forked from lijiext/lammps
451 lines
17 KiB
Plaintext
451 lines
17 KiB
Plaintext
.. index:: kspace_style
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kspace_style command
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====================
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Syntax
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""""""
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.. parsed-literal::
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kspace_style style value
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* style = *none* or *ewald* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/omp* or *pppm/cg/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp*
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.. parsed-literal::
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*none* value = none
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*ewald* value = accuracy
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accuracy = desired relative error in forces
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*ewald/disp* value = accuracy
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accuracy = desired relative error in forces
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*ewald/omp* value = accuracy
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accuracy = desired relative error in forces
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*pppm* value = accuracy
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accuracy = desired relative error in forces
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*pppm/cg* value = accuracy (smallq)
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accuracy = desired relative error in forces
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smallq = cutoff for charges to be considered (optional) (charge units)
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*pppm/disp* value = accuracy
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accuracy = desired relative error in forces
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*pppm/tip4p* value = accuracy
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accuracy = desired relative error in forces
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*pppm/disp/tip4p* value = accuracy
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accuracy = desired relative error in forces
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*pppm/gpu* value = accuracy
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accuracy = desired relative error in forces
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*pppm/omp* value = accuracy
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accuracy = desired relative error in forces
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*pppm/cg/omp* value = accuracy
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accuracy = desired relative error in forces
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*pppm/tip4p/omp* value = accuracy
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accuracy = desired relative error in forces
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*pppm/stagger* value = accuracy
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accuracy = desired relative error in forces
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*msm* value = accuracy
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accuracy = desired relative error in forces
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*msm/cg* value = accuracy (smallq)
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accuracy = desired relative error in forces
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smallq = cutoff for charges to be considered (optional) (charge units)
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*msm/omp* value = accuracy
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accuracy = desired relative error in forces
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*msm/cg/omp* value = accuracy (smallq)
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accuracy = desired relative error in forces
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smallq = cutoff for charges to be considered (optional) (charge units)
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Examples
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""""""""
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.. parsed-literal::
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kspace_style pppm 1.0e-4
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kspace_style pppm/cg 1.0e-5 1.0e-6
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kspace style msm 1.0e-4
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kspace_style none
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Description
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"""""""""""
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Define a long-range solver for LAMMPS to use each timestep to compute
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long-range Coulombic interactions or long-range 1/r^6 interactions.
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Most of the long-range solvers perform their computation in K-space,
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hence the name of this command.
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When such a solver is used in conjunction with an appropriate pair
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style, the cutoff for Coulombic or 1/r^N interactions is effectively
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infinite. If the Coulombic case, this means each charge in the system
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interacts with charges in an infinite array of periodic images of the
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simulation domain.
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Note that using a long-range solver requires use of a matching :doc:`pair style <pair>` to perform consistent short-range pairwise
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calculations. This means that the name of the pair style contains a
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matching keyword to the name of the KSpace style, as in this table:
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+----------------------+-----------------------+
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| Pair style | KSpace style |
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+----------------------+-----------------------+
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| coul/long | ewald or pppm |
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+----------------------+-----------------------+
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| coul/msm | msm |
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+----------------------+-----------------------+
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| lj/long or buck/long | disp (for dispersion) |
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+----------------------+-----------------------+
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| tip4p/long | tip4p |
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+----------------------+-----------------------+
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----------
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The *ewald* style performs a standard Ewald summation as described in
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any solid-state physics text.
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The *ewald/disp* style adds a long-range dispersion sum option for
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1/r^6 potentials and is useful for simulation of interfaces
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:ref:`(Veld) <Veld>`. It also performs standard Coulombic Ewald summations,
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but in a more efficient manner than the *ewald* style. The 1/r^6
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capability means that Lennard-Jones or Buckingham potentials can be
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used without a cutoff, i.e. they become full long-range potentials.
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The *ewald/disp* style can also be used with point-dipoles
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:ref:`(Toukmaji) <Toukmaji>` and is currently the only kspace solver in
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LAMMPS with this capability.
