From f2b5004d78d66f973d7e031eb6bb531d320df5ab Mon Sep 17 00:00:00 2001 From: robinzhuang <38876805+robinzyb@users.noreply.github.com> Date: Fri, 14 Aug 2020 16:03:12 +0800 Subject: [PATCH 01/19] parse virial info in cp2k --- dpdata/cp2k/output.py | 31 +- dpdata/system.py | 61 +- tests/cp2k/cp2k_output | 2953 +++++++++++++++---------------------- tests/cp2k/ref_cell | 6 +- tests/cp2k/ref_coord | 43 +- tests/cp2k/ref_force | 43 +- tests/cp2k/ref_type | 30 + tests/cp2k/ref_virial | 3 + tests/cp2k/test.py | 21 +- tests/test_cp2k_output.py | 61 +- 10 files changed, 1361 insertions(+), 1891 deletions(-) create mode 100644 tests/cp2k/ref_type create mode 100644 tests/cp2k/ref_virial diff --git a/dpdata/cp2k/output.py b/dpdata/cp2k/output.py index 469ccbdd4..dc9dae0fb 100644 --- a/dpdata/cp2k/output.py +++ b/dpdata/cp2k/output.py @@ -210,13 +210,16 @@ def handle_single_xyz_frame(self, lines): def get_frames (fname) : coord_flag = False force_flag = False + stress_flag = False eV = 2.72113838565563E+01 # hatree to eV - angstrom = 5.29177208590000E-01 # Bohrto Angstrom + angstrom = 5.29177208590000E-01 # Bohr to Angstrom + GPa = 160.21766208 # 1 eV/(Angstrom^3) = 160.21 GPa fp = open(fname) atom_symbol_list = [] cell = [] coord = [] force = [] + stress = [] coord_count = 0 for idx, ii in enumerate(fp) : if 'CELL| Vector' in ii : @@ -244,10 +247,23 @@ def get_frames (fname) : force_flag = False else : force.append(ii.split()[3:6]) + # add reading stress tensor + if 'STRESS TENSOR [GPa' in ii : + stress_flag = True + stress_idx = idx + if stress_flag : + if (idx > stress_idx + 2): + if (ii == '\n') : + stress_flag = False + else : + stress.append(ii.split()[1:4]) + + fp.close() assert(coord), "cannot find coords" assert(energy), "cannot find energies" assert(force), "cannot find forces" + assert(stress), "cannot find stress" #conver to float array and add extra dimension for nframes cell = np.array(cell) @@ -260,10 +276,21 @@ def get_frames (fname) : force = np.array(force) force = force.astype(np.float) force = force[np.newaxis, :, :] + stress = np.array(stress) + stress = stress.astype(np.float) + stress = stress[np.newaxis, :, :] + # force unit conversion, default unit in cp2k is hartree/bohr force = force * eV / angstrom + # energy unit conversion, default unit in cp2k is hartree energy = float(energy) * eV energy = np.array(energy) energy = energy[np.newaxis] + # stress to virial conversion, default unit in cp2k is GPa + # note the stress is virial = stress * volume + virial = stress * np.linalg.det(cell[0])/GPa + + + tmp_names, symbol_idx = np.unique(atom_symbol_list, return_index=True) atom_types = [] atom_numbs = [] @@ -278,7 +305,7 @@ def get_frames (fname) : atom_types = np.array(atom_types) - return list(atom_names), atom_numbs, atom_types, cell, coord, energy, force + return list(atom_names), atom_numbs, atom_types, cell, coord, energy, force, virial diff --git a/dpdata/system.py b/dpdata/system.py index 656563f25..5f3eb4dd1 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -136,7 +136,7 @@ def from_fmt(self, file_name, fmt='auto', **kwargs): func(self, file_name, **kwargs) else : raise RuntimeError('unknow data format ' + fmt) - + def to(self, fmt, *args, **kwargs): fmt = fmt.lower() to_funcs = self.register_to_funcs.funcs @@ -349,7 +349,7 @@ def append(self, system) : for ii in ['coords', 'cells'] : self.data[ii] = np.concatenate((self.data[ii], system[ii]), axis = 0) if self.nopbc and not system.nopbc: - # appended system uses PBC, cancel nopbc + # appended system uses PBC, cancel nopbc self.data['nopbc'] = False return True @@ -357,7 +357,7 @@ def sort_atom_names(self, type_map=None): """ Sort atom_names of the system and reorder atom_numbs and atom_types accoarding to atom_names. If type_map is not given, atom_names will be sorted by - alphabetical order. If type_map is given, atom_names will be type_map. + alphabetical order. If type_map is given, atom_names will be type_map. Parameters ---------- @@ -394,7 +394,7 @@ def check_type_map(self, type_map): Parameters ---------- type_map : list - type_map + type_map """ if type_map is not None and type_map != self.data['atom_names']: self.sort_atom_names(type_map=type_map) @@ -416,13 +416,13 @@ def formula(self): """ Return the formula of this system, like C3H5O2 """ - return ''.join(["{}{}".format(symbol,numb) for symbol,numb in + return ''.join(["{}{}".format(symbol,numb) for symbol,numb in zip(self.data['atom_names'], self.data['atom_numbs'])]) @property def uniq_formula(self): """ - Return the uniq_formula of this system. + Return the uniq_formula of this system. The uniq_formula sort the elements in formula by names. Systems with the same uniq_formula can be append together. """ @@ -456,9 +456,9 @@ def apply_pbc(self) : def remove_pbc(self, protect_layer = 9): """ This method does NOT delete the definition of the cells, it - (1) revises the cell to a cubic cell and ensures that the cell + (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than `protect_layer` - (2) translates the system such that the center-of-geometry of the system + (2) translates the system such that the center-of-geometry of the system locates at the center of the cell. Parameters @@ -474,12 +474,12 @@ def remove_pbc(self, protect_layer = 9): cog = np.average(tmpcoord, axis = 0) dist = tmpcoord - np.tile(cog, [natoms, 1]) max_dist = np.max(np.linalg.norm(dist, axis = 1)) - h_cell_size = max_dist + protect_layer + h_cell_size = max_dist + protect_layer cell_size = h_cell_size * 2 shift = np.array([1,1,1]) * h_cell_size - cog self.data['coords'][ff] = self.data['coords'][ff] + np.tile(shift, [natoms, 1]) - self.data['cells'][ff] = cell_size * np.eye(3) - + self.data['cells'][ff] = cell_size * np.eye(3) + @register_from_funcs.register_funcs("lmp") @register_from_funcs.register_funcs("lammps/lmp") @@ -508,7 +508,7 @@ def to_pymatgen_structure(self): structure=Structure(system.data['cells'][0],species,system.data['coords'][0],coords_are_cartesian=True) structures.append(structure) return structures - + @register_to_funcs.register_funcs("ase/structure") def to_ase_structure(self): @@ -570,7 +570,7 @@ def from_vasp_poscar(self, file_name) : def to_vasp_string(self, frame_idx=0): """ Dump the system in vasp POSCAR format string - + Parameters ---------- frame_idx : int @@ -579,7 +579,7 @@ def to_vasp_string(self, frame_idx=0): assert(frame_idx < len(self.data['coords'])) w_str = dpdata.vasp.poscar.from_system_data(self.data, frame_idx) return w_str - + @register_to_funcs.register_funcs("vasp/poscar") def to_vasp_poscar(self, file_name, frame_idx = 0) : """ @@ -660,7 +660,7 @@ def to_deepmd_raw(self, folder) : """ Dump the system in deepmd raw format to `folder` """ - dpdata.deepmd.raw.dump(folder, self.data) + dpdata.deepmd.raw.dump(folder, self.data) @register_from_funcs.register_funcs('siesta/output') def from_siesta_output(self, fname): @@ -761,7 +761,7 @@ def replicate(self, ncopy): Parameters ---------- - ncopy : + ncopy : list: [4,2,3] or tuple: (4,2,3,) make `ncopy[0]` copys in x dimensions, @@ -778,7 +778,7 @@ def replicate(self, ncopy): for ii in ncopy: if type(ii) is not int: raise RuntimeError('ncopy must be a list or tuple must with 3 int') - + tmp = System() nframes = self.get_nframes() data = self.data @@ -799,10 +799,10 @@ def replicate(self, ncopy): tmp.data['coords'] = np.reshape(np.transpose(tmp.data['coords'], [3,4,0,1,2,5]), (nframes, -1 , 3)) return tmp - def perturb(self, - pert_num, + def perturb(self, + pert_num, cell_pert_fraction, - atom_pert_distance, + atom_pert_distance, atom_pert_style='normal'): """ Perturb each frame in the system randomly. @@ -816,8 +816,8 @@ def perturb(self, That means the system to be returned will contain `pert_num` * frame_num of the input system. cell_pert_fraction : float A fraction determines how much (relatively) will cell deform. - The cell of each frame is deformed by a symmetric matrix perturbed from identity. - The perturbation to the diagonal part is subject to a uniform distribution in [-cell_pert_fraction, cell_pert_fraction), + The cell of each frame is deformed by a symmetric matrix perturbed from identity. + The perturbation to the diagonal part is subject to a uniform distribution in [-cell_pert_fraction, cell_pert_fraction), and the perturbation to the off-diagonal part is subject to a uniform distribution in [-0.5*cell_pert_fraction, 0.5*cell_pert_fraction). atom_pert_distance: float unit: Angstrom. A distance determines how far atoms will move. @@ -839,7 +839,7 @@ def perturb(self, The perturbed_system. It contains `pert_num` * frame_num of the input system frames. """ perturbed_system = System() - nframes = self.get_nframes() + nframes = self.get_nframes() for ii in range(nframes): for jj in range(pert_num): tmp_system = self[ii].copy() @@ -921,7 +921,7 @@ def get_atom_perturb_vector(atom_pert_distance, atom_pert_style='normal'): random_vector = None if atom_pert_distance < 0: raise RuntimeError('atom_pert_distance can not be negative') - + if atom_pert_style == 'normal': e = np.random.randn(3) random_vector=(atom_pert_distance/np.sqrt(3))*e @@ -1173,7 +1173,7 @@ def from_qe_cp_traj(self, prefix, begin = 0, step = 1) : ) self.data['energies'], self.data['forces'], es \ = dpdata.qe.traj.to_system_label(prefix + '.in', prefix, begin = begin, step = step) - assert(cs == es), "the step key between files are not consistent" + assert(cs == es), "the step key between files are not consistent" self.rot_lower_triangular() @register_from_funcs.register_funcs('qe/pw/scf') @@ -1188,7 +1188,7 @@ def from_qe_pw_scf(self, file_name) : self.data['virials'], \ = dpdata.qe.scf.get_frame(file_name) self.rot_lower_triangular() - + @register_from_funcs.register_funcs('siesta/output') def from_siesta_output(self, file_name) : self.data['atom_names'], \ @@ -1213,7 +1213,7 @@ def from_siesta_aiMD_output(self, file_name): self.data['forces'], \ self.data['virials'] \ = dpdata.siesta.aiMD_output.get_aiMD_frame(file_name) - + @register_from_funcs.register_funcs('gaussian/log') def from_gaussian_log(self, file_name, md=False): try: @@ -1221,7 +1221,7 @@ def from_gaussian_log(self, file_name, md=False): except AssertionError: self.data['energies'], self.data['forces']= [], [] self.data['nopbc'] = True - + @register_from_funcs.register_funcs('gaussian/md') def from_gaussian_md(self, file_name): self.from_gaussian_log(file_name, md=True) @@ -1248,6 +1248,7 @@ def from_cp2k_output(self, file_name) : self.data['coords'], \ self.data['energies'], \ self.data['forces'], \ + self.data['virials'] \ = dpdata.cp2k.output.get_frames(file_name) @register_from_funcs.register_funcs('movement') @register_from_funcs.register_funcs('MOVEMENT') @@ -1405,7 +1406,7 @@ def __add__(self, others) : elif isinstance(others, list): return self.__class__(self, *others) raise RuntimeError("Unspported data structure") - + @classmethod def from_file(cls,file_name,fmt): multi_systems = cls() @@ -1547,7 +1548,7 @@ def check_System(data): if len(data['coords']) > 0 : assert( len(data['coords'][0])==len(data['atom_types'])==sum(data['atom_numbs']) ) else : - assert( len(data['atom_types'])==sum(data['atom_numbs']) ) + assert( len(data['atom_types'])==sum(data['atom_numbs']) ) assert( len(data['cells']) == len(data['coords']) ) assert( len(data['atom_names'])==len(data['atom_numbs']) ) diff --git a/tests/cp2k/cp2k_output b/tests/cp2k/cp2k_output index 48f04b615..0aa678f37 100644 --- a/tests/cp2k/cp2k_output +++ b/tests/cp2k/cp2k_output @@ -1,9 +1,8 @@ - DBCSR| Multiplication driver BLAS + DBCSR| Multiplication driver XSMM 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 @@ -12,805 +11,31 @@ 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 + **** **** ****** ** PROGRAM STARTED AT 2020-08-14 06:09:53.115 + ***** ** *** *** ** PROGRAM STARTED ON c026.hpc.xmu + ** **** ****** PROGRAM STARTED BY ch2_101 + ***** ** ** ** ** PROGRAM PROCESS ID 19586 + **** ** ******* ** PROGRAM STARTED IN /data/ch2_101/ybzhuang/project02/prin + t_stress/small_system - 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| version string: CP2K version 6.1 + CP2K| source code revision number: svn:18464 + CP2K| cp2kflags: libint fftw3 libxc parallel mpi3 scalapack xsmm libderiv_max_a + CP2K| m1=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| Program compiled at Sun May 24 15:58:16 CST 2020 + CP2K| Program compiled on login01 + CP2K| Program compiled for local + CP2K| Data directory path /data/ch2_101/ybzhuang/basis 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 - - 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| Basis set file name BASIS_MOLOPT + 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 Solv_0.37-0.0 + GLOBAL| Project name PROJECT GLOBAL| Preferred FFT library FFTW3 GLOBAL| Preferred diagonalization lib. SL GLOBAL| Run type ENERGY_FORCE @@ -824,13 +49,13 @@ 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 + MEMORY| MemTotal 65401984 65401984 65401984 65401984 + MEMORY| MemFree 61249532 61249532 61249532 61249532 + MEMORY| Buffers 130692 130692 130692 130692 + MEMORY| Cached 1878912 1878912 1878912 1878912 + MEMORY| Slab 248924 248924 248924 248924 + MEMORY| SReclaimable 59404 59404 59404 59404 + MEMORY| MemLikelyFree 63318540 63318540 63318540 63318540 *** Fundamental physical constants (SI units) *** @@ -877,35 +102,35 @@ [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| Volume [angstrom^3]: 302.722 + CELL_TOP| Vector a [angstrom 5.038 0.000 0.000 |a| = 5.038 + CELL_TOP| Vector b [angstrom -2.519 4.363 0.000 |b| = 5.038 + CELL_TOP| Vector c [angstrom 0.000 0.000 13.772 |c| = 13.772 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 - + CELL_TOP| Angle (a,b), gamma [degree]: 120.000 + CELL_TOP| Numerically orthorhombic: NO + 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| Volume [angstrom^3]: 302.722 + CELL| Vector a [angstrom]: 5.038 0.000 0.000 |a| = 5.038 + CELL| Vector b [angstrom]: -2.519 4.363 0.000 |b| = 5.038 + CELL| Vector c [angstrom]: 0.000 0.000 13.772 |c| = 13.772 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| Angle (a,b), gamma [degree]: 120.000 + CELL| Numerically orthorhombic: NO - 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| Volume [angstrom^3]: 302.722 + CELL_REF| Vector a [angstrom 5.038 0.000 0.000 |a| = 5.038 + CELL_REF| Vector b [angstrom -2.519 4.363 0.000 |b| = 5.038 + CELL_REF| Vector c [angstrom 0.000 0.000 13.772 |c| = 13.772 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 + CELL_REF| Angle (a,b), gamma [degree]: 120.000 + CELL_REF| Numerically orthorhombic: NO ******************************************************************************* ******************************************************************************* @@ -922,189 +147,542 @@ ** ** ** ... make the atoms dance ** ** ** - ** Copyright (C) by CP2K developers group (2000 - 2016) ** + ** Copyright (C) by CP2K developers group (2000 - 2018) ** ** ** ******************************************************************************* - DFT| Spin restricted Kohn-Sham (RKS) calculation RKS + DFT| Spin unrestricted (spin-polarized) Kohn-Sham calculation UKS DFT| Multiplicity 1 - DFT| Number of spin states 1 + DFT| Number of spin states 2 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 + DFT| XC density smoothing NONE + DFT| XC derivatives PW + + DFT+U| Method MULLIKEN + DFT+U| Check atomic kind information for details 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} + FUNCTIONAL| PBE: + FUNCTIONAL| J.P.Perdew, K.Burke, M.Ernzerhof, Phys. Rev. Letter, vol. 77, n 18, + FUNCTIONAL| pp. 3865-3868, (1996){spin polarized} 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| sr6 Scaling Factor: 1.2170 + vdW POTENTIAL| s8 Scaling Factor: 0.7220 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| Density cutoff [a.u.]: 200.0 + QS| Multi grid cutoff [a.u.]: 1) grid level 200.0 + QS| 2) grid level 66.7 + QS| 3) grid level 22.2 + QS| 4) grid level 7.4 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| Interaction thresholds: eps_pgf_orb: 3.2E-07 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_core_charge: 1.0E-15 + QS| eps_rho_gspace: 1.0E-13 + QS| eps_rho_rspace: 1.0E-13 + QS| eps_gvg_rspace: 3.2E-07 QS| eps_ppl: 1.0E-02 - QS| eps_ppnl: 1.0E-08 + QS| eps_ppnl: 3.2E-09 ATOMIC KIND INFORMATION - 1. Atomic kind: C Number of atoms: 4 + 1. Atomic kind: Fe1 Number of atoms: 6 - Orbital Basis Set DZVP-GTH + Orbital Basis Set DZVP-MOLOPT-SR-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 + Number of orbital shell sets: 1 + Number of orbital shells: 8 + Number of primitive Cartesian functions: 6 + Number of Cartesian basis functions: 31 + Number of spherical basis functions: 26 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 + 1 1 2s 8.424366 -0.545589 + 4.825220 -0.832336 + 2.198939 0.958990 + 0.891661 0.416271 + 0.316231 0.012631 + 0.103474 -0.013505 + + 1 2 3s 8.424366 -0.106056 + 4.825220 -0.104587 + 2.198939 0.052318 + 0.891661 -0.169042 + 0.316231 0.061854 + 0.103474 0.122891 + + 1 3 4s 8.424366 -0.333477 + 4.825220 -0.289267 + 2.198939 -0.125861 + 0.891661 -1.004000 + 0.316231 0.780774 + 0.103474 -0.187846 + + 1 4 3px 8.424366 -1.658234 + 4.825220 1.618912 + 2.198939 1.969078 + 0.891661 0.523780 + 0.316231 0.024574 + 0.103474 -0.000798 + 1 4 3py 8.424366 -1.658234 + 4.825220 1.618912 + 2.198939 1.969078 + 0.891661 0.523780 + 0.316231 0.024574 + 0.103474 -0.000798 + 1 4 3pz 8.424366 -1.658234 + 4.825220 1.618912 + 2.198939 1.969078 + 0.891661 0.523780 + 0.316231 0.024574 + 0.103474 -0.000798 + + 1 5 4px 8.424366 -0.105249 + 4.825220 -0.126123 + 2.198939 -0.349657 + 0.891661 -0.133470 + 0.316231 0.170554 + 0.103474 0.054381 + 1 5 4py 8.424366 -0.105249 + 4.825220 -0.126123 + 2.198939 -0.349657 + 0.891661 -0.133470 + 0.316231 0.170554 + 0.103474 0.054381 + 1 5 4pz 8.424366 -0.105249 + 4.825220 -0.126123 + 2.198939 -0.349657 + 0.891661 -0.133470 + 0.316231 0.170554 + 0.103474 0.054381 + + 1 6 4dx2 8.424366 7.918298 + 4.825220 5.112663 + 2.198939 2.118663 + 0.891661 0.465004 + 0.316231 0.065856 + 0.103474 0.002769 + 1 6 4dxy 8.424366 13.714895 + 4.825220 8.855393 + 2.198939 3.669632 + 0.891661 0.805411 + 0.316231 0.114066 + 0.103474 0.004796 + 1 6 4dxz 8.424366 13.714895 + 4.825220 8.855393 + 2.198939 3.669632 + 0.891661 0.805411 + 0.316231 0.114066 + 0.103474 0.004796 + 1 6 4dy2 8.424366 7.918298 + 4.825220 5.112663 + 2.198939 2.118663 + 0.891661 0.465004 + 0.316231 0.065856 + 0.103474 0.002769 + 1 6 4dyz 8.424366 13.714895 + 4.825220 8.855393 + 2.198939 3.669632 + 0.891661 0.805411 + 0.316231 0.114066 + 0.103474 0.004796 + 1 6 4dz2 8.424366 7.918298 + 4.825220 5.112663 + 2.198939 2.118663 + 0.891661 0.465004 + 0.316231 0.065856 + 0.103474 0.002769 + + 1 7 5dx2 8.424366 -4.223614 + 4.825220 -1.970584 + 2.198939 -1.543490 + 0.891661 -0.041381 + 0.316231 0.082821 + 0.103474 0.021964 + 1 7 5dxy 8.424366 -7.315513 + 4.825220 -3.413151 + 2.198939 -2.673404 + 0.891661 -0.071673 + 0.316231 0.143450 + 0.103474 0.038042 + 1 7 5dxz 8.424366 -7.315513 + 4.825220 -3.413151 + 2.198939 -2.673404 + 0.891661 -0.071673 + 0.316231 0.143450 + 0.103474 0.038042 + 1 7 5dy2 8.424366 -4.223614 + 4.825220 -1.970584 + 2.198939 -1.543490 + 0.891661 -0.041381 + 0.316231 0.082821 + 0.103474 0.021964 + 1 7 5dyz 8.424366 -7.315513 + 4.825220 -3.413151 + 2.198939 -2.673404 + 0.891661 -0.071673 + 0.316231 0.143450 + 0.103474 0.038042 + 1 7 5dz2 8.424366 -4.223614 + 4.825220 -1.970584 + 2.198939 -1.543490 + 0.891661 -0.041381 + 0.316231 0.082821 + 0.103474 0.021964 + + 1 8 5fx3 8.424366 -1.141046 + 4.825220 0.521593 + 2.198939 -0.648365 + 0.891661 -0.481511 + 0.316231 -0.065954 + 0.103474 0.007610 + 1 8 5fx2y 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fx2z 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fxy2 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fxyz 8.424366 -4.419252 + 4.825220 2.020120 + 2.198939 -2.511108 + 0.891661 -1.864883 + 0.316231 -0.255438 + 0.103474 0.029474 + 1 8 5fxz2 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fy3 8.424366 -1.141046 + 4.825220 0.521593 + 2.198939 -0.648365 + 0.891661 -0.481511 + 0.316231 -0.065954 + 0.103474 0.007610 + 1 8 5fy2z 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fyz2 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fz3 8.424366 -1.141046 + 4.825220 0.521593 + 2.198939 -0.648365 + 0.891661 -0.481511 + 0.316231 -0.065954 + 0.103474 0.007610 + + GTH Potential information for GTH-PBE-q16 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 + Gaussian exponent of the core charge distribution: 3.858025 + Electronic configuration (s p d ...): 4 6 6 Parameters of the local part of the GTH pseudopotential: rloc C1 C2 C3 C4 - 0.338066 -9.136269 1.429260 + 0.360000 6.756789 -0.228833 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 + 0 0.278263 0.629506 7.913132 + 7.913132 -10.215810 + 1 0.251383 -7.932133 7.697079 + 7.697079 -9.107307 + 2 0.222856 -12.385799 - 2. Atomic kind: H Number of atoms: 6 + A DFT+U correction is applied to atoms of this atomic kind: + Angular quantum momentum number L: 2 + U(eff) = (U - J) value in [eV]: 3.000 - Orbital Basis Set DZVP-GTH + 2. Atomic kind: Fe2 Number of atoms: 6 - 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 + Orbital Basis Set DZVP-MOLOPT-SR-GTH + + Number of orbital shell sets: 1 + Number of orbital shells: 8 + Number of primitive Cartesian functions: 6 + Number of Cartesian basis functions: 31 + Number of spherical basis functions: 26 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 + 1 1 2s 8.424366 -0.545589 + 4.825220 -0.832336 + 2.198939 0.958990 + 0.891661 0.416271 + 0.316231 0.012631 + 0.103474 -0.013505 + + 1 2 3s 8.424366 -0.106056 + 4.825220 -0.104587 + 2.198939 0.052318 + 0.891661 -0.169042 + 0.316231 0.061854 + 0.103474 0.122891 + + 1 3 4s 8.424366 -0.333477 + 4.825220 -0.289267 + 2.198939 -0.125861 + 0.891661 -1.004000 + 0.316231 0.780774 + 0.103474 -0.187846 + + 1 4 3px 8.424366 -1.658234 + 4.825220 1.618912 + 2.198939 1.969078 + 0.891661 0.523780 + 0.316231 0.024574 + 0.103474 -0.000798 + 1 4 3py 8.424366 -1.658234 + 4.825220 1.618912 + 2.198939 1.969078 + 0.891661 0.523780 + 0.316231 0.024574 + 0.103474 -0.000798 + 1 4 3pz 8.424366 -1.658234 + 4.825220 1.618912 + 2.198939 1.969078 + 0.891661 0.523780 + 0.316231 0.024574 + 0.103474 -0.000798 + + 1 5 4px 8.424366 -0.105249 + 4.825220 -0.126123 + 2.198939 -0.349657 + 0.891661 -0.133470 + 0.316231 0.170554 + 0.103474 0.054381 + 1 5 4py 8.424366 -0.105249 + 4.825220 -0.126123 + 2.198939 -0.349657 + 0.891661 -0.133470 + 0.316231 0.170554 + 0.103474 0.054381 + 1 5 4pz 8.424366 -0.105249 + 4.825220 -0.126123 + 2.198939 -0.349657 + 0.891661 -0.133470 + 0.316231 0.170554 + 0.103474 0.054381 + + 1 6 4dx2 8.424366 7.918298 + 4.825220 5.112663 + 2.198939 2.118663 + 0.891661 0.465004 + 0.316231 0.065856 + 0.103474 0.002769 + 1 6 4dxy 8.424366 13.714895 + 4.825220 8.855393 + 2.198939 3.669632 + 0.891661 0.805411 + 0.316231 0.114066 + 0.103474 0.004796 + 1 6 4dxz 8.424366 13.714895 + 4.825220 8.855393 + 2.198939 3.669632 + 0.891661 0.805411 + 0.316231 0.114066 + 0.103474 0.004796 + 1 6 4dy2 8.424366 7.918298 + 4.825220 5.112663 + 2.198939 2.118663 + 0.891661 0.465004 + 0.316231 0.065856 + 0.103474 0.002769 + 1 6 4dyz 8.424366 13.714895 + 4.825220 8.855393 + 2.198939 3.669632 + 0.891661 0.805411 + 0.316231 0.114066 + 0.103474 0.004796 + 1 6 4dz2 8.424366 7.918298 + 4.825220 5.112663 + 2.198939 2.118663 + 0.891661 0.465004 + 0.316231 0.065856 + 0.103474 0.002769 + + 1 7 5dx2 8.424366 -4.223614 + 4.825220 -1.970584 + 2.198939 -1.543490 + 0.891661 -0.041381 + 0.316231 0.082821 + 0.103474 0.021964 + 1 7 5dxy 8.424366 -7.315513 + 4.825220 -3.413151 + 2.198939 -2.673404 + 0.891661 -0.071673 + 0.316231 0.143450 + 0.103474 0.038042 + 1 7 5dxz 8.424366 -7.315513 + 4.825220 -3.413151 + 2.198939 -2.673404 + 0.891661 -0.071673 + 0.316231 0.143450 + 0.103474 0.038042 + 1 7 5dy2 8.424366 -4.223614 + 4.825220 -1.970584 + 2.198939 -1.543490 + 0.891661 -0.041381 + 0.316231 0.082821 + 0.103474 0.021964 + 1 7 5dyz 8.424366 -7.315513 + 4.825220 -3.413151 + 2.198939 -2.673404 + 0.891661 -0.071673 + 0.316231 0.143450 + 0.103474 0.038042 + 1 7 5dz2 8.424366 -4.223614 + 4.825220 -1.970584 + 2.198939 -1.543490 + 0.891661 -0.041381 + 0.316231 0.082821 + 0.103474 0.021964 + + 1 8 5fx3 8.424366 -1.141046 + 4.825220 0.521593 + 2.198939 -0.648365 + 0.891661 -0.481511 + 0.316231 -0.065954 + 0.103474 0.007610 + 1 8 5fx2y 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fx2z 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fxy2 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fxyz 8.424366 -4.419252 + 4.825220 2.020120 + 2.198939 -2.511108 + 0.891661 -1.864883 + 0.316231 -0.255438 + 0.103474 0.029474 + 1 8 5fxz2 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fy3 8.424366 -1.141046 + 4.825220 0.521593 + 2.198939 -0.648365 + 0.891661 -0.481511 + 0.316231 -0.065954 + 0.103474 0.007610 + 1 8 5fy2z 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fyz2 8.424366 -2.551456 + 4.825220 1.166317 + 2.198939 -1.449789 + 0.891661 -1.076690 + 0.316231 -0.147477 + 0.103474 0.017017 + 1 8 5fz3 8.424366 -1.141046 + 4.825220 0.521593 + 2.198939 -0.648365 + 0.891661 -0.481511 + 0.316231 -0.065954 + 0.103474 0.007610 + + GTH Potential information for GTH-PBE-q16 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 + Gaussian exponent of the core charge distribution: 3.858025 + Electronic configuration (s p d ...): 4 6 6 Parameters of the local part of the GTH pseudopotential: rloc C1 C2 C3 C4 - 0.200000 -4.195961 0.730498 + 0.360000 6.756789 -0.228833 + + Parameters of the non-local part of the GTH pseudopotential: + + l r(l) h(i,j,l) + + 0 0.278263 0.629506 7.913132 + 7.913132 -10.215810 + 1 0.251383 -7.932133 7.697079 + 7.697079 -9.107307 + 2 0.222856 -12.385799 + + A DFT+U correction is applied to atoms of this atomic kind: + Angular quantum momentum number L: 2 + U(eff) = (U - J) value in [eV]: 3.000 - 3. Atomic kind: O Number of atoms: 3 + 3. Atomic kind: O Number of atoms: 18 - Orbital Basis Set DZVP-GTH + Orbital Basis Set DZVP-MOLOPT-SR-GTH - Number of orbital shell sets: 2 + Number of orbital shell sets: 1 Number of orbital shells: 5 Number of primitive Cartesian functions: 5 Number of Cartesian basis functions: 14 @@ -1115,70 +693,102 @@ 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 + 1 1 2s 10.389228 0.396646 + 3.849621 0.208811 + 1.388401 -0.301641 + 0.496955 -0.274061 + 0.162492 -0.033677 + + 1 2 3s 10.389228 0.303673 + 3.849621 0.240943 + 1.388401 -0.313066 + 0.496955 -0.043055 + 0.162492 0.213991 + + 1 3 3px 10.389228 -1.530415 + 3.849621 -1.371928 + 1.388401 -0.761951 + 0.496955 -0.253695 + 0.162492 -0.035541 + 1 3 3py 10.389228 -1.530415 + 3.849621 -1.371928 + 1.388401 -0.761951 + 0.496955 -0.253695 + 0.162492 -0.035541 + 1 3 3pz 10.389228 -1.530415 + 3.849621 -1.371928 + 1.388401 -0.761951 + 0.496955 -0.253695 + 0.162492 -0.035541 + + 1 4 4px 10.389228 -0.565392 + 3.849621 -0.038231 + 1.388401 -0.382373 + 0.496955 0.179070 + 0.162492 0.122714 + 1 4 4py 10.389228 -0.565392 + 3.849621 -0.038231 + 1.388401 -0.382373 + 0.496955 0.179070 + 0.162492 0.122714 + 1 4 4pz 10.389228 -0.565392 + 3.849621 -0.038231 + 1.388401 -0.382373 + 0.496955 0.179070 + 0.162492 0.122714 + + 1 5 4dx2 10.389228 1.867377 + 3.849621 0.670994 + 1.388401 1.353441 + 0.496955 0.273538 + 0.162492 0.006620 + 1 5 4dxy 10.389228 3.234392 + 3.849621 1.162195 + 1.388401 2.344229 + 0.496955 0.473781 + 0.162492 0.011466 + 1 5 4dxz 10.389228 3.234392 + 3.849621 1.162195 + 1.388401 2.344229 + 0.496955 0.473781 + 0.162492 0.011466 + 1 5 4dy2 10.389228 1.867377 + 3.849621 0.670994 + 1.388401 1.353441 + 0.496955 0.273538 + 0.162492 0.006620 + 1 5 4dyz 10.389228 3.234392 + 3.849621 1.162195 + 1.388401 2.344229 + 0.496955 0.473781 + 0.162492 0.011466 + 1 5 4dz2 10.389228 1.867377 + 3.849621 0.670994 + 1.388401 1.353441 + 0.496955 0.273538 + 0.162492 0.006620 + + GTH Potential information for GTH-PBE-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 + Gaussian exponent of the core charge distribution: 8.360253 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 + 0.244554 -16.667215 2.487311 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 + 0 0.220956 18.337458 + 1 0.211332 MOLECULE KIND INFORMATION @@ -1190,310 +800,303 @@ 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 + - Atoms: 30 + - Shell sets: 30 + - Shells: 186 + - Primitive Cartesian functions: 162 + - Cartesian basis functions: 624 + - Spherical basis functions: 546 + + Maximum angular momentum of- Orbital basis functions: 3 - Local part of the GTH pseudopotential: 2 - - Non-local part of the GTH pseudopotential: 0 + - Non-local part of the GTH pseudopotential: 3 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 + 1 1 Fe 26 0.000000 0.000000 1.992808 16.00 55.8450 + 2 2 Fe 26 0.000000 0.000000 8.878808 16.00 55.8450 + 3 1 Fe 26 0.000000 0.000000 11.779192 16.00 55.8450 + 4 2 Fe 26 0.000000 0.000000 4.893192 16.00 55.8450 + 5 1 Fe 26 2.519000 1.454345 6.583475 16.00 55.8450 + 6 2 Fe 26 2.519000 1.454345 13.469475 16.00 55.8450 + 7 1 Fe 26 2.519000 1.454345 2.597858 16.00 55.8450 + 8 2 Fe 26 2.519000 1.454345 9.483858 16.00 55.8450 + 9 1 Fe 26 0.000000 2.908691 11.174142 16.00 55.8450 + 10 2 Fe 26 0.000000 2.908691 4.288142 16.00 55.8450 + 11 1 Fe 26 0.000000 2.908691 7.188525 16.00 55.8450 + 12 2 Fe 26 0.000000 2.908691 0.302525 16.00 55.8450 + 13 3 O 8 1.541124 0.000000 3.443000 6.00 15.9994 + 14 3 O 8 1.748438 3.028383 3.443000 6.00 15.9994 + 15 3 O 8 -0.770562 1.334653 3.443000 6.00 15.9994 + 16 3 O 8 0.770562 1.334653 10.329000 6.00 15.9994 + 17 3 O 8 -1.748438 3.028383 10.329000 6.00 15.9994 + 18 3 O 8 3.496876 0.000000 10.329000 6.00 15.9994 + 19 3 O 8 4.060124 1.454345 8.033667 6.00 15.9994 + 20 3 O 8 1.748438 0.119693 8.033667 6.00 15.9994 + 21 3 O 8 1.748438 2.788998 8.033667 6.00 15.9994 + 22 3 O 8 3.289562 2.788998 1.147667 6.00 15.9994 + 23 3 O 8 3.289562 0.119693 1.147667 6.00 15.9994 + 24 3 O 8 0.977876 1.454345 1.147667 6.00 15.9994 + 25 3 O 8 1.541124 2.908691 12.624333 6.00 15.9994 + 26 3 O 8 -0.770562 1.574038 12.624333 6.00 15.9994 + 27 3 O 8 -0.770562 4.243343 12.624333 6.00 15.9994 + 28 3 O 8 0.770562 4.243343 5.738333 6.00 15.9994 + 29 3 O 8 0.770562 1.574038 5.738333 6.00 15.9994 + 30 3 O 8 -1.541124 2.908691 5.738333 6.00 15.9994 + + + + + SCF PARAMETERS Density guess: ATOMIC -------------------------------------------------------- - max_scf: 50 + max_scf: 1 max_scf_history: 0 max_diis: 4 -------------------------------------------------------- - eps_scf: 1.00E-06 + eps_scf: 3.00E-07 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 + No outer SCF 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| Cutoff [a.u.] 200.0 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| Bounds 1 -32 31 Points: 64 + PW_GRID| Bounds 2 -32 31 Points: 64 + PW_GRID| Bounds 3 -90 89 Points: 180 + PW_GRID| Volume element (a.u.^3) 0.2771E-02 Volume (a.u.^3) 2042.8693 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| G-Vectors 26331.4 26368 26304 + PW_GRID| G-Rays 411.4 412 411 + PW_GRID| Real Space Points 26331.4 34560 23040 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| Cutoff [a.u.] 66.7 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| Bounds 1 -18 17 Points: 36 + PW_GRID| Bounds 2 -18 17 Points: 36 + PW_GRID| Bounds 3 -48 47 Points: 96 + PW_GRID| Volume element (a.u.^3) 0.1642E-01 Volume (a.u.^3) 2042.8693 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| G-Vectors 4443.4 4680 4212 + PW_GRID| G-Rays 123.4 130 117 + PW_GRID| Real Space Points 4443.4 6912 3456 PW_GRID| Information for grid number 3 PW_GRID| Grid distributed over 28 processors - PW_GRID| Real space group dimensions 28 1 + PW_GRID| Real space group dimensions 2 14 PW_GRID| the grid is blocked: NO - PW_GRID| Cutoff [a.u.] 27.8 + PW_GRID| Cutoff [a.u.] 22.2 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| Bounds 1 -12 11 Points: 24 + PW_GRID| Bounds 2 -12 11 Points: 24 + PW_GRID| Bounds 3 -30 29 Points: 60 + PW_GRID| Volume element (a.u.^3) 0.5911E-01 Volume (a.u.^3) 2042.8693 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| G-Vectors 1234.3 1320 1176 + PW_GRID| G-Rays 51.4 55 49 + PW_GRID| Real Space Points 1234.3 1440 720 PW_GRID| Information for grid number 4 PW_GRID| Grid distributed over 28 processors - PW_GRID| Real space group dimensions 28 1 + PW_GRID| Real space group dimensions 2 14 PW_GRID| the grid is blocked: NO - PW_GRID| Cutoff [a.u.] 9.3 + PW_GRID| Cutoff [a.u.] 7.4 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| Bounds 1 -6 5 Points: 12 + PW_GRID| Bounds 2 -6 5 Points: 12 + PW_GRID| Bounds 3 -16 15 Points: 32 + PW_GRID| Volume element (a.u.^3) 0.4433 Volume (a.u.^3) 2042.8693 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 + PW_GRID| G-Vectors 164.6 216 108 + PW_GRID| G-Rays 13.7 18 9 + PW_GRID| Real Space Points 164.6 192 0 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| Bounds 1 -32 31 Points: 64 + RS_GRID| Bounds 2 -32 31 Points: 64 + RS_GRID| Bounds 3 -90 89 Points: 180 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 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| Bounds 1 -18 17 Points: 36 + RS_GRID| Bounds 2 -18 17 Points: 36 + RS_GRID| Bounds 3 -48 47 Points: 96 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 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| Bounds 1 -12 11 Points: 24 + RS_GRID| Bounds 2 -12 11 Points: 24 + RS_GRID| Bounds 3 -30 29 Points: 60 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| Bounds 1 -6 5 Points: 12 + RS_GRID| Bounds 2 -6 5 Points: 12 + RS_GRID| Bounds 3 -16 15 Points: 32 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 + Spin 1 - Extrapolation method: initial_guess + Number of electrons: 150 + Number of occupied orbitals: 150 + Number of molecular orbitals: 150 + + Spin 2 - *** 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. *** + Number of electrons: 150 + Number of occupied orbitals: 150 + Number of molecular orbitals: 150 + Number of orbital functions: 546 + Number of independent orbital functions: 546 + + 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: C + Guess for atomic kind: Fe1 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 - + Total number of core electrons 10.00 + Total number of valence electrons 13.00 + Total number of electrons 23.00 + Multiplicity sextet + Alpha Electrons + S [ 1.00 1.00] 1.00 + P [ 3.00] 3.00 + D 5.00 + Beta Electrons + S [ 1.00 1.00] 1.00 + P [ 3.00] 3.00 + D 0.00 + ******************************************************************************* 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 + 1 2.54209 -120.150614842433 + 2 1.43784 -120.903351751461 + 3 0.736235E-01 -120.985109878427 + 4 0.120693E-01 -120.985393690991 + 5 0.262156E-02 -120.985401118823 + 6 0.157468E-02 -120.985401426562 + 7 0.698268E-04 -120.985401612034 + 8 0.487778E-04 -120.985401612190 + 9 0.441372E-04 -120.985401612211 + 10 0.115128E-05 -120.985401612298 + 11 0.585531E-06 -120.985401612298 + + Energy components [Hartree] Total Energy :: -120.985401612298 + Band Energy :: -39.640843232782 + Kinetic Energy :: 64.276269679946 + Potential Energy :: -185.261671292244 + Virial (-V/T) :: 2.882271672185 + Core Energy :: -194.271167227349 + XC Energy :: -11.804081492160 + Coulomb Energy :: 85.089847107212 + Total Pseudopotential Energy :: -258.570236844263 + Local Pseudopotential Energy :: -236.048731410826 + Nonlocal Pseudopotential Energy :: -22.521505433437 + Confinement :: 0.227999369674 + + Orbital energies State Spin L Occupation Energy[a.u.] Energy[eV] + + 1 alpha 0 1.000 -5.019588 -136.589933 + 1 beta 0 1.000 -4.775625 -129.951372 + + 1 alpha 1 3.000 -3.674975 -100.001167 + 1 beta 1 3.000 -3.438324 -93.561566 + + 1 alpha 2 5.000 -1.701146 -46.290539 + 1 beta 2 0.000 -1.485400 -40.419800 + + + Total Electron Density at R=0: 0.000188 + + Guess for atomic kind: Fe2 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 - + Total number of core electrons 10.00 + Total number of valence electrons 13.00 + Total number of electrons 23.00 + Multiplicity sextet + Alpha Electrons + S [ 1.00 1.00] 1.00 + P [ 3.00] 3.00 + D 0.00 + Beta Electrons + S [ 1.00 1.00] 1.00 + P [ 3.00] 3.00 + D 5.00 + ******************************************************************************* 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 + 1 2.54209 -120.150614842433 + 2 1.43784 -120.903351751461 + 3 0.736235E-01 -120.985109878427 + 4 0.120693E-01 -120.985393690991 + 5 0.262156E-02 -120.985401118823 + 6 0.157468E-02 -120.985401426562 + 7 0.698268E-04 -120.985401612034 + 8 0.487778E-04 -120.985401612190 + 9 0.441372E-04 -120.985401612210 + 10 0.115128E-05 -120.985401612297 + 11 0.585535E-06 -120.985401612298 + + Energy components [Hartree] Total Energy :: -120.985401612298 + Band Energy :: -39.640843232767 + Kinetic Energy :: 64.276269679939 + Potential Energy :: -185.261671292237 + Virial (-V/T) :: 2.882271672185 + Core Energy :: -194.271167227344 + XC Energy :: -11.804081492159 + Coulomb Energy :: 85.089847107206 + Total Pseudopotential Energy :: -258.570236844251 + Local Pseudopotential Energy :: -236.048731410817 + Nonlocal