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Implementation of pair_style uf3 and uf3/kk #4110

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Implementation of pair_style uf3 and uf3/kk #4110

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Commits on Mar 25, 2024

  1. Added ml-uf3 src files

    @monk-04
    monk-04 committed Mar 25, 2024
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  2. Added src files for uf3/kk

    @monk-04
    monk-04 committed Mar 25, 2024
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  3. Added ml-uf3 to cmake and make files

    @monk-04
    monk-04 committed Mar 25, 2024
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  4. Added documentation for ml-uf3

    @monk-04
    monk-04 committed Mar 25, 2024
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  5. Added ml-uf3 potential files

    @monk-04
    monk-04 committed Mar 25, 2024
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  6. Added ml-uf3 unittest

    @monk-04
    monk-04 committed Mar 25, 2024
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  7. Fixed typos in the UF3 equation

    @monk-04
    monk-04 committed Mar 25, 2024
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  8. Fixed lammps developer email-id and contributing authors section. Rem… 

    …oved some old comments
    @monk-04
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  9. Removed LAMMPS errordocs

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  10. fixed trailing whitespaces

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Commits on Mar 26, 2024

  1. Added uf3 details to Commands_pair, Packages_details and Packages_list

    @monk-04
    monk-04 committed Mar 26, 2024
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  2. Added uf3 examples to the examples directory

    @monk-04
    monk-04 committed Mar 26, 2024
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  3. Removed trailing whitespaces

    @monk-04
    monk-04 committed Mar 26, 2024
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  4. Added example potential files for W

    @monk-04
    monk-04 committed Mar 26, 2024
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Commits on Mar 27, 2024

  1. add ML-UF3 to compatible CMake preset files

    @akohlmey
    akohlmey committed Mar 27, 2024
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  2. update .gitignore

    @akohlmey
    akohlmey committed Mar 27, 2024
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  3. update code owners list

    @akohlmey
    akohlmey committed Mar 27, 2024
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  4. move examples

    @akohlmey
    akohlmey committed Mar 27, 2024
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  5. reformat and fix spelling and related issues

    @akohlmey
    akohlmey committed Mar 27, 2024
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  6. update ML-UF3 examples

    @akohlmey
    akohlmey committed Mar 27, 2024
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  7. some style cleanup and simplified pair_style and pair_coeff input

    @akohlmey
    akohlmey committed Mar 27, 2024
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Commits on Mar 28, 2024

  1. examples folder was moved

    @akohlmey
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  2. manybody and single flag need to be changed from the default when 2-b… 

    …ody/3-body is selected
    @akohlmey
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  3. update more files and docs for .uf3 potential file extension 

    also remove redundant files
    @akohlmey
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  4. some formatting and logic cleanup.

    @akohlmey
    akohlmey committed Mar 28, 2024
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  5. Merge pull request #1 from akohlmey/ml-uf3 

    Updates for ml-uf3 pull request
    @monk-04
    monk-04 committed Mar 28, 2024
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Commits on Mar 29, 2024

  1. update example logs

    @akohlmey
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  2. remove dead code

    @akohlmey
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  3. add system error message with failure to open potential

    @akohlmey
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  4. apply clang-format

    @akohlmey
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  5. call utils::logmesg() only on rank 0, use c++ string comparisons, rem… 

    …ove debug comments
    @akohlmey
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  6. don't use pow() function for simple square

    @akohlmey
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  7. remove num_of_elements class variable, just use local copy of atom->n… 

    …types
    @akohlmey
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  8. initialize all class pointers to null, delete all allocated storage

    @akohlmey
    akohlmey committed Mar 29, 2024
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  9. drop log messages

    @akohlmey
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  10. replace pow(x,2) and pow(x,3) with square() and cube()

    @akohlmey
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Commits on Apr 1, 2024

  1. Merge pull request #2 from akohlmey/ml-uf3 

    More updates to PR 4110
    @monk-04
    monk-04 committed Apr 1, 2024
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  2. Pimplifying the code Attempt-1

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  3. Merge branch 'lammps:develop' into ml-uf3

    @monk-04
    monk-04 committed Apr 1, 2024
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Commits on Apr 2, 2024

  1. Removed commented out code

    @monk-04
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  2. Added code to check if 'UNITS:' metadata is present in the pot file o… 

    …r not
    @monk-04
    monk-04 committed Apr 2, 2024
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  3. Replaced the A_A.uf3 and A_A_A.uf3 with uf3 lammps pot files for Nb

    @monk-04
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  4. Updated A_A.uf3 to Nb_Nb.uf3 and A_A_A.uf3 to Nb_Nb_Nb.uf3

    @monk-04
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  5. Removed old pot files

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  6. Updated documentation about METADATA in the uf3 lammps pot files

    @monk-04
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  7. Fixed trailing whitespace

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Commits on Apr 13, 2024

  1. Merge branch 'lammps:develop' into ml-uf3

    @monk-04
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Commits on Apr 15, 2024

  1. Added uf3_read_unified_pot_file() to read single potential file on ra… 

    …nk 0 and communicate() to broadcast the data to other ranks

Added one_ceoff
    @monk-04
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  2. Added new constructor functions in uf3_pair_bspline and uf3_triplet_b… 

    …spline to construct std::vectors of knots and coefficients rom memory block
    @monk-04
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  3. Updated pair_coeff in unittest to read only one potential file; added… 

    … Nb.uf3 unified potential file
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  4. Updated the code as we are no longer using std::vector for knots and … 

    …coefficients
    @monk-04
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  5. Removed reference to std::vector knots and coefficients; commented ou… 

    …t getter functions
    @monk-04
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Commits on Apr 17, 2024

  1. Updated the documentation about UF3 LAMMPS potential file

    @monk-04
    monk-04 committed Apr 17, 2024
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  2. Merge pull request #4 from monk-04/ml-uf3 

    Updates to pair_uf3- Reading potential from single file, arrays from memory class, MPI to communicate the arrays
    @monk-04
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  3. Fixed trailing whitespaces

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  4. Merge branch 'lammps:develop' into ml-uf3

    @monk-04
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Commits on May 2, 2024

  1. Made 'constants' variable public

    @monk-04
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  2. Removed UFBS2b and UFBS3b std::vector objects. 

    These objects held the bspline basis set object (uf3_pair_bspline and uf3_triplet_bspline) for 2- and 3-body interaction at UFBS2b[itype][jtype] and UFBS3b[itype][jtype][ktype].
These std:vectors were removed. New arrays (cached_constants_2b, cached_constants_2b_deri, cached_constants_3b, cached_constants_3b_deri) were added that holds the cached coefficients of the bspline basis set. The UF3Impl PIMPLE was also removed as it is not longer needed. The memory_usage function needs to updated
    @monk-04
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  3. Removed trailing whitespace

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  4. constants was changed from std::vector to fixed length array

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  5. Removed uf3_pair_bspline and uf3_triplet_bspline

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  6. Commented out the uniform knot spacing logic as for more than 1 proce… 

    …ssors was getting some weird errors.

Deleted commented (dead) code.
Updated the memory_usage function.
Reordered some functions to refelect the calling order
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  7. Removed unused variables and reordered the code

    @monk-04
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  8. Fixed trailing whitespace

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  9. Removed dead code, fixed trailing whitespace

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  10. Merge pull request #5 from monk-04/ml-uf3 

    Remove std::vector completely
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  11. Merge branch 'lammps:develop' into ml-uf3

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Commits on May 3, 2024

  1. Fixed bug with uniform knot spacing

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  2. Initialize setflag, n2b_coeff_array_size, n2b_knots_array_size, n3b_c… 

    …oeff_array_size, n3b_knots_array_size arrays to 0; fixed memory leaks; removed some dead code
    @monk-04
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  3. Removed trailing whitespace

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Commits on May 4, 2024

  1. Merge pull request #6 from monk-04/ml-uf3 

    Bug Fixes- uniform knot spacing, memory leaks, array initialization
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Commits on May 13, 2024

  1. Merge branch 'lammps:develop' into ml-uf3

    @monk-04
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Commits on May 14, 2024

  1. Merge branch 'develop' into ml-uf3

    @akohlmey
    akohlmey committed May 14, 2024
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  2. fix spelling

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    akohlmey committed May 14, 2024
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  3. remove unused variables

    @akohlmey
    akohlmey committed May 14, 2024
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  4. update ML-UF3 example

    @akohlmey
    akohlmey committed May 14, 2024
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  5. Merge pull request #7 from akohlmey/ml-uf3 

    Update example with new syntax
    @monk-04
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