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!