diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py index bc6fceab06e73a2f06164addf566a3f9bfcddc61..81fab939fb05f86227e10fc7f78d01b128382948 100644 --- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py +++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py @@ -246,6 +246,8 @@ class CP2KInputParser(BasicParser): self.input_tree.root_section.accessed = True for line in self.input_lines: + + # Remove comments and whitespaces line = line.split('!', 1)[0].strip() # Skip empty lines @@ -283,6 +285,8 @@ class CP2KInputParser(BasicParser): # Contents (keywords, default keywords) else: split = line.split(' ', 1) + if len(split) <= 1: + raise IndexError("A keyword in the CP2K input had no value associated with it. The line causing this is: '{}'".format(line)) keyword_name = split[0].upper() keyword_value = split[1] self.input_tree.set_keyword(path + "/" + keyword_name, keyword_value) diff --git a/test/unittests/cp2k_2.6.2/input_preprocessing/comments/si_bulk8.inp b/test/unittests/cp2k_2.6.2/input_preprocessing/comments/si_bulk8.inp new file mode 100644 index 0000000000000000000000000000000000000000..7701cb015289fceb9080984e7f8dfbb533131877 --- /dev/null +++ b/test/unittests/cp2k_2.6.2/input_preprocessing/comments/si_bulk8.inp @@ -0,0 +1,65 @@ +! Starting comment +&GLOBAL + PROJECT Si_bulk8 ! Keyword comment + RUN_TYPE ENERGY_FORCE + PRINT_LEVEL MEDIUM +&END GLOBAL +&FORCE_EVAL ! Section comment + METHOD Quickstep + &SUBSYS + &KIND Si + ELEMENT Si + BASIS_SET DZVP-GTH-PADE + POTENTIAL GTH-PADE-q4 + &END KIND + &CELL + A 5.430697500 0.000000000 0.000000000 ! test + B 0.000000000 5.430697500 0.000000000 + C 0.000000000 0.000000000 5.430697500 + &END CELL ! Comment in end tag + &COORD ! Comment where default keyword starts + Si 0.000000000 0.000000000 0.000000000 + Si 0.000000000 2.715348700 2.715348700 + Si 2.715348700 2.715348700 0.000000000 + Si 2.715348700 0.000000000 2.715348700 + Si 4.073023100 1.357674400 4.073023100 + Si 1.357674400 1.357674400 1.357674400 + Si 1.357674400 4.073023100 4.073023100 + Si 4.073023100 4.073023100 1.357674400 + &END COORD + &END SUBSYS + &DFT + BASIS_SET_FILE_NAME ../../BASIS_SET + POTENTIAL_FILE_NAME ../../GTH_POTENTIALS + &QS + EPS_DEFAULT 1.0E-10 + &END QS + &MGRID + NGRIDS 4 + CUTOFF 120 + REL_CUTOFF 40 + &END MGRID + &XC + &XC_FUNCTIONAL PADE + &END XC_FUNCTIONAL + &END XC + &SCF + SCF_GUESS ATOMIC + EPS_SCF 1.0E-5 + MAX_SCF 50 + &DIAGONALIZATION ON + ALGORITHM STANDARD + &END DIAGONALIZATION + &MIXING T + METHOD BROYDEN_MIXING + ALPHA 0.4 + NBROYDEN 8 + &END MIXING + &END SCF + &END DFT + &PRINT + &FORCES ON + &END FORCES + &END PRINT +&END FORCE_EVAL +! Comment at the end diff --git a/test/unittests/cp2k_2.6.2/input_preprocessing/comments/unittest.out b/test/unittests/cp2k_2.6.2/input_preprocessing/comments/unittest.out new file mode 100644 index 0000000000000000000000000000000000000000..ae48935fbc7cfa5d47d53cf6c955bc5c8c301b32 --- /dev/null +++ b/test/unittests/cp2k_2.6.2/input_preprocessing/comments/unittest.out @@ -0,0 +1,748 @@ + DBCSR| Multiplication driver SMM + DBCSR| Multrec recursion limit 512 + DBCSR| Multiplication stack size 1000 + DBCSR| Multiplication size stacks 3 + DBCSR| Use subcommunicators T + DBCSR| Use MPI combined types F + DBCSR| Use MPI memory allocation T + DBCSR| Use Communication thread T + DBCSR| Communication thread load 87 + + + **** **** ****** ** PROGRAM STARTED AT 2016-06-01 18:30:29.854 + ***** ** *** *** ** PROGRAM STARTED ON lauri-Lenovo-Z50-70 + ** **** ****** PROGRAM STARTED BY lauri + ***** ** ** ** ** PROGRAM PROCESS ID 28472 + **** ** ******* ** PROGRAM STARTED IN /home/lauri/Dropbox/nomad-dev/nomad-l + ab-base/parsers/cp2k/test/unittests/c + p2k_2.6.2/input_preprocessing/comment + s + + CP2K| version string: CP2K version 2.6.2 + CP2K| source code revision number: svn:15893 + CP2K| is freely available from http://www.cp2k.org/ + CP2K| Program compiled at ke 4.11.2015 08.48.42 +0200 + CP2K| Program compiled on lauri-Lenovo-Z50-70 + CP2K| Program compiled for Linux-x86-64-gfortran_basic + CP2K| Input file name si_bulk8.inp + + GLOBAL| Force Environment number 1 + GLOBAL| Basis set file name ../../BASIS_SET + GLOBAL| Geminal file name BASIS_GEMINAL + GLOBAL| Potential file name ../../GTH_POTENTIALS + GLOBAL| MM Potential file name MM_POTENTIAL + GLOBAL| Coordinate file name __STD_INPUT__ + GLOBAL| Method name CP2K + GLOBAL| Project name Si_bulk8 + GLOBAL| Preferred FFT library FFTW3 + GLOBAL| Preferred diagonalization lib. SL + GLOBAL| Run type ENERGY_FORCE + GLOBAL| All-to-all communication in single precision F + GLOBAL| FFTs using library dependent lengths F + GLOBAL| Global print level MEDIUM + GLOBAL| Total number of message passing processes 1 + GLOBAL| Number of threads for this process 1 + GLOBAL| This output is from process 0 + + MEMORY| system memory details [Kb] + MEMORY| rank 0 min max average + MEMORY| MemTotal 8070360 8070360 8070360 8070360 + MEMORY| MemFree 1594624 1594624 1594624 1594624 + MEMORY| Buffers 965532 965532 965532 965532 + MEMORY| Cached 2762996 2762996 2762996 2762996 + MEMORY| Slab 589936 589936 589936 589936 + MEMORY| SReclaimable 545876 545876 545876 545876 + MEMORY| MemLikelyFree 5869028 5869028 5869028 5869028 + + + *** Fundamental physical constants (SI units) *** + + *** Literature: B. J. Mohr and B. N. Taylor, + *** CODATA recommended values of the fundamental physical + *** constants: 2006, Web Version 5.1 + *** http://physics.nist.gov/constants + + Speed of light in vacuum [m/s] 2.99792458000000E+08 + Magnetic constant or permeability of vacuum [N/A**2] 1.25663706143592E-06 + Electric constant or permittivity of vacuum [F/m] 8.85418781762039E-12 + Planck constant (h) [J*s] 6.62606896000000E-34 + Planck constant (h-bar) [J*s] 1.05457162825177E-34 + Elementary charge [C] 1.60217648700000E-19 + Electron mass [kg] 9.10938215000000E-31 + Electron g factor [ ] -2.00231930436220E+00 + Proton mass [kg] 1.67262163700000E-27 + Fine-structure constant 7.29735253760000E-03 + Rydberg constant [1/m] 1.09737315685270E+07 + Avogadro constant [1/mol] 6.02214179000000E+23 + Boltzmann constant [J/K] 1.38065040000000E-23 + Atomic mass unit [kg] 1.66053878200000E-27 + Bohr radius [m] 5.29177208590000E-11 + + *** Conversion factors *** + + [u] -> [a.u.] 1.82288848426455E+03 + [Angstrom] -> [Bohr] = [a.u.] 1.88972613288564E+00 + [a.u.] = [Bohr] -> [Angstrom] 5.29177208590000E-01 + [a.u.] -> [s] 2.41888432650478E-17 + [a.u.] -> [fs] 2.41888432650478E-02 + [a.u.] -> [J] 4.35974393937059E-18 + [a.u.] -> [N] 8.23872205491840E-08 + [a.u.] -> [K] 3.15774647902944E+05 + [a.u.] -> [kJ/mol] 2.62549961709828E+03 + [a.u.] -> [kcal/mol] 6.27509468713739E+02 + [a.u.] -> [Pa] 2.94210107994716E+13 + [a.u.] -> [bar] 2.94210107994716E+08 + [a.u.] -> [atm] 2.90362800883016E+08 + [a.u.] -> [eV] 2.72113838565563E+01 + [a.u.] -> [Hz] 6.57968392072181E+15 + [a.u.] -> [1/cm] (wave numbers) 2.19474631370540E+05 + [a.u./Bohr**2] -> [1/cm] 5.14048714338585E+03 + + + CELL_TOP| Volume [angstrom^3]: 160.165 + CELL_TOP| Vector a [angstrom 5.431 0.000 0.000 |a| = 5.431 + CELL_TOP| Vector b [angstrom 0.000 5.431 0.000 |b| = 5.431 + CELL_TOP| Vector c [angstrom 0.000 0.000 5.431 |c| = 5.431 + CELL_TOP| Angle (b,c), alpha [degree]: 90.000 + CELL_TOP| Angle (a,c), beta [degree]: 90.000 + CELL_TOP| Angle (a,b), gamma [degree]: 90.000 + CELL_TOP| Numerically orthorhombic: YES + + GENERATE| Preliminary Number of Bonds generated: 0 + GENERATE| Achieved consistency in connectivity generation. + + CELL| Volume [angstrom^3]: 160.165 + CELL| Vector a [angstrom]: 5.431 0.000 0.000 |a| = 5.431 + CELL| Vector b [angstrom]: 0.000 5.431 0.000 |b| = 5.431 + CELL| Vector c [angstrom]: 0.000 0.000 5.431 |c| = 5.431 + CELL| Angle (b,c), alpha [degree]: 90.000 + CELL| Angle (a,c), beta [degree]: 90.000 + CELL| Angle (a,b), gamma [degree]: 90.000 + CELL| Numerically orthorhombic: YES + + CELL_REF| Volume [angstrom^3]: 160.165 + CELL_REF| Vector a [angstrom 5.431 0.000 0.000 |a| = 5.431 + CELL_REF| Vector b [angstrom 0.000 5.431 0.000 |b| = 5.431 + CELL_REF| Vector c [angstrom 0.000 0.000 5.431 |c| = 5.431 + CELL_REF| Angle (b,c), alpha [degree]: 90.000 + CELL_REF| Angle (a,c), beta [degree]: 90.000 + CELL_REF| Angle (a,b), gamma [degree]: 90.000 + CELL_REF| Numerically orthorhombic: YES + + ******************************************************************************* + ******************************************************************************* + ** ** + ** ##### ## ## ** + ** ## ## ## ## ## ** + ** ## ## ## ###### ** + ** ## ## ## ## ## ##### ## ## #### ## ##### ##### ** + ** ## ## ## ## ## ## ## ## ## ## ## ## ## ## ** + ** ## ## ## ## ## ## ## #### ### ## ###### ###### ** + ** ## ### ## ## ## ## ## ## ## ## ## ## ** + ** ####### ##### ## ##### ## ## #### ## ##### ## ** + ** ## ## ** + ** ** + ** ... make the atoms dance ** + ** ** + ** Copyright (C) by CP2K Developers Group (2000 - 2014) ** + ** ** + ******************************************************************************* + + DFT| Spin restricted Kohn-Sham (RKS) calculation RKS + DFT| Multiplicity 1 + DFT| Number of spin states 1 + DFT| Charge 0 + DFT| Self-interaction correction (SIC) NO + DFT| Cutoffs: density 1.000000E-10 + DFT| gradient 1.000000E-10 + DFT| tau 1.000000E-10 + DFT| cutoff_smoothing_range 0.000000E+00 + DFT| XC density smoothing NONE + DFT| XC derivatives PW + FUNCTIONAL| ROUTINE=NEW + FUNCTIONAL| PADE: + FUNCTIONAL| S. Goedecker, M. Teter and J. Hutter, Phys. Rev. B 54, 1703 (1996) + + QS| Method: GPW + QS| Density plane wave grid type NON-SPHERICAL FULLSPACE + QS| Number of grid levels: 4 + QS| Density cutoff [a.u.]: 60.0 + QS| Multi grid cutoff [a.u.]: 1) grid level 60.0 + QS| 2) grid level 20.0 + QS| 3) grid level 6.7 + QS| 4) grid level 2.2 + QS| Grid level progression factor: 3.0 + QS| Relative density cutoff [a.u.]: 20.0 + QS| Consistent realspace mapping and integration + QS| Interaction thresholds: eps_pgf_orb: 1.0E-05 + QS| eps_filter_matrix: 0.0E+00 + QS| eps_core_charge: 1.0E-12 + QS| eps_rho_gspace: 1.0E-10 + QS| eps_rho_rspace: 1.0E-10 + QS| eps_gvg_rspace: 1.0E-05 + QS| eps_ppl: 1.0E-02 + QS| eps_ppnl: 1.0E-07 + + + ATOMIC KIND INFORMATION + + 1. Atomic kind: Si Number of atoms: 8 + + Orbital Basis Set DZVP-GTH-PADE + + Number of orbital shell sets: 2 + Number of orbital shells: 5 + Number of primitive Cartesian functions: 5 + Number of Cartesian basis functions: 14 + Number of spherical basis functions: 13 + Norm type: 2 + + Normalised Cartesian orbitals: + + Set Shell Orbital Exponent Coefficient + + 1 1 3s 1.203242 0.269412 + 0.468841 -0.102290 + 0.167986 -0.147195 + 0.057562 -0.015996 + + 1 2 4s 1.203242 0.000000 + 0.468841 0.000000 + 0.167986 0.000000 + 0.057562 0.083755 + + 1 3 4px 1.203242 0.085242 + 0.468841 -0.143473 + 0.167986 -0.083408 + 0.057562 -0.014565 + 1 3 4py 1.203242 0.085242 + 0.468841 -0.143473 + 0.167986 -0.083408 + 0.057562 -0.014565 + 1 3 4pz 1.203242 0.085242 + 0.468841 -0.143473 + 0.167986 -0.083408 + 0.057562 -0.014565 + + 1 4 5px 1.203242 0.000000 + 0.468841 0.000000 + 0.167986 0.000000 + 0.057562 0.040189 + 1 4 5py 1.203242 0.000000 + 0.468841 0.000000 + 0.167986 0.000000 + 0.057562 0.040189 + 1 4 5pz 1.203242 0.000000 + 0.468841 0.000000 + 0.167986 0.000000 + 0.057562 0.040189 + + 2 1 3dx2 0.450000 0.406941 + 2 1 3dxy 0.450000 0.704842 + 2 1 3dxz 0.450000 0.704842 + 2 1 3dy2 0.450000 0.406941 + 2 1 3dyz 0.450000 0.704842 + 2 1 3dz2 0.450000 0.406941 + + Potential information for GTH-PADE-q4 + + Description: Goedecker-Teter-Hutter pseudopotential + Goedecker et al., PRB 54, 1703 (1996) + Hartwigsen et al., PRB 58, 3641 (1998) + Krack, TCA 114, 145 (2005) + + Gaussian exponent of the core charge distribution: 2.582645 + Electronic configuration (s p d ...): 2 2 + + Parameters of the local part of the GTH pseudopotential: + + rloc C1 C2 C3 C4 + 0.440000 -7.336103 + + Parameters of the non-local part of the GTH pseudopotential: + + l r(l) h(i,j,l) + + 0 0.422738 5.906928 -1.261894 + -1.261894 3.258196 + 1 0.484278 2.727013 + + + MOLECULE KIND INFORMATION + + + All atoms are their own molecule, skipping detailed information + + + TOTAL NUMBERS AND MAXIMUM NUMBERS + + Total number of - Atomic kinds: 1 + - Atoms: 8 + - Shell sets: 16 + - Shells: 40 + - Primitive Cartesian functions: 40 + - Cartesian basis functions: 112 + - Spherical basis functions: 104 + + Maximum angular momentum of- Orbital basis functions: 2 + - Local part of the GTH pseudopotential: 0 + - Non-local part of the GTH pseudopotential: 2 + + + MODULE QUICKSTEP: ATOMIC COORDINATES IN angstrom + + Atom Kind Element X Y Z Z(eff) Mass + + 1 1 Si 14 0.000000 0.000000 0.000000 4.00 28.0855 + 2 1 Si 14 0.000000 2.715349 2.715349 4.00 28.0855 + 3 1 Si 14 2.715349 2.715349 0.000000 4.00 28.0855 + 4 1 Si 14 2.715349 0.000000 2.715349 4.00 28.0855 + 5 1 Si 14 4.073023 1.357674 4.073023 4.00 28.0855 + 6 1 Si 14 1.357674 1.357674 1.357674 4.00 28.0855 + 7 1 Si 14 1.357674 4.073023 4.073023 4.00 28.0855 + 8 1 Si 14 4.073023 4.073023 1.357674 4.00 28.0855 + + + + + SCF PARAMETERS Density guess: ATOMIC + -------------------------------------------------------- + max_scf: 50 + max_scf_history: 0 + max_diis: 4 + -------------------------------------------------------- + eps_scf: 1.00E-05 + eps_scf_history: 0.00E+00 + eps_diis: 1.00E-01 + eps_eigval: 1.00E-05 + -------------------------------------------------------- + level_shift [a.u.]: 0.00 + -------------------------------------------------------- + Mixing method: BROYDEN_MIXING + charge density mixing in g-space + -------------------------------------------------------- + No outer SCF + + PW_GRID| Information for grid number 1 + PW_GRID| Cutoff [a.u.] 60.0 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -18 17 Points: 36 + PW_GRID| Bounds 2 -18 17 Points: 36 + PW_GRID| Bounds 3 -18 17 Points: 36 + PW_GRID| Volume element (a.u.^3) 0.2317E-01 Volume (a.u.^3) 1080.8451 + PW_GRID| Grid span FULLSPACE + + PW_GRID| Information for grid number 2 + PW_GRID| Cutoff [a.u.] 20.0 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -12 11 Points: 24 + PW_GRID| Bounds 2 -12 11 Points: 24 + PW_GRID| Bounds 3 -12 11 Points: 24 + PW_GRID| Volume element (a.u.^3) 0.7819E-01 Volume (a.u.^3) 1080.8451 + PW_GRID| Grid span FULLSPACE + + PW_GRID| Information for grid number 3 + PW_GRID| Cutoff [a.u.] 6.7 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -6 5 Points: 12 + PW_GRID| Bounds 2 -6 5 Points: 12 + PW_GRID| Bounds 3 -6 5 Points: 12 + PW_GRID| Volume element (a.u.^3) 0.6255 Volume (a.u.^3) 1080.8451 + PW_GRID| Grid span FULLSPACE + + PW_GRID| Information for grid number 4 + PW_GRID| Cutoff [a.u.] 2.2 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -4 3 Points: 8 + PW_GRID| Bounds 2 -4 3 Points: 8 + PW_GRID| Bounds 3 -4 3 Points: 8 + PW_GRID| Volume element (a.u.^3) 2.111 Volume (a.u.