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Close #419 We now use qcelemental to fetch Bondi radii, and use alpha=1.2 for hydrogen --------- Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com>
* cavity function used directly instead of projected first * clear d_V * Update SCRF.cpp define ranks in accelerator, so that all mpi ranks use kain * cavity function used directly instead of projected first * clear d_V * Update SCRF.cpp define ranks in accelerator, so that all mpi ranks use kain * manage to pull down to 12.2 and 30.0 gb * reduced memory usage to ca. 3 gb from 8 gb * Remove print statement for memory * Small changes to desctructor and clear * Use latest MRCPP * Use default initialization in header file * Do some cleaning after feedback * Remove ´optimizer´ option from inputs * Fix tests --------- Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> Co-authored-by: Gabrielgerez <gsa017@uit.no>
* Convert default radii to bohr when input units are not angstrom * Update template.yml (formatting and documentation) * Refine fix for unit conversion of cavity params, add tests
* Refactor the Permittivity function for ease of future implementation work. * Add ShiftFunction to CMakeLists * Add virtual and override where necessary * Remove evalf definition from shiftFunction * Rename ShiftFunction to StepFunction * Update src/environment/Permittivity.cpp Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> * Update src/environment/StepFunction.cpp Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> * Update src/environment/StepFunction.cpp Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> * Update src/environment/StepFunction.cpp Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> * Update src/environment/StepFunction.h Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> * Update src/environment/StepFunction.h Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> * Pass cavity as a shared_ptr to save memory. * Fix rebase error * Remove use for `flipFunction` in Permittivity * Update src/environment/Permittivity.h Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> * Update src/environment/StepFunction.cpp Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> * Add print_header to detail namespace * Update src/environment/StepFunction.h Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> --------- Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com>
* Use C++17
* Use std::tie to unpack tuple return value
* Remove some cruft from Cavity and Permittivity
* SCRF deals in densities only, not orbitals
* Refactor Reaction{Potential,Operator} following Coulomb example
In preparation for the computation of the response terms, we make ReactionPotential abstract and add
subclass ReactionPotentialD1 to deal with one single set of orbitals.
* Modify input to accept static and dynamic permittivities
* Handle nonequilibrium solvation more gracefully
* Sign change was necessary
* Update input parser
* Small fixes to include order
* Rename section for permittivity outside
* Add tests
* add compile definition for xcfun settings * Change test reference for unit test "xc_hessian_pbe" * Remove debug prints * Remove typo in new reference data * attempting loosening threshold for pipeline to pass * trying debug print in pipeline * loosen threshold even more
Adding aliases for libxc funtionals, so that "normal" functional names can be written in the input file when using libxc, instead of functional IDS. The following shorthands will now be available for use with libxc (aka the functional list found in python/mrchem/helpers.py + some): slaterx, vwn3, vwn5, svwn3, svwn5, beckex, pbe, pbe0, bpw91, bp86, b3p86, b3p86-g, blyp, b3lyp, b3lyp-g, olyp, kt1, kt2, kt3 Changes made: Made a new file xc_aliases for the functional list instead of having mapFunctionalName in Factory The list of libxc functional objects is now a list of pointers Variable for explicitly defining exact exchange in mapFunctionalName added (not used yet, but was useful when testing different functional combinations to find most accurate functional combinations) Updated user_inp.rst Adding line break in libxc functional references printed in .out file
Updating the tests in mrchem, this includes: - [x] Increase tolerance of tests - [x] Reconstruct into three sets of tests: 1) run every time something is committed, 2) run once for a pull request etc, 3) Extensive set that can be ran sometimes (one folder for each) - [x] Add xc library name in label + input file - [x] Increase tolerance and update reference for libxc tests - [x] Update documentation - [x] Update the `config.yml` for CircleCI to allow for staging of pipelines and the test splitting - [x] Reformatting input files that use json format - [x] All tests should have one of the three labels: short (default), medium (can be ran locally), long (should not be in ctest)) - [x] Folder should have the same name as the test in lower case - Labels should at least include: mrchem, method, molecule, short/medium/long, tests should not have its name as a label - [x] imom tests does not have to run every time - [x] dft tests using xcfun should be similar to libxc (restricted/unrestricted, hyb-gga/lda) --------- Co-authored-by: MarcusTL12 <marcuspaafjellet@gmail.com> Co-authored-by: Niklas Goellmann <ngoellmann@gmail.com>
Added code to project gto initial guesses including g orbitals. This allows starting from e.g. def2-QZVP or cc-pVQZ calculations for most atoms.
When specifying functionals using the "functionals" keyword in the input file (instead of eg "method = pbe"), mrchem does not say which functionals are used. When using the libxc library, the output file prints the information of the used library together with the specific xc functionals under the "XC Functional" header. This is now done for xcfun as well. --------- Co-authored-by: Marcus Takvam Lexander <marcuspaafjellet@gmail.com>
…564) Generalize the code in gto_utils to allow for arbitrary angular momentum. Also update the from_orca.py script to allow for 'i' orbitals in gto initial guess. --------- Co-authored-by: Niklas Göllmann <153195865+msnik1999@users.noreply.github.com>
Synchrinizes MRChem with mrcpp. mrcpp::map changed to mrcpp::treeMap mrcpp tag updated accordingly
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