Name change, add example
This commit is contained in:
Gabriel Alkuino
@ -58,6 +58,7 @@ OPT.
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* :doc:`dt/reset (k) <fix_dt_reset>`
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* :doc:`dt/reset (k) <fix_dt_reset>`
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* :doc:`edpd/source <fix_dpd_source>`
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* :doc:`edpd/source <fix_dpd_source>`
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* :doc:`efield (k) <fix_efield>`
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* :doc:`efield (k) <fix_efield>`
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* :doc:`efield/lepton <fix_efield_lepton>`
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* :doc:`efield/tip4p <fix_efield>`
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* :doc:`efield/tip4p <fix_efield>`
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* :doc:`ehex <fix_ehex>`
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* :doc:`ehex <fix_ehex>`
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* :doc:`electrode/conp (i) <fix_electrode>`
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* :doc:`electrode/conp (i) <fix_electrode>`
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@ -69,7 +70,6 @@ OPT.
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* :doc:`eos/cv <fix_eos_cv>`
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* :doc:`eos/cv <fix_eos_cv>`
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* :doc:`eos/table <fix_eos_table>`
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* :doc:`eos/table <fix_eos_table>`
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* :doc:`eos/table/rx (k) <fix_eos_table_rx>`
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* :doc:`eos/table/rx (k) <fix_eos_table_rx>`
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* :doc:`epot/lepton <fix_epot_lepton>`
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* :doc:`evaporate <fix_evaporate>`
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* :doc:`evaporate <fix_evaporate>`
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* :doc:`external <fix_external>`
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* :doc:`external <fix_external>`
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* :doc:`ffl <fix_ffl>`
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* :doc:`ffl <fix_ffl>`
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@ -237,6 +237,7 @@ accelerated styles exist.
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* :doc:`dt/reset <fix_dt_reset>` - reset the timestep based on velocity, forces
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* :doc:`dt/reset <fix_dt_reset>` - reset the timestep based on velocity, forces
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* :doc:`edpd/source <fix_dpd_source>` - add heat source to eDPD simulations
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* :doc:`edpd/source <fix_dpd_source>` - add heat source to eDPD simulations
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* :doc:`efield <fix_efield>` - impose electric field on system
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* :doc:`efield <fix_efield>` - impose electric field on system
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* :doc:`efield/lepton <fix_efield_lepton>` - impose electric field on system using a Lepton expression for the potential
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* :doc:`efield/tip4p <fix_efield>` - impose electric field on system with TIP4P molecules
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* :doc:`efield/tip4p <fix_efield>` - impose electric field on system with TIP4P molecules
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* :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
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* :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
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* :doc:`electrode/conp <fix_electrode>` - impose electric potential
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* :doc:`electrode/conp <fix_electrode>` - impose electric potential
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@ -248,7 +249,6 @@ accelerated styles exist.
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* :doc:`eos/cv <fix_eos_cv>` - applies a mesoparticle equation of state to relate the particle internal energy to the particle internal temperature
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* :doc:`eos/cv <fix_eos_cv>` - applies a mesoparticle equation of state to relate the particle internal energy to the particle internal temperature
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* :doc:`eos/table <fix_eos_table>` - applies a tabulated mesoparticle equation of state to relate the particle internal energy to the particle internal temperature
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* :doc:`eos/table <fix_eos_table>` - applies a tabulated mesoparticle equation of state to relate the particle internal energy to the particle internal temperature
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* :doc:`eos/table/rx <fix_eos_table_rx>` - applies a tabulated mesoparticle equation of state to relate the concentration-dependent particle internal energy to the particle internal temperature
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* :doc:`eos/table/rx <fix_eos_table_rx>` - applies a tabulated mesoparticle equation of state to relate the concentration-dependent particle internal energy to the particle internal temperature
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* :doc:`epot/lepton <fix_epot_lepton>` - apply electric potential on system using Lepton expression
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* :doc:`evaporate <fix_evaporate>` - remove atoms from simulation periodically
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* :doc:`evaporate <fix_evaporate>` - remove atoms from simulation periodically
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* :doc:`external <fix_external>` - callback to an external driver program
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* :doc:`external <fix_external>` - callback to an external driver program
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* :doc:`ffl <fix_ffl>` - apply a Fast-Forward Langevin equation thermostat
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* :doc:`ffl <fix_ffl>` - apply a Fast-Forward Langevin equation thermostat
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@ -45,8 +45,9 @@ Description
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Add a force :math:`\vec{F} = q\vec{E}` to each charged atom in the group due to an
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Add a force :math:`\vec{F} = q\vec{E}` to each charged atom in the group due to an
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external electric field being applied to the system. If the system
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external electric field being applied to the system. If the system
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contains point-dipoles, also add a torque on the dipoles due to the
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contains point-dipoles, also add a torque :math:`\vec{T} = \vec{p} \times \vec{E}` on the dipoles due to the
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external electric field.
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external electric field. This fix does not compute the dipole force :math:`\vec{F} = (\vec{p} \cdot \nabla) \vec{E}`,
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and the :doc:`fix efield/lepton <fix_efield_lepton>` command should be used instead.
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.. versionadded:: 28Mar2023
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.. versionadded:: 28Mar2023
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@ -68,6 +69,7 @@ For point-dipoles, equal-style variables can be used, but atom-style
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variables are not currently supported, since they imply a spatial
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variables are not currently supported, since they imply a spatial
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gradient in the electric field which means additional terms with
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gradient in the electric field which means additional terms with
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gradients of the field are required for the force and torque on dipoles.
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gradients of the field are required for the force and torque on dipoles.
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The :doc:`fix efield/lepton <fix_efield_lepton>` command should be used instead.
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Equal-style variables can specify formulas with various mathematical
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Equal-style variables can specify formulas with various mathematical
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functions, and include :doc:`thermo_style <thermo_style>` command
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functions, and include :doc:`thermo_style <thermo_style>` command
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@ -229,7 +231,7 @@ Fix style *efield/tip4p* can only be used with tip4p pair styles.
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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 addforce <fix_addforce>`
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:doc:`fix addforce <fix_addforce>`, :doc:`fix efield/lepton <fix_efield_lepton>`
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Default
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Default
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"""""""
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"""""""
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@ -1,138 +1,143 @@
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.. index:: fix epot/lepton
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.. index:: fix efield/lepton
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fix epot/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 epot/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 = *epot/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 epot/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 epot/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 epot/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 epot/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 epot/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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The `Lepton library <https://simtk.org/projects/lepton>`_, that the *epot/lepton* fix style interfaces with, evaluates
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.. note::
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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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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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.. math::
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:doc:`fix efield <fix_efield>` should be used since it is faster.
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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 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 Lepton expression must be either enclosed in quotes or must not contain any whitespace so that LAMMPS
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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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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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.. math::
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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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\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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----------
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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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.. include:: lepton_expression.rst
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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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----------
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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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If the *region* keyword is used, the atom must also be in the specified
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----------
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geometric :doc:`region <region>` in order to be affected by the potential.
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.. include:: lepton_expression.rst
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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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If you only want to apply a uniform electric field, the :doc:`fix efield <fix_efield>` command will be faster.
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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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geometric :doc:`region <region>` in order to be affected by the potential.
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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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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No information about this fix is written to :doc:`binary restart files
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----------
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<restart>`.
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Restart, fix_modify, output, run start/stop, minimize info
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The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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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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No information about this fix is written to :doc:`binary restart files
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The default setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
|
<restart>`.
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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>` *energy* option is supported by this
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fix to add the contribution due to the added ***forces*** on charges and dipoles
|
fix to add the potential energy defined above to the global potential energy
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to both the global pressure and per-atom stress of the system via the
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of the system as part of :doc:`thermodynamic output <thermo_style>`.
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:doc:`compute pressure <compute_pressure>` and :doc:`compute stress/atom
|
The default setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
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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
|
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
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this fix is :doc:`fix_modify virial no <fix_modify>`.
|
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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The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
|
:doc:`compute pressure <compute_pressure>` and :doc:`compute stress/atom
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fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
|
<compute_stress_atom>` commands. The former can be accessed by
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integrator the fix adding its forces. Default is the outermost level.
|
: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 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>`.
|
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
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The scalar is the potential energy discussed above.
|
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
|
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The vector is the total force added to the group of atoms.
|
integrator the fix adding its forces. Default is the outermost level.
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The scalar and vector values calculated by this fix are "extensive".
|
|
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|
This fix computes a global scalar and a global 3-vector of forces,
|
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This fix cannot be used with the *start/stop* keywords of
|
which can be accessed by various :doc:`output commands <Howto_output>`.
|
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the :doc:`run <run>` command.
|
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 forces due to this fix are imposed during an energy minimization,
|
The scalar and vector values calculated by this fix are "extensive".
|
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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
|
This fix cannot be used with the *start/stop* keywords of
|
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use with a minimizer, since the minimizer increments the timestep as
|
the :doc:`run <run>` command.
|
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the iteration count during the minimization.
|
|
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|
The forces due to this fix are imposed during an energy minimization,
|
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.. note::
|
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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If you want the electric potential energy to be included in the
|
use with a minimizer, since the minimizer increments the timestep as
|
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total potential energy of the system (the quantity being minimized),
|
the iteration count during the minimization.
|
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you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for this fix.
|
|
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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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Restrictions
|
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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|
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Fix style *epot/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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|
Restrictions
|
||||||
|
""""""""""""
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Related commands
|
|
||||||
""""""""""""""""
|
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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:doc:`fix efield <fix_efield>`
|
|
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|
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Default
|
Related commands
|
||||||
"""""""
|
""""""""""""""""
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||||||
|
|
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none
|
:doc:`fix efield <fix_efield>`
