forked from lijiext/lammps
error our when Fix:set_molecule() is called with unsupported fixes
also add example input for using fix rigid/small with fix deposit
This commit is contained in:
Axel Kohlmeyer
parent
57ad6d50f4
commit
71dbf43e09
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@ -0,0 +1,56 @@
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# sample surface deposition script for molecules
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units lj
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atom_style bond
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boundary p p f
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lattice fcc 1.0
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region box block 0 5 0 5 0 10
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create_box 3 box bond/types 1 extra/bond/per/atom 1
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region substrate block INF INF INF INF INF 3
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create_atoms 1 region substrate
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff 1 2 1.0 1.0 5.0
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mass * 1.0
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bond_style harmonic
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bond_coeff 1 5.0 1.0
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neigh_modify delay 0
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molecule dimer molecule.dimer
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region slab block 0 5 0 5 8 9
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group addatoms empty
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region mobile block 0 5 0 5 2 INF
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group mobile region mobile
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compute add addatoms temp
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compute_modify add dynamic/dof yes extra/dof 0
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fix 1 addatoms rigid/small molecule mol dimer
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fix 2 mobile langevin 0.1 0.1 0.1 587283
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fix 3 mobile nve
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fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 &
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mol dimer vz -1.0 -1.0 rigid 1
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fix 5 addatoms wall/reflect zhi EDGE
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thermo_style custom step atoms temp epair etotal press
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thermo 100
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thermo_modify temp add lost/bond ignore lost warn
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#dump 1 all atom 50 dump.deposit.atom
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#dump 2 all image 50 image.*.jpg type type &
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# axes yes 0.8 0.02 view 80 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 50 tmp.mpg type type &
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# axes yes 0.8 0.02 view 80 -30
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#dump_modify 3 pad 5
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run 10000
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@ -21,11 +21,11 @@ bond_coeff 1 5.0 1.0
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neigh_modify delay 0
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group addatoms type 2
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group addatoms empty
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region mobile block 0 5 0 5 2 INF
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group mobile region mobile
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compute add addatoms temp
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compute add addatoms temp
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compute_modify add dynamic/dof yes extra/dof 0
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fix 1 addatoms nve
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@ -0,0 +1,218 @@
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LAMMPS (10 Mar 2021)
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using 1 OpenMP thread(s) per MPI task
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# sample surface deposition script for molecules
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units lj
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atom_style bond
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boundary p p f
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lattice fcc 1.0
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Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
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region box block 0 5 0 5 0 10
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create_box 3 box bond/types 1 extra/bond/per/atom 1
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
