Merge pull request #4370 from jtclemm/small-patches
Fixing potential segfaults in granular/nstencil classes and other minor clean ups
This commit is contained in:
Axel Kohlmeyer
@ -5,7 +5,11 @@ The BPM package implements bonded particle models which can be used to
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simulate mesoscale solids. Solids are constructed as a collection of
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particles, which each represent a coarse-grained region of space much
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larger than the atomistic scale. Particles within a solid region are
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then connected by a network of bonds to provide solid elasticity.
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then connected by a network of bonds to model solid elasticity.
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There are many names for methods that are based on similar (or
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equivalent) capabilities to those in this package, including, but not
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limited to, cohesive beam models, bonded DEMs, lattice spring models,
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mass spring models, and lattice particle methods.
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Unlike traditional bonds in molecular dynamics, the equilibrium bond
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length can vary between bonds. Bonds store the reference state. This
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File diff suppressed because it is too large
Load Diff
@ -11,7 +11,7 @@ mass 1 1.0
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mass 2 1.0
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velocity all create 2.0 87287 loop geom
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pair_style hybrid/overlay lj/cut 2.5 tracker
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pair_style hybrid/overlay lj/cut 2.5 tracker trackfix 1000 id1 id2 time/created time/broken time/total time/min 0.5
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pair_coeff * * lj/cut 1.0 1.0 2.5
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pair_coeff * * tracker 2.5
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@ -19,10 +19,9 @@ neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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fix 2 all pair/tracker 1000 id1 id2 time/created time/broken time/total time/min 0.5
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fix 3 all ave/histo 1000 1 1000 0 6 30 f_2[5] mode vector kind local file lifetime_hist.dat
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fix 2 all ave/histo 1000 1 1000 0 6 30 f_trackfix[5] mode vector kind local file lifetime_hist.dat
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dump 1 all local 1000 contact_history.dat f_2[1] f_2[2] f_2[3] f_2[4]
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dump 1 all local 1000 contact_history.dat f_trackfix[1] f_trackfix[2] f_trackfix[3] f_trackfix[4]
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dump_modify 1 header no
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# compute 1 all property/local patom1 patom2
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@ -1,4 +1,4 @@
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# Histogrammed data for fix 3
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# Histogrammed data for fix 2
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# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value
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# Bin Coord Count Count/Total
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0 30 0 0 1e+20 -1e+20
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@ -32,34 +32,34 @@
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28 5.5 0 0
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29 5.7 0 0
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30 5.9 0 0
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1000 30 8122 0 0.5 5
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1000 30 528 20285 1 1000
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1 0.1 0 0
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2 0.3 0 0
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3 0.5 910 0.112041
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4 0.7 1253 0.154272
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5 0.9 953 0.117336
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6 1.1 747 0.0919724
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7 1.3 559 0.0688254
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8 1.5 501 0.0616843
