diff --git a/examples/README b/examples/README index e476df30f4..7f38b31bf5 100644 --- a/examples/README +++ b/examples/README @@ -49,6 +49,7 @@ prd: parallel replica dynamics of a vacancy diffusion in bulk Si reax: RDX and TATB models using the ReaxFF rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void +srd: stochastic rotation dynamics (SRD) particles as solvent Here is how you might run and visualize one of the sample problems: diff --git a/examples/srd/in.srd.mixture b/examples/srd/in.srd.mixture new file mode 100644 index 0000000000..77d95eac0b --- /dev/null +++ b/examples/srd/in.srd.mixture @@ -0,0 +1,102 @@ +# 2d SRD test: big + small particles + +units lj +atom_style colloid +atom_modify first big +dimension 2 + +# create big particles with sigma 1.0 + +lattice sq 0.4 +region box block 0 10 0 10 -0.5 0.5 +create_box 2 box +create_atoms 1 region box +mass 1 1.0 +mass 2 0.01 + +shape 1 1.0 1.0 1.0 +shape 2 0.0 0.0 0.0 + +group big type 1 +velocity big create 1.44 87287 loop geom + +# equilibrate big particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 big nve +fix 2 all enforce2d + +run 1000 + +unfix 1 +unfix 2 + +# add small particles as hi density lattice + +lattice sq 0.4 +region plane block 0 10 0 10 -0.001 0.001 +lattice sq 85.0 +create_atoms 2 region plane + +group small type 2 + +velocity small create 1.0 593849 loop geom + +# delete overlaps +# must set 1-2 cutoff to non-zero value + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.5 + +delete_atoms overlap 0.5 small big + +# SRD run + +reset_timestep 0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +communicate multi group big vel yes +neigh_modify include big + +# no pairwise interactions with small particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +# use fix SRD to push small particles out from inside big ones + +timestep 0.001 + +fix 1 big nve +fix 2 small srd 20 big 1.0 0.25 49894 & + radius 0.88 search 0.2 collision slip +fix 3 all enforce2d + +# diagnostics + +compute tbig big temp +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press & + f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & + f_2[6] f_2[8] f_2[9] f_2[10] + +thermo_modify temp tbig +thermo 100 +dump 1 all atom 250 dump.srd.mixture + +run 5000 + diff --git a/examples/srd/in.srd.pure b/examples/srd/in.srd.pure new file mode 100644 index 0000000000..c9b9e588a1 --- /dev/null +++ b/examples/srd/in.srd.pure @@ -0,0 +1,46 @@ +# 2d SRD only test + +units lj +atom_style atomic +atom_modify first empty +dimension 2 + +# create box with big lattice + +lattice sq 0.4 +region box block 0 10 0 10 -0.5 0.5 +create_box 1 box + +# add SRD particles as hi density lattice + +lattice sq 0.4 +region plane block 0 10 0 10 -0.001 0.001 +lattice sq 85.0 +create_atoms 1 region plane + +group empty type 2 + +mass 1 0.01 +velocity all create 1.0 593849 loop geom + +# settings - need dummy empty group to enable no communication + +neighbor 0.3 bin +neigh_modify delay 1 every 1 check no + +communicate single group empty + +# timestep is big and SRD frequency is 1 + +timestep 0.02 + +fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip +fix 2 all enforce2d + +# diagnostics + +thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6] +thermo 100 +dump 1 all atom 250 dump.srd.pure + +run 5000 diff --git a/examples/srd/log.srd.mixture.10Sep10.linux.1 b/examples/srd/log.srd.mixture.10Sep10.linux.1 new file mode 100644 index 0000000000..2002a07512 --- /dev/null +++ b/examples/srd/log.srd.mixture.10Sep10.linux.1 @@ -0,0 +1,220 @@ +LAMMPS (1 Oct 2010) +# 2d SRD test: big + small particles + +units lj +atom_style colloid +atom_modify first big +dimension 2 + +# create big particles with sigma 1.0 + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 +region box block 0 10 0 10 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569) + 