diff --git a/dpdata/cp2k/output.py b/dpdata/cp2k/output.py index f9b96eb42..469ccbdd4 100644 --- a/dpdata/cp2k/output.py +++ b/dpdata/cp2k/output.py @@ -20,7 +20,7 @@ class Cp2kSystems(object): """ - deal with cp2k outputfile + deal with cp2k outputfile """ def __init__(self, log_file_name, xyz_file_name): self.log_file_object = open(log_file_name, 'r') @@ -69,7 +69,7 @@ def get_log_block_generator(self): break if delimiter_flag is True: raise RuntimeError('This file lacks some content, please check') - + def get_xyz_block_generator(self): p3 = re.compile(r'^\s*(\d+)\s*') while True: @@ -116,7 +116,7 @@ def handle_single_log_frame(self, lines): if cell_length_pattern.match(line): cell_A = float(cell_length_pattern.match(line).groupdict()['A']) * AU_TO_ANG cell_B = float(cell_length_pattern.match(line).groupdict()['B']) * AU_TO_ANG - cell_C = float(cell_length_pattern.match(line).groupdict()['C']) * AU_TO_ANG + cell_C = float(cell_length_pattern.match(line).groupdict()['C']) * AU_TO_ANG cell_flag+=1 if cell_angle_pattern.match(line): cell_alpha = np.deg2rad(float(cell_angle_pattern.match(line).groupdict()['alpha'])) @@ -148,10 +148,10 @@ def handle_single_log_frame(self, lines): element_index +=1 element_dict[line_list[2]]=[element_index,1] atom_types_list.append(element_dict[line_list[2]][0]) - forces_list.append([float(line_list[3])*AU_TO_EV_EVERY_ANG, - float(line_list[4])*AU_TO_EV_EVERY_ANG, + forces_list.append([float(line_list[3])*AU_TO_EV_EVERY_ANG, + float(line_list[4])*AU_TO_EV_EVERY_ANG, float(line_list[5])*AU_TO_EV_EVERY_ANG]) - + atom_names=list(element_dict.keys()) atom_numbs=[] for ii in atom_names: @@ -190,8 +190,8 @@ def handle_single_xyz_frame(self, lines): element_index +=1 element_dict[line_list[0]]=[element_index,1] atom_types_list.append(element_dict[line_list[0]][0]) - coords_list.append([float(line_list[1])*AU_TO_ANG, - float(line_list[2])*AU_TO_ANG, + coords_list.append([float(line_list[1])*AU_TO_ANG, + float(line_list[2])*AU_TO_ANG, float(line_list[3])*AU_TO_ANG]) atom_names=list(element_dict.keys()) atom_numbs=[] @@ -203,7 +203,7 @@ def handle_single_xyz_frame(self, lines): info_dict['coords'] = np.asarray([coords_list]).astype('float32') info_dict['energies'] = np.array([energy]).astype('float32') info_dict['orig']=[0,0,0] - return info_dict + return info_dict #%% @@ -211,21 +211,22 @@ def get_frames (fname) : coord_flag = False force_flag = False eV = 2.72113838565563E+01 # hatree to eV - angstrom = 5.29177208590000E-01 # Bohrto Angstrom + angstrom = 5.29177208590000E-01 # Bohrto Angstrom fp = open(fname) atom_symbol_list = [] cell = [] coord = [] force = [] - + coord_count = 0 for idx, ii in enumerate(fp) : if 'CELL| Vector' in ii : cell.append(ii.split()[4:7]) if 'Atom Kind Element' in ii : coord_flag = True coord_idx = idx + coord_count += 1 # get the coord block info - if coord_flag : + if coord_flag and (coord_count == 1): if (idx > coord_idx + 1) : if (ii == '\n') : coord_flag = False diff --git a/tests/cp2k/cp2k_output b/tests/cp2k/cp2k_output index bb162d359..48f04b615 100644 --- a/tests/cp2k/cp2k_output +++ b/tests/cp2k/cp2k_output @@ -770,6 +770,780 @@ 40 40.000 1.000 + SCF WAVEFUNCTION OPTIMIZATION + + DBCSR| Multiplication driver BLAS + DBCSR| Multrec recursion limit 512 + DBCSR| Multiplication stack size 1000 + DBCSR| Maximum elements for images UNLIMITED + DBCSR| Multiplicative factor virtual images 1 + DBCSR| Randmat seed 12341313 + DBCSR| Multiplication size stacks 3 + DBCSR| Number of 3D layers SINGLE + DBCSR| Use MPI memory allocation T + DBCSR| Use RMA algorithm F + DBCSR| Use Communication thread T + DBCSR| Communication thread load 87 + + + **** **** ****** ** PROGRAM STARTED AT 2019-08-10 12:43:41.832 + ***** ** *** *** ** PROGRAM STARTED ON c038 + ** **** ****** PROGRAM STARTED BY fengw + ***** ** ** ** ** PROGRAM PROCESS ID 21094 + **** ** ******* ** PROGRAM STARTED IN /data/fengw/PC-LiTFSI/energy/BLYP/0.3 + 7_CBM_VBM/KS/29000/test + + CP2K| version string: CP2K version 4.1 + CP2K| source code revision number: svn:17462 + CP2K| cp2kflags: omp libint fftw3 libxc parallel mpi3 scalapack libderiv_max_am + CP2K| 1=5 libint_max_am=6 + CP2K| is freely available from https://www.cp2k.org/ + CP2K| Program compiled at Tue May 2 22:33:05 CST 2017 + CP2K| Program compiled on mgt + CP2K| Program compiled for Linux-x86-64-gfortran + CP2K| Data directory path /share/soft/cp2k-4.1/data + CP2K| Input file name input.inp + + GLOBAL| Force Environment number 1 + GLOBAL| Basis set file name /data/fengw/data/GTH_BASIS_SETS + GLOBAL| Potential file name /data/fengw/data/GTH_POTENTIALS + GLOBAL| MM Potential file name MM_POTENTIAL + GLOBAL| Coordinate file name __STD_INPUT__ + GLOBAL| Method name CP2K + GLOBAL| Project name Solv_0.37-0.0 + 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 28 + GLOBAL| Number of threads for this process 1 + GLOBAL| This output is from process 0 + GLOBAL| CPU model name : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz + + MEMORY| system memory details [Kb] + MEMORY| rank 0 min max average + MEMORY| MemTotal 65125420 65125420 65125420 65125420 + MEMORY| MemFree 44849788 44849788 44849788 44849788 + MEMORY| Buffers 144020 144020 144020 144020 + MEMORY| Cached 18013976 18013976 18013976 18013976 + MEMORY| Slab 402832 402832 402832 402832 + MEMORY| SReclaimable 174504 174504 174504 174504 + MEMORY| MemLikelyFree 63182288 63182288 63182288 63182288 + + + *** 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]: 4499.480 + CELL_TOP| Vector a [angstrom 16.509 0.000 0.000 |a| = 16.509 + CELL_TOP| Vector b [angstrom 0.000 16.509 0.000 |b| = 16.509 + CELL_TOP| Vector c [angstrom 0.000 0.000 16.509 |c| = 16.509 + 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]: 4499.480 + CELL| Vector a [angstrom]: 16.509 0.000 0.000 |a| = 16.509 + CELL| Vector b [angstrom]: 0.000 16.509 0.000 |b| = 16.509 + CELL| Vector c [angstrom]: 0.000 0.000 16.509 |c| = 16.509 + 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]: 4499.480 + CELL_REF| Vector a [angstrom 16.509 0.000 0.000 |a| = 16.509 + CELL_REF| Vector b [angstrom 0.000 16.509 0.000 |b| = 16.509 + CELL_REF| Vector c [angstrom 0.000 0.000 16.509 |c| = 16.509 + 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 - 2016) ** + ** ** + ******************************************************************************* + + 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 NN50 + DFT| XC derivatives NN50_SMOOTH + FUNCTIONAL| ROUTINE=NEW + FUNCTIONAL| BECKE88: + FUNCTIONAL| A. Becke, Phys. Rev. A 38, 3098 (1988) {LDA version} + FUNCTIONAL| LYP: + FUNCTIONAL| C. Lee, W. Yang, R.G. Parr, Phys. Rev. B, 37, 785 (1988) {LDA versi + FUNCTIONAL| on} + vdW POTENTIAL| Pair Potential + vdW POTENTIAL| DFT-D3 (Version 3.1) + vdW POTENTIAL| Potential Form: S. Grimme et al, JCP 132: 154104 (2010) + vdW POTENTIAL| Zero Damping + vdW POTENTIAL| Cutoff Radius [Bohr]: 20.00 + vdW POTENTIAL| s6 Scaling Factor: 1.0000 + vdW POTENTIAL| sr6 Scaling Factor: 1.0940 + vdW POTENTIAL| s8 Scaling Factor: 1.6820 + vdW POTENTIAL| Cutoff for CN calculation: 0.1000E-05 + + QS| Method: GPW + QS| Density plane wave grid type NON-SPHERICAL FULLSPACE + QS| Number of grid levels: 4 + QS| Density cutoff [a.u.]: 250.0 + QS| Multi grid cutoff [a.u.]: 1) grid level 250.0 + QS| 2) grid level 83.3 + QS| 3) grid level 27.8 + QS| 4) grid level 9.3 + QS| Grid level progression factor: 3.0 + QS| Relative density cutoff [a.u.]: 30.0 + QS| Consistent realspace mapping and integration + QS| Interaction thresholds: eps_pgf_orb: 1.0E-15 + QS| eps_filter_matrix: 0.0E+00 + QS| eps_core_charge: 1.0E-14 + QS| eps_rho_gspace: 1.0E-12 + QS| eps_rho_rspace: 1.0E-12 + QS| eps_gvg_rspace: 1.0E-06 + QS| eps_ppl: 1.0E-02 + QS| eps_ppnl: 1.0E-08 + + + ATOMIC KIND INFORMATION + + 1. Atomic kind: C Number of atoms: 4 + + Orbital Basis Set DZVP-GTH + + 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 2s 4.336238 0.319274 + 1.288184 -0.025219 + 0.403777 -0.248447 + 0.118788 -0.057170 + + 1 2 3s 4.336238 0.000000 + 1.288184 0.000000 + 0.403777 0.000000 + 0.118788 0.144208 + + 1 3 3px 4.336238 -0.783226 + 1.288184 -0.542954 + 0.403777 -0.216197 + 0.118788 -0.040339 + 1 3 3py 4.336238 -0.783226 + 1.288184 -0.542954 + 0.403777 -0.216197 + 0.118788 -0.040339 + 1 3 3pz 4.336238 -0.783226 + 1.288184 -0.542954 + 0.403777 -0.216197 + 0.118788 -0.040339 + + 1 4 4px 4.336238 0.000000 + 1.288184 0.000000 + 0.403777 0.000000 + 0.118788 0.099404 + 1 4 4py 4.336238 0.000000 + 1.288184 0.000000 + 0.403777 0.000000 + 0.118788 0.099404 + 1 4 4pz 4.336238 0.000000 + 1.288184 0.000000 + 0.403777 0.000000 + 0.118788 0.099404 + + 2 1 3dx2 0.550000 0.578155 + 2 1 3dxy 0.550000 1.001394 + 2 1 3dxz 0.550000 1.001394 + 2 1 3dy2 0.550000 0.578155 + 2 1 3dyz 0.550000 1.001394 + 2 1 3dz2 0.550000 0.578155 + + Potential information for GTH-BLYP-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: 4.374886 + Electronic configuration (s p d ...): 2 2 + + Parameters of the local part of the GTH pseudopotential: + + rloc C1 C2 C3 C4 + 0.338066 -9.136269 1.429260 + + Parameters of the non-local part of the GTH pseudopotential: + + l r(l) h(i,j,l) + + 0 0.302322 9.665512 + 1 0.286379 + + 2. Atomic kind: H Number of atoms: 6 + + Orbital Basis Set DZVP-GTH + + Number of orbital shell sets: 2 + Number of orbital shells: 3 + Number of primitive Cartesian functions: 5 + Number of Cartesian basis functions: 5 + Number of spherical basis functions: 5 + Norm type: 2 + + Normalised Cartesian orbitals: + + Set Shell Orbital Exponent Coefficient + + 1 1 1s 8.374435 -0.099425 + 1.805868 -0.148088 + 0.485253 -0.165568 + 0.165824 -0.102436 + + 1 2 2s 8.374435 0.000000 + 1.805868 0.000000 + 0.485253 0.000000 + 0.165824 0.185202 + + 2 1 2px 0.727000 0.956881 + 2 1 2py 0.727000 0.956881 + 2 1 2pz 0.727000 0.956881 + + Potential information for GTH-BLYP-q1 + + 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: 12.500000 + Electronic configuration (s p d ...): 1 + + Parameters of the local part of the GTH pseudopotential: + + rloc C1 C2 C3 C4 + 0.200000 -4.195961 0.730498 + + 3. Atomic kind: O Number of atoms: 3 + + Orbital Basis Set DZVP-GTH + + 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 2s 8.304386 0.526521 + 2.457948 -0.055011 + 0.759737 -0.404341 + 0.213639 -0.086026 + + 1 2 3s 8.304386 0.000000 + 2.457948 0.000000 + 0.759737 0.000000 + 0.213639 0.223960 + + 1 3 3px 8.304386 -2.000755 + 2.457948 -1.321076 + 0.759737 -0.480332 + 0.213639 -0.078647 + 1 3 3py 8.304386 -2.000755 + 2.457948 -1.321076 + 0.759737 -0.480332 + 0.213639 -0.078647 + 1 3 3pz 8.304386 -2.000755 + 2.457948 -1.321076 + 0.759737 -0.480332 + 0.213639 -0.078647 + + 1 4 4px 8.304386 0.000000 + 2.457948 0.000000 + 0.759737 0.000000 + 0.213639 0.207033 + 1 4 4py 8.304386 0.000000 + 2.457948 0.000000 + 0.759737 0.000000 + 0.213639 0.207033 + 1 4 4pz 8.304386 0.000000 + 2.457948 0.000000 + 0.759737 0.000000 + 0.213639 0.207033 + + 2 1 3dx2 1.185000 2.215218 + 2 1 3dxy 1.185000 3.836871 + 2 1 3dxz 1.185000 3.836871 + 2 1 3dy2 1.185000 2.215218 + 2 1 3dyz 1.185000 3.836871 + 2 1 3dz2 1.185000 2.215218 + + Potential information for GTH-BLYP-q6 + + 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: 8.438331 + Electronic configuration (s p d ...): 2 4 + + Parameters of the local part of the GTH pseudopotential: + + rloc C1 C2 C3 C4 + 0.243420 -16.991892 2.566142 + + Parameters of the non-local part of the GTH pseudopotential: + + l r(l) h(i,j,l) + + 0 0.220831 18.388851 + 1 0.217201 + + + MOLECULE KIND INFORMATION + + + All atoms are their own molecule, skipping detailed information + + + TOTAL NUMBERS AND MAXIMUM NUMBERS + + Total number of - Atomic kinds: 3 + - Atoms: 13 + - Shell sets: 26 + - Shells: 53 + - Primitive Cartesian functions: 65 + - Cartesian basis functions: 128 + - Spherical basis functions: 121 + + Maximum angular momentum of- Orbital basis functions: 2 + - Local part of the GTH pseudopotential: 2 + - Non-local part of the GTH pseudopotential: 0 + + + MODULE QUICKSTEP: ATOMIC COORDINATES IN angstrom + + Atom Kind Element X Y Z Z(eff) Mass + + 1 1 C 6 8.502557 13.615841 13.959087 4.00 12.0107 + 2 1 C 6 7.337961 15.436979 13.231602 4.00 12.0107 + 3 1 C 6 7.898228 15.711577 14.610790 4.00 12.0107 + 4 2 H 1 6.191067 15.347699 13.085878 1.00 1.0079 + 5 3 O 8 7.966143 14.222136 12.790193 6.00 15.9994 + 6 1 C 6 7.734765 16.557145 12.069222 4.00 12.0107 + 7 2 H 1 7.130790 15.862453 15.339187 1.00 1.0079 + 8 2 H 1 8.737614 16.468567 14.497932 1.00 1.0079 + 9 3 O 8 8.496264 14.451055 14.990319 6.00 15.9994 + 10 3 O 8 8.899322 12.523607 13.901094 6.00 15.9994 + 11 2 H 1 7.514778 17.615787 12.389690 1.00 1.0079 + 12 2 H 1 8.850553 16.479587 11.921136 1.00 1.0079 + 13 2 H 1 7.059051 16.153899 11.247693 1.00 1.0079 + + + + + SCF PARAMETERS Density guess: RESTART + -------------------------------------------------------- + max_scf: 50 + max_scf_history: 0 + max_diis: 4 + -------------------------------------------------------- + eps_scf: 1.00E-06 + eps_scf_history: 0.00E+00 + eps_diis: 1.00E-01 + eps_eigval: 1.00E-05 + -------------------------------------------------------- + level_shift [a.u.]: 0.00 + -------------------------------------------------------- + Outer loop SCF in use + No variables optimised in outer loop + eps_scf 1.00E-06 + max_scf 10 + No outer loop optimization + step_size 3.00E-02 + + PW_GRID| Information for grid number 1 + PW_GRID| Grid distributed over 28 processors + PW_GRID| Real space group dimensions 28 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 250.0 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -112 112 Points: 225 + PW_GRID| Bounds 2 -112 112 Points: 225 + PW_GRID| Bounds 3 -112 112 Points: 225 + PW_GRID| Volume element (a.u.^3) 0.2666E-02 Volume (a.u.^3) 30363.9949 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 406808.0 407025 406800 + PW_GRID| G-Rays 1808.0 1809 1808 + PW_GRID| Real Space Points 406808.0 455625 405000 + + PW_GRID| Information for grid number 2 + PW_GRID| Grid distributed over 28 processors + PW_GRID| Real space group dimensions 28 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 83.3 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -67 67 Points: 135 + PW_GRID| Bounds 2 -67 67 Points: 135 + PW_GRID| Bounds 3 -67 67 Points: 135 + PW_GRID| Volume element (a.u.^3) 0.1234E-01 Volume (a.u.^3) 30363.9949 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 87870.5 88020 87750 + PW_GRID| G-Rays 650.9 652 650 + PW_GRID| Real Space Points 87870.5 91125 72900 + + PW_GRID| Information for grid number 3 + PW_GRID| Grid distributed over 28 processors + PW_GRID| Real space group dimensions 28 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 27.8 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -37 37 Points: 75 + PW_GRID| Bounds 2 -37 37 Points: 75 + PW_GRID| Bounds 3 -37 37 Points: 75 + PW_GRID| Volume element (a.u.^3) 0.7197E-01 Volume (a.u.^3) 30363.9949 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 15067.0 15150 14850 + PW_GRID| G-Rays 200.9 202 198 + PW_GRID| Real Space Points 15067.0 16875 11250 + + PW_GRID| Information for grid number 4 + PW_GRID| Grid distributed over 28 processors + PW_GRID| Real space group dimensions 28 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 9.3 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -22 22 Points: 45 + PW_GRID| Bounds 2 -22 22 Points: 45 + PW_GRID| Bounds 3 -22 22 Points: 45 + PW_GRID| Volume element (a.u.^3) 0.3332 Volume (a.u.^3) 30363.9949 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 3254.5 3285 3195 + PW_GRID| G-Rays 72.3 73 71 + PW_GRID| Real Space Points 3254.5 4050 2025 + + POISSON| Solver PERIODIC + POISSON| Periodicity XYZ + + RS_GRID| Information for grid number 1 + RS_GRID| Bounds 1 -112 112 Points: 225 + RS_GRID| Bounds 2 -112 112 Points: 225 + RS_GRID| Bounds 3 -112 112 Points: 225 + RS_GRID| Real space distribution over 4 groups + RS_GRID| Real space distribution along direction 2 + RS_GRID| Border size 25 + RS_GRID| Real space distribution over 7 groups + RS_GRID| Real space distribution along direction 3 + RS_GRID| Border size 25 + RS_GRID| Distribution Average Max Min + RS_GRID| Planes 106.2 107 106 + RS_GRID| Distribution Average Max Min + RS_GRID| Planes 82.1 83 82 + + RS_GRID| Information for grid