diff --git a/.github/workflows/mirror_gitee.yml b/.github/workflows/mirror_gitee.yml new file mode 100644 index 000000000..97ea2e48a --- /dev/null +++ b/.github/workflows/mirror_gitee.yml @@ -0,0 +1,19 @@ +name: Mirror to Gitee Repo + +on: [ push, delete, create ] + +# Ensures that only one mirror task will run at a time. +concurrency: + group: git-mirror + +jobs: + git-mirror: + runs-on: ubuntu-latest + steps: + - uses: wearerequired/git-mirror-action@v1 + env: + ORGANIZATION: deepmodeling + SSH_PRIVATE_KEY: ${{ secrets.SYNC_GITEE_PRIVATE_KEY }} + with: + source-repo: "https://github.com/deepmodeling/dpdata.git" + destination-repo: "git@gitee.com:deepmodeling/dpdata.git" diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index fa40e3e73..350186d9f 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -23,7 +23,7 @@ jobs: - name: Install rdkit run: conda create -c conda-forge -n my-rdkit-env python=${{ matrix.python-version }} rdkit openbabel; - name: Install dependencies - run: source $CONDA/bin/activate my-rdkit-env && pip install .[amber] coverage codecov + run: source $CONDA/bin/activate my-rdkit-env && pip install .[amber,ase,pymatgen] coverage codecov - name: Test run: source $CONDA/bin/activate my-rdkit-env && cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report - name: Run codecov diff --git a/README.md b/README.md index e62802992..8702166e8 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -**dpdata** is a python package for manipulating DeePMD-kit, VASP, LAMMPS data formats. +**dpdata** is a python package for manipulating data formats of software in computational science, including DeePMD-kit, VASP, LAMMPS, GROMACS, Gaussian. dpdata only works with python 3.x. @@ -80,6 +80,8 @@ The `System` or `LabeledSystem` can be constructed from the following file forma | Amber | multi | True | True | LabeledSystem | 'amber/md' | | Amber/sqm | sqm.out | False | False | System | 'sqm/out' | | Gromacs | gro | True | False | System | 'gromacs/gro' | +| ABACUS | STRU | False | True | LabeledSystem | 'abacus/scf' | +| ABACUS | cif | True | True | LabeledSystem | 'abacus/md' | The Class `dpdata.MultiSystems` can read data from a dir which may contains many files of different systems, or from single xyz file which contains different systems. @@ -116,7 +118,7 @@ xyz_multi_systems.to_deepmd_raw('./my_deepmd_data/') ``` You may also use the following code to parse muti-system: -``` +```python from dpdata import LabeledSystem,MultiSystems from glob import glob """ @@ -255,7 +257,7 @@ If a valence of 3 is detected on carbon, the formal charge will be assigned to - # Plugins -One can follow [a simple example](plugin_example/) to add their own format by creating and installing plugins. It's crirical to add the [Format](dpdata/format.py) class to `entry_points['dpdata.plugins']` in `setup.py`: +One can follow [a simple example](plugin_example/) to add their own format by creating and installing plugins. It's critical to add the [Format](dpdata/format.py) class to `entry_points['dpdata.plugins']` in `setup.py`: ```py entry_points={ 'dpdata.plugins': [ diff --git a/docs/conf.py b/docs/conf.py index 51e185639..bed869fd7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -14,13 +14,14 @@ # import os import sys +from datetime import date sys.path.insert(0, os.path.abspath('..')) # -- Project information ----------------------------------------------------- project = 'dpdata' -copyright = '2019, Han Wang' +copyright = '2019-%d, Deep Modeling ' % date.today().year author = 'Han Wang' # The short X.Y version @@ -39,11 +40,12 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - 'sphinxcontrib.napoleon', + 'sphinx_rtd_theme', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', - 'sphinx.ext.githubpages', - 'm2r', + 'sphinx.ext.intersphinx', + 'numpydoc', + 'm2r2', ] # Add any paths that contain templates here, relative to this directory. @@ -79,7 +81,7 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'alabaster' +html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the @@ -90,7 +92,7 @@ # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +#html_static_path = ['_static'] # Custom sidebar templates, must be a dictionary that maps document names # to template names. @@ -161,3 +163,18 @@ # -- Extension configuration ------------------------------------------------- +def run_apidoc(_): + from sphinx.ext.apidoc import main + sys.path.append(os.path.join(os.path.dirname(__file__), '..')) + cur_dir = os.path.abspath(os.path.dirname(__file__)) + module = os.path.join(cur_dir, "..", "dpdata") + main(['-M', '--tocfile', 'api', '-H', 'API documentation', '-o', os.path.join(cur_dir, "api"), module, '--force']) + +def setup(app): + app.connect('builder-inited', run_apidoc) + + +intersphinx_mapping = { + "numpy": ("https://docs.scipy.org/doc/numpy/", None), + "python": ("https://docs.python.org/", None), +} diff --git a/docs/index.rst b/docs/index.rst index 5ea8253f2..116e3f690 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -10,22 +10,11 @@ Welcome to dpdata's documentation! :maxdepth: 2 :caption: Contents: + api/api .. mdinclude:: ../README.md -API documentation -================= - -.. automodule:: dpdata - -.. autoclass:: System - :members: __init__, __getitem__, get_nframes, get_natoms, sub_system, append, apply_pbc, to_lammps_lmp, to_vasp_poscar - -.. autoclass:: LabeledSystem - :members: __init__, sub_system, to_deepmd_raw, to_deepmd_npy - - Indices and tables ================== diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 000000000..e9704b8eb --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1 @@ +.[docs] diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py new file mode 100644 index 000000000..5b6a1730c --- /dev/null +++ b/dpdata/abacus/md.py @@ -0,0 +1,192 @@ +import os,sys +import numpy as np +from .scf import ry2ev, kbar2evperang3, get_block, get_geometry_in, get_cell, get_coords + +# Read in geometries from an ABACUS MD trajectory. +# The atomic coordinates are read in from generated files in OUT.XXXX. +# Energies, forces +# IMPORTANT: the program defaultly takes STRU input file as standard cell information, +# therefore the direct and cartesan coordinates read could be different from the ones in +# the output cif files!!! +# It is highly recommanded to use ORTHOGANAL coordinates in STRU file if you wish to get +# same coordinates in both dpdata and output cif files. + +def get_path_out(fname, inlines): + # This function is different from the same-name function in scf.py. + # This function returns OUT.XXXX's base directory. + path_out = os.path.join(fname, "OUT.ABACUS/") + for line in inlines: + if len(line)>0 and "suffix" in line and "suffix"==line.split()[0]: + suffix = line.split()[1] + path_out = os.path.join(fname, "OUT.%s/" % suffix) + break + return path_out + +def get_coord_dump_freq(inlines): + for line in inlines: + if len(line)>0 and "md_dumpmdfred" in line and "md_dumpmdfred" == line.split()[0]: + return int(line.split()[1]) + return 1 + +# set up a cell according to cell info in cif file. +# maybe useful later +''' +def setup_cell(a, b, c, alpha, beta, gamma): + cell = np.zeros(3, 3) + cell[0, 0] = a + cell[1, 0] = b*np.cos(gamma/180*np.pi) + cell[1, 1] = b*np.sin(gamma/180*np.pi) + cell[2, 0] = c*np.cos(beta/180*np.pi) + cell[2, 1] = c*(b*np.cos(alpha/180*np.pi) - cell[1, 0]*np.cos(beta/180*np.pi))/cell[1, 1] + cell[2, 2] = np.sqrt(c**2 - cell[2, 0]**2 - cell[2, 1]**2) + return cell +''' + +def get_single_coord_from_cif(pos_file, atom_names, natoms, cell): + assert(len(atom_names) == len(natoms)) + nele = len(atom_names) + total_natoms = sum(natoms) + coord = np.zeros([total_natoms, 3]) + a = 0 + b = 0 + c = 0 + alpha = 0 + beta = 0 + gamma = 0 + with open(pos_file, "r") as fp: + lines = fp.read().split("\n") + for line in lines: + if "_cell_length_a" in line: + a = float(line.split()[1]) + if "_cell_length_b" in line: + b = float(line.split()[1]) + if "_cell_length_c" in line: + c = float(line.split()[1]) + if "_cell_angle_alpha" in line: + alpha = float(line.split()[1]) + if "_cell_angle_beta" in line: + beta = float(line.split()[1]) + if "_cell_angle_gamma" in line: + gamma = float(line.split()[1]) + assert(a > 0 and b > 0 and c > 0 and alpha > 0 and beta > 0 and gamma > 0) + #cell = setup_cell(a, b, c, alpha, beta, gamma) + coord_lines = get_block(lines=lines, keyword="_atom_site_fract_z", skip=0, nlines = total_natoms) + + ia_idx = 0 + for it in range(nele): + for ia in range(natoms[it]): + coord_line = coord_lines[ia_idx].split() + assert(coord_line[0] == atom_names[it]) + coord[ia_idx, 0] = float(coord_line[1]) + coord[ia_idx, 1] = float(coord_line[2]) + coord[ia_idx, 2] = float(coord_line[3]) + ia_idx+=1 + coord = np.matmul(coord, cell) + # important! Coordinates are converted to Cartesian coordinate. + return coord + + +def get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell): + total_natoms = sum(natoms) + #cell = np.zeros(ndump, 3, 3) + coords = np.zeros([ndump, total_natoms, 3]) + pos_file = os.path.join(path_out, "STRU_READIN_ADJUST.cif") + # frame 0 file is different from any other frames + coords[0] = get_single_coord_from_cif(pos_file, atom_names, natoms, cell) + for dump_idx in range(1, ndump): + pos_file = os.path.join(path_out, "md_pos_%d.cif" %(dump_idx*dump_freq)) + #print("dump_idx = %s" %dump_idx) + coords[dump_idx] = get_single_coord_from_cif(pos_file, atom_names, natoms, cell) + return coords + +def get_energy_force_stress(outlines, inlines, dump_freq, ndump, natoms, atom_names): + stress = None + total_natoms = sum(natoms) + for line in inlines: + if len(line)>0 and "stress" in line and "stress" == line.split()[0] and "1" == line.split()[1]: + stress = np.zeros([ndump, 3, 3]) + break + if type(stress) != np.ndarray: + print("The ABACUS program has no stress output. Stress will not be read.") + nenergy = 0 + nforce = 0 + nstress = 0 + energy = np.zeros(ndump) + force = np.zeros([ndump, total_natoms, 3]) + + for line_idx, line in enumerate(outlines): + if "final etot is" in line: + if nenergy%dump_freq == 0: + energy[int(nenergy/dump_freq)] = float(line.split()[-2]) + nenergy+=1 + if "TOTAL-FORCE (eV/Angstrom)" in line: + for iatom in range(0, total_natoms): + force_line = outlines[line_idx+5+iatom] + atom_force = [float(i) for i in force_line.split()[1:]] + assert(len(atom_force) == 3) + atom_force = np.array(atom_force) + if nforce%dump_freq == 0: + force[int(nforce/dump_freq), iatom] = atom_force + nforce+=1 + assert(nforce==nenergy) + if "TOTAL-STRESS (KBAR)" in line: + for idx in range(0, 3): + stress_line = outlines[line_idx+4+idx] + single_stress = [float(i) for i in stress_line.split()] + if len(single_stress) != 3: + print(single_stress) + assert(len(single_stress) == 3) + single_stress = np.array(single_stress) + if nstress%dump_freq == 0: + stress[int(nstress/dump_freq), idx] = single_stress + nstress+=1 + assert(nstress==nforce) + if type(stress) == np.ndarray: + stress *= kbar2evperang3 + return energy, force, stress + + +def get_frame (fname): + if type(fname) == str: + # if the input parameter is only one string, it is assumed that it is the + # base directory containing INPUT file; + path_in = os.path.join(fname, "INPUT") + else: + raise RuntimeError('invalid input') + with open(path_in, 'r') as fp: + inlines = fp.read().split('\n') + geometry_path_in = get_geometry_in(fname, inlines) # base dir of STRU + path_out = get_path_out(fname, inlines) + + with open(geometry_path_in, 'r') as fp: + geometry_inlines = fp.read().split('\n') + celldm, cell = get_cell(geometry_inlines) + atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines) + # This coords is not to be used. + dump_freq = get_coord_dump_freq(inlines = inlines) + ndump = int(os.popen("ls -l %s | grep 'md_pos_' | wc -l" %path_out).readlines()[0]) + # number of dumped geometry files + coords = get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell) + + # TODO: Read in energies, forces and pressures. + with open(os.path.join(path_out, "running_md.log"), 'r') as fp: + outlines = fp.read().split('\n') + energy, force, stress = get_energy_force_stress(outlines, inlines, dump_freq, ndump, natoms, atom_names) + if type(stress) == np.ndarray: + stress *= np.linalg.det(cell) + data = {} + data['atom_names'] = atom_names + data['atom_numbs'] = natoms + data['atom_types'] = types + data['cells'] = np.zeros([ndump, 3, 3]) + for idx in range(ndump): + data['cells'][:, :, :] = cell + data['coords'] = coords + data['energies'] = energy + data['forces'] = force + data['virials'] = stress + if type(data['virials']) != np.ndarray: + del data['virials'] + data['orig'] = np.zeros(3) + + return data diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py index 3a42b853c..41dd40a70 100644 --- a/dpdata/abacus/scf.py +++ b/dpdata/abacus/scf.py @@ -1,11 +1,10 @@ import os,sys import numpy as np +from ..unit import EnergyConversion, PressureConversion, LengthConversion -bohr2ang = 0.5291770 -ry2ev = 13.605698 -kbar2evperang3 = 1e3 / 1.6021892e6 -# The consts are cited from $ABACUS_ROOT/source/src_global/constant.h - +bohr2ang = LengthConversion("bohr", "angstrom").value() +ry2ev = EnergyConversion("rydberg", "eV").value() +kbar2evperang3 = PressureConversion("kbar", "eV/angstrom^3").value() def get_block (lines, keyword, skip = 0, nlines = None): ret = [] @@ -175,6 +174,6 @@ def get_frame (fname): # print("virial = ", data['virials']) return data -if __name__ == "__main__": - path = "/home/lrx/work/12_ABACUS_dpgen_interface/dpdata/dpdata/tests/abacus.scf" - data = get_frame(path) \ No newline at end of file +#if __name__ == "__main__": +# path = "/home/lrx/work/12_ABACUS_dpgen_interface/dpdata/dpdata/tests/abacus.scf" +# data = get_frame(path) \ No newline at end of file diff --git a/dpdata/amber/md.py b/dpdata/amber/md.py index eb9d21b9f..64227a6a6 100644 --- a/dpdata/amber/md.py +++ b/dpdata/amber/md.py @@ -3,9 +3,11 @@ from scipy.io import netcdf import numpy as np from dpdata.amber.mask import pick_by_amber_mask +from dpdata.unit import EnergyConversion +from ..periodic_table import ELEMENTS -kcalmol2eV= 0.04336410390059322 -symbols = ['X', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og'] +kcalmol2eV = EnergyConversion("kcal_mol", "eV").value() +symbols = ['X'] + ELEMENTS energy_convert = kcalmol2eV force_convert = energy_convert diff --git a/dpdata/amber/sqm.py b/dpdata/amber/sqm.py index 6d5843126..f569ebe4b 100644 --- a/dpdata/amber/sqm.py +++ b/dpdata/amber/sqm.py @@ -1,11 +1,15 @@ import numpy as np +from dpdata.periodic_table import ELEMENTS +from dpdata.unit import EnergyConversion +kcal2ev = EnergyConversion("kcal_mol", "eV").value() START = 0 -READ_CHARGE = 1 -READ_CHARGE_SUCCESS = 2 +READ_ENERGY = 1 +READ_CHARGE = 2 READ_COORDS_START = 3 READ_COORDS = 6 +READ_FORCES = 7 def parse_sqm_out(fname): ''' @@ -14,15 +18,26 @@ def parse_sqm_out(fname): atom_symbols = [] coords = [] charges = [] + forces = [] + energies = [] + with open(fname) as f: - flag = 0 + flag = START for line in f: - if line.startswith(" Atom Element Mulliken Charge"): + if line.startswith(" Total SCF energy"): + flag = READ_ENERGY + elif line.startswith(" Atom Element Mulliken Charge"): flag = READ_CHARGE elif line.startswith(" Total Mulliken Charge"): - flag = READ_CHARGE_SUCCESS + flag = START elif line.startswith(" Final Structure"): flag = READ_COORDS_START + elif line.startswith("QMMM: Forces on QM atoms"): + flag = READ_FORCES + elif flag == READ_ENERGY: + energy = float(line.strip().split()[-2]) + energies.append(energy) + flag = START elif flag == READ_CHARGE: ls = line.strip().split() atom_symbols.append(ls[-2]) @@ -30,25 +45,61 @@ def parse_sqm_out(fname): elif READ_COORDS_START <= flag < READ_COORDS: flag += 1 elif flag == READ_COORDS: - ls = line.strip() - if not ls: - break - else: - symbol = line.strip().split()[-4] - coord = list(map(float, line.strip().split()[-3:])) - coords.append(coord) - return atom_symbols, charges, np.array(coords) - - -def to_system_data(fname): + coords.append([float(x) for x in line.strip().split()[-3:]]) + if len(coords) == len(charges): + flag = START + elif flag == READ_FORCES: + ll = line.strip() + forces.append([float(ll[-60:-40]), float(ll[-40:-20]), float(ll[-20:])]) + if len(forces) == len(charges): + flag = START + data = {} - atom_symbols, charges, coords = parse_sqm_out(fname) atom_names, data['atom_types'], atom_numbs = np.unique(atom_symbols, return_inverse=True, return_counts=True) + data['charges'] = np.array(charges) data['atom_names'] = list(atom_names) data['atom_numbs'] = list(atom_numbs) - data['charges'] = np.array([charges]) - data['coords'] = np.array([coords]) data['orig'] = np.array([0, 0, 0]) data['cells'] = np.array([[[100., 0., 0.], [0., 100., 0.], [0., 0., 100.]]]) data['nopbc'] = True + data['coords'] = np.array([coords]) + + energies = np.array(energies) + forces = np.array([forces], dtype=np.float32) * kcal2ev + if len(forces) > 0: + data['energies'] = energies + data['forces'] = forces + return data + +def make_sqm_in(data, fname=None, frame_idx=0, **kwargs): + symbols = [data['atom_names'][ii] for ii in data['atom_types']] + atomic_numbers = [ELEMENTS.index(ss) + 1 for ss in symbols] + charge = kwargs.get("charge", 0) + + # multiplicity + mult = kwargs.get("mult", 1) + if mult != 1 : + raise RuntimeError("Multiplicity is not 1, which is not supported by sqm") + + maxcyc = kwargs.get("maxcyc", 0) # 0 represents a single-point calculation + theory = kwargs.get("qm_theory", "DFTB3") + ret = "Run semi-emperical minimization\n" + ret += " &qmmm\n" + ret += f" qm_theory='{theory}'\n" + ret += f" qmcharge={charge}\n" + ret += f" maxcyc={maxcyc}\n" + ret += " verbosity=4\n" + ret += " /\n" + for ii in range(len(data['atom_types'])): + ret += "{:>4s}{:>6s}{:>14s}{:>14s}{:>14s}\n".format( + str(atomic_numbers[ii]), + str(symbols[ii]), + f"{data['coords'][frame_idx][ii, 0]:.4f}", + f"{data['coords'][frame_idx][ii, 1]:.4f}", + f"{data['coords'][frame_idx][ii, 2]:.4f}" + ) + if fname is not None: + with open(fname, 'w') as fp: + fp.write(ret) + return ret diff --git a/dpdata/bond_order_system.py b/dpdata/bond_order_system.py index 6b0869a9f..0a43bda5f 100644 --- a/dpdata/bond_order_system.py +++ b/dpdata/bond_order_system.py @@ -4,6 +4,7 @@ import dpdata.rdkit.utils from dpdata.rdkit.sanitize import Sanitizer, SanitizeError from copy import deepcopy +from rdkit.Chem import Conformer # import dpdata.rdkit.mol2 def check_BondOrderSystem(data): @@ -95,6 +96,12 @@ def from_fmt_obj(self, fmtobj, file_name, **kwargs): return self def to_fmt_obj(self, fmtobj, *args, **kwargs): + self.rdkit_mol.RemoveAllConformers() + for ii in range(self.get_nframes()): + conf = Conformer() + for idx in range(self.get_natoms()): + conf.SetAtomPosition(idx, self.data["coords"][ii][idx]) + self.rdkit_mol.AddConformer(conf, assignId=True) return fmtobj.to_bond_order_system(self.data, self.rdkit_mol, *args, **kwargs) def __repr__(self): @@ -151,7 +158,8 @@ def copy(self): self.__class__(data=deepcopy(self.data), rdkit_mol=new_mol) - # def __add__(self, other): + def __add__(self, other): + raise NotImplementedError("magic method '+' has not been implemented on BondOrderSystem") # ''' # magic method "+" operation # ''' diff --git a/dpdata/cp2k/output.py b/dpdata/cp2k/output.py index a38413719..9d13f7c99 100644 --- a/dpdata/cp2k/output.py +++ b/dpdata/cp2k/output.py @@ -3,11 +3,12 @@ import re from collections import OrderedDict from .cell import cell_to_low_triangle +from ..unit import EnergyConversion, LengthConversion, ForceConversion, PressureConversion #%% -AU_TO_ANG = 5.29177208590000E-01 -AU_TO_EV = 2.72113838565563E+01 -AU_TO_EV_EVERY_ANG = AU_TO_EV/AU_TO_ANG +AU_TO_ANG = LengthConversion("bohr", "angstrom").value() +AU_TO_EV = EnergyConversion("hartree", "eV").value() +AU_TO_EV_EVERY_ANG = ForceConversion("hartree/bohr", "eV/angstrom").value() delimiter_patterns=[] delimiter_p1 = re.compile(r'^ \* GO CP2K GO! \*+') delimiter_p2 = re.compile(r'^ \*+') @@ -221,10 +222,9 @@ def get_frames (fname) : coord_flag = False force_flag = False stress_flag = False - eV = 2.72113838565563E+01 # hatree to eV - angstrom = 5.29177208590000E-01 # Bohr to Angstrom - GPa = 160.21766208 # 1 eV/(Angstrom^3) = 160.21 GPa - fp = open(fname) + eV = EnergyConversion("hartree", "eV").value() + angstrom = LengthConversion("bohr", "angstrom").value() + GPa = PressureConversion("eV/angstrom^3", "GPa").value() atom_symbol_list = [] cell = [] coord = [] @@ -232,6 +232,15 @@ def get_frames (fname) : stress = [] cell_count = 0 coord_count = 0 + + fp = open(fname) + # check if output is converged, if not, return sys = 0 + content = fp.read() + count = content.count('SCF run converged') + if count == 0: + return [], [], [], [], [], [], [], [] + + fp.seek(0) for idx, ii in enumerate(fp) : if ('CELL| Vector' in ii) and (cell_count < 3) : cell.append(ii.split()[4:7]) diff --git a/dpdata/deepmd/hdf5.py b/dpdata/deepmd/hdf5.py new file mode 100644 index 000000000..ea373ae49 --- /dev/null +++ b/dpdata/deepmd/hdf5.py @@ -0,0 +1,149 @@ +"""Utils for deepmd/hdf5 format.""" +import h5py +import numpy as np + +from wcmatch.glob import globfilter + + +__all__ = ['to_system_data', 'dump'] + +def to_system_data(f: h5py.File, + folder: str, + type_map: list = None, + labels: bool = True) : + """Load a HDF5 file. + + Parameters + ---------- + f : h5py.File + HDF5 file object + folder : str + path in the HDF5 file + type_map : list + type map + labels : bool + labels + """ + g = f[folder] if folder else f + + data = {} + data['atom_types'] = g['type.raw'][:] + ntypes = np.max(data['atom_types']) + 1 + natoms = data['atom_types'].size + data['atom_numbs'] = [] + for ii in range (ntypes) : + data['atom_numbs'].append(np.count_nonzero(data['atom_types'] == ii)) + data['atom_names'] = [] + # if find type_map.raw, use it + if 'type_map.raw' in g.keys(): + my_type_map = list(np.char.decode(g['type_map.raw'][:])) + # else try to use arg type_map + elif type_map is not None: + my_type_map = type_map + # in the last case, make artificial atom names + else: + my_type_map = [] + for ii in range(ntypes) : + my_type_map.append('Type_%d' % ii) + assert(len(my_type_map) >= len(data['atom_numbs'])) + for ii in range(len(data['atom_numbs'])) : + data['atom_names'].append(my_type_map[ii]) + + data['orig'] = np.zeros([3]) + if 'nopbc' in g.keys(): + data['nopbc'] = True + sets = globfilter(g.keys(), 'set.*') + + data_types = { + 'cells': {'fn': 'box', 'labeled': False, 'shape': (3,3), 'required': 'nopbc' not in data}, + 'coords': {'fn': 'coord', 'labeled': False, 'shape': (natoms,3), 'required': True}, + 'energies': {'fn': 'energy', 'labeled': True, 'shape': tuple(), 'required': False}, + 'forces': {'fn': 'force', 'labeled': True, 'shape': (natoms,3), 'required': False}, + 'virials': {'fn': 'virial', 'labeled': True, 'shape': (3,3), 'required': False}, + } + + for dt, prop in data_types.items(): + all_data = [] + + for ii in sets: + set = g[ii] + fn = '%s.npy' % prop['fn'] + if fn in set.keys(): + dd = set[fn][:] + nframes = dd.shape[0] + all_data.append(np.reshape(dd, (nframes, *prop['shape']))) + elif prop['required']: + raise RuntimeError("%s/%s/%s not found" % (folder, ii, fn)) + + if len(all_data) > 0 : + data[dt] = np.concatenate(all_data, axis = 0) + return data + +def dump(f: h5py.File, + folder: str, + data: dict, + set_size = 5000, + comp_prec = np.float32, + ) -> None: + """Dump data to a HDF5 file. + + Parameters + ---------- + f : h5py.File + HDF5 file object + folder : str + path in the HDF5 file + data : dict + System or LabeledSystem data + set_size : int, default: 5000 + size of a set + comp_prec : np.dtype, default: np.float32 + precision of data + """ + # if folder is None, use the root of the file + if folder: + if folder in f: + del f[folder] + g = f.create_group(folder) + else: + g = f + # dump raw (array in fact) + g.create_dataset('type.raw', data=data['atom_types']) + g.create_dataset('type_map.raw', data=np.array(data['atom_names'], dtype='S')) + # BondOrder System + if "bonds" in data: + g.create_dataset("bonds.raw", data=data['bonds']) + if "formal_charges" in data: + g.create_dataset("formal_charges.raw", data=data['formal_charges']) + # reshape frame properties and convert prec + nframes = data['cells'].shape[0] + + nopbc = data.get("nopbc", False) + reshaped_data = {} + + data_types = { + 'cells': {'fn': 'box', 'shape': (nframes, 9), 'dump': not nopbc}, + 'coords': {'fn': 'coord', 'shape': (nframes, -1), 'dump': True}, + 'energies': {'fn': 'energy', 'shape': (nframes,), 'dump': True}, + 'forces': {'fn': 'force', 'shape': (nframes, -1), 'dump': True}, + 'virials': {'fn': 'virial', 'shape': (nframes, 9), 'dump': True}, + } + for dt, prop in data_types.items(): + if dt in data: + if prop['dump']: + reshaped_data[dt] = np.reshape(data[dt], prop['shape']).astype(comp_prec) + + # dump frame properties: cell, coord, energy, force and virial + nsets = nframes // set_size + if set_size * nsets < nframes : + nsets += 1 + for ii in range(nsets) : + set_stt = ii * set_size + set_end = (ii+1) * set_size + set_folder = g.create_group('set.%03d' % ii) + for dt, prop in data_types.items(): + if dt in reshaped_data: + set_folder.create_dataset('%s.npy' % prop['fn'], data=reshaped_data[dt][set_stt:set_end]) + + if nopbc: + g.create_dataset("nopbc", True) diff --git a/dpdata/format.py b/dpdata/format.py index ee495d60f..b96c374a3 100644 --- a/dpdata/format.py +++ b/dpdata/format.py @@ -106,11 +106,11 @@ def from_multi_systems(self, directory, **kwargs): list of filenames """ if self.MultiMode == self.MultiModes.Directory: - return [name for name in os.listdir(directory) if os.path.isdir(os.path.join(directory, name))] + return [os.path.join(directory, name) for name in os.listdir(directory) if os.path.isdir(os.path.join(directory, name))] raise NotImplementedError("%s doesn't support MultiSystems.from" %(self.__class__.__name__)) def to_multi_systems(self, formulas, directory, **kwargs): if self.MultiMode == self.MultiModes.Directory: return [os.path.join(directory, ff) for ff in formulas] raise NotImplementedError("%s doesn't support MultiSystems.to" %(self.__class__.__name__)) - \ No newline at end of file + diff --git a/dpdata/gaussian/log.py b/dpdata/gaussian/log.py index 9c20977db..5ed976fea 100644 --- a/dpdata/gaussian/log.py +++ b/dpdata/gaussian/log.py @@ -1,14 +1,12 @@ import numpy as np +from ..unit import LengthConversion, EnergyConversion, ForceConversion +from ..periodic_table import ELEMENTS +length_convert = LengthConversion("bohr", "angstrom").value() +energy_convert = EnergyConversion("hartree", "eV").value() +force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value() -hartree2ev = 27.211386018 -bohr2ang = 0.52917721067 - -length_convert = bohr2ang -energy_convert = hartree2ev -force_convert = energy_convert / length_convert - -symbols = ['X', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og'] +symbols = ["X"] + ELEMENTS def to_system_data(file_name, md=False): data = {} diff --git a/dpdata/gromacs/gro.py b/dpdata/gromacs/gro.py index b2473a03b..2114810ef 100644 --- a/dpdata/gromacs/gro.py +++ b/dpdata/gromacs/gro.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 import re import numpy as np -import json -import os +from ..unit import LengthConversion -nm2ang = 10. -ang2nm = 1. / nm2ang +nm2ang = LengthConversion("nm", "angstrom").value() +ang2nm = LengthConversion("angstrom", "nm").value() cell_idx_gmx2dp = [0, 4, 8, 1, 2, 3, 5, 6, 7] def _format_atom_name(atom_name): @@ -41,7 +40,7 @@ def _get_cell(line): cell = cell * nm2ang return cell -def file_to_system_data(fname, format_atom_name=True): +def file_to_system_data(fname, format_atom_name=True, **kwargs): system = {'coords': [], 'cells': []} with open(fname) as fp: frame = 0 @@ -74,7 +73,9 @@ def file_to_system_data(fname, format_atom_name=True): system['cells'] = np.array(system['cells']) return system -def from_system_data(system, f_idx=0): +def from_system_data(system, f_idx=0, **kwargs): + resname = kwargs.get("resname", "MOL") + shift = kwargs.get("shift", 0) ret = "" ret += " molecule" + "\n" n_atoms = sum(system["atom_numbs"]) @@ -83,8 +84,8 @@ def from_system_data(system, f_idx=0): atom_type = system["atom_types"][i] atom_name = system["atom_names"][atom_type] coords = system["coords"][f_idx] * ang2nm - ret += "{:>5d}{:<5s}{:>5s}{:5d}{:8.3f}{:8.3f}{:8.3f}\n".format(1, "MOL", atom_name, i+1, *tuple(coords[i])) + ret += "{:>5d}{:<5s}{:>5s}{:5d}{:8.3f}{:8.3f}{:8.3f}\n".format(1, resname, atom_name, i+shift+1, *tuple(coords[i])) cell = (system["cells"][f_idx].flatten() * ang2nm)[cell_idx_gmx2dp] - ret += " " + " ".join([str(x) for x in cell]) + ret += " " + " ".join([f"{x:.3f}" for x in cell]) return ret diff --git a/dpdata/lammps/dump.py b/dpdata/lammps/dump.py index 74fdb6530..7136d3e63 100644 --- a/dpdata/lammps/dump.py +++ b/dpdata/lammps/dump.py @@ -51,45 +51,38 @@ def get_natoms_vec(lines) : assert (sum(natoms_vec) == get_natoms(lines)) return natoms_vec -def get_posi(lines) : +def get_coordtype_and_scalefactor(keys): + # 4 types in total,with different scaling factor + key_pc=['x','y','z'] # plain cartesian, sf = 1 + key_uc=['xu','yu','zu'] # unwraped cartesian, sf = 1 + key_s=['xs','ys','zs'] # scaled by lattice parameter, sf = lattice parameter + key_su = ['xsu','ysu','zsu'] #scaled and unfolded,sf = lattice parameter + lmp_coor_type = [key_pc,key_uc,key_s,key_su] + sf = [0,0,1,1] + for k in range(4): + if all(i in keys for i in lmp_coor_type[k]): + return lmp_coor_type[k],sf[k] + +def safe_get_posi(lines,cell,orig=np.zeros(3)) : blk, head = _get_block(lines, 'ATOMS') keys = head.split() + coord_tp_and_sf = get_coordtype_and_scalefactor(keys) + assert coord_tp_and_sf is not None, 'Dump file does not contain atomic coordinates!' + coordtype, sf = coord_tp_and_sf id_idx = keys.index('id') - 2 - xidx = keys.index('x') - 2 - yidx = keys.index('y') - 2 - zidx = keys.index('z') - 2 + xidx = keys.index(coordtype[0])-2 + yidx = keys.index(coordtype[1])-2 + zidx = keys.index(coordtype[2])-2 sel = (xidx, yidx, zidx) posis = [] for ii in blk : words = ii.split() posis.append([float(words[id_idx]), float(words[xidx]), float(words[yidx]), float(words[zidx])]) posis.sort() - posis = np.array(posis) - return posis[:,1:4] - -def get_posi_frac(lines) : - blk, head = _get_block(lines, 'ATOMS') - keys = head.split() - id_idx = keys.index('id') - 2 - xidx = keys.index('xs') - 2 - yidx = keys.index('ys') - 2 - zidx = keys.index('zs') - 2 - sel = (xidx, yidx, zidx) - posis = [] - for ii in blk : - words = ii.split() - posis.append([float(words[id_idx]), float(words[xidx]), float(words[yidx]), float(words[zidx])]) - posis.sort() - posis = np.array(posis) - return posis[:,1:4] - -def safe_get_posi(lines, cell, orig = np.zeros(3)): - try: - posis = get_posi(lines) - orig - except ValueError: - fposis = get_posi_frac(lines) - posis = fposis @ cell - return posis + posis = np.array(posis)[:,1:4] + if not sf: + posis = (posis-orig)@np.linalg.inv(cell)# Convert to scaled coordinates for unscaled coordinates + return (posis%1)@cell # Convert scaled coordinates back to Cartesien coordinates def get_dumpbox(lines) : blk, h = _get_block(lines, 'BOX BOUNDS') @@ -211,8 +204,6 @@ def split_traj(dump_lines) : # # print(get_natomtypes(lines)) # # print(get_natoms_vec(lines)) # posi = get_posi(lines) - # dbox, tilt = get_dumpbox(lines) - # orig, box = dumpbox2box(dbox, tilt) # dbox1, tilt1 = box2dumpbox(orig, box) # print(dbox - dbox1) # print(tilt - tilt1) @@ -220,7 +211,9 @@ def split_traj(dump_lines) : # print(box) # np.savetxt('tmp.out', posi - orig, fmt='%.6f') # print(system_data(lines)) - - lines = load_file('conf.5.dump', begin = 0, step = 2) - with open('tmp.out', 'w') as fp: - fp.write('\n'.join(lines)) + lines = load_file('conf_unfold.dump', begin = 0, step = 1) + al = split_traj(lines) + s = system_data(lines,['O','H']) + #l = np.linalg.norm(s['cells'][1],axis=1) + #p = s['coords'][0] + l + #np.savetxt('p',p,fmt='%1.10f') diff --git a/dpdata/plugins/abacus.py b/dpdata/plugins/abacus.py index ad37cdfa2..43403772a 100644 --- a/dpdata/plugins/abacus.py +++ b/dpdata/plugins/abacus.py @@ -1,10 +1,19 @@ import dpdata.abacus.scf +import dpdata.abacus.md from dpdata.format import Format @Format.register("abacus/scf") @Format.register("abacus/pw/scf") class AbacusSCFFormat(Format): - @Format.post("rot_lower_triangular") + #@Format.post("rot_lower_triangular") def from_labeled_system(self, file_name, **kwargs): return dpdata.abacus.scf.get_frame(file_name) + +@Format.register("abacus/md") +@Format.register("abacus/pw/md") +@Format.register("abacus/lcao/md") +class AbacusMDFormat(Format): + #@Format.post("rot_lower_triangular") + def from_labeled_system(self, file_name, **kwargs): + return dpdata.abacus.md.get_frame(file_name) diff --git a/dpdata/plugins/amber.py b/dpdata/plugins/amber.py index 81e279138..2c6fa56a5 100644 --- a/dpdata/plugins/amber.py +++ b/dpdata/plugins/amber.py @@ -5,7 +5,7 @@ @Format.register("amber/md") class AmberMDFormat(Format): - def from_system(self, file_name=None, parm7_file=None, nc_file=None, use_element_symbols=None): + def from_system(self, file_name=None, parm7_file=None, nc_file=None, use_element_symbols=None, **kwargs): # assume the prefix is the same if the spefic name is not given if parm7_file is None: parm7_file = file_name + ".parm7" @@ -34,4 +34,20 @@ def from_system(self, fname, **kwargs): ''' Read from ambertools sqm.out ''' - return dpdata.amber.sqm.to_system_data(fname) + return dpdata.amber.sqm.parse_sqm_out(fname) + + def from_labeled_system(self, fname, **kwargs): + ''' + Read from ambertools sqm.out + ''' + data = dpdata.amber.sqm.parse_sqm_out(fname) + assert "forces" in list(data.keys()), f"No forces in {fname}" + return data + +@Format.register("sqm/in") +class SQMINFormat(Format): + def to_system(self, data, fname=None, frame_idx=0, **kwargs): + """ + Generate input files for semi-emperical calculation in sqm software + """ + return dpdata.amber.sqm.make_sqm_in(data, fname, frame_idx, **kwargs) diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py index 4d0e0aedb..a116e2162 100644 --- a/dpdata/plugins/ase.py +++ b/dpdata/plugins/ase.py @@ -1,8 +1,50 @@ from dpdata.format import Format +import numpy as np +try: + import ase.io + from ase.calculators.calculator import PropertyNotImplementedError +except ImportError: + pass @Format.register("ase/structure") class ASEStructureFormat(Format): + def from_labeled_system(self, data, **kwargs): + return data + + def from_multi_systems(self, file_name, begin=None, end=None, step=None, fmt='traj', **kwargs): + frames = ase.io.read(file_name, format=fmt, index=slice(begin, end, step)) + for atoms in frames: + symbols = atoms.get_chemical_symbols() + atom_names = list(set(symbols)) + atom_numbs = [symbols.count(symbol) for symbol in atom_names] + atom_types = np.array([atom_names.index(symbol) for symbol in symbols]).astype(int) + + cells = atoms.cell[:] + coords = atoms.get_positions() + try: + energies = atoms.get_potential_energy(force_consistent=True) + except PropertyNotImplementedError: + energies = atoms.get_potential_energy() + forces = atoms.get_forces() + info_dict = { + 'atom_names': atom_names, + 'atom_numbs': atom_numbs, + 'atom_types': atom_types, + 'cells': np.array([cells]).astype('float32'), + 'coords': np.array([coords]).astype('float32'), + 'energies': np.array([energies]).astype('float32'), + 'forces': np.array([forces]).astype('float32'), + 'orig': [0,0,0], + } + try: + stress = atoms.get_stress(False) + virials = np.array([-atoms.get_volume() * stress]).astype('float32') + info_dict['virials'] = virials + except PropertyNotImplementedError: + pass + yield info_dict + def to_system(self, data, **kwargs): ''' convert System to ASE Atom obj @@ -42,9 +84,10 @@ def to_labeled_system(self, data, *args, **kwargs): } if "virials" in data: # convert to GPa as this is ase convention - v_pref = 1 * 1e4 / 1.602176621e6 + # v_pref = 1 * 1e4 / 1.602176621e6 vol = structure.get_volume() - results['stress'] = data["virials"][ii] / (v_pref * vol) + # results['stress'] = data["virials"][ii] / (v_pref * vol) + results['stress'] = -data["virials"][ii] / vol structure.calc = SinglePointCalculator(structure, **results) structures.append(structure) diff --git a/dpdata/plugins/deepmd.py b/dpdata/plugins/deepmd.py index 6910cc60a..6fd209a3f 100644 --- a/dpdata/plugins/deepmd.py +++ b/dpdata/plugins/deepmd.py @@ -1,6 +1,8 @@ import dpdata.deepmd.raw import dpdata.deepmd.comp +import dpdata.deepmd.hdf5 import numpy as np +import h5py from dpdata.format import Format @@ -15,7 +17,7 @@ def to_system(self, data, file_name, **kwargs): """ dpdata.deepmd.raw.dump(file_name, data) - def from_labeled_system(self, file_name, type_map, **kwargs): + def from_labeled_system(self, file_name, type_map=None, **kwargs): return dpdata.deepmd.raw.to_system_data(file_name, type_map=type_map, labels=True) MultiMode = Format.MultiModes.Directory @@ -50,7 +52,53 @@ def to_system(self, data, file_name, set_size=5000, prec=np.float32, **kwargs): dpdata.deepmd.comp.dump( file_name, data, set_size=set_size, comp_prec=prec) - def from_labeled_system(self, file_name, type_map, **kwargs): + def from_labeled_system(self, file_name, type_map=None, **kwargs): return dpdata.deepmd.comp.to_system_data(file_name, type_map=type_map, labels=True) MultiMode = Format.MultiModes.Directory + +@Format.register("deepmd/hdf5") +class DeePMDCompFormat(Format): + """HDF5 format for DeePMD-kit. + + Examples + -------- + Dump a MultiSystems to a HDF5 file: + >>> import dpdata + >>> dpdata.MultiSystems().from_deepmd_npy("data").to_deepmd_hdf5("data.hdf5") + """ + def from_system(self, file_name, type_map=None, **kwargs): + s = file_name.split("#") + name = s[1] if len(s) > 1 else "" + with h5py.File(s[0], 'r') as f: + return dpdata.deepmd.hdf5.to_system_data(f, name, type_map=type_map, labels=False) + + def from_labeled_system(self, file_name, type_map=None, **kwargs): + s = file_name.split("#") + name = s[1] if len(s) > 1 else "" + with h5py.File(s[0], 'r') as f: + return dpdata.deepmd.hdf5.to_system_data(f, name, type_map=type_map, labels=True) + + def to_system(self, + data : dict, + file_name : str, + set_size : int = 5000, + comp_prec : np.dtype = np.float32, + **kwargs): + s = file_name.split("#") + name = s[1] if len(s) > 1 else "" + mode = 'a' if name else 'w' + with h5py.File(s[0], mode) as f: + dpdata.deepmd.hdf5.dump(f, name, data, set_size = set_size, comp_prec = comp_prec) + + def from_multi_systems(self, + directory, + **kwargs): + with h5py.File(directory, 'r') as f: + return ["%s#%s" % (directory, ff) for ff in f.keys()] + + def to_multi_systems(self, + formulas, + directory, + **kwargs): + return ["%s#%s" % (directory, ff) for ff in formulas] diff --git a/dpdata/plugins/gromacs.py b/dpdata/plugins/gromacs.py index a061918ba..f4e3d5285 100644 --- a/dpdata/plugins/gromacs.py +++ b/dpdata/plugins/gromacs.py @@ -14,7 +14,7 @@ def from_system(self, file_name, format_atom_name=True, **kwargs): file_name : str The input file name """ - return dpdata.gromacs.gro.file_to_system_data(file_name, format_atom_name=format_atom_name) + return dpdata.gromacs.gro.file_to_system_data(file_name, format_atom_name=format_atom_name, **kwargs) def to_system(self, data, file_name=None, frame_idx=-1, **kwargs): """ @@ -31,12 +31,13 @@ def to_system(self, data, file_name=None, frame_idx=-1, **kwargs): if frame_idx == -1: strs = [] for idx in range(data['coords'].shape[0]): - gro_str = dpdata.gromacs.gro.from_system_data(data, f_idx=idx) + gro_str = dpdata.gromacs.gro.from_system_data(data, f_idx=idx, + **kwargs) strs.append(gro_str) gro_str = "\n".join(strs) else: gro_str = dpdata.gromacs.gro.from_system_data( - data, f_idx=frame_idx) + data, f_idx=frame_idx, **kwargs) if file_name is None: return gro_str diff --git a/dpdata/plugins/pymatgen.py b/dpdata/plugins/pymatgen.py index a047249e1..f29ac382b 100644 --- a/dpdata/plugins/pymatgen.py +++ b/dpdata/plugins/pymatgen.py @@ -1,4 +1,6 @@ from dpdata.format import Format +import dpdata.pymatgen.molecule +import numpy as np @Format.register("pymatgen/structure") @@ -8,7 +10,7 @@ def to_system(self, data, **kwargs): """ structures = [] try: - from pymatgen import Structure + from pymatgen.core import Structure except ModuleNotFoundError as e: raise ImportError('No module pymatgen.Structure') from e @@ -22,6 +24,37 @@ def to_system(self, data, **kwargs): return structures +@Format.register("pymatgen/molecule") +class PyMatgenMoleculeFormat(Format): + @Format.post("remove_pbc") + def from_system(self, file_name, **kwargs): + try: + from pymatgen.core import Molecule + except ModuleNotFoundError as e: + raise ImportError('No module pymatgen.Molecule') from e + + return dpdata.pymatgen.molecule.to_system_data(file_name) + + def to_system(self, data, **kwargs): + """convert System to Pymatgen Molecule obj + """ + molecules = [] + try: + from pymatgen.core import Molecule + except ModuleNotFoundError as e: + raise ImportError('No module pymatgen.Molecule') from e + + species = [] + for name, numb in zip(data['atom_names'], data['atom_numbs']): + species.extend([name]*numb) + data = dpdata.system.remove_pbc(data) + for ii in range(np.array(data['coords']).shape[0]): + molecule = Molecule( + species, data['coords'][ii]) + molecules.append(molecule) + return molecules + + @Format.register("pymatgen/computedstructureentry") @Format.register_to("to_pymatgen_ComputedStructureEntry") class PyMatgenCSEFormat(Format): @@ -44,3 +77,5 @@ def to_labeled_system(self, data, *args, **kwargs): entry = ComputedStructureEntry(structure, energy, data=csedata) entries.append(entry) return entries + + diff --git a/dpdata/plugins/rdkit.py b/dpdata/plugins/rdkit.py index 20e5696b2..9d40257a7 100644 --- a/dpdata/plugins/rdkit.py +++ b/dpdata/plugins/rdkit.py @@ -1,9 +1,9 @@ from dpdata.format import Format try: import rdkit.Chem + import dpdata.rdkit.utils except ModuleNotFoundError: pass -import dpdata.rdkit.utils @Format.register("mol") @@ -13,8 +13,8 @@ def from_bond_order_system(self, file_name, **kwargs): return rdkit.Chem.MolFromMolFile(file_name, sanitize=False, removeHs=False) - def to_bond_order_system(self, mol, data, file_name, frame_idx=0, **kwargs): - assert (frame_idx < self.get_nframes()) + def to_bond_order_system(self, data, mol, file_name, frame_idx=0, **kwargs): + assert (frame_idx < mol.GetNumConformers()) rdkit.Chem.MolToMolFile(mol, file_name, confId=frame_idx) @@ -32,12 +32,12 @@ def from_bond_order_system(self, file_name, **kwargs): mol = mols[0] return mol - def to_bond_order_system(self, mol, data, file_name, frame_idx=-1, **kwargs): + def to_bond_order_system(self, data, mol, file_name, frame_idx=-1, **kwargs): sdf_writer = rdkit.Chem.SDWriter(file_name) if frame_idx == -1: - for ii in range(data['coords'].shape[0]): + for ii in range(mol.GetNumConformers()): sdf_writer.write(mol, confId=ii) else: - assert (frame_idx < data['coords'].shape[0]) + assert (frame_idx < mol.GetNumConformers()) sdf_writer.write(mol, confId=frame_idx) sdf_writer.close() \ No newline at end of file diff --git a/dpdata/pwmat/atomconfig.py b/dpdata/pwmat/atomconfig.py index 13034e70d..6535edc64 100644 --- a/dpdata/pwmat/atomconfig.py +++ b/dpdata/pwmat/atomconfig.py @@ -1,5 +1,5 @@ #!/usr/bin/python3 - +from ..periodic_table import ELEMENTS import numpy as np def _to_system_data_lower(lines) : @@ -39,13 +39,6 @@ def _to_system_data_lower(lines) : for jj in range(ii) : atom_types.append(idx) system['atom_types'] = np.array(atom_types, dtype = int) - ELEMENTS=['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', \ - 'Sc', 'Ti', 'V', 'Cr','Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', \ - 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd',\ - 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', \ - 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', \ - 'Md', 'No', 'Lr'] - system['atom_names'] = [ELEMENTS[ii-1] for ii in np.unique(sorted(atomic_number))] return system @@ -80,12 +73,6 @@ def from_system_data(system, f_idx = 0, skip_zeros = True) : for ii, jj in zip(atom_numbs, atom_names): for kk in range(ii): symbal.append(jj) - ELEMENTS=['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', \ - 'Sc', 'Ti', 'V', 'Cr','Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', \ - 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd',\ - 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', \ - 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', \ - 'Md', 'No', 'Lr'] atomic_numbers = [] for ii in symbal: atomic_numbers.append(ELEMENTS.index(ii)+1) diff --git a/dpdata/pwmat/movement.py b/dpdata/pwmat/movement.py index ef79906a7..121f38855 100644 --- a/dpdata/pwmat/movement.py +++ b/dpdata/pwmat/movement.py @@ -1,4 +1,5 @@ import numpy as np +from ..periodic_table import ELEMENTS def system_info (lines, type_idx_zero = False) : atom_names = [] @@ -32,12 +33,6 @@ def system_info (lines, type_idx_zero = False) : atom_types.append(idx) else : atom_types.append(idx+1) - ELEMENTS=['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', \ - 'Sc', 'Ti', 'V', 'Cr','Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', \ - 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd',\ - 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', \ - 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', \ - 'Md', 'No', 'Lr'] for ii in np.unique(sorted(atomic_number)): atom_names.append(ELEMENTS[ii-1]) return atom_names, atom_numbs, np.array(atom_types, dtype = int), nelm diff --git a/dpdata/pymatgen/__init__.py b/dpdata/pymatgen/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/dpdata/pymatgen/molecule.py b/dpdata/pymatgen/molecule.py new file mode 100644 index 000000000..f671d6ea8 --- /dev/null +++ b/dpdata/pymatgen/molecule.py @@ -0,0 +1,26 @@ +import numpy as np +from pymatgen.core import Molecule +from collections import Counter +import dpdata + +def to_system_data(file_name, protect_layer = 9) : + mol = Molecule.from_file(file_name) + elem_mol = list(str(site.species.elements[0]) for site in mol.sites) + elem_counter = Counter(elem_mol) + atom_names = list(elem_counter.keys()) + atom_numbs = list(elem_counter.values()) + atom_types = [list(atom_names).index(e) for e in elem_mol] + natoms = np.sum(atom_numbs) + + tmpcoord = np.copy(mol.cart_coords) + + system = {} + system['atom_names'] = atom_names + system['atom_numbs'] = atom_numbs + system['atom_types'] = np.array(atom_types, dtype = int) + # center = [c - h_cell_size for c in mol.center_of_mass] + system['orig'] = np.array([0, 0, 0]) + + system['coords'] = [tmpcoord] + system['cells'] = [10.0 * np.eye(3)] + return system diff --git a/dpdata/qe/traj.py b/dpdata/qe/traj.py index e98003307..49d3338dd 100644 --- a/dpdata/qe/traj.py +++ b/dpdata/qe/traj.py @@ -1,16 +1,14 @@ #!/usr/bin/python3 - import numpy as np -import dpdata,warnings +import dpdata, warnings +from ..unit import EnergyConversion, LengthConversion, ForceConversion, PressureConversion -ry2ev = 13.605693009 -hartree2ev = 27.211386018 -bohr2ang = 0.52917721067 -kbar2evperang3 = 1e3 / 1.602176621e6 +ry2ev = EnergyConversion("rydberg", "eV").value() +kbar2evperang3 = PressureConversion("kbar", "eV/angstrom^3").value() -length_convert = bohr2ang -energy_convert = hartree2ev -force_convert = energy_convert / length_convert +length_convert = LengthConversion("bohr", "angstrom").value() +energy_convert = EnergyConversion("hartree", "eV").value() +force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value() def load_key (lines, key) : for ii in lines : diff --git a/dpdata/rdkit/utils.py b/dpdata/rdkit/utils.py index a8a52be86..5cf0df323 100644 --- a/dpdata/rdkit/utils.py +++ b/dpdata/rdkit/utils.py @@ -1,5 +1,8 @@ -from rdkit import Chem -from rdkit.Chem import AllChem +try: + from rdkit import Chem + from rdkit.Chem import AllChem +except ModuleNotFoundError: + pass import numpy as np def mol_to_system_data(mol): @@ -60,7 +63,7 @@ def system_data_to_mol(data): mol = mol_ed.GetMol() # set formal charges for idx, atom in enumerate(mol.GetAtoms()): - atom.SetFormalCharge(data['formal_charges'][idx]) + atom.SetFormalCharge(int(data['formal_charges'][idx])) # set mol name if '_name' in list(data.keys()): mol.SetProp("_Name", data['_name']) @@ -105,4 +108,4 @@ def combine_molecules(mols): mols[0].AddConformer(conf, assignId=True) return mols[0] else: - raise ValueError("molecules are not of the same topology.") \ No newline at end of file + raise ValueError("molecules are not of the same topology.") diff --git a/dpdata/system.py b/dpdata/system.py index b0b9345b3..3c3423c6d 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -9,6 +9,7 @@ from monty.serialization import loadfn,dumpfn from dpdata.periodic_table import Element from dpdata.amber.mask import pick_by_amber_mask, load_param_file +import dpdata # ensure all plugins are loaded! import dpdata.plugins @@ -76,7 +77,8 @@ def __init__ (self, - ``vasp/poscar``: vasp POSCAR - ``qe/cp/traj``: Quantum Espresso CP trajectory files. should have: file_name+'.in' and file_name+'.pos' - ``qe/pw/scf``: Quantum Espresso PW single point calculations. Both input and output files are required. If file_name is a string, it denotes the output file name. Input file name is obtained by replacing 'out' by 'in' from file_name. Or file_name is a list, with the first element being the input file name and the second element being the output filename. - - ``abacus/scf``: ABACUS plane wave scf. The directory containing INPUT file is required. + - ``abacus/scf``: ABACUS pw/lcao scf. The directory containing INPUT file is required. + - ``abacus/md``: ABACUS pw/lcao MD. The directory containing INPUT file is required. - ``siesta/output``: siesta SCF output file - ``siesta/aimd_output``: siesta aimd output file - ``pwmat/atom.config``: pwmat atom.config @@ -418,7 +420,7 @@ def extend(self, systems): for system in systems: self.append(system.copy()) - + def apply_pbc(self) : """ Append periodic boundary condition @@ -428,6 +430,7 @@ def apply_pbc(self) : self.data['coords'] = np.matmul(ncoord, self.data['cells']) + @post_funcs.register("remove_pbc") def remove_pbc(self, protect_layer = 9): """ This method does NOT delete the definition of the cells, it @@ -441,19 +444,8 @@ def remove_pbc(self, protect_layer = 9): protect_layer : the protect layer between the atoms and the cell boundary """ - nframes = self.get_nframes() - natoms = self.get_natoms() assert(protect_layer >= 0), "the protect_layer should be no less than 0" - for ff in range(nframes): - tmpcoord = self.data['coords'][ff] - 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 - 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) + remove_pbc(self.data, protect_layer) def affine_map(self, trans, f_idx = 0) : assert(np.linalg.det(trans) != 0) @@ -661,7 +653,7 @@ def predict(self, dp): Returns ------- - labeled_sys LabeledSystem + labeled_sys : LabeledSystem The labeled system. """ try: @@ -679,19 +671,33 @@ def predict(self, dp): labeled_sys = LabeledSystem() - for ss in self: - coord = ss['coords'].reshape((-1,1)) - if not ss.nopbc: - cell = ss['cells'].reshape((-1,1)) + if 'auto_batch_size' not in DeepPot.__init__.__code__.co_varnames: + for ss in self: + coord = ss['coords'].reshape((1, ss.get_natoms()*3)) + if not ss.nopbc: + cell = ss['cells'].reshape((1, 9)) + else: + cell = None + e, f, v = dp.eval(coord, cell, atype) + data = ss.data + data['energies'] = e.reshape((1, 1)) + data['forces'] = f.reshape((1, ss.get_natoms(), 3)) + data['virials'] = v.reshape((1, 3, 3)) + this_sys = LabeledSystem.from_dict({'data': data}) + labeled_sys.append(this_sys) + else: + # since v2.0.2, auto batch size is supported + coord = self.data['coords'].reshape((self.get_nframes(), self.get_natoms()*3)) + if not self.nopbc: + cell = self.data['cells'].reshape((self.get_nframes(), 9)) else: cell = None e, f, v = dp.eval(coord, cell, atype) - data = ss.data - data['energies'] = e.reshape((1, 1)) - data['forces'] = f.reshape((1, -1, 3)) - data['virials'] = v.reshape((1, 3, 3)) - this_sys = LabeledSystem.from_dict({'data': data}) - labeled_sys.append(this_sys) + data = self.data.copy() + data['energies'] = e.reshape((self.get_nframes(), 1)) + data['forces'] = f.reshape((self.get_nframes(), self.get_natoms(), 3)) + data['virials'] = v.reshape((self.get_nframes(), 3, 3)) + labeled_sys = LabeledSystem.from_dict({'data': data}) return labeled_sys def pick_atom_idx(self, idx, nopbc=None): @@ -1300,3 +1306,18 @@ def elements_index_map(elements,standard=False,inverse=False): else: return dict(zip(elements,range(len(elements)))) # %% + +def remove_pbc(system, protect_layer = 9): + nframes = len(system["coords"]) + natoms = len(system['coords'][0]) + for ff in range(nframes): + tmpcoord = system['coords'][ff] + 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 + cell_size = h_cell_size * 2 + shift = np.array([1,1,1]) * h_cell_size - cog + system['coords'][ff] = system['coords'][ff] + np.tile(shift, [natoms, 1]) + system['cells'][ff] = cell_size * np.eye(3) + return system diff --git a/dpdata/unit.py b/dpdata/unit.py new file mode 100644 index 000000000..7b5aeffc4 --- /dev/null +++ b/dpdata/unit.py @@ -0,0 +1,169 @@ +from abc import ABC +from scipy import constants + +AVOGADRO = constants.Avogadro # Avagadro constant +ELE_CHG = constants.elementary_charge # Elementary Charge, in C +BOHR = constants.value("atomic unit of length") # Bohr, in m +HARTREE = constants.value("atomic unit of energy") # Hartree, in Jole +RYDBERG = constants.Rydberg * constants.h * constants.c # Rydberg, in Jole + +# energy conversions +econvs = { + "eV": 1.0, + "hartree": HARTREE / ELE_CHG, + "kJ_mol": 1 / (ELE_CHG * AVOGADRO / 1000), + "kcal_mol": 1 / (ELE_CHG * AVOGADRO / 1000 / 4.184), + "rydberg": RYDBERG / ELE_CHG, + "J": 1 / ELE_CHG, + "kJ": 1000 / ELE_CHG +} + +# length conversions +lconvs = { + "angstrom": 1.0, + "bohr": BOHR * 1E10, + "nm": 10.0, + "m": 1E10, +} + +def check_unit(unit): + if unit not in econvs.keys() and unit not in lconvs.keys(): + try: + eunit = unit.split("/")[0] + lunit = unit.split("/")[1] + if eunit not in econvs.keys(): + raise RuntimeError(f"Invaild unit: {unit}") + if lunit not in lconvs.keys(): + raise RuntimeError(f"Invalid unit: {unit}") + except: + raise RuntimeError(f"Invalid unit: {unit}") + +class Conversion(ABC): + def __init__(self, unitA, unitB, check=True): + """ + Parent class for unit conversion + + Parameters + ---------- + unitA : str, unit to be converted + unitB : str, unit which unitA is converted to, i.e. `1 unitA = self._value unitB` + check : bool, whether to check unit validity + + Examples + -------- + >>> conv = Conversion("foo", "bar", check=False) + >>> conv.set_value("10.0") + >>> print(conv) + 1 foo = 10.0 bar + >>> conv.value() + 10.0 + """ + if check: + check_unit(unitA) + check_unit(unitB) + self.unitA = unitA + self.unitB = unitB + self._value = 0.0 + + def value(self): + return self._value + + def set_value(self, value): + self._value = value + + def __repr__(self): + return f"1 {self.unitA} = {self._value} {self.unitB}" + + def __str__(self): + return self.__repr__() + +class EnergyConversion(Conversion): + def __init__(self, unitA, unitB): + """ + Class for energy conversion + + Examples + -------- + >>> conv = LengthConversion("eV", "kcal_mol") + >>> conv.value() + 23.06054783061903 + """ + super().__init__(unitA, unitB) + self.set_value(econvs[unitA] / econvs[unitB]) + +class LengthConversion(Conversion): + def __init__(self, unitA, unitB): + """ + Class for length conversion + + Examples + -------- + >>> conv = LengthConversion("angstrom", "nm") + >>> conv.value() + 0.1 + """ + super().__init__(unitA, unitB) + self.set_value(lconvs[unitA] / lconvs[unitB]) + +class ForceConversion(Conversion): + def __init__(self, unitA, unitB): + """ + Class for force conversion + + Parameters + ---------- + unitA, unitB : str, in format of "energy_unit/length_unit" + + Examples + -------- + >>> conv = ForceConversion("kJ_mol/nm", "eV/angstrom") + >>> conv.value() + 0.0010364269656262175 + """ + super().__init__(unitA, unitB) + econv = EnergyConversion(unitA.split("/")[0], unitB.split("/")[0]).value() + lconv = LengthConversion(unitA.split("/")[1], unitB.split("/")[1]).value() + self.set_value(econv / lconv) + +class PressureConversion(Conversion): + def __init__(self, unitA, unitB): + """ + Class for pressure conversion + + Parameters + ---------- + unitA, unitB : str, in format of "energy_unit/length_unit^3", or in `["Pa", "pa", "kPa", "kpa", "bar", "kbar"]` + + Examples + -------- + >>> conv = PressureConversion("kbar", "eV/angstrom^3") + >>> conv.value() + 0.0006241509074460763 + """ + super().__init__(unitA, unitB, check=False) + unitA, factorA = self._convert_unit(unitA) + unitB, factorB = self._convert_unit(unitB) + eunitA, lunitA = self._split_unit(unitA) + eunitB, lunitB = self._split_unit(unitB) + econv = EnergyConversion(eunitA, eunitB).value() * factorA / factorB + lconv = LengthConversion(lunitA, lunitB).value() + self.set_value(econv / lconv**3) + + def _convert_unit(self, unit): + if unit == "Pa" or unit == "pa": + return "J/m^3", 1 + elif unit == "kPa" or unit == "kpa": + return "kJ/m^3", 1 + elif unit == "GPa" or unit == "Gpa": + return "kJ/m^3", 1E6 + elif unit == "bar": + return "J/m^3", 1E5 + elif unit == "kbar": + return "kJ/m^3", 1E5 + else: + return unit, 1 + + def _split_unit(self, unit): + eunit = unit.split("/")[0] + lunit = unit.split("/")[1][:-2] + return eunit, lunit \ No newline at end of file diff --git a/setup.py b/setup.py index 8fb19676c..428a2bfe7 100644 --- a/setup.py +++ b/setup.py @@ -12,7 +12,7 @@ readme = f.read() # install_requires = ['xml'] -install_requires=['numpy>=1.14.3', 'monty', 'scipy'] +install_requires=['numpy>=1.14.3', 'monty', 'scipy', 'h5py', 'wcmatch'] setuptools.setup( name="dpdata", @@ -41,6 +41,7 @@ 'dpdata/abacus', 'dpdata/rdkit', 'dpdata/plugins', + 'dpdata/pymatgen', ], package_data={'dpdata':['*.json']}, classifiers=[ @@ -52,6 +53,8 @@ extras_require={ 'ase': ['ase'], 'amber': ['parmed'], + 'pymatgen': ['pymatgen'], + 'docs': ['sphinx', 'recommonmark', 'sphinx_rtd_theme>=1.0.0rc1', 'numpydoc', 'm2r2'], } ) diff --git a/tests/abacus.md/INPUT b/tests/abacus.md/INPUT new file mode 100644 index 000000000..d169ddf95 --- /dev/null +++ b/tests/abacus.md/INPUT @@ -0,0 +1,30 @@ +INPUT_PARAMETERS +#Parameters (General) +suffix autotest +pseudo_dir ./ +ntype 1 +nbands 8 +calculation md +read_file_dir ./ + +#Parameters (Accuracy) +ecutwfc 20 +niter 20 + +basis_type pw +nstep 21 # number of MD/relaxation steps + +stress 1 +stress_thr 1e-6 +force 1 +force_thr_ev 1.0e-3 + +ks_solver cg +mixing_type pulay +mixing_beta 0.7 + +md_mdtype 1 # 0 for NVE; 1 for NVT with Nose Hoover; 2 for NVT with velocity rescaling +md_tfirst 10 # temperature, unit: K +md_dt 1 # unit: fs +md_rstmd 0 # 1 for restart +md_dumpmdfred 5 diff --git a/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif b/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif new file mode 100644 index 000000000..24779f6c0 --- /dev/null +++ b/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0 0 0 +Si 0.245 0.237 0.265 diff --git a/tests/abacus.md/OUT.autotest/md_pos_1.cif b/tests/abacus.md/OUT.autotest/md_pos_1.cif new file mode 100644 index 000000000..832aaef0a --- /dev/null +++ b/tests/abacus.md/OUT.autotest/md_pos_1.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0.00106888 0.99849 0.000247409 +Si 0.245535 0.237394 0.262886 diff --git a/tests/abacus.md/OUT.autotest/md_pos_10.cif b/tests/abacus.md/OUT.autotest/md_pos_10.cif new file mode 100644 index 000000000..a7546cea6 --- /dev/null +++ b/tests/abacus.md/OUT.autotest/md_pos_10.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0.00711478 0.993904 0.9916 +Si 0.253316 0.23197 0.255312 diff --git a/tests/abacus.md/OUT.autotest/md_pos_15.cif b/tests/abacus.md/OUT.autotest/md_pos_15.cif new file mode 100644 index 000000000..51f15b4ea --- /dev/null +++ b/tests/abacus.md/OUT.autotest/md_pos_15.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0.00722617 0.979891 0.000667301 +Si 0.260608 0.240666 0.237553 diff --git a/tests/abacus.md/OUT.autotest/md_pos_20.cif b/tests/abacus.md/OUT.autotest/md_pos_20.cif new file mode 100644 index 000000000..3d01862a9 --- /dev/null +++ b/tests/abacus.md/OUT.autotest/md_pos_20.