Merge release 20251210 #400
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* add libROM to CMakelists.txt * Add shell_script * Minor changes * Add module file
* Update script to analyze forces on constraints * initial ci workflow files. * default branch name release. * create build directory for compilation. * minor fix --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov>
* changed the Signal.h header file name. * additional routine to find scalapack library, if nothing is found. * ci workflow with test and format * changed branch name * ctest verbose * added --oversubscribe to cmake MPIEXEC_PREFLAGS variable. * parallel hdf5 package fix. also librom is included. * ci workflow only checks the first 20 tests. * minor fix * rom-fpmd driver and librom dependency in cmake. librom must be compiled before mgmol cmake. * cmake fix and toolchain file for LC quartz. * bug fix on FindSCALAPACK.cmake * librom-mgmol installation script for LC quartz.
* Fix build with HDF5P on (#231) * LoadOrbitalsFromRestartFile and miscellaneous changes (#226) * Signal.h -> mgmol_Signal.h * Carbyne example files. * fixed FindSCALAPACK.cmake to search for default paths * MGmol::loadOrbitalFromRestartFile * nullptr initialization --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov>
* librom compilation setup. * rom config options. * parsing rom config option to Control.
on-the-fly FOM orbital snapshot saving
* rom load restart file and POD basis training. * example rom config file for carbyne. * update docker container with hdf5-tools
Update ROMFPMD with release branch
* Reenable testShortSighted test (#248) * Make new driver to check input (#247) * clean up/reorganize main.cc * use shared_ptr in class MGmol * Add possible periodic dimensions to xyz2in.py (#249) * Add possible periodic dimensions to xyz2in.py * Remove unused/untested option extrapolateH (#250) * Exit with failure if density off by more than 2% (#251) * Exit with failure if density off by more than 2% * adapt SiH4 test to catch that * fix bug in DFTsolver that was leading to wrong density * Example driver (#252) * add example driver, showing use of MGmol as a force/energy computational engine * clean up related functions in class Ions * loadOrbitalsFromRestartFile -> loadRestartFile * update the rom main driver. * update rom main driver again * temporary fix before the next PR --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov>
* offline workflow with potential POD training * update rom main driver again * ci workflow include librom in compilation * add config option
* rom workflow for buildROMPoissonOperator * change from total to hartree potential * test routine for Poisson ROM operator. * POD reconstruction * test Poisson ROM operator verified. * buildROMPoissonOperator updated. * ci test for Poisson ROM operator
* Reenable testShortSighted test (#248) * Make new driver to check input (#247) * clean up/reorganize main.cc * use shared_ptr in class MGmol * Add possible periodic dimensions to xyz2in.py (#249) * Add possible periodic dimensions to xyz2in.py * Remove unused/untested option extrapolateH (#250) * Exit with failure if density off by more than 2% (#251) * Exit with failure if density off by more than 2% * adapt SiH4 test to catch that * fix bug in DFTsolver that was leading to wrong density * Example driver (#252) * add example driver, showing use of MGmol as a force/energy computational engine * clean up related functions in class Ions * loadOrbitalsFromRestartFile -> loadRestartFile (#253) * Add SG15 PBE potential for N (#258) * Update 2-pyridone example (#259) * Adjust verbosity in some functions (#260) * Add new example: pinned H2O (#261) * Print out eigenvalues out of MVP solver (#262) Previously, the wrong eigenvalues (0) were printed out because eigenvalues outside solver were not up-to-date. * Add Li2 example with local GTH potential (#263) * Fix LBFGS termination when converged (#264) * Remove unused code to extrapolate rho (#265) * Fix and test EnergyAndForces interface (#266) * Atomic potentials were not updated when atomic positions were changed * Added test to make sure energies and forces are the same after positions move by one mesh spacing * Add new functionality to compute energy and forces (#267) * use specified initial conditions for wavefunctions --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> Co-authored-by: Kevin" Seung Whan Chung <seung.chung@austin.utexas.edu>
* Add libROM snapshot frequency option * make install enabled * Add scripts * Add postprocessing script
* base for rho hyperreduction test * compute rho on sample points, on carom space. * computeRhoOnSamplePts checked. does not seem to have the factor 2.. * exact equivalence cannot be accomplished due to rescaleTotalCharge. adjusting tolerance. * save hyperreduction operator in build rom phase.
