forked from lijiext/lammps
347 lines
16 KiB
Plaintext
347 lines
16 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :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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thermo_style command :h3
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[Syntax:]
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thermo_style style args :pre
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style = {one} or {multi} or {custom} :ulb,l
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args = list of arguments for a particular style :l
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{one} args = none
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{multi} args = none
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{custom} args = list of attributes
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possible attributes = step, elapsed, elaplong, dt, time,
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cpu, tpcpu, spcpu, cpuremain, part,
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atoms, temp, press, pe, ke, etotal, enthalpy,
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evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
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emol, elong, etail,
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vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
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xy, xz, yz, xlat, ylat, zlat,
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pxx, pyy, pzz, pxy, pxz, pyz,
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fmax, fnorm,
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cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
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c_ID, c_ID\[I\], c_ID\[I\]\[J\],
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f_ID, f_ID\[I\], f_ID\[I\]\[J\],
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v_name
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step = timestep
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elapsed = timesteps since start of this run
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elaplong = timesteps since start of initial run in a series of runs
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dt = timestep size
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time = simulation time
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cpu = elapsed CPU time in seconds
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tpcpu = time per CPU second
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spcpu = timesteps per CPU second
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cpuremain = estimated CPU time remaining in run
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part = which partition (0 to Npartition-1) this is
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atoms = # of atoms
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temp = temperature
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press = pressure
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pe = total potential energy
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ke = kinetic energy
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etotal = total energy (pe + ke)
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enthalpy = enthalpy (etotal + press*vol)
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evdwl = VanderWaal pairwise energy
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ecoul = Coulombic pairwise energy
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epair = pairwise energy (evdwl + ecoul + elong + etail)
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ebond = bond energy
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eangle = angle energy
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edihed = dihedral energy
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eimp = improper energy
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emol = molecular energy (ebond + eangle + edihed + eimp)
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elong = long-range kspace energy
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etail = VanderWaal energy long-range tail correction
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vol = volume
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density = mass density of system
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lx,ly,lz = box lengths in x,y,z
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xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
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xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
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xlat,ylat,zlat = lattice spacings as calculated by "lattice"_lattice.html command
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pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
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fmax = max component of force on any atom in any dimension
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fnorm = length of force vector for all atoms
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cella,cellb,cellc = periodic cell lattice constants a,b,c
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cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma
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c_ID = global scalar value calculated by a compute with ID
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c_ID\[I\] = Ith component of global vector calculated by a compute with ID
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c_ID\[I\]\[J\] = I,J component of global array calculated by a compute with ID
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f_ID = global scalar value calculated by a fix with ID
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f_ID\[I\] = Ith component of global vector calculated by a fix with ID
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f_ID\[I\]\[J\] = I,J component of global array calculated by a fix with ID
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v_name = scalar value calculated by an equal-style variable with name :pre
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:ule
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[Examples:]
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thermo_style multi
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thermo_style custom step temp pe etotal press vol
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thermo_style custom step temp etotal c_myTemp v_abc :pre
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[Description:]
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Set the style and content for printing thermodynamic data to the
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screen and log file.
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Style {one} prints a one-line summary of thermodynamic info that is
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the equivalent of "thermo_style custom step temp epair emol etotal
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press". The line contains only numeric values.
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Style {multi} prints a multiple-line listing of thermodynamic info
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that is the equivalent of "thermo_style custom etotal ke temp pe ebond
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eangle edihed eimp evdwl ecoul elong press". The listing contains
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numeric values and a string ID for each quantity.
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Style {custom} is the most general setting and allows you to specify
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which of the keywords listed above you want printed on each
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thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are
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references to "computes"_compute.html, "fixes"_fix.html, and
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equal-style "variables"_variable.html" that have been defined
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elsewhere in the input script or can even be new styles which users
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have added to LAMMPS (see the "Section_modify"_Section_modify.html
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section of the documentation). Thus the {custom} style provides a
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flexible means of outputting essentially any desired quantity as a
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simulation proceeds.
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All styles except {custom} have {vol} appended to their list of
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outputs if the simulation box volume changes during the simulation.
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The values printed by the various keywords are instantaneous values,
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calculated on the current timestep. Time-averaged quantities, which
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include values from previous timesteps, can be output by using the
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f_ID keyword and accessing a fix that does time-averaging such as the
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"fix ave/time"_fix_ave_time.html command.
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Options invoked by the "thermo_modify"_thermo_modify.html command can
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be used to set the one- or multi-line format of the print-out, the
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normalization of thermodynamic output (total values versus per-atom
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values for extensive quantities (ones which scale with the number of
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atoms in the system), and the numeric precision of each printed value.
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IMPORTANT NOTE: When you use a "thermo_style" command, all
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thermodynamic settings are restored to their default values, including
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those previously set by a "thermo_modify"_thermo_modify.html command.
