replace CR-LF with LF
This commit is contained in:
Axel Kohlmeyer
@ -1,143 +1,143 @@
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.. index:: fix efield/lepton
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.. index:: fix efield/lepton
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fix efield/lepton command
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fix efield/lepton command
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=========================
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=========================
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Syntax
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Syntax
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""""""
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""""""
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.. code-block:: LAMMPS
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.. code-block:: LAMMPS
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fix ID group-ID efield/lepton V ...
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fix ID group-ID efield/lepton V ...
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* ID, group-ID are documented in the :doc:`fix <fix>` command
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* ID, group-ID are documented in the :doc:`fix <fix>` command
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* style = *efield/lepton*
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* style = *efield/lepton*
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* V = electric potential (electric field * distance units)
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* V = electric potential (electric field * distance units)
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* V must be a Lepton expression (see below)
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* V must be a Lepton expression (see below)
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* zero or more keyword/value pairs may be appended to args
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* zero or more keyword/value pairs may be appended to args
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* keyword = *region* or *step*
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* keyword = *region* or *step*
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.. parsed-literal::
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.. parsed-literal::
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*region* value = region-ID
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*region* value = region-ID
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region-ID = ID of region atoms must be in to have effect
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region-ID = ID of region atoms must be in to have effect
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*step* value = h
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*step* value = h
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h = step size for numerical differentiation (distance units)
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h = step size for numerical differentiation (distance units)
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Examples
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Examples
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""""""""
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""""""""
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.. code-block:: LAMMPS
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.. code-block:: LAMMPS
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fix ex all efield/lepton "-E*x; E=1"
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fix ex all efield/lepton "-E*x; E=1"
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fix dexx all efield/lepton "-0.5*x^2" step 1
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fix dexx all efield/lepton "-0.5*x^2" step 1
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fix yukawa all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1" step 1e-6
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fix yukawa all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1" step 1e-6
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fix infp all efield/lepton "-abs(x)" step 1
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fix infp all efield/lepton "-abs(x)" step 1
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variable th equal 2*PI*ramp(0,1)
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variable th equal 2*PI*ramp(0,1)
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fix erot all efield/lepton "-(x*cos(v_th)+y*sin(v_th))"
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fix erot all efield/lepton "-(x*cos(v_th)+y*sin(v_th))"
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Description
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Description
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"""""""""""
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"""""""""""
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.. versionadded:: TBD
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.. versionadded:: TBD
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Add an electric potential :math:`V` that applies to a group of charged atoms a force :math:`\vec{F} = q \vec{E}`,
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Add an electric potential :math:`V` that applies to a group of charged atoms a force :math:`\vec{F} = q \vec{E}`,
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and to dipoles a force :math:`\vec{F} = (\vec{p} \cdot \nabla) \vec{E}` and torque :math:`\vec{T} = \vec{p} \times \vec{E}`,
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and to dipoles a force :math:`\vec{F} = (\vec{p} \cdot \nabla) \vec{E}` and torque :math:`\vec{T} = \vec{p} \times \vec{E}`,
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where :math:`\vec{E} = - \nabla V`. The fix also evaluates the electrostatic energy (:math:`U_{q} = q V` and :math:`U_{p} = - \vec{p} \cdot \vec{E}`)
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where :math:`\vec{E} = - \nabla V`. The fix also evaluates the electrostatic energy (:math:`U_{q} = q V` and :math:`U_{p} = - \vec{p} \cdot \vec{E}`)
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due to this potential when the :doc:`fix_modify energy yes <fix_modify>` command is specified (see below).
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due to this potential when the :doc:`fix_modify energy yes <fix_modify>` command is specified (see below).
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.. note::
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.. note::
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This command should be used instead of :doc:`fix efield <fix_efield>` if you want to impose a non-uniform electric field on a system with dipoles
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This command should be used instead of :doc:`fix efield <fix_efield>` if you want to impose a non-uniform electric field on a system with dipoles
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since the latter does not include the dipole force term. If you only have charges or if the electric field gradient is negligible,
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since the latter does not include the dipole force term. If you only have charges or if the electric field gradient is negligible,
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:doc:`fix efield <fix_efield>` should be used since it is faster.