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9 1.7 421 0.0518345
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10 1.9 356 0.0438316
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11 2.1 300 0.0369367
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12 2.3 281 0.0345974
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13 2.5 242 0.0297956
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14 2.7 226 0.0278257
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15 2.9 175 0.0215464
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16 3.1 168 0.0206846
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17 3.3 162 0.0199458
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18 3.5 129 0.0158828
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19 3.7 151 0.0185915
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20 3.9 137 0.0168678
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21 4.1 98 0.012066
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22 4.3 104 0.0128047
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23 4.5 83 0.0102192
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24 4.7 77 0.00948042
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25 4.9 86 0.0105885
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26 5.1 3 0.000369367
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3 0.5 0 0
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4 0.7 0 0
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5 0.9 0 0
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6 1.1 17 0.032197
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7 1.3 0 0
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8 1.5 0 0
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9 1.7 0 0
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10 1.9 0 0
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11 2.1 51 0.0965909
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12 2.3 0 0
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13 2.5 0 0
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14 2.7 0 0
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15 2.9 0 0
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16 3.1 80 0.151515
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17 3.3 0 0
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18 3.5 0 0
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19 3.7 0 0
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20 3.9 0 0
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21 4.1 91 0.172348
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22 4.3 0 0
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23 4.5 0 0
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24 4.7 0 0
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25 4.9 0 0
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26 5.1 117 0.221591
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27 5.3 0 0
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28 5.5 0 0
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29 5.7 0 0
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30 5.9 0 0
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30 5.9 172 0.325758
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108
examples/tracker/log.29Aug24.tracker.g++.1
Normal file
108
examples/tracker/log.29Aug24.tracker.g++.1
Normal file
@ -0,0 +1,108 @@
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LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-731-g5ce635757f)
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# 3d Lennard-Jones melt with tracking
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 4 0 4 0 4
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create_box 2 box
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Created orthogonal box = (0 0 0) to (6.7183848 6.7183848 6.7183848)
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1 by 1 by 1 MPI processor grid
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create_atoms 2 box
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Created 256 atoms
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using lattice units in orthogonal box = (0 0 0) to (6.7183848 6.7183848 6.7183848)
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create_atoms CPU = 0.000 seconds
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mass 1 1.0
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mass 2 1.0
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velocity all create 2.0 87287 loop geom
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pair_style hybrid/overlay lj/cut 2.5 tracker trackfix 1000 id1 id2 time/created time/broken time/total time/min 0.5
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pair_coeff * * lj/cut 1.0 1.0 2.5
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pair_coeff * * tracker 2.5
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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fix 2 all ave/histo 1000 1 1000 0 6 30 f_trackfix[5] mode vector kind local file lifetime_hist.dat
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dump 1 all local 1000 contact_history.dat f_trackfix[1] f_trackfix[2] f_trackfix[3] f_trackfix[4]
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dump_modify 1 header no
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# compute 1 all property/local patom1 patom2
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# dump 2 all local 1 pairs.dat c_1[1] c_1[2]
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# dump 3 all atom 1 atoms.dat
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thermo 50
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run 1000 #0
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 20 steps, delay = 0 steps, check = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 5 5 5
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2 neighbor lists, perpetual/occasional/extra = 2 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/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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(2) pair tracker, perpetual, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 8.679 | 8.679 | 8.679 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 2 -6.7733681 0 -3.7850868 -4.5535126
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50 1.0540428 -5.3670859 0 -3.7921977 2.3386375
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100 1.0402713 -5.3493439 0 -3.7950323 2.4553748
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150 1.0570745 -5.3738961 0 -3.7944781 2.3767396
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200 1.0431846 -5.3518647 0 -3.7932002 2.5010135
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250 1.070121 -5.3902744 0 -3.791363 2.4908658
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300 1.0667723 -5.3866302 0 -3.7927224 2.3589344
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350 1.000601 -5.2859643 0 -3.7909257 2.9065274
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400 0.99256113 -5.2738812 0 -3.7908553 2.8595867
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450 1.0482542 -5.357452 0 -3.7912128 2.4707397
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500 1.0196176 -5.3123538 0 -3.7889017 2.7230338
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550 0.98274535 -5.2586303 0 -3.7902706 2.9156947
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600 1.0683914 -5.3863229 0 -3.789996 2.3002719
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650 1.0130779 -5.303917 0 -3.7902362 2.8726423
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700 1.0583333 -5.3737358 0 -3.792437 2.5770307
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750 0.98274506 -5.2612464 0 -3.792887 2.9447027
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800 1.0294191 -5.332001 0 -3.7939042 2.5293193
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850 0.99240027 -5.2735754 0 -3.7907899 2.7672711
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900 1.0293488 -5.3306241 0 -3.7926323 2.6054041
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950 0.97137182 -5.2424403 0 -3.7910742 3.129989
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1000 1.0009431 -5.2864286 0 -3.7908788 2.7536598
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Loop time of 0.286151 on 1 procs for 1000 steps with 256 atoms
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Performance: 1509690.552 tau/day, 3494.654 timesteps/s, 894.631 katom-step/s
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99.4% CPU use with 1 MPI tasks x no 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 | 0.21578 | 0.21578 | 0.21578 | 0.0 | 75.41
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Neigh | 0.020262 | 0.020262 | 0.020262 | 0.0 | 7.08
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Comm | 0.0051679 | 0.0051679 | 0.0051679 | 0.0 | 1.81
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Output | 0.021204 | 0.021204 | 0.021204 | 0.0 | 7.41
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Modify | 0.02307 | 0.02307 | 0.02307 | 0.0 | 8.06
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Other | | 0.0006654 | | | 0.23
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Nlocal: 256 ave 256 max 256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1327 ave 1327 max 1327 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 9612 ave 9612 max 9612 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9612
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Ave neighs/atom = 37.546875
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Neighbor list builds = 50
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Dangerous builds not checked
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Total wall time: 0:00:00
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@ -1,107 +0,0 @@
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LAMMPS (8 Apr 2021)
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# 3d Lennard-Jones melt with tracking
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 4 0 4 0 4
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create_box 2 box
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
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1 by 1 by 1 MPI processor grid
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create_atoms 2 box
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Created 256 atoms
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create_atoms CPU = 0.001 seconds
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mass 1 1.0
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mass 2 1.0
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velocity all create 2.0 87287 loop geom
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pair_style hybrid/overlay lj/cut 2.5 tracker
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pair_coeff * * lj/cut 1.0 1.0 2.5
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pair_coeff * * tracker 2.5
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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fix 2 all pair/tracker 1000 id1 id2 time/created time/broken time/total time/min 0.5
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fix 3 all ave/histo 1000 1 1000 0 6 30 f_2[5] mode vector kind local file lifetime_hist.dat
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dump 1 all local 1000 contact_history.dat f_2[1] f_2[2] f_2[3] f_2[4]
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dump_modify 1 header no
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# compute 1 all property/local patom1 patom2
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# dump 2 all local 1 pairs.dat c_1[1] c_1[2]
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# dump 3 all atom 1 atoms.dat
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thermo 50
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run 1000 #0
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 5 5 5
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2 neighbor lists, perpetual/occasional/extra = 2 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/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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(2) pair tracker, perpetual
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attributes: half, newton on, history
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 10.46 | 10.46 | 10.46 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 2 -6.7733681 0 -3.7850868 -4.5535126
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50 1.0540428 -5.3670859 0 -3.7921977 2.3386375
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100 1.0402713 -5.3493439 0 -3.7950323 2.4553748
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150 1.0570745 -5.3738961 0 -3.7944781 2.3767396
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200 1.0431846 -5.3518647 0 -3.7932002 2.5010135
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250 1.070121 -5.3902744 0 -3.791363 2.4908658
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300 1.0667723 -5.3866302 0 -3.7927224 2.3589344
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350 1.000601 -5.2859643 0 -3.7909257 2.9065274
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400 0.99256113 -5.2738812 0 -3.7908553 2.8595867
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450 1.0482542 -5.357452 0 -3.7912128 2.4707397
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500 1.0196176 -5.3123538 0 -3.7889017 2.7230338
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550 0.98274535 -5.2586303 0 -3.7902706 2.9156947
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600 1.0683914 -5.3863229 0 -3.789996 2.3002719
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650 1.0130779 -5.303917 0 -3.7902362 2.8726423
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700 1.0583333 -5.3737358 0 -3.792437 2.5770307
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750 0.98274506 -5.2612464 0 -3.792887 2.9447027
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800 1.0294191 -5.332001 0 -3.7939042 2.5293193
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850 0.99240027 -5.2735754 0 -3.7907899 2.7672711
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900 1.0293488 -5.3306241 0 -3.7926323 2.6054041
