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Merge pull request lammps#4129 from akohlmey/pedone-potentials
Add pair style for analytic form of Pedone potential non-Coulomb
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| Original file line number | Diff line number | Diff line change |
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| .. index:: pair_style pedone | ||
| .. index:: pair_style pedone/omp | ||
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| pair_style pedone command | ||
| ========================= | ||
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| Accelerator Variants: *pedone/omp* | ||
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| Syntax | ||
| """""" | ||
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| .. code-block:: LAMMPS | ||
| pair_style style args | ||
| * style = pedone* | ||
| * args = list of arguments for a particular style | ||
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| .. parsed-literal:: | ||
| *pedone* args = cutoff | ||
| cutoff = global cutoff for Pedone interactions (distance units) | ||
| Examples | ||
| """""""" | ||
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| .. code-block:: LAMMPS | ||
| pair_style hybrid/overlay pedone 15.0 coul/long 15.0 | ||
| kspace_style pppm 1.0e-5 | ||
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| pair_coeff * * coul/long | ||
| pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 | ||
| pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 | ||
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| Used in input scripts: | ||
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| .. parsed-literal:: | ||
| examples/PACKAGES/pedone/in.pedone.relax | ||
| examples/PACKAGES/pedone/in.pedone.melt | ||
| Description | ||
| """"""""""" | ||
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| .. versionadded:: TBD | ||
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| Pair style *pedone* computes the **non-Coulomb** interactions of the Pedone | ||
| (or PMMCS) potential :ref:`(Pedone) <Pedone>` which combines Coulomb | ||
| interactions, Morse potential, and repulsive :math:`r^{-12}` | ||
| Lennard-Jones terms (see below). The *pedone* pair style is meant | ||
| to be used in addition to a :doc:`Coulomb pair style <pair_coul>` via | ||
| pair style :doc:`hybrid/overlay <pair_hybrid>` (see example above). | ||
| Using *coul/long* or *could/dsf* (for solids) is recommended. | ||
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| The full Pedone potential function from :ref:`(Pedone) <Pedone>` for each | ||
| pair of atoms is: | ||
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| .. math:: | ||
| E = \frac{C q_i q_j}{\epsilon r} | ||
| + D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] | ||
| + \frac{B_0}{r^{12}} \qquad r < r_c | ||
| :math:`r_c` is the cutoff and :math:`C` is a conversion factor that is | ||
| specific to the choice of :doc:`units <units>` so that the entire | ||
| Coulomb term is in energy units with :math:`q_i` and :math:`q_j` as the | ||
| assigned charges in multiples of the elementary charge. | ||
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| The following coefficients must be defined for the selected pairs of | ||
| atom types via the :doc:`pair_coeff <pair_coeff>` command as in the | ||
| example above: | ||
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| * :math:`D_0` (energy units) | ||
| * :math:`\alpha` (1/distance units) | ||
| * :math:`r_0` (distance units) | ||
| * :math:`C_0` (energy units) | ||
| * cutoff (distance units) | ||
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| The last coefficient is optional. If not specified, the global *pedone* | ||
| cutoff is used. | ||
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| ---------- | ||
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| .. include:: accel_styles.rst | ||
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| ---------- | ||
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| Mixing, shift, table, tail correction, restart, rRESPA info | ||
| """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" | ||
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| This pair style does not support mixing. | ||
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| This pair style support the :doc:`pair_modify <pair_modify>` shift | ||
| option for the energy of the pair interaction. | ||
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| This pair style does not support the :doc:`pair_modify <pair_modify>` | ||
| tail option for adding long-range tail corrections to energy and | ||
| pressure. | ||
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| This pair style writes its information to :doc:`binary restart files <restart>`, | ||
| so pair_style and pair_coeff commands does not need to be specified in an input | ||
| script that reads a restart file. | ||
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| This pair style can only be used via the *pair* keyword of the | ||
| :doc:`run_style respa <run_style>` command. It does not support the | ||
| *inner*, *middle*, or *outer* keywords. | ||
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| ---------- | ||
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| Restrictions | ||
| """""""""""" | ||
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| The *pedone* pair style is only enabled if LAMMPS was built with the | ||
| EXTRA-PAIR package. See the :doc:`Build package <Build_package>` page | ||
| for more info. | ||
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| Related commands | ||
| """""""""""""""" | ||
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| :doc:`pair_coeff <pair_coeff>`, :doc:`pair_style <pair_style>`, | ||
| :doc:`pair style coul/long and coul/dsf <pair_coul>`, | ||
| :doc:`pair style morse <pair_morse>` | ||
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| Default | ||
| """"""" | ||
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| none | ||
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| ------------- | ||
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| .. _Pedone: | ||
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| **(Pedone)** A. Pedone, G. Malavasi, M. C. Menziani, A. N. Cormack, and U. Segre, J. Phys. Chem. B, 110, 11780 (2006) |
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| Original file line number | Diff line number | Diff line change |
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| # Ca-O melt with Pedone potential | ||
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| units metal | ||
| atom_style charge | ||
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| lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations | ||
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| region box block 0 4 0 4 0 4 | ||
| create_box 2 box | ||
| create_atoms 1 box | ||
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| lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell | ||
| create_atoms 2 box | ||
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| mass 1 40.078 | ||
| mass 2 15.999 | ||
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| set type 1 charge 1.2 | ||
| set type 2 charge -1.2 | ||
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| timestep 0.002 | ||
| neigh_modify delay 5 every 1 check yes | ||
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| pair_style hybrid/overlay pedone 15.0 coul/long 15.0 | ||
| kspace_style pppm 1.0e-6 | ||
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| pair_coeff * * coul/long | ||
| pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 | ||
| pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 | ||
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| velocity all create 6000.0 98347 | ||
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| fix 1 all nvt temp 3000.0 3000.0 0.1 | ||
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| # dump 1 all atom 500 Ca-O-melt.lammpstrj | ||
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| thermo 100 | ||
| run 1000 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| # Ca-O crystal with Pedone potential | ||
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| units metal | ||
| atom_style charge | ||
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| lattice fcc 4.8105 # experimental lattice parameter for fcc-lattice Ca cations | ||
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| region box block 0 4 0 4 0 4 | ||
| create_box 2 box | ||
| create_atoms 1 box | ||
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| lattice fcc 4.8105 origin 0.5 0.5 0.5 # O anion lattice shifted by half a unit cell | ||
| create_atoms 2 box | ||
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| mass 1 40.078 | ||
| mass 2 15.999 | ||
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| displace_atoms all random 0.01 0.01 0.01 9084544 | ||
| set type 1 charge 1.2 | ||
| set type 2 charge -1.2 | ||
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| timestep 0.002 | ||
| neigh_modify delay 5 every 1 check yes | ||
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| pair_style hybrid/overlay pedone 15.0 coul/long 15.0 | ||
| kspace_style pppm 1.0e-6 | ||
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| pair_coeff * * coul/long | ||
| pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 | ||
| pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 | ||
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| variable len equal lx*0.25 | ||
| thermo_style custom step v_len lx pe press | ||
| thermo 100 | ||
| fix 1 all box/relax iso 0.0 | ||
| minimize 0.0 0.0 1000 10000 | ||
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| print "Expected lattice parameter: 4.7748, computed: $(v_len:%6.4f)" |
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