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Commit aa6df075 authored by Lauri Himanen's avatar Lauri Himanen
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Support for most basic metainfos, some XC functionals now supported, adding... 

Support for most basic metainfos, some XC functionals now supported, adding more. Added proper scala integration.
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parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/forces_posinp.xyz 0 → 100644
View file @ aa6df075
2 angstroemd0 -1.98834837256869932E+01 (Ha) Geometry + metaData forces
free
N 0.00000000000000000E+00 0.00000000000000000E+00 0.00000000000000000E+00
N 0.00000000000000000E+00 0.00000000000000000E+00 1.11498999595642090E+00
forces
N -1.69406589450860068E-21 -1.69406589450860068E-21 5.67055414067696439E-02
N 1.69406589450860068E-21 1.69406589450860068E-21 -5.67055414067696439E-02
parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/input_minimal.yaml 0 → 100644
View file @ aa6df075
#---------------------------------------------------------------------- Minimal input file
#This file indicates the minimal set of input variables which has to be given to perform
#the run. The code would produce the same output if this file is used as input.
posinp:
units: angstroem
positions:
- N: [0.0, 0.0, 0.0]
- N: [0.0, 0.0, 1.114989995956421]
properties:
format: xyz
source: posinp.xyz
psolver:
environment:
gammaS: water
alphaS: water
betaV: water
parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/time.yaml 0 → 100644
View file @ aa6df075
---
INIT: # % , Time (s)
Classes:
Flib LowLevel : [ 10.9, 6.84E-02]
Communications : [ 0.0, 2.15E-05]
BLAS-LAPACK : [ 0.8, 5.05E-03]
PS Computation : [ 36.6, 0.23]
Potential : [ 6.7, 4.25E-02]
Convolutions : [ 12.4, 7.83E-02]
Other : [ 0.2, 1.21E-03]
Initialization : [ 5.0, 3.12E-02]
Total : [ 72.5, 0.63]
Categories: #Ordered by time consumption
PSolver Kernel Creation:
Data : [ 19.2, 0.12]
Class : PS Computation
Info : ISF operations and creation of the kernel
PSolver Computation:
Data : [ 17.4, 0.11]
Class : PS Computation
Info : 3D SG_FFT and related operations
Init to Zero:
Data : [ 7.1, 4.49E-02]
Class : Flib LowLevel
Info : Memset of storage space
ApplyLocPotKin:
Data : [ 7.1, 4.48E-02]
Class : Convolutions
Info : OpenCL ported
Exchange-Correlation:
Data : [ 6.7, 4.25E-02]
Class : Potential
Info : Operations needed to construct local XC potential
Rho_comput:
Data : [ 5.3, 3.35E-02]
Class : Convolutions
Info : OpenCL ported
wavefunction:
Data : [ 4.2, 2.63E-02]
Class : Initialization
Info : Miscellaneous
Array allocations:
Data : [ 2.4, 1.51E-02]
Class : Flib LowLevel
Info : Heap storage allocation and associated profiling
Blas (d-s-c-z)GeMM:
Data : [ 0.8, 5.05E-03]
Class : BLAS-LAPACK
Info : Blas General Matrix-Matrix multiplications of any float type
Routine Profiling:
Data : [ 0.7, 4.26E-03]
Class : Flib LowLevel
Info : Profiling performances for debugging
Vector copy:
Data : [ 0.7, 4.15E-03]
Class : Flib LowLevel
Info : Memory copy of arrays (excluded allocations)
CrtLocPot:
Data : [ 0.3, 2.20E-03]
Class : Initialization
Info : Miscellaneous
Input_comput:
Data : [ 0.2, 1.45E-03]
Class : Initialization
Info : Miscellaneous
CrtDescriptors:
Data : [ 0.2, 1.27E-03]
Class : Initialization
Info : RMA Pattern
ApplyProj:
Data : [ 0.1, 7.44E-04]
Class : Other
Info : RMA pattern
ionic_energy:
Data : [ 0.1, 3.89E-04]
Class : Other
Info : Miscellaneous
calc_bounds:
Data : [ 0.0, 3.91E-05]
Class : Other
Info : Miscellaneous
Un-TransSwitch:
Data : [ 0.0, 2.96E-05]
Class : Other
Info : RMA pattern
Allreduce, Large Size:
Data : [ 0.0, 1.38E-05]
Class : Communications
Info : Allreduce operations for more than 5 elements
Pot_after_comm:
Data : [ 0.0, 7.87E-06]
Class : Other
Info : global_to_loca
Pot_commun:
Data : [ 0.0, 5.96E-06]
Class : Communications
Info : AllGathrv grid
Allreduce, Small Size:
Data : [ 0.0, 1.67E-06]
Class : Communications
Info : Allreduce operations for less than 5 elements
WFN_OPT: # % , Time (s)
Classes:
Flib LowLevel : [ 17.7, 0.39]
Communications : [ 0.0, 5.29E-05]
BLAS-LAPACK : [ 0.4, 9.37E-03]
PS Computation : [ 18.1, 0.40]
Potential : [ 17.5, 0.39]
Convolutions : [ 33.7, 0.75]
Linear Algebra : [ 0.4, 8.93E-03]
Other : [ 9.9, 0.22]
Total : [ 97.8, 2.2]
Categories: #Ordered by time consumption
PSolver Computation:
Data : [ 18.1, 0.40]
Class : PS Computation
Info : 3D SG_FFT and related operations
Exchange-Correlation:
Data : [ 17.5, 0.39]
Class : Potential
Info : Operations needed to construct local XC potential
ApplyLocPotKin:
Data : [ 13.5, 0.30]
Class : Convolutions
Info : OpenCL ported
Rho_comput:
Data : [ 10.9, 0.24]
Class : Convolutions
Info : OpenCL ported
Init to Zero:
Data : [ 10.3, 0.23]
Class : Flib LowLevel
Info : Memset of storage space
Precondition:
Data : [ 9.3, 0.21]
Class : Convolutions
Info : OpenCL ported
ApplyProj:
Data : [ 8.9, 0.20]
Class : Other
Info : RMA pattern
Array allocations:
Data : [ 2.8, 6.12E-02]
Class : Flib LowLevel
Info : Heap storage allocation and associated profiling
Routine Profiling:
Data : [ 2.5, 5.55E-02]
Class : Flib LowLevel
Info : Profiling performances for debugging
Vector copy:
Data : [ 2.2, 4.82E-02]
Class : Flib LowLevel
Info : Memory copy of arrays (excluded allocations)
Diis:
Data : [ 1.0, 2.21E-02]
Class : Other
Info : Other
Blas (d-s-c-z)GeMM:
Data : [ 0.4, 9.37E-03]
Class : BLAS-LAPACK
Info : Blas General Matrix-Matrix multiplications of any float type
Chol_comput:
Data : [ 0.4, 8.81E-03]
Class : Linear Algebra
