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@ -37,13 +37,13 @@ of a compute com/chunk command defined in the input script. It is
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used to compute the COMs of each chunk.
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At the beginning of the first :doc:`run <run>` or
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:doc:`minimize <miminize>` command after this fix is defined, the
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initial COM of each chunk is calculated and stored as R0c, where C is
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:doc:`minimize <minimize>` command after this fix is defined, the
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initial COM of each chunk is calculated and stored as R0m, where M is
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the chunk number. Thereafter, at every timestep (or minimization
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iteration), the current COM of each chunk is calculated as Rc. A
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restoring force of magnitude K (Rc - R0c) Mi / Mc is applied to each
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iteration), the current COM of each chunk is calculated as Rm. A
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restoring force of magnitude K (Rm - R0m) Mi / Mm is applied to each
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atom in each chunk where *K* is the specified spring constant, Mi is
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the mass of the atom, and Mc is the total mass of all atoms in the
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the mass of the atom, and Mm is the total mass of all atoms in the
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chunk. Note that *K* thus represents the spring constant for the
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total force on each chunk of atoms, not for a spring applied to each
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atom.
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@ -156,13 +156,13 @@ input script. It is used to define the chunks. The <em>comID</em> is the ID
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of a compute com/chunk command defined in the input script. It is
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used to compute the COMs of each chunk.</p>
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<p>At the beginning of the first <a class="reference internal" href="run.html"><span class="doc">run</span></a> or
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<span class="xref doc">minimize</span> command after this fix is defined, the
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initial COM of each chunk is calculated and stored as R0c, where C is
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<a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command after this fix is defined, the
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initial COM of each chunk is calculated and stored as R0m, where M is
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the chunk number. Thereafter, at every timestep (or minimization
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iteration), the current COM of each chunk is calculated as Rc. A
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restoring force of magnitude K (Rc - R0c) Mi / Mc is applied to each
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iteration), the current COM of each chunk is calculated as Rm. A
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restoring force of magnitude K (Rm - R0m) Mi / Mm is applied to each
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atom in each chunk where <em>K</em> is the specified spring constant, Mi is
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the mass of the atom, and Mc is the total mass of all atoms in the
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the mass of the atom, and Mm is the total mass of all atoms in the
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chunk. Note that <em>K</em> thus represents the spring constant for the
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total force on each chunk of atoms, not for a spring applied to each
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atom.</p>
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File diff suppressed because one or more lines are too long
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@ -35,13 +35,13 @@ of a compute com/chunk command defined in the input script. It is
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used to compute the COMs of each chunk.
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At the beginning of the first "run"_run.html or
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"minimize"_miminize.html command after this fix is defined, the
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initial COM of each chunk is calculated and stored as R0c, where C is
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"minimize"_minimize.html command after this fix is defined, the
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initial COM of each chunk is calculated and stored as R0m, where M is
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the chunk number. Thereafter, at every timestep (or minimization
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iteration), the current COM of each chunk is calculated as Rc. A
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restoring force of magnitude K (Rc - R0c) Mi / Mc is applied to each
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iteration), the current COM of each chunk is calculated as Rm. A
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restoring force of magnitude K (Rm - R0m) Mi / Mm is applied to each
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atom in each chunk where {K} is the specified spring constant, Mi is
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the mass of the atom, and Mc is the total mass of all atoms in the
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the mass of the atom, and Mm is the total mass of all atoms in the
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chunk. Note that {K} thus represents the spring constant for the
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total force on each chunk of atoms, not for a spring applied to each
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atom.
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