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Thus if your input script specifies a thermo_style command, you should
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use the thermo_modify command after it.
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:line
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Several of the thermodynamic quantities require a temperature to be
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computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx", etc. By
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default this is done by using a {temperature} compute which is created
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when LAMMPS starts up, as if this command had been issued:
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compute thermo_temp all temp :pre
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See the "compute temp"_compute_temp.html command for details. Note
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that the ID of this compute is {thermo_temp} and the group is {all}.
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You can change the attributes of this temperature (e.g. its
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degrees-of-freedom) via the "compute_modify"_compute_modify.html
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command. Alternatively, you can directly assign a new compute (that
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calculates temperature) which you have defined, to be used for
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calculating any thermodynamic quantity that requires a temperature.
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This is done via the "thermo_modify"_thermo_modify.html command.
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Several of the thermodynamic quantities require a pressure to be
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computed: "press", "enthalpy", "pxx", etc. By default this is done by
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using a {pressure} compute which is created when LAMMPS starts up, as
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if this command had been issued:
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compute thermo_press all pressure thermo_temp :pre
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See the "compute pressure"_compute_pressure.html command for details.
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Note that the ID of this compute is {thermo_press} and the group is
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{all}. You can change the attributes of this pressure via the
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"compute_modify"_compute_modify.html command. Alternatively, you can
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directly assign a new compute (that calculates pressure) which you
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have defined, to be used for calculating any thermodynamic quantity
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that requires a pressure. This is done via the
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"thermo_modify"_thermo_modify.html command.
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Several of the thermodynamic quantities require a potential energy to
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be computed: "pe", "etotal", "ebond", etc. This is done by using a
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{pe} compute which is created when LAMMPS starts up, as if this
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command had been issued:
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compute thermo_pe all pe :pre
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See the "compute pe"_compute_pe.html command for details. Note that
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the ID of this compute is {thermo_pe} and the group is {all}. You can
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change the attributes of this potential energy via the
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"compute_modify"_compute_modify.html command.
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:line
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The kinetic energy of the system {ke} is inferred from the temperature
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of the system with 1/2 Kb T of energy for each degree of freedom.
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Thus, using different "compute commands"_compute.html for calculating
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temperature, via the "thermo_modify temp"_thermo_modify.html command,
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may yield different kinetic energies, since different computes that
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calculate temperature can subtract out different non-thermal
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components of velocity and/or include different degrees of freedom
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(translational, rotational, etc).
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The potential energy of the system {pe} will include contributions
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from fixes if the "fix_modify thermo"_fix_modify.html option is set
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for a fix that calculates such a contribution. For example, the "fix
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wall/lj93"_fix_wall.html fix calculates the energy of atoms
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interacting with the wall. See the doc pages for "individual fixes"
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to see which ones contribute.
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A long-range tail correction {etail} for the VanderWaal pairwise
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energy will be non-zero only if the "pair_modify
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tail"_pair_modify.html option is turned on. The {etail} contribution
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is included in {evdwl}, {pe}, and {etotal}, and the corresponding tail
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correction to the pressure is included in {press} and {pxx}, {pyy},
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etc.
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:line
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The {step}, {elapsed}, and {elaplong} keywords refer to timestep
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count. {Step} is the current timestep, or iteration count when a
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"minimization"_minimize.html is being performed. {Elapsed} is the
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number of timesteps elapsed since the beginning of this run.
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{Elaplong} is the number of timesteps elapsed since the beginning of
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an initial run in a series of runs. See the {start} and {stop}
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keywords for the "run"_run.html for info on how to invoke a series of
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runs that keep track of an initial starting time. If these keywords
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are not used, then {elapsed} and {elaplong} are the same value.
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The {dt} keyword is the current timestep size in time
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"units"_units.html. The {time} keyword is the current elapsed
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simulation time, also in time "units"_units.html, which is simply
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(step*dt) if the timestep size has not changed and the timestep has
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not been reset. If the timestep has changed (e.g. via "fix
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dt/reset"_fix_dt_reset.html) or the timestep has been reset (e.g. via
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the "reset_timestep" command), then the simulation time is effectively
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a cummulative value up to the current point.
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The {cpu} keyword is elapsed CPU seconds since the beginning of this
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run. The {tpcpu} and {spcpu} keywords are measures of how fast your
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simulation is currently running. The {tpcpu} keyword is simulation
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time per CPU second, where simulation time is in time
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"units"_units.html. E.g. for metal units, the {tpcpu} value would be
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picoseconds per CPU second. The {spcpu} keyword is the number of
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timesteps per CPU second. Both quantities are on-the-fly metrics,
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measured relative to the last time they were invoked. Thus if you are
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printing out thermodyamic output every 100 timesteps, the two keywords
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will continually output the time and timestep rate for the last 100
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steps. The {tpcpu} keyword does not attempt to track any changes in
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timestep size, e.g. due to using the "fix dt/reset"_fix_dt_reset.html
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command.
