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add difference part in fix pimd doc

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Yifan Li
2023-03-27 23:06:05 -04:00
parent f6d94a95dd
commit 849933a687
1 changed files with 14 additions and 2 deletions
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doc/src/fix_pimd.rst
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@ -269,13 +269,25 @@ related tasks for each of the partitions, e.g.
read_restart system_${ibead}.restart2
.. note::
Fix *pimd/langevin* dumps the Catersian coordinates, but dumps the velocities and
forces in the normal mode representation. If the Catersian velocities and forces are
Fix *pimd/langevin* dumps the Cartesian coordinates, but dumps the velocities and
forces in the normal mode representation. If the Cartesian velocities and forces are
needed, it is easy to perform the transformation when doing post-processing.
It is recommended to dump the image flags (*ix iy iz*) for fix *pimd/langevin*. It
will be useful if you want to calculate some estimators during post-processing.
Major differences of *fix pimd/nvt* and *fix pimd/langevin* are:
#. *Fix pimd/nvt* includes Cartesian pimd, normal mode pimd, and centroid md. *Fix pimd/langevin* only intends to support normal mode pimd, as it is commonly enough for thermodynamic sampling.
#. *Fix pimd/nvt* uses Nose-Hoover chain thermostat. *Fix pimd/langevin* uses Langevin thermostat.
#. *Fix pimd/langevin* provides barostat, so the npt ensemble can be sampled. *Fix pimd/nvt* only support nvt ensemble.
#. *Fix pimd/langevin* provides several quantum estimators in output.
#. *Fix pimd/langevin* allows multiple processes for each bead. For *fix pimd/nvt*, there is a large chance that multi-process tasks for each bead may fail.
#. The dump of *fix pimd/nvt* are all Cartesian. *Fix pimd/langevin* dumps normal-mode velocities and forces, and Cartesian coordinates.
Initially, the inter-replica communication and normal mode transformation parts of *fix pimd/langevin* are written based on
those of *fix pimd/nvt*, but are significantly revised.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""