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595 lines
20 KiB
Plaintext
"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_example.html :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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4. How-to discussions :h3
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The following sections describe what commands can be used to perform
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certain kinds of LAMMPS simulations.
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4.1 "Restarting a simulation"_#4_1
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4.2 "2d simulations"_#4_2
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4.3 "CHARMM and AMBER force fields"_#4_3
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4.4 "Running multiple simulations from one input script"_#4_4
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4.5 "Parallel tempering"_#4_5
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4.6 "Granular models"_#4_6
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4.7 "TIP3P water model"_#4_7
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4.8 "TIP4P water model"_#4_8
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4.9 "SPC water model"_#4_9
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4.10 "Coupling LAMMPS to other codes"_#4_10 :all(b)
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The example input scripts included in the LAMMPS distribution and
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highlighted in "this section"_Section_example.html also show how to
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setup and run various kinds of problems.
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:line
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4.1 Restarting a simulation :link(4_1),h4
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There are 3 ways to continue a long LAMMPS simulation. Multiple
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"run"_run.html commands can be used in the same input script. Each
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run will continue from where the previous run left off. Or binary
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restart files can be saved to disk using the "restart"_restart.html
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command. At a later time, these binary files can be read via a
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"read_restart"_read_restart.html command in a new script. Or they can
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be converted to text data files and read by a
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"read_data"_read_data.html command in a new script. "This
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section"_Section_tools.html discusses the {restart2data} tool that is
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used to perform the conversion.
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Here we give examples of 2 scripts that read either a binary restart
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file or a converted data file and then issue a new run command to
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continue where the previous run left off. They illustrate what
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settings must be made in the new script. Details are discussed in the
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documentation for the "read_restart"_read_restart.html and
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"read_data"_read_data.html commands.
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Look at the {in.chain} input script provided in the {bench} directory
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of the LAMMPS distribution to see the original script that these 2
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scripts are based on. If that script had the line
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restart 50 tmp.restart :pre
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added to it, it would produce 2 binary restart files (tmp.restart.50
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and tmp.restart.100) as it ran.
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This script could be used to read the 1st restart file and re-run the
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last 50 timesteps:
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read_restart tmp.restart.50 :pre
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neighbor 0.4 bin
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neigh_modify every 1 delay 1 :pre
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fix 1 all nve
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fix 2 all langevin 1.0 1.0 10.0 904297 :pre
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timestep 0.012 :pre
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run 50 :pre
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Note that the following commands do not need to be repeated because
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their settings are included in the restart file: {units, atom_style,
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special_bonds, pair_style, bond_style}. However these commands do
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need to be used, since their settings are not in the restart file:
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{neighbor, fix, timestep}.
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If you actually use this script to perform a restarted run, you will
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notice that the thermodynamic data match at step 50 (if you also put a
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"thermo 50" command in the original script), but do not match at step
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100. This is because the "fix langevin"_fix_langevin.html command
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uses random numbers in a way that does not allow for perfect restarts.
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As an alternate approach, the restart file could be converted to a data
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file using this tool:
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restart2data tmp.restart.50 tmp.restart.data :pre
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Then, this script could be used to re-run the last 50 steps:
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units lj
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atom_style bond
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pair_style lj/cut 1.12
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pair_modify shift yes
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bond_style fene
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special_bonds 0.0 1.0 1.0 :pre
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read_data tmp.restart.data :pre
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neighbor 0.4 bin
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neigh_modify every 1 delay 1 :pre
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fix 1 all nve
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fix 2 all langevin 1.0 1.0 10.0 904297 :pre
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timestep 0.012 :pre
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reset_timestep 50
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run 50 :pre
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Note that nearly all the settings specified in the original {in.chain}
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script must be repeated, except the {pair_coeff} and {bond_coeff}
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commands since the new data file lists the force field coefficients.
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Also, the "reset_timestep"_reset_timestep.html command is used to tell
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LAMMPS the current timestep. This value is stored in restart files,
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but not in data files.
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:line
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4.2 2d simulations :link(4_2),h4
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Use the "dimension"_dimension.html command to specify a 2d simulation.
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Make the simulation box periodic in z via the "boundary"_boundary.html
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command. This is the default.
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If using the "create box"_create_box.html command to define a
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simulation box, set the z dimensions narrow, but finite, so that the
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create_atoms command will tile the 3d simulation box with a single z
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plane of atoms - e.g.
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"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre
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If using the "read data"_read_data.html command to read in a file of
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atom coordinates, set the "zlo zhi" values to be finite but narrow,
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similar to the create_box command settings just described. For each
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atom in the file, assign a z coordinate so it falls inside the
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z-boundaries of the box - e.g. 0.0.
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Use the "fix enforce2d"_fix_enforce2d.html command as the last
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defined fix to insure that the z-components of velocities and forces
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are zeroed out every timestep. The reason to make it the last fix is
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so that any forces induced by other fixes will be zeroed out.
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Many of the example input scripts included in the LAMMPS distribution
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are for 2d models.
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:line
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4.3 CHARMM and AMBER force fields :link(4_3),h4
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There are many different ways to compute forces in the "CHARMM"_charmm
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and "AMBER"_amber molecular dynamics codes, only some of which are
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available as options in LAMMPS. A force field has 2 parts: the
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formulas that define it and the coefficients used for a particular
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system. Here we only discuss formulas implemented in LAMMPS. Setting
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coefficients is done in the input data file via the
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"read_data"_read_data.html command or in the input script with
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commands like "pair_coeff"_pair_coeff.html or
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"bond_coeff"_bond_coeff.html. See "this section"_Section_tools.html for
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additional tools that can use CHARMM or AMBER to assign force field
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coefficients and convert their output into LAMMPS input.
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See "(MacKerell)"_#MacKerell for a description of the CHARMM force
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field. See "(Cornell)"_#Cornell for a description of the AMBER force
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field.
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:link(charmm,http://www.scripps.edu/brooks)
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:link(amber,http://amber.scripps.edu)
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These style choices compute force field formulas that are consistent
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with common options in CHARMM or AMBER. See each command's
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documentation for the formula it computes.
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"bond_style"_bond_style.html harmonic
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"angle_style"_angle_style.html charmm
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"dihedral_style"_dihedral_style.html charmm
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"pair_style"_pair_style.html lj/charmm/coul/charmm
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"pair_style"_pair_style.html lj/charmm/coul/charmm/implicit
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"pair_style"_pair_style.html lj/charmm/coul/long :ul
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"special_bonds"_special_bonds.html charmm
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"special_bonds"_special_bonds.html amber :ul
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:line
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4.4 Running multiple simulations from one input script :link(4_4),h4
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This can be done in several ways. See the documentation for
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individual commands for more details on how these examples work.
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If "multiple simulations" means continue a previous simulation for
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more timesteps, then you simply use the "run"_run.html command
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multiple times. For example, this script
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units lj
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atom_style atomic
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read_data data.lj
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run 10000
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run 10000
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run 10000
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run 10000
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run 10000 :pre
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would run 5 successive simulations of the same system for a total of
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50,000 timesteps.
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If you wish to run totally different simulations, one after the other,
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the "clear"_clear.html command can be used in between them to
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re-initialize LAMMPS. For example, this script
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units lj
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atom_style atomic
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read_data data.lj
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run 10000
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clear
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units lj
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atom_style atomic
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read_data data.lj.new
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run 10000 :pre
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would run 2 independent simulations, one after the other.
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For large numbers of independent simulations, you can use
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"variables"_variable.html and the "next"_next.html and
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"jump"_jump.html commands to loop over the same input script
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multiple times with different settings. For example, this
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script, named in.polymer
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variable d index run1 run2 run3 run4 run5 run6 run7 run8
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cd $d
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read_data data.polymer
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run 10000
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cd ..
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clear
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next d
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jump in.polymer :pre
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would run 8 simulations in different directories, using a data.polymer
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file in each directory. The same concept could be used to run the
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same system at 8 different temperatures, using a temperature variable
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and storing the output in different log and dump files, for example
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variable a loop 8
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variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
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log log.$a
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read data.polymer
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velocity all create $t 352839
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fix 1 all nvt $t $t 100.0
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dump 1 all atom 1000 dump.$a
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run 100000
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next t
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next a
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jump in.polymer :pre
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All of the above examples work whether you are running on 1 or
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multiple processors, but assumed you are running LAMMPS on a single
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partition of processors. LAMMPS can be run on multiple partitions via
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the "-partition" command-line switch as described in "this
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section"_Section_start.html#2_4 of the manual.
