mirror of https://github.com/lammps/lammps.git
bug-fix for slope() function in variable
This commit is contained in:
Steven J. Plimpton
parent
1b0a8fdc9b
commit
5789ef9128
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@ -47,7 +47,7 @@ compute the diffusion coefficient. You can see that both measures
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give roughly the same answer and rapidly become roughly constant for
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the 100K step simulation.
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Dcoeff = 0.36
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Dcoeff = 0.33
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(2) in.vacf.2d
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@ -58,4 +58,4 @@ that point in time, converted into the diffusion coefficient. You can
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see the VACF approach gives a more noise, fluctuating value for the
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diffusion coefficient, compared to the MSD approach.
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Dcoeff = 0.25 to 0.45
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Dcoeff = ~0.25
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@ -1,245 +0,0 @@
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LAMMPS (13 Oct 2016)
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# sample LAMMPS input script for diffusion of 2d LJ liquid
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# mean-squared displacement via compute msd
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# settings
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variable x equal 40
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variable y equal 40
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variable rho equal 0.6
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variable t equal 1.0
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variable rc equal 2.5
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# problem setup
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units lj
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dimension 2
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atom_style atomic
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neigh_modify delay 0 every 1
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lattice sq2 ${rho}
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lattice sq2 0.6
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Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
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region simbox block 0 $x 0 $y -0.1 0.1
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region simbox block 0 40 0 $y -0.1 0.1
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region simbox block 0 40 0 40 -0.1 0.1
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create_box 1 simbox
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Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
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4 by 2 by 1 MPI processor grid
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create_atoms 1 box
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Created 3200 atoms
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pair_style lj/cut ${rc}
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pair_style lj/cut 2.5
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pair_coeff * * 1 1
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mass * 1.0
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velocity all create $t 97287
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velocity all create 1 97287
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fix 1 all nve
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fix 2 all langevin $t $t 0.1 498094
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fix 2 all langevin 1 $t 0.1 498094
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fix 2 all langevin 1 1 0.1 498094
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fix 3 all enforce2d
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# equilibration run
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thermo 1000
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run 5000
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Neighbor list info ...
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1 neighbor list requests
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4 -> bins = 53 53 1
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Memory usage per processor = 2.478 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 -1.56492 0 -0.5652325 -1.5346995
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1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
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2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
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3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
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4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
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5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
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Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms
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Performance: 3896017.421 tau/day, 9018.559 timesteps/s
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98.9% CPU use with 8 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 | 0.23992 | 0.24608 | 0.25161 | 0.7 | 44.39
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Neigh | 0.063106 | 0.064417 | 0.066279 | 0.4 | 11.62
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Comm | 0.072465 | 0.085066 | 0.094837 | 2.3 | 15.34
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Output | 0.00013208 | 0.00013691 | 0.00014591 | 0.0 | 0.02
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Modify | 0.11441 | 0.11621 | 0.11769 | 0.3 | 20.96
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Other | | 0.04251 | | | 7.67
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Nlocal: 400 ave 406 max 394 min
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Histogram: 1 1 0 1 0 2 1 0 1 1
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Nghost: 202.5 ave 212 max 191 min
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Histogram: 1 0 0 0 3 1 0 2 0 1
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Neighs: 2800.88 ave 2903 max 2690 min
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Histogram: 1 1 0 0 1 2 1 0 1 1
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Total # of neighbors = 22407
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Ave neighs/atom = 7.00219
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Neighbor list builds = 599
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Dangerous builds = 0
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unfix 2
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# data gathering run
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reset_timestep 0
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# factor of 4 in 2 variables is for 2d
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compute msd all msd com yes
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variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
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fix 9 all vector 10 c_msd[4]
