diff --git a/examples/PACKAGES/alchemy/in.twowater b/examples/PACKAGES/alchemy/in.twowater index 63089d23c5..8c19eab215 100644 --- a/examples/PACKAGES/alchemy/in.twowater +++ b/examples/PACKAGES/alchemy/in.twowater @@ -73,18 +73,18 @@ else & velocity all create 300.0 5463576 timestep 0.2 -# since the trajectory and forces are kept identical through fix alchemy -# we can even do fix npt simulations, but we need to use the "mixed" pressure +# since the trajectory and forces are kept identical through fix alchemy, +# we can do fix npt simulations, but we must use the "mixed" pressure fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0 fix transform all alchemy compute pressure all pressure/alchemy transform fix_modify integrate press pressure -# only need to output a dump file form one partition -if "${name} == twowater" then & - "dump 1 all atom 100 ${name}.lammpstrj" & - "dump_modify 1 sort id" +# only need to output a dump file from one partition +# if "${name} == twowater" then & +# "dump 1 all atom 100 ${name}.lammpstrj" & +# "dump_modify 1 sort id" thermo_style custom step temp press etotal density pe ke f_transform[1] f_transform[4] thermo_modify colname f_transform[1] lambda colname f_transform[4] EPot_mixed diff --git a/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4 b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4 new file mode 100644 index 0000000000..18375012d0 --- /dev/null +++ b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4 @@ -0,0 +1,13 @@ +LAMMPS (8 Feb 2023) +Running on 2 partitions of processors +Starting alchemical transformation at 0% + Alchemical transformation progress: 10% + Alchemical transformation progress: 20% + Alchemical transformation progress: 30% + Alchemical transformation progress: 40% + Alchemical transformation progress: 50% + Alchemical transformation progress: 60% + Alchemical transformation progress: 70% + Alchemical transformation progress: 80% + Alchemical transformation progress: 90% + Alchemical transformation progress: 100% diff --git a/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.0 b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.0 new file mode 100644 index 0000000000..7717dae784 --- /dev/null +++ b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.0 @@ -0,0 +1,408 @@ +LAMMPS (8 Feb 2023) +Processor partition = 0 + using 1 OpenMP thread(s) per MPI task +# Example for alchemical transformation of two water molecules into a hydronium and hydroxyl ion +# WARNING: This input is intended for demonstrating the method, only +# The force field parameters are made up and NOT suitable for production simulations. + +# set up different names for two partitions +variable name world twowater twoions + +units real +atom_style full +atom_modify map array +region box block -5 5 -5 5 -5 5 +boundary p p p +create_box 2 box bond/types 2 angle/types 2 extra/bond/per/atom 3 extra/angle/per/atom 3 extra/special/per/atom 3 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 2 MPI processor grid + +mass 1 15.9994 +mass 2 1.008 + +pair_style lj/cut/coul/cut 10.0 +pair_coeff 1 1 0.1553 3.166 +pair_coeff 1 2 0.0 1.0 +pair_coeff 2 2 0.0 1.0 + +bond_style harmonic +bond_coeff * 1000.0 1.0 + +angle_style harmonic +angle_coeff * 100.0 109.47 + +molecule water h2o.mol +Read molecule template water: + 1 molecules + 0 fragments + 3 atoms with max type 2 + 2 bonds with max type 1 + 1 angles with max type 1 + 0 dihedrals with max type 0 + 0 impropers with max type 0 + +# create the two molecules we want to transform ... +create_atoms 0 single -2.0 0.0 0.0 mol water 453624 +Created 3 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.003 seconds +create_atoms 0 single 2.0 0.0 0.0 mol water 767353 +Created 3 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds + +# ... and put them in a group +group transform id 1:6 +6 atoms in group transform + +# now fill the rest of the box with more water +create_atoms 0 random 32 34564 NULL mol water 25367 overlap 1.33 +Created 96 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.001 seconds + +# change topology and settings for the two states +# we cannot simply create a different topology directly or +# load a different data file because the order and position +# of all atoms must be maintained across both replica + +# we first have to remove all topology data in the transform group +delete_bonds transform bond 1 +System init for delete_bonds ... +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Deleting bonds ... + 68 total bonds, 64 turned on, 4 turned off + 34 total angles, 34 turned on, 0 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off +delete_bonds transform angle 1 remove +System init for delete_bonds ... +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Deleting bonds ... + 64 total bonds, 64 turned on, 0 turned off + 32 total angles, 32 turned on, 0 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +# then generate different topologies for the two partitions. select by name. +if "${name} == twowater" then "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 1 3" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 2 1 3" "create_bonds single/angle 2 5 4 6" else "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 3 4" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 3 4 5" "create_bonds single/angle 2 5 4 6" "create_bonds single/angle 2 3 4 6" "set atom 1 charge -1.1354" "set atom 2 charge 0.1354" "set atom 3 charge 0.56775" "set atom 4 charge -0.70305" "set atom 5*6 charge 0.56775" +create_bonds single/bond 2 1 2 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 2 1 3 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 2 4 5 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 2 4 6 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/angle 2 2 1 3 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/angle 2 5 4 6 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds + +velocity all create 300.0 5463576 +timestep 0.2 + +# since the trajectory and forces are kept identical through fix alchemy, +# we can do fix npt simulations, but we must use the "mixed" pressure + +fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0 +fix transform all alchemy +compute pressure all pressure/alchemy transform +fix_modify integrate press pressure + +# only need to output a dump file from one partition +# if "${name} == twowater" then # "dump 1 all atom 100 ${name}.lammpstrj" # "dump_modify 1 sort id" + +thermo_style custom step temp press etotal density pe ke f_transform[1] f_transform[4] +thermo_modify colname f_transform[1] lambda colname f_transform[4] EPot_mixed +thermo_modify press pressure + +thermo 100 +run 20000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 7.535 | 7.535 | 7.535 Mbytes + Step Temp Press TotEng Density PotEng KinEng lambda EPot_mixed + 0 300 184631.17 -802.19609 1.0171193 -892.51464 90.318545 1 -892.51464 + 100 293.4335 -513.97927 189.09028 0.3029684 100.74865 88.341623 0.995 207.29243 + 200 320.81838 1513.3 111.09325 0.64509407 14.507087 96.586165 0.99 46.402434 + 300 261.53825 -3808.6942 -538.67351 0.88817871 -617.41269 78.739179 0.985 -614.76481 + 400 308.32444 1375.0327 -804.08042 0.97694485 -896.90513 92.824715 0.98 -897.24386 + 500 292.60623 -12843.384 -1141.5985 1.0140814 -1229.691 88.092563 0.975 -1221.948 + 600 326.16112 91608.645 2882.4855 1.0263567 2784.2908 98.194659 0.97 2786.0743 + 700 317.22811 -60420.408 -1517.0601 0.9919143 -1612.5654 95.505272 0.965 -1616.7677 + 800 309.94673 -56793.931 -1549.4612 1.0024958 -1642.7743 93.313126 0.96 -1640.8606 + 900 272.80718 -5076.2282 -1266.6775 1.0141078 -1348.8093 82.131824 0.955 -1357.1812 + 1000 346.52557 -16919.192 -1406.675 1.0170322 -1511.0006 104.32562 0.95 -1514.1398 + 1100 300.62984 -51826.972 -2469.2821 1.0063592 -2559.7903 90.508164 0.945 -2565.9668 + 1200 293.72767 45222.698 2039.1938 1.0272336 1950.7636 88.430186 0.94 1951.1683 + 1300 289.4971 94600.203 2184.5096 1.0298091 2097.3531 87.156524 0.935 2088.1011 + 1400 328.98666 35468.53 1816.723 1.0198467 1717.6777 99.045321 0.93 1716.9268 + 1500 392.9407 41220.21 1820.7312 1.0194044 1702.4317 118.29944 0.925 1690.6416 + 1600 284.90093 -37995.141 -2439.9256 1.0068497 -2525.6984 85.772791 0.92 -2529.5874 + 1700 267.67454 25275.255 1612.5912 1.0313556 1532.0046 80.586582 0.915 1520.9695 + 1800 247.16495 -68222.994 -2699.1903 1.0018048 -2773.6022 74.41193 0.91 -2788.9545 + 1900 328.41849 -51979.665 -2339.7432 1.0154952 -2438.6175 98.874268 0.905 -2461.3422 + 2000 313.8715 21726.003 1473.9594 1.018831 1379.4647 94.494725 0.9 1363.0739 + 2100 296.07341 66130.11 1379.1597 1.0224882 1290.0233 89.136398 0.895 1272.1884 + 2200 282.67889 51746.464 2376.377 1.0362683 2291.2732 85.103821 0.89 2276.1488 + 2300 281.04207 -71937.759 -2791.0867 1.0111968 -2875.6977 84.611035 0.885 -2892.2526 + 2400 321.00806 -51658.758 -2507.6376 1.0168161 -2604.2809 96.643269 0.88 -2622.9732 + 2500 288.95906 49645.753 2361.024 1.0355648 2274.0295 86.99454 0.875 2275.0348 + 2600 303.0064 -48470.216 -1973.9561 1.000439 -2065.1798 91.223657 0.87 -2082.5895 + 2700 361.7083 54973.584 1929.0772 1.0223169 1820.1806 108.89656 0.865 1817.1972 + 2800 289.27827 33564.017 1783.5154 1.0257088 1696.4248 87.090642 0.86 1682.9162 + 2900 283.94365 -47190.274 -2286.9529 1.0059224 -2372.4375 85.484591 0.855 -2395.9575 + 3000 337.10996 61988.686 2289.363 1.0258 2187.8721 101.49094 0.85 2168.1085 + 3100 305.28249 -50123.109 -1913.7375 1.0143567 -2005.6464 91.9089 0.845 -2040.3453 + 3200 270.19471 -18114.265 -1961.3048 1.0132413 -2042.6502 81.345309 0.84 -2076.9595 + 3300 263.39996 -109301.89 -2351.6647 0.99956867 -2430.9643 79.299671 0.835 -2471.0269 + 3400 249.01722 -37585.949 -2423.3849 1.0080932 -2498.3544 74.969576 0.83 -2537.734 + 3500 267.88868 65528.865 2164.3882 1.0390872 2083.7372 80.651054 0.825 2061.6421 + 3600 351.46458 -67583.574 -2861.4561 1.0059621 -2967.2687 105.81256 0.82 -3004.5028 + 3700 332.82565 -61204.843 -2275.2765 1.0053485 -2375.4776 100.20109 0.815 -2415.4435 + 3800 298.0279 61123.085 1951.1943 1.020672 1861.4695 89.724819 0.81 1831.9734 + 3900 317.04715 43210.045 1848.3875 1.0287838 1752.9367 95.450792 0.805 1721.1961 + 4000 261.75174 -111920.72 -3274.707 0.99457106 -3353.5105 78.803455 0.8 -3394.3528 + 4100 338.34245 89763.083 2115.4809 1.0318272 2013.6189 101.86199 0.795 1973.419 + 4200 288.52623 19989.792 1758.0617 1.0204119 1671.1975 86.86423 0.79 1633.1439 + 4300 322.05593 -33791.403 -2107.1643 1.0155065 -2204.1231 96.958741 0.785 -2246.4353 + 4400 280.59054 -27839.599 -1534.3265 1.0123506 -1618.8016 84.475096 0.78 -1672.1425 + 4500 296.08336 75206.112 2789.7494 1.0329133 2700.61 89.139393 0.775 2670.4908 + 4600 288.02094 -67445.101 -2983.5242 0.99579107 -3070.2363 86.712106 0.77 -3132.6352 + 4700 332.21641 -83964.647 -2746.0748 1.0053915 -2846.0925 100.01768 0.765 -2916.6652 + 4800 305.52557 -93111.682 -2354.6562 0.99824941 -2446.6383 91.982082 0.76 -2514.039 + 4900 272.82262 -53664.198 -2790.1342 0.99527907 -2872.2707 82.136472 0.755 -2947.2062 + 5000 288.96388 39846.089 1975.7895 1.0371205 1888.7935 86.99599 0.75 1833.3716 + 5100 293.25543 -71819.425 -2916.8817 0.99452016 -3005.1697 88.288011 0.745 -3069.7618 + 5200 296.16486 -64484.821 -2416.0381 1.0153125 -2505.2021 89.163931 0.74 -2589.6878 + 5300 342.07246 60255.985 1749.8984 1.0306374 1646.9134 102.98496 0.735 1608.5673 + 5400 295.53315 61421.189 1620.6432 1.0334762 1531.6695 88.973746 0.73 1492.0969 + 5500 285.1755 24845.113 1144.9009 1.0335035 1059.0454 85.855455 0.725 1014.0263 + 5600 276.79246 66244.072 1523.3405 1.0251134 1440.0089 83.331641 0.72 1390.9078 + 5700 288.43485 14629.129 1208.7278 1.02997 1121.8911 86.836719 0.715 1074.3779 + 5800 276.64233 59262.97 914.26981 1.0332305 830.98336 83.286443 0.71 763.27415 + 5900 358.25384 -111203.23 -3370.7104 1.006331 -3478.567 107.85655 0.705 -3561.6283 + 6000 327.82233 -62936.335 -1881.2426 1.0106476 -1979.9373 98.694786 0.7 -2062.107 + 6100 309.86553 -59110.381 -2698.4147 1.0076375 -2791.7034 93.28868 0.695 -2870.9566 + 6200 294.95752 -58011.845 -1819.201 1.0161986 -1908.0014 88.800448 0.69 -1971.2586 + 6300 307.27252 59016.127 1186.0709 1.0225343 1093.5629 92.508022 0.685 1032.9616 + 6400 292.21611 -118857.83 -2992.9227 1.0031304 -3080.8978 87.975114 0.68 -3175.9068 + 6500 332.21108 97132.547 2290.2726 1.0349752 2190.2565 100.01607 0.675 2121.4674 + 6600 321.93985 -50017.836 -2484.5919 1.0076385 -2581.5157 96.923796 0.67 -2673.6819 + 6700 299.07231 -98136.241 -3013.1584 1.0106261 -3103.1976 90.039252 0.665 -3194.0694 + 6800 285.33731 28487.407 455.68104 1.017186 369.77687 85.904169 0.66 294.02418 + 6900 296.41387 50054.533 2028.1018 1.0445934 1938.8629 89.238897 0.655 1851.1397 + 7000 318.34109 -71579.897 -3114.0324 1.007304 -3209.8728 95.840345 0.65 -3305.5715 + 7100 317.2192 12370.315 1139.7687 1.0177238 1044.2661 95.502589 0.645 961.68146 + 7200 289.91091 43944.333 1213.4685 1.0302599 1126.1874 87.281105 0.64 1039.3329 + 7300 324.81227 42859.173 1288.5297 1.0300698 1190.7411 97.788572 0.635 1083.5764 + 7400 305.72634 76516.72 2404.9462 1.0580673 2312.9036 92.042527 0.63 2218.3674 + 7500 283.77479 -87225.247 -3401.4354 0.9936609 -3486.8692 85.433754 0.625 -3581.9003 + 7600 318.72048 16084.995 1848.3396 1.0296163 1752.385 95.954566 0.62 1653.5125 + 7700 307.36895 74007.024 1754.8928 1.0363553 1662.3558 92.537054 0.615 1572.8568 + 7800 297.44704 28693.429 1261.5958 1.0206402 1172.0459 89.549946 0.61 1093.5903 + 7900 288.47173 -94644.76 -2455.4369 1.0095244 -2542.2847 86.847823 0.605 -2648.2974 + 8000 280.5001 63255.987 1584.7287 1.020587 1500.2808 84.44787 0.6 1418.7144 + 8100 320.23351 68383.584 2300.142 1.0419027 2203.7319 96.410082 0.595 2111.2616 + 8200 354.86765 50012.316 1350.3752 1.0292074 1243.5381 106.8371 0.59 1149.0631 + 8300 278.8859 24200.145 772.82478 1.0232468 688.86288 83.961894 0.585 569.83331 + 8400 295.95754 -12010.401 1078.6687 1.0200526 989.56716 89.101514 0.58 872.63254 + 8500 289.57525 -64114.236 -3017.5291 1.0062613 -3104.7091 87.18005 0.575 -3227.8592 + 8600 329.23192 15948.893 1427.4791 1.0271511 1328.3599 99.119161 0.57 1211.3868 + 8700 327.45998 39407.811 1697.908 1.0343756 1599.3223 98.585695 0.565 1480.9482 + 8800 296.99753 18017.036 871.11717 1.0178295 781.70256 89.414616 0.56 657.09357 + 8900 289.10016 79527.35 2536.8041 1.0462904 2449.7671 87.037018 0.555 2338.4742 + 9000 260.53308 -51430.717 -2680.1664 1.0040128 -2758.603 78.436561 0.55 -2894.7913 + 9100 314.17867 40043.249 2043.6144 1.0361707 1949.0272 94.5872 0.545 1836.5399 + 9200 362.21236 -55153.163 -2232.4614 1.0102652 -2341.5097 109.04831 0.54 -2497.8765 + 9300 266.62049 -72193.959 -2980.9254 1.0063615 -3061.1946 80.269248 0.535 -3225.2604 + 9400 259.59316 7674.9295 1378.2484 1.0326879 1300.0948 78.153588 0.53 1171.7119 + 9500 278.72962 -33127.835 -2581.8908 1.0163553 -2665.8057 83.914845 0.525 -2805.1711 + 9600 299.09039 24570.664 1839.3275 1.025317 1749.2828 90.044695 0.52 1631.8392 + 9700 336.65655 37767.059 1415.9074 1.0245842 1314.5529 101.35443 0.515 1218.4022 + 9800 279.68112 -55007.939 -2548.4947 1.0129837 -2632.696 84.201305 0.51 -2775.6909 + 9900 300.55694 14964.424 1332.287 1.0176315 1241.8008 90.486218 0.505 1127.7276 + 10000 276.77193 -75638.817 -3100.7483 1.0019055 -3184.0738 83.325459 0.5 -3341.663 + 10100 316.26926 61548.301 2406.8933 1.0427988 2311.6767 95.216598 0.495 2206.7159 + 10200 297.28171 56814.839 2073.2348 1.0270036 1983.7347 89.500171 0.49 1859.0176 + 10300 276.84774 83572.576 1920.2202 1.0322243 1836.8719 83.348283 0.485 1704.2233 + 10400 263.28687 -16549.994 1144.9186 1.0177296 1065.6529 79.265623 0.48 940.36339 + 10500 332.79252 47379.311 1538.8168 1.0223403 1438.6257 100.19112 0.475 1301.3762 + 10600 329.01105 39299.248 1330.9914 1.0230094 1231.9387 99.052663 0.47 1077.5639 + 10700 339.21335 -4217.0313 981.9193 1.0235915 879.79511 102.12419 0.465 741.87272 + 10800 297.11192 -80013.424 -3682.9794 1.0009566 -3772.4285 89.449054 0.46 -3958.8283 + 10900 299.63096 47783.864 1833.1832 1.0435283 1742.9757 90.207441 0.455 1620.9328 + 11000 363.58243 67370.65 1769.9236 1.0450565 1660.4628 109.46079 0.45 1543.803 + 11100 306.04664 50246.004 1323.7676 1.0341876 1231.6287 92.138957 0.445 1063.5345 + 11200 255.68488 43750.967 2205.2392 1.0530607 2128.2623 76.976955 0.44 1986.9636 + 11300 271.71957 -40289.299 -3083.4093 1.0168497 -3165.2137 81.804388 0.435 -3344.1558 + 11400 291.74007 -115249.24 -3319.2153 1.0067921 -3407.0471 87.831795 0.43 -3569.0256 + 11500 270.22077 28235.119 596.78348 1.0195886 515.43032 81.353155 0.425 373.78255 + 11600 297.08506 29790.701 1031.3514 1.0317561 941.91046 89.440969 0.42 803.92835 + 11700 295.33119 -101140.58 -3068.1166 1.0107252 -3157.0295 88.912943 0.415 -3348.5652 + 11800 308.77287 -120312.75 -3553.1266 0.99681611 -3646.0863 92.95972 0.41 -3835.4663 + 11900 293.86337 82287.969 1847.0953 1.0331446 1758.6242 88.47104 0.405 1625.4846 + 12000 279.9866 27919.689 2249.3175 1.0384909 2165.0242 84.293273 0.4 2028.6311 + 12100 292.19439 47035.018 1220.3593 1.0210948 1132.3908 87.968573 0.395 976.68113 + 12200 317.78325 46886.483 2039.3721 1.0310567 1943.6997 95.672401 0.39 1763.6359 + 12300 357.44038 51492.35 1898.3396 1.0414835 1790.7279 107.61165 0.385 1638.1905 + 12400 288.16042 -50528.478 -2837.5599 1.0130798 -2924.314 86.7541 0.38 -3115.1383 + 12500 300.37356 -114034.29 -3091.586 1.0130272 -3182.017 90.431009 0.375 -3364.511 + 12600 265.4402 73960.28 1297.3012 1.0343798 1217.3873 79.913907 0.37 1094.544 + 12700 287.07994 22722.337 1711.9055 1.0268893 1625.4767 86.428809 0.365 1490.443 + 12800 315.39745 46072.191 926.21362 1.0205906 831.25949 94.954129 0.36 662.83753 + 12900 307.48549 -120472.73 -3181.5418 1.005689 -3274.1139 92.57214 0.355 -3469.7834 + 13000 291.00577 -59154.878 -2652.0402 1.012821 -2739.6509 87.610727 0.35 -2966.2448 + 13100 318.37718 86703.775 2087.145 1.036209 1991.2938 95.851211 0.345 1819.7078 + 13200 280.41509 -107033.79 -2683.9682 1.0135499 -2768.3905 84.422277 0.34 -2953.8355 + 13300 275.01919 112086.85 2632.1169 1.0437945 2549.3192 82.797775 0.335 2394.6707 + 13400 299.46547 -111959.62 -3475.4354 0.98732074 -3565.593 90.157617 0.33 -3792.6798 + 13500 275.65631 17625.49 1762.6531 1.0255473 1679.6636 82.989588 0.325 1521.2745 + 13600 302.63525 122466.63 2853.8095 1.0438137 2762.6976 91.111917 0.32 2611.7188 + 13700 302.21323 -94399.663 -3003.7573 1.0068914 -3094.7422 90.984863 0.315 -3328.4539 + 13800 305.70483 30039.825 1792.3286 1.0225478 1700.2926 92.036052 0.31 1502.8476 + 13900 273.15564 -27822.597 -2346.6702 1.0131002 -2428.9069 82.236732 0.305 -2683.7804 + 14000 257.14635 -1821.0012 1378.2522 1.0172653 1300.8352 77.416947 0.3 1067.8821 + 14100 323.74174 -76139.363 -2747.4152 1.0139806 -2844.8814 97.466276 0.295 -3052.598 + 14200 