From af8103433c63ee4ef6ea9b8ae4ad764d109820f9 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Sun, 30 Jun 2019 22:13:12 -0600 Subject: [PATCH] add stabilized vs unstabilized examples --- ...in.tiny_nylon => in.tiny_nylon.stabilized} | 2 + .../tiny_nylon/in.tiny_nylon.unstabilized | 48 +++ .../tiny_nylon/log.20Apr18.tiny_nylon.g++.1 | 370 ------------------ .../tiny_nylon/log.20Apr18.tiny_nylon.g++.4 | 370 ------------------ .../log.5Jun19.tiny_nylon.stabilized.g++.1 | 148 +++++++ .../log.5Jun19.tiny_nylon.stabilized.g++.4 | 148 +++++++ .../log.5Jun19.tiny_nylon.unstabilized.g++.1 | 147 +++++++ .../log.5Jun19.tiny_nylon.unstabilized.g++.4 | 147 +++++++ 8 files changed, 640 insertions(+), 740 deletions(-) rename examples/USER/misc/bond_react/tiny_nylon/{in.tiny_nylon => in.tiny_nylon.stabilized} (88%) create mode 100644 examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized delete mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 delete mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 create mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 create mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 create mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 create mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized similarity index 88% rename from examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon rename to examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized index 73cb2eb270..b152dec00a 100644 --- a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon +++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized @@ -38,6 +38,8 @@ fix myrxns all bond/react stabilization yes statted_grp .03 & fix 1 statted_grp_REACT nvt temp 300 300 100 +# optionally, you can customize behavior of reacting atoms, +# by using the internally-created 'bond_react_MASTER_group', like so: fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized new file mode 100644 index 0000000000..1e5a493821 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized @@ -0,0 +1,48 @@ +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.data + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +molecule mol2 rxn1_stp1_reacted.data_template +molecule mol3 rxn1_stp2_unreacted.data_template +molecule mol4 rxn1_stp2_reacted.data_template + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization no & + react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & + react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map + +fix 1 all nve/limit .03 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 1000 + +# write_restart restart_longrun +# write_data restart_longrun.data diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 deleted file mode 100644 index 344439f94c..0000000000 --- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 +++ /dev/null @@ -1,370 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# two monomer nylon example -# reaction produces a condensed water molecule - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data tiny_nylon.data - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 300.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 - -thermo 50 - -# dump 1 all xyz 1 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map -WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -fix 1 statted_grp nvt temp 300 300 100 - -fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 - -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] - -# restart 100 restart1 restart2 - -run 10000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 343 8 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10.5 - ghost atom cutoff = 10.5 - binsize = 5.25, bins = 10 10 10 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) pair lj/class2/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard - (2) fix bond/react, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -WARNING: Inconsistent image flags (../domain.cpp:786) -Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 296.70408 -51.30066 0.0034851739 1 0 - 100 274.25324 46.715512 0.0034851739 1 1 - 150 471.61579 