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variable fitslope equal slope(f_9)/4/(10*dt)
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thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
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# only need to run for 10K steps to make a good 100-frame movie
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#dump 1 all custom 1 tmp.dump id type vx vy vz
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#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
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thermo 1000
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run 100000
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Memory usage per processor = 2.853 Mbytes
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Step Temp c_msd[4] v_twopoint v_fitslope
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0 0.97069905 0 0 5e+20
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1000 0.98138076 4.0484996 0.20242494 0.18046446
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2000 0.97606079 9.2121392 0.23030346 0.2091528
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3000 0.97924866 14.815034 0.24691721 0.22619184
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4000 0.98568451 20.516817 0.25646019 0.23715506
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5000 0.97551815 27.33922 0.27339219 0.24709999
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6000 0.98482252 34.37734 0.28647782 0.25735178
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7000 0.9672559 41.696689 0.29783348 0.26654059
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8000 0.9836541 48.340277 0.30212673 0.27440308
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9000 0.99087147 56.042692 0.31134828 0.28113047
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10000 0.99663166 63.69663 0.31848314 0.28767921
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11000 0.97776688 71.144109 0.32338231 0.29344527
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12000 0.98246011 78.301774 0.32625739 0.29849471
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13000 0.98788732 85.061923 0.32716124 0.3026655
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14000 0.96872483 91.1658 0.32559214 0.30601023
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15000 0.98955796 97.278388 0.32426129 0.3084275
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16000 0.99855196 104.23997 0.3257499 0.31049883
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17000 0.98600861 110.66055 0.3254722 0.31220348
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18000 0.98696963 116.90111 0.32472531 0.31352676
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19000 0.9881192 124.21305 0.32687644 0.31480062
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20000 0.98527319 131.09874 0.32774685 0.31596198
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21000 0.99015191 137.89263 0.32831579 0.31705324
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22000 0.97972418 146.68982 0.33338595 0.31833889
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23000 0.98911012 155.1264 0.33723129 0.31979515
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24000 0.98810498 162.88634 0.33934653 0.32131187
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25000 0.96961962 170.37907 0.34075814 0.32276215
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26000 0.99118408 179.26511 0.34474059 0.32427111
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27000 0.98515159 185.90764 0.3442734 0.32574529
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28000 0.98951677 192.12183 0.34307469 0.32700292
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29000 0.9832026 196.99457 0.33964581 0.32799023
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30000 0.98449493 203.48475 0.33914124 0.3287171
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31000 0.96585993 210.06193 0.33880956 0.32935775
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32000 0.98758117 218.94174 0.34209646 0.33001591
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33000 0.98875584 225.96489 0.34237104 0.33072947
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34000 0.98007229 233.5792 0.34349882 0.3314385
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35000 0.98415295 241.98148 0.34568783 0.33216634
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36000 0.98101154 250.30876 0.34765106 0.33295272
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37000 0.97606878 258.2127 0.34893608 0.33377673
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38000 0.97220293 266.40464 0.35053242 0.33459273
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39000 0.979783 272.8578 0.34981769 0.33539728
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40000 0.98375673 279.87598 0.34984497 0.33609699
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41000 0.97506523 288.07676 0.35131312 0.33677708
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42000 0.97106749 296.11647 0.3525196 0.33751312
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43000 0.97717259 304.46747 0.35403194 0.33823441
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44000 0.98541435 312.57228 0.35519578 0.3389771
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45000 0.97678287 321.82674 0.35758527 0.33973306
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46000 0.98169719 329.78197 0.35845866 0.34051748
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47000 0.99471466 337.11283 0.35863066 0.34127239
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48000 0.98332437 346.0754 0.3604952 0.34202442
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49000 0.98126947 356.11859 0.36338631 0.34282132
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50000 0.98809751 365.65248 0.36565248 0.34368171
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51000 0.95919516 373.91833 0.36658659 0.34454516
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52000 0.98097913 381.26492 0.36660089 0.34538506
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53000 0.97774072 388.81031 0.36680218 0.34618232
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54000 0.99096915 395.56767 0.36626636 0.3469296
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55000 0.97652739 401.72735 0.36520668 0.34760374
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56000 0.99185306 407.28834 0.3636503 0.34819906
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57000 0.96289342 414.75298 0.3638184 0.34871992
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58000 0.97871716 424.69443 0.36611588 0.34927986
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59000 0.98637393 433.14205 0.36706953 0.34986296
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60000 0.98009845 438.14533 0.36512111 0.35040349
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61000 0.99416712 446.08007 0.3656394 0.35088379
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62000 0.97612483 450.90846 0.36363585 0.35132647
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63000 0.97786531 455.36749 0.36140277 0.35167458
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64000 0.99080668 458.04873 0.35785057 0.3519105
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65000 0.97952497 461.31241 0.3548557 0.3520506
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66000 0.98095955 463.91727 0.35145248 0.35207764
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67000 0.98370788 468.93 0.34994776 0.35204043
