diff --git a/doc/html/_sources/compute_dpd.txt b/doc/html/_sources/compute_dpd.txt index 5975dfd4c4..61241d83ee 100644 --- a/doc/html/_sources/compute_dpd.txt +++ b/doc/html/_sources/compute_dpd.txt @@ -55,8 +55,11 @@ Restrictions """""""""""" -The compute *dpd* is only available if LAMMPS is built with the -USER-DPD package and requires the :doc:`atom_style dpd `. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This command also requires use of the :doc:`atom_style dpd ` +command. Related commands """""""""""""""" diff --git a/doc/html/_sources/compute_dpd_atom.txt b/doc/html/_sources/compute_dpd_atom.txt index ba36cfacbe..b3919f67e2 100644 --- a/doc/html/_sources/compute_dpd_atom.txt +++ b/doc/html/_sources/compute_dpd_atom.txt @@ -46,8 +46,11 @@ Restrictions """""""""""" -The compute *dpd/atom* is only available if LAMMPS is built with the -USER-DPD package. +This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This command also requires use of the :doc:`atom_style dpd ` +command. Related commands """""""""""""""" diff --git a/doc/html/_sources/fix.txt b/doc/html/_sources/fix.txt index 9259c93f07..e27a3b2b96 100644 --- a/doc/html/_sources/fix.txt +++ b/doc/html/_sources/fix.txt @@ -186,6 +186,7 @@ of :ref:`this page `. * :doc:`drag ` - drag atoms towards a defined coordinate * :doc:`dt/reset ` - reset the timestep based on velocity, forces * :doc:`efield ` - impose electric field on system +* :doc:`ehex ` - ehanced heat exchange algorithm * :doc:`enforce2d ` - zero out z-dimension velocity and force * :doc:`evaporate ` - remove atoms from simulation periodically * :doc:`external ` - callback to an external driver program diff --git a/doc/html/_sources/fix_ehex.txt b/doc/html/_sources/fix_ehex.txt index 7e94b40341..b2278c9c80 100644 --- a/doc/html/_sources/fix_ehex.txt +++ b/doc/html/_sources/fix_ehex.txt @@ -71,69 +71,33 @@ hundred (LJ and SPC/E water) with little computational overhead. In both algorithms (non-translational) kinetic energy is constantly swapped between regions (reservoirs) to impose a heat flux onto the system. The equations of motion are therefore modified if a particle -*i* is located inside a reservoir - -.. image:: Eqs/fix_ehex01.jpg - :align: center - -where - -.. image:: Eqs/fix_ehex02.jpg - :align: center - -We use - -.. image:: Eqs/fix_ehex03.jpg - :align: center - -to label those parts of the simulation box which are not -thermostatted.) The input parameter *region-ID* of this fix -corresponds to *k*\ . The energy swap is modelled by introducing an +:math:`i` is located inside a reservoir :math:`\Gamma_\ *k*\` where :math:`k>0`. We +use :math:`\Gamma_\ *0*\` to label those parts of the simulation box which +are not thermostatted.) The input parameter *region-ID* of this fix +corresponds to :math:`k`. The energy swap is modelled by introducing an additional thermostatting force to the equations of motion, such that -the time evolution of coordinates and momenta of particle *i* becomes -:ref:`(Wirnsberger) ` +the time evolution of coordinates and momenta of particle :math:`i` +becomes :ref:`(Wirnsberger) ` -.. image:: Eqs/fix_ehex04.jpg +.. image:: src/Eqs/fix_ehex_eom.jpg :align: center The thermostatting force is given by -.. image:: Eqs/fix_ehex05.jpg +.. image:: src/Eqs/fix_ehex_f.jpg :align: center -where - -.. image:: Eqs/fix_ehex06.jpg - :align: center - -is the mass and - -.. image:: Eqs/fix_ehex07.jpg - :align: center - -maps the particle position to the respective reservoir. The quantity - -.. image:: Eqs/fix_ehex08.jpg - :align: center - -corresponds to the input parameter *F*\ , which is the energy flux into -the reservoir. Furthermore, - -.. image:: Eqs/fix_ehex09.jpg - :align: center - -and - -.. image:: Eqs/fix_ehex10.jpg - :align: center - -denote the non-translational kinetic -energy and the centre of mass velocity of that reservoir. The -thermostatting force does not affect the centre of mass velocities of -the individual reservoirs and the entire simulation box. A derivation -of the equations and details on the numerical implementation with -velocity Verlet in LAMMPS can be found in reference -"(Wirnsberger)"#_Wirnsberger. +where :math:`m_i` is the mass and :math:`k(\mathbf r_i)` maps the particle +position to the respective reservoir. The quantity +:math:`F_*\Gamma_*k(\mathbf r_i)**` corresponds to the input parameter +*F*\ , which is the energy flux into the reservoir. Furthermore, +:math:`K_*\Gamma_*k(\mathbf r_i)**` and :math:`v_*\Gamma_*k(\mathbf r_i)**` +denote the non-translational kinetic energy and the centre of mass +velocity of that reservoir. The thermostatting force does not affect +the centre of mass velocities of the individual reservoirs and the +entire simulation box. A derivation of the equations and details on +the numerical implementation with velocity Verlet in LAMMPS can be +found in reference "(Wirnsberger)"#_Wirnsberger. .. note:: @@ -193,7 +157,7 @@ constraints will be satisfied. bond distances, which goes to zero with order three in the timestep. For example, in a simulation of SPC/E water with a timestep of 2 fs the maximum relative error in the bond distances was found to - be on the order of :c,image(Eqs/fix_ehex07.jpg) for relatively large + be on the order of :math:`10^\ *-7*\` for relatively large temperature gradients. A higher precision can be achieved by decreasing the timestep. @@ -220,8 +184,7 @@ was built with that package. See the :ref:`Making LAMMPS ` section for Related commands """""""""""""""" -:doc:`fix heat `, :doc:`fix thermal/conductivity `, -:doc:`compute temp `, :doc:`compute temp/region ` +:doc:`fix heat `, :doc:`fix thermal/conductivity `, :doc:`compute temp `, :doc:`compute temp/region ` **Default:** none diff --git a/doc/html/compute_dpd.html b/doc/html/compute_dpd.html index 2fecd4eef0..d65587a9aa 100644 --- a/doc/html/compute_dpd.html +++ b/doc/html/compute_dpd.html @@ -164,8 +164,10 @@ output options.

Restrictions

-

The compute dpd is only available if LAMMPS is built with the -USER-DPD package and requires the atom_style dpd.

+

This command is part of the USER-DPD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS section for more info.

+

This command also requires use of the atom_style dpd +command.