31.321598 0.0034851739 1 1 - 200 362.87766 42.061118 0.0034851739 1 1 - 250 367.58058 65.303109 0.0034851739 1 1 - 300 372.38236 -52.421725 0.0034851739 1 1 - 350 297.69957 17.869945 0.0034851739 1 1 - 400 258.30433 49.19156 0.0034851739 1 1 - 450 253.34384 -5.8162637 0.0034851739 1 1 - 500 269.96465 -43.337517 0.0034851739 1 1 - 550 303.23718 10.180246 0.0034851739 1 1 - 600 329.59579 -48.97461 0.0034851739 1 1 - 650 350.42568 50.983183 0.0034851739 1 1 - 700 342.03272 35.43465 0.0034851739 1 1 - 750 269.23405 -41.873166 0.0034851739 1 1 - 800 245.15025 13.953092 0.0034851739 1 1 - 850 257.85421 -3.1492141 0.0034851739 1 1 - 900 316.15644 7.7798301 0.0034851739 1 1 - 950 299.9124 -15.77014 0.0034851739 1 1 - 1000 302.89968 -17.049693 0.0034851739 1 1 - 1050 308.91651 71.84632 0.0034851739 1 1 - 1100 348.43932 -18.742012 0.0034851739 1 1 - 1150 309.03036 50.536311 0.0034851739 1 1 - 1200 318.9761 -16.905746 0.0034851739 1 1 - 1250 320.42806 -0.057975092 0.0034851739 1 1 - 1300 289.7824 18.200772 0.0034851739 1 1 - 1350 284.79836 -9.1978427 0.0034851739 1 1 - 1400 325.43292 42.082833 0.0034851739 1 1 - 1450 261.5041 -37.823325 0.0034851739 1 1 - 1500 298.88723 -5.1647385 0.0034851739 1 1 - 1550 291.37403 -7.7764201 0.0034851739 1 1 - 1600 293.83475 22.2458 0.0034851739 1 1 - 1650 293.80611 24.202512 0.0034851739 1 1 - 1700 291.70205 -23.397884 0.0034851739 1 1 - 1750 292.32437 -10.671214 0.0034851739 1 1 - 1800 302.01367 -11.671025 0.0034851739 1 1 - 1850 322.1651 24.438331 0.0034851739 1 1 - 1900 310.45076 45.343592 0.0034851739 1 1 - 1950 325.91745 -19.847809 0.0034851739 1 1 - 2000 276.89662 63.387098 0.0034851739 1 1 - 2050 311.33783 -24.683247 0.0034851739 1 1 - 2100 346.2336 -27.526891 0.0034851739 1 1 - 2150 345.30604 -15.722411 0.0034851739 1 1 - 2200 346.7718 -17.857633 0.0034851739 1 1 - 2250 304.28676 -1.9965581 0.0034851739 1 1 - 2300 322.56372 -31.786868 0.0034851739 1 1 - 2350 282.64326 6.1982735 0.0034851739 1 1 - 2400 286.65759 -63.207781 0.0034851739 1 1 - 2450 257.05528 32.931491 0.0034851739 1 1 - 2500 283.64386 26.912373 0.0034851739 1 1 - 2550 299.54005 27.277039 0.0034851739 1 1 - 2600 283.92503 14.660972 0.0034851739 1 1 - 2650 321.93453 -18.977358 0.0034851739 1 1 - 2700 376.7189 31.826935 0.0034851739 1 1 - 2750 372.20075 -32.821697 0.0034851739 1 1 - 2800 361.40604 83.035183 0.0034851739 1 1 - 2850 332.27269 -23.927452 0.0034851739 1 1 - 2900 331.14638 -0.12328446 0.0034851739 1 1 - 2950 303.67489 -24.078857 0.0034851739 1 1 - 3000 311.40462 21.563537 0.0034851739 1 1 - 3050 284.72849 -23.849667 0.0034851739 1 1 - 3100 303.48477 39.347763 0.0034851739 1 1 - 3150 264.2739 -0.22299879 0.0034851739 1 1 - 3200 300.03351 31.545323 0.0034851739 1 1 - 3250 288.56663 5.7225228 0.0034851739 1 1 - 3300 200.13238 -31.239655 0.0034851739 1 1 - 3350 231.32512 16.631728 0.0034851739 1 1 - 3400 260.57402 2.1717992 0.0034851739 1 1 - 3450 301.47128 -42.210623 0.0034851739 1 1 - 3500 321.77414 40.074365 0.0034851739 1 1 - 3550 353.21858 28.387783 0.0034851739 1 1 - 3600 331.45989 -57.800858 0.0034851739 1 1 - 3650 303.88123 44.86596 0.0034851739 1 1 - 3700 329.73833 -0.80615652 0.0034851739 1 1 - 3750 297.55588 -0.49626039 0.0034851739 1 1 - 3800 286.38794 -10.010003 0.0034851739 1 1 - 3850 290.17417 -43.51187 0.0034851739 1 1 - 3900 247.88933 51.23735 0.0034851739 1 1 - 3950 332.31324 -18.194985 0.0034851739 1 1 - 4000 325.56802 18.402825 0.0034851739 1 1 - 4050 338.37593 36.430977 0.0034851739 1 1 - 4100 370.95478 39.290285 0.0034851739 1 1 - 4150 348.47859 -7.0779678 0.0034851739 1 1 - 4200 241.30632 -33.371788 0.0034851739 1 1 - 4250 242.17258 -9.986197 0.0034851739 1 1 - 4300 300.85311 -7.9244294 0.0034851739 1 1 - 4350 273.15684 -21.257283 0.0034851739 1 1 - 4400 305.77463 -5.8720722 0.0034851739 1 1 - 4450 314.97697 45.0373 0.0034851739 1 1 - 4500 310.77723 16.958773 0.0034851739 1 1 - 4550 302.1742 12.156862 0.0034851739 1 1 - 4600 319.74799 6.84889 0.0034851739 1 1 - 4650 270.86805 -13.767905 0.0034851739 1 1 - 4700 249.81731 -31.197487 0.0034851739 1 1 - 4750 285.86481 -9.8916364 0.0034851739 