Info : ALLReduce orbs
Un-TransSwitch:
Data : [ 0.0, 2.54E-04]
Class : Other
Info : RMA pattern
LagrM_comput:
Data : [ 0.0, 1.21E-04]
Class : Linear Algebra
Info : DGEMM
Pot_after_comm:
Data : [ 0.0, 8.37E-05]
Class : Other
Info : global_to_loca
Pot_commun:
Data : [ 0.0, 5.29E-05]
Class : Communications
Info : AllGathrv grid
LAST: # % , Time (s)
Classes:
Flib LowLevel : [ 15.4, 5.02E-02]
Communications : [ 0.0, 1.38E-05]
BLAS-LAPACK : [ 0.3, 1.01E-03]
PS Computation : [ 25.0, 8.17E-02]
Potential : [ 11.7, 3.83E-02]
Convolutions : [ 25.7, 8.40E-02]
Other : [ 8.0, 2.62E-02]
Finalization : [ 0.8, 2.69E-03]
Total : [ 87.0, 0.33]
Categories: #Ordered by time consumption
PSolver Computation:
Data : [ 25.0, 8.17E-02]
Class : PS Computation
Info : 3D SG_FFT and related operations
Rho_comput:
Data : [ 14.6, 4.78E-02]
Class : Convolutions
Info : OpenCL ported
Exchange-Correlation:
Data : [ 11.7, 3.83E-02]
Class : Potential
Info : Operations needed to construct local XC potential
ApplyLocPotKin:
Data : [ 11.1, 3.61E-02]
Class : Convolutions
Info : OpenCL ported
Init to Zero:
Data : [ 10.4, 3.40E-02]
Class : Flib LowLevel
Info : Memset of storage space
ApplyProj:
Data : [ 8.0, 2.62E-02]
Class : Other
Info : RMA pattern
Vector copy:
Data : [ 2.8, 9.08E-03]
Class : Flib LowLevel
Info : Memory copy of arrays (excluded allocations)
Array allocations:
Data : [ 1.2, 4.05E-03]
Class : Flib LowLevel
Info : Heap storage allocation and associated profiling
Routine Profiling:
Data : [ 0.9, 3.06E-03]
Class : Flib LowLevel
Info : Profiling performances for debugging
Forces:
Data : [ 0.8, 2.69E-03]
Class : Finalization
Info : Miscellaneous
Blas (d-s-c-z)GeMM:
Data : [ 0.3, 9.85E-04]
Class : BLAS-LAPACK
Info : Blas General Matrix-Matrix multiplications of any float type
Lapack (dsy-ssy-che-zhe)eev:
Data : [ 0.0, 3.00E-05]
Class : BLAS-LAPACK
Info : Lapack Eigenvalue Problem
Un-TransSwitch:
Data : [ 0.0, 1.22E-05]
Class : Other
Info : RMA pattern
Pot_after_comm:
Data : [ 0.0, 7.15E-06]
Class : Other
Info : global_to_loca
Pot_commun:
Data : [ 0.0, 5.48E-06]
Class : Communications
Info : AllGathrv grid
Allreduce, Small Size:
Data : [ 0.0, 5.25E-06]
Class : Communications
Info : Allreduce operations for less than 5 elements
Allreduce, Large Size:
Data : [ 0.0, 3.10E-06]
Class : Communications
Info : Allreduce operations for more than 5 elements
SUMMARY: # % , Time (s)
INIT : [ 19.9, 0.63]
WFN_OPT : [ 69.8, 2.2]
LAST : [ 10.3, 0.33]
Total : [ 100.0, 3.2]
Routines timing and number of calls:
- Main_program: [ 3.93, 1, ~*]
Subroutines:
- process_run (id="posinp"): [ 3.18, 1, 80.83%*]
Subroutines:
- bigdft_state: [ 3.18, 1, 99.90%*]
Subroutines:
- quantum_mechanical_state: [ 3.17, 1, 99.76%*]
Subroutines:
- cluster: [ 3.17, 1, 100.03%]
