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one more doc fix

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2021-04-23 20:09:41 +02:00
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doc/src/pair_dpd_ext.rst
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@ -1,9 +1,10 @@
.. index:: pair_style dpdext
.. index:: pair_style dpd/ext
.. index:: pair_style dpd/ext/tstat
pair_style dpdext command
pair_style dpd/ext command
==========================
pair_style dpdext/tstat command
pair_style dpd/ext/tstat command
================================
Syntax
@ -12,8 +13,8 @@ Syntax
.. code-block:: LAMMPS
pair_style dpdext T cutoff seed
pair_style dpdext/tstat Tstart Tstop cutoff seed
pair_style dpd/ext T cutoff seed
pair_style dpd/ext/tstat Tstart Tstop cutoff seed
* T = temperature (temperature units)
* Tstart,Tstop = desired temperature at start/end of run (temperature units)
@ -26,22 +27,22 @@ Examples
.. code-block:: LAMMPS
pair_style dpdext 1.0 2.5 34387
pair_style dpd/ext 1.0 2.5 34387
pair_coeff 1 1 25.0 4.5 4.5 0.5 0.5 1.2
pair_coeff 1 2 40.0 4.5 4.5 0.5 0.5 1.2
pair_style dpdext/tstat 1.0 1.0 2.5 34387
pair_style dpd/ext/tstat 1.0 1.0 2.5 34387
pair_coeff 1 1 4.5 4.5 0.5 0.5 1.2
pair_coeff 1 2 4.5 4.5 0.5 0.5 1.2
Description
"""""""""""
The style *dpdext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) <Groot>`, :ref:`(Junghans) <Junghans>`.
The style *dpd/ext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) <Groot>`, :ref:`(Junghans) <Junghans>`.
Style *dpdext/tstat* invokes an extended DPD thermostat on pairwise interactions, which is equivalent to the non-conservative portion of the extended DPD force field. To use *dpdext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay <pair_hybrid>` command to compute both the desired pair interaction and the thermostat for each pair of particles.
Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise interactions, equivalent to the non-conservative portion of the extended DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay <pair_hybrid>` command to compute both the desired pair interaction and the thermostat for each pair of particles.
For the style *dpdext*\ , the force on atom I due to atom J is given as a sum
For the style *dpd/ext*\ , the force on atom I due to atom J is given as a sum
of 3 terms
.. math::
@ -54,15 +55,15 @@ of 3 terms
where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command.
For the style *dpdext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop.
For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop.
For the style *dpdext*\ , the pairwise energy associated with style *dpdext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. For style *dpdext/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial.
For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial.
For the style *dpdext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop.
For the style *dpd/ext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop.
For the style *dpdext*\ , the pairwise energy associated with style *dpdext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. For style *dpdext/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial.
For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial.
For the style *dpdext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in the examples above:
For the style *dpd/ext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in the examples above:
* A (force units)
* :math:`\gamma_{\perp}` (force/velocity units)
@ -74,7 +75,7 @@ For the style *dpdext*, the following coefficients must be defined for each pair
The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style <pair_style>` command so it does not need to be specified.
For the style *dpdext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command is the same, except that A is not included.
For the style *dpd/ext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command is the same, except that A is not included.
.. note::
@ -89,17 +90,17 @@ For the style *dpdext/tstat*, the coefficients defined for each pair of atoms ty
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
The style *dpdext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly.
The style *dpd/ext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly.
The pair styles do not support the :doc:`pair_modify <pair_modify>` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`.
The :doc:`pair_modify <pair_modify>` table option is not relevant for the style *dpdext*.
The :doc:`pair_modify <pair_modify>` table option is not relevant for the style *dpd/ext*.
The style *dpdext* does not support the :doc:`pair_modify <pair_modify>` tail option for adding long-range tail corrections to energy and pressure.
The style *dpd/ext* does not support the :doc:`pair_modify <pair_modify>` tail option for adding long-range tail corrections to energy and pressure.
The pair styles can only be used via the pair keyword of the :doc:`run_style respa <run_style>` command. They do not support the *inner*\ , *middle*\ , and *outer*\ keywords.
The style *dpdext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run <run>` command. See the :doc:`run <run>` command for details of how to do this.
The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run <run>` command. See the :doc:`run <run>` command for details of how to do this.
----------
@ -107,7 +108,7 @@ The style *dpdext/tstat* can ramp its target temperature over multiple runs, usi
Restrictions
""""""""""""
The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify <neigh_modify>` command). This may be too infrequent for style *dpdext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change.
The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify <neigh_modify>` command). This may be too infrequent for style *dpd/ext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change.
The pair styles require to use the :doc:`comm_modify vel yes <comm_modify>` command so that velocities are stored by ghost atoms.