0   -10.899901            0   -10.899905 4.363308e-06            0   -10.899901
   43000  0.099133015            0   -10.900527            0   -10.900532 4.3634556e-06            0   -10.900527
   44000   0.10136509            0   -10.901154            0   -10.901159 4.3636032e-06            0   -10.901154
   45000    0.1036191            0   -10.901781            0   -10.901786 4.363751e-06 4.1569098e-12   -10.901781
   46000   0.10583019            0   -10.902409            0   -10.902413 4.3638988e-06            0   -10.902409
   47000   0.10806417            0   -10.903037            0   -10.903041 4.3640467e-06 4.1569098e-12   -10.903037
   48000   0.11031508            0   -10.903665            0   -10.903669 4.3641947e-06            0   -10.903665
   49000   0.11259317            0   -10.904294            0   -10.904298 4.3643428e-06            0   -10.904294
   50000   0.11562109            0   -10.904923            0   -10.904927 4.3644909e-06            0   -10.904923
Loop time of 0.115642 on 1 procs for 50000 steps with 4 atoms

Performance: 9339.162 ns/day, 0.003 hours/ns, 432368.598 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0062993  | 0.0062993  | 0.0062993  |   0.0 |  5.45
Bond    | 0.043074   | 0.043074   | 0.043074   |   0.0 | 37.25
Neigh   | 1.3828e-05 | 1.3828e-05 | 1.3828e-05 |   0.0 |  0.01
Comm    | 0.0033088  | 0.0033088  | 0.0033088  |   0.0 |  2.86
Output  | 0.0026288  | 0.0026288  | 0.0026288  |   0.0 |  2.27
Modify  | 0.053799   | 0.053799   | 0.053799   |   0.0 | 46.52
Other   |            | 0.006519   |            |       |  5.64

Nlocal:    4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 4
Ave neighs/atom = 1
Ave special neighs/atom = 1.5
Neighbor list builds = 11
Dangerous builds = 1

write_restart equil.restart2
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:925)
Total wall time: 0:00:00




DATA FILE

LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.5 on Tue Jun 13 17:03:39 EDT 2017
 4 atoms
 3 bonds
 2 angles
 1 dihedrals
 0 impropers
 1 atom types
 1 bond types
 1 angle types
 1 dihedral types
 0 improper types

 -5.500000 23.500000  xlo xhi
 -5.00000 5.00000  ylo yhi
 -5.000000 5.00000  zlo zhi

 Masses

 1 162.1406


 Atoms

1 1 1 0.000000 0.000000 0.000000 0.000000 #  Chain1
2 1 1 0.000000 5.640000 0.000000 0.000000 # Chain1
3 1 1 0.000000 11.280000 0.000000 0.000000 # Chain1
4 1 1 0.000000 16.920000 0.000000 0.000000 # Chain1


 Bonds

1 1 1 2
2 1 2 3
3 1 3 4

 Angles

1 1 1 2 3
2 1 2 3 4

 Dihedrals

1 1 1 2 3 4





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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.