Dear all
While I was trying to simulate a single chain polyisoprene being pulled against a graphene layer I got the following error message:
ERROR on proc 14: Angle atoms 314 333 331 missing on proc 14 at step 0 (neigh_bond.cpp:131)
ERROR on proc 10: Angle atoms 356 362 364 missing on proc 10 at step 0 (neigh_bond.cpp:131)
Could you please help me to sort out this error?
The input script, output file and data file are added at the end of the mail.
Yours faithfully
Jeeno Jose
Input script
VARIABLES
variable fname index data.naturalrubbergraphene
variable simname index datarestart_naturalrubbergraphene
Initialization
units real
boundary s s s
atom_style full
log log.{simname}.txt
read_data {fname}
neighbor 5 bin
neigh_modify page 10000000 one 1000000 every 2
dielectric 1.0
potentials
pair_style lj/charmm/coul/charmm 50.0 55.0
pair_coeff 2 2 0.068 3.7239
pair_coeff 2 3 0.068 3.7239
pair_coeff 2 4 0.06171 3.6527
pair_coeff 2 5 0.04878 3.0558
pair_coeff 2 6 0.0459 2.9756
pair_coeff 1 2 1.0 3.0
pair_coeff 3 3 0.068 3.7239
pair_coeff 3 4 0.06171 3.6527
pair_coeff 3 5 0.04878 3.0558
pair_coeff 3 6 0.0459 2.9756
pair_coeff 1 3 1.0 3.0
pair_coeff 4 4 0.056 3.5814
pair_coeff 4 5 0.04427 2.9845
pair_coeff 4 6 0.04166 2.9043
pair_coeff 1 4 1.0 3.0
pair_coeff 5 5 0.035 2.3876
pair_coeff 5 6 0.03294 2.3074
pair_coeff 1 5 0.8 3.7
pair_coeff 6 6 0.031 2.2272
pair_coeff 1 6 0.8 3.7
pair_coeff 1 1 0.0 2.9756
bond_style harmonic
bond_coeff 1 365 1.5020
bond_coeff 2 360 1.1
bond_coeff 3 365 1.5020
bond_coeff 4 0 1.5020
bond_coeff 5 440 1.34
bond_coeff 6 309 1.1110
bond_coeff 7 0 1.5020
bond_coeff 8 0 1.5020
bond_coeff 9 222 1.53
angle_style charmm # U-B term
angle_coeff 1 45 111.5 0 0.0
angle_coeff 2 36 109.0 5 1.802
angle_coeff 3 32 112.2 0 0.0
angle_coeff 4 48 123.5 0 0.0
angle_coeff 5 40 116.0 0 0.0
angle_coeff 6 0 119.5 0 0.0
angle_coeff 7 0 119.5 0 0.0
angle_coeff 8 0 119.5 0 0.0
angle_coeff 9 0 119.5 0 0.0
angle_coeff 10 48 123.5 0 0.0 #
angle_coeff 11 52 119.5 0 0.0 #
angle_coeff 12 32 112.2 0 0.0
angle_coeff 13 0 119.5 0 0.0
angle_coeff 14 0 119.5 0 0.0
angle_coeff 15 0 119.5 0 0.0
angle_coeff 16 35 110.10 22 2.179
angle_coeff 17 0 119.5 0 0.0
angle_coeff 18 0 119.5 0 0.0
angle_coeff 19 48 123.5 0 0.0 #
angle_coeff 20 45 111.5 0 0.0
dihedral_style charmm
dihedral_coeff 1 0.0 3 0 0.2
dihedral_coeff 2 0.19 3 0 0.2
dihedral_coeff 3 0.19 3 0 0.2
dihedral_coeff 4 0.0 3 0 0.2
dihedral_coeff 5 0.0 3 0 0.2
dihedral_coeff 6 0.0 3 0 0.2
dihedral_coeff 7 0.12 3 0 0.2
dihedral_coeff 8 0.22 3 0 0.2
dihedral_coeff 9 0.19 3 0 0.2
dihedral_coeff 10 0.0 3 0 0.2
dihedral_coeff 11 0.0 3 0 0.2
dihedral_coeff 12 0.0 3 0 0.2
dihedral_coeff 13 0.0 3 0 0.2
dihedral_coeff 14 0.0 3 0 0.2
dihedral_coeff 15 0.3 3 180 0.2 #
dihedral_coeff 16 0.17 2 0 0.2 #
dihedral_coeff 17 0.5 1 180 0.2 #
dihedral_coeff 18 0.45 1 180 0.2 #
dihedral_coeff 19 5.2 2 180 0.2 # *
dihedral_coeff 20 0.0 3 0 0.2
dihedral_coeff 21 0.0 3 0 0.2
dihedral_coeff 22 0.0 3 0 0.2
dihedral_coeff 23 0.0 3 0 0.2
dihedral_coeff 24 0.0 3 0 0.2
dihedral_coeff 25 0.0 3 0 0.2
dihedral_coeff 26 0.0 3 0 0.2
dihedral_coeff 27 0.0 3 0 0.2
dihedral_coeff 28 0.0 3 0 0.2
dihedral_coeff 29 0.0 3 0 0.2
dihedral_coeff 30 0.0 3 0 0.2
dihedral_coeff 31 0.1 3 0 0.2 #
dihedral_coeff 32 0.0 3 0 0.2
dihedral_coeff 33 1.3 3 180 0.2 #
dihedral_coeff 34 0.195 3 0 0.2 #
special_bonds charmm
group graphene id > 392
group polymer id < 393
fix rgd graphene move linear 0.0 0.0 0.0 units box
dump 1 all dcd 50 c_naturalrubbersinglechaingraphene.dcd
timestep 0.005
Minimization
thermo_style custom step temp etotal evdwl eangle ebond edihed ecoul eimp lx ly lz vol press
thermo 1
min_style cg
minimize 1e-20 1e-20 500000 1000000
equilibration to 1500 K
velocity polymer create 1500 12318 dist gaussian mom yes
fix 1 polymer nve
timestep 0.005
fix 2 polymer langevin 1500 1500 0.1 904297
thermo_style custom step temp etotal evdwl eangle ebond edihed ecoul eimp lx ly lz vol press
thermo 200
run 1000
unfix 1
unfix 2
equilibration to 300 K
velocity 1 create 300 12318 dist gaussian mom yes
fix 1 polymer nve
timestep 0.005
fix 2 polymer langevin 300 300 0.3 904297
thermo_style custom step temp etotal evdwl eangle ebond edihed ecoul eimp lx ly lz vol press
thermo 200
run 10000
unfix 1
unfix 2
dump_modify 1 every 100
Minimization
reset_timestep 0
thermo 100
thermo_style custom step temp etotal evdwl eangle ebond edihed ecoul eimp lx ly lz vol press
min_style cg
minimize 1e-20 1e-20 500000 1000000
group pull id 378 379 380 381 382 383 384 385 386 387 388 389 390 391
compute inter polymer group/group graphene boundary no
dump 3 all dcd 20 singlepolyisoprenepullinggraphene.dcd
dump 2 all custom 20 dump.singlepolyisoprenepullinggraphene id type x y z xs ys zs mass fx fy fz vx vy vz
timestep 0.005
fix 1 pull move linear 0.0 0.0 1.0
thermo_style custom step temp etotal evdwl eangle ebond edihed ecoul eimp c_inter c_inter[1] c_inter[2] c_inter[3] vol press lx ly lz pxx pyy pzz pxy pxz pyz
thermo 1
run 100000
unfix 1
write_restart ${simname}.txt
unfix rgd
https://icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_Polymer for the explanation of the various aspects of code. see the movie shown below.
Output file
LAMMPS (13 Dec 2011)
Scanning data file …
5 = max bonds/atom
15 = max angles/atom
50 = max dihedrals/atom
Reading data file …
orthogonal box = (-100 -100 -100) to (250 250 250)
2 by 2 by 4 MPI processor grid
3592 atoms
5078 bonds
9957 angles
19133 dihedrals
Finding 1-2 1-3 1-4 neighbors …
6 = max # of 1-2 neighbors
14 = max # of 1-3 neighbors
44 = max # of 1-4 neighbors
26 = max # of special neighbors
3200 atoms in group graphene
392 atoms in group polymer
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Setting up minimization …
ERROR on proc 14: Angle atoms 314 333 331 missing on proc 14 at step 0 (neigh_bond.cpp:131)
ERROR on proc 10: Angle atoms 356 362 364 missing on proc 10 at step 0 (neigh_bond.cpp:131)
Data file (part which contains angles and atom coordinates)
300 1 5 0.064473 82.602997 60.771999 9.598000 # H2 NAT
301 1 4 -0.147368 77.223999 59.506001 12.036000 # CG9 NAT
302 1 5 0.064473 77.221001 58.848999 11.165000 # H2 NAT
303 1 5 0.064473 76.371002 60.174999 11.890000 # H2 NAT
304 1 3 0.000000 78.467003 60.278999 12.111000 # CG3D NAT
305 1 2 -0.073684 79.664001 59.834999 11.661000 # CG2D NAT
306 1 6 0.064473 80.439003 60.458000 11.723000 # H4 NAT
307 1 4 -0.147368 79.977997 58.528999 11.088000 # CG9 NAT
308 1 5 0.064473 79.226997 57.775002 11.328000 # H2 NAT
309 1 5 0.064473 80.915001 58.174999 11.526000 # H2 NAT
310 1 4 -0.147368 78.410004 61.617001 12.700000 # CG9 NAT
311 1 5 0.064473 77.443001 61.837002 13.156000 # H2 NAT
312 1 5 0.064473 78.597000 62.366001 11.928000 # H2 NAT
313 1 5 0.064473 79.165001 61.720001 13.485000 # H2 NAT
314 1 4 -0.147368 76.707001 55.661999 12.727000 # CG9 NAT
315 1 5 0.064473 77.517998 56.174999 12.209000 # H2 NAT
316 1 5 0.064473 76.390999 54.868999 12.044000 # H2 NAT
317 1 3 0.000000 75.588997 56.575001 12.995000 # CG3D NAT
318 1 2 -0.073684 75.734001 57.902000 13.219000 # CG2D NAT
319 1 6 0.064473 74.903999 58.438000 13.350000 # H4 NAT
320 1 4 -0.147368 76.973999 58.667999 13.305000 # CG9 NAT
321 1 5 0.064473 77.845001 58.036999 13.488000 # H2 NAT
322 1 5 0.064473 76.904999 59.346001 14.160000 # H2 NAT
323 1 4 -0.147368 74.237000 56.020000 13.010000 # CG9 NAT
324 1 5 0.064473 74.227997 54.930000 12.956000 # H2 NAT
325 1 5 0.064473 73.671997 56.403999 12.158000 # H2 NAT
326 1 5 0.064473 73.722000 56.299000 13.932000 # H2 NAT
327 1 4 -0.147368 75.234001 55.029999 16.326000 # CG9 NAT
328 1 5 0.064473 74.834999 54.749001 15.350000 # H2 NAT
329 1 5 0.064473 74.405998 55.528999 16.836000 # H2 NAT
330 1 3 0.000000 76.372002 55.945000 16.190001 # CG3D NAT
331 1 2 -0.073684 77.232002 55.931999 15.144000 # CG2D NAT
332 1 6 0.064473 77.947998 56.626999 15.130000 # H4 NAT
333 1 4 -0.147368 77.253998 55.011002 14.011000 # CG9 NAT
334 1 5 0.064473 76.698997 54.091999 14.207000 # H2 NAT
335 1 5 0.064473 78.289001 54.708000 13.831000 # H2 NAT
336 1 4 -0.147368 76.584999 56.938000 17.240999 # CG9 NAT
337 1 5 0.064473 75.931999 56.785999 18.103001 # H2 NAT
338 1 5 0.064473 76.394997 57.938000 16.847000 # H2 NAT
339 1 5 0.064473 77.613998 56.890999 17.607000 # H2 NAT
340 1 4 -0.147368 75.102997 51.175999 15.518000 # CG9 NAT
341 1 5 0.064473 75.587997 51.987000 14.972000 # H2 NAT
342 1 5 0.064473 74.514000 50.643002 14.768000 # H2 NAT
343 1 3 0.000000 74.228996 51.696999 16.573999 # CG3D NAT
344 1 2 -0.073684 74.455002 52.852001 17.243000 # CG2D NAT
345 1 6 0.064473 73.774002 53.133999 17.914000 # H4 NAT
346 1 4 -0.147368 75.594002 53.755001 17.113001 # CG9 NAT
347 1 5 0.064473 76.455002 53.280998 16.639999 # H2 NAT
348 1 5 0.064473 75.920998 54.048000 18.115000 # H2 NAT
349 1 4 -0.147368 73.033997 50.926998 16.920000 # CG9 NAT
350 1 5 0.064473 73.004997 49.951000 16.430000 # H2 NAT
351 1 5 0.064473 72.141998 51.480000 16.621000 # H2 NAT
352 1 5 0.064473 72.996002 50.745998 17.996000 # H2 NAT
353 1 4 -0.147368 79.042000 51.134998 15.424000 # CG9 NAT
354 1 5 0.064473 78.360001 51.912998 15.770000 # H2 NAT
355 1 5 0.064473 79.725998 51.643002 14.738000 # H2 NAT
356 1 3 0.000000 78.317001 50.073002 14.719000 # CG3D NAT
357 1 2 -0.073684 77.044998 49.706001 15.005000 # CG2D NAT
358 1 6 0.064473 76.632004 48.999001 14.436000 # H4 NAT
359 1 4 -0.147368 76.179001 50.219002 16.063999 # CG9 NAT
360 1 5 0.064473 76.737999 50.727001 16.851999 # H2 NAT
361 1 5 0.064473 75.679001 49.372002 16.542000 # H2 NAT
362 1 4 -0.147368 79.004997 49.370998 13.637000 # CG9 NAT
363 1 5 0.064473 80.063004 49.634998 13.568000 # H2 NAT
364 1 5 0.064473 78.533997 49.615002 12.682000 # H2 NAT
365 1 5 0.064473 78.954002 48.291000 13.791000 # H2 NAT
366 1 4 -0.147368 82.865997 50.417000 16.041000 # CG9 NAT
367 1 5 0.064473 82.372002 51.331001 15.706000 # H2 NAT
368 1 5 0.064473 83.667000 50.245998 15.317000 # H2 NAT
369 1 3 0.000000 81.933998 49.284000 16.044001 # CG3D NAT
370 1 2 -0.073684 80.606003 49.396999 16.275000 # CG2D NAT
371 1 6 0.064473 80.056000 48.568001 16.212000 # H4 NAT
372 1 4 -0.147368 79.852997 50.601002 16.618999 # CG9 NAT
373 1 5 0.064473 80.491997 51.400002 16.997999 # H2 NAT
374 1 5 0.064473 79.158997 50.356998 17.427000 # H2 NAT
375 1 4 -0.147368 82.472000 47.951000 15.770000 # CG9 NAT
376 1 5 0.064473 83.563004 47.936001 15.731000 # H2 NAT
377 1 5 0.064473 82.096001 47.594002 14.809000 # H2 NAT
378 1 5 0.064473 82.168999 47.250999 16.552000 # H2 NAT
379 1 4 -0.147368 82.970001 53.483002 18.511000 # CG9 NAT
380 1 5 0.064473 82.952003 53.349998 19.452000 # H2 NAT
381 1 5 0.064473 82.113998 52.978001 18.061001 # H2 NAT
382 1 5 0.064473 82.810997 54.544998 18.308001 # H2 NAT
383 1 3 0.000000 84.226997 53.033001 17.907000 # CG3D NAT
384 1 2 -0.073684 84.426003 51.789001 17.409000 # CG2D NAT
385 1 6 0.064473 85.306999 51.601002 16.982000 # H4 NAT
386 1 4 -0.147368 83.500999 50.659000 17.422001 # CG9 NAT
387 1 5 0.064473 82.706001 50.777000 18.160999 # H2 NAT
388 1 5 0.064473 84.054001 49.761002 17.712000 # H2 NAT
389 1 4 -0.147368 85.332001 53.987000 17.825001 # CG9 NAT
390 1 5 0.064473 85.130997 54.912998 18.368000 # H2 NAT
391 1 5 0.064473 85.519997 54.244999 16.781000 # H2 NAT
392 1 5 0.064473 86.239998 53.556000 18.254000 # H2 NAT
393 1 1 0.000000 38.137001 11.167000 0.000000 # C MOL
394 1 1 0.000000 39.442001 11.729000 0.000000 # C MOL
395 1 1 0.000000 37.164001 13.426000 0.000000 # C MOL
396 1 1 0.000000 38.467999 13.988000 0.000000 # C MOL
397 1 1 0.000000 36.191002 15.686000 0.000000 # C MOL
398 1 1 0.000000 37.494999 16.247999 0.000000 # C MOL
399 1 1 0.000000 35.216999 17.945000 0.000000 # C MOL
567 2 302 301 303
568 1 302 301 304
569 16 302 301 320
570 1 303 301 304
571 16 303 301 320
572 3 304 301 320
573 10 301 304 305
574 4 301 304 310
575 10 305 304 310
576 11 304 305 306
577 19 304 305 307
578 5 306 305 307
579 12 288 307 305
580 16 288 307 309
581 16 288 307 308
582 20 305 307 309
583 20 305 307 308
584 2 308 307 309
585 1 304 310 313
586 1 304 310 311
587 1 304 310 312
588 2 311 310 313
589 2 312 310 313
590 2 311 310 312
591 1 316 314 317
592 2 315 314 316
593 16 316 314 333
594 1 315 314 317
595 3 317 314 333
596 16 315 314 333
597 4 314 317 323
598 10 314 317 318
599 10 318 317 323
600 19 317 318 320
601 11 317 318 319
602 5 319 318 320
603 12 301 320 318
604 16 301 320 321
605 16 301 320 322
606 20 318 320 321
607 20 318 320 322
608 2 321 320 322
609 1 317 323 326
610 1 317 323 325
611 1 317 323 324
612 2 325 323 326
613 2 324 323 326
614 2 324 323 325
615 1 328 327 330
616 16 328 327 346
617 2 328 327 329
618 3 330 327 346
619 1 329 327 330
620 16 329 327 346
621 10 327 330 331
622 4 327 330 336
623 10 331 330 336
624 19 330 331 333
625 11 330 331 332
626 5 332 331 333
627 12 314 333 331
628 16 314 333 334
629 16 314 333 335
630 20 331 333 334
631 20 331 333 335
632 2 334 333 335
633 1 330 336 337
634 1 330 336 339
635 1 330 336 338
636 2 337 336 339
637 2 337 336 338
638 2 338 336 339
639 2 341 340 342
640 1 342 340 343
641 16 342 340 359
642 1 341 340 343
643 16 341 340 359
644 3 343 340 359
645 4 340 343 349
646 10 340 343 344
647 10 344 343 349
648 11 343 344 345
649 19 343 344 346
650 5 345 344 346
651 12 327 346 344
652 16 327 346 347
653 16 327 346 348
654 20 344 346 347
655 20 344 346 348
656 2 347 346 348
657 1 343 349 350
658 1 343 349 352
659 1 343 349 351
660 2 350 349 352
661 2 350 349 351
662 2 351 349 352
663 2 354 353 355
664 16 354 353 372
665 1 354 353 356
666 16 355 353 372
667 1 355 353 356
668 3 356 353 372
669 10 353 356 357
670 4 353 356 362
671 10 357 356 362
672 11 356 357 358
673 19 356 357 359
674 5 358 357 359
675 12 340 359 357
676 16 340 359 360
677 16 340 359 361
678 20 357 359 360
679 20 357 359 361
680 2 360 359 361
681 1 356 362 364
682 1 356 362 363
683 1 356 362 365
684 2 363 362 364
685 2 364 362 365
686 2 363 362 365
687 1 368 366 369
688 2 367 366 368
689 16 368 366 386
690 1 367 366 369
691 3 369 366 386
692 16 367 366 386
693 10 366 369 370
694 4 366 369 375
695 10 370 369 375
696 11 369 370 371
697 19 369 370 372
698 5 371 370 372
699 12 353 372 370
700 16 353 372 373
701 16 353 372 374
702 20 370 372 373
703 20 370 372 374
704 2 373 372 374
705 1 369 375 376
706 1 369 375 377
707 1 369 375 378
708 2 376 375 377
709 2 376 375 378
710 2 377 375 378
711 2 380 379 381
712 1 381 379 383
713 2 381 379 382
714 1 380 379 383
715 2 380 379 382
716 1 382 379 383
717 10 379 383 384
718 4 379 383 389
719 10 384 383 389
720 11 383 384 385
721 19 383 384 386
722 5 385 384 386
723 12 366 386 384
724 16 366 386 387
725 16 366 386 388
726 20 384 386 387
727 20 384 386 388
728 2 387 386 388
729 1 383 389 391
730 1 383 389 392
731 1 383 389 390
732 2 391 389 392
733 2 390 389 391
734 2 390 389 392
735 9 393 394 473
736 9 393 394 475
737 9 473 394 475
738 9 395 396 475
739 9 395 396 477
740 9 475 396 477
741 9 397 398 477
742 9 397 398 479
743 9 477 398 479
744 9 399 400 481
745 9 399 400 479
746 9 479 400 481
747 9 401 402 481
748 9 401 402 483
749 9 481 402 483
750 9 403 404 485
751 9 403 404 483
752 9 483 404 485
753 9 405 406 485
754 9 405 406 487