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:doc:`fix efield <fix_efield>` should be used since it is faster.
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The `Lepton library <https://simtk.org/projects/lepton>`_, that the *efield/lepton* fix style interfaces with, evaluates
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The `Lepton library <https://simtk.org/projects/lepton>`_, that the *efield/lepton* fix style interfaces with, evaluates
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the expression string at run time to compute the energy, forces, and torques. It creates an analytical representation
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the expression string at run time to compute the energy, forces, and torques. It creates an analytical representation
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of :math:`V` and :math:`\vec{E}`, while the gradient force is computed using a central difference scheme
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of :math:`V` and :math:`\vec{E}`, while the gradient force is computed using a central difference scheme
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.. math::
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.. math::
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\vec{F} = \frac{|\vec{p}|}{2h} \left[ \vec{E}(\vec{x} + h \hat{p}) - \vec{E}(\vec{x} - h \hat{p}) \right] .
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\vec{F} = \frac{|\vec{p}|}{2h} \left[ \vec{E}(\vec{x} + h \hat{p}) - \vec{E}(\vec{x} - h \hat{p}) \right] .
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The Lepton expression must be either enclosed in quotes or must not contain any whitespace so that LAMMPS
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The Lepton expression must be either enclosed in quotes or must not contain any whitespace so that LAMMPS
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recognizes it as a single keyword. More on valid Lepton expressions below. The final Lepton expression must
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recognizes it as a single keyword. More on valid Lepton expressions below. The final Lepton expression must
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be a function of only :math:`x, y, z`, which refer to the current *unwrapped* coordinates of the atoms to ensure continuity.
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be a function of only :math:`x, y, z`, which refer to the current *unwrapped* coordinates of the atoms to ensure continuity.
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Special care must be taken when using this fix with periodic boundary conditions or box-changing commands.
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Special care must be taken when using this fix with periodic boundary conditions or box-changing commands.
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----------
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----------
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.. include:: lepton_expression.rst
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.. include:: lepton_expression.rst
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----------
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----------
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If the *region* keyword is used, the atom must also be in the specified
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If the *region* keyword is used, the atom must also be in the specified
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geometric :doc:`region <region>` in order to be affected by the potential.
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geometric :doc:`region <region>` in order to be affected by the potential.
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The *step* keyword is required when :doc:`atom_style dipole <atom_style>` is used and the electric field is non-uniform.
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The *step* keyword is required when :doc:`atom_style dipole <atom_style>` is used and the electric field is non-uniform.
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----------
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files
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No information about this fix is written to :doc:`binary restart files
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<restart>`.
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<restart>`.
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The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
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The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
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fix to add the potential energy defined above to the global potential energy
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fix to add the potential energy defined above to the global potential energy
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of the system as part of :doc:`thermodynamic output <thermo_style>`.
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of the system as part of :doc:`thermodynamic output <thermo_style>`.
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The default setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
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The default setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
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The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
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The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
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fix to add the contribution due to the added ***forces*** on charges and dipoles
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fix to add the contribution due to the added ***forces*** on charges and dipoles
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to both the global pressure and per-atom stress of the system via the
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to both the global pressure and per-atom stress of the system via the
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:doc:`compute pressure <compute_pressure>` and :doc:`compute stress/atom
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:doc:`compute pressure <compute_pressure>` and :doc:`compute stress/atom
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<compute_stress_atom>` commands. The former can be accessed by
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<compute_stress_atom>` commands. The former can be accessed by
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:doc:`thermodynamic output <thermo_style>`. The default setting for
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:doc:`thermodynamic output <thermo_style>`. The default setting for
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this fix is :doc:`fix_modify virial no <fix_modify>`.
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this fix is :doc:`fix_modify virial no <fix_modify>`.
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The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
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The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
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fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
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fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
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integrator the fix adding its forces. Default is the outermost level.
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integrator the fix adding its forces. Default is the outermost level.
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This fix computes a global scalar and a global 3-vector of forces,
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This fix computes a global scalar and a global 3-vector of forces,
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which can be accessed by various :doc:`output commands <Howto_output>`.
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which can be accessed by various :doc:`output commands <Howto_output>`.
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The scalar is the potential energy discussed above.
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The scalar is the potential energy discussed above.