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----------
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The *pppm* style invokes a particle-particle particle-mesh solver
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:ref:`(Hockney) <Hockney>` which maps atom charge to a 3d mesh, uses 3d FFTs
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to solve Poisson's equation on the mesh, then interpolates electric
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fields on the mesh points back to the atoms. It is closely related to
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the particle-mesh Ewald technique (PME) :ref:`(Darden) <Darden>` used in
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AMBER and CHARMM. The cost of traditional Ewald summation scales as
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N^(3/2) where N is the number of atoms in the system. The PPPM solver
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scales as Nlog(N) due to the FFTs, so it is almost always a faster
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choice :ref:`(Pollock) <Pollock>`.
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The *pppm/cg* style is identical to the *pppm* style except that it
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has an optimization for systems where most particles are uncharged.
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Similarly the *msm/cg* style implements the same optimization for *msm*\ .
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The optional *smallq* argument defines the cutoff for the absolute
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charge value which determines whether a particle is considered charged
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or not. Its default value is 1.0e-5.
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The *pppm/tip4p* style is identical to the *pppm* style except that it
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adds a charge at the massless 4th site in each TIP4P water molecule.
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It should be used with :doc:`pair styles <pair_style>` with a
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*tip4p/long* in their style name.
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The *pppm/stagger* style performs calculations using two different
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meshes, one shifted slightly with respect to the other. This can
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reduce force aliasing errors and increase the accuracy of the method
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for a given mesh size. Or a coarser mesh can be used for the same
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target accuracy, which saves CPU time. However, there is a trade-off
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since FFTs on two meshes are now performed which increases the
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compuation required. See :ref:`(Cerutti) <Cerutti>`, :ref:`(Neelov) <Neelov>`,
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and :ref:`(Hockney) <Hockney>` for details of the method.
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For high relative accuracy, using staggered PPPM allows the mesh size
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to be reduced by a factor of 2 in each dimension as compared to
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regular PPPM (for the same target accuracy). This can give up to a 4x
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speedup in the KSpace time (8x less mesh points, 2x more expensive).
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However, for low relative accuracy, the staggered PPPM mesh size may
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be essentially the same as for regular PPPM, which means the method
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will be up to 2x slower in the KSpace time (simply 2x more expensive).
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For more details and timings, see
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:doc:`Section_accelerate <Section_accelerate>`.
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.. note::
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Using *pppm/stagger* may not give the same increase in the
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accuracy of energy and pressure as it does in forces, so some caution
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must be used if energy and/or pressure are quantities of interest,
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such as when using a barostat.
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----------
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The *pppm/disp* and *pppm/disp/tip4p* styles add a mesh-based long-range
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dispersion sum option for 1/r^6 potentials :ref:`(Isele-Holder) <Isele-Holder>`,
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similar to the *ewald/disp* style. The 1/r^6 capability means
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that Lennard-Jones or Buckingham potentials can be used without a cutoff,
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i.e. they become full long-range potentials.
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For these styles, you will possibly want to adjust the default choice of
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parameters by using the :doc:`kspace_modify <kspace_modify>` command.
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This can be done by either choosing the Ewald and grid parameters, or
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by specifying separate accuracies for the real and kspace
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calculations. When not making any settings, the simulation will stop with
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an error message. Further information on the influence of the parameters
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and how to choose them is described in :ref:`(Isele-Holder) <Isele-Holder>`,
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:ref:`(Isele-Holder2) <Isele-Holder2>` and the
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:ref:`How-To <howto_24>` discussion.
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----------
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.. note::
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All of the PPPM styles can be used with single-precision FFTs by
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using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
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lo-level Makefile. This setting also changes some of the PPPM
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operations (e.g. mapping charge to mesh and interpolating electric
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fields to particles) to be performed in single precision. This option
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can speed-up long-range calulations, particularly in parallel or on
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GPUs. The use of the -DFFT_SINGLE flag is discussed in :ref:`this section <start_2_4>` of the manual. MSM does not
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currently support the -DFFT_SINGLE compiler switch.