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0.0136053 0.987589 0.984304 +Si 0.261345 0.227707 0.245529 diff --git a/tests/abacus.md/OUT.autotest/md_pos_5.cif b/tests/abacus.md/OUT.autotest/md_pos_5.cif new file mode 100644 index 000000000..b35b1102d --- /dev/null +++ b/tests/abacus.md/OUT.autotest/md_pos_5.cif @@ -0,0 +1,21 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 3.81668 +_cell_length_b 3.81668 +_cell_length_c 3.81668 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Si 0.999048 0.984501 0.010401 +Si 0.2538 0.246892 0.24541 diff --git a/tests/abacus.md/OUT.autotest/running_md.log b/tests/abacus.md/OUT.autotest/running_md.log new file mode 100644 index 000000000..16f460507 --- /dev/null +++ b/tests/abacus.md/OUT.autotest/running_md.log @@ -0,0 +1,2608 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 1 + Start Time is Fri Oct 15 14:37:16 2021 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.autotest/ + global_in_card = INPUT + pseudo_dir = ./ + orbital_dir = ./ + pseudo_type = auto + DRANK = 1 + DSIZE = 1 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 1 + atom label for species 1 = Si + lattice constant (Bohr) = 10.2 + lattice constant (Angstrom) = 5.39761 + + READING ATOM TYPE 1 + atom label = Si + L=0, number of zeta = 1 + L=1, number of zeta = 1 + L=2, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 2 + + CARTESIAN COORDINATES ( UNIT = 10.2 Bohr ). + atom x y z mag vx vy vz + tauc_Si1 0 0 0 0 0 0 0 + tauc_Si2 0.241 0.255 0.250999999999 0 0 0 0 + + + Volume (Bohr^3) = 265.302 + Volume (A^3) = 39.3136533177 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +0.5 +0.5 +0 + +0.5 +0 +0.5 + +0 +0.5 +0.5 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +1 +1 -1 + +1 -1 +1 + -1 +1 +1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is ./Si_ONCV_PBE-1.0.upf + pseudopotential type = NC + functional Ex = PBE + functional Ec = + functional GCEx = + functional GCEc = + nonlocal core correction = 0 + valence electrons = 4 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + initial pseudo atomic orbital number = 0 + NLOCAL = 18 + + SETUP THE ELECTRONS NUMBER + electron number of element Si = 4 + total electron number of element Si = 8 + occupied bands = 4 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0648149461485 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 8 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 0.125 + 2 0.5 0 0 0.125 + 3 0 0.5 0 0.125 + 4 0.5 0.5 0 0.125 + 5 0 0 0.5 0.125 + 6 0.5 0 0.5 0.125 + 7 0 0.5 0.5 0.125 + 8 0.5 0.5 0.5 0.125 + + k-point number in this process = 8 + minimum distributed K point number = 8 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 0.25 + 2 0.5 0.5 -0.5 0.25 + 3 0.5 -0.5 0.5 0.25 + 4 1 0 0 0.25 + 5 -0.5 0.5 0.5 0.25 + 6 0 1 0 0.25 + 7 0 0 1 0.25 + 8 0.5 0.5 0.5 0.25 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 0.25 + 2 0.5 0 0 0.25 + 3 0 0.5 0 0.25 + 4 0.5 0.5 0 0.25 + 5 0 0 0.5 0.25 + 6 0.5 0 0.5 0.25 + 7 0 0.5 0.5 0.25 + 8 0.5 0.5 0.5 0.25 + DONE : INIT K-POINTS Time : 0.0652149026282 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for wavefunc (unit:Ry) = 20 + [fft grid for wave functions] = 24, 24, 24 + [fft grid for charge/potential] = 24, 24, 24 + [fft grid division] = 1, 1, 1 + [big fft grid for charge/potential] = 24, 24, 24 + nbxx = 13824 + nrxx = 13824 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 3143 + number of sticks = 283 + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + number of plane waves = 609 + number of sticks = 91 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 283 3143 + --------------- sum ------------------- + 1 283 3143 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(W) PW + 1 91 609 + --------------- sum ------------------- + 1 91 609 + + SETUP COORDINATES OF PLANE WAVES + number of total plane waves = 3143 + + SETUP COORDINATES OF PLANE WAVES + number of |g| = 72 + max |g| = 208 + min |g| = 0 + DONE : INIT PLANEWAVE Time : 0.0986429497134 (SEC) + + npwx = 411 + + SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS + Si non-local projectors: + projector 1 L=0 + projector 2 L=0 + projector 3 L=1 + projector 4 L=1 + TOTAL NUMBER OF NONLOCAL PROJECTORS = 16 + DONE : LOCAL POTENTIAL Time : 0.109992648242 (SEC) + + + Init Non-Local PseudoPotential table : + Init Non-Local-Pseudopotential done. + DONE : NON-LOCAL POTENTIAL Time : 0.122797146207 (SEC) + + start_pot = atomic + DONE : INIT POTENTIAL Time : 0.135785 (SEC) + + + Make real space PAO into reciprocal space. + max mesh points in Pseudopotential = 601 + dq(describe PAO in reciprocal space) = 0.01 + max q = 542 + + number of pseudo atomic orbitals for Si is 0 + DONE : INIT BASIS Time : 0.184089 (SEC) + + ...............Nose-Hoover Chain parameter initialization............... + Temperature = 3.16682e-05 + Temperature2 = 10.0004 + NHC frequency = 0.00120944 + NHC chain = 4 + Qmass = 1823.61 + ............................................................... + + PW ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + K-point CG iter num Time(Sec) + 1 6.125000 0.314119 + 2 6.500000 0.327905 + 3 6.750000 0.334448 + 4 6.125000 0.309547 + 5 6.750000 0.112520 + 6 6.125000 0.024925 + 7 5.875000 0.024036 + 8 6.250000 0.025291 + + Density error is 0.108050841230 + + PW ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + K-point CG iter num Time(Sec) + 1 2.500000 0.012342 + 2 2.250000 0.011339 + 3 2.625000 0.012621 + 4 3.250000 0.014770 + 5 2.500000 0.012183 + 6 3.125000 0.014333 + 7 2.125000 0.010831 + 8 2.625000 0.012575 + + Density error is 0.004334778560 + + PW ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + K-point CG iter num Time(Sec) + 1 3.375000 0.015399 + 2 3.250000 0.014874 + 3 3.125000 0.014380 + 4 4.000000 0.017413 + 5 3.250000 0.014776 + 6 4.000000 0.017425 + 7 3.750000 0.016523 + 8 2.875000 0.013438 + + Density error is 0.000134739187 + + PW ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + K-point CG iter num Time(Sec) + 1 3.750000 0.016717 + 2 3.250000 0.014854 + 3 3.375000 0.015229 + 4 4.000000 0.017399 + 5 3.500000 0.015669 + 6 4.000000 0.017380 + 7 4.500000 0.019148 + 8 3.375000 0.015188 + + Density error is 0.000014649703 + + PW ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + K-point CG iter num Time(Sec) + 1 2.750000 0.013183 + 2 2.625000 0.012728 + 3 2.750000 0.013067 + 4 2.750000 0.013018 + 5 2.875000 0.013453 + 6 2.750000 0.013008 + 7 2.625000 0.012593 + 8 2.625000 0.012567 + + Density error is 0.000000599415 + + PW ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + K-point CG iter num Time(Sec) + 1 3.125000 0.014489 + 2 3.625000 0.016131 + 3 3.250000 0.014781 + 4 4.375000 0.018739 + 5 3.375000 0.015250 + 6 4.000000 0.017425 + 7 4.250000 0.018253 + 8 3.375000 0.015213 + + Density error is 0.000000048534 + + PW ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + K-point CG iter num Time(Sec) + 1 3.250000 0.015027 + 2 3.000000 0.013998 + 3 3.125000 0.014375 + 4 3.625000 0.016117 + 5 3.000000 0.013941 + 6 4.125000 0.017842 + 7 3.500000 0.015638 + 8 3.125000 0.014323 + + Density error is 0.000000002823 + + PW ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + K-point CG iter num Time(Sec) + 1 3.500000 0.015909 + 2 3.125000 0.014437 + 3 3.000000 0.013954 + 4 3.500000 0.015692 + 5 3.250000 0.014873 + 6 3.250000 0.014791 + 7 3.375000 0.015237 + 8 3.125000 0.014335 + + Density error is 0.000000000061 + + charge density convergence is achieved + final etot is -211.771832657158 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.885363 +0.500467 +0.150240 + Si2 +0.885363 -0.500467 -0.150240 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.045273 -3.807537 -13.541448 + -3.807537 +124.421298 +24.047975 + -13.541448 +24.047975 +125.016023 + +output Pressure for check! +Virtual Pressure is +124.231102 Kbar +Virial is +124.160865 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 1 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564005 (Rydberg) + NVT Temperature : +10.000364 (K) + NVT Kinetic energy : +0.000190 (Rydberg) + NVT Potential energy : -15.564937 (Rydberg) + maxForce : +0.000400 + maxStep : +0.012800 + MD_STEP SystemE Conserved DeltaE Temperature + +1 -7.782469 -7.782003 +0.000000 +14.311776 + + PW ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +34.500000 +1.482434 + +2 +24.125000 +0.314735 + +3 +24.250000 +0.087904 + +4 +27.625000 +0.099392 + +5 +25.000000 +0.090634 + +6 +29.875000 +0.107431 + +7 +31.875000 +0.113921 + +8 +26.750000 +0.096067 + + Density error is +0.000008438536 + + PW ALGORITHM --------------- ION=+2 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010623 + +2 +2.000000 +0.010501 + +3 +2.000000 +0.010437 + +4 +2.000000 +0.010430 + +5 +2.000000 +0.010417 + +6 +2.000000 +0.010392 + +7 +2.000000 +0.010413 + +8 +2.000000 +0.010431 + + Density error is +0.000000589537 + + PW ALGORITHM --------------- ION=+2 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.375000 +0.011909 + +2 +2.125000 +0.010960 + +3 +2.125000 +0.010853 + +4 +2.750000 +0.013046 + +5 +2.000000 +0.010421 + +6 +2.750000 +0.013030 + +7 +3.375000 +0.015237 + +8 +2.125000 +0.010850 + + Density error is +0.000000029687 + + PW ALGORITHM --------------- ION=+2 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.375000 +0.015446 + +2 +3.500000 +0.015794 + +3 +3.125000 +0.014440 + +4 +3.500000 +0.015678 + +5 +3.625000 +0.016125 + +6 +3.500000 +0.015643 + +7 +3.250000 +0.014765 + +8 +3.500000 +0.015638 + + Density error is +0.000000000296 + + charge density convergence is achieved + final etot is -211.778481425683 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.815731 +0.355757 +0.109618 + Si2 +0.815731 -0.355757 -0.109618 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.843178 -2.800524 -9.609977 + -2.800524 +124.232437 +22.152784 + -9.609977 +22.152784 +124.529670 + +output Pressure for check! +Virtual Pressure is +123.968947 Kbar +Virial is +123.868428 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 2 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564050 (Rydberg) + NVT Temperature : +33.255982 (K) + NVT Kinetic energy : +0.000632 (Rydberg) + NVT Potential energy : -15.565426 (Rydberg) + maxForce : +0.000304 + maxStep : +0.026509 + MD_STEP SystemE Conserved DeltaE Temperature + +2 -7.782713 -7.782025 +0.000000 +66.542608 + + PW ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +33.625000 +1.455297 + +2 +23.000000 +0.344287 + +3 +23.250000 +0.084591 + +4 +27.250000 +0.097961 + +5 +24.625000 +0.089419 + +6 +28.375000 +0.101985 + +7 +26.625000 +0.096635 + +8 +24.625000 +0.089249 + + Density error is +0.000021869323 + + PW ALGORITHM --------------- ION=+3 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010696 + +2 +2.000000 +0.010427 + +3 +2.000000 +0.010429 + +4 +2.000000 +0.010408 + +5 +2.000000 +0.010427 + +6 +2.375000 +0.011750 + +7 +2.000000 +0.010404 + +8 +2.000000 +0.010397 + + Density error is +0.000001763699 + + PW ALGORITHM --------------- ION=+3 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011012 + +2 +2.250000 +0.011394 + +3 +2.250000 +0.011290 + +4 +2.875000 +0.013481 + +5 +2.250000 +0.011358 + +6 +3.000000 +0.013927 + +7 +2.875000 +0.013486 + +8 +2.375000 +0.011717 + + Density error is +0.000000036065 + + PW ALGORITHM --------------- ION=+3 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016348 + +2 +3.750000 +0.016579 + +3 +3.750000 +0.016547 + +4 +4.375000 +0.018704 + +5 +3.500000 +0.015695 + +6 +4.125000 +0.017849 + +7 +4.625000 +0.019620 + +8 +3.625000 +0.016087 + + Density error is +0.000000002244 + + PW ALGORITHM --------------- ION=+3 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013691 + +2 +3.000000 +0.013966 + +3 +2.875000 +0.013492 + +4 +3.875000 +0.016984 + +5 +3.250000 +0.014831 + +6 +3.750000 +0.016559 + +7 +3.000000 +0.013909 + +8 +3.000000 +0.013880 + + Density error is +0.000000000184 + + charge density convergence is achieved + final etot is -211.794269556733 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.462515 +0.083202 +0.018773 + Si2 +0.462515 -0.083202 -0.018773 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.815311 -0.492388 -2.246119 + -0.492388 +123.347654 +12.547878 + -2.246119 +12.547878 +123.364301 + +output Pressure for check! +Virtual Pressure is +123.643118 Kbar +Virial is +123.175755 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 3 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564151 (Rydberg) + NVT Temperature : +88.343003 (K) + NVT Kinetic energy : +0.001679 (Rydberg) + NVT Potential energy : -15.566586 (Rydberg) + maxForce : +0.000084 + maxStep : +0.033756 + MD_STEP SystemE Conserved DeltaE Temperature + +3 -7.783293 -7.782076 +0.000000 +112.977290 + + PW ALGORITHM --------------- ION=+4 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +37.125000 +1.584397 + +2 +24.625000 +0.212187 + +3 +25.750000 +0.092986 + +4 +29.250000 +0.104765 + +5 +27.000000 +0.097458 + +6 +31.875000 +0.113833 + +7 +28.250000 +0.101426 + +8 +25.250000 +0.091166 + + Density error is +0.000033429323 + + PW ALGORITHM --------------- ION=+4 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010606 + +2 +2.000000 +0.010470 + +3 +2.000000 +0.010394 + +4 +2.000000 +0.010391 + +5 +2.000000 +0.010403 + +6 +2.000000 +0.010374 + +7 +2.000000 +0.010374 + +8 +2.000000 +0.010432 + + Density error is +0.000002801781 + + PW ALGORITHM --------------- ION=+4 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011027 + +2 +2.500000 +0.012197 + +3 +2.250000 +0.011338 + +4 +2.375000 +0.011707 + +5 +2.250000 +0.011301 + +6 +2.625000 +0.012578 + +7 +2.875000 +0.013474 + +8 +2.375000 +0.011758 + + Density error is +0.000000035628 + + PW ALGORITHM --------------- ION=+4 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.875000 +0.017185 + +2 +3.875000 +0.017012 + +3 +3.750000 +0.016533 + +4 +4.000000 +0.017359 + +5 +3.750000 +0.016991 + +6 +3.875000 +0.017340 + +7 +4.625000 +0.019603 + +8 +3.750000 +0.016469 + + Density error is +0.000000003655 + + PW ALGORITHM --------------- ION=+4 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013239 + +2 +2.625000 +0.012645 + +3 +2.750000 +0.013035 + +4 +3.750000 +0.016496 + +5 +2.750000 +0.013016 + +6 +3.250000 +0.014762 + +7 +3.000000 +0.013915 + +8 +2.625000 +0.012541 + + Density error is +0.000000000196 + + charge density convergence is achieved + final etot is -211.798998994521 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.045801 -0.211053 -0.052135 + Si2 -0.045801 +0.211053 +0.052135 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.007250 +1.421851 +5.725860 + +1.421851 +122.897686 -1.245212 + +5.725860 -1.245212 +123.005310 + +output Pressure for check! +Virtual Pressure is +123.763579 Kbar +Virial is +122.970082 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 4 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564177 (Rydberg) + NVT Temperature : +103.974513 (K) + NVT Kinetic energy : +0.001976 (Rydberg) + NVT Potential energy : -15.566934 (Rydberg) + maxForce : +0.000019 + maxStep : +0.030839 + MD_STEP SystemE Conserved DeltaE Temperature + +4 -7.783467 -7.782089 +0.000000 +94.653093 + + PW ALGORITHM --------------- ION=+5 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.125000 +1.541803 + +2 +24.500000 +0.265063 + +3 +26.125000 +0.094359 + +4 +30.250000 +0.108286 + +5 +25.500000 +0.091682 + +6 +28.875000 +0.104719 + +7 +29.250000 +0.105021 + +8 +25.125000 +0.090821 + + Density error is +0.000028572302 + + PW ALGORITHM --------------- ION=+5 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010595 + +2 +2.000000 +0.010418 + +3 +2.000000 +0.010451 + +4 +2.000000 +0.010412 + +5 +2.000000 +0.010426 + +6 +2.000000 +0.010384 + +7 +2.000000 +0.010373 + +8 +2.000000 +0.010418 + + Density error is +0.000002384066 + + PW ALGORITHM --------------- ION=+5 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011011 + +2 +2.375000 +0.011743 + +3 +2.250000 +0.011317 + +4 +2.625000 +0.012578 + +5 +2.250000 +0.011279 + +6 +2.750000 +0.013007 + +7 +2.875000 +0.013443 + +8 +2.375000 +0.011684 + + Density error is +0.000000035575 + + PW ALGORITHM --------------- ION=+5 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.016778 + +2 +3.875000 +0.017042 + +3 +3.750000 +0.016539 + +4 +4.125000 +0.017849 + +5 +3.750000 +0.016577 + +6 +3.625000 +0.016055 + +7 +4.625000 +0.019602 + +8 +3.625000 +0.016048 + + Density error is +0.000000003086 + + PW ALGORITHM --------------- ION=+5 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013198 + +2 +2.625000 +0.012687 + +3 +2.875000 +0.013502 + +4 +3.750000 +0.016536 + +5 +2.750000 +0.013120 + +6 +3.375000 +0.015253 + +7 +2.875000 +0.013430 + +8 +2.875000 +0.013424 + + Density error is +0.000000000189 + + charge density convergence is achieved + final etot is -211.787163106063 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.531795 -0.423861 -0.074943 + Si2 -0.531795 +0.423861 +0.074943 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.156562 +2.191352 +11.539648 + +2.191352 +123.421604 -14.461358 + +11.539648 -14.461358 +123.871961 + +output Pressure for check! +Virtual Pressure is +124.148173 Kbar +Virial is +123.483375 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 5 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564100 (Rydberg) + NVT Temperature : +61.015343 (K) + NVT Kinetic energy : +0.001159 (Rydberg) + NVT Potential energy : -15.566064 (Rydberg) + maxForce : +0.000177 + maxStep : +0.019294 + MD_STEP SystemE Conserved DeltaE Temperature + +5 -7.783032 -7.782050 +0.000000 +35.600513 + + PW ALGORITHM --------------- ION=+6 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +35.750000 +1.538779 + +2 +23.375000 +0.281560 + +3 +26.625000 +0.096030 + +4 +29.375000 +0.105067 + +5 +25.125000 +0.090691 + +6 +30.000000 +0.107285 + +7 +30.125000 +0.107224 + +8 +23.875000 +0.086308 + + Density error is +0.000013559050 + + PW ALGORITHM --------------- ION=+6 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010587 + +2 +2.000000 +0.010411 + +3 +2.000000 +0.010387 + +4 +2.000000 +0.010385 + +5 +2.000000 +0.010401 + +6 +2.000000 +0.010372 + +7 +2.000000 +0.010373 + +8 +2.000000 +0.010387 + + Density error is +0.000001049378 + + PW ALGORITHM --------------- ION=+6 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.010993 + +2 +2.125000 +0.010884 + +3 +2.125000 +0.010912 + +4 +2.500000 +0.012157 + +5 +2.125000 +0.010852 + +6 +2.750000 +0.013010 + +7 +3.000000 +0.013908 + +8 +2.125000 +0.010824 + + Density error is +0.000000034124 + + PW ALGORITHM --------------- ION=+6 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016280 + +2 +3.625000 +0.016107 + +3 +3.625000 +0.016126 + +4 +3.875000 +0.016930 + +5 +3.625000 +0.016102 + +6 +3.625000 +0.016047 + +7 +4.375000 +0.018675 + +8 +3.625000 +0.016036 + + Density error is +0.000000001047 + + PW ALGORITHM --------------- ION=+6 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.250000 +0.015029 + +2 +3.250000 +0.014818 + +3 +3.125000 +0.014333 + +4 +4.500000 +0.019099 + +5 +3.125000 +0.014369 + +6 +4.250000 +0.018282 + +7 +3.250000 +0.014734 + +8 +3.250000 +0.014725 + + Density error is +0.000000000093 + + charge density convergence is achieved + final etot is -211.773976096239 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.830073 -0.488698 -0.076368 + Si2 -0.830073 +0.488698 +0.076368 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.079115 +2.349387 +13.341463 + +2.349387 +124.240376 -22.607891 + +13.341463 -22.607891 +124.847553 + +output Pressure for check! +Virtual Pressure is +124.305722 Kbar +Virial is +124.055681 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 6 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564017 (Rydberg) + NVT Temperature : +13.869106 (K) + NVT Kinetic energy : +0.000264 (Rydberg) + NVT Potential energy : -15.565095 (Rydberg) + maxForce : +0.000353 + maxStep : +0.009591 + MD_STEP SystemE Conserved DeltaE Temperature + +6 -7.782547 -7.782009 +0.000000 +9.461554 + + PW ALGORITHM --------------- ION=+7 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.250000 +1.548029 + +2 +24.625000 +0.276619 + +3 +27.375000 +0.098665 + +4 +30.375000 +0.108527 + +5 +26.375000 +0.095093 + +6 +30.625000 +0.109686 + +7 +31.000000 +0.110332 + +8 +25.250000 +0.091074 + + Density error is +0.000006867857 + + PW ALGORITHM --------------- ION=+7 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010576 + +2 +2.000000 +0.010440 + +3 +2.000000 +0.010510 + +4 +2.000000 +0.010413 + +5 +2.000000 +0.010403 + +6 +2.125000 +0.010838 + +7 +2.000000 +0.010376 + +8 +2.000000 +0.010387 + + Density error is +0.000000471169 + + PW ALGORITHM --------------- ION=+7 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013211 + +2 +2.000000 +0.010520 + +3 +2.000000 +0.010489 + +4 +2.750000 +0.013013 + +5 +2.125000 +0.010843 + +6 +2.500000 +0.012183 + +7 +3.250000 +0.014821 + +8 +2.000000 +0.010417 + + Density error is +0.000000026949 + + PW ALGORITHM --------------- ION=+7 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.000000 +0.014095 + +2 +3.250000 +0.014863 + +3 +3.000000 +0.013942 + +4 +3.125000 +0.014354 + +5 +3.250000 +0.014813 + +6 +3.250000 +0.014752 + +7 +3.500000 +0.015640 + +8 +3.250000 +0.014764 + + Density error is +0.000000000178 + + charge density convergence is achieved + final etot is -211.775966500996 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.841211 -0.388251 -0.083865 + Si2 -0.841211 +0.388251 +0.083865 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.888185 +2.498229 +10.607911 + +2.498229 +124.324706 -22.903208 + +10.607911 -22.903208 +124.699212 + +output Pressure for check! +Virtual Pressure is +124.037154 Kbar +Virial is +123.970701 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 7 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564029 (Rydberg) + NVT Temperature : +20.830773 (K) + NVT Kinetic energy : +0.000396 (Rydberg) + NVT Potential energy : -15.565241 (Rydberg) + maxForce : +0.000327 + maxStep : +0.022260 + MD_STEP SystemE Conserved DeltaE Temperature + +7 -7.782620 -7.782015 +0.000000 +47.763680 + + PW ALGORITHM --------------- ION=+8 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +34.625000 +1.498024 + +2 +22.500000 +0.296778 + +3 +24.500000 +0.088638 + +4 +28.750000 +0.103008 + +5 +24.000000 +0.086877 + +6 +29.375000 +0.105138 + +7 +26.250000 +0.094433 + +8 +22.375000 +0.081172 + + Density error is +0.000016498376 + + PW ALGORITHM --------------- ION=+8 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010574 + +2 +2.000000 +0.010443 + +3 +2.000000 +0.010379 + +4 +2.000000 +0.010399 + +5 +2.000000 +0.010420 + +6 +2.000000 +0.010425 + +7 +2.500000 +0.012164 + +8 +2.000000 +0.010416 + + Density error is +0.000001314992 + + PW ALGORITHM --------------- ION=+8 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011051 + +2 +2.250000 +0.011345 + +3 +2.125000 +0.010869 + +4 +2.750000 +0.013016 + +5 +2.250000 +0.011286 + +6 +2.750000 +0.013011 + +7 +3.125000 +0.014347 + +8 +2.250000 +0.011259 + + Density error is +0.000000033932 + + PW ALGORITHM --------------- ION=+8 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.017140 + +2 +3.625000 +0.016310 + +3 +3.750000 +0.016631 + +4 +4.000000 +0.017495 + +5 +3.500000 +0.015705 + +6 +4.125000 +0.017878 + +7 +4.250000 +0.018300 + +8 +3.500000 +0.015635 + + Density error is +0.000000001483 + + PW ALGORITHM --------------- ION=+8 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013210 + +2 +3.125000 +0.014428 + +3 +3.125000 +0.014340 + +4 +4.000000 +0.017385 + +5 +3.125000 +0.014518 + +6 +3.625000 +0.016115 + +7 +3.500000 +0.015627 + +8 +3.375000 +0.015173 + + Density error is +0.000000000115 + + charge density convergence is achieved + final etot is -211.790638622284 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.562521 -0.158433 -0.082597 + Si2 -0.562521 +0.158433 +0.082597 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.818911 +2.300863 +4.331819 + +2.300863 +123.569280 -15.284717 + +4.331819 -15.284717 +123.616732 + +output Pressure for check! +Virtual Pressure is +123.670443 Kbar +Virial is +123.334974 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 8 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564121 (Rydberg) + NVT Temperature : +72.197413 (K) + NVT Kinetic energy : +0.001372 (Rydberg) + NVT Potential energy : -15.566319 (Rydberg) + maxForce : +0.000132 + maxStep : +0.031989 + MD_STEP SystemE Conserved DeltaE Temperature + +8 -7.783160 -7.782060 +0.000000 +101.706395 + + PW ALGORITHM --------------- ION=+9 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +35.875000 +1.531937 + +2 +26.875000 +0.264962 + +3 +26.750000 +0.096733 + +4 +30.375000 +0.108739 + +5 +27.000000 +0.097620 + +6 +31.875000 +0.114026 + +7 +28.000000 +0.100499 + +8 +25.250000 +0.092090 + + Density error is +0.000030268617 + + PW ALGORITHM --------------- ION=+9 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010942 + +2 +2.000000 +0.010442 + +3 +2.000000 +0.010413 + +4 +2.000000 +0.010444 + +5 +2.000000 +0.010413 + +6 +2.000000 +0.010372 + +7 +2.000000 +0.010379 + +8 +2.000000 +0.010382 + + Density error is +0.000002526424 + + PW ALGORITHM --------------- ION=+9 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011021 + +2 +2.500000 +0.012194 + +3 +2.250000 +0.011346 + +4 +2.375000 +0.011731 + +5 +2.250000 +0.011785 + +6 +2.750000 +0.013400 + +7 +2.875000 +0.013483 + +8 +2.500000 +0.012132 + + Density error is +0.000000035287 + + PW ALGORITHM --------------- ION=+9 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016272 + +2 +3.750000 +0.016595 + +3 +3.625000 +0.016152 + +4 +3.875000 +0.016950 + +5 +3.625000 +0.016113 + +6 +3.750000 +0.016497 + +7 +4.625000 +0.019580 + +8 +3.750000 +0.016488 + + Density error is +0.000000003280 + + PW ALGORITHM --------------- ION=+9 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013195 + +2 +2.750000 +0.013069 + +3 +2.875000 +0.013452 + +4 +4.250000 +0.018388 + +5 +2.875000 +0.013480 + +6 +3.500000 +0.015655 + +7 +3.000000 +0.013869 + +8 +2.625000 +0.012553 + + Density error is +0.000000000193 + + charge density convergence is achieved + final etot is -211.799689533651 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.088600 +0.125590 -0.036123 + Si2 -0.088600 -0.125590 +0.036123 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.942319 +0.972401 -3.404364 + +0.972401 +122.922036 -2.403271 + -3.404364 -2.403271 +122.959321 + +output Pressure for check! +Virtual Pressure is +123.655562 Kbar +Virial is +122.941225 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 9 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564178 (Rydberg) + NVT Temperature : +102.774866 (K) + NVT Kinetic energy : +0.001953 (Rydberg) + NVT Potential energy : -15.566984 (Rydberg) + maxForce : +0.000009 + maxStep : +0.032288 + MD_STEP SystemE Conserved DeltaE Temperature + +9 -7.783492 -7.782089 +0.000000 +102.692994 + + PW ALGORITHM --------------- ION=+10 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.000000 +1.538429 + +2 +24.875000 +0.260502 + +3 +25.750000 +0.093167 + +4 +29.875000 +0.106972 + +5 +26.000000 +0.094130 + +6 +30.000000 +0.107537 + +7 +31.000000 +0.110836 + +8 +25.375000 +0.091698 + + Density error is +0.000030737201 + + PW ALGORITHM --------------- ION=+10 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010666 + +2 +2.000000 +0.010444 + +3 +2.000000 +0.010477 + +4 +2.000000 +0.010404 + +5 +2.000000 +0.010414 + +6 +2.000000 +0.010377 + +7 +2.000000 +0.010374 + +8 +2.000000 +0.010388 + + Density error is +0.000002560646 + + PW ALGORITHM --------------- ION=+10 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.250000 +0.011451 + +2 +2.500000 +0.012257 + +3 +2.250000 +0.011301 + +4 +2.750000 +0.013040 + +5 +2.250000 +0.011288 + +6 +2.625000 +0.012593 + +7 +3.000000 +0.013923 + +8 +2.500000 +0.012151 + + Density error is +0.000000033975 + + PW ALGORITHM --------------- ION=+10 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016339 + +2 +3.875000 +0.017015 + +3 +3.750000 +0.016527 + +4 +4.250000 +0.018269 + +5 +3.750000 +0.016535 + +6 +3.750000 +0.016493 + +7 +4.625000 +0.019590 + +8 +3.750000 +0.016482 + + Density error is +0.000000003387 + + PW ALGORITHM --------------- ION=+10 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013682 + +2 +2.625000 +0.012626 + +3 +2.750000 +0.013042 + +4 +3.750000 +0.016591 + +5 +3.000000 +0.013926 + +6 +3.500000 +0.015660 + +7 +3.000000 +0.013942 + +8 +2.625000 +0.012582 + + Density error is +0.000000000211 + + charge density convergence is achieved + final etot is -211.791757080168 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.416931 +0.372190 +0.054656 + Si2 +0.416931 -0.372190 -0.054656 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.112004 -1.386177 -10.090684 + -1.386177 +123.202765 +11.305489 + -10.090684 +11.305489 +123.552704 + +output Pressure for check! +Virtual Pressure is +124.010423 Kbar +Virial is +123.289157 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 10 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564126 (Rydberg) + NVT Temperature : +73.190993 (K) + NVT Kinetic energy : +0.001391 (Rydberg) + NVT Potential energy : -15.566401 (Rydberg) + maxForce : +0.000119 + maxStep : +0.022835 + MD_STEP SystemE Conserved DeltaE Temperature + +10 -7.783201 -7.782063 +0.000000 +48.734190 + + PW ALGORITHM --------------- ION=+11 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +35.875000 +1.541778 + +2 +25.500000 +0.266144 + +3 +25.250000 +0.091185 + +4 +29.250000 +0.104785 + +5 +24.875000 +0.090153 + +6 +30.625000 +0.109517 + +7 +28.875000 +0.103393 + +8 +27.500000 +0.098937 + + Density error is +0.000016935127 + + PW ALGORITHM --------------- ION=+11 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010679 + +2 +2.000000 +0.010521 + +3 +2.000000 +0.010402 + +4 +2.000000 +0.010379 + +5 +2.000000 +0.010446 + +6 +2.000000 +0.010416 + +7 +2.000000 +0.010382 + +8 +2.000000 +0.010370 + + Density error is +0.000001343508 + + PW ALGORITHM --------------- ION=+11 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.010997 + +2 +2.125000 +0.010874 + +3 +2.250000 +0.011252 + +4 +2.625000 +0.012581 + +5 +2.125000 +0.010886 + +6 +2.625000 +0.012585 + +7 +3.000000 +0.013888 + +8 +2.375000 +0.011709 + + Density error is +0.000000032255 + + PW ALGORITHM --------------- ION=+11 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.016894 + +2 +3.750000 +0.016617 + +3 +3.625000 +0.016129 + +4 +3.875000 +0.016962 + +5 +3.750000 +0.016549 + +6 +3.750000 +0.016487 + +7 +4.500000 +0.019118 + +8 +3.500000 +0.015592 + + Density error is +0.000000001579 + + PW ALGORITHM --------------- ION=+11 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013663 + +2 +3.125000 +0.014367 + +3 +2.875000 +0.013494 + +4 +4.125000 +0.017819 + +5 +3.125000 +0.014308 + +6 +4.000000 +0.017389 + +7 +3.125000 +0.014286 + +8 +3.125000 +0.014297 + + Density error is +0.000000000113 + + charge density convergence is achieved + final etot is -211.777136772291 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.774114 +0.493555 +0.132287 + Si2 +0.774114 -0.493555 -0.132287 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.125513 -3.354234 -13.360634 + -3.354234 +124.042603 +21.012997 + -13.360634 +21.012997 +124.630461 + +output Pressure for check! +Virtual Pressure is +124.275144 Kbar +Virial is +123.932859 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 11 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564029 (Rydberg) + NVT Temperature : +20.916618 (K) + NVT Kinetic energy : +0.000397 (Rydberg) + NVT Potential energy : -15.565327 (Rydberg) + maxForce : +0.000325 + maxStep : +0.009427 + MD_STEP SystemE Conserved DeltaE