rename lj/sphere to lj/cut/sphere and add (yet non-functional) lj/expand/sphere
This commit is contained in:
Axel Kohlmeyer
@ -172,12 +172,14 @@ OPT.
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* :doc:`lj/cut/dipole/long (g) <pair_dipole>`
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* :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
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* :doc:`lj/cut/soft (o) <pair_fep_soft>`
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* :doc:`lj/cut/sphere (o) <pair_lj_cut_sphere>`
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* :doc:`lj/cut/thole/long (o) <pair_thole>`
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* :doc:`lj/cut/tip4p/cut (o) <pair_lj_cut_tip4p>`
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* :doc:`lj/cut/tip4p/long (got) <pair_lj_cut_tip4p>`
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* :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
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* :doc:`lj/expand (gko) <pair_lj_expand>`
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* :doc:`lj/expand/coul/long (gk) <pair_lj_expand>`
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* :doc:`lj/expand/sphere (o) <pair_lj_expand_sphere>`
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* :doc:`lj/gromacs (gko) <pair_gromacs>`
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* :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
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* :doc:`lj/long/coul/long (iot) <pair_lj_long>`
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@ -186,7 +188,6 @@ OPT.
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* :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
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* :doc:`lj/mdf <pair_mdf>`
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* :doc:`lj/relres (o) <pair_lj_relres>`
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* :doc:`lj/sphere (o) <pair_lj_sphere>`
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* :doc:`lj/spica (gko) <pair_spica>`
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* :doc:`lj/spica/coul/long (go) <pair_spica>`
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* :doc:`lj/spica/coul/msm (o) <pair_spica>`
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@ -1,10 +1,10 @@
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.. index:: pair_style lj/sphere
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.. index:: pair_style lj/sphere/omp
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.. index:: pair_style lj/cut/sphere
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.. index:: pair_style lj/cut/sphere/omp
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pair_style lj/sphere command
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============================
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pair_style lj/cut/sphere command
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================================
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Accelerator Variant: *lj/sphere/omp*
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Accelerator Variant: *lj/cut/sphere/omp*
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Syntax
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""""""
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@ -13,12 +13,12 @@ Syntax
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pair_style style args
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* style = *lj/sphere*
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* style = *lj/cut/sphere*
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* args = list of arguments for a particular style
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.. parsed-literal::
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*lj/sphere* args = cutoff ratio
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*lj/cut/sphere* args = cutoff ratio
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cutoff = global cutoff ratio for Lennard Jones interactions (unitless)
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Examples
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@ -26,14 +26,14 @@ Examples
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.. code-block:: LAMMPS
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pair_style lj/sphere 2.5
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pair_style lj/cut/sphere 2.5
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pair_coeff * * 1.0
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pair_coeff 1 1 1.1 2.8
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Description
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"""""""""""
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The *lj/sphere* style compute the standard 12/6 Lennard-Jones potential,
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The *lj/cut/sphere* style compute the standard 12/6 Lennard-Jones potential,
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given by
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.. math::
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@ -106,7 +106,7 @@ is at :math:`2^{\frac{1}{6}} \sigma_{ij}`.
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group large variable large
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set group largea type 2
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pair_style lj/sphere 2.5
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pair_style lj/cut/sphere 2.5
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pair_coeff * * 1.0
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neighbor 0.3 multi
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@ -139,18 +139,18 @@ Mixing, shift, table, tail correction, restart, rRESPA info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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For atom type pairs I,J and I != J, the epsilon coefficients and cutoff
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ratio for the *lj/sphere* pair style can be mixed. The default mixing
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ratio for the *lj/cut/sphere* pair style can be mixed. The default mixing
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style is *geometric*. See the :doc:`pair_modify command <pair_modify>`
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for details.
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The *lj/sphere* pair style supports the :doc:`pair_modify shift <pair_modify>`
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The *lj/cut/sphere* pair style supports the :doc:`pair_modify shift <pair_modify>`
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option for the energy of the Lennard-Jones portion of the pair interaction.
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The *lj/sphere* pair style does *not* support the :doc:`pair_modify
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The *lj/cut/sphere* pair style does *not* support the :doc:`pair_modify
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<pair_modify>` tail option for adding a long-range tail corrections to
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the energy and pressure.
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The *lj/sphere* pair style writes its information to :doc:`binary
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The *lj/cut/sphere* pair style writes its information to :doc:`binary
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restart files <restart>`, so pair_style and pair_coeff commands do not
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need to be specified in an input script that reads a restart file.
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@ -163,11 +163,11 @@ This pair style can only be used via the *pair* keyword of the
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Restrictions
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""""""""""""
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The *lj/sphere* pair style is only enabled if LAMMPS was built with the
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The *lj/cut/sphere* pair style is only enabled if LAMMPS was built with the
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EXTRA-PAIR package. See the :doc:`Build package <Build_package>` page
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for more info.
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The *lj/sphere* pair style does not support the *sixthpower* mixing rule.
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The *lj/cut/sphere* pair style does not support the *sixthpower* mixing rule.
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----------
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@ -176,6 +176,7 @@ Related commands
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* :doc:`pair_coeff <pair_coeff>`
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* :doc:`pair_style lj/cut <pair_lj>`
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* :doc:`pair_style lj/expnd/sphere <pair_lj_expand_sphere>`
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Default
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"""""""
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184
doc/src/pair_lj_expand_sphere.rst
Normal file
184
doc/src/pair_lj_expand_sphere.rst
Normal file
@ -0,0 +1,184 @@
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.. index:: pair_style lj/expand/sphere
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.. index:: pair_style lj/expand/sphere/omp
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pair_style lj/expand/sphere command
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===================================
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Accelerator Variant: *lj/expand/sphere/omp*
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Syntax
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""""""
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.. code-block:: LAMMPS
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pair_style style args
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* style = *lj/expand/sphere*
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* args = list of arguments for a particular style
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.. parsed-literal::
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*lj/expand/sphere* args = cutoff ratio
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cutoff = global cutoff ratio for Lennard Jones interactions (unitless)
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Examples
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""""""""
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.. code-block:: LAMMPS
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pair_style lj/expand/sphere 2.5
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pair_coeff * * 1.0
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pair_coeff 1 1 1.1 2.8
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Description
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"""""""""""
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The *lj/expand/sphere* style compute the standard 12/6 Lennard-Jones potential,
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given by
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.. math::
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E = 4 \epsilon \left[ \left(\frac{\sigma_{ij}}{r}\right)^{12} -
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\left(\frac{\sigma_{ij}}{r}\right)^6 \right] \qquad r < r_c * \sigma_{ij}
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:math:`r_c` is the cutoff ratio.
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This is the same potential function used by the :doc:`lj/cut
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<pair_lj>` pair style, but the :math:`\sigma_{ij}` parameter is not
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set as a per-type parameter via the :doc:`pair_coeff command
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<pair_coeff>`. Instead it is calculated individually for each pair
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using the per-atom diameter attribute of :doc:`atom_style sphere
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<atom_style>` for the two atoms as :math:`\sigma_{i}` and
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:math:`\sigma_{j}`; :math:`\sigma_{ij}` is then computed by the mixing
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rule for pair coefficients as set by the :doc:`pair_modify mix
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<pair_modify>` command (defaults to geometric mixing). The cutoff is
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not specified as a distance, but as ratio that is internally
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multiplied by :math:`\sigma_{ij}` to obtain the actual cutoff for each
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pair of atoms.
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Note that :math:`\sigma_{ij}` is defined in the LJ formula above as the
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zero-crossing distance for the potential, *not* as the energy minimum which
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is at :math:`2^{\frac{1}{6}} \sigma_{ij}`.
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.. admonition:: Notes on cutoffs, neighbor lists, and efficiency
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:class: note
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If your system is mildly polydisperse, meaning the ratio of the
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diameter of the largest particle to the smallest is less than 2.0,
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then the neighbor lists built by the code should be resonably
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efficient. Which means they will not contain too many particle
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pairs that do not interact. However, if your system is highly
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polydisperse (ratio > 2.0), the neighbor list build and force
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computations may be inefficient. There are two ways to try and
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speed up the computations.
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The first is to assign multiple atom types so that atoms of each
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type are similar in size. E.g. if particle diameters range from 1
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to 5 use 4 atom types, ensuring atoms of type 1 have diameters from
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1.0-2.0, type 2 from 2.0-3.0, etc.
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The second is to try the :doc:`neighbor multi <neighbor>` command
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which uses a different algorithm for buliding neighbor lists. This
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will also require that you assign multiple atom types as in the
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preceeding paragraph.
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Here are example input script commands using both ideas for a
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highly polydisperse system:
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.. code-block:: c++
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units lj
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atom_style sphere
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lattice fcc 0.8442
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region box block 0 10 0 10 0 10
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create_box 2 box
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create_atoms 1 box
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# create atoms with random diameters from bimodal distribution
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variable switch atom random(0.0,1.0,345634)
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variable diam atom (v_switch<0.75)*normal(0.4,0.075,325)+(v_switch>=0.7)*normal(1.2,0.2,453)
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set group all diameter v_diam
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# assign type 2 to atoms with diameter > 0.5
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variable large atom 2.0*radius>0.5
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group large variable large
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set group largea type 2
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pair_style lj/expand/sphere 2.5
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pair_coeff * * 1.0
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neighbor 0.3 multi
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Coefficients
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""""""""""""
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The following coefficients must be defined for each pair of atoms types via the
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:doc:`pair_coeff <pair_coeff>` command as in the examples above, or in the data
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file or restart files read by the :doc:`read_data <read_data>` or
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:doc:`read_restart <read_restart>` commands, or by mixing as described below:
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* :math:`\epsilon` (energy units)
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* LJ cutoff ratio (unitless) (optional)
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The last coefficient is optional. If not specified, the global LJ
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cutoff ratio specified in the :doc:`pair_style command <pair_style>` is
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used.
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If a repulsive only LJ interaction is desired, the coefficient for the cutoff
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ratio should be set to the minimum of the LJ potential using ``$(2.0^(1.0/6.0))``
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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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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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For atom type pairs I,J and I != J, the epsilon coefficients and cutoff
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ratio for the *lj/expand/sphere* pair style can be mixed. The default mixing
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style is *geometric*. See the :doc:`pair_modify command <pair_modify>`
|
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for details.
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The *lj/expand/sphere* pair style supports the :doc:`pair_modify shift <pair_modify>`
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option for the energy of the Lennard-Jones portion of the pair interaction.
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The *lj/expand/sphere* pair style does *not* support the :doc:`pair_modify
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<pair_modify>` tail option for adding a long-range tail corrections to
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the energy and pressure.
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The *lj/expand/sphere* pair style writes its information to :doc:`binary
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restart files <restart>`, so pair_style and pair_coeff commands do not
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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
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:doc:`run_style respa <run_style>` command. It does *not* support the
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*inner*, *middle*, *outer* keywords.
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----------
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Restrictions
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""""""""""""
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The *lj/expand/sphere* pair style is only enabled if LAMMPS was built with the
|
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EXTRA-PAIR package. See the :doc:`Build package <Build_package>` page
|
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for more info.
|
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|
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The *lj/expand/sphere* pair style does not support the *sixthpower* mixing rule.
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----------
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Related commands
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""""""""""""""""
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* :doc:`pair_coeff <pair_coeff>`
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* :doc:`pair_style lj/cut <pair_lj>`
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* :doc:`pair_style lj/cut/sphere <pair_lj_cut_sphere>`
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Default
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"""""""
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none
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@ -250,12 +250,14 @@ accelerated styles exist.