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950 0.97137182 -5.2424403 0 -3.7910742 3.129989
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1000 1.0009431 -5.2864286 0 -3.7908788 2.7536598
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Loop time of 0.310363 on 1 procs for 1000 steps with 256 atoms
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Performance: 1391918.252 tau/day, 3222.033 timesteps/s
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100.7% CPU use with 1 MPI tasks x no 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 | 0.22132 | 0.22132 | 0.22132 | 0.0 | 71.31
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Neigh | 0.03458 | 0.03458 | 0.03458 | 0.0 | 11.14
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Comm | 0.0087938 | 0.0087938 | 0.0087938 | 0.0 | 2.83
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Output | 0.014075 | 0.014075 | 0.014075 | 0.0 | 4.54
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Modify | 0.02818 | 0.02818 | 0.02818 | 0.0 | 9.08
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Other | | 0.003411 | | | 1.10
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Nlocal: 256.000 ave 256 max 256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1327.00 ave 1327 max 1327 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 9612.00 ave 9612 max 9612 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9612
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Ave neighs/atom = 37.546875
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Neighbor list builds = 50
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Dangerous builds not checked
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Total wall time: 0:00:00
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@ -146,11 +146,17 @@ void BondBPM::init_style()
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"weights = 1,1,1");
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if (id_fix_dummy_special && break_flag) {
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id_fix_update_special_bonds = utils::strdup("BPM_UPDATE_SPECIAL_BONDS");
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auto newfix = modify->replace_fix(
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// check if an update fix already exists, if so use it
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auto fixes = modify->get_fix_by_style("UPDATE_SPECIAL_BONDS");
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if (fixes.size() > 0 ) {
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fix_update_special_bonds = dynamic_cast<FixUpdateSpecialBonds *>(fixes[0]);
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} else {
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id_fix_update_special_bonds = utils::strdup("BPM_UPDATE_SPECIAL_BONDS");
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auto newfix = modify->replace_fix(
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id_fix_dummy_special,
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fmt::format("{} all UPDATE_SPECIAL_BONDS", id_fix_update_special_bonds), 1);
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fix_update_special_bonds = dynamic_cast<FixUpdateSpecialBonds *>(newfix);
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fix_update_special_bonds = dynamic_cast<FixUpdateSpecialBonds *>(newfix);
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}
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delete[] id_fix_dummy_special;
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id_fix_dummy_special = nullptr;
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}
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@ -162,10 +168,12 @@ void BondBPM::init_style()
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error->all(FLERR, "Bond style bpm requires 1-3 and 1-4 special weights of 1.0");
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}
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if (force->angle || force->dihedral || force->improper)
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error->all(FLERR, "Bond style bpm cannot be used with 3,4-body interactions");
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if (atom->molecular == 2)
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error->all(FLERR, "Bond style bpm cannot be used with atom style template");
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if (break_flag) {
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if (force->angle || force->dihedral || force->improper)
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error->all(FLERR, "Bond style bpm cannot break with 3,4-body interactions");
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if (atom->molecular == 2)