274.99913 54440.943 983.27131 1.0186356 900.47957 82.791736 0.29 767.64274 + 14300 291.8774 1281.7286 1258.7881 1.0214356 1170.915 87.873139 0.285 1042.8585 + 14400 308.97245 -47961.551 -2680.7892 1.0155221 -2773.809 93.019806 0.28 -3007.3204 + 14500 311.05309 86026.739 2115.2413 1.0311818 2021.5951 93.646208 0.275 1830.5463 + 14600 269.27432 -12972.747 971.48792 1.0172239 890.41971 81.068214 0.27 711.81484 + 14700 262.20739 -77722.459 -3215.6796 1.0029421 -3294.6202 78.940634 0.265 -3537.1929 + 14800 300.33592 -107332.8 -2798.6664 1.0126785 -2889.086 90.419677 0.26 -3125.8439 + 14900 307.0173 -73204.94 -2652.7275 1.016875 -2745.1587 92.431185 0.255 -3016.0143 + 15000 334.08711 64440.709 1615.3385 1.0369481 1514.7576 100.58087 0.25 1323.9179 + 15100 293.46703 35179.395 2020.1996 1.0331703 1931.8479 88.351717 0.245 1768.9681 + 15200 307.80546 54006.291 1111.7619 1.0246134 1019.0935 92.668471 0.24 822.22754 + 15300 336.59792 33832.907 1282.8271 1.0242407 1181.4903 101.33678 0.235 956.25285 + 15400 285.46526 -99629.94 -2336.7535 1.0041261 -2422.6962 85.942688 0.23 -2730.1887 + 15500 269.15938 122546.45 3012.0792 1.0318941 2931.0456 81.033612 0.225 2695.4331 + 15600 294.50818 -104733.19 -1914.0242 1.0017241 -2002.6894 88.665166 0.22 -2281.5773 + 15700 321.05125 -40438.501 -1721.9536 1.0125007 -1818.6099 96.656271 0.215 -2084.0893 + 15800 303.22185 -42224.408 -2145.481 1.0090867 -2236.7695 91.288521 0.21 -2506.3355 + 15900 281.65025 78652.063 2791.9418 1.0460521 2707.1477 84.794136 0.205 2500.7128 + 16000 286.5056 63174.412 1725.0409 1.0185277 1638.785 86.255897 0.2 1442.2427 + 16100 271.74574 -75051.584 -2101.5778 1.0091727 -2183.3901 81.812265 0.195 -2447.1967 + 16200 266.40007 -64120.09 -2223.3693 1.0064388 -2303.5722 80.202888 0.19 -2525.4243 + 16300 330.67137 46204.124 1837.3168 1.0271037 1737.7643 99.552523 0.185 1529.8186 + 16400 310.94573 18510.676 1531.823 1.0188695 1438.2091 93.613887 0.18 1195.3041 + 16500 270.29191 79005.409 1989.9392 1.0354088 1908.5646 81.374574 0.175 1678.7342 + 16600 334.24108 17143.221 1644.1483 1.0230561 1543.521 100.62723 0.17 1379.3215 + 16700 292.28721 -78618.031 -2768.3997 0.99940789 -2856.3962 87.996518 0.165 -3087.379 + 16800 346.09157 -69398.937 -2647.1375 1.0153026 -2751.3325 104.19496 0.16 -3011.3476 + 16900 284.37042 39314.526 2287.7061 1.0343186 2202.093 85.613074 0.155 2045.8316 + 17000 281.69389 86032.163 1817.9125 1.0237583 1733.1052 84.807275 0.15 1528.8391 + 17100 297.2629 55128.393 2617.4156 1.0419182 2527.9211 89.494508 0.145 2369.0347 + 17200 328.81472 47063.86 1880.9768 1.0364627 1781.9832 98.993555 0.14 1526.7115 + 17300 313.41363 -46685.063 -2310.803 1.008117 -2405.1599 94.356878 0.135 -2685.8034 + 17400 288.17114 68721.523 2771.6788 1.0429105 2684.9215 86.757326 0.13 2490.5845 + 17500 260.01702 -23324.539 -1436.6738 1.0100415 -1514.955 78.281195 0.125 -1812.4813 + 17600 297.6633 72795.463 2635.741 1.0362827 2546.126 89.615054 0.12 2336.0152 + 17700 301.02937 93833.118 2690.518 1.0276466 2599.8896 90.628448 0.115 2364.8751 + 17800 238.92837 -78317.212 -2175.2589 1.0084077 -2247.1911 71.932208 0.11 -2579.4429 + 17900 299.27724 -65278.891 -2589.1173 1.0034773 -2679.2182 90.10095 0.105 -2987.498 + 18000 315.15753 -72437.481 -2338.6068 1.0136139 -2433.4887 94.881898 0.1 -2718.125 + 18100 268.39411 -42194.209 -2285.3824 1.0108104 -2366.1856 80.803219 0.095 -2656.3853 + 18200 284.91941 40905.162 2045.1299 1.0266185 1959.3515 85.778354 0.09 1723.6803 + 18300 329.41629 -56526.814 -2104.8386 1.0137784 -2204.0133 99.174667 0.085 -2540.6829 + 18400 293.16732 -22085.551 -1652.5444 1.0163557 -1740.8059 88.261484 0.08 -2052.7864 + 18500 276.28141 29367.359 2314.5497 1.0270087 2231.3719 83.177784 0.075 1971.9405 + 18600 331.18031 94669.124 2466.3928 1.0225403 2366.6871 99.705745 0.07 2081.8675 + 18700 265.4491 49872.536 2571.9864 1.0255308 2492.0698 79.916587 0.065 2260.4261 + 18800 314.51042 60758.629 2560.3258 1.0300818 2465.6387 94.687078 0.06 2219.6547 + 18900 317.70309 66345.835 1768.2041 1.0248229 1672.5558 95.648268 0.055 1410.3087 + 19000 291.39831 -96336.931 -2448.6251 1.0100498 -2536.354 87.728905 0.05 -2805.9396 + 19100 303.37353 -21421.495 -2012.0929 0.99771284 -2103.4271 91.334186 0.045 -2436.2173 + 19200 293.92948 36383.881 2042.0163 1.0251299 1953.5254 88.490944 0.04 1633.579 + 19300 287.24409 -46691.027 -2399.698 1.0112067 -2486.1762 86.478228 0.035 -2811.3506 + 19400 333.42205 21152.63 1524.8699 1.0189912 1424.4893 100.38065 0.03 1118.2463 + 19500 309.17989 60445.761 2298.6966 1.0338543 2205.6144 93.082259 0.025 1928.6181 + 19600 255.92246 -32795.547 -1724.7933 1.0157044 -1801.8418 77.04848 0.02 -2213.9484 + 19700 342.62332 33538.746 2439.138 1.0225905 2335.9872 103.1508 0.015 2081.9185 + 19800 295.68946 81474.342 2308.3249 1.0240743 2219.3041 89.020804 0.01 1910.5545 + 19900 306.4947 43488.052 2330.4958 1.0222707 2238.222 92.27385 0.005 1957.4368 + 20000 313.31679 -25133.284 -1161.6979 1.0163289 -1256.0256 94.327722 0 -1649.7551 +Loop time of 11.8252 on 2 procs for 20000 steps with 102 atoms + +Performance: 29.226 ns/day, 0.821 hours/ns, 1691.296 timesteps/s, 172.512 katom-step/s +99.3% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.8298 | 8.6298 | 10.43 | 61.3 | 72.98 +Bond | 0.045072 | 0.045296 | 0.045519 | 0.1 | 0.38 +Neigh | 0.10567 | 0.10572 | 0.10577 | 0.0 | 0.89 +Comm | 0.73714 | 2.5381 | 4.3392 | 113.0 | 21.46 +Output | 0.0032977 | 0.0035468 | 0.003796 | 0.4 | 0.03 +Modify | 0.43872 | 0.44155 | 0.44438 | 0.4 | 3.73 +Other | | 0.06121 | | | 0.52 + +Nlocal: 51 ave 51 max 51 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 3317 ave 3317 max 3317 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 18320 ave 21941 max 14699 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 36640 +Ave neighs/atom = 359.21569 +Ave special neighs/atom = 2 +Neighbor list builds = 181 +Dangerous builds = 0 +Total wall time: 0:00:11 diff --git a/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.1 b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.1 new file mode 100644 index 0000000000..8fa06d5677 --- /dev/null +++ b/examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4.1 @@ -0,0 +1,433 @@ +LAMMPS (8 Feb 2023) +Processor partition = 1 + using 1 OpenMP thread(s) per MPI task +# Example for alchemical transformation of two water molecules into a hydronium and hydroxyl ion +# WARNING: This input is intended for demonstrating the method, only +# The force field parameters are made up and NOT suitable for production simulations. + +# set up different names for two partitions +variable name world twowater twoions + +units real +atom_style full +atom_modify map array +region box block -5 5 -5 5 -5 5 +boundary p p p +create_box 2 box bond/types 2 angle/types 2 extra/bond/per/atom 3 extra/angle/per/atom 3 extra/special/per/atom 3 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 2 MPI processor grid + +mass 1 15.9994 +mass 2 1.008 + +pair_style lj/cut/coul/cut 10.0 +pair_coeff 1 1 0.1553 3.166 +pair_coeff 1 2 0.0 1.0 +pair_coeff 2 2 0.0 1.0 + +bond_style harmonic +bond_coeff * 1000.0 1.0 + +angle_style harmonic +angle_coeff * 100.0 109.47 + +molecule water h2o.mol +Read molecule template water: + 1 molecules + 0 fragments + 3 atoms with max type 2 + 2 bonds with max type 1 + 1 angles with max type 1 + 0 dihedrals with max type 0 + 0 impropers with max type 0 + +# create the two molecules we want to transform ... +create_atoms 0 single -2.0 0.0 0.0 mol water 453624 +Created 3 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.004 seconds +create_atoms 0 single 2.0 0.0 0.0 mol water 767353 +Created 3 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds + +# ... and put them in a group +group transform id 1:6 +6 atoms in group transform + +# now fill the rest of the box with more water +create_atoms 0 random 32 34564 NULL mol water 25367 overlap 1.33 +Created 96 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.001 seconds + +# change topology and settings for the two states +# we cannot simply create a different topology directly or +# load a different data file because the order and position +# of all atoms must be maintained across both replica + +# we first have to remove all topology data in the transform group +delete_bonds transform bond 1 +System init for delete_bonds ... +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Deleting bonds ... + 68 total bonds, 64 turned on, 4 turned off + 34 total angles, 34 turned on, 0 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off +delete_bonds transform angle 1 remove +System init for delete_bonds ... +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Deleting bonds ... + 64 total bonds, 64 turned on, 0 turned off + 32 total angles, 32 turned on, 0 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +# then generate different topologies for the two partitions. select by name. +if "${name} == twowater" then "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 1 3" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 2 1 3" "create_bonds single/angle 2 5 4 6" else "create_bonds single/bond 2 1 2" "create_bonds single/bond 2 3 4" "create_bonds single/bond 2 4 5" "create_bonds single/bond 2 4 6" "create_bonds single/angle 2 3 4 5" "create_bonds single/angle 2 5 4 6" "create_bonds single/angle 2 3 4 6" "set atom 1 charge -1.1354" "set atom 2 charge 0.1354" "set atom 3 charge 0.56775" "set atom 4 charge -0.70305" "set atom 5*6 charge 0.56775" +create_bonds single/bond 2 1 2 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 2 3 4 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 2 4 5 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/bond 2 4 6 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/angle 2 3 4 5 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/angle 2 5 4 6 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds single/angle 2 3 4 6 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds +set atom 1 charge -1.1354 +Setting atom values ... + 1 settings made for charge +set atom 2 charge 0.1354 +Setting atom values ... + 1 settings made for charge +set atom 3 charge 0.56775 +Setting atom values ... + 1 settings made for charge +set atom 4 charge -0.70305 +Setting atom values ... + 1 settings made for charge +set atom 5*6 charge 0.56775 +Setting atom values ... + 2 settings made for charge + +velocity all create 300.0 5463576 +timestep 0.2 + +# since the trajectory and forces are kept identical through fix alchemy, +# we can do fix npt simulations, but we must use the "mixed" pressure + +fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0 +fix transform all alchemy +compute pressure all pressure/alchemy transform +fix_modify integrate press pressure + +# only need to output a dump file from one partition +# if "${name} == twowater" then # "dump 1 all atom 100 ${name}.lammpstrj" # "dump_modify 1 sort id" + +thermo_style custom step temp press etotal density pe ke f_transform[1] f_transform[4] +thermo_modify colname f_transform[1] lambda colname f_transform[4] EPot_mixed +thermo_modify press pressure + +thermo 100 +run 20000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Per MPI rank memory allocation (min/avg/max) = 7.535 | 7.535 | 7.535 Mbytes + Step Temp Press TotEng Density PotEng KinEng lambda EPot_mixed + 0 300 184631.17 10769.267 1.0171193 10678.948 90.318545 0 -892.51464 + 100 293.4335 -513.97927 21497.846 0.3029684 21409.505 88.341623 0.005 207.29243 + 200 320.81838 1513.3 3300.6279 0.64509407 3204.0418 96.586165 0.01 46.402434 + 300 261.53825 -3808.6942 -362.14861 0.88817871 -440.88779 78.739179 0.015 -614.76481 + 400 308.32444 1375.0327 -821.01681 0.97694485 -913.84152 92.824715 0.02 -897.24386 + 500 292.60623 -12843.384 -831.87625 1.0140814 -919.96881 88.092563 0.025 -1221.948 + 600 326.16112 91608.645 2941.9339 1.0263567 2843.7393 98.194659 0.03 2786.0743 + 700 317.22811 -60420.408 -1637.1259 0.9919143 -1732.6311 95.505272 0.035 -1616.7677 + 800 309.94673 -56793.931 -1501.6195 1.0024958 -1594.9326 93.313126 0.04 -1640.8606 + 900 272.80718 -5076.2282 -1452.719 1.0141078 -1534.8508 82.131824 0.045 -1357.1812 + 1000 346.52557 -16919.192 -1469.4601 1.0170322 -1573.7857 104.32562 0.05 -1514.1398 + 1100 300.62984 -51826.972 -2581.5818 1.0063592 -2672.09 90.508164 0.055 -2565.9668 + 1200 293.72767 45222.698 2045.9381 1.0272336 1957.5079 88.430186 0.06 1951.1683 + 1300 289.4971 94600.203 2042.1709 1.0298091 1955.0144 87.156524 0.065 2088.1011 + 1400 328.98666 35468.53 1805.9965 1.0198467 1706.9512 99.045321 0.07 1716.9268 + 1500 392.9407 41220.21 1663.5291 1.0194044 1545.2297 118.29944 0.075 1690.6416 + 1600 284.90093 -37995.141 -2488.5372 1.0068497 -2574.31 85.772791 0.08 -2529.5874 + 1700 267.67454 25275.255 1482.7666 1.0313556 1402.18 80.586582 0.085 1520.9695 + 1800 247.16495 -68222.994 -2869.7712 1.0018048 -2944.1832 74.41193 0.09 -2788.9545 + 1900 328.41849 -51979.665 -2578.9515 1.0154952 -2677.8258 98.874268 0.095 -2461.3422 + 2000 313.8715 21726.003 1310.0519 1.018831 1215.5571 94.494725 0.1 1363.0739 + 2100 296.07341 66130.11 1209.3035 1.0224882 1120.1671 89.136398 0.105 1272.1884 + 2200 282.67889 51746.464 2238.8823 1.0362683 2153.7785 85.103821 0.11 2276.1488 + 2300 281.04207 -71937.759 -2935.0422 1.0111968 -3019.6532 84.611035 0.115 -2892.2526 + 2400 321.00806 -51658.758 -2663.4071 1.0168161 -2760.0503 96.643269 0.12 -2622.9732 + 2500 288.95906 49645.753 2369.0667 1.0355648 2282.0722 86.99454 0.125 2275.0348 + 2600 303.0064 -48470.216 -2107.8769 1.000439 -2199.1005 91.223657 0.13 -2082.5895 + 2700 361.7083 54973.584 1906.9779 1.0223169 1798.0813 108.89656 0.135 1817.1972 + 2800 289.27827 33564.017 1687.0255 1.0257088 1599.9349 87.090642 0.14 1682.9162 + 2900 283.94365 -47190.274 -2449.1599 1.0059224 -2534.6445 85.484591 0.145 -2395.9575 + 3000 337.10996 61988.686 2157.6059 1.0258 2056.115 101.49094 0.15 2168.1085 + 3100 305.28249 -50123.109 -2137.6015 1.0143567 -2229.5104 91.9089 0.155 -2040.3453 + 3200 270.19471 -18114.265 -2175.7381 1.0132413 -2257.0834 81.345309 0.16 -2076.9595 + 3300 263.39996 -109301.89 -2594.4684 0.99956867 -2673.7681 79.299671 0.165 -2471.0269 + 3400 249.01722 -37585.949 -2655.0291 1.0080932 -2729.9987 74.969576 0.17 -2537.734 + 3500 267.88868 65528.865 2038.1308 1.0390872 1957.4797 80.651054 0.175 2061.6421 + 3600 351.46458 -67583.574 -3068.3126 1.0059621 -3174.1251 105.81256 0.18 -3004.5028 + 3700 332.82565 -61204.843 -2491.3087 1.0053485 -2591.5097 100.20109 0.185 -2415.4435 + 3800 298.0279 61123.085 1795.9521 1.020672 1706.2273 89.724819 0.19 1831.9734 + 3900 317.04715 43210.045 1685.6151 1.0287838 1590.1643 95.450792 0.195 1721.1961 + 4000 261.75174 -111920.72 -3478.9188 0.99457106 -3557.7223 78.803455 0.2 -3394.3528 + 4100 338.34245 89763.083 1919.3836 1.0318272 1817.5216 101.86199 0.205 1973.419 + 4200 288.52623 19989.792 1576.8543 1.0204119 1489.99 86.86423 0.21 1633.1439 + 4300 322.05593 -33791.403 -2303.9654 1.0155065 -2400.9242 96.958741 0.215 -2246.4353 + 4400 280.59054 -27839.599 -1776.7852 1.0123506 -1861.2603 84.475096 0.22 -1672.1425 + 4500 296.08336 75206.112 2655.8862 1.0329133 2566.7468 89.139393 0.225 2670.4908 + 4600 288.02094 -67445.101 -3254.8238 0.99579107 -3341.5359 86.712106 0.23 -3132.6352 + 4700 332.21641 -83964.647 -3046.3841 1.0053915 -3146.4017 100.01768 0.235 -2916.6652 + 4800 305.52557 -93111.682 -2635.4926 0.99824941 -2727.4747 91.982082 0.24 -2514.039 + 4900 272.82262 -53664.198 -3095.9932 0.99527907 -3178.1297 82.136472 0.245 -2947.2062 + 5000 288.96388 39846.089 1754.1018 1.0371205 1667.1058 86.99599 0.25 1833.3716 + 5100 293.25543 -71819.425 -3170.1841 0.99452016 -3258.4721 88.288011 0.255 -3069.7618 + 5200 296.16486 -64484.821 -2740.9832 1.0153125 -2830.1471 89.163931 0.26 -2589.6878 + 5300 342.07246 60255.985 1605.1961 1.0306374 1502.2111 102.98496 0.265 1608.5673 + 5400 295.53315 61421.189 1474.0782 1.0334762 1385.1045 88.973746 0.27 1492.0969 + 5500 285.1755 24845.113 981.19505 1.0335035 895.3396 85.855455 0.275 1014.0263 + 5600 276.79246 66244.072 1347.9794 1.0251134 1264.6478 83.331641 0.28 1390.9078 + 5700 288.43485 14629.129 1042.0147 1.02997 955.17799 86.836719 0.285 1074.3779 + 5800 276.64233 59262.97 680.78976 1.0332305 597.50331 83.286443 0.29 763.27415 + 5900 358.25384 -111203.23 -3652.2742 1.006331 -3760.1307 107.85655 0.295 -3561.6283 + 6000 327.82233 -62936.335 -2155.1414 1.0106476 -2253.8362 98.694786 0.3 -2062.107 + 6100 309.86553 -59110.381 -2958.2613 1.0076375 -3051.5499 93.28868 0.305 -2870.9566 + 6200 294.95752 -58011.845 -2023.2564 1.0161986 -2112.0569 88.800448 0.31 -1971.2586 + 6300 307.27252 59016.127 993.68575 1.0225343 901.17773 92.508022 0.315 1032.9616 + 6400 292.21611 -118857.83 -3289.8257 1.0031304 -3377.8009 87.975114 0.32 -3175.9068 + 6500 332.21108 97132.547 2078.6137 1.0349752 1978.5976 100.01607 0.325 2121.4674 + 6600 321.93985 -50017.836 -2763.8832 1.0076385 -2860.807 96.923796 0.33 -2673.6819 + 6700 299.07231 -98136.241 -3284.4174 1.0106261 -3374.4566 90.039252 0.335 -3194.0694 + 6800 285.33731 28487.407 232.87902 1.017186 146.97485 85.904169 0.34 294.02418 + 6900 296.41387 50054.533 1773.8315 1.0445934 1684.5926 89.238897 0.345 1851.1397 + 7000 318.34109 -71579.897 -3387.4573 1.007304 -3483.2977 95.840345 0.35 -3305.5715 + 7100 317.2192 12370.315 907.13585 1.0177238 811.63326 95.502589 0.355 961.68146 + 7200 289.91091 43944.333 972.20602 1.0302599 884.92492 87.281105 0.36 1039.3329 + 7300 324.81227 42859.173 994.92755 1.0300698 897.13897 97.788572 0.365 1083.5764 + 7400 305.72634 76516.72 2149.4427 1.0580673 2057.4002 92.042527 0.37 2218.3674 + 7500 283.77479 -87225.247 -3654.8517 0.9936609 -3740.2855 85.433754 0.375 -3581.9003 + 7600 318.72048 16084.995 1588.1487 1.0296163 1492.1941 95.954566 0.38 1653.5125 + 7700 307.36895 74007.024 1522.4279 1.0363553 1429.8909 92.537054 0.385 1572.8568 + 7800 297.44704 28693.429 1060.4277 1.0206402 970.87774 89.549946 0.39 1093.5903 + 7900 288.47173 -94644.76 -2723.8234 1.0095244 -2810.6712 86.847823 0.395 -2648.2974 + 8000 280.5001 63255.987 1380.8125 1.020587 1296.3647 84.44787 0.4 1418.7144 + 8100 320.23351 68383.584 2071.8202 1.0419027 1975.4101 96.410082 0.405 2111.2616 + 8200 354.86765 50012.316 1119.9483 1.0292074 1013.1112 106.8371 0.41 1149.0631 + 8300 278.8859 24200.145 486.00653 1.0232468 402.04464 83.961894 0.415 569.83331 + 8400 295.95754 -12010.401 800.25292 1.0200526 711.1514 89.101514 0.42 872.63254 + 8500 289.57525 -64114.236 -3307.2939 1.0062613 -3394.4739 87.18005 0.425 -3227.8592 + 8600 329.23192 15948.893 1155.4486 1.0271511 1056.3294 99.119161 0.43 1211.3868 + 8700 327.45998 39407.811 1425.7837 1.0343756 1327.198 98.585695 0.435 1480.9482 + 8800 296.99753 18017.036 587.91493 1.0178295 498.50031 89.414616 0.44 657.09357 + 8900 289.10016 79527.35 2286.7077 1.0462904 2199.6707 87.037018 0.445 2338.4742 + 9000 260.53308 -51430.717 -2982.8072 1.0040128 -3061.2437 78.436561 0.45 -2894.7913 + 9100 314.17867 40043.249 1796.3896 1.0361707 1701.8024 94.5872 0.455 1836.5399 + 9200 362.21236 -55153.163 -2572.3893 1.0102652 -2681.4376 109.04831 0.46 -2497.8765 + 9300 266.62049 -72193.959 -3333.755 1.0063615 -3414.0242 80.269248 0.465 -3225.2604 + 9400 259.59316 7674.9295 1105.0933 1.0326879 1026.9397 78.153588 0.47 1171.7119 + 9500 278.72962 -33127.835 -2875.2917 1.0163553 -2959.2065 83.914845 0.475 -2805.1711 + 9600 299.09039 24570.664 1594.6533 1.025317 1504.6086 90.044695 0.48 1631.8392 + 9700 336.65655 37767.059 1217.6584 1.0245842 1116.3039 101.35443 0.485 1218.4022 + 9800 279.68112 -55007.939 -2840.321 1.0129837 -2924.5223 84.201305 0.49 -2775.6909 + 9900 300.55694 14964.424 1101.8362 1.0176315 1011.35 90.486218 0.495 1127.7276 + 10000 276.77193 -75638.817 -3415.9268 1.0019055 -3499.2523 83.325459 0.5 -3341.663 + 10100 316.26926 61548.301 2199.0502 1.0427988 2103.8336 95.216598 0.505 2206.7159 + 10200 297.28171 56814.839 1828.6916 1.0270036 1739.1915 89.500171 0.51 1859.0176 + 10300 276.84774 83572.576 1662.6501 1.0322243 1579.3018 83.348283 0.515 1704.2233 + 10400 263.28687 -16549.994 903.97712 1.0177296 824.71149 79.265623 0.52 940.36339 + 10500 332.79252 47379.311 1277.3892 1.0223403 1177.1981 100.19112 0.525 1301.3762 + 10600 329.01105 39299.248 1039.7181 1.0230094 940.66548 99.052663 0.53 1077.5639 + 10700 339.21335 -4217.0313 724.12043 1.0235915 621.99624 102.12419 0.535 741.87272 + 10800 297.11192 -80013.424 -4028.1643 1.0009566 -4117.6134 89.449054 0.54 -3958.8283 + 10900 299.63096 47783.864 1609.2512 1.0435283 1519.0437 90.207441 0.545 1620.9328 + 11000 363.58243 67370.65 1557.8148 1.0450565 1448.354 109.46079 0.55 1543.803 + 11100 306.04664 50246.004 1020.8953 1.0341876 928.75637 92.138957 0.555 1063.5345 + 11200 255.68488 43750.967 1952.9201 1.0530607 1875.9431 76.976955 0.56 1986.9636 + 11300 271.71957 -40289.299 -3400.121 1.0168497 -3481.9254 81.804388 0.565 -3344.1558 + 11400 291.74007 -115249.24 -3603.3881 1.0067921 -3691.2199 87.831795 0.57 -3569.0256 + 11500 270.22077 28235.119 350.43952 1.0195886 269.08637 81.353155 0.575 373.78255 + 11600 297.08506 29790.701 793.45124 1.0317561 704.01027 89.440969 0.58 803.92835 + 11700 295.33119 -101140.58 -3395.5279 1.0107252 -3484.4409 88.912943 0.585 -3348.5652 + 11800 308.77287 -120312.75 -3874.1096 0.99681611 -3967.0693 92.95972 0.59 -3835.4663 + 11900 293.86337 82287.969 1623.3312 1.0331446 1534.8602 88.47104 0.595 1625.4846 + 12000 279.9866 27919.689 2021.9956 1.0384909 1937.7024 84.293273 0.6 2028.6311 + 12100 292.19439 47035.018 962.98803 1.0210948 875.01946 87.968573 0.605 976.68113 + 12200 317.78325 46886.483 1744.1855 1.0310567 1648.5131 95.672401 0.61 1763.6359 + 12300 357.44038 51492.35 1650.3113 1.0414835 1542.6996 107.61165 0.615 1638.1905 + 12400 288.16042 -50528.478 -3145.341 1.0130798 -3232.0951 86.7541 0.62 -3115.1383 + 12500 300.37356 -114034.29 -3383.5763 1.0130272 -3474.0074 90.431009 0.625 -3364.511 + 12600 265.4402 73960.28 1102.3119 1.0343798 1022.398 79.913907 0.63 1094.544 + 12700 287.07994 22722.337 1499.2541 1.0268893 1412.8252 86.428809 0.635 1490.443 + 12800 315.39745 46072.191 663.05431 1.0205906 568.10018 94.954129 0.64 662.83753 + 12900 307.48549 -120472.73 -3484.9054 1.005689 -3577.4775 92.57214 0.645 -3469.7834 + 13000 291.00577 -59154.878 -3000.6461 1.012821 -3088.2569 87.610727 0.65 -2966.2448 + 13100 318.37718 86703.775 1825.1817 1.036209 1729.3305 95.851211 0.655 1819.7078 + 13200 280.41509 -107033.79 -2964.9455 1.0135499 -3049.3678 84.422277 0.66 -2953.8355 + 13300 275.01919 112086.85 2399.5628 1.0437945 2316.765 82.797775 0.665 2394.6707 + 13400 299.46547 -111959.62 -3814.3709 0.98732074 -3904.5286 90.157617 0.67 -3792.6798 + 13500 275.65631 17625.49 1528.0027 1.0255473 1445.0131 82.989588 0.675 1521.2745 + 13600 302.63525 122466.63 2631.7819 1.0438137 2540.67 91.111917 0.68 2611.7188 + 13700 302.21323 -94399.663 -3344.9423 1.0068914 -3435.9271 90.984863 0.685 -3328.4539 + 13800 305.70483 30039.825 1506.1765 1.0225478 1414.1404 92.036052 0.69 1502.8476 + 13900 273.15564 -27822.597 -2713.3946 1.0131002 -2795.6313 82.236732 0.695 -2683.7804 + 14000 257.14635 -1821.0012 1045.462 1.0172653 968.04508 77.416947 0.7 1067.8821 + 14100 323.74174 -76139.363 -3042.0486 1.0139806 -3139.5149 97.466276 0.705 -3052.598 + 14200 274.99913 54440.943 796.17718 1.0186356 713.38545 82.791736 0.71 767.64274 + 14300 291.8774 1281.7286 1079.6881 1.0214356 991.81498 87.873139 0.715 1042.8585 + 14400 308.97245 -47961.551 -3005.1106 1.0155221 -3098.1304 93.019806 0.72 -3007.3204 + 14500 311.05309 86026.739 1851.7257 1.0311818 1758.0795 93.646208 0.725 1830.5463 + 14600 269.27432 -12972.747 726.82371 1.0172239 645.7555 81.068214 0.73 711.81484 + 14700 262.20739 -77722.459 -3545.7104 1.0029421 -3624.651 78.940634 0.735 -3537.1929 + 14800 300.33592 -107332.8 -3118.6094 1.0126785 -3209.0291 90.419677 0.74 -3125.8439 + 14900 307.0173 -73204.94 -3016.2921 1.016875 -3108.7233 92.431185 0.745 -3016.0143 + 15000 334.08711 64440.709 1360.8856 1.0369481 1260.3047 100.58087 0.75 1323.9179 + 15100 293.46703 35179.395 1804.4648 1.0331703 1716.1131 88.351717 0.755 1768.9681 + 15200 307.80546 54006.291 852.72781 1.0246134 760.05934 92.668471 0.76 822.22754 + 15300 336.59792 33832.907 988.39905 1.0242407 887.06227 101.33678 0.765 956.25285 + 15400 285.46526 -99629.94 -2736.0944 1.0041261 -2822.0371 85.942688 0.77 -2730.1887 + 15500 269.15938 122546.45 2708.063 1.0318941 2627.0294 81.033612 0.775 2695.4331 + 15600 294.50818 -104733.19 -2271.5729 1.0017241 -2360.238 88.665166 0.78 -2281.5773 + 15700 321.05125 -40438.501 -2060.144 1.0125007 -2156.8002 96.656271 0.785 -2084.0893 + 15800 303.22185 -42224.408 -2486.7037 1.0090867 -2577.9922 91.288521 0.79 -2506.3355 + 15900 281.65025 78652.063 2532.2753 1.0460521 2447.4812 84.794136 0.795 2500.7128 + 16000 286.5056 63174.412 1479.3631 1.0185277 1393.1072 86.255897 0.8 1442.2427 + 16100 271.74574 -75051.584 -2429.2879 1.0091727 -2511.1002 81.812265 0.805 -2447.1967 + 16200 266.40007 -64120.09 -2497.2609 1.0064388 -2577.4638 80.202888 0.81 -2525.4243 + 16300 330.67137 46204.124 1582.1688 1.0271037 1482.6162 99.552523 0.815 1529.8186 + 16400 310.94573 18510.676 1235.5974 1.0188695 1141.9835 93.613887 0.82 1195.3041 + 16500 270.29191 79005.409 1711.3568 1.0354088 1629.9822 81.374574 0.825 1678.7342 + 16600 334.24108 17143.221 1446.3175 1.0230561 1345.6903 100.62723 0.83 1379.3215 + 16700 292.28721 -78618.031 -3045.0258 0.99940789 -3133.0223 87.996518 0.835 -3087.379 + 16800 346.09157 -69398.937 -2956.6793 1.0153026 -3060.8742 104.19496 0.84 -3011.3476 + 16900 284.37042 39314.526 2102.7814 1.0343186 2017.1683 85.613074 0.845 2045.8316 + 17000 281.69389 86032.163 1577.5995 1.0237583 1492.7922 84.807275 0.85 1528.8391 + 17100 297.2629 55128.393 2431.5835 1.0419182 2342.089 89.494508 0.855 2369.0347 + 17200 328.81472 47063.86 1584.1492 1.0364627 1485.1556 98.993555 0.86 1526.7115 + 17300 313.41363 -46685.063 -2635.2463 1.008117 -2729.6032 94.356878 0.865 -2685.8034 + 17400 288.17114 68721.523 2548.303 1.0429105 2461.5456 86.757326 0.87 2490.5845 + 17500 260.01702 -23324.539 -1776.7039 1.0100415 -1854.9851 78.281195 0.875 -1812.4813 + 17600 297.6633 72795.463 2396.9788 1.0362827 2307.3638 89.615054 0.88 2336.0152 + 17700 301.02937 93833.118 2424.9649 1.0276466 2334.3364 90.628448 0.885 2364.8751 + 17800 238.92837 -78317.212 -2548.5755 1.0084077 -2620.5077 71.932208 0.89 -2579.4429 + 17900 299.27724 -65278.891 -2933.564 1.0034773 -3023.6649 90.10095 0.895 -2987.498 + 18000 315.15753 -72437.481 -2654.8693 1.0136139 -2749.7512 94.881898 0.9 -2718.125 + 18100 268.39411 -42194.209 -2606.045 1.0108104 -2686.8482 80.803219 0.905 -2656.3853 + 18200 284.91941 40905.162 1786.1505 1.0266185 1700.3722 85.778354 0.91 1723.6803 + 18300 329.41629 -56526.814 -2472.7835 1.0137784 -2571.9582 99.174667 0.915 -2540.6829 + 18400 293.16732 -22085.551 -1991.6537 1.0163557 -2079.9152 88.261484 0.92 -2052.7864 + 18500 276.28141 29367.359 2034.0833 1.0270087 1950.9056 83.177784 0.925 1971.9405 + 18600 331.18031 94669.124 2160.1352 1.0225403 2060.4295 99.705745 0.93 2081.8675 + 18700 265.4491 49872.536 2324.2391 1.0255308 2244.3225 79.916587 0.935 2260.4261 + 18800 314.51042 60758.629 2298.6407 1.0300818 2203.9536 94.687078 0.94 2219.6547 + 18900 317.70309 66345.835 1490.6939 1.0248229 1395.0457 95.648268 0.945 1410.3087 + 19000 291.39831 -96336.931 -2732.3994 1.0100498 -2820.1283 87.728905 0.95 -2805.9396 + 19100 303.37353 -21421.495 -2360.5644 0.99771284 -2451.8986 91.334186 0.955 -2436.2173 + 19200 293.92948 36383.881 1708.7388 1.0251299 1620.2479 88.490944 0.96 1633.579 + 19300 287.24409 -46691.027 -2736.6663 1.0112067 -2823.1445 86.478228 0.965 -2811.3506 + 19400 333.42205 21152.63 1209.1556 1.0189912 1108.7749 100.38065 0.97 1118.2463 + 19500 309.17989 60445.761 2014.5979 1.0338543 1921.5157 93.082259 0.975 1928.6181 + 19600 255.92246 -32795.547 -2145.3103 1.0157044 -2222.3587 77.04848 0.98 -2213.9484 + 19700 342.62332 33538.746 2181.2002 1.0225905 2078.0494 103.1508 0.985 2081.9185 + 19800 295.68946 81474.342 1996.4567 1.0240743 1907.4359 89.020804 0.99 1910.5545 + 19900 306.4947 43488.052 2048.2997 1.0222707 1956.0258 92.27385 0.995 1957.4368 + 20000 313.31679 -25133.284 -1555.4274 1.0163289 -1649.7551 94.327722 1 -1649.7551 +Loop time of 11.8253 on 2 procs for 20000 steps with 102 atoms + +Performance: 29.226 ns/day, 0.821 hours/ns, 1691.295 timesteps/s, 172.512 katom-step/s +99.3% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.8508 | 8.6272 | 10.404 | 60.5 | 72.96 +Bond | 0.045829 | 0.046542 | 0.047256 | 0.3 | 0.39 +Neigh | 0.10781 | 0.10791 | 0.108 | 0.0 | 0.91 +Comm | 0.75178 | 2.5281 | 4.3045 | 111.7 | 21.38 +Output | 0.0032916 | 0.0035722 | 0.0038527 | 0.5 | 0.03 +Modify | 0.44867 | 0.45212 | 0.45556 | 0.5 | 3.82 +Other | | 0.05976 | | | 0.51 + +Nlocal: 51 ave 51 max 51 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 3317 ave 3317 max 3317 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 18319.5 ave 21940 max 14699 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 36639 +Ave neighs/atom = 359.20588 +Ave special neighs/atom = 2.0196078 +Neighbor list builds = 181 +Dangerous builds = 0 +Total wall time: 0:00:11 diff --git a/src/REPLICA/fix_alchemy.cpp b/src/REPLICA/fix_alchemy.cpp index 75b4c4cb73..b0c8d6799d 100644 --- a/src/REPLICA/fix_alchemy.cpp +++ b/src/REPLICA/fix_alchemy.cpp @@ -45,6 +45,7 @@ FixAlchemy::FixAlchemy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), if (narg != 3) error->all(FLERR, "Incorrect number of arguments for fix alchemy"); lambda = epot[0] = epot[1] = 0.0; + progress = 0; for (int i = 0; i < 6; ++i) pressure[i] = 0.0; no_change_box = 1; @@ -125,6 +126,13 @@ void FixAlchemy::setup(int vflag) } else { post_force(vflag); } + + if (universe->me == 0) { + progress = static_cast(100.0 - lambda * 100.0); + auto msg = fmt::format("Starting alchemical transformation at {:>3d}%\n", progress); + if (universe->uscreen) fmt::print(universe->uscreen, msg); + if (universe->ulogfile) fmt::print(universe->ulogfile, msg); + } } /* ---------------------------------------------------------------------- */ @@ -164,6 +172,17 @@ void FixAlchemy::post_force(int /*vflag*/) for (int i = 0; i < 6; ++i) commbuf[i] = lambda * scalefac * press->vector[i]; MPI_Allreduce(commbuf, pressure, 6, MPI_DOUBLE, MPI_SUM, universe->uworld); press->addstep(update->ntimestep + 1); + + // print progress info + if (universe->me == 0) { + int status = static_cast(100.0 - lambda * 100.0); + if ((status / 10) > (progress / 10)) { + progress = status; + auto msg = fmt::format(" Alchemical transformation progress: {:>3d}%\n", progress); + if (universe->uscreen) fmt::print(universe->uscreen, msg); + if (universe->ulogfile) fmt::print(universe->ulogfile, msg); + } + } } /* ---------------------------------------------------------------------- */ diff --git a/src/REPLICA/fix_alchemy.h b/src/REPLICA/fix_alchemy.h index 9794629db3..f0dd7bde04 100644 --- a/src/REPLICA/fix_alchemy.h +++ b/src/REPLICA/fix_alchemy.h @@ -45,6 +45,7 @@ class FixAlchemy : public Fix { double lambda; // changes from 0 to 1 during run double epot[3]; // last (unscaled) potential energy from each replica and combined energy double pressure[6]; // joined pressure + int progress; // for progress indicator int ilevel_respa; int nmax; };