* Reenable testShortSighted test (#248) * Make new driver to check input (#247) * clean up/reorganize main.cc * use shared_ptr in class MGmol * Add possible periodic dimensions to xyz2in.py (#249) * Add possible periodic dimensions to xyz2in.py * Remove unused/untested option extrapolateH (#250) * Exit with failure if density off by more than 2% (#251) * Exit with failure if density off by more than 2% * adapt SiH4 test to catch that * fix bug in DFTsolver that was leading to wrong density * Example driver (#252) * add example driver, showing use of MGmol as a force/energy computational engine * clean up related functions in class Ions * loadOrbitalsFromRestartFile -> loadRestartFile (#253) * Add SG15 PBE potential for N (#258) * Update 2-pyridone example (#259) * Adjust verbosity in some functions (#260) * Add new example: pinned H2O (#261) * Print out eigenvalues out of MVP solver (#262) Previously, the wrong eigenvalues (0) were printed out because eigenvalues outside solver were not up-to-date. * Add Li2 example with local GTH potential (#263) * Fix LBFGS termination when converged (#264) * Remove unused code to extrapolate rho (#265) * Fix and test EnergyAndForces interface (#266) * Atomic potentials were not updated when atomic positions were changed * Added test to make sure energies and forces are the same after positions move by one mesh spacing * Add new functionality to compute energy and forces (#267) * use specified initial conditions for wavefunctions * Add functionality to compute energy and forces (#270) * use specified wavefunctions as solution, with unknown DM * Add ONCV for Sulfur + example (#275) * Fix CMakeList * Fix test * Bypass build error * Fix merge mistake --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> Co-authored-by: Kevin" Seung Whan Chung <seung.chung@austin.utexas.edu>
* Reenable testShortSighted test (#248) * Make new driver to check input (#247) * clean up/reorganize main.cc * use shared_ptr in class MGmol * Add possible periodic dimensions to xyz2in.py (#249) * Add possible periodic dimensions to xyz2in.py * Remove unused/untested option extrapolateH (#250) * Exit with failure if density off by more than 2% (#251) * Exit with failure if density off by more than 2% * adapt SiH4 test to catch that * fix bug in DFTsolver that was leading to wrong density * Example driver (#252) * add example driver, showing use of MGmol as a force/energy computational engine * clean up related functions in class Ions * loadOrbitalsFromRestartFile -> loadRestartFile (#253) * Add SG15 PBE potential for N (#258) * Update 2-pyridone example (#259) * Adjust verbosity in some functions (#260) * Add new example: pinned H2O (#261) * Print out eigenvalues out of MVP solver (#262) Previously, the wrong eigenvalues (0) were printed out because eigenvalues outside solver were not up-to-date. * Add Li2 example with local GTH potential (#263) * Fix LBFGS termination when converged (#264) * Remove unused code to extrapolate rho (#265) * Fix and test EnergyAndForces interface (#266) * Atomic potentials were not updated when atomic positions were changed * Added test to make sure energies and forces are the same after positions move by one mesh spacing * Add new functionality to compute energy and forces (#267) * use specified initial conditions for wavefunctions * Add functionality to compute energy and forces (#270) * use specified wavefunctions as solution, with unknown DM * Add ONCV for Sulfur + example (#275) * Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov>
* save/load poisson rom operator. * test routine for ion density * ion density hyper-reduction verified. * added rom ion test in ci workflow. * fixed ci workflow * setting ion configuration using Ions::setPositions.