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1 by 1 by 1 MPI processor grid
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region substrate block INF INF INF INF INF 3
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create_atoms 1 region substrate
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Created 350 atoms
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create_atoms CPU = 0.001 seconds
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff 1 2 1.0 1.0 5.0
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mass * 1.0
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bond_style harmonic
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bond_coeff 1 5.0 1.0
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neigh_modify delay 0
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molecule dimer molecule.dimer
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Read molecule template dimer:
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1 molecules
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2 atoms with max type 3
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1 bonds with max type 1
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0 angles with max type 0
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0 dihedrals with max type 0
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0 impropers with max type 0
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region slab block 0 5 0 5 8 9
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group addatoms empty
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0 atoms in group addatoms
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region mobile block 0 5 0 5 2 INF
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group mobile region mobile
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150 atoms in group mobile
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compute add addatoms temp
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compute_modify add dynamic/dof yes extra/dof 0
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fix 1 addatoms rigid/small molecule mol dimer
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create bodies CPU = 0.000 seconds
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0 rigid bodies with 0 atoms
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1.0000000 = max distance from body owner to body atom
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fix 2 mobile langevin 0.1 0.1 0.1 587283
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fix 3 mobile nve
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fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
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fix 5 addatoms wall/reflect zhi EDGE
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thermo_style custom step atoms temp epair etotal press
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thermo 100
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thermo_modify temp add lost/bond ignore lost warn
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WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
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#dump 1 all atom 50 dump.deposit.atom
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#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
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#dump_modify 3 pad 5
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run 10000
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WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.3
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ghost atom cutoff = 5.3
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binsize = 2.65, bins = 3 3 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes
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Step Atoms Temp E_pair TotEng Press
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0 350 0 -6.9215833 -6.9215833 -1.0052629
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100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914
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200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276
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300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826
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400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699
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500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307
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600 362 1.026148 -6.7105231 -6.6680032 -0.68314418
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700 364 1.0683344 -6.6725162 -6.621154 -0.65747369
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800 366 1.0958952 -6.6412275 -6.5813425 -0.68789614
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900 368 1.1250033 -6.6101882 -6.541404 -0.66674346
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1000 370 1.2326373 -6.5993719 -6.5160856 -0.6968868