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----------
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The *msm* style invokes a multi-level summation method MSM solver,
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:ref:`(Hardy) <Hardy>` or :ref:`(Hardy2) <Hardy2>`, which maps atom charge to a 3d
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mesh, and uses a multi-level hierarchy of coarser and coarser meshes
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on which direct coulomb solves are done. This method does not use
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FFTs and scales as N. It may therefore be faster than the other
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K-space solvers for relatively large problems when running on large
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core counts. MSM can also be used for non-periodic boundary conditions and
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for mixed periodic and non-periodic boundaries.
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MSM is most competitive versus Ewald and PPPM when only relatively
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low accuracy forces, about 1e-4 relative error or less accurate,
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are needed. Note that use of a larger coulomb cutoff (i.e. 15
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angstroms instead of 10 angstroms) provides better MSM accuracy for
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both the real space and grid computed forces.
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Currently calculation of the full pressure tensor in MSM is expensive.
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Using the :doc:`kspace_modify <kspace_modify>` *pressure/scalar yes*
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command provides a less expensive way to compute the scalar pressure
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(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
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to run an isotropic barostat. If the full pressure tensor is needed,
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then calculating the pressure at every timestep or using a fixed
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pressure simulation with MSM will cause the code to run slower.
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----------
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The specified *accuracy* determines the relative RMS error in per-atom
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forces calculated by the long-range solver. It is set as a
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dimensionless number, relative to the force that two unit point
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charges (e.g. 2 monovalent ions) exert on each other at a distance of
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1 Angstrom. This reference value was chosen as representative of the
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magnitude of electrostatic forces in atomic systems. Thus an accuracy
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value of 1.0e-4 means that the RMS error will be a factor of 10000
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smaller than the reference force.
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The accuracy setting is used in conjunction with the pairwise cutoff
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to determine the number of K-space vectors for style *ewald* or the
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grid size for style *pppm* or *msm*\ .
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Note that style *pppm* only computes the grid size at the beginning of
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a simulation, so if the length or triclinic tilt of the simulation
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cell increases dramatically during the course of the simulation, the
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accuracy of the simulation may degrade. Likewise, if the
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:doc:`kspace_modify slab <kspace_modify>` option is used with
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shrink-wrap boundaries in the z-dimension, and the box size changes
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dramatically in z. For example, for a triclinic system with all three
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tilt factors set to the maximum limit, the PPPM grid should be
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increased roughly by a factor of 1.5 in the y direction and 2.0 in the
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z direction as compared to the same system using a cubic orthogonal
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simulation cell. One way to ensure the accuracy requirement is being
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met is to run a short simulation at the maximum expected tilt or
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length, note the required grid size, and then use the
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:doc:`kspace_modify <kspace_modify>` *mesh* command to manually set the
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PPPM grid size to this value.
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RMS force errors in real space for *ewald* and *pppm* are estimated
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using equation 18 of :ref:`(Kolafa) <Kolafa>`, which is also referenced as
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equation 9 of :ref:`(Petersen) <Petersen>`. RMS force errors in K-space for
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*ewald* are estimated using equation 11 of :ref:`(Petersen) <Petersen>`,
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which is similar to equation 32 of :ref:`(Kolafa) <Kolafa>`. RMS force
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errors in K-space for *pppm* are estimated using equation 38 of
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:ref:`(Deserno) <Deserno>`. RMS force errors for *msm* are estimated
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using ideas from chapter 3 of :ref:`(Hardy) <Hardy>`, with equation 3.197
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of particular note. When using *msm* with non-periodic boundary
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conditions, it is expected that the error estimation will be too
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pessimistic. RMS force errors for dipoles when using *ewald/disp*
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are estimated using equations 33 and 46 of :ref:`(Wang) <Wang>`.
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See the :doc:`kspace_modify <kspace_modify>` command for additional
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options of the K-space solvers that can be set, including a *force*
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option for setting an absoulte RMS error in forces, as opposed to a
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relative RMS error.