Orbital projection tests
3-parameter Pinned H2O
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * remove a redundant assignment in DensityMatrix::DensityMatrix --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov>
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * set up offline procedure * Parametric file * Add basis script * Add postprocessing scripts * Add files via upload * Add restore check. Make H1 shorter than H2 in original system for verification * Minor change * Add C++ translation * Add restoring test * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * Set up test * Update cfg * Fix conversions * Add new script * Add CMake * Restore * Updates * Changes * Relocate set * Refactor * Remove unused function in Control (#294) * Change symlink to restart in tests (#295) * enable tests when old link present * Extract number empty orbitals from restart file (#296) * Merge release to ROMFPMD * updates * Updates * Fixes * Add computeGramAndInvS * Add * Debug * Clean up * Turn on MVP solver for nempty > 0 case * Add getForces for evaluateDMandEnergyAndForces * Add new tests * Remove redundant line * Fix filename * Add quench and MVP comparison for main executable * minor changes * Changes in setting of Quench and MVP comparison * Add number of quench iterations for convergence * Update job scripts * Update config files * Update toy example * Remove redundant script * Updates * Update scripts * Add functional script * Templatize scripts * Add postprocessing script * Add units to plot --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov>
* Minor change * Fix calculations * Rename * Add rotation * Clean up
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * Remove unused function in Control (#294) * Change symlink to restart in tests (#295) * enable tests when old link present * Extract number empty orbitals from restart file (#296) * Clean up MD_IonicStepper restart data write (#297) * Clean up code based on compiler warnings (#299) * Add getForces for evaluateDMandEnergyAndForces (#300) * Add check for compatibility MVP/Mehrstellen (#301) * Add support for Br atom (#302) * Clean up some HDFrestart functions (#303) * Fix and test restart single hdf5 file (#305) * Save Hartree potential for write in restart file (#306) * Add commit number temporarily * Fix merge --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov>
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * Remove unused function in Control (#294) * Change symlink to restart in tests (#295) * enable tests when old link present * Extract number empty orbitals from restart file (#296) * Clean up MD_IonicStepper restart data write (#297) * Clean up code based on compiler warnings (#299) * Add getForces for evaluateDMandEnergyAndForces (#300) * Add check for compatibility MVP/Mehrstellen (#301) * Add support for Br atom (#302) * Clean up some HDFrestart functions (#303) * Fix and test restart single hdf5 file (#305) * Save Hartree potential for write in restart file (#306) * Speed-up recently added tests (#309) * simply use a smaller domain/mesh * Encapsulate some functions in Potentials (#310) * some functions were called at random places and confusing * Remove confusing 0 in naming restart files (#308) * use added integer only in case of fail/retry * Add functionalities for extra info in restart file (#312) * MPI abort (#313) * Fix error code used by MPI_Abort * Rho and VH restart (#311) * enable restart with consistent rho and VHartree --------- Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu> * Strenghten testIons (#315) * More clean up in class Potentials (#316) * remove some unused functions * make use of class MGmol_MPI * change some function names for clarity * fix some minor bug in iterative indexes * Misc code fixes (#317) * exposed by porting on new environment * Use unique restart filenames in test HDF5single (#318) * Swap ions in existing test (#319) * strengthen testing by swapping ions in testRestartEnergyAndForces * Code clean up (#320) * use more const * use initNuc() instead of moveVnuc() * remove incorrect assert * use MGmol_MPI in more cases * setup g_kbpsi_ inside initNuc() * rename initNuc() into setupPotentials() * Added functionalities to set local forces (#321) --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu>
