thermo_style command

Syntax

thermo_style style args
  • style = one or multi or custom

  • args = list of arguments for a particular style

    one args = none
    multi args = none
    custom args = list of keywords
      possible keywords = step, elapsed, elaplong, dt, time,
                          cpu, tpcpu, spcpu, cpuremain, part, timeremain,
                          atoms, temp, press, pe, ke, etotal, enthalpy,
                          evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
                          emol, elong, etail,
                          vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
                          xy, xz, yz, xlat, ylat, zlat,
                          bonds, angles, dihedrals, impropers,
                          pxx, pyy, pzz, pxy, pxz, pyz,
                          fmax, fnorm, nbuild, ndanger,
                          cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
                          c_ID, c_ID[I], c_ID[I][J],
                          f_ID, f_ID[I], f_ID[I][J],
                          v_name, v_name[I]
        step = timestep
        elapsed = timesteps since start of this run
        elaplong = timesteps since start of initial run in a series of runs
        dt = timestep size
        time = simulation time
        cpu = elapsed CPU time in seconds since start of this run
        tpcpu = time per CPU second
        spcpu = timesteps per CPU second
        cpuremain = estimated CPU time remaining in run
        part = which partition (0 to Npartition-1) this is
        timeremain = remaining time in seconds on timer timeout.
        atoms = # of atoms
        temp = temperature
        press = pressure
        pe = total potential energy
        ke = kinetic energy
        etotal = total energy (pe + ke)
        enthalpy = enthalpy (etotal + press*vol)
        evdwl = VanderWaal pairwise energy (includes etail)
        ecoul = Coulombic pairwise energy
        epair = pairwise energy (evdwl + ecoul + elong)
        ebond = bond energy
        eangle = angle energy
        edihed = dihedral energy
        eimp = improper energy
        emol = molecular energy (ebond + eangle + edihed + eimp)
        elong = long-range kspace energy
        etail = VanderWaal energy long-range tail correction
        vol = volume
        density = mass density of system
        lx,ly,lz = box lengths in x,y,z
        xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
        xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
        xlat,ylat,zlat = lattice spacings as calculated by lattice command
        bonds,angles,dihedrals,impropers = # of these interactions defined
        pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
        fmax = max component of force on any atom in any dimension
        fnorm = length of force vector for all atoms
        nbuild = # of neighbor list builds
        ndanger = # of dangerous neighbor list builds
        cella,cellb,cellc = periodic cell lattice constants a,b,c
        cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma
        c_ID = global scalar value calculated by a compute with ID
        c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
        c_ID[I][J] = I,J component of global array calculated by a compute with ID
        f_ID = global scalar value calculated by a fix with ID
        f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
        f_ID[I][J] = I,J component of global array calculated by a fix with ID
        v_name = value calculated by an equal-style variable with name
        v_name[I] = value calculated by a vector-style variable with name
    

Examples

thermo_style multi
thermo_style custom step temp pe etotal press vol
thermo_style custom step temp etotal c_myTemp v_abc
thermo_style custom step temp etotal c_myTemp[*] v_abc

Description

Set the style and content for printing thermodynamic data to the screen and log file.

Style one prints a one-line summary of thermodynamic info that is the equivalent of “thermo_style custom step temp epair emol etotal press”. The line contains only numeric values.

Style multi prints a multiple-line listing of thermodynamic info that is the equivalent of “thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press”. The listing contains numeric values and a string ID for each quantity.

Style custom is the most general setting and allows you to specify which of the keywords listed above you want printed on each thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are references to computes, fixes, and equal-style variables that have been defined elsewhere in the input script or can even be new styles which users have added to LAMMPS (see the Section 10 section of the documentation). Thus the custom style provides a flexible means of outputting essentially any desired quantity as a simulation proceeds.

All styles except custom have vol appended to their list of outputs if the simulation box volume changes during the simulation.

The values printed by the various keywords are instantaneous values, calculated on the current timestep. Time-averaged quantities, which include values from previous timesteps, can be output by using the f_ID keyword and accessing a fix that does time-averaging such as the fix ave/time command.

Options invoked by the thermo_modify command can be used to set the one- or multi-line format of the print-out, the normalization of thermodynamic output (total values versus per-atom values for extensive quantities (ones which scale with the number of atoms in the system), and the numeric precision of each printed value.

Note

When you use a “thermo_style” command, all thermodynamic settings are restored to their default values, including those previously set by a thermo_modify command. Thus if your input script specifies a thermo_style command, you should use the thermo_modify command after it.


Several of the thermodynamic quantities require a temperature to be computed: “temp”, “press”, “ke”, “etotal”, “enthalpy”, “pxx”, etc. By default this is done by using a temperature compute which is created when LAMMPS starts up, as if this command had been issued:

compute thermo_temp all temp

See the compute temp command for details. Note that the ID of this compute is thermo_temp and the group is all. You can change the attributes of this temperature (e.g. its degrees-of-freedom) via the compute_modify command. Alternatively, you can directly assign a new compute (that calculates temperature) which you have defined, to be used for calculating any thermodynamic quantity that requires a temperature. This is done via the thermo_modify command.

Several of the thermodynamic quantities require a pressure to be computed: “press”, “enthalpy”, “pxx”, etc. By default this is done by using a pressure compute which is created when LAMMPS starts up, as if this command had been issued:

compute thermo_press all pressure thermo_temp

See the compute pressure command for details. Note that the ID of this compute is thermo_press and the group is all. You can change the attributes of this pressure via the compute_modify command. Alternatively, you can directly assign a new compute (that calculates pressure) which you have defined, to be used for calculating any thermodynamic quantity that requires a pressure. This is done via the thermo_modify command.

Several of the thermodynamic quantities require a potential energy to be computed: “pe”, “etotal”, “ebond”, etc. This is done by using a pe compute which is created when LAMMPS starts up, as if this command had been issued:

compute thermo_pe all pe

See the compute pe command for details. Note that the ID of this compute is thermo_pe and the group is all. You can change the attributes of this potential energy via the compute_modify command.


The kinetic energy of the system ke is inferred from the temperature of the system with 1/2 Kb T of energy for each degree of freedom. Thus, using different compute commands for calculating temperature, via the thermo_modify temp command, may yield different kinetic energies, since different computes that calculate temperature can subtract out different non-thermal components of velocity and/or include different degrees of freedom (translational, rotational, etc).

The potential energy of the system pe will include contributions from fixes if the fix_modify thermo option is set for a fix that calculates such a contribution. For example, the fix wall/lj93 fix calculates the energy of atoms interacting with the wall. See the doc pages for “individual fixes” to see which ones contribute.

A long-range tail correction etail for the VanderWaal pairwise energy will be non-zero only if the pair_modify tail option is turned on. The etail contribution is included in evdwl, epair, pe, and etotal, and the corresponding tail correction to the pressure is included in press and pxx, pyy, etc.


The step, elapsed, and elaplong keywords refer to timestep count. Step is the current timestep, or iteration count when a minimization is being performed. Elapsed is the number of timesteps elapsed since the beginning of this run. Elaplong is the number of timesteps elapsed since the beginning of an initial run in a series of runs. See the start and stop keywords for the run for info on how to invoke a series of runs that keep track of an initial starting time. If these keywords are not used, then elapsed and elaplong are the same value.

The dt keyword is the current timestep size in time units. The time keyword is the current elapsed simulation time, also in time units, which is simply (step*dt) if the timestep size has not changed and the timestep has not been reset. If the timestep has changed (e.g. via fix dt/reset) or the timestep has been reset (e.g. via the “reset_timestep” command), then the simulation time is effectively a cumulative value up to the current point.

The cpu keyword is elapsed CPU seconds since the beginning of this run. The tpcpu and spcpu keywords are measures of how fast your simulation is currently running. The tpcpu keyword is simulation time per CPU second, where simulation time is in time units. E.g. for metal units, the tpcpu value would be picoseconds per CPU second. The spcpu keyword is the number of timesteps per CPU second. Both quantities are on-the-fly metrics, measured relative to the last time they were invoked. Thus if you are printing out thermodynamic output every 100 timesteps, the two keywords will continually output the time and timestep rate for the last 100 steps. The tpcpu keyword does not attempt to track any changes in timestep size, e.g. due to using the fix dt/reset command.

The cpuremain keyword estimates the CPU time remaining in the current run, based on the time elapsed thus far. It will only be a good estimate if the CPU time/timestep for the rest of the run is similar to the preceding timesteps. On the initial timestep the value will be 0.0 since there is no history to estimate from. For a minimization run performed by the “minimize” command, the estimate is based on the maxiter parameter, assuming the minimization will proceed for the maximum number of allowed iterations.

The part keyword is useful for multi-replica or multi-partition simulations to indicate which partition this output and this file corresponds to, or for use in a variable to append to a filename for output specific to this partition. See Section 2.6 of the manual for details on running in multi-partition mode.

The timeremain keyword returns the remaining seconds when a timeout has been configured via the timer timeout command. If the timeout timer is inactive, the value of this keyword is 0.0 and if the timer is expired, it is negative. This allows for example to exit loops cleanly, if the timeout is expired with:

if "$(timeremain) < 0.0" then "quit 0"

The fmax and fnorm keywords are useful for monitoring the progress of an energy minimization. The fmax keyword calculates the maximum force in any dimension on any atom in the system, or the infinity-norm of the force vector for the system. The fnorm keyword calculates the 2-norm or length of the force vector.