1 by 1 by 1 processor grid +create_atoms 1 region box +Created 100 atoms +mass 1 1.0 +mass 2 0.01 + +shape 1 1.0 1.0 1.0 +shape 2 0.0 0.0 0.0 + +group big type 1 +100 atoms in group big +velocity big create 1.44 87287 loop geom + +# equilibrate big particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 big nve +fix 2 all enforce2d + +run 1000 +Memory usage per processor = 2.1298 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -0.54272 0 0.88288 -0.041088 + 1000 1.8791467 -0.97185784 0 0.8884974 0.61487656 +Loop time of 0.0272841 on 1 procs for 1000 steps with 100 atoms + +Pair time (%) = 0.0153759 (56.3545) +Neigh time (%) = 0.00355697 (13.0368) +Comm time (%) = 0.00313544 (11.4918) +Outpt time (%) = 2.7895e-05 (0.102239) +Other time (%) = 0.00518799 (19.0147) + +Nlocal: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 88 ave 88 max 88 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 459 ave 459 max 459 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 459 +Ave neighs/atom = 4.59 +Neighbor list builds = 129 +Dangerous builds = 0 + +unfix 1 +unfix 2 + +# add small particles as hi density lattice + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 +region plane block 0 10 0 10 -0.001 0.001 +lattice sq 85.0 +Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 +create_atoms 2 region plane +Created 21316 atoms + +group small type 2 +21316 atoms in group small + +velocity small create 1.0 593849 loop geom + +# delete overlaps +# must set 1-2 cutoff to non-zero value + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.5 + +delete_atoms overlap 0.5 small big +Deleted 6700 atoms, new total = 14716 + +# SRD run + +reset_timestep 0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +communicate multi group big vel yes +neigh_modify include big + +# no pairwise interactions with small particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +# use fix SRD to push small particles out from inside big ones + +timestep 0.001 + +fix 1 big nve +fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip +fix 3 all enforce2d + +# diagnostics + +compute tbig big temp +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10] + +thermo_modify temp tbig +WARNING: Temperature for thermo pressure is not for group all +thermo 100 +dump 1 all atom 250 dump.srd.mixture + +run 5000 +SRD info: + SRD/big particles = 14616 100 + big particle diameter max/min = 0.88 0.88 + SRD temperature & lamda = 1 0.2 + SRD max distance & max velocity = 0.8 40 + SRD grid counts: 63 63 1 + SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114 + SRD per actual grid cell = 4.86648 + SRD viscosity = 0.463448 + big/SRD mass density ratio = 2.12808 +WARNING: Fix srd grid size > 1/4 of big particle diameter + # of rescaled SRD velocities = 0 + ave/max small velocity = 13.2944 24.262 + ave/max big velocity = 1.69284 5.10989 +Memory usage per processor = 9.18853 Mbytes +Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10] + 0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487656 0 0 0 0 0 0 0 0 0 + 100 1.1854519 3969 0.0020564907 -0.8709642 0.30263317 0.89895867 7567 82 82 0 0 12996 3018 1.0025076 0 + 200 1.0912203 3969 0.00077322095 -0.96652094 0.11378719 0.53220883 7617 91 91 0 0 12996 3019 1.0315077 0 + 300 0.99609974 3969 -8.9958107e-05 -0.99937698 -0.013238235 0.30744437 7686 92 92 0 0 12996 3014 1.0224789 0 + 400 0.97378829 3969 -1.0310777e-06 -0.96420214 -0.00015173339 0.29401458 7517 104 104 0 0 12996 3015 1.0354258 0 + 500 1.0704853 3969 0.00045875378 -0.99227027 0.067510207 0.23723623 7507 90 90 0 0 12996 3013 1.0255432 0 + 600 0.98490603 3969 -0.00036594295 -1.0289091 -0.053852164 0.17457127 7475 84 84 0 0 12996 2994 1.0362491 0 + 700 1.1128816 3969 0.00061003578 -1.0119799 0.089772865 0.44497962 7680 97 97 0 0 12996 3017 1.0076201 0 + 800 0.96861977 3969 -0.00069285411 -1.060894 -0.10196041 0.3497781 7534 74 74 0 0 12996 3008 1.0271614 0 + 900 1.0407967 3969 0.00047726289 -0.9601547 0.070234006 0.70144271 7521 97 97 0 0 12996 2988 1.0115957 0 + 1000 1.0543264 3969 7.8805118e-05 -1.0321862 0.011596961 0.41617549 7499 82 82 0 0 12996 3022 1.0039293 0 + 1100 0.79276143 3969 -0.0014999076 -1.0055602 -0.22072641 0.38874703 7333 100 100 0 0 12996 3013 1.0389616 0 + 1200 1.084432 3969 0.00068593846 -0.97264494 0.1009427 0.60176004 7348 81 81 0 0 12996 2999 1.0009925 0 + 1300 1.0487612 3969 0.00032122262 -0.9910025 0.047271121 0.49732554 7551 94 94 0 0 12996 2988 1.0221747 0 + 1400 1.0098443 3969 4.0826801e-05 -0.99373776 0.006008072 0.51403259 7619 89 89 0 0 12996 3007 1.0344942 0 + 1500 1.218401 3969 0.00097129173 -1.0632817 0.14293529 0.38730792 7414 87 87 0 0 12996 3015 1.0519305 0 + 1600 1.1501145 3969 0.00047446251 -1.0687914 0.069821903 0.35607234 7383 80 80 0 0 12996 3014 1.0203142 0 + 1700 0.94258444 3969 -0.0007994931 -1.050812 -0.1176534 0.40572317 7597 92 92 0 0 12996 3002 1.0469204 0 + 1800 1.1205745 3969 0.00014712615 -1.0877177 0.021651085 0.37897578 7585 82 82 0 0 12996 2991 1.0389588 0 + 1900 0.95430392 3969 -0.0010155747 -1.0942129 -0.14945198 0.24556839 7703 85 85 0 0 12996 3001 1.0246638 0 + 2000 0.92246887 3969 -0.0011696335 -1.0853675 -0.17212327 0.23953568 7636 100 100 0 0 12996 3022 1.0204788 0 + 2100 0.91529221 3969 -0.0012601691 -1.0915858 -0.18544648 0.22735286 7481 80 80 0 0 12996 3026 1.0280942 0 + 2200 0.89505853 3969 -0.00064151149 -0.98051277 -0.094404831 0.51723842 7418 87 87 0 0 12996 3000 1.027661 0 + 2300 0.98485557 3969 -0.00075152689 -1.0856017 -0.1105947 0.24927644 7590 80 80 0 0 12996 2999 1.0258603 0 + 2400 0.91841201 3969 -0.0010505855 -1.0638321 -0.15460417 0.23326098 7587 103 103 0 0 12996 3001 1.0282876 0 + 2500 1.0358998 3969 6.5299645e-05 -1.0159313 0.0096094958 0.34899097 7452 93 93 0 0 12996 2975 1.0426326 0 + 2600 0.94743566 3969 -0.00053875484 -1.0172445 -0.079283162 0.22735975 7560 66 66 0 0 12996 2996 1.0211493 0 + 2700 0.87106832 3969 -0.0010996524 -1.0241825 -0.16182485 0.25604039 7329 83 83 0 0 12996 3005 1.0305366 0 + 2800 1.0803159 3969 0.00030634738 -1.0244307 0.045082081 0.45643311 7418 108 108 0 0 12996 3023 1.0340188 0 + 2900 1.1283591 3969 0.00084010869 -0.99344512 0.12363039 0.83746145 7308 91 91 0 0 12996 2981 1.0189882 0 + 3000 1.1876657 3969 0.0016273526 -0.93630787 0.23948121 0.97168782 7453 87 87 0 0 12996 2979 1.0166656 0 + 3100 1.0004566 3969 -0.00032761995 -1.0386645 -0.048212552 0.61341839 7470 87 87 0 0 12996 3031 1.017823 0 + 3200 1.2257669 3969 0.00099290366 -1.0673936 0.1461157 0.61730027 7545 86 86 0 1 12996 2963 1.0419479 0 + 3300 1.0483473 3969 -0.00031074739 -1.0835934 -0.045729586 0.52991291 7442 84 84 0 0 12996 3010 1.015561 0 + 3400 1.1060909 3969 0.00030818848 -1.049677 0.045353017 0.7068218 7459 87 87 0 0 12996 3002 1.0231151 0 + 3500 1.0538669 3969 -0.00036380882 -1.0968664 -0.053538106 0.45965228 7648 81 81 0 0 12996 3020 1.0228882 0 + 3600 0.9403379 3969 -0.00095052032 -1.0708131 -0.13987857 0.29232958 7731 104 104 0 0 12996 3015 1.0308016 0 + 3700 0.87576431 3969 -0.0013620431 -1.0674449 -0.20043826 0.20807819 7570 93 93 0 0 12996 2999 1.027521 0 + 3800 1.0214205 3969 -0.00025908571 -1.0493333 -0.038127053 0.35110253 7480 95 95 0 0 12996 3023 1.0189546 0 + 3900 1.0399628 3969 -0.0004657163 -1.098098 -0.068534811 0.14477785 7597 84 84 0 0 12996 3001 1.0391639 0 + 4000 0.96223871 3969 -0.00087553027 -1.0814594 -0.12884303 0.32672058 7506 91 91 0 0 12996 3026 1.0273983 0 + 4100 0.9978966 3969 -0.00014719261 -1.0095785 -0.021660865 0.54900472 7553 89 89 0 0 12996 3008 1.0214976 0 + 4200 0.99324797 3969 -0.00014342613 -1.0044221 -0.02110659 0.5121817 7423 77 77 0 0 12996 3008 1.0621727 0 + 4300 0.90689211 3969 -0.00089523015 -1.0295653 -0.13174207 0.41794731 7614 77 77 0 0 12996 3009 1.0361369 0 + 4400 0.94201541 3969 -0.00126231 -1.1183568 -0.18576154 0.16778284 7600 91 91 0 0 12996 3004 1.035561 0 + 4500 0.97003803 3969 -0.00090250856 -1.0931508 -0.13281316 0.37787471 7505 96 96 0 0 12996 2998 1.0335568 0 + 4600 0.96052354 3969 -0.00093721969 -1.0888396 -0.13792125 0.48917838 7532 72 72 0 0 12996 2999 1.0124728 0 + 4700 0.95086208 3969 -0.00076105324 -1.0533501 -0.11199659 0.60704145 7429 104 104 0 0 12996 2988 1.0095829 0 + 4800 0.94826516 3969 -0.0010878926 -1.0988768 -0.16009427 0.50867751 7351 93 93 0 0 12996 2968 1.0212405 0 + 4900 1.0540371 3969 -4.230244e-06 -1.0441192 -0.00062252271 0.6999864 7454 91 91 0 0 12996 2998 1.0019459 0 + 5000 0.94814157 3969 -0.0007896491 -1.0548649 -0.11620476 0.61244147 7362 76 76 0 0 12996 2976 1.0250728 0 +Loop time of 5.65139 on 1 procs for 5000 steps with 14716 atoms + +Pair time (%) = 0.0861783 (1.5249) +Neigh time (%) = 0.310817 (5.49982) +Comm time (%) = 0.0628221 (1.11162) +Outpt time (%) = 0.457241 (8.09077) +Other time (%) = 4.73433 (83.7729) + +Nlocal: 14716 ave 14716 max 14716 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 87 ave 87 max 87 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 480 ave 480 max 480 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 480 +Ave neighs/atom = 0.0326176 +Neighbor list builds = 250 +Dangerous builds = 0 + diff --git a/examples/srd/log.srd.mixture.10Sep10.linux.4 b/examples/srd/log.srd.mixture.10Sep10.linux.4 new file mode 100644 index 0000000000..9ff674770e --- /dev/null +++ b/examples/srd/log.srd.mixture.10Sep10.linux.4 @@ -0,0 +1,220 @@ +LAMMPS (1 Oct 2010) +# 2d SRD test: big + small particles + +units lj +atom_style colloid +atom_modify first big +dimension 2 + +# create big particles with sigma 1.0 + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 +region box block 0 10 0 10 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569) + 2 by 2 by 1 processor grid +create_atoms 1 region box +Created 100 atoms +mass 1 1.0 +mass 2 0.01 + +shape 1 1.0 1.0 1.0 +shape 2 0.0 0.0 0.0 + +group big type 1 +100 atoms in group big +velocity big create 1.44 87287 loop geom + +# equilibrate big particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 big nve +fix 2 all enforce2d + +run 1000 +Memory usage per processor = 2.12925 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -0.54272 0 0.88288 -0.041088 + 1000 1.8791467 -0.97185784 0 0.8884974 0.61487657 +Loop time of 0.032092 on 4 procs for 1000 steps with 100 atoms + +Pair time (%) = 0.00402153 (12.5312) +Neigh time (%) = 0.000997305 (3.10764) +Comm time (%) = 0.0206033 (64.2007) +Outpt time (%) = 8.10027e-05 (0.252408) +Other time (%) = 0.0063889 (19.9081) + +Nlocal: 25 ave 26 max 23 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 47 ave 48 max 46 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 114.75 ave 124 max 100 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 459 +Ave neighs/atom = 4.59 +Neighbor list builds = 129 +Dangerous builds = 0 + +unfix 1 +unfix 2 + +# add small particles as hi density lattice + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 +region plane block 0 10 0 10 -0.001 0.001 +lattice sq 85.0 +Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 +create_atoms 2 region plane +Created 21316 atoms + +group small type 2 +21316 atoms in group small + +velocity small create 1.0 593849 loop geom + +# delete overlaps +# must set 1-2 cutoff to non-zero value + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.5 + +delete_atoms overlap 0.5 small big +Deleted 6700 atoms, new total = 14716 + +# SRD run + +reset_timestep 0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +communicate multi group big vel yes +neigh_modify include big + +# no pairwise interactions with small particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +# use fix SRD to push small particles out from inside big ones + +timestep 0.001 + +fix 1 big nve +fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip +fix 3 all enforce2d + +# diagnostics + +compute tbig big temp +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10] + +thermo_modify temp tbig +WARNING: Temperature for thermo pressure is not for group all +thermo 100 +dump 1 all atom 250 dump.srd.mixture + +run 5000 +SRD info: + SRD/big particles = 14616 100 + big particle diameter max/min = 0.88 0.88 + SRD temperature & lamda = 1 0.2 + SRD max distance & max velocity = 0.8 40 + SRD grid counts: 63 63 1 + SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114 + SRD per actual grid cell = 4.86648 + SRD viscosity = 0.463448 + big/SRD mass density ratio = 2.12808 +WARNING: Fix srd grid size > 1/4 of big particle diameter + # of rescaled SRD velocities = 0 + ave/max small velocity = 13.2944 24.262 + ave/max big velocity = 1.69284 5.10989 +Memory usage per processor = 4.74632 Mbytes +Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10] + 0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487657 0 0 0 0 0 0 0 0 0 + 100 1.3582446 3969 0.0026789295 -0.95043087 0.39423126 0.73581726 7479 87 87 0 0 22500 2999 1.0285157 0 + 200 1.2572907 3969 0.0019616669 -0.95603884 0.28867891 0.62749376 7394 98 98 0 0 22500 2994 1.0253343 0 + 300 1.12798 3969 0.00057755533 -1.0317072 0.084993042 0.30262448 7311 88 88 0 0 22500 2997 1.022263 0 + 400 1.1466105 3969 0.00088785773 -1.0044873 0.13065714 0.40537124 7467 82 82 0 0 22500 2993 1.0139003 0 + 500 1.0151043 3969 -0.00021014381 -1.0358781 -0.030924763 0.19673928 7587 81 81 0 0 22500 2994 1.0145019 0 + 600 0.99210691 3969 -0.0002577968 -1.0201232 -0.037937377 0.2625174 7449 92 92 0 0 22500 2968 0.98574736 0 + 700 0.92572874 3969 -0.00067753277 -1.0161772 -0.099705722 0.19520999 7537 78 78 0 0 22500 2998 1.0064032 0 + 800 0.94627244 3969 -0.0003639106 -0.9903628 -0.053553084 0.22241336 7602 79 79 0 1 22500 3010 1.0134331 0 + 900 0.92523394 3969 -0.00080502966 -1.0344498 -0.11846816 0.18846804 7576 72 72 0 1 22500 3015 1.0136704 0 + 1000 1.0322972 3969 -0.00037569219 -1.0772611 -0.055286863 0.13263626 7601 88 88 0 0 22500 3000 1.0224061 0 + 1100 0.9726161 3969 -0.00041776377 -1.0243681 -0.061478117 0.3120931 7425 87 87 0 0 22500 2991 1.0216981 0 + 1200 0.9785542 3969 -0.00036217362 -1.0220661 -0.053297471 0.37956001 7634 94 94 0 0 22500 3022 1.0055215 0 + 1300 1.102684 3969 0.00056306573 -1.0087964 0.082860753 0.50039902 7380 94 94 0 0 22500 3011 1.0298198 0 + 1400 1.2416072 3969 0.0016380507 -0.98813558 0.24105553 0.6709785 7532 95 95 0 0 22500 3005 1.0272106 0 + 1500 1.1009579 3969 0.00041059416 -1.0295252 0.060423037 0.4271012 7443 86 86 0 0 22500 2990 1.0322439 0 + 1600 0.97932726 3969 -0.00044406974 -1.0348833 -0.065349303 0.23710215 7541 85 85 0 0 22500 3005 1.0504545 0 + 1700 1.07156 3969 0.0003309407 -1.0121432 0.048701233 0.32615222 7660 90 90 0 1 22500 3010 1.0192163 0 + 1800 0.94379054 3969 -0.00060529206 -1.0234274 -0.08907478 0.28437994 7706 92 92 0 0 22500 2983 1.0197247 0 + 1900 1.1935542 3969 0.001087796 -1.0215386 0.16008006 0.32082985 7633 102 102 0 0 22500 3026 1.0227294 0 + 2000 1.0794535 3969 0.00017035747 -1.0435892 0.025069805 0.12933714 7547 76 76 0 0 22500 3028 1.0339312 0 + 2100 1.11728 3969 0.001197717 -0.92985122 0.17625603 0.4877601 7424 88 88 0 0 22500 2986 1.0268223 0 + 2200 1.022726 3969 -0.00017383526 -1.0380804 -0.025581597 0.18522494 7414 92 92 0 0 22500 3004 1.0254694 0 + 2300 1.2289681 3969 0.0014918151 -0.99714295 0.21953551 0.56571933 7669 90 90 0 0 22500 3008 1.0265701 0 + 2400 1.0261081 3969 0.00016550325 -0.99149158 0.024355459 0.53332928 7499 83 83 0 0 22500 3019 1.0160353 0 + 2500 1.0155015 3969 -0.00056230464 -1.0880952 -0.082748751 0.22398562 7712 79 79 0 0 22500 3017 