Subroutines:
- Electrostatic_Solver: [ 0.629, 11, 19.85%]
Subroutines:
- apply_kernel: [ 0.605, 11, 96.13%]
Subroutines:
- G_PoissonSolver: [ 0.420, 11, 69.37%]
- XC_potential: [ 0.440, 11, 13.88%]
Subroutines:
- xc_energy_new: [ 0.416, 11, 94.65%]
Subroutines:
- xc_getvxc: [ 0.393, 11, 94.49%]
- LocalHamiltonianApplication: [ 0.401, 11, 12.65%]
Subroutines:
- psir_to_vpsi: [ 8.427E-02, 55, 21.02%]
Subroutines:
- apply_potential_lr_bounds: [ 8.006E-02, 55, 95.00%]
- orbital_basis_associate: [ 7.374E-04, 11, 0.18%]
- input_wf: [ 0.400, 1, 12.62%]
Subroutines:
- updatePotential: [ 9.890E-02, 1, 24.73%]
Subroutines:
- Electrostatic_Solver: [ 5.146E-02, 1, 52.04%]
Subroutines:
- apply_kernel: [ 4.950E-02, 1, 96.18%]
Subroutines:
- G_PoissonSolver: [ 4.089E-02, 1, 82.61%]
- XC_potential: [ 4.481E-02, 1, 45.30%]
Subroutines:
- xc_energy_new: [ 4.171E-02, 1, 93.08%]
Subroutines:
- xc_getvxc: [ 3.893E-02, 1, 93.32%]
- LocalHamiltonianApplication: [ 4.885E-02, 1, 12.21%]
Subroutines:
- psir_to_vpsi: [ 1.043E-02, 8, 21.35%]
Subroutines:
- apply_potential_lr_bounds: [ 9.872E-03, 8, 94.65%]
- orbital_basis_associate: [ 7.438E-05, 1, 0.15%]
- daub_to_isf: [ 2.496E-02, 8, 6.24%]
- LDiagHam: [ 6.851E-03, 1, 1.71%]
- check_linear_and_create_Lzd: [ 1.257E-03, 1, 0.31%]
- NonLocalHamiltonianApplication: [ 1.087E-03, 1, 0.27%]
Subroutines:
- atom_projector: [ 4.037E-04, 2, 37.14%]
Subroutines:
- crtproj: [ 3.028E-04, 2, 75.01%]
- orbital_basis_associate: [ 7.897E-05, 1, 7.27%]
- local_potential_dimensions: [ 2.057E-04, 3, 0.05%]
- deallocate_work_arrays_sumrho: [ 1.086E-04, 1, 0.03%]
- initialize_work_arrays_sumrho: [ 8.927E-05, 1, 0.02%]
- full_local_potential: [ 6.645E-05, 1, 0.02%]
- SynchronizeHamiltonianApplication: [ 1.804E-05, 1, 0.00%]
- preconditionall2: [ 0.298, 10, 9.41%]
Subroutines:
- precondition_preconditioner: [ 8.735E-02, 50, 29.31%]
Subroutines:
- prec_diag: [ 8.165E-02, 50, 93.48%]
- calculate_rmr_new: [ 2.798E-02, 300, 9.39%]
- compress_forstandard: [ 1.280E-02, 350, 4.29%]
- finalise_precond_residue: [ 1.502E-03, 50, 0.50%]
- NonLocalHamiltonianApplication: [ 0.244, 11, 7.70%]
Subroutines:
- atom_projector: [ 0.203, 22, 83.21%]
Subroutines:
- crtproj: [ 0.200, 22, 98.38%]
- orbital_basis_associate: [ 7.821E-04, 11, 0.32%]
- daub_to_isf: [ 0.158, 55, 4.97%]
- system_initialization: [ 0.152, 1, 4.79%]
Subroutines:
- pkernel_set: [ 0.130, 1, 85.60%]
Subroutines:
- mpi_environment_set: [ 1.627E-05, 1, 0.01%]
- createWavefunctionsDescriptors: [ 2.176E-03, 1, 1.43%]
Subroutines:
- fill_logrid: [ 1.882E-04, 2, 8.65%]
- segkeys: [ 1.310E-04, 2, 6.02%]
- num_segkeys: [ 6.667E-05, 2, 3.06%]
- createProjectorsArrays: [ 1.970E-03, 1, 1.30%]
Subroutines:
- localize_projectors: [ 3.041E-04, 1, 15.44%]
Subroutines:
- fill_logrid: [ 1.101E-04, 4, 36.21%]
- num_segkeys: [ 8.109E-05, 4, 26.66%]
- set_wfd_to_wfd: [ 1.631E-04, 2, 8.28%]
Subroutines:
- init_tolr: [ 9.121E-05, 2, 55.92%]
- fill_logrid: [ 1.066E-04, 4, 5.41%]
- segkeys: [ 9.551E-05, 4, 4.85%]
- transform_keyglob_to_keygloc: [ 8.327E-05, 4, 4.23%]
- allocate_arrays: [ 8.077E-05, 1, 4.10%]
- gaussian_basis_from_psp: [ 3.932E-05, 1, 2.00%]
- nullify_structure: [ 1.577E-05, 1, 0.80%]
- orbital_basis_associate: [ 7.075E-05, 1, 0.05%]
- mpi_environment_set: [ 2.706E-05, 1, 0.02%]
- kswfn_post_treatments: [ 0.117, 1, 3.68%]
Subroutines:
- Electrostatic_Solver: [ 4.524E-02, 1, 38.67%]
Subroutines:
- apply_kernel: [ 4.347E-02, 1, 96.09%]
Subroutines:
- G_PoissonSolver: [ 4.070E-02, 1, 93.64%]
- calculate_dipole_moment: [ 3.421E-02, 1, 29.24%]
- daub_to_isf: [ 1.492E-02, 5, 12.75%]
- calculate_forces: [ 3.409E-03, 1, 2.91%]
Subroutines:
- nonlocal_forces: [ 1.813E-03, 1, 53.17%]
Subroutines:
- atom_projector: [ 1.313E-03, 8, 72.43%]
Subroutines:
- crtproj: [ 1.029E-03, 8, 78.41%]
- local_forces: [ 1.481E-03, 1, 43.43%]
- rhocore_forces: [ 1.499E-05, 1, 0.44%]
- deallocate_work_arrays_sumrho: [ 1.051E-04, 1, 0.09%]
- initialize_work_arrays_sumrho: [ 9.186E-05, 1, 0.08%]
- orbital_basis_associate: [ 8.129E-05, 1, 0.07%]
- createEffectiveIonicPotential: [ 7.749E-02, 1, 2.44%]
Subroutines:
- createIonicPotential: [ 7.745E-02, 1, 99.94%]
Subroutines:
- Electrostatic_Solver: [ 6.985E-02, 1, 90.18%]
Subroutines:
- apply_kernel: [ 6.825E-02, 1, 97.71%]
Subroutines:
- G_PoissonSolver: [ 6.418E-02, 1, 94.04%]
- timing_dump_results: [ 1.666E-03, 2, 0.05%]
- deallocate_work_arrays_sumrho: [ 1.243E-03, 11, 0.04%]
- initialize_work_arrays_sumrho: [ 1.158E-03, 11, 0.04%]
- full_local_potential: [ 8.629E-04, 11, 0.03%]
- IonicEnergyandForces: [ 5.133E-04, 1, 0.02%]
Subroutines:
- vdwcorrection_calculate_energy: [ 2.188E-05, 1, 4.26%]
- vdwcorrection_calculate_forces: [ 1.581E-05, 1, 3.08%]
- SynchronizeHamiltonianApplication: [ 2.722E-04, 11, 0.01%]
- interaction_multipoles_ions: [ 1.312E-04, 1, 0.00%]
- ionic_energy_of_external_charges: [ 5.234E-05, 1, 0.00%]
- potential_from_charge_multipoles: [ 1.835E-05, 1, 0.00%]
- timing_dump_results: [ 7.660E-04, 1, 0.02%]
- bigdft_init: [ 0.713, 1, 18.13%]
Subroutines:
- mpi_environment_set: [ 7.590E-05, 1, 0.01%]
- run_objects_init: [ 4.323E-02, 1, 1.10%]
Subroutines:
- set_run_objects: [ 2.204E-02, 1, 50.98%]
Subroutines:
- inputs_from_dict: [ 2.197E-02, 1, 99.68%]
Subroutines:
- input_keys_fill_all: [ 9.360E-03, 1, 42.61%]
Subroutines:
- input_keys_init: [ 5.172E-03, 1, 55.26%]
- PS_input_dict: [ 8.858E-04, 1, 9.46%]
- input_keys_dump: [ 5.086E-03, 1, 23.15%]
- atomic_data_set_from_dict: [ 3.365E-03, 1, 15.32%]
- psp_dict_fill_all: [ 9.859E-04, 1, 4.49%]