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In the last 2 examples, if LAMMPS were run on 3 partitions, the same
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scripts could be used if the "index" and "loop" variables were
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replaced with {universe}-style variables, as described in the
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"variable"_variable.html command. Also, the "next t" and "next a"
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commands would need to be replaced with a single "next a t" command.
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With these modifications, the 8 simulations of each script would run
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on the 3 partitions one after the other until all were finished.
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Initially, 3 simulations would be started simultaneously, one on each
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partition. When one finished, that partition would then start
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the 4th simulation, and so forth, until all 8 were completed.
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:line
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4.5 Parallel tempering :link(4_5),h4
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The "temper"_temper.html command can be used to perform a parallel
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tempering or replica-exchange simulation where multiple copies of a
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simulation are run at different temperatures on different sets of
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processors, and Monte Carlo temperature swaps are performed between
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pairs of copies.
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Use the -procs and -in "command-line switches"_Section_start.html#2_4
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to launch LAMMPS on multiple partitions.
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In your input script, define a set of temperatures, one for each
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processor partition, using the "variable"_variable.html command:
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variable t proc 300.0 310.0 320.0 330.0 :pre
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Define a fix of style "nvt"_fix_nvt.html or "langevin"_fix_langevin.html
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to control the temperature of each simulation:
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fix myfix all nvt $t $t 100.0 :pre
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Use the "temper"_temper.html command in place of a "run"_run.html
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command to perform a simulation where tempering exchanges will take
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place:
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temper 100000 100 $t myfix 3847 58382 :pre
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:line
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4.6 Granular models :link(4_6),h4
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To run a simulation of a granular model, you will want to use
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the following commands:
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"atom_style"_atom_style.html granular
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"fix nve/gran"_fix_nve_gran.html
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"fix gravity"_fix_gravity.html
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"thermo_style"_thermo_style.html gran :ul
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Use one of these 3 pair potentials:
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"pair_style"_pair_style.html gran/history
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"pair_style"_pair_style.html gran/no_history
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"pair_style"_pair_style.html gran/hertzian :ul
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These commands implement fix options specific to granular systems:
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"fix freeze"_fix_freeze.html
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"fix gran/diag"_fix_gran_diag.html
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"fix insert"_fix_insert.html
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"fix viscous"_fix_viscous.html
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"fix wall/gran"_fix_wall_gran.html :ul
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The fix style {freeze} zeroes both the force and torque of frozen
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atoms, and should be used for granular system instead of the fix style
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{setforce}.
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For computational efficiency, you can eliminate needless pairwise
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computations between frozen atoms by using this command:
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"neigh_modify"_neigh_modify.html exclude :ul
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:line
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4.7 TIP3P water model :link(4_7),h4
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The TIP3P water model as implemented in CHARMM
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"(MacKerell)"_#MacKerell specifies a 3-site rigid water molecule with
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charges and Lennard-Jones parameters assigned to each of the 3 atoms.
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In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
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the two O-H bonds and the H-O-H angle rigid. A bond style of
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{harmonic} and an angle style of {harmonic} or {charmm} should also be
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used.
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These are the additional parameters (in real units) to set for O and H
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atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
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cutoff. The K values can be used if a flexible TIP3P model (without
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fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
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set to 0.0, it corresponds to the original 1983 TIP3P model
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"(Jorgensen)"_#Jorgensen.
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O mass = 15.9994
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H mass = 1.008 :all(b),p
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O charge = -0.834
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H charge = 0.417 :all(b),p
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LJ epsilon of OO = 0.1521
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LJ sigma of OO = 3.1507
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LJ epsilon of HH = 0.0460
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LJ sigma of HH = 0.4000
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LJ epsilon of OH = 0.0836
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LJ sigma of OH = 1.7753 :all(b),p
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K of OH bond = 450
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r0 of OH bond = 0.9572 :all(b),p
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K of HOH angle = 55
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theta of HOH angle = 104.52 :all(b),p
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These are the parameters to use for TIP3P with a long-range Coulombic
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solver (Ewald or PPPM in LAMMPS):
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O mass = 15.9994
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H mass = 1.008 :all(b),p
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O charge = -0.830
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H charge = 0.415 :all(b),p
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LJ epsilon of OO = 0.102
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LJ sigma of OO = 3.1507
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LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
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K of OH bond = 450
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r0 of OH bond = 0.9572 :all(b),p
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K of HOH angle = 55
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theta of HOH angle = 104.52 :all(b),p
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:line
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4.8 TIP4P water model :link(4_8),h4
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The four-point TIP4P rigid water model extends the traditional
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three-point TIP3P model by adding an additional site, usually
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massless, where the charge associated with the oxygen atom is placed.