number 2 + RS_GRID| Bounds 1 -67 67 Points: 135 + RS_GRID| Bounds 2 -67 67 Points: 135 + RS_GRID| Bounds 3 -67 67 Points: 135 + RS_GRID| Real space distribution over 4 groups + RS_GRID| Real space distribution along direction 2 + RS_GRID| Border size 28 + RS_GRID| Real space distribution over 7 groups + RS_GRID| Real space distribution along direction 3 + RS_GRID| Border size 28 + RS_GRID| Distribution Average Max Min + RS_GRID| Planes 89.8 90 89 + RS_GRID| Distribution Average Max Min + RS_GRID| Planes 75.3 76 75 + + RS_GRID| Information for grid number 3 + RS_GRID| Bounds 1 -37 37 Points: 75 + RS_GRID| Bounds 2 -37 37 Points: 75 + RS_GRID| Bounds 3 -37 37 Points: 75 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + RS_GRID| Information for grid number 4 + RS_GRID| Bounds 1 -22 22 Points: 45 + RS_GRID| Bounds 2 -22 22 Points: 45 + RS_GRID| Bounds 3 -22 22 Points: 45 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + DISTRIBUTION OF THE PARTICLES (ROWS) + Process row Number of particles Number of matrix rows + 0 7 -1 + 1 6 -1 + Sum 13 -1 + + DISTRIBUTION OF THE PARTICLES (COLUMNS) + Process col Number of particles Number of matrix columns + 0 1 -1 + 1 1 -1 + 2 1 -1 + 3 1 -1 + 4 1 -1 + 5 1 -1 + 6 1 -1 + 7 1 -1 + 8 1 -1 + 9 1 -1 + 10 1 -1 + 11 1 -1 + 12 1 -1 + 13 0 -1 + Sum 13 -1 + + DISTRIBUTION OF THE NEIGHBOR LISTS + Total number of particle pairs: 261 + Total number of matrix elements: 26357 + Average number of particle pairs: 10 + Maximum number of particle pairs: 25 + Average number of matrix element: 942 + Maximum number of matrix elements: 3393 + + + DISTRIBUTION OF THE OVERLAP MATRIX + Number of non-zero blocks: 91 + Percentage non-zero blocks: 100.00 + Average number of blocks per CPU: 4 + Maximum number of blocks per CPU: 5 + Average number of matrix elements per CPU: 295 + Maximum number of matrix elements per CPU: 647 + + Number of electrons: 40 + Number of occupied orbitals: 20 + Number of molecular orbitals: 20 + + Number of orbital functions: 121 + Number of independent orbital functions: 121 + + Extrapolation method: initial_guess + + *** WARNING in qs_initial_guess.F:262 :: User requested to restart the *** + *** wavefunction from the file named: ./Solv_0.37-0.0-RESTART.wfn. This *** + *** file does not exist. Please check the existence of the file or change *** + *** properly the value of the keyword WFN_RESTART_FILE_NAME. Calculation *** + *** continues using ATOMIC 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: C + + Electronic structure + Total number of core electrons 2.00 + Total number of valence electrons 4.00 + Total number of electrons 6.00 + Multiplicity not specified + S [ 2.00] 2.00 + P 2.00 + + + ******************************************************************************* + Iteration Convergence Energy [au] + ******************************************************************************* + 1 0.327231 -5.171846354414 + 2 0.243406 -5.237407211855 + 3 0.585645E-03 -5.283736081319 + 4 0.113344E-04 -5.283736390449 + 5 0.562146E-05 -5.283736390525 + 6 0.373780E-05 -5.283736390538 + 7 0.387614E-07 -5.283736390549 + + Energy components [Hartree] Total Energy :: -5.283736390549 + Band Energy :: -1.318690543615 + Kinetic Energy :: 3.419941553466 + Potential