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* :doc:`lj/cut/dipole/cut <pair_dipole>` - point dipoles with cutoff
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* :doc:`lj/cut/dipole/long <pair_dipole>` - point dipoles with long-range Ewald
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* :doc:`lj/cut/soft <pair_fep_soft>` - LJ with a soft core
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* :doc:`lj/cut/sphere <pair_lj_cut_sphere>` - LJ where per-atom radius is used as LJ sigma
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* :doc:`lj/cut/thole/long <pair_thole>` - LJ with Coulomb with thole damping
|
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* :doc:`lj/cut/tip4p/cut <pair_lj_cut_tip4p>` - LJ with cutoff Coulomb for TIP4P water
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* :doc:`lj/cut/tip4p/long <pair_lj_cut_tip4p>` - LJ with long-range Coulomb for TIP4P water
|
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* :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>` - LJ with cutoff Coulomb for TIP4P water with a soft core
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* :doc:`lj/expand <pair_lj_expand>` - Lennard-Jones for variable size particles
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* :doc:`lj/expand/coul/long <pair_lj_expand>` - Lennard-Jones for variable size particles with long-range Coulomb
|
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* :doc:`lj/expand/sphere <pair_lj_sphere>` - Variable size LJ where per-atom radius is used as delta (size)
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* :doc:`lj/gromacs <pair_gromacs>` - GROMACS-style Lennard-Jones potential
|
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* :doc:`lj/gromacs/coul/gromacs <pair_gromacs>` - GROMACS-style LJ and Coulomb potential
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* :doc:`lj/long/coul/long <pair_lj_long>` - long-range LJ and long-range Coulomb
|
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@ -264,7 +266,6 @@ accelerated styles exist.
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* :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulomb for TIP4P water
|
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* :doc:`lj/mdf <pair_mdf>` - LJ potential with a taper function
|
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* :doc:`lj/relres <pair_lj_relres>` - LJ using multiscale Relative Resolution (RelRes) methodology :ref:`(Chaimovich) <Chaimovich2>`.
|
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* :doc:`lj/sphere <pair_lj_sphere>` - LJ where per-atom radius is used as LJ sigma
|
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* :doc:`lj/spica <pair_spica>` - LJ for SPICA coarse-graining
|
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* :doc:`lj/spica/coul/long <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb
|
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* :doc:`lj/spica/coul/msm <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb via MSM
|
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|
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4
src/.gitignore
vendored
4
src/.gitignore
vendored
@ -1249,6 +1249,8 @@
|
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/pair_lj_cut_dipole_long.h
|
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/pair_lj_cut_*hars_*.cpp
|
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/pair_lj_cut_*hars_*.h
|
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/pair_lj_cut_sphere.cpp
|
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/pair_lj_cut_sphere.h
|
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/pair_lj_cut_soft.cpp
|
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/pair_lj_cut_soft.h
|
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/pair_lj_cut_tip4p_long.cpp
|
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@ -1263,6 +1265,8 @@
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/pair_lj_long_tip4p_long.h
|
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/pair_lj_cut_tgpu.cpp
|
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/pair_lj_cut_tgpu.h
|
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/pair_lj_expand_sphere.cpp
|
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/pair_lj_expand_sphere.h
|
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/pair_lj_spica.cpp
|
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/pair_lj_spica.h
|
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/pair_lj_spica_coul_long.cpp
|
||||
|
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@ -11,7 +11,7 @@
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
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|
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#include "pair_lj_sphere.h"
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#include "pair_lj_cut_sphere.h"
|
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|
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#include "atom.h"
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#include "comm.h"
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@ -32,14 +32,15 @@ using MathSpecial::square;
|
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|
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/* ---------------------------------------------------------------------- */
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|
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PairLJSphere::PairLJSphere(LAMMPS *lmp) : Pair(lmp), rmax(nullptr), cut(nullptr), epsilon(nullptr)
|
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PairLJCutSphere::PairLJCutSphere(LAMMPS *lmp) :
|
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Pair(lmp), rmax(nullptr), cut(nullptr), epsilon(nullptr)
|
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{
|
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writedata = 1;
|
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}
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|
||||
/* ---------------------------------------------------------------------- */
|
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|
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PairLJSphere::~PairLJSphere()
|
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PairLJCutSphere::~PairLJCutSphere()
|
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{
|
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if (allocated) {
|
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memory->destroy(setflag);
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@ -53,7 +54,7 @@ PairLJSphere::~PairLJSphere()
|
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|
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/* ---------------------------------------------------------------------- */
|
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|
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void PairLJSphere::compute(int eflag, int vflag)
|
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void PairLJCutSphere::compute(int eflag, int vflag)
|
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{
|
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int i, j, ii, jj, inum, jnum, itype, jtype;
|
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double xtmp, ytmp, ztmp, rtmp, delx, dely, delz, evdwl, sigma, sigma6, fpair;
|
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@ -145,7 +146,7 @@ void PairLJSphere::compute(int eflag, int vflag)
|
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allocate all arrays
|
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------------------------------------------------------------------------- */
|
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|
||||
void PairLJSphere::allocate()
|
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void PairLJCutSphere::allocate()
|
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{
|
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allocated = 1;
|
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int n = atom->ntypes + 1;
|
||||
@ -165,7 +166,7 @@ void PairLJSphere::allocate()
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJSphere::settings(int narg, char **arg)
|
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void PairLJCutSphere::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR, "Illegal pair_style command");
|
||||
|
||||
@ -185,7 +186,7 @@ void PairLJSphere::settings(int narg, char **arg)
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJSphere::coeff(int narg, char **arg)
|
||||
void PairLJCutSphere::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
@ -215,13 +216,14 @@ void PairLJSphere::coeff(int narg, char **arg)
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJSphere::init_style()
|
||||
void PairLJCutSphere::init_style()
|
||||
{
|
||||
Pair::init_style();
|
||||
|
||||
if (!atom->radius_flag) error->all(FLERR, "Pair style lj/sphere requires atom attribute radius");
|
||||
if (!atom->radius_flag)
|
||||
error->all(FLERR, "Pair style lj/cut/sphere requires atom attribute radius");
|
||||
if (mix_flag == SIXTHPOWER)
|
||||
error->all(FLERR, "Pair_modify mix sixthpower is not compatible with pair style lj/sphere");
|
||||
error->all(FLERR, "Pair_modify mix sixthpower is not compatible with pair style lj/cut/sphere");
|
||||
|
||||
// determine max radius per type
|
||||
|
||||
@ -241,7 +243,7 @@ void PairLJSphere::init_style()
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJSphere::init_one(int i, int j)
|
||||
double PairLJCutSphere::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], 0.0, 0.0);
|
||||
@ -260,7 +262,7 @@ double PairLJSphere::init_one(int i, int j)
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJSphere::write_restart(FILE *fp)
|
||||
void PairLJCutSphere::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
@ -279,7 +281,7 @@ void PairLJSphere::write_restart(FILE *fp)
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJSphere::read_restart(FILE *fp)
|
||||
void PairLJCutSphere::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
@ -305,7 +307,7 @@ void PairLJSphere::read_restart(FILE *fp)
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJSphere::write_restart_settings(FILE *fp)
|
||||
void PairLJCutSphere::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_global, sizeof(double), 1, fp);
|
||||
fwrite(&offset_flag, sizeof(int), 1, fp);
|
||||
@ -316,7 +318,7 @@ void PairLJSphere::write_restart_settings(FILE *fp)
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJSphere::read_restart_settings(FILE *fp)
|
||||
void PairLJCutSphere::read_restart_settings(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) {
|
||||
@ -333,7 +335,7 @@ void PairLJSphere::read_restart_settings(FILE *fp)
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJSphere::write_data(FILE *fp)
|
||||
void PairLJCutSphere::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d %g\n", i, epsilon[i][i]);
|
||||
}
|
||||
@ -342,7 +344,7 @@ void PairLJSphere::write_data(FILE *fp)
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJSphere::write_data_all(FILE *fp)
|
||||
void PairLJCutSphere::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
@ -351,8 +353,8 @@ void PairLJSphere::write_data_all(FILE *fp)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJSphere::single(int i, int j, int itype, int jtype, double rsq, double /*factor_coul*/,
|
||||
double factor_lj, double &fforce)
|
||||
double PairLJCutSphere::single(int i, int j, int itype, int jtype, double rsq,
|
||||
double /*factor_coul*/, double factor_lj, double &fforce)
|
||||
{
|
||||
double r2inv, r6inv, rcutsq, sigma, sigma6, forcelj, philj;
|
||||
|
||||
@ -374,7 +376,7 @@ double PairLJSphere::single(int i, int j, int itype, int jtype, double rsq, doub
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairLJSphere::extract(const char *str, int &dim)
|
||||
void *PairLJCutSphere::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 2;
|
||||
if (strcmp(str, "epsilon") == 0) return (void *) epsilon;
|
||||
@ -13,21 +13,21 @@