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68000 0.96931818 471.07765 0.34638063 0.35192685
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69000 0.98512552 474.59146 0.34390685 0.35174053
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70000 0.98065743 478.66071 0.3419005 0.35149002
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71000 0.98971283 482.57357 0.33984054 0.35119434
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72000 0.99890324 485.32018 0.3370279 0.35084345
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73000 0.98649924 490.19497 0.33574998 0.35043722
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74000 0.98723422 496.04991 0.33516886 0.35003351
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75000 1.0025633 501.6313 0.33442087 0.34962094
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76000 0.97859959 505.97813 0.33288035 0.34921013
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77000 0.97973006 510.55334 0.33152814 0.3487692
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78000 0.9903944 515.06966 0.33017286 0.34830833
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79000 0.96847518 518.76483 0.32833217 0.3478214
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80000 0.99171112 524.18127 0.32761329 0.34733349
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81000 0.97202573 529.09959 0.32660468 0.3468315
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82000 0.99368438 535.80271 0.32670897 0.34633058
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83000 0.97932483 543.08233 0.32715803 0.34586259
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84000 0.99078651 547.57861 0.32593965 0.34540839
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85000 0.98973457 552.24581 0.32485048 0.34493584
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86000 0.9835873 557.3493 0.32404029 0.34446152
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87000 0.97180564 564.93434 0.32467491 0.34400358
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88000 0.99743353 571.39837 0.32465817 0.3435667
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89000 0.98993437 577.81703 0.32461631 0.3431411
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90000 0.9926071 583.39378 0.32410765 0.342724
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91000 0.98800458 591.08741 0.3247733 0.34232767
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92000 0.98501879 596.10133 0.32396811 0.34193949
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93000 0.98810082 604.02652 0.32474544 0.3415681
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94000 0.97563748 609.43676 0.32416849 0.341209
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95000 0.97283448 615.15754 0.32376713 0.34084828
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96000 0.9883071 622.30912 0.32411933 0.34049871
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97000 0.97717678 628.84457 0.32414669 0.34016355
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98000 0.97190208 634.37377 0.32366009 0.3398341
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99000 0.98687379 640.66666 0.32356902 0.33950845
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100000 0.97559757 646.96406 0.32348203 0.33919036
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Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms
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Performance: 4505729.040 tau/day, 10429.928 timesteps/s
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99.4% CPU use with 8 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 | 4.8572 | 4.9363 | 4.9822 | 1.7 | 51.49
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Neigh | 1.3583 | 1.376 | 1.3991 | 1.2 | 14.35
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Comm | 1.5192 | 1.7079 | 1.8264 | 7.2 | 17.81
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Output | 0.0085125 | 0.0086059 | 0.0089455 | 0.1 | 0.09
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Modify | 0.77663 | 0.7903 | 0.81378 | 1.3 | 8.24
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Other | | 0.7686 | | | 8.02
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Nlocal: 400 ave 413 max 391 min
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Histogram: 2 1 0 2 0 0 1 1 0 1
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Nghost: 204.75 ave 213 max 197 min
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Histogram: 1 1 0 1 0 3 0 1 0 1
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Neighs: 2800.62 ave 2959 max 2661 min
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Histogram: 1 1 1 2 0 0 0 1 1 1
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Total # of neighbors = 22405
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Ave neighs/atom = 7.00156
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Neighbor list builds = 12728
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Dangerous builds = 0
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Total wall time: 0:00:10
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@ -0,0 +1,251 @@
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LAMMPS (2 Aug 2018)
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# sample LAMMPS input script for diffusion of 2d LJ liquid
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# mean-squared displacement via compute msd
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# settings
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variable x equal 40
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variable y equal 40
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variable rho equal 0.6
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variable t equal 1.0
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variable rc equal 2.5
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# problem setup
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units lj
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dimension 2
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atom_style atomic
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neigh_modify delay 0 every 1
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lattice sq2 ${rho}
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lattice sq2 0.6
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Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
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region simbox block 0 $x 0 $y -0.1 0.1
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region simbox block 0 40 0 $y -0.1 0.1
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region simbox block 0 40 0 40 -0.1 0.1
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create_box 1 simbox
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Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
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4 by 2 by 1 MPI processor grid
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create_atoms 1 box
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Created 3200 atoms
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Time spent = 0.000706911 secs
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pair_style lj/cut ${rc}
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pair_style lj/cut 2.5
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pair_coeff * * 1 1
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mass * 1.0
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velocity all create $t 97287
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velocity all create 1 97287
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fix 1 all nve
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fix 2 all langevin $t $t 0.1 498094
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fix 2 all langevin 1 $t 0.1 498094
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fix 2 all langevin 1 1 0.1 498094
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fix 3 all enforce2d
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# equilibration run
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thermo 1000
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run 5000
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 53 53 1
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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/atomonly/newton
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stencil: half/bin/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 -1.56492 0 -0.5652325 -1.5346995
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1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
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2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
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3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
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4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
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5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
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Loop time of 0.667446 on 8 procs for 5000 steps with 3200 atoms
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Performance: 3236214.756 tau/day, 7491.238 timesteps/s
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99.9% CPU use with 8 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 | 0.22913 | 0.24877 | 0.28382 | 3.6 | 37.27
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Neigh | 0.064419 | 0.071256 | 0.080013 | 1.7 | 10.68
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Comm | 0.103 | 0.14054 | 0.17204 | 5.5 | 21.06
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Output | 0.00010705 | 0.00013995 | 0.00021911 | 0.0 | 0.02
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Modify | 0.13457 | 0.14973 | 0.16887 | 2.6 | 22.43
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Other | | 0.05701 | | | 8.54
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Nlocal: 400 ave 406 max 394 min
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Histogram: 1 1 0 1 0 2 1 0 1 1
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Nghost: 202.5 ave 212 max 191 min
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Histogram: 1 0 0 0 3 1 0 2 0 1
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Neighs: 2800.88 ave 2903 max 2690 min
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Histogram: 1 1 0 0 1 2 1 0 1 1
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Total # of neighbors = 22407
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Ave neighs/atom = 7.00219
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Neighbor list builds = 599
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Dangerous builds = 0
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unfix 2
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# data gathering run
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reset_timestep 0
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# factor of 4 in 2 variables is for 2d
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compute msd all msd com yes
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variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
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fix 9 all vector 10 c_msd[4]
|
||||
variable fitslope equal slope(f_9)/4/(10*dt)
|
||||
|
||||
thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
|
||||
|
||||
# only need to run for 10K steps to make a good 100-frame movie
|
||||
|
||||
#dump 1 all custom 1 tmp.dump id type vx vy vz
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
|
||||
|
||||
thermo 1000
|
||||
run 100000
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
|
||||
Step Temp c_msd[4] v_twopoint v_fitslope
|
||||
0 0.97069905 0 0 5e+20
|
||||
1000 0.98138076 4.0484996 0.20242494 0.20685564
|
||||
2000 0.97606079 9.2121392 0.23030346 0.23687918
|
||||
3000 0.97924866 14.815034 0.24691721 0.25405247
|
||||
4000 0.98568451 20.516817 0.25646019 0.26353644
|
||||
5000 0.97551815 27.33922 0.27339219 0.27544492
|
||||
6000 0.98482252 34.37734 0.28647782 0.28966619
|
||||
7000 0.9672559 41.696689 0.29783348 0.30165524
|
||||
8000 0.9836541 48.340277 0.30212673 0.31085371
|
||||
9000 0.99087147 56.042692 0.31134828 0.31811489
|
||||
10000 0.99663166 63.69663 0.31848314 0.32589374
|
||||
11000 0.97776688 71.144109 0.32338231 0.33219745
|
||||
12000 0.98246011 78.301774 0.32625739 0.33723
|
||||
13000 0.98788732 85.061923 0.32716124 0.34053027
|
||||
14000 0.96872483 91.1658 0.32559214 0.34231162
|
||||
15000 0.98955796 97.278388 0.32426129 0.34229511
|
||||
16000 0.99855196 104.23997 0.3257499 0.34217252
|
||||
17000 0.98600861 110.66055 0.3254722 0.34172446
|
||||
18000 0.98696963 116.90111 0.32472531 0.3408227
|
||||
19000 0.9881192 124.21305 0.32687644 0.34036538
|
||||
20000 0.98527319 131.09874 0.32774685 0.34003478
|
||||
21000 0.99015191 137.89263 0.32831579 0.33987868
|
||||
22000 0.97972418 146.68982 0.33338595 0.34060035
|
||||
23000 0.98911012 155.1264 0.33723129 0.34201036
|
||||
24000 0.98810498 162.88634 0.33934653 0.34371488
|
||||
25000 0.96961962 170.37907 0.34075814 0.34531409
|
||||
26000 0.99118408 179.26511 0.34474059 0.34717195
|
||||
27000 0.98515159 185.90764 0.3442734 0.34898035
|
||||
28000 0.98951677 192.12183 0.34307469 0.35021808
|
||||
29000 0.9832026 196.99457 0.33964581 0.35075459
|
||||
30000 0.98449493 203.48475 0.33914124 0.35066186
|
||||
31000 0.96585993 210.06193 0.33880956 0.35046715
|
||||
32000 0.98758117 218.94174 0.34209646 0.35046623
|
||||
33000 0.98875584 225.96489 0.34237104 0.35073944
|
||||
34000 0.98007229 233.5792 0.34349882 0.35109188
|
||||
35000 0.98415295 241.98148 0.34568783 0.35157879
|
||||
36000 0.98101154 250.30876 0.34765106 0.3523013
|
||||
37000 0.97606878 258.2127 0.34893608 0.35318097
|
||||
38000 0.97220293 266.40464 0.35053242 0.3540743
|
||||
39000 0.979783 272.8578 0.34981769 0.35496561
|
||||
40000 0.98375673 279.87598 0.34984497 0.35558182
|
||||
41000 0.97506523 288.07676 0.35131312 0.35618259
|
||||
42000 0.97106749 296.11647 0.3525196 0.35698571
|
||||
43000 0.97717259 304.46747 0.35403194 0.3577736
|
||||
44000 0.98541435 312.57228 0.35519578 0.35865003
|
||||
45000 0.97678287 321.82674 0.35758527 0.35958623
|
||||
46000 0.98169719 329.78197 0.35845866 0.36062236
|
||||
47000 0.99471466 337.11283 0.35863066 0.36158322
|
||||
48000 0.98332437 346.0754 0.3604952 0.36255042
|
||||
49000 0.98126947 356.11859 0.36338631 0.3636628
|
||||
50000 0.98809751 365.65248 0.36565248 0.36496809
|
||||
51000 0.95919516 373.91833 0.36658659 0.36628073
|
||||
52000 0.98097913 381.26492 0.36660089 0.36752237
|
||||
53000 0.97774072 388.81031 0.36680218 0.36863962
|
||||
54000 0.99096915 395.56767 0.36626636 0.36961521
|
||||
55000 0.97652739 401.72735 0.36520668 0.37038579
|
||||
56000 0.99185306 407.28834 0.3636503 0.37094092
|
||||
57000 0.96289342 414.75298 0.3638184 0.37130039
|
||||
58000 0.97871716 424.69443 0.36611588 0.37180428
|
||||
59000 0.98637393 433.14205 0.36706953 0.37239862
|
||||
60000 0.98009845 438.14533 0.36512111 0.37288487
|
||||
61000 0.99416712 446.08007 0.3656394 0.37321496
|
||||
62000 0.97612483 450.90846 0.36363585 0.37345792
|
||||
63000 0.97786531 455.36749 0.36140277 0.37344803
|
||||
64000 0.99080668 458.04873 0.35785057 0.37313914
|
||||
65000 0.97952497 461.31241 0.3548557 0.3725875
|
||||
66000 0.98095955 463.91727 0.35145248 0.37174735
|
||||
67000 0.98370788 468.93 0.34994776 0.37076942
|
||||
68000 0.96931818 471.07765 0.34638063 0.36961868
|
||||
69000 0.98512552 474.59146 0.34390685 0.36830908
|
||||
70000 0.98065743 478.66071 0.3419005 0.36686789
|
||||
71000 0.98971283 482.57357 0.33984054 0.36535224
|
||||
72000 0.99890324 485.32018 0.3370279 0.36373174
|
||||
73000 0.98649924 490.19497 0.33574998 0.36200692
|
||||
74000 0.98723422 496.04991 0.33516886 0.36034919
|
||||
75000 1.0025633 501.6313 0.33442087 0.35872052
|
||||
76000 0.97859959 505.97813 0.33288035 0.35714939
|
||||
77000 0.97973006 510.55334 0.33152814 0.35553808
|
||||
78000 0.9903944 515.06966 0.33017286 0.35391584
|
||||
79000 0.96847518 518.76483 0.32833217 0.35226287
|
||||
80000 0.99171112 524.18127 0.32761329 0.35065267
|
||||
81000 0.97202573 529.09959 0.32660468 0.34904364
|
||||
82000 0.99368438 535.80271 0.32670897 0.34747913
|
||||
83000 0.97932483 543.08233 0.32715803 0.34605097
|
||||
84000 0.99078651 547.57861 0.32593965 0.34469765
|
||||
85000 0.98973457 552.24581 0.32485048 0.34332115
|
||||
86000 0.9835873 557.3493 0.32404029 0.34197018
|
||||
87000 0.97180564 564.93434 0.32467491 0.34069702
|
||||
88000 0.99743353 571.39837 0.32465817 0.33951258
|
||||
89000 0.98993437 577.81703 0.32461631 0.33838511
|
||||
90000 0.9926071 583.39378 0.32410765 0.33730429
|
||||
91000 0.98800458 591.08741 0.3247733 0.33630505
|
||||
92000 0.98501879 596.10133 0.32396811 0.33534725
|
||||
93000 0.98810082 604.02652 0.32474544 0.33445545
|
||||
94000 0.97563748 609.43676 0.32416849 0.33361404
|
||||
95000 0.97283448 615.15754 0.32376713 0.33278044
|
||||
96000 0.9883071 622.30912 0.32411933 0.33199212
|
||||
97000 0.97717678 628.84457 0.32414669 0.33125729
|
||||
98000 0.97190208 634.37377 0.32366009 0.33054877
|
||||
99000 0.98687379 640.66666 0.32356902 0.32986014
|
||||
100000 0.97559757 646.96406 0.32348203 0.32920186
|
||||
Loop time of 7.61838 on 8 procs for 100000 steps with 3200 atoms
|
||||
|
||||
Performance: 5670494.518 tau/day, 13126.145 timesteps/s
|
||||
100.0% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.5458 | 3.6709 | 3.8234 | 4.3 | 48.19
|
||||
Neigh | 1.1363 | 1.1513 | 1.1753 | 1.0 | 15.11
|
||||
Comm | 1.5901 | 1.7017 | 1.8664 | 6.9 | 22.34
|
||||
Output | 0.0041966 | 0.0043583 | 0.0050626 | 0.4 | 0.06
|
||||
Modify | 0.63816 | 0.65537 | 0.68918 | 2.0 | 8.60
|
||||
Other | | 0.4348 | | | 5.71
|
||||
|
||||
Nlocal: 400 ave 413 max 391 min
|
||||
Histogram: 2 1 0 2 0 0 1 1 0 1
|
||||
Nghost: 204.75 ave 213 max 197 min
|
||||
Histogram: 1 1 0 1 0 3 0 1 0 1
|
||||
Neighs: 2800.62 ave 2959 max 2661 min
|
||||
Histogram: 1 1 1 2 0 0 0 1 1 1
|
||||
|
||||
Total # of neighbors = 22405
|
||||
Ave neighs/atom = 7.00156
|
||||
Neighbor list builds = 12728
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (13 Oct 2016)
|
||||
LAMMPS (2 Aug 2018)
|
||||
# sample LAMMPS input script for diffusion of 2d LJ liquid
|
||||
# mean-squared displacement via compute msd
|
||||
|
||||
|
|
@ -29,6 +29,7 @@ Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
|
|||
4 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3200 atoms
|
||||
Time spent = 0.000712872 secs
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_style lj/cut 2.5
|
||||
|
|
@ -49,13 +50,18 @@ fix 3 all enforce2d
|
|||
thermo 1000
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 53 53 1
|
||||
Memory usage per processor = 2.478 Mbytes
|
||||
binsize = 1.4, bins = 53 53 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -1.56492 0 -0.5652325 -1.5346995
|
||||
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
|
||||
|
|
@ -63,20 +69,20 @@ Step Temp E_pair E_mol TotEng Press
|
|||
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
|
||||
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
|
||||
5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
|
||||
Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms
|
||||
Loop time of 0.648098 on 8 procs for 5000 steps with 3200 atoms
|
||||
|
||||
Performance: 3873826.669 tau/day, 8967.191 timesteps/s
|
||||
99.1% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
Performance: 3332829.949 tau/day, 7714.884 timesteps/s
|
||||
99.9% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.23784 | 0.24683 | 0.25594 | 1.0 | 44.27
|
||||
Neigh | 0.062975 | 0.06439 | 0.0662 | 0.4 | 11.55
|
||||
Comm | 0.083826 | 0.092564 | 0.1035 | 2.1 | 16.60
|
||||
Output | 0.00011778 | 0.00012615 | 0.00014257 | 0.1 | 0.02
|
||||
Modify | 0.11466 | 0.11648 | 0.1187 | 0.4 | 20.89
|
||||
Other | | 0.0372 | | | 6.67
|
||||
Pair | 0.22614 | 0.24602 | 0.27481 | 2.8 | 37.96
|
||||
Neigh | 0.066875 | 0.07135 | 0.077825 | 1.2 | 11.01
|
||||
Comm | 0.098293 | 0.12744 | 0.1569 | 5.6 | 19.66
|
||||
Output | 0.0001049 | 0.00012228 | 0.00014496 | 0.0 | 0.02
|
||||
Modify | 0.13725 | 0.14919 | 0.16903 | 2.4 | 23.02
|
||||
Other | | 0.05398 | | | 8.33
|
||||
|
||||
Nlocal: 400 ave 406 max 394 min
|
||||
Histogram: 1 1 0 1 0 2 1 0 1 1
|
||||
|
|
@ -114,7 +120,7 @@ thermo_style custom step temp c_vacf[4] v_vacf
|
|||
|
||||
thermo 1000
|
||||
run 100000
|
||||
Memory usage per processor = 2.853 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
|
||||
Step Temp c_vacf[4] v_vacf
|
||||
0 0.97069905 1.9407914 0
|
||||
1000 0.98138076 0.029239763 0.22157396
|
||||
|
|
@ -217,20 +223,20 @@ Step Temp c_vacf[4] v_vacf
|
|||
98000 0.97190208 0.015065013 0.20906937
|
||||
99000 0.98687379 -0.036869401 0.22993959
|
||||
100000 0.97559757 0.045464091 0.23369283
|
||||
Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms
|
||||
Loop time of 8.16691 on 8 procs for 100000 steps with 3200 atoms
|
||||
|
||||
Performance: 3987213.825 tau/day, 9229.662 timesteps/s
|
||||
99.5% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
Performance: 5289636.190 tau/day, 12244.528 timesteps/s
|
||||
100.0% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.8486 | 4.9469 | 5.0248 | 2.8 | 45.66
|
||||
Neigh | 1.3613 | 1.374 | 1.3916 | 0.8 | 12.68
|
||||
Comm | 1.8181 | 1.9534 | 2.0665 | 5.7 | 18.03
|
||||
Output | 0.016565 | 0.016701 | 0.017039 | 0.1 | 0.15
|
||||
Modify | 1.8395 | 1.9053 | 1.9704 | 2.8 | 17.59
|
||||
Other | | 0.6383 | | | 5.89
|
||||
Pair | 3.5668 | 3.6612 | 3.7867 | 4.0 | 44.83
|
||||
Neigh | 1.1409 | 1.1555 | 1.1804 | 1.4 | 14.15
|
||||
Comm | 1.581 | 1.711 | 1.8239 | 7.1 | 20.95
|
||||
Output | 0.016626 | 0.016831 | 0.017569 | 0.2 | 0.21
|
||||
Modify | 1.225 | 1.2594 | 1.3008 | 2.0 | 15.42
|
||||
Other | | 0.363 | | | 4.45
|
||||
|
||||
Nlocal: 400 ave 413 max 391 min
|
||||
Histogram: 2 1 0 2 0 0 1 1 0 1
|
||||
|
|
@ -243,4 +249,4 @@ Total # of neighbors = 22405
|
|||
Ave neighs/atom = 7.00156
|
||||
Neighbor list builds = 12728
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:11
|
||||
Total wall time: 0:00:08
|
||||
189
src/variable.cpp
189
src/variable.cpp
|
|
@ -1576,7 +1576,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
newtree->nextra = 0;
|
||||
treestack[ntreestack++] = newtree;
|
||||
|
||||
} else print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
|
||||
} else print_var_error(FLERR,
|
||||
"Mismatched compute in variable formula",ivar);
|
||||
|
||||
// ----------------
|
||||