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * Remove unused function in Control (#294) * Change symlink to restart in tests (#295) * enable tests when old link present * Extract number empty orbitals from restart file (#296) * Clean up MD_IonicStepper restart data write (#297) * Clean up code based on compiler warnings (#299) * Add getForces for evaluateDMandEnergyAndForces (#300) * Add check for compatibility MVP/Mehrstellen (#301) * Add support for Br atom (#302) * Clean up some HDFrestart functions (#303) * Fix and test restart single hdf5 file (#305) * Save Hartree potential for write in restart file (#306) * Speed-up recently added tests (#309) * simply use a smaller domain/mesh * Encapsulate some functions in Potentials (#310) * some functions were called at random places and confusing * Remove confusing 0 in naming restart files (#308) * use added integer only in case of fail/retry * Add functionalities for extra info in restart file (#312) * MPI abort (#313) * Fix error code used by MPI_Abort * Rho and VH restart (#311) * enable restart with consistent rho and VHartree --------- Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu> * Strenghten testIons (#315) * More clean up in class Potentials (#316) * remove some unused functions * make use of class MGmol_MPI * change some function names for clarity * fix some minor bug in iterative indexes * Misc code fixes (#317) * exposed by porting on new environment * Use unique restart filenames in test HDF5single (#318) * Swap ions in existing test (#319) * strengthen testing by swapping ions in testRestartEnergyAndForces * Code clean up (#320) * use more const * use initNuc() instead of moveVnuc() * remove incorrect assert * use MGmol_MPI in more cases * setup g_kbpsi_ inside initNuc() * rename initNuc() into setupPotentials() * Added functionalities to set local forces (#321) * Update mixed precision code (#322) * enable cmake build with mixed precision * enable use of BLIS * isolate blas3 loop rewrite in separate files * fix misc issues with mixed precision code * Clean up and fixes Ions (#326) * reset static index counter ion Ion when needed * simplify some loops * make Ions copy constructor private --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu>
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * Remove unused function in Control (#294) * Change symlink to restart in tests (#295) * enable tests when old link present * Extract number empty orbitals from restart file (#296) * Clean up MD_IonicStepper restart data write (#297) * Clean up code based on compiler warnings (#299) * Add getForces for evaluateDMandEnergyAndForces (#300) * Add check for compatibility MVP/Mehrstellen (#301) * Add support for Br atom (#302) * Clean up some HDFrestart functions (#303) * Fix and test restart single hdf5 file (#305) * Save Hartree potential for write in restart file (#306) * Speed-up recently added tests (#309) * simply use a smaller domain/mesh * Encapsulate some functions in Potentials (#310) * some functions were called at random places and confusing * Remove confusing 0 in naming restart files (#308) * use added integer only in case of fail/retry * Add functionalities for extra info in restart file (#312) * MPI abort (#313) * Fix error code used by MPI_Abort * Rho and VH restart (#311) * enable restart with consistent rho and VHartree --------- Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu> * Strenghten testIons (#315) * More clean up in class Potentials (#316) * remove some unused functions * make use of class MGmol_MPI * change some function names for clarity * fix some minor bug in iterative indexes * Misc code fixes (#317) * exposed by porting on new environment * Use unique restart filenames in test HDF5single (#318) * Swap ions in existing test (#319) * strengthen testing by swapping ions in testRestartEnergyAndForces * Code clean up (#320) * use more const * use initNuc() instead of moveVnuc() * remove incorrect assert * use MGmol_MPI in more cases * setup g_kbpsi_ inside initNuc() * rename initNuc() into setupPotentials() * Added functionalities to set local forces (#321) * Update mixed precision code (#322) * enable cmake build with mixed precision * enable use of BLIS * isolate blas3 loop rewrite in separate files * fix misc issues with mixed precision code * Clean up and fixes Ions (#326) * reset static index counter ion Ion when needed * simplify some loops * make Ions copy constructor private * Fixes for build without HDF5P (#324) * Fix testRhoVhRestart (#325) * Fix a few more issues with class Ions (#328) --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu>
