\(\renewcommand{\AA}{\text{Å}}\)
thermo_style command
Syntax
thermo_style style args
style = one or multi or yaml or custom
args = list of arguments for a particular style
one args = none multi args = none yaml 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, evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail, enthalpy, ecouple, econserve, vol, density, xlo, xhi, ylo, yhi, zlo, zhi, xy, xz, yz, avecx, avecy, avecz, bvecx, bvecy, bvecz, cvecx, cvecy, cvecz, lx, ly, lz, xlat, ylat, zlat, cella, cellb, cellc, cellalpha, cellbeta, cellgamma, pxx, pyy, pzz, pxy, pxz, pyz, bonds, angles, dihedrals, impropers, fmax, fnorm, nbuild, ndanger, 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) evdwl = van der Waals 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 = van der Waals energy long-range tail correction enthalpy = enthalpy (etotal + press*vol) ecouple = cumulative energy change due to thermo/baro statting fixes econserve = pe + ke + ecouple = etotal + ecouple vol = volume density = mass density of system xlo,xhi,ylo,yhi,zlo,zhi = box boundaries xy,xz,yz = box tilt for restricted triclinic (non-orthogonal) simulation boxes avecx,avecy,avecz = components of edge vector A of the simulation box bvecx,bvecy,bvecz = components of edge vector B of the simulation box cvecx,cvecy,cvecz = components of edge vector C of the simulation box lx,ly,lz = box lengths in x,y,z xlat,ylat,zlat = lattice spacings as calculated by lattice command cella,cellb,cellc = periodic cell lattice constants a,b,c cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor bonds,angles,dihedrals,impropers = # of these interactions defined 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 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, I can include wildcard (see below)
Examples
thermo_style multi
thermo_style yaml
thermo_style one
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 files. The units for each column of output corresponding to the list of keywords is determined by the units command for the simulation. E.g. energies will be in energy units, temperature in temperature units, pressure in pressure units.
Style one prints a single line 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.
Added in version 24Mar2022.
Style yaml is similar to style one but prints the output in YAML format which can be easily read by a variety of
script languages and data handling packages. Since LAMMPS may print
other output before, after, or in between thermodynamic output, the
YAML format content needs to be separated from the rest. All YAML
format thermodynamic output can be matched with a regular expression
and can thus be extracted with commands like egrep as follows:
egrep '^(keywords:|data:$|---$|\.\.\.$| - \[)' log.lammps > log.yaml
Information about processing such YAML files is in the structured data output howto.
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 Modify page for details on the latter. 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 \(\frac{1}{2} k_B T\) 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 energy yes 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 and whether their default fix_modify energy setting is yes or no.
A long-range tail correction etail for the van der Waals 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.
Here is more information on other keywords whose meaning may not be clear.
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 discussion of the -partition command-line switch for details on running in multi-partition mode.
The timeremain keyword is the seconds remaining 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 ecouple keyword is cumulative energy change in the system due to any thermostatting or barostatting fixes that are being used. A positive value means that energy has been subtracted from the system (added to the coupling reservoir). See the econserve keyword for an explanation of why this sign choice makes sense.
The econserve keyword is the sum of the potential and kinetic energy of the system as well as the energy that has been transferred by thermostatting or barostatting to their coupling reservoirs – that is, econserve = pe + ke + ecouple. Ideally, for a simulation in the NVT, NPH, or NPT ensembles, the econserve quantity should remain constant over time even though etotal may change.
In LAMMPS, the simulation box can be defined as orthogonal or triclinic (non-orthogonal). See the Howto_triclinic doc page for a detailed explanation of orthogonal, restricted triclinic, and general triclinic simulation boxes and how LAMMPS rotates a general triclinic box to be restricted triclinic internally.
The lx, ly, lz keywords are the extent of the simulation box in each dimension. The xlo, xhi, ylo, yhi, zlo, zhi keywords are the lower and upper bounds of the simulation box in each dimension. I.e. lx = xhi - xlo). These 9 values are the same for all 3 kinds of boxes. I.e. for a restricted triclinic box, they are the values as if the box were not tilted. For a general triclinic box, they are the values after it is internally rotated to be a restricted triclinic box.
The xy, xz, yz are the current tilt factors for a triclinic box. They are the same for restricted and general triclinic boxes.
The avecx, avecy, avecz, bvecx, bvecy, bvecz, cvecx, cvecy, cvecz are the components of the 3 edge vectors of the current general simulation box. If it is an orthogonal box the vectors are along the x, y, z coordinate axes. If it is a restricted triclinic box, the A vector is along the x axis, the B vector is in the xy plane with a +y coordinate, and the C vector has a +z coordinate, as explained on the Howto_triclinic doc page. If the thermo_modify triclinic/general option is set then they are the A, B, C vector which define the general triclinic box.
The cella, cellb, cellc, cellalpha, cellbeta, cellgamma keywords correspond to the usual crystallographic quantities that define the periodic simulation box of a crystalline system. See the Howto triclinic page for a precise definition of these quantities in terms of the LAMMPS representation of a restricted triclinic simulation box via lx, ly, lz, yz, xz, xy.
The pxx,pyy,pzz,pxy,pxz,pyz keywords are the 6 components of the symmetric pressure tensor for the system. See the compute pressure command doc page for details of how it is calculated.
If the thermo_modify triclinic/general option is set then the 6 components will be output as values consistent with the orientation of the general triclinic box relative to the standard xyz coordinate axes. If this keyword is not used, the values will be consistent with the orientation of the restricted triclinic box (which aligns with the xyz coordinate axes). As explained on the Howto_triclinic doc page, even if the simulation box is created as a general triclinic box, internally LAMMPS uses a restricted triclinic box.
Note that because the pressure tensor components are computed using force vectors and atom coordinates, both of which are rotated in the general versus restricted triclinic representation, the values will typically be different for the two cases.
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 ensure no force interactions are missed by atoms moving beyond the neighbor skin distance before a rebuild takes place.
For output values from a compute or fix or variable, the bracketed index I used to index a vector, as in c_ID[I] or f_ID[I] or v_name[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, 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]
Note
For a vector-style variable, only the wildcard forms “*n” or “m*n” are allowed. You must specify the upper bound, because vector-style variable lengths are not determined until the variable is evaluated. If n is specified larger than the vector length turns out to be, zeroes are output for missing vector values.
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, local, and per-grid values. Only global values can be referenced by this command. However, per-atom compute values for an individual atom can be referenced in a equal-style 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, local, and per-grid values. Only global values can be referenced by this command. However, per-atom fix values can be referenced for an individual atom in a equal-style 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 equal-style variable can use an atom-style variable in its formula indexed by the ID of an individual atom. This is a way to output a specific atom’s per-atom coordinates or other per-atom properties in thermo output. See the variable command for details. Note that 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