From 2a9a1aeeabe6665799286228cc5d14937935108f Mon Sep 17 00:00:00 2001 From: ofirblumer Date: Wed, 15 Jan 2025 11:43:32 +0200 Subject: [PATCH] Updated doc/src/fix_pimdb.rst --- doc/src/fix_pimd.rst | 3 +++ doc/src/fix_pimdb.rst | 9 ++++++--- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index 09b6552adc..d56dd6cfae 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -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: diff --git a/doc/src/fix_pimdb.rst b/doc/src/fix_pimdb.rst index df4ddaf5b5..55f3016b81 100644 --- a/doc/src/fix_pimdb.rst +++ b/doc/src/fix_pimdb.rst @@ -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 `. The quantities #. potential energy of the bead, #. total energy of all beads (conserved if *ensemble* is *nve*) #. primitive kinetic energy estimator :ref:`(Hirshberg1) ` - #. virial energy estimator :ref:`(Herman) `. + #. virial energy estimator :ref:`(Herman) ` (see the justification in the supporting information of :ref:`(Hirshberg2) `). 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: