diff --git a/doc/src/fix_tgnh_drude.rst b/doc/src/fix_tgnh_drude.rst index 9afb35c8f6..92781cd9e8 100644 --- a/doc/src/fix_tgnh_drude.rst +++ b/doc/src/fix_tgnh_drude.rst @@ -65,10 +65,13 @@ Examples Description """"""""""" -These commands are variants of the Nose-Hoover fix styles :doc:`fix nvt ` and :doc:`fix npt ` for thermalized Drude polarizable models. -They apply temperature-grouped Nose-Hoover thermostat (TGNH) proposed by :ref:`(Son) `. -When there are fast vibrational modes with frequencies close to Drude oscillators (e.g. double bonds or out-of-plane torsions), -this thermostat can provide better kinetic energy equipartition. +These commands are variants of the Nose-Hoover fix styles :doc:`fix nvt +` and :doc:`fix npt ` for thermalized Drude polarizable +models. They apply temperature-grouped Nose-Hoover thermostat (TGNH) +proposed by :ref:`(Son) `. When there are fast vibrational +modes with frequencies close to Drude oscillators (e.g. double bonds or +out-of-plane torsions), this thermostat can provide better kinetic +energy equipartitioning. The difference between TGNH and the original Nose-Hoover thermostat is that, TGNH separates the kinetic energy of the group into three contributions: @@ -108,8 +111,8 @@ Here :math:`N_\mathrm{mol}` and :math:`N_\mathrm{mol,sys}` are the numbers of mo not. You must therefore use the :doc:`fix drude ` command to specify the Drude status of each atom type. - Because that TGNH thermostat thermalizes the molecular COM motion, - all atoms belong to the same molecule must be in the same group. + Because the TGNH thermostat thermostats the molecular COM motion, + all atoms belonging to the same molecule must be in the same group. That is, these fixes can not be applied to a subset of a molecule. For this fix to act correctly, ghost atoms need to know their velocity. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 0563ac1499..de2065c1e3 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -533,6 +533,7 @@ cuda Cuda CUDA CuH +Cui cuFFT Cummins Curk @@ -869,6 +870,7 @@ equilibrating equilibration Equilibria equilization +equipartitioning Ercolessi Erdmann eradius @@ -3071,9 +3073,11 @@ tex tfac tfmc tfMC -th +tgnpt +tgnvt Thakkar Thaokar +th thb thei Theodorou @@ -3479,6 +3483,7 @@ Yc ycm Yeh yellowgreen +Yethiraj yflag yhi yi