diff --git a/examples/USER/cg-cmm/README b/examples/USER/cg-cmm/README index d444a4023..6a283114b 100644 --- a/examples/USER/cg-cmm/README +++ b/examples/USER/cg-cmm/README @@ -1,33 +1,19 @@ -LAMMPS cmm-cg example problems +LAMMPS USER-CMM-CG example problems -Each of these sub-directories contains a sample problem for the CMM -coarse grained MD potentials that you can run with LAMMPS. The -represent some typical uses and are also used to verify the -implmentation in LAMMPS. +Each of these sub-directories contains a sample problem for the SDK +coarse grained MD potentials that you can run with LAMMPS. -Each problem has an input script (in.*) and produces a log file -(log.*) and trajectory file in compressed .xtc format (*.xtc) when it -runs. Inputs are usually set up to read the start configuration and -topology from a data file (data.*) and the matching force field -parameter from an include file (parms.*). - -A few sample log file outputs on different machines and different -numbers of processors are included in the directories to compare your -answers to. E.g. a log file like log.crack.date.foo.P means it ran on -P processors of machine "foo" with the dated version of LAMMPS. Note -that these problems should get statistically similar answers when run -on different machines or different numbers of processors, but not -identical answers to those in the log of dump files included here. -See the Errors section of the LAMMPS documentation for more -discussion. - -The examples also provide matching topology files for visualization -(*.psf) so that the .xtc trajectories can be visualized with VMD. - -These are the sample systems the various sub-directories: +These are the two sample systems peg-verlet: coarse grained PEG surfactant/water mixture lamella verlet version - this example uses the plain LJ term only, no charges + this example uses the plain LJ term only, no charges. + two variants are provided regular harmonic angles and + the SDK variant that includes 1-3 LJ repulsion. -(more to come) +sds-monolayer: coarse grained SDS surfactant monolayers at water/vapor + interface. + this example uses the SDK LJ term with coulomb and shows + how to use the combined coulomb style vs. hybrid/overlay + with possible optimizations due to the small number of + charged particles in this system diff --git a/examples/USER/cg-cmm/sds-monolayer/data.sds.gz b/examples/USER/cg-cmm/sds-monolayer/data.sds.gz new file mode 100644 index 000000000..7b7e44659 Binary files /dev/null and b/examples/USER/cg-cmm/sds-monolayer/data.sds.gz differ diff --git a/examples/USER/cg-cmm/sds-monolayer/in.sds-hybrid b/examples/USER/cg-cmm/sds-monolayer/in.sds-hybrid new file mode 100644 index 000000000..046181f55 --- /dev/null +++ b/examples/USER/cg-cmm/sds-monolayer/in.sds-hybrid @@ -0,0 +1,50 @@ +# coarse grained SDS surfactant monolayer + +units real +dimension 3 +atom_style full +processors * * 1 + +pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5 +bond_style harmonic +angle_style sdk +special_bonds lj/coul 0.0 0.0 1.0 + +read_data data.sds.gz + +pair_coeff 1 4 coul/long # SO4 SOD +pair_coeff 4 4 coul/long # SOD SOD +pair_coeff 1 1 lj/sdk lj9_6 0.7000 4.3210 # SO4 SO4 +pair_coeff 1 2 lj/sdk lj9_6 0.3830 4.4135 # SO4 CM +pair_coeff 1 3 lj/sdk lj9_6 0.4050 4.4530 # SO4 CT +pair_coeff 1 4 lj/sdk lj12_4 1.1000 4.1000 # SO4 SOD +pair_coeff 1 5 lj/sdk lj12_4 1.1000 4.1000 # SO4 W +pair_coeff 2 2 lj/sdk lj9_6 0.4200 4.5060 # CM CM +pair_coeff 2 3 lj/sdk lj9_6 0.4440 4.5455 # CT CM +pair_coeff 2 4 lj/sdk lj12_4 0.3400 4.4385 # SOD CM +pair_coeff 2 5 lj/sdk lj12_4 0.3400 4.4385 # W CM +pair_coeff 3 3 lj/sdk lj9_6 0.4690 4.5850 # CT CT +pair_coeff 3 4 lj/sdk lj12_4 0.3600 4.4780 # SOD CT +pair_coeff 3 5 lj/sdk lj12_4 0.3600 4.4780 # W CT +pair_coeff 4 4 lj/sdk lj12_4 0.3500 4.3710 # SOD SOD +pair_coeff 4 5 lj/sdk lj12_4 0.8950 4.3710 # SOD W +pair_coeff 5 5 lj/sdk lj12_4 0.8950 4.3710 # W W + + +group charged type 1 4 +atom_modify first charged + +kspace_style pppm/cg 0.00001 +kspace_modify order 3 + +communicate multi +neighbor 2.0 multi +neigh_modify delay 4 every 2 check yes + +timestep 10.0 + +fix 1 all nvt temp 310.0 310.0 100.0 + +thermo 10 + +run 100 diff --git a/examples/USER/cg-cmm/sds-monolayer/in.sds-regular b/examples/USER/cg-cmm/sds-monolayer/in.sds-regular new file mode 100644 index 000000000..217c15697 --- /dev/null +++ b/examples/USER/cg-cmm/sds-monolayer/in.sds-regular @@ -0,0 +1,43 @@ +# coarse grained SDS surfactant monolayer + +units real +dimension 3 +atom_style full +processors * * 1 + +pair_style lj/sdk/coul/long 15.0 +bond_style harmonic +angle_style sdk +special_bonds lj/coul 0.0 0.0 1.0 + +read_data data.sds.gz + +pair_coeff 1 1 lj9_6 0.7000 4.3210 # SO4 SO4 +pair_coeff 1 2 lj9_6 0.3830 4.4135 # SO4 CM +pair_coeff 1 3 lj9_6 0.4050 4.4530 # SO4 CT +pair_coeff 1 4 lj12_4 1.1000 4.1000 # SO4 SOD +pair_coeff 1 5 lj12_4 1.1000 4.1000 # SO4 W +pair_coeff 2 2 lj9_6 0.4200 4.5060 # CM CM +pair_coeff 2 3 lj9_6 0.4440 4.5455 # CT CM +pair_coeff 2 4 lj12_4 0.3400 4.4385 # SOD CM +pair_coeff 2 5 lj12_4 0.3400 4.4385 # W CM +pair_coeff 3 3 lj9_6 0.4690 4.5850 # CT CT +pair_coeff 3 4 lj12_4 0.3600 4.4780 # SOD CT +pair_coeff 3 5 lj12_4 0.3600 4.4780 # W CT +pair_coeff 4 4 lj12_4 0.3500 4.3710 # SOD SOD +pair_coeff 4 5 lj12_4 0.8950 4.3710 # SOD W +pair_coeff 5 5 lj12_4 0.8950 4.3710 # W W + +kspace_style pppm/cg 0.00001 +kspace_modify order 3 + +neighbor 2.0 bin +neigh_modify delay 4 every 2 check yes + +timestep 10.0 + +fix 1 all nvt temp 310.0 310.0 100.0 + +thermo 10 + +run 100 diff --git a/examples/USER/cg-cmm/sds-monolayer/log.sds-hybrid b/examples/USER/cg-cmm/sds-monolayer/log.sds-hybrid new file mode 100644 index 000000000..1a8e3b65f --- /dev/null +++ b/examples/USER/cg-cmm/sds-monolayer/log.sds-hybrid @@ -0,0 +1,127 @@ +LAMMPS (20 Mar 2014-ICMS) +WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) + using 1 OpenMP thread(s) per MPI task +# coarse grained SDS surfactant monolayer + +units real +dimension 3 +atom_style full +processors * * 1 + +pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5 +bond_style harmonic +angle_style sdk +special_bonds lj/coul 0.0 0.0 1.0 + +read_data data.sds.gz + orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 31280 atoms + reading velocities ... + 31280 velocities + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 4096 bonds + reading angles ... + 3072 angles + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of special neighbors + +pair_coeff 1 4 coul/long # SO4 SOD +pair_coeff 4 4 coul/long # SOD SOD +pair_coeff 1 1 lj/sdk lj9_6 0.7000 4.3210 # SO4 SO4 +pair_coeff 1 2 lj/sdk lj9_6 0.3830 4.4135 # SO4 CM +pair_coeff 1 3 lj/sdk lj9_6 0.4050 4.4530 # SO4 CT +pair_coeff 1 4 lj/sdk lj12_4 1.1000 4.1000 # SO4 SOD +pair_coeff 1 5 lj/sdk lj12_4 1.1000 4.1000 # SO4 W +pair_coeff 2 2 lj/sdk lj9_6 0.4200 4.5060 # CM CM +pair_coeff 2 3 lj/sdk lj9_6 0.4440 4.5455 # CT CM +pair_coeff 2 4 lj/sdk lj12_4 0.3400 4.4385 # SOD CM +pair_coeff 2 5 lj/sdk lj12_4 0.3400 4.4385 # W CM +pair_coeff 3 3 lj/sdk lj9_6 0.4690 4.5850 # CT CT +pair_coeff 3 4 lj/sdk lj12_4 0.3600 4.4780 # SOD CT +pair_coeff 3 5 lj/sdk lj12_4 0.3600 4.4780 # W CT +pair_coeff 4 4 lj/sdk lj12_4 0.3500 4.3710 # SOD SOD +pair_coeff 4 5 lj/sdk lj12_4 0.8950 4.3710 # SOD W +pair_coeff 5 5 lj/sdk lj12_4 0.8950 4.3710 # W W + + +group charged type 1 4 +2048 atoms in group charged +atom_modify first charged + +kspace_style pppm/cg 0.00001 +kspace_modify order 3 + +communicate multi +neighbor 2.0 multi +neigh_modify delay 4 every 2 check yes + +timestep 10.0 + +fix 1 all nvt temp 310.0 310.0 100.0 + +thermo 10 + +run 100 +PPPM initialization ... + G vector (1/distance) = 0.0416781 + grid = 8 4 12 + stencil order = 3 + estimated absolute RMS force accuracy = 0.00248777 + estimated relative force accuracy = 7.49185e-06 + using double precision FFTs + 3d grid and FFT values/proc = 525 96 + PPPM/cg optimization cutoff: 1e-05 + Total charged atoms: 6.5% + Min/max charged atoms/proc: 6.4% 6.7% +Memory usage per processor = 7.66668 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516 + 10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262 + 20 310.33025 -249325.09 2543.0138 -217847.89 -30.069751 + 30 308.24273 -249331.54 2604.3227 -217987.66 -28.033129 + 40 309.41339 -249363.5 2560.6727 -217954.13 -25.802838 + 50 309.16857 -249071.94 2571.9117 -217674.15 -17.946457 + 60 312.67237 -249288.77 2621.0185 -217515.19 -25.723545 + 70 310.13623 -249262.32 2595.874 -217750.35 -26.276067 + 80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924 + 90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575 + 100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823 + +Loop time of 4.07239 on 4 procs for 100 steps with 31280 atoms +98.6% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 21.216 ns/day 1.131 hours/ns 24.556 timesteps/s + +MPI task timings breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.082 | 3.0928 | 3.1091 | 0.6 | 75.95 +Bond | 0.021077 | 0.021421 | 0.021823 | 0.2 | 0.53 +Kspace | 0.042646 | 0.058859 | 0.069797 | 4.1 | 1.45 +Neigh | 0.79689 | 0.79696 | 0.79711 | 0.0 | 19.57 +Comm | 0.048668 | 0.049552 | 0.050446 | 0.3 | 1.22 +Output | 0.00072145 | 0.00095147 | 0.0016341 | 1.3 | 0.02 +Modify | 0.034767 | 0.035175 | 0.035714 | 0.2 | 0.86 +Other | | 0.01665 | | | 0.41 + +Nlocal: 7820 ave 7866 max 7774 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 9179.5 ave 9199 max 9157 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 850419 ave 853627 max 846921 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 3401676 +Ave neighs/atom = 108.749 +Ave special neighs/atom = 0.458312 +Neighbor list builds = 10 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + diff --git a/examples/USER/cg-cmm/sds-monolayer/log.sds-regular b/examples/USER/cg-cmm/sds-monolayer/log.sds-regular new file mode 100644 index 000000000..7ab9d1a76 --- /dev/null +++ b/examples/USER/cg-cmm/sds-monolayer/log.sds-regular @@ -0,0 +1,116 @@ +LAMMPS (20 Mar 2014-ICMS) +WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) + using 1 OpenMP thread(s) per MPI task +# coarse grained SDS surfactant monolayer + +units real +dimension 3 +atom_style full +processors * * 1 + +pair_style lj/sdk/coul/long 15.0 +bond_style harmonic +angle_style sdk +special_bonds lj/coul 0.0 0.0 1.0 + +read_data data.sds.gz + orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 31280 atoms + reading velocities ... + 31280 velocities + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 4096 bonds + reading angles ... + 3072 angles + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of special neighbors + +pair_coeff 1 1 lj9_6 0.7000 4.3210 # SO4 SO4 +pair_coeff 1 2 lj9_6 0.3830 4.4135 # SO4 CM +pair_coeff 1 3 lj9_6 0.4050 4.4530 # SO4 CT +pair_coeff 1 4 lj12_4 1.1000 4.1000 # SO4 SOD +pair_coeff 1 5 lj12_4 1.1000 4.1000 # SO4 W +pair_coeff 2 2 lj9_6 0.4200 4.5060 # CM CM +pair_coeff 2 3 lj9_6 0.4440 4.5455 # CT CM +pair_coeff 2 4 lj12_4 0.3400 4.4385 # SOD CM +pair_coeff 2 5 lj12_4 0.3400 4.4385 # W CM +pair_coeff 3 3 lj9_6 0.4690 4.5850 # CT CT +pair_coeff 3 4 lj12_4 0.3600 4.4780 # SOD CT +pair_coeff 3 5 lj12_4 0.3600 4.4780 # W CT +pair_coeff 4 4 lj12_4 0.3500 4.3710 # SOD SOD +pair_coeff 4 5 lj12_4 0.8950 4.3710 # SOD W +pair_coeff 5 5 lj12_4 0.8950 4.3710 # W W + +kspace_style pppm/cg 0.00001 +kspace_modify order 3 + +neighbor 2.0 bin +neigh_modify delay 4 every 2 check yes + +timestep 10.0 + +fix 1 all nvt temp 310.0 310.0 100.0 + +thermo 10 + +run 100 +PPPM initialization ... + G vector (1/distance) = 0.0789325 + grid = 15 8 25 + stencil order = 3 + estimated absolute RMS force accuracy = 0.00275556 + estimated relative force accuracy = 8.29828e-06 + using double precision FFTs + 3d grid and FFT values/proc = 2156 840 + PPPM/cg optimization cutoff: 1e-05 + Total charged atoms: 6.5% + Min/max charged atoms/proc: 6.4% 6.7% +Memory usage per processor = 8.05923 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 310.0934 -247030.21 2566.2036 -215551.9 -14.547393 + 10 310.89138 -247061.61 2549.4854 -215525.62 -18.043512 + 20 310.29287 -247017.8 2542.4491 -215544.65 -19.148631 + 30 308.13371 -247024.82 2602.1061 -215693.32 -17.390902 + 40 309.40426 -247058.41 2558.7402 -215651.82 -15.445066 + 50 309.11317 -246753.92 2570.8603 -215362.36 -7.4232007 + 60 312.52974 -246964.73 2618.8108 -215206.66 -15.23965 + 70 310.11675 -246941.68 2591.8668 -215435.53 -16.153691 + 80 310.48262 -247090.02 2595.0493 -215546.58 -18.080368 + 90 309.60017 -247067.1 2604.6545 -215596.33 -14.583764 + 100 309.7356 -247004.05 2604.8729 -215520.43 -12.78624 + +Loop time of 3.44972 on 4 procs for 100 steps with 31280 atoms +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 25.046 ns/day 0.958 hours/ns 28.988 timesteps/s + +MPI task timings breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.7883 | 2.817 | 2.8415 | 1.1 | 81.66 +Bond | 0.017868 | 0.018973 | 0.020636 | 0.7 | 0.55 +Kspace | 0.063881 | 0.088012 | 0.11571 | 6.2 | 2.55 +Neigh | 0.42765 | 0.42828 | 0.42882 | 0.1 | 12.41 +Comm | 0.043887 | 0.044575 | 0.045079 | 0.2 | 1.29 +Output | 0.00072694 | 0.00096422 | 0.0016718 | 1.3 | 0.03 +Modify | 0.035513 | 0.035955 | 0.036887 | 0.3 | 1.04 +Other | | 0.01597 | | | 0.46 + +Nlocal: 7820 ave 7866 max 7775 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Nghost: 8679.75 ave 8699 max 8666 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 838026 ave 841202 max 834819 min +Histogram: 1 1 0 0 0 0 0 0 1 1 + +Total # of neighbors = 3352103 +Ave neighs/atom = 107.164 +Ave special neighs/atom = 0.458312 +Neighbor list builds = 10 +Dangerous builds = 0