// fix
|
||||
|
|
@ -1584,7 +1585,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
|
||||
} else if (strncmp(word,"f_",2) == 0 || strncmp(word,"F_",2) == 0) {
|
||||
if (domain->box_exist == 0)
|
||||
print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
|
||||
print_var_error(FLERR,"Variable evaluation before "
|
||||
"simulation box is defined",ivar);
|
||||
|
||||
// uppercase used to force access of
|
||||
// global vector vs global scalar, and global array vs global vector
|
||||
|
|
@ -1667,11 +1669,14 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
|
||||
if (index1 > fix->size_array_rows &&
|
||||
fix->size_array_rows_variable == 0)
|
||||
print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar);
|
||||
print_var_error(FLERR,"Variable formula fix array is "
|
||||
"accessed out-of-range",ivar);
|
||||
if (index2 > fix->size_array_cols)
|
||||
print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar);
|
||||
print_var_error(FLERR,"Variable formula fix array is "
|
||||
"accessed out-of-range",ivar);
|
||||
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
|
||||
print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
|
||||
print_var_error(FLERR,"Fix in variable not computed at a "
|
||||
"compatible time",ivar);
|
||||
|
||||
value1 = fix->compute_array(index1-1,index2-1);
|
||||
if (tree) {
|
||||
|
|
@ -1688,13 +1693,17 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
} else if (nbracket == 0 && fix->vector_flag) {
|
||||
|
||||
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
|
||||
print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
|
||||
print_var_error(FLERR,"Fix in variable not computed at "
|
||||
"compatible time",ivar);
|
||||
if (tree == NULL)
|
||||
print_var_error(FLERR,"Fix global vector in ""equal-style variable formula",ivar);
|
||||
print_var_error(FLERR,"Fix global vector in "
|
||||
"equal-style variable formula",ivar);
|
||||
if (treetype == ATOM)
|
||||
print_var_error(FLERR,"Fix global vector in ""atom-style variable formula",ivar);
|
||||
print_var_error(FLERR,"Fix global vector in "
|
||||
"atom-style variable formula",ivar);
|
||||
if (fix->size_vector == 0)
|
||||
print_var_error(FLERR,"Variable formula fix vector is zero length",ivar);
|
||||
print_var_error(FLERR,"Variable formula "
|
||||
"fix vector is zero length",ivar);
|
||||
|
||||
int nvec = fix->size_vector;
|
||||
double *vec;
|
||||
|
|
@ -1726,7 +1735,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
print_var_error(FLERR,"Fix global vector in "
|
||||
"atom-style variable formula",ivar);
|
||||
if (fix->size_array_rows == 0)
|
||||
print_var_error(FLERR,"Variable formula fix array is zero length",ivar);
|
||||
print_var_error(FLERR,"Variable formula fix array is "
|
||||
"zero length",ivar);
|
||||
|
||||
int nvec = fix->size_array_rows;
|
||||
double *vec;
|
||||
|
|
@ -1785,10 +1795,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
fix->size_peratom_cols == 0) {
|
||||
|
||||
if (tree == NULL)
|
||||
print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar);
|
||||
print_var_error(FLERR,"Per-atom fix in "
|
||||
"equal-style variable formula",ivar);
|
||||
if (update->whichflag > 0 &&
|
||||
update->ntimestep % fix->peratom_freq)
|
||||
print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
|
||||
print_var_error(FLERR,"Fix in variable not computed at "
|
||||
"compatible time",ivar);
|
||||
|
||||
Tree *newtree = new Tree();
|
||||
newtree->type = ATOMARRAY;
|
||||
|
|
@ -1805,13 +1817,15 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
fix->size_peratom_cols > 0) {
|
||||
|
||||
if (tree == NULL)
|
||||
print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar);
|
||||
print_var_error(FLERR,"Per-atom fix in "
|
||||
"equal-style variable formula",ivar);
|
||||
if (index1 > fix->size_peratom_cols)
|
||||
print_var_error(FLERR,"Variable formula fix array "
|
||||
"is accessed out-of-range",ivar);
|
||||
if (update->whichflag > 0 &&
|
||||
update->ntimestep % fix->peratom_freq)
|
||||
print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
|
||||
print_var_error(FLERR,"Fix in variable not computed at "
|
||||
"compatible time",ivar);
|
||||
|
||||
Tree *newtree = new Tree();
|
||||
newtree->type = ATOMARRAY;
|
||||
|
|
@ -1878,7 +1892,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
|
||||
char *var = retrieve(word+2);
|
||||
if (var == NULL)
|
||||
print_var_error(FLERR,"Invalid variable evaluation in variable formula",ivar);
|
||||
print_var_error(FLERR,"Invalid variable evaluation in "
|
||||
"variable formula",ivar);
|
||||
if (tree) {
|
||||
Tree *newtree = new Tree();
|
||||
newtree->type = VALUE;
|
||||
|
|
@ -1977,7 +1992,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
double *vec;
|
||||
int nvec = compute_vector(ivar,&vec);
|
||||
if (index <= 0 || index > nvec)
|
||||
print_var_error(FLERR,"Invalid index into vector-style variable",ivar);
|
||||
print_var_error(FLERR,"Invalid index into "
|
||||
"vector-style variable",ivar);
|
||||
int m = index; // convert from tagint to int
|
||||
|
||||
if (tree) {
|
||||
|
|
@ -1989,7 +2005,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
treestack[ntreestack++] = newtree;
|
||||
} else argstack[nargstack++] = vec[m-1];
|
||||
|
||||
} else print_var_error(FLERR,"Mismatched variable in variable formula",ivar);
|
||||
} else print_var_error(FLERR,"Mismatched variable in "
|
||||
"variable formula",ivar);
|
||||
|
||||
// ----------------
|
||||
// math/group/special function or atom value/vector or
|
||||
|
|
@ -2194,7 +2211,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
|||
if (value2 == 0.0)
|
||||
argstack[nargstack++] = 1.0;
|
||||
else if ((value1 == 0.0) && (value2 < 0.0))
|
||||
print_var_error(FLERR,"Invalid power expression in variable formula",ivar);
|
||||
print_var_error(FLERR,"Invalid power expression in "
|
||||
"variable formula",ivar);
|
||||
else argstack[nargstack++] = pow(value1,value2);
|
||||
} else if (opprevious == UNARY) {
|
||||
argstack[nargstack++] = -value2;
|
||||
|
|
@ -3368,7 +3386,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
|
|||
if (tree) newtree->type = LN;
|
||||
else {
|
||||
if (value1 <= 0.0)
|
||||
print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar);
|
||||
print_var_error(FLERR,"Log of zero/negative value in "
|
||||
"variable formula",ivar);
|
||||
argstack[nargstack++] = log(value1);
|
||||
}
|
||||
} else if (strcmp(word,"log") == 0) {
|
||||
|
|
@ -3377,7 +3396,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
|
|||
if (tree) newtree->type = LOG;
|
||||
else {
|
||||
if (value1 <= 0.0)
|
||||
print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar);
|
||||
print_var_error(FLERR,"Log of zero/negative value in "
|
||||
"variable formula",ivar);
|
||||
argstack[nargstack++] = log10(value1);
|
||||
}
|
||||
} else if (strcmp(word,"abs") == 0) {
|
||||
|
|
@ -3482,7 +3502,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
|
|||
if (narg != 2)
|
||||
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
|
||||
if (update->whichflag == 0)
|
||||
print_var_error(FLERR,"Cannot use ramp in variable formula between runs",ivar);
|
||||
print_var_error(FLERR,"Cannot use ramp in "
|
||||
"variable formula between runs",ivar);
|
||||
if (tree) newtree->type = RAMP;
|
||||
else {
|
||||
double delta = update->ntimestep - update->beginstep;
|
||||
|
|
@ -3617,7 +3638,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
|
|||
if (narg != 2)
|
||||
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
|
||||
if (update->whichflag == 0)
|
||||
print_var_error(FLERR,"Cannot use vdisplace in variable formula between runs",ivar);
|
||||
print_var_error(FLERR,"Cannot use vdisplace in "
|
||||
"variable formula between runs",ivar);
|
||||
if (tree) newtree->type = VDISPLACE;
|
||||
else {
|
||||
double delta = update->ntimestep - update->beginstep;
|
||||
|
|
@ -3629,7 +3651,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
|
|||
if (narg != 3)
|
||||
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
|
||||
if (update->whichflag == 0)
|
||||
print_var_error(FLERR,"Cannot use swiggle in variable formula between runs",ivar);
|
||||
print_var_error(FLERR,"Cannot use swiggle in "
|
||||
"variable formula between runs",ivar);
|
||||
if (tree) newtree->type = CWIGGLE;
|
||||
else {
|
||||
if (values[0] == 0.0)
|
||||
|
|
@ -3644,7 +3667,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
|
|||
if (narg != 3)
|
||||
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
|
||||
if (update->whichflag == 0)
|
||||
print_var_error(FLERR,"Cannot use cwiggle in variable formula between runs",ivar);
|
||||
print_var_error(FLERR,"Cannot use cwiggle in "
|
||||
"variable formula between runs",ivar);
|
||||
if (tree) newtree->type = CWIGGLE;
|
||||
else {
|
||||
if (values[0] == 0.0)
|
||||
|
|
@ -3709,7 +3733,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
|
||||
if (strcmp(word,"count") == 0) {
|
||||
if (narg == 1) value = group->count(igroup);
|
||||
else if (narg == 2) value = group->count(igroup,region_function(args[1],ivar));
|
||||
else if (narg == 2)
|
||||
value = group->count(igroup,region_function(args[1],ivar));
|
||||
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
|
||||
|
||||
} else if (strcmp(word,"mass") == 0) {
|
||||
|
|
@ -3719,7 +3744,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
|
||||
} else if (strcmp(word,"charge") == 0) {
|
||||
if (narg == 1) value = group->charge(igroup);
|
||||
else if (narg == 2) value = group->charge(igroup,region_function(args[1],ivar));
|
||||
else if (narg == 2)
|
||||
value = group->charge(igroup,region_function(args[1],ivar));
|
||||
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
|
||||
|
||||
} else if (strcmp(word,"xcm") == 0) {
|
||||
|
|
@ -3732,7 +3758,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
int iregion = region_function(args[2],ivar);
|
||||
double masstotal = group->mass(igroup,iregion);
|
||||
group->xcm(igroup,masstotal,xcm,iregion);
|
||||
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
|
||||
} else print_var_error(FLERR,"Invalid group function in "
|
||||
"variable formula",ivar);
|
||||
if (strcmp(args[1],"x") == 0) value = xcm[0];
|
||||
else if (strcmp(args[1],"y") == 0) value = xcm[1];
|
||||
else if (strcmp(args[1],"z") == 0) value = xcm[2];
|
||||
|
|
@ -3748,7 +3775,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
int iregion = region_function(args[2],ivar);
|
||||
double masstotal = group->mass(igroup,iregion);
|
||||
group->vcm(igroup,masstotal,vcm,iregion);
|
||||
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
|
||||
} else print_var_error(FLERR,"Invalid group function in "
|
||||
"variable formula",ivar);
|
||||
if (strcmp(args[1],"x") == 0) value = vcm[0];
|
||||
else if (strcmp(args[1],"y") == 0) value = vcm[1];
|
||||
else if (strcmp(args[1],"z") == 0) value = vcm[2];
|
||||
|
|
@ -3767,7 +3795,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
} else if (strcmp(word,"bound") == 0) {
|
||||
double minmax[6];
|
||||
if (narg == 2) group->bounds(igroup,minmax);
|
||||
else if (narg == 3) group->bounds(igroup,minmax,region_function(args[2],ivar));
|
||||
else if (narg == 3)
|
||||
group->bounds(igroup,minmax,region_function(args[2],ivar));
|
||||
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
|
||||
if (strcmp(args[1],"xmin") == 0) value = minmax[0];
|
||||
else if (strcmp(args[1],"xmax") == 0) value = minmax[1];
|
||||
|
|
@ -3789,7 +3818,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
double masstotal = group->mass(igroup,iregion);
|
||||
group->xcm(igroup,masstotal,xcm,iregion);
|
||||
value = group->gyration(igroup,masstotal,xcm,iregion);
|
||||
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
|
||||
} else print_var_error(FLERR,"Invalid group function in "
|
||||
"variable formula",ivar);
|
||||
|
||||
} else if (strcmp(word,"ke") == 0) {
|
||||
if (narg == 1) value = group->ke(igroup);
|
||||
|
|
@ -3808,7 +3838,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
double masstotal = group->mass(igroup,iregion);
|
||||
group->xcm(igroup,masstotal,xcm,iregion);
|
||||
group->angmom(igroup,xcm,lmom,iregion);
|
||||
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
|
||||
} else print_var_error(FLERR,"Invalid group function in "
|
||||
"variable formula",ivar);
|
||||
if (strcmp(args[1],"x") == 0) value = lmom[0];
|
||||
else if (strcmp(args[1],"y") == 0) value = lmom[1];
|
||||
else if (strcmp(args[1],"z") == 0) value = lmom[2];
|
||||
|
|
@ -3826,7 +3857,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
double masstotal = group->mass(igroup,iregion);
|
||||
group->xcm(igroup,masstotal,xcm,iregion);
|
||||
group->torque(igroup,xcm,tq,iregion);
|
||||
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
|
||||
} else print_var_error(FLERR,"Invalid group function in "
|
||||
"variable formula",ivar);
|
||||
if (strcmp(args[1],"x") == 0) value = tq[0];
|
||||
else if (strcmp(args[1],"y") == 0) value = tq[1];
|
||||
else if (strcmp(args[1],"z") == 0) value = tq[2];
|
||||
|
|
@ -3844,7 +3876,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
double masstotal = group->mass(igroup,iregion);
|
||||
group->xcm(igroup,masstotal,xcm,iregion);
|
||||
group->inertia(igroup,xcm,inertia,iregion);
|
||||
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
|
||||
} else print_var_error(FLERR,"Invalid group function in "
|
||||
"variable formula",ivar);
|
||||
if (strcmp(args[1],"xx") == 0) value = inertia[0][0];
|
||||
else if (strcmp(args[1],"yy") == 0) value = inertia[1][1];
|
||||
else if (strcmp(args[1],"zz") == 0) value = inertia[2][2];
|
||||
|
|
@ -3869,7 +3902,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
|||
group->angmom(igroup,xcm,angmom,iregion);
|
||||
group->inertia(igroup,xcm,inertia,iregion);
|
||||
group->omega(angmom,inertia,omega);
|
||||
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
|
||||
} else print_var_error(FLERR,"Invalid group function in "
|
||||
"variable formula",ivar);
|
||||
if (strcmp(args[1],"x") == 0) value = omega[0];
|
||||
else if (strcmp(args[1],"y") == 0) value = omega[1];
|
||||
else if (strcmp(args[1],"z") == 0) value = omega[2];
|
||||
|
|
@ -3924,7 +3958,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
Tree **treestack, int &ntreestack,
|
||||
double *argstack, int &nargstack, int ivar)
|
||||
{
|
||||
double value,xvalue,sx,sy,sxx,sxy;
|
||||
bigint sx,sxx;
|
||||
double value,xvalue,sy,sxy;
|
||||
|
||||
// word not a match to any special function
|
||||
|
||||
|
|
@ -4020,11 +4055,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
} else index = 0;
|
||||
|
||||
int ifix = modify->find_fix(&args[0][2]);
|
||||
if (ifix < 0) print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
|
||||
if (ifix < 0)
|
||||
print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
|
||||
fix = modify->fix[ifix];
|
||||
if (index == 0 && fix->vector_flag) {
|
||||
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
|
||||
print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
|
||||
print_var_error(FLERR,"Fix in variable not computed at "
|
||||
"compatible time",ivar);
|
||||
nvec = fix->size_vector;
|
||||
nstride = 1;
|
||||
} else if (index && fix->array_flag) {
