(6b593f0c) · Commits · 郑智淋 / lammps

doc/_sources/Manual.txt

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		@@ -101,6 +101,27 @@ assignments for the Nth replica by comparing the Nth column of screen
		output to the thermodynamic data in the corresponding log.lammps.N or
		screen.N files as time proceeds.

		You can have each replica create its own dump file in the following
		manner:

		.. parsed-literal::

		variable rep world 0 1 2 3 4 5 6 7
		dump 1 all atom 1000 dump.temper.$rep

		.. note::

		Each replica's dump file will contain a continuous trajectory
		for its atoms where the temperature varies over time as swaps take
		place involving that replica. If you want a series of dump files,
		each with snapshots (from all replicas) that are all at a single
		temperature, then you will need to post-process the dump files using
		the information from the log.lammps file. E.g. you could produce one
		dump file with snapshots at 300K (from all replicas), another with
		snapshots at 310K, etc. Note that these new dump files will not
		contain "continuous trajectories" for individual atoms, because two
		successive snapshots (in time) may be from different replicas.

		The last argument index in the temper command is optional and is
		used when restarting a tempering run from a set of restart files (one
		for each replica) which had previously swapped to new temperatures.

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		@@ -48,9 +48,9 @@ Syntax
		ke = kinetic energy
		etotal = total energy (pe + ke)
		enthalpy = enthalpy (etotal + press*vol)
		evdwl = VanderWaal pairwise energy
		evdwl = VanderWaal pairwise energy (includes etail)
		ecoul = Coulombic pairwise energy
		epair = pairwise energy (evdwl + ecoul + elong + etail)
		epair = pairwise energy (evdwl + ecoul + elong)
		ebond = bond energy
		eangle = angle energy
		edihed = dihedral energy
		@@ -215,9 +215,9 @@ to see which ones contribute.

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


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		@@ -212,6 +212,25 @@ temperature. You can verify this time sequence of temperature
		assignments for the Nth replica by comparing the Nth column of screen
		output to the thermodynamic data in the corresponding log.lammps.N or
		screen.N files as time proceeds.</p>
		<p>You can have each replica create its own dump file in the following
		manner:</p>
		<div class="highlight-python"><div class="highlight"><pre>variable rep world 0 1 2 3 4 5 6 7
		dump 1 all atom 1000 dump.temper.$rep
		</pre></div>
		</div>
		<div class="admonition note">
		<p class="first admonition-title">Note</p>
		<p class="last">Each replica’s dump file will contain a continuous trajectory
		for its atoms where the temperature varies over time as swaps take
		place involving that replica. If you want a series of dump files,
		each with snapshots (from all replicas) that are all at a single
		temperature, then you will need to post-process the dump files using
		the information from the log.lammps file. E.g. you could produce one
		dump file with snapshots at 300K (from all replicas), another with
		snapshots at 310K, etc. Note that these new dump files will not
		contain “continuous trajectories” for individual atoms, because two
		successive snapshots (in time) may be from different replicas.</p>
		</div>
		<p>The last argument <em>index</em> in the temper command is optional and is
		used when restarting a tempering run from a set of restart files (one
		for each replica) which had previously swapped to new temperatures.