1.. index:: fix wall/ees 2.. index:: fix wall/region/ees 3 4fix wall/ees command 5==================== 6 7fix wall/region/ees command 8=========================== 9 10Syntax 11"""""" 12 13.. parsed-literal:: 14 15 fix ID group-ID style args 16 17* ID, group-ID are documented in :doc:`fix <fix>` command 18* style = *wall/ees* or *wall/region/ees* 19 20 .. parsed-literal:: 21 22 args for style *wall/ees*\ : one or more *face parameters* groups may be appended 23 face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi* 24 parameters = coord epsilon sigma cutoff 25 coord = position of wall = EDGE or constant or variable 26 EDGE = current lo or hi edge of simulation box 27 constant = number like 0.0 or -30.0 (distance units) 28 variable = :doc:`equal-style variable <variable>` like v_x or v_wiggle 29 epsilon = strength factor for wall-particle interaction (energy or energy/distance\^2 units) 30 epsilon can be a variable (see below) 31 sigma = size factor for wall-particle interaction (distance units) 32 sigma can be a variable (see below) 33 cutoff = distance from wall at which wall-particle interaction is cut off (distance units) 34 35 .. parsed-literal:: 36 37 args for style *wall/region/ees*\ : *region-ID* *epsilon* *sigma* *cutoff* 38 region-ID = region whose boundary will act as wall 39 epsilon = strength factor for wall-particle interaction (energy or energy/distance\^2 units) 40 sigma = size factor for wall-particle interaction (distance units) 41 cutoff = distance from wall at which wall-particle interaction is cut off (distance units) 42 43Examples 44"""""""" 45 46.. code-block:: LAMMPS 47 48 fix wallhi all wall/ees xlo -1.0 1.0 1.0 2.5 units box 49 fix wallhi all wall/ees xhi EDGE 1.0 1.0 2.5 50 fix wallhi all wall/ees v_wiggle 23.2 1.0 1.0 2.5 51 fix zwalls all wall/ees zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 52 53 fix ees_cube all wall/region/ees myCube 1.0 1.0 2.5 54 55Description 56""""""""""" 57 58Fix *wall/ees* bounds the simulation domain on one or more of its 59faces with a flat wall that interacts with the ellipsoidal atoms in 60the group by generating a force on the atom in a direction 61perpendicular to the wall and a torque parallel with the wall. The 62energy of wall-particle interactions E is given by: 63 64.. math:: 65 66 E = \epsilon \left[ \frac{2 \sigma_{LJ}^{12} \left(7 r^5+14 r^3 67 \sigma_{n}^2+3 r \sigma_{n}^4\right) }{945 68 \left(r^2-\sigma_{n}^2\right)^7} -\frac{ \sigma_{LJ}^6 \left(2 r 69 \sigma_{n}^3+\sigma_{n}^2 \left(r^2-\sigma_{n}^2\right)\log{ 70 \left[\frac{r-\sigma_{n}}{r+\sigma_{n}}\right]}\right) }{12 71 \sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n 72 < r < r_c 73 74Introduced by Babadi and Ejtehadi in :ref:`(Babadi) 75<BabadiEjtehadi>`. Here, *r* is the distance from the particle to the 76wall at position *coord*, and Rc is the *cutoff* distance at which 77the particle and wall no longer interact. Also, :math:`\sigma_n` is 78the distance between center of ellipsoid and the nearest point of its 79surface to the wall as shown below. 80 81.. image:: JPG/fix_wall_ees_image.jpg 82 :align: center 83 84Details of using this command and specifications are the same as 85fix/wall command. You can also find an example in USER/ees/ under 86examples/ directory. 87 88The prefactor :math:`\epsilon` can be thought of as an 89effective Hamaker constant with energy units for the strength of the 90ellipsoid-wall interaction. More specifically, the :math:`\epsilon` 91pre-factor is 92 93.. math:: 94 95 8 \pi^2 \quad \rho_{wall} \quad \rho_{ellipsoid} \quad \epsilon 96 \quad \sigma_a \quad \sigma_b \quad \sigma_c 97 98where :math:`\epsilon` is the LJ energy parameter for the constituent 99LJ particles and :math:`\sigma_a`, :math:`\sigma_b`, and 100:math:`\sigma_c` are the radii of the ellipsoidal 101particles. :math:`\rho_{wall}` and :math:`\rho_{ellipsoid}` are the 102number density of the constituent particles, in the wall and ellipsoid 103respectively, in units of 1/volume. 104 105.. note:: 106 107 You must insure that r is always bigger than :math:`\sigma_n` for 108 all particles in the group, or LAMMPS will generate an error. This 109 means you cannot start your simulation with particles touching the wall 110 position *coord* (:math:`r = \sigma_n`) or with particles penetrating 111 the wall (:math:`0 =< r < \sigma_n`) or with particles on the wrong 112 side of the wall (:math:`r < 0`). 113 114Fix *wall/region/ees* treats the surface of the geometric region defined 115by the *region-ID* as a bounding wall which interacts with nearby 116ellipsoidal particles according to the EES potential introduced above. 117 118Other details of this command are the same as for the :doc:`fix 119wall/region <fix_wall_region>` command. One may also find an example 120of using this fix in the examples/PACKAGES/ees/ directory. 121 122---------- 123 124Restart, fix_modify, output, run start/stop, minimize info 125""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 126 127No information about these fixes are written to :doc:`binary restart 128files <restart>`. 129 130The :doc:`fix_modify <fix_modify>` *energy* option is supported by 131these fixes to add the energy of interaction between atoms and all the 132specified walls or region wall to the global potential energy of the 133system as part of :doc:`thermodynamic output <thermo_style>`. The 134default settings for these fixes are :doc:`fix_modify energy no 135<fix_modify>`. 136 137The :doc:`fix_modify <fix_modify>` *respa* option is supported by 138these fixes. This allows to set at which level of the :doc:`r-RESPA 139<run_style>` integrator the fix is adding its forces. Default is the 140outermost level. 141 142These fixes computes a global scalar and a global vector of forces, 143which can be accessed by various :doc:`output commands 144<Howto_output>`. See the :doc:`fix wall <fix_wall>` command for a 145description of the scalar and vector. 146 147No parameter of these fixes can be used with the *start/stop* keywords of 148the :doc:`run <run>` command. 149 150The forces due to these fixes are imposed during an energy 151minimization, invoked by the :doc:`minimize <minimize>` command. 152 153.. note:: 154 155 If you want the atom/wall interaction energy to be included in 156 the total potential energy of the system (the quantity being 157 minimized), you MUST enable the :doc:`fix_modify <fix_modify>` *energy* 158 option for this fix. 159 160Restrictions 161"""""""""""" 162 163These fixes are part of the EXTRA-FIX package. They are only enabled 164if LAMMPS was built with that package. See the :doc:`Build package 165<Build_package>` page for more info. 166 167These fixes requires that atoms be ellipsoids as defined by the 168:doc:`atom_style ellipsoid <atom_style>` command. 169 170Related commands 171"""""""""""""""" 172 173:doc:`fix wall <fix_wall>`, 174:doc:`pair resquared <pair_resquared>` 175 176Default 177""""""" 178 179none 180 181---------- 182 183.. _BabadiEjtehadi: 184 185**(Babadi)** Babadi and Ejtehadi, EPL, 77 (2007) 23002. 186