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----------
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Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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More specifically, the *pppm/gpu* style performs charge assignment and
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force interpolation calculations on the GPU. These processes are
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performed either in single or double precision, depending on whether
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the -DFFT_SINGLE setting was specified in your lo-level Makefile, as
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discussed above. The FFTs themselves are still calculated on the CPU.
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If *pppm/gpu* is used with a GPU-enabled pair style, part of the PPPM
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calculation can be performed concurrently on the GPU while other
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calculations for non-bonded and bonded force calculation are performed
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on the CPU.
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These accelerated styles are part of the GPU, USER-INTEL,
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KOKKOS, USER-OMP, and OPT packages respectively. They are only
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enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
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See :doc:`Section_accelerate <Section_accelerate>` of the manual for
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more instructions on how to use the accelerated styles effectively.
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Restrictions
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""""""""""""
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Note that the long-range electrostatic solvers in LAMMPS assume conducting
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metal (tinfoil) boundary conditions for both charge and dipole
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interactions. Vacuum boundary conditions are not currently supported.
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The *ewald/disp*\ , *ewald*\ , *pppm*\ , and *msm* styles support
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non-orthogonal (triclinic symmetry) simulation boxes. However,
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triclinic simulation cells may not yet be supported by suffix versions
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of these styles.
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All of the kspace styles are part of the KSPACE package. They are
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only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info. Note that
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the KSPACE package is installed by default.
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For MSM, a simulation must be 3d and one can use any combination of
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periodic, non-periodic, or shrink-wrapped boundaries (specified using
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the :doc:`boundary <boundary>` command).
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For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions.
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The only exception is if the slab option is set with :doc:`kspace_modify <kspace_modify>`,
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in which case the xy dimensions must be periodic and the z dimension must be
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non-periodic.
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Related commands
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""""""""""""""""
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:doc:`kspace_modify <kspace_modify>`, :doc:`pair_style lj/cut/coul/long <pair_lj>`, :doc:`pair_style lj/charmm/coul/long <pair_charmm>`, :doc:`pair_style lj/long/coul/long <pair_lj_long>`, :doc:`pair_style buck/coul/long <pair_buck>`
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Default
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"""""""
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.. parsed-literal::
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kspace_style none
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----------
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.. _Darden:
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**(Darden)** Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
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.. _Deserno:
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**(Deserno)** Deserno and Holm, J Chem Phys, 109, 7694 (1998).
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.. _Hockney:
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**(Hockney)** Hockney and Eastwood, Computer Simulation Using Particles,
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Adam Hilger, NY (1989).
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.. _Kolafa:
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**(Kolafa)** Kolafa and Perram, Molecular Simualtion, 9, 351 (1992).
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.. _Petersen:
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**(Petersen)** Petersen, J Chem Phys, 103, 3668 (1995).
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.. _Wang:
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**(Wang)** Wang and Holm, J Chem Phys, 115, 6277 (2001).
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.. _Pollock:
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**(Pollock)** Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
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.. _Cerutti:
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**(Cerutti)** Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory
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and Computation 5, 2322 (2009)
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.. _Neelov:
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**(Neelov)** Neelov, Holm, J Chem Phys 132, 234103 (2010)
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.. _Veld:
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**(Veld)** In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
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.. _Toukmaji:
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**(Toukmaji)** Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
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10913 (2000).
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.. _Isele-Holder:
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**(Isele-Holder)** Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).
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.. _Isele-Holder2:
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**(Isele-Holder2)** Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory
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Comput 9, 5412 (2013).
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.. _Hardy:
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**(Hardy)** David Hardy thesis: Multilevel Summation for the Fast
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Evaluation of Forces for the Simulation of Biomolecules, University of
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Illinois at Urbana-Champaign, (2006).
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.. _Hardy2:
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**(Hardy)** Hardy, Stone, Schulten, Parallel Computing 35 (2009)
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164-177.
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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