- astruct_set_from_dict: [ 4.273E-04, 1, 1.94%]
- psp_dict_analyse: [ 2.290E-04, 1, 1.04%]
- allocateBasicArraysInputLin: [ 7.826E-05, 1, 0.36%]
- kpt_input_analyse: [ 4.855E-05, 1, 0.22%]
- atomic_gamma_from_dict: [ 2.668E-05, 1, 0.12%]
- occupation_set_from_dict: [ 2.611E-05, 1, 0.12%]
- input_analyze: [ 1.795E-05, 1, 0.08%]
- read_n_orbitals: [ 1.721E-05, 1, 0.08%]
- astruct_file_merge_to_dict: [ 1.736E-02, 1, 40.16%]
- read_input_dict_from_files: [ 1.218E-04, 1, 0.28%]
CPU parallelism:
MPI tasks : 1
OMP threads : 8
Report timestamp : 2016-12-02 08:53:41.913
parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/forces_posinp.xyz 0 → 100644
View file @ aa6df075
2 angstroemd0 -1.98842958295531673E+01 (Ha) Geometry + metaData forces
periodic 7.00000000000000000E+00 7.00000000000000000E+00 7.00000000000000000E+00
N 0.00000000000000000E+00 0.00000000000000000E+00 0.00000000000000000E+00
N 0.00000000000000000E+00 0.00000000000000000E+00 1.11498999595642090E+00
forces
N 0.00000000000000000E+00 0.00000000000000000E+00 5.62611962577510491E-02
N 0.00000000000000000E+00 0.00000000000000000E+00 -5.62611962577510630E-02
parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/input_minimal.yaml 0 → 100644
View file @ aa6df075
#---------------------------------------------------------------------- Minimal input file
#This file indicates the minimal set of input variables which has to be given to perform
#the run. The code would produce the same output if this file is used as input.
posinp:
units: angstroem
cell: [ 7.0, 7.0, 7.0]
positions:
- N: [0.0, 0.0, 0.0]
- N: [0.0, 0.0, 1.114989995956421]
properties:
format: xyz
source: posinp.xyz
psolver:
environment:
gammaS: water
alphaS: water
betaV: water
parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/time.yaml 0 → 100644
View file @ aa6df075
---
INIT: # % , Time (s)
Classes:
Flib LowLevel : [ 7.2, 3.69E-02]
Communications : [ 0.0, 3.81E-06]
BLAS-LAPACK : [ 0.9, 4.81E-03]
PS Computation : [ 1.3, 6.82E-03]
Potential : [ 2.4, 1.20E-02]
Convolutions : [ 22.3, 0.11]
Other : [ 16.7, 8.53E-02]
Initialization : [ 12.5, 6.41E-02]
Total : [ 63.4, 0.51]
Categories: #Ordered by time consumption
ionic_energy:
Data : [ 16.5, 8.45E-02]
Class : Other
Info : Miscellaneous
ApplyLocPotKin:
Data : [ 13.0, 6.64E-02]
Class : Convolutions
Info : OpenCL ported
wavefunction:
Data : [ 11.9, 6.10E-02]
Class : Initialization
Info : Miscellaneous
Rho_comput:
Data : [ 9.3, 4.76E-02]
Class : Convolutions
Info : OpenCL ported
Init to Zero:
Data : [ 5.1, 2.61E-02]
Class : Flib LowLevel
Info : Memset of storage space
Exchange-Correlation:
Data : [ 2.4, 1.20E-02]
Class : Potential
Info : Operations needed to construct local XC potential
Array allocations:
Data : [ 1.1, 5.86E-03]
Class : Flib LowLevel