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * Remove unused function in Control (#294) * Change symlink to restart in tests (#295) * enable tests when old link present * Extract number empty orbitals from restart file (#296) * Clean up MD_IonicStepper restart data write (#297) * Clean up code based on compiler warnings (#299) * Add getForces for evaluateDMandEnergyAndForces (#300) * Add check for compatibility MVP/Mehrstellen (#301) * Add support for Br atom (#302) * Clean up some HDFrestart functions (#303) * Fix and test restart single hdf5 file (#305) * Save Hartree potential for write in restart file (#306) * Speed-up recently added tests (#309) * simply use a smaller domain/mesh * Encapsulate some functions in Potentials (#310) * some functions were called at random places and confusing * Remove confusing 0 in naming restart files (#308) * use added integer only in case of fail/retry * Add functionalities for extra info in restart file (#312) * MPI abort (#313) * Fix error code used by MPI_Abort * Rho and VH restart (#311) * enable restart with consistent rho and VHartree --------- Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu> * Strenghten testIons (#315) * More clean up in class Potentials (#316) * remove some unused functions * make use of class MGmol_MPI * change some function names for clarity * fix some minor bug in iterative indexes * Misc code fixes (#317) * exposed by porting on new environment * Use unique restart filenames in test HDF5single (#318) * Swap ions in existing test (#319) * strengthen testing by swapping ions in testRestartEnergyAndForces * Code clean up (#320) * use more const * use initNuc() instead of moveVnuc() * remove incorrect assert * use MGmol_MPI in more cases * setup g_kbpsi_ inside initNuc() * rename initNuc() into setupPotentials() * Added functionalities to set local forces (#321) * Update mixed precision code (#322) * enable cmake build with mixed precision * enable use of BLIS * isolate blas3 loop rewrite in separate files * fix misc issues with mixed precision code * Clean up and fixes Ions (#326) * reset static index counter ion Ion when needed * simplify some loops * make Ions copy constructor private * Fixes for build without HDF5P (#324) * Fix testRhoVhRestart (#325) * Fix a few more issues with class Ions (#328) * Introduce new constructor for class Ions (#330) * modify various functions to use argument of type Ions instead of MGmol::ions_ --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu>
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * Remove unused function in Control (#294) * Change symlink to restart in tests (#295) * enable tests when old link present * Extract number empty orbitals from restart file (#296) * Clean up MD_IonicStepper restart data write (#297) * Clean up code based on compiler warnings (#299) * Add getForces for evaluateDMandEnergyAndForces (#300) * Add check for compatibility MVP/Mehrstellen (#301) * Add support for Br atom (#302) * Clean up some HDFrestart functions (#303) * Fix and test restart single hdf5 file (#305) * Save Hartree potential for write in restart file (#306) * Speed-up recently added tests (#309) * simply use a smaller domain/mesh * Encapsulate some functions in Potentials (#310) * some functions were called at random places and confusing * Remove confusing 0 in naming restart files (#308) * use added integer only in case of fail/retry * Add functionalities for extra info in restart file (#312) * MPI abort (#313) * Fix error code used by MPI_Abort * Rho and VH restart (#311) * enable restart with consistent rho and VHartree --------- Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu> * Strenghten testIons (#315) * More clean up in class Potentials (#316) * remove some unused functions * make use of class MGmol_MPI * change some function names for clarity * fix some minor bug in iterative indexes * Misc code fixes (#317) * exposed by porting on new environment * Use unique restart filenames in test HDF5single (#318) * Swap ions in existing test (#319) * strengthen testing by swapping ions in testRestartEnergyAndForces * Code clean up (#320) * use more const * use initNuc() instead of moveVnuc() * remove incorrect assert * use MGmol_MPI in more cases * setup g_kbpsi_ inside initNuc() * rename initNuc() into setupPotentials() * Added functionalities to set local forces (#321) * Update mixed precision code (#322) * enable cmake build with mixed precision * enable use of BLIS * isolate blas3 loop rewrite in separate files * fix misc issues with mixed precision code * Clean up and fixes Ions (#326) * reset static index counter ion Ion when needed * simplify some loops * make Ions copy constructor private * Fixes for build without HDF5P (#324) * Fix testRhoVhRestart (#325) * Fix a few more issues with class Ions (#328) * Introduce new constructor for class Ions (#330) * modify various functions to use argument of type Ions instead of MGmol::ions_ * Add cleanup and MGmolInterface (#331) * Add function to set local forces (#333) * based on matching coordinates to local ions --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu>