1 1 - 4800 233.98321 7.1338571 0.0034851739 1 1 - 4850 302.60551 49.262889 0.0034851739 1 1 - 4900 316.55056 34.663247 0.0034851739 1 1 - 4950 357.32741 11.583006 0.0034851739 1 1 - 5000 400.21045 -8.1781061 0.0034851739 1 1 - 5050 390.01845 -20.490275 0.0034851739 1 1 - 5100 378.84247 -41.328757 0.0034851739 1 1 - 5150 324.02038 -15.023862 0.0034851739 1 1 - 5200 262.08429 10.937354 0.0034851739 1 1 - 5250 255.75508 16.381455 0.0034851739 1 1 - 5300 277.84989 40.68232 0.0034851739 1 1 - 5350 302.92832 9.1989494 0.0034851739 1 1 - 5400 283.7196 -1.6584671 0.0034851739 1 1 - 5450 300.71266 -4.7030295 0.0034851739 1 1 - 5500 343.5499 -0.30550044 0.0034851739 1 1 - 5550 369.51271 21.691649 0.0034851739 1 1 - 5600 372.69789 -38.67994 0.0034851739 1 1 - 5650 327.41266 11.352137 0.0034851739 1 1 - 5700 278.98614 -23.827304 0.0034851739 1 1 - 5750 308.30054 -20.756187 0.0034851739 1 1 - 5800 341.45594 28.058441 0.0034851739 1 1 - 5850 322.97844 -10.731921 0.0034851739 1 1 - 5900 304.53591 32.825279 0.0034851739 1 1 - 5950 287.1752 -36.780091 0.0034851739 1 1 - 6000 296.52681 18.781896 0.0034851739 1 1 - 6050 314.25442 15.992829 0.0034851739 1 1 - 6100 313.86576 3.4342714 0.0034851739 1 1 - 6150 325.64196 32.392039 0.0034851739 1 1 - 6200 367.42931 -27.160706 0.0034851739 1 1 - 6250 369.30798 39.020934 0.0034851739 1 1 - 6300 328.92285 -23.175157 0.0034851739 1 1 - 6350 305.63077 4.9024453 0.0034851739 1 1 - 6400 241.70341 -13.676629 0.0034851739 1 1 - 6450 265.66717 2.40612 0.0034851739 1 1 - 6500 249.36037 13.420255 0.0034851739 1 1 - 6550 294.53814 10.853462 0.0034851739 1 1 - 6600 308.2025 18.995308 0.0034851739 1 1 - 6650 305.43797 -49.56785 0.0034851739 1 1 - 6700 320.27344 11.336281 0.0034851739 1 1 - 6750 321.78666 -23.463899 0.0034851739 1 1 - 6800 303.40388 7.6224553 0.0034851739 1 1 - 6850 297.18966 51.52256 0.0034851739 1 1 - 6900 284.18909 -8.4947203 0.0034851739 1 1 - 6950 331.03663 13.233655 0.0034851739 1 1 - 7000 311.37928 -43.265479 0.0034851739 1 1 - 7050 286.81661 -14.174683 0.0034851739 1 1 - 7100 302.84119 12.048954 0.0034851739 1 1 - 7150 297.19357 -43.111968 0.0034851739 1 1 - 7200 332.47359 26.048249 0.0034851739 1 1 - 7250 262.70677 41.176242 0.0034851739 1 1 - 7300 250.61405 -23.413982 0.0034851739 1 1 - 7350 296.91117 35.88133 0.0034851739 1 1 - 7400 245.09229 -13.447194 0.0034851739 1 1 - 7450 272.28131 -23.322585 0.0034851739 1 1 - 7500 209.04985 13.871239 0.0034851739 1 1 - 7550 255.00955 4.9325621 0.0034851739 1 1 - 7600 312.30937 -37.368274 0.0034851739 1 1 - 7650 305.65903 55.245496 0.0034851739 1 1 - 7700 325.09504 -18.347711 0.0034851739 1 1 - 7750 363.28282 -22.479686 0.0034851739 1 1 - 7800 350.17429 26.849547 0.0034851739 1 1 - 7850 271.70853 -17.764575 0.0034851739 1 1 - 7900 272.66484 -11.701967 0.0034851739 1 1 - 7950 298.60202 -12.765675 0.0034851739 1 1 - 8000 274.58852 49.641532 0.0034851739 1 1 - 8050 304.72347 -0.55414183 0.0034851739 1 1 - 8100 328.30757 -39.861301 0.0034851739 1 1 - 8150 406.67601 2.8999409 0.0034851739 1 1 - 8200 332.20083 -51.217399 0.0034851739 1 1 - 8250 354.50609 53.128769 0.0034851739 1 1 - 8300 337.2758 20.68562 0.0034851739 1 1 - 8350 361.89708 -54.185869 0.0034851739 1 1 - 8400 305.63496 24.058529 0.0034851739 1 1 - 8450 303.27461 4.304683 0.0034851739 1 1 - 8500 253.53694 -10.909021 0.0034851739 1 1 - 8550 277.03017 23.241479 0.0034851739 1 1 - 8600 291.41844 -22.240665 0.0034851739 1 1 - 8650 307.85368 31.919587 0.0034851739 1 1 - 8700 309.19724 0.53529642 0.0034851739 1 1 - 8750 354.6583 11.565515 0.0034851739 1 1 - 8800 329.78598 19.5996 0.0034851739 1 1 - 8850 240.79198 21.803515 0.0034851739 1 1 - 8900 318.40749 -59.816923 0.0034851739 1 1 - 8950 308.47211 -57.808635 0.0034851739 1 1 - 9000 271.51207 50.943482 0.0034851739 1 1 - 9050 249.4005 6.7529187 0.0034851739 1 1 - 9100 221.8772 47.196092 0.0034851739 1 1 - 9150 297.9351 4.0058184 0.0034851739 1 1 - 9200 274.85051 -24.774393 0.0034851739 1 1 - 9250 336.04757 5.3799028 0.0034851739 1 1 - 9300 380.44956 -22.389381 0.0034851739 1 1 - 9350 336.9824 23.050616 0.0034851739 1 1 - 9400 304.46425 32.530218 0.0034851739 1 1 - 9450 317.55591 -22.265425 0.0034851739 1 1 - 9500 323.70901 -7.0159787 0.0034851739 1 1 - 9550 316.07308 28.062131 0.0034851739 1 1 - 9600 262.74608 -0.78519192 0.0034851739 1 1 - 9650 271.55045 -21.430123 0.0034851739 1 1 - 9700 239.6022 14.483637 0.0034851739 1 1 - 9750 338.1437 -0.72765302 0.0034851739 1 1 - 9800 334.50189 19.495144 0.0034851739 1 1 - 9850 354.87554 19.272719 0.0034851739 1 1 - 9900 334.02141 -22.393457 0.0034851739 1 1 - 9950 293.63651 19.178873 0.0034851739 1 1 - 10000 319.81736 21.904414 0.0034851739 1 1 -Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms - -Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14 -Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04 -Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49 -Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62 -Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22 -Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19 -Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40 -Other | | 0.01666 | | | 0.90 - -Nlocal: 44 ave 44 max 44 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 44 ave 44 max 44 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 823 ave 823 max 823 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 823 -Ave neighs/atom = 18.7045 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 10000 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 deleted file mode 100644 index 377781f48f..0000000000 --- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 +++ /dev/null @@ -1,370 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# two monomer nylon example -# reaction produces a condensed water molecule - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data tiny_nylon.data - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 300.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 - -thermo 50 - -# dump 1 all xyz 1 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map -WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -fix 1 statted_grp nvt temp 300 300 100 - -fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 - -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] - -# restart 100 restart1 restart2 - -run 10000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 252 2 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10.5 - ghost atom cutoff = 10.5 - binsize = 5.25, bins = 10 10 10 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) pair lj/class2/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard - (2) fix bond/react, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -WARNING: Inconsistent image flags (../domain.cpp:786) -Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 296.70408 -51.30066 0.0034851739 1 0 - 100 274.25324 46.715512 0.0034851739 1 1 - 150 471.61579 31.321598 0.0034851739 1 1 - 200 362.87766 42.061118 0.0034851739 1 1 - 250 367.58058 65.303109 0.0034851739 1 1 - 300 372.38236 -52.421725 0.0034851739 1 1 - 350 297.69957 17.869945 0.0034851739 1 1 - 400 258.30433 49.19156 0.0034851739 1 1 - 450 253.34384 -5.8162637 0.0034851739 1 1 - 500 269.96465 -43.337517 0.0034851739 1 1 - 550 303.23718 10.180246 0.0034851739 1 1 - 600 329.59579 -48.97461 0.0034851739 1 1 - 650 350.42568 50.983183 0.0034851739 1 1 - 700 342.03272 35.43465 0.0034851739 1 1 - 750 269.23405 -41.873166 0.0034851739 1 1 - 800 245.15025 13.953092 0.0034851739 1 1 - 850 257.85421 -3.1492141 0.0034851739 1 1 - 900 316.15644 7.7798301 0.0034851739 1 1 - 950 299.9124 -15.77014 0.0034851739 1 1 - 1000 302.89968 -17.049693 0.0034851739 1 1 - 1050 308.91651 71.84632 0.0034851739 1 1 - 1100 348.43932 -18.742012 0.0034851739 1 1 - 1150 309.03036 50.536311 0.0034851739 1 1 - 1200 318.9761 -16.905746 0.0034851739 1 1 - 1250 320.42806 -0.057975092 0.0034851739 1 1 - 1300 289.7824 18.200772 0.0034851739 1 1 - 1350 284.79836 -9.1978427 0.0034851739 1 1 - 1400 325.43292 42.082833 0.0034851739 1 1 - 1450 261.5041 -37.823325 0.0034851739 1 1 - 1500 298.88723 -5.1647385 0.0034851739 1 1 - 1550 291.37403 -7.7764201 0.0034851739 1 1 - 1600 293.83475 