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error->all(FLERR, "Bond style bpm cannot break with atom style template");
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}
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// find all instances of bond history to delete/shift data
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// (bond hybrid may create multiple)
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@ -454,14 +454,12 @@ void BondBPMRotational::damping_forces(int i1, int i2, int type, double *rhat, d
|
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void BondBPMRotational::compute(int eflag, int vflag)
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{
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||||
|
||||
if (!fix_bond_history->stored_flag) {
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fix_bond_history->stored_flag = true;
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store_data();
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}
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if (hybrid_flag)
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fix_bond_history->compress_history();
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if (hybrid_flag) fix_bond_history->compress_history();
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int i1, i2, itmp, n, type;
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double r[3], r0[3], rhat[3];
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@ -544,33 +542,36 @@ void BondBPMRotational::compute(int eflag, int vflag)
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// Apply forces and torques to particles
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||||
// ------------------------------------------------------//
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||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] -= force1on2[0] * smooth;
|
||||
f[i1][1] -= force1on2[1] * smooth;
|
||||
f[i1][2] -= force1on2[2] * smooth;
|
||||
MathExtra::scale3(smooth, force1on2);
|
||||
|
||||
torque[i1][0] += torque2on1[0] * smooth;
|
||||
torque[i1][1] += torque2on1[1] * smooth;
|
||||
torque[i1][2] += torque2on1[2] * smooth;
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] -= force1on2[0];
|
||||
f[i1][1] -= force1on2[1];
|
||||
f[i1][2] -= force1on2[2];
|
||||
|
||||
MathExtra::scale3(smooth, torque2on1);
|
||||
torque[i1][0] += torque2on1[0];
|
||||
torque[i1][1] += torque2on1[1];
|
||||
torque[i1][2] += torque2on1[2];
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] += force1on2[0] * smooth;
|
||||
f[i2][1] += force1on2[1] * smooth;
|
||||
f[i2][2] += force1on2[2] * smooth;
|
||||
f[i2][0] += force1on2[0];
|
||||
f[i2][1] += force1on2[1];
|
||||
f[i2][2] += force1on2[2];
|
||||
|
||||
torque[i2][0] += torque1on2[0] * smooth;
|
||||
torque[i2][1] += torque1on2[1] * smooth;
|
||||
torque[i2][2] += torque1on2[2] * smooth;
|
||||
MathExtra::scale3(smooth, torque1on2);
|
||||
torque[i2][0] += torque1on2[0];
|
||||
torque[i2][1] += torque1on2[1];
|
||||
torque[i2][2] += torque1on2[2];
|
||||
}
|
||||
|
||||
if (evflag)
|
||||
ev_tally_xyz(i1, i2, nlocal, newton_bond, 0.0, -force1on2[0] * smooth, -force1on2[1] * smooth,
|
||||
-force1on2[2] * smooth, r[0], r[1], r[2]);
|
||||
ev_tally_xyz(i1, i2, nlocal, newton_bond, 0.0, -force1on2[0], -force1on2[1],
|
||||
-force1on2[2], r[0], r[1], r[2]);
|
||||
}
|
||||
|
||||
if (hybrid_flag)
|
||||
fix_bond_history->uncompress_history();
|
||||
if (hybrid_flag) fix_bond_history->uncompress_history();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -817,21 +818,22 @@ double BondBPMRotational::single(int type, double rsq, int i, int j, double &ffo
|
||||
|
||||
// set single_extra quantities
|
||||
|
||||
MathExtra::scale3(smooth, force1on2);
|
||||
svector[0] = r0_mag;
|
||||
if (flipped) {
|
||||
svector[1] = -r0[0];
|
||||
svector[2] = -r0[1];
|
||||
svector[3] = -r0[2];
|
||||
svector[4] = force1on2[0] * smooth;
|
||||
svector[5] = force1on2[1] * smooth;
|
||||
svector[6] = force1on2[2] * smooth;
|
||||
svector[4] = force1on2[0];
|
||||
svector[5] = force1on2[1];
|
||||
svector[6] = force1on2[2];
|
||||
} else {
|
||||
svector[1] = r0[0];
|
||||
svector[2] = r0[1];
|
||||
svector[3] = r0[2];
|
||||
svector[4] = -force1on2[0] * smooth;
|
||||
svector[5] = -force1on2[1] * smooth;
|
||||
svector[6] = -force1on2[2] * smooth;
|
||||
svector[4] = -force1on2[0];
|
||||
svector[5] = -force1on2[1];
|
||||
svector[6] = -force1on2[2];
|
||||
}
|
||||
|
||||
return 0.0;
|
||||
|
||||
@ -149,8 +149,6 @@ void BondBPMSpring::store_data()
|
||||
|
||||
void BondBPMSpring::compute(int eflag, int vflag)
|
||||
{
|
||||
if (hybrid_flag) fix_bond_history->compress_history();
|
||||
|
||||
int i, bond_change_flag;
|
||||
double *vol0, *vol;
|
||||
|
||||
@ -195,6 +193,8 @@ void BondBPMSpring::compute(int eflag, int vflag)