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1100 372 1.1397426 -6.5912861 -6.5070309 -0.63330356
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1200 374 1.0514292 -6.5905747 -6.5062354 -0.71020362
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1300 376 1.003296 -6.5747765 -6.4880555 -0.65459732
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1400 378 0.82999289 -6.5681797 -6.4913285 -0.60438126
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1500 380 0.90239175 -6.575298 -6.4862461 -0.66528725
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1600 382 0.86399799 -6.5692206 -6.4787496 -0.65027781
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1700 384 0.64747231 -6.5644237 -6.4927634 -0.6304614
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1800 386 0.74288971 -6.5515735 -6.4649672 -0.67772325
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1900 388 0.7257202 -6.5565091 -6.4676644 -0.66173549
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2000 390 0.73381036 -6.5631515 -6.4690733 -0.64685916
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2100 392 0.76476562 -6.5574124 -6.4549885 -0.68866192
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2200 394 0.65932468 -6.5511557 -6.459118 -0.71728829
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2300 396 0.70269509 -6.5728146 -6.4707819 -0.64362081
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2400 398 0.60528919 -6.5845991 -6.4933494 -0.63956327
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2500 400 0.51025744 -6.5812452 -6.5015175 -0.68706961
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2600 402 0.5245131 -6.6003894 -6.5155801 -0.68972215
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2700 404 0.46330251 -6.5659175 -6.4885092 -0.72870942
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2800 406 0.48039778 -6.5715192 -6.488692 -0.753758
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2900 408 0.53698616 -6.5813154 -6.4858951 -0.67117541
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3000 410 0.50231419 -6.5886963 -6.4968096 -0.71905351
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3100 412 0.49420225 -6.596733 -6.5037702 -0.65947518
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3200 414 0.42703699 -6.5879338 -6.5054146 -0.80033546
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3300 416 0.44306009 -6.580249 -6.4923825 -0.76503083
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3400 418 0.55620672 -6.5923388 -6.4792346 -0.69367877
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3500 420 0.39815033 -6.5911154 -6.5081674 -0.65569211
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3600 422 0.44197847 -6.6026382 -6.5083774 -0.73299102
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3700 424 0.45049389 -6.6060616 -6.5077817 -0.7552914
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3800 426 0.43047295 -6.6079275 -6.51193 -0.71501328
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3900 428 0.43779129 -6.6099306 -6.5102001 -0.71539515
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4000 430 0.41113503 -6.6123009 -6.5166881 -0.74177096
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4100 432 0.32800011 -6.5983566 -6.5205325 -0.71688103
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4200 434 0.39168203 -6.6110342 -6.5162724 -0.78927697
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4300 436 0.48151013 -6.6183315 -6.4996106 -0.70523035
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4400 438 0.45391027 -6.6331732 -6.5191775 -0.7270855
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4500 440 0.349126 -6.6091657 -6.5199006 -0.76974115
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4600 442 0.43375023 -6.6219188 -6.5090653 -0.74576212
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4700 444 0.40071749 -6.6184164 -6.5123707 -0.71919052
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4800 446 0.414292 -6.6298132 -6.5183445 -0.76237313
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4900 448 0.44210681 -6.6364174 -6.5155288 -0.78753121
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5000 450 0.36101771 -6.6232703 -6.5229876 -0.73927083
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5100 452 0.41481171 -6.6442404 -6.5272305 -0.76316209
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5200 454 0.40283527 -6.6512252 -6.5358759 -0.79645689
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5300 456 0.3642061 -6.6530346 -6.5472072 -0.77458364
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5400 458 0.38449826 -6.6514864 -6.5381518 -0.73083784
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5500 460 0.42559408 -6.6769326 -6.5497169 -0.78932279
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5600 462 0.38905756 -6.6698705 -6.5519743 -0.77118812
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5700 464 0.38354955 -6.6706904 -6.5528977 -0.75067129
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5800 466 0.36760943 -6.6942519 -6.5798669 -0.685487