|
||||
|
|
@ -4032,7 +4069,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
print_var_error(FLERR,"Variable formula fix array "
|
||||
"is accessed out-of-range",ivar);
|
||||
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
|
||||
print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
|
||||
print_var_error(FLERR,"Fix in variable not computed at "
|
||||
"compatible time",ivar);
|
||||
nvec = fix->size_array_rows;
|
||||
nstride = fix->size_array_cols;
|
||||
} else print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
|
||||
|
|
@ -4048,10 +4086,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
} else index = 0;
|
||||
|
||||
if (index)
|
||||
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
|
||||
print_var_error(FLERR,"Invalid special function in "
|
||||
"variable formula",ivar);
|
||||
ivar = find(&args[0][2]);
|
||||
if (ivar < 0)
|
||||
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
|
||||
print_var_error(FLERR,"Invalid special function in "
|
||||
"variable formula",ivar);
|
||||
if (style[ivar] != VECTOR)
|
||||
print_var_error(FLERR,"Mis-matched special function variable "
|
||||
"in variable formula",ivar);
|
||||
|
|
@ -4062,12 +4102,16 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
nvec = compute_vector(ivar,&vec);
|
||||
nstride = 1;
|
||||
|
||||
} else print_var_error(FLERR,"Invalid special function in variable formula",ivar);
|
||||
} else print_var_error(FLERR,"Invalid special function in "
|
||||
"variable formula",ivar);
|
||||
|
||||
value = 0.0;
|
||||
if (method == SLOPE) sx = sy = sxx = sxy = 0.0;
|
||||
if (method == XMIN) value = BIG;
|
||||
if (method == XMAX) value = -BIG;
|
||||
if (method == SLOPE) {
|
||||
sx = sxx = 0;
|
||||
sy = sxy = 0.0;
|
||||
}
|
||||
else if (method == XMIN) value = BIG;
|
||||
else if (method == XMAX) value = -BIG;
|
||||
|
||||
if (compute) {
|
||||
double *vec;
|
||||
|
|
@ -4084,12 +4128,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
else if (method == AVE) value += vec[j];
|
||||
else if (method == TRAP) value += vec[j];
|
||||
else if (method == SLOPE) {
|
||||
if (nvec > 1) xvalue = (double) i / (nvec-1);
|
||||
else xvalue = 0.0;
|
||||
sx += xvalue;
|
||||
sx += i;
|
||||
sy += vec[j];
|
||||
sxx += xvalue*xvalue;
|
||||
sxy += xvalue*vec[j];
|
||||
sxx += i*i;
|
||||
sxy += i*vec[j];
|
||||
}
|
||||
j += nstride;
|
||||
}
|
||||
|
|
@ -4107,12 +4149,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
else if (method == AVE) value += one;
|
||||
else if (method == TRAP) value += one;
|
||||
else if (method == SLOPE) {
|
||||
if (nvec > 1) xvalue = (double) i / (nvec-1);
|
||||
else xvalue = 0.0;
|
||||
sx += xvalue;
|
||||
sx += i;
|
||||
sy += one;
|
||||
sxx += xvalue*xvalue;
|
||||
sxy += xvalue*one;
|
||||
sxx += i*i;
|
||||
sxy += i*one;
|
||||
}
|
||||
}
|
||||
if (method == TRAP) {
|
||||
|
|
@ -4134,12 +4174,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
else if (method == AVE) value += one;
|
||||
else if (method == TRAP) value += one;
|
||||
else if (method == SLOPE) {
|
||||
if (nvec > 1) xvalue = (double) i / (nvec-1);
|
||||
else xvalue = 0.0;
|
||||
sx += xvalue;
|
||||
sx += i;
|
||||
sy += one;
|
||||
sxx += xvalue*xvalue;
|
||||
sxy += xvalue*one;
|
||||
sxx += i*i;
|
||||
sxy += i*one;
|
||||
}
|
||||
}
|
||||
if (method == TRAP) value -= 0.5*vec[0] + 0.5*vec[nvec-1];
|
||||
|
|
@ -4148,9 +4186,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
if (method == AVE) value /= nvec;
|
||||
|
||||
if (method == SLOPE) {
|
||||
double numerator = sxy - sx*sy;
|
||||
double denominator = sxx - sx*sx;
|
||||
if (denominator != 0.0) value = numerator/denominator / nvec;
|
||||
double numerator = nvec*sxy - sx*sy;
|
||||
double denominator = nvec*sxx - sx*sx;
|
||||
if (denominator != 0.0) value = numerator/denominator;
|
||||
else value = BIG;
|
||||
}
|
||||
|
||||
|
|
@ -4169,7 +4207,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
|
||||
} else if (strcmp(word,"gmask") == 0) {
|
||||
if (tree == NULL)
|
||||
print_var_error(FLERR,"Gmask function in equal-style variable formula",ivar);
|
||||
print_var_error(FLERR,"Gmask function in equal-style "
|
||||
"variable formula",ivar);
|
||||
if (narg != 1)
|
||||
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
|
||||
|
||||
|
|
@ -4186,7 +4225,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
|
||||
} else if (strcmp(word,"rmask") == 0) {
|
||||
if (tree == NULL)
|
||||
print_var_error(FLERR,"Rmask function in equal-style variable formula",ivar);
|
||||
print_var_error(FLERR,"Rmask function in equal-style "
|
||||
"variable formula",ivar);
|
||||
if (narg != 1)
|
||||
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
|
||||
|
||||
|
|
@ -4202,7 +4242,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
|
||||
} else if (strcmp(word,"grmask") == 0) {
|
||||
if (tree == NULL)
|
||||
print_var_error(FLERR,"Grmask function in equal-style variable formula",ivar);
|
||||
print_var_error(FLERR,"Grmask function in equal-style "
|
||||
"variable formula",ivar);
|
||||
if (narg != 2)
|
||||
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
|
||||
|
||||
|
|
@ -4228,7 +4269,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
|
||||
int ivar = find(args[0]);
|
||||
if (ivar < 0)
|
||||
print_var_error(FLERR,"Variable ID in variable formula does not exist",ivar);
|
||||
print_var_error(FLERR,"Variable ID in "
|
||||
"variable formula does not exist",ivar);
|
||||
|
||||
// SCALARFILE has single current value, read next one
|
||||
// save value in tree or on argstack
|
||||
|
|
@ -4253,7 +4295,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
|
||||
} else if (style[ivar] == ATOMFILE) {
|
||||
if (tree == NULL)
|
||||
print_var_error(FLERR,"Atomfile variable in equal-style variable formula",ivar);
|
||||
print_var_error(FLERR,"Atomfile variable in "
|
||||
"equal-style variable formula",ivar);
|
||||
|
||||
double *result;
|
||||
memory->create(result,atom->nlocal,"variable:result");
|
||||
|
|
@ -4271,11 +4314,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
newtree->nextra = 0;
|
||||
treestack[ntreestack++] = newtree;
|
||||
|
||||
} else print_var_error(FLERR,"Invalid variable style in special function next",ivar);
|
||||
} else print_var_error(FLERR,"Invalid variable style in "
|
||||
"special function next",ivar);
|
||||
|
||||
} else if (strcmp(word,"is_active") == 0) {
|
||||
if (narg != 2)
|
||||
print_var_error(FLERR,"Invalid is_active() function in variable formula",ivar);
|
||||
print_var_error(FLERR,"Invalid is_active() function in "
|
||||
"variable formula",ivar);
|
||||
|
||||
Info info(lmp);
|
||||
value = (info.is_active(args[0],args[1])) ? 1.0 : 0.0;
|
||||
|
|
@ -4293,7 +4338,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
|
||||
} else if (strcmp(word,"is_available") == 0) {
|
||||
if (narg != 2)
|
||||
print_var_error(FLERR,"Invalid is_available() function in variable formula",ivar);
|
||||
print_var_error(FLERR,"Invalid is_available() function in "
|
||||
"variable formula",ivar);
|
||||
|
||||
Info info(lmp);
|
||||
value = (info.is_available(args[0],args[1])) ? 1.0 : 0.0;
|
||||
|
|
@ -4311,7 +4357,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
|
|||
|
||||
} else if (strcmp(word,"is_defined") == 0) {
|
||||
if (narg != 2)
|
||||
print_var_error(FLERR,"Invalid is_defined() function in variable formula",ivar);
|
||||
print_var_error(FLERR,"Invalid is_defined() function in "
|
||||
"variable formula",ivar);
|
||||
|
||||
Info info(lmp);
|
||||
value = (info.is_defined(args[0],args[1])) ? 1.0 : 0.0;
|
||||
|
|
|
|||
Loading…
Reference in New Issue