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518 lines
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<title>thermo_style command — LAMMPS 15 May 2015 version documentation</title>
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<li>thermo_style command</li>
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<div class="section" id="thermo-style-command">
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<span id="index-0"></span><h1>thermo_style command<a class="headerlink" href="#thermo-style-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>thermo_style style args
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</pre></div>
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</div>
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<ul class="simple">
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<li>style = <em>one</em> or <em>multi</em> or <em>custom</em></li>
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<li>args = list of arguments for a particular style</li>
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</ul>
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<pre class="literal-block">
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<em>one</em> args = none
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<em>multi</em> args = none
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<em>custom</em> args = list of keywords
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possible keywords = 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, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
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xy, xz, yz, xlat, ylat, zlat,
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bonds, angles, dihedrals, impropers,
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pxx, pyy, pzz, pxy, pxz, pyz,
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fmax, fnorm, nbuild, ndanger,
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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 <a class="reference internal" href="lattice.html"><em>lattice</em></a> command
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bonds,angles,dihedrals,impropers = # of these interactions defined
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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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nbuild = # of neighbor list builds
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ndanger = # of dangerous neighbor list builds
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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
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>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
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Set the style and content for printing thermodynamic data to the
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screen and log file.</p>
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<p>Style <em>one</em> 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.</p>
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<p>Style <em>multi</em> 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.</p>
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<p>Style <em>custom</em> 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 <a class="reference internal" href="compute.html"><em>computes</em></a>, <a class="reference internal" href="fix.html"><em>fixes</em></a>, and
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equal-style <a class="reference external" href="variable.html"">variables</a> 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 <a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a>
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section of the documentation). Thus the <em>custom</em> style provides a
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flexible means of outputting essentially any desired quantity as a
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simulation proceeds.</p>
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<p>All styles except <em>custom</em> have <em>vol</em> appended to their list of
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outputs if the simulation box volume changes during the simulation.</p>
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<p>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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<a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a> command.</p>
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<p>Options invoked by the <a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> 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.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">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 <a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> 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.</p>
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</div>
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<hr class="docutils" />
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<p>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 <em>temperature</em> compute which is created
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when LAMMPS starts up, as if this command had been issued:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute thermo_temp all temp
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</pre></div>
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</div>
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<p>See the <a class="reference internal" href="compute_temp.html"><em>compute temp</em></a> command for details. Note
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that the ID of this compute is <em>thermo_temp</em> and the group is <em>all</em>.
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You can change the attributes of this temperature (e.g. its
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degrees-of-freedom) via the <a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a>
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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 <a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> command.</p>
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<p>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 <em>pressure</em> compute which is created when LAMMPS starts up, as
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if this command had been issued:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute thermo_press all pressure thermo_temp
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</pre></div>
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</div>
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<p>See the <a class="reference internal" href="compute_pressure.html"><em>compute pressure</em></a> command for details.
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Note that the ID of this compute is <em>thermo_press</em> and the group is
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<em>all</em>. You can change the attributes of this pressure via the
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<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> 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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<a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> command.</p>
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<p>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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<em>pe</em> compute which is created when LAMMPS starts up, as if this
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command had been issued:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute thermo_pe all pe
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</pre></div>
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</div>
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<p>See the <a class="reference internal" href="compute_pe.html"><em>compute pe</em></a> command for details. Note that
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the ID of this compute is <em>thermo_pe</em> and the group is <em>all</em>. You can
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change the attributes of this potential energy via the
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<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command.</p>
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<hr class="docutils" />
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<p>The kinetic energy of the system <em>ke</em> 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 <a class="reference internal" href="compute.html"><em>compute commands</em></a> for calculating
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temperature, via the <a class="reference internal" href="thermo_modify.html"><em>thermo_modify temp</em></a> 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).</p>
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<p>The potential energy of the system <em>pe</em> will include contributions
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from fixes if the <a class="reference internal" href="fix_modify.html"><em>fix_modify thermo</em></a> option is set
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for a fix that calculates such a contribution. For example, the <a class="reference internal" href="fix_wall.html"><em>fix wall/lj93</em></a> 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.</p>
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<p>A long-range tail correction <em>etail</em> for the VanderWaal pairwise
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energy will be non-zero only if the <a class="reference internal" href="pair_modify.html"><em>pair_modify tail</em></a> option is turned on. The <em>etail</em> contribution
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is included in <em>evdwl</em>, <em>pe</em>, and <em>etotal</em>, and the corresponding tail
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correction to the pressure is included in <em>press</em> and <em>pxx</em>, <em>pyy</em>,
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etc.</p>
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<hr class="docutils" />
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<p>The <em>step</em>, <em>elapsed</em>, and <em>elaplong</em> keywords refer to timestep
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count. <em>Step</em> is the current timestep, or iteration count when a
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<a class="reference internal" href="minimize.html"><em>minimization</em></a> is being performed. <em>Elapsed</em> is the
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number of timesteps elapsed since the beginning of this run.