|
||||
}
|
||||
}
|
||||
|
||||
if (hybrid_flag) fix_bond_history->compress_history();
|
||||
|
||||
int i1, i2, itmp, n, type;
|
||||
double delx, dely, delz, delvx, delvy, delvz;
|
||||
double e, rsq, r, r0, rinv, smooth, fbond, dot;
|
||||
|
||||
@ -20,8 +20,6 @@
|
||||
|
||||
#include <cmath>
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace Granular_NS;
|
||||
using namespace MathConst;
|
||||
@ -159,6 +157,8 @@ GranSubModDampingCoeffRestitution::GranSubModDampingCoeffRestitution(GranularMod
|
||||
allow_cohesion = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void GranSubModDampingCoeffRestitution::init()
|
||||
{
|
||||
// Calculate prefactor, assume Hertzian as default
|
||||
@ -172,6 +172,8 @@ void GranSubModDampingCoeffRestitution::init()
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double GranSubModDampingCoeffRestitution::calculate_forces()
|
||||
{
|
||||
// in case argument <= 0 due to precision issues
|
||||
|
||||
@ -12,6 +12,7 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "gran_sub_mod_normal.h"
|
||||
|
||||
#include "error.h"
|
||||
#include "granular_model.h"
|
||||
#include "math_const.h"
|
||||
|
||||
@ -77,10 +77,11 @@ void GranSubModRollingSDS::calculate_forces()
|
||||
|
||||
Frcrit = mu * gm->normal_model->get_fncrit();
|
||||
|
||||
hist_temp[0] = gm->history[rhist0];
|
||||
hist_temp[1] = gm->history[rhist1];
|
||||
hist_temp[2] = gm->history[rhist2];
|
||||
|
||||
if (gm->history_update) {
|
||||
hist_temp[0] = gm->history[rhist0];
|
||||
hist_temp[1] = gm->history[rhist1];
|
||||
hist_temp[2] = gm->history[rhist2];
|
||||
rolldotn = dot3(hist_temp, gm->nx);
|
||||
|
||||
frameupdate = (fabs(rolldotn) * k) > (EPSILON * Frcrit);
|
||||
|
||||
@ -231,13 +231,13 @@ void PairSPHTaitwater::coeff(int narg, char **arg)
|
||||
allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
utils::bounds(FLERR,arg[0], 1, atom->ntypes, ilo, ihi, error);
|
||||
utils::bounds(FLERR,arg[1], 1, atom->ntypes, jlo, jhi, error);
|
||||
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
|
||||
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
|
||||
|
||||
double rho0_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double soundspeed_one = utils::numeric(FLERR,arg[3],false,lmp);
|
||||
double viscosity_one = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
double cut_one = utils::numeric(FLERR,arg[5],false,lmp);
|
||||
double rho0_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double soundspeed_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double viscosity_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
double cut_one = utils::numeric(FLERR, arg[5], false, lmp);
|
||||
double B_one = soundspeed_one * soundspeed_one * rho0_one / 7.0;
|
||||
|
||||
int count = 0;
|
||||
@ -254,7 +254,7 @@ void PairSPHTaitwater::coeff(int narg, char **arg)
|
||||
}
|
||||
|
||||
if (count == 0)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
error->all(FLERR, "Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -264,7 +264,7 @@ void PairSPHTaitwater::coeff(int narg, char **arg)
|
||||
double PairSPHTaitwater::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
error->all(FLERR,"All pair sph/taitwater coeffs are set");
|
||||
error->all(FLERR, "All pair sph/taitwater coeffs are not set");
|
||||
}
|
||||
|
||||
cut[j][i] = cut[i][j];
|
||||
|
||||
@ -223,15 +223,15 @@ void NStencil::create_setup()
|
||||
// smax = max possible size of entire 3d stencil
|
||||
// stencil will be empty if cutneighmax = 0.0
|
||||
|
||||
sx = static_cast<int>(cutneighmax*bininvx);
|
||||
if (sx*binsizex < cutneighmax) sx++;
|
||||
sy = static_cast<int>(cutneighmax*bininvy);
|
||||
if (sy*binsizey < cutneighmax) sy++;
|
||||
sz = static_cast<int>(cutneighmax*bininvz);
|
||||
if (sz*binsizez < cutneighmax) sz++;
|
||||
sx = static_cast<int>(cutneighmax * bininvx);
|
||||
if (sx * binsizex < cutneighmax) sx++;
|
||||
sy = static_cast<int>(cutneighmax * bininvy);
|
||||
if (sy * binsizey < cutneighmax) sy++;
|
||||
sz = static_cast<int>(cutneighmax * bininvz);
|
||||
if (sz * binsizez < cutneighmax) sz++;
|
||||
if (dimension == 2) sz = 0;
|
||||
|
||||
int smax = (2*sx+1) * (2*sy+1) * (2*sz+1);
|
||||
int smax = (2 * sx + 1) * (2 * sy + 1) * (2 * sz + 1);
|
||||
|
||||
// reallocate stencil structs if necessary
|
||||
// for BIN and MULTI_OLD styles
|
||||
@ -240,10 +240,10 @@ void NStencil::create_setup()
|
||||
if (smax > maxstencil) {
|
||||
maxstencil = smax;
|
||||
memory->destroy(stencil);
|
||||
memory->create(stencil,maxstencil,"neighstencil:stencil");
|
||||
memory->create(stencil, maxstencil, "neighstencil:stencil");
|
||||
if (xyzflag) {
|
||||
memory->destroy(stencilxyz);
|
||||
memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz");
|
||||
memory->create(stencilxyz, maxstencil, 3, "neighstencil:stencilxyz");
|
||||
}
|
||||
}
|
||||
|
||||
@ -251,9 +251,9 @@ void NStencil::create_setup()
|
||||
int i;
|
||||
int n = atom->ntypes;
|
||||
if (maxstencil_multi_old == 0) {
|
||||
nstencil_multi_old = new int[n+1];
|
||||
stencil_multi_old = new int*[n+1];
|
||||
distsq_multi_old = new double*[n+1];
|
||||
nstencil_multi_old = new int[n + 1];
|
||||
stencil_multi_old = new int*[n + 1];
|
||||
distsq_multi_old = new double*[n + 1];
|
||||
for (i = 1; i <= n; i++) {
|
||||
nstencil_multi_old[i] = 0;
|
||||
stencil_multi_old[i] = nullptr;
|
||||
@ -265,9 +265,9 @@ void NStencil::create_setup()
|
||||
for (i = 1; i <= n; i++) {
|
||||
memory->destroy(stencil_multi_old[i]);
|
||||
memory->destroy(distsq_multi_old[i]);
|
||||
memory->create(stencil_multi_old[i],maxstencil_multi_old,
|
||||
memory->create(stencil_multi_old[i], maxstencil_multi_old,
|
||||
"neighstencil:stencil_multi_old");
|
||||
memory->create(distsq_multi_old[i],maxstencil_multi_old,
|
||||
memory->create(distsq_multi_old[i], maxstencil_multi_old,
|
||||
"neighstencil:distsq_multi_old");
|
||||
}
|
||||
}
|
||||
@ -280,7 +280,7 @@ void NStencil::create_setup()
|
||||
if (nb) copy_bin_info_multi();
|
||||
|
||||
// Deallocate arrays if previously allocated
|
||||
if((n > maxcollections) && stencil_multi){
|
||||
if ((n > maxcollections) && stencil_multi){
|
||||
memory->destroy(nstencil_multi);
|
||||
for (i = 0; i < maxcollections; i++) {
|
||||
for (j = 0; j < maxcollections; j++)
|
||||
@ -339,10 +339,10 @@ void NStencil::create_setup()
|
||||
memory->create(maxstencil_multi, n, n, "neighstencil::maxstencil_multi");
|
||||
memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi");
|
||||
stencil_multi = new int**[n]();
|
||||
for (i = 0; i < n; ++i) {
|
||||
for (i = 0; i < n; i++) {
|
||||
stencil_multi[i] = new int*[n]();
|
||||
for (j = 0; j < n; ++j) {
|
||||
maxstencil_multi[i][j] = 0;
|
||||
for (j = 0; j < n; j++) {
|
||||
maxstencil_multi[i][j] = 0;
|
||||
nstencil_multi[i][j] = 0;
|
||||
stencil_multi[i][j] = nullptr;
|
||||
}
|
||||
@ -378,23 +378,23 @@ void NStencil::create_setup()
|
||||
|
||||
stencil_range = sqrt(cutcollectionsq[i][j]);
|
||||
|
||||
sx = static_cast<int> (stencil_range*bininvx_multi[bin_collection]);
|
||||
if (sx*binsizex_multi[bin_collection] < stencil_range) sx++;
|
||||
sy = static_cast<int> (stencil_range*bininvy_multi[bin_collection]);
|
||||
if (sy*binsizey_multi[bin_collection] < stencil_range) sy++;
|
||||
sz = static_cast<int> (stencil_range*bininvz_multi[bin_collection]);
|
||||
if (sz*binsizez_multi[bin_collection] < stencil_range) sz++;
|
||||
sx = static_cast<int> (stencil_range * bininvx_multi[bin_collection]);
|
||||
if (sx * binsizex_multi[bin_collection] < stencil_range) sx++;
|
||||
sy = static_cast<int> (stencil_range * bininvy_multi[bin_collection]);
|
||||
if (sy * binsizey_multi[bin_collection] < stencil_range) sy++;
|
||||
sz = static_cast<int> (stencil_range * bininvz_multi[bin_collection]);
|
||||
if (sz * binsizez_multi[bin_collection] < stencil_range) sz++;
|
||||
if (dimension == 2) sz = 0;
|
||||
|
||||
stencil_sx_multi[i][j] = sx;
|
||||
stencil_sy_multi[i][j] = sy;
|
||||
stencil_sz_multi[i][j] = sz;
|
||||
|
||||
smax = ((2*sx+1) * (2*sy+1) * (2*sz+1));
|
||||
smax = ((2 * sx + 1) * (2 * sy + 1) * (2 * sz + 1));
|
||||
|
||||
if (smax > maxstencil_multi[i][j]) {
|
||||
maxstencil_multi[i][j] = smax;
|
||||
if(stencil_multi[i][j])
|
||||
if (stencil_multi[i][j])
|
||||
memory->destroy(stencil_multi[i][j]);
|
||||
memory->create(stencil_multi[i][j], smax,
|
||||
"neighstencil::stencil_multi");
|
||||
@ -457,16 +457,20 @@ double NStencil::memory_usage()
|
||||
{
|
||||
double bytes = 0;
|
||||
if (neighstyle == Neighbor::BIN) {
|
||||
bytes += memory->usage(stencil,maxstencil);
|
||||
bytes += memory->usage(stencilxyz,maxstencil,3);
|
||||
bytes += memory->usage(stencil, maxstencil);
|
||||
bytes += memory->usage(stencilxyz, maxstencil, 3);
|
||||
} else if (neighstyle == Neighbor::MULTI_OLD) {
|
||||
bytes += (double)atom->ntypes*maxstencil_multi_old * sizeof(int);
|
||||
bytes += (double)atom->ntypes*maxstencil_multi_old * sizeof(double);
|
||||
bytes += (double)atom->ntypes * maxstencil_multi_old * sizeof(int);
|
||||
bytes += (double)atom->ntypes * maxstencil_multi_old * sizeof(double);
|
||||
} else if (neighstyle == Neighbor::MULTI) {
|
||||
int n = ncollections;
|
||||
for (int i = 0; i < n; i++) {
|
||||
for (int j = 0; j < n; j++) {
|
||||
bytes += (double)maxstencil_multi[i][j] * sizeof(int);
|
||||
|
||||
// May not yet be initialized for occasional lists
|
||||
if (maxstencil_multi) {
|
||||
for (int i = 0; i < n; i++) {
|
||||
for (int j = 0; j < n; j++) {
|
||||
bytes += (double)maxstencil_multi[i][j] * sizeof(int);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user