Dear all,
Recently, I fitted a ADP potential by using a large DFT dataset. The energy of all structures consistent very well with the DFT value (average loss: 0.006 eV/structure).
After compiling this potential into lammps, I used this potential to do simulation. It can predict the Fe lattice constant well. However, the relaxing simulation is not good. The pressure along all three directions slowly become large which corresponds to box expansion and then simulation is broken.
Please have a look on the input file and log.lammps.
Thanks.
echo both
processors 1 1 1
package gpu 1 neigh no
newton off
units metal
atom_style atomic
boundary p p p
timestep 0.001
neighbor 2.0 bin
neigh_modify every 5 delay 5 check yes
variable temperature equal 300
variable datafile string fe_st.dat
#variable datafile string fe.dat
#------------chose potential and minimize energy--------
read_data ${datafile}
pair_style pinn_adp
pair_coeff * * fe_adp_potential_238_129e458.pinn Fe
mass 1 55.845
minimize 1.0e-6 1.0e-6 1000 10000
min_style cg
#-----------------------relaxing------------------------
reset_timestep 0
thermo 1
velocity all create ${temperature} 4928459
fix 1 all npt temp ${temperature} ${temperature} $(100.0*dt) x 0 0 1 y 0 0 1 z 0 0 1
thermo_style custom step temp pe ke lx ly lz press vol pxx pyy pzz
dump 1 all custom 100 relaxing*.FILE id type x y z
dump_modify 1 first yes
dump_modify 1 sort id
run 1000
No protocol specified
LAMMPS (29 Sep 2021)
processors 1 1 1
package gpu 1 neigh no
newton off
units metal
atom_style atomic
boundary p p p
timestep 0.001
neighbor 2.0 bin
neigh_modify every 5 delay 5 check yes
variable temperature equal 300
variable datafile string fe_st.dat
#variable datafile string fe.dat
#------------chose potential and minimize energy--------
read_data ${datafile}
read_data fe_st.dat
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (184.00000 85.659000 112.50000)
1 by 1 by 1 MPI processor grid
reading atoms ...
152880 atoms
read_data CPU = 0.099 seconds
pair_style pinn_adp
pair_coeff * * fe_adp_potential_238_129e458.pinn Fe
MPI_checking.....
number of potentials.......: 0 1
mass 1 55.845
minimize 1.0e-6 1.0e-6 1000 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- GPU package (short-range, long-range and three-body potentials):
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:188)
gpu.cpp.....init 152880 152880 0
--------------------------------------------------------------------------
- Using acceleration for pinn_adp/gpu:
- with 1 proc(s) per device.
- Horizontal vector operations: ENABLED
- Shared memory system: No
--------------------------------------------------------------------------
Device 0: NVIDIA RTX A5000, 64 CUs, 4.6/24 GB, 1.7 GHZ (Mixed Precision)
--------------------------------------------------------------------------
Initializing Device and compiling on process 0...Done.
Initializing Device 0 on core 0...Done.
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.055
ghost atom cutoff = 7.055
binsize = 3.5275, bins = 53 25 32
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair pinn_adp/gpu, perpetual
attributes: full, newton off
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 0
calculate_short_time(ms)....3.789248
calculate_energy(ms)....191.176697
calculate_force(ms)....25.057728
Per MPI rank memory allocation (min/avg/max) = 141.5 | 141.5 | 141.5 Mbytes
Step Temp E_pair E_mol TotEng Press
compute_pressure.240..667145.772261 46836.455189 2741554.265216
0 0 -6.8454996e+08 0 -6.8454996e+08 1040785.5
calculate_short_time(ms)....0.879328
calculate_energy(ms)....177.698822
calculate_force(ms)....24.698977
calculate_short_time(ms)....0.895232
calculate_energy(ms)....175.935486
calculate_force(ms)....26.050400
calculate_short_time(ms)....0.888000
calculate_energy(ms)....178.088959
calculate_force(ms)....23.495136
calculate_short_time(ms)....0.889504
calculate_energy(ms)....173.526016
calculate_force(ms)....24.618080
calculate_short_time(ms)....0.884512
calculate_energy(ms)....177.272827
calculate_force(ms)....24.691839
calculate_short_time(ms)....0.885600
calculate_energy(ms)....177.223679
calculate_force(ms)....22.481888
calculate_short_time(ms)....0.888384
calculate_energy(ms)....174.655487
calculate_force(ms)....24.574207
calculate_short_time(ms)....0.888672
calculate_energy(ms)....174.788605
calculate_force(ms)....22.481407
calculate_short_time(ms)....0.884512
calculate_energy(ms)....174.384125
calculate_force(ms)....23.130848
compute_pressure.240..59412.842566 56999.912303 60784.171386 (this is virial force: virial[0], virial[1], virial[2])
6 0 -6.8487667e+08 0 -6.8487667e+08 53370.582
Loop time of 1.90279 on 1 procs for 6 steps with 152880 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-684549956.656995 -684876432.248793 -684876668.74023
Force two-norm initial, final = 78245.649 71.623334
Force max component initial, final = 1221.0045 0.99900012
Final line search alpha, max atom move = 0.037349021 0.037311677
Iterations, force evaluations = 6 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8635 | 1.8635 | 1.8635 | 0.0 | 97.94
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0025246 | 0.0025246 | 0.0025246 | 0.0 | 0.13
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 2.7e-06 | 2.7e-06 | 2.7e-06 | 0.0 | 0.00
Other | | 0.03673 | | | 1.93
Nlocal: 152880.0 ave 152880 max 152880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 60846.0 ave 60846 max 60846 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.06897e+07 ave 2.06897e+07 max 2.06897e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 20689740
Ave neighs/atom = 135.33320
Neighbor list builds = 0
Dangerous builds = 0
min_style cg
#-----------------------relaxing------------------------
reset_timestep 0
thermo 1
velocity all create ${temperature} 4928459
velocity all create 300 4928459
fix 1 all npt temp ${temperature} ${temperature} $(100.0*dt) x 0 0 1 y 0 0 1 z 0 0 1
fix 1 all npt temp 300 ${temperature} $(100.0*dt) x 0 0 1 y 0 0 1 z 0 0 1
fix 1 all npt temp 300 300 $(100.0*dt) x 0 0 1 y 0 0 1 z 0 0 1
fix 1 all npt temp 300 300 0.10000000000000000555 x 0 0 1 y 0 0 1 z 0 0 1
thermo_style custom step temp pe ke lx ly lz press vol pxx pyy pzz
dump 1 all custom 100 relaxing*.FILE id type x y z
dump_modify 1 first yes
dump_modify 1 sort id
run 1000
gpu.cpp.....init 152880 152880 0
---------------------------------------------------------------------
Device Time Info (average):
---------------------------------------------------------------------
Data Transfer: 0.0231 s.
Neighbor copy: 0.0371 s.
Neighbor unpack: 0.0000 s.
Force calc: 2.0096 s.
Device Overhead: 0.0004 s.
Average split: 1.0000.
Lanes / atom: 4.
Vector width: 32.
Max Mem / Proc: 131.56 MB.
CPU Cast/Pack: 0.0159 s.
CPU Driver_Time: 0.0001 s.
CPU Idle_Time: 0.0073 s.
---------------------------------------------------------------------
--------------------------------------------------------------------------
- Using acceleration for pinn_adp/gpu:
- with 1 proc(s) per device.
- Horizontal vector operations: ENABLED
- Shared memory system: No
--------------------------------------------------------------------------
Device 0: NVIDIA RTX A5000, 64 CUs, 4.4/24 GB, 1.7 GHZ (Mixed Precision)
--------------------------------------------------------------------------
Initializing Device and compiling on process 0...Done.
Initializing Device 0 on core 0...Done.