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The {cpuremain} keyword estimates the CPU time remaining in the
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current run, based on the time elapsed thus far. It will only be a
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good estimate if the CPU time/timestep for the rest of the run is
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similar to the preceding timesteps. On the initial timestep the value
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will be 0.0 since there is no history to estimate from. For a
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minimization run performed by the "minimize" command, the estimate is
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based on the {maxiter} parameter, assuming the minimization will
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proceed for the maximum number of allowed iterations.
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The {part} keyword is useful for multi-replica or multi-partition
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simulations to indicate which partition this output and this file
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corresponds to, or for use in a "variable"_variable.html to append to
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a filename for output specific to this partition. See "Section_start
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7"_Section_start.html#start_7 of the manual for details on running in
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multi-partition mode.
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The {fmax} and {fnorm} keywords are useful for monitoring the progress
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of an "energy minimization"_minimize.html. The {fmax} keyword
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calculates the maximum force in any dimension on any atom in the
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system, or the infinity-norm of the force vector for the system. The
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{fnorm} keyword calculates the 2-norm or length of the force vector.
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The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta},
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{cellgamma}, correspond to the usual crystallographic quantities that
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define the periodic unit cell of a crystal. See "this
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section"_Section_howto.html#howto_12 of the doc pages for a geometric
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description of triclinic periodic cells, including a precise defintion
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of these quantities in terms of the internal LAMMPS cell dimensions
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{lx}, {ly}, {lz}, {yz}, {xz}, {xy}.
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:line
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The {c_ID} and {c_ID\[I\]} and {c_ID\[I\]\[J\]} keywords allow global
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values calculated by a compute to be output. As discussed on the
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"compute"_compute.html doc page, computes can calculate global,
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per-atom, or local values. Only global values can be referenced by
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this command. However, per-atom compute values can be referenced in a
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"variable"_variable.html and the variable referenced by thermo_style
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custom, as discussed below.
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The ID in the keyword should be replaced by the actual ID of a compute
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that has been defined elsewhere in the input script. See the
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"compute"_compute.html command for details. If the compute calculates
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a global scalar, vector, or array, then the keyword formats with 0, 1,
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or 2 brackets will reference a scalar value from the compute.
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Note that some computes calculate "intensive" global quantities like
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temperature; others calculate "extensive" global quantities like
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kinetic energy that are summed over all atoms in the compute group.
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Intensive quantities are printed directly without normalization by
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thermo_style custom. Extensive quantities may be normalized by the
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total number of atoms in the simulation (NOT the number of atoms in
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the compute group) when output, depending on the "thermo_modify
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norm"_thermo_modify.html option being used.
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The {f_ID} and {f_ID\[I\]} and {f_ID\[I\]\[J\]} keywords allow global
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values calculated by a fix to be output. As discussed on the
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"fix"_fix.html doc page, fixes can calculate global, per-atom, or
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local values. Only global values can be referenced by this command.
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However, per-atom fix values can be referenced in a
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"variable"_variable.html and the variable referenced by thermo_style
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custom, as discussed below.
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The ID in the keyword should be replaced by the actual ID of a fix
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that has been defined elsewhere in the input script. See the
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"fix"_fix.html command for details. If the fix calculates a global
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scalar, vector, or array, then the keyword formats with 0, 1, or 2
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brackets will reference a scalar value from the fix.
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Note that some fixes calculate "intensive" global quantities like
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timestep size; others calculate "extensive" global quantities like
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energy that are summed over all atoms in the fix group. Intensive
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quantities are printed directly without normalization by thermo_style
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custom. Extensive quantities may be normalized by the total number of
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atoms in the simulation (NOT the number of atoms in the fix group)
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when output, depending on the "thermo_modify norm"_thermo_modify.html
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option being used.
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The {v_name} keyword allow the current value of a variable to be
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output. The name in the keyword should be replaced by the variable
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name that has been defined elsewhere in the input script. Only
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equal-style variables can be referenced. See the
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"variable"_variable.html command for details. Variables of style
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{equal} can reference per-atom properties or thermodynamic keywords,
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or they can invoke other computes, fixes, or variables when evaluated,
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so this is a very general means of creating thermodynamic output.
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Note that equal-style variables are assumed to be "intensive" global
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quantities, which are thus printed as-is, without normalization by
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thermo_style custom. You can include a division by "natoms" in the
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variable formula if this is not the case.
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:line
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[Restrictions:]
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This command must come after the simulation box is defined by a
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"read_data"_read_data.html, "read_restart"_read_restart.html, or
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"create_box"_create_box.html command.
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[Related commands:]
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"thermo"_thermo.html, "thermo_modify"_thermo_modify.html,
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"fix_modify"_fix_modify.html, "compute temp"_compute_temp.html,
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"compute pressure"_compute_pressure.html
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[Default:]
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thermo_style one :pre
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