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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
Small fix to ease compilation under MAC
needs to be close to the class definition
Removed the unused get_my_chunk function from orbital_utils.cpp.
More consistent numerical results and repaired exchange
Add missing template parameters
* first version two electron integrals * print times for two electron integrals * bug shared potential (code hangs) * 2 el integrals test and change indices order * add two electron integrals test file * remove obsolete rescaling for Zora (taken care by mrcpp now) * update test results for new mrcpp (default for crop is absprec=true) * more test results updates for new mrcpp (default for crop is absprec=true) * lower test threshold for xc_hessian_pbe * Update tests/qmoperators/two_el_int.cpp Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com> --------- Co-authored-by: Luca Frediani <luca.frediani@gmail.com> Co-authored-by: gitpeterwind <peterw@met.no> Co-authored-by: Roberto Di Remigio Eikås <robertodr@users.noreply.github.com>
* rebased master; fixed some last warnings * fetched wrong MRCPP
* initial conversion of occupancies from integer to double * Initial implementation of core hole calculations * Switching logic so that restricted checks depend on doubly occ (only happens for rest) not singly occ (which could be unrest or rest with a hole) * XX with occupancies * updating input file for explicit occupancies * fixing occupancies/spin factors for XX in restricted calculations * removing unneeded print statement * adding positions of the orbitals to enable association with a particular atomic orbital * first try * restricted MOM * first try for IMOM; only IMOM in this version * first cleanup, code now readable, but longer * small bugfix * added input in input parser for MOM/IMOM * small bugfix * new logic to treat different occupation numbers; cleanup * small formatting * small temporary fix in restricted occupations * print orbital occupations as doubles instead of integers * for now only removal of one electron possible# * small bugfix in ExchangePotentialD2.cpp * bugfix in initial guess * IMOM: fetch Orbitals before calculation of initial guess energy; some general cleanup; added first test for DeltaSCF * small bugfix in test * small bugfix in driver.cpp and some changes to the core-hole test * added tests * changing copies to deep_copies * some cleanup + some more output depending on print level * - Implemented partial localization for different occupations - Fixed values for tests - some cleanup * small bugfix for unrestricted MOM/IMOM calculations * remove partial localization * added tests for unrestricted IMOM; some cleanup * small cleanup * incorporated PR comments * first try * first try for IMOM; only IMOM in this version * first cleanup, code now readable, but longer * added input in input parser for MOM/IMOM * new logic to treat different occupation numbers; cleanup * small formatting * IMOM: fetch Orbitals before calculation of initial guess energy; some general cleanup; added first test for DeltaSCF * small bugfix in test * small bugfix in driver.cpp and some changes to the core-hole test * added tests * changing copies to deep_copies * some cleanup + some more output depending on print level * - Implemented partial localization for different occupations - Fixed values for tests - some cleanup * small bugfix for unrestricted MOM/IMOM calculations * remove partial localization * added tests for unrestricted IMOM; some cleanup * small cleanup * make code mostly compilable * cleanup * fixed bug in calculation of number of electrons that lead to failing tests * updated test references for core-hole and IMOM tests * fixed MPI print issues, split tests to avoid timeout * added missing files * updated tests * storing mom orbitals in the Molecule object --------- Co-authored-by: Laura Ratcliff <laura_ratcliff@hotmail.com> Co-authored-by: Niklas Göllmann <niklas@tromso-eksterne-763.wifi.uit.no> Co-authored-by: Niklas Göllmann <niklas@tromso-eksterne-2394.wifi.uit.no>
* implement nlcc pps * get rid of numpy dependency * print nlcc data * implement f projectors untested * remove print * add getatomic number function * make sad work for pp * new way to project rho * clean things up * remove more prints * speed things up * add basis for all elements * test spherical harmonics * make test work or other alphas * remove writing of user dict for debug purposes * add a couple of virtual orbitals * renove virt. orbs * improve test * make projector not function * deepcopy to be safe * debug print * lots of debyug * make sure projector is projected * remove some copies * make sure nlcc rho gets projected * mix it a bit * move mixing calculation to sad initial guess * new parameters * calcuclate mixing energies * go to pbe * adnjust test * for marco * add orbitals * read file * make it run again * add getter * improve switch_sperics * this does nearly work * fix bug * sp[in changes * maybe * rescale intitial charge * more orbitalsfor gold * precompute kin and nuc mat * remove print * start migrating stuff * restore sad initial guess * add new initial guess type * parse new mixing parameters * implement nao intial guess in driver * fix bug * add timer * revert gsf * revert core * fix projection * better prints * gold has even f orbital * update template and helper * update parser * fix typo * change yet another thing * add nao directory logic to mrchem * include unoccupied orbitals in nao basis. * add na pseudopotential test * better tolerances * quick and dirty * improve code * (un)safe changes * add doc * fix bug reading c * start on good pp * improve pp * add one to lmax * remove old implementation of data type * clean up code * rename stuff * move files * add multi elements * add first draft of projector * add exponential factor * improvements * add sketch of projectoroperator * add some docs * more docs * introduce shift * change types * add constructor * doc * fix silly errors * reintroduce old stuff * minor fix in file format * fix qmfunctionvector naming * improve constructor * make parent class public * start dotting * apply compiles * make it segfault * add prints * add more prints * more prints * more prints and fix bugs * single s projector working * printprintprint * fix bug * p orbitals working * add pp section * start python stuff * update params * first logic done, todo parse psppar * add parsing of psppar files * json mess * small change * use different format * example in driver working * add getters * integrate pp-data * add new constructor to nuclei and add function that checks if a pp exists * put pp into molecult * add other constructor to get rid of final occurence of set_charge * update mechanism from pp nucleus * mixed sims working * update parser * input logic working * compute molecular charge differently * fix bug * comment a lot of print * make core initial guess work for pps * add has pp function to molecule * force core initial guess if pps are used * remove r^-l factor for numerical stability * remove a lot of prints * parse nlcc terms * implement nlcc pps * get rid of numpy dependency * print nlcc data * implement f projectors untested * remove print * add getatomic number function * make sad work for pp * new way to project rho * clean things up * remove more prints * speed things up * add basis for all elements * test spherical harmonics * make test work or other alphas * remove writing of user dict for debug purposes * add a couple of virtual orbitals * renove virt. orbs * improve test * make projector not function * deepcopy to be safe * debug print * lots of debyug * make sure projector is projected * remove some copies * make sure nlcc rho gets projected * mix it a bit * move mixing calculation to sad initial guess * new parameters * calcuclate mixing energies * go to pbe * adnjust test * for marco * add orbitals * read file * make it run again * add getter * improve switch_sperics * this does nearly work * fix bug * sp[in changes * maybe * rescale intitial charge * more orbitalsfor gold * precompute kin and nuc mat * remove print * start migrating stuff * restore sad initial guess * add new initial guess type * parse new mixing parameters * implement nao intial guess in driver * fix bug * add timer * revert gsf * revert core * fix projection * better prints * gold has even f orbital * update template and helper * update parser * fix typo * change yet another thing * add nao directory logic to mrchem * include unoccupied orbitals in nao basis. * add na pseudopotential test * better tolerances * adjust catch include * quick fix of dft functional error. * update psp test * update for new mrcpp * new interface * change filename in docs * add some documentation * remove duplicate docs * add explanations * cleaner prints * use mrchem logging * update test values * add manual * fix typo * run update_input_parser * fix brace * set has_pp_data in constructor * explain scaling of k * use ang_mom_char * use eigen maps * minor formatting * revert type set to int * add commented debub print again * fix typo in abort message * remove tightening of precision for debugging * use std::tgamma * remove unnecessary comments * remove uneccessary comment * move docstring to header * use gaussian from mrcpp * fix typo in mrchem and regenerate docs * make new helper functions const * formating * remove unnecessary fields * adjust print * remove debug prints * change loop type to size_t * Added override to all six methods that override virtuals from QMOperator: setup, clear, apply(Orbital), dagger, evalf, and apply(shared_ptr<QMOperator>&). * delete empty line * use || * make projection cleaner * add integration weights and update readme * use previous value for broad sigma in max * increase print level of orbital widths --------- Co-authored-by: Moritz Gubler <moritz.gubler@e.email> Co-authored-by: gitpeterwind <peter.wind@met.no>
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