1.03801 0 + 2600 0.8756954 3969 -0.0014956069 -1.087032 -0.22009351 0.10400097 7542 85 85 0 0 22500 2985 1.024091 0 + 2700 0.97964461 3969 -0.00075911535 -1.0815596 -0.11171141 0.27927544 7449 86 86 0 0 22500 2993 1.0166909 0 + 2800 0.97102332 3969 -0.00081115436 -1.0806826 -0.11936948 0.36647698 7662 85 85 0 0 22500 3014 1.0148134 0 + 2900 1.1405082 3969 0.00078035444 -1.0142661 0.11483696 0.73653576 7451 82 82 0 0 22500 3007 1.0296379 0 + 3000 1.0460256 3969 -0.00031837206 -1.082417 -0.046851633 0.25310003 7494 83 83 0 0 22500 3013 1.043192 0 + 3100 1.128752 3969 0.00043203186 -1.0538867 0.063577808 0.37101933 7458 89 89 0 1 22500 2981 1.0082866 0 + 3200 1.0546223 3969 0.00023156986 -1.0099982 0.034077821 0.66191884 7451 92 92 0 0 22500 2988 1.0254862 0 + 3300 1.0859707 3969 -5.4375056e-05 -1.0831128 -0.0080018333 0.3552947 7441 74 74 0 0 22500 2978 1.0252244 0 + 3400 0.90831095 3969 -0.0011506108 -1.0685517 -0.16932389 0.26027658 7478 76 76 0 0 22500 2997 1.0306308 0 + 3500 1.0971397 3969 0.00047675241 -1.0160094 0.070158884 0.39394719 7510 87 87 0 0 22500 2999 1.0303505 0 + 3600 1.0758592 3969 5.1451605e-05 -1.057529 0.0075716182 0.23217468 7505 98 98 0 0 22500 3022 1.0133265 0 + 3700 0.99184036 3969 -0.00051911023 -1.0583142 -0.076392262 0.2659259 7566 104 104 0 0 22500 3006 1.0284719 0 + 3800 0.86950687 3969 -0.0014525295 -1.074566 -0.21375425 0.27380224 7552 80 80 0 0 22500 3013 1.0351337 0 + 3900 0.86286132 3969 -0.0010595017 -1.010149 -0.15591627 0.56043933 7547 104 104 0 0 22500 2992 1.0313609 0 + 4000 0.76083626 3969 -0.0014009914 -0.9593978 -0.2061699 0.64813923 7448 101 101 0 0 22500 3032 1.0109258 0 + 4100 1.0071575 3969 -0.00018734554 -1.0246557 -0.027569769 0.55964495 7489 76 76 0 0 22500 3016 1.0175384 0 + 4200 0.88374612 3969 -0.0010981928 -1.0365187 -0.16161005 0.41352036 7481 92 92 0 0 22500 2995 1.0123735 0 + 4300 0.98819505 3969 -0.00066821798 -1.0766481 -0.098334958 0.41489158 7557 79 79 0 0 22500 2998 1.0400745 0 + 4400 1.1772685 3969 0.0010725317 -1.007662 0.15783376 0.7912903 7522 76 76 0 0 22500 2991 1.0176624 0 + 4500 1.0836741 3969 0.00021867511 -1.0406572 0.032180229 0.58489302 7800 93 93 0 0 22500 2997 1.0023484 0 + 4600 1.0334731 3969 -0.00015378918 -1.04577 -0.022631616 0.53872329 7542 94 94 0 0 22500 2996 0.98823241 0 + 4700 1.2126127 3969 0.0011423373 -1.0323802 0.16810636 0.49583696 7387 81 81 0 0 22500 3001 1.0425378 0 + 4800 1.1593219 3969 0.0010239969 -0.99703726 0.15069139 0.37192735 7374 80 80 0 1 22500 2988 1.0278368 0 + 4900 0.87223689 3969 -0.00099601272 -1.0100878 -0.14657323 0.11585542 7448 89 89 0 0 22500 3000 1.0267238 0 + 5000 0.87426493 3969 -0.0010817587 -1.0247139 -0.15919161 0.15322481 7587 100 100 0 0 22500 2988 1.0030228 0 +Loop time of 1.93728 on 4 procs for 5000 steps with 14716 atoms + +Pair time (%) = 0.0232192 (1.19854) +Neigh time (%) = 0.0877846 (4.53133) +Comm time (%) = 0.182241 (9.40704) +Outpt time (%) = 0.381904 (19.7134) +Other time (%) = 1.26213 (65.1497) + +Nlocal: 3679 ave 3872 max 3379 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Nghost: 48.25 ave 51 max 45 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 118 ave 167 max 87 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 472 +Ave neighs/atom = 0.0320739 +Neighbor list builds = 250 +Dangerous builds = 0 + diff --git a/examples/srd/log.srd.pure.10Sep10.linux.1 b/examples/srd/log.srd.pure.10Sep10.linux.1 new file mode 100644 index 0000000000..14eb96e297 --- /dev/null +++ b/examples/srd/log.srd.pure.10Sep10.linux.1 @@ -0,0 +1,138 @@ +LAMMPS (1 Oct 2010) +# 2d SRD only test + +units lj +atom_style atomic +atom_modify first empty +dimension 2 + +# create box with big lattice + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 +region box block 0 10 0 10 -0.5 0.5 +create_box 1 box +Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569) + 