^3) 1080.8451 + PW_GRID| Grid span FULLSPACE + + POISSON| Solver PERIODIC + POISSON| Periodicity XYZ + + RS_GRID| Information for grid number 1 + RS_GRID| Bounds 1 -18 17 Points: 36 + RS_GRID| Bounds 2 -18 17 Points: 36 + RS_GRID| Bounds 3 -18 17 Points: 36 + + RS_GRID| Information for grid number 2 + RS_GRID| Bounds 1 -12 11 Points: 24 + RS_GRID| Bounds 2 -12 11 Points: 24 + RS_GRID| Bounds 3 -12 11 Points: 24 + + RS_GRID| Information for grid number 3 + RS_GRID| Bounds 1 -6 5 Points: 12 + RS_GRID| Bounds 2 -6 5 Points: 12 + RS_GRID| Bounds 3 -6 5 Points: 12 + + RS_GRID| Information for grid number 4 + RS_GRID| Bounds 1 -4 3 Points: 8 + RS_GRID| Bounds 2 -4 3 Points: 8 + RS_GRID| Bounds 3 -4 3 Points: 8 + + DISTRIBUTION OF THE PARTICLES (ROWS) + Process row Number of particles Number of matrix rows + 0 8 -1 + Sum 8 -1 + + DISTRIBUTION OF THE PARTICLES (COLUMNS) + Process col Number of particles Number of matrix columns + 0 8 -1 + Sum 8 -1 + + DISTRIBUTION OF THE NEIGHBOR LISTS + Total number of particle pairs: 2952 + Total number of matrix elements: 498888 + Average number of particle pairs: 2952 + Maximum number of particle pairs: 2952 + Average number of matrix element: 498888 + Maximum number of matrix elements: 498888 + + + DISTRIBUTION OF THE OVERLAP MATRIX + Number of non-zero blocks: 36 + Percentage non-zero blocks: 100.00 + Average number of blocks per CPU: 36 + Maximum number of blocks per CPU: 36 + Average number of matrix elements per CPU: 6094 + Maximum number of matrix elements per CPU: 6094 + + Number of electrons: 32 + Number of occupied orbitals: 16 + Number of molecular orbitals: 16 + + Number of orbital functions: 104 + Number of independent orbital functions: 104 + + Extrapolation method: initial_guess + + Atomic guess: The first density matrix is obtained in terms of atomic orbitals + and electronic configurations assigned to each atomic kind + + Guess for atomic kind: Si + + Electronic structure + Total number of core electrons 10.00 + Total number of valence electrons 4.00 + Total number of electrons 14.00 + Multiplicity not specified + S [ 2.00 2.00] 2.00 + P [ 6.00] 2.00 + + + ******************************************************************************* + Iteration Convergence Energy [au] + ******************************************************************************* + 1 0.191310 -3.618313869735 + 2 0.731569E-01 -3.691159009622 + 3 0.405574E-02 -3.699900512584 + 4 0.328704E-02 -3.699908407293 + 5 0.320845E-02 -3.699909118998 + 6 0.316809E-02 -3.699909477757 + 7 0.331859E-05 -3.699923449535 + 8 0.110258E-06 -3.699923449550 + + Energy components [Hartree] Total Energy :: -3.699923449550 + Band Energy :: -1.012729790251 + Kinetic Energy :: 1.397012768229 + Potential Energy :: -5.096936217779 + Virial (-V/T) :: 3.648453567279 + Core Energy :: -5.703543362687 + XC Energy :: -0.980691562795 + Coulomb Energy :: 2.984311475932 + Total Pseudopotential Energy :: -7.145739758818 + Local Pseudopotential Energy :: -7.987908627736 + Nonlocal Pseudopotential Energy :: 0.842168868918 + Confinement :: 0.451836279031 + + Orbital energies State L Occupation Energy[a.u.] Energy[eV] + + 1 0 2.000 -0.378230 -10.292155 + + 1 1 2.000 -0.128135 -3.486734 + + Re-scaling the density matrix to get the right number of electrons + # Electrons Trace(P) Scaling factor + 32 31.129 1.028 + + + SCF WAVEFUNCTION OPTIMIZATION + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + + Trace(PS): 32.0000000000 + Electronic density on regular grids: -31.9999999989 0.0000000011 + Core density on regular grids: 31.9999999944 -0.0000000056 + Total charge density on r-space grids: -0.0000000045 + Total charge density g-space grids: -0.0000000045 + + 1 NoMix/Diag. 0.40E+00 0.6 0.75558199 -32.2320851846 -3.22E+01 + + Trace(PS): 32.0000000000 + Electronic density on regular grids: -31.9999999973 0.0000000027 + Core density on regular grids: 31.9999999944 -0.0000000056 + Total charge density on r-space grids: -0.0000000029 + Total charge density g-space grids: -0.0000000029 + + 2 Broy./Diag. 0.40E+00 1.1 0.05667988 -31.1418132241 1.09E+00 + + Trace(PS): 32.0000000000 + Electronic density