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The vector is the total force added to the group of atoms.
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The vector is the total force added to the group of atoms.
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The scalar and vector values calculated by this fix are "extensive".
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The scalar and vector values calculated by this fix are "extensive".
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This fix cannot be used with the *start/stop* keywords of
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This fix cannot be used with the *start/stop* keywords of
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the :doc:`run <run>` command.
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the :doc:`run <run>` command.
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The forces due to this fix are imposed during an energy minimization,
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The forces due to this fix are imposed during an energy minimization,
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invoked by the :doc:`minimize <minimize>` command. You should not
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invoked by the :doc:`minimize <minimize>` command. You should not
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specify force components with a variable that has time-dependence for
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specify force components with a variable that has time-dependence for
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use with a minimizer, since the minimizer increments the timestep as
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use with a minimizer, since the minimizer increments the timestep as
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the iteration count during the minimization.
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the iteration count during the minimization.
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.. note::
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.. note::
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If you want the electric potential energy to be included in the
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If you want the electric potential energy to be included in the
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total potential energy of the system (the quantity being minimized),
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total potential energy of the system (the quantity being minimized),
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you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for this fix.
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you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for this fix.
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----------
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----------
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Restrictions
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Restrictions
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""""""""""""
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""""""""""""
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Fix style *efield/lepton* is part of the LEPTON package. It is only enabled if LAMMPS was built with that package.
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Fix style *efield/lepton* is part of the LEPTON package. It is only enabled if LAMMPS was built with that package.
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See the :doc:`Build package <Build_package>` page for more info.
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See the :doc:`Build package <Build_package>` page for more info.
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Related commands
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Related commands
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""""""""""""""""
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""""""""""""""""
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:doc:`fix efield <fix_efield>`
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:doc:`fix efield <fix_efield>`
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Default
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Default
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"""""""
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"""""""
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none
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none
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@ -1,50 +1,50 @@
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# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions)
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# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions)
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units lj
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units lj
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atom_style hybrid sphere dipole
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atom_style hybrid sphere dipole
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dimension 3
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dimension 3
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boundary s s s
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boundary s s s
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region box block -2 2 -2 2 -2 2
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region box block -2 2 -2 2 -2 2
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create_box 1 box
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create_box 1 box
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create_atoms 1 random 100 12345 NULL
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create_atoms 1 random 100 12345 NULL
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# need both mass settings due to hybrid atom style
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# need both mass settings due to hybrid atom style
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mass 1 1.0
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mass 1 1.0
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set group all mass 1.0
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set group all mass 1.0
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set group all diameter 0.1
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set group all diameter 0.1
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set group all dipole/random 98934 0.01
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set group all dipole/random 98934 0.01
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pair_style none
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pair_style none
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comm_modify cutoff 3.0
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comm_modify cutoff 3.0
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velocity all create 0.0 87287 mom yes rot yes
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velocity all create 0.0 87287 mom yes rot yes
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fix 1 all nve/sphere update dipole
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fix 1 all nve/sphere update dipole
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###############################################################################################################
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###############################################################################################################
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## Yukawa potential
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## Yukawa potential
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#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8
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#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8
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## Gradually increasing uniform field
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## Gradually increasing uniform field
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#variable E equal ramp(0,1)
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#variable E equal ramp(0,1)
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#fix 2 all efield/lepton "-v_E*(x+y+z)"
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#fix 2 all efield/lepton "-v_E*(x+y+z)"
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## Linear gradient field
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## Linear gradient field
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fix 2 all efield/lepton "-1/6*x^3" step 1e-6
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fix 2 all efield/lepton "-1/6*x^3" step 1e-6
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fix_modify 2 energy yes
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fix_modify 2 energy yes
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###############################################################################################################
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###############################################################################################################
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timestep 1e-3
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timestep 1e-3
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compute erot all erotate/sphere
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compute erot all erotate/sphere
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variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot
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variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot
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thermo_style custom step temp ke c_erot pe v_etotal
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thermo_style custom step temp ke c_erot pe v_etotal
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thermo 500
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thermo 500
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thermo_modify norm no
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thermo_modify norm no
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#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz
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#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz
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run 10000
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run 10000
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Reference in New Issue
Block a user