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5900 468 0.30783118 -6.6838159 -6.5867965 -0.79233808
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6000 470 0.33145368 -6.6733504 -6.5675673 -0.84390449
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6100 472 0.39252324 -6.6912189 -6.5643973 -0.83342022
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6200 474 0.32342144 -6.6906083 -6.5848481 -0.71262158
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6300 476 0.34445238 -6.7008453 -6.5868721 -0.76650756
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6400 478 0.38152782 -6.7017838 -6.5740758 -0.77113022
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6500 480 0.37540166 -6.7119996 -6.5849105 -0.79907635
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6600 482 0.3579419 -6.7034721 -6.5809401 -0.8141269
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6700 484 0.33538235 -6.6916682 -6.575601 -0.83265486
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6800 486 0.34081871 -6.6931924 -6.573976 -0.80582583
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6900 488 0.3555283 -6.6939997 -6.5683263 -0.74771423
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7000 490 0.3543769 -6.7093364 -6.5827732 -0.77643516
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7100 492 0.31263107 -6.698361 -6.5855723 -0.73108333
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7200 494 0.32107 -6.6959056 -6.5789166 -0.7575478
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7300 496 0.32908165 -6.7137605 -6.592677 -0.86538023
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7400 498 0.32539571 -6.7030353 -6.5821554 -0.79337428
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7500 500 0.33902577 -6.7078178 -6.5806832 -0.85408988
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7600 502 0.35530921 -6.707507 -6.5730274 -0.79914613
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7700 504 0.32391812 -6.6978823 -6.5741635 -0.78603595
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7800 506 0.36390015 -6.7151325 -6.5748943 -0.83164222
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7900 508 0.3372561 -6.7086718 -6.5775535 -0.7949992
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8000 510 0.36612946 -6.7225238 -6.5789437 -0.80322866
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8100 512 0.34622305 -6.7229825 -6.5860486 -0.70478659
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8200 514 0.3212233 -6.7202524 -6.5921381 -0.91836713
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8300 516 0.3402461 -6.721488 -6.5846642 -0.88273592
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8400 518 0.34070258 -6.7268378 -6.5887152 -0.76057264
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8500 520 0.36267747 -6.744602 -6.5963924 -0.81051317
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8600 522 0.3439948 -6.7376267 -6.595943 -0.84600203
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8700 524 0.30960289 -6.7276471 -6.5991382 -0.90965986
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8800 526 0.28868972 -6.7159628 -6.595218 -0.876093
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8900 528 0.31020216 -6.7162903 -6.5855707 -0.83193125
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9000 530 0.31836275 -6.7171479 -6.5819939 -0.82093897
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9100 532 0.32543293 -6.724167 -6.5850016 -0.7690143
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9200 534 0.32644265 -6.7139575 -6.5733549 -0.86903096
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9300 536 0.33050759 -6.7254715 -6.5821077 -0.94504522
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9400 538 0.30372582 -6.7139931 -6.5813247 -0.91128612
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9500 540 0.32943659 -6.7206223 -6.5757312 -0.87818439
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9600 542 0.30911968 -6.708091 -6.5712114 -0.79092372
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9700 544 0.33909826 -6.7222948 -6.5711342 -0.80266151
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9800 546 0.29015141 -6.7086869 -6.5784908 -0.87763769
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9900 548 0.33838474 -6.7384955 -6.5856667 -0.85630604
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10000 550 0.30213198 -6.7338924 -6.5965597 -0.75738882
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Loop time of 17.2852 on 1 procs for 10000 steps with 550 atoms
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Performance: 249924.414 tau/day, 578.529 timesteps/s
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99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 9.637 | 9.637 | 9.637 | 0.0 | 55.75
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Bond | 0.025444 | 0.025444 | 0.025444 | 0.0 | 0.15
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Neigh | 4.6852 | 4.6852 | 4.6852 | 0.0 | 27.11
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Comm | 0.65556 | 0.65556 | 0.65556 | 0.0 | 3.79
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Output | 0.0099883 | 0.0099883 | 0.0099883 | 0.0 | 0.06
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Modify | 2.1895 | 2.1895 | 2.1895 | 0.0 | 12.67
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Other | | 0.08248 | | | 0.48
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Nlocal: 550.000 ave 550 max 550 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2367.00 ave 2367 max 2367 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 36781.0 ave 36781 max 36781 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 36781
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Ave neighs/atom = 66.874545
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Ave special neighs/atom = 0.36363636
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Neighbor list builds = 840
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Dangerous builds = 0
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Total wall time: 0:00:17
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@ -0,0 +1,218 @@
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LAMMPS (10 Mar 2021)
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using 1 OpenMP thread(s) per MPI task
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# sample surface deposition script for molecules
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units lj
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atom_style bond
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boundary p p f
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lattice fcc 1.0
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Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
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region box block 0 5 0 5 0 10
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create_box 3 box bond/types 1 extra/bond/per/atom 1
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
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1 by 1 by 4 MPI processor grid
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region substrate block INF INF INF INF INF 3
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create_atoms 1 region substrate
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Created 350 atoms
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create_atoms CPU = 0.139 seconds
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff 1 2 1.0 1.0 5.0
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mass * 1.0
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bond_style harmonic
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bond_coeff 1 5.0 1.0
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neigh_modify delay 0
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molecule dimer molecule.dimer
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Read molecule template dimer:
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1 molecules
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2 atoms with max type 3
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1 bonds with max type 1
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0 angles with max type 0
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0 dihedrals with max type 0
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0 impropers with max type 0
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region slab block 0 5 0 5 8 9
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group addatoms empty
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0 atoms in group addatoms
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region mobile block 0 5 0 5 2 INF
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group mobile region mobile
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150 atoms in group mobile
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compute add addatoms temp
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compute_modify add dynamic/dof yes extra/dof 0
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fix 1 addatoms rigid/small molecule mol dimer
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create bodies CPU = 0.006 seconds
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0 rigid bodies with 0 atoms
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1.0000000 = max distance from body owner to body atom
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fix 2 mobile langevin 0.1 0.1 0.1 587283
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fix 3 mobile nve
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fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
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fix 5 addatoms wall/reflect zhi EDGE
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thermo_style custom step atoms temp epair etotal press
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thermo 100
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thermo_modify temp add lost/bond ignore lost warn
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WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
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#dump 1 all atom 50 dump.deposit.atom
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#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
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#dump_modify 3 pad 5
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run 10000
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WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
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Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65, bins = 3 3 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes
|
||||
Step Atoms Temp E_pair TotEng Press
|
||||
0 350 0 -6.9215833 -6.9215833 -1.0052629
|
||||
100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337
|
||||
200 354 1.0081552 -6.8645575 -6.850318 -0.69629729
|
||||
300 356 1.0085803 -6.821677 -6.8004288 -0.69532657
|
||||
400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568
|
||||
500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641
|
||||
600 362 1.026146 -6.7129201 -6.6704003 -0.67063836
|
||||
700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472
|
||||
800 366 1.0958893 -6.6402029 -6.5803182 -0.66307281
|
||||
900 368 1.1231768 -6.6050912 -6.5364187 -0.64076928
|
||||
1000 370 1.1976283 -6.5942507 -6.5133299 -0.69249019
|
||||
1100 372 1.0506263 -6.5772313 -6.499564 -0.63072939
|
||||
1200 374 0.93724351 -6.5732957 -6.4981157 -0.64963897
|
||||
1300 376 0.93899686 -6.5578406 -6.4766773 -0.65096289
|
||||
1400 378 0.8704974 -6.5468498 -6.4662482 -0.67613931
|
||||
1500 380 0.84490693 -6.5401094 -6.4567304 -0.64385968
|
||||
1600 382 0.9243154 -6.5611604 -6.4643734 -0.62096869
|
||||
1700 384 0.67202953 -6.5590557 -6.4846775 -0.67807465
|
||||
1800 386 0.8712464 -6.5654953 -6.4639251 -0.65860236
|
||||
1900 388 0.70011668 -6.5808612 -6.495151 -0.65146463
|
||||
2000 390 0.64019295 -6.5652168 -6.4831408 -0.70291888
|
||||
2100 392 0.67578277 -6.5596196 -6.469113 -0.63315981
|
||||
2200 394 0.60785287 -6.558941 -6.4740885 -0.7133822
|
||||
2300 396 0.8155086 -6.5756022 -6.4571887 -0.69176417
|
||||
2400 398 0.69028748 -6.5875474 -6.483484 -0.63743938
|
||||
2500 400 0.5013913 -6.5871851 -6.5088427 -0.65872179
|
||||
2600 402 0.51268385 -6.5782356 -6.495339 -0.74289067
|
||||
2700 404 0.57745388 -6.5815718 -6.4850912 -0.67922914
|
||||
2800 406 0.47317895 -6.5974978 -6.5159152 -0.64657562
|
||||
2900 408 0.50593124 -6.6019054 -6.5120034 -0.64211427
|
||||
3000 410 0.44423233 -6.5956684 -6.5144064 -0.66526127
|
||||
3100 412 0.40808865 -6.5949863 -6.5182221 -0.62722445
|
||||
3200 414 0.40692632 -6.5866689 -6.5080358 -0.76440608
|
||||
3300 416 0.43908529 -6.5851721 -6.4980939 -0.69345883
|
||||
3400 418 0.53825907 -6.5880076 -6.478553 -0.69726204
|
||||
3500 420 0.46363057 -6.6135193 -6.5169296 -0.58015901
|
||||
3600 422 0.39262699 -6.621857 -6.5381213 -0.74921264
|
||||
3700 424 0.42679205 -6.6146579 -6.5215488 -0.69040431
|
||||
3800 426 0.38997492 -6.6139725 -6.5270063 -0.78237667
|
||||
3900 428 0.5222531 -6.6403886 -6.5214174 -0.78298122
|
||||
4000 430 0.47841128 -6.6502681 -6.5390097 -0.68125967
|
||||
4100 432 0.44609186 -6.6610827 -6.5552392 -0.81157037
|
||||
4200 434 0.4591431 -6.6858064 -6.5747234 -0.79000753
|
||||
4300 436 0.40690573 -6.6800195 -6.579693 -0.6781696
|
||||
4400 438 0.43023944 -6.6849804 -6.5769294 -0.7620548
|
||||
4500 440 0.40889421 -6.6783124 -6.5737656 -0.8577593
|
||||
4600 442 0.41452051 -6.6968565 -6.5890061 -0.70427746
|
||||
4700 444 0.36740394 -6.6920933 -6.5948636 -0.69303162
|
||||
4800 446 0.40112316 -6.6869413 -6.5790158 -0.84792822
|
||||
4900 448 0.42437165 -6.6789835 -6.5629444 -0.82278531
|
||||
5000 450 0.41822898 -6.6770254 -6.5608507 -0.72224472
|
||||
5100 452 0.38445688 -6.6738997 -6.5654522 -0.7022418
|
||||
5200 454 0.39998238 -6.6670536 -6.5525212 -0.73639959
|
||||
5300 456 0.39471029 -6.6728592 -6.5581681 -0.70419927
|
||||
5400 458 0.35817807 -6.6702423 -6.5646658 -0.81657219
|
||||
5500 460 0.37151428 -6.6690855 -6.558035 -0.78076653
|
||||
5600 462 0.32642513 -6.6622352 -6.5633185 -0.69118644
|
||||
5700 464 0.43665879 -6.6811227 -6.5470195 -0.77500043
|
||||
5800 466 0.40704721 -6.6858874 -6.5592311 -0.72683597
|
||||
5900 468 0.3861903 -6.6896953 -6.5679794 -0.78001958
|
||||
6000 470 0.34073346 -6.6833717 -6.574627 -0.78170837
|
||||
6100 472 0.39953874 -6.7083668 -6.5792785 -0.81791744
|
||||
6200 474 0.36685189 -6.7114648 -6.5915027 -0.80545451
|
||||
6300 476 0.35851799 -6.7261023 -6.607475 -0.77350495
|
||||
6400 478 0.41771823 -6.7427425 -6.6029205 -0.85319003
|
||||
6500 480 0.36519478 -6.732662 -6.6090284 -0.78712805
|
||||
6600 482 0.30669571 -6.7269784 -6.6219892 -0.76698134
|
||||
6700 484 0.3384344 -6.7261448 -6.6090213 -0.79935239
|
||||
6800 486 0.36420902 -6.7320259 -6.6046277 -0.84650552
|
||||
6900 488 0.40181215 -6.7490619 -6.6070279 -0.75753238
|
||||
7000 490 0.30536068 -6.7398924 -6.6308351 -0.73210162
|
||||
7100 492 0.28813004 -6.7257287 -6.6217794 -0.92178435
|
||||
7200 494 0.30956277 -6.7342688 -6.6214727 -0.77532949
|
||||
