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[lammps-users] Bead -Spring model temperature not going up


From: George Ray <uraykol12@...24...>
Date: Mon, 31 Jul 2017 11:31:07 -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. The bond, angle and dihedral coefficients match close to this paper (Table 1) (https://link.springer.com/article/10.1007/s10570-014-0481-2)

However, when I am running the simulations, I see that the energy is extremely high and the temperature is not increasing at all. Reducing the time step does not help. For ease, I simplified the system to just 4 beads in a chain and am producing the log file, data file and input script below.

When I am visualizing the trajectories, I am seeing that the beads are  going far apart and then again coming back together. But the final position of the chain is perpendicular to the initial position. This definitely should not happen.

Can someone please help me out with this? Thank you so much for your help.


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


##POTENTIAL SPECIFICATION

pair_style lj/cut 7.0
pair_modify shift yes
pair_coeff 1 1 9.02 4.42

bond_style harmonic
bond_coeff 1 90.283 5.6393

angle_style harmonic
angle_coeff 1 366068.3768 163.272

dihedral_style harmonic
dihedral_coeff 1 37442.11445 1 1

special_bonds lj/coul 1 1 1



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
fix 1 all nve
run 100
minimize 1.0e-4 1.0e-6 100 1000


write_restart equil.restart1


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

unfix 1




fix 2 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    0.002 bin
#neigh_modify    delay 50 every 10 check yes


##POTENTIAL SPECIFICATION

pair_style lj/cut 7.0
pair_modify shift yes
pair_coeff 1 1 9.02 4.42

bond_style harmonic
bond_coeff 1 90.283 5.6393

angle_style harmonic
angle_coeff 1 366068.3768 163.272

dihedral_style harmonic
dihedral_coeff 1 37442.11445 1 1

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





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
fix 1 all nve
run 100
Neighbor list info ...
  1 neighbor list requests
  update every 10 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 9
  ghost atom cutoff = 9
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:925)
Memory usage per processor = 6.71467 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
       0          300   -12.840924    99849.356    99839.198 -2.6169035e+10  6.77032e-05
     100 1.2745609e+11            0 8.481596e+08 1.9879268e+09     10253693    1312916.1
Loop time of 0.000164986 on 1 procs for 100 steps with 4 atoms

Performance: 52368.189 ns/day, 0.000 hours/ns, 606113.295 timesteps/s
64.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 |   0.0 |  3.61
Bond    | 7.844e-05  | 7.844e-05  | 7.844e-05  |   0.0 | 47.54
Neigh   | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 |   0.0 |  3.61
Comm    | 8.1062e-06 | 8.1062e-06 | 8.1062e-06 |   0.0 |  4.91
Output  | 2.2173e-05 | 2.2173e-05 | 2.2173e-05 |   0.0 | 13.44
Modify  | 2.0742e-05 | 2.0742e-05 | 2.0742e-05 |   0.0 | 12.57
Other   |            | 2.36e-05   |            |       | 14.31

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:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 1.5
Neighbor list builds = 10
Dangerous builds = 10
minimize 1.0e-4 1.0e-6 100 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 9
  ghost atom cutoff = 9
Memory usage per processor = 7.83967 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
     100 1.2745609e+11            0 8.481596e+08 1.9879268e+09     10253693    1312916.1
     200 1.2745609e+11            0 8.3250017e+08 1.9722674e+09     11067444    1281157.6
Loop time of 0.000170946 on 1 procs for 100 steps with 4 atoms

64.3% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = max iterations
  Energy initial, next-to-last, final =
         848159603.188      832656042.585       832500170.99
  Force two-norm initial, final = 1.01367e+06 1.00414e+06
  Force max component initial, final = 653130 646901
  Final line search alpha, max atom move = 1.54568e-07 0.0999904
  Iterations, force evaluations = 100 100

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 9.2983e-06 | 9.2983e-06 | 9.2983e-06 |   0.0 |  5.44
Bond    | 6.6757e-05 | 6.6757e-05 | 6.6757e-05 |   0.0 | 39.05
Neigh   | 7.1526e-06 | 7.1526e-06 | 7.1526e-06 |   0.0 |  4.18
Comm    | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 |   0.0 |  3.49
Output  | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 |   0.0 | 11.16
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 6.27e-05   |            |       | 36.68

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:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 1.5
Neighbor list builds = 10
Dangerous builds = 0

#min_style    cg
#min_modify    line quadratic
#minimize    1.0e-20 1.0e-15 100000000 1000000000
#minimize 1.0e-4 1.0e-6 100 1000

write_restart equil.restart1
Neighbor list info ...
  1 neighbor list requests
  update every 10 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 9
  ghost atom cutoff = 9


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


#min_style    cg
#min_modify    line quadratic
#minimize    1.0e-20 1.0e-15 100000000 1000000000
#velocity all create 300.0 4928459 dist gaussian mom yes rot yes loop local units box
#fix 1 all nve
#run 500000
#unfix 1

#velocity all scale 300.0
unfix 1




fix 2 all nvt temp 300.0 300.0 10
run 50000
Memory usage per processor = 6.71467 Mbytes
Step CPU Temp PotEng KinEng E_bond E_angle E_dihed TotEng
       0            0 1.2745609e+11 8.3250017e+08 1.1397672e+09 8.269226e+08    5502686.5    74881.395 1.9722674e+09
    1000 0.0029017925            0 7.5508884e+08            0 7.4951903e+08    5494929.2    74881.248 7.5508884e+08
    2000 0.0052688122            0 6.8497982e+08            0 6.7941787e+08    5487068.5    74881.092 6.8497982e+08
    3000 0.0074679852            0 6.2148287e+08            0 6.1592888e+08    5479103.3    74880.927 6.2148287e+08
    4000 0.0096409321            0 5.6397304e+08            0 5.5842713e+08    5471032.2     74880.75 5.6397304e+08
    5000   0.01154995            0 5.1188449e+08            0 5.0634676e+08    5462853.8    74880.563 5.1188449e+08
    6000  0.013285875            0 4.6470489e+08            0 4.5917544e+08    5454566.6    74880.362 4.6470489e+08
    7000  0.015064001            0 4.2197035e+08            0 4.164493e+08    5446168.6    74880.149 4.2197035e+08
    8000  0.017179966            0 3.8326088e+08            0 3.7774834e+08    5437657.8     74879.92 3.8326088e+08
    9000  0.019134998            0 3.4819618e+08            0 3.4269227e+08    5429031.8    74879.675 3.4819618e+08
   10000  0.020870924            0 3.1643193e+08            0 3.1093676e+08      5420288    74879.412 3.1643193e+08
   11000  0.022675991            0 2.8765634e+08            0 2.8217004e+08    5411423.4     74879.13 2.8765634e+08
   12000  0.024457932            0 2.6158714e+08            0 2.5610983e+08    5402434.7    74878.826 2.6158714e+08
   13000  0.026168823            0 2.3796872e+08            0 2.3250052e+08    5393318.1    74878.498 2.3796872e+08
   14000  0.027909994            0 2.1656965e+08            0 2.111107e+08    5384069.6    74878.144 2.1656965e+08
   15000  0.029618979            0 1.9718037e+08            0 1.917308e+08    5374684.4     74877.76 1.9718037e+08
   16000  0.031370878            0 1.7961113e+08            0 1.7417109e+08    5365157.4    74877.342 1.7961113e+08
   17000   0.03309083            0 1.6369012e+08            0 1.5825977e+08      5355483    74876.887 1.6369012e+08
   18000  0.034863949            0 1.4926179e+08            0 1.4384126e+08    5345654.8    74876.389 1.4926179e+08
   19000  0.036565781            0 1.3618525e+08            0 1.3077471e+08    5335666.1    74875.842 1.3618525e+08
   20000  0.038306952            0 1.2433296e+08            0 1.1893257e+08    5325509.2     74875.24 1.2433296e+08
   21000  0.040010929            0 1.1358941e+08            0 1.0819936e+08    5315175.9    74874.573 1.1358941e+08
   22000    0.0417099            0 1.0385002e+08            0     98470485    5304657.1    74873.831 1.0385002e+08
