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


From: George Ray <uraykol12@...24...>
Date: Tue, 1 Aug 2017 12:10:55 -0400

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.

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.

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