Error while using fix thermal/conductivity command using Lammps MARCH 21 version

LAMMPS LAMMPS Beginners
1

Hello,

I am trying to compute the thermal conductivity of a polymer composite using fix thermal/conductivity command. The command runs like this:

fix thermal all thermal/conductivity 300 z 100
thermo_style custom step temp pe ke etotal press lx ly lz f_thermal
run 7000000

The simulation is running as I see from the trajectory file but the value of f_thermal is 0. I am pasting the input and log files below. Also, uploading the relevant files.

The simulation box length is ~40 nm in Z direction and there are periodic boundary conditions all around. Can you please help me with this?

Thank you so much.

restart.AfterEquilibration-2 (5.0 MB)
INPUT FILE
read_restart restart.AfterEquilibration-2
pair_style reax/c NULL checkqeq yes safezone 16 mincap 1000
pair_coeff * * HCONSB.ff C H O B N
fix 7 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

variable t equal 15000
thermo $t

dump 1 all custom 500 hybrid.lammpstrj id type x y z

reset_timestep 0

fix NVT all nvt temp 300.0 300.0 0.1

compute ke all ke/atom
variable temperature atom c_ke/(1.5*8.617e-5)

fix thermal all thermal/conductivity 300 z 100
thermo_style custom step temp pe ke etotal press lx ly lz f_thermal
run 7000000

write_restart equil.restart3

compute cc1 all chunk/atom bin/1d z lower 3 units box
fix TEP all ave/chunk 1 100 100 cc1 v_temperature file temp.hybrid_thermal
run 1000000
write_restart equil.restart4

LOG FILE

LAMMPS (10 Mar 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
Reading restart file …
restart file = 10 Mar 2021, LAMMPS = 10 Mar 2021
restoring atom style full from restart
orthogonal box = (-11.925711 -12.270832 -2.1317216) to (11.925711 16.270832 809.13172)
1 by 2 by 30 MPI processor grid
pair style reax/c stores no restart info
38432 atoms
Finding 1-2 1-3 1-4 neighbors …
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.086 seconds
read_restart CPU = 0.225 seconds

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

  • pair reax/c command:
  • fix qeq/reax command:
    The log file lists these citations in BibTeX format.

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Neighbor list info …
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 = 4 5 136
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Setting up Verlet run …
Unit style : real
Current step : 0
Time step : 0.5
Per MPI rank memory allocation (min/avg/max) = 1462.0 | 1572.0 | 1680.0 Mbytes
Step Temp PotEng KinEng TotEng Press Lx Ly Lz f_thermal
0 299.47419 -4966357.4 34306.419 -4932051 1842.0198 23.851422 28.541664 811.26344 0
15000 0 -5001062 0 -5001062 -51.197548 23.851422 28.541664 811.26344 0
30000 0 -5001670 0 -5001670 -341.36846 23.851422 28.541664 811.26344 0
in.thermal (3.2 KB)
ffield.reax (16.7 KB)
restart.AfterEquilibration-2 (5.0 MB)

2

Here, the thermal conductivity is calculated in the z direction. At the end, the job stops with this error:

Per MPI rank memory allocation (min/avg/max) = 1462.0 | 1572.0 | 1680.0 Mbytes
Step Temp PotEng KinEng TotEng Press Lx Ly Lz f_thermal
0 299.47419 -4966357.4 34306.419 -4932051 1842.0198 23.851422 28.541664 811.26344 0
15000 0 -5001062 0 -5001062 -51.197548 23.851422 28.541664 811.26344 0
30000 0 -5001670 0 -5001670 -341.36846 23.851422 28.541664 811.26344 0
ERROR on proc 59: step40649-hbondchk failed: H=0 end(H)=29 str(H+1)=25

3

If you search through the archives with those two keywords (or use google), you should find multiple recommendations for workarounds for this issue.