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
// clang-format off
|
||||
PairStyle(lj/sphere,PairLJSphere);
|
||||
PairStyle(lj/cut/sphere,PairLJCutSphere);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_SPHERE_H
|
||||
#define LMP_PAIR_LJ_SPHERE_H
|
||||
#ifndef LMP_PAIR_LJ_CUT_SPHERE_H
|
||||
#define LMP_PAIR_LJ_CUT_SPHERE_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJSphere : public Pair {
|
||||
class PairLJCutSphere : public Pair {
|
||||
public:
|
||||
PairLJSphere(class LAMMPS *);
|
||||
~PairLJSphere() override;
|
||||
PairLJCutSphere(class LAMMPS *);
|
||||
~PairLJCutSphere() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
385
src/EXTRA-PAIR/pair_lj_expand_sphere.cpp
Normal file
385
src/EXTRA-PAIR/pair_lj_expand_sphere.cpp
Normal file
@ -0,0 +1,385 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_lj_expand_sphere.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_special.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neighbor.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using MathSpecial::powint;
|
||||
using MathSpecial::square;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJExpandSphere::PairLJExpandSphere(LAMMPS *lmp) :
|
||||
Pair(lmp), rmax(nullptr), cut(nullptr), epsilon(nullptr)
|
||||
{
|
||||
writedata = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJExpandSphere::~PairLJExpandSphere()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(rmax);
|
||||
memory->destroy(cut);
|
||||
memory->destroy(epsilon);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphere::compute(int eflag, int vflag)
|
||||
{
|
||||
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||
double xtmp, ytmp, ztmp, rtmp, delx, dely, delz, evdwl, sigma, sigma6, fpair;
|
||||
double rcutsq, rsq, r2inv, r6inv, forcelj, factor_lj;
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *radius = atom->radius;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
rtmp = radius[i];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
|
||||
// cutsq is maximum cutoff per type. Now compute and apply real cutoff
|
||||
|
||||
sigma = 2.0 * mix_distance(rtmp, radius[j]);
|
||||
rcutsq = square(cut[itype][jtype] * sigma);
|
||||
if (rsq < rcutsq) {
|
||||
|
||||
r2inv = 1.0 / rsq;
|
||||
r6inv = r2inv * r2inv * r2inv;
|
||||
sigma6 = powint(sigma, 6);
|
||||
forcelj = r6inv * 24.0 * epsilon[itype][jtype] * (2.0 * sigma6 * sigma6 * r6inv - sigma6);
|
||||
fpair = factor_lj * forcelj * r2inv;
|
||||
|
||||
f[i][0] += delx * fpair;
|
||||
f[i][1] += dely * fpair;
|
||||
f[i][2] += delz * fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx * fpair;
|
||||
f[j][1] -= dely * fpair;
|
||||
f[j][2] -= delz * fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
evdwl = r6inv * 4.0 * epsilon[itype][jtype];
|
||||
evdwl *= sigma6 * sigma6 * r6inv - sigma6;
|
||||
if (offset_flag && (rcutsq > 0.0)) {
|
||||
double ratio6 = sigma6 / powint(rcutsq, 3);
|
||||
evdwl -= 4.0 * epsilon[itype][jtype] * (ratio6 * ratio6 - ratio6);
|
||||
}
|
||||
evdwl *= factor_lj;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphere::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes + 1;
|
||||
|
||||
memory->create(setflag, n, n, "pair:setflag");
|
||||
for (int i = 1; i < n; i++)
|
||||
for (int j = i; j < n; j++) setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq, n, n, "pair:cutsq");
|
||||
|
||||
memory->create(rmax, n, "pair:rmax");
|
||||
memory->create(cut, n, n, "pair:cut");
|
||||
memory->create(epsilon, n, n, "pair:epsilon");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphere::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR, "Illegal pair_style command");
|
||||
|
||||
cut_global = utils::numeric(FLERR, arg[0], false, lmp);
|
||||
|
||||
// reset cutoffs that have been explicitly set
|
||||
|
||||
if (allocated) {
|
||||
int i, j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++)
|
||||
if (setflag[i][j]) cut[i][j] = cut_global;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphere::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
|
||||
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
|
||||
|
||||
double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double cut_one = cut_global;
|
||||
if (narg == 5) cut_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo, i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
cut[i][j] = cut_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphere::init_style()
|
||||
{
|
||||
Pair::init_style();
|
||||
|
||||
if (!atom->radius_flag)
|
||||
error->all(FLERR, "Pair style lj/expand/sphere requires atom attribute radius");
|
||||
if (mix_flag == SIXTHPOWER)
|
||||
error->all(FLERR,
|
||||
"Pair_modify mix sixthpower is not compatible with pair style lj/expand/sphere");
|
||||
|
||||
// determine max radius per type
|
||||
|
||||
int *type = atom->type;
|
||||
double *radius = atom->radius;
|
||||
rmax[0] = 0.0;
|
||||
for (int itype = 1; itype <= atom->ntypes; ++itype) {
|
||||
double rmax_one = 0.0;
|
||||
for (int i = 0; i < atom->nlocal; ++i) {
|
||||
if (type[i] == itype) rmax_one = MAX(rmax_one, radius[i]);
|
||||
}
|
||||
MPI_Allreduce(&rmax_one, &rmax[itype], 1, MPI_DOUBLE, MPI_MAX, world);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJExpandSphere::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], 0.0, 0.0);
|
||||
cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
|
||||
}
|
||||
|
||||
epsilon[j][i] = epsilon[i][j];
|
||||
cut[j][i] = cut[i][j];
|
||||
|
||||
// since cut is a scaled by the mixed diameter, report maximum possible cutoff.
|
||||
|
||||
return cut[i][j] * 2.0 * mix_distance(rmax[i], rmax[j]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphere::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i, j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j], sizeof(int), 1, fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&epsilon[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&cut[i][j], sizeof(double), 1, fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphere::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