1 by 1 by 1 processor grid + +# add SRD particles as hi density lattice + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 +region plane block 0 10 0 10 -0.001 0.001 +lattice sq 85.0 +Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 +create_atoms 1 region plane +Created 21316 atoms + +group empty type 2 +0 atoms in group empty + +mass 1 0.01 +velocity all create 1.0 593849 loop geom + +# settings - need dummy empty group to enable no communication + +neighbor 0.3 bin +neigh_modify delay 1 every 1 check no + +communicate single group empty + +# timestep is big and SRD frequency is 1 + +timestep 0.02 + +fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip +fix 2 all enforce2d + +# diagnostics + +thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6] +thermo 100 +dump 1 all atom 250 dump.srd.pure + +run 5000 +SRD info: + SRD/big particles = 21316 0 + big particle diameter max/min = 0 1e+20 + SRD temperature & lamda = 1 0.2 + SRD max distance & max velocity = 0.8 40 + SRD grid counts: 63 63 1 + SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114 + SRD per actual grid cell = 5.37062 + SRD viscosity = 0.439647 + big/SRD mass density ratio = 0 + # of rescaled SRD velocities = 0 + ave/max all velocity = 13.2735 24.2873 +Memory usage per processor = 4.2049 Mbytes +Step Temp 1[7] TotEng Press 1[3] 1[4] 1[6] + 0 1 0 0.99995309 85.26 0 0 0 + 100 1 3969 0.99995309 85.26 0 0 0 + 200 1 3969 0.99995309 85.26 0 0 0 + 300 1 3969 0.99995309 85.26 0 0 0 + 400 1 3969 0.99995309 85.26 0 0 0 + 500 1 3969 0.99995309 85.26 0 0 0 + 600 1 3969 0.99995309 85.26 0 0 0 + 700 1 3969 0.99995309 85.26 0 0 0 + 800 1 3969 0.99995309 85.26 0 0 0 + 900 1 3969 0.99995309 85.26 0 0 0 + 1000 1 3969 0.99995309 85.26 0 0 0 + 1100 1 3969 0.99995309 85.26 0 0 0 + 1200 1 3969 0.99995309 85.26 0 0 0 + 1300 1 3969 0.99995309 85.26 0 0 0 + 1400 1 3969 0.99995309 85.26 0 0 0 + 1500 1 3969 0.99995309 85.26 0 0 0 + 1600 1 3969 0.99995309 85.26 0 0 0 + 1700 1 3969 0.99995309 85.26 0 0 0 + 1800 1 3969 0.99995309 85.26 0 0 0 + 1900 1 3969 0.99995309 85.26 0 0 0 + 2000 1 3969 0.99995309 85.26 0 0 0 + 2100 1 3969 0.99995309 85.26 0 0 0 + 2200 1 3969 0.99995309 85.26 0 0 0 + 2300 1 3969 0.99995309 85.26 0 0 0 + 2400 1 3969 0.99995309 85.26 0 0 0 + 2500 1 3969 0.99995309 85.26 0 0 0 + 2600 1 3969 0.99995309 85.26 0 0 0 + 2700 1 3969 0.99995309 85.26 0 0 0 + 2800 1 3969 0.99995309 85.26 0 0 0 + 2900 1 3969 0.99995309 85.26 0 0 0 + 3000 1 3969 0.99995309 85.26 0 0 0 + 3100 1 3969 0.99995309 85.26 0 0 0 + 3200 1 3969 0.99995309 85.26 0 0 0 + 3300 1 3969 0.99995309 85.26 0 0 0 + 3400 1 3969 0.99995309 85.26 0 0 0 + 3500 1 3969 0.99995309 85.26 0 0 0 + 3600 1 3969 0.99995309 85.26 0 0 0 + 3700 1 3969 0.99995309 85.26 0 0 0 + 3800 1 3969 0.99995309 85.26 0 0 0 + 3900 1 3969 0.99995309 85.26 0 0 0 + 4000 1 3969 0.99995309 85.26 0 0 0 + 4100 1 3969 0.99995309 85.26 0 0 0 + 4200 1 3969 0.99995309 85.26 0 0 0 + 4300 1 3969 0.99995309 85.26 0 0 0 + 4400 1 3969 0.99995309 85.26 0 0 0 + 4500 1 3969 0.99995309 85.26 0 0 0 + 4600 1 3969 0.99995309 85.26 0 0 0 + 4700 1 3969 0.99995309 85.26 0 0 0 + 4800 1 3969 0.99995309 85.26 0 0 0 + 4900 1 3969 0.99995309 85.26 0 0 0 + 5000 1 3969 0.99995309 85.26 0 0 0 +Loop time of 10.4217 on 1 procs for 5000 steps with 21316 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 5.80617 (55.7125) +Comm time (%) = 0.917962 (8.80821) +Outpt time (%) = 0.66245 (6.35647) +Other time (%) = 3.03508 (29.1228) + +Nlocal: 21316 ave 21316 max 21316 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5000 +Dangerous builds = 0 diff --git a/examples/srd/log.srd.pure.10Sep10.linux.4 b/examples/srd/log.srd.pure.10Sep10.linux.4 new file mode 100644 index 0000000000..f2251269ce --- /dev/null +++ b/examples/srd/log.srd.pure.10Sep10.linux.4 @@ -0,0 +1,138 @@ +LAMMPS (1 Oct 2010) +# 2d SRD only