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This site M is located at a fixed distance away from the oxygen along
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the bisector of the HOH bond angle. A bond style of {harmonic} and an
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angle style of {harmonic} or {charmm} should also be used.
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Two different four-point models (cutoff and long-range Coulombics) can
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be implemented using LAMMPS pair styles with {tip4p} in their style
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name. For both models, the bond lengths and bond angles should be
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held fixed using the "fix shake"_fix_shake.html command.
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These are the additional parameters (in real units) to set for O and H
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atoms and the water molecule to run a rigid TIP4P model with a cutoff
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"(Jorgensen)"_#Jorgensen. Note that the OM distance is specified in
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the "pair_style"_pair_style.html command, not as part of the pair
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coefficients.
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O mass = 15.9994
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H mass = 1.008 :all(b),p
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O charge = -1.040
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H charge = 0.520 :all(b),p
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r0 of OH bond = 0.9572
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theta of HOH angle = 104.52 :all(b),p
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OM distance = 0.15 :all(b),p
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LJ epsilon of O-O = 0.1550
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LJ sigma of O-O = 3.1536
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LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
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These are the parameters to use for TIP4P with a long-range Coulombic
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solver (Ewald or PPPM in LAMMPS):
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O mass = 15.9994
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H mass = 1.008 :all(b),p
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O charge = -1.0484
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H charge = 0.5242 :all(b),p
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r0 of OH bond = 0.9572
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theta of HOH angle = 104.52 :all(b),p
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OM distance = 0.1250 :all(b),p
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LJ epsilon of O-O = 0.16275
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LJ sigma of O-O = 3.16435
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LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
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:line
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4.9 SPC water model :link(4_9),h4
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The SPC water model specifies a 3-site rigid water molecule with
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charges and Lennard-Jones parameters assigned to each of the 3 atoms.
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In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
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the two O-H bonds and the H-O-H angle rigid. A bond style of
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{harmonic} and an angle style of {harmonic} or {charmm} should also be
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used.
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These are the additional parameters (in real units) to set for O and H
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atoms and the water molecule to run a rigid SPC model with long-range
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Coulombics (Ewald or PPPM in LAMMPS).
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O mass = 15.9994
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H mass = 1.008 :all(b),p
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O charge = -0.820
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H charge = 0.410 :all(b),p
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LJ epsilon of OO = 0.1553
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LJ sigma of OO = 3.166
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LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
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r0 of OH bond = 1.0
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theta of HOH angle = 109.47 :all(b),p
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:line
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4.10 Coupling LAMMPS to other codes :link(4_10),h4
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LAMMPS is designed to allow it to be coupled to other codes. For
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example, a quantum mechanics code might compute forces on a subset of
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atoms and pass those forces to LAMMPS. Or a continuum finite element
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(FE) simulation might use atom positions as boundary conditions on FE
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nodal points, compute a FE solution, and return interpolated forces on
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MD atoms.
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LAMMPS can be coupled to other codes in at least 3 ways. Each has
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advantages and disadvantages, which you'll have to think about in the
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context of your application.
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(1) Define a new "fix"_fix.html command that calls the other code. In
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this scenario, LAMMPS is the driver code. During its timestepping,
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the fix is invoked, and can make library calls to the other code,
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|
which has been linked to LAMMPS as a library. This is the way the
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|
"POEMS"_poems package that performs constrained rigid-body motion on
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|
groups of atoms is hooked to LAMMPS. See the
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"fix_poems"_fix_poems.html command for more details. See "this
|
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section"_Section_modify.html of the documentation for info on how to add
|
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a new fix to LAMMPS.
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|
|
|
:link(poems,http://www.rpi.edu/~anderk5/lab)
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(2) Define a new LAMMPS command that calls the other code. This is
|
|
conceptually similar to method (1), but in this case LAMMPS and the
|
|
other code are on a more equal footing. Note that now the other
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|
code is not called during the timesteps of a LAMMPS run, but between
|
|
runs. The LAMMPS input script can be used to alternate LAMMPS runs
|
|
with calls to the other code, invoked via the new command. The
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|
"run"_run.html command facilitates this with its {every} option, which
|
|
makes it easy to run a few steps, invoke the command, run a few steps,
|
|
invoke the command, etc.
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|
|
|
In this scenario, the other code can be a library, called by the
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|
command, or it could be a stand-alone code, invoked by a system() call
|
|
made by the command (assuming your parallel machine allows one or more
|
|
processors to start up another program). In the latter case the
|
|
stand-alone code could communicate with LAMMPS thru files that the
|
|
command writes and reads.
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|
|
|
See "this section"_Section_modify.html of the documentation for how to
|
|
add a new command to LAMMPS.
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|
|
|
(3) Use LAMMPS as a library called by another code. In this case the
|
|
other code is the driver and calls LAMMPS as needed. Or a wrapper
|
|
code could link and call both LAMMPS and another code as libraries.
|
|
Again, the "run"_run.html command has options that allow it to be
|
|
invoked with minimal overhead (no setup or clean-up) if you wish to do
|
|
multiple short runs, driven by another program.
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|
|
|
"This section"_Section_start.html#2_2 of the documentation describes
|
|
how to build LAMMPS as a library. Once this is done, you can interface
|
|
with LAMMPS either via C++, C, or Fortran (or any other language that
|
|
supports a vanilla C-like interface, e.g. a scripting language). For
|
|
example, from C++ you could create an "instance" of LAMMPS, and
|
|
initialize it, pass it an input script to process, or execute
|
|
individual commands, all by invoking the correct class methods in
|
|
LAMMPS. From C or Fortran you would make function calls to do the
|
|
same things. Library.cpp and library.h contain such a C interface
|
|
that illustrates this with the functions:
|
|
|
|
void lammps_open(int, char **, MPI_Comm);
|
|
void lammps_close();
|
|
void lammps_file(char *);
|
|
char *lammps_command(char *); :pre
|
|
|
|
The functions contain the C++ code you would need to put in a C++
|
|
application that was invoking LAMMPS directly.
|
|
|
|
Two of the routines in library.cpp are of particular note. The
|
|
lammps_open() function initiates LAMMPS and takes an MPI communicator
|
|
as an argument. LAMMPS will run on the set of processors in the
|
|
communicator. This means the calling code can run LAMMPS on all or a
|
|
subset of processors. For example, a wrapper script might decide to
|
|
alternate between LAMMPS and another code, allowing them both to run
|
|
on all the processors. Or it might allocate half the processors to
|
|
LAMMPS and half to the other code and run both codes simultaneously
|
|
before syncing them up periodically.
|
|
|
|
Library.cpp also contains a lammps_command() function to which the
|
|
caller passes a single LAMMPS command (a string). Thus the calling
|
|
code can read or generate a series of LAMMPS commands (e.g. an input
|
|
script) one line at a time and pass it thru the library interface to
|
|
setup a problem and then run it.
|
|
|
|
A few other sample routines are included in library.cpp, but the key
|
|
idea is that you can write any routines you wish to define an
|
|
interface for how your code talks to LAMMPS and add them to
|
|
library.cpp and library.h. The routines you add can access any LAMMPS
|
|
data. The umbrella.cpp code in examples/couple is a simple example of
|
|
how a stand-alone code can link LAMMPS as a library, run LAMMPS on a
|
|
subset of processors, grab data from LAMMPS, change it, and put it
|
|
back into LAMMPS.
|
|
|
|
:line
|
|
|
|
:link(Cornell)
|
|
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
|
|
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
|
|
|
|
:link(Horn)
|
|
[(Horn)] Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
|
|
J Chem Phys, 120, 9665 (2004).
|
|
|
|
:link(MacKerell)
|
|
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
|
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
|
|
|
:link(Jorgensen)
|
|
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
|
|
Phys, 79, 926 (1983).
|