int i, j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
|
||||
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
|
||||
if (setflag[i][j]) {
|
||||
if (me == 0) {
|
||||
utils::sfread(FLERR, &epsilon[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphere::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_global, sizeof(double), 1, fp);
|
||||
fwrite(&offset_flag, sizeof(int), 1, fp);
|
||||
fwrite(&mix_flag, sizeof(int), 1, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphere::read_restart_settings(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) {
|
||||
utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world);
|
||||
MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphere::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d %g\n", i, epsilon[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphere::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp, "%d %d %g %g\n", i, j, epsilon[i][j], cut[i][j]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJExpandSphere::single(int i, int j, int itype, int jtype, double rsq,
|
||||
double /*factor_coul*/, double factor_lj, double &fforce)
|
||||
{
|
||||
double r2inv, r6inv, rcutsq, sigma, sigma6, forcelj, philj;
|
||||
|
||||
sigma = 2.0 * mix_distance(atom->radius[i], atom->radius[j]);
|
||||
rcutsq = square(cut[itype][jtype] * sigma);
|
||||
sigma6 = powint(sigma, 6);
|
||||
r2inv = 1.0 / rsq;
|
||||
r6inv = r2inv * r2inv * r2inv;
|
||||
forcelj = r6inv * 24.0 * epsilon[itype][jtype] * (sigma6 * sigma6 * r6inv - sigma6);
|
||||
fforce = factor_lj * forcelj * r2inv;
|
||||
|
||||
philj = r6inv * 4.0 * epsilon[itype][jtype] * (sigma6 * sigma6 * r6inv - sigma6);
|
||||
if (offset_flag && (rcutsq > 0.0)) {
|
||||
double ratio6 = sigma6 / powint(rcutsq, 3);
|
||||
philj -= 4.0 * epsilon[itype][jtype] * (ratio6 * ratio6 - ratio6);
|
||||
}
|
||||
return factor_lj * philj;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairLJExpandSphere::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 2;
|
||||
if (strcmp(str, "epsilon") == 0) return (void *) epsilon;
|
||||
return nullptr;
|
||||
}
|
||||
58
src/EXTRA-PAIR/pair_lj_expand_sphere.h
Normal file
58
src/EXTRA-PAIR/pair_lj_expand_sphere.h
Normal file
@ -0,0 +1,58 @@
|
||||
/* -*- 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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
// clang-format off
|
||||
PairStyle(lj/expand/sphere,PairLJExpandSphere);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_EXPAND_SPHERE_H
|
||||
#define LMP_PAIR_LJ_EXPAND_SPHERE_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJExpandSphere : public Pair {
|
||||
public:
|
||||
PairLJExpandSphere(class LAMMPS *);
|
||||
~PairLJExpandSphere() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
void write_data_all(FILE *) override;
|
||||
double single(int, int, int, int, double, double, double, double &) override;
|
||||
void *extract(const char *, int &) override;
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double *rmax;
|
||||
double **cut;
|
||||
double **epsilon;
|
||||
double **sigma;
|
||||
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -12,7 +12,7 @@
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_lj_sphere_omp.h"
|
||||
#include "pair_lj_cut_sphere_omp.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
@ -28,14 +28,14 @@ using MathSpecial::square;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJSphereOMP::PairLJSphereOMP(LAMMPS *lmp) : PairLJSphere(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
PairLJCutSphereOMP::PairLJCutSphereOMP(LAMMPS *lmp) : PairLJCutSphere(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJSphereOMP::compute(int eflag, int vflag)
|
||||
void PairLJCutSphereOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
@ -78,7 +78,7 @@ void PairLJSphereOMP::compute(int eflag, int vflag)
|
||||
}
|
||||
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void PairLJSphereOMP::eval(int iifrom, int iito, ThrData *const thr)
|
||||
void PairLJCutSphereOMP::eval(int iifrom, int iito, ThrData *const thr)
|
||||
{
|
||||
const auto *_noalias const x = (dbl3_t *) atom->x[0];
|
||||
auto *_noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
@ -172,10 +172,10 @@ void PairLJSphereOMP::eval(int iifrom, int iito, ThrData *const thr)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJSphereOMP::memory_usage()
|
||||
double PairLJCutSphereOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJSphere::memory_usage();
|
||||
bytes += PairLJCutSphere::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
@ -17,22 +17,22 @@
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
// clang-format off
|
||||
PairStyle(lj/sphere/omp,PairLJSphereOMP);
|
||||
PairStyle(lj/cut/sphere/omp,PairLJCutSphereOMP);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_SPHERE_OMP_H
|
||||
#define LMP_PAIR_LJ_SPHERE_OMP_H
|
||||
#ifndef LMP_PAIR_LJ_CUT_SPHERE_OMP_H
|
||||
#define LMP_PAIR_LJ_CUT_SPHERE_OMP_H
|
||||
|
||||
#include "pair_lj_sphere.h"
|
||||
#include "pair_lj_cut_sphere.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJSphereOMP : public PairLJSphere, public ThrOMP {
|
||||
class PairLJCutSphereOMP : public PairLJCutSphere, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJSphereOMP(class LAMMPS *);
|
||||
PairLJCutSphereOMP(class LAMMPS *);
|
||||
|
||||
void compute(int, int) override;
|
||||
double memory_usage() override;
|
||||
181
src/OPENMP/pair_lj_expand_sphere_omp.cpp
Normal file
181
src/OPENMP/pair_lj_expand_sphere_omp.cpp
Normal file
@ -0,0 +1,181 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
This software is distributed under the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_lj_expand_sphere_omp.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "math_special.h"
|
||||
#include "neigh_list.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#include "omp_compat.h"
|
||||
using namespace LAMMPS_NS;
|
||||
using MathSpecial::powint;
|
||||
using MathSpecial::square;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJExpandSphereOMP::PairLJExpandSphereOMP(LAMMPS *lmp) : PairLJExpandSphere(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJExpandSphereOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
const int nall = atom->nlocal + atom->nghost;
|
||||
const int nthreads = comm->nthreads;
|
||||
const int inum = list->inum;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag, vflag)
|
||||
#endif
|
||||
{
|
||||
int ifrom, ito, tid;
|
||||
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr);
|
||||
|
||||
if (evflag) {
|
||||
if (eflag) {
|
||||
if (force->newton_pair)
|
||||
eval<1, 1, 1>(ifrom, ito, thr);
|
||||
else
|
||||
eval<1, 1, 0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (force->newton_pair)
|
||||
eval<1, 0, 1>(ifrom, ito, thr);
|
||||
else
|
||||
eval<1, 0, 0>(ifrom, ito, thr);
|
||||
}
|
||||
} else {
|
||||
if (force->newton_pair)
|
||||
eval<0, 0, 1>(ifrom, ito, thr);
|
||||
else
|
||||
eval<0, 0, 0>(ifrom, ito, thr);
|
||||
}
|
||||
thr->timer(Timer::PAIR);
|
||||
reduce_thr(this, eflag, vflag, thr);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void PairLJExpandSphereOMP::eval(int iifrom, int iito, ThrData *const thr)
|
||||
{
|
||||
const auto *_noalias const x = (dbl3_t *) atom->x[0];
|
||||
auto *_noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
const double *_noalias const radius = atom->radius;
|
||||
const int *_noalias const type = atom->type;
|
||||
const double *_noalias const special_lj = force->special_lj;
|
||||
const int *_noalias const ilist = list->ilist;
|
||||
const int *_noalias const numneigh = list->numneigh;
|
||||
const int *const *const firstneigh = list->firstneigh;
|
||||
|
||||
double xtmp, ytmp, ztmp, rtmp, delx, dely, delz, fxtmp, fytmp, fztmp;
|
||||
double rcutsq, rsq, r2inv, r6inv, forcelj, factor_lj, evdwl, sigma, sigma6, fpair;
|
||||
|
||||
const int nlocal = atom->nlocal;
|
||||
int j, jj, jnum, jtype;
|
||||
|
||||
evdwl = 0.0;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (int ii = iifrom; ii < iito; ++ii) {
|
||||
const int i = ilist[ii];
|
||||
const int itype = type[i];
|
||||
const int *_noalias const jlist = firstneigh[i];
|
||||
const double *_noalias const epsiloni = epsilon[itype];
|
||||
const double *_noalias const cutsqi = cutsq[itype];
|
||||
|
||||
xtmp = x[i].x;
|
||||
ytmp = x[i].y;
|
||||
ztmp = x[i].z;
|
||||
rtmp = radius[i];
|
||||
jnum = numneigh[i];
|
||||
fxtmp = fytmp = fztmp = 0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j].x;
|
||||
dely = ytmp - x[j].y;
|
||||
delz = ztmp - x[j].z;
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsqi[jtype]) {
|
||||
|
||||
// cutsq is maximum cutoff per type. Now compute and apply real cutoff
|
||||
|
||||
sigma = 2.0 * mix_distance(rtmp, radius[j]);
|
||||
rcutsq = square(cut[itype][jtype] * sigma);
|
||||
|
||||
if (rsq < rcutsq) {
|
||||
|
||||
r2inv = 1.0 / rsq;
|
||||
r6inv = r2inv * r2inv * r2inv;
|
||||
|
||||
sigma6 = powint(sigma, 6);
|
||||
forcelj = r6inv * 24.0 * epsiloni[jtype] * (2.0 * sigma6 * sigma6 * r6inv - sigma6);
|
||||
fpair = factor_lj * forcelj * r2inv;
|
||||
|
||||
fxtmp += delx * fpair;
|
||||
fytmp += dely * fpair;
|
||||
fztmp += delz * fpair;
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
f[j].x -= delx * fpair;
|
||||
f[j].y -= dely * fpair;
|
||||
f[j].z -= delz * fpair;
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
evdwl = r6inv * 4.0 * epsiloni[jtype];
|
||||
evdwl *= sigma6 * sigma6 * r6inv - sigma6;
|
||||
if (offset_flag && (cutsqi[jtype] > 0.0)) {
|
||||
const double ratio6 = sigma6 / powint(rcutsq, 3);
|
||||
evdwl -= 4.0 * epsiloni[jtype] * (ratio6 * ratio6 - ratio6);
|
||||
}
|
||||
evdwl *= factor_lj;
|
||||
}
|
||||
|
||||
if (EVFLAG)
|
||||
ev_tally_thr(this, i, j, nlocal, NEWTON_PAIR, evdwl, 0.0, fpair, delx, dely, delz, thr);
|
||||
}
|
||||
}
|
||||
}
|
||||
f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJExpandSphereOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJExpandSphere::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
46
src/OPENMP/pair_lj_expand_sphere_omp.h
Normal file
46
src/OPENMP/pair_lj_expand_sphere_omp.h
Normal file
@ -0,0 +1,46 @@
|
||||
/* -*- 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: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
// clang-format off
|
||||
PairStyle(lj/expand/sphere/omp,PairLJExpandSphereOMP);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_EXPAND_SPHERE_OMP_H
|
||||
#define LMP_PAIR_LJ_EXPAND_SPHERE_OMP_H
|
||||
|
||||
#include "pair_lj_expand_sphere.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJExpandSphereOMP : public PairLJExpandSphere, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJExpandSphereOMP(class LAMMPS *);
|
||||
|
||||
void compute(int, int) override;
|
||||
double memory_usage() override;
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData *const thr);
|
||||
};
|
||||
} // namespace LAMMPS_NS
|
||||
#endif
|
||||
#endif
|
||||
@ -4,7 +4,7 @@ date_generated: Thu Mar 30 14:38:22 2023
|
||||
epsilon: 7.5e-13
|
||||
skip_tests: single
|
||||
prerequisites: ! |
|
||||
pair lj/sphere
|
||||
pair lj/cut/sphere
|
||||
atom sphere
|
||||
pre_commands: ! |
|
||||
echo screen
|
||||
@ -21,7 +21,7 @@ pre_commands: ! |
|
||||
velocity all create 3.0 4534624 loop geom
|
||||
post_commands: ! ""
|
||||
input_file: in.empty
|
||||
pair_style: lj/sphere 2.5
|
||||
pair_style: lj/cut/sphere 2.5
|
||||
pair_coeff: ! |
|
||||
1 1 1.0
|
||||
extract: ! |
|
||||
104
unittest/force-styles/tests/atomic-pair-lj_expand_sphere.yaml
Normal file
104
unittest/force-styles/tests/atomic-pair-lj_expand_sphere.yaml
Normal file
@ -0,0 +1,104 @@
|
||||
---
|
||||
lammps_version: 28 Mar 2023
|
||||
date_generated: Thu Mar 30 14:38:22 2023
|
||||
epsilon: 7.5e-13
|
||||
skip_tests: single
|
||||
prerequisites: ! |
|
||||
pair lj/expand/sphere
|
||||
atom sphere
|
||||
pre_commands: ! |
|
||||
echo screen
|
||||
atom_modify map array
|
||||
units lj
|
||||
atom_style sphere
|
||||
lattice fcc 0.8442
|
||||
region box block 0 2 0 2 0 2
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
displace_atoms all random 0.1 0.1 0.1 623426
|
||||
set group all diameter 1.0
|
||||
set group all mass 1.0
|
||||
velocity all create 3.0 4534624 loop geom
|
||||
post_commands: ! ""
|
||||
input_file: in.empty
|
||||
pair_style: lj/expand/sphere 2.5
|
||||
pair_coeff: ! |
|
||||
1 1 1.0
|
||||
extract: ! |
|
||||
epsilon 2
|
||||
natoms: 32
|
||||
init_vdwl: -116.44208632277189
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
2.8031747808711788e+02 3.3753332096206151e+02 3.6161491443553058e+02 9.1207933030798330e+01 1.5243342905404037e+02 -9.9498392667113833e+01
|
||||
init_forces: ! |2
|
||||
1 -1.4586568952535859e+02 -2.1931945697523867e+02 8.3668114906961620e+01
|
||||
2 1.5110060734448868e+02 1.6194983298501683e+02 5.1680305209387697e+01
|
||||
3 -4.1775824251599438e+01 1.2867107093830445e+00 -3.6313865233596999e+01
|
||||
4 2.9472326459801721e+01 8.8486535373136732e+01 -4.2617580722552610e+01
|
||||
5 5.2397837003192160e+00 2.0459375918115779e+01 -2.3426042702551680e+01
|
||||
6 9.6723821245494683e+00 -4.1806082480411575e+01 1.2511584321172965e+01
|
||||
7 -5.1675096093601567e+01 -4.0551926756618926e+01 -1.3294327178693157e+01
|
||||
8 -8.2578663162446531e+01 -2.0603180343277316e+02 1.1080781077571790e+02
|
||||
9 6.6563366218520699e+00 -1.3576270514928492e+01 -6.2990879039987373e+00
|
||||
10 1.2562028508263918e+01 7.1383899379197500e+00 -7.4200177576219133e+00
|
||||
11 -4.0616225569260138e+01 2.9426535484086656e+01 -1.5194870287132140e+01
|
||||
12 -1.2185920630572705e+01 2.0903918930070052e+01 2.3935223952337630e+01
|
||||
13 -1.0168289428829605e+02 1.2181428476742342e+02 -2.4970463716793029e+02
|
||||
14 1.1276607360598639e+01 2.0932524903784913e+00 -8.4445936145127263e+00
|
||||
15 2.1147814932644917e+02 7.2455411745058896e+01 1.3994698736930633e+02
|
||||
16 2.1307381939437682e+00 -9.7110437674312617e+00 1.6772426774878742e+01
|
||||
17 1.3917131309134271e+01 -4.3979124892489672e+01 5.9765040597753625e+01
|
||||
18 2.0607405082480078e+01 -3.0878340639707460e+01 1.4167531514432428e+01
|
||||
19 4.6190203936710283e+01 -1.1202702997067846e+01 -3.9476561053715500e+01
|
||||
20 -4.0392151835430383e+01 7.6413322558301815e+01 -9.9315439072912369e+01
|
||||
21 3.9812181220755775e+01 -8.0229922011073427e+00 4.8494181799577049e+01
|
||||
22 3.5117168233481337e+01 -5.0880287326141598e+01 8.1590667313257761e+00
|
||||
23 -3.3183438691899802e+01 5.8452017613468186e+01 1.3689689859305707e+01
|
||||
24 -7.0085612135333859e+00 -1.4882951194443576e+01 -1.6978104605753799e+01
|
||||
25 -2.6945478276353324e+01 1.4989629752987154e+01 2.2837312716809768e+00
|
||||
26 1.5934827401819398e+00 1.0517784981514938e+01 1.1915938970456459e+01
|
||||
27 2.8342468546108526e+00 3.3183558717337318e+00 -9.9597072230404908e+00
|
||||
28 1.0973021677369854e+02 -1.8959241094027011e+01 1.1838770808181975e+02
|
||||
29 -3.7698386363756697e+01 4.4468578018428147e+01 1.1140943290101237e+01
|
||||
30 -8.2712093475021490e+01 -4.7423589066212351e+01 -1.3330169888378890e+02
|
||||
31 -2.8868167685733068e+00 2.1403398282492340e+01 -3.1026283179188514e+01
|
||||
32 -2.1837556456164062e+00 1.6484779190829122e+00 5.4465311607738585e+00
|
||||
run_vdwl: -117.1001111727232
|
||||
run_coul: 0
|
||||
run_stress: ! |2-
|
||||
2.7695385711446124e+02 3.3278546187873974e+02 3.6006476859072728e+02 8.6715925372879269e+01 1.5264294056452928e+02 -9.6728681863809229e+01
|
||||
run_forces: ! |2
|
||||
1 -1.4371784794329676e+02 -2.1498566778457018e+02 8.3095590725041319e+01
|
||||
2 1.4875978675032550e+02 1.5837418598684059e+02 5.1936572842869772e+01
|
||||
3 -4.1902045381131956e+01 1.3746278031477663e+00 -3.7012679382131516e+01
|
||||
4 2.7963282998007497e+01 8.7029018636752809e+01 -4.2734730369263040e+01
|
||||
5 5.0038082469556810e+00 2.0394292459977670e+01 -2.3158066316063287e+01
|
||||
6 9.8078855865137822e+00 -4.1221556143424770e+01 1.2111606884041064e+01
|
||||
7 -4.9916678949523160e+01 -3.9032632064977967e+01 -1.3057662213781221e+01
|
||||
8 -7.9404298765990461e+01 -2.0228919740312625e+02 1.0842014530532373e+02
|
||||
9 6.5305851467989928e+00 -1.3836534088482027e+01 -6.3753564084228440e+00
|
||||
10 1.2948519162479368e+01 7.1663216684672859e+00 -7.9026502950718713e+00
|
||||
11 -4.0485527318703632e+01 2.9658129253905681e+01 -1.5413396670143056e+01
|
||||
12 -1.2384564654464873e+01 2.0906797996653175e+01 2.4583702026262241e+01
|
||||
13 -1.0117689275037893e+02 1.1973355069764031e+02 -2.4623920962306576e+02
|
||||
14 1.1129073511061154e+01 1.9554924379279703e+00 -8.3457798988948593e+00
|
||||
15 2.0816516562230623e+02 7.0803370473935900e+01 1.3842506215462157e+02
|
||||
16 2.1310828504091881e+00 -9.8135507177243841e+00 1.6536268967032719e+01
|
||||
17 1.3641628242862716e+01 -4.4119911040585336e+01 5.9614054383878042e+01
|
||||
18 2.1006853310301640e+01 -3.1211293326535454e+01 1.4241007813718358e+01
|
||||
19 4.6009040579610449e+01 -1.1345944054890328e+01 -3.9459071459686321e+01
|
||||
20 -4.0397130717929159e+01 7.5279993851872220e+01 -9.8511341807527316e+01
|
||||
21 4.0039315283046079e+01 -8.0137748724521511e+00 4.8660642711420813e+01
|
||||
22 3.5708168073593527e+01 -5.1821322839622454e+01 8.2819277512096683e+00
|
||||
23 -3.3113759560430822e+01 5.9072079885315674e+01 1.4264033179943622e+01
|
||||
24 -6.9593081581622727e+00 -1.4886965489878571e+01 -1.6947529042442767e+01
|
||||
25 -2.7405937853181872e+01 1.5364157291023506e+01 2.2982650066647481e+00
|
||||
26 1.5890405119239828e+00 1.0786544007531514e+01 1.2070193510601317e+01
|
||||
27 2.8643954209448790e+00 3.4431707338380022e+00 -1.0003156259622884e+01
|
||||
28 1.1184386324630830e+02 -1.8203684205576618e+01 1.2042827913401095e+02
|
||||
29 -3.8541921364351666e+01 4.5525124123081802e+01 1.1427605135155794e+01
|
||||
30 -8.4505523479161951e+01 -4.8548646933958288e+01 -1.3594721117648746e+02
|
||||
31 -2.9919458949399576e+00 2.0910279091646661e+01 -3.0672195920243109e+01
|
||||
32 -2.2381117518014042e+00 1.5535445662463561e+00 5.3850793110514772e+00
|
||||
...
|
||||
Reference in New Issue
Block a user