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|
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|
Default
|
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|
"""""""
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none
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@ -1020,7 +1020,6 @@ eos
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epair
|
epair
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epcc
|
epcc
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epl
|
epl
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epot
|
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Epp
|
Epp
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Epq
|
Epq
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eps
|
eps
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49
examples/LEPTON/in.efield-lepton
Normal file
49
examples/LEPTON/in.efield-lepton
Normal file
@ -0,0 +1,49 @@
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|
# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions)
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|
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|
units lj
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|
atom_style hybrid sphere dipole
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|
dimension 3
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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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|
|
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|
create_box 1 box
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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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|
mass 1 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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|
|
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|
set group all dipole/random 98934 0.01
|
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|
pair_style none
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|
|
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|
velocity all create 0.0 87287 mom yes rot yes
|
||||||
|
|
||||||
|
fix 1 all nve/sphere update dipole
|
||||||
|
|
||||||
|
###############################################################################################################
|
||||||
|
## Yukawa potential
|
||||||
|
#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
|
||||||
|
|
||||||
|
## Gradually increasing uniform field
|
||||||
|
#variable E equal ramp(0,1)
|
||||||
|
#fix 2 all efield/lepton "-v_E*(x+y+z)"
|
||||||
|
|
||||||
|
## Linear gradient field
|
||||||
|
fix 2 all efield/lepton "-1/6*x^3" step 1e-6
|
||||||
|
|
||||||
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
|
###############################################################################################################
|
||||||
|
|
||||||
|
timestep 1e-3
|
||||||
|
|
||||||
|
compute erot all erotate/sphere
|
||||||
|
variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot
|
||||||
|
thermo_style custom step temp ke c_erot pe v_etotal
|
||||||
|
thermo 500
|
||||||
|
thermo_modify norm no
|
||||||
|
|
||||||
|
#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz
|
||||||
|
|
||||||
|
run 10000
|
||||||
4
src/.gitignore
vendored
4
src/.gitignore
vendored
@ -95,8 +95,8 @@
|
|||||||
/angle_lepton.h
|
/angle_lepton.h
|
||||||
/dihedral_lepton.cpp
|
/dihedral_lepton.cpp
|
||||||
/dihedral_lepton.h
|
/dihedral_lepton.h
|
||||||
/fix_epot_lepton.cpp
|
/fix_efield_lepton.cpp
|
||||||
/fix_epot_lepton.h
|
/fix_efield_lepton.h
|
||||||
/fix_wall_lepton.cpp
|
/fix_wall_lepton.cpp
|
||||||
/fix_wall_lepton.h
|
/fix_wall_lepton.h
|
||||||
/lepton_utils.cpp
|
/lepton_utils.cpp
|
||||||
|
|||||||
@ -1,495 +0,0 @@
|
|||||||
/* ----------------------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
Contributing author: Gabriel Alkuino (Syracuse University) - gsalkuin@syr.edu
|
|
||||||
Modified from fix_efield
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#include "fix_epot_lepton.h"
|
|
||||||
|
|
||||||
#include "atom.h"
|
|
||||||
#include "comm.h"
|
|
||||||
#include "domain.h"
|
|
||||||
#include "error.h"
|
|
||||||
#include "force.h"
|
|
||||||
#include "input.h"
|
|
||||||
#include "modify.h"
|
|
||||||
#include "region.h"
|
|
||||||
#include "respa.h"
|
|
||||||
#include "update.h"
|
|
||||||
|
|
||||||
#include <array>
|
|
||||||
|
|
||||||
#include "Lepton.h"
|
|
||||||
#include "lepton_utils.h"
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
|
||||||
using namespace FixConst;
|
|
||||||
|
|
||||||
#define EPSILON 1.0e-10
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
FixEpotLepton::FixEpotLepton(LAMMPS *lmp, int narg, char **arg) :
|
|
||||||
Fix(lmp, narg, arg), idregion(nullptr), region(nullptr)
|
|
||||||
{
|
|
||||||
if (domain->xperiodic || domain->yperiodic || domain->zperiodic) {
|
|
||||||
error->warning(FLERR, "Fix {} uses unwrapped coordinates", style);
|
|
||||||
}
|
|
||||||
if (narg < 4) utils::missing_cmd_args(FLERR, std::string("fix ") + style, error);
|
|
||||||
|
|
||||||
scalar_flag = 1;
|
|
||||||
global_freq = 1;
|
|
||||||
extscalar = 1;
|
|
||||||
energy_global_flag = 1;
|
|
||||||
virial_global_flag = virial_peratom_flag = 1;
|
|
||||||
respa_level_support = 1;
|
|
||||||
ilevel_respa = 0;
|
|
||||||
|
|
||||||
// optional args
|
|
||||||
int iarg = 4;
|
|
||||||
while (iarg < narg) {
|
|
||||||
if (strcmp(arg[iarg], "region") == 0) {
|
|
||||||
if (iarg + 2 > narg)
|
|
||||||
utils::missing_cmd_args(FLERR, std::string("fix ") + style + " region", error);
|
|
||||||
region = domain->get_region_by_id(arg[iarg + 1]);
|
|
||||||
if (!region) error->all(FLERR, "Region {} for fix {} does not exist", arg[iarg + 1], style);
|
|
||||||
idregion = utils::strdup(arg[iarg + 1]);
|
|
||||||
iarg += 2;
|
|
||||||
} else if (strcmp(arg[iarg], "step") == 0) {
|
|
||||||
if (iarg + 2 > narg)
|
|
||||||
utils::missing_cmd_args(FLERR, std::string("fix ") + style + "step", error);
|
|
||||||
h = utils::numeric(FLERR, arg[iarg+1], false, lmp);
|
|
||||||
iarg += 2;
|
|
||||||
} else {
|
|
||||||
error->all(FLERR, "Unknown keyword for fix {} command: {}", style, arg[iarg]);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// check validity of Lepton expression
|
|
||||||
// remove whitespace and quotes from expression string and then
|
|
||||||
// check if the expression can be parsed without error
|
|
||||||
expr = LeptonUtils::condense(arg[3]);
|
|
||||||
try {
|
|
||||||
auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(expr, lmp));
|
|
||||||