Pseudopotential Energy :: -22.521505433434 + Confinement :: 0.227999369674 + + Orbital energies State Spin L Occupation Energy[a.u.] Energy[eV] + + 1 alpha 0 1.000 -4.775625 -129.951372 + 1 beta 0 1.000 -5.019588 -136.589933 + + 1 alpha 1 3.000 -3.438324 -93.561566 + 1 beta 1 3.000 -3.674975 -100.001167 + + 1 alpha 2 0.000 -1.485400 -40.419800 + 1 beta 2 5.000 -1.701146 -46.290539 + + + Total Electron Density at R=0: 0.000188 Guess for atomic kind: O @@ -1504,44 +1107,52 @@ 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 + 1 1.67054 -14.836051221656 + 2 2.12470 -14.897900780399 + 3 0.100150 -15.654295189160 + 4 0.189307E-01 -15.655828842238 + 5 0.464435E-02 -15.655882433232 + 6 0.259395E-02 -15.655884790195 + 7 0.516014E-04 -15.655885857622 + 8 0.157374E-05 -15.655885858066 + 9 0.783512E-06 -15.655885858066 + + Energy components [Hartree] Total Energy :: -15.655885858066 + Band Energy :: -2.983129541149 + Kinetic Energy :: 11.754767937471 + Potential Energy :: -27.410653795537 + Virial (-V/T) :: 2.331875366774 + Core Energy :: -26.153524299614 + XC Energy :: -3.157392735430 + Coulomb Energy :: 13.655031176977 + Total Pseudopotential Energy :: -37.943031004163 + Local Pseudopotential Energy :: -39.220423834999 + Nonlocal Pseudopotential Energy :: 1.277392830837 + Confinement :: 0.347387670777 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 - + 1 0 2.000 -0.861523 -23.443221 + + 1 1 4.000 -0.315021 -8.572160 + - Total Electron Density at R=0: 0.000665 - Re-scaling the density matrix to get the right number of electrons + Total Electron Density at R=0: 0.000093 + + Spin 1 + Re-scaling the density matrix to get the right number of electrons for spin 1 + # Electrons Trace(P) Scaling factor + 150 131.956 1.137 + + Spin 2 + Re-scaling the density matrix to get the right number of electrons for spin 2 # Electrons Trace(P) Scaling factor - 40 40.000 1.000 + 150 131.956 1.137 SCF WAVEFUNCTION OPTIMIZATION @@ -1561,472 +1172,180 @@ Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 1 OT DIIS 0.80E-01 0.6 0.12211697 -69.9227646320 -6.99E+01 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 2 OT DIIS 0.80E-01 0.8 0.08397991 -71.5488849278 -1.63E+00 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 3 OT DIIS 0.80E-01 0.8 0.06432705 -72.3568418033 -8.08E-01 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 4 OT DIIS 0.80E-01 0.8 0.05737364 -73.1900458544 -8.33E-01 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 5 OT DIIS 0.80E-01 0.8 0.03623630 -73.7413152872 -5.51E-01 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 6 OT DIIS 0.80E-01 0.8 0.02687733 -73.9835995051 -2.42E-01 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 7 OT DIIS 0.80E-01 0.8 0.01682164 -74.0451613466 -6.16E-02 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 8 OT DIIS 0.80E-01 0.8 0.01172379 -74.1060462003 -6.09E-02 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 9 OT DIIS 0.80E-01 0.9 0.00685204 -74.1347934213 -2.87E-02 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 10 OT DIIS 0.80E-01 0.8 0.00557939 -74.1452592701 -1.05E-02 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 11 OT DIIS 0.80E-01 0.8 0.00529907 -74.1545329360 -9.27E-03 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 12 OT DIIS 0.80E-01 0.8 0.00204013 -74.1583772496 -3.84E-03 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 13 OT DIIS 0.80E-01 0.8 0.00125361 -74.1604256086 -2.05E-03 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 14 OT DIIS 0.80E-01 0.8 0.00081727 -74.1611323749 -7.07E-04 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 15 OT DIIS 0.80E-01 0.8 0.00059499 -74.1614246428 -2.92E-04 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 16 OT DIIS 0.80E-01 0.8 0.00040833 -74.1616124349 -1.88E-04 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 17 OT DIIS 0.80E-01 0.8 0.00032383 -74.1616836330 -7.12E-05 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 18 OT DIIS 0.80E-01 0.8 0.00024259 -74.1617425930 -5.90E-05 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 19 OT DIIS 0.80E-01 0.8 0.00019028 -74.1617752692 -3.27E-05 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 20 OT DIIS 0.80E-01 0.8 0.00014769 -74.1617987237 -2.35E-05 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 21 OT DIIS 0.80E-01 0.8 0.00011570 -74.1618110663 -1.23E-05 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 22 OT DIIS 0.80E-01 0.8 0.00009372 -74.1618181547 -7.09E-06 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 23 OT DIIS 0.80E-01 0.8 0.00007276 -74.1618237906 -5.64E-06 + *** WARNING in dft_plus_u.F:1457 :: DFT+U energy contibution is negative *** + *** possibly due to unphysical Mulliken charges. Check your input, if *** + *** this warning persists or try a different method! *** - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 + 1 OT DIIS 0.80E-01 1.8 0.02028625 -1761.4177347284 -1.76E+03 - 24 OT DIIS 0.80E-01 0.8 0.00005773 -74.1618267716 -2.98E-06 + Leaving inner SCF loop after reaching 1 steps. - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - 25 OT DIIS 0.80E-01 0.8 0.00004629 -74.1618286021 -1.83E-06 + Electronic density on regular grids: -299.9999999986 0.0000000014 + Core density on regular grids: 300.0000000000 -0.0000000000 + Total charge density on r-space grids: 0.0000000014 + Total charge density g-space grids: 0.0000000014 - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 + Overlap energy of the core charge distribution: 0.00000000000003 + Self energy of the core charge distribution: -3154.68061722574021 + Core Hamiltonian energy: 935.66202309714276 + Hartree energy: 690.69767703020932 + Exchange-correlation energy: -232.91317595479714 + Dispersion energy: -0.14404267231287 - 26 OT DIIS 0.80E-01 0.8 0.00003663 -74.1618296881 -1.09E-06 + DFT+U energy: -0.03959900290022 - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 + Total energy: -1761.41773472839827 - 27 OT DIIS 0.80E-01 0.8 0.00002919 -74.1618303402 -6.52E-07 + *** WARNING in qs_scf.F:542 :: SCF run NOT converged *** - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 28 OT DIIS 0.80E-01 0.8 0.00002316 -74.1618307348 -3.95E-07 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 29 OT DIIS 0.80E-01 0.8 0.00001912 -74.1618309323 -1.98E-07 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 30 OT DIIS 0.80E-01 0.8 0.00001585 -74.1618310522 -1.20E-07 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 31 OT DIIS 0.80E-01 0.8 0.00001283 -74.1618311407 -8.86E-08 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 32 OT DIIS 0.80E-01 0.8 0.00001054 -74.1618311976 -5.69E-08 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 33 OT DIIS 0.80E-01 0.8 0.00000864 -74.1618312407 -4.31E-08 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 34 OT DIIS 0.80E-01 0.8 0.00000720 -74.1618312662 -2.54E-08 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 35 OT DIIS 0.80E-01 0.8 0.00000603 -74.1618312851 -1.89E-08 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 36 OT DIIS 0.80E-01 0.8 0.00000510 -74.1618313004 -1.53E-08 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 37 OT DIIS 0.80E-01 0.8 0.00000446 -74.1618313105 -1.01E-08 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 38 OT DIIS 0.80E-01 0.8 0.00000385 -74.1618313187 -8.25E-09 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 39 OT DIIS 0.80E-01 0.8 0.00000332 -74.1618313255 -6.75E-09 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 40 OT DIIS 0.80E-01 0.8 0.00000288 -74.1618313308 -5.30E-09 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 41 OT DIIS 0.80E-01 0.8 0.00000245 -74.1618313356 -4.81E-09 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 42 OT DIIS 0.80E-01 0.8 0.00000212 -74.1618313387 -3.05E-09 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 43 OT DIIS 0.80E-01 0.8 0.00000178 -74.1618313411 -2.49E-09 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 44 OT DIIS 0.80E-01 0.8 0.00000148 -74.1618313429 -1.80E-09 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 45 OT DIIS 0.80E-01 0.8 0.00000124 -74.1618313441 -1.15E-09 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 46 OT DIIS 0.80E-01 0.9 0.00000101 -74.1618313448 -7.33E-10 - - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - 47 OT DIIS 0.80E-01 0.8 0.00000081 -74.1618313453 -4.29E-10 - - *** SCF run converged in 47 steps *** - - - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 - - Overlap energy of the core charge distribution: 0.00000242417664 - Self energy of the core charge distribution: -187.02580487381152 - Core Hamiltonian energy: 55.54257423380538 - Hartree energy: 76.76711718225495 - Exchange-correlation energy: -19.43594060717809 - Dispersion energy: -0.00977970450525 - - Total energy: -74.16183134525791 - - outer SCF iter = 1 RMS gradient = 0.81E-06 energy = -74.1618313453 - outer SCF loop converged in 1 iterations or 47 steps + Integrated absolute spin density : 58.8663280160 + Ideal and single determinant S**2 : 0.000000 29.993294 !-----------------------------------------------------------------------------! Mulliken Population Analysis - # Atom Element Kind Atomic population Net charge - 1 C 1 3.984867 0.015133 - 2 C 1 4.077879 -0.077879 - 3 C 1 3.913577 0.086423 - 4 H 2 0.898355 0.101645 - 5 O 3 6.208620 -0.208620 - 6 C 1 4.255056 -0.255056 - 7 H 2 0.878166 0.121834 - 8 H 2 0.895576 0.104424 - 9 O 3 6.133234 -0.133234 - 10 O 3 6.093371 -0.093371 - 11 H 2 0.894525 0.105475 - 12 H 2 0.886697 0.113303 - 13 H 2 0.880075 0.119925 - # Total charge 40.000000 0.000000 + # Atom Element Kind Atomic population (alpha,beta) Net charge Spin moment + 1 Fe 1 9.198415 4.240345 2.561240 4.958071 + 2 Fe 2 4.240344 9.198416 2.561240 -4.958072 + 3 Fe 1 9.198415 4.240345 2.561240 4.958071 + 4 Fe 2 4.240344 9.198416 2.561240 -4.958072 + 5 Fe 1 9.198399 4.240321 2.561279 4.958078 + 6 Fe 2 4.240321 9.198399 2.561280 -4.958079 + 7 Fe 1 9.198413 4.240337 2.561250 4.958076 + 8 Fe 2 4.240336 9.198413 2.561251 -4.958077 + 9 Fe 1 9.198413 4.240337 2.561250 4.958076 + 10 Fe 2 4.240336 9.198413 2.561251 -4.958077 + 11 Fe 1 9.198399 4.240321 2.561279 4.958078 + 12 Fe 2 4.240321 9.198399 2.561280 -4.958079 + 13 O 3 3.853738 3.853757 -1.707495 -0.000019 + 14 O 3 3.853764 3.853764 -1.707528 0.000000 + 15 O 3 3.853757 3.853738 -1.707495 0.000019 + 16 O 3 3.853764 3.853764 -1.707528 0.000000 + 17 O 3 3.853757 3.853738 -1.707495 0.000019 + 18 O 3 3.853738 3.853757 -1.707495 -0.000019 + 19 O 3 3.853736 3.853756 -1.707492 -0.000019 + 20 O 3 3.853764 3.853763 -1.707528 0.000001 + 21 O 3 3.853755 3.853737 -1.707492 0.000017 + 22 O 3 3.853764 3.853764 -1.707528 -0.000000 + 23 O 3 3.853756 3.853736 -1.707492 0.000020 + 24 O 3 3.853738 3.853755 -1.707492 -0.000017 + 25 O 3 3.853738 3.853755 -1.707492 -0.000017 + 26 O 3 3.853764 3.853764 -1.707528 -0.000000 + 27 O 3 3.853756 3.853736 -1.707492 0.000020 + 28 O 3 3.853764 3.853763 -1.707528 0.000001 + 29 O 3 3.853755 3.853737 -1.707492 0.000017 + 30 O 3 3.853736 3.853756 -1.707492 -0.000019 + # Total charge and spin 150.000000 150.000000 0.000000 -0.000000 !-----------------------------------------------------------------------------! !-----------------------------------------------------------------------------! Hirshfeld Charges - #Atom Element Kind Ref Charge Population Net charge - 1 C 1 4.000 3.350 0.650 - 2 C 1 4.000 3.767 0.233 - 3 C 1 4.000 3.835 0.165 - 4 H 2 1.000 0.952 0.048 - 5 O 3 6.000 6.476 -0.476 - 6 C 1 4.000 4.086 -0.086 - 7 H 2 1.000 0.909 0.091 - 8 H 2 1.000 0.929 0.071 - 9 O 3 6.000 6.428 -0.428 - 10 O 3 6.000 6.407 -0.407 - 11 H 2 1.000 0.961 0.039 - 12 H 2 1.000 0.952 0.048 - 13 H 2 1.000 0.948 0.052 + #Atom Element Kind Ref Charge Population Spin moment Net charge + 1 Fe 1 16.000 10.314 5.463 4.851 0.223 + 2 Fe 2 16.000 5.463 10.314 -4.851 0.223 + 3 Fe 1 16.000 10.314 5.463 4.851 0.223 + 4 Fe 2 16.000 5.463 10.314 -4.851 0.223 + 5 Fe 1 16.000 10.314 5.463 4.851 0.223 + 6 Fe 2 16.000 5.463 10.314 -4.851 0.223 + 7 Fe 1 16.000 10.314 5.463 4.851 0.223 + 8 Fe 2 16.000 5.463 10.314 -4.851 0.223 + 9 Fe 1 16.000 10.314 5.463 4.851 0.223 + 10 Fe 2 16.000 5.463 10.314 -4.851 0.223 + 11 Fe 1 16.000 10.314 5.463 4.851 0.223 + 12 Fe 2 16.000 5.463 10.314 -4.851 0.223 + 13 O 3 6.000 3.074 3.074 -0.000 -0.148 + 14 O 3 6.000 3.074 3.074 0.000 -0.148 + 15 O 3 6.000 3.074 3.074 0.000 -0.148 + 16 O 3 6.000 3.074 3.074 0.000 -0.148 + 17 O 3 6.000 3.074 3.074 0.000 -0.148 + 18 O 3 6.000 3.074 3.074 -0.000 -0.148 + 19 O 3 6.000 3.074 3.074 -0.000 -0.148 + 20 O 3 6.000 3.074 3.074 0.000 -0.148 + 21 O 3 6.000 3.074 3.074 0.000 -0.148 + 22 O 3 6.000 3.074 3.074 -0.000 -0.148 + 23 O 3 6.000 3.074 3.074 0.000 -0.148 + 24 O 3 6.000 3.074 3.074 -0.000 -0.148 + 25 O 3 6.000 3.074 3.074 -0.000 -0.148 + 26 O 3 6.000 3.074 3.074 -0.000 -0.148 + 27 O 3 6.000 3.074 3.074 0.000 -0.148 + 28 O 3 6.000 3.074 3.074 0.000 -0.148 + 29 O 3 6.000 3.074 3.074 0.000 -0.148 + 30 O 3 6.000 3.074 3.074 -0.000 -0.148 Total Charge 0.000 !-----------------------------------------------------------------------------! - Trace(PS): 40.0000000000 - Electronic density on regular grids: -40.0000000000 0.0000000000 - Core density on regular grids: 40.0000000000 -0.0000000000 - Total charge density on r-space grids: -0.0000000000 - Total charge density g-space grids: -0.0000000000 + *** WARNING in dft_plus_u.F:1457 :: DFT+U energy contibution is negative *** + *** possibly due to unphysical Mulliken charges. Check your input, if *** + *** this warning persists or try a different method! *** + + *** WARNING in dft_plus_u.F:1457 :: DFT+U energy contibution is negative *** + *** possibly due to unphysical Mulliken charges. Check your input, if *** + *** this warning persists or try a different method! *** - ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -74.161831345521179 + + ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -1766.225653832774242 ATOMIC FORCES in [a.u.] # Atom Kind Element X Y Z - 1 1 C -0.02543205 0.04647274 -0.04576210 - 2 1 C -0.02384518 0.04070368 -0.06382020 - 3 1 C 0.02413716 0.00267013 -0.01594700 - 4 2 H 0.02331229 -0.00303660 0.01752014 - 5 3 O -0.00330258 -0.00031879 0.01926047 - 6 1 C -0.01124607 -0.02554273 0.02814433 - 7 2 H -0.01321314 0.01947427 0.01821504 - 8 2 H -0.01528903 -0.00477150 0.01334457 - 9 3 O 0.00705728 0.00564402 0.03059922 - 10 3 O 0.03607999 -0.08625169 0.01012960 - 11 2 H -0.00531559 -0.01159595 -0.00486571 - 12 2 H -0.01370828 -0.00250871 -0.00716084 - 13 2 H 0.02104090 0.01869862 0.00050029 - SUM OF ATOMIC FORCES 0.00027571 -0.00036251 0.00015781 0.00048201 + 1 1 Fe 0.00021561 0.00034116 0.00317438 + 2 2 Fe -0.00021697 -0.00027978 0.00317440 + 3 1 Fe -0.00017983 -0.00032126 -0.00315870 + 4 2 Fe 0.00018114 0.00029976 -0.00315876 + 5 1 Fe 0.00017702 0.00029234 0.00344790 + 6 2 Fe -0.00019383 -0.00022206 0.00344792 + 7 1 Fe -0.00015795 -0.00026945 -0.00342977 + 8 2 Fe 0.00014710 0.00025482 -0.00342982 + 9 1 Fe 0.00019366 0.00028930 0.00344520 + 10 2 Fe -0.00018286 -0.00023491 0.00344521 + 11 1 Fe -0.00014131 -0.00027253 -0.00343196 + 12 2 Fe 0.00015806 0.00024194 -0.00343201 + 13 3 O 0.01425438 -0.00005072 -0.00001088 + 14 3 O -0.00708841 -0.01231098 0.00004367 + 15 3 O -0.00713118 0.01235320 0.00000748 + 16 3 O 0.00709789 0.01231643 -0.00001565 + 17 3 O 0.00712170 -0.01234776 0.00002053 + 18 3 O -0.01425432 0.00002189 0.00003555 + 19 3 O 0.01182370 -0.00334309 -0.00003683 + 20 3 O -0.00879899 -0.00851906 0.00001763 + 21 3 O -0.00295797 0.01180748 0.00001105 + 22 3 O 0.00297960 0.01189104 -0.00001362 + 23 3 O 0.00875765 -0.00859646 -0.00000546 + 24 3 O -0.01169411 -0.00334302 0.00001109 + 25 3 O 0.01170457 0.00329778 -0.00007042 + 26 3 O -0.00296861 -0.01189738 -0.00001440 + 27 3 O -0.00875812 0.00859734 0.00000546 + 28 3 O 0.00879946 0.00851995 -0.00001764 + 29 3 O 0.00294698 -0.01181382 -0.00003905 + 30 3 O -0.01183406 0.00329784 -0.00002250 + SUM OF ATOMIC FORCES 0.00000000 0.00000000 -0.00000000 0.00000000 + + STRESS TENSOR [GPa] + + X Y Z + X -7.95728223 -0.07686533 0.00049141 + Y -0.07686533 -8.05678106 -0.01863861 + Z 0.00049141 -0.01863861 -8.18444753 + + 1/3 Trace(stress tensor): -8.06617027E+00 + + Det(stress tensor) : -5.24654468E+02 + + + EIGENVECTORS AND EIGENVALUES OF THE STRESS TENSOR + + -8.18769093 -8.09567402 -7.91514587 + + 0.05548079 0.47828752 0.87644905 + 0.17259431 0.85999286 -0.48023273 + 0.98342925 -0.17791381 0.03483662 ------------------------------------------------------------------------------- - - @@ -2034,67 +1353,118 @@ - - ------------------------------------------------------------------------------- COUNTER TOTAL BLAS SMM ACC - flops 5 x 20 x 20 24000 100.0% 0.0% 0.0% - flops 13 x 20 x 20 72800 100.0% 0.0% 0.0% - flops 5 x 5 x 20 1050000 100.0% 0.0% 0.0% - flops 5 x 13 x 20 2730000 100.0% 0.0% 0.0% - flops 13 x 5 x 20 2730000 100.0% 0.0% 0.0% - flops 54 x 20 x 5 3110400 100.0% 0.0% 0.0% - flops 5 x 20 x 5 3636000 100.0% 0.0% 0.0% - flops 67 x 20 x 5 3859200 100.0% 0.0% 0.0% - flops 20 x 20 x 5 4512000 100.0% 0.0% 0.0% - flops 20 x 20 x 20 6672000 100.0% 0.0% 0.0% - flops 54 x 20 x 13 9434880 100.0% 0.0% 0.0% - flops 13 x 13 x 20 9464000 100.0% 0.0% 0.0% - flops 54 x 20 x 20 10108800 100.0% 0.0% 0.0% - flops 5 x 20 x 13 11029200 100.0% 0.0% 0.0% - flops 13 x 20 x 5 11029200 100.0% 0.0% 0.0% - flops 67 x 20 x 13 11706240 100.0% 0.0% 0.0% - flops 67 x 20 x 20 12542400 100.0% 0.0% 0.0% - flops 20 x 20 x 13 13686400 100.0% 0.0% 0.0% - flops 13 x 20 x 13 33455240 100.0% 0.0% 0.0% - flops total 150.852760E+06 100.0% 0.0% 0.0% - flops max/rank 87.058120E+06 100.0% 0.0% 0.0% + flops 22 x 22 x 26 100672 0.0% 100.0% 0.0% + flops 22 x 22 x 52 201344 0.0% 100.0% 0.0% + flops 32 x 22 x 26 292864 0.0% 100.0% 0.0% + flops 22 x 32 x 26 292864 0.0% 100.0% 0.0% + flops 64 x 22 x 22 371712 0.0% 100.0% 0.0% + flops 86 x 22 x 22 499488 0.0% 100.0% 0.0% + flops 32 x 22 x 52 585728 0.0% 100.0% 0.0% + flops 22 x 32 x 52 585728 0.0% 100.0% 0.0% + flops 22 x 22 x 39 755040 0.0% 100.0% 0.0% + flops 64 x 22 x 26 878592 0.0% 100.0% 0.0% + flops 13 x 22 x 22 906048 0.0% 100.0% 0.0% + flops 86 x 22 x 26 1180608 0.0% 100.0% 0.0% + flops 26 x 22 x 22 1208064 0.0% 100.0% 0.0% + flops 64 x 22 x 52 1757184 0.0% 100.0% 0.0% + flops 32 x 32 x 26 2129920 0.0% 100.0% 0.0% + flops 64 x 22 x 32 2162688 0.0% 100.0% 0.0% + flops 64 x 32 x 22 2162688 0.0% 100.0% 0.0% + flops 32 x 22 x 39 2196480 0.0% 100.0% 0.0% + flops 22 x 32 x 39 2196480 0.0% 100.0% 0.0% + flops 86 x 22 x 52 2361216 0.0% 100.0% 0.0% + flops 13 x 32 x 22 2635776 0.0% 100.0% 0.0% + flops 13 x 22 x 32 2635776 0.0% 100.0% 0.0% + flops 86 x 32 x 22 2906112 0.0% 100.0% 0.0% + flops 86 x 22 x 32 2906112 0.0% 100.0% 0.0% + flops 273 x 22 x 22 3171168 0.0% 100.0% 0.0% + flops 26 x 32 x 22 3514368 0.0% 100.0% 0.0% + flops 26 x 22 x 32 3514368 0.0% 100.0% 0.0% + flops 32 x 32 x 52 4259840 0.0% 100.0% 0.0% + flops 273 x 22 x 26 4996992 0.0% 100.0% 0.0% + flops 64 x 32 x 26 5111808 0.0% 100.0% 0.0% + flops 64 x 22 x 39 6589440 0.0% 100.0% 0.0% + flops 86 x 32 x 26 6868992 0.0% 100.0% 0.0% + flops 86 x 22 x 39 8854560 0.0% 100.0% 0.0% + flops 273 x 22 x 52 9993984 0.0% 100.0% 0.0% + flops 13 x 13 x 22 10172448 0.0% 100.0% 0.0% + flops 64 x 32 x 52 10223616 0.0% 100.0% 0.0% + flops 64 x 32 x 32 12582912 0.0% 100.0% 0.0% + flops 26 x 13 x 22 12849408 0.0% 100.0% 0.0% + flops 13 x 26 x 22 12849408 0.0% 100.0% 0.0% + flops 86 x 32 x 52 13737984 0.0% 100.0% 0.0% + flops 32 x 32 x 39 15974400 0.0% 100.0% 0.0% + flops 86 x 32 x 32 16908288 0.0% 100.0% 0.0% + flops 273 x 32 x 22 18450432 0.0% 100.0% 0.0% + flops 273 x 22 x 32 18450432 0.0% 100.0% 0.0% + flops 26 x 26 x 22 18560256 0.0% 100.0% 0.0% + flops 13 x 32 x 32 19169280 0.0% 100.0% 0.0% + flops 26 x 32 x 32 25559040 0.0% 100.0% 0.0% + flops 273 x 32 x 26 29073408 0.0% 100.0% 0.0% + flops 273 x 22 x 39 37477440 0.0% 100.0% 0.0% + flops 64 x 32 x 39 38338560 0.0% 100.0% 0.0% + flops 13 x 22 x 13 45776016 0.0% 100.0% 0.0% + flops 86 x 32 x 39 51517440 0.0% 100.0% 0.0% + flops 273 x 32 x 52 58146816 0.0% 100.0% 0.0% + flops 13 x 13 x 32 59185152 0.0% 100.0% 0.0% + flops 26 x 22 x 13 61034688 0.0% 100.0% 0.0% + flops 13 x 22 x 26 61034688 0.0% 100.0% 0.0% + flops 26 x 13 x 32 74760192 0.0% 100.0% 0.0% + flops 13 x 26 x 32 74760192 0.0% 100.0% 0.0% + flops 26 x 22 x 26 81379584 0.0% 100.0% 0.0% + flops 273 x 32 x 32 107347968 0.0% 100.0% 0.0% + flops 26 x 26 x 32 107986944 0.0% 100.0% 0.0% + flops 273 x 32 x 39 218050560 0.0% 100.0% 0.0% + flops 13 x 32 x 13 266333184 0.0% 100.0% 0.0% + flops 26 x 32 x 13 355110912 0.0% 100.0% 0.0% + flops 13 x 32 x 26 355110912 0.0% 100.0% 0.0% + flops 26 x 32 x 26 473481216 0.0% 100.0% 0.0% + flops inhomo. stacks 0 0.0% 0.0% 0.0% + flops total 2.852178E+09 0.0% 100.0% 0.0% + flops max/rank 282.340320E+06 0.0% 100.0% 0.0% matmuls inhomo. stacks 0 0.0% 0.0% 0.0% - matmuls total 26209 100.0% 0.0% 0.0% - number of processed stacks 12233 100.0% 0.0% 0.0% - average stack size 2.1 0.0 0.0 - marketing flops 164.257696E+06 + matmuls total 108320 0.0% 100.0% 0.0% + number of processed stacks 16588 0.0% 100.0% 0.0% + average stack size 0.0 6.5 0.0 + marketing flops 3.304377E+09 ------------------------------------------------------------------------------- - # multiplications 1040 - max memory usage/rank 311.861248E+06 + # multiplications 57 + max memory usage/rank 120.508416E+06 # max total images/rank 7 - # MPI messages exchanged 3028480 - # MPI messages filtered 0 - MPI messages size (elements): - total size 60.974020E+06 + # max 3D layers 1 + # MPI messages exchanged 165984 + MPI messages size (bytes): + total size 1.314490E+09 min size 0.000000E+00 - max size 1.340000E+03 - average size 20.133539E+00 + max size 113.568000E+03 + average size 7.919377E+03 MPI breakdown and total messages size (bytes): - size <= 128 2859636 0 - 128 < size <= 8192 161434 416063336 - 8192 < size <= 32768 7410 71728800 - 32768 < size <= 131072 0 0 + size <= 128 111410 0 + 128 < size <= 8192 14196 96515744 + 8192 < size <= 32768 29458 344122688 + 32768 < size <= 131072 10920 873851680 131072 < size <= 4194304 0 0 4194304 < size <= 16777216 0 0 16777216 < size 0 0 ------------------------------------------------------------------------------- - Warning: using a non-square number of MPI ranks might lead to poor performance. - used ranks: 28 - suggested : 25 49 + + *** WARNING in dbcsr/mm/dbcsr_mm.F:268 :: Using a non-square number of *** + *** MPI ranks might lead to poor performance. *** + *** Used ranks: 28 *** + *** Suggested: 25 49 *** + ------------------------------------------------------------------------------- - - MEMORY| Estimated peak process memory [MiB] 298 + + MEMORY| Estimated peak process memory [MiB] 116 ------------------------------------------------------------------------------- ---- MULTIGRID INFO ---- ------------------------------------------------------------------------------- - count for grid 1: 110888 cutoff [a.u.] 250.00 - count for grid 2: 67832 cutoff [a.u.] 83.33 - count for grid 3: 38068 cutoff [a.u.] 27.78 - count for grid 4: 7104 cutoff [a.u.] 9.26 - total gridlevel count : 223892 + count for grid 1: 1237230 cutoff [a.u.] 200.00 + count for grid 2: 263362 cutoff [a.u.] 66.67 + count for grid 3: 171414 cutoff [a.u.] 22.22 + count for grid 4: 34210 cutoff [a.u.] 7.41 + total gridlevel count : 1706216 ------------------------------------------------------------------------------- - - @@ -2102,20 +1472,20 @@ - - ------------------------------------------------------------------------------- - ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s] - MP_Group 5 0.000 - MP_Bcast 2370 0.009 120247. 30442.16 - MP_Allreduce 8751 1.290 181. 1.23 - MP_Sync 51 0.003 - MP_Alltoall 4123 1.548 1382531. 3682.81 - MP_SendRecv 876 0.907 355083. 342.97 - MP_ISendRecv 5184 0.013 83700. 34235.90 - MP_Wait 145452 2.740 - MP_comm_split 47 0.001 - MP_ISend 230604 0.097 10294. 24486.66 - MP_IRecv 227748 0.046 10386. 51680.72 - MP_Recv 27 0.000 1936. 2128.59 - MP_Memory 153498 0.028 + ROUTINE CALLS AVE VOLUME [Bytes] + MP_Group 28 + MP_Bcast 1208 431092. + MP_Allreduce 3663 449. + MP_Sync 6 + MP_Alltoall 678 1547382. + MP_SendRecv 108 2586. + MP_ISendRecv 999 111920. + MP_Wait 8295 + MP_comm_split 2 + MP_ISend 12520 5845. + MP_IRecv 12448 5670. + MP_Recv 26 48048. + MP_Memory 7740 ------------------------------------------------------------------------------- @@ -2125,7 +1495,7 @@ - - ------------------------------------------------------------------------------- - CP2K version 4.1, the CP2K developers group (2016). + CP2K version 6.1, the CP2K developers group (2018). CP2K is freely available from https://www.cp2k.org/ . Schuett, Ole; Messmer, Peter; Hutter, Juerg; VandeVondele, Joost. @@ -2160,6 +1530,13 @@ http://dx.doi.org/10.1063/1.3382344 + VandeVondele, J; Hutter, J. + JOURNAL OF CHEMICAL PHYSICS, 127 (11), 114105 (2007). + Gaussian basis sets for accurate calculations on molecular systems in + gas and condensed phases. + http://dx.doi.org/10.1063/1.2770708 + + Krack, M. THEORETICAL CHEMISTRY ACCOUNTS, 114 (1-3), 145-152 (2005). Pseudopotentials for H to Kr optimized for gradient-corrected @@ -2193,29 +1570,36 @@ http://dx.doi.org/10.1103/PhysRevB.58.3641 + Dudarev, SL; Botton, GA; Savrasov, SY; Humphreys, CJ; Sutton, AP. + PHYSICAL REVIEW B, 57 (3), 1505-1509 (1998). + Electron-energy-loss spectra and the structural stability of + nickel oxide: An LSDA+U study. + http://dx.doi.org/10.1103/PhysRevB.57.1505 + + 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 + Dudarev, SL; Manh, DN; Sutton, AP. + PHILOSOPHICAL MAGAZINE B, 75 (5), 613-628 (1997). + Effect of Mott-Hubbard correlations on the electronic + structure and structural stability of uranium dioxide. + http://dx.doi.org/10.1080/13642819708202343 - BECKE, AD. PHYSICAL REVIEW A, 38 (6), 3098-3100 (1988). - DENSITY-FUNCTIONAL EXCHANGE-ENERGY APPROXIMATION WITH CORRECT - ASYMPTOTIC-BEHAVIOR. - http://dx.doi.org/10.1103/PhysRevA.38.3098 + Perdew, JP; Burke, K; Ernzerhof, M. + PHYSICAL REVIEW LETTERS, 77 (18), 3865-3868 (1996). + Generalized gradient approximation made simple. + http://dx.doi.org/10.1103/PhysRevLett.77.3865 - LEE, CT; YANG, WT; PARR, RG. - PHYSICAL REVIEW B, 37 (2), 785-789 (1988). - DEVELOPMENT OF THE COLLE-SALVETTI CORRELATION-ENERGY FORMULA INTO A - FUNCTIONAL OF THE ELECTRON-DENSITY. - http://dx.doi.org/10.1103/PhysRevB.37.785 + 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 ------------------------------------------------------------------------------- @@ -2225,64 +1609,49 @@ ------------------------------------------------------------------------------- SUBROUTINE CALLS ASD SELF TIME TOTAL TIME MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM - CP2K 1 1.0 0.019 0.025 39.922 39.924 - qs_forces 1 2.0 0.000 0.000 39.637 39.637 - qs_energies 1 3.0 0.000 0.000 38.957 38.957 - scf_env_do_scf 1 4.0 0.000 0.000 38.327 38.327 - scf_env_do_scf_inner_loop 47 5.0 0.001 0.005 37.802 37.802 - rebuild_ks_matrix 48 6.9 0.000 0.000 23.473 23.482 - qs_ks_build_kohn_sham_matrix 48 7.9 0.007 0.019 23.473 23.482 - qs_ks_update_qs_env 48 6.0 0.001 0.001 22.800 22.809 - pw_transfer 577 10.1 0.036 0.046 14.984 16.075 - fft_wrap_pw1pw2 481 11.2 0.004 0.005 14.528 15.602 - fft_wrap_pw1pw2_250 193 11.7 1.131 1.163 13.168 14.450 - qs_rho_update_rho 48 6.0 0.000 0.000 13.711 13.711 - calculate_rho_elec 48 7.0 0.274 1.101 13.711 13.711 - fft3d_ps 481 13.2 7.329 8.819 11.213 12.356 - density_rs2pw 48 8.0 0.002 0.003 11.575 12.218 - sum_up_and_integrate 48 8.9 0.228 0.259 10.386 10.429 - integrate_v_rspace 48 9.9 0.141 0.758 10.158 10.205 - rs_pw_transfer 388 10.4 0.004 0.005 9.600 9.797 - potential_pw2rs 48 10.9 0.021 0.022 9.421 9.433 - qs_vxc_create 48 8.9 0.001 0.002 7.730 7.831 - xc_vxc_pw_create 48 9.9 0.492 0.555 7.729 7.829 - pw_nn_compose_r 384 11.4 4.267 4.305 5.466 5.844 - xc_rho_set_and_dset_create 48 10.9 0.570 0.626 4.004 4.710 - rs_pw_transfer_PW2RS_250 50 12.8 1.750 1.811 3.392 3.494 - mp_waitany 6464 12.4 2.891 3.200 2.891 3.200 - rs_pw_transfer_RS2PW_250 50 9.9 1.491 1.642 2.775 2.984 - mp_alltoall_z22v 481 15.2 2.139 2.779 2.139 2.779 - rs_grid_zero 292 10.0 2.509 2.571 2.509 2.571 - dbcsr_multiply_generic 1040 11.1 0.024 0.026 1.794 2.384 - x_to_yz 240 14.8 1.019 1.087 2.154 2.252 - yz_to_x 241 13.6 0.717 0.847 1.720 1.981 - qs_scf_new_mos 47 6.0 0.000 0.000 1.844 1.846 - qs_scf_loop_do_ot 47 7.0 0.000 0.000 1.844 1.846 - ot_scf_mini 47 8.0 0.001 0.001 1.759 1.761 - rs_pw_transfer_PW2RS_90 48 12.9 0.579 0.614 1.488 1.608 - mp_sendrecv_dm2 768 12.4 1.200 1.590 1.200 1.590 - fft_wrap_pw1pw2_90 96 12.5 0.080 0.101 1.141 1.498 - pw_poisson_solve 48 8.9 0.890 0.904 1.376 1.377 - mp_sum_d 2457 10.1 0.852 1.334 0.852 1.334 - make_m2s 2080 12.1 0.026 0.026 0.646 1.215 - pw_scatter_p 240 13.8 1.113 1.188 1.113 1.188 - ot_mini 47 9.0 0.000 0.000 1.171 1.173 - rs_pw_transfer_RS2PW_90 48 10.0 0.663 0.697 1.130 1.154 - xc_functional_eval 96 11.9 0.001 0.001 0.540 1.082 - qs_ot_get_derivative 47 10.0 0.001 0.001 1.057 1.059 - make_images 2080 13.1 0.130 0.140 0.455 1.027 - pw_gather_p 241 12.6 0.970 1.016 0.970 1.016 - multiply_cannon 1040 12.1 0.137 0.145 0.885 0.972 - mp_waitall_1 138988 14.3 0.603 0.825 0.603 0.825 - qs_ot_get_derivative_diag 46 11.0 0.002 0.002 0.807 0.808 + CP2K 1 1.0 0.006 0.019 9.191 9.198 + qs_forces 1 2.0 0.000 0.000 8.755 8.755 + rebuild_ks_matrix 2 5.5 0.000 0.000 4.942 4.943 + qs_ks_build_kohn_sham_matrix 2 6.5 0.000 0.000 4.942 4.942 + sum_up_and_integrate 2 7.5 0.000 0.000 4.392 4.784 + integrate_v_rspace 4 8.5 3.939 4.722 4.391 4.784 + qs_energies 1 3.0 0.000 0.000 4.781 4.781 + qs_ks_update_qs_env_forces 1 3.0 0.000 0.000 3.376 3.376 + scf_env_do_scf 1 4.0 0.000 0.000 3.103 3.103 + qs_rho_update_rho 2 6.0 0.000 0.000 2.660 2.660 + calculate_rho_elec 4 7.0 2.168 2.582 2.660 2.660 + init_scf_loop 1 5.0 0.000 0.000 1.668 1.668 + qs_ks_update_qs_env 2 6.0 0.000 0.000 1.567 1.567 + scf_env_do_scf_inner_loop 1 5.0 0.000 0.000 1.420 1.432 + init_scf_run 1 4.0 0.000 0.000 1.391 1.391 + scf_env_initial_rho_setup 1 5.0 0.000 0.000 1.391 1.391 + mp_sum_d 925 6.6 0.497 0.965 0.497 0.965 + rs_pw_transfer 37 9.5 0.000 0.000 0.556 0.939 + mp_waitall_1 8295 12.8 0.516 0.910 0.516 0.910 + pw_transfer 71 9.6 0.002 0.003 0.517 0.900 + fft_wrap_pw1pw2 67 10.7 0.000 0.000 0.514 0.897 + fft_wrap_pw1pw2_200 43 11.6 0.008 0.010 0.506 0.889 + fft3d_ps 67 12.7 0.050 0.060 0.490 0.874 + rs_pw_transfer_RS2PW_200 6 9.5 0.018 0.021 0.481 0.863 + density_rs2pw 4 8.0 0.000 0.000 0.477 0.856 + potential_pw2rs 4 9.5 0.000 0.000 0.452 0.832 + mp_alltoall_z22v 67 14.7 0.430 0.816 0.430 0.816 + yz_to_x 25 13.4 0.003 0.004 0.422 0.808 + plus_u 3 6.0 0.000 0.000 0.400 0.778 + mulliken 3 7.0 0.000 0.001 0.399 0.778 + build_core_hamiltonian_matrix_ 1 3.0 0.000 0.000 0.524 0.597 + build_core_ppnl_forces 1 4.0 0.298 0.333 0.298 0.333 + qs_init_subsys 1 2.0 0.001 0.002 0.295 0.296 + qs_energies_init_hamiltonians 1 4.0 0.000 0.000 0.212 0.212 + calculate_ecore_overlap 2 4.0 0.000 0.000 0.074 0.193 ------------------------------------------------------------------------------- - The number of warnings for this run is : 1 + The number of warnings for this run is : 5 ------------------------------------------------------------------------------- - **** **** ****** ** PROGRAM ENDED AT 2019-08-10 12:44:21.899 - ***** ** *** *** ** PROGRAM RAN ON c038 - ** **** ****** PROGRAM RAN BY fengw - ***** ** ** ** ** PROGRAM PROCESS ID 21094 - **** ** ******* ** PROGRAM STOPPED IN /data/fengw/PC-LiTFSI/energy/BLYP/0.3 - 7_CBM_VBM/KS/29000/test + **** **** ****** ** PROGRAM ENDED AT 2020-08-14 06:10:02.425 + ***** ** *** *** ** PROGRAM RAN ON c026.hpc.xmu + ** **** ****** PROGRAM RAN BY ch2_101 + ***** ** ** ** ** PROGRAM PROCESS ID 19586 + **** ** ******* ** PROGRAM STOPPED IN /data/ch2_101/ybzhuang/project02/prin + t_stress/small_system diff --git a/tests/cp2k/ref_cell b/tests/cp2k/ref_cell index 555d04d38..0ad570a93 100644 --- a/tests/cp2k/ref_cell +++ b/tests/cp2k/ref_cell @@ -1,3 +1,3 @@ - 16.509 0.000 0.000 - 0.000 16.509 0.000 - 0.000 0.000 16.509 +5.038000000000000256e+00 0.000000000000000000e+00 0.000000000000000000e+00 +-2.519000000000000128e+00 4.363000000000000433e+00 0.000000000000000000e+00 +0.000000000000000000e+00 0.000000000000000000e+00 1.377200000000000024e+01 diff --git a/tests/cp2k/ref_coord b/tests/cp2k/ref_coord index e8653d15a..bdb94d354 100644 --- a/tests/cp2k/ref_coord +++ b/tests/cp2k/ref_coord @@ -1,13 +1,30 @@ - 8.502557 13.615841 13.959087 - 7.337961 15.436979 13.231602 - 7.898228 15.711577 14.610790 - 6.191067 15.347699 13.085878 - 7.966143 14.222136 12.790193 - 7.734765 16.557145 12.069222 - 7.130790 15.862453 15.339187 - 8.737614 16.468567 14.497932 - 8.496264 14.451055 14.990319 - 8.899322 12.523607 13.901094 - 7.514778 17.615787 12.389690 - 8.850553 16.479587 11.921136 - 7.059051 16.153899 11.247693 +0.000000000000000000e+00 0.000000000000000000e+00 1.992807999999999913e+00 +0.000000000000000000e+00 0.000000000000000000e+00 8.878807999999999367e+00 +0.000000000000000000e+00 0.000000000000000000e+00 1.177919200000000011e+01 +0.000000000000000000e+00 0.000000000000000000e+00 4.893191999999999986e+00 +2.519000000000000128e+00 1.454344999999999999e+00 6.583474999999999966e+00 +2.519000000000000128e+00 1.454344999999999999e+00 1.346947499999999920e+01 +2.519000000000000128e+00 1.454344999999999999e+00 2.597858000000000001e+00 +2.519000000000000128e+00 1.454344999999999999e+00 9.483857999999999677e+00 +0.000000000000000000e+00 2.908691000000000138e+00 1.117414199999999980e+01 +0.000000000000000000e+00 2.908691000000000138e+00 4.288141999999999676e+00 +0.000000000000000000e+00 2.908691000000000138e+00 7.188525000000000276e+00 +0.000000000000000000e+00 2.908691000000000138e+00 3.025249999999999884e-01 +1.541123999999999938e+00 0.000000000000000000e+00 3.443000000000000060e+00 +1.748437999999999937e+00 3.028382999999999825e+00 3.443000000000000060e+00 +-7.705619999999999692e-01 1.334653000000000089e+00 3.443000000000000060e+00 +7.705619999999999692e-01 1.334653000000000089e+00 1.032900000000000063e+01 +-1.748437999999999937e+00 3.028382999999999825e+00 1.032900000000000063e+01 +3.496875999999999873e+00 0.000000000000000000e+00 1.032900000000000063e+01 +4.060124000000000066e+00 1.454344999999999999e+00 8.033666999999999447e+00 +1.748437999999999937e+00 1.196929999999999938e-01 8.033666999999999447e+00 +1.748437999999999937e+00 2.788997999999999866e+00 8.033666999999999447e+00 +3.289562000000000097e+00 2.788997999999999866e+00 1.147666999999999993e+00 +3.289562000000000097e+00 1.196929999999999938e-01 1.147666999999999993e+00 +9.778759999999999675e-01 1.454344999999999999e+00 1.147666999999999993e+00 +1.541123999999999938e+00 2.908691000000000138e+00 1.262433300000000003e+01 +-7.705619999999999692e-01 1.574038000000000048e+00 1.262433300000000003e+01 +-7.705619999999999692e-01 4.243343000000000309e+00 1.262433300000000003e+01 +7.705619999999999692e-01 4.243343000000000309e+00 5.738332999999999906e+00 +7.705619999999999692e-01 1.574038000000000048e+00 5.738332999999999906e+00 +-1.541123999999999938e+00 2.908691000000000138e+00 5.738332999999999906e+00 diff --git a/tests/cp2k/ref_force b/tests/cp2k/ref_force index f0b57d2ac..2f96c3e9f 100644 --- a/tests/cp2k/ref_force +++ b/tests/cp2k/ref_force @@ -1,13 +1,30 @@ - -0.02543205 0.04647274 -0.04576210 - -0.02384518 0.04070368 -0.06382020 - 0.02413716 0.00267013 -0.01594700 - 0.02331229 -0.00303660 0.01752014 - -0.00330258 -0.00031879 0.01926047 - -0.01124607 -0.02554273 0.02814433 - -0.01321314 0.01947427 0.01821504 - -0.01528903 -0.00477150 0.01334457 - 0.00705728 0.00564402 0.03059922 - 0.03607999 -0.08625169 0.01012960 - -0.00531559 -0.01159595 -0.00486571 - -0.01370828 -0.00250871 -0.00716084 - 0.02104090 0.01869862 0.00050029 +1.108711104347243244e-02 1.754315107643919860e-02 1.632331689354762083e-01 +-1.115704504940500871e-02 -1.438686483809988904e-02 1.632341973767398868e-01 +-9.247229622687480610e-03 -1.651985201904342809e-02 -1.624268709847241643e-01 +9.314592525460768657e-03 1.541427766055051586e-02 -1.624299563085153109e-01 +9.102733625135616888e-03 1.503272595171249552e-02 1.772981316580334865e-01 +-9.967138507287517935e-03 -1.141878335102030836e-02 1.772991600992972205e-01 +-8.122114880183993121e-03 -1.385567492539143547e-02 -1.763658496524764530e-01 +7.564185494618964889e-03 1.310337014098439390e-02 -1.763684207556357464e-01 +9.958396756545946985e-03 1.487640287962791602e-02 1.771592920874320576e-01 +-9.403038474140203509e-03 -1.207955686295677199e-02 1.771598063080639107e-01 +-7.266451748773662157e-03 -1.401405488000344139e-02 -1.764784639708531777e-01 +8.127771307134422710e-03 1.244105396715236046e-02 -1.764810350740124434e-01 +7.329896290332200692e-01 -2.608127044779564186e-03 -5.594720474606004312e-04 +-3.645006669062679228e-01 -6.330559914380976538e-01 2.245601499320259466e-03 +-3.666999885487210453e-01 6.352270309457986874e-01 3.846370326291628371e-04 +3.649881480652685251e-01 6.333362416824599439e-01 -8.047552888564704155e-04 +3.662125073897204430e-01 -6.349472949220683615e-01 1.055694957202769121e-03 +-7.329865437094289504e-01 1.125628963135344093e-03 1.828054346252237566e-03 +6.079990484889615798e-01 -1.719085852155384786e-01 -1.893874587129955366e-03 +-4.524622197504916121e-01 -4.380676416029138931e-01 9.065709739641898864e-04 +-1.521049202414551660e-01 6.071649826240892445e-01 5.682137982021722485e-04 +1.532171794681622401e-01 6.114618102238877917e-01 -7.003685005894649948e-04 +4.503364316583940985e-01 -4.420477092934883556e-01 -2.807644649940145630e-04 +-6.013352633207245113e-01 -1.719049856711155067e-01 5.702706807296011602e-04 +6.018731381016471094e-01 1.695786515325936605e-01 -3.621141689538187863e-03 +-1.526520509937512038e-01 -6.117878261044852328e-01 -7.404777098743240554e-04 +-4.503606000280913624e-01 4.420929607090918756e-01 2.807644649940145630e-04 +4.524863881201889315e-01 4.381134072391492107e-01 -9.070851945960471414e-04 +1.515397917670441574e-01 -6.074909985046866856e-01 -2.008031567402247114e-03 +-6.085317810635656466e-01 1.695817368563847793e-01 -1.156996421678631662e-03 diff --git a/tests/cp2k/ref_type b/tests/cp2k/ref_type new file mode 100644 index 000000000..4524534da --- /dev/null +++ b/tests/cp2k/ref_type @@ -0,0 +1,30 @@ +0.000000000000000000e+00 +0.000000000000000000e+00 +0.000000000000000000e+00 +0.000000000000000000e+00 +0.000000000000000000e+00 +0.000000000000000000e+00 +0.000000000000000000e+00 +0.000000000000000000e+00 +0.000000000000000000e+00 +0.000000000000000000e+00 +0.000000000000000000e+00 +0.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 +1.000000000000000000e+00 diff --git a/tests/cp2k/ref_virial b/tests/cp2k/ref_virial new file mode 100644 index 000000000..e1cdf306b --- /dev/null +++ b/tests/cp2k/ref_virial @@ -0,0 +1,3 @@ +-1.503469983715443092e+01 -1.452313906973011215e-01 9.284830716600153992e-04 +-1.452313906973011215e-01 -1.522269556232277843e+01 -3.521628347871041259e-02 +9.284830716600153992e-04 -3.521628347871041259e-02 -1.546391197267989526e+01 diff --git a/tests/cp2k/test.py b/tests/cp2k/test.py index 3a9bf48c4..5b299c5ed 100755 --- a/tests/cp2k/test.py +++ b/tests/cp2k/test.py @@ -1,14 +1,29 @@ import dpdata +import numpy as np -cp2k_output = dpdata.LabeledSystem('cp2k_output', fmt = 'cp2k/output') +cp2k_output = dpdata.LabeledSystem('output_40847', fmt = 'cp2k/output') +print("atom name") print(cp2k_output['atom_names']) +print("atom number") print(cp2k_output['atom_numbs']) +print("atom type") print(cp2k_output['atom_types']) +np.savetxt("ref_type", cp2k_output['atom_types']) +print("atom cell") print(cp2k_output['cells']) +np.savetxt("ref_cell", cp2k_output['cells'][0]) +print("atom coord") print(cp2k_output['coords']) +np.savetxt("ref_coord", cp2k_output['coords'][0]) +print("energyies") print(cp2k_output['energies']) +print("forces") print(cp2k_output['forces']) +np.savetxt("ref_force", cp2k_output['forces'][0]) +print("virials") +print(cp2k_output['virials']) +np.savetxt("ref_virial", cp2k_output['virials'][0]) # no virial -cp2k_output.to_deepmd_raw('dpmd_raw') -cp2k_output.to_deepmd_npy('dpmd_npy') +#cp2k_output.to_deepmd_raw('dpmd_raw') +#cp2k_output.to_deepmd_npy('dpmd_npy') diff --git a/tests/test_cp2k_output.py b/tests/test_cp2k_output.py index 5575fd17a..2ed548c12 100644 --- a/tests/test_cp2k_output.py +++ b/tests/test_cp2k_output.py @@ -4,55 +4,46 @@ from context import dpdata class TestCP2KSinglePointEnergy: - def test_atom_names(self) : - self.assertEqual(self.system.data['atom_names'], ['C','H','O']) - def test_atom_numbs(self) : - self.assertEqual(self.system.data['atom_numbs'], [4,6,3]) - def test_atom_types(self) : - ref_type = [0,0,0,1,2,0,1,1,2,2,1,1,1] - ref_type = np.array(ref_type) + def test_atom_names(self): + self.assertEqual(self.system.data['atom_names'], ['Fe','O']) + def test_atom_numbs(self): + self.assertEqual(self.system.data['atom_numbs'], [12,18]) + def test_atom_types(self): + ref_type = np.loadtxt('cp2k/ref_type') for ii in range(ref_type.shape[0]) : self.assertEqual(self.system.data['atom_types'][ii], ref_type[ii]) - def test_cell(self) : - fp = open('cp2k/ref_cell') - cell = [] - for ii in fp : - cell.append([float(jj) for jj in ii.split()]) - cell = np.array(cell) + def test_cell(self): + cell = np.loadtxt('cp2k/ref_cell') for ii in range(cell.shape[0]) : for jj in range(cell.shape[1]) : self.assertEqual(self.system.data['cells'][0][ii][jj], cell[ii][jj]) - fp.close() - def test_coord(self) : - fp = open('cp2k/ref_coord') - coord = [] - for ii in fp : - coord.append([float(jj) for jj in ii.split()]) - coord = np.array(coord) + def test_coord(self): + coord = np.loadtxt('cp2k/ref_coord') for ii in range(coord.shape[0]) : for jj in range(coord.shape[1]) : self.assertEqual(self.system.data['coords'][0][ii][jj], coord[ii][jj]) - fp.close() - def test_force(self) : - eV = 2.72113838565563E+01 - angstrom = 5.29177208590000E-01 - fp = open('cp2k/ref_force') - force = [] - for ii in fp : - force.append([float(jj) for jj in ii.split()]) - force = np.array(force) + def test_force(self): + #eV = 2.72113838565563E+01 + #angstrom = 5.29177208590000E-01 + force = np.loadtxt('cp2k/ref_force') for ii in range(force.shape[0]) : for jj in range(force.shape[1]) : - self.assertEqual(self.system.data['forces'][0][ii][jj], force[ii][jj]*eV/angstrom) - fp.close() + self.assertEqual(self.system.data['forces'][0][ii][jj], force[ii][jj]) + + def test_energy(self): + #eV = 2.72113838565563E+01 + ref_energy = -48061.44424374075 + self.assertEqual(self.system.data['energies'][0], ref_energy) + + def test_virial(self): + virial = np.loadtxt("cp2k/ref_virial") + for ii in range(virial.shape[0]) : + for jj in range(virial.shape[1]) : + self.assertEqual(self.system.data['virials'][0][ii][jj], virial[ii][jj]) - def test_energy(self) : - eV = 2.72113838565563E+01 - ref_energy = -74.161831345521179 - self.assertEqual(self.system.data['energies'][0], ref_energy*eV) From 7c5b719fa937ead8c9adcf1a8e54c4e784c1e230 Mon Sep 17 00:00:00 2001 From: robinzyb Date: Sat, 24 Oct 2020 20:08:47 +0800 Subject: [PATCH 02/19] fix double cell bug and no virial information --- dpdata/cp2k/output.py | 23 +- dpdata/system.py | 4 +- tests/cp2k/cp2k_output_2 | 2288 ++++++++++++++++++++++++++++++++++++++ tests/cp2k/test.py | 45 +- 4 files changed, 2342 insertions(+), 18 deletions(-) create mode 100644 tests/cp2k/cp2k_output_2 diff --git a/dpdata/cp2k/output.py b/dpdata/cp2k/output.py index dc9dae0fb..c29e0e859 100644 --- a/dpdata/cp2k/output.py +++ b/dpdata/cp2k/output.py @@ -220,10 +220,12 @@ def get_frames (fname) : coord = [] force = [] stress = [] + cell_count = 0 coord_count = 0 for idx, ii in enumerate(fp) : - if 'CELL| Vector' in ii : + if ('CELL| Vector' in ii) and (cell_count < 3) : cell.append(ii.split()[4:7]) + cell_count += 1 if 'Atom Kind Element' in ii : coord_flag = True coord_idx = idx @@ -263,7 +265,6 @@ def get_frames (fname) : assert(coord), "cannot find coords" assert(energy), "cannot find energies" assert(force), "cannot find forces" - assert(stress), "cannot find stress" #conver to float array and add extra dimension for nframes cell = np.array(cell) @@ -276,18 +277,24 @@ def get_frames (fname) : force = np.array(force) force = force.astype(np.float) force = force[np.newaxis, :, :] - stress = np.array(stress) - stress = stress.astype(np.float) - stress = stress[np.newaxis, :, :] + + # virial is not necessary + if stress: + stress = np.array(stress) + stress = stress.astype(np.float) + stress = stress[np.newaxis, :, :] + # stress to virial conversion, default unit in cp2k is GPa + # note the stress is virial = stress * volume + virial = stress * np.linalg.det(cell[0])/GPa + else: + virial = None + # force unit conversion, default unit in cp2k is hartree/bohr force = force * eV / angstrom # energy unit conversion, default unit in cp2k is hartree energy = float(energy) * eV energy = np.array(energy) energy = energy[np.newaxis] - # stress to virial conversion, default unit in cp2k is GPa - # note the stress is virial = stress * volume - virial = stress * np.linalg.det(cell[0])/GPa diff --git a/dpdata/system.py b/dpdata/system.py index 5f3eb4dd1..d2be7f879 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -1248,8 +1248,10 @@ def from_cp2k_output(self, file_name) : self.data['coords'], \ self.data['energies'], \ self.data['forces'], \ - self.data['virials'] \ + tmp_virial \ = dpdata.cp2k.output.get_frames(file_name) + if tmp_virial is not None: + self.data['virials'] = tmp_virial @register_from_funcs.register_funcs('movement') @register_from_funcs.register_funcs('MOVEMENT') @register_from_funcs.register_funcs('mlmd') diff --git a/tests/cp2k/cp2k_output_2 b/tests/cp2k/cp2k_output_2 new file mode 100644 index 000000000..48f04b615 --- /dev/null +++ b/tests/cp2k/cp2k_output_2 @@ -0,0 +1,2288 @@ + 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 + + 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 --------------------------------------- + Minimizer : DIIS : direct inversion + in the iterative subspace + using 7 DIIS vectors + safer DIIS on + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 1 OT DIIS 0.80E-01 0.6 0.12211697 -69.9227646320 -6.99E+01 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 2 OT DIIS 0.80E-01 0.8 0.08397991 -71.5488849278 -1.63E+00 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 3 OT DIIS 0.80E-01 0.8 0.06432705 -72.3568418033 -8.08E-01 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 4 OT DIIS 0.80E-01 0.8 0.05737364 -73.1900458544 -8.33E-01 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 5 OT DIIS 0.80E-01 0.8 0.03623630 -73.7413152872 -5.51E-01 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 6 OT DIIS 0.80E-01 0.8 0.02687733 -73.9835995051 -2.42E-01 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 7 OT DIIS 0.80E-01 0.8 0.01682164 -74.0451613466 -6.16E-02 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 8 OT DIIS 0.80E-01 0.8 0.01172379 -74.1060462003 -6.09E-02 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 9 OT DIIS 0.80E-01 0.9 0.00685204 -74.1347934213 -2.87E-02 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 10 OT DIIS 0.80E-01 0.8 0.00557939 -74.1452592701 -1.05E-02 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 11 OT DIIS 0.80E-01 0.8 0.00529907 -74.1545329360 -9.27E-03 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 12 OT DIIS 0.80E-01 0.8 0.00204013 -74.1583772496 -3.84E-03 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 13 OT DIIS 0.80E-01 0.8 0.00125361 -74.1604256086 -2.05E-03 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 14 OT DIIS 0.80E-01 0.8 0.00081727 -74.1611323749 -7.07E-04 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 15 OT DIIS 0.80E-01 0.8 0.00059499 -74.1614246428 -2.92E-04 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 16 OT DIIS 0.80E-01 0.8 0.00040833 -74.1616124349 -1.88E-04 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 17 OT DIIS 0.80E-01 0.8 0.00032383 -74.1616836330 -7.12E-05 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 18 OT DIIS 0.80E-01 0.8 0.00024259 -74.1617425930 -5.90E-05 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 19 OT DIIS 0.80E-01 0.8 0.00019028 -74.1617752692 -3.27E-05 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 20 OT DIIS 0.80E-01 0.8 0.00014769 -74.1617987237 -2.35E-05 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 21 OT DIIS 0.80E-01 0.8 0.00011570 -74.1618110663 -1.23E-05 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 22 OT DIIS 0.80E-01 0.8 0.00009372 -74.1618181547 -7.09E-06 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 23 OT DIIS 0.80E-01 0.8 0.00007276 -74.1618237906 -5.64E-06 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 24 OT DIIS 0.80E-01 0.8 0.00005773 -74.1618267716 -2.98E-06 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 25 OT DIIS 0.80E-01 0.8 0.00004629 -74.1618286021 -1.83E-06 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 26 OT DIIS 0.80E-01 0.8 0.00003663 -74.1618296881 -1.09E-06 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 27 OT DIIS 0.80E-01 0.8 0.00002919 -74.1618303402 -6.52E-07 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 28 OT DIIS 0.80E-01 0.8 0.00002316 -74.1618307348 -3.95E-07 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 29 OT DIIS 0.80E-01 0.8 0.00001912 -74.1618309323 -1.98E-07 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 30 OT DIIS 0.80E-01 0.8 0.00001585 -74.1618310522 -1.20E-07 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 31 OT DIIS 0.80E-01 0.8 0.00001283 -74.1618311407 -8.86E-08 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 32 OT DIIS 0.80E-01 0.8 0.00001054 -74.1618311976 -5.69E-08 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 33 OT DIIS 0.80E-01 0.8 0.00000864 -74.1618312407 -4.31E-08 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 34 OT DIIS 0.80E-01 0.8 0.00000720 -74.1618312662 -2.54E-08 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 35 OT DIIS 0.80E-01 0.8 0.00000603 -74.1618312851 -1.89E-08 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 36 OT DIIS 0.80E-01 0.8 0.00000510 -74.1618313004 -1.53E-08 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 37 OT DIIS 0.80E-01 0.8 0.00000446 -74.1618313105 -1.01E-08 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 38 OT DIIS 0.80E-01 0.8 0.00000385 -74.1618313187 -8.25E-09 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 39 OT DIIS 0.80E-01 0.8 0.00000332 -74.1618313255 -6.75E-09 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 40 OT DIIS 0.80E-01 0.8 0.00000288 -74.1618313308 -5.30E-09 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 41 OT DIIS 0.80E-01 0.8 0.00000245 -74.1618313356 -4.81E-09 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 42 OT DIIS 0.80E-01 0.8 0.00000212 -74.1618313387 -3.05E-09 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 43 OT DIIS 0.80E-01 0.8 0.00000178 -74.1618313411 -2.49E-09 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 44 OT DIIS 0.80E-01 0.8 0.00000148 -74.1618313429 -1.80E-09 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 45 OT DIIS 0.80E-01 0.8 0.00000124 -74.1618313441 -1.15E-09 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 46 OT DIIS 0.80E-01 0.9 0.00000101 -74.1618313448 -7.33E-10 + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + 47 OT DIIS 0.80E-01 0.8 0.00000081 -74.1618313453 -4.29E-10 + + *** SCF run converged in 47 steps *** + + + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + Overlap energy of the core charge distribution: 0.00000242417664 + Self energy of the core charge distribution: -187.02580487381152 + Core Hamiltonian energy: 55.54257423380538 + Hartree energy: 76.76711718225495 + Exchange-correlation energy: -19.43594060717809 + Dispersion energy: -0.00977970450525 + + Total energy: -74.16183134525791 + + outer SCF iter = 1 RMS gradient = 0.81E-06 energy = -74.1618313453 + outer SCF loop converged in 1 iterations or 47 steps + + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population Net charge + 1 C 1 3.984867 0.015133 + 2 C 1 4.077879 -0.077879 + 3 C 1 3.913577 0.086423 + 4 H 2 0.898355 0.101645 + 5 O 3 6.208620 -0.208620 + 6 C 1 4.255056 -0.255056 + 7 H 2 0.878166 0.121834 + 8 H 2 0.895576 0.104424 + 9 O 3 6.133234 -0.133234 + 10 O 3 6.093371 -0.093371 + 11 H 2 0.894525 0.105475 + 12 H 2 0.886697 0.113303 + 13 H 2 0.880075 0.119925 + # Total charge 40.000000 0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Net charge + 1 C 1 4.000 3.350 0.650 + 2 C 1 4.000 3.767 0.233 + 3 C 1 4.000 3.835 0.165 + 4 H 2 1.000 0.952 0.048 + 5 O 3 6.000 6.476 -0.476 + 6 C 1 4.000 4.086 -0.086 + 7 H 2 1.000 0.909 0.091 + 8 H 2 1.000 0.929 0.071 + 9 O 3 6.000 6.428 -0.428 + 10 O 3 6.000 6.407 -0.407 + 11 H 2 1.000 0.961 0.039 + 12 H 2 1.000 0.952 0.048 + 13 H 2 1.000 0.948 0.052 + + Total Charge 0.000 + !-----------------------------------------------------------------------------! + + Trace(PS): 40.0000000000 + Electronic density on regular grids: -40.0000000000 0.0000000000 + Core density on regular grids: 40.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000000 + Total charge density g-space grids: -0.0000000000 + + + ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -74.161831345521179 + + + ATOMIC FORCES in [a.u.] + + # Atom Kind Element X Y Z + 1 1 C -0.02543205 0.04647274 -0.04576210 + 2 1 C -0.02384518 0.04070368 -0.06382020 + 3 1 C 0.02413716 0.00267013 -0.01594700 + 4 2 H 0.02331229 -0.00303660 0.01752014 + 5 3 O -0.00330258 -0.00031879 0.01926047 + 6 1 C -0.01124607 -0.02554273 0.02814433 + 7 2 H -0.01321314 0.01947427 0.01821504 + 8 2 H -0.01528903 -0.00477150 0.01334457 + 9 3 O 0.00705728 0.00564402 0.03059922 + 10 3 O 0.03607999 -0.08625169 0.01012960 + 11 2 H -0.00531559 -0.01159595 -0.00486571 + 12 2 H -0.01370828 -0.00250871 -0.00716084 + 13 2 H 0.02104090 0.01869862 0.00050029 + SUM OF ATOMIC FORCES 0.00027571 -0.00036251 0.00015781 0.00048201 + + ------------------------------------------------------------------------------- + - - + - DBCSR STATISTICS - + - - + ------------------------------------------------------------------------------- + COUNTER TOTAL BLAS SMM ACC + flops 5 x 20 x 20 24000 100.0% 0.0% 0.0% + flops 13 x 20 x 20 72800 100.0% 0.0% 0.0% + flops 5 x 5 x 20 1050000 100.0% 0.0% 0.0% + flops 5 x 13 x 20 2730000 100.0% 0.0% 0.0% + flops 13 x 5 x 20 2730000 100.0% 0.0% 0.0% + flops 54 x 20 x 5 3110400 100.0% 0.0% 0.0% + flops 5 x 20 x 5 3636000 100.0% 0.0% 0.0% + flops 67 x 20 x 5 3859200 100.0% 0.0% 0.0% + flops 20 x 20 x 5 4512000 100.0% 0.0% 0.0% + flops 20 x 20 x 20 6672000 100.0% 0.0% 0.0% + flops 54 x 20 x 13 9434880 100.0% 0.0% 0.0% + flops 13 x 13 x 20 9464000 100.0% 0.0% 0.0% + flops 54 x 20 x 20 10108800 100.0% 0.0% 0.0% + flops 5 x 20 x 13 11029200 100.0% 0.0% 0.0% + flops 13 x 20 x 5 11029200 100.0% 0.0% 0.0% + flops 67 x 20 x 13 11706240 100.0% 0.0% 0.0% + flops 67 x 20 x 20 12542400 100.0% 0.0% 0.0% + flops 20 x 20 x 13 13686400 100.0% 0.0% 0.0% + flops 13 x 20 x 13 33455240 100.0% 0.0% 0.0% + flops total 150.852760E+06 100.0% 0.0% 0.0% + flops max/rank 87.058120E+06 100.0% 0.0% 0.0% + matmuls inhomo. stacks 0 0.0% 0.0% 0.0% + matmuls total 26209 100.0% 0.0% 0.0% + number of processed stacks 12233 100.0% 0.0% 0.0% + average stack size 2.1 0.0 0.0 + marketing flops 164.257696E+06 + ------------------------------------------------------------------------------- + # multiplications 1040 + max memory usage/rank 311.861248E+06 + # max total images/rank 7 + # MPI messages exchanged 3028480 + # MPI messages filtered 0 + MPI messages size (elements): + total size 60.974020E+06 + min size 0.000000E+00 + max size 1.340000E+03 + average size 20.133539E+00 + MPI breakdown and total messages size (bytes): + size <= 128 2859636 0 + 128 < size <= 8192 161434 416063336 + 8192 < size <= 32768 7410 71728800 + 32768 < size <= 131072 0 0 + 131072 < size <= 4194304 0 0 + 4194304 < size <= 16777216 0 0 + 16777216 < size 0 0 + ------------------------------------------------------------------------------- + Warning: using a non-square number of MPI ranks might lead to poor performance. + used ranks: 28 + suggested : 25 49 + ------------------------------------------------------------------------------- + + MEMORY| Estimated peak process memory [MiB] 298 + + ------------------------------------------------------------------------------- + ---- MULTIGRID INFO ---- + ------------------------------------------------------------------------------- + count for grid 1: 110888 cutoff [a.u.] 250.00 + count for grid 2: 67832 cutoff [a.u.] 83.33 + count for grid 3: 38068 cutoff [a.u.] 27.78 + count for grid 4: 7104 cutoff [a.u.] 9.26 + total gridlevel count : 223892 + + ------------------------------------------------------------------------------- + - - + - MESSAGE PASSING PERFORMANCE - + - - + ------------------------------------------------------------------------------- + + ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s] + MP_Group 5 0.000 + MP_Bcast 2370 0.009 120247. 30442.16 + MP_Allreduce 8751 1.290 181. 1.23 + MP_Sync 51 0.003 + MP_Alltoall 4123 1.548 1382531. 3682.81 + MP_SendRecv 876 0.907 355083. 342.97 + MP_ISendRecv 5184 0.013 83700. 34235.90 + MP_Wait 145452 2.740 + MP_comm_split 47 0.001 + MP_ISend 230604 0.097 10294. 24486.66 + MP_IRecv 227748 0.046 10386. 51680.72 + MP_Recv 27 0.000 1936. 2128.59 + MP_Memory 153498 0.028 + ------------------------------------------------------------------------------- + + + ------------------------------------------------------------------------------- + - - + - R E F E R E N C E S - + - - + ------------------------------------------------------------------------------- + + CP2K version 4.1, the CP2K developers group (2016). + CP2K is freely available from https://www.cp2k.org/ . + + Schuett, Ole; Messmer, Peter; Hutter, Juerg; VandeVondele, Joost. + Electronic Structure Calculations on Graphics Processing Units, John Wiley & Sons, Ltd, 173-190 (2016). + GPU-Accelerated Sparse Matrix-Matrix Multiplication for Linear Scaling Density Functional Theory. + http://dx.doi.org/10.1002/9781118670712.ch8 + + + 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 + + + Grimme, S; Ehrlich, S; Goerigk, L. + JOURNAL OF COMPUTATIONAL CHEMISTRY, 32, 1456 (2011). + Effect of the damping function in dispersion corrected density functional theory. + http://dx.doi.org/10.1002/jcc.21759 + + + Grimme, S; Antony, J; Ehrlich, S; Krieg, H. + JOURNAL OF CHEMICAL PHYSICS, 132 (15), 154104 (2010). + A consistent and accurate ab initio parametrization of density + functional dispersion correction (DFT-D) for the 94 elements H-Pu. + http://dx.doi.org/10.1063/1.3382344 + + + 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 + + + VandeVondele, J; Hutter, J. + JOURNAL OF CHEMICAL PHYSICS, 118 (10), 4365-4369 (2003). + An efficient orbital transformation method for electronic structure + calculations. + http://dx.doi.org/10.1063/1.1543154 + + + 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 + + + BECKE, AD. PHYSICAL REVIEW A, 38 (6), 3098-3100 (1988). + DENSITY-FUNCTIONAL EXCHANGE-ENERGY APPROXIMATION WITH CORRECT + ASYMPTOTIC-BEHAVIOR. + http://dx.doi.org/10.1103/PhysRevA.38.3098 + + + LEE, CT; YANG, WT; PARR, RG. + PHYSICAL REVIEW B, 37 (2), 785-789 (1988). + DEVELOPMENT OF THE COLLE-SALVETTI CORRELATION-ENERGY FORMULA INTO A + FUNCTIONAL OF THE ELECTRON-DENSITY. + http://dx.doi.org/10.1103/PhysRevB.37.785 + + + ------------------------------------------------------------------------------- + - - + - T I M I N G - + - - + ------------------------------------------------------------------------------- + SUBROUTINE CALLS ASD SELF TIME TOTAL TIME + MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM + CP2K 1 1.0 0.019 0.025 39.922 39.924 + qs_forces 1 2.0 0.000 0.000 39.637 39.637 + qs_energies 1 3.0 0.000 0.000 38.957 38.957 + scf_env_do_scf 1 4.0 0.000 0.000 38.327 38.327 + scf_env_do_scf_inner_loop 47 5.0 0.001 0.005 37.802 37.802 + rebuild_ks_matrix 48 6.9 0.000 0.000 23.473 23.482 + qs_ks_build_kohn_sham_matrix 48 7.9 0.007 0.019 23.473 23.482 + qs_ks_update_qs_env 48 6.0 0.001 0.001 22.800 22.809 + pw_transfer 577 10.1 0.036 0.046 14.984 16.075 + fft_wrap_pw1pw2 481 11.2 0.004 0.005 14.528 15.602 + fft_wrap_pw1pw2_250 193 11.7 1.131 1.163 13.168 14.450 + qs_rho_update_rho 48 6.0 0.000 0.000 13.711 13.711 + calculate_rho_elec 48 7.0 0.274 1.101 13.711 13.711 + fft3d_ps 481 13.2 7.329 8.819 11.213 12.356 + density_rs2pw 48 8.0 0.002 0.003 11.575 12.218 + sum_up_and_integrate 48 8.9 0.228 0.259 10.386 10.429 + integrate_v_rspace 48 9.9 0.141 0.758 10.158 10.205 + rs_pw_transfer 388 10.4 0.004 0.005 9.600 9.797 + potential_pw2rs 48 10.9 0.021 0.022 9.421 9.433 + qs_vxc_create 48 8.9 0.001 0.002 7.730 7.831 + xc_vxc_pw_create 48 9.9 0.492 0.555 7.729 7.829 + pw_nn_compose_r 384 11.4 4.267 4.305 5.466 5.844 + xc_rho_set_and_dset_create 48 10.9 0.570 0.626 4.004 4.710 + rs_pw_transfer_PW2RS_250 50 12.8 1.750 1.811 3.392 3.494 + mp_waitany 6464 12.4 2.891 3.200 2.891 3.200 + rs_pw_transfer_RS2PW_250 50 9.9 1.491 1.642 2.775 2.984 + mp_alltoall_z22v 481 15.2 2.139 2.779 2.139 2.779 + rs_grid_zero 292 10.0 2.509 2.571 2.509 2.571 + dbcsr_multiply_generic 1040 11.1 0.024 0.026 1.794 2.384 + x_to_yz 240 14.8 1.019 1.087 2.154 2.252 + yz_to_x 241 13.6 0.717 0.847 1.720 1.981 + qs_scf_new_mos 47 6.0 0.000 0.000 1.844 1.846 + qs_scf_loop_do_ot 47 7.0 0.000 0.000 1.844 1.846 + ot_scf_mini 47 8.0 0.001 0.001 1.759 1.761 + rs_pw_transfer_PW2RS_90 48 12.9 0.579 0.614 1.488 1.608 + mp_sendrecv_dm2 768 12.4 1.200 1.590 1.200 1.590 + fft_wrap_pw1pw2_90 96 12.5 0.080 0.101 1.141 1.498 + pw_poisson_solve 48 8.9 0.890 0.904 1.376 1.377 + mp_sum_d 2457 10.1 0.852 1.334 0.852 1.334 + make_m2s 2080 12.1 0.026 0.026 0.646 1.215 + pw_scatter_p 240 13.8 1.113 1.188 1.113 1.188 + ot_mini 47 9.0 0.000 0.000 1.171 1.173 + rs_pw_transfer_RS2PW_90 48 10.0 0.663 0.697 1.130 1.154 + xc_functional_eval 96 11.9 0.001 0.001 0.540 1.082 + qs_ot_get_derivative 47 10.0 0.001 0.001 1.057 1.059 + make_images 2080 13.1 0.130 0.140 0.455 1.027 + pw_gather_p 241 12.6 0.970 1.016 0.970 1.016 + multiply_cannon 1040 12.1 0.137 0.145 0.885 0.972 + mp_waitall_1 138988 14.3 0.603 0.825 0.603 0.825 + qs_ot_get_derivative_diag 46 11.0 0.002 0.002 0.807 0.808 + ------------------------------------------------------------------------------- + + The number of warnings for this run is : 1 + + ------------------------------------------------------------------------------- + **** **** ****** ** PROGRAM ENDED AT 2019-08-10 12:44:21.899 + ***** ** *** *** ** PROGRAM RAN ON c038 + ** **** ****** PROGRAM RAN BY fengw + ***** ** ** ** ** PROGRAM PROCESS ID 21094 + **** ** ******* ** PROGRAM STOPPED IN /data/fengw/PC-LiTFSI/energy/BLYP/0.3 + 7_CBM_VBM/KS/29000/test diff --git a/tests/cp2k/test.py b/tests/cp2k/test.py index 5b299c5ed..dbfdae36e 100755 --- a/tests/cp2k/test.py +++ b/tests/cp2k/test.py @@ -1,29 +1,56 @@ - import dpdata import numpy as np -cp2k_output = dpdata.LabeledSystem('output_40847', fmt = 'cp2k/output') + +# simple test for cp2k +# first case: with force and virial information +print("first case") +print("--------------------------------------------------------------") +cp2k_output = dpdata.LabeledSystem('cp2k_output', fmt = 'cp2k/output') print("atom name") print(cp2k_output['atom_names']) print("atom number") print(cp2k_output['atom_numbs']) print("atom type") print(cp2k_output['atom_types']) -np.savetxt("ref_type", cp2k_output['atom_types']) print("atom cell") print(cp2k_output['cells']) -np.savetxt("ref_cell", cp2k_output['cells'][0]) print("atom coord") print(cp2k_output['coords']) -np.savetxt("ref_coord", cp2k_output['coords'][0]) print("energyies") print(cp2k_output['energies']) print("forces") print(cp2k_output['forces']) -np.savetxt("ref_force", cp2k_output['forces'][0]) print("virials") print(cp2k_output['virials']) -np.savetxt("ref_virial", cp2k_output['virials'][0]) # no virial -#cp2k_output.to_deepmd_raw('dpmd_raw') -#cp2k_output.to_deepmd_npy('dpmd_npy') + +cp2k_output.to_deepmd_raw('dpmd_raw') +cp2k_output.to_deepmd_npy('dpmd_npy') + +# second case: with force and no! virial information +# double header information is contained, to test robustness of this parser +print("\n") +print("\n") +print("second case") +print("---------------------------------------------------------------") + +cp2k_output = dpdata.LabeledSystem('cp2k_output_2', fmt = 'cp2k/output') +print("atom name") +print(cp2k_output['atom_names']) +print("atom number") +print(cp2k_output['atom_numbs']) +print("atom type") +print(cp2k_output['atom_types']) +#np.savetxt("ref_type", cp2k_output['atom_types']) +print("atom cell") +print(cp2k_output['cells']) +#np.savetxt("ref_cell", cp2k_output['cells'][0]) +print("atom coord") +print(cp2k_output['coords']) +#np.savetxt("ref_coord", cp2k_output['coords'][0]) +print("energyies") +print(cp2k_output['energies']) +print("forces") +print(cp2k_output['forces']) + From 5e6da87abaa96c1a250250f98efebd0df13657f3 Mon Sep 17 00:00:00 2001 From: Yuan Fengbo Date: Fri, 27 Nov 2020 20:28:32 +0800 Subject: [PATCH 03/19] add the replace method to system, using for randomly substitute atom of specific type to anothor type --- dpdata/system.py | 34 +++++++++ tests/poscars/POSCAR.P42nmc | 104 ++++++++++++++++++++++++++++ tests/poscars/POSCAR.P42nmc.replace | 104 ++++++++++++++++++++++++++++ tests/test_replace.py | 40 +++++++++++ 4 files changed, 282 insertions(+) create mode 100644 tests/poscars/POSCAR.P42nmc create mode 100644 tests/poscars/POSCAR.P42nmc.replace create mode 100644 tests/test_replace.py diff --git a/dpdata/system.py b/dpdata/system.py index d2be7f879..bba7446f0 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -799,6 +799,40 @@ def replicate(self, ncopy): tmp.data['coords'] = np.reshape(np.transpose(tmp.data['coords'], [3,4,0,1,2,5]), (nframes, -1 , 3)) return tmp + def replace(self, initial_atom_type, end_atom_type, replace_num): + if type(self) is not dpdata.System: + raise RuntimeError('Must use method replace() of the instance of class dpdata.System') + if type(replace_num) is not int: + raise ValueError("replace_num must be a integer. Now is {replace_num}".format(replace_num=replace_num)) + if replace_num <= 0: + raise ValueError("replace_num must be larger than 0.Now is {replace_num}".format(replace_num=replace_num)) + + try: + initial_atom_index = self.data['atom_names'].index(initial_atom_type) + except ValueError as e: + raise ValueError("atom_type {initial_atom_type} not in {atom_names}" + .format(initial_atom_type=initial_atom_type, atom_names=self.data['atom_names'])) + max_replace_num = self.data['atom_numbs'][initial_atom_index] + + if replace_num > max_replace_num: + raise RuntimeError("not enough {initial_atom_type} atom, only {max_replace_num} available, less than {replace_num}.Please check." + .format(initial_atom_type=initial_atom_type,max_replace_num=max_replace_num, replace_num=replace_num)) + + may_replace_indices = [i for i, x in enumerate(self.data['atom_types']) if x == initial_atom_index] + to_replace_indices = np.random.choice(may_replace_indices, size=replace_num, replace=False) + + if end_atom_type not in self.data['atom_names']: + self.data['atom_names'].append(end_atom_type) + self.data['atom_numbs'].append(0) + + end_atom_index = self.data['atom_names'].index(end_atom_type) + for ii in to_replace_indices: + self.data['atom_types'][ii] = end_atom_index + self.data['atom_numbs'][initial_atom_index] -= replace_num + self.data['atom_numbs'][end_atom_index] += replace_num + self.sort_atom_types() + + def perturb(self, pert_num, cell_pert_fraction, diff --git a/tests/poscars/POSCAR.P42nmc b/tests/poscars/POSCAR.P42nmc new file mode 100644 index 000000000..130daa127 --- /dev/null +++ b/tests/poscars/POSCAR.P42nmc @@ -0,0 +1,104 @@ +Hf32 O64 +1.0 +10.001280 0.000000 0.000000 +0.000000 10.001280 0.000000 +0.000000 0.000000 10.163840 +Hf O +32 64 +direct +0.000000 0.000000 0.000000 Hf +0.000000 0.000000 0.500000 Hf +0.000000 0.500000 1.000000 Hf +0.000000 0.500000 0.500000 Hf +0.500000 0.000000 1.000000 Hf +0.500000 0.000000 0.500000 Hf +0.500000 0.500000 1.000000 Hf 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0.353880 O +0.125000 0.375000 0.853880 O +0.125000 0.875000 0.353880 O +0.125000 0.875000 0.853880 O +0.625000 0.375000 0.353880 O +0.625000 0.375000 0.853880 O +0.625000 0.875000 0.353880 O +0.625000 0.875000 0.853880 O +0.125000 0.125000 0.146120 O +0.125000 0.125000 0.646120 O +0.125000 0.625000 0.146120 O +0.125000 0.625000 0.646120 O +0.625000 0.125000 0.146120 O +0.625000 0.125000 0.646120 O +0.625000 0.625000 0.146120 O +0.625000 0.625000 0.646120 O +0.125000 0.125000 0.396120 O +0.125000 0.125000 0.896120 O +0.125000 0.625000 0.396120 O +0.125000 0.625000 0.896120 O +0.625000 0.125000 0.396120 O +0.625000 0.125000 0.896120 O +0.625000 0.625000 0.396120 O +0.625000 0.625000 0.896120 O diff --git a/tests/poscars/POSCAR.P42nmc.replace b/tests/poscars/POSCAR.P42nmc.replace new file mode 100644 index 000000000..e785d1286 --- /dev/null +++ b/tests/poscars/POSCAR.P42nmc.replace @@ -0,0 +1,104 @@ +Hf24 O64 Zr8 +1.0 +1.0001280000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 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5.0006400000 5.0006400000 5.0819200000 + 5.0006400000 5.0006400000 10.1638400000 + 0.0000000000 5.0006400000 10.1638400000 diff --git a/tests/test_replace.py b/tests/test_replace.py new file mode 100644 index 000000000..a8dd917b5 --- /dev/null +++ b/tests/test_replace.py @@ -0,0 +1,40 @@ +import os +import numpy as np +import unittest +from context import dpdata +from comp_sys import CompSys, IsPBC + +from unittest.mock import Mock +from unittest.mock import patch, MagicMock + + +class ConstGenerator(object): + def __init__(self): + self.choice_generator = self.get_choice_generator() + def choice(self, a, size=None, replace=True, p=None): + return next(self.choice_generator) + + @staticmethod + def get_choice_generator(): + yield np.asarray([20, 6, 7, 22, 29, 2, 23, 10]) + +class TestReplace(unittest.TestCase, CompSys, IsPBC): + @patch('numpy.random') + def setUp(self, random_mock): + random_mock.choice = ConstGenerator().choice + self.system_1 = dpdata.System('poscars/POSCAR.P42nmc',fmt='vasp/poscar') + self.system_1.replace('Hf', 'Zr', 8) + # print(self.system_1.data) + self.system_2 = dpdata.System('poscars/POSCAR.P42nmc.replace',fmt='vasp/poscar') + # print(self.system_2.data) + self.places = 6 + +# class TestReplicate123_not_change_origin(unittest.TestCase, CompSys, IsPBC): +# def setUp (self) : +# self.system_1 = dpdata.System('poscars/POSCAR.SiC',fmt='vasp/poscar') +# self.system_1.replicate((1,2,3,)) +# self.system_2 = dpdata.System('poscars/POSCAR.SiC',fmt='vasp/poscar') +# self.places = 6 + +if __name__ == '__main__': + unittest.main() From b293324d7b0863e1e52c29114c458dbc064c47e2 Mon Sep 17 00:00:00 2001 From: Yuan Fengbo Date: Fri, 27 Nov 2020 20:39:34 +0800 Subject: [PATCH 04/19] add documents for replace() method --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/README.md b/README.md index 8dd9c8649..2f3dc0d3a 100644 --- a/README.md +++ b/README.md @@ -197,3 +197,13 @@ perturbed_system = dpdata.System('./POSCAR').perturb(pert_num=3, atom_pert_style='normal') print(perturbed_system.data) ``` + +## replace +By the following example, Random 8 Hf atoms in the system will be replaced by Zr atoms with the atom postion unchanged. +```python +s=dpdata.System('tests/poscars/POSCAR.P42nmc',fmt='vasp/poscar') +s.replace('Hf', 'Zr', 8) +s.to_vasp_poscar('POSCAR.P42nmc.replace') +``` + + From 8380aa78d2cf69a6f9da9c0c49781921b5dd8f27 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mari=C3=A1n=20Rynik?= Date: Tue, 1 Dec 2020 12:19:15 +0100 Subject: [PATCH 05/19] export energy, forces and virials to se atoms --- dpdata/system.py | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/dpdata/system.py b/dpdata/system.py index bba7446f0..2de9b1e18 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -309,9 +309,14 @@ def sub_system(self, f_idx) : tmp = System() for ii in ['atom_numbs', 'atom_names', 'atom_types', 'orig'] : tmp.data[ii] = self.data[ii] + tmp.data['cells'] = self.data['cells'][f_idx].reshape(-1, 3, 3) + tmp.data['virials'] = self.data['virials'][f_idx].reshape(-1, 3, 3) tmp.data['coords'] = self.data['coords'][f_idx].reshape(-1, self.data['coords'].shape[1], 3) + tmp.data['forces'] = self.data['forces'][f_idx].reshape(-1, self.data['forces'].shape[1], 3) + tmp.data['energies'] = self.data['energies'][f_idx] tmp.data['nopbc'] = self.nopbc + return tmp @@ -519,12 +524,20 @@ def to_ase_structure(self): structures=[] try: from ase import Atoms - except: - raise ImportError('No module ase.Atoms') + from ase.calculators.singlepoint import SinglePointCalculator + except ImportError: + raise ImportError('No module ase') for system in self.to_list(): species=[system.data['atom_names'][tt] for tt in system.data['atom_types']] structure=Atoms(symbols=species,positions=system.data['coords'][0],pbc=True,cell=system.data['cells'][0]) + calc = SinglePointCalculator( + structure, + energy=system.data["energies"][0], + forces=system.data['forces'][0], + stresses=system.data['virials'][0] + ) + structure.calc = calc structures.append(structure) return structures From c487f05223a24f2ade8e36b47c89d6cda287c32f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mari=C3=A1n=20Rynik?= Date: Tue, 1 Dec 2020 12:21:41 +0100 Subject: [PATCH 06/19] remove try-except block for import it is not necessary --- dpdata/system.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/dpdata/system.py b/dpdata/system.py index 2de9b1e18..df83f7f94 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -521,12 +521,10 @@ def to_ase_structure(self): convert System to ASE Atom obj ''' + from ase import Atoms + from ase.calculators.singlepoint import SinglePointCalculator + structures=[] - try: - from ase import Atoms - from ase.calculators.singlepoint import SinglePointCalculator - except ImportError: - raise ImportError('No module ase') for system in self.to_list(): species=[system.data['atom_names'][tt] for tt in system.data['atom_types']] From 0901cfde96809f45e962bfb7ab39042ed243501c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mari=C3=A1n=20Rynik?