Temperature + +11 -7.782663 -7.782015 +0.000000 +9.036895 + + PW ALGORITHM --------------- ION=+12 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.125000 +1.547415 + +2 +26.375000 +0.264168 + +3 +25.375000 +0.091673 + +4 +29.500000 +0.105644 + +5 +26.125000 +0.094314 + +6 +31.500000 +0.112479 + +7 +29.875000 +0.106803 + +8 +28.625000 +0.102367 + + Density error is +0.000006530970 + + PW ALGORITHM --------------- ION=+12 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010577 + +2 +2.000000 +0.010466 + +3 +2.000000 +0.010402 + +4 +2.000000 +0.010371 + +5 +2.000000 +0.010404 + +6 +2.000000 +0.010385 + +7 +2.000000 +0.010377 + +8 +2.000000 +0.010356 + + Density error is +0.000000440898 + + PW ALGORITHM --------------- ION=+12 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.625000 +0.012786 + +2 +2.000000 +0.010477 + +3 +2.000000 +0.010393 + +4 +2.750000 +0.013027 + +5 +2.125000 +0.010923 + +6 +2.750000 +0.012995 + +7 +3.125000 +0.014337 + +8 +2.000000 +0.010365 + + Density error is +0.000000024207 + + PW ALGORITHM --------------- ION=+12 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.000000 +0.014107 + +2 +3.125000 +0.014392 + +3 +3.000000 +0.013912 + +4 +3.375000 +0.015251 + +5 +3.375000 +0.015234 + +6 +3.125000 +0.014438 + +7 +3.250000 +0.014784 + +8 +3.250000 +0.014731 + + Density error is +0.000000000170 + + charge density convergence is achieved + final etot is -211.774943325509 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.854779 +0.436696 +0.135045 + Si2 +0.854779 -0.436696 -0.135045 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.950297 -3.436598 -11.810037 + -3.436598 +124.343261 +23.217684 + -11.810037 +23.217684 +124.792605 + +output Pressure for check! +Virtual Pressure is +124.092191 Kbar +Virial is +124.028721 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 12 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564015 (Rydberg) + NVT Temperature : +13.061843 (K) + NVT Kinetic energy : +0.000248 (Rydberg) + NVT Potential energy : -15.565166 (Rydberg) + maxForce : +0.000355 + maxStep : +0.019395 + MD_STEP SystemE Conserved DeltaE Temperature + +12 -7.782583 -7.782007 +0.000000 +34.185920 + + PW ALGORITHM --------------- ION=+13 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +34.000000 +1.465002 + +2 +23.000000 +0.338683 + +3 +23.500000 +0.085138 + +4 +27.875000 +0.099984 + +5 +24.000000 +0.086926 + +6 +28.875000 +0.103425 + +7 +30.250000 +0.108009 + +8 +24.000000 +0.086816 + + Density error is +0.000013073792 + + PW ALGORITHM --------------- ION=+13 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010625 + +2 +2.000000 +0.010427 + +3 +2.000000 +0.010396 + +4 +2.000000 +0.010386 + +5 +2.000000 +0.010431 + +6 +2.000000 +0.010378 + +7 +2.000000 +0.010379 + +8 +2.000000 +0.010393 + + Density error is +0.000001008013 + + PW ALGORITHM --------------- ION=+13 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011016 + +2 +2.250000 +0.011351 + +3 +2.125000 +0.010831 + +4 +2.750000 +0.013017 + +5 +2.125000 +0.010830 + +6 +2.750000 +0.013067 + +7 +3.125000 +0.014333 + +8 +2.250000 +0.011270 + + Density error is +0.000000030793 + + PW ALGORITHM --------------- ION=+13 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016352 + +2 +3.500000 +0.015679 + +3 +3.625000 +0.016117 + +4 +3.875000 +0.016947 + +5 +3.625000 +0.016079 + +6 +3.750000 +0.016476 + +7 +4.250000 +0.018229 + +8 +3.500000 +0.015618 + + Density error is +0.000000001065 + + PW ALGORITHM --------------- ION=+13 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013652 + +2 +3.375000 +0.015279 + +3 +3.125000 +0.014327 + +4 +4.125000 +0.017830 + +5 +3.250000 +0.014748 + +6 +4.250000 +0.018231 + +7 +3.500000 +0.015621 + +8 +3.375000 +0.015172 + + Density error is +0.000000000097 + + charge density convergence is achieved + final etot is -211.787892336077 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.634765 +0.219902 +0.063772 + Si2 +0.634765 -0.219902 -0.063772 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.810989 -1.646977 -5.949715 + -1.646977 +123.724465 +17.235456 + -5.949715 +17.235456 +123.839274 + +output Pressure for check! +Virtual Pressure is +123.698348 Kbar +Virial is +123.458243 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 13 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564100 (Rydberg) + NVT Temperature : +58.268396 (K) + NVT Kinetic energy : +0.001107 (Rydberg) + NVT Potential energy : -15.566117 (Rydberg) + maxForce : +0.000172 + maxStep : +0.030214 + MD_STEP SystemE Conserved DeltaE Temperature + +13 -7.783059 -7.782050 +0.000000 +89.458675 + + PW ALGORITHM --------------- ION=+14 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +35.875000 +1.542133 + +2 +26.125000 +0.252769 + +3 +27.000000 +0.097434 + +4 +31.125000 +0.111257 + +5 +27.250000 +0.098368 + +6 +30.375000 +0.108770 + +7 +28.125000 +0.101032 + +8 +27.000000 +0.097412 + + Density error is +0.000027152014 + + PW ALGORITHM --------------- ION=+14 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010571 + +2 +2.000000 +0.010418 + +3 +2.000000 +0.010469 + +4 +2.000000 +0.010378 + +5 +2.000000 +0.010391 + +6 +2.125000 +0.010816 + +7 +2.000000 +0.010413 + +8 +2.000000 +0.010387 + + Density error is +0.000002253887 + + PW ALGORITHM --------------- ION=+14 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011042 + +2 +2.375000 +0.011756 + +3 +2.250000 +0.011280 + +4 +2.750000 +0.013020 + +5 +2.250000 +0.011259 + +6 +2.625000 +0.012556 + +7 +2.875000 +0.013452 + +8 +2.500000 +0.012282 + + Density error is +0.000000033052 + + PW ALGORITHM --------------- ION=+14 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.875000 +0.017209 + +2 +3.750000 +0.016568 + +3 +3.625000 +0.016133 + +4 +4.250000 +0.018248 + +5 +3.625000 +0.016119 + +6 +4.250000 +0.018240 + +7 +4.750000 +0.020036 + +8 +3.625000 +0.016022 + + Density error is +0.000000002963 + + PW ALGORITHM --------------- ION=+14 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013700 + +2 +2.750000 +0.013049 + +3 +2.750000 +0.012990 + +4 +3.500000 +0.015607 + +5 +3.000000 +0.013859 + +6 +3.375000 +0.015179 + +7 +2.875000 +0.013422 + +8 +2.750000 +0.012955 + + Density error is +0.000000000187 + + charge density convergence is achieved + final etot is -211.799136169946 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.198870 -0.070672 -0.020734 + Si2 +0.198870 +0.070672 +0.020734 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.902575 +0.551658 +1.913429 + +0.551658 +122.991496 +5.397063 + +1.913429 +5.397063 +123.003398 + +output Pressure for check! +Virtual Pressure is +123.594137 Kbar +Virial is +122.965823 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 14 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564168 (Rydberg) + NVT Temperature : +96.770497 (K) + NVT Kinetic energy : +0.001839 (Rydberg) + NVT Potential energy : -15.566944 (Rydberg) + maxForce : +0.000017 + maxStep : +0.032116 + MD_STEP SystemE Conserved DeltaE Temperature + +14 -7.783472 -7.782084 +0.000000 +103.109630 + + PW ALGORITHM --------------- ION=+15 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +35.375000 +1.505918 + +2 +24.375000 +0.254664 + +3 +24.625000 +0.089084 + +4 +30.625000 +0.109605 + +5 +26.625000 +0.095625 + +6 +29.125000 +0.104515 + +7 +27.875000 +0.100128 + +8 +24.500000 +0.088547 + + Density error is +0.000030393373 + + PW ALGORITHM --------------- ION=+15 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010563 + +2 +2.000000 +0.010432 + +3 +2.000000 +0.010404 + +4 +2.000000 +0.010375 + +5 +2.000000 +0.010381 + +6 +2.000000 +0.010377 + +7 +2.000000 +0.010377 + +8 +2.000000 +0.010354 + + Density error is +0.000002547296 + + PW ALGORITHM --------------- ION=+15 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.250000 +0.011476 + +2 +2.500000 +0.012193 + +3 +2.250000 +0.011277 + +4 +2.750000 +0.013015 + +5 +2.250000 +0.011319 + +6 +2.750000 +0.013017 + +7 +2.750000 +0.013009 + +8 +2.500000 +0.012125 + + Density error is +0.000000032257 + + PW ALGORITHM --------------- ION=+15 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016335 + +2 +3.875000 +0.016993 + +3 +3.750000 +0.016491 + +4 +4.375000 +0.018723 + +5 +3.750000 +0.016532 + +6 +3.500000 +0.015608 + +7 +4.375000 +0.018691 + +8 +3.750000 +0.016462 + + Density error is +0.000000003366 + + PW ALGORITHM --------------- ION=+15 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013287 + +2 +2.625000 +0.012630 + +3 +2.875000 +0.013438 + +4 +3.500000 +0.015728 + +5 +2.750000 +0.013063 + +6 +3.125000 +0.014314 + +7 +3.250000 +0.014752 + +8 +2.625000 +0.012547 + + Density error is +0.000000000185 + + charge density convergence is achieved + final etot is -211.794739884606 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.297987 -0.327806 -0.066082 + Si2 -0.297987 +0.327806 +0.066082 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.100328 +1.856002 +8.909136 + +1.856002 +123.052207 -8.099784 + +8.909136 -8.099784 +123.317967 + +output Pressure for check! +Virtual Pressure is +123.881026 Kbar +Virial is +123.156834 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 15 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564136 (Rydberg) + NVT Temperature : +79.642870 (K) + NVT Kinetic energy : +0.001513 (Rydberg) + NVT Potential energy : -15.566621 (Rydberg) + maxForce : +0.000076 + maxStep : +0.024468 + MD_STEP SystemE Conserved DeltaE Temperature + +15 -7.783310 -7.782068 +0.000000 +58.786721 + + PW ALGORITHM --------------- ION=+16 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.000000 +1.550421 + +2 +24.125000 +0.253604 + +3 +26.125000 +0.094431 + +4 +29.625000 +0.106054 + +5 +25.500000 +0.091700 + +6 +29.500000 +0.105684 + +7 +29.125000 +0.104354 + +8 +23.750000 +0.086118 + + Density error is +0.000019003017 + + PW ALGORITHM --------------- ION=+16 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010587 + +2 +2.000000 +0.010446 + +3 +2.000000 +0.010445 + +4 +2.000000 +0.010404 + +5 +2.000000 +0.010390 + +6 +2.000000 +0.010379 + +7 +2.000000 +0.010378 + +8 +2.000000 +0.010370 + + Density error is +0.000001546864 + + PW ALGORITHM --------------- ION=+16 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011046 + +2 +2.375000 +0.011756 + +3 +2.250000 +0.011289 + +4 +2.500000 +0.012140 + +5 +2.250000 +0.011313 + +6 +2.750000 +0.013017 + +7 +2.875000 +0.013462 + +8 +2.250000 +0.011249 + + Density error is +0.000000031769 + + PW ALGORITHM --------------- ION=+16 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.016761 + +2 +3.500000 +0.015694 + +3 +3.750000 +0.016521 + +4 +4.000000 +0.017360 + +5 +3.500000 +0.015655 + +6 +3.625000 +0.016032 + +7 +4.625000 +0.019569 + +8 +3.625000 +0.016039 + + Density error is +0.000000001918 + + PW ALGORITHM --------------- ION=+16 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013196 + +2 +3.125000 +0.014455 + +3 +2.875000 +0.013481 + +4 +4.000000 +0.017394 + +5 +3.000000 +0.013924 + +6 +3.750000 +0.016493 + +7 +3.000000 +0.013924 + +8 +3.125000 +0.014310 + + Density error is +0.000000000142 + + charge density convergence is achieved + final etot is -211.780796729120 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.685454 -0.466777 -0.074732 + Si2 -0.685454 +0.466777 +0.074732 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.145046 +2.237882 +12.724721 + +2.237882 +123.794533 -18.656690 + +12.724721 -18.656690 +124.345426 + +output Pressure for check! +Virtual Pressure is +124.174558 Kbar +Virial is +123.761668 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 16 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564047 (Rydberg) + NVT Temperature : +29.284447 (K) + NVT Kinetic energy : +0.000556 (Rydberg) + NVT Potential energy : -15.565596 (Rydberg) + maxForce : +0.000262 + maxStep : +0.011494 + MD_STEP SystemE Conserved DeltaE Temperature + +16 -7.782798 -7.782023 +0.000000 +12.500370 + + PW ALGORITHM --------------- ION=+17 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.250000 +1.548769 + +2 +24.250000 +0.238733 + +3 +26.875000 +0.097094 + +4 +30.500000 +0.109091 + +5 +25.500000 +0.092283 + +6 +29.500000 +0.106987 + +7 +30.375000 +0.108359 + +8 +24.000000 +0.086977 + + Density error is +0.000007183223 + + PW ALGORITHM --------------- ION=+17 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010577 + +2 +2.000000 +0.010427 + +3 +2.000000 +0.010496 + +4 +2.000000 +0.010394 + +5 +2.000000 +0.010418 + +6 +2.125000 +0.010931 + +7 +2.000000 +0.010379 + +8 +2.000000 +0.010422 + + Density error is +0.000000511477 + + PW ALGORITHM --------------- ION=+17 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.375000 +0.011921 + +2 +2.125000 +0.010910 + +3 +2.125000 +0.010844 + +4 +2.875000 +0.013531 + +5 +2.000000 +0.010405 + +6 +2.625000 +0.012594 + +7 +3.375000 +0.015197 + +8 +2.125000 +0.010844 + + Density error is +0.000000026283 + + PW ALGORITHM --------------- ION=+17 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.375000 +0.015456 + +2 +3.625000 +0.016132 + +3 +3.250000 +0.014828 + +4 +3.500000 +0.015635 + +5 +3.375000 +0.015239 + +6 +3.375000 +0.015161 + +7 +3.125000 +0.014336 + +8 +3.500000 +0.015643 + + Density error is +0.000000000237 + + charge density convergence is achieved + final etot is -211.774985509926 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.833310 -0.445812 -0.078719 + Si2 -0.833310 +0.445812 +0.078719 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.994195 +2.379118 +12.171980 + +2.379118 +124.272817 -22.694125 + +12.171980 -22.694125 +124.774373 + +output Pressure for check! +Virtual Pressure is +124.101591 Kbar +Virial is +124.013795 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 17 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564010 (Rydberg) + NVT Temperature : +8.524394 (K) + NVT Kinetic energy : +0.000162 (Rydberg) + NVT Potential energy : -15.565169 (Rydberg) + maxForce : +0.000340 + maxStep : +0.014988 + MD_STEP SystemE Conserved DeltaE Temperature + +17 -7.782584 -7.782005 +0.000000 +21.039416 + + PW ALGORITHM --------------- ION=+18 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +34.250000 +1.473409 + +2 +22.000000 +0.326542 + +3 +24.000000 +0.087028 + +4 +28.000000 +0.100599 + +5 +24.000000 +0.086910 + +6 +29.000000 +0.103884 + +7 +27.125000 +0.097431 + +8 +21.625000 +0.078627 + + Density error is +0.000009301236 + + PW ALGORITHM --------------- ION=+18 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010625 + +2 +2.000000 +0.010448 + +3 +2.000000 +0.010394 + +4 +2.000000 +0.010369 + +5 +2.000000 +0.010395 + +6 +2.125000 +0.010809 + +7 +2.000000 +0.010374 + +8 +2.000000 +0.010352 + + Density error is +0.000000698839 + + PW ALGORITHM --------------- ION=+18 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.250000 +0.011468 + +2 +2.125000 +0.010873 + +3 +2.125000 +0.010841 + +4 +2.875000 +0.013464 + +5 +2.125000 +0.010821 + +6 +2.500000 +0.012141 + +7 +3.125000 +0.014320 + +8 +2.125000 +0.010803 + + Density error is +0.000000028756 + + PW ALGORITHM --------------- ION=+18 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.500000 +0.015856 + +2 +3.625000 +0.016113 + +3 +3.500000 +0.015631 + +4 +3.625000 +0.016042 + +5 +3.625000 +0.016071 + +6 +3.750000 +0.016468 + +7 +4.000000 +0.017389 + +8 +3.625000 +0.016045 + + Density error is +0.000000000545 + + charge density convergence is achieved + final etot is -211.784530531570 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.693682 -0.275109 -0.084557 + Si2 -0.693682 +0.275109 +0.084557 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.844932 +2.424056 +7.513685 + +2.424056 +123.890142 -18.864028 + +7.513685 -18.864028 +124.067900 + +output Pressure for check! +Virtual Pressure is +123.748762 Kbar +Virial is +123.600991 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 18 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564069 (Rydberg) + NVT Temperature : +42.047874 (K) + NVT Kinetic energy : +0.000799 (Rydberg) + NVT Potential energy : -15.565870 (Rydberg) + maxForce : +0.000213 + maxStep : +0.027051 + MD_STEP SystemE Conserved DeltaE Temperature + +18 -7.782935 -7.782034 +0.000000 +72.297418 + + PW ALGORITHM --------------- ION=+19 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +33.625000 +1.446761 + +2 +22.750000 +0.337746 + +3 +24.500000 +0.088664 + +4 +26.875000 +0.096374 + +5 +24.375000 +0.088118 + +6 +27.625000 +0.099005 + +7 +26.125000 +0.093894 + +8 +23.000000 +0.083275 + + Density error is +0.000022341414 + + PW ALGORITHM --------------- ION=+19 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010590 + +2 +2.000000 +0.010429 + +3 +2.000000 +0.010400 + +4 +2.500000 +0.012143 + +5 +2.000000 +0.010418 + +6 +2.000000 +0.010354 + +7 +2.375000 +0.011685 + +8 +2.000000 +0.010357 + + Density error is +0.000001840522 + + PW ALGORITHM --------------- ION=+19 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011068 + +2 +2.375000 +0.011775 + +3 +2.250000 +0.011276 + +4 +2.500000 +0.012134 + +5 +2.250000 +0.011291 + +6 +2.500000 +0.012133 + +7 +3.000000 +0.013910 + +8 +2.375000 +0.011695 + + Density error is +0.000000031328 + + PW ALGORITHM --------------- ION=+19 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.016750 + +2 +3.750000 +0.016541 + +3 +3.750000 +0.016522 + +4 +4.000000 +0.017360 + +5 +3.625000 +0.016071 + +6 +3.875000 +0.016922 + +7 +4.125000 +0.017815 + +8 +3.875000 +0.016914 + + Density error is +0.000000002386 + + PW ALGORITHM --------------- ION=+19 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.750000 +0.013224 + +2 +2.875000 +0.013511 + +3 +2.875000 +0.013467 + +4 +3.875000 +0.016967 + +5 +2.875000 +0.013449 + +6 +3.500000 +0.015602 + +7 +3.500000 +0.015614 + +8 +2.500000 +0.012112 + + Density error is +0.000000000165 + + charge density convergence is achieved + final etot is -211.797509996802 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 +0.315435 -0.012610 -0.062567 + Si2 -0.315435 +0.012610 +0.062567 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +122.869560 +1.699030 +0.355976 + +1.699030 +123.125358 -8.562365 + +0.355976 -8.562365 +123.115733 + +output Pressure for check! +Virtual Pressure is +123.544666 Kbar +Virial is +123.036884 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 19 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564150 (Rydberg) + NVT Temperature : +86.724314 (K) + NVT Kinetic energy : +0.001648 (Rydberg) + NVT Potential energy : -15.566824 (Rydberg) + maxForce : +0.000039 + maxStep : +0.031849 + MD_STEP SystemE Conserved DeltaE Temperature + +19 -7.783412 -7.782075 +0.000000 +101.072847 + + PW ALGORITHM --------------- ION=+20 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.000000 +1.535621 + +2 +25.500000 +0.274161 + +3 +26.125000 +0.094184 + +4 +29.875000 +0.106798 + +5 +26.375000 +0.095103 + +6 +30.750000 +0.109985 + +7 +31.875000 +0.114172 + +8 +25.750000 +0.092841 + + Density error is +0.000029792721 + + PW ALGORITHM --------------- ION=+20 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011051 + +2 +2.000000 +0.010426 + +3 +2.000000 +0.010378 + +4 +2.125000 +0.010793 + +5 +2.000000 +0.010367 + +6 +2.000000 +0.010355 + +7 +2.000000 +0.010362 + +8 +2.000000 +0.010354 + + Density error is +0.000002500903 + + PW ALGORITHM --------------- ION=+20 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.375000 +0.011932 + +2 +2.500000 +0.012164 + +3 +2.250000 +0.011253 + +4 +2.500000 +0.012117 + +5 +2.250000 +0.011252 + +6 +2.750000 +0.012983 + +7 +2.750000 +0.013005 + +8 +2.500000 +0.012105 + + Density error is +0.000000031164 + + PW ALGORITHM --------------- ION=+20 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.750000 +0.016752 + +2 +3.875000 +0.016963 + +3 +3.750000 +0.016481 + +4 +3.875000 +0.016934 + +5 +3.750000 +0.016474 + +6 +3.625000 +0.016019 + +7 +4.750000 +0.019994 + +8 +3.750000 +0.016447 + + Density error is +0.000000003269 + + PW ALGORITHM --------------- ION=+20 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013655 + +2 +2.625000 +0.012594 + +3 +2.625000 +0.012553 + +4 +3.750000 +0.016475 + +5 +2.875000 +0.013402 + +6 +3.500000 +0.015683 + +7 +2.750000 +0.012961 + +8 +2.625000 +0.012526 + + Density error is +0.000000000179 + + charge density convergence is achieved + final etot is -211.797737534802 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.171785 +0.257041 +0.008602 + Si2 +0.171785 -0.257041 -0.008602 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.033300 -0.204765 -6.972062 + -0.204765 +122.939153 +4.657249 + -6.972062 +4.657249 +123.108999 + +output Pressure for check! +Virtual Pressure is +123.737037 Kbar +Virial is +123.027151 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 20 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564150 (Rydberg) + NVT Temperature : +85.566203 (K) + NVT Kinetic energy : +0.001626 (Rydberg) + NVT Potential energy : -15.566841 (Rydberg) + maxForce : +0.000036 + maxStep : +0.026933 + MD_STEP SystemE Conserved DeltaE Temperature + +20 -7.783421 -7.782075 +0.000000 +70.314105 + + PW ALGORITHM --------------- ION=+21 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +36.125000 +1.533770 + +2 +24.250000 +0.243025 + +3 +24.750000 +0.089487 + +4 +29.750000 +0.106362 + +5 +24.875000 +0.089914 + +6 +29.875000 +0.106912 + +7 +32.125000 +0.114500 + +8 +27.125000 +0.097630 + + Density error is +0.000022029241 + + PW ALGORITHM --------------- ION=+21 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.010617 + +2 +2.000000 +0.010405 + +3 +2.000000 +0.010373 + +4 +2.000000 +0.010365 + +5 +2.000000 +0.010388 + +6 +2.000000 +0.010360 + +7 +2.000000 +0.010347 + +8 +2.000000 +0.010369 + + Density error is +0.000001807441 + + PW ALGORITHM --------------- ION=+21 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.125000 +0.011063 + +2 +2.375000 +0.011747 + +3 +2.250000 +0.011261 + +4 +2.500000 +0.012112 + +5 +2.250000 +0.011278 + +6 +2.625000 +0.012552 + +7 +3.000000 +0.013891 + +8 +2.375000 +0.011680 + + Density error is +0.000000029382 + + PW ALGORITHM --------------- ION=+21 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.625000 +0.016299 + +2 +3.625000 +0.016094 + +3 +3.750000 +0.016491 + +4 +3.875000 +0.016919 + +5 +3.750000 +0.016502 + +6 +3.750000 +0.016462 + +7 +4.625000 +0.019557 + +8 +3.625000 +0.016026 + + Density error is +0.000000002371 + + PW ALGORITHM --------------- ION=+21 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.875000 +0.013673 + +2 +2.875000 +0.013455 + +3 +2.875000 +0.013422 + +4 +4.125000 +0.017806 + +5 +3.000000 +0.013879 + +6 +3.875000 +0.016927 + +7 +3.000000 +0.013878 + +8 +2.875000 +0.013406 + + Density error is +0.000000000178 + + charge density convergence is achieved + final etot is -211.785114277951 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.597076 +0.443380 +0.097410 + Si2 +0.597076 -0.443380 -0.097410 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +123.145634 -2.476538 -12.011339 + -2.476538 +123.557627 +16.195950 + -12.011339 +16.195950 +124.041967 + +output Pressure for check! +Virtual Pressure is +124.075595 Kbar +Virial is +123.581743 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 21 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -15.564066 (Rydberg) + NVT Temperature : +39.619227 (K) + NVT Kinetic energy : +0.000753 (Rydberg) + NVT Potential energy : -15.565913 (Rydberg) + maxForce : +0.000213 + maxStep : +0.014552 + MD_STEP SystemE Conserved DeltaE Temperature + +21 -7.782957 -7.782033 +0.000000 +19.004126 + + + -------------------------------------------- + !FINAL_ETOT_IS -211.7851142779510099 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total +35.575 15 +2.37 +100.00 % + Run_pw plane_wave_line +35.54 1 +35.54 +99.91 % + Run_MD_PW md_cells_pw +35.47 1 +35.47 +99.70 % + Potential init_pot +0.21 22 +0.01 +0.59 % + FFT FFT3D +21.26 126906 +0.00 +59.76 % + Potential v_of_rho +1.13 125 +0.01 +3.17 % + H_XC_pw v_xc +1.20 146 +0.01 +3.36 % + wavefunc wfcinit +0.97 22 +0.04 +2.73 % + pp_cell_vnl getvnl +0.46 1336 +0.00 +1.29 % + Hamilt_PW diagH_subspace +3.41 984 +0.00 +9.57 % + Hamilt_PW h_psi +24.29 52236 +0.00 +68.28 % + Hamilt_PW vloc +22.85 52236 +0.00 +64.24 % + Hamilt_PW vnl +1.29 52236 +0.00 +3.63 % + Hamilt_PW add_nonlocal_pp +0.75 52236 +0.00 +2.12 % + Run_MD_PW md_ions_pw +35.39 1 +35.39 +99.48 % + Electrons self_consistent +29.43 21 +1.40 +82.73 % + Electrons c_bands +25.56 103 +0.25 +71.86 % + Hamilt diagH_pw +25.14 824 +0.03 +70.67 % + Diago_CG diag +22.34 824 +0.03 +62.80 % + Charge sum_band +1.54 103 +0.01 +4.32 % + Charge mix_rho +0.20 103 +0.00 +0.57 % + Forces cal_force_nl +0.59 21 +0.03 +1.66 % + Stress_PW cal_stress +3.97 21 +0.19 +11.16 % + Stress_Func stress_ew +16.82 11 +1.53 +47.27 % + Force_Func stress_ew +16.82 11 +1.53 +47.27 % + Stress_Func stress_gga +0.11 21 +0.01 +0.31 % + Stress_Func stres_nl +3.76 21 +0.18 +10.57 % + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + +5.1730 + ---------------------------------------------------------- + + Start Time : Fri Oct 15 14:37:16 2021 + Finish Time : Fri Oct 15 14:37:52 2021 + Total Time : 0 h 0 mins 36 secs diff --git a/tests/abacus.md/STRU b/tests/abacus.md/STRU new file mode 100644 index 000000000..c3765e9bc --- /dev/null +++ b/tests/abacus.md/STRU @@ -0,0 +1,21 @@ +ATOMIC_SPECIES +Si 1.000 ./Si_ONCV_PBE-1.0.upf #Element, Mass, Pseudopotential + +NUMERICAL_ORBITAL +./Si_gga_8au_60Ry_2s2p1d.orb + +LATTICE_CONSTANT +10.2 #Lattice constant + +LATTICE_VECTORS +0.5 0.5 0.0 #Lattice vector 1 +0.5 0.0 0.5 #Lattice vector 2 +0.0 0.5 0.5 #Lattice vector 3 + +ATOMIC_POSITIONS +Cartesian #Cartesian(Unit is LATTICE_CONSTANT) +Si #Name of element +0.0 #Magnetic for this element. +2 #Number of atoms +0.00 0.00 0.00 1 1 1 #x,y,z, move_x, move_y, move_z +0.241 0.255 0.251 1 1 1 diff --git a/tests/abacus.md/Si_coord b/tests/abacus.md/Si_coord new file mode 100644 index 000000000..fb8c5a8df --- /dev/null +++ b/tests/abacus.md/Si_coord @@ -0,0 +1,10 @@ +0 0 0 +1.30082342 1.37638993 1.3547995 +5.35320953 2.72430477 2.68504527 +1.35126946 1.34726983 1.3286265 +2.70155326 2.69533522 5.35848569 +1.30969169 1.37268717 1.3150785 +2.66403555 0.02130293 2.64633444 +1.35284016 1.34443879 1.29061924 +2.70202696 2.69316139 5.32175227 +1.31985538 1.36795346 1.2771711 diff --git a/tests/abacus.md/Si_force b/tests/abacus.md/Si_force new file mode 100644 index 000000000..b22dd3cc1 --- /dev/null +++ b/tests/abacus.md/Si_force @@ -0,0 +1,10 @@ +-0.885363 0.500467 0.15024 +0.885363 -0.500467 -0.15024 +0.830073 -0.488698 -0.076368 +-0.830073 0.488698 0.076368 +-0.774114 0.493555 0.132287 +0.774114 -0.493555 -0.132287 +0.685454 -0.466777 -0.074732 +-0.685454 0.466777 0.074732 +-0.597076 0.44338 0.09741 +0.597076 -0.44338 -0.09741 diff --git a/tests/abacus.md/Si_virial b/tests/abacus.md/Si_virial new file mode 100644 index 000000000..8ee021799 --- /dev/null +++ b/tests/abacus.md/Si_virial @@ -0,0 +1,15 @@ +-3.01924575 0.09342813 0.33227574 +0.09342813 -3.05301021 -0.59008156 +0.33227574 -0.59008156 -3.06760338 +-3.02007615 -0.05764851 -0.32736857 +-0.05764851 -3.0485708 0.55474523 +-0.32736857 0.55474523 -3.06346952 +-3.02121465 0.08230513 0.32783898 +0.08230513 -3.04371791 -0.51561023 +0.32783898 -0.51561023 -3.05814259 +-3.02169395 -0.05491244 -0.31223515 +-0.05491244 -3.03763085 0.45779192 +-0.31223515 0.45779192 -3.05114849 +-3.02170837 0.0607685 0.29473041 +0.0607685 -3.03181773 -0.39741107 +0.29473041 -0.39741107 -3.04370231 diff --git a/tests/amber/methane.mol b/tests/amber/methane.mol new file mode 100644 index 000000000..bc9be67b6 --- /dev/null +++ b/tests/amber/methane.mol @@ -0,0 +1,14 @@ + + RDKit 3D + + 5 4 0 0 0 0 0 0 0 0999 V2000 + -0.0221 0.0032 0.0165 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6690 0.8894 -0.1009 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3778 -0.8578 -0.5883 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0964 -0.3151 1.0638 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9725 0.2803 -0.3911 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 1 3 1 0 + 1 4 1 0 + 1 5 1 0 +M END diff --git a/tests/amber/sqm.in b/tests/amber/sqm.in new file mode 100644 index 000000000..8f4120085 --- /dev/null +++ b/tests/amber/sqm.in @@ -0,0 +1,12 @@ +Run semi-emperical minimization + &qmmm + qm_theory='DFTB3' + qmcharge=0 + maxcyc=0 + verbosity=4 + / + 6 C -0.0221 0.0032 0.0165 + 1 H -0.6690 0.8894 -0.1009 + 1 H -0.3778 -0.8578 -0.5883 + 1 H 0.0964 -0.3151 1.0638 + 1 H 0.9725 0.2803 -0.3911 diff --git a/tests/amber/sqm_forces.out b/tests/amber/sqm_forces.out new file mode 100644 index 000000000..e4c2405d4 --- /dev/null +++ b/tests/amber/sqm_forces.out @@ -0,0 +1,392 @@ + -------------------------------------------------------- + AMBER SQM VERSION 19 + + By + Ross C. Walker, Michael F. Crowley, Scott Brozell, + Tim Giese, Andreas W. Goetz, + Tai-Sung Lee and David A. Case + + -------------------------------------------------------- + + +-------------------------------------------------------------------------------- + QM CALCULATION INFO +-------------------------------------------------------------------------------- + +| QMMM: Citation for AMBER QMMM Run: +| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008 + +| QMMM: DFTB Calculation - Additional citation for AMBER DFTB QMMM Run: +| QMMM: Seabra, G.M., Walker, R.C. et al., J. PHYS. CHEM. A., 111, 5655, (2007) + +| QMMM: DFTB3 - Additional citation to follow. Implementation by: +| QMMM: A.W. Goetz +| QMMM: +| QMMM: DFTB3 method citation: +| QMMM: M. Gaus, Q. Cui, M. Elstner, J. CHEM. THEORY COMPUT. 