on regular grids: -31.9999999941 0.0000000059 + Core density on regular grids: 31.9999999944 -0.0000000056 + Total charge density on r-space grids: 0.0000000003 + Total charge density g-space grids: 0.0000000003 + + 3 Broy./Diag. 0.40E+00 1.1 0.09691373 -31.1974010218 -5.56E-02 + + Trace(PS): 32.0000000000 + Electronic density on regular grids: -31.9999999933 0.0000000067 + Core density on regular grids: 31.9999999944 -0.0000000056 + Total charge density on r-space grids: 0.0000000011 + Total charge density g-space grids: 0.0000000011 + + 4 Broy./Diag. 0.40E+00 1.1 0.00246215 -31.3377989104 -1.40E-01 + + Trace(PS): 32.0000000000 + Electronic density on regular grids: -31.9999999925 0.0000000075 + Core density on regular grids: 31.9999999944 -0.0000000056 + Total charge density on r-space grids: 0.0000000018 + Total charge density g-space grids: 0.0000000018 + + 5 Broy./Diag. 0.40E+00 1.1 0.00235081 -31.3009549062 3.68E-02 + + Trace(PS): 32.0000000000 + Electronic density on regular grids: -31.9999999926 0.0000000074 + Core density on regular grids: 31.9999999944 -0.0000000056 + Total charge density on r-space grids: 0.0000000018 + Total charge density g-space grids: 0.0000000018 + + 6 Broy./Diag. 0.40E+00 1.1 0.00007565 -31.2972179358 3.74E-03 + + Trace(PS): 32.0000000000 + Electronic density on regular grids: -31.9999999926 0.0000000074 + Core density on regular grids: 31.9999999944 -0.0000000056 + Total charge density on r-space grids: 0.0000000018 + Total charge density g-space grids: 0.0000000018 + + 7 Broy./Diag. 0.40E+00 1.1 0.00008972 -31.2977306332 -5.13E-04 + + Trace(PS): 32.0000000000 + Electronic density on regular grids: -31.9999999926 0.0000000074 + Core density on regular grids: 31.9999999944 -0.0000000056 + Total charge density on r-space grids: 0.0000000018 + Total charge density g-space grids: 0.0000000018 + + 8 Broy./Diag. 0.40E+00 1.1 0.00000174 -31.2978462605 -1.16E-04 + + *** SCF run converged in 8 steps *** + + + Electronic density on regular grids: -31.9999999926 0.0000000074 + Core density on regular grids: 31.9999999944 -0.0000000056 + Total charge density on r-space grids: 0.0000000018 + Total charge density g-space grids: 0.0000000018 + + Overlap energy of the core charge distribution: 0.00000000005320 + Self energy of the core charge distribution: -82.06393942512820 + Core Hamiltonian energy: 18.06859044546266 + Hartree energy: 42.41176248696382 + Exchange-correlation energy: -9.71425976785727 + + Total energy: -31.29784626050581 + + + MULLIKEN POPULATION ANALYSIS + + # Atom Element Kind Atomic population Net charge + 1 Si 1 4.000001 -0.000001 + 2 Si 1 4.000000 0.000000 + 3 Si 1 4.000000 0.000000 + 4 Si 1 4.000000 0.000000 + 5 Si 1 4.000000 0.000000 + 6 Si 1 4.000000 0.000000 + 7 Si 1 4.000000 0.000000 + 8 Si 1 4.000000 0.000000 + # Total charge 32.000000 -0.000000 + + + !-----------------------------------------------------------------------------! + Hirschfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 Si 1 4.000 4.000 -0.000 + 2 Si 1 4.000 4.000 -0.000 + 3 Si 1 4.000 4.000 -0.000 + 4 Si 1 4.000 4.000 -0.000 + 5 Si 1 4.000 4.000 -0.000 + 6 Si 1 4.000 4.000 0.000 + 7 Si 1 4.000 4.000 -0.000 + 8 Si 1 4.000 4.000 -0.000 + + Total Charge -0.000 + !-----------------------------------------------------------------------------! + + Trace(PS): 32.0000000000 + Electronic density on regular grids: -31.9999999926 0.0000000074 + Core density on regular grids: 31.9999999944 -0.0000000056 + Total charge density on r-space grids: 0.0000000018 + Total charge density g-space grids: 0.0000000018 + + + ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -31.297886315837690 + + + ATOMIC FORCES in [a.u.] + + # Atom Kind Element X Y Z + 1 1 Si 0.00000000 0.00000000 0.00000000 + 2 1 Si 0.00000000 0.00000001 0.00000001 + 3 1 Si 0.00000001 0.00000001 0.00000000 + 4 1 Si 0.00000001 0.00000000 0.00000001 + 5 1 Si -0.00000000 -0.00000001 -0.00000001 + 6 1 Si -0.00000001 -0.00000001 -0.00000001 + 7 1 Si -0.00000001 -0.00000001 -0.00000001 + 8 1 Si -0.00000000 -0.00000001 -0.00000001 + SUM OF ATOMIC FORCES -0.00000000 -0.00000000 -0.00000000 0.00000000 + + ------------------------------------------------------------------------------- + - - + - DBCSR STATISTICS - + - - + ------------------------------------------------------------------------------- + COUNTER CPU ACC ACC% + number of processed stacks 9 0 0.0 + matmuls inhomo. stacks 0 0 0.0 + matmuls total 324 0 0.0 + flops 13 x 13 x 16 1752192 0 0.0 + flops total 1752192 0 0.0 + marketing flops 3115008 + ------------------------------------------------------------------------------- + + ------------------------------------------------------------------------------- + ---- MULTIGRID INFO ---- + ------------------------------------------------------------------------------- + count for grid 1: 2568 cutoff [a.u.] 60.00 + count for grid 2: 7088 cutoff [a.u.] 20.00 + count for grid 3: 6056 cutoff [a.u.] 6.67 + count for grid 4: 16 cutoff [a.u.] 2.22 + total gridlevel count : 15728 + + ------------------------------------------------------------------------------- + - - + - MESSAGE PASSING PERFORMANCE - + - - + ------------------------------------------------------------------------------- + + ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s] + MP_Group 5 0.000 + MP_Bcast 10 0.000 6. 0.23 + MP_Allreduce 155 0.000 43. 37.99 + MP_Sync 4 0.000 + MP_Alltoall 151 0.000 15676. 8003.92 + MP_Wait 216 0.000 + MP_ISend 72 0.001 13472. 1404.11 + MP_IRecv 72 0.000 13472. 10374.60 + MP_Memory 216 0.000 + ------------------------------------------------------------------------------- + + + ------------------------------------------------------------------------------- + - - + - R E F E R E N C E S - + - - + ------------------------------------------------------------------------------- + + CP2K version 2.6.2, the CP2K developers group (2015). + CP2K is freely available from http://www.cp2k.org/ . + + Borstnik, U; VandeVondele, J; Weber, V; Hutter, J. + PARALLEL COMPUTING, 40 (5-6), 47-58 (2014). + Sparse matrix multiplication: The distributed block-compressed sparse + row library. + http://dx.doi.org/10.1016/j.parco.2014.03.012 + + + Hutter, J; Iannuzzi, M; Schiffmann, F; VandeVondele, J. + WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 4 (1), 15-25 (2014). + CP2K: atomistic simulations of condensed matter systems. + http://dx.doi.org/10.1002/wcms.1159 + + + Krack, M. + THEORETICAL CHEMISTRY ACCOUNTS, 114 (1-3), 145-152 (2005). + Pseudopotentials for H to Kr optimized for gradient-corrected + exchange-correlation functionals. + http://dx.doi.org/10.1007/s00214-005-0655-y + + + VandeVondele, J; Krack, M; Mohamed, F; Parrinello, M; Chassaing, T; + Hutter, J. COMPUTER PHYSICS COMMUNICATIONS, 167 (2), 103-128 (2005). + QUICKSTEP: Fast and accurate density functional calculations using a + mixed Gaussian and plane waves approach. + http://dx.doi.org/10.1016/j.cpc.2004.12.014 + + + Frigo, M; Johnson, SG. + PROCEEDINGS OF THE IEEE, 93 (2), 216-231 (2005). + The design and implementation of FFTW3. + http://dx.doi.org/10.1109/JPROC.2004.840301 + + + Hartwigsen, C; Goedecker, S; Hutter, J. + PHYSICAL REVIEW B, 58 (7), 3641-3662 (1998). + Relativistic separable dual-space Gaussian pseudopotentials from H to Rn. + http://dx.doi.org/10.1103/PhysRevB.58.3641 + + + Lippert, G; Hutter, J; Parrinello, M. + MOLECULAR PHYSICS, 92 (3), 477-487 (1997). + A hybrid Gaussian and plane wave density functional scheme. + http://dx.doi.org/10.1080/002689797170220 + + + Goedecker, S; Teter, M; Hutter, J. + PHYSICAL REVIEW B, 54 (3), 1703-1710 (1996). + Separable dual-space Gaussian pseudopotentials. + http://dx.doi.org/10.1103/PhysRevB.54.1703 + + + ------------------------------------------------------------------------------- + - - + - T I M I N G - + - - + ------------------------------------------------------------------------------- + SUBROUTINE CALLS ASD SELF TIME TOTAL TIME + MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM + CP2K 1 1.0 0.003 0.003 11.026 11.026 + qs_forces 1 2.0 0.000 0.000 10.985 10.985 + qs_energies_scf 1 3.0 0.000 0.000 9.448 9.448 + scf_env_do_scf 1 4.0 0.000 0.000 8.666 8.666 + scf_env_do_scf_inner_loop 8 5.0 0.001 0.001 8.666 8.666 + rebuild_ks_matrix 9 6.7 0.000 0.000 5.865 5.865 + qs_ks_build_kohn_sham_matrix 9 7.7 0.001 0.001 5.865 5.865 + sum_up_and_integrate 9 8.7 0.001 0.001 5.815 5.815 + integrate_v_rspace 9 9.7 5.790 5.790 5.814 5.814 + qs_ks_update_qs_env 8 6.0 0.000 0.000 5.016 5.016 + qs_rho_update_rho 9 6.0 0.000 0.000 3.995 3.995 + calculate_rho_elec 9 7.0 3.943 3.943 3.995 3.995 + qs_ks_update_qs_env_forces 1 3.0 0.000 0.000 0.850 0.850 + build_core_hamiltonian_matrix_ 1 3.0 0.000 0.000 0.687 0.687 + init_scf_run 1 4.0 0.000 0.000 0.462 0.462 + scf_env_initial_rho_setup 1 5.0 0.000 0.000 0.461 0.461 + build_core_ppnl_forces 1 4.0 0.367 0.367 0.367 0.367 + qs_energies_init_hamiltonians 1 4.0 0.000 0.000 0.306 0.306 + build_core_hamiltonian_matrix 1 5.0 0.000 0.000 0.259 0.259 + build_core_ppl_forces 1 4.0 0.252 0.252 0.252 0.252 + ------------------------------------------------------------------------------- + + **** **** ****** ** PROGRAM ENDED AT 2016-06-01 18:30:40.935 + ***** ** *** *** ** PROGRAM RAN ON lauri-Lenovo-Z50-70 + ** **** ****** PROGRAM RAN BY lauri + ***** ** ** ** ** PROGRAM PROCESS ID 28472 + **** ** ******* ** PROGRAM STOPPED IN /home/lauri/Dropbox/nomad-dev/nomad-l + ab-base/parsers/cp2k/test/unittests/c + p2k_2.6.2/input_preprocessing/comment + s diff --git a/test/unittests/cp2k_2.6.2/run_tests.py b/test/unittests/cp2k_2.6.2/run_tests.py index 6f89522c7f4feeb3c968bb825a8c4ad46f65569c..f2268a6982828b3714be3aa40d2fae83c399da26 100644 --- a/test/unittests/cp2k_2.6.2/run_tests.py +++ b/test/unittests/cp2k_2.6.2/run_tests.py @@ -446,6 +446,10 @@ class TestPreprocessor(unittest.TestCase): result = get_result("input_preprocessing/variable_multiple", "x_cp2k_CP2K_INPUT.FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False) self.assertEqual(result, 50) + def test_comments(self): + result = get_result("input_preprocessing/comments", "x_cp2k_CP2K_INPUT.FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False) + self.assertEqual(result, 120) + #=============================================================================== class TestGeoOpt(unittest.TestCase): @@ -611,13 +615,13 @@ if __name__ == '__main__': suites = [] # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors)) # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional)) - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce)) + # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce)) # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestStressTensorMethods)) # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSelfInteractionCorrectionMethod)) # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestConfigurationPeriodicDimensions)) # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSCFConvergence)) # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestForceFiles)) - # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPreprocessor)) + suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPreprocessor)) # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt)) # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajFormats)) # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptOptimizers))