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