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * Remove unused function in Control (#294) * Change symlink to restart in tests (#295) * enable tests when old link present * Extract number empty orbitals from restart file (#296) * Clean up MD_IonicStepper restart data write (#297) * Clean up code based on compiler warnings (#299) * Add getForces for evaluateDMandEnergyAndForces (#300) * Add check for compatibility MVP/Mehrstellen (#301) * Add support for Br atom (#302) * Clean up some HDFrestart functions (#303) * Fix and test restart single hdf5 file (#305) * Save Hartree potential for write in restart file (#306) * Add commit number temporarily * Fix merge * Speed-up recently added tests (#309) * simply use a smaller domain/mesh * Encapsulate some functions in Potentials (#310) * some functions were called at random places and confusing * Remove confusing 0 in naming restart files (#308) * use added integer only in case of fail/retry * Move geometric transforms to tools in library * Add functionalities for extra info in restart file (#312) * Add ROM MVP solver to MD * Changes to scripts * MPI abort (#313) * Fix error code used by MPI_Abort * Partial updates * Rho and VH restart (#311) * enable restart with consistent rho and VHartree --------- Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu> * Attempt to fix bugs * Fix config file * Debug * Debug * Debug * Debug * Strenghten testIons (#315) * More clean up in class Potentials (#316) * remove some unused functions * make use of class MGmol_MPI * change some function names for clarity * fix some minor bug in iterative indexes * Fix ROM stage * Debug * Add initialization to evaluateDMandEnergyandForces if it is ROM MVP * Misc code fixes (#317) * exposed by porting on new environment * Use unique restart filenames in test HDF5single (#318) * Swap ions in existing test (#319) * strengthen testing by swapping ions in testRestartEnergyAndForces * Code clean up (#320) * use more const * use initNuc() instead of moveVnuc() * remove incorrect assert * use MGmol_MPI in more cases * setup g_kbpsi_ inside initNuc() * rename initNuc() into setupPotentials() * Pass by reference * Make global version of setForces * Added functionalities to set local forces (#321) * Update mixed precision code (#322) * enable cmake build with mixed precision * enable use of BLIS * isolate blas3 loop rewrite in separate files * fix misc issues with mixed precision code * Use new setLocalForce * Write PinnedH2O into original ordering. This is better for MD * names should be obtained before rotate * Fixing ion names * Clean up and fixes Ions (#326) * reset static index counter ion Ion when needed * simplify some loops * make Ions copy constructor private * Fixes for build without HDF5P (#324) * Fix testRhoVhRestart (#325) * Fix a few more issues with class Ions (#328) * Debugging * Introduce new constructor for class Ions (#330) * modify various functions to use argument of type Ions instead of MGmol::ions_ * Add cleanup and MGmolInterface (#331) * Using new constructor for ROM ions * Add function to set local forces (#333) * based on matching coordinates to local ions * Use new setLocalForces with positions instead of names * Cleanup * only pe0 prints bondlengths and bondangle * Fix setLocalForces * Updates * Minor changes * Auxiliary scripts * Auxiliary script * Auxiliary scripts * fix job scripts * Renaming and adding new test * Rename * Minor change in auxiliary script * config files * update tests * Minor changes in names --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu>
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * Remove unused function in Control (#294) * Change symlink to restart in tests (#295) * enable tests when old link present * Extract number empty orbitals from restart file (#296) * Clean up MD_IonicStepper restart data write (#297) * Clean up code based on compiler warnings (#299) * Add getForces for evaluateDMandEnergyAndForces (#300) * Add check for compatibility MVP/Mehrstellen (#301) * Add support for Br atom (#302) * Clean up some HDFrestart functions (#303) * Fix and test restart single hdf5 file (#305) * Save Hartree potential for write in restart file (#306) * Speed-up recently added tests (#309) * simply use a smaller domain/mesh * Encapsulate some functions in Potentials (#310) * some functions were called at random places and confusing * Remove confusing 0 in naming restart files (#308) * use added integer only in case of fail/retry * Add functionalities for extra info in restart file (#312) * MPI abort (#313) * Fix error code used by MPI_Abort * Rho and VH restart (#311) * enable restart with consistent rho and VHartree --------- Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu> * Strenghten testIons (#315) * More clean up in class Potentials (#316) * remove some unused functions * make use of class MGmol_MPI * change some function names for clarity * fix some minor bug in iterative indexes * Misc code fixes (#317) * exposed by porting on new environment * Use unique restart filenames in test HDF5single (#318) * Swap ions in existing test (#319) * strengthen testing by swapping ions in testRestartEnergyAndForces * Code clean up (#320) * use more const * use initNuc() instead of moveVnuc() * remove incorrect assert * use MGmol_MPI in more cases * setup g_kbpsi_ inside initNuc() * rename initNuc() into setupPotentials() * Added functionalities to set local forces (#321) * Update mixed precision code (#322) * enable cmake build with mixed precision * enable use of BLIS * isolate blas3 loop rewrite in separate files * fix misc issues with mixed precision code * Clean up and fixes Ions (#326) * reset static index counter ion Ion when needed * simplify some loops * make Ions copy constructor private * Fixes for build without HDF5P (#324) * Fix testRhoVhRestart (#325) * Fix a few more issues with class Ions (#328) * Introduce new constructor for class Ions (#330) * modify various functions to use argument of type Ions instead of MGmol::ions_ * Add cleanup and MGmolInterface (#331) * Add function to set local forces (#333) * based on matching coordinates to local ions * Fix setLocalForces (#335) * Fix test WFEnergyAndForces (#336) * writing restart twice in same directory was failing * Add mixing option in MVP (#337) * Timer * Update MVP with mixing (#339) * use tolerance to terminate iterations * tune verbosity * Updates * use setupPotentials * Setup potentials again * setupRhoc is done within setupPotentials * Avoid setPositions * Rescaling ROM ion density * Relax threshold * Increase tolerance for testROMIonDensity --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu>
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * Remove unused function in Control (#294) * Change symlink to restart in tests (#295) * enable tests when old link present * Extract number empty orbitals from restart file (#296) * Clean up MD_IonicStepper restart data write (#297) * Clean up code based on compiler warnings (#299) * Add getForces for evaluateDMandEnergyAndForces (#300) * Add check for compatibility MVP/Mehrstellen (#301) * Add support for Br atom (#302) * Clean up some HDFrestart functions (#303) * Fix and test restart single hdf5 file (#305) * Save Hartree potential for write in restart file (#306) * Speed-up recently added tests (#309) * simply use a smaller domain/mesh * Encapsulate some functions in Potentials (#310) * some functions were called at random places and confusing * Remove confusing 0 in naming restart files (#308) * use added integer only in case of fail/retry * Add functionalities for extra info in restart file (#312) * MPI abort (#313) * Fix error code used by MPI_Abort * Rho and VH restart (#311) * enable restart with consistent rho and VHartree --------- Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu> * Strenghten testIons (#315) * More clean up in class Potentials (#316) * remove some unused functions * make use of class MGmol_MPI * change some function names for clarity * fix some minor bug in iterative indexes * Misc code fixes (#317) * exposed by porting on new environment * Use unique restart filenames in test HDF5single (#318) * Swap ions in existing test (#319) * strengthen testing by swapping ions in testRestartEnergyAndForces * Code clean up (#320) * use more const * use initNuc() instead of moveVnuc() * remove incorrect assert * use MGmol_MPI in more cases * setup g_kbpsi_ inside initNuc() * rename initNuc() into setupPotentials() * Added functionalities to set local forces (#321) * Update mixed precision code (#322) * enable cmake build with mixed precision * enable use of BLIS * isolate blas3 loop rewrite in separate files * fix misc issues with mixed precision code * Clean up and fixes Ions (#326) * reset static index counter ion Ion when needed * simplify some loops * make Ions copy constructor private * Fixes for build without HDF5P (#324) * Fix testRhoVhRestart (#325) * Fix a few more issues with class Ions (#328) * Introduce new constructor for class Ions (#330) * modify various functions to use argument of type Ions instead of MGmol::ions_ * Add cleanup and MGmolInterface (#331) * Add function to set local forces (#333) * based on matching coordinates to local ions * Fix setLocalForces (#335) * Fix test WFEnergyAndForces (#336) * writing restart twice in same directory was failing * Add mixing option in MVP (#337) * Update MVP with mixing (#339) * use tolerance to terminate iterations * tune verbosity * Update DensityMatrix class (#342) * add extrapolation function * remove unused function * simplify use of iterative index * Fixing DM tolerance (#341) * Fix Density Matrix tolerance read --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> * Rm oversubscribe from CMakeLists.txt (#346) * already set in build script * Adapt to new environment on condo @ ORNL (#348) --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu>