= Date: Tue, 1 Dec 2020 12:46:36 +0100 Subject: [PATCH 07/19] convert ASE stress tensot to GPa --- dpdata/system.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/dpdata/system.py b/dpdata/system.py index df83f7f94..1b8407876 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -529,11 +529,14 @@ def to_ase_structure(self): for system in self.to_list(): species=[system.data['atom_names'][tt] for tt in system.data['atom_types']] structure=Atoms(symbols=species,positions=system.data['coords'][0],pbc=True,cell=system.data['cells'][0]) + # convert to GPa as this is ase convention + v_pref = 1 * 1e4 / 1.602176621e6 + vol = structure.get_volume() calc = SinglePointCalculator( structure, energy=system.data["energies"][0], forces=system.data['forces'][0], - stresses=system.data['virials'][0] + stresses=system.data['virials'][0] / (v_pref * vol) ) structure.calc = calc structures.append(structure) From 931c606d8eefbff75f7377cde828c1d084952933 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mari=C3=A1n=20Rynik?= Date: Tue, 1 Dec 2020 14:23:41 +0100 Subject: [PATCH 08/19] account for energies, forces or virials not present --- dpdata/system.py | 27 ++++++++++++++++++--------- 1 file changed, 18 insertions(+), 9 deletions(-) diff --git a/dpdata/system.py b/dpdata/system.py index 1b8407876..8091ad32d 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -311,11 +311,15 @@ def sub_system(self, f_idx) : tmp.data[ii] = self.data[ii] tmp.data['cells'] = self.data['cells'][f_idx].reshape(-1, 3, 3) - tmp.data['virials'] = self.data['virials'][f_idx].reshape(-1, 3, 3) tmp.data['coords'] = self.data['coords'][f_idx].reshape(-1, self.data['coords'].shape[1], 3) - tmp.data['forces'] = self.data['forces'][f_idx].reshape(-1, self.data['forces'].shape[1], 3) - tmp.data['energies'] = self.data['energies'][f_idx] tmp.data['nopbc'] = self.nopbc + + if 'forces' in self.data: + tmp.data['forces'] = self.data['forces'][f_idx].reshape(-1, self.data['forces'].shape[1], 3) + if 'virials' in self.data: + tmp.data['virials'] = self.data['virials'][f_idx].reshape(-1, 3, 3) + if 'energies' in self.data: + tmp.data['energies'] = self.data['energies'][f_idx] return tmp @@ -532,14 +536,19 @@ def to_ase_structure(self): # convert to GPa as this is ase convention v_pref = 1 * 1e4 / 1.602176621e6 vol = structure.get_volume() - calc = SinglePointCalculator( - structure, - energy=system.data["energies"][0], - forces=system.data['forces'][0], - stresses=system.data['virials'][0] / (v_pref * vol) - ) + + results = {} + if "energies" in system.data: + results['energy'] = system.data["energies"][0] + if "forces" in system.data: + results['forces'] = system.data["forces"][0] + if "virials" in system.data: + results['stress'] = system.data["virials"][0] / (v_pref * vol) + + calc = SinglePointCalculator(structure, **results) structure.calc = calc structures.append(structure) + return structures @register_to_funcs.register_funcs("lammps/lmp") From 4288f5209a3e2e3f47724e8959607cf40c686f49 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mari=C3=A1n=20Rynik?= Date: Wed, 2 Dec 2020 11:01:25 +0100 Subject: [PATCH 09/19] reimplement to_ase_structure in labeled system --- dpdata/system.py | 53 ++++++++++++++++++++++++++++-------------------- 1 file changed, 31 insertions(+), 22 deletions(-) diff --git a/dpdata/system.py b/dpdata/system.py index 8091ad32d..d3542e52e 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -313,13 +313,6 @@ def sub_system(self, f_idx) : tmp.data['cells'] = self.data['cells'][f_idx].reshape(-1, 3, 3) tmp.data['coords'] = self.data['coords'][f_idx].reshape(-1, self.data['coords'].shape[1], 3) tmp.data['nopbc'] = self.nopbc - - if 'forces' in self.data: - tmp.data['forces'] = self.data['forces'][f_idx].reshape(-1, self.data['forces'].shape[1], 3) - if 'virials' in self.data: - tmp.data['virials'] = self.data['virials'][f_idx].reshape(-1, 3, 3) - if 'energies' in self.data: - tmp.data['energies'] = self.data['energies'][f_idx] return tmp @@ -526,27 +519,12 @@ def to_ase_structure(self): ''' from ase import Atoms - from ase.calculators.singlepoint import SinglePointCalculator structures=[] for system in self.to_list(): species=[system.data['atom_names'][tt] for tt in system.data['atom_types']] structure=Atoms(symbols=species,positions=system.data['coords'][0],pbc=True,cell=system.data['cells'][0]) - # convert to GPa as this is ase convention - v_pref = 1 * 1e4 / 1.602176621e6 - vol = structure.get_volume() - - results = {} - if "energies" in system.data: - results['energy'] = system.data["energies"][0] - if "forces" in system.data: - results['forces'] = system.data["forces"][0] - if "virials" in system.data: - results['stress'] = system.data["virials"][0] / (v_pref * vol) - - calc = SinglePointCalculator(structure, **results) - structure.calc = calc structures.append(structure) return structures @@ -1361,6 +1339,37 @@ def sub_system(self, f_idx) : tmp_sys.data['virials'] = self.data['virials'][f_idx].reshape(-1, 3, 3) return tmp_sys + @register_to_funcs.register_funcs("ase/structure") + def to_ase_structure(self): + '''Convert System to ASE Atoms object.''' + from ase import Atoms + from ase.calculators.singlepoint import SinglePointCalculator + + structures = [] + + for system in self.to_list(): + species=[system.data['atom_names'][tt] for tt in system.data['atom_types']] + structure=Atoms( + symbols=species, + positions=system.data['coords'][0], + pbc=True, + cell=system.data['cells'][0] + ) + + results = { + 'energy': system.data["energies"][0], + 'forces': system.data["forces"][0] + } + if "virials" in system.data: + # convert to GPa as this is ase convention + v_pref = 1 * 1e4 / 1.602176621e6 + vol = structure.get_volume() + results['stress'] = system.data["virials"][0] / (v_pref * vol) + + structure.calc = SinglePointCalculator(structure, **results) + structures.append(structure) + + return structures def append(self, system): """ From 79bc35b08ac8b83238b139c6d2208a8e00c553cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mari=C3=A1n=20Rynik?= Date: Wed, 2 Dec 2020 14:04:37 +0100 Subject: [PATCH 10/19] bugfix - register to_ase_structure correctly --- dpdata/system.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dpdata/system.py b/dpdata/system.py index d3542e52e..f5e1ffb3e 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -40,6 +40,10 @@ def decorator(func): return func return decorator + def __add__(self, other): + self.funcs.update(other.funcs) + return self + class System (MSONable) : ''' @@ -1046,6 +1050,7 @@ def __init__ (self, self.apply_type_map(type_map) register_from_funcs = Register() + register_to_funcs = System.register_to_funcs + Register() def __repr__(self): return self.__str__() From e9d689f6fdf4a42b43b2a06b8aab26d8e5f73f62 Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 6 Jan 2021 12:45:46 +0800 Subject: [PATCH 11/19] add pbc_coords for water --- dpdata/md/water.py | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/dpdata/md/water.py b/dpdata/md/water.py index 8c38a108a..75ad1ad2d 100644 --- a/dpdata/md/water.py +++ b/dpdata/md/water.py @@ -1,5 +1,6 @@ import numpy as np from .pbc import posi_diff +from .pbc import posi_shift def compute_bonds (box, posis, @@ -179,3 +180,26 @@ def find_ions (atype, else : raise RuntimeError("unknow case: numb of O bonded to H > 1") return no, noh, noh2, noh3, nh + + + +def pbc_coords(cells, + coords, + atom_types, + oh_sel = [0, 1], + max_roh = 1.3): + bonds = compute_bonds(cells, coords, atom_types, oh_sel = oh_sel, max_roh = max_roh, uniq_hbond = True) + + new_coords = np.copy(coords) + natoms = len(atom_types) + o_type = oh_sel[0] + h_type = oh_sel[1] + for ii in range(natoms): + if atom_types[ii] == o_type: + assert(len(bonds[ii]) == 2), 'O has more than 2 bonded Hs, stop' + for jj in bonds[ii]: + assert(atom_types[jj] == h_type), 'The atom bonded to O is not H, stop' + shift = posi_shift(cells, coords[jj], coords[ii]) + new_coords[jj] = coords[jj] + np.matmul(shift, cells) + return new_coords + From 4c6c6fb01c3ea6c4dad99ad7f34fcc915dfc05e6 Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 6 Jan 2021 12:45:59 +0800 Subject: [PATCH 12/19] add coordination number calculation to rdf --- dpdata/md/rdf.py | 24 +++++++++++++++++++++--- 1 file changed, 21 insertions(+), 3 deletions(-) diff --git a/dpdata/md/rdf.py b/dpdata/md/rdf.py index 6c514ca0b..e1fd50a23 100644 --- a/dpdata/md/rdf.py +++ b/dpdata/md/rdf.py @@ -21,6 +21,15 @@ def rdf(sys, Maximal range of rdf calculation nbins: int Number of bins for rdf calculation + + Returns + ------- + xx: np.array + The lattice of r + rdf: np.array + The value of rdf at r + coord: np.array + The coordination number up to r """ return compute_rdf(sys['cells'], sys['coords'], sys['atom_types'], sel_type = sel_type, @@ -36,12 +45,16 @@ def compute_rdf(box, nframes = box.shape[0] xx = None all_rdf = [] + all_cod = [] for ii in range(nframes): - xx, rdf = _compute_rdf_1frame(box[ii], posis[ii], atype, sel_type, max_r, nbins) + xx, rdf, cod = _compute_rdf_1frame(box[ii], posis[ii], atype, sel_type, max_r, nbins) all_rdf.append(rdf) + all_cod.append(cod) all_rdf = np.array(all_rdf).reshape([nframes, -1]) + all_cod = np.array(all_cod).reshape([nframes, -1]) all_rdf = np.average(all_rdf, axis = 0) - return xx, all_rdf + all_cod = np.average(all_cod, axis = 0) + return xx, all_rdf, all_cod def _compute_rdf_1frame(box, posis, @@ -65,6 +78,7 @@ def _compute_rdf_1frame(box, nlist = ase.neighborlist.NeighborList(max_r, self_interaction=False, bothways=True, primitive=ase.neighborlist.NewPrimitiveNeighborList) nlist.update(atoms) stat = np.zeros(nbins) + stat_acc = np.zeros(nbins) hh = max_r / float(nbins) for ii in range(natoms) : # atom "0" @@ -90,13 +104,17 @@ def _compute_rdf_1frame(box, for ii in sel_type[1]: c1 += np.sum(atype == ii) rho1 = c1 / np.linalg.det(box) + # compute coordination number + for ii in range(1, nbins): + stat_acc[ii] = stat_acc[ii-1] + stat[ii-1] + stat_acc = stat_acc / c0 # compute rdf for ii in range(nbins): vol = 4./3. * np.pi * ( ((ii+1)*hh) ** 3 - ((ii)*hh) ** 3 ) rho = stat[ii] / vol stat[ii] = rho / rho1 / c0 xx = np.arange(0, max_r-1e-12, hh) - return xx, stat + return xx, stat, stat_acc if __name__ == '__main__': import dpdata From a843feec3149226197bb4c22e091e8b4cbbd4d32 Mon Sep 17 00:00:00 2001 From: Chentao168 Date: Sat, 9 Jan 2021 21:10:25 +0800 Subject: [PATCH 13/19] new_energy --- dpdata/qe/scf.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dpdata/qe/scf.py b/dpdata/qe/scf.py index 33bbdbc9a..613bed4d7 100755 --- a/dpdata/qe/scf.py +++ b/dpdata/qe/scf.py @@ -64,10 +64,11 @@ def get_coords (lines) : return list(atom_names), atom_numbs, atom_types, coord def get_energy (lines) : + energy = None for ii in lines : if '! total energy' in ii : - return ry2ev * float(ii.split('=')[1].split()[0]) - return None + energy = ry2ev * float(ii.split('=')[1].split()[0]) + return energy def get_force (lines) : blk = get_block(lines, 'Forces acting on atoms', skip = 1) From bcda8688017862ddd111503572f8b1f5dce3a48b Mon Sep 17 00:00:00 2001 From: Chentao168 Date: Mon, 1 Feb 2021 23:15:46 +0800 Subject: [PATCH 14/19] test --- tests/qe.scf/Al.in | 43 +++ tests/qe.scf/Al.out | 557 +++++++++++++++++++++++++++++ tests/test_qe_pw_scf_energy_bug.py | 24 ++ 3 files changed, 624 insertions(+) create mode 100755 tests/qe.scf/Al.in create mode 100644 tests/qe.scf/Al.out create mode 100644 tests/test_qe_pw_scf_energy_bug.py diff --git a/tests/qe.scf/Al.in b/tests/qe.scf/Al.in new file mode 100755 index 000000000..e3a430142 --- /dev/null +++ b/tests/qe.scf/Al.in @@ -0,0 +1,43 @@ +&CONTROL + calculation = "scf", + pseudo_dir = "../", + prefix = "Aluminium", + wf_collect = .True., + tstress = .True., + tprnfor = .True., + outdir = "./", + iprint = 1, +/ +&SYSTEM + ibrav = 0, + nat = 4, + ntyp = 1, + occupations ='smearing', + smearing ='fermi-dirac', + degauss = 0.001d0, + nosym = .true., + ecutwfc = 50, + nbnd = 12, +/ +&ELECTRONS + electron_maxstep = 200, + mixing_mode = 'plain', + conv_thr = 1.0D-8, + mixing_beta = 0.7D0, +/ +CELL_PARAMETERS (angstrom) +4.04 0 0 +0 4.04 0 +0 0 4.04 + +ATOMIC_SPECIES +Al 26.98 Al.pbe-n-nc.UPF + +ATOMIC_POSITIONS (crystal) +Al 0 0 0 +Al 0 0.5 0.5 +Al 0.5 0 0.5 +Al 0.5 0.5 0 + +K_POINTS (automatic) +2 2 2 0 0 0 diff --git a/tests/qe.scf/Al.out b/tests/qe.scf/Al.out new file mode 100644 index 000000000..882ccba83 --- /dev/null +++ b/tests/qe.scf/Al.out @@ -0,0 +1,557 @@ + + Program PWSCF v.6.7MaX starts on 1Feb2021 at 22:29:45 + + This program is part of the open-source Quantum ESPRESSO suite + for quantum simulation of materials; please cite + "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); + "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017); + URL http://www.quantum-espresso.org", + in publications or presentations arising from this work. More details at + http://www.quantum-espresso.org/quote + + Parallel version (MPI), running on 8 processors + + MPI processes distributed on 1 nodes + R & G space division: proc/nbgrp/npool/nimage = 8 + Reading input from Al.in + + Current dimensions of program PWSCF are: + Max number of different atomic species (ntypx) = 10 + Max number of k-points (npk) = 40000 + Max angular momentum in pseudopotentials (lmaxx) = 3 + + Subspace diagonalization in iterative solution of the eigenvalue problem: + one sub-group per band group will be used + scalapack distributed-memory algorithm (size of sub-group: 2* 2 procs) + + Found symmetry operation: I + ( 0.0000 -0.5000 -0.5000) + This is a supercell, fractional translations are disabled + + Parallelization info + -------------------- + sticks: dense smooth PW G-vecs: dense smooth PW + Min 116 116 35 2654 2654 446 + Max 117 117 37 2657 2657 447 + Sum 933 933 285 21247 21247 3575 + + + + bravais-lattice index = 0 + lattice parameter (alat) = 7.6345 a.u. + unit-cell volume = 444.9802 (a.u.)^3 + number of atoms/cell = 4 + number of atomic types = 1 + number of electrons = 12.00 + number of Kohn-Sham states= 12 + kinetic-energy cutoff = 50.0000 Ry + charge density cutoff = 200.0000 Ry + scf convergence threshold = 1.0E-08 + mixing beta = 0.7000 + number of iterations used = 8 plain mixing + Exchange-correlation= PBE + ( 1 4 3 4 0 0 0) + + celldm(1)= 7.634494 celldm(2)= 0.000000 celldm(3)= 0.000000 + celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 + + crystal axes: (cart. coord. in units of alat) + a(1) = ( 1.000000 0.000000 0.000000 ) + a(2) = ( 0.000000 1.000000 0.000000 ) + a(3) = ( 0.000000 0.000000 1.000000 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( 1.000000 0.000000 0.000000 ) + b(2) = ( 0.000000 1.000000 0.000000 ) + b(3) = ( 0.000000 0.000000 1.000000 ) + + + PseudoPot. # 1 for Al read from file: + ../Al.pbe-n-nc.UPF + MD5 check sum: f1c8cd6d2c6964a193fa1ea9a097ceb9 + Pseudo is Norm-conserving + core correction, Zval = 3.0 + Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9656 + Using radial grid of 1135 points, 2 beta functions with: + l(1) = 0 + l(2) = 1 + + atomic species valence mass pseudopotential + Al 3.00 26.98000 Al( 1.00) + + No symmetry found + + + + Cartesian axes + + site n. atom positions (alat units) + 1 Al tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) + 2 Al tau( 2) = ( 0.0000000 0.5000000 0.5000000 ) + 3 Al tau( 3) = ( 0.5000000 0.0000000 0.5000000 ) + 4 Al tau( 4) = ( 0.5000000 0.5000000 0.0000000 ) + + number of k points= 8 Fermi-Dirac smearing, width (Ry)= 0.0010 + cart. coord. in units 2pi/alat + k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.2500000 + k( 2) = ( 0.0000000 0.0000000 -0.5000000), wk = 0.2500000 + k( 3) = ( 0.0000000 -0.5000000 0.0000000), wk = 0.2500000 + k( 4) = ( 0.0000000 -0.5000000 -0.5000000), wk = 0.2500000 + k( 5) = ( -0.5000000 0.0000000 0.0000000), wk = 0.2500000 + k( 6) = ( -0.5000000 0.0000000 -0.5000000), wk = 0.2500000 + k( 7) = ( -0.5000000 -0.5000000 0.0000000), wk = 0.2500000 + k( 8) = ( -0.5000000 -0.5000000 -0.5000000), wk = 0.2500000 + + Dense grid: 21247 G-vectors FFT dimensions: ( 36, 36, 36) + + Estimated max dynamical RAM per process > 2.53 MB + + Estimated total dynamical RAM > 20.22 MB + + Check: negative core charge= -0.000005 + + Initial potential from superposition of free atoms + + starting charge 11.99084, renormalised to 12.00000 + Starting wfcs are 16 randomized atomic wfcs + + total cpu time spent up to now is 0.2 secs + + Self-consistent Calculation + + iteration # 1 ecut= 50.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.00E-02, avg # of iterations = 2.8 + + Threshold (ethr) on eigenvalues was too large: + Diagonalizing with lowered threshold + + Davidson diagonalization with overlap + ethr = 3.17E-04, avg # of iterations = 1.9 + + total cpu time spent up to now is 0.6 secs + + k = 0.0000 0.0000 0.0000 band energies (ev): + + -3.2360 5.0027 5.0027 5.0027 6.3490 6.3490 6.3490 13.5555 + 13.5556 13.5556 13.5556 13.5556 + + k = 0.0000 0.0000-0.5000 band energies (ev): + + -0.9727 -0.9727 7.0885 7.0885 7.0886 7.0886 8.0679 8.0679 + 9.1152 9.1152 15.4767 15.4768 + + k = 0.0000-0.5000 0.0000 band energies (ev): + + -0.9727 -0.9727 7.0885 7.0885 7.0885 7.0886 8.0679 8.0679 + 9.1152 9.1152 15.4767 15.4767 + + k = 0.0000-0.5000-0.5000 band energies (ev): + + 1.2520 1.2520 1.2520 1.2520 9.1779 9.1779 9.1779 9.1780 + 10.6997 10.6997 10.6997 10.6997 + + k =-0.5000 0.0000 0.0000 band energies (ev): + + -0.9727 -0.9727 7.0885 7.0885 7.0886 7.0886 8.0679 8.0679 + 9.1152 9.1152 15.4767 15.4768 + + k =-0.5000 0.0000-0.5000 band energies (ev): + + 1.2520 1.2520 1.2520 1.2520 9.1779 9.1779 9.1780 9.1780 + 10.6997 10.6997 10.6997 10.6997 + + k =-0.5000-0.5000 0.0000 band energies (ev): + + 1.2520 1.2520 1.2520 1.2520 9.1779 9.1779 9.1780 9.1780 + 10.6997 10.6997 10.6997 10.6997 + + k =-0.5000-0.5000-0.5000 band energies (ev): + + 3.3086 3.3086 3.3086 3.3087 3.5896 3.5896 3.5896 3.5896 + 19.3649 19.3650 19.3650 19.3651 + + the Fermi energy is 8.0679 ev + +! total energy = -21.76174003 Ry + estimated scf accuracy < 0.03820994 Ry + smearing contrib. (-TS) = -0.00103972 Ry + internal energy E=F+TS = -21.76070031 Ry + + The total energy is F=E-TS. E is the sum of the following terms: + one-electron contribution = 11.87797707 Ry + hartree contribution = 0.02122794 Ry + xc contribution = -12.10349065 Ry + ewald contribution = -21.61964430 Ry + scf correction = 0.06322963 Ry + + iteration # 2 ecut= 50.