auto phi = parsed.createCompiledExpression();
|
|
||||||
} catch (std::exception &e) {
|
|
||||||
error->all(FLERR, e.what());
|
|
||||||
}
|
|
||||||
|
|
||||||
force_flag = 0;
|
|
||||||
fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
FixEpotLepton::~FixEpotLepton()
|
|
||||||
{
|
|
||||||
delete[] idregion;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
int FixEpotLepton::setmask()
|
|
||||||
{
|
|
||||||
int mask = 0;
|
|
||||||
mask |= POST_FORCE;
|
|
||||||
mask |= POST_FORCE_RESPA;
|
|
||||||
mask |= MIN_POST_FORCE;
|
|
||||||
return mask;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixEpotLepton::init()
|
|
||||||
{
|
|
||||||
if (!atom->q_flag && !atom->mu_flag)
|
|
||||||
error->all(FLERR, "Fix {} requires atom attribute q or mu", style);
|
|
||||||
if (atom->mu_flag && !atom->torque_flag)
|
|
||||||
error->all(FLERR, "Dipoles must be finite-sized to rotate", style);
|
|
||||||
|
|
||||||
// set index and check validity of region
|
|
||||||
if (idregion) {
|
|
||||||
region = domain->get_region_by_id(idregion);
|
|
||||||
if (!region) error->all(FLERR, "Region {} for fix {} does not exist", idregion, style);
|
|
||||||
}
|
|
||||||
|
|
||||||
if (utils::strmatch(update->integrate_style, "^respa")) {
|
|
||||||
ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels - 1;
|
|
||||||
if (respa_level >= 0) ilevel_respa = MIN(respa_level, ilevel_respa);
|
|
||||||
}
|
|
||||||
|
|
||||||
// unit conversion factors and restrictions (see issue #1377)
|
|
||||||
char *unit_style = update->unit_style;
|
|
||||||
qe2f = force->qe2f;
|
|
||||||
mue2e = qe2f;
|
|
||||||
if (strcmp(unit_style, "electron") == 0 || strcmp(unit_style, "micro") == 0 || strcmp(unit_style, "nano") == 0) {
|
|
||||||
error->all(FLERR, "Fix {} does not support {} units", style, unit_style);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixEpotLepton::setup(int vflag)
|
|
||||||
{
|
|
||||||
if (utils::strmatch(update->integrate_style, "^respa")) {
|
|
||||||
auto respa = dynamic_cast<Respa *>(update->integrate);
|
|
||||||
respa->copy_flevel_f(ilevel_respa);
|
|
||||||
post_force_respa(vflag, ilevel_respa, 0);
|
|
||||||
respa->copy_f_flevel(ilevel_respa);
|
|
||||||
} else {
|
|
||||||
post_force(vflag);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixEpotLepton::min_setup(int vflag)
|
|
||||||
{
|
|
||||||
post_force(vflag);
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
Apply F = qE,
|
|
||||||
F = (mu . D) E,
|
|
||||||
T = mu x E
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixEpotLepton::post_force(int vflag)
|
|
||||||
{
|
|
||||||
double **f = atom->f;
|
|
||||||
double **x = atom->x;
|
|
||||||
int *mask = atom->mask;
|
|
||||||
imageint *image = atom->image;
|
|
||||||
int nlocal = atom->nlocal;
|
|
||||||
|
|
||||||
auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(expr, lmp)).optimize();
|
|
||||||
Lepton::CompiledExpression phi;
|
|
||||||
auto dphi_x = parsed.differentiate("x").createCompiledExpression();
|
|
||||||
auto dphi_y = parsed.differentiate("y").createCompiledExpression();
|
|
||||||
auto dphi_z = parsed.differentiate("z").createCompiledExpression();
|
|
||||||
std::vector<Lepton::CompiledExpression*> dphis = {&dphi_x, &dphi_y, &dphi_z};
|
|
||||||
|
|
||||||
// check if reference to x, y, z exist
|
|
||||||
const std::array<std::string, 3> variableNames = {"x", "y", "z"};
|
|
||||||
std::array<bool, 3> phi_has_ref = {true, true, true};
|
|
||||||
if (atom->q_flag){
|
|
||||||
phi = parsed.createCompiledExpression();
|
|
||||||
for (size_t i = 0; i < 3; i++) {
|
|
||||||
try {
|
|
||||||
phi.getVariableReference(variableNames[i]);
|
|
||||||
}
|
|
||||||
catch (Lepton::Exception &) {
|
|
||||||
phi_has_ref[i] = false;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
std::vector<std::array<bool, 3>> dphis_has_ref;
|
|
||||||
bool e_uniform = true;
|
|
||||||
for (auto &dphi : dphis) {
|
|
||||||
dphis_has_ref.push_back({false, false, false});
|
|
||||||
for (size_t i = 0; i < 3; i++) {
|
|
||||||
try {
|
|
||||||
(*dphi).getVariableReference(variableNames[i]);
|
|
||||||
dphis_has_ref.back()[i] = true;
|
|
||||||
e_uniform = false;
|
|
||||||
}
|
|
||||||
catch (Lepton::Exception &) {
|
|
||||||
// do nothing
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
if (!e_uniform && atom->mu_flag && h < 0) {
|
|
||||||
error->all(FLERR, "Fix {} requires keyword `step' for dipoles in a non-uniform electric field", style);
|
|
||||||
}
|
|
||||||
|
|
||||||
// virial setup
|
|
||||||
v_init(vflag);
|
|
||||||
|
|
||||||
// update region if necessary
|
|
||||||
if (region) region->prematch();
|
|
||||||
|
|
||||||
// fsum[0] = "potential energy" for added force
|
|
||||||
// fsum[123] = extra force added to atoms
|
|
||||||
fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
|
|
||||||
force_flag = 0;
|
|
||||||
|
|
||||||
double ex, ey, ez;
|
|
||||||
double fx, fy, fz;
|
|
||||||
double v[6], unwrap[3];
|
|
||||||
double xf, yf, zf, xb, yb, zb;
|
|
||||||
double exf, eyf, ezf, exb, eyb, ezb;
|
|
||||||
double tx, ty, tz;
|
|
||||||
double mu_norm, h_mu;
|
|
||||||
|
|
||||||
if (atom->q_flag && atom->mu_flag) {
|
|
||||||
double *q = atom->q;
|
|
||||||
double **mu = atom->mu;
|
|
||||||
double **t = atom->torque;
|
|
||||||
for (int i = 0; i < nlocal; i++) {
|
|
||||||
if (mask[i] & groupbit) {
|
|
||||||
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
|
|
||||||
domain->unmap(x[i], image[i], unwrap);
|
|
||||||
|
|
||||||
// evaluate e-field, used by q and mu
|
|
||||||
for (size_t j = 0; j < 3; j++) {
|
|
||||||
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = unwrap[0];
|
|
||||||
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = unwrap[1];
|
|
||||||
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = unwrap[2];
|
|
||||||
}
|
|
||||||
ex = -dphi_x.evaluate();
|
|
||||||
ey = -dphi_y.evaluate();
|
|
||||||
ez = -dphi_z.evaluate();
|
|
||||||
|
|
||||||
if (phi_has_ref[0]) phi.getVariableReference("x") = unwrap[0];
|
|
||||||
if (phi_has_ref[1]) phi.getVariableReference("y") = unwrap[1];
|
|
||||||
if (phi_has_ref[2]) phi.getVariableReference("z") = unwrap[2];
|
|
||||||
|
|
||||||
// charges
|
|
||||||
// force = q E
|
|
||||||
fx = qe2f * q[i] * ex;
|
|
||||||
fy = qe2f * q[i] * ey;
|
|
||||||
fz = qe2f * q[i] * ez;
|
|
||||||
// potential energy = q phi
|
|
||||||
fsum[0] += qe2f * q[i] * phi.evaluate();
|
|
||||||
|
|
||||||
// dipoles
|
|
||||||
mu_norm = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]);
|
|
||||||
if (mu_norm > EPSILON) {
|
|
||||||
// torque = mu cross E
|
|
||||||
t[i][0] += mue2e * (ez * mu[i][1] - ey * mu[i][2]);
|
|
||||||