Energy :: -8.703677944015 + Virial (-V/T) :: 2.544978564091 + Core Energy :: -8.294092137394 + XC Energy :: -1.376676470246 + Coulomb Energy :: 4.387032217090 + Total Pseudopotential Energy :: -11.748318778537 + Local Pseudopotential Energy :: -12.388386202901 + Nonlocal Pseudopotential Energy :: 0.640067424364 + Confinement :: 0.342850876775 + + Orbital energies State L Occupation Energy[a.u.] Energy[eV] + + 1 0 2.000 -0.483269 -13.150417 + + 1 1 2.000 -0.176076 -4.791281 + + + Total Electron Density at R=0: 0.000246 + + Guess for atomic kind: H + + Electronic structure + Total number of core electrons 0.00 + Total number of valence electrons 1.00 + Total number of electrons 1.00 + Multiplicity not specified + S 1.00 + + + ******************************************************************************* + Iteration Convergence Energy [au] + ******************************************************************************* + 1 0.146049E-02 -0.421767924009 + 2 0.155986E-03 -0.421770124406 + 3 0.193312E-07 -0.421770149791 + + Energy components [Hartree] Total Energy :: -0.421770149791 + Band Energy :: -0.187795475903 + Kinetic Energy :: 0.476713143506 + Potential Energy :: -0.898483293297 + Virial (-V/T) :: 1.884746215910 + Core Energy :: -0.480212605621 + XC Energy :: -0.252068122890 + Coulomb Energy :: 0.310510578720 + Total Pseudopotential Energy :: -0.973576798689 + Local Pseudopotential Energy :: -0.973576798689 + Nonlocal Pseudopotential Energy :: 0.000000000000 + Confinement :: 0.166510495623 + + Orbital energies State L Occupation Energy[a.u.] Energy[eV] + + 1 0 1.000 -0.187795 -5.110175 + + + Total Electron Density at R=0: 0.223082 + + Guess for atomic kind: O + + Electronic structure + Total number of core electrons 2.00 + Total number of valence electrons 6.00 + Total number of electrons 8.00 + Multiplicity not specified + S [ 2.00] 2.00 + P 4.00 + + + ******************************************************************************* + Iteration Convergence Energy [au] + ******************************************************************************* + 1 1.69938 -14.798518114414 + 2 2.16886 -14.874253792865 + 3 0.907499E-01 -15.651960249323 + 4 0.348940E-02 -15.653277219447 + 5 0.142526E-02 -15.653278829294 + 6 0.884102E-03 -15.653279027439 + 7 0.268715E-04 -15.653279151165 + 8 0.171415E-06 -15.653279151285 + + Energy components [Hartree] Total Energy :: -15.653279151285 + Band Energy :: -2.985013233435 + Kinetic Energy :: 11.847839736451 + Potential Energy :: -27.501118887736 + Virial (-V/T) :: 2.321192681492 + Core Energy :: -26.146913442065 + XC Energy :: -3.156740274181 + Coulomb Energy :: 13.650374564961 + Total Pseudopotential Energy :: -38.029576734215 + Local Pseudopotential Energy :: -39.318981387664 + Nonlocal Pseudopotential Energy :: 1.289404653450 + Confinement :: 0.348235556985 + + Orbital energies State L Occupation Energy[a.u.] Energy[eV] + + 1 0 2.000 -0.860035 -23.402743 + + 1 1 4.000 -0.316236 -8.605214 + + + Total Electron Density at R=0: 0.000665 + Re-scaling the density matrix to get the right number of electrons + # Electrons Trace(P) Scaling factor + 40 40.000 1.000 + + SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT ---------------------------------------