option to calculate only subset of atoms in local representations #26
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Looks good! Can you add a test to show that a generated coulomb matrix gives same result before and after this pull request? Then I'll merge right away. I would prefer a test case similar to: https://github.com/qmlcode/qml/blob/slatm/tests/test_slatm.py#L73 |
andersx
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Mar 2, 2018
* option to calculate only subset of atoms in local representations (#26) * option to calculate only subset of atoms in local representations * added reference calculation of representations * finalized reference testing * fixed error in test * Atomic kernels memory (#27) * Added local kernels and tests for local kernels * Slatm (#28) * Updated SLATM, removed ASE, updated docs, updated SLATM tests case * Added F90 version of get_sbot in SLATM * Added F2py implementation of get_sbop in slatm * Fixed remaining issues with f90-slatm, works for global and local now. * Added testcases for local SLATM * Removed dead code from slatm.py * Linear kernel (#29) * Added linear kernel and test * Updated documentation for kernels and removed compiler warning (from frepresentations) * Added global ARAD kernel and test * Linalg (#30) * Added MKL discovery * Updated cho_solve and cho_invert, so input is conserved * Added busch-kaufman factorization solver and inversion (DSYTRS) * Linear kernel (#31) * Added linear kernel and test * Updated documentation for kernels and removed compiler warning (from frepresentations) * Added global ARAD and linear global kernel * Corrected ARAD global kernel to L2 distance * Bob bug (#33) * Fixed ordering in Bob, added integration test * Tightened threshold in Bob integration test to 2.8 kcal/mol * Fchl main (#37) * Added ARAS->FCHL code * updated fchl kernels code * Cleaned up FCHL code, parallelized weight ksi functions * Factor 4 speed in three-body term * Updated alchemy and speed * Added global FCHL kernel * Fixed initialization bug in FCHL global kernel * Fixed clearing of self-dotprodicts, and removed excessive OMP memory use * More parallelization issues fixed in FCHL * Fixed 3-body parallelization, added atomic kernels, added option for no alchemy * Fixed parallelization memory, added force kernels to FCHL * Added two- and three-body exponenets as parameters * Added alchemy module, added custom alchemy vectors. * Updated parallelization etc. * Fchl module (#34) * Updated to module and added screening function * Fixed bug in cut-off function. * Removed debug output from cut-off function. * Added FCHL to develop branch * Updated clang->gcc in macos installation instructions, hattip geoff hutchison * Updated autodeployment to GH pages and PyPI
andersx
added a commit
that referenced
this pull request
Mar 2, 2018
* option to calculate only subset of atoms in local representations (#26) * option to calculate only subset of atoms in local representations * added reference calculation of representations * finalized reference testing * fixed error in test * Atomic kernels memory (#27) * Added local kernels and tests for local kernels * Slatm (#28) * Updated SLATM, removed ASE, updated docs, updated SLATM tests case * Added F90 version of get_sbot in SLATM * Added F2py implementation of get_sbop in slatm * Fixed remaining issues with f90-slatm, works for global and local now. * Added testcases for local SLATM * Removed dead code from slatm.py * Linear kernel (#29) * Added linear kernel and test * Updated documentation for kernels and removed compiler warning (from frepresentations) * Added global ARAD kernel and test * Linalg (#30) * Added MKL discovery * Updated cho_solve and cho_invert, so input is conserved * Added busch-kaufman factorization solver and inversion (DSYTRS) * Linear kernel (#31) * Added linear kernel and test * Updated documentation for kernels and removed compiler warning (from frepresentations) * Added global ARAD and linear global kernel * Corrected ARAD global kernel to L2 distance * Bob bug (#33) * Fixed ordering in Bob, added integration test * Tightened threshold in Bob integration test to 2.8 kcal/mol * Fchl main (#37) * Added ARAS->FCHL code * updated fchl kernels code * Cleaned up FCHL code, parallelized weight ksi functions * Factor 4 speed in three-body term * Updated alchemy and speed * Added global FCHL kernel * Fixed initialization bug in FCHL global kernel * Fixed clearing of self-dotprodicts, and removed excessive OMP memory use * More parallelization issues fixed in FCHL * Fixed 3-body parallelization, added atomic kernels, added option for no alchemy * Fixed parallelization memory, added force kernels to FCHL * Added two- and three-body exponenets as parameters * Added alchemy module, added custom alchemy vectors. * Updated parallelization etc. * Fchl module (#34) * Updated to module and added screening function * Fixed bug in cut-off function. * Removed debug output from cut-off function. * Added FCHL to develop branch * Updated clang->gcc in macos installation instructions, hattip geoff hutchison * Updated autodeployment to GH pages and PyPI * Updated version number
zaspel
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to zaspel/qml
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Jul 29, 2019
* option to calculate only subset of atoms in local representations (qmlcode#26) * option to calculate only subset of atoms in local representations * added reference calculation of representations * finalized reference testing * fixed error in test * Atomic kernels memory (qmlcode#27) * Added local kernels and tests for local kernels * Slatm (qmlcode#28) * Updated SLATM, removed ASE, updated docs, updated SLATM tests case * Added F90 version of get_sbot in SLATM * Added F2py implementation of get_sbop in slatm * Fixed remaining issues with f90-slatm, works for global and local now. * Added testcases for local SLATM * Removed dead code from slatm.py * Linear kernel (qmlcode#29) * Added linear kernel and test * Updated documentation for kernels and removed compiler warning (from frepresentations) * Added global ARAD kernel and test * Linalg (qmlcode#30) * Added MKL discovery * Updated cho_solve and cho_invert, so input is conserved * Added busch-kaufman factorization solver and inversion (DSYTRS) * Linear kernel (qmlcode#31) * Added linear kernel and test * Updated documentation for kernels and removed compiler warning (from frepresentations) * Added global ARAD and linear global kernel * Corrected ARAD global kernel to L2 distance * Bob bug (qmlcode#33) * Fixed ordering in Bob, added integration test * Tightened threshold in Bob integration test to 2.8 kcal/mol * Fchl main (qmlcode#37) * Added ARAS->FCHL code * updated fchl kernels code * Cleaned up FCHL code, parallelized weight ksi functions * Factor 4 speed in three-body term * Updated alchemy and speed * Added global FCHL kernel * Fixed initialization bug in FCHL global kernel * Fixed clearing of self-dotprodicts, and removed excessive OMP memory use * More parallelization issues fixed in FCHL * Fixed 3-body parallelization, added atomic kernels, added option for no alchemy * Fixed parallelization memory, added force kernels to FCHL * Added two- and three-body exponenets as parameters * Added alchemy module, added custom alchemy vectors. * Updated parallelization etc. * Fchl module (qmlcode#34) * Updated to module and added screening function * Fixed bug in cut-off function. * Removed debug output from cut-off function. * Added FCHL to develop branch * Updated clang->gcc in macos installation instructions, hattip geoff hutchison * Updated autodeployment to GH pages and PyPI
zaspel
pushed a commit
to zaspel/qml
that referenced
this pull request
Jul 29, 2019
* option to calculate only subset of atoms in local representations (qmlcode#26) * option to calculate only subset of atoms in local representations * added reference calculation of representations * finalized reference testing * fixed error in test * Atomic kernels memory (qmlcode#27) * Added local kernels and tests for local kernels * Slatm (qmlcode#28) * Updated SLATM, removed ASE, updated docs, updated SLATM tests case * Added F90 version of get_sbot in SLATM * Added F2py implementation of get_sbop in slatm * Fixed remaining issues with f90-slatm, works for global and local now. * Added testcases for local SLATM * Removed dead code from slatm.py * Linear kernel (qmlcode#29) * Added linear kernel and test * Updated documentation for kernels and removed compiler warning (from frepresentations) * Added global ARAD kernel and test * Linalg (qmlcode#30) * Added MKL discovery * Updated cho_solve and cho_invert, so input is conserved * Added busch-kaufman factorization solver and inversion (DSYTRS) * Linear kernel (qmlcode#31) * Added linear kernel and test * Updated documentation for kernels and removed compiler warning (from frepresentations) * Added global ARAD and linear global kernel * Corrected ARAD global kernel to L2 distance * Bob bug (qmlcode#33) * Fixed ordering in Bob, added integration test * Tightened threshold in Bob integration test to 2.8 kcal/mol * Fchl main (qmlcode#37) * Added ARAS->FCHL code * updated fchl kernels code * Cleaned up FCHL code, parallelized weight ksi functions * Factor 4 speed in three-body term * Updated alchemy and speed * Added global FCHL kernel * Fixed initialization bug in FCHL global kernel * Fixed clearing of self-dotprodicts, and removed excessive OMP memory use * More parallelization issues fixed in FCHL * Fixed 3-body parallelization, added atomic kernels, added option for no alchemy * Fixed parallelization memory, added force kernels to FCHL * Added two- and three-body exponenets as parameters * Added alchemy module, added custom alchemy vectors. * Updated parallelization etc. * Fchl module (qmlcode#34) * Updated to module and added screening function * Fixed bug in cut-off function. * Removed debug output from cut-off function. * Added FCHL to develop branch * Updated clang->gcc in macos installation instructions, hattip geoff hutchison * Updated autodeployment to GH pages and PyPI * Updated version number
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Only for local/atomic CM