t[i][1] += mue2e * (ex * mu[i][2] - ez * mu[i][0]);
|
|
||||||
t[i][2] += mue2e * (ey * mu[i][0] - ex * mu[i][1]);
|
|
||||||
// potential energy = - mu dot E
|
|
||||||
fsum[0] -= mue2e * (mu[i][0] * ex + mu[i][1] * ey + mu[i][2] * ez);
|
|
||||||
|
|
||||||
// force = (mu dot D) E
|
|
||||||
// using central difference method
|
|
||||||
h_mu = h / mu_norm;
|
|
||||||
|
|
||||||
xf = unwrap[0] + h_mu * mu[i][0];
|
|
||||||
yf = unwrap[1] + h_mu * mu[i][1];
|
|
||||||
zf = unwrap[2] + h_mu * mu[i][2];
|
|
||||||
for (size_t j = 0; j < 3; j++) {
|
|
||||||
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = xf;
|
|
||||||
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = yf;
|
|
||||||
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = zf;
|
|
||||||
}
|
|
||||||
exf = -dphi_x.evaluate();
|
|
||||||
eyf = -dphi_y.evaluate();
|
|
||||||
ezf = -dphi_z.evaluate();
|
|
||||||
|
|
||||||
xb = unwrap[0] - h_mu * mu[i][0];
|
|
||||||
yb = unwrap[1] - h_mu * mu[i][1];
|
|
||||||
zb = unwrap[2] - h_mu * mu[i][2];
|
|
||||||
for (size_t j = 0; j < 3; j++) {
|
|
||||||
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = xb;
|
|
||||||
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = yb;
|
|
||||||
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = zb;
|
|
||||||
}
|
|
||||||
exb = -dphi_x.evaluate();
|
|
||||||
eyb = -dphi_y.evaluate();
|
|
||||||
ezb = -dphi_z.evaluate();
|
|
||||||
|
|
||||||
fx += qe2f * (exf - exb) / 2.0 / h_mu;
|
|
||||||
fy += qe2f * (eyf - eyb) / 2.0 / h_mu;
|
|
||||||
fz += qe2f * (ezf - ezb) / 2.0 / h_mu;
|
|
||||||
}
|
|
||||||
|
|
||||||
f[i][0] += fx;
|
|
||||||
f[i][1] += fy;
|
|
||||||
f[i][2] += fz;
|
|
||||||
|
|
||||||
fsum[1] += fx;
|
|
||||||
fsum[2] += fy;
|
|
||||||
fsum[3] += fz;
|
|
||||||
|
|
||||||
if (evflag) {
|
|
||||||
v[0] = fx * unwrap[0];
|
|
||||||
v[1] = fy * unwrap[1];
|
|
||||||
v[2] = fz * unwrap[2];
|
|
||||||
v[3] = fx * unwrap[1];
|
|
||||||
v[4] = fx * unwrap[2];
|
|
||||||
v[5] = fy * unwrap[2];
|
|
||||||
v_tally(i, v);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
} else if (atom->q_flag && !atom->mu_flag) {
|
|
||||||
double *q = atom->q;
|
|
||||||
for (int i = 0; i < nlocal; i++) {
|
|
||||||
if (mask[i] & groupbit) {
|
|
||||||
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
|
|
||||||
domain->unmap(x[i], image[i], unwrap);
|
|
||||||
|
|
||||||
for (size_t j = 0; j < 3; j++) {
|
|
||||||
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = unwrap[0];
|
|
||||||
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = unwrap[1];
|
|
||||||
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = unwrap[2];
|
|
||||||
}
|
|
||||||
ex = -dphi_x.evaluate();
|
|
||||||
ey = -dphi_y.evaluate();
|
|
||||||
ez = -dphi_z.evaluate();
|
|
||||||
|
|
||||||
if (phi_has_ref[0]) phi.getVariableReference("x") = unwrap[0];
|
|
||||||
if (phi_has_ref[1]) phi.getVariableReference("y") = unwrap[1];
|
|
||||||
if (phi_has_ref[2]) phi.getVariableReference("z") = unwrap[2];
|
|
||||||
|
|
||||||
// force = q E
|
|
||||||
fx = qe2f * q[i] * ex;
|
|
||||||
fy = qe2f * q[i] * ey;
|
|
||||||
fz = qe2f * q[i] * ez;
|
|
||||||
// potential energy = q phi
|
|
||||||
fsum[0] += qe2f * q[i] * phi.evaluate();
|
|
||||||
|
|
||||||
f[i][0] += fx;
|
|
||||||
f[i][1] += fy;
|
|
||||||
f[i][2] += fz;
|
|
||||||
|
|
||||||
fsum[1] += fx;
|
|
||||||
fsum[2] += fy;
|
|
||||||
fsum[3] += fz;
|
|
||||||
|
|
||||||
if (evflag) {
|
|
||||||
v[0] = fx * unwrap[0];
|
|
||||||
v[1] = fy * unwrap[1];
|
|
||||||
v[2] = fz * unwrap[2];
|
|
||||||
v[3] = fx * unwrap[1];
|
|
||||||
v[4] = fx * unwrap[2];
|
|
||||||
v[5] = fy * unwrap[2];
|
|
||||||
v_tally(i, v);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
} else if (!atom->q_flag && atom->mu_flag) {
|
|
||||||
double **mu = atom->mu;
|
|
||||||
double **t = atom->torque;
|
|
||||||
for (int i = 0; i < nlocal; i++) {
|
|
||||||
if (mask[i] & groupbit) {
|
|
||||||
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
|
|
||||||
|
|
||||||
mu_norm = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]);
|
|
||||||
if (mu_norm > EPSILON) continue;
|
|
||||||
|
|
||||||
domain->unmap(x[i], image[i], unwrap);
|
|
||||||
|
|
||||||
for (size_t j = 0; j < 3; j++) {
|
|
||||||
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = unwrap[0];
|
|
||||||
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = unwrap[1];
|
|
||||||
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = unwrap[2];
|
|
||||||
}
|
|
||||||
ex = -dphi_x.evaluate();
|
|
||||||
ey = -dphi_y.evaluate();
|
|
||||||
ez = -dphi_z.evaluate();
|
|
||||||
|
|
||||||
// torque = mu cross E
|
|
||||||
t[i][0] += mue2e * (ez * mu[i][1] - ey * mu[i][2]);
|
|
||||||
t[i][1] += mue2e * (ex * mu[i][2] - ez * mu[i][0]);
|
|
||||||
t[i][2] += mue2e * (ey * mu[i][0] - ex * mu[i][1]);
|
|
||||||
// potential energy = - mu dot E
|
|
||||||
fsum[0] -= mue2e * (mu[i][0] * ex + mu[i][1] * ey + mu[i][2] * ez);
|
|
||||||
|
|
||||||
// force = (mu dot D) E
|
|
||||||
// using central difference method
|
|
||||||
h_mu = h / sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]);
|
|
||||||
|
|
||||||
xf = unwrap[0] + h_mu * mu[i][0];
|
|
||||||
yf = unwrap[1] + h_mu * mu[i][1];
|
|
||||||
zf = unwrap[2] + h_mu * mu[i][2];
|
|
||||||
for (size_t j = 0; j < 3; j++) {
|
|
||||||
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = xf;
|
|
||||||
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = yf;
|
|
||||||
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = zf;
|
|
||||||
}
|
|
||||||
exf = -dphi_x.evaluate();
|
|
||||||
eyf = -dphi_y.evaluate();
|
|
||||||
ezf = -dphi_z.evaluate();
|
|
||||||
|
|
||||||
xb = unwrap[0] - h_mu * mu[i][0];
|
|
||||||
yb = unwrap[1] - h_mu * mu[i][1];
|
|
||||||
zb = unwrap[2] - h_mu * mu[i][2];
|
|
||||||
for (size_t j = 0; j < 3; j++) {
|
|
||||||
if (dphis_has_ref[j][0]) (*dphis[j]).getVariableReference("x") = xb;
|
|
||||||
if (dphis_has_ref[j][1]) (*dphis[j]).getVariableReference("y") = yb;
|
|
||||||
if (dphis_has_ref[j][2]) (*dphis[j]).getVariableReference("z") = zb;
|
|
||||||
}
|
|
||||||
exb = -dphi_x.evaluate();
|
|
||||||
eyb = -dphi_y.evaluate();
|
|
||||||
ezb = -dphi_z.evaluate();
|
|
||||||
|
|
||||||
fx = qe2f * (exf - exb) / 2.0 / h_mu;
|
|
||||||
fy = qe2f * (eyf - eyb) / 2.0 / h_mu;
|
|
||||||
fz = qe2f * (ezf - ezb) / 2.0 / h_mu;
|
|
||||||
|
|
||||||
f[i][0] += fx;
|
|
||||||
f[i][1] += fy;
|
|
||||||
f[i][2] += fz;
|
|
||||||
|
|
||||||
fsum[1] += fx;
|
|
||||||
fsum[2] += fy;
|
|
||||||
fsum[3] += fz;
|
|
||||||
|
|
||||||
if (evflag) {
|
|
||||||
v[0] = fx * unwrap[0];
|
|
||||||
v[1] = fy * unwrap[1];
|
|
||||||
v[2] = fz * unwrap[2];
|
|
||||||
v[3] = fx * unwrap[1];
|
|
||||||
v[4] = fx * unwrap[2];
|
|
||||||
v[5] = fy * unwrap[2];
|
|
||||||
v_tally(i, v);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixEpotLepton::post_force_respa(int vflag, int ilevel, int /*iloop*/)
|
|
||||||
{
|
|
||||||
if (ilevel == ilevel_respa) post_force(vflag);
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixEpotLepton::min_post_force(int vflag)
|
|
||||||
{
|
|
||||||
post_force(vflag);
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
return energy added by fix
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
double FixEpotLepton::compute_scalar()
|
|
||||||
{
|
|
||||||
if (force_flag == 0) {
|
|
||||||
MPI_Allreduce(fsum, fsum_all, 4, MPI_DOUBLE, MPI_SUM, world);
|
|
||||||
force_flag = 1;
|
|
||||||
}
|
|
||||||
return fsum_all[0];
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
return total extra force due to fix
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
double FixEpotLepton::compute_vector(int n)
|
|
||||||
{
|
|
||||||
if (force_flag == 0) {
|
|
||||||
MPI_Allreduce(fsum, fsum_all, 4, MPI_DOUBLE, MPI_SUM, world);
|
|
||||||
force_flag = 1;
|
|
||||||
}
|
|
||||||
return fsum_all[n + 1];
|
|
||||||
}
|
|
||||||
@ -1,60 +0,0 @@
|
|||||||
/* -*- c++ -*- ----------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
Contributing author: Gabriel Alkuino (Syracuse University) - gsalkuin@syr.edu
|
|
||||||
Modified from fix_efield
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#ifdef FIX_CLASS
|
|
||||||
// clang-format off
|
|
||||||
FixStyle(epot/lepton,FixEpotLepton);
|
|
||||||
// clang-format on
|
|
||||||
#else
|
|
||||||
|
|
||||||
#ifndef LMP_FIX_EPOT_LEPTON_H
|
|
||||||
#define LMP_FIX_EPOT_LEPTON_H
|
|
||||||
|
|
||||||
#include "fix.h"
|
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
|
||||||
|
|
||||||
class FixEpotLepton : public Fix {
|
|
||||||
|
|
||||||
public:
|
|
||||||
FixEpotLepton(class LAMMPS *, int, char **);
|
|
||||||
~FixEpotLepton() override;
|
|
||||||
int setmask() override;
|
|
||||||
void init() override;
|
|
||||||
void setup(int) override;
|
|
||||||
void min_setup(int) override;
|
|
||||||
void post_force(int) override;
|
|
||||||
void post_force_respa(int, int, int) override;
|
|
||||||
void min_post_force(int) override;
|
|
||||||
double compute_scalar() override;
|
|
||||||
double compute_vector(int) override;
|
|
||||||
|
|
||||||
protected:
|
|
||||||
char *idregion;
|
|
||||||
class Region *region;
|
|
||||||
int ilevel_respa;
|
|
||||||
std::string expr;
|
|
||||||
|
|
||||||
int force_flag;
|
|
||||||
double h = -1.0;
|
|
||||||
double qe2f, mue2e;
|
|
||||||
double fsum[4], fsum_all[4];
|
|
||||||
};
|
|
||||||
} // namespace LAMMPS_NS
|
|
||||||
#endif
|
|
||||||
#endif
|
|
||||||
@ -1,77 +1,78 @@
|
|||||||
---
|
---
|
||||||
lammps_version: 27 Jun 2024
|
lammps_version: 29 Aug 2024
|
||||||
date_generated: Tue Sep 17 08:38:51 2024
|
tags: generated
|
||||||
epsilon: 2e-13
|
date_generated: Tue Nov 12 08:53:18 2024
|
||||||
skip_tests:
|
epsilon: 2e-13
|
||||||
prerequisites: ! |
|
skip_tests:
|
||||||
atom full
|
prerequisites: ! |
|
||||||
fix efield
|
atom full
|
||||||
pre_commands: ! ""
|
fix efield
|
||||||
post_commands: ! |
|
pre_commands: ! ""
|
||||||
region half block 0 EDGE EDGE EDGE EDGE EDGE
|
post_commands: ! |
|
||||||
fix move all nve
|
region half block 0 EDGE EDGE EDGE EDGE EDGE
|
||||||
fix test solute epot/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1"
|
fix move all nve
|
||||||
input_file: in.fourmol
|
fix test solute efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1"
|
||||||
natoms: 29
|
input_file: in.fourmol
|
||||||
global_scalar: 1.6704454516566274
|
natoms: 29
|
||||||
run_pos: ! |2
|
global_scalar: 1.6704454516566274
|
||||||
1 -2.7045174040786113e-01 2.4911873718363386e+00 -1.6695654631491835e-01
|
run_pos: ! |2
|
||||||
2 3.1004221019407835e-01 2.9612623619618166e+00 -8.5467074498303619e-01
|
1 -2.7045174040786113e-01 2.4911873718363386e+00 -1.6695654631491835e-01
|
||||||
3 -7.0398277208953364e-01 1.2305442007296870e+00 -6.2777337959095758e-01
|
2 3.1004221019407835e-01 2.9612623619618166e+00 -8.5467074498303619e-01
|
||||||
4 -1.5818277418447926e+00 1.4837528245352911e+00 -1.2538808796681880e+00
|
3 -7.0398277208953364e-01 1.2305442007296870e+00 -6.2777337959095758e-01
|
||||||
5 -9.0729118448236790e-01 9.2661863916543652e-01 3.9958383542336978e-01
|
4 -1.5818277418447926e+00 1.4837528245352911e+00 -1.2538808796681880e+00
|
||||||
6 2.4837968642651539e-01 2.8318965710323424e-01 -1.2316675533799510e+00
|
5 -9.0729118448236790e-01 9.2661863916543652e-01 3.9958383542336978e-01
|
||||||
7 3.4143233737928985e-01 -2.2652080889821399e-02 -2.5292246648830696e+00
|
6 2.4837968642651539e-01 2.8318965710323424e-01 -1.2316675533799510e+00
|
||||||
8 1.1742106633496632e+00 -4.8857819177533296e-01 -6.3774855832878818e-01
|
7 3.4143233737928985e-01 -2.2652080889821399e-02 -2.5292246648830696e+00
|
||||||
9 1.3804619006746952e+00 -2.5282186304504617e-01 2.8361638661486044e-01
|
8 1.1742106633496632e+00 -4.8857819177533296e-01 -6.3774855832878818e-01
|
||||||
10 2.0510714422715428e+00 -1.4603992238436605e+00 -9.8323613298241641e-01
|
9 1.3804619006746952e+00 -2.5282186304504617e-01 2.8361638661486044e-01
|
||||||
11 1.7878067664442001e+00 -1.9921902225913919e+00 -1.8890639278278800e+00
|
10 2.0510714422715428e+00 -1.4603992238436605e+00 -9.8323613298241641e-01
|
||||||
12 3.0062962291402449e+00 -4.9013271581056822e-01 -1.6231874104184338e+00
|
11 1.7878067664442001e+00 -1.9921902225913919e+00 -1.8890639278278800e+00
|
||||||
13 4.0515414154880354e+00 -8.9202039400328714e-01 -1.6400010189207204e+00
|
12 3.0062962291402449e+00 -4.9013271581056822e-01 -1.6231874104184338e+00
|
||||||
14 2.6066986955414859e+00 -4.1789289874186603e-01 -2.6634027530740045e+00
|
13 4.0515414154880354e+00 -8.9202039400328714e-01 -1.6400010189207204e+00
|
||||||
15 2.9695346087268195e+00 5.5422728642528218e-01 -1.2342046800948778e+00
|
14 2.6066986955414859e+00 -4.1789289874186603e-01 -2.6634027530740045e+00
|
||||||
16 2.6747089246970055e+00 -2.4124172919180635e+00 -2.3435358040545039e-02
|
15 2.9695346087268195e+00 5.5422728642528218e-01 -1.2342046800948778e+00
|
||||||
17 2.2153515161424591e+00 -2.0897925974376559e+00 1.1963115055447653e+00
|
16 2.6747089246970055e+00 -2.4124172919180635e+00 -2.3435358040545039e-02
|
||||||
18 2.1369701703995672e+00 3.0158507413483879e+00 -3.5179348337128169e+00
|
17 2.2153515161424591e+00 -2.0897925974376559e+00 1.1963115055447653e+00
|
||||||
19 1.5355837136075503e+00 2.6255292355356850e+00 -4.2353987779858899e+00
