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[lammps-users] Verify hydrogen bond energy and van der Waals energy using Reax/c potential
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[lammps-users] Verify hydrogen bond energy and van der Waals energy using Reax/c potential


From: George Ray <uraykol12@...24...>
Date: Sat, 1 Jul 2017 09:40:53 -0700

Hello everyone,

I am trying to equilibrate a cellulose molecule (just 2 repeat units) using REAX/c (mattsson) potential in Lammps 14May-2016 version. A similar paper doing this is given here (https://link.springer.com/article/10.1007/s10570-014-0481-2).

My question is with the intermolecular van der waals forces and hydrogen bonding captured in this paper by a standard lj12/6 potential. The paper quotes " The intermolecular potential must describe van der Waals interactions and hydrogen bonding. Because the coarse-grained beads are neutral, electrostatic interactions are not considered. We represent the van der Waals interactions with a 6-12 Lennard-Jones potential"

I also want to capture the vdw and hydrogen bond energy by a standard lj potential. When I am carrying my simulations,the value of epsilon is much much higher. My value of epsilon is coming around 60kcal/mole (~2.4 ev) using the hydrogen bond energy contribution of REAX force field. The value in the existing paper came around 0.1 kcal/mole. This is orders of magnitude higher and made me think of the effectiveness of my results. The sigma value is comparable though (5.04 Angstorm). We can output a separate hydrogen bond energy using Reax, which the existing paper wasn't using, but will this value be so different? Also the vdw forces are much higher (~1900kcal/mole). Can someone please help me understand where I am going wrong?

I am attaching the input files and log files for your understanding.

Thank you so much for your help.

Regards,


Input file

dimension    3
boundary    s s s
units        real

atom_style    full
newton        on

read_data    data.2beads


###SPECIFYING THE POTENTIAL
pair_style reax/c NULL checkqeq yes safezone 16 mincap 1000
pair_coeff * * ffield.reax C H O 
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c

neighbor    2.0 bin
neigh_modify    delay 50 every 10 check yes


###SPECIFYING THE GROUPS
region        1 block -5.0 0.15 -5.0 5.0 -5.0 5.0 units box
region        2 block 0.3 5.0 -5.0 5.0 -5.0 5.0 units box

group bead id <= 42
group bead1 region 1
group bead2 region 2

displace_atoms bead2 move 0.5 0 0 units box

compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]


thermo_style    custom step cpu temp pe evdwl v_eb v_ea v_elp v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew  
thermo        500
thermo_modify flush yes
timestep    0.5 

dump 1 bead1 custom 500 releasedall_equilibrate_bead1.lammpstrj id type x y z 
dump 2 bead2 custom 500 releasedall_equilibrate_bead2.lammpstrj id type x y z 
dump 4 bead custom 500 releasedall_equilibrate_bead.lammpstrj id type x y z


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 2 all nvt temp 300.0 300.0 50
run 50000
unfix 2

write_restart equil.restart1




















Log file

LAMMPS (14 May 2016)
dimension    3
boundary    s s s
units        real

atom_style    full
newton        on

read_data    data.2beads
  orthogonal box = (-5.5 -5.5 -4.5) to (5.5 3 4.5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  42 atoms
  0 = max # of 1-2 neighbors
  0 = max # of 1-3 neighbors
  0 = max # of 1-4 neighbors
  1 = max # of special neighbors


###SPECIFYING THE POTENTIAL
pair_style reax/c NULL checkqeq yes safezone 16 mincap 1000
pair_coeff * * ffield.reax C H O
Reading potential file ffield.reax with DATE: 2010-02-19
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c

neighbor    2.0 bin
neigh_modify    delay 50 every 10 check yes


###SPECIFYING THE GROUPS
region        1 block -5.0 0.15 -5.0 5.0 -5.0 5.0 units box
region        2 block 0.3 5.0 -5.0 5.0 -5.0 5.0 units box

group bead id <= 42
42 atoms in group bead
group bead1 region 1
21 atoms in group bead1
group bead2 region 2
21 atoms in group bead2

displace_atoms bead2 move 0.5 0 0 units box

compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]


thermo_style    custom step cpu temp pe evdwl v_eb v_ea v_elp v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew
thermo        500
thermo_modify flush yes
timestep    0.5

dump 1 bead1 custom 500 releasedall_equilibrate_bead1.lammpstrj id type x y z
dump 2 bead2 custom 500 releasedall_equilibrate_bead2.lammpstrj id type x y z
dump 4 bead custom 500 releasedall_equilibrate_bead.lammpstrj id type x y z


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 = 12
  ghost atom cutoff = 12
  binsize = 6 -> bins = 2 2 1
Memory usage per processor = 18.3661 Mbytes
Step CPU Temp PotEng E_vdwl eb ea elp ev epen ecoa ehb et eco ew 
       0            0            0   -4454.1246   -4213.8495   -6490.7237   -51.936002   0.35154844    82.751806 0.0019810209            0   -23.720825    143.24071   -14.868565    2141.0535 
     200     1.458657            0   -4666.7758   -4431.8118   -6452.1606   -108.23699    7.7570673    59.108315  0.004845264            0   -26.835471    139.09144    -11.93034      1961.39 
Loop time of 1.45871 on 1 procs for 200 steps with 42 atoms

100.0% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = linesearch alpha is zero
  Energy initial, next-to-last, final = 
        -4454.12456652     -4666.77584578      -4666.7758412
  Force two-norm initial, final = 637.489 39.6633
  Force max component initial, final = 200.621 19.0886
  Final line search alpha, max atom move = 1.34355e-11 2.56464e-10
  Iterations, force evaluations = 200 1161

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.256      | 1.256      | 1.256      |   0.0 | 86.10
Bond    | 0.00012946 | 0.00012946 | 0.00012946 |   0.0 |  0.01
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0002327  | 0.0002327  | 0.0002327  |   0.0 |  0.02
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.20001    | 0.20001    | 0.20001    |   0.0 | 13.71
Other   |            | 0.002365   |            |       |  0.16

Nlocal:    42 ave 42 max 42 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:    861 ave 861 max 861 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 861
Ave neighs/atom = 20.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0

velocity all create 300.0 4928459 dist gaussian mom yes rot yes loop local units box



fix 2 all nvt temp 300.0 300.0 50
run 50000
Neighbor list info ...
  2 neighbor list requests
  update every 10 steps, delay 50 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6 -> bins = 2 2 1
Memory usage per processor = 18.3632 Mbytes
Step CPU Temp PotEng E_vdwl eb ea elp ev epen ecoa ehb et eco ew 
     200            0          300   -4666.7758   -4431.8118   -6452.1606   -108.23699    7.7570673    59.108315  0.004845264            0   -26.835471    139.09144    -11.93034      1961.39 
     500   0.36317611     323.2542    -4662.182   -4427.2049   -6441.7365   -113.23341    7.4780197    78.366524 0.0052528189            0   -43.530009    138.19823   -13.208184    1960.4552 
    1000   0.96616006    283.48796   -4666.7537   -4422.1257   -6446.4854   -101.69546    8.5351309    80.359165 0.0055152928            0   -51.670625     139.8173   -12.832566    1961.8412 
    1500    1.5720019    307.49755   -4672.2002   -4436.2856   -6446.6355   -121.12505    9.7128278    70.395459 0.00076852475            0   -46.597139    141.07075   -12.495519    1969.3878 
    2000     2.186136    237.77823    -4661.697   -4421.0459   -6458.8594   -117.14233    10.341593    78.262338 0.0014461823            0   -48.935312    143.74285   -12.743959    1984.2869 
    2500     2.792275     272.3355   -4672.2369   -4432.2035   -6424.7731   -110.63535    7.7859823     67.75178 0.0022189269            0   -41.396089    140.10757   -12.399683    1941.3532 
    3000     3.400897    311.04527   -4676.7499   -4439.5846   -6413.2173   -122.82569    7.3032281    71.451647 0.0013719693            0   -51.262515    136.19205    -12.46477    1945.2374 
    3500     4.005414    382.50013   -4660.7796   -4421.4044   -6454.7646   -118.87805    12.972605    73.422732 0.00074608067            0   -47.341771    141.97555   -11.781952    1982.9904 
    4000    4.6121621    218.15732   -4671.0864    -4430.119   -6440.2244   -107.32237    6.9556748    68.751343  0.013176161            0   -54.046933    135.55931   -15.164716    1975.3599 
    4500    5.2122161    249.42103   -4667.3536   -4430.1878    -6425.201    -121.9831    6.8226577    71.897661 0.0063251844            0   -56.881032    136.52996   -16.209616    1974.8304 
    5000     5.810802    447.06483   -4677.2412   -4436.6968   -6438.0259   -116.55941    7.3390091    70.307999 0.0091528005            0   -51.024153    136.33284   -14.337822    1969.2615 
    5500     6.399256    365.14449    -4663.967   -4424.1497   -6469.8962   -94.477394    11.178061    75.604697  0.013468443            0   -43.718836    132.33195   -14.488287    1979.3029 
    6000     7.006716    254.04552   -4673.5604   -4433.6344   -6450.3514   -103.12012    6.2446992    71.904951  0.016516402            0   -46.895308    135.64911    -15.50543    1968.4225 
    6500     7.600939    254.84014   -4661.3968   -4417.8177   -6426.6769   -112.63709    13.024331    81.440508  0.015354352            0   -44.605388    134.32878   -13.363915    1950.6566 
    7000    8.1967862    252.20353   -4667.1337   -4424.8438   -6482.8153   -89.665875    9.8457546    74.518751 0.0089038252            0   -47.484831    134.64918    -15.06993    1991.1695 
    7500    8.7934701    300.18706   -4678.5068   -4437.8052   -6472.5659   -90.903852    8.6337346     61.04272  0.020427978            0   -47.809284    132.30655    -14.88009    1986.3505 
    8000    9.3986731    354.80271   -4679.5304   -4437.1563   -6425.3101   -113.24685    7.9651094    67.898013  0.015370639            0   -47.448107     135.7288   -14.142366    1951.3838 
    8500    10.008633    305.21399   -4668.2811   -4428.8664   -6432.0423   -96.690961    9.5040805    79.029047  0.018731543            0   -51.200534    134.98104   -14.777476    1942.3119 
    9000    10.627788    264.30105    -4669.467   -4428.2855    -6449.236   -118.04956    8.0629736    63.878951 0.0019929333            0   -49.548623    144.21757   -13.250695    1985.6379 
    9500    11.283511    309.72643   -4672.2073   -4427.3323   -6422.4297   -104.21717    8.1449961    69.450948 0.0084838155            0   -49.603932    129.37202   -12.931834    1954.8739 
   10000     11.91096     270.5621   -4675.5808   -4434.5341   -6411.7198   -120.20886    7.3730281    71.616638 0.0055713649            0   -48.388533    136.68323   -14.923703    1945.0283 
   10500    12.657229    309.56492   -4671.4943   -4431.6203   -6393.1093   -127.64395     7.835846    63.919598 0.0042727812            0   -49.637124      134.881   -14.486522    1946.6158 
   11000    13.333863    334.75335   -4666.4676   -4421.3347   -6473.0778   -97.497699    8.3885144    70.332957 0.0047385263            0   -47.860858    136.66197   -14.364335    1996.0778 
   11500    14.050043    324.02692   -4665.5144   -4423.9741   -6433.2646   -110.98781    8.0182989     73.20362 0.0028132656            0   -46.575595    133.69621   -13.398191    1965.3312 
   12000    14.820009    232.23824   -4651.8505    -4409.162   -6440.1569   -91.225033    8.4049553    68.844392 0.0057924746            0   -44.284591     137.2523   -14.113406    1966.1105 
   12500    15.507524    238.00269   -4669.3157   -4426.9981   -6465.8494   -98.910946    7.9484254    74.480771 0.0046441628            0    -51.53376    131.28505   -14.294679    1989.8718 
   13000    16.207219    304.64951   -4675.2571   -4429.9984   -6475.1386   -105.96349    7.7219976    72.825091 0.0058719818            0   -50.360024    133.77808   -14.791298     2001.924 
   13500     16.83668    376.25528   -4665.1261   -4423.8419   -6424.4238   -110.36635    9.2131175    73.543021 0.0049746001            0   -49.890816     138.6477   -14.728476    1954.1587 
   14000     17.49331    281.18422   -4653.9004   -4414.6704   -6455.9753   -109.87762    10.155821    84.014603 0.0066392658            0   -46.578176     138.7477   -15.084262    1979.9202 
   14500     18.10469    301.32142   -4677.0219   -4434.2567   -6449.9135   -115.13201    7.7770663    67.903144 0.0037633791            0   -51.659748    134.11537   -14.847607    1987.4968 
   15000    18.707863    345.54337   -4675.9691   -4433.1078   -6452.6607   -102.06548    12.588749    72.163541 0.0021293738            0   -48.352579    134.50961   -14.004535    1964.7114 
   15500    19.328893    304.80933   -4672.6864   -4429.2357   -6483.9017    -86.28655    13.778485    71.310584 0.0058618519            0   -54.661672    134.48238   -13.881098     1989.918 
   16000    19.935807    276.16463   -4673.6807   -4434.6725   -6435.5793   -96.395703    7.6322007    67.820975 0.0036624122            0   -49.333142    136.05185   -15.651977    1950.7789 
   16500    20.530683    266.46372   -4662.1253   -4422.1123   -6472.9414   -87.387624    11.587381    81.376696 0.0048796028            0   -49.980651    130.14808   -14.622447    1979.7028 
   17000    21.124628    266.47447    -4665.393   -4422.8076   -6439.9614   -115.93127    7.1538329    67.654139 0.0029389347            0   -52.857895    137.64762   -14.018006    1987.5025 
   17500    21.742838     297.1702   -4672.2894   -4430.9158   -6454.3944   -105.31804    7.9634401     69.22603 0.0071449684            0   -51.006462    139.86772   -15.247196     1977.986 
   18000    22.338851    249.78956   -4671.3469   -4429.7132    -6438.115    -99.95556    6.9980161     65.29701 0.0069006993            0   -48.105734    133.26749   -14.800273    1965.6939 
   18500    22.929616    335.80836   -4671.8735   -4430.6617    -6476.701   -101.17437    5.6441968    71.506505  0.011900272            0    -47.48733    136.60283   -15.589459     1996.525 
   19000    23.540888    326.48628    -4668.364   -4427.5846   -6407.7726   -125.43989    12.155422    72.601615 0.0014053976            0   -47.731942    140.43306   -14.067994    1942.2363 
   19500    24.147696    305.08079    -4668.725   -4427.5335   -6405.3324   -117.29129    7.9936113    67.066608 0.00076770689            0   -46.992531    141.21285   -13.427582    1939.2364 
   20000    24.755297    265.37632   -4668.6361   -4425.6148   -6425.0032   -109.51106     6.648713    77.273494 0.0050588697            0   -49.744291    133.65802   -14.309926    1955.3684 
   20500    25.364733    283.37606   -4676.0218   -4433.1587   -6476.9416   -106.87077    7.3043857    66.704058 0.0070381867            0    -53.67835    137.03182   -15.257565    2008.5422 
   21000    25.961028    342.40585    -4689.364   -4447.8546   -6429.1595   -119.18842    6.5464587    59.909589 0.0036341212            0    -50.71205    137.23531   -15.230033    1962.7404 
   21500     26.55605    309.11524    -4673.889   -4430.6937   -6429.5635   -111.40124    7.0913235    73.319613 0.0032137026            0   -47.089051    134.21112   -13.481107    1956.2159 
   22000    27.156069    264.19694   -4664.0884   -4420.6736   -6491.9192   -91.967802    14.375805    75.766671 0.0042248002            0   -45.911149    140.05993   -13.462874    1992.3808 
   22500    27.752653    280.32673   -4670.7211   -4427.6207   -6436.7259   -111.48583    11.289399    79.461515 0.0075422257            0   -44.986063    136.70526   -13.847624     1951.961 
   23000    28.347034    355.64714   -4678.4751   -4435.6679   -6418.0962   -111.54352    7.0614895    66.985261  0.010043492            0   -48.682993    132.00597   -14.203365    1950.7954 
   23500    29.008307    286.02865   -4673.4438   -4430.8535   -6421.1525   -114.00535    6.8605905     66.43517 0.0020256278            0   -48.806696    130.19416   -13.041757    1962.6609 
   24000    29.636043    290.06429   -4662.9862   -4420.6601   -6403.5054   -114.67804    7.1025459     66.88858 0.0051873089            0   -48.662613    139.18381   -14.001759    1947.0076 
   24500    30.250597    271.19785   -4671.5481   -4427.5645   -6462.1612   -107.45502    6.0322071    72.599142 0.0036957232            0   -48.029737    133.62682   -14.063582    1991.8832 
   25000    30.858949    254.87279   -4673.9414   -4432.9992   -6438.6889   -106.53016    9.4629217    68.615782  0.004414856            0   -46.912925    135.53254   -14.241332    1959.7585 
   25500    31.458123    273.69875   -4671.3119   -4429.5541   -6458.5066   -99.845768    11.003261    71.996839 0.0028491166            0   -48.229017    134.21233   -15.388691    1975.2006 
   26000    32.051169    298.78978    -4670.631    -4429.012   -6459.3658   -96.558216    7.2401153    67.587245 0.0071988555            0   -51.181443    144.45602   -15.145888    1973.9488 
   26500     32.68374    380.88809   -4666.1929   -4423.1702   -6458.9516   -120.44174    12.911379    76.176741 0.0013641711            0    -48.25675    141.76892   -13.062802    1986.6842 
   27000    33.297435    252.18373    -4667.961   -4425.8605   -6390.6826   -137.50835     6.699015    72.556787 0.0025327541            0   -50.117205    137.38981   -14.068971    1949.8685 
   27500     33.89825    270.32346   -4668.8299   -4423.9545   -6501.2967   -94.080395    7.9800115    76.250755 0.0052510447            0   -54.868083    142.33474   -15.438977    2015.1588 
   28000    34.509532    317.93381   -4663.7077   -4422.1039   -6423.4323   -89.093245    7.8423254    73.252601 0.0032047345            0   -49.972405    135.14976   -14.470496    1938.6166 
   28500    35.139705    358.09126   -4663.8437    -4420.373   -6476.9319   -89.559616    12.891187     72.95369 0.00059081796            0   -51.137986    141.64204   -12.068371    1981.8374 
   29000    35.742638    272.46798    -4666.133   -4426.4687   -6356.3008    -136.9559    7.3690309    70.477606  0.001548969            0   -53.638793    137.76334   -13.449158    1918.2644 
   29500    36.358421    324.91838    -4668.796   -4426.3511   -6434.5399   -109.40426    7.5652199     70.92383 0.0020375482            0    -50.26535    140.98375   -13.728149    1962.1117 
   30000    36.980087    293.97952   -4669.6499   -4429.4566   -6448.2161    -92.57712    11.514179    69.314476 0.00074638476            0   -49.894518    141.72008   -12.372062    1951.0537 
   30500     37.59557    321.74253   -4677.6184   -4437.3994   -6381.6868   -141.31541    7.2203339    64.165628 0.0006765648            0   -51.967298    137.76262   -13.075487    1941.4963 
   31000     38.20494    250.81325   -4675.2874   -4433.9261   -6425.5521   -135.90373    10.736951    68.242819   0.00118426            0   -52.070255    138.78988   -12.697277    1974.5265 
   31500    38.808455    267.48194   -4666.5381   -4427.0706     -6433.95   -101.43996    8.0179122    72.619167 0.00097540886            0   -46.592501    136.59533   -13.752201    1951.4307 
   32000    39.413871     321.8419   -4677.0375   -4436.7649   -6426.0985   -95.476367    11.835755    66.809035 0.0012453649            0   -48.546818    139.65068   -13.309707    1928.3698 
   32500    40.010014    232.61716   -4675.1019   -4432.7768   -6419.3122   -118.96964    7.4846632    70.508415 0.0026147793            0    -51.54851    131.43781   -13.394282    1961.0143 
   33000    40.625978    333.70647   -4683.0873   -4443.2139   -6405.0781   -142.67827    6.8957756     61.73504 0.0012141119            0   -52.998953    136.54347   -12.909203    1965.2751 
   33500    41.268639    290.26701   -4671.8834   -4429.9453   -6429.8053   -130.16489    7.7283114    64.186439 0.0016726485            0   -52.651803    143.50168   -13.491636    1980.7502 
   34000    41.881919    330.49029   -4673.2174   -4429.6418   -6429.2457   -132.12901    7.1258314    70.396845 0.0011541538            0   -47.042208    136.00461   -13.692985    1978.9397 
   34500    42.492572    303.16602   -4666.1014   -4425.1375   -6388.7303   -124.34046    12.463561    75.142116 0.0048355099            0   -47.045652    133.23979   -13.946993    1928.0756 
   35000    43.089272    250.75027   -4665.2823   -4423.6054   -6455.3198   -114.72855    6.1996533    81.001055 0.0051318413            0   -53.208763     138.4859   -15.136306    1989.0963 
   35500    43.676489     296.9642   -4682.5296   -4439.4256    -6455.257   -108.30881    7.2930085    62.437093   0.00579283            0   -52.600421    132.92783   -14.949363    1989.0262 
   36000    44.273447    282.92222   -4677.3579    -4436.052    -6406.244   -111.03659    7.8062974    63.223409 0.0024725189            0   -50.993981     130.7158   -14.157305    1944.6319 
   36500    44.873022    318.32383   -4666.5958   -4425.3772   -6417.9155    -106.1285    8.7661577    73.091087 0.0022717735            0   -50.800196    133.59663   -15.447363    1949.4583 
   37000    45.484801    301.70449   -4669.8518   -4428.6563   -6491.9592   -87.105323    16.656185    80.500785 0.0069339287            0   -48.477613    142.33529   -14.339655    1973.7263 
   37500    46.088296    280.64875   -4672.6853   -4430.0235    -6429.884   -102.06626    7.4279578    75.004351 0.0098350429            0   -50.279726    128.50244   -14.387971    1955.6499 
   38000    46.699201    262.99177   -4663.8301   -4422.9468   -6438.6967   -96.394159    7.8988862    71.408122 0.0057491613            0   -52.967525     131.2731   -14.727617    1969.2534 
   38500    47.300592    323.75097   -4661.4149   -4420.9485   -6390.7571   -127.57943    7.3257311    76.823511 0.0029106816            0   -53.956402    132.79494   -14.257567    1948.6549 
   39000    47.919204    337.81744    -4669.358   -4426.9729   -6445.3704   -117.97332    7.6445072    62.778501 0.0013705549            0   -50.526935    136.53983   -13.419336    1993.3529 
   39500    48.529485    305.40629    -4674.893   -4432.7779   -6435.1304   -128.13484    10.309611    70.490719 0.00085550495            0   -49.450808    142.45587   -13.923658    1970.6048 
   40000    49.136645    322.45725     -4675.58   -4433.1517   -6453.5691   -127.27278    7.5730198    73.563466 0.00070299091            0   -51.405075    134.58354   -13.154865    1996.5294 
   40500    49.737637    329.83886   -4667.4369   -4426.2707   -6403.5436   -125.94577    14.298535    76.990904 0.00053184321            0   -51.212462    141.58016   -12.202798    1933.7638 
   41000    50.362683    343.55579    -4671.422   -4429.6311   -6356.3054   -148.53022     7.609246    72.812375 0.0006411695            0   -51.177946    130.97671   -11.853168    1926.8367 
   41500    50.983423    226.61473   -4678.9684   -4438.3604   -6407.4746     -141.322    7.7947815    66.739361 0.00066010327            0   -54.255686    131.99245   -13.471163    1971.6358 
   42000    51.616973    311.20195   -4672.4712     -4431.65   -6437.3957   -120.29504    10.365529    66.027178  0.001718793            0   -51.537517    148.86432   -13.961145    1966.2807 
   42500    52.227666    318.65404   -4667.4785    -4424.023   -6442.0229   -118.94511    7.1778901    66.505635 0.00091736675            0   -52.464399    132.42095   -13.374601    1996.6786 
   43000    52.833757    265.92946   -4669.2405   -4427.3198    -6406.559   -132.04351    7.4451324     77.28799 0.00066757138            0   -51.011462    131.99759   -12.443307    1958.0061 
   43500    53.442778    321.97282    -4680.711   -4439.3286   -6424.7375   -127.96692    6.6477422    68.032297 0.0010231182            0    -53.81541    137.56401   -12.944112    1967.8902 
   44000    54.034851    292.88229   -4673.1544   -4433.6339   -6394.0064   -100.05837     7.819124    67.670546  0.004710989            0   -51.049227    134.79384   -14.987755    1916.1797 
   44500     54.63396    309.91585   -4671.9476   -4428.7187    -6463.038   -77.192515    10.045269    75.405551 0.0091357509            0    -50.75105    129.19123   -14.546029    1962.1577 
   45000    55.228883    315.72297   -4673.0496   -4430.8719   -6420.6316    -116.2018     7.148619    69.742576 0.0084056345            0   -50.000533     138.2504   -15.028886    1955.8409 
   45500    55.838865    229.63075   -4674.2379   -4434.4033   -6399.5417   -125.52209    7.3138994    62.034067 0.0012887121            0   -51.540424     137.4968   -13.793282    1949.1482 
   46000    56.451767    274.31744   -4672.6817   -4431.7477   -6439.0119   -114.69425    8.4614396    78.111574 0.0011410495            0   -50.626965    138.24412    -13.20372    1960.9708 
   46500    57.062798    312.63292   -4674.8573   -4433.1243    -6384.821   -137.69982    6.8313325    67.927697 0.0008518875            0   -51.072082    138.94484   -12.363228    1939.1272 
   47000    57.667273    233.33805   -4668.2846   -4425.2917   -6446.5803   -108.00385    13.048232    76.086543 0.00074676044            0   -50.267754    138.19296   -13.882984    1966.1148 
   47500    58.285003    277.78081    -4671.933   -4430.5359     -6447.49    -110.9793    9.3979368    67.630284 0.0012909062            0   -49.433449    140.26144   -13.182817    1973.2588 
   48000     58.88841     300.3376    -4662.269   -4419.6027   -6450.9972   -124.06051    11.550887    75.642969 0.00086354455            0   -50.074557    138.80074   -12.260885     1991.795 
   48500    59.495306    366.70782   -4668.7668   -4427.5419   -6439.8235   -116.76496    9.8234848       67.894 0.0007849912            0    -47.26334     138.5984   -13.070721     1973.064 
   49000    60.093332    282.32561   -4668.2126   -4427.4247     -6411.62   -120.44109    8.0641556    68.194399 0.00088662265            0   -51.024083    139.72044    -13.31416    1952.9948 
   49500    60.697442    262.06579   -4666.1614   -4424.6156   -6399.6924   -128.18004    8.5691116    74.328957 0.00092856928            0   -52.129837    135.54682   -13.226218    1950.1671 
   50000     61.29713    307.88338   -4669.9599   -4428.6023   -6445.3603   -114.52487    8.2044566    75.948174 0.0010269855            0   -47.352983    140.68024   -12.822521    1966.6245 
   50200    61.543509    263.18501   -4664.4908   -4420.7628   -6440.1946   -114.06089    7.0979636    73.897433 0.0056866387            0   -48.857294    141.65395   -14.928077    1974.6231 
Loop time of 61.5436 on 1 procs for 50000 steps with 42 atoms

Performance: 35.097 ns/day, 0.684 hours/ns, 812.432 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 54.491     | 54.491     | 54.491     |  -nan | 88.54
Bond    | 0.0061998  | 0.0061998  | 0.0061998  |   0.0 |  0.01
Neigh   | 0.0059302  | 0.0059302  | 0.0059302  |   0.0 |  0.01
Comm    | 0.011688   | 0.011688   | 0.011688   |   0.0 |  0.02
Output  | 0.022183   | 0.022183   | 0.022183   |   0.0 |  0.04
Modify  | 6.9766     | 6.9766     | 6.9766     |   0.0 | 11.34
Other   |            | 0.02974    |            |       |  0.05

Nlocal:    42 ave 42 max 42 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:    861 ave 861 max 861 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 861
Ave neighs/atom = 20.5
Ave special neighs/atom = 0
Neighbor list builds = 177
Dangerous builds = 14
unfix 2

write_restart equil.restart1

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:01:03