22.2458 0.0034851739 1 1 - 1650 293.80611 24.202512 0.0034851739 1 1 - 1700 291.70205 -23.397884 0.0034851739 1 1 - 1750 292.32437 -10.671214 0.0034851739 1 1 - 1800 302.01367 -11.671025 0.0034851739 1 1 - 1850 322.1651 24.438331 0.0034851739 1 1 - 1900 310.45076 45.343592 0.0034851739 1 1 - 1950 325.91745 -19.847809 0.0034851739 1 1 - 2000 276.89662 63.387098 0.0034851739 1 1 - 2050 311.33783 -24.683247 0.0034851739 1 1 - 2100 346.2336 -27.526891 0.0034851739 1 1 - 2150 345.30604 -15.722411 0.0034851739 1 1 - 2200 346.7718 -17.857633 0.0034851739 1 1 - 2250 304.28676 -1.9965581 0.0034851739 1 1 - 2300 322.56372 -31.786868 0.0034851739 1 1 - 2350 282.64326 6.1982735 0.0034851739 1 1 - 2400 286.65759 -63.207781 0.0034851739 1 1 - 2450 257.05528 32.931491 0.0034851739 1 1 - 2500 283.64386 26.912373 0.0034851739 1 1 - 2550 299.54005 27.277039 0.0034851739 1 1 - 2600 283.92503 14.660972 0.0034851739 1 1 - 2650 321.93453 -18.977358 0.0034851739 1 1 - 2700 376.7189 31.826935 0.0034851739 1 1 - 2750 372.20075 -32.821697 0.0034851739 1 1 - 2800 361.40604 83.035183 0.0034851739 1 1 - 2850 332.27269 -23.927452 0.0034851739 1 1 - 2900 331.14638 -0.12328446 0.0034851739 1 1 - 2950 303.67489 -24.078857 0.0034851739 1 1 - 3000 311.40462 21.563537 0.0034851739 1 1 - 3050 284.72849 -23.849667 0.0034851739 1 1 - 3100 303.48477 39.347763 0.0034851739 1 1 - 3150 264.2739 -0.22299878 0.0034851739 1 1 - 3200 300.03351 31.545323 0.0034851739 1 1 - 3250 288.56663 5.7225229 0.0034851739 1 1 - 3300 200.13238 -31.239655 0.0034851739 1 1 - 3350 231.32512 16.631728 0.0034851739 1 1 - 3400 260.57402 2.1717992 0.0034851739 1 1 - 3450 301.47128 -42.210623 0.0034851739 1 1 - 3500 321.77414 40.074365 0.0034851739 1 1 - 3550 353.21858 28.387783 0.0034851739 1 1 - 3600 331.45989 -57.800858 0.0034851739 1 1 - 3650 303.88123 44.86596 0.0034851739 1 1 - 3700 329.73833 -0.8061567 0.0034851739 1 1 - 3750 297.55588 -0.49626022 0.0034851739 1 1 - 3800 286.38794 -10.010003 0.0034851739 1 1 - 3850 290.17417 -43.51187 0.0034851739 1 1 - 3900 247.88933 51.23735 0.0034851739 1 1 - 3950 332.31324 -18.194985 0.0034851739 1 1 - 4000 325.56802 18.402825 0.0034851739 1 1 - 4050 338.37594 36.430977 0.0034851739 1 1 - 4100 370.95478 39.290285 0.0034851739 1 1 - 4150 348.47859 -7.0779683 0.0034851739 1 1 - 4200 241.30632 -33.371789 0.0034851739 1 1 - 4250 242.17258 -9.9861962 0.0034851739 1 1 - 4300 300.85311 -7.924429 0.0034851739 1 1 - 4350 273.15684 -21.257282 0.0034851739 1 1 - 4400 305.77464 -5.8720712 0.0034851739 1 1 - 4450 314.97697 45.037299 0.0034851739 1 1 - 4500 310.77723 16.958771 0.0034851739 1 1 - 4550 302.17421 12.156862 0.0034851739 1 1 - 4600 319.74799 6.8488914 0.0034851739 1 1 - 4650 270.86805 -13.767907 0.0034851739 1 1 - 4700 249.81731 -31.197484 0.0034851739 1 1 - 4750 285.86481 -9.8916332 0.0034851739 1 1 - 4800 233.98321 7.1338518 0.0034851739 1 1 - 4850 302.60551 49.262886 0.0034851739 1 1 - 4900 316.55055 34.663238 0.0034851739 1 1 - 4950 357.32741 11.583013 0.0034851739 1 1 - 5000 400.21044 -8.1780861 0.0034851739 1 1 - 5050 390.01845 -20.490268 0.0034851739 1 1 - 5100 378.84249 -41.328772 0.0034851739 1 1 - 5150 324.02039 -15.023852 0.0034851739 1 1 - 5200 262.08427 10.937367 0.0034851739 1 1 - 5250 255.75506 16.381495 0.0034851739 1 1 - 5300 277.84991 40.682283 0.0034851739 1 1 - 5350 302.92834 9.1989644 0.0034851739 1 1 - 5400 283.71964 -1.6583895 0.0034851739 1 1 - 5450 300.71261 -4.703054 0.0034851739 1 1 - 5500 343.54987 -0.30546396 0.0034851739 1 1 - 5550 369.51272 21.691639 0.0034851739 1 1 - 5600 372.69786 -38.679919 0.0034851739 1 1 - 5650 327.41256 11.352201 0.0034851739 1 1 - 5700 278.9861 -23.82728 0.0034851739 1 1 - 5750 308.30037 -20.756238 0.0034851739 1 1 - 5800 341.4559 28.058314 0.0034851739 1 1 - 5850 322.9786 -10.731862 0.0034851739 1 1 - 5900 304.53598 32.825105 0.0034851739 1 1 - 5950 287.17515 -36.780057 0.0034851739 1 1 - 6000 296.52688 18.782156 0.0034851739 1 1 - 6050 314.25411 15.99272 0.0034851739 1 1 - 6100 313.86572 3.4344108 0.0034851739 1 1 - 6150 325.64197 32.39212 0.0034851739 1 1 - 6200 367.4298 -27.161154 