|
18 2.1369701703995672e+00 3.0158507413483879e+00 -3.5179348337128169e+00
|
||||||
20 2.7727573005675157e+00 3.6923910449606199e+00 -3.9330842459130921e+00
|
19 1.5355837136075503e+00 2.6255292355356850e+00 -4.2353987779858899e+00
|
||||||
21 4.9040128073216458e+00 -4.0752348172972228e+00 -3.6210314709902178e+00
|
20 2.7727573005675157e+00 3.6923910449606199e+00 -3.9330842459130921e+00
|
||||||
22 4.3582355554441330e+00 -4.2126119427287785e+00 -4.4612844196314905e+00
|
21 4.9040128073216458e+00 -4.0752348172972228e+00 -3.6210314709902178e+00
|
||||||
23 5.7439382849308398e+00 -3.5821957939275575e+00 -3.8766361295936442e+00
|
22 4.3582355554441330e+00 -4.2126119427287785e+00 -4.4612844196314905e+00
|
||||||
24 2.0689243582420707e+00 3.1513346907257525e+00 3.1550389754825381e+00
|
23 5.7439382849308398e+00 -3.5821957939275575e+00 -3.8766361295936442e+00
|
||||||
25 1.3045351331495809e+00 3.2665125705836533e+00 2.5111855257438469e+00
|
24 2.0689243582420707e+00 3.1513346907257525e+00 3.1550389754825381e+00
|
||||||
26 2.5809237402711407e+00 4.0117602605482343e+00 3.2212060529090203e+00
|
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|
||||||
27 -1.9611343130355228e+00 -4.3563411931353464e+00 2.1098293115521636e+00
|
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|
||||||
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|
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|
||||||
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|
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|
||||||
run_vel: ! |2
|
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|
||||||
1 8.1748902719248895e-03 1.6488825063890555e-02 4.7920575746796803e-03
|
run_vel: ! |2
|
||||||
2 5.4511084007743318e-03 5.2051261388670498e-03 -1.4434422725438370e-03
|
1 8.1748902719248895e-03 1.6488825063890555e-02 4.7920575746796803e-03
|
||||||
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|
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|
||||||
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|
||||||
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|
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|
||||||
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|
||||||
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|
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|
||||||
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|
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|
||||||
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|
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|
||||||
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|
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|
||||||
11 -4.7800378310285741e-03 -3.7519133265433713e-03 -2.3499734597008941e-03
|
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|
||||||
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|
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|
||||||
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|
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|
||||||
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|
||||||
15 -1.8489707819649144e-03 -5.8542853523402688e-03 6.2913780244787517e-03
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
21 -1.4689220345082588e-03 -2.7352130061578030e-04 7.0581623990333337e-04
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|
||||||
22 -7.0694199253619090e-03 -4.2577148926459460e-03 2.8079117595322244e-04
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|
||||||
23 6.0446963119181341e-03 -1.4000131615895693e-03 2.5819754845648850e-03
|
22 -7.0694199253619090e-03 -4.2577148926459460e-03 2.8079117595322244e-04
|
||||||
24 3.1926367864219455e-04 -9.9445665025542493e-04 1.4999996888246658e-04
|
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|
||||||
25 1.3789754587624503e-04 -4.4335894897561037e-03 -8.1808136628206090e-04
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|
||||||
26 2.0485904035354775e-03 2.7813358632583834e-03 4.3245727149805969e-03
|
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|
||||||
27 4.5604120337294426e-04 -1.0305523013893942e-03 2.1188058337867958e-04
|
26 2.0485904035354775e-03 2.7813358632583834e-03 4.3245727149805969e-03
|
||||||
28 -6.2544520861285771e-03 1.4127711177082084e-03 -1.8429821885090839e-03
|
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|
||||||
29 6.4110631550796319e-04 3.1273432723457764e-03 3.7253671103666878e-03
|
28 -6.2544520861285771e-03 1.4127711177082084e-03 -1.8429821885090839e-03
|
||||||
...
|
29 6.4110631550796319e-04 3.1273432723457764e-03 3.7253671103666878e-03
|
||||||
|
...
|
||||||
@ -1,77 +1,78 @@
|
|||||||
---
|
---
|
||||||
lammps_version: 27 Jun 2024
|
lammps_version: 29 Aug 2024
|
||||||
date_generated: Tue Sep 17 08:42:57 2024
|
tags: generated
|
||||||
epsilon: 2e-13
|
date_generated: Tue Nov 12 08:53:32 2024
|
||||||
skip_tests:
|
epsilon: 2e-13
|
||||||
prerequisites: ! |
|
skip_tests:
|
||||||
atom full
|
prerequisites: ! |
|
||||||
fix efield
|
atom full
|
||||||
pre_commands: ! ""
|
fix efield
|
||||||
post_commands: ! |
|
pre_commands: ! ""
|
||||||
region half block 0 EDGE EDGE EDGE EDGE EDGE
|
post_commands: ! |
|
||||||
fix move all nve
|
region half block 0 EDGE EDGE EDGE EDGE EDGE
|
||||||
fix test solute epot/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1" region half
|
fix move all nve
|
||||||
input_file: in.fourmol
|
fix test solute efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1" region half
|
||||||
natoms: 29
|
input_file: in.fourmol
|
||||||
global_scalar: 1.6224257709052041
|
natoms: 29
|
||||||
run_pos: ! |2
|
global_scalar: 1.6224257709052041
|
||||||
1 -2.7045550227503484e-01 2.4912161552650542e+00 -1.6695870672991683e-01
|
run_pos: ! |2
|
||||||
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|
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|
||||||
3 -7.0398509489328243e-01 1.2305505728672561e+00 -6.2777617667397034e-01
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|
||||||
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|
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|
||||||
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|
||||||
6 2.4837966543189102e-01 2.8318973351568738e-01 -1.2316676191454061e+00
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|
||||||
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|
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
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|
||||||
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|
||||||
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|
||||||
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|
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|
||||||
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|
||||||
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|
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|
||||||
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|
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|
||||||
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|
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|
||||||
21 4.9040128073216458e+00 -4.0752348172972228e+00 -3.6210314709902178e+00
|
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|
||||||
22 4.3582355554441330e+00 -4.2126119427287785e+00 -4.4612844196314905e+00
|
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|
||||||
23 5.7439382849308398e+00 -3.5821957939275575e+00 -3.8766361295936442e+00
|
22 4.3582355554441330e+00 -4.2126119427287785e+00 -4.4612844196314905e+00
|
||||||
24 2.0689243582419663e+00 3.1513346907264923e+00 3.1550389754824169e+00
|
23 5.7439382849308398e+00 -3.5821957939275575e+00 -3.8766361295936442e+00
|
||||||
25 1.3045351331492137e+00 3.2665125705841698e+00 2.5111855257432798e+00
|
24 2.0689243582419663e+00 3.1513346907264923e+00 3.1550389754824169e+00
|
||||||
26 2.5809237402711096e+00 4.0117602605482601e+00 3.2212060529089785e+00
|
25 1.3045351331492137e+00 3.2665125705841698e+00 2.5111855257432798e+00
|
||||||
27 -1.9611343130355403e+00 -4.3563411931354130e+00 2.1098293115521884e+00
|
26 2.5809237402711096e+00 4.0117602605482601e+00 3.2212060529089785e+00
|
||||||
28 -2.7473562684513166e+00 -4.0200819932378939e+00 1.5830052163433843e+00
|
27 -1.9611343130355403e+00 -4.3563411931354130e+00 2.1098293115521884e+00
|
||||||
29 -1.3126000191359157e+00 -3.5962518039481259e+00 2.2746342468736964e+00
|
28 -2.7473562684513166e+00 -4.0200819932378939e+00 1.5830052163433843e+00
|
||||||
run_vel: ! |2
|
29 -1.3126000191359157e+00 -3.5962518039481259e+00 2.2746342468736964e+00
|
||||||
1 8.1707610252536762e-03 1.6516729522797459e-02 4.7898444127747793e-03
|
run_vel: ! |2
|
||||||
2 5.4518750405498674e-03 5.2058557730251687e-03 -1.4441331386370641e-03
|
1 8.1707610252536762e-03 1.6516729522797459e-02 4.7898444127747793e-03
|
||||||
3 -8.2289377254294322e-03 -1.2927459179389453e-02 -4.1002423460516626e-03
|
2 5.4518750405498674e-03 5.2058557730251687e-03 -1.4441331386370641e-03
|
||||||
4 -3.7700883579582412e-03 -6.5718761179186279e-03 -1.1180449896675260e-03
|
3 -8.2289377254294322e-03 -1.2927459179389453e-02 -4.1002423460516626e-03
|
||||||
5 -1.1021377362739846e-02 -9.8914014766124762e-03 -2.8411972311159365e-03
|
4 -3.7700883579582412e-03 -6.5718761179186279e-03 -1.1180449896675260e-03
|
||||||
6 -3.9614514600574871e-02 4.6885283311817079e-02 3.6916556408268048e-02
|
5 -1.1021377362739846e-02 -9.8914014766124762e-03 -2.8411972311159365e-03
|
||||||
7 9.0823995329068752e-04 -1.0137213428025349e-02 -5.1576824114592634e-02
|
6 -3.9614514600574871e-02 4.6885283311817079e-02 3.6916556408268048e-02
|
||||||
8 7.7662014866174776e-03 -3.3034295723750589e-03 3.4641871541434638e-02
|
7 9.0823995329068752e-04 -1.0137213428025349e-02 -5.1576824114592634e-02
|
||||||
9 1.9711566911953310e-03 3.6632928332818136e-03 1.5119486593282045e-02
|
8 7.7662014866174776e-03 -3.3034295723750589e-03 3.4641871541434638e-02
|
||||||
10 2.9189761435066477e-02 -2.9234948184549876e-02 -1.5014329155936850e-02
|
9 1.9711566911953310e-03 3.6632928332818136e-03 1.5119486593282045e-02
|
||||||
11 -4.7800378317950521e-03 -3.7519133256272356e-03 -2.3499734593625606e-03
|
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|
||||||
12 2.2651912749160931e-03 -3.4688766464208300e-04 -3.0617028620660344e-03
|
11 -4.7800378317950521e-03 -3.7519133256272356e-03 -2.3499734593625606e-03
|
||||||
13 2.7541524308356854e-03 5.8168212241007178e-03 -7.9509320188147147e-04
|
12 2.2651912749160931e-03 -3.4688766464208300e-04 -3.0617028620660344e-03
|
||||||
14 3.5269195770455336e-03 -5.7943367273509527e-03 -3.9501557655038776e-03
|
13 2.7541524308356854e-03 5.8168212241007178e-03 -7.9509320188147147e-04
|
||||||
15 -1.8489707807796338e-03 -5.8542853526596435e-03 6.2913780240085072e-03
|
14 3.5269195770455336e-03 -5.7943367273509527e-03 -3.9501557655038776e-03
|
||||||
16 1.8687298458816809e-02 -1.3267695592172753e-02 -4.5638131306663686e-02
|
15 -1.8489707807796338e-03 -5.8542853526596435e-03 6.2913780240085072e-03
|
||||||
17 -1.2902476275417624e-02 9.7586450753110940e-03 3.7292773490567067e-02
|
16 1.8687298458816809e-02 -1.3267695592172753e-02 -4.5638131306663686e-02
|
||||||
18 -8.0065797374504898e-04 -8.6270476028742454e-04 -1.4483040514595652e-03
|
17 -1.2902476275417624e-02 9.7586450753110940e-03 3.7292773490567067e-02
|
||||||
19 1.2452390810788788e-03 -2.5061097156065682e-03 7.2998631050903854e-03
|
18 -8.0065797374504898e-04 -8.6270476028742454e-04 -1.4483040514595652e-03
|
||||||
20 3.5930060220034791e-03 3.6938860299639783e-03 3.2322732695251408e-03
|
19 1.2452390810788788e-03 -2.5061097156065682e-03 7.2998631050903854e-03
|
||||||
21 -1.4689220345081530e-03 -2.7352130061585414e-04 7.0581623990322755e-04
|
20 3.5930060220034791e-03 3.6938860299639783e-03 3.2322732695251408e-03
|
||||||
22 -7.0694199253619021e-03 -4.2577148926459503e-03 2.8079117595321425e-04
|
21 -1.4689220345081530e-03 -2.7352130061585414e-04 7.0581623990322755e-04
|
||||||
23 6.0446963119181419e-03 -1.4000131615895712e-03 2.5819754845648798e-03
|
22 -7.0694199253619021e-03 -4.2577148926459503e-03 2.8079117595321425e-04
|
||||||
24 3.1926367843162763e-04 -9.9445664874966543e-04 1.4999996864545090e-04
|
23 6.0446963119181419e-03 -1.4000131615895712e-03 2.5819754845648798e-03
|
||||||
25 1.3789754514824566e-04 -4.4335894886887352e-03 -8.1808136740210897e-04
|
24 3.1926367843162763e-04 -9.9445664874966543e-04 1.4999996864545090e-04
|
||||||
26 2.0485904034778955e-03 2.7813358633230435e-03 4.3245727148973397e-03
|
25 1.3789754514824566e-04 -4.4335894886887352e-03 -8.1808136740210897e-04
|
||||||
27 4.5604120333659156e-04 -1.0305523015253445e-03 2.1188058342984497e-04
|
26 2.0485904034778955e-03 2.7813358633230435e-03 4.3245727148973397e-03
|
||||||
28 -6.2544520861335402e-03 1.4127711176935673e-03 -1.8429821885043371e-03
|
27 4.5604120333659156e-04 -1.0305523015253445e-03 2.1188058342984497e-04
|
||||||
29 6.4110631550259628e-04 3.1273432723195943e-03 3.7253671103774067e-03
|
28 -6.2544520861335402e-03 1.4127711176935673e-03 -1.8429821885043371e-03
|
||||||
...
|
29 6.4110631550259628e-04 3.1273432723195943e-03 3.7253671103774067e-03
|
||||||
|
...
|
||||||
Reference in New Issue
Block a user