The origin is that plain ReaxFF implementation in LAMMPS has heuristic based fixed size buffers for bonded interaction data. When the system changes significantly, those buffer sizes may be wrong. This is likely enhanced by the number of parallel processes, as for smaller sub-domains, changes have a relative larger impact.

1 Like
4

Try using the Kokkos version of ReaxFF, it is much more memory robust and should never encounter these types of errors (unless you truly exceed the total system RAM).

1 Like
5

Hello,

Thank you so much for both of your reply. After that I built LAMMPS with the kokkos package in the cluster I use. Unfortunaltely, I am still getting this error with a simpler model. I am explaining with the details below.

The LAMMPS version I am using is 23 Jun 2022 - Update 4.

**Output from ./lmp -h is attached and KOKKOS was built.
lmp-h OUTPUT.txt (12.7 KB)

My problem -

Now, I started with a simpler experiment. There are 14 polymeric chains aligned with each other and fixed at the ends. The part which are not fixed are in the “mobile” group used for computation. The thermal conductivity is attempted to be computed along Z direction (length of polymer). There is periodic boundary condition along Z direction and -s boundary condition along X and Y. I am using REAXFF potential and trying to compute the thermal conductivity by the RNEMD (fix thermal/conductivity) method.

An image of the equilibrated structure is attached below.
image

Whenerver, I am issuing a command like this below, there is no compute by the fix
fix NVT mobile nvt temp 300.0 300.0 10
compute ke mobile ke/atom
variable temperature atom c_ke/(1.58.617e-5)*
fix thermal mobile thermal/conductivity 300 z 100
thermo_style custom step temp pe ke etotal press lx ly lz f_thermal
run 7000000

Also attaching the log file below, which shows that the value of f_thermal is always coming to be 0. But the simulation is running and the structure looks stable as in the snapshot posted above. Can you please help me with this?

LOG FILE--------

Currently Loaded Modulefiles:

  1. hpcc/zaratan(default) 3) openmpi/gcc/9.4.0/zen2/4.1.1
  2. gcc/9.4.0(default)
    /cvmfs/hpcsw.umd.edu/spack-software/2022.06.15/linux-rhel8-zen2/gcc-9.4.0/openmpi-4.1.1-hm2fkyfi7d5ggq4hg2xn4dtzf2o5r2rx/bin/mpirun

The library attempted to open the following supporting CUDA libraries,
but each of them failed. CUDA-aware support is disabled.
libcuda.so.1: cannot open shared object file: No such file or directory
libcuda.dylib: cannot open shared object file: No such file or directory
/usr/lib64/libcuda.so.1: cannot open shared object file: No such file or directory
/usr/lib64/libcuda.dylib: cannot open shared object file: No such file or directory
If you are not interested in CUDA-aware support, then run with
–mca opal_warn_on_missing_libcuda 0 to suppress this message. If you are interested
in CUDA-aware support, then try setting LD_LIBRARY_PATH to the location
of libcuda.so.1 to get passed this issue.

Kokkos::OpenMP::initialize WARNING: OMP_PROC_BIND environment variable not set
In general, for best performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads
For best performance with OpenMP 3.1 set OMP_PROC_BIND=true
For unit testing set OMP_PROC_BIND=false
LAMMPS (23 Jun 2022 - Update 4)
KOKKOS mode is enabled (src/KOKKOS/kokkos.cpp:106)
will use up to 0 GPU(s) per node
WARNING: When using a single thread, the Kokkos Serial backend (i.e. Makefile.kokkos_mpi_only) gives better performance than the OpenMP backend (src/KOKKOS/kokkos.cpp:218)
Kokkos::OpenMP::initialize WARNING: OMP_PROC_BIND environment variable not set
In general, for best performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads
For best performance with OpenMP 3.1 set OMP_PROC_BIND=true
For unit testing set OMP_PROC_BIND=false
using 1 OpenMP thread(s) per MPI task
Reading data file …
orthogonal box = (-50.2845 -50.0175 -7.025989) to (60.7155 80.9825 407.101)
2 by 2 by 4 MPI processor grid
reading atoms …
22358 atoms
Finding 1-2 1-3 1-4 neighbors …
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.140 seconds
6384 atoms in group Carbon
10668 atoms in group Hydrogen
5306 atoms in group Oxygen
294 atoms in group leftend
154 atoms in group rightend
448 atoms in group Ends
21910 atoms in group mobile
Displacing atoms …

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

  • pair reaxff command:
  • fix qeq/reaxff command:
    The log file lists these citations in BibTeX format.

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Neighbor list info …
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 = 19 22 70
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c/kk, perpetual
attributes: half, newton off, ghost, kokkos_device
pair build: half/bin/newtoff/ghost/kk/device
stencil: full/ghost/bin/3d
bin: kk/device
(2) fix qeq/reax/kk, perpetual, copy from (1)
attributes: half, newton off, kokkos_device
pair build: copy/kk/device
stencil: none
bin: none
Setting up Verlet run …
Unit style : real
Current step : 0
Time step : 0.5
Per MPI rank memory allocation (min/avg/max) = 17.33 | 18.75 | 20.52 Mbytes
Step CPU Temp Press Volume PotEng E_vdwl v_eb v_ea v_elp v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew Lx Ly Lz Pxx Pyy Pzz
0 0 0 8828.8495 6021820.6 -2379978.3 -2321236.3 -3240461.9 -39378.314 53.658969 82141.52 0.36457227 -18.848419 -394.70039 68960.271 -13192.68 821054.33 111 131 414.12699 -194.18434 11784.645 14896.088
50 3.2412442 472.89605 4361.4346 6021820.6 -2412017.8 -2342064.9 -3343222.3 -95435.014 0.0091842318 91944.846 0.29749198 -83.758785 -480.65672 58796.868 -10319.435 956734.26 111 131 414.12699 7125.4433 1247.8409 4711.0195
Loop time of 3.24144 on 16 procs for 50 steps with 22358 atoms

Performance: 0.666 ns/day, 36.016 hours/ns, 15.425 timesteps/s
99.3% CPU use with 16 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total

Pair | 1.3966 | 1.9591 | 2.5623 | 23.2 | 60.44
Bond | 4.235e-06 | 9.0704e-06 | 1.9638e-05 | 0.0 | 0.00
Neigh | 0.00514 | 0.0065032 | 0.011911 | 1.9 | 0.20
Comm | 0.016386 | 0.6198 | 1.1823 | 41.3 | 19.12
Output | 0.00020707 | 0.00024406 | 0.00031789 | 0.0 | 0.01
Modify | 0.64905 | 0.65508 | 0.65717 | 0.2 | 20.21
Other | | 0.0006688 | | | 0.02

Nlocal: 1397.38 ave 1876 max 978 min
Histogram: 1 3 1 2 3 2 0 1 1 2
Nghost: 2427.38 ave 2968 max 1851 min
Histogram: 2 0 2 2 2 2 2 1 1 2
Neighs: 139229 ave 186670 max 97790 min
Histogram: 1 1 4 1 2 3 1 0 1 2