The nbuild and ndanger keywords are useful for monitoring neighbor list builds during a run. Note that both these values are also printed with the end-of-run statistics. The nbuild keyword is the number of re-builds during the current run. The ndanger keyword is the number of re-builds that LAMMPS considered potentially “dangerous”. If atom movement triggered neighbor list rebuilding (see the neigh_modify command), then dangerous reneighborings are those that were triggered on the first timestep atom movement was checked for. If this count is non-zero you may wish to reduce the delay factor to insure no force interactions are missed by atoms moving beyond the neighbor skin distance before a rebuild takes place.

The keywords cella, cellb, cellc, cellalpha, cellbeta, cellgamma, correspond to the usual crystallographic quantities that define the periodic unit cell of a crystal. See this section of the doc pages for a geometric description of triclinic periodic cells, including a precise definition of these quantities in terms of the internal LAMMPS cell dimensions lx, ly, lz, yz, xz, xy.


For output values from a compute or fix, the bracketed index I used to index a vector, as in c_ID[I] or f_ID[I], can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the size of the vector (for mode = scalar) or the number of columns in the array (for mode = vector), then an asterisk with no numeric values means all indices from 1 to N. A leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive).

Using a wildcard is the same as if the individual elements of the vector had been listed one by one. E.g. these 2 thermo_style commands are equivalent, since the compute temp command creates a global vector with 6 values.

compute myTemp all temp
thermo_style custom step temp etotal c_myTemp[*]
thermo_style custom step temp etotal &
             c_myTemp[1] c_myTemp[2] c_myTemp[3] &
             c_myTemp[4] c_myTemp[5] c_myTemp[6]

The c_ID and c_ID[I] and c_ID[I][J] keywords allow global values calculated by a compute to be output. As discussed on the compute doc page, computes can calculate global, per-atom, or local values. Only global values can be referenced by this command. However, per-atom compute values for an individual atom can be referenced in a variable and the variable referenced by thermo_style custom, as discussed below. See the discussion above for how the I in c_ID[I] can be specified with a wildcard asterisk to effectively specify multiple values from a global compute vector.

The ID in the keyword should be replaced by the actual ID of a compute that has been defined elsewhere in the input script. See the compute command for details. If the compute calculates a global scalar, vector, or array, then the keyword formats with 0, 1, or 2 brackets will reference a scalar value from the compute.

Note that some computes calculate “intensive” global quantities like temperature; others calculate “extensive” global quantities like kinetic energy that are summed over all atoms in the compute group. Intensive quantities are printed directly without normalization by thermo_style custom. Extensive quantities may be normalized by the total number of atoms in the simulation (NOT the number of atoms in the compute group) when output, depending on the thermo_modify norm option being used.

The f_ID and f_ID[I] and f_ID[I][J] keywords allow global values calculated by a fix to be output. As discussed on the fix doc page, fixes can calculate global, per-atom, or local values. Only global values can be referenced by this command. However, per-atom fix values can be referenced for an individual atom in a variable and the variable referenced by thermo_style custom, as discussed below. See the discussion above for how the I in f_ID[I] can be specified with a wildcard asterisk to effectively specify multiple values from a global fix vector.

The ID in the keyword should be replaced by the actual ID of a fix that has been defined elsewhere in the input script. See the fix command for details. If the fix calculates a global scalar, vector, or array, then the keyword formats with 0, 1, or 2 brackets will reference a scalar value from the fix.

Note that some fixes calculate “intensive” global quantities like timestep size; others calculate “extensive” global quantities like energy that are summed over all atoms in the fix group. Intensive quantities are printed directly without normalization by thermo_style custom. Extensive quantities may be normalized by the total number of atoms in the simulation (NOT the number of atoms in the fix group) when output, depending on the thermo_modify norm option being used.

The v_name keyword allow the current value of a variable to be output. The name in the keyword should be replaced by the variable name that has been defined elsewhere in the input script. Only equal-style and vector-style variables can be referenced; the latter requires a bracketed term to specify the Ith element of the vector calculated by the variable. However, an atom-style variable can be referenced for an individual atom by an equal-style variable and that variable referenced. See the variable command for details. Variables of style equal and vector and atom define a formula which can reference per-atom properties or thermodynamic keywords, or they can invoke other computes, fixes, or variables when evaluated, so this is a very general means of creating thermodynamic output.

Note that equal-style and vector-style variables are assumed to produce “intensive” global quantities, which are thus printed as-is, without normalization by thermo_style custom. You can include a division by “natoms” in the variable formula if this is not the case.


Restrictions

This command must come after the simulation box is defined by a read_data, read_restart, or create_box command.

Default

thermo_style one