0.0034851739 1 1 - 6250 369.30937 39.020881 0.0034851739 1 1 - 6300 328.92245 -23.175612 0.0034851739 1 1 - 6350 305.6293 4.9011587 0.0034851739 1 1 - 6400 241.70456 -13.675247 0.0034851739 1 1 - 6450 265.66574 2.4049735 0.0034851739 1 1 - 6500 249.3592 13.420453 0.0034851739 1 1 - 6550 294.5367 10.856753 0.0034851739 1 1 - 6600 308.20246 18.992923 0.0034851739 1 1 - 6650 305.43756 -49.57151 0.0034851739 1 1 - 6700 320.27395 11.339101 0.0034851739 1 1 - 6750 321.7875 -23.463361 0.0034851739 1 1 - 6800 303.40316 7.6256997 0.0034851739 1 1 - 6850 297.18652 51.52186 0.0034851739 1 1 - 6900 284.19084 -8.496294 0.0034851739 1 1 - 6950 331.04173 13.227745 0.0034851739 1 1 - 7000 311.38027 -43.26105 0.0034851739 1 1 - 7050 286.82046 -14.171194 0.0034851739 1 1 - 7100 302.81691 12.058085 0.0034851739 1 1 - 7150 297.18018 -43.110658 0.0034851739 1 1 - 7200 332.46131 26.051496 0.0034851739 1 1 - 7250 262.72288 41.161451 0.0034851739 1 1 - 7300 250.62739 -23.440907 0.0034851739 1 1 - 7350 296.92141 35.869216 0.0034851739 1 1 - 7400 245.06807 -13.467896 0.0034851739 1 1 - 7450 272.2659 -23.292836 0.0034851739 1 1 - 7500 209.05776 13.888665 0.0034851739 1 1 - 7550 255.03716 4.9662624 0.0034851739 1 1 - 7600 312.26011 -37.350427 0.0034851739 1 1 - 7650 305.5823 55.208039 0.0034851739 1 1 - 7700 325.13382 -18.370791 0.0034851739 1 1 - 7750 363.24898 -22.473126 0.0034851739 1 1 - 7800 350.19254 26.792307 0.0034851739 1 1 - 7850 271.76418 -17.843445 0.0034851739 1 1 - 7900 272.70301 -11.709349 0.0034851739 1 1 - 7950 298.5993 -12.736235 0.0034851739 1 1 - 8000 274.52611 49.657345 0.0034851739 1 1 - 8050 304.73711 -0.52485689 0.0034851739 1 1 - 8100 328.29239 -39.901891 0.0034851739 1 1 - 8150 406.52096 2.8669076 0.0034851739 1 1 - 8200 332.17309 -51.168754 0.0034851739 1 1 - 8250 354.68419 53.003157 0.0034851739 1 1 - 8300 337.28934 20.766408 0.0034851739 1 1 - 8350 361.81133 -54.159227 0.0034851739 1 1 - 8400 305.59597 24.011667 0.0034851739 1 1 - 8450 303.25823 4.423341 0.0034851739 1 1 - 8500 253.50747 -11.026949 0.0034851739 1 1 - 8550 277.13504 23.204625 0.0034851739 1 1 - 8600 291.40211 -22.253861 0.0034851739 1 1 - 8650 307.93765 32.14162 0.0034851739 1 1 - 8700 309.1529 0.36279434 0.0034851739 1 1 - 8750 355.10326 11.677219 0.0034851739 1 1 - 8800 330.21328 19.235269 0.0034851739 1 1 - 8850 241.29109 21.707386 0.0034851739 1 1 - 8900 319.15363 -60.010115 0.0034851739 1 1 - 8950 308.88552 -57.637014 0.0034851739 1 1 - 9000 272.22373 51.15837 0.0034851739 1 1 - 9050 248.84947 7.3390565 0.0034851739 1 1 - 9100 221.91564 48.387079 0.0034851739 1 1 - 9150 298.03506 2.9058639 0.0034851739 1 1 - 9200 274.25114 -24.597819 0.0034851739 1 1 - 9250 334.08373 5.1079577 0.0034851739 1 1 - 9300 383.07285 -23.274763 0.0034851739 1 1 - 9350 335.00581 20.94212 0.0034851739 1 1 - 9400 309.23862 34.074744 0.0034851739 1 1 - 9450 312.62262 -28.468057 0.0034851739 1 1 - 9500 324.54274 2.851136 0.0034851739 1 1 - 9550 313.32781 22.468182 0.0034851739 1 1 - 9600 269.04372 4.064934 0.0034851739 1 1 - 9650 270.98476 -21.520127 0.0034851739 1 1 - 9700 236.8736 16.250728 0.0034851739 1 1 - 9750 333.94686 1.6864148 0.0034851739 1 1 - 9800 330.91875 12.150018 0.0034851739 1 1 - 9850 343.8603 25.338853 0.0034851739 1 1 - 9900 330.93364 -28.292992 0.0034851739 1 1 - 9950 291.25518 25.795948 0.0034851739 1 1 - 10000 319.25565 25.323846 0.0034851739 1 1 -Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms - -Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s -93.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94 -Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22 -Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39 -Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51 -Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91 -Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33 -Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03 -Other | | 0.02359 | | | 0.66 - -Nlocal: 11 ave 44 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 33 ave 44 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 3 -Neighs: 205.75 ave 823 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 823 -Ave neighs/atom = 18.7045 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 10000 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 new file mode 100644 index 0000000000..de1167c652 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 @@ -0,0 +1,148 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000181113 secs + read_data CPU = 0.0251833 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 343 8 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 293.70542 -52.547388 0.0034851739 1 0 + 100 276.36755 54.81826 0.0034851739 1 1 + 150 448.65869 16.874435 0.0034851739 1 1 + 200 379.84257 11.578545 0.0034851739 1 1 + 250 298.21983 90.656585 0.0034851739 1 1 + 300 333.3111 -30.139607 0.0034851739 1 1 + 350 266.57108 6.4505134 0.0034851739 1 1 + 400 264.05476 10.513204 0.0034851739 1 1 + 450 250.70418 -18.635379 0.0034851739 1 1 + 500 261.21632 10.231013 0.0034851739 1 1 + 550 309.89024 -8.8299506 0.0034851739 1 1 + 600 373.45851 30.368993 0.0034851739 1 1 + 650 338.26242 9.0362267 0.0034851739 1 1 + 700 295.67794 -5.6007538 0.0034851739 1 1 + 750 310.86563 -59.228181 0.0034851739 1 1 + 800 286.22678 -9.9022407 0.0034851739 1 1 + 850 218.42135 27.845352 0.0034851739 1 1 + 900 259.62551 24.216336 0.0034851739 1 1 + 950 250.21307 -14.560985 0.0034851739 1 1 + 1000 274.29245 -0.38768626 0.0034851739 1 1 +Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms + +Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s +87.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031135 | 0.031135 | 0.031135 | 0.0 | 9.13 +Bond | 0.12623 | 0.12623 | 0.12623 | 0.0 | 37.01 +Kspace | 0.036491 | 0.036491 | 0.036491 | 0.0 | 10.70 +Neigh | 0.046395 | 0.046395 | 0.046395 | 0.0 | 13.60 +Comm | 0.0025396 | 0.0025396 | 0.0025396 | 0.0 | 0.74 +Output | 0.07775 | 0.07775 | 0.07775 | 0.0 | 22.80 +Modify | 0.019219 | 0.019219 | 0.019219 | 0.0 | 5.64 +Other | | 0.001306 | | | 0.38 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 740 ave 740 max 740 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 740 +Ave neighs/atom = 16.8182 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 new file mode 100644 index 0000000000..b9c7a3ba15 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 @@ -0,0 +1,148 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000178751 secs + read_data CPU = 0.0385782 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 252 2 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 293.70542 -52.547388 0.0034851739 1 0 + 100 276.36755 54.81826 0.0034851739 1 1 + 150 448.65869 16.874435 0.0034851739 1 1 + 200 379.84257 11.578545 0.0034851739 1 1 + 250 298.21983 90.656585 0.0034851739 1 1 + 300 333.3111 -30.139607 0.0034851739 1 1 + 350 266.57108 6.4505134 0.0034851739 1 1 + 400 264.05476 10.513204 0.0034851739 1 1 + 450 250.70418 -18.635379 0.0034851739 1 1 + 500 261.21632 10.231013 0.0034851739 1 1 + 550 309.89024 -8.8299506 0.0034851739 1 1 + 600 373.45851 30.368993 0.0034851739 1 1 + 650 338.26242 9.0362267 0.0034851739 1 1 + 700 295.67794 -5.6007538 0.0034851739 1 1 + 750 310.86563 -59.228181 0.0034851739 1 1 + 800 286.22678 -9.9022407 0.0034851739 1 1 + 850 218.42135 27.845352 0.0034851739 1 1 + 900 259.62551 24.216336 0.0034851739 1 1 + 950 250.21307 -14.560985 0.0034851739 1 1 + 1000 274.29245 -0.38768626 0.0034851739 1 1 +Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms + +Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s +98.