test + +units lj +atom_style atomic +atom_modify first empty +dimension 2 + +# create box with big lattice + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 +region box block 0 10 0 10 -0.5 0.5 +create_box 1 box +Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569) + 2 by 2 by 1 processor grid + +# add SRD particles as hi density lattice + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 +region plane block 0 10 0 10 -0.001 0.001 +lattice sq 85.0 +Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 +create_atoms 1 region plane +Created 21316 atoms + +group empty type 2 +0 atoms in group empty + +mass 1 0.01 +velocity all create 1.0 593849 loop geom + +# settings - need dummy empty group to enable no communication + +neighbor 0.3 bin +neigh_modify delay 1 every 1 check no + +communicate single group empty + +# timestep is big and SRD frequency is 1 + +timestep 0.02 + +fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip +fix 2 all enforce2d + +# diagnostics + +thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6] +thermo 100 +dump 1 all atom 250 dump.srd.pure + +run 5000 +SRD info: + SRD/big particles = 21316 0 + big particle diameter max/min = 0 1e+20 + SRD temperature & lamda = 1 0.2 + SRD max distance & max velocity = 0.8 40 + SRD grid counts: 63 63 1 + SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114 + SRD per actual grid cell = 5.37062 + SRD viscosity = 0.439647 + big/SRD mass density ratio = 0 + # of rescaled SRD velocities = 0 + ave/max all velocity = 13.2735 24.2873 +Memory usage per processor = 1.31651 Mbytes +Step Temp 1[7] TotEng Press 1[3] 1[4] 1[6] + 0 1 0 0.99995309 85.26 0 0 0 + 100 1 3969 0.99995309 85.26 0 0 0 + 200 1 3969 0.99995309 85.26 0 0 0 + 300 1 3969 0.99995309 85.26 0 0 0 + 400 1 3969 0.99995309 85.26 0 0 0 + 500 1 3969 0.99995309 85.26 0 0 0 + 600 1 3969 0.99995309 85.26 0 0 0 + 700 1 3969 0.99995309 85.26 0 0 0 + 800 1 3969 0.99995309 85.26 0 0 0 + 900 1 3969 0.99995309 85.26 0 0 0 + 1000 1 3969 0.99995309 85.26 0 0 0 + 1100 1 3969 0.99995309 85.26 0 0 0 + 1200 1 3969 0.99995309 85.26 0 0 0 + 1300 1 3969 0.99995309 85.26 0 0 0 + 1400 1 3969 0.99995309 85.26 0 0 0 + 1500 1 3969 0.99995309 85.26 0 0 0 + 1600 1 3969 0.99995309 85.26 0 0 0 + 1700 1 3969 0.99995309 85.26 0 0 0 + 1800 1 3969 0.99995309 85.26 0 0 0 + 1900 1 3969 0.99995309 85.26 0 0 0 + 2000 1 3969 0.99995309 85.26 0 0 0 + 2100 1 3969 0.99995309 85.26 0 0 0 + 2200 1 3969 0.99995309 85.26 0 0 0 + 2300 1 3969 0.99995309 85.26 0 0 0 + 2400 1 3969 0.99995309 85.26 0 0 0 + 2500 1 3969 0.99995309 85.26 0 0 0 + 2600 1 3969 0.99995309 85.26 0 0 0 + 2700 1 3969 0.99995309 85.26 0 0 0 + 2800 1 3969 0.99995309 85.26 0 0 0 + 2900 1 3969 0.99995309 85.26 0 0 0 + 3000 1 3969 0.99995309 85.26 0 0 0 + 3100 1 3969 0.99995309 85.26 0 0 0 + 3200 1 3969 0.99995309 85.26 0 0 0 + 3300 1 3969 0.99995309 85.26 0 0 0 + 3400 1 3969 0.99995309 85.26 0 0 0 + 3500 1 3969 0.99995309 85.26 0 0 0 + 3600 1 3969 0.99995309 85.26 0 0 0 + 3700 1 3969 0.99995309 85.26 0 0 0 + 3800 1 3969 0.99995309 85.26 0 0 0 + 3900 1 3969 0.99995309 85.26 0 0 0 + 4000 1 3969 0.99995309 85.26 0 0 0 + 4100 1 3969 0.99995309 85.26 0 0 0 + 4200 1 3969 0.99995309 85.26 0 0 0 + 4300 1 3969 0.99995309 85.26 0 0 0 + 4400 1 3969 0.99995309 85.26 0 0 0 + 4500 1 3969 0.99995309 85.26 0 0 0 + 4600 1 3969 0.99995309 85.26 0 0 0 + 4700 1 3969 0.99995309 85.26 0 0 0 + 4800 1 3969 0.99995309 85.26 0 0 0 + 4900 1 3969 0.99995309 85.26 0 0 0 + 5000 1 3969 0.99995309 85.26 0 0 0 +Loop time of 3.48791 on 4 procs for 5000 steps with 21316 atoms + +Pair time (%) = 0 (0) +Neigh time (%) = 1.4364 (41.1823) +Comm time (%) = 0.740496 (21.2303) +Outpt time (%) = 0.541988 (15.5391) +Other time (%) = 0.769027 (22.0483) + +Nlocal: 5329 ave 5381 max 5260 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5000 +Dangerous builds = 0