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
calculate_short_time(ms)....1.313824
calculate_energy(ms)....175.074310
calculate_force(ms)....24.644833
Per MPI rank memory allocation (min/avg/max) = 151.8 | 151.8 | 151.8 Mbytes
Step Temp PotEng KinEng Lx Ly Lz Press Volume Pxx Pyy Pzz
compute_pressure.240..59412.840600 56999.909925 60784.169052
0 300 -6.8487667e+08 5928.3485 184 85.659 112.5 56941.742 1773141.3 57256.698 55079.669 58488.858
calculate_short_time(ms)....0.874848
calculate_energy(ms)....175.364090
calculate_force(ms)....23.180767
compute_pressure.240..59436.765517 57019.910836 60817.667433 (this is virial force virial[0], virial[1], virial[2])
1 299.7462 -6.8487666e+08 5923.3332 184.00148 85.659661 112.50092 56960.678 1773183.7 57273.947 55093.265 58514.821
calculate_short_time(ms)....0.882336
calculate_energy(ms)....175.773697
calculate_force(ms)....23.698048
compute_pressure.240..59512.870298 57085.184950 60904.438647
2 298.99206 -6.8487662e+08 5908.4305 184.0059 85.661643 112.50369 57016.325 1773311 57329.719 55138.834 58580.421
calculate_short_time(ms)....0.883616
calculate_energy(ms)....174.519333
calculate_force(ms)....25.145023
compute_pressure.240..59640.796088 57195.419074 61043.846280
3 297.74331 -6.8487656e+08 5883.7537 184.01328 85.664947 112.50829 57108.339 1773523.1 57423.736 55216.144 58685.136
calculate_short_time(ms)....0.885696
calculate_energy(ms)....174.332932
calculate_force(ms)....25.336128
compute_pressure.240..59819.671386 57349.925523 61234.748116 (this is virial force virial[0], virial[1], virial[2])
4 296.0095 -6.8487648e+08 5849.4917 184.02361 85.669571 112.51475 57235.995 1773820.1 57555.294 55324.665 58828.027
calculate_short_time(ms)....0.883072
calculate_energy(ms)....176.412674
calculate_force(ms)....25.343296
compute_pressure.240..60048.257426 57547.767049 61475.581241
5 293.80397 -6.8487638e+08 5805.9078 184.03687 85.67551 112.52304 57398.303 1774201.7 57723.396 55463.686 59007.827
calculate_short_time(ms)....0.880320
calculate_energy(ms)....175.244293
calculate_force(ms)....25.318945
compute_pressure.240..60325.057670 57787.795979 61764.428872
6 291.14369 -6.8487625e+08 5753.3375 184.05304 85.682749 112.53314 57594.074 1774666.8 57926.864 55632.356 59223.002
calculate_short_time(ms)....0.887744
calculate_energy(ms)....175.844345
calculate_force(ms)....25.360607
compute_pressure.240..60648.349991 58068.711874 62099.103656 (this is virial force virial[0], virial[1], virial[2])
7 288.04916 -6.848761e+08 5692.186 184.07206 85.691257 112.54502 57821.991 1775213.8 58164.379 55829.75 59471.844
calculate_short_time(ms)....0.881664
calculate_energy(ms)....174.546951
calculate_force(ms)....26.773504
compute_pressure.240..61016.220097 58389.111431 62477.189794 (this is virial force virial[0], virial[1], virial[2])
8 284.5442 -6.8487594e+08 5622.9239 184.0938 85.700986 112.55861 58080.652 1775839.4 58434.52 56054.92 59752.516
calculate_short_time(ms)....0.890880
calculate_energy(ms)....176.638977
calculate_force(ms)....24.069281
compute_pressure.240..61426.632293 58747.525094 62896.137120 (this is virial force virial[0], virial[1], virial[2])
9 280.65573 -6.8487575e+08 5546.0832 184.11811 85.711861 112.5738 58368.645 1776539.1 58735.842 56306.942 60063.15
calculate_short_time(ms)....0.884352
calculate_energy(ms)....176.113663
calculate_force(ms)....23.096001
compute_pressure.240..61877.477595 59142.451625 63353.289754 (this is virial force virial[0], virial[1], virial[2])
10 276.41349 -6.8487554e+08 5462.2518 184.14476 85.723777 112.59045 58684.588 1777306.1 59066.928 56584.957 60401.88
calculate_short_time(ms)....0.880608
calculate_energy(ms)....175.706116
calculate_force(ms)....25.518623
compute_pressure.240..62366.609438 59572.398607 63845.974918
11 271.8497 -6.8487532e+08 5372.0658 184.17343 85.736598 112.60838 59027.184 1778131.7 59426.427 56888.202 60766.924
calculate_short_time(ms)....0.883776
calculate_energy(ms)....179.087418
calculate_force(ms)....23.293407
compute_pressure.240..62891.843253 60035.897103 64371.563842 (this is virial force virial[0], virial[1], virial[2])
12 266.9986 -6.8487509e+08 5276.2026 184.20378 85.750159 112.62734 59395.236 1779005.5 59813.047 57216.027 61156.634
calculate_short_time(ms)....0.892256
calculate_energy(ms)....178.168839
calculate_force(ms)....23.276960
compute_pressure.240..63450.969258 60531.458912 64927.400541 (this is virial force virial[0], virial[1], virial[2])
13 261.89608 -6.8487483e+08 5175.3708 184.23536 85.764272 112.64709 59787.598 1779915.4 60225.549 57567.836 61569.41
calculate_short_time(ms)....0.884352
calculate_energy(ms)....177.204224
calculate_force(ms)....25.515425
compute_pressure.240..64041.732423 61057.541253 65510.864567 (this is virial force virial[0], virial[1], virial[2])
14 256.57909 -6.8487457e+08 5070.3008 184.26775 85.778737 112.66733 60203.156 1780848.6 60662.708 57943.031 62003.73
calculate_short_time(ms)....0.899808
calculate_energy(ms)....177.029114
calculate_force(ms)....25.580511
compute_pressure.240..64661.744895 61612.526710 66119.306234 (this is virial force virial[0], virial[1], virial[2])
15 251.08516 -6.8487429e+08 4961.7344 184.30051 85.79336 112.6878 60640.734 1781792.5 61123.193 58340.957 62458.053
calculate_short_time(ms)....0.896576
calculate_energy(ms)....175.642624
calculate_force(ms)....25.399937
compute_pressure.240..65308.488695 62194.591806 66749.990205 (this is virial force virial[0], virial[1], virial[2])
16 245.45188 -6.8487401e+08 4850.4143 184.33324 85.807965 112.70826 61099.001 1782735.9 61605.529 58760.751 62930.722
calculate_short_time(ms)....0.889376
calculate_energy(ms)....177.623108
calculate_force(ms)....23.269793
compute_pressure.240..65979.207836 62801.717934 67400.092525 (this is virial force virial[0], virial[1], virial[2])
17 239.71642 -6.8487371e+08 4737.0749 184.36563 85.822412 112.72851 61576.401 1783669.7 62107.966 59201.312 63419.925
calculate_short_time(ms)....0.893280
calculate_energy(ms)....175.901703
calculate_force(ms)....23.888384
compute_pressure.240..66670.952277 63431.635166 68066.641180 (this is virial force virial[0], virial[1], virial[2])
18 233.91507 -6.8487341e+08 4622.4336 184.39747 85.836605 112.7484 62071.107 1784587.6 62628.486 59661.226 63923.608
calculate_short_time(ms)....0.897216
calculate_energy(ms)....176.110596
calculate_force(ms)....25.369921
ERROR: Non-numeric pressure - simulation unstable (../fix_nh.cpp:1069)
Last command: run 1000
Cuda driver error 4 in call at file 'geryon/nvd_timer.h' in line 98.
Cuda driver error 4 in call at file 'geryon/nvd_timer.h' in line 99.
Cuda driver error 4 in call at file 'geryon/nvd_timer.h' in line 98.
Cuda driver error 4 in call at file 'geryon/nvd_timer.h' in line 99.
Cuda driver error 4 in call at file 'geryon/nvd_timer.h' in line 98.
Cuda driver error 4 in call at file 'geryon/nvd_timer.h' in line 99.
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[7971,1],0]
Exit code: 1
Kind regards,
Meng Zhang