* Fix EnergyAndForces tests (#277) * have them work in debug mode too * Move factor 4pi out og linear solvers (#278) * Move some code into PoissonSolverFactory (#279) * Clean up class Potentials (#280) * Clean up class Ions, add test for it (#281) * Add test MD_MVP (#290) * Clean up code related to DM restart data (#292) * Write dm (#291) * Update use of DM in restart * Remove unused function in Control (#294) * Change symlink to restart in tests (#295) * enable tests when old link present * Extract number empty orbitals from restart file (#296) * Clean up MD_IonicStepper restart data write (#297) * Clean up code based on compiler warnings (#299) * Add getForces for evaluateDMandEnergyAndForces (#300) * Add check for compatibility MVP/Mehrstellen (#301) * Add support for Br atom (#302) * Clean up some HDFrestart functions (#303) * Fix and test restart single hdf5 file (#305) * Save Hartree potential for write in restart file (#306) * Speed-up recently added tests (#309) * simply use a smaller domain/mesh * Encapsulate some functions in Potentials (#310) * some functions were called at random places and confusing * Remove confusing 0 in naming restart files (#308) * use added integer only in case of fail/retry * Add functionalities for extra info in restart file (#312) * MPI abort (#313) * Fix error code used by MPI_Abort * Rho and VH restart (#311) * enable restart with consistent rho and VHartree --------- Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu> * Strenghten testIons (#315) * More clean up in class Potentials (#316) * remove some unused functions * make use of class MGmol_MPI * change some function names for clarity * fix some minor bug in iterative indexes * Misc code fixes (#317) * exposed by porting on new environment * Use unique restart filenames in test HDF5single (#318) * Swap ions in existing test (#319) * strengthen testing by swapping ions in testRestartEnergyAndForces * Code clean up (#320) * use more const * use initNuc() instead of moveVnuc() * remove incorrect assert * use MGmol_MPI in more cases * setup g_kbpsi_ inside initNuc() * rename initNuc() into setupPotentials() * Added functionalities to set local forces (#321) * Update mixed precision code (#322) * enable cmake build with mixed precision * enable use of BLIS * isolate blas3 loop rewrite in separate files * fix misc issues with mixed precision code * Clean up and fixes Ions (#326) * reset static index counter ion Ion when needed * simplify some loops * make Ions copy constructor private * Fixes for build without HDF5P (#324) * Fix testRhoVhRestart (#325) * Fix a few more issues with class Ions (#328) * Introduce new constructor for class Ions (#330) * modify various functions to use argument of type Ions instead of MGmol::ions_ * Add cleanup and MGmolInterface (#331) * Add function to set local forces (#333) * based on matching coordinates to local ions * Fix setLocalForces (#335) * Fix test WFEnergyAndForces (#336) * writing restart twice in same directory was failing * Add mixing option in MVP (#337) * Update MVP with mixing (#339) * use tolerance to terminate iterations * tune verbosity * Update DensityMatrix class (#342) * add extrapolation function * remove unused function * simplify use of iterative index * Fixing DM tolerance (#341) * Fix Density Matrix tolerance read --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> * Rm oversubscribe from CMakeLists.txt (#346) * already set in build script * Adapt to new environment on condo @ ORNL (#348) * Remove unused function * Clean up use of coords file when restarting * use coordinates file to override atomic coordinates when using restart wavefunctions * Add test restart with override atomic coordinates * Add some missing include files * required for gcc12 * Print MVP timers --------- Co-authored-by: Jean-Luc Fattebert <fattebertj@ornl.gov> Co-authored-by: Seung Whan Chung <seung.chung@austin.utexas.edu>
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This is just to compare ROM latest version with release