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 3.18E-04, avg # of iterations = 1.0 + + total cpu time spent up to now is 0.8 secs + + k = 0.0000 0.0000 0.0000 band energies (ev): + + -3.2685 4.9748 4.9748 4.9748 6.3005 6.3005 6.3006 13.4945 + 13.4945 13.4946 13.4946 13.4947 + + k = 0.0000 0.0000-0.5000 band energies (ev): + + -1.0064 -1.0062 7.0578 7.0578 7.0580 7.0580 8.0797 8.0798 + 8.9742 8.9743 15.4122 15.4124 + + k = 0.0000-0.5000 0.0000 band energies (ev): + + -1.0067 -1.0060 7.0576 7.0576 7.0582 7.0583 8.0797 8.0798 + 8.9742 8.9743 15.4120 15.4123 + + k = 0.0000-0.5000-0.5000 band energies (ev): + + 1.2169 1.2173 1.2178 1.2180 9.1439 9.1442 9.1447 9.1448 + 10.6348 10.6351 10.6357 10.6359 + + k =-0.5000 0.0000 0.0000 band energies (ev): + + -1.0065 -1.0062 7.0577 7.0578 7.0581 7.0581 8.0797 8.0798 + 8.9742 8.9743 15.4122 15.4123 + + k =-0.5000 0.0000-0.5000 band energies (ev): + + 1.2172 1.2174 1.2176 1.2178 9.1442 9.1444 9.1445 9.1447 + 10.6351 10.6353 10.6355 10.6357 + + k =-0.5000-0.5000 0.0000 band energies (ev): + + 1.2169 1.2173 1.2177 1.2180 9.1439 9.1442 9.1446 9.1449 + 10.6348 10.6352 10.6356 10.6360 + + k =-0.5000-0.5000-0.5000 band energies (ev): + + 3.3028 3.3030 3.3030 3.3031 3.5193 3.5194 3.5194 3.5195 + 19.2453 19.2454 19.2454 19.2455 + + the Fermi energy is 8.0798 ev + +! total energy = -21.76159248 Ry + estimated scf accuracy < 0.00229810 Ry + smearing contrib. (-TS) = -0.00103972 Ry + internal energy E=F+TS = -21.76055276 Ry + + The total energy is F=E-TS. E is the sum of the following terms: + one-electron contribution = 11.88942524 Ry + hartree contribution = 0.02870492 Ry + xc contribution = -12.06302033 Ry + ewald contribution = -21.61964430 Ry + scf correction = 0.00398171 Ry + + iteration # 3 ecut= 50.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 1.92E-05, avg # of iterations = 1.2 + + total cpu time spent up to now is 1.0 secs + + k = 0.0000 0.0000 0.0000 band energies (ev): + + -3.2755 4.9705 4.9705 4.9705 6.2861 6.2863 6.2865 13.4778 + 13.4779 13.4779 13.4780 13.4780 + + k = 0.0000 0.0000-0.5000 band energies (ev): + + -1.0139 -1.0135 7.0525 7.0526 7.0529 7.0529 8.0850 8.0855 + 8.9312 8.9313 15.3944 15.3946 + + k = 0.0000-0.5000 0.0000 band energies (ev): + + -1.0139 -1.0135 7.0525 7.0525 7.0530 7.0530 8.0850 8.0855 + 8.9313 8.9313 15.3944 15.3946 + + k = 0.0000-0.5000-0.5000 band energies (ev): + + 1.2094 1.2098 1.2098 1.2102 9.1379 9.1383 9.1384 9.1387 + 10.6162 10.6165 10.6166 10.6169 + + k =-0.5000 0.0000 0.0000 band energies (ev): + + -1.0138 -1.0137 7.0527 7.0527 7.0528 7.0528 8.0852 8.0853 + 8.9313 8.9313 15.3945 15.3945 + + k =-0.5000 0.0000-0.5000 band energies (ev): + + 1.2095 1.2097 1.2099 1.2100 9.1380 9.1382 9.1384 9.1386 + 10.6164 10.6165 10.6166 10.6167 + + k =-0.5000-0.5000 0.0000 band energies (ev): + + 1.2095 1.2097 1.2100 1.2101 9.1380 9.1382 9.1385 9.1386 + 10.6163 10.6164 10.6167 10.6168 + + k =-0.5000-0.5000-0.5000 band energies (ev): + + 3.3040 3.3044 3.3045 3.3049 3.5002 3.5004 3.5005 3.5007 + 19.2100 19.2101 19.2101 19.2103 + + the Fermi energy is 8.0853 ev + +! total energy = -21.76175335 Ry + estimated scf accuracy < 0.00000644 Ry + smearing contrib. (-TS) = -0.00103967 Ry + internal energy E=F+TS = -21.76071368 Ry + + The total energy is F=E-TS. E is the sum of the following terms: + one-electron contribution = 11.89482626 Ry + hartree contribution = 0.02889136 Ry + xc contribution = -12.06507400 Ry + ewald contribution = -21.61964430 Ry + scf correction = 0.00028700 Ry + + iteration # 4 ecut= 50.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 5.36E-08, avg # of iterations = 2.1 + + total cpu time spent up to now is 1.2 secs + + k = 0.0000 0.0000 0.0000 band energies (ev): + + -3.2748 4.9713 4.9713 4.9713 6.2860 6.2870 6.2883 13.4785 + 13.4790 13.4791 13.4794 13.4796 + + k = 0.0000 0.0000-0.5000 band energies (ev): + + -1.0139 -1.0121 7.0526 7.0527 7.0545 7.0545 8.0837 8.0863 + 8.9336 8.9338 15.3949 15.3959 + + k = 0.0000-0.5000 0.0000 band energies (ev): + + -1.0141 -1.0119 7.0524 7.0524 7.0547 7.0547 8.0834 8.0866 + 8.9335 8.9339 15.3953 15.3964 + + k = 0.0000-0.5000-0.5000 band energies (ev): + + 1.2086 1.2103 1.2107 1.2126 9.1371 9.1390 9.1394 9.1413 + 10.6160 10.6174 10.6178 10.6193 + + k =-0.5000 0.0000 0.0000 band energies (ev): + + -1.0131 -1.0128 7.0535 7.0535 7.0537 7.0537 8.0849 8.0851 + 8.9337 8.9337 15.3956 15.3957 + + k =-0.5000 0.0000-0.5000 band energies (ev): + + 1.2094 1.2100 1.2110 1.2119 9.1380 9.1385 9.1397 9.1406 + 10.6168 10.6170 10.6181 10.6185 + + k =-0.5000-0.5000 0.0000 band energies (ev): + + 1.2092 1.2097 1.2113 1.2120 9.1378 9.1383 9.1400 9.1407 + 10.6166 10.6168 10.6183 10.6187 + + k =-0.5000-0.5000-0.5000 band energies (ev): + + 3.3023 3.3044 3.3048 3.3073 3.5005 3.5018 3.5020 3.5032 + 19.2114 19.2121 19.2126 19.2131 + + the Fermi energy is 8.0850 ev + +! total energy = -21.76175564 Ry + estimated scf accuracy < 0.00002038 Ry + smearing contrib. (-TS) = -0.00103827 Ry + internal energy E=F+TS = -21.76071737 Ry + + The total energy is F=E-TS. E is the sum of the following terms: + one-electron contribution = 11.89466555 Ry + hartree contribution = 0.02891972 Ry + xc contribution = -12.06506812 Ry + ewald contribution = -21.61964430 Ry + scf correction = 0.00040978 Ry + + iteration # 5 ecut= 50.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 5.36E-08, avg # of iterations = 1.0 + + total cpu time spent up to now is 1.3 secs + + k = 0.0000 0.0000 0.0000 band energies (ev): + + -3.2748 4.9713 4.9713 4.9713 6.2870 6.2871 6.2871 13.4791 + 13.4791 13.4791 13.4791 13.4791 + + k = 0.0000 0.0000-0.5000 band energies (ev): + + -1.0130 -1.0129 7.0535 7.0535 7.0537 7.0537 8.0849 8.0851 + 8.9337 8.9337 15.3957 15.3958 + + k = 0.0000-0.5000 0.0000 band energies (ev): + + -1.0131 -1.0128 7.0535 7.0535 7.0537 7.0537 8.0849 8.0851 + 8.9337 8.9337 15.3956 15.3957 + + k = 0.0000-0.5000-0.5000 band energies (ev): + + 1.2104 1.2105 1.2107 1.2108 9.1390 9.1391 9.1393 9.1394 + 10.6174 10.6175 10.6177 10.6179 + + k =-0.5000 0.0000 0.0000 band energies (ev): + + -1.0130 -1.0129 7.0535 7.0535 7.0537 7.0537 8.0850 8.0850 + 8.9337 8.9337 15.3957 15.3957 + + k =-0.5000 0.0000-0.5000 band energies (ev): + + 1.2104 1.2106 1.2106 1.2107 9.1391 9.1392 9.1392 9.1393 + 10.6175 10.6176 10.6176 10.6178 + + k =-0.5000-0.5000 0.0000 band energies (ev): + + 1.2103 1.2105 1.2107 1.2108 9.1390 9.1391 9.1393 9.1394 + 10.6174 10.6175 10.6177 10.6179 + + k =-0.5000-0.5000-0.5000 band energies (ev): + + 3.3046 3.3047 3.3047 3.3048 3.5018 3.5019 3.5019 3.5020 + 19.2123 19.2123 19.2123 19.2124 + + the Fermi energy is 8.0850 ev + +! total energy = -21.76175739 Ry + estimated scf accuracy < 0.00000029 Ry + smearing contrib. (-TS) = -0.00103972 Ry + internal energy E=F+TS = -21.76071767 Ry + + The total energy is F=E-TS. E is the sum of the following terms: + one-electron contribution = 11.89466503 Ry + hartree contribution = 0.02898289 Ry + xc contribution = -12.06473946 Ry + ewald contribution = -21.61964430 Ry + scf correction = 0.00001818 Ry + + iteration # 6 ecut= 50.00 Ry beta= 0.70 + Davidson diagonalization with overlap + ethr = 2.43E-09, avg # of iterations = 1.5 + + total cpu time spent up to now is 1.5 secs + + End of self-consistent calculation + + k = 0.0000 0.0000 0.0000 ( 2601 PWs) bands (ev): + + -3.2749 4.9712 4.9712 4.9712 6.2870 6.2870 6.2870 13.4789 + 13.4789 13.4790 13.4790 13.4790 + + k = 0.0000 0.0000-0.5000 ( 2666 PWs) bands (ev): + + -1.0131 -1.0130 7.0535 7.0535 7.0536 7.0536 8.0851 8.0851 + 8.9332 8.9333 15.3955 15.3956 + + k = 0.0000-0.5000 0.0000 ( 2666 PWs) bands (ev): + + -1.0131 -1.0129 7.0535 7.0535 7.0536 7.0536 8.0851 8.0851 + 8.9332 8.9333 15.3955 15.3956 + + k = 0.0000-0.5000-0.5000 ( 2680 PWs) bands (ev): + + 1.2104 1.2105 1.2106 1.2106 9.1390 9.1391 9.1392 9.1393 + 10.6173 10.6174 10.6175 10.6176 + + k =-0.5000 0.0000 0.0000 ( 2666 PWs) bands (ev): + + -1.0131 -1.0130 7.0535 7.0535 7.0536 7.0536 8.0851 8.0851 + 8.9333 8.9333 15.3955 15.3956 + + k =-0.5000 0.0000-0.5000 ( 2680 PWs) bands (ev): + + 1.2104 1.2105 1.2105 1.2106 9.1391 9.1391 9.1392 9.1392 + 10.6174 10.6174 10.6175 10.6175 + + k =-0.5000-0.5000 0.0000 ( 2680 PWs) bands (ev): + + 1.2104 1.2105 1.2106 1.2106 9.1390 9.1391 9.1392 9.1393 + 10.6173 10.6174 10.6175 10.6176 + + k =-0.5000-0.5000-0.5000 ( 2608 PWs) bands (ev): + + 3.3047 3.3047 3.3047 3.3047 3.5016 3.5017 3.5017 3.5018 + 19.2120 19.2120 19.2120 19.2121 + + the Fermi energy is 8.0851 ev + +! total energy = -21.76175741 Ry + estimated scf accuracy < 7.0E-09 Ry + smearing contrib. (-TS) = -0.00103972 Ry + internal energy E=F+TS = -21.76071769 Ry + + The total energy is F=E-TS. E is the sum of the following terms: + one-electron contribution = 11.89471334 Ry + hartree contribution = 0.02897992 Ry + xc contribution = -12.06476665 Ry + ewald contribution = -21.61964430 Ry + + convergence has been achieved in 6 iterations + + Forces acting on atoms (cartesian axes, Ry/au): + + atom 1 type 1 force = -0.00000064 0.00000288 -0.00000097 + atom 2 type 1 force = -0.00000087 -0.00000194 0.00000106 + atom 3 type 1 force = 0.00000054 0.00000195 0.00000063 + atom 4 type 1 force = 0.00000096 -0.00000289 -0.00000071 + + Total force = 0.000005 Total SCF correction = 0.000050 + SCF correction compared to forces is large: reduce conv_thr to get better values + + + Computing stress (Cartesian axis) and pressure + + total stress (Ry/bohr**3) (kbar) P= -37.45 + -0.00025459 -0.00000000 -0.00000000 -37.45 -0.00 -0.00 + -0.00000000 -0.00025458 -0.00000000 -0.00 -37.45 -0.00 + -0.00000000 -0.00000000 -0.00025458 -0.00 -0.00 -37.45 + + + Writing output data file ./Aluminium.save/ + + init_run : 0.10s CPU 0.12s WALL ( 1 calls) + electrons : 1.10s CPU 1.35s WALL ( 1 calls) + forces : 0.02s CPU 0.02s WALL ( 1 calls) + stress : 0.05s CPU 0.06s WALL ( 1 calls) + + Called by init_run: + wfcinit : 0.08s CPU 0.08s WALL ( 1 calls) + potinit : 0.01s CPU 0.01s WALL ( 1 calls) + hinit0 : 0.01s CPU 0.01s WALL ( 1 calls) + + Called by electrons: + c_bands : 0.90s CPU 1.13s WALL ( 7 calls) + sum_band : 0.15s CPU 0.16s WALL ( 7 calls) + v_of_rho : 0.04s CPU 0.05s WALL ( 7 calls) + mix_rho : 0.01s CPU 0.01s WALL ( 7 calls) + + Called by c_bands: + init_us_2 : 0.02s CPU 0.02s WALL ( 136 calls) + cegterg : 0.88s CPU 1.10s WALL ( 56 calls) + + Called by *egterg: + cdiaghg : 0.26s CPU 0.36s WALL ( 140 calls) + h_psi : 0.58s CPU 0.69s WALL ( 156 calls) + g_psi : 0.00s CPU 0.00s WALL ( 92 calls) + + Called by h_psi: + h_psi:calbec : 0.02s CPU 0.02s WALL ( 156 calls) + vloc_psi : 0.55s CPU 0.65s WALL ( 156 calls) + add_vuspsi : 0.01s CPU 0.01s WALL ( 156 calls) + + General routines + calbec : 0.02s CPU 0.03s WALL ( 196 calls) + fft : 0.03s CPU 0.03s WALL ( 95 calls) + ffts : 0.00s CPU 0.00s WALL ( 7 calls) + fftw : 0.61s CPU 0.71s WALL ( 3988 calls) + + Parallel routines + fft_scatt_xy : 0.09s CPU 0.11s WALL ( 4090 calls) + fft_scatt_yz : 0.30s CPU 0.36s WALL ( 4090 calls) + + PWSCF : 1.33s CPU 1.63s WALL + + + This run was terminated on: 22:29:47 1Feb2021 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/tests/test_qe_pw_scf_energy_bug.py b/tests/test_qe_pw_scf_energy_bug.py new file mode 100644 index 000000000..975aca487 --- /dev/null +++ b/tests/test_qe_pw_scf_energy_bug.py @@ -0,0 +1,24 @@ +import os +import numpy as np +import unittest +from context import dpdata + +class TestPWSCFSinglePointEnergy: + + def test_energy(self) : + ref_energy = -296.08379065679094669 + self.assertAlmostEqual(self.system_al.data['energies'][0], ref_energy) + +class TestPWSCFLabeledOutput(unittest.TestCase, TestPWSCFSinglePointEnergy): + + def setUp(self): + self.system_al = dpdata.LabeledSystem('qe.scf/Al.out',fmt='qe/pw/scf') + +class TestPWSCFLabeledOutputListInput(unittest.TestCase, TestPWSCFSinglePointEnergy): + + def setUp(self): + self.system_al = dpdata.LabeledSystem(['qe.scf/Al.in', 'qe.scf/Al.out'], fmt='qe/pw/scf') + +if __name__ == '__main__': + unittest.main() + From c89efa0d1d8226bc76ac972d343e4349faefe001 Mon Sep 17 00:00:00 2001 From: Yuan Fengbo Date: Tue, 9 Feb 2021 17:24:02 +0800 Subject: [PATCH 15/19] fix bug in cp2k coord units convert --- tests/cp2k/aimd/deepmd/coord.raw | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/cp2k/aimd/deepmd/coord.raw b/tests/cp2k/aimd/deepmd/coord.raw index 73c94e941..2f65ed6d8 100644 --- a/tests/cp2k/aimd/deepmd/coord.raw +++ b/tests/cp2k/aimd/deepmd/coord.raw @@ -1,3 +1,3 @@ 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3.209767580032348633e+00 6.404254436492919922e+00 6.404428482055664062e+00 3.212347269058227539e+00 8.956408500671386719e+00 6.400252819061279297e+00 3.210726499557495117e+00 1.280919551849365234e+00 8.961791992187500000e+00 3.212758541107177734e+00 3.836170196533203125e+00 8.964490890502929688e+00 3.206373691558837891e+00 6.403016090393066406e+00 8.961875915527343750e+00 3.207864284515380859e+00 8.961993217468261719e+00 8.960158348083496094e+00 3.210070610046386719e+00 -3.502698242664337158e-02 3.746033832430839539e-02 4.997550964355468750e+00 2.520578861236572266e+00 3.585025668144226074e-02 5.025019168853759766e+00 5.083852291107177734e+00 3.335775062441825867e-02 5.008239269256591797e+00 7.640606403350830078e+00 3.966629877686500549e-02 4.989236354827880859e+00 3.948704898357391357e-02 2.593201875686645508e+00 5.033899307250976562e+00 2.598308086395263672e+00 2.528058767318725586e+00 5.007804870605468750e+00 5.162371635437011719e+00 2.603828430175781250e+00 5.058613300323486328e+00 7.726068973541259766e+00 2.600023269653320312e+00 4.999958515167236328e+00 -3.637440875172615051e-02 5.090862274169921875e+00 5.011786460876464844e+00 2.593329668045043945e+00 5.081934452056884766e+00 5.055696487426757812e+00 5.151907444000244141e+00 5.160426139831542969e+00 4.993530273437500000e+00 7.648036956787109375e+00 5.159348964691162109e+00 5.034187316894531250e+00 3.586012497544288635e-02 7.644814491271972656e+00 5.007235527038574219e+00 2.599578857421875000e+00 7.725337028503417969e+00 5.046085357666015625e+00 5.163563251495361328e+00 7.721114635467529297e+00 5.031165599822998047e+00 7.725455760955810547e+00 7.723210811614990234e+00 5.011199474334716797e+00 From af8a7de34bb67c1a6413b91beea3d17fc8edfb6f Mon Sep 17 00:00:00 2001 From: Yuan Fengbo Date: Tue, 9 Feb 2021 17:27:51 +0800 Subject: [PATCH 16/19] fix bug in cp2k coord units convert 2 --- dpdata/cp2k/output.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/dpdata/cp2k/output.py b/dpdata/cp2k/output.py index c29e0e859..a488a7e15 100644 --- a/dpdata/cp2k/output.py +++ b/dpdata/cp2k/output.py @@ -190,9 +190,12 @@ 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, - float(line_list[3])*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]) + coords_list.append([float(line_list[1]), + float(line_list[2]), + float(line_list[3])]) atom_names=list(element_dict.keys()) atom_numbs=[] for ii in atom_names: From 73942e0e4d2f450d0626108ec93b526f2d27a283 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Fri, 12 Feb 2021 19:22:19 -0500 Subject: [PATCH 17/19] migirate to github actions --- .github/workflows/test.yml | 24 ++++++++++++++++++++++++ .travis.yml | 16 ---------------- 2 files changed, 24 insertions(+), 16 deletions(-) create mode 100644 .github/workflows/test.yml delete mode 100644 .travis.yml diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 000000000..7887343f8 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,24 @@ +name: Python package + +on: + - push + - pull_request + +jobs: + build: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.5, 3.6] + + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: pip install . coverage codecov + - name: Test + run: cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report + - run: codecov diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 379837c0b..000000000 --- a/.travis.yml +++ /dev/null @@ -1,16 +0,0 @@ -language: python -python: - - "3.5" - - "3.5-dev" # 3.5 development branch - - "3.6" - - "3.6-dev" # 3.6 development branch -# command to install dependencies -before_install: - - pip install coverage codecov -install: - - pip install . -# command to run tests -script: - - cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report -after_success: - - codecov From 95a48ea72daeb206d8595d2bde0fd722ef9cc4e9 Mon Sep 17 00:00:00 2001 From: robinzyb Date: Wed, 24 Feb 2021 15:45:22 +0800 Subject: [PATCH 18/19] remove useless py --- tests/cp2k/test.py | 56 ---------------------------------------------- 1 file changed, 56 deletions(-) delete mode 100755 tests/cp2k/test.py diff --git a/tests/cp2k/test.py b/tests/cp2k/test.py deleted file mode 100755 index dbfdae36e..000000000 --- a/tests/cp2k/test.py +++ /dev/null @@ -1,56 +0,0 @@ -import dpdata -import numpy as np - - -# simple test for cp2k -# first case: with force and virial information -print("first case") -print("--------------------------------------------------------------") -cp2k_output = dpdata.LabeledSystem('cp2k_output', fmt = 'cp2k/output') -print("atom name") -print(cp2k_output['atom_names']) -print("atom number") -print(cp2k_output['atom_numbs']) -print("atom type") -print(cp2k_output['atom_types']) -print("atom cell") -print(cp2k_output['cells']) -print("atom coord") -print(cp2k_output['coords']) -print("energyies") -print(cp2k_output['energies']) -print("forces") -print(cp2k_output['forces']) -print("virials") -print(cp2k_output['virials']) -# no virial - -cp2k_output.to_deepmd_raw('dpmd_raw') -cp2k_output.to_deepmd_npy('dpmd_npy') - -# second case: with force and no! virial information -# double header information is contained, to test robustness of this parser -print("\n") -print("\n") -print("second case") -print("---------------------------------------------------------------") - -cp2k_output = dpdata.LabeledSystem('cp2k_output_2', fmt = 'cp2k/output') -print("atom name") -print(cp2k_output['atom_names']) -print("atom number") -print(cp2k_output['atom_numbs']) -print("atom type") -print(cp2k_output['atom_types']) -#np.savetxt("ref_type", cp2k_output['atom_types']) -print("atom cell") -print(cp2k_output['cells']) -#np.savetxt("ref_cell", cp2k_output['cells'][0]) -print("atom coord") -print(cp2k_output['coords']) -#np.savetxt("ref_coord", cp2k_output['coords'][0]) -print("energyies") -print(cp2k_output['energies']) -print("forces") -print(cp2k_output['forces']) - From 94b97e362ce71b310c3153dce8f0613172f50db1 Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 24 Mar 2021 21:15:08 +0800 Subject: [PATCH 19/19] do not support py3.5 anymore. unit test under py 3.7 and 3.8 --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 7887343f8..3f805dd1a 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.5, 3.6] + python-version: [3.6, 3.7, 3.8] steps: - uses: actions/checkout@v2