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…added to atom_vec_shperatom.cpp/.h. So far this atom style load in files and sets class specific arrays to hold the data specific to each spherical harmonic type. These arrays are then associated with each atom in set.cpp/.h. Currently arrays are directly copied across to each per_atom array. The time integration scheme hasn't been tested yet nor has a contact model been developed. I also haven't finished the expansion factors method in the atom class.
…stigate whether the new atom style needs to be included in the main directory so as to work with set.cpp and others. Ignore the SphericalHarm folder, this contains older attempts. Relevant code is in USER-SPHERHARM.
…the cut_global in the atom_style just for testing.
… the methods in atom_vec_shperatom
…peratom to directly access array stored in the atom style (this may break using MPI, needs checking). Wrote a basic pair style based on the the overlap distance between gauss points and analytical radii of neighbouring particles (completely unphysical but could be useful for testing). Just uses F=-kx where the user specifies "k". Updated the input script in the Examples/User folder to use the new pair style.
…by the set command if all that is needed is to store the per_atom variable shtype. Also fixed the pair style such that serial and 2-proc MPI give the same results. Problem was that I was calculating forces w.r.t atom j, when this should have been for atom i.
…by the set command if all that is needed is to store the per_atom variable shtype. Also fixed the pair style such that serial and 2-proc MPI give the same results. Problem was that I was calculating forces w.r.t atom j, when this should have been for atom i.
…atom style and to this file.
…sing the in-built PotentialFileReader.
…Wrote a class intended for unti tests.
# Conflicts: # examples/granular/in.pour.drum # src/atom.cpp # src/atom_vec.cpp # src/set.cpp
… access per-shape arrays. Per-shape arrays are not in the atom scope, but the memory for them are allocated within the atom style itself. The result is that they can be accessed via atom->shape_array. Now referring to "shapes" instead of "shtypes" to avoid the confusion with the LAMMPS type. Added flags to the pair_style so that it can switch between using the points of Gaussian quadrature and the patch approach. Both are flawed (contact is not equal and opposite due to the non-equal distance between surface points).
… the pair style. Also fixed the bug where the shape A radius was overwritten in the pair style.
… from the centre of the volume of overlap, which is an arbitrary guess as to where the moment should act from. About to implement Feng's method, which conserves energy and requires direct caclulation of the moment from integral form (rather than multiplying the force by the distance from the particle COM to the centre of the volume of overlap). Added documentation, but this is just for LAMMPS review rather than final documentation.
…m has two bugs. (1) The caps should not be calculated from the lens of sphere-sphere overlap but from the tangents of the spheres. (2) protruding contacts are not accounted for.
…h particles persepctive now converges. The force is incorrect for the second particle as y and z are swapped. Some problem with rotating back to the contact.
…the integration on the spherical cap takes place over the spherical cap that is rotated to the contact.
…the work done by the contact potential. Adding functions to implement flat wall boundaries (cylindrical boundary does not yet work)
… currently this is just used to access individual elements of the quaternion form the input script.
…tyle Removed pair_sh_resquared.h/cpp as this was just used to test ellipsoid particles generated by spherical harmonics. The pair style itself only worked for ellipsoids and was really only testing if the SH series generated the ellipsoids properly. Removing the factorial math from math_spherharm and gaussquad_const. This seems to have been added to math_special, so just calling the method from here now.
…example numex1 file
Had to add "quat" to fields_border_vel in atom_vec_spherharm in order for the quaternion of atoms on different processors to be communicated compute_efunction_spherharm needed to be updated as it was still loading mass based on types rather than rmass. This was resulting in a mass=0 and a divion by zero leading to NANS. This has been fixed. Tidying up the pair_style: Deleting the bisection gradient method as this is WIP and will only serve to confuse at present. Knock on effect of removing calc_nearest_point and skew_lines_check. Removing get_contact_point_bounds as this seems not to be called anywhere. May be called in commented out code but that remains to be seen.
Deleting the write_ellipsoid method from pair_sh, it is not used at present. Moved the spherharmunittest into its own package. This way BOOST is only required for the testing but not for the stand-alone spherharm package
Updates from Imaran with original names
kevinstratford
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Apr 19, 2024
Update to current develop and some cosmetic changes
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By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
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