7, 931 (2011) +| QMMM: +| QMMM: DFTB3 dispersion correction [D3(BJ)] and halogen correction not available. + +| QMMM: Please cite also the appropriate references for the DFTB parameters +| QMMM: that you are using (see the manual and www.dftb.org). + + +QMMM: SINGLET STATE CALCULATION +QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 66 + +| QMMM: *** SCF convergence criteria *** +| QMMM: Energy change : 0.1D-09 kcal/mol +| QMMM: Error matrix |FP-PF| : 0.1D+00 au +| QMMM: Density matrix change : 0.5D-06 +| QMMM: Maximum number of SCF cycles : 1000 + DFTB: Number of atom types = 6 + + Parameter files: + TYP (AT) TYP (AT) SK integral FILE +| 1 1 (H ) 1 (H ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/H-H.skf +| 2 1 (H ) 2 (Cl) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/H-Cl.skf +| 3 1 (H ) 3 (N ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/H-N.skf +| 4 1 (H ) 4 (F ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/H-F.skf +| 5 1 (H ) 5 (C ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/H-C.skf +| 6 1 (H ) 6 (O ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/H-O.skf +| 7 2 (Cl) 1 (H ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/Cl-H.skf +| 8 2 (Cl) 2 (Cl) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/Cl-Cl.skf +| 9 2 (Cl) 3 (N ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/Cl-N.skf +| 10 2 (Cl) 4 (F ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/Cl-F.skf +| 11 2 (Cl) 5 (C ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/Cl-C.skf +| 12 2 (Cl) 6 (O ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/Cl-O.skf +| 13 3 (N ) 1 (H ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/N-H.skf +| 14 3 (N ) 2 (Cl) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/N-Cl.skf +| 15 3 (N ) 3 (N ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/N-N.skf +| 16 3 (N ) 4 (F ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/N-F.skf +| 17 3 (N ) 5 (C ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/N-C.skf +| 18 3 (N ) 6 (O ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/N-O.skf +| 19 4 (F ) 1 (H ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/F-H.skf +| 20 4 (F ) 2 (Cl) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/F-Cl.skf +| 21 4 (F ) 3 (N ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/F-N.skf +| 22 4 (F ) 4 (F ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/F-F.skf +| 23 4 (F ) 5 (C ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/F-C.skf +| 24 4 (F ) 6 (O ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/F-O.skf +| 25 5 (C ) 1 (H ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/C-H.skf +| 26 5 (C ) 2 (Cl) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/C-Cl.skf +| 27 5 (C ) 3 (N ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/C-N.skf +| 28 5 (C ) 4 (F ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/C-F.skf +| 29 5 (C ) 5 (C ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/C-C.skf +| 30 5 (C ) 6 (O ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/C-O.skf +| 31 6 (O ) 1 (H ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/O-H.skf +| 32 6 (O ) 2 (Cl) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/O-Cl.skf +| 33 6 (O ) 3 (N ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/O-N.skf +| 34 6 (O ) 4 (F ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/O-F.skf +| 35 6 (O ) 5 (C ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/O-C.skf +| 36 6 (O ) 6 (O ) /opt/anaconda3/envs/deepchem/dat/slko/3ob-3-1/O-O.skf + +QMMM: Hubbard Derivatives dU/dq: +QMMM: H -0.185700 +QMMM: Cl -0.069700 +QMMM: N -0.153500 +QMMM: F -0.157500 +QMMM: C -0.149200 +QMMM: O -0.157500 + +QMMM: zeta = 4.000000 + + QMMM: QM Region Cartesian Coordinates (*=link atom) + QMMM: QM_NO. MM_NO. ATOM X Y Z + QMMM: 1 1 H -3.2480 16.7500 48.5690 + QMMM: 2 2 H -5.8110 17.5130 48.7760 + QMMM: 3 3 H -5.2480 19.0560 49.7070 + QMMM: 4 4 H 1.5010 14.9330 51.1720 + QMMM: 5 5 Cl 1.4590 28.6690 49.7060 + QMMM: 6 6 N 1.5970 22.7720 52.6590 + QMMM: 7 7 F 3.2720 26.3910 49.9790 + QMMM: 8 8 C -0.6920 25.3770 50.5860 + QMMM: 9 9 C -0.3220 26.6740 50.2790 + QMMM: 10 10 C 2.4140 21.7490 53.2910 + QMMM: 11 11 C 1.5860 24.7340 50.4600 + QMMM: 12 12 C -0.2430 20.2390 50.6080 + QMMM: 13 13 C 1.4860 18.6010 51.9670 + QMMM: 14 14 C 1.6900 16.0010 51.2810 + QMMM: 15 15 C -3.5540 17.6700 49.0670 + QMMM: 16 16 O -3.0180 19.5790 50.3580 + QMMM: 17 17 C -2.5910 18.6340 49.7030 + QMMM: 18 18 C 0.2560 24.3780 50.6770 + QMMM: 19 19 C 1.9850 26.0320 50.1740 + QMMM: 20 20 C -0.2890 18.8740 50.3880 + QMMM: 21 21 C 1.0090 26.9990 50.0810 + QMMM: 22 22 C 0.5890 18.0550 51.0710 + QMMM: 23 23 C 0.6790 22.1640 51.7100 + QMMM: 24 24 C 1.5360 19.9630 52.1990 + QMMM: 25 25 C 0.6610 20.7900 51.4970 + QMMM: 26 26 C -5.0110 18.1230 49.1960 + QMMM: 27 27 N 2.4160 20.4320 53.0930 + QMMM: 28 28 N -1.2370 18.3410 49.4770 + QMMM: 29 29 N -0.1760 23.0610 51.0220 + QMMM: 30 30 O 0.5230 16.6890 50.8330 + QMMM: 31 31 H -1.6870 25.1540 50.7490 + QMMM: 32 32 H -1.0450 27.4060 50.1970 + QMMM: 33 33 H 3.0750 22.1330 53.9840 + QMMM: 34 34 H 2.3080 23.9980 50.5140 + QMMM: 35 35 H -0.8950 20.8570 50.1000 + QMMM: 36 36 H 2.1340 17.9790 52.4750 + QMMM: 37 37 H 1.8940 16.2470 52.3020 + QMMM: 38 38 H 2.5460 16.2790 50.7020 + QMMM: 39 39 H -0.9560 17.7860 48.7140 + QMMM: 40 40 H -1.0840 22.7710 50.7770 + +-------------------------------------------------------------------------------- + RESULTS +-------------------------------------------------------------------------------- + + QMMM SCC-DFTB: No external charges defined. + + QMMM SCC-DFTB: QM Region Input Cartesian Coordinates + QMMM SCC-DFTB: NO. TYP L AT# SYM X Y Z Charge + QMMM SCC-DFTB: 1 1 1 1 H -3.2480000000 16.7500000000 48.5690000000 0.0000000000 + QMMM SCC-DFTB: 2 1 1 1 H -5.8110000000 17.5130000000 48.7760000000 0.0000000000 + QMMM SCC-DFTB: 3 1 1 1 H -5.2480000000 19.0560000000 49.7070000000 0.0000000000 + QMMM SCC-DFTB: 4 1 1 1 H 1.5010000000 14.9330000000 51.1720000000 0.0000000000 + QMMM SCC-DFTB: 5 2 3 17 Cl 1.4590000000 28.6690000000 49.7060000000 0.0000000000 + QMMM SCC-DFTB: 6 3 2 7 N 1.5970000000 22.7720000000 52.6590000000 0.0000000000 + QMMM SCC-DFTB: 7 4 2 9 F 3.2720000000 26.3910000000 49.9790000000 0.0000000000 + QMMM SCC-DFTB: 8 5 2 6 C -0.6920000000 25.3770000000 50.5860000000 0.0000000000 + QMMM SCC-DFTB: 9 5 2 6 C -0.3220000000 26.6740000000 50.2790000000 0.0000000000 + QMMM SCC-DFTB: 10 5 2 6 C 2.4140000000 21.7490000000 53.2910000000 0.0000000000 + QMMM SCC-DFTB: 11 5 2 6 C 1.5860000000 24.7340000000 50.4600000000 0.0000000000 + QMMM SCC-DFTB: 12 5 2 6 C -0.2430000000 20.2390000000 50.6080000000 0.0000000000 + QMMM SCC-DFTB: 13 5 2 6 C 1.4860000000 18.6010000000 51.9670000000 0.0000000000 + QMMM SCC-DFTB: 14 5 2 6 C 1.6900000000 16.0010000000 51.2810000000 0.0000000000 + QMMM SCC-DFTB: 15 5 2 6 C -3.5540000000 17.6700000000 49.0670000000 0.0000000000 + QMMM SCC-DFTB: 16 6 2 8 O -3.0180000000 19.5790000000 50.3580000000 0.0000000000 + QMMM SCC-DFTB: 17 5 2 6 C -2.5910000000 18.6340000000 49.7030000000 0.0000000000 + QMMM SCC-DFTB: 18 5 2 6 C 0.2560000000 24.3780000000 50.6770000000 0.0000000000 + QMMM SCC-DFTB: 19 5 2 6 C 1.9850000000 26.0320000000 50.1740000000 0.0000000000 + QMMM SCC-DFTB: 20 5 2 6 C -0.2890000000 18.8740000000 50.3880000000 0.0000000000 + QMMM SCC-DFTB: 21 5 2 6 C 1.0090000000 26.9990000000 50.0810000000 0.0000000000 + QMMM SCC-DFTB: 22 5 2 6 C 0.5890000000 18.0550000000 51.0710000000 0.0000000000 + QMMM SCC-DFTB: 23 5 2 6 C 0.6790000000 22.1640000000 51.7100000000 0.0000000000 + QMMM SCC-DFTB: 24 5 2 6 C 1.5360000000 19.9630000000 52.1990000000 0.0000000000 + QMMM SCC-DFTB: 25 5 2 6 C 0.6610000000 20.7900000000 51.4970000000 0.0000000000 + QMMM SCC-DFTB: 26 5 2 6 C -5.0110000000 18.1230000000 49.1960000000 0.0000000000 + QMMM SCC-DFTB: 27 3 2 7 N 2.4160000000 20.4320000000 53.0930000000 0.0000000000 + QMMM SCC-DFTB: 28 3 2 7 N -1.2370000000 18.3410000000 49.4770000000 0.0000000000 + QMMM SCC-DFTB: 29 3 2 7 N -0.1760000000 23.0610000000 51.0220000000 0.0000000000 + QMMM SCC-DFTB: 30 6 2 8 O 0.5230000000 16.6890000000 50.8330000000 0.0000000000 + QMMM SCC-DFTB: 31 1 1 1 H -1.6870000000 25.1540000000 50.7490000000 0.0000000000 + QMMM SCC-DFTB: 32 1 1 1 H -1.0450000000 27.4060000000 50.1970000000 0.0000000000 + QMMM SCC-DFTB: 33 1 1 1 H 3.0750000000 22.1330000000 53.9840000000 0.0000000000 + QMMM SCC-DFTB: 34 1 1 1 H 2.3080000000 23.9980000000 50.5140000000 0.0000000000 + QMMM SCC-DFTB: 35 1 1 1 H -0.8950000000 20.8570000000 50.1000000000 0.0000000000 + QMMM SCC-DFTB: 36 1 1 1 H 2.1340000000 17.9790000000 52.4750000000 0.0000000000 + QMMM SCC-DFTB: 37 1 1 1 H 1.8940000000 16.2470000000 52.3020000000 0.0000000000 + QMMM SCC-DFTB: 38 1 1 1 H 2.5460000000 16.2790000000 50.7020000000 0.0000000000 + QMMM SCC-DFTB: 39 1 1 1 H -0.9560000000 17.7860000000 48.7140000000 0.0000000000 + QMMM SCC-DFTB: 40 1 1 1 H -1.0840000000 22.7710000000 50.7770000000 0.0000000000 + + QMMM SCC-DFTB: SCC convergence criteria: + QMMM SCC-DFTB: Energy: 1.0E-10 + QMMM SCC-DFTB: Charge: 5.0E-07 + QMMM SCC-DFTB: Telec : 0.000K + QMMM SCC-DFTB: It# Energy Diff MaxChDiff At# Index Symb MullikCh + QMMM SCC-DFTB: 1 -60.798600944606008 + QMMM SCC-DFTB: 2 -60.761310277605311 0.037290667000697 0.595754712212091 16 16 O -0.77468 + QMMM SCC-DFTB: 3 -60.690761389922393 0.070548887682918 0.162169321675918 28 28 N -0.34943 + QMMM SCC-DFTB: 4 -60.693582112240911 -0.002820722318518 0.057212899956027 26 26 C -0.18805 + QMMM SCC-DFTB: 5 -60.693810112125625 -0.000227999884714 0.034126287054791 26 26 C -0.18625 + QMMM SCC-DFTB: 6 -60.694758814978442 -0.000948702852817 0.006280640593352 10 10 C 0.26492 + QMMM SCC-DFTB: 7 -60.694683794994447 0.000075019983996 0.001188656812445 14 14 C 0.02853 + QMMM SCC-DFTB: 8 -60.694671884036232 0.000011910958214 0.000754530995241 24 24 C 0.24619 + QMMM SCC-DFTB: 9 -60.694667355499796 0.000004528536437 0.000226900277553 14 14 C 0.02864 + QMMM SCC-DFTB: 10 -60.694665432744969 0.000001922754826 0.000062045483471 18 18 C 0.19381 + QMMM SCC-DFTB: 11 -60.694668962789393 -0.000003530044424 0.000015615528849 11 11 C -0.22899 + QMMM SCC-DFTB: 12 -60.694667911003613 0.000001051785780 0.000009751821261 26 26 C -0.17321 + QMMM SCC-DFTB: 13 -60.694667846256891 0.000000064746722 0.000002027486490 12 12 C -0.14319 + QMMM SCC-DFTB: 14 -60.694667872515218 -0.000000026258327 0.000000853761193 12 12 C -0.14320 + QMMM SCC-DFTB: 15 -60.694667834521049 0.000000037994170 0.000000335782053 26 26 C -0.17321 + QMMM SCC-DFTB: 16 -60.694667845507233 -0.000000010986184 0.000000061336410 22 22 C 0.27074 + QMMM SCC-DFTB: 17 -60.694667845634164 -0.000000000126931 0.000000011315413 13 13 C -0.25843 + QMMM SCC-DFTB: 18 -60.694667845907794 -0.000000000273630 0.000000009087084 28 28 N -0.30551 + QMMM SCC-DFTB: 19 -60.694667845785801 0.000000000121993 0.000000002561571 9 9 C -0.11560 + QMMM SCC-DFTB: 20 -60.694667845807182 -0.000000000021380 0.000000000342425 14 14 C 0.02867 + QMMM SCC-DFTB: SCC-DFTB for step 0 converged in 20 cycles. + + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (eV) = -1425.999680715001 + QMMM SCC-DFTB: Electronic Energy (eV) = -1651.501912084414 + QMMM SCC-DFTB: Repulsive Energy (eV) = 27.941863707373 + QMMM SCC-DFTB: Total Energy (eV) = -1623.560048377041 + QMMM SCC-DFTB: SCF Energy (eV) = -197.560367662040 + QMMM SCC-DFTB: + QMMM SCC-DFTB: + QMMM SCC-DFTB: Atomization Energy (a.u.) = -52.407191500000 + QMMM SCC-DFTB: Electronic Energy (a.u.) = -60.694667845807 + QMMM SCC-DFTB: Repulsive Energy (a.u.) = 1.026896865394 + QMMM SCC-DFTB: Total Energy (a.u.) = -59.667770980413 + QMMM SCC-DFTB: SCF Energy (a.u.) = -7.260579480413 + QMMM SCC-DFTB: +QMMM: +QMMM: SCF Energy = -4555.93963865431033 KCal/mol, -19062.05144812963408 KJ/mol +QMMM: +QMMM: Electronic energy = -1651.50191208 eV ( -38085.28559458 KCal/mol) +QMMM: Repulsive energy = 27.94186371 eV ( 644.36731896 KCal/mol) +QMMM: Total energy = -1623.56004838 eV ( -37440.91827562 KCal/mol) + + Final MO eigenvalues (au): + -1.0678 -0.9168 -0.8819 -0.8091 -0.7922 -0.7767 -0.7663 -0.7146 + -0.7040 -0.6908 -0.6470 -0.6399 -0.6319 -0.6195 -0.6123 -0.5854 + -0.5491 -0.5352 -0.5223 -0.5130 -0.5092 -0.4936 -0.4794 -0.4578 + -0.4553 -0.4438 -0.4275 -0.4160 -0.4109 -0.4081 -0.4035 -0.4018 + -0.3975 -0.3919 -0.3896 -0.3838 -0.3733 -0.3707 -0.3675 -0.3562 + -0.3556 -0.3519 -0.3486 -0.3408 -0.3388 -0.3341 -0.3307 -0.3258 + -0.3231 -0.3211 -0.3141 -0.3067 -0.3021 -0.2999 -0.2874 -0.2770 + -0.2707 -0.2682 -0.2618 -0.2562 -0.2505 -0.2329 -0.2320 -0.2265 + -0.2248 -0.2086 -0.1292 -0.1036 -0.0653 -0.0615 -0.0509 -0.0262 + -0.0147 0.0102 0.0235 0.0502 0.0541 0.0702 0.0974 0.1356 + 0.1625 0.3045 0.3303 0.3330 0.3578 0.3670 0.3792 0.3898 + 0.3945 0.4153 0.4226 0.4356 0.4547 0.4654 0.5158 0.5206 + 0.5342 0.5503 0.5853 0.5957 0.5997 0.6140 0.6254 0.6388 + 0.6557 0.6633 0.6742 0.7431 0.7823 0.7996 0.8108 0.8206 + 0.8616 0.9009 0.9073 0.9275 0.9732 1.0088 1.0131 1.0738 + 1.1570 1.1766 1.2328 + + Heat of formation = -4555.93963865 kcal/mol ( -197.56036766 eV) + + Total SCF energy = -37440.91827562 kcal/mol ( -1623.56004838 eV) + Electronic energy = -38085.28559458 kcal/mol ( -1651.50191208 eV) + Core-core repulsion = 644.36731896 kcal/mol ( 27.94186371 eV) + + Atomic Charges for Step 1 : + Atom Element Mulliken Charge + 1 H 0.114 + 2 H 0.109 + 3 H 0.149 + 4 H 0.065 + 5 Cl -0.117 + 6 N -0.449 + 7 F -0.241 + 8 C -0.189 + 9 C -0.116 + 10 C 0.267 + 11 C -0.229 + 12 C -0.143 + 13 C -0.258 + 14 C 0.029 + 15 C -0.229 + 16 O -0.561 + 17 C 0.575 + 18 C 0.194 + 19 C 0.360 + 20 C 0.087 + 21 C 0.053 + 22 C 0.271 + 23 C 0.332 + 24 C 0.246 + 25 C -0.084 + 26 C -0.173 + 27 N -0.375 + 28 N -0.306 + 29 N -0.257 + 30 O -0.317 + 31 H 0.101 + 32 H 0.107 + 33 H 0.062 + 34 H 0.121 + 35 H 0.109 + 36 H 0.111 + 37 H 0.065 + 38 H 0.058 + 39 H 0.227 + 40 H 0.229 + Total Mulliken Charge = -0.000 + + X Y Z TOTAL + QM DIPOLE -1.681 -6.267 -2.968 7.135 + + Final Structure + + QMMM: QM Region Cartesian Coordinates (*=link atom) + QMMM: QM_NO. MM_NO. ATOM X Y Z + QMMM: 1 1 H -3.2480 16.7500 48.5690 + QMMM: 2 2 H -5.8110 17.5130 48.7760 + QMMM: 3 3 H -5.2480 19.0560 49.7070 + QMMM: 4 4 H 1.5010 14.9330 51.1720 + QMMM: 5 5 Cl 1.4590 28.6690 49.7060 + QMMM: 6 6 N 1.5970 22.7720 52.6590 + QMMM: 7 7 F 3.2720 26.3910 49.9790 + QMMM: 8 8 C -0.6920 25.3770 50.5860 + QMMM: 9 9 C -0.3220 26.6740 50.2790 + QMMM: 10 10 C 2.4140 21.7490 53.2910 + QMMM: 11 11 C 1.5860 24.7340 50.4600 + QMMM: 12 12 C -0.2430 20.2390 50.6080 + QMMM: 13 13 C 1.4860 18.6010 51.9670 + QMMM: 14 14 C 1.6900 16.0010 51.2810 + QMMM: 15 15 C -3.5540 17.6700 49.0670 + QMMM: 16 16 O -3.0180 19.5790 50.3580 + QMMM: 17 17 C -2.5910 18.6340 49.7030 + QMMM: 18 18 C 0.2560 24.3780 50.6770 + QMMM: 19 19 C 1.9850 26.0320 50.1740 + QMMM: 20 20 C -0.2890 18.8740 50.3880 + QMMM: 21 21 C 1.0090 26.9990 50.0810 + QMMM: 22 22 C 0.5890 18.0550 51.0710 + QMMM: 23 23 C 0.6790 22.1640 51.7100 + QMMM: 24 24 C 1.5360 19.9630 52.1990 + QMMM: 25 25 C 0.6610 20.7900 51.4970 + QMMM: 26 26 C -5.0110 18.1230 49.1960 + QMMM: 27 27 N 2.4160 20.4320 53.0930 + QMMM: 28 28 N -1.2370 18.3410 49.4770 + QMMM: 29 29 N -0.1760 23.0610 51.0220 + QMMM: 30 30 O 0.5230 16.6890 50.8330 + QMMM: 31 31 H -1.6870 25.1540 50.7490 + QMMM: 32 32 H -1.0450 27.4060 50.1970 + QMMM: 33 33 H 3.0750 22.1330 53.9840 + QMMM: 34 34 H 2.3080 23.9980 50.5140 + QMMM: 35 35 H -0.8950 20.8570 50.1000 + QMMM: 36 36 H 2.1340 17.9790 52.4750 + QMMM: 37 37 H 1.8940 16.2470 52.3020 + QMMM: 38 38 H 2.5460 16.2790 50.7020 + QMMM: 39 39 H -0.9560 17.7860 48.7140 + QMMM: 40 40 H -1.0840 22.7710 50.7770 +QMMM: +QMMM: Forces on QM atoms from SCF calculation +QMMM: Atm 1: 4.42339900482660 -1.84568335347418 -0.24491557798460 +QMMM: Atm 2: -3.23209970326899 -1.85584446015013 -2.20135365689389 +QMMM: Atm 3: -5.54210962602182 4.34957265805574 1.85035027143676 +QMMM: Atm 4: -0.64965287663571 1.94602348403655 -0.17030626388226 +QMMM: Atm 5: -0.54449676554692 11.45822560763962 -2.23770926902059 +QMMM: Atm 6: 19.47767949569608 114.02040828112732 39.17663967370635 +QMMM: Atm 7: 12.28770551313949 9.37687303025295 -2.02590726598390 +QMMM: Atm 8: -4.17307911860172 -18.69156102467198 8.61144913000140 +QMMM: Atm 9: -20.91151485959386 13.33542543081089 0.98315413859869 +QMMM: Atm 10: 57.81213096995776 -43.13681964739768 50.26857285156537 +QMMM: Atm 11: -14.70155414401897 2.29929204647827 1.84376932601349 +QMMM: Atm 12: 4.28968365278840 35.79519808443145 9.42895880861141 +QMMM: Atm 13: 11.76171363201617 19.00313683654644 18.40255685642010 +QMMM: Atm 14: 22.59203204962653 19.11376183395772 6.26353761850374 +QMMM: Atm 15: 152.71558007062131 -68.12292270331908 -19.48655475555291 +QMMM: Atm 16: -11.49476927523302 -14.61363615332107 -14.50049097275524 +QMMM: Atm 17: 7.28101898453634 32.58120230458048 30.69803359813822 +QMMM: Atm 18: 9.48563330633164 19.48973417471588 -14.39963078054814 +QMMM: Atm 19: -2.57982902102892 -2.92469180692160 0.27432319603930 +QMMM: Atm 20: 16.42510244833950 -31.10011261537555 26.07624637232345 +QMMM: Atm 21: 5.95178221473678 -32.84667693126916 5.72361951573615 +QMMM: Atm 22: -18.14365819340035 45.09266296196960 -10.97576744543044 +QMMM: Atm 23: -49.99748863934114 -104.43344069703645 -58.63304911115858 +QMMM: Atm 24: 3.59176294072371 11.23725074178902 2.97938234668701 +QMMM: Atm 25: 14.25157155772366 -12.74688632731251 -0.57220250477898 +QMMM: Atm 26: -143.19251827591333 60.79644824364138 22.33937110909451 +QMMM: Atm 27: -24.79071168291482 -36.88401899016046 -28.12203350267119 +QMMM: Atm 28: 28.91417842070531 -25.77427818785100 -30.66892606163460 +QMMM: Atm 29: -65.89101186031054 -5.88522174153298 -15.16631581275175 +QMMM: Atm 30: -10.73880633055260 -17.96543583547968 -1.06061838010930 +QMMM: Atm 31: 40.65299260949839 8.02283309252694 -6.07635657301762 +QMMM: Atm 32: 27.20908459427808 -29.72514804363591 2.48242778109588 +QMMM: Atm 33: -34.45616935317404 -17.96764452127526 -35.82036618876448 +QMMM: Atm 34: -31.01578164575134 30.29115946335486 -3.86716445062276 +QMMM: Atm 35: 26.66256743652963 -22.40890209908388 21.54264045155386 +QMMM: Atm 36: -26.57370510314600 16.55720434422381 -22.58257785285205 +QMMM: Atm 37: -2.11072325158175 6.70223481725448 -18.68189818816325 +QMMM: Atm 38: -15.33603012995946 -5.01932540898593 13.24968460082511 +QMMM: Atm 39: -7.53701805911437 25.50230569784656 15.96574322862577 +QMMM: Atm 40: 27.82710899111730 6.97729738125887 9.33368373960077 + + --------- Calculation Completed ---------- + diff --git a/tests/amber/sqm.out b/tests/amber/sqm_no_forces.out similarity index 100% rename from tests/amber/sqm.out rename to tests/amber/sqm_no_forces.out diff --git a/tests/ase/Al0He4O0/box.raw b/tests/ase/Al0He4O0/box.raw new file mode 100644 index 000000000..1c2cfa7ae --- /dev/null +++ b/tests/ase/Al0He4O0/box.raw @@ -0,0 +1 @@ +1.788616180419921875e+00 0.000000000000000000e+00 -0.000000000000000000e+00 -0.000000000000000000e+00 1.788616180419921875e+00 -0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 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-0.000000000000000000e+00 3.571599960327148438e+01 diff --git a/tests/ase/Al2He1O3/box.raw b/tests/ase/Al2He1O3/box.raw new file mode 100644 index 000000000..0dd4e0493 --- /dev/null +++ b/tests/ase/Al2He1O3/box.raw @@ -0,0 +1 @@ +2.135493040084838867e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 2.135493040084838867e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 4.186914920806884766e+00 diff --git a/tests/ase/Al2He1O3/coord.raw b/tests/ase/Al2He1O3/coord.raw new file mode 100644 index 000000000..9ba95bb20 --- /dev/null +++ b/tests/ase/Al2He1O3/coord.raw @@ -0,0 +1 @@ +0.000000000000000000e+00 1.067746520042419434e+00 3.076044321060180664e+00 1.067746520042419434e+00 0.000000000000000000e+00 1.110870838165283203e+00 0.000000000000000000e+00 1.067746520042419434e+00 1.504464030265808105e+00 1.067746520042419434e+00 0.000000000000000000e+00 2.682451248168945312e+00 0.000000000000000000e+00 0.000000000000000000e+00 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-0.000000000000000000e+00 -0.000000000000000000e+00 2.074619987979531288e-03 -0.000000000000000000e+00 0.000000000000000000e+00 2.074619987979531288e-03 -0.000000000000000000e+00 -0.000000000000000000e+00 -1.876299967989325523e-03 -0.000000000000000000e+00 -0.000000000000000000e+00 -1.876299967989325523e-03 -0.000000000000000000e+00 -0.000000000000000000e+00 5.152570083737373352e-03 -0.000000000000000000e+00 -0.000000000000000000e+00 5.152570083737373352e-03 -0.000000000000000000e+00 -0.000000000000000000e+00 -1.141160028055310249e-03 -0.000000000000000000e+00 -0.000000000000000000e+00 -1.141160028055310249e-03 diff --git a/tests/ase/Al8He8O12/type.raw b/tests/ase/Al8He8O12/type.raw new file mode 100644 index 000000000..96922a7fe --- /dev/null +++ b/tests/ase/Al8He8O12/type.raw @@ -0,0 +1,28 @@ +0 +0 +0 +0 +2 +2 +2 +2 +0 +0 +0 +0 +2 +2 +2 +2 +2 +2 +2 +2 +1 +1 +1 +1 +1 +1 +1 +1 diff --git a/tests/ase/Al8He8O12/type_map.raw b/tests/ase/Al8He8O12/type_map.raw new file mode 100644 index 000000000..b25e54214 --- /dev/null +++ b/tests/ase/Al8He8O12/type_map.raw @@ -0,0 +1,3 @@ +Al +He +O diff --git a/tests/ase/Al8He8O12/virial.raw b/tests/ase/Al8He8O12/virial.raw new file mode 100644 index 000000000..89908573d --- /dev/null +++ b/tests/ase/Al8He8O12/virial.raw @@ -0,0 +1 @@ +5.049785766601562500e+02 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 5.050623474121093750e+02 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 5.049291992187500000e+02 diff --git a/tests/ase/HeAlO.traj b/tests/ase/HeAlO.traj new file mode 100644 index 000000000..c3564ecfc Binary files /dev/null and b/tests/ase/HeAlO.traj differ diff --git a/tests/comp_sys.py b/tests/comp_sys.py index ca70e6076..d4934c1cb 100644 --- a/tests/comp_sys.py +++ b/tests/comp_sys.py @@ -35,13 +35,10 @@ def test_nframs(self): def test_cell(self): self.assertEqual(self.system_1.get_nframes(), self.system_2.get_nframes()) - for ff in range(self.system_1.get_nframes()) : - for ii in range(3) : - for jj in range(3) : - self.assertAlmostEqual(self.system_1.data['cells'][ff][ii][jj], - self.system_2.data['cells'][ff][ii][jj], - places = self.places, - msg = 'cell[%d][%d][%d] failed' % (ff,ii,jj)) + np.testing.assert_almost_equal(self.system_1.data['cells'], + self.system_2.data['cells'], + decimal = self.places, + err_msg = 'cell failed') def test_coord(self): self.assertEqual(self.system_1.get_nframes(), @@ -49,14 +46,11 @@ def test_coord(self): # think about direct coord tmp_cell = self.system_1.data['cells'] tmp_cell = np.reshape(tmp_cell, [-1, 3]) - tmp_cell_norm = np.reshape(np.linalg.norm(tmp_cell, axis = 1), [-1, 3]) - for ff in range(self.system_1.get_nframes()) : - for ii in range(sum(self.system_1.data['atom_numbs'])) : - for jj in range(3) : - self.assertAlmostEqual(self.system_1.data['coords'][ff][ii][jj] / tmp_cell_norm[ff][jj], - self.system_2.data['coords'][ff][ii][jj] / tmp_cell_norm[ff][jj], - places = self.places, - msg = 'coord[%d][%d][%d] failed' % (ff,ii,jj)) + tmp_cell_norm = np.reshape(np.linalg.norm(tmp_cell, axis = 1), [-1, 1, 3]) + np.testing.assert_almost_equal(self.system_1.data['coords'] / tmp_cell_norm, + self.system_2.data['coords'] / tmp_cell_norm, + decimal = self.places, + err_msg = 'coord failed') def test_nopbc(self): self.assertEqual(self.system_1.nopbc, self.system_2.nopbc) @@ -66,22 +60,18 @@ class CompLabeledSys (CompSys) : def test_energy(self) : self.assertEqual(self.system_1.get_nframes(), self.system_2.get_nframes()) - for ff in range(self.system_1.get_nframes()) : - self.assertAlmostEqual(self.system_1.data['energies'][ff], - self.system_2.data['energies'][ff], - places = self.e_places, - msg = 'energies[%d] failed' % (ff)) + np.testing.assert_almost_equal(self.system_1.data['energies'], + self.system_2.data['energies'], + decimal = self.e_places, + err_msg = 'energies failed') def test_force(self) : self.assertEqual(self.system_1.get_nframes(), self.system_2.get_nframes()) - for ff in range(self.system_1.get_nframes()) : - for ii in range(self.system_1.data['forces'].shape[1]) : - for jj in range(3) : - self.assertAlmostEqual(self.system_1.data['forces'][ff][ii][jj], - self.system_2.data['forces'][ff][ii][jj], - places = self.f_places, - msg = 'forces[%d][%d][%d] failed' % (ff,ii,jj)) + np.testing.assert_almost_equal(self.system_1.data['forces'], + self.system_2.data['forces'], + decimal = self.f_places, + err_msg = 'forces failed') def test_virial(self) : self.assertEqual(self.system_1.get_nframes(), @@ -92,13 +82,10 @@ def test_virial(self) : if not 'virials' in self.system_1: self.assertFalse('virials' in self.system_2) return - for ff in range(self.system_1.get_nframes()) : - for ii in range(3) : - for jj in range(3) : - self.assertAlmostEqual(self.system_1['virials'][ff][ii][jj], - self.system_2['virials'][ff][ii][jj], - places = self.v_places, - msg = 'virials[%d][%d][%d] failed' % (ff,ii,jj)) + np.testing.assert_almost_equal(self.system_1['virials'], + self.system_2['virials'], + decimal = self.v_places, + err_msg = 'virials failed') class MultiSystems: diff --git a/tests/cp2k/aimd/deepmd/energy.raw b/tests/cp2k/aimd/deepmd/energy.raw index 5944c7889..ed4325d62 100644 --- a/tests/cp2k/aimd/deepmd/energy.raw +++ b/tests/cp2k/aimd/deepmd/energy.raw @@ -1,3 +1,3 @@ -7.597057812500000000e+04 --7.597049218750000000e+04 --7.597026562500000000e+04 +-7.597050000000000000e+04 +-7.597027343750000000e+04 diff --git a/tests/cp2k/aimd/deepmd/force.raw b/tests/cp2k/aimd/deepmd/force.raw index d17e071a8..e3dd01762 100644 --- a/tests/cp2k/aimd/deepmd/force.raw +++ b/tests/cp2k/aimd/deepmd/force.raw @@ -1,3 +1,3 @@ --1.181987579911947250e-02 -6.981573533266782761e-03 -2.535107731819152832e-02 2.352045150473713875e-03 6.612877477891743183e-04 -1.095135696232318878e-02 9.170096367597579956e-03 3.188682254403829575e-03 -1.015020068734884262e-02 4.770424682646989822e-03 7.456199382431805134e-04 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5.263562873005867004e-02 1.400428563356399536e-01 2.000724673271179199e-01 -3.160451725125312805e-02 -1.877728290855884552e-02 1.365667283535003662e-01 1.508774887770414352e-02 -2.999140694737434387e-02 2.362376004457473755e-01 -5.841958150267601013e-02 -2.730511769186705351e-04 2.864455878734588623e-01 -3.346033859997987747e-03 3.664439544081687927e-02 1.374090164899826050e-01 3.791400417685508728e-02 -1.554489135742187500e-03 1.316636353731155396e-01 -7.310777902603149414e-02 -2.165897516533732414e-03 7.529733236879110336e-03 2.937588468194007874e-02 -1.078212782740592957e-01 -2.507854253053665161e-02 -4.747645184397697449e-02 2.562515810132026672e-02 -1.774123013019561768e-01 -2.635998092591762543e-02 5.408058688044548035e-02 6.827719509601593018e-02 -1.295218989253044128e-02 -4.677094146609306335e-02 5.198719725012779236e-02 -3.239590208977460861e-03 3.646956011652946472e-02 -1.268860101699829102e-01 -7.840836420655250549e-03 -8.373003453016281128e-02 2.224750071763992310e-01 3.069074638187885284e-02 5.268705077469348907e-03 -1.480256170034408569e-01 -3.176289796829223633e-02 3.841331228613853455e-02 -1.046835035085678101e-01 8.282604068517684937e-02 3.443067520856857300e-02 1.815867424011230469e-02 9.441194683313369751e-02 5.159073323011398315e-02 -1.701041939668357372e-03 3.985930234193801880e-02 1.937892101705074310e-02 9.308422915637493134e-03 3.155926614999771118e-02 2.736631035804748535e-02 -1.607952564954757690e-01 3.609520569443702698e-02 -6.125190854072570801e-02 7.475946098566055298e-02 6.751203443855047226e-03 -8.983435109257698059e-03 1.465528970584273338e-03 -6.945424526929855347e-02 -3.552904725074768066e-02 -7.128743827342987061e-02 diff --git a/tests/cp2k/cp2k_nocon_output b/tests/cp2k/cp2k_nocon_output new file mode 100644 index 000000000..48f54f9ec --- /dev/null +++ b/tests/cp2k/cp2k_nocon_output @@ -0,0 +1,4344 @@ + DBCSR| CPU 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| Use multiplication densification T + 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 2021-07-01 17:46:52.971 + ***** ** *** *** ** PROGRAM STARTED ON c53-018 + ** **** ****** PROGRAM STARTED BY ybzhuang + ***** ** ** ** ** PROGRAM PROCESS ID 394775 + **** ** ******* ** PROGRAM STARTED IN /data/ybzhuang/workdirs/CoO100-ml/wor + kdirs/fp/52dbdd53-8307-41df-80be-dc25 + da11e058/task.000.000178 + + CP2K| version string: CP2K version 7.1 + CP2K| source code revision number: git:e635599 + CP2K| cp2kflags: libint fftw3 libxc elpa parallel mpi3 scalapack xsmm spglib + CP2K| is freely available from https://www.cp2k.org/ + CP2K| Program compiled at Mon Mar 8 20:53:19 CST 2021 + CP2K| Program compiled on mgt01 + CP2K| Program compiled for local + CP2K| Data directory path /data/share/apps/cp2k/7.1/data + CP2K| Input file name input.inp + + GLOBAL| Force Environment number 1 + 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 DPGEN + GLOBAL| Preferred FFT library FFTW3 + GLOBAL| Preferred diagonalization lib. ELPA + 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| MPI I/O enabled T + GLOBAL| Total number of message passing processes 96 + GLOBAL| Number of threads for this process 1 + GLOBAL| This output is from process 0 + GLOBAL| CPU model name Intel(R) Xeon(R) Gold 6226R CPU @ 2.90GHz + GLOBAL| CPUID 1003 + GLOBAL| Compiled for CPUID 1002 + HINT in environment.F:814 The compiler target flags (x86_avx2) used to build + this binary cannot exploit all extensions of this CPU model (x86_avx512). + Consider compiler target flags as part of FCFLAGS and CFLAGS (ARCH file). + + MEMORY| system memory details [Kb] + MEMORY| rank 0 min max average + MEMORY| MemTotal 196481368 196472820 196481368 196475781 + MEMORY| MemFree 188584196 188577732 190659272 189601323 + MEMORY| Buffers 1092 0 2196 1096 + MEMORY| Cached 2405608 619200 2405920 1524383 + MEMORY| Slab 589336 445376 589336 495520 + MEMORY| SReclaimable 202560 161368 202624 175905 + MEMORY| MemLikelyFree 191193456 191187368 191442208 191302707 + + + *** 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]: 2814.757 + CELL_TOP| Vector a [angstrom 8.533 0.000 0.000 |a| = 8.533 + CELL_TOP| Vector b [angstrom 0.000 8.533 0.000 |b| = 8.533 + CELL_TOP| Vector c [angstrom 0.000 0.000 38.654 |c| = 38.654 + 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]: 2814.757 + CELL| Vector a [angstrom]: 8.533 0.000 0.000 |a| = 8.533 + CELL| Vector b [angstrom]: 0.000 8.533 0.000 |b| = 8.533 + CELL| Vector c [angstrom]: 0.000 0.000 38.654 |c| = 38.654 + 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]: 2814.757 + CELL_REF| Vector a [angstrom 8.533 0.000 0.000 |a| = 8.533 + CELL_REF| Vector b [angstrom 0.000 8.533 0.000 |b| = 8.533 + CELL_REF| Vector c [angstrom 0.000 0.000 38.654 |c| = 38.654 + 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 - 2019) ** + ** ** + ******************************************************************************* + + DFT| Spin unrestricted (spin-polarized) Kohn-Sham calculation UKS + DFT| Multiplicity 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 NONE + DFT| XC derivatives PW + + DFT+U| Method MULLIKEN_CHARGES + DFT+U| Check atomic kind information for details + FUNCTIONAL| ROUTINE=NEW + 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: 1.2170 + 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.]: 600.0 + QS| Multi grid cutoff [a.u.]: 1) grid level 600.0 + QS| 2) grid level 200.0 + QS| 3) grid level 66.7 + QS| 4) grid level 22.2 + 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: 3.2E-07 + QS| eps_filter_matrix: 0.0E+00 + 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: 3.2E-09 + + + ATOMIC KIND INFORMATION + + 1. Atomic kind: Al Number of atoms: 20 + + 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 2s 8.365268 1.064825 + 4.376458 0.104866 + 1.999998 -0.862858 + 0.834300 -0.262031 + 0.307482 -0.018089 + 0.095840 -0.010281 + + 1 2 3s 8.365268 0.314661 + 4.376458 0.067973 + 1.999998 -0.381507 + 0.834300 -0.269316 + 0.307482 0.083179 + 0.095840 0.115036 + + 1 3 4s 8.365268 -0.139380 + 4.376458 0.299832 + 1.999998 0.115427 + 0.834300 0.879401 + 0.307482 -0.824138 + 0.095840 0.204433 + + 1 4 3px 8.365268 1.285965 + 4.376458 -2.371337 + 1.999998 -1.725706 + 0.834300 -0.389232 + 0.307482 -0.014707 + 0.095840 0.000199 + 1 4 3py 8.365268 1.285965 + 4.376458 -2.371337 + 1.999998 -1.725706 + 0.834300 -0.389232 + 0.307482 -0.014707 + 0.095840 0.000199 + 1 4 3pz 8.365268 1.285965 + 4.376458 -2.371337 + 1.999998 -1.725706 + 0.834300 -0.389232 + 0.307482 -0.014707 + 0.095840 0.000199 + + 1 5 4px 8.365268 -0.139636 + 4.376458 -0.041761 + 1.999998 -0.203152 + 0.834300 -0.062856 + 0.307482 0.217329 + 0.095840 0.036248 + 1 5 4py 8.365268 -0.139636 + 4.376458 -0.041761 + 1.999998 -0.203152 + 0.834300 -0.062856 + 0.307482 0.217329 + 0.095840 0.036248 + 1 5 4pz 8.365268 -0.139636 + 4.376458 -0.041761 + 1.999998 -0.203152 + 0.834300 -0.062856 + 0.307482 0.217329 + 0.095840 0.036248 + + 1 6 4dx2 8.365268 10.317377 + 4.376458 5.299795 + 1.999998 1.799234 + 0.834300 0.387793 + 0.307482 0.052793 + 0.095840 0.001852 + 1 6 4dxy 8.365268 17.870222 + 4.376458 9.179514 + 1.999998 3.116365 + 0.834300 0.671678 + 0.307482 0.091440 + 0.095840 0.003207 + 1 6 4dxz 8.365268 17.870222 + 4.376458 9.179514 + 1.999998 3.116365 + 0.834300 0.671678 + 0.307482 0.091440 + 0.095840 0.003207 + 1 6 4dy2 8.365268 10.317377 + 4.376458 5.299795 + 1.999998 1.799234 + 0.834300 0.387793 + 0.307482 0.052793 + 0.095840 0.001852 + 1 6 4dyz 8.365268 17.870222 + 4.376458 9.179514 + 1.999998 3.116365 + 0.834300 0.671678 + 0.307482 0.091440 + 0.095840 0.003207 + 1 6 4dz2 8.365268 10.317377 + 4.376458 5.299795 + 1.999998 1.799234 + 0.834300 0.387793 + 0.307482 0.052793 + 0.095840 0.001852 + + 1 7 5dx2 8.365268 -6.769324 + 4.376458 -3.376985 + 1.999998 -1.595477 + 0.834300 0.024020 + 0.307482 0.083232 + 0.095840 0.017285 + 1 7 5dxy 8.365268 -11.724813 + 4.376458 -5.849110 + 1.999998 -2.763447 + 0.834300 0.041604 + 0.307482 0.144162 + 0.095840 0.029938 + 1 7 5dxz 8.365268 -11.724813 + 4.376458 -5.849110 + 1.999998 -2.763447 + 0.834300 0.041604 + 0.307482 0.144162 + 0.095840 0.029938 + 1 7 5dy2 8.365268 -6.769324 + 4.376458 -3.376985 + 1.999998 -1.595477 + 0.834300 0.024020 + 0.307482 0.083232 + 0.095840 0.017285 + 1 7 5dyz 8.365268 -11.724813 + 4.376458 -5.849110 + 1.999998 -2.763447 + 0.834300 0.041604 + 0.307482 0.144162 + 0.095840 0.029938 + 1 7 5dz2 8.365268 -6.769324 + 4.376458 -3.376985 + 1.999998 -1.595477 + 0.834300 0.024020 + 0.307482 0.083232 + 0.095840 0.017285 + + 1 8 5fx3 8.365268 -0.608021 + 4.376458 -0.793512 + 1.999998 -0.517880 + 0.834300 -0.502812 + 0.307482 -0.065982 + 0.095840 0.003032 + 1 8 5fx2y 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fx2z 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fxy2 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fxyz 8.365268 -2.354856 + 4.376458 -3.073258 + 1.999998 -2.005739 + 0.834300 -1.947383 + 0.307482 -0.255547 + 0.095840 0.011745 + 1 8 5fxz2 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fy3 8.365268 -0.608021 + 4.376458 -0.793512 + 1.999998 -0.517880 + 0.834300 -0.502812 + 0.307482 -0.065982 + 0.095840 0.003032 + 1 8 5fy2z 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fyz2 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fz3 8.365268 -0.608021 + 4.376458 -0.793512 + 1.999998 -0.517880 + 0.834300 -0.502812 + 0.307482 -0.065982 + 0.095840 0.003032 + + GTH Potential information for GTH-PBE-q17 + + 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: 3.967467 + Electronic configuration (s p d ...): 4 6 7 + + Parameters of the local part of the GTH pseudopotential: + + rloc C1 C2 C3 C4 + 0.355000 4.828197 0.368143 + + Parameters of the non-local part of the GTH pseudopotential: + + l r(l) h(i,j,l) + + 0 0.276801 -0.584496 9.286293 + 9.286293 -11.988552 + 1 0.268158 -6.851953 5.680133 + 5.680133 -6.720824 + 2 0.222584 -12.333150 + + 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]: 3.600 + + 2. Atomic kind: Co Number of atoms: 20 + + 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 2s 8.365268 1.064825 + 4.376458 0.104866 + 1.999998 -0.862858 + 0.834300 -0.262031 + 0.307482 -0.018089 + 0.095840 -0.010281 + + 1 2 3s 8.365268 0.314661 + 4.376458 0.067973 + 1.999998 -0.381507 + 0.834300 -0.269316 + 0.307482 0.083179 + 0.095840 0.115036 + + 1 3 4s 8.365268 -0.139380 + 4.376458 0.299832 + 1.999998 0.115427 + 0.834300 0.879401 + 0.307482 -0.824138 + 0.095840 0.204433 + + 1 4 3px 8.365268 1.285965 + 4.376458 -2.371337 + 1.999998 -1.725706 + 0.834300 -0.389232 + 0.307482 -0.014707 + 0.095840 0.000199 + 1 4 3py 8.365268 1.285965 + 4.376458 -2.371337 + 1.999998 -1.725706 + 0.834300 -0.389232 + 0.307482 -0.014707 + 0.095840 0.000199 + 1 4 3pz 8.365268 1.285965 + 4.376458 -2.371337 + 1.999998 -1.725706 + 0.834300 -0.389232 + 0.307482 -0.014707 + 0.095840 0.000199 + + 1 5 4px 8.365268 -0.139636 + 4.376458 -0.041761 + 1.999998 -0.203152 + 0.834300 -0.062856 + 0.307482 0.217329 + 0.095840 0.036248 + 1 5 4py 8.365268 -0.139636 + 4.376458 -0.041761 + 1.999998 -0.203152 + 0.834300 -0.062856 + 0.307482 0.217329 + 0.095840 0.036248 + 1 5 4pz 8.365268 -0.139636 + 4.376458 -0.041761 + 1.999998 -0.203152 + 0.834300 -0.062856 + 0.307482 0.217329 + 0.095840 0.036248 + + 1 6 4dx2 8.365268 10.317377 + 4.376458 5.299795 + 1.999998 1.799234 + 0.834300 0.387793 + 0.307482 0.052793 + 0.095840 0.001852 + 1 6 4dxy 8.365268 17.870222 + 4.376458 9.179514 + 1.999998 3.116365 + 0.834300 0.671678 + 0.307482 0.091440 + 0.095840 0.003207 + 1 6 4dxz 8.365268 17.870222 + 4.376458 9.179514 + 1.999998 3.116365 + 0.834300 0.671678 + 0.307482 0.091440 + 0.095840 0.003207 + 1 6 4dy2 8.365268 10.317377 + 4.376458 5.299795 + 1.999998 1.799234 + 0.834300 0.387793 + 0.307482 0.052793 + 0.095840 0.001852 + 1 6 4dyz 8.365268 17.870222 + 4.376458 9.179514 + 1.999998 3.116365 + 0.834300 0.671678 + 0.307482 0.091440 + 0.095840 0.003207 + 1 6 4dz2 8.365268 10.317377 + 4.376458 5.299795 + 1.999998 1.799234 + 0.834300 0.387793 + 0.307482 0.052793 + 0.095840 0.001852 + + 1 7 5dx2 8.365268 -6.769324 + 4.376458 -3.376985 + 1.999998 -1.595477 + 0.834300 0.024020 + 0.307482 0.083232 + 0.095840 0.017285 + 1 7 5dxy 8.365268 -11.724813 + 4.376458 -5.849110 + 1.999998 -2.763447 + 0.834300 0.041604 + 0.307482 0.144162 + 0.095840 0.029938 + 1 7 5dxz 8.365268 -11.724813 + 4.376458 -5.849110 + 1.999998 -2.763447 + 0.834300 0.041604 + 0.307482 0.144162 + 0.095840 0.029938 + 1 7 5dy2 8.365268 -6.769324 + 4.376458 -3.376985 + 1.999998 -1.595477 + 0.834300 0.024020 + 0.307482 0.083232 + 0.095840 0.017285 + 1 7 5dyz 8.365268 -11.724813 + 4.376458 -5.849110 + 1.999998 -2.763447 + 0.834300 0.041604 + 0.307482 0.144162 + 0.095840 0.029938 + 1 7 5dz2 8.365268 -6.769324 + 4.376458 -3.376985 + 1.999998 -1.595477 + 0.834300 0.024020 + 0.307482 0.083232 + 0.095840 0.017285 + + 1 8 5fx3 8.365268 -0.608021 + 4.376458 -0.793512 + 1.999998 -0.517880 + 0.834300 -0.502812 + 0.307482 -0.065982 + 0.095840 0.003032 + 1 8 5fx2y 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fx2z 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fxy2 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fxyz 8.365268 -2.354856 + 4.376458 -3.073258 + 1.999998 -2.005739 + 0.834300 -1.947383 + 0.307482 -0.255547 + 0.095840 0.011745 + 1 8 5fxz2 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fy3 8.365268 -0.608021 + 4.376458 -0.793512 + 1.999998 -0.517880 + 0.834300 -0.502812 + 0.307482 -0.065982 + 0.095840 0.003032 + 1 8 5fy2z 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fyz2 8.365268 -1.359576 + 4.376458 -1.774347 + 1.999998 -1.158014 + 0.834300 -1.124322 + 0.307482 -0.147540 + 0.095840 0.006781 + 1 8 5fz3 8.365268 -0.608021 + 4.376458 -0.793512 + 1.999998 -0.517880 + 0.834300 -0.502812 + 0.307482 -0.065982 + 0.095840 0.003032 + + GTH Potential information for GTH-PBE-q17 + + 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: 3.967467 + Electronic configuration (s p d ...): 4 6 7 + + Parameters of the local part of the GTH pseudopotential: + + rloc C1 C2 C3 C4 + 0.355000 4.828197 0.368143 + + Parameters of the non-local part of the GTH pseudopotential: + + l r(l) h(i,j,l) + + 0 0.276801 -0.584496 9.286293 + 9.286293 -11.988552 + 1 0.268158 -6.851953 5.680133 + 5.680133 -6.720824 + 2 0.222584 -12.333150 + + 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]: 3.600 + + 3. Atomic kind: H Number of atoms: 148 + + Orbital Basis Set DZVP-MOLOPT-SR-GTH + + Number of orbital shell sets: 1 + 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 2s 10.068468 -0.133023 + 2.680223 -0.177618 + 0.791502 -0.258419 + 0.239116 -0.107525 + 0.082193 -0.014019 + + 1 2 3s 10.068468 0.344673 + 2.680223 1.819821 + 0.791502 -0.999069 + 0.239116 0.017430 + 0.082193 0.082660 + + 1 3 3px 10.068468 0.155326 + 2.680223 0.367157 + 0.791502 0.311480 + 0.239116 0.080105 + 0.082193 0.033440 + 1 3 3py 10.068468 0.155326 + 2.680223 0.367157 + 0.791502 0.311480 + 0.239116 0.080105 + 0.082193 0.033440 + 1 3 3pz 10.068468 0.155326 + 2.680223 0.367157 + 0.791502 0.311480 + 0.239116 0.080105 + 0.082193 0.033440 + + GTH Potential information for GTH-PBE-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 -4.178900 0.724463 + + 4. Atomic kind: O Number of atoms: 114 + + Orbital Basis Set DZVP-MOLOPT-SR-GTH + + Number of orbital shell sets: 1 + 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 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: 8.360253 + Electronic configuration (s p d ...): 2 4 + + Parameters of the local part of the GTH pseudopotential: + + rloc C1 C2 C3 C4 + 0.244554 -16.667215 2.487311 + + Parameters of the non-local part of the GTH pseudopotential: + + l r(l) h(i,j,l) + + 0 0.220956 18.337458 + 1 0.211332 + + + MOLECULE KIND INFORMATION + + + All atoms are their own molecule, skipping detailed information + + + TOTAL NUMBERS AND MAXIMUM NUMBERS + + Total number of - Atomic kinds: 4 + - Atoms: 302 + - Shell sets: 302 + - Shells: 1334 + - Primitive Cartesian functions: 1550 + - Cartesian basis functions: 3576 + - Spherical basis functions: 3262 + + Maximum angular momentum of- Orbital basis functions: 3 + - Local part of the GTH pseudopotential: 2 + - 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 Co 27 0.772952 1.046610 4.349800 17.00 58.9332 + 2 1 Co 27 0.673906 2.986320 2.311110 17.00 58.9332 + 3 1 Co 27 2.955400 0.860018 2.248680 17.00 58.9332 + 4 1 Co 27 5.011510 7.306510 2.226850 17.00 58.9332 + 5 1 Co 27 7.047330 7.542630 38.603300 17.00 58.9332 + 6 1 Co 27 2.877810 3.039910 0.121442 17.00 58.9332 + 7 1 Co 27 0.975833 5.167600 0.055087 17.00 58.9332 + 8 1 Co 27 2.947490 7.310700 4.305750 17.00 58.9332 + 9 1 Co 27 4.935640 5.163860 4.262020 17.00 58.9332 + 10 1 Co 27 7.153490 2.979880 4.337570 17.00 58.9332 + 11 1 Co 27 7.061260 5.269620 2.067850 17.00 58.9332 + 12 1 Co 27 0.852413 7.390160 6.287700 17.00 58.9332 + 13 1 Co 27 5.033300 3.025440 6.290610 17.00 58.9332 + 14 1 Co 27 7.106820 0.829033 6.377540 17.00 58.9332 + 15 1 Co 27 2.901900 5.099150 6.286920 17.00 58.9332 + 16 1 Co 27 4.919970 0.965284 38.616600 17.00 58.9332 + 17 1 Co 27 7.294490 7.173990 8.538250 17.00 58.9332 + 18 1 Co 27 2.852160 3.252690 8.661040 17.00 58.9332 + 19 1 Co 27 0.919714 5.381210 8.568090 17.00 58.9332 + 20 1 Co 27 4.899360 0.905979 8.505370 17.00 58.9332 + 21 2 Co 27 5.165050 2.974370 2.385420 17.00 58.9332 + 22 2 Co 27 0.610294 5.230330 4.326880 17.00 58.9332 + 23 2 Co 27 5.064000 0.756750 4.376250 17.00 58.9332 + 24 2 Co 27 4.855800 5.181700 8.594120 17.00 58.9332 + 25 2 Co 27 2.814010 7.405070 8.691370 17.00 58.9332 + 26 2 Co 27 7.233910 7.267070 4.227820 17.00 58.9332 + 27 2 Co 27 7.189510 0.962452 2.229400 17.00 58.9332 + 28 2 Co 27 2.815640 3.053650 4.228070 17.00 58.9332 + 29 2 Co 27 2.875870 7.274390 38.613200 17.00 58.9332 + 30 2 Co 27 0.707087 0.931557 38.633000 17.00 58.9332 + 31 2 Co 27 2.816990 5.054250 2.218100 17.00 58.9332 + 32 2 Co 27 5.106550 7.274550 6.464920 17.00 58.9332 + 33 2 Co 27 7.164210 2.946920 38.647000 17.00 58.9332 + 34 2 Co 27 0.735849 3.096210 6.427060 17.00 58.9332 + 35 2 Co 27 7.134030 5.204710 6.253510 17.00 58.9332 + 36 2 Co 27 7.241260 3.065130 8.513850 17.00 58.9332 + 37 2 Co 27 0.721020 7.434140 2.105460 17.00 58.9332 + 38 2 Co 27 0.863058 0.888601 8.740710 17.00 58.9332 + 39 2 Co 27 2.887530 1.018790 6.429970 17.00 58.9332 + 40 2 Co 27 4.967980 5.230290 0.072048 17.00 58.9332 + 41 3 H 1 6.644060 5.287860 20.976900 1.00 1.0079 + 42 3 H 1 6.198890 5.044290 22.417000 1.00 1.0079 + 43 3 H 1 6.154080 2.515080 30.160300 1.00 1.0079 + 44 3 H 1 5.619880 5.796950 30.113800 1.00 1.0079 + 45 3 H 1 7.819140 3.583730 11.232400 1.00 1.0079 + 46 3 H 1 7.901440 5.946750 27.259700 1.00 1.0079 + 47 3 H 1 7.914150 6.770960 21.431800 1.00 1.0079 + 48 3 H 1 6.608970 5.263300 27.964000 1.00 1.0079 + 49 3 H 1 2.363930 4.825250 19.992500 1.00 1.0079 + 50 3 H 1 2.945180 0.763929 19.801900 1.00 1.0079 + 51 3 H 1 1.566490 6.642650 28.215500 1.00 1.0079 + 52 3 H 1 5.718950 5.198960 12.314700 1.00 1.0079 + 53 3 H 1 7.909680 5.811100 12.745100 1.00 1.0079 + 54 3 H 1 5.880110 2.429970 32.855800 1.00 1.0079 + 55 3 H 1 3.320320 3.923890 19.250700 1.00 1.0079 + 56 3 H 1 5.482380 1.511290 34.110700 1.00 1.0079 + 57 3 H 1 8.395200 7.123790 20.010500 1.00 1.0079 + 58 3 H 1 3.075890 0.848378 18.158300 1.00 1.0079 + 59 3 H 1 1.231690 7.188990 25.600500 1.00 1.0079 + 60 3 H 1 0.303601 0.375479 16.664000 1.00 1.0079 + 61 3 H 1 1.790370 3.330880 14.205100 1.00 1.0079 + 62 3 H 1 2.780440 6.003410 34.221500 1.00 1.0079 + 63 3 H 1 4.926090 7.813100 17.368000 1.00 1.0079 + 64 3 H 1 1.042400 7.897760 15.594200 1.00 1.0079 + 65 3 H 1 5.023140 0.380817 12.198800 1.00 1.0079 + 66 3 H 1 3.892800 7.911460 11.992500 1.00 1.0079 + 67 3 H 1 0.174405 7.494680 28.253500 1.00 1.0079 + 68 3 H 1 1.761340 6.303020 24.480700 1.00 1.0079 + 69 3 H 1 0.496777 4.273490 16.265900 1.00 1.0079 + 70 3 H 1 1.032160 5.167430 17.289200 1.00 1.0079 + 71 3 H 1 5.867890 8.364160 28.494400 1.00 1.0079 + 72 3 H 1 5.202250 7.904460 27.244800 1.00 1.0079 + 73 3 H 1 7.490880 7.276510 17.119300 1.00 1.0079 + 74 3 H 1 7.037670 6.488150 18.359000 1.00 1.0079 + 75 3 H 1 0.840109 4.699380 13.828300 1.00 1.0079 + 76 3 H 1 2.216580 5.664870 22.132400 1.00 1.0079 + 77 3 H 1 7.653140 1.512160 12.847400 1.00 1.0079 + 78 3 H 1 0.758159 1.406950 11.459400 1.00 1.0079 + 79 3 H 1 4.824370 4.831340 35.904600 1.00 1.0079 + 80 3 H 1 4.604640 8.009510 30.864800 1.00 1.0079 + 81 3 H 1 7.673980 0.894675 29.387800 1.00 1.0079 + 82 3 H 1 7.705090 2.320980 28.615900 1.00 1.0079 + 83 3 H 1 2.726650 7.890510 13.549100 1.00 1.0079 + 84 3 H 1 6.360430 4.500020 19.065200 1.00 1.0079 + 85 3 H 1 7.936260 4.734700 18.903400 1.00 1.0079 + 86 3 H 1 3.317600 2.287100 27.319300 1.00 1.0079 + 87 3 H 1 7.399870 7.853040 30.095500 1.00 1.0079 + 88 3 H 1 7.954440 4.706340 34.054900 1.00 1.0079 + 89 3 H 1 0.592326 2.704670 30.022900 1.00 1.0079 + 90 3 H 1 1.822710 6.589940 20.980300 1.00 1.0079 + 91 3 H 1 1.099110 2.723880 33.604600 1.00 1.0079 + 92 3 H 1 5.473840 6.895440 21.533200 1.00 1.0079 + 93 3 H 1 5.351070 5.665960 14.076400 1.00 1.0079 + 94 3 H 1 7.121550 2.419870 26.174300 1.00 1.0079 + 95 3 H 1 7.308230 3.757060 26.948100 1.00 1.0079 + 96 3 H 1 0.706245 7.383180 33.408400 1.00 1.0079 + 97 3 H 1 7.633500 7.501150 33.427700 1.00 1.0079 + 98 3 H 1 3.200390 3.811850 35.331700 1.00 1.0079 + 99 3 H 1 4.296090 3.467720 34.317400 1.00 1.0079 + 100 3 H 1 4.395070 0.337303 22.875800 1.00 1.0079 + 101 3 H 1 4.321720 8.294250 24.407100 1.00 1.0079 + 102 3 H 1 5.430410 2.754150 18.849100 1.00 1.0079 + 103 3 H 1 5.432680 3.259540 17.359300 1.00 1.0079 + 104 3 H 1 4.990700 5.979630 28.739500 1.00 1.0079 + 105 3 H 1 3.941110 0.558654 29.256500 1.00 1.0079 + 106 3 H 1 1.045250 3.780920 23.450500 1.00 1.0079 + 107 3 H 1 8.378820 4.437570 22.685900 1.00 1.0079 + 108 3 H 1 2.015190 6.713890 11.023500 1.00 1.0079 + 109 3 H 1 0.539704 5.314780 11.810500 1.00 1.0079 + 110 3 H 1 7.270480 3.493890 35.914800 1.00 1.0079 + 111 3 H 1 5.384830 7.649310 32.200700 1.00 1.0079 + 112 3 H 1 6.027370 1.143370 24.520600 1.00 1.0079 + 113 3 H 1 7.601410 1.057830 24.051600 1.00 1.0079 + 114 3 H 1 1.272770 3.902640 31.724300 1.00 1.0079 + 115 3 H 1 1.696590 4.794390 32.947100 1.00 1.0079 + 116 3 H 1 4.191230 1.679670 30.286400 1.00 1.0079 + 117 3 H 1 5.174050 3.694740 29.981200 1.00 1.0079 + 118 3 H 1 5.609910 6.656660 25.489700 1.00 1.0079 + 119 3 H 1 4.001300 6.436610 25.647200 1.00 1.0079 + 120 3 H 1 3.782950 6.024270 14.546100 1.00 1.0079 + 121 3 H 1 6.777760 1.006490 18.904200 1.00 1.0079 + 122 3 H 1 5.752300 0.449664 20.050300 1.00 1.0079 + 123 3 H 1 0.004540 8.393440 22.286000 1.00 1.0079 + 124 3 H 1 0.948099 8.213180 23.538400 1.00 1.0079 + 125 3 H 1 3.001460 5.266570 29.653000 1.00 1.0079 + 126 3 H 1 1.801520 4.536750 29.374600 1.00 1.0079 + 127 3 H 1 3.479130 3.951680 25.935200 1.00 1.0079 + 128 3 H 1 3.013080 3.918820 24.559300 1.00 1.0079 + 129 3 H 1 2.745460 2.826020 20.934900 1.00 1.0079 + 130 3 H 1 3.894520 2.854330 21.866600 1.00 1.0079 + 131 3 H 1 5.041030 4.018410 24.262600 1.00 1.0079 + 132 3 H 1 6.257420 3.111840 23.687600 1.00 1.0079 + 133 3 H 1 2.789790 7.382890 33.494500 1.00 1.0079 + 134 3 H 1 3.964150 7.162940 21.364600 1.00 1.0079 + 135 3 H 1 5.806410 1.496810 15.284400 1.00 1.0079 + 136 3 H 1 4.375090 2.093000 14.888600 1.00 1.0079 + 137 3 H 1 0.575598 0.998240 35.913700 1.00 1.0079 + 138 3 H 1 2.279520 0.969842 34.596300 1.00 1.0079 + 139 3 H 1 5.980310 0.117152 13.822000 1.00 1.0079 + 140 3 H 1 7.279060 8.415660 14.872600 1.00 1.0079 + 141 3 H 1 2.873130 6.927220 17.154100 1.00 1.0079 + 142 3 H 1 1.521010 7.180220 17.929500 1.00 1.0079 + 143 3 H 1 0.156304 1.406130 33.773900 1.00 1.0079 + 144 3 H 1 3.423820 3.646070 27.983200 1.00 1.0079 + 145 3 H 1 4.480720 0.338486 16.368400 1.00 1.0079 + 146 3 H 1 3.776620 6.117530 10.670700 1.00 1.0079 + 147 3 H 1 5.624640 1.675040 36.051100 1.00 1.0079 + 148 3 H 1 1.999590 2.197570 36.287900 1.00 1.0079 + 149 3 H 1 7.279420 5.022490 9.602130 1.00 1.0079 + 150 3 H 1 2.133960 2.426080 30.025800 1.00 1.0079 + 151 3 H 1 0.878684 3.544010 9.509750 1.00 1.0079 + 152 3 H 1 4.221730 1.408070 10.647200 1.00 1.0079 + 153 3 H 1 5.224540 2.810440 9.581820 1.00 1.0079 + 154 3 H 1 5.312060 7.374120 9.595880 1.00 1.0079 + 155 3 H 1 1.712440 4.276030 10.609900 1.00 1.0079 + 156 3 H 1 4.843790 3.115410 37.663000 1.00 1.0079 + 157 3 H 1 7.133540 5.238240 37.567600 1.00 1.0079 + 158 3 H 1 4.190790 6.028960 36.566800 1.00 1.0079 + 159 3 H 1 7.210180 6.722060 35.863500 1.00 1.0079 + 160 3 H 1 7.622660 1.916680 36.463300 1.00 1.0079 + 161 3 H 1 6.258920 6.606300 11.977300 1.00 1.0079 + 162 3 H 1 2.761360 8.233730 35.557200 1.00 1.0079 + 163 3 H 1 2.102020 6.416760 36.574300 1.00 1.0079 + 164 3 H 1 5.245290 7.613990 37.497500 1.00 1.0079 + 165 3 H 1 7.707750 8.191270 36.366200 1.00 1.0079 + 166 3 H 1 4.187600 1.013170 35.917300 1.00 1.0079 + 167 3 H 1 8.503010 5.193570 35.499700 1.00 1.0079 + 168 3 H 1 1.395290 4.383040 36.496000 1.00 1.0079 + 169 3 H 1 2.297900 2.343840 10.698300 1.00 1.0079 + 170 3 H 1 7.905590 7.288510 10.923900 1.00 1.0079 + 171 3 H 1 1.854000 0.064567 10.943000 1.00 1.0079 + 172 3 H 1 7.182260 0.658034 9.558690 1.00 1.0079 + 173 3 H 1 5.214100 6.506150 34.125300 1.00 1.0079 + 174 3 H 1 5.755130 7.638980 35.140400 1.00 1.0079 + 175 3 H 1 0.734180 1.767030 26.768200 1.00 1.0079 + 176 3 H 1 1.283890 7.186610 13.235600 1.00 1.0079 + 177 3 H 1 1.604350 0.625366 27.114200 1.00 1.0079 + 178 3 H 1 3.953020 4.557310 10.812500 1.00 1.0079 + 179 3 H 1 1.841440 1.888620 25.316500 1.00 1.0079 + 180 3 H 1 1.101530 3.128700 37.760900 1.00 1.0079 + 181 3 H 1 6.534040 2.872540 11.206300 1.00 1.0079 + 182 3 H 1 3.964340 3.372420 13.975900 1.00 1.0079 + 183 3 H 1 1.562420 1.625050 23.828700 1.00 1.0079 + 184 3 H 1 0.937763 7.504530 37.647200 1.00 1.0079 + 185 3 H 1 3.430890 2.911990 12.590900 1.00 1.0079 + 186 3 H 1 0.100028 2.648560 13.280600 1.00 1.0079 + 187 3 H 1 1.072450 1.449550 18.529000 1.00 1.0079 + 188 3 H 1 0.439810 2.699390 17.964500 1.00 1.0079 + 189 4 O 8 2.961710 5.124160 0.189070 6.00 15.9994 + 190 4 O 8 0.771144 1.004600 2.220810 6.00 15.9994 + 191 4 O 8 2.867570 3.013000 2.202010 6.00 15.9994 + 192 4 O 8 6.833890 0.488006 14.217800 6.00 15.9994 + 193 4 O 8 7.204350 1.008780 0.271000 6.00 15.9994 + 194 4 O 8 4.990710 2.016630 15.679800 6.00 15.9994 + 195 4 O 8 5.276940 5.321920 29.329800 6.00 15.9994 + 196 4 O 8 0.644149 5.274050 2.042290 6.00 15.9994 + 197 4 O 8 5.099210 0.893161 2.243930 6.00 15.9994 + 198 4 O 8 7.085170 7.257200 1.998070 6.00 15.9994 + 199 4 O 8 2.999070 7.288220 2.080810 6.00 15.9994 + 200 4 O 8 5.028260 5.167280 2.207510 6.00 15.9994 + 201 4 O 8 2.706890 0.883313 0.233754 6.00 15.9994 + 202 4 O 8 4.751470 7.078880 25.542600 6.00 15.9994 + 203 4 O 8 7.067910 5.263490 38.542300 6.00 15.9994 + 204 4 O 8 7.124540 3.165410 2.089340 6.00 15.9994 + 205 4 O 8 0.707124 7.146870 38.540100 6.00 15.9994 + 206 4 O 8 3.087110 0.427154 34.931600 6.00 15.9994 + 207 4 O 8 2.146010 6.492140 17.786600 6.00 15.9994 + 208 4 O 8 0.747010 7.278970 4.221060 6.00 15.9994 + 209 4 O 8 0.795137 3.187720 4.410500 6.00 15.9994 + 210 4 O 8 7.130100 5.246080 4.265090 6.00 15.9994 + 211 4 O 8 7.108660 3.132690 6.515250 6.00 15.9994 + 212 4 O 8 0.375206 5.869770 12.621000 6.00 15.9994 + 213 4 O 8 2.879070 3.061360 6.456280 6.00 15.9994 + 214 4 O 8 7.261630 0.918413 8.585390 6.00 15.9994 + 215 4 O 8 5.125700 7.300610 31.318900 6.00 15.9994 + 216 4 O 8 7.049070 5.142840 8.635820 6.00 15.9994 + 217 4 O 8 0.620773 5.193980 6.590650 6.00 15.9994 + 218 4 O 8 2.762920 0.932001 8.575630 6.00 15.9994 + 219 4 O 8 5.135840 3.169620 8.627520 6.00 15.9994 + 220 4 O 8 2.887180 5.124850 8.295050 6.00 15.9994 + 221 4 O 8 1.060120 4.143720 32.619800 6.00 15.9994 + 222 4 O 8 0.744789 2.943880 8.688430 6.00 15.9994 + 223 4 O 8 4.998490 7.381080 8.668580 6.00 15.9994 + 224 4 O 8 4.184560 8.015280 16.732200 6.00 15.9994 + 225 4 O 8 6.890640 1.582510 24.568200 6.00 15.9994 + 226 4 O 8 7.615990 2.799780 26.981300 6.00 15.9994 + 227 4 O 8 0.760173 4.607610 22.949500 6.00 15.9994 + 228 4 O 8 4.998400 5.118560 6.400550 6.00 15.9994 + 229 4 O 8 5.099390 7.229940 4.274480 6.00 15.9994 + 230 4 O 8 8.470920 8.041400 33.381000 6.00 15.9994 + 231 4 O 8 2.843630 5.112450 4.275520 6.00 15.9994 + 232 4 O 8 2.794060 0.807156 4.366620 6.00 15.9994 + 233 4 O 8 3.792800 4.207400 34.671500 6.00 15.9994 + 234 4 O 8 4.861620 7.567900 21.156000 6.00 15.9994 + 235 4 O 8 5.053560 0.840494 6.436600 6.00 15.9994 + 236 4 O 8 7.172150 0.986709 4.387570 6.00 15.9994 + 237 4 O 8 4.943720 2.983220 4.327410 6.00 15.9994 + 238 4 O 8 2.946110 7.396450 6.345970 6.00 15.9994 + 239 4 O 8 5.082770 3.426710 18.248700 6.00 15.9994 + 240 4 O 8 0.812978 0.971389 6.438180 6.00 15.9994 + 241 4 O 8 7.137550 7.307100 6.383680 6.00 15.9994 + 242 4 O 8 3.478570 0.958035 30.006700 6.00 15.9994 + 243 4 O 8 4.265470 0.565433 23.841900 6.00 15.9994 + 244 4 O 8 4.946070 7.395590 38.421500 6.00 15.9994 + 245 4 O 8 3.948160 3.072260 27.386700 6.00 15.9994 + 246 4 O 8 5.704470 3.930300 23.549600 6.00 15.9994 + 247 4 O 8 5.060370 5.483540 36.631000 6.00 15.9994 + 248 4 O 8 0.894651 3.843200 14.332800 6.00 15.9994 + 249 4 O 8 6.980220 3.568430 10.759000 6.00 15.9994 + 250 4 O 8 1.444220 3.103110 30.327400 6.00 15.9994 + 251 4 O 8 2.854380 3.181940 10.641800 6.00 15.9994 + 252 4 O 8 7.518300 8.116820 29.160000 6.00 15.9994 + 253 4 O 8 7.155680 4.876260 19.457600 6.00 15.9994 + 254 4 O 8 2.306920 2.960800 36.768900 6.00 15.9994 + 255 4 O 8 7.700610 2.011000 29.535900 6.00 15.9994 + 256 4 O 8 7.029280 2.764150 36.613700 6.00 15.9994 + 257 4 O 8 7.583580 5.065860 34.917500 6.00 15.9994 + 258 4 O 8 8.380060 2.060230 12.527100 6.00 15.9994 + 259 4 O 8 0.334416 1.764690 17.989800 6.00 15.9994 + 260 4 O 8 2.611570 6.244830 21.448900 6.00 15.9994 + 261 4 O 8 6.855600 7.276180 17.858000 6.00 15.9994 + 262 4 O 8 3.382580 2.702680 13.570800 6.00 15.9994 + 263 4 O 8 4.930770 7.975590 28.159000 6.00 15.9994 + 264 4 O 8 1.571900 2.359600 24.440700 6.00 15.9994 + 265 4 O 8 0.304014 4.550860 17.139700 6.00 15.9994 + 266 4 O 8 1.834000 7.202260 24.837300 6.00 15.9994 + 267 4 O 8 1.721180 1.547720 26.936300 6.00 15.9994 + 268 4 O 8 4.471590 8.226770 12.720000 6.00 15.9994 + 269 4 O 8 5.516820 7.440450 34.204800 6.00 15.9994 + 270 4 O 8 0.205106 8.051200 16.058600 6.00 15.9994 + 271 4 O 8 2.364770 6.512750 33.503100 6.00 15.9994 + 272 4 O 8 5.327960 2.879340 30.551800 6.00 15.9994 + 273 4 O 8 0.703309 3.085930 0.062619 6.00 15.9994 + 274 4 O 8 2.504540 0.614667 18.919200 6.00 15.9994 + 275 4 O 8 0.940087 7.117510 27.637800 6.00 15.9994 + 276 4 O 8 5.113780 3.098690 38.573600 6.00 15.9994 + 277 4 O 8 0.780725 4.740940 10.423900 6.00 15.9994 + 278 4 O 8 3.240540 2.228810 21.516200 6.00 15.9994 + 279 4 O 8 3.543700 4.522780 25.061500 6.00 15.9994 + 280 4 O 8 5.231160 1.310220 10.530900 6.00 15.9994 + 281 4 O 8 2.415010 5.187820 28.942700 6.00 15.9994 + 282 4 O 8 7.066310 7.457840 10.491500 6.00 15.9994 + 283 4 O 8 0.368771 0.367397 23.077100 6.00 15.9994 + 284 4 O 8 6.148430 1.289440 19.668700 6.00 15.9994 + 285 4 O 8 2.686260 7.270310 10.655400 6.00 15.9994 + 286 4 O 8 4.527220 5.345150 14.583300 6.00 15.9994 + 287 4 O 8 4.437800 5.412440 10.593600 6.00 15.9994 + 288 4 O 8 0.819409 2.006100 34.240800 6.00 15.9994 + 289 4 O 8 1.896670 7.575920 13.930000 6.00 15.9994 + 290 4 O 8 1.381970 0.931575 10.803900 6.00 15.9994 + 291 4 O 8 6.649320 5.692530 21.869100 6.00 15.9994 + 292 4 O 8 6.906960 7.480220 36.384500 6.00 15.9994 + 293 4 O 8 7.100410 5.306390 27.068500 6.00 15.9994 + 294 4 O 8 2.424960 4.009620 19.502800 6.00 15.9994 + 295 4 O 8 0.807042 5.157930 36.705000 6.00 15.9994 + 296 4 O 8 0.091167 7.265980 20.934600 6.00 15.9994 + 297 4 O 8 4.914290 1.088110 36.581900 6.00 15.9994 + 298 4 O 8 5.825060 2.428650 33.838900 6.00 15.9994 + 299 4 O 8 6.186320 5.961810 12.773200 6.00 15.9994 + 300 4 O 8 2.714060 7.179650 36.687600 6.00 15.9994 + 301 4 O 8 0.255691 0.716359 36.786400 6.00 15.9994 + 302 4 O 8 0.759642 7.411320 8.300850 6.00 15.9994 + + + + + SCF PARAMETERS Density guess: RESTART + -------------------------------------------------------- + max_scf: 50 + max_scf_history: 0 + max_diis: 4 + -------------------------------------------------------- + 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 3.00E-07 + max_scf 15 + No outer loop optimization + step_size 5.00E-01 + + PW_GRID| Information for grid number 1 + PW_GRID| Grid distributed over 96 processors + PW_GRID| Real space group dimensions 96 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 600.0 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -90 89 Points: 180 + PW_GRID| Bounds 2 -90 89 Points: 180 + PW_GRID| Bounds 3 -405 404 Points: 810 + PW_GRID| Volume element (a.u.^3) 0.7238E-03 Volume (a.u.^3) 18994.9215 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 273375.0 273420 273240 + PW_GRID| G-Rays 1518.8 1519 1518 + PW_GRID| Real Space Points 273375.0 291600 145800 + + PW_GRID| Information for grid number 2 + PW_GRID| Number of the reference grid 1 + PW_GRID| Grid distributed over 96 processors + PW_GRID| Real space group dimensions 96 1 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 200.0 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -54 53 Points: 108 + PW_GRID| Bounds 2 -54 53 Points: 108 + PW_GRID| Bounds 3 -240 239 Points: 480 + PW_GRID| Volume element (a.u.^3) 0.3393E-02 Volume (a.u.^3) 18994.9215 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 58320.0 59184 57240 + PW_GRID| G-Rays 540.0 548 530 + PW_GRID| Real Space Points 58320.0 103680 51840 + + PW_GRID| Information for grid number 3 + PW_GRID| Number of the reference grid 1 + PW_GRID| Grid distributed over 96 processors + PW_GRID| Real space group dimensions 8 12 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 66.7 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -30 29 Points: 60 + PW_GRID| Bounds 2 -30 29 Points: 60 + PW_GRID| Bounds 3 -135 134 Points: 270 + PW_GRID| Volume element (a.u.^3) 0.1954E-01 Volume (a.u.^3) 18994.9215 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 10125.0 10440 9780 + PW_GRID| G-Rays 168.8 174 163 + PW_GRID| Real Space Points 10125.0 10800 9450 + + PW_GRID| Information for grid number 4 + PW_GRID| Number of the reference grid 1 + PW_GRID| Grid distributed over 96 processors + PW_GRID| Real space group dimensions 8 12 + PW_GRID| the grid is blocked: NO + PW_GRID| Cutoff [a.u.] 22.2 + PW_GRID| spherical cutoff: NO + PW_GRID| Bounds 1 -18 17 Points: 36 + PW_GRID| Bounds 2 -18 17 Points: 36 + PW_GRID| Bounds 3 -80 79 Points: 160 + PW_GRID| Volume element (a.u.^3) 0.9160E-01 Volume (a.u.^3) 18994.9215 + PW_GRID| Grid span FULLSPACE + PW_GRID| Distribution Average Max Min + PW_GRID| G-Vectors 2160.0 2484 1728 + PW_GRID| G-Rays 60.0 69 48 + PW_GRID| Real Space Points 2160.0 2400 1920 + + POISSON| Solver PERIODIC + POISSON| Periodicity XYZ + + RS_GRID| Information for grid number 1 + RS_GRID| Bounds 1 -90 89 Points: 180 + RS_GRID| Bounds 2 -90 89 Points: 180 + RS_GRID| Bounds 3 -405 404 Points: 810 + RS_GRID| Real space distribution over 4 groups + RS_GRID| Real space distribution along direction 2 + RS_GRID| Border size 35 + RS_GRID| Real space distribution over 24 groups + RS_GRID| Real space distribution along direction 3 + RS_GRID| Border size 35 + RS_GRID| Distribution Average Max Min + RS_GRID| Planes 115.0 115 115 + RS_GRID| Distribution Average Max Min + RS_GRID| Planes 103.8 104 103 + + RS_GRID| Information for grid number 2 + RS_GRID| Bounds 1 -54 53 Points: 108 + RS_GRID| Bounds 2 -54 53 Points: 108 + RS_GRID| Bounds 3 -240 239 Points: 480 + RS_GRID| Real space distribution over 4 groups + RS_GRID| Real space distribution along direction 2 + RS_GRID| Border size 30 + RS_GRID| Real space distribution over 24 groups + RS_GRID| Real space distribution along direction 3 + RS_GRID| Border size 30 + RS_GRID| Distribution Average Max Min + RS_GRID| Planes 87.0 87 87 + RS_GRID| Distribution Average Max Min + RS_GRID| Planes 80.0 80 80 + + RS_GRID| Information for grid number 3 + RS_GRID| Bounds 1 -30 29 Points: 60 + RS_GRID| Bounds 2 -30 29 Points: 60 + RS_GRID| Bounds 3 -135 134 Points: 270 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + RS_GRID| Information for grid number 4 + RS_GRID| Bounds 1 -18 17 Points: 36 + RS_GRID| Bounds 2 -18 17 Points: 36 + RS_GRID| Bounds 3 -80 79 Points: 160 + RS_GRID| Real space fully replicated + RS_GRID| Group size 1 + + Spin 1 + + Number of electrons: 756 + Number of occupied orbitals: 756 + Number of molecular orbitals: 756 + + Spin 2 + + Number of electrons: 756 + Number of occupied orbitals: 756 + Number of molecular orbitals: 756 + + Number of orbital functions: 3262 + Number of independent orbital functions: 3262 + + Extrapolation method: initial_guess + + *** WARNING in qs_initial_guess.F:280 :: User requested to restart the *** + *** wavefunction from the file named: DPGEN-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: Al + + Electronic structure + Total number of core electrons 10.00 + Total number of valence electrons 15.00 + Total number of electrons 25.00 + Multiplicity quartet + 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 2.00 + + + ******************************************************************************* + Iteration Convergence Energy [au] + ******************************************************************************* + 1 3.04992 -142.792613309736 + 2 9.38670 -141.393967195469 + 3 0.493816 -143.914365551236 + 4 0.902072E-01 -143.922741133468 + 5 0.330034E-01 -143.923385186826 + 6 0.879178E-01 -143.922868243225 + 7 0.635733E-01 -143.923519213985 + 8 0.696867E-01 -143.923481182864 + 9 0.161759 -143.922720130419 + 10 0.686786E-02 -143.923663275204 + 11 0.106180E-01 -143.923658166179 + 12 0.846532E-02 -143.923661997206 + 13 0.903049E-02 -143.923660604258 + 14 0.886428E-02 -143.923660808485 + 15 0.582658E-02 -143.923666909339 + 16 0.380707E-02 -143.923670276375 + 17 0.622896E-02 -143.923671738055 + 18 0.636438E-02 -143.923671691135 + 19 0.656526E-02 -143.923671598138 + 20 0.655799E-02 -143.923671596368 + 21 0.601183E-02 -143.923671841808 + 22 0.125136E-02 -143.923673161271 + 23 0.129934E-02 -143.923673165713 + 24 0.130220E-02 -143.923673164896 + 25 0.130974E-02 -143.923673162226 + 26 0.131719E-02 -143.923673159449 + 27 0.117247E-02 -143.923673208735 + 28 0.100055E-02 -143.923673397633 + 29 0.100449E-02 -143.923673397635 + 30 0.100480E-02 -143.923673397614 + 31 0.100566E-02 -143.923673397551 + 32 0.100716E-02 -143.923673397438 + 33 0.673413E-03 -143.923673417919 + 34 0.205773E-03 -143.923673434453 + 35 0.205780E-03 -143.923673434452 + 36 0.205802E-03 -143.923673434451 + 37 0.205852E-03 -143.923673434448 + 38 0.206136E-03 -143.923673434431 + 39 0.216122E-03 -143.923673439497 + 40 0.158451E-03 -143.923673440264 + 41 0.158465E-03 -143.923673440263 + 42 0.158473E-03 -143.923673440264 + 43 0.158473E-03 -143.923673440264 + 44 0.158081E-03 -143.923673440268 + 45 0.106295E-03 -143.923673440768 + 46 0.324777E-04 -143.923673441180 + 47 0.324758E-04 -143.923673441180 + 48 0.324750E-04 -143.923673441180 + 49 0.324759E-04 -143.923673441180 + 50 0.325435E-04 -143.923673441180 + No convergence within maximum number of iterations + + Energy components [Hartree] Total Energy :: -143.923673441180 + Band Energy :: -34.750628451159 + Kinetic Energy :: 82.204907789880 + Potential Energy :: -226.128581231060 + Virial (-V/T) :: 2.750791738725 + Core Energy :: -243.507792497973 + XC Energy :: -14.037196260317 + Coulomb Energy :: 113.621315317111 + Total Pseudopotential Energy :: -325.740769048217 + Local Pseudopotential Energy :: -294.653926123523 + Nonlocal Pseudopotential Energy :: -31.086842924694 + Confinement :: 0.280687603640 + + Orbital energies State Spin L Occupation Energy[a.u.] Energy[eV] + + 1 alpha 0 1.000 -4.644931 -126.394991 + 1 beta 0 1.000 -4.506275 -122.621982 + + 1 alpha 1 3.000 -3.155520 -85.866070 + 1 beta 1 3.000 -3.021384 -82.216045 + + 1 alpha 2 5.000 -1.043107 -28.384388 + 1 beta 2 2.000 -0.926587 -25.213717 + + + Total Electron Density at R=0: 0.000416 + + Guess for atomic kind: Co + + Electronic structure + Total number of core electrons 10.00 + Total number of valence electrons 15.00 + Total number of electrons 25.00 + Multiplicity quartet + Alpha Electrons + S [ 1.00 1.00] 1.00 + P [ 3.00] 3.00 + D 2.00 + Beta Electrons + S [ 1.00 1.00] 1.00 + P [ 3.00] 3.00 + D 5.00 + + + ******************************************************************************* + Iteration Convergence Energy [au] + ******************************************************************************* + 1 3.04992 -142.792613309736 + 2 9.38670 -141.393967195469 + 3 0.493816 -143.914365551236 + 4 0.902072E-01 -143.922741133468 + 5 0.330034E-01 -143.923385186826 + 6 0.879178E-01 -143.922868243225 + 7 0.635733E-01 -143.923519213985 + 8 0.696867E-01 -143.923481182864 + 9 0.161759 -143.922720130419 + 10 0.686786E-02 -143.923663275204 + 11 0.106180E-01 -143.923658166179 + 12 0.846532E-02 -143.923661997206 + 13 0.903049E-02 -143.923660604258 + 14 0.886428E-02 -143.923660808485 + 15 0.582658E-02 -143.923666909339 + 16 0.380707E-02 -143.923670276375 + 17 0.622896E-02 -143.923671738055 + 18 0.636438E-02 -143.923671691135 + 19 0.656526E-02 -143.923671598138 + 20 0.655799E-02 -143.923671596368 + 21 0.601183E-02 -143.923671841808 + 22 0.125136E-02 -143.923673161271 + 23 0.129934E-02 -143.923673165713 + 24 0.130220E-02 -143.923673164896 + 25 0.130974E-02 -143.923673162226 + 26 0.131719E-02 -143.923673159449 + 27 0.117247E-02 -143.923673208735 + 28 0.100055E-02 -143.923673397633 + 29 0.100449E-02 -143.923673397635 + 30 0.100480E-02 -143.923673397614 + 31 0.100566E-02 -143.923673397551 + 32 0.100716E-02 -143.923673397438 + 33 0.673413E-03 -143.923673417919 + 34 0.205773E-03 -143.923673434453 + 35 0.205780E-03 -143.923673434452 + 36 0.205802E-03 -143.923673434451 + 37 0.205852E-03 -143.923673434448 + 38 0.206136E-03 -143.923673434431 + 39 0.216122E-03 -143.923673439497 + 40 0.158451E-03 -143.923673440264 + 41 0.158465E-03 -143.923673440263 + 42 0.158473E-03 -143.923673440264 + 43 0.158473E-03 -143.923673440264 + 44 0.158081E-03 -143.923673440268 + 45 0.106295E-03 -143.923673440768 + 46 0.324777E-04 -143.923673441180 + 47 0.324758E-04 -143.923673441180 + 48 0.324750E-04 -143.923673441180 + 49 0.324759E-04 -143.923673441180 + 50 0.325435E-04 -143.923673441180 + No convergence within maximum number of iterations + + Energy components [Hartree] Total Energy :: -143.923673441180 + Band Energy :: -34.750628451159 + Kinetic Energy :: 82.204907789880 + Potential Energy :: -226.128581231060 + Virial (-V/T) :: 2.750791738725 + Core Energy :: -243.507792497973 + XC Energy :: -14.037196260317 + Coulomb Energy :: 113.621315317111 + Total Pseudopotential Energy :: -325.740769048217 + Local Pseudopotential Energy :: -294.653926123523 + Nonlocal Pseudopotential Energy :: -31.086842924694 + Confinement :: 0.280687603640 + + Orbital energies State Spin L Occupation Energy[a.u.] Energy[eV] + + 1 alpha 0 1.000 -4.506275 -122.621982 + 1 beta 0 1.000 -4.644931 -126.394991 + + 1 alpha 1 3.000 -3.021384 -82.216045 + 1 beta 1 3.000 -3.155520 -85.866070 + + 1 alpha 2 2.000 -0.926587 -25.213717 + 1 beta 2 5.000 -1.043107 -28.384388 + + + Total Electron Density at R=0: 0.000416 + + 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 0.250972E-02 -0.375256815885 + 2 0.570752E-04 -0.375258666164 + 3 0.832405E-09 -0.375258667122 + + Energy components [Hartree] Total Energy :: -0.375258667122 + Band Energy :: -0.076317618391 + Kinetic Energy :: 0.771356566341 + Potential Energy :: -1.146615233463 + Virial (-V/T) :: 1.486491829455 + Core Energy :: -0.456090715790 + XC Energy :: -0.314218627334 + Coulomb Energy :: 0.395050676003 + Total Pseudopotential Energy :: -1.238482237174 + Local Pseudopotential Energy :: -1.238482237174 + Nonlocal Pseudopotential Energy :: 0.000000000000 + Confinement :: 0.110349550431 + + Orbital energies State L Occupation Energy[a.u.] Energy[eV] + + 1 0 1.000 -0.076318 -2.076708 + + + Total Electron Density at R=0: 0.425022 + + 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 0.702811 -15.577904332270 + 2 0.612408 -15.588447180504 + 3 0.955344E-02 -15.655871208406 + 4 0.223754E-02 -15.655885053552 + 5 0.157183E-02 -15.655885461027 + 6 0.124953E-02 -15.655885607150 + 7 0.312011E-06 -15.655885858066 + + Energy components [Hartree] Total Energy :: -15.655885858066 + Band Energy :: -2.983128125584 + Kinetic Energy :: 11.754765134683 + Potential Energy :: -27.410650992749 + Virial (-V/T) :: 2.331875684345 + Core Energy :: -26.153522949071 + XC Energy :: -3.157392363346 + Coulomb Energy :: 13.655029454351 + Total Pseudopotential Energy :: -37.943026860963 + Local Pseudopotential Energy :: -39.220419683052 + Nonlocal Pseudopotential Energy :: 1.277392822089 + Confinement :: 0.347387772086 + + Orbital energies State L Occupation Energy[a.u.] Energy[eV] + + 1 0 2.000 -0.861522 -23.443215 + + 1 1 4.000 -0.315021 -8.572154 + + + 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 + 756 716.000 1.056 + + Spin 2 + Re-scaling the density matrix to get the right number of electrons for spin 2 + # Electrons Trace(P) Scaling factor + 756 716.000 1.056 + + + SCF WAVEFUNCTION OPTIMIZATION + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 3.1 0.02810212 -7457.4351580507 -7.46E+03 + 2 OT LS 0.83E-01 1.8 -7618.7710694284 + 3 OT CG 0.83E-01 3.4 0.00636647 -7618.2185401772 -1.61E+02 + 4 OT LS 0.33E+00 1.8 -7631.1028706834 + 5 OT CG 0.33E+00 3.4 0.00358973 -7657.5447589502 -3.93E+01 + 6 OT LS 0.26E+00 1.7 -7665.3110799172 + 7 OT CG 0.26E+00 3.4 0.00478039 -7665.7834064179 -8.24E+00 + 8 OT LS 0.33E+00 1.7 -7683.7420994201 + 9 OT CG 0.33E+00 3.4 0.00332067 -7684.7111054093 -1.89E+01 + 10 OT LS 0.31E+00 1.7 -7693.2876223544 + 11 OT CG 0.31E+00 3.4 0.00233919 -7693.3577252495 -8.65E+00 + 12 OT LS 0.51E+00 1.7 -7698.9656639509 + 13 OT CG 0.51E+00 3.4 0.00280091 -7700.0662956310 -6.71E+00 + 14 OT LS 0.29E+00 1.7 -7702.6237189557 + 15 OT CG 0.29E+00 3.4 0.00220070 -7705.6215361384 -5.56E+00 + 16 OT LS 0.39E+00 1.7 -7709.8898890845 + 17 OT CG 0.39E+00 3.4 0.00179639 -7710.2071319986 -4.59E+00 + 18 OT LS 0.53E+00 1.7 -7714.1666386195 + 19 OT CG 0.53E+00 3.4 0.00168715 -7714.4518024724 -4.24E+00 + 20 OT LS 0.43E+00 1.7 -7717.3291478621 + 21 OT CG 0.43E+00 3.4 0.00140602 -7717.4513083344 -3.00E+00 + 22 OT LS 0.48E+00 1.8 -7719.7703408236 + 23 OT CG 0.48E+00 3.4 0.00124909 -7719.7927390022 -2.34E+00 + 24 OT LS 0.49E+00 1.8 -7721.7055930953 + 25 OT CG 0.49E+00 3.4 0.00104646 -7721.7089800161 -1.92E+00 + 26 OT LS 0.49E+00 1.8 -7723.0403498153 + 27 OT CG 0.49E+00 3.4 0.00098535 -7723.0405466772 -1.33E+00 + 28 OT LS 0.49E+00 1.7 -7724.2095733689 + 29 OT CG 0.49E+00 3.4 0.00084313 -7724.2096344594 -1.17E+00 + 30 OT LS 0.52E+00 1.7 -7725.1162664079 + 31 OT CG 0.52E+00 3.4 0.00076263 -7725.1184371803 -9.09E-01 + 32 OT LS 0.46E+00 1.8 -7725.7737301788 + 33 OT CG 0.46E+00 3.4 0.00070350 -7725.7823312963 -6.64E-01 + 34 OT LS 0.56E+00 1.8 -7726.4470094323 + 35 OT CG 0.56E+00 3.4 0.00064876 -7726.4688224263 -6.86E-01 + 36 OT LS 0.47E+00 1.7 -7726.9436539757 + 37 OT CG 0.47E+00 3.4 0.00058170 -7726.9612013170 -4.92E-01 + 38 OT LS 0.55E+00 1.7 -7727.4110886109 + 39 OT CG 0.55E+00 3.4 0.00054549 -7727.4196917213 -4.58E-01 + 40 OT LS 0.48E+00 1.8 -7727.7626539042 + 41 OT CG 0.48E+00 3.4 0.00048955 -7727.7704108755 -3.51E-01 + 42 OT LS 0.55E+00 1.7 -7728.0907123790 + 43 OT CG 0.55E+00 3.4 0.00047772 -7728.0963861697 -3.26E-01 + 44 OT LS 0.48E+00 1.7 -7728.3597506557 + 45 OT CG 0.48E+00 3.4 0.00042894 -7728.3660588153 -2.70E-01 + 46 OT LS 0.54E+00 1.7 -7728.6092488488 + 47 OT CG 0.54E+00 3.4 0.00042442 -7728.6126781879 -2.47E-01 + 48 OT LS 0.53E+00 1.8 -7728.8480369769 + 49 OT CG 0.53E+00 3.4 0.00039936 -7728.8481910915 -2.36E-01 + 50 OT LS 0.55E+00 1.7 -7729.0646873724 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1512.0000000000 0.0000000000 + Core density on regular grids: 1512.0000000000 -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: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4019.68880194058966 + Hartree energy: 3434.21476142080064 + Exchange-correlation energy: -1056.13298464055651 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 2.71524387404235 + + Total energy: -7729.06468737235718 + + outer SCF iter = 1 RMS gradient = 0.40E-03 energy = -7729.0646873724 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.6 0.00122807 -7729.0649722487 -2.17E-01 + 2 OT LS 0.99E-01 1.7 -7729.4204685397 + 3 OT CG 0.99E-01 3.4 0.00165708 -7729.4343551159 -3.69E-01 + 4 OT LS 0.60E-01 1.8 -7729.6706945187 + 5 OT CG 0.60E-01 3.4 0.00193177 -7729.8416052171 -4.07E-01 + 6 OT LS 0.45E-01 1.8 -7730.2132320207 + 7 OT CG 0.45E-01 3.4 0.00184656 -7730.2573168813 -4.16E-01 + 8 OT LS 0.38E-01 1.7 -7730.5641269088 + 9 OT CG 0.38E-01 3.4 0.00157155 -7730.5743365684 -3.17E-01 + 10 OT LS 0.39E-01 1.7 -7730.8142448000 + 11 OT CG 0.39E-01 3.4 0.00124925 -7730.8145454957 -2.40E-01 + 12 OT LS 0.54E-01 1.7 -7731.0075896009 + 13 OT CG 0.54E-01 3.4 0.00115150 -7731.0236381318 -2.09E-01 + 14 OT LS 0.45E-01 1.8 -7731.1659489428 + 15 OT CG 0.45E-01 3.4 0.00098373 -7731.1715417801 -1.48E-01 + 16 OT LS 0.66E-01 1.7 -7731.3128078068 + 17 OT CG 0.66E-01 3.4 0.00105240 -7731.3278131414 -1.56E-01 + 18 OT LS 0.54E-01 1.8 -7731.4692042879 + 19 OT CG 0.54E-01 3.4 0.00089338 -7731.4754220136 -1.48E-01 + 20 OT LS 0.58E-01 1.7 -7731.5892041585 + 21 OT CG 0.58E-01 3.4 0.00082802 -7731.5896587753 -1.14E-01 + 22 OT LS 0.59E-01 1.7 -7731.6894860003 + 23 OT CG 0.59E-01 3.4 0.00076456 -7731.6895181408 -9.99E-02 + 24 OT LS 0.59E-01 1.7 -7731.7750652016 + 25 OT CG 0.59E-01 3.4 0.00072110 -7731.7750675554 -8.55E-02 + 26 OT LS 0.70E-01 1.8 -7731.8630031531 + 27 OT CG 0.70E-01 3.4 0.00074076 -7731.8649942057 -8.99E-02 + 28 OT LS 0.60E-01 1.7 -7731.9429518815 + 29 OT CG 0.60E-01 3.4 0.00067867 -7731.9455390107 -8.05E-02 + 30 OT LS 0.64E-01 1.8 -7732.0175262717 + 31 OT CG 0.64E-01 3.4 0.00063071 -7732.0177717915 -7.22E-02 + 32 OT LS 0.62E-01 1.7 -7732.0778589082 + 33 OT CG 0.62E-01 3.4 0.00060898 -7732.0779468589 -6.02E-02 + 34 OT LS 0.70E-01 1.7 -7732.1406136242 + 35 OT CG 0.70E-01 3.4 0.00060531 -7732.1413598329 -6.34E-02 + 36 OT LS 0.66E-01 1.7 -7732.2004526052 + 37 OT CG 0.66E-01 3.4 0.00058296 -7732.2006719767 -5.93E-02 + 38 OT LS 0.65E-01 1.7 -7732.2551241985 + 39 OT CG 0.65E-01 3.4 0.00055719 -7732.2551388216 -5.45E-02 + 40 OT LS 0.63E-01 1.7 -7732.3029928428 + 41 OT CG 0.63E-01 3.4 0.00052367 -7732.3030821092 -4.79E-02 + 42 OT LS 0.66E-01 1.7 -7732.3472878200 + 43 OT CG 0.66E-01 3.4 0.00050985 -7732.3473498699 -4.43E-02 + 44 OT LS 0.66E-01 1.7 -7732.3896578216 + 45 OT CG 0.66E-01 3.4 0.00048633 -7732.3896569220 -4.23E-02 + 46 OT LS 0.66E-01 1.7 -7732.4277933791 + 47 OT CG 0.66E-01 3.4 0.00045956 -7732.4278010638 -3.81E-02 + 48 OT LS 0.66E-01 1.7 -7732.4621616015 + 49 OT CG 0.66E-01 3.4 0.00043147 -7732.4621612072 -3.44E-02 + 50 OT LS 0.65E-01 1.7 -7732.4917262923 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1512.0000000000 0.0000000000 + Core density on regular grids: 1512.0000000000 -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: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.95971197794370 + Hartree energy: 3437.05009726644312 + Exchange-correlation energy: -1057.64009463223738 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.68906906282677 + + Total energy: -7732.49172629225632 + + outer SCF iter = 2 RMS gradient = 0.43E-03 energy = -7732.4917262923 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.6 0.00044000 -7732.4917486737 -2.96E-02 + 2 OT LS 0.42E-01 1.7 -7732.4952003062 + 3 OT CG 0.42E-01 3.3 0.00047483 -7732.5117418030 -2.00E-02 + 4 OT LS 0.80E-01 1.7 -7732.5461641109 + 5 OT CG 0.80E-01 3.4 0.00071128 -7732.5562575810 -4.45E-02 + 6 OT LS 0.44E-01 1.7 -7732.5723075218 + 7 OT CG 0.44E-01 3.4 0.00049969 -7732.6107701819 -5.45E-02 + 8 OT LS 0.46E-01 1.7 -7732.6391261910 + 9 OT CG 0.46E-01 3.4 0.00034773 -7732.6392042254 -2.84E-02 + 10 OT LS 0.44E-01 1.7 -7732.6522875894 + 11 OT CG 0.44E-01 3.4 0.00024700 -7732.6523179234 -1.31E-02 + 12 OT LS 0.55E-01 1.7 -7732.6602694553 + 13 OT CG 0.55E-01 3.4 0.00021515 -7732.6606037068 -8.29E-03 + 14 OT LS 0.47E-01 1.7 -7732.6657949166 + 15 OT CG 0.47E-01 3.4 0.00020408 -7732.6659560034 -5.35E-03 + 16 OT LS 0.53E-01 1.7 -7732.6713537634 + 17 OT CG 0.53E-01 3.4 0.00021324 -7732.6714335524 -5.48E-03 + 18 OT LS 0.57E-01 1.7 -7732.6777975981 + 19 OT CG 0.57E-01 3.4 0.00021344 -7732.6778222160 -6.39E-03 + 20 OT LS 0.62E-01 1.7 -7732.6846844227 + 21 OT CG 0.62E-01 3.4 0.00020379 -7732.6847162107 -6.89E-03 + 22 OT LS 0.53E-01 1.8 -7732.6900305747 + 23 OT CG 0.53E-01 3.4 0.00018584 -7732.6901611581 -5.44E-03 + 24 OT LS 0.51E-01 1.7 -7732.6944869026 + 25 OT CG 0.51E-01 3.4 0.00017582 -7732.6944974934 -4.34E-03 + 26 OT LS 0.54E-01 1.8 -7732.6985620820 + 27 OT CG 0.54E-01 3.4 0.00015417 -7732.6985694998 -4.07E-03 + 28 OT LS 0.61E-01 1.7 -7732.7020733297 + 29 OT CG 0.61E-01 3.4 0.00014172 -7732.7021213639 -3.55E-03 + 30 OT LS 0.60E-01 1.8 -7732.7050834756 + 31 OT CG 0.60E-01 3.4 0.00013768 -7732.7050840661 -2.96E-03 + 32 OT LS 0.49E-01 1.8 -7732.7072231995 + 33 OT CG 0.49E-01 3.4 0.00012256 -7732.7073515021 -2.27E-03 + 34 OT LS 0.57E-01 1.8 -7732.7094118166 + 35 OT CG 0.57E-01 3.4 0.00011118 -7732.7094552300 -2.10E-03 + 36 OT LS 0.58E-01 1.7 -7732.7112109558 + 37 OT CG 0.58E-01 3.4 0.00010232 -7732.7112112658 -1.76E-03 + 38 OT LS 0.50E-01 1.8 -7732.7124695434 + 39 OT CG 0.50E-01 3.4 0.00009141 -7732.7125006712 -1.29E-03 + 40 OT LS 0.51E-01 1.7 -7732.7135485193 + 41 OT CG 0.51E-01 3.4 0.00008129 -7732.7135488270 -1.05E-03 + 42 OT LS 0.58E-01 1.7 -7732.7144752519 + 43 OT CG 0.58E-01 3.4 0.00007536 -7732.7144880826 -9.39E-04 + 44 OT LS 0.54E-01 1.7 -7732.7152415139 + 45 OT CG 0.54E-01 3.4 0.00007068 -7732.7152449597 -7.57E-04 + 46 OT LS 0.54E-01 1.8 -7732.7159152989 + 47 OT CG 0.54E-01 3.4 0.00006513 -7732.7159153236 -6.70E-04 + 48 OT LS 0.54E-01 1.7 -7732.7164830260 + 49 OT CG 0.54E-01 3.4 0.00005909 -7732.7164830321 -5.68E-04 + 50 OT LS 0.51E-01 1.8 -7732.7169199664 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1512.0000000000 0.0000000000 + Core density on regular grids: 1512.0000000000 -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: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.64516980690360 + Hartree energy: 3437.41335551075235 + Exchange-correlation energy: -1057.73803396397307 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.51309864713360 + + Total energy: -7732.71691996641675 + + outer SCF iter = 3 RMS gradient = 0.59E-04 energy = -7732.7169199664 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.5 0.00005932 -7732.7169218506 -4.39E-04 + 2 OT LS 0.27E-01 1.7 -7732.7162791758 + 3 OT CG 0.27E-01 3.3 0.00004987 -7732.7171590896 -2.37E-04 + 4 OT LS 0.81E-01 1.7 -7732.7174380778 + 5 OT CG 0.81E-01 3.3 0.00006310 -7732.7176577444 -4.99E-04 + 6 OT LS 0.54E-01 1.7 -7732.7180411736 + 7 OT CG 0.54E-01 3.3 0.00005988 -7732.7181834341 -5.26E-04 + 8 OT LS 0.49E-01 1.7 -7732.7186093948 + 9 OT CG 0.49E-01 3.3 0.00005551 -7732.7186137659 -4.30E-04 + 10 OT LS 0.52E-01 1.7 -7732.7190060594 + 11 OT CG 0.52E-01 3.3 0.00005463 -7732.7190075162 -3.94E-04 + 12 OT LS 0.50E-01 1.7 -7732.7193724231 + 13 OT CG 0.50E-01 3.3 0.00005343 -7732.7193731315 -3.66E-04 + 14 OT LS 0.56E-01 1.7 -7732.7197623691 + 15 OT CG 0.56E-01 3.3 0.00005740 -7732.7197671821 -3.94E-04 + 16 OT LS 0.60E-01 1.7 -7732.7202488465 + 17 OT CG 0.60E-01 3.3 0.00006248 -7732.7202501746 -4.83E-04 + 18 OT LS 0.55E-01 1.7 -7732.7207727205 + 19 OT CG 0.55E-01 3.3 0.00006504 -7732.7207774729 -5.27E-04 + 20 OT LS 0.53E-01 1.7 -7732.7213243632 + 21 OT CG 0.53E-01 3.3 0.00006690 -7732.7213257845 -5.48E-04 + 22 OT LS 0.52E-01 1.7 -7732.7218904490 + 23 OT CG 0.52E-01 3.3 0.00006320 -7732.7218910675 -5.65E-04 + 24 OT LS 0.53E-01 1.7 -7732.7224113122 + 25 OT CG 0.53E-01 3.3 0.00005908 -7732.7224116313 -5.21E-04 + 26 OT LS 0.49E-01 1.7 -7732.7228269656 + 27 OT CG 0.49E-01 3.3 0.00005474 -7732.7228305543 -4.19E-04 + 28 OT LS 0.50E-01 1.7 -7732.7232003606 + 29 OT CG 0.50E-01 3.3 0.00005191 -7732.7232005786 -3.70E-04 + 30 OT LS 0.51E-01 1.7 -7732.7235405162 + 31 OT CG 0.51E-01 3.4 0.00005009 -7732.7235406593 -3.40E-04 + 32 OT LS 0.51E-01 1.7 -7732.7238545597 + 33 OT CG 0.51E-01 3.3 0.00004833 -7732.7238545885 -3.14E-04 + 34 OT LS 0.48E-01 1.7 -7732.7241314846 + 35 OT CG 0.48E-01 3.4 0.00004514 -7732.7241322852 -2.78E-04 + 36 OT LS 0.56E-01 1.7 -7732.7244074084 + 37 OT CG 0.56E-01 3.3 0.00004476 -7732.7244124448 -2.80E-04 + 38 OT LS 0.53E-01 1.7 -7732.7246752844 + 39 OT CG 0.53E-01 3.3 0.00004460 -7732.7246758634 -2.63E-04 + 40 OT LS 0.51E-01 1.7 -7732.7249238936 + 41 OT CG 0.51E-01 3.3 0.00004101 -7732.7249245955 -2.49E-04 + 42 OT LS 0.56E-01 1.7 -7732.7251540798 + 43 OT CG 0.56E-01 3.3 0.00003918 -7732.7251559302 -2.31E-04 + 44 OT LS 0.50E-01 1.7 -7732.7253440124 + 45 OT CG 0.50E-01 3.3 0.00003747 -7732.7253463099 -1.90E-04 + 46 OT LS 0.53E-01 1.7 -7732.7255292879 + 47 OT CG 0.53E-01 3.3 0.00003552 -7732.7255297269 -1.83E-04 + 48 OT LS 0.53E-01 1.7 -7732.7256942076 + 49 OT CG 0.53E-01 3.3 0.00003193 -7732.7256942088 -1.64E-04 + 50 OT LS 0.51E-01 1.7 -7732.7258209835 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1511.9999999748 0.0000000252 + Core density on regular grids: 1512.0000000000 -0.0000000000 + Total charge density on r-space grids: 0.0000000251 + Total charge density g-space grids: 0.0000000251 + + Overlap energy of the core charge distribution: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.65560464291957 + Hartree energy: 3437.40651462958522 + Exchange-correlation energy: -1057.74732700589834 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50989671714404 + + Total energy: -7732.72582098348266 + + outer SCF iter = 4 RMS gradient = 0.32E-04 energy = -7732.7258209835 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.4 0.00003233 -7732.7258213076 -1.27E-04 + 2 OT LS 0.27E-01 1.7 -7732.7256230431 + 3 OT CG 0.27E-01 3.3 0.00002762 -7732.7258909564 -6.96E-05 + 4 OT LS 0.77E-01 1.7 -7732.7259746896 + 5 OT CG 0.77E-01 3.3 0.00003433 -7732.7260352425 -1.44E-04 + 6 OT LS 0.48E-01 1.7 -7732.7261217346 + 7 OT CG 0.48E-01 3.3 0.00003164 -7732.7261735627 -1.38E-04 + 8 OT LS 0.41E-01 1.7 -7732.7262737400 + 9 OT CG 0.41E-01 3.4 0.00002684 -7732.7262759710 -1.02E-04 + 10 OT LS 0.39E-01 1.7 -7732.7263449218 + 11 OT CG 0.39E-01 3.3 0.00002271 -7732.7263452059 -6.92E-05 + 12 OT LS 0.41E-01 1.7 -7732.7263976126 + 13 OT CG 0.41E-01 3.3 0.00001925 -7732.7263977862 -5.26E-05 + 14 OT LS 0.47E-01 1.7 -7732.7264402617 + 15 OT CG 0.47E-01 3.3 0.00001668 -7732.7264409189 -4.31E-05 + 16 OT LS 0.48E-01 1.7 -7732.7264735945 + 17 OT CG 0.48E-01 3.3 0.00001548 -7732.7264735972 -3.27E-05 + 18 OT LS 0.50E-01 1.7 -7732.7265032999 + 19 OT CG 0.50E-01 3.3 0.00001597 -7732.7265033916 -2.98E-05 + 20 OT LS 0.55E-01 1.7 -7732.7265376667 + 21 OT CG 0.55E-01 3.3 0.00001735 -7732.7265378910 -3.45E-05 + 22 OT LS 0.58E-01 1.7 -7732.7265809060 + 23 OT CG 0.58E-01 3.3 0.00002000 -7732.7265810354 -4.31E-05 + 24 OT LS 0.53E-01 1.7 -7732.7266323100 + 25 OT CG 0.53E-01 3.3 0.00002206 -7732.7266328997 -5.19E-05 + 26 OT LS 0.54E-01 1.7 -7732.7266969526 + 27 OT CG 0.54E-01 3.3 0.00002409 -7732.7266969624 -6.41E-05 + 28 OT LS 0.51E-01 1.7 -7732.7267699733 + 29 OT CG 0.51E-01 3.4 0.00002505 -7732.7267701360 -7.32E-05 + 30 OT LS 0.50E-01 1.7 -7732.7268478908 + 31 OT CG 0.50E-01 3.4 0.00002540 -7732.7268479254 -7.78E-05 + 32 OT LS 0.47E-01 1.7 -7732.7269219791 + 33 OT CG 0.47E-01 3.3 0.00002464 -7732.7269224252 -7.45E-05 + 34 OT LS 0.51E-01 1.7 -7732.7269979618 + 35 OT CG 0.51E-01 3.3 0.00002495 -7732.7269983800 -7.60E-05 + 36 OT LS 0.51E-01 1.7 -7732.7270763304 + 37 OT CG 0.51E-01 3.3 0.00002674 -7732.7270763300 -7.79E-05 + 38 OT LS 0.48E-01 1.7 -7732.7271599819 + 39 OT CG 0.48E-01 3.3 0.00002587 -7732.7271604062 -8.41E-05 + 40 OT LS 0.59E-01 1.7 -7732.7272537280 + 41 OT CG 0.59E-01 3.4 0.00002928 -7732.7272568891 -9.65E-05 + 42 OT LS 0.51E-01 1.7 -7732.7273612531 + 43 OT CG 0.51E-01 3.3 0.00003044 -7732.7273642154 -1.07E-04 + 44 OT LS 0.52E-01 1.7 -7732.7274808898 + 45 OT CG 0.52E-01 3.4 0.00003073 -7732.7274808622 -1.17E-04 + 46 OT LS 0.51E-01 1.7 -7732.7275973954 + 47 OT CG 0.51E-01 3.3 0.00003420 -7732.7275974481 -1.17E-04 + 48 OT LS 0.50E-01 1.7 -7732.7277390447 + 49 OT CG 0.50E-01 3.3 0.00003437 -7732.7277392318 -1.42E-04 + 50 OT LS 0.47E-01 1.7 -7732.7278748317 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1512.0000090882 -0.0000090882 + Core density on regular grids: 1512.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000090882 + Total charge density g-space grids: -0.0000090882 + + Overlap energy of the core charge distribution: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.64238455346731 + Hartree energy: 3437.41412368791316 + Exchange-correlation energy: -1057.74515525350057 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.51128214765234 + + Total energy: -7732.72787483170032 + + outer SCF iter = 5 RMS gradient = 0.34E-04 energy = -7732.7278748317 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.4 0.00003379 -7732.7278753187 -1.36E-04 + 2 OT LS 0.30E-01 1.7 -7732.7277285758 + 3 OT CG 0.30E-01 3.3 0.00003188 -7732.7279606440 -8.53E-05 + 4 OT LS 0.75E-01 1.7 -7732.7280812729 + 5 OT CG 0.75E-01 3.3 0.00003804 -7732.7281484379 -1.88E-04 + 6 OT LS 0.50E-01 1.7 -7732.7282855164 + 7 OT CG 0.50E-01 3.3 0.00003712 -7732.7283282081 -1.80E-04 + 8 OT LS 0.59E-01 1.7 -7732.7285243315 + 9 OT CG 0.59E-01 3.3 0.00003930 -7732.7285288168 -2.01E-04 + 10 OT LS 0.50E-01 1.7 -7732.7287152213 + 11 OT CG 0.50E-01 3.3 0.00003891 -7732.7287210542 -1.92E-04 + 12 OT LS 0.53E-01 1.7 -7732.7289191290 + 13 OT CG 0.53E-01 3.3 0.00003881 -7732.7289196415 -1.99E-04 + 14 OT LS 0.53E-01 1.7 -7732.7291167430 + 15 OT CG 0.53E-01 3.3 0.00003710 -7732.7291167434 -1.97E-04 + 16 OT LS 0.43E-01 1.7 -7732.7292543051 + 17 OT CG 0.43E-01 3.3 0.00003366 -7732.7292626055 -1.46E-04 + 18 OT LS 0.55E-01 1.7 -7732.7294089119 + 19 OT CG 0.55E-01 3.3 0.00003591 -7732.7294161906 -1.54E-04 + 20 OT LS 0.57E-01 1.7 -7732.7295974140 + 21 OT CG 0.57E-01 3.3 0.00003760 -7732.7295975804 -1.81E-04 + 22 OT LS 0.51E-01 1.7 -7732.7297695208 + 23 OT CG 0.51E-01 3.3 0.00003609 -7732.7297728882 -1.75E-04 + 24 OT LS 0.52E-01 1.7 -7732.7299376276 + 25 OT CG 0.52E-01 3.3 0.00003622 -7732.7299376788 -1.65E-04 + 26 OT LS 0.52E-01 1.7 -7732.7301042757 + 27 OT CG 0.52E-01 3.3 0.00003458 -7732.7301042764 -1.67E-04 + 28 OT LS 0.49E-01 1.7 -7732.7302482145 + 29 OT CG 0.49E-01 3.3 0.00003219 -7732.7302486357 -1.44E-04 + 30 OT LS 0.49E-01 1.7 -7732.7303753553 + 31 OT CG 0.49E-01 3.3 0.00003148 -7732.7303753742 -1.27E-04 + 32 OT LS 0.55E-01 1.7 -7732.7305083742 + 33 OT CG 0.55E-01 3.3 0.00003064 -7732.7305096370 -1.34E-04 + 34 OT LS 0.52E-01 1.7 -7732.7306289051 + 35 OT CG 0.52E-01 3.3 0.00003090 -7732.7306293838 -1.20E-04 + 36 OT LS 0.57E-01 1.7 -7732.7307619156 + 37 OT CG 0.57E-01 3.3 0.00003384 -7732.7307628462 -1.33E-04 + 38 OT LS 0.54E-01 1.7 -7732.7309144965 + 39 OT CG 0.54E-01 3.4 0.00003544 -7732.7309149131 -1.52E-04 + 40 OT LS 0.55E-01 1.7 -7732.7310836966 + 41 OT CG 0.55E-01 3.4 0.00003616 -7732.7310837084 -1.69E-04 + 42 OT LS 0.57E-01 1.7 -7732.7312671400 + 43 OT CG 0.57E-01 3.4 0.00003802 -7732.7312674550 -1.84E-04 + 44 OT LS 0.54E-01 1.7 -7732.7314590902 + 45 OT CG 0.54E-01 3.4 0.00003723 -7732.7314597599 -1.92E-04 + 46 OT LS 0.56E-01 1.7 -7732.7316493093 + 47 OT CG 0.56E-01 3.4 0.00003810 -7732.7316494125 -1.90E-04 + 48 OT LS 0.49E-01 1.7 -7732.7318197218 + 49 OT CG 0.49E-01 3.4 0.00003888 -7732.7318233793 -1.74E-04 + 50 OT LS 0.77E-01 1.7 -7732.7320704526 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1512.0000000000 0.0000000000 + Core density on regular grids: 1512.0000000000 -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: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.66401977063197 + Hartree energy: 3437.39999770714348 + Exchange-correlation energy: -1057.75345816817935 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50788020499482 + + Total energy: -7732.73207045264371 + + outer SCF iter = 6 RMS gradient = 0.39E-04 energy = -7732.7320704526 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.5 0.00005064 -7732.7321055697 -2.82E-04 + 2 OT LS 0.24E-01 1.7 -7732.7314600003 + 3 OT CG 0.24E-01 3.3 0.00003454 -7732.7322599823 -1.54E-04 + 4 OT LS 0.55E-01 1.7 -7732.7323720132 + 5 OT CG 0.55E-01 3.3 0.00003562 -7732.7324232166 -1.63E-04 + 6 OT LS 0.50E-01 1.7 -7732.7325761041 + 7 OT CG 0.50E-01 3.3 0.00003518 -7732.7325782984 -1.55E-04 + 8 OT LS 0.56E-01 1.7 -7732.7327473482 + 9 OT CG 0.56E-01 3.3 0.00003870 -7732.7327497286 -1.71E-04 + 10 OT LS 0.54E-01 1.7 -7732.7329478032 + 11 OT CG 0.54E-01 3.3 0.00003981 -7732.7329482440 -1.99E-04 + 12 OT LS 0.47E-01 1.7 -7732.7331295207 + 13 OT CG 0.47E-01 3.3 0.00003760 -7732.7331330783 -1.85E-04 + 14 OT LS 0.52E-01 1.7 -7732.7333129634 + 15 OT CG 0.52E-01 3.3 0.00004039 -7732.7333144284 -1.81E-04 + 16 OT LS 0.56E-01 1.7 -7732.7335373569 + 17 OT CG 0.56E-01 3.3 0.00004446 -7732.7335382612 -2.24E-04 + 18 OT LS 0.46E-01 1.7 -7732.7337501831 + 19 OT CG 0.46E-01 3.3 0.00004369 -7732.7337611020 -2.23E-04 + 20 OT LS 0.51E-01 1.7 -7732.7339969447 + 21 OT CG 0.51E-01 3.3 0.00004507 -7732.7339989077 -2.38E-04 + 22 OT LS 0.54E-01 1.7 -7732.7342683279 + 23 OT CG 0.54E-01 3.3 0.00004633 -7732.7342691245 -2.70E-04 + 24 OT LS 0.49E-01 1.7 -7732.7345206027 + 25 OT CG 0.49E-01 3.4 0.00004335 -7732.7345248557 -2.56E-04 + 26 OT LS 0.49E-01 1.7 -7732.7347498279 + 27 OT CG 0.49E-01 3.4 0.00004155 -7732.7347498060 -2.25E-04 + 28 OT LS 0.51E-01 1.7 -7732.7349643893 + 29 OT CG 0.51E-01 3.4 0.00004065 -7732.7349645761 -2.15E-04 + 30 OT LS 0.46E-01 1.7 -7732.7351497364 + 31 OT CG 0.46E-01 3.4 0.00003849 -7732.7351518248 -1.87E-04 + 32 OT LS 0.45E-01 1.7 -7732.7353169195 + 33 OT CG 0.45E-01 3.4 0.00003478 -7732.7353169957 -1.65E-04 + 34 OT LS 0.41E-01 1.7 -7732.7354389201 + 35 OT CG 0.41E-01 3.4 0.00003069 -7732.7354400780 -1.23E-04 + 36 OT LS 0.46E-01 1.8 -7732.7355452028 + 37 OT CG 0.46E-01 3.4 0.00002841 -7732.7355461822 -1.06E-04 + 38 OT LS 0.51E-01 1.7 -7732.7356474113 + 39 OT CG 0.51E-01 3.3 0.00002721 -7732.7356487271 -1.03E-04 + 40 OT LS 0.48E-01 1.7 -7732.7357364893 + 41 OT CG 0.48E-01 3.3 0.00002458 -7732.7357368111 -8.81E-05 + 42 OT LS 0.43E-01 1.7 -7732.7358011681 + 43 OT CG 0.43E-01 3.3 0.00002221 -7732.7358019468 -6.51E-05 + 44 OT LS 0.49E-01 1.7 -7732.7358610135 + 45 OT CG 0.49E-01 3.3 0.00002174 -7732.7358618366 -5.99E-05 + 46 OT LS 0.46E-01 1.7 -7732.7359157544 + 47 OT CG 0.46E-01 3.3 0.00001994 -7732.7359159526 -5.41E-05 + 48 OT LS 0.48E-01 1.8 -7732.7359630404 + 49 OT CG 0.48E-01 3.3 0.00001856 -7732.7359630980 -4.71E-05 + 50 OT LS 0.47E-01 1.7 -7732.7360026158 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1512.0000150570 -0.0000150570 + Core density on regular grids: 1512.