7300 496 0.36625115 -6.7528159 -6.6180561 -0.76247835
|
||||
7400 498 0.30935271 -6.7401433 -6.6252231 -0.82809158
|
||||
7500 500 0.33222282 -6.7410421 -6.6164585 -0.81948236
|
||||
7600 502 0.33318693 -6.7488106 -6.622704 -0.82395904
|
||||
7700 504 0.34570598 -6.7547394 -6.6226989 -0.85644369
|
||||
7800 506 0.34587242 -6.7446006 -6.6113099 -0.82476511
|
||||
7900 508 0.2969166 -6.7305429 -6.6151078 -0.8210214
|
||||
8000 510 0.32355758 -6.7437629 -6.6168776 -0.81719054
|
||||
8100 512 0.33784479 -6.7545537 -6.6209335 -0.78082067
|
||||
8200 514 0.32351289 -6.7525032 -6.6234757 -0.87093587
|
||||
8300 516 0.31900134 -6.7550972 -6.6268166 -0.79928704
|
||||
8400 518 0.3338521 -6.7588757 -6.6235302 -0.81699503
|
||||
8500 520 0.33115184 -6.7614854 -6.6261589 -0.79958489
|
||||
8600 522 0.29478929 -6.7490188 -6.6276018 -0.81954456
|
||||
8700 524 0.267993 -6.7467764 -6.6355389 -0.76642994
|
||||
8800 526 0.28792085 -6.7527118 -6.6322887 -0.86911619
|
||||
8900 528 0.32430992 -6.75901 -6.6223453 -0.87087898
|
||||
9000 530 0.33151321 -6.7534845 -6.6127478 -0.79309499
|
||||
9100 532 0.32760982 -6.7599992 -6.6199028 -0.7506309
|
||||
9200 534 0.32579101 -6.7671489 -6.6268269 -0.94238755
|
||||
9300 536 0.35144354 -6.7782581 -6.625813 -0.77952234
|
||||
9400 538 0.33689976 -6.7804455 -6.6332867 -0.75768501
|
||||
9500 540 0.3052486 -6.7745436 -6.6402908 -0.89621525
|
||||
9600 542 0.30617581 -6.7648172 -6.6292412 -0.90623541
|
||||
9700 544 0.30097715 -6.7714379 -6.6372707 -0.85534149
|
||||
9800 546 0.31297479 -6.7814978 -6.6410604 -0.88651064
|
||||
9900 548 0.31832347 -6.790661 -6.6468926 -1.006
|
||||
10000 550 0.29239559 -6.7823137 -6.6494066 -1.0337518
|
||||
Loop time of 34.7661 on 4 procs for 10000 steps with 550 atoms
|
||||
|
||||
Performance: 124259.065 tau/day, 287.637 timesteps/s
|
||||
73.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0076709 | 3.1286 | 9.1834 | 211.7 | 9.00
|
||||
Bond | 0.0040276 | 0.010416 | 0.022169 | 7.0 | 0.03
|
||||
Neigh | 0.052413 | 1.5948 | 4.885 | 155.3 | 4.59
|
||||
Comm | 4.9736 | 12.242 | 20.073 | 166.2 | 35.21
|
||||
Output | 0.053549 | 0.10104 | 0.21642 | 21.0 | 0.29
|
||||
Modify | 13.435 | 16.191 | 23.851 | 110.0 | 46.57
|
||||
Other | | 1.499 | | | 4.31
|
||||
|
||||
Nlocal: 137.500 ave 299 max 2 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 1898.75 ave 2679 max 524 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 9204.00 ave 23014 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 36816
|
||||
Ave neighs/atom = 66.938182
|
||||
Ave special neighs/atom = 0.36363636
|
||||
Neighbor list builds = 832
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:34
|
||||
|
|
@ -1365,6 +1365,19 @@ int FixRigidNHSmall::modify_param(int narg, char **arg)
|
|||
return FixRigidSmall::modify_param(narg,arg);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
disallow using fix rigid/n??/small fixes with fix deposit
|
||||
we would need custom functionality to update data structures
|
||||
used by all fixes derived from this class but not fix rigid/small
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidNHSmall::set_molecule(int, tagint, int,
|
||||
double *, double *, double *)
|
||||
{
|
||||
error->all(FLERR,fmt::format("Molecule update not (yet) implemented for "
|
||||
"fix {}", style));
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidNHSmall::allocate_chain()
|
||||
|
|
|
|||
|
|
@ -80,6 +80,7 @@ class FixRigidNHSmall : public FixRigidSmall {
|
|||
void nh_epsilon_dot();
|
||||
void compute_dof();
|
||||
|
||||
void set_molecule(int, tagint, int, double *, double *, double *);
|
||||
void allocate_chain();
|
||||
void allocate_order();
|
||||
void deallocate_chain();
|
||||
|
|
|
|||
|
|
@ -43,7 +43,7 @@ class FixRigidSmall : public Fix {
|
|||
void grow_arrays(int);
|
||||
void copy_arrays(int, int, int);
|
||||
void set_arrays(int);
|
||||
void set_molecule(int, tagint, int, double *, double *, double *);
|
||||
virtual void set_molecule(int, tagint, int, double *, double *, double *);
|
||||
|
||||
int pack_exchange(int, double *);
|
||||
int unpack_exchange(int, double *);
|
||||
|
|
|
|||
|
|
@ -174,6 +174,12 @@ void Fix::modify_params(int narg, char **arg)
|
|||
}
|
||||
}
|
||||
|
||||
void::Fix::set_molecule(int, tagint, int, double *, double *, double *)
|
||||
{
|
||||
error->all(FLERR,fmt::format("Molecule update not implemented for "
|
||||
"fix {}", style));
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
setup for peratom energy and global/peratom virial computation
|
||||
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
|
||||
|
|
|
|||
|
|
@ -155,7 +155,7 @@ class Fix : protected Pointers {
|
|||
virtual void copy_arrays(int, int, int) {}
|
||||
virtual void set_arrays(int) {}
|
||||
virtual void update_arrays(int, int) {}
|
||||
virtual void set_molecule(int, tagint, int, double *, double *, double *) {}
|
||||
virtual void set_molecule(int, tagint, int, double *, double *, double *);
|
||||
virtual void clear_bonus() {}
|
||||
|
||||
virtual int pack_border(int, int *, double *) {return 0;}
|
||||
|
|
|
|||
Loading…
Reference in New Issue