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85 +Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84 +Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16 +Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78 +Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03 +Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93 +Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10 +Other | | 0.0008281 | | | 0.31 + +Nlocal: 11 ave 21 max 0 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 32.5 ave 43 max 23 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 185 ave 376 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 740 +Ave neighs/atom = 16.8182 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 new file mode 100644 index 0000000000..14cac1dfad --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 @@ -0,0 +1,147 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000217102 secs + read_data CPU = 0.00630778 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 343 8 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 416.49412 -20.293038 0.0034851739 1 0 + 100 746.49323 91.912227 0.0034851739 1 1 + 150 515.15907 -1.4024709 0.0034851739 1 1 + 200 441.14572 -19.333087 0.0034851739 1 1 + 250 376.40996 30.717679 0.0034851739 1 1 + 300 326.15127 -3.0433799 0.0034851739 1 1 + 350 326.21116 6.235391 0.0034851739 1 1 + 400 366.48556 3.9807338 0.0034851739 1 1 + 450 313.79097 7.6674629 0.0034851739 1 1 + 500 278.89836 14.102052 0.0034851739 1 1 + 550 267.50214 18.241417 0.0034851739 1 1 + 600 276.28064 7.4649611 0.0034851739 1 1 + 650 255.26713 -8.5258573 0.0034851739 1 1 + 700 258.59752 -5.3341215 0.0034851739 1 1 + 750 263.71264 33.369869 0.0034851739 1 1 + 800 246.22976 -15.349137 0.0034851739 1 1 + 850 255.93887 16.331669 0.0034851739 1 1 + 900 239.72525 -0.20075789 0.0034851739 1 1 + 950 213.73064 12.17619 0.0034851739 1 1 + 1000 218.25094 -9.0955642 0.0034851739 1 1 +Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms + +Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s +91.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031941 | 0.031941 | 0.031941 | 0.0 | 9.17 +Bond | 0.13031 | 0.13031 | 0.13031 | 0.0 | 37.42 +Kspace | 0.037554 | 0.037554 | 0.037554 | 0.0 | 10.78 +Neigh | 0.047397 | 0.047397 | 0.047397 | 0.0 | 13.61 +Comm | 0.0025814 | 0.0025814 | 0.0025814 | 0.0 | 0.74 +Output | 0.083526 | 0.083526 | 0.083526 | 0.0 | 23.98 +Modify | 0.013602 | 0.013602 | 0.013602 | 0.0 | 3.91 +Other | | 0.001336 | | | 0.38 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 818 ave 818 max 818 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 818 +Ave neighs/atom = 18.5909 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 new file mode 100644 index 0000000000..6b13dd60d3 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 @@ -0,0 +1,147 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000163256 secs + read_data CPU = 0.0244579 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 252 2 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 416.49412 -20.293038 0.0034851739 1 0 + 100 746.49323 91.912227 0.0034851739 1 1 + 150 515.15907 -1.4024709 0.0034851739 1 1 + 200 441.14572 -19.333087 0.0034851739 1 1 + 250 376.40996 30.717679 0.0034851739 1 1 + 300 326.15127 -3.0433799 0.0034851739 1 1 + 350 326.21116 6.235391 0.0034851739 1 1 + 400 366.48556 3.9807338 0.0034851739 1 1 + 450 313.79097 7.6674629 0.0034851739 1 1 + 500 278.89836 14.102052 0.0034851739 1 1 + 550 267.50214 18.241417 0.0034851739 1 1 + 600 276.28064 7.4649611 0.0034851739 1 1 + 650 255.26713 -8.5258573 0.0034851739 1 1 + 700 258.59752 -5.3341215 0.0034851739 1 1 + 750 263.71264 33.369869 0.0034851739 1 1 + 800 246.22976 -15.349137 0.0034851739 1 1 + 850 255.93887 16.331669 0.0034851739 1 1 + 900 239.72525 -0.20075789 0.0034851739 1 1 + 950 213.73064 12.17619 0.0034851739 1 1 + 1000 218.25094 -9.0955642 0.0034851739 1 1 +Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms + +Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56 +Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62 +Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04 +Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16 +Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31 +Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13 +Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91 +Other | | 0.0007123 | | | 0.28 + +Nlocal: 11 ave 29 max 0 min +Histogram: 1 1 0 0 1 0 0 0 0 1 +Nghost: 25 ave 31 max 12 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 204.5 ave 443 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 818 +Ave neighs/atom = 18.5909 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00