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000150571 + Total charge density g-space grids: -0.0000150571 + + Overlap energy of the core charge distribution: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.63622318329544 + Hartree energy: 3437.42246519040236 + Exchange-correlation energy: -1057.75031532306230 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50613430081053 + + Total energy: -7732.73600261578849 + + outer SCF iter = 7 RMS gradient = 0.19E-04 energy = -7732.7360026158 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.4 0.00001715 -7732.7360026587 -3.96E-05 + 2 OT LS 0.26E-01 1.7 -7732.7359377827 + 3 OT CG 0.26E-01 3.3 0.00001485 -7732.7360220230 -1.94E-05 + 4 OT LS 0.77E-01 1.7 -7732.7360451594 + 5 OT CG 0.77E-01 3.3 0.00001980 -7732.7360635900 -4.16E-05 + 6 OT LS 0.50E-01 1.7 -7732.7360975831 + 7 OT CG 0.50E-01 3.3 0.00002018 -7732.7361117242 -4.81E-05 + 8 OT LS 0.45E-01 1.7 -7732.7361567646 + 9 OT CG 0.45E-01 3.3 0.00001874 -7732.7361572104 -4.55E-05 + 10 OT LS 0.45E-01 1.7 -7732.7361959287 + 11 OT CG 0.45E-01 3.3 0.00001670 -7732.7361959361 -3.87E-05 + 12 OT LS 0.51E-01 1.7 -7732.7362303268 + 13 OT CG 0.51E-01 3.3 0.00001610 -7732.7362308156 -3.49E-05 + 14 OT LS 0.48E-01 1.7 -7732.7362610872 + 15 OT CG 0.48E-01 3.3 0.00001471 -7732.7362612189 -3.04E-05 + 16 OT LS 0.41E-01 1.7 -7732.7362822237 + 17 OT CG 0.41E-01 3.3 0.00001260 -7732.7362828699 -2.17E-05 + 18 OT LS 0.42E-01 1.7 -7732.7362993030 + 19 OT CG 0.42E-01 3.3 0.00001156 -7732.7362993222 -1.65E-05 + 20 OT LS 0.49E-01 1.7 -7732.7363151964 + 21 OT CG 0.49E-01 3.3 0.00001160 -7732.7363155488 -1.62E-05 + 22 OT LS 0.48E-01 1.7 -7732.7363314759 + 23 OT CG 0.48E-01 3.3 0.00001096 -7732.7363314864 -1.59E-05 + 24 OT LS 0.49E-01 1.7 -7732.7363461234 + 25 OT CG 0.49E-01 3.3 0.00001111 -7732.7363461354 -1.46E-05 + 26 OT LS 0.51E-01 1.7 -7732.7363615911 + 27 OT CG 0.51E-01 3.3 0.00001123 -7732.7363616028 -1.55E-05 + 28 OT LS 0.53E-01 1.7 -7732.7363779538 + 29 OT CG 0.53E-01 3.3 0.00001195 -7732.7363779727 -1.64E-05 + 30 OT LS 0.50E-01 1.7 -7732.7363953745 + 31 OT CG 0.50E-01 3.3 0.00001199 -7732.7363954409 -1.75E-05 + 32 OT LS 0.44E-01 1.7 -7732.7364106359 + 33 OT CG 0.44E-01 3.3 0.00001158 -7732.7364109269 -1.55E-05 + 34 OT LS 0.45E-01 1.8 -7732.7364257307 + 35 OT CG 0.45E-01 3.3 0.00001181 -7732.7364257404 -1.48E-05 + 36 OT LS 0.52E-01 1.7 -7732.7364431526 + 37 OT CG 0.52E-01 3.3 0.00001204 -7732.7364434463 -1.77E-05 + 38 OT LS 0.54E-01 1.7 -7732.7364626554 + 39 OT CG 0.54E-01 3.3 0.00001187 -7732.7364626917 -1.92E-05 + 40 OT LS 0.58E-01 1.7 -7732.7364826361 + 41 OT CG 0.58E-01 3.3 0.00001317 -7732.7364827180 -2.00E-05 + 42 OT LS 0.52E-01 1.7 -7732.7365044211 + 43 OT CG 0.52E-01 3.3 0.00001363 -7732.7365047510 -2.20E-05 + 44 OT LS 0.43E-01 1.7 -7732.7365236576 + 45 OT CG 0.43E-01 3.3 0.00001234 -7732.7365244550 -1.97E-05 + 46 OT LS 0.44E-01 1.7 -7732.7365409344 + 47 OT CG 0.44E-01 3.3 0.00001143 -7732.7365409408 -1.65E-05 + 48 OT LS 0.50E-01 1.7 -7732.7365568288 + 49 OT CG 0.50E-01 3.3 0.00001167 -7732.7365570646 -1.61E-05 + 50 OT LS 0.44E-01 1.8 -7732.7365715214 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1512.0000000011 -0.0000000011 + Core density on regular grids: 1512.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000011 + Total charge density g-space grids: -0.0000000011 + + Overlap energy of the core charge distribution: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.64743711844540 + Hartree energy: 3437.41259396097303 + Exchange-correlation energy: -1057.75221082692724 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50611819330350 + + Total energy: -7732.73657152144006 + + outer SCF iter = 8 RMS gradient = 0.12E-04 energy = -7732.7365715214 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.5 0.00001097 -7732.7365718110 -1.47E-05 + 2 OT LS 0.28E-01 1.7 -7732.7365503787 + 3 OT CG 0.28E-01 3.3 0.00000885 -7732.7365799816 -8.17E-06 + 4 OT LS 0.48E-01 1.7 -7732.7365875905 + 5 OT CG 0.48E-01 3.3 0.00000857 -7732.7365893246 -9.34E-06 + 6 OT LS 0.45E-01 1.7 -7732.7365974372 + 7 OT CG 0.45E-01 3.3 0.00000806 -7732.7365974815 -8.16E-06 + 8 OT LS 0.45E-01 1.7 -7732.7366046830 + 9 OT CG 0.45E-01 3.3 0.00000773 -7732.7366046830 -7.20E-06 + 10 OT LS 0.47E-01 1.7 -7732.7366115709 + 11 OT CG 0.47E-01 3.3 0.00000710 -7732.7366115825 -6.90E-06 + 12 OT LS 0.46E-01 1.7 -7732.7366172384 + 13 OT CG 0.46E-01 3.3 0.00000618 -7732.7366172435 -5.66E-06 + 14 OT LS 0.47E-01 1.7 -7732.7366216358 + 15 OT CG 0.47E-01 3.3 0.00000560 -7732.7366216386 -4.40E-06 + 16 OT LS 0.45E-01 1.7 -7732.7366251081 + 17 OT CG 0.45E-01 3.3 0.00000523 -7732.7366251135 -3.47E-06 + 18 OT LS 0.42E-01 1.7 -7732.7366279127 + 19 OT CG 0.42E-01 3.3 0.00000484 -7732.7366279289 -2.82E-06 + 20 OT LS 0.43E-01 1.7 -7732.7366304337 + 21 OT CG 0.43E-01 3.3 0.00000471 -7732.7366304372 -2.51E-06 + 22 OT LS 0.46E-01 1.7 -7732.7366329321 + 23 OT CG 0.46E-01 3.3 0.00000437 -7732.7366329384 -2.50E-06 + 24 OT LS 0.43E-01 1.7 -7732.7366349567 + 25 OT CG 0.43E-01 3.3 0.00000372 -7732.7366349644 -2.03E-06 + 26 OT LS 0.46E-01 1.7 -7732.7366365234 + 27 OT CG 0.46E-01 3.3 0.00000336 -7732.7366365293 -1.56E-06 + 28 OT LS 0.47E-01 1.7 -7732.7366378292 + 29 OT CG 0.47E-01 3.3 0.00000319 -7732.7366378296 -1.30E-06 + 30 OT LS 0.51E-01 1.7 -7732.7366390920 + 31 OT CG 0.51E-01 3.3 0.00000329 -7732.7366391002 -1.27E-06 + 32 OT LS 0.48E-01 1.7 -7732.7366403677 + 33 OT CG 0.48E-01 3.3 0.00000337 -7732.7366403728 -1.27E-06 + 34 OT LS 0.48E-01 1.7 -7732.7366417172 + 35 OT CG 0.48E-01 3.3 0.00000350 -7732.7366417172 -1.34E-06 + 36 OT LS 0.49E-01 1.7 -7732.7366431939 + 37 OT CG 0.49E-01 3.3 0.00000365 -7732.7366431943 -1.48E-06 + 38 OT LS 0.51E-01 1.7 -7732.7366448753 + 39 OT CG 0.51E-01 3.3 0.00000376 -7732.7366448788 -1.68E-06 + 40 OT LS 0.49E-01 1.7 -7732.7366465896 + 41 OT CG 0.49E-01 3.3 0.00000358 -7732.7366465926 -1.71E-06 + 42 OT LS 0.47E-01 1.7 -7732.7366480690 + 43 OT CG 0.47E-01 3.3 0.00000345 -7732.7366480728 -1.48E-06 + 44 OT LS 0.44E-01 1.7 -7732.7366493549 + 45 OT CG 0.44E-01 3.3 0.00000340 -7732.7366493603 -1.29E-06 + 46 OT LS 0.45E-01 1.7 -7732.7366506506 + 47 OT CG 0.45E-01 3.3 0.00000322 -7732.7366506519 -1.29E-06 + 48 OT LS 0.43E-01 1.7 -7732.7366517636 + 49 OT CG 0.43E-01 3.3 0.00000262 -7732.7366517657 -1.11E-06 + 50 OT LS 0.35E-01 1.7 -7732.7366523192 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1512.0000000001 -0.0000000001 + Core density on regular grids: 1512.0000000000 -0.0000000000 + Total charge density on r-space grids: -0.0000000001 + Total charge density g-space grids: -0.0000000001 + + Overlap energy of the core charge distribution: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.63570506047381 + Hartree energy: 3437.42243009623689 + Exchange-correlation energy: -1057.75043294182751 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50615543317347 + + Total energy: -7732.73665231917767 + + outer SCF iter = 9 RMS gradient = 0.26E-05 energy = -7732.7366523192 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.3 0.00000225 -7732.7366523547 -5.89E-07 + 2 OT LS 0.32E-01 1.7 -7732.7366518237 + 3 OT CG 0.32E-01 3.3 0.00000204 -7732.7366527495 -3.95E-07 + 4 OT LS 0.59E-01 1.7 -7732.7366532279 + 5 OT CG 0.59E-01 3.3 0.00000232 -7732.7366533626 -6.13E-07 + 6 OT LS 0.48E-01 1.7 -7732.7366539561 + 7 OT CG 0.48E-01 3.3 0.00000228 -7732.7366539947 -6.32E-07 + 8 OT LS 0.43E-01 1.7 -7732.7366545451 + 9 OT CG 0.43E-01 3.3 0.00000215 -7732.7366545509 -5.56E-07 + 10 OT LS 0.46E-01 1.7 -7732.7366550694 + 11 OT CG 0.46E-01 3.3 0.00000204 -7732.7366550707 -5.20E-07 + 12 OT LS 0.49E-01 1.7 -7732.7366555673 + 13 OT CG 0.49E-01 3.3 0.00000201 -7732.7366555693 -4.99E-07 + 14 OT LS 0.47E-01 1.7 -7732.7366560370 + 15 OT CG 0.47E-01 3.3 0.00000189 -7732.7366560374 -4.68E-07 + 16 OT LS 0.45E-01 1.7 -7732.7366564306 + 17 OT CG 0.45E-01 3.3 0.00000173 -7732.7366564316 -3.94E-07 + 18 OT LS 0.43E-01 1.7 -7732.7366567509 + 19 OT CG 0.43E-01 3.3 0.00000160 -7732.7366567514 -3.20E-07 + 20 OT LS 0.43E-01 1.7 -7732.7366570230 + 21 OT CG 0.43E-01 3.3 0.00000150 -7732.7366570231 -2.72E-07 + 22 OT LS 0.46E-01 1.7 -7732.7366572771 + 23 OT CG 0.46E-01 3.3 0.00000140 -7732.7366572781 -2.55E-07 + 24 OT LS 0.50E-01 1.7 -7732.7366575151 + 25 OT CG 0.50E-01 3.3 0.00000139 -7732.7366575166 -2.39E-07 + 26 OT LS 0.53E-01 1.7 -7732.7366577710 + 27 OT CG 0.53E-01 3.3 0.00000147 -7732.7366577723 -2.56E-07 + 28 OT LS 0.56E-01 1.7 -7732.7366580690 + 29 OT CG 0.56E-01 3.3 0.00000160 -7732.7366580696 -2.97E-07 + 30 OT LS 0.48E-01 1.7 -7732.7366583661 + 31 OT CG 0.48E-01 3.3 0.00000155 -7732.7366583735 -3.04E-07 + 32 OT LS 0.44E-01 1.7 -7732.7366586325 + 33 OT CG 0.44E-01 3.3 0.00000151 -7732.7366586348 -2.61E-07 + 34 OT LS 0.45E-01 1.7 -7732.7366588862 + 35 OT CG 0.45E-01 3.3 0.00000151 -7732.7366588862 -2.51E-07 + 36 OT LS 0.47E-01 1.7 -7732.7366591473 + 37 OT CG 0.47E-01 3.3 0.00000146 -7732.7366591477 -2.62E-07 + 38 OT LS 0.50E-01 1.7 -7732.7366594087 + 39 OT CG 0.50E-01 3.3 0.00000142 -7732.7366594099 -2.62E-07 + 40 OT LS 0.52E-01 1.7 -7732.7366596703 + 41 OT CG 0.52E-01 3.3 0.00000145 -7732.7366596708 -2.61E-07 + 42 OT LS 0.47E-01 1.7 -7732.7366599101 + 43 OT CG 0.47E-01 3.3 0.00000141 -7732.7366599135 -2.43E-07 + 44 OT LS 0.43E-01 1.7 -7732.7366601229 + 45 OT CG 0.43E-01 3.3 0.00000132 -7732.7366601242 -2.11E-07 + 46 OT LS 0.47E-01 1.7 -7732.7366603256 + 47 OT CG 0.47E-01 3.3 0.00000124 -7732.7366603271 -2.03E-07 + 48 OT LS 0.47E-01 1.7 -7732.7366605076 + 49 OT CG 0.47E-01 3.3 0.00000115 -7732.7366605076 -1.80E-07 + 50 OT LS 0.50E-01 1.7 -7732.7366606695 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1511.9999999997 0.0000000003 + Core density on regular grids: 1512.0000000000 -0.0000000000 + Total charge density on r-space grids: 0.0000000002 + Total charge density g-space grids: 0.0000000002 + + Overlap energy of the core charge distribution: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.63603182322095 + Hartree energy: 3437.42203978754151 + Exchange-correlation energy: -1057.75045652855715 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50623421556727 + + Total energy: -7732.73666066946225 + + outer SCF iter = 10 RMS gradient = 0.11E-05 energy = -7732.7366606695 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.4 0.00000147 -7732.7366606698 -1.62E-07 + 2 OT LS 0.24E-01 1.7 -7732.7366600997 + 3 OT CG 0.24E-01 3.3 0.00000095 -7732.7366607980 -1.28E-07 + 4 OT LS 0.53E-01 1.7 -7732.7366608808 + 5 OT CG 0.53E-01 3.3 0.00000095 -7732.7366609158 -1.18E-07 + 6 OT LS 0.51E-01 1.7 -7732.7366610295 + 7 OT CG 0.51E-01 3.3 0.00000090 -7732.7366610296 -1.14E-07 + 8 OT LS 0.52E-01 1.7 -7732.7366611337 + 9 OT CG 0.52E-01 3.3 0.00000089 -7732.7366611337 -1.04E-07 + 10 OT LS 0.54E-01 1.7 -7732.7366612375 + 11 OT CG 0.54E-01 3.3 0.00000087 -7732.7366612377 -1.04E-07 + 12 OT LS 0.52E-01 1.7 -7732.7366613341 + 13 OT CG 0.52E-01 3.3 0.00000081 -7732.7366613342 -9.65E-08 + 14 OT LS 0.52E-01 1.7 -7732.7366614197 + 15 OT CG 0.52E-01 3.3 0.00000081 -7732.7366614197 -8.54E-08 + 16 OT LS 0.48E-01 1.8 -7732.7366614977 + 17 OT CG 0.48E-01 3.3 0.00000077 -7732.7366614982 -7.85E-08 + 18 OT LS 0.50E-01 1.7 -7732.7366615708 + 19 OT CG 0.50E-01 3.3 0.00000077 -7732.7366615709 -7.27E-08 + 20 OT LS 0.53E-01 1.7 -7732.7366616479 + 21 OT CG 0.53E-01 3.3 0.00000078 -7732.7366616482 -7.73E-08 + 22 OT LS 0.54E-01 1.7 -7732.7366617292 + 23 OT CG 0.54E-01 3.3 0.00000076 -7732.7366617293 -8.11E-08 + 24 OT LS 0.49E-01 1.7 -7732.7366617977 + 25 OT CG 0.49E-01 3.3 0.00000070 -7732.7366617987 -6.94E-08 + 26 OT LS 0.51E-01 1.7 -7732.7366618596 + 27 OT CG 0.51E-01 3.3 0.00000069 -7732.7366618598 -6.10E-08 + 28 OT LS 0.52E-01 1.7 -7732.7366619211 + 29 OT CG 0.52E-01 3.3 0.00000070 -7732.7366619211 -6.14E-08 + 30 OT LS 0.55E-01 1.7 -7732.7366619873 + 31 OT CG 0.55E-01 3.3 0.00000076 -7732.7366619875 -6.64E-08 + 32 OT LS 0.56E-01 1.7 -7732.7366620671 + 33 OT CG 0.56E-01 3.3 0.00000079 -7732.7366620672 -7.97E-08 + 34 OT LS 0.58E-01 1.7 -7732.7366621559 + 35 OT CG 0.58E-01 3.3 0.00000085 -7732.7366621560 -8.88E-08 + 36 OT LS 0.55E-01 1.7 -7732.7366622543 + 37 OT CG 0.55E-01 3.3 0.00000088 -7732.7366622545 -9.85E-08 + 38 OT LS 0.54E-01 1.7 -7732.7366623564 + 39 OT CG 0.54E-01 3.3 0.00000093 -7732.7366623565 -1.02E-07 + 40 OT LS 0.50E-01 1.7 -7732.7366624629 + 41 OT CG 0.50E-01 3.3 0.00000090 -7732.7366624634 -1.07E-07 + 42 OT LS 0.54E-01 1.7 -7732.7366625708 + 43 OT CG 0.54E-01 3.3 0.00000091 -7732.7366625713 -1.08E-07 + 44 OT LS 0.58E-01 1.7 -7732.7366626880 + 45 OT CG 0.58E-01 3.3 0.00000097 -7732.7366626886 -1.17E-07 + 46 OT LS 0.47E-01 1.7 -7732.7366627935 + 47 OT CG 0.47E-01 3.3 0.00000082 -7732.7366627989 -1.10E-07 + 48 OT LS 0.55E-01 1.7 -7732.7366628870 + 49 OT CG 0.55E-01 3.3 0.00000097 -7732.7366628886 -8.98E-08 + 50 OT LS 0.93E-01 1.7 -7732.7366630681 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1512.0000000000 0.0000000000 + Core density on regular grids: 1512.0000000000 -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: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.63530137391035 + Hartree energy: 3437.42271991201005 + Exchange-correlation energy: -1057.75037626102039 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50620187421356 + + Total energy: -7732.73666306811992 + + outer SCF iter = 11 RMS gradient = 0.97E-06 energy = -7732.7366630681 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.3 0.00000172 -7732.7366631045 -2.16E-07 + 2 OT LS 0.21E-01 1.7 -7732.7366620940 + 3 OT CG 0.21E-01 3.3 0.00000089 -7732.7366632611 -1.57E-07 + 4 OT LS 0.43E-01 1.7 -7732.7366633245 + 5 OT CG 0.43E-01 3.3 0.00000076 -7732.7366633462 -8.51E-08 + 6 OT LS 0.56E-01 1.7 -7732.7366634231 + 7 OT CG 0.56E-01 3.3 0.00000082 -7732.7366634275 -8.13E-08 + 8 OT LS 0.51E-01 1.7 -7732.7366635123 + 9 OT CG 0.51E-01 3.3 0.00000079 -7732.7366635131 -8.56E-08 + 10 OT LS 0.54E-01 1.7 -7732.7366635956 + 11 OT CG 0.54E-01 3.3 0.00000079 -7732.7366635958 -8.27E-08 + 12 OT LS 0.51E-01 1.7 -7732.7366636755 + 13 OT CG 0.51E-01 3.3 0.00000080 -7732.7366636757 -7.99E-08 + 14 OT LS 0.48E-01 1.7 -7732.7366637509 + 15 OT CG 0.48E-01 3.3 0.00000074 -7732.7366637512 -7.54E-08 + 16 OT LS 0.52E-01 1.7 -7732.7366638207 + 17 OT CG 0.52E-01 3.3 0.00000072 -7732.7366638210 -6.98E-08 + 18 OT LS 0.54E-01 1.7 -7732.7366638897 + 19 OT CG 0.54E-01 3.3 0.00000069 -7732.7366638899 -6.89E-08 + 20 OT LS 0.51E-01 1.7 -7732.7366639495 + 21 OT CG 0.51E-01 3.3 0.00000065 -7732.7366639498 -5.99E-08 + 22 OT LS 0.50E-01 1.7 -7732.7366640021 + 23 OT CG 0.50E-01 3.3 0.00000063 -7732.7366640021 -5.22E-08 + 24 OT LS 0.52E-01 1.7 -7732.7366640533 + 25 OT CG 0.52E-01 3.3 0.00000064 -7732.7366640535 -5.14E-08 + 26 OT LS 0.53E-01 1.7 -7732.7366641067 + 27 OT CG 0.53E-01 3.3 0.00000065 -7732.7366641067 -5.32E-08 + 28 OT LS 0.55E-01 1.7 -7732.7366641628 + 29 OT CG 0.55E-01 3.3 0.00000068 -7732.7366641629 -5.62E-08 + 30 OT LS 0.59E-01 1.7 -7732.7366642297 + 31 OT CG 0.59E-01 3.3 0.00000072 -7732.7366642301 -6.72E-08 + 32 OT LS 0.53E-01 1.7 -7732.7366642962 + 33 OT CG 0.53E-01 3.3 0.00000070 -7732.7366642971 -6.70E-08 + 34 OT LS 0.49E-01 1.7 -7732.7366643561 + 35 OT CG 0.49E-01 3.3 0.00000068 -7732.7366643565 -5.93E-08 + 36 OT LS 0.54E-01 1.7 -7732.7366644179 + 37 OT CG 0.54E-01 3.3 0.00000071 -7732.7366644184 -6.19E-08 + 38 OT LS 0.52E-01 1.7 -7732.7366644826 + 39 OT CG 0.52E-01 3.3 0.00000072 -7732.7366644827 -6.44E-08 + 40 OT LS 0.57E-01 1.7 -7732.7366645543 + 41 OT CG 0.57E-01 3.3 0.00000074 -7732.7366645549 -7.22E-08 + 42 OT LS 0.53E-01 1.7 -7732.7366646268 + 43 OT CG 0.53E-01 3.3 0.00000075 -7732.7366646271 -7.22E-08 + 44 OT LS 0.53E-01 1.7 -7732.7366646991 + 45 OT CG 0.53E-01 3.3 0.00000075 -7732.7366646992 -7.20E-08 + 46 OT LS 0.58E-01 1.7 -7732.7366647782 + 47 OT CG 0.58E-01 3.3 0.00000080 -7732.7366647788 -7.96E-08 + 48 OT LS 0.49E-01 1.7 -7732.7366648540 + 49 OT CG 0.49E-01 3.3 0.00000073 -7732.7366648565 -7.77E-08 + 50 OT LS 0.57E-01 1.7 -7732.7366649301 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1511.9999999956 0.0000000044 + Core density on regular grids: 1512.0000000000 -0.0000000000 + Total charge density on r-space grids: 0.0000000043 + Total charge density g-space grids: 0.0000000043 + + Overlap energy of the core charge distribution: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.63580924551388 + Hartree energy: 3437.42220310096945 + Exchange-correlation energy: -1057.75041482910433 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50624751977732 + + Total energy: -7732.73666493007750 + + outer SCF iter = 12 RMS gradient = 0.73E-06 energy = -7732.7366649301 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.4 0.00000103 -7732.7366649318 -7.53E-08 + 2 OT LS 0.25E-01 1.7 -7732.7366646782 + 3 OT CG 0.25E-01 3.3 0.00000069 -7732.7366649962 -6.44E-08 + 4 OT LS 0.61E-01 1.7 -7732.7366650423 + 5 OT CG 0.61E-01 3.3 0.00000076 -7732.7366650676 -7.14E-08 + 6 OT LS 0.49E-01 1.7 -7732.7366651329 + 7 OT CG 0.49E-01 3.3 0.00000071 -7732.7366651371 -6.96E-08 + 8 OT LS 0.51E-01 1.7 -7732.7366651999 + 9 OT CG 0.51E-01 3.3 0.00000068 -7732.7366652000 -6.28E-08 + 10 OT LS 0.53E-01 1.7 -7732.7366652606 + 11 OT CG 0.53E-01 3.3 0.00000068 -7732.7366652607 -6.07E-08 + 12 OT LS 0.53E-01 1.7 -7732.7366653207 + 13 OT CG 0.53E-01 3.3 0.00000065 -7732.7366653207 -6.01E-08 + 14 OT LS 0.51E-01 1.7 -7732.7366653751 + 15 OT CG 0.51E-01 3.3 0.00000064 -7732.7366653751 -5.44E-08 + 16 OT LS 0.49E-01 1.7 -7732.7366654247 + 17 OT CG 0.49E-01 3.3 0.00000061 -7732.7366654249 -4.98E-08 + 18 OT LS 0.53E-01 1.7 -7732.7366654737 + 19 OT CG 0.53E-01 3.3 0.00000063 -7732.7366654741 -4.92E-08 + 20 OT LS 0.56E-01 1.7 -7732.7366655289 + 21 OT CG 0.56E-01 3.2 0.00000065 -7732.7366655290 -5.49E-08 + 22 OT LS 0.54E-01 1.7 -7732.7366655853 + 23 OT CG 0.54E-01 3.3 0.00000062 -7732.7366655854 -5.64E-08 + 24 OT LS 0.50E-01 1.7 -7732.7366656329 + 25 OT CG 0.50E-01 3.3 0.00000060 -7732.7366656331 -4.77E-08 + 26 OT LS 0.52E-01 1.7 -7732.7366656790 + 27 OT CG 0.52E-01 3.3 0.00000060 -7732.7366656791 -4.60E-08 + 28 OT LS 0.51E-01 1.7 -7732.7366657233 + 29 OT CG 0.51E-01 3.3 0.00000058 -7732.7366657233 -4.42E-08 + 30 OT LS 0.53E-01 1.7 -7732.7366657676 + 31 OT CG 0.53E-01 3.3 0.00000060 -7732.7366657678 -4.45E-08 + 32 OT LS 0.57E-01 1.7 -7732.7366658180 + 33 OT CG 0.57E-01 3.3 0.00000063 -7732.7366658182 -5.04E-08 + 34 OT LS 0.58E-01 1.7 -7732.7366658750 + 35 OT CG 0.58E-01 3.3 0.00000065 -7732.7366658750 -5.68E-08 + 36 OT LS 0.54E-01 1.7 -7732.7366659302 + 37 OT CG 0.54E-01 3.3 0.00000065 -7732.7366659305 -5.54E-08 + 38 OT LS 0.55E-01 1.7 -7732.7366659881 + 39 OT CG 0.55E-01 3.3 0.00000068 -7732.7366659882 -5.77E-08 + 40 OT LS 0.50E-01 1.7 -7732.7366660455 + 41 OT CG 0.50E-01 3.3 0.00000067 -7732.7366660460 -5.79E-08 + 42 OT LS 0.52E-01 1.7 -7732.7366661034 + 43 OT CG 0.52E-01 3.3 0.00000065 -7732.7366661035 -5.75E-08 + 44 OT LS 0.55E-01 1.7 -7732.7366661610 + 45 OT CG 0.55E-01 3.3 0.00000066 -7732.7366661611 -5.76E-08 + 46 OT LS 0.49E-01 1.7 -7732.7366662142 + 47 OT CG 0.49E-01 3.3 0.00000062 -7732.7366662148 -5.37E-08 + 48 OT LS 0.58E-01 1.7 -7732.7366662688 + 49 OT CG 0.58E-01 3.3 0.00000070 -7732.7366662700 -5.52E-08 + 50 OT LS 0.76E-01 1.7 -7732.7366663566 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1511.9999999966 0.0000000034 + Core density on regular grids: 1512.0000000000 -0.0000000000 + Total charge density on r-space grids: 0.0000000034 + Total charge density g-space grids: 0.0000000034 + + Overlap energy of the core charge distribution: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.63543071195272 + Hartree energy: 3437.42257702024563 + Exchange-correlation energy: -1057.75037898002734 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50621485851141 + + Total energy: -7732.73666635655172 + + outer SCF iter = 13 RMS gradient = 0.70E-06 energy = -7732.7366663566 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.3 0.00000124 -7732.7366663619 -9.19E-08 + 2 OT LS 0.22E-01 1.7 -7732.7366658463 + 3 OT CG 0.22E-01 3.3 0.00000067 -7732.7366664435 -8.17E-08 + 4 OT LS 0.46E-01 1.7 -7732.7366664797 + 5 OT CG 0.46E-01 3.3 0.00000059 -7732.7366664935 -5.00E-08 + 6 OT LS 0.56E-01 1.7 -7732.7366665395 + 7 OT CG 0.56E-01 3.3 0.00000062 -7732.7366665411 -4.76E-08 + 8 OT LS 0.52E-01 1.7 -7732.7366665910 + 9 OT CG 0.52E-01 3.3 0.00000060 -7732.7366665913 -5.01E-08 + 10 OT LS 0.55E-01 1.7 -7732.7366666404 + 11 OT CG 0.55E-01 3.3 0.00000062 -7732.7366666405 -4.92E-08 + 12 OT LS 0.52E-01 1.7 -7732.7366666888 + 13 OT CG 0.52E-01 3.3 0.00000062 -7732.7366666890 -4.85E-08 + 14 OT LS 0.50E-01 1.7 -7732.7366667367 + 15 OT CG 0.50E-01 3.3 0.00000059 -7732.7366667368 -4.79E-08 + 16 OT LS 0.53E-01 1.7 -7732.7366667819 + 17 OT CG 0.53E-01 3.3 0.00000058 -7732.7366667820 -4.52E-08 + 18 OT LS 0.55E-01 1.7 -7732.7366668281 + 19 OT CG 0.55E-01 3.3 0.00000057 -7732.7366668283 -4.62E-08 + 20 OT LS 0.52E-01 1.7 -7732.7366668690 + 21 OT CG 0.52E-01 3.3 0.00000054 -7732.7366668693 -4.10E-08 + 22 OT LS 0.51E-01 1.7 -7732.7366669059 + 23 OT CG 0.51E-01 3.3 0.00000053 -7732.7366669059 -3.67E-08 + 24 OT LS 0.53E-01 1.7 -7732.7366669426 + 25 OT CG 0.53E-01 3.3 0.00000054 -7732.7366669427 -3.68E-08 + 26 OT LS 0.53E-01 1.7 -7732.7366669812 + 27 OT CG 0.53E-01 3.3 0.00000055 -7732.7366669812 -3.85E-08 + 28 OT LS 0.54E-01 1.7 -7732.7366670210 + 29 OT CG 0.54E-01 3.3 0.00000056 -7732.7366670210 -3.98E-08 + 30 OT LS 0.58E-01 1.7 -7732.7366670663 + 31 OT CG 0.58E-01 3.3 0.00000058 -7732.7366670666 -4.56E-08 + 32 OT LS 0.52E-01 1.7 -7732.7366671095 + 33 OT CG 0.52E-01 3.3 0.00000056 -7732.7366671101 -4.35E-08 + 34 OT LS 0.50E-01 1.7 -7732.7366671485 + 35 OT CG 0.50E-01 3.3 0.00000054 -7732.7366671486 -3.85E-08 + 36 OT LS 0.53E-01 1.7 -7732.7366671861 + 37 OT CG 0.53E-01 3.3 0.00000055 -7732.7366671863 -3.76E-08 + 38 OT LS 0.52E-01 1.7 -7732.7366672252 + 39 OT CG 0.52E-01 3.3 0.00000055 -7732.7366672252 -3.89E-08 + 40 OT LS 0.56E-01 1.7 -7732.7366672669 + 41 OT CG 0.56E-01 3.3 0.00000056 -7732.7366672671 -4.19E-08 + 42 OT LS 0.53E-01 1.7 -7732.7366673079 + 43 OT CG 0.53E-01 3.3 0.00000056 -7732.7366673081 -4.10E-08 + 44 OT LS 0.53E-01 1.7 -7732.7366673491 + 45 OT CG 0.53E-01 3.3 0.00000057 -7732.7366673491 -4.10E-08 + 46 OT LS 0.57E-01 1.7 -7732.7366673939 + 47 OT CG 0.57E-01 3.3 0.00000060 -7732.7366673941 -4.50E-08 + 48 OT LS 0.49E-01 1.7 -7732.7366674370 + 49 OT CG 0.49E-01 3.3 0.00000054 -7732.7366674381 -4.41E-08 + 50 OT LS 0.54E-01 1.7 -7732.7366674761 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1511.9999999983 0.0000000017 + Core density on regular grids: 1512.0000000000 -0.0000000000 + Total charge density on r-space grids: 0.0000000017 + Total charge density g-space grids: 0.0000000017 + + Overlap energy of the core charge distribution: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.63563221075719 + Hartree energy: 3437.42233695673121 + Exchange-correlation energy: -1057.75038038567163 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50625370934173 + + Total energy: -7732.73666747607513 + + outer SCF iter = 14 RMS gradient = 0.54E-06 energy = -7732.7366674761 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.4 0.00000075 -7732.7366674764 -3.83E-08 + 2 OT LS 0.25E-01 1.7 -7732.7366673472 + 3 OT CG 0.25E-01 3.3 0.00000052 -7732.7366675117 -3.53E-08 + 4 OT LS 0.62E-01 1.7 -7732.7366675382 + 5 OT CG 0.62E-01 3.3 0.00000057 -7732.7366675524 -4.07E-08 + 6 OT LS 0.50E-01 1.7 -7732.7366675904 + 7 OT CG 0.50E-01 3.3 0.00000054 -7732.7366675928 -4.04E-08 + 8 OT LS 0.51E-01 1.7 -7732.7366676292 + 9 OT CG 0.51E-01 3.4 0.00000052 -7732.7366676292 -3.64E-08 + 10 OT LS 0.53E-01 1.7 -7732.7366676647 + 11 OT CG 0.53E-01 3.3 0.00000052 -7732.7366676648 -3.55E-08 + 12 OT LS 0.53E-01 1.7 -7732.7366677002 + 13 OT CG 0.53E-01 3.3 0.00000050 -7732.7366677002 -3.54E-08 + 14 OT LS 0.52E-01 1.7 -7732.7366677327 + 15 OT CG 0.52E-01 3.3 0.00000050 -7732.7366677327 -3.25E-08 + 16 OT LS 0.50E-01 1.7 -7732.7366677634 + 17 OT CG 0.50E-01 3.3 0.00000049 -7732.7366677635 -3.08E-08 + 18 OT LS 0.54E-01 1.7 -7732.7366677945 + 19 OT CG 0.54E-01 3.3 0.00000050 -7732.7366677946 -3.12E-08 + 20 OT LS 0.56E-01 1.7 -7732.7366678296 + 21 OT CG 0.56E-01 3.3 0.00000052 -7732.7366678296 -3.50E-08 + 22 OT LS 0.55E-01 1.7 -7732.7366678662 + 23 OT CG 0.55E-01 3.3 0.00000051 -7732.7366678663 -3.66E-08 + 24 OT LS 0.51E-01 1.7 -7732.7366678981 + 25 OT CG 0.51E-01 3.3 0.00000049 -7732.7366678983 -3.20E-08 + 26 OT LS 0.52E-01 1.7 -7732.7366679290 + 27 OT CG 0.52E-01 3.3 0.00000049 -7732.7366679290 -3.08E-08 + 28 OT LS 0.50E-01 1.7 -7732.7366679583 + 29 OT CG 0.50E-01 3.3 0.00000047 -7732.7366679583 -2.93E-08 + 30 OT LS 0.53E-01 1.7 -7732.7366679870 + 31 OT CG 0.53E-01 3.3 0.00000048 -7732.7366679871 -2.87E-08 + 32 OT LS 0.56E-01 1.7 -7732.7366680183 + 33 OT CG 0.56E-01 3.3 0.00000049 -7732.7366680184 -3.14E-08 + 34 OT LS 0.57E-01 1.7 -7732.7366680531 + 35 OT CG 0.57E-01 3.3 0.00000050 -7732.7366680531 -3.47E-08 + 36 OT LS 0.53E-01 1.7 -7732.7366680859 + 37 OT CG 0.53E-01 3.3 0.00000050 -7732.7366680861 -3.30E-08 + 38 OT LS 0.54E-01 1.7 -7732.7366681195 + 39 OT CG 0.54E-01 3.3 0.00000052 -7732.7366681195 -3.34E-08 + 40 OT LS 0.50E-01 1.7 -7732.7366681522 + 41 OT CG 0.50E-01 3.3 0.00000050 -7732.7366681525 -3.29E-08 + 42 OT LS 0.52E-01 1.7 -7732.7366681847 + 43 OT CG 0.52E-01 3.3 0.00000049 -7732.7366681848 -3.23E-08 + 44 OT LS 0.55E-01 1.7 -7732.7366682165 + 45 OT CG 0.55E-01 3.3 0.00000049 -7732.7366682166 -3.18E-08 + 46 OT LS 0.49E-01 1.7 -7732.7366682458 + 47 OT CG 0.49E-01 3.3 0.00000046 -7732.7366682461 -2.95E-08 + 48 OT LS 0.57E-01 1.7 -7732.7366682757 + 49 OT CG 0.57E-01 3.3 0.00000052 -7732.7366682763 -3.02E-08 + 50 OT LS 0.71E-01 1.7 -7732.7366683212 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1511.9999999988 0.0000000012 + Core density on regular grids: 1512.0000000000 -0.0000000000 + Total charge density on r-space grids: 0.0000000012 + Total charge density g-space grids: 0.0000000012 + + Overlap energy of the core charge distribution: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.63547394347825 + Hartree energy: 3437.42251743308861 + Exchange-correlation energy: -1057.75037507949128 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50622534896116 + + Total energy: -7732.73666832119761 + + outer SCF iter = 15 RMS gradient = 0.52E-06 energy = -7732.7366683212 + + ----------------------------------- OT --------------------------------------- + Minimizer : CG : conjugate gradient + Preconditioner : FULL_SINGLE_INVERSE : inversion of + H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T + Precond_solver : DEFAULT + Line search : 2PNT : 2 energies, one gradient + stepsize : 0.08000000 energy_gap : 0.10000000 + eps_taylor : 0.10000E-15 max_taylor : 4 + ----------------------------------- OT --------------------------------------- + + Step Update method Time Convergence Total energy Change + ------------------------------------------------------------------------------ + 1 OT CG 0.80E-01 5.4 0.00000088 -7732.7366683230 -4.67E-08 + 2 OT LS 0.22E-01 1.7 -7732.7366680773 + 3 OT CG 0.22E-01 3.3 0.00000050 -7732.7366683659 -4.29E-08 + 4 OT LS 0.46E-01 1.7 -7732.7366683863 + 5 OT CG 0.46E-01 3.3 0.00000044 -7732.7366683936 -2.77E-08 + 6 OT LS 0.56E-01 1.7 -7732.7366684192 + 7 OT CG 0.56E-01 3.3 0.00000047 -7732.7366684201 -2.66E-08 + 8 OT LS 0.52E-01 1.7 -7732.7366684480 + 9 OT CG 0.52E-01 3.3 0.00000045 -7732.7366684482 -2.81E-08 + 10 OT LS 0.55E-01 1.7 -7732.7366684759 + 11 OT CG 0.55E-01 3.3 0.00000046 -7732.7366684760 -2.78E-08 + 12 OT LS 0.52E-01 1.7 -7732.7366685035 + 13 OT CG 0.52E-01 3.3 0.00000047 -7732.7366685036 -2.76E-08 + 14 OT LS 0.50E-01 1.7 -7732.7366685312 + 15 OT CG 0.50E-01 3.3 0.00000045 -7732.7366685312 -2.76E-08 + 16 OT LS 0.53E-01 1.7 -7732.7366685578 + 17 OT CG 0.53E-01 3.3 0.00000045 -7732.7366685579 -2.66E-08 + 18 OT LS 0.55E-01 1.7 -7732.7366685853 + 19 OT CG 0.55E-01 3.3 0.00000044 -7732.7366685854 -2.75E-08 + 20 OT LS 0.52E-01 1.7 -7732.7366686099 + 21 OT CG 0.52E-01 3.3 0.00000042 -7732.7366686100 -2.47E-08 + 22 OT LS 0.51E-01 1.7 -7732.7366686324 + 23 OT CG 0.51E-01 3.3 0.00000042 -7732.7366686325 -2.24E-08 + 24 OT LS 0.53E-01 1.7 -7732.7366686552 + 25 OT CG 0.53E-01 3.3 0.00000043 -7732.7366686552 -2.28E-08 + 26 OT LS 0.53E-01 1.7 -7732.7366686791 + 27 OT CG 0.53E-01 3.3 0.00000043 -7732.7366686791 -2.38E-08 + 28 OT LS 0.54E-01 1.7 -7732.7366687035 + 29 OT CG 0.54E-01 3.3 0.00000044 -7732.7366687035 -2.44E-08 + 30 OT LS 0.57E-01 1.7 -7732.7366687307 + 31 OT CG 0.57E-01 3.3 0.00000045 -7732.7366687308 -2.73E-08 + 32 OT LS 0.51E-01 1.7 -7732.7366687559 + 33 OT CG 0.51E-01 3.3 0.00000043 -7732.7366687562 -2.54E-08 + 34 OT LS 0.49E-01 1.7 -7732.7366687784 + 35 OT CG 0.49E-01 3.3 0.00000041 -7732.7366687785 -2.23E-08 + 36 OT LS 0.52E-01 1.7 -7732.7366687998 + 37 OT CG 0.52E-01 3.3 0.00000041 -7732.7366687999 -2.14E-08 + 38 OT LS 0.52E-01 1.7 -7732.7366688216 + 39 OT CG 0.52E-01 3.3 0.00000041 -7732.7366688216 -2.17E-08 + 40 OT LS 0.56E-01 1.7 -7732.7366688445 + 41 OT CG 0.56E-01 3.3 0.00000042 -7732.7366688447 -2.31E-08 + 42 OT LS 0.53E-01 1.7 -7732.7366688671 + 43 OT CG 0.53E-01 3.3 0.00000041 -7732.7366688672 -2.25E-08 + 44 OT LS 0.53E-01 1.7 -7732.7366688896 + 45 OT CG 0.53E-01 3.3 0.00000042 -7732.7366688896 -2.25E-08 + 46 OT LS 0.57E-01 1.7 -7732.7366689141 + 47 OT CG 0.57E-01 3.3 0.00000044 -7732.7366689142 -2.45E-08 + 48 OT LS 0.49E-01 1.7 -7732.7366689374 + 49 OT CG 0.49E-01 3.3 0.00000039 -7732.7366689380 -2.38E-08 + 50 OT LS 0.52E-01 1.7 -7732.7366689579 + + Leaving inner SCF loop after reaching 50 steps. + + + Electronic density on regular grids: -1511.9999999994 0.0000000006 + Core density on regular grids: 1512.0000000000 -0.0000000000 + Total charge density on r-space grids: 0.0000000006 + Total charge density g-space grids: 0.0000000006 + + Overlap energy of the core charge distribution: 0.00000239243369 + Self energy of the core charge distribution: -14128.69773293553044 + Core Hamiltonian energy: 4016.63553276686162 + Hartree energy: 3437.42241333064430 + Exchange-correlation energy: -1057.75036120151526 + Dispersion energy: -0.85277942413643 + + DFT+U energy: 0.50625611336018 + + Total energy: -7732.73666895788210 + + outer SCF iter = 16 RMS gradient = 0.39E-06 energy = -7732.7366689579 + outer SCF loop FAILED to converge after 16 iterations or 800 steps + + + *** WARNING in qs_scf.F:542 :: SCF run NOT converged *** + + + Integrated absolute spin density : 108.9943318149 + Ideal and single determinant S**2 : 0.000000 57.165097 + + !-----------------------------------------------------------------------------! + Mulliken Population Analysis + + # Atom Element Kind Atomic population (alpha,beta) Net charge Spin moment + 1 Co 1 9.430663 6.746650 0.822686 2.684013 + 2 Co 1 9.421822 6.705500 0.872678 2.716323 + 3 Co 1 9.433255 6.739727 0.827018 2.693528 + 4 Co 1 9.421765 6.727921 0.850314 2.693844 + 5 Co 1 9.377002 6.670813 0.952185 2.706189 + 6 Co 1 9.392612 6.684676 0.922712 2.707936 + 7 Co 1 9.395023 6.686533 0.918444 2.708490 + 8 Co 1 9.422790 6.729119 0.848091 2.693