Total # of neighbors = 2227666
Ave neighs/atom = 99.636193
Ave special neighs/atom = 0
Neighbor list builds = 1
Dangerous builds = 1
WARNING: Using ‘neigh_modify every 1 delay 0 check yes’ setting during minimization (src/min.cpp:187)
Setting up cg/kk style minimization …
Unit style : real
Current step : 50
Per MPI rank memory allocation (min/avg/max) = 18.01 | 19.32 | 20.8 Mbytes
Step CPU Temp Press Volume PotEng E_vdwl v_eb v_ea v_elp v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew Lx Ly Lz Pxx Pyy Pzz
50 0 472.89605 4361.4335 6021820.6 -2412017.8 -2342064.9 -3343222.3 -95435.014 0.0091842318 91944.846 0.29749198 -83.758785 -480.65672 58796.868 -10319.435 956734.26 111 131 414.12699 7125.4406 1247.8407 4711.019
[compute-b7-50.zaratan.umd.edu:1063439] 15 more processes have sent help message help-mpi-common-cuda.txt / dlopen failed
[compute-b7-50.zaratan.umd.edu:1063439] Set MCA parameter “orte_base_help_aggregate” to 0 to see all help / error messages
500 160.48713 472.89605 452.45967 6021820.6 -2467164 -2402519.7 -3279952.5 -109202.33 -2.5752608e-06 83793.361 0.090378073 -59.671075 -518.22963 47526.249 -10590.91 866484.21 111 131 414.12699 202.24285 267.3579 887.77825
552 182.31407 472.89605 441.72687 6021820.6 -2467516 -2402671.3 -3279570.9 -109336.21 -2.5687561e-06 83820.633 0.089701245 -59.278863 -549.36288 47242.741 -10611.802 866392.87 111 131 414.12699 216.04129 264.35128 844.78803
Loop time of 182.314 on 16 procs for 502 steps with 22358 atoms

99.5% CPU use with 16 MPI tasks x 1 OpenMP threads

Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2412017.83510368 -2467516.02200665 -2467516.02176074
Force two-norm initial, final = 16044.011 493.76582
Force max component initial, final = 267.80848 61.144764
Final line search alpha, max atom move = 0.00020443243 0.012499973
Iterations, force evaluations = 502 2618

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total

Pair | 77.515 | 105.71 | 136.42 | 161.9 | 57.98
Bond | 0.00022993 | 0.00041284 | 0.00091056 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.56355 | 31.086 | 59.222 | 297.2 | 17.05
Output | 0.059045 | 0.059053 | 0.059086 | 0.0 | 0.03
Modify | 45.08 | 45.127 | 45.187 | 0.6 | 24.75
Other | | 0.3341 | | | 0.18

Nlocal: 1397.38 ave 1876 max 978 min
Histogram: 1 3 1 2 3 2 0 1 1 2
Nghost: 2427.38 ave 2968 max 1851 min
Histogram: 2 0 2 2 2 2 2 1 1 2
Neighs: 139229 ave 186670 max 97790 min
Histogram: 1 1 4 1 2 3 1 0 1 2

Total # of neighbors = 2227666
Ave neighs/atom = 99.636193
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
System init for write_restart …
Setting up Verlet run …
Unit style : real
Current step : 552
Time step : 0.5
Per MPI rank memory allocation (min/avg/max) = 17.79 | 19.08 | 20.52 Mbytes
Step CPU Temp Press Volume PotEng E_vdwl v_eb v_ea v_elp v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew Lx Ly Lz Pxx Pyy Pzz
552 0 293.98846 351.22054 6021820.6 -2467516 -2402671.3 -3279570.9 -109336.21 -2.5687561e-06 83820.633 0.089701245 -59.278863 -549.36288 47242.741 -10611.802 866392.87 111 131 414.12699 166.64003 155.53647 731.48513
1000 28.857037 293.8783 56.628429 6021820.6 -2454066.1 -2385227.2 -3266904 -112373.27 -4.6739323e-06 91964.198 0.097382092 -64.505944 -2381.1752 50325.62 -10197.807 864403.63 111 131 414.12699 -46.409526 -0.64368165 216.9385
1500 61.32138 294.98119 -72.683825 6021820.6 -2454635.6 -2385611.1 -3267159.9 -112309.67 -4.6339226e-06 93644.801 0.097286942 -66.158802 -2011.2742 48591.268 -10211.998 863911.72 111 131 414.12699 -90.54505 -73.256375 -54.25005
2000 93.954531 292.94402 -88.002495 6021820.6 -2455196.7 -2386196.1 -3266682.3 -112231.54 -4.5739619e-06 94176.388 0.097166855 -66.723477 -1966.59 47487.079 -10212.713 863300.21 111 131 414.12699 -22.119555 5.8568246 -247.74475
2500 126.95164 296.89558 -85.643639 6021820.6 -2455898.1 -2386653.7 -3267451.3 -112090.61 -4.6511661e-06 94064.02 0.096809483 -67.833999 -2077.3809 47335.619 -10223.408 863857.03 111 131 414.12699 -62.134473 38.847607 -233.64405
3000 160.48192 294.2264 -122.90436 6021820.6 -2456326 -2387071.2 -3267820.5 -111827.64 -4.6996283e-06 94017.074 0.098726374 -66.045379 -2077.9106 46962.98 -10251.903 863992.66 111 131 414.12699 -71.054019 11.818622 -309.47767
3500 194.31028 294.06109 -134.60921 6021820.6 -2457285.6 -2387807.5 -3267566.5 -112139.36 -4.7291073e-06 93811.645 0.097725225 -66.126272 -2225.1286 46683.384 -10243.209 863937.67 111 131 414.12699 -41.768468 -59.315772 -302.74338
4000 228.95997 294.23599 -40.740347 6021820.6 -2457555.1 -2387941.9 -3268556.7 -111621.07 -4.683541e-06 93803.315 0.099577611 -66.485962 -2267.128 46548.804 -10274.594 864491.93 111 131 414.12699 57.563251 23.957401 -203.74169
4500 264.32793 290.98896 -89.687102 6021820.6 -2457903.8 -2388306.7 -3267702.9 -111804.48 -4.7286792e-06 93865.774 0.099065418 -67.098987 -2291.7807 46074.877 -10259.677 863878.56 111 131 414.12699 -23.219679 -35.706731 -210.1349
5000 300.36455 293.15896 -91.728048 6021820.6 -2458570.8 -2388725.4 -3268335.5 -111619.2 -4.7366289e-06 93589.966 0.099709156 -66.254085 -2389.4289 46173.069 -10264.263 864186.11 111 131 414.12699 -69.646136 16.236923 -221.77493
5500 337.04904 293.36685 -56.245028 6021820.6 -2458745.5 -2388870.5 -3268205.6 -111631.17 -4.7396857e-06 93880.9 0.099707829 -66.809767 -2433.8268 45828.53 -10262.765 864020.18 111 131 414.12699 22.895986 34.929253 -226.56032
6000 374.21946 295.01512 -106.80537 6021820.6 -2459187.3 -2389243 -3267614 -111867.43 -4.7885297e-06 93675.592 0.099070724 -66.632145 -2512.9341 45698.229 -10259.038 863703.08 111 131 414.12699 -26.76769 -49.345921 -244.3025
6500 411.71482 292.88214 -44.745911 6021820.6 -2459353.7 -2389306.4 -3267912.2 -111560.55 1.0417292e-05 93568.3 0.10013268 -68.644727 -2512.3374 45721.111 -10266.971 863724.74 111 131 414.12699 -4.0570271 37.585979 -167.76668
7000 449.92759 294.59569 -45.636714 6021820.6 -2459760.4 -2389604.5 -3268362.9 -111408.5 -4.6778013e-06 93445.476 0.10090968 -66.215937 -2590.3242 45849.419 -10279.24 863807.67 111 131 414.12699 7.2630146 26.300834 -170.47399
7500 488.57388 294.59494 -14.988278 6021820.6 -2459880.6 -2389714.1 -3268488.2 -111461.26 -4.6711421e-06 93638.918 0.099694711 -65.500546 -2610.2716 45434.846 -10274.594 864111.83 111 131 414.12699 47.266258 37.086672 -129.31776
8000 527.48245 296.09744 -78.703549 6021820.6 -2460157.8 -2389847.9 -3268733.7 -111487.71 1.8459419e-05 93523.824 0.09990421 -66.201218 -2592.0513 45389.254 -10265.797 864384.4 111 131 414.12699 -37.797656 -9.7843521 -188.52864
8500 566.40912 294.30908 -44.264269 6021820.6 -2460453.5 -2390103.1 -3268554.9 -111359.52 0.00019102209 93563.639 0.099957039 -66.816704 -2749.9666 45473.475 -10273.368 863864.27 111 131 414.12699 46.39223 2.5627208 -181.74776
9000 605.95432 292.9753 -56.683407 6021820.6 -2460463.9 -2390137.9 -3268012.4 -111700.74 -4.8275546e-06 93672.634 0.10058048 -65.870698 -2663.9136 45249.582 -10274.257 863656.94 111 131 414.12699 22.360664 4.4644719 -196.87536
9500 646.46054 294.93961 -71.384307 6021820.6 -2460599.2 -2390117.2 -3269117.5 -111368.69 0.0017364977 93691.788 0.10042214 -65.229158 -2719.3601 45383.829 -10281.04 864358.89 111 131 414.12699 -9.2876732 19.055384 -223.92063