   23000  0.043429852            0     95020078            0     89651262      5293943    74873.002     95020078
   24000  0.045136929            0     87013836            0     81655941    5283022.9     74872.07     87013836
   25000  0.046867847            0     79753630            0     74406874    5271885.2    74871.015     79753630
   26000  0.048596859            0     73169138            0     67833751    5260517.5    74869.812     73169138
   27000  0.051007986            0     67196679            0     61872904    5248906.3     74868.43     67196679
   28000  0.052762985            0     61778582            0     56466678    5237037.1    74866.828     61778582
   29000  0.054547787            0     56862624            0     51562864    5224894.5    74864.952     56862624
   30000  0.056252003            0     52401508            0     47114183    5212461.7    74862.732     52401508
   31000  0.057978868            0     48352402            0     43077821    5199720.9    74860.072     48352402
   32000  0.059690952            0     44676515            0     39415005    5186653.3    74856.841     44676515
   33000  0.061381817            0     41338714            0     36090623    5173238.3    74852.854     41338714
   34000   0.06307888            0     38307181            0     33072879    5159454.1    74847.849     38307181
   35000  0.064860821            0     35553093            0     30332975    5145277.2    74841.439     35553093
   36000  0.066574812            0     33050347            0     27844832    5130681.7     74833.04     33050347
   37000  0.068271875            0     30775291            0     25584830    5115639.1    74821.744     30775291
   38000  0.069976807            0     28706499            0     23531577    5100116.4    74806.085     28706499
   39000  0.071679831            0     26824554            0     21665697    5084073.6    74783.595     26824554
   40000  0.073370934            0     25111844            0     19969636    5067458.5    74749.916     25111844
   41000  0.075089931            0     23552381            0     18427490    5050194.3    74696.905     23552381
   42000  0.076786995            0     22131600            0     17024840    5032152.3    74608.304     22131600
   43000  0.078513861            0     20836123            0     15748592      5013082    74449.004     20836123
   44000  0.080533981            0     19653361            0     14586810    4992415.4    74135.827     19653361
   45000  0.082799911            0     18570577            0     13528472    4968655.5    73449.552     18570577
   46000  0.084667921            0     17571897            0     12562948    4937203.2    71745.199     17571897
   47000  0.086378813            0     16627202            0     11678368    4881821.7    67012.232     16627202
   48000  0.088130951            0     15653857            0     10856010    4743551.1    54296.512     15653857
   49000  0.089857817            0     14460024            0     10058225    4369425.2    32373.793     14460024
   50000  0.091587782            0     12849862            0      9230850    3603864.8     15147.62     12849862
Loop time of 0.0916119 on 1 procs for 50000 steps with 4 atoms

Performance: 11788.866 ns/day, 0.002 hours/ns, 545780.850 timesteps/s
98.8% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0027101  | 0.0027101  | 0.0027101  |   0.0 |  2.96
Bond    | 0.02532    | 0.02532    | 0.02532    |   0.0 | 27.64
Neigh   | 0.00051594 | 0.00051594 | 0.00051594 |   0.0 |  0.56
Comm    | 0.0041747  | 0.0041747  | 0.0041747  |   0.0 |  4.56
Output  | 0.0029523  | 0.0029523  | 0.0029523  |   0.0 |  3.22
Modify  | 0.048834   | 0.048834   | 0.048834   |   0.0 | 53.31
Other   |            | 0.007105   |            |       |  7.76

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:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 1.5
Neighbor list builds = 845
Dangerous builds = 0
#unfix 2

write_restart equil.restart2
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