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clarify one of the outputs of fix ti/spring

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Plimpton
2021-02-03 15:01:35 -07:00
parent f2479e7d05
commit 1ee27e2bc2
1 changed files with 17 additions and 11 deletions
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doc/src/fix_ti_spring.rst
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@ -120,22 +120,28 @@ increase in computational resources cost.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the original coordinates of tethered atoms to :doc:`binary restart files <restart>`, so that the spring effect will be the
same in a restarted simulation. See the :doc:`read restart <read_restart>` command for info on how to re-specify a fix
in an input script that reads a restart file, so that the operation of
the fix continues in an uninterrupted fashion.
This fix writes the original coordinates of tethered atoms to
:doc:`binary restart files <restart>`, so that the spring effect will
be the same in a restarted simulation. See the :doc:`read restart
<read_restart>` command for info on how to re-specify a fix in an
input script that reads a restart file, so that the operation of the
fix continues in an uninterrupted fashion.
The :doc:`fix modify <fix_modify>` *energy* option is supported by this
fix to add the energy stored in the per-atom springs to the system's
potential energy as part of :doc:`thermodynamic output <thermo_style>`.
The :doc:`fix modify <fix_modify>` *energy* option is supported by
this fix to add the energy stored in the per-atom springs to the
system's potential energy as part of :doc:`thermodynamic output
<thermo_style>`.
This fix computes a global scalar and a global vector quantities which
can be accessed by various :doc:`output commands <Howto_output>`. The
scalar is an energy which is the sum of the spring energy for each
atom, where the per-atom energy is 0.5 \* k \* r\^2. The vector has 2
positions, the first one is the coupling parameter lambda and the
second one is the time derivative of lambda. The scalar and vector
values calculated by this fix are "extensive".
atom, where the per-atom energy is 0.5 \* k \* r\^2. The vector stores
2 values. The first value is the coupling parameter lambda. The
second value is the derivative of lambda with respect to the integer
timestep *s*, i.e. d lambda / ds. In order to obtain d lambda / dt,
where t is simulation time, this 2nd value needs to be divided by the
timestep size (e.g. 0.5 fs). The scalar and vector values calculated
by this fix are "extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.