 10000   688.39074      295.04625     -61.199027      6021820.6     -2460916.9     -2390411.6     -3268012.4     -111405.49     -4.7928136e-06  93541.96       0.10060033    -66.656757     -2773.4285      45364.277     -10290.322      863230.33      111            131            414.12699     -42.45192       12.68096      -153.82612    
 93500   12183.105      292.65149     -165.17339      6021820.6     -2466332.6     -2393616.9     -3268244.8     -111488.99      7.52835e-06    94125.315      0.10057305    -65.487852     -4147.6679      44119.805     -10275.619      862360.49      111            131            414.12699     -91.737421     -86.149112     -317.63363    
 94000   12261.814      293.06901     -103.91467      6021820.6     -2466103       -2393431.3     -3267978.7     -111380.45      0.0010248413   93922.335      0.10168618    -67.485362     -4116.1487      44239.265     -10285.474      862235.31      111            131            414.12699     -13.364838     -15.496277     -282.8829     
 94500   12340.774      292.92508     -57.682861      6021820.6     -2466329.5     -2393671.2     -3267950.3     -111282.75     -4.9143445e-06  93728.361      0.10228358    -65.618595     -4145.4519      44343.665     -10297.257      861998.12      111            131            414.12699     -6.6345409      10.495906     -176.90995    
 95000   12419.162      291.66753     -64.621737      6021820.6     -2466006       -2393300.7     -3268254.9     -111341.63     -4.9823446e-06  93895.76       0.10248137    -67.860252     -4162.7847      44413.222     -10290.255      862507.68      111            131            414.12699     -1.5792883      18.784212     -211.07013    
 95500   12496.316      291.90056     -121.68537      6021820.6     -2466372.8     -2393689.6     -3267673.7     -111442.81      0.0041056328   93728.802      0.10115168    -65.9251       -4129.073       44299.936     -10285.003      861878.01      111            131            414.12699     -49.77014      -59.301938     -255.98402    
 96000   12573.808      295.56186     -60.255667      6021820.6     -2466236.8     -2393529.3     -3268705       -111121.7       0.0012254607   93723.252      0.10287899    -66.144502     -4104.7748      44416.271     -10299.735      862628.4       111            131            414.12699     -10.599739     -0.33430233    -169.83296    
 96500   12651.339      294.20856     -157.60895      6021820.6     -2466241.5     -2393645.6     -3267791.8     -111483.79      1.0352677e-05  93930.746      0.1008419     -66.030455     -4089.0023      44192.494     -10283.519      861945.28      111            131            414.12699     -72.686984     -74.436534     -325.70333    
 97000   12728.881      294.68983      42.168012      6021820.6     -2466122.9     -2393383.7     -3269206.1     -110765.27      0.00031317334  93813.006      0.10290118    -66.110846     -4114.5207      44442.735     -10307.528      862820.02      111            131            414.12699      159.82452      69.783446     -103.10393    
 97500   12806.22       292.83516     -126.09759      6021820.6     -2465997.8     -2393383.3     -3268133.2     -111324.55      0.00010345185  94060.914      0.10205916    -66.411865     -4093.8484      44280.965     -10285.449      862178.23      111            131            414.12699     -0.28177503    -76.22646      -301.78452    
 98000   12883.587      295.2778      -62.762301      6021820.6     -2466308.9     -2393578.7     -3267760.3     -111415.02      0.00023447357  94050.257      0.10143733    -66.660047     -4151.7936      44213.69      -10284.9        861835.91      111            131            414.12699      21.602924      15.568224     -225.45805    
 98500   12960.246      293.52578     -71.727615      6021820.6     -2466251.6     -2393520.3     -3268215.8     -111221.25     -4.8570346e-06  94024.456      0.10224376    -66.487624     -4144.2457      44288.031     -10296.689      862111.57      111            131            414.12699      42.30513      -50.164368     -207.32361    
 99000   13036.644      295.82687     -162.55076      6021820.6     -2465991.9     -2393299.2     -3267537       -111573.54      0.00063503709  94264.669      0.10216623    -66.23871      -4090.0091      44227.464     -10274.601      861749.95      111            131            414.12699     -45.461948     -125.17241     -317.01793    
 99500   13112.674      295.4157      -27.91636       6021820.6     -2466138.7     -2393465.7     -3268230.6     -111218.48     -4.9497562e-06  93974.093      0.102782      -66.392743     -4118.7615      44224.353     -10292.068      862261.96      111            131            414.12699      45.841217      40.70597      -170.29627    
100000   13188.955      292.79008     -81.393212      6021820.6     -2466408.5     -2393686       -3268443       -111324.95      0.00078575882  93877.631      0.10181618    -67.187041     -4136.5965      44310.745     -10293.458      862390.68      111            131            414.12699      33.797286     -49.382506     -228.59442    
100500   13265.007      295.88343     -68.084446      6021820.6     -2466104.3     -2393407.9     -3268129.6     -111345.51     -4.8412291e-06  94324.884      0.10037727    -66.728911     -4182.1389      44124.13      -10286.867      862153.78      111            131            414.12699      17.683375     -9.3206983     -212.61601    
100552   13272.952      294.86783     -127.09374      6021820.6     -2466401.7     -2393712.8     -3267339.7     -111585.09      0.00046836992  93970.719      0.10175848    -68.157062     -4180.8981      44186.311     -10277.705      861581.59      111            131            414.12699     -38.945025     -31.247571     -311.08863

