Hi, everone. I'm using lammps to calculate the thermal conductivity of Mg-MOF-74. I firstly perform NPT, NVT ensemble to get a stable equilibrium, with a total energy fluctuation within 0.5%. Then, when changing into NVE ensemble, the temperature strats to grow gradually at 230000 steps, and an error happened in 1639242 steps due to angle atoms missing.

Here are some details about my input file and log file. Hope anyone can help me or give some suggestions.

minimize 1.0e-4 1.0e-8 100 1000000

neighbor 2 bin

neigh_modify delay 0

variable T equal 300

variable V equal vol

variable dt equal 1

variable p equal 10000

variable s equal 1

variable d equal $p*$s

variable kB equal 1.3806504e-23 #[J/K] Boltzmann

variable kCal12J equal 4186.0/6.02214e23

variable fs2s equal 1.0e-15

variable A2m equal 1.0e-10

variable convert equal ${kCal12J}*${kCal12J}/${fs2s}/${A2m}

thermo $d

thermo_style custom step elapsed time temp pe ke etotal press vol xlo xhi ylo yhi zlo zhi density

thermo_modify flush yes line one

timestep ${dt}

dump dtrj all custom 10000 Mg-MOF-74.lammpstrj id type element x y z

dump dxyz all xyz 10000 Mg-MOF-74.xyz

dump_modify dtrj element O O C H Mg O O O b b b

dump_modify dxyz element O O C H Mg O O O b b b

restart 100000 restart/Mg-MOF-74.restart

velocity all create $T 135790 mom yes rot yes dist gaussian

fix NPT all npt temp 300.0 300.0 100.0 iso 1.0 1.0 100

run 2000000

unfix NPT

fix NVT all nvt temp $T $T 100 drag 0.2

run 2000000

unfix NVT

fix NVE all nve

reset_timestep 0

compute myKE all ke/atom

compute myPE all pe/atom

compute myStress all stress/atom NULL virial

compute flux all heat/flux myKE myPE myStress

fix JJ all ave/correlate $s $p $d &

c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running

variable Jx equal c_flux[1]/vol

variable Jy equal c_flux[2]/vol

variable Jz equal c_flux[3]/vol

variable scale equal ${convert}/${kB}/$T/$T/$V*$s*${dt}

variable k11 equal trap(f_JJ[3])*${scale}

variable k22 equal trap(f_JJ[4])*${scale}

variable k33 equal trap(f_JJ[5])*${scale}

variable kall equal (v_k11+v_k22+v_k33)/3.0

thermo $d

thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 v_kall

restart 100000 restart/Mg-MOF-74.restart

run 2000000

variable k equal (v_k11+v_k22+v_k33)/3.0

variable ndens equal count(all)/vol

print "average conductivity: $k[W/mK] @ $T K "

log:

NPT(last 0.1ns):

Step Elapsed Time Temp PotEng KinEng TotEng Press Volume Xlo Xhi Ylo Yhi Zlo Zhi Density

1900000 1899924 1899924 300.19589 -72370.237 3864.7575 -68505.48 299.43364 61487.115 0.54900172 51.848998 0.47544944 44.902551 0.28871887 27.267281 0.943907

1910000 1909924 1909924 304.39345 -72373.125 3918.7974 -68454.327 569.0023 62045.487 0.47159199 51.926408 0.40841065 44.969589 0.24800925 27.307991 0.93541241

1920000 1919924 1919924 296.47968 -72332.43 3816.9145 -68515.515 -1001.0074 61854.713 0.49798744 51.900013 0.43126978 44.94673 0.26189056 27.294109 0.93829743

1930000 1929924 1929924 300.84356 -72258.982 3873.0957 -68385.886 -532.9097 61938.096 0.48644389 51.911556 0.42127278 44.956727 0.25581984 27.30018 0.93703426

1940000 1939924 1939924 300.69654 -72261.493 3871.2029 -68390.29 1354.783 61796.867 0.50600174 51.891998 0.43821037 44.93979 0.26610527 27.289895 0.93917574

1950000 1949924 1949924 294.40876 -72216.855 3790.2533 -68426.601 -116.07429 61438.444 0.55577131 51.842229 0.48131209 44.896688 0.29227899 27.263721 0.94465475

1960000 1959924 1959924 298.22917 -72236.965 3839.4377 -68397.527 467.83331 61744.472 0.51326511 51.884735 0.44450063 44.933499 0.26992506 27.286075 0.9399727

