ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Updated doc/src/fix_pimdb.rst

Browse Source
This commit is contained in:
ofirblumer
2025-01-15 11:43:32 +02:00
parent 1b79f34b22
commit 2a9a1aeeab
2 changed files with 9 additions and 3 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
doc/src/fix_pimd.rst
View File

@ -419,6 +419,9 @@ Default
The keyword defaults for fix *pimd/nvt* are method = pimd, fmass = 1.0, sp
= 1.0, temp = 300.0, and nhc = 2.
The keyord defaults for fix *pimd/langevin* are integrator = obabo, method = nmpimd, ensemble = nvt, fmmode = physical, fmass = 1.0,
scale = 1, temp = 298.15, thermostat = PILE_L, tau = 1.0, iso = 1.0, taup = 1.0, barostat = BZP, fixcom = yes, and lj = 1 for all its arguments.
----------
.. _Feynman:

9
doc/src/fix_pimdb.rst
View File

@ -84,9 +84,9 @@ distinguishable particles. The sum is over all permutations :math:`\sigma`. Reca
.. math::
E^\sigma = \frac{mP}{2\beta^2 \hbar^2} \sum_{\ell=1}^N \sum_{j=1}^P \left(\bf{q}_\ell^j - \bf{q}_\ell^{j+1}\right)^2,
E^\sigma = \frac{mP}{2\beta^2 \hbar^2} \sum_{\ell=1}^N \sum_{j=1}^P \left(\mathbf{q}_\ell^j - \mathbf{q}_\ell^{j+1}\right)^2,
where :math:`P` is the number of beads and :math:`\bf{q}_\ell^{P+1}=\bf{q}_{\sigma(\ell)}^1.`
where :math:`P` is the number of beads and :math:`\mathbf{q}_\ell^{P+1}=\mathbf{q}_{\sigma(\ell)}^1.`
Hirshberg et. al. showed that the ring polymer potential
:math:`-\frac{1}{\beta}\textrm{ln}\left[ \frac{1}{N!} \sum_\sigma e ^ { -\beta E^\sigma } \right]`, which scales exponentially with :math:`N`,
@ -129,9 +129,10 @@ can be accessed by various :doc:`output commands <Howto_output>`. The quantities
#. potential energy of the bead,
#. total energy of all beads (conserved if *ensemble* is *nve*)
#. primitive kinetic energy estimator :ref:`(Hirshberg1) <Hirshberg>`
#. virial energy estimator :ref:`(Herman) <HermanBB>`.
#. virial energy estimator :ref:`(Herman) <HermanBB>` (see the justification in the supporting information of :ref:`(Hirshberg2) <HirshbergInvernizzi>`).
The first three are different for different log files, and the others are the same for different log files.
All vector values calculated by fix *pimdb/langevin* are "extensive".
Restrictions
""""""""""""
@ -148,6 +149,8 @@ Default
The keyword defaults for fix *pimdb/nvt* are method = pimd, fmass = 1.0, sp
= 1.0, temp = 300.0, and nhc = 2.
The keyord defaults for fix *pimdb/langevin* are integrator = obabo, method = pimd, ensemble = nvt, fmass = 1.0,
temp = 298.15, thermostat = PILE_L, tau = 1.0, fixcom = yes, and lj = 1 for all its arguments.
----------
.. _book-Tuckerman: