I am facing a problem while using the dump cfg option during a NEB run.
Although everything is working fine and LAMMPS is dumping the files at the specified timesteps, some of the dump files are not properly written during the run.
When I manually check the erroneous dump files, I can see that some garbage data is being written in some lines.
I think this is a bug with LAMMPS itself. If not any help would be appreciated.
Regards,
Subham Mridha
I am facing a problem while using the dump cfg option during a NEB run.
Although everything is working fine and LAMMPS is dumping the files at the specified timesteps, some of the dump files are not properly written during the run.
When I manually check the erroneous dump files, I can see that some garbage data is being written in some lines.
I think this is a bug with LAMMPS itself. If not any help would be appreciated.
How should anybody give any help based on such a vague and incomplete description?
Most likely, there is an error on your side. It usually is the safest assumption unless you can provide convincing evidence to the contrary.
Axel
Sorry, my mistake.
Below is my input file for the NEB run
clear
units metal
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify check yes
atom_style atomic
atom_modify map hash sort 0 0.0 #important to convert it to hash for NEB and sorting is to be turned off
variable etol equal 1.0e-15
variable ftol equal 1.0e-15
variable maxiter equal 20000
variable maxeval equal 20000
#variable a equal 4.06
variable a equal 4.0486702
#read_data data.alMg
lattice fcc $a
region bulk block 0 5 0 5 0 5 units lattice
region vac sphere 1.5 1.5 1.0 0.1 units lattice
create_box 1 bulk
#lattice fcc 4.04958 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
create_atoms 1 region bulk #inserts Al atoms to the bulk_al region
delete_atoms region vac compress no
group all type 1
group diffatom id 149
#Define interatomic potentials
pair_style eam/alloy
pair_coeff * * …/…/potentials/Al99.eam.alloy Al
timestep 0.001
reset_timestep 0
compute csym all centro/atom fcc
compute cordn all coord/atom 3.0
compute eng all pe/atom
compute eatoms all reduce sum c_eng
#compute eng1 diffatom reduce c_eng
#----compute stress on the diffusing atom
compute patom all stress/atom
#------------Configure output data-----------------
thermo 1000
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms
dump 1 all cfg 1000 dump.alneb.*.cfg mass type xs ys zs c_csym c_cordn c_eng
dump_modify 1 element Al
#-----------Run----------------------------------
fix 5 all neb 30.0
min_style fire
neb {etol} {ftol} {maxiter} {maxeval} 100 final FinalConfig.txt
print “All done!”
Now, the first two dump files at step 0 and 2000 are OK.
But, the later dump files show errors. snapshot of the erroneous regions are below.
dumpfile@…4887… (lines 1511-1515)
Al
0.899989 0.800009 0.900295 4.07896e-05 12 -3.35606 499
0.900294 4.05258e-05 12 -3.35606 499
Al
dumpfile@…4888… (lines 1393-end)
Al
0.899948 0.399943 0.900163 5.58035e-05 12 -3.35596 45815 0.600139 0.800075 6.00458e-05 12 -3.35629 461
26.982000
Al
0.0998492 0.700192 0.800069 6.13387e-05 12 -3.35639 462
26.982000
Al
0.0997953 0.600195 0.899989 0.000311885 12 -3.35661 463
26.982000
Al
0.999941 0.700059 0.900246 6.56846e-05 12 -3.35615 464
26.982000
Al
0.199802 0.600332 0.799839 0.000305078 12 -3.35654 465
26.982000
Al
0.299976 0.700256 0.800012 0.000158883 12 -3.35533 466
26.982000
Al
0.299985 0.600469 0.899614 0.0024508 12 -3.35257 467
26.982000
Al
0.199936 0.70017 0.900101 0.000185188 12 -3.3563 468
26.982000
Al
0.400078 0.600353 0.799784 0.000443964 12 -3.35584 469
26.982000
Al
0.500095 0.700212 0.800046 9.52304e-05 12 -3.35582 470
26.982000
Al
0.500137 0.60031 0.899824 0.000985783 12 -3.35627 471
26.982000
Al
0.400033 0.700044 0.900193 0.000414783 12 -3.35772 472
26.982000
Al
0.600218 0.600218 0.799986 0.000125929 12 -3.35692 473
26.982000
Al
0.700103 0.700103 0.800128 2.88029e-05 12 -3.35633 474
26.982000
Al
0.700088 0.600053 0.900185 9.30106e-05 12 -3.35615 475
26.982000
Al
0.600053 0.700088 0.900185 9.30106e-05 12 -3.35615 476
26.982000
Al
0.80005 0.600078 0.800139 2.07169e-05 12 -3.35611 477
26.982000
Al
0.899948 0.700077 0.800154 1.79764e-05 12 -3.35622 478
26.982000
Al
0.899965 0.600004 0.900264 5.66167e-05 12 -3.35613 479
26.982000
Al
0.800007 0.700008 0.900282 4.34174e-05 12 -3.3561 480
26.982000
Al
0.999923 0.800059 0.800154 1.77307e-05 12 -3.35623 481
26.982000
Al
0.0999279 0.899971 0.800143 2.0811e-05 12 -3.35609 482
26.982000
Al
0.0999899 0.800056 0.900261 5.75265e-05 12 -3.35616 483
26.982000
Al
0.999999 0.900006 0.900283 4.15976e-05 12 -3.35609 484
26.982000
Al
0.199944 0.800104 0.800123 2.73899e-05 12 -3.35598 485
26.982000
Al
0.299981 0.899959 0.800146 4.80736e-05 12 -3.35664 486
26.982000
Al
0.300019 0.800035 0.900257 0.000154462 12 -3.3562 487
26.982000
Al
0.200029 0.900023 0.900263 0.000100657 12 -3.35569 488
26.982000
Al
0.400019 0.800078 0.800137 4.00636e-05 12 -3.35655 489
26.982000
Al
0.500049 0.899923 0.800129 2.56861e-05 12 -3.35595 490
26.982000
Al
0.49998 0.800018 0.900257 9.58911e-05 12 -3.35587 491
26.982000
Al
0.399974 0.900018 0.900271 0.000174823 12 -3.35616 492
26.982000
Al
0.600078 0.80005 0.800139 2.07169e-05 12 -3.35611 493
26.982000
Al
0.700077 0.899948 0.800154 1.79764e-05 12 -3.35622 494
26.982000
Al
0.700008 0.800007 0.900282 4.34174e-05 12 -3.3561 495
26.982000
Al
0.600004 0.899965 0.900264 5.66167e-05 12 -3.35613 496
26.982000
Al
0.800027 0.800027 0.800167 1.28352e-05 12 -3.35622 497
26.982000
Al
0.899979 0.899979 0.800168 1.23653e-05 12 -3.35622 498
26.982000
Al
0.899992 0.800012 0.900294 4.05228e-05 12 -3.35606 499
35624 498
26.982000
Al
0.899954 0.799952 0.900215 2.14585e-05 12 -3.35618 499
00049 0.800046 0.900214 2.11304e-05 12 -3.35618 499
These are some of the dumpfiles just to show what error is occuring.
Sorry, my mistake.
have you even *looked* at the example files in examples/neb ?
also, have you read about multi-partition runs in the manual?
if not, please do so. if you did, please read them again, and pay
special attention to the explanations for output. what you see, is
what i would expect from multiple partitions trying to (over)write the
same file.
i think we can declare this a non-bug, but rather a user/input problem.
axel.
Right,
I also have a separate line where I do use a loop variable to dump files from separate partitions.
But i did not modify this line.
Extremely sorry for this mistake.
Regards,
Subham
Right,
I also have a separate line where I do use a loop variable to dump files from separate partitions.
But i did not modify this line.
I have no idea what you want to say with these statements.
I have corrected my code.
Following is my corrected code (just the line where dump is issued)
dump 1 all cfg 1000 dump.alneb.*.$u.cfg mass type xs ys zs c_csym c_cordn c_eng id
where $u is a uloop variable.
Now everything is working fine.
Thanks again.
Subham