1970000 1969924 1969924 300.94669 -72282.289 3874.4233 -68407.865 2188.0688 61582.774 0.53570686 51.862293 0.46393576 44.914064 0.28172713 27.274273 0.94244079

1980000 1979924 1979924 299.61245 -72340.45 3857.2463 -68483.204 662.75969 61799.319 0.50566188 51.892338 0.43791604 44.940084 0.26592654 27.290073 0.93913847

1990000 1989924 1989924 298.56203 -72204.753 3843.723 -68361.03 330.52411 61829.602 0.50146577 51.896534 0.43428211 44.943718 0.26371981 27.29228 0.9386785

2000000 1999924 1999924 300.84392 -72332.003 3873.1003 -68458.902 114.02159 61177.299 0.59215519 51.805845 0.51282145 44.865179 0.31141319 27.244587 0.94868716

2000076 2000000 2000000 300.77454 -72260.156 3872.207 -68387.949 -195.10172 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

NVT(last 0.1ns)

3900000 1899924 3899924 303.16078 -72306.041 3902.9278 -68403.113 -2245.6907 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

3910000 1909924 3909924 297.23095 -72357.734 3826.5866 -68531.147 -1626.6059 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

3920000 1919924 3919924 307.35255 -72388.507 3956.8932 -68431.614 1089.8766 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

3930000 1929924 3929924 305.8046 -72358.423 3936.9646 -68421.459 189.14304 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

3940000 1939924 3939924 303.90881 -72381.89 3912.5581 -68469.332 3028.6707 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

3950000 1949924 3949924 304.507 -72381.785 3920.2593 -68461.526 -230.57069 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

3960000 1959924 3959924 301.92666 -72228.085 3887.0397 -68341.045 91.686489 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

3970000 1969924 3969924 304.5679 -72424.318 3921.0433 -68503.275 1519.0109 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

3980000 1979924 3979924 301.65781 -72297.044 3883.5784 -68413.466 -271.48268 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

3990000 1989924 3989924 307.00495 -72360.954 3952.4181 -68408.535 -2521.9574 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

4000000 1999924 3999924 299.67001 -72401.719 3857.9873 -68543.732 -1943.6075 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

4000076 2000000 4000000 302.62485 -72438.022 3896.0282 -68541.994 893.07637 61447.341 0.55453353 51.843466 0.48024013 44.89776 0.29162804 27.264372 0.94451797

NVE(part of it):

Step Temp

0 302.6249

10000 297.02

20000 298.0575

30000 299.9917

40000 300.5121

50000 300.1069

60000 295.1424

70000 301.0109

80000 304.1412

90000 298.6296

100000 306.4158

110000 305.5104

120000 302.2589

130000 302.5609

140000 302.2362

150000 308.1364

160000 300.0563

170000 299.8534

180000 301.2992

190000 300.5985

200000 297.9644

210000 306.8841

220000 301.2316

230000 309.1059

240000 308.7167

250000 308.4066

260000 312.7306

270000 312.1801

280000 309.4838

290000 307.1806

300000 311.2416

310000 309.7554

320000 305.7033

330000 309.8235

340000 306.4184

350000 314.2227

360000 308.5119

370000 309.2281

380000 311.6083

390000 313.6745

400000 310.9765

410000 310.7669

420000 309.8643

430000 311.8931

440000 312.4852

450000 312.7968

460000 308.2947

470000 313.6332

480000 317.9289

490000 316.7104

500000 316.3063

510000 313.6752

520000 314.1453

530000 319.4908

540000 316.4856

550000 315.7817

560000 322.8026

570000 318.0926

580000 321.9529

590000 319.9658

600000 321.1059

610000 317.1512

620000 321.6389

630000 316.6208

640000 327.5142

650000 326.9689

660000 320.0033

670000 318.9957

680000 324.4062

...

1530000 390.3848

1540000 392.2057

1550000 394.7468

1560000 394.4621

1570000 391.4525

1580000 396.4241

1590000 397.9968

1600000 403.3611

1610000 405.7124

1620000 408.3486

1630000 407.2747

and here is the wrong message

ERROR on proc 3: Angle atoms 307 2702 2704 missing on proc 3 at step 1639242 (../ntopo_angle_all.cpp:68)

Last command: run 2000000

any help will be appreciated!

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