Loop time of 13273 on 16 procs for 100000 steps with 22358 atoms

Performance: 0.325 ns/day, 73.739 hours/ns, 7.534 timesteps/s
99.5% CPU use with 16 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total

Pair | 4733.7 | 6951.5 | 9115 |1821.8 | 52.37
Bond | 0.0086036 | 0.019122 | 0.044236 | 6.1 | 0.00
Neigh | 17.027 | 21.807 | 27.518 | 81.7 | 0.16
Comm | 715.63 | 3138.8 | 5033.8 |2616.6 | 23.65
Output | 3.1283 | 3.1293 | 3.1371 | 0.1 | 0.02
Modify | 2928.2 | 3156.8 | 3695 | 557.7 | 23.78
Other | | 0.8993 | | | 0.01

Nlocal: 1397.38 ave 2274 max 237 min
Histogram: 1 2 0 1 2 3 1 0 3 3
Nghost: 3568.06 ave 5414 max 2489 min
Histogram: 3 1 4 2 1 3 0 0 1 1
Neighs: 377001 ave 617766 max 86187 min
Histogram: 2 1 1 1 0 5 0 2 3 1

Total # of neighbors = 6032015
Ave neighs/atom = 269.79224
Ave special neighs/atom = 0
Neighbor list builds = 2000
Dangerous builds = 2000
System init for write_restart …
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
Setting up Verlet run …
Unit style : real
Current step : 100552
Time step : 0.5
Per MPI rank memory allocation (min/avg/max) = 26.52 | 31.95 | 39.42 Mbytes
Step Temp PotEng KinEng TotEng Press Lx Ly Lz f_thermal
100552 294.86783 -2466401.7 19650.573 -2446751.1 -127.09328 111 131 414.12699 0
105000 293.25831 -2466232.7 19543.312 -2446689.4 -104.53902 111 131 414.12699 0
120000 292.26325 -2466357.1 19476.999 -2446880.1 -139.52807 111 131 414.12699 0
135000 293.24414 -2466582.9 19542.367 -2447040.6 -62.821061 111 131 414.12699 0

The input files and data files are attached below. Thank you so much for the help.
in.thermal (2.9 KB)
data.hybrid (990.7 KB)
ffield.reax (16.7 KB)

Regards,

6

Also, I have tried this experiment with a single polymer chain in place of a bundle shown above. I got the same error. Please help me solve this. Thank you so much.

7

What error are you getting with the Kokkos version?

8

Hello,

I am not getting any error as such after using the Kokkos version. From what I see from the trajectory, the atoms are evolving with time as expected. When I am consistently getting the compute by the “fix thermal/conductivity” (here f_thermal=0) command to be zero, I am cancelling the experiment.

In details, the commands in the input file are like this:-

fix NVT mobile nvt temp 300.0 300.0 10
compute ke mobile ke/atom
variable temperature atom c_ke/(1.5*8.617e-5)
fix thermal mobile thermal/conductivity 300 z 100
thermo_style custom step temp pe ke etotal press lx ly lz f_thermal
run 7000000

The corresponding output as in the log file is like this:-

Per MPI rank memory allocation (min/avg/max) = 26.52 | 31.95 | 39.42 Mbytes
Step Temp PotEng KinEng TotEng Press Lx Ly Lz f_thermal
100552 294.86783 -2466401.7 19650.573 -2446751.1 -127.09328 111 131 414.12699 0
105000 293.25831 -2466232.7 19543.312 -2446689.4 -104.53902 111 131 414.12699 0
120000 292.26325 -2466357.1 19476.999 -2446880.1 -139.52807 111 131 414.12699 0
135000 293.24414 -2466582.9 19542.367 -2447040.6 -62.821061 111 131 414.12699 0
slurmstepd: error: *** JOB 2760009 ON compute-b7-50 CANCELLED AT 2023-06-25T18:06:37 ***

The error at the end is only because I stopped the experiment.

The relevant input and log files are attached below. Thank you so much in helping me resolve this.

in.thermal (2.9 KB)
slurm-2760009.out (79.8 KB)
data.hybrid (990.7 KB)
ffield.reax (16.7 KB)

9

You’ve fixed the “ends” of your simulation volume, including a group from z=0 to z=9 of your 400 angstrom box.

Your fix thermal/conductivity settings are to swap atoms every 300 steps in the mobile group, dividing the box into 100 bins.

From documentation, the fix works by exchanging momenta and kinetic energies from the first bin to the middle bin.

But there are no mobile atoms in the first bin of the box (0-4 angstrom, which you have defined as a different group and explicitly omitted from integration).

Hence, I am guessing, the fix doesn’t change anything. In my opinion this should be an error or at least a warning, but it’s all there in the documentation for you to check.

Additionally, I can’t see the physical logic in freezing out an entire slice of your polymer and then still trying to calculate a thermal conductivity across it.

1 Like
10

Hello,

Thank you so much for your reply.

Yes, I fixed the “Ends” forming a group from z=0 to z=9.

But when I do the fix thermal/conductivity, I want to exchange momenta and kinetic energies only from the “mobile” group which is not part of “Ends” [group mobile subtract all Ends].

I read the documentation and was under the impression that when I issue the “fix thermal mobile thermal/conductivity 300 z 100” command, the first bin will start (swapping atoms) from the “mobile” group which is not under any constraint.

I agree with you that freezing an entire slice of polymer at the ends might not be a good idea. So I am already running another experiment now unfreezing all. I will update as I get the results of that.

Thank you so much for your time and help.