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<em>Elaplong</em> is the number of timesteps elapsed since the beginning of
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an initial run in a series of runs. See the <em>start</em> and <em>stop</em>
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keywords for the <a class="reference internal" href="run.html"><em>run</em></a> 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 <em>elapsed</em> and <em>elaplong</em> are the same value.</p>
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<p>The <em>dt</em> keyword is the current timestep size in time
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<a class="reference internal" href="units.html"><em>units</em></a>. The <em>time</em> keyword is the current elapsed
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simulation time, also in time <a class="reference internal" href="units.html"><em>units</em></a>, 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 <a class="reference internal" href="fix_dt_reset.html"><em>fix dt/reset</em></a>) 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.</p>
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<p>The <em>cpu</em> keyword is elapsed CPU seconds since the beginning of this
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run. The <em>tpcpu</em> and <em>spcpu</em> keywords are measures of how fast your
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simulation is currently running. The <em>tpcpu</em> keyword is simulation
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time per CPU second, where simulation time is in time
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<a class="reference internal" href="units.html"><em>units</em></a>. E.g. for metal units, the <em>tpcpu</em> value would be
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picoseconds per CPU second. The <em>spcpu</em> 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 <em>tpcpu</em> keyword does not attempt to track any changes in
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timestep size, e.g. due to using the <a class="reference internal" href="fix_dt_reset.html"><em>fix dt/reset</em></a>
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command.</p>
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<p>The <em>cpuremain</em> 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 <em>maxiter</em> parameter, assuming the minimization will
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proceed for the maximum number of allowed iterations.</p>
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<p>The <em>part</em> 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 <a class="reference internal" href="variable.html"><em>variable</em></a> to append to
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a filename for output specific to this partition. See <a class="reference internal" href="Section_start.html#start-7"><span>Section_start 7</span></a> of the manual for details on running in
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multi-partition mode.</p>
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<p>The <em>fmax</em> and <em>fnorm</em> keywords are useful for monitoring the progress
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of an <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>. The <em>fmax</em> 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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<em>fnorm</em> keyword calculates the 2-norm or length of the force vector.</p>
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<p>The <em>nbuild</em> and <em>ndanger</em> keywords are useful for monitoring neighbor
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list builds during a run. Note that both these values are also
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printed with the end-of-run statistics. The <em>nbuild</em> keyword is the
|
|
number of re-builds during the current run. The <em>ndanger</em> keyword is
|
|
the number of re-builds that LAMMPS considered potentially
|
|
“dangerous”. If atom movement triggered neighbor list rebuilding (see
|
|
the <a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a> 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.</p>
|
|
<p>The keywords <em>cella</em>, <em>cellb</em>, <em>cellc</em>, <em>cellalpha</em>, <em>cellbeta</em>,
|
|
<em>cellgamma</em>, correspond to the usual crystallographic quantities that
|
|
define the periodic unit cell of a crystal. See <a class="reference internal" href="Section_howto.html#howto-12"><span>this section</span></a> of the doc pages for a geometric
|
|
description of triclinic periodic cells, including a precise defintion
|
|
of these quantities in terms of the internal LAMMPS cell dimensions
|
|
<em>lx</em>, <em>ly</em>, <em>lz</em>, <em>yz</em>, <em>xz</em>, <em>xy</em>.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>c_ID</em> and <em>c_ID[I]</em> and <em>c_ID[I][J]</em> keywords allow global
|
|
values calculated by a compute to be output. As discussed on the
|
|
<a class="reference internal" href="compute.html"><em>compute</em></a> 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 can be referenced in a
|
|
<a class="reference internal" href="variable.html"><em>variable</em></a> and the variable referenced by thermo_style
|
|
custom, as discussed below.</p>
|
|
<p>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
|
|
<a class="reference internal" href="compute.html"><em>compute</em></a> 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.</p>
|
|
<p>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 <a class="reference internal" href="thermo_modify.html"><em>thermo_modify norm</em></a> option being used.</p>
|
|
<p>The <em>f_ID</em> and <em>f_ID[I]</em> and <em>f_ID[I][J]</em> keywords allow global
|
|
values calculated by a fix to be output. As discussed on the
|
|
<a class="reference internal" href="fix.html"><em>fix</em></a> 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 in a
|
|
<a class="reference internal" href="variable.html"><em>variable</em></a> and the variable referenced by thermo_style
|
|
custom, as discussed below.</p>
|
|
<p>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
|
|
<a class="reference internal" href="fix.html"><em>fix</em></a> 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.</p>
|
|
<p>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 <a class="reference internal" href="thermo_modify.html"><em>thermo_modify norm</em></a>
|
|
option being used.</p>
|
|
<p>The <em>v_name</em> 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 variables can be referenced. See the
|
|
<a class="reference internal" href="variable.html"><em>variable</em></a> command for details. Variables of style
|
|
<em>equal</em> 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.</p>
|
|
<p>Note that equal-style variables are assumed to be “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.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<p>This command must come after the simulation box is defined by a
|
|
<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>, or
|
|
<a class="reference internal" href="create_box.html"><em>create_box</em></a> command.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="thermo.html"><em>thermo</em></a>, <a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a>,
|
|
<a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a>, <a class="reference internal" href="compute_temp.html"><em>compute temp</em></a>,
|
|
<a class="reference internal" href="compute_pressure.html"><em>compute pressure</em></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
|
<div class="highlight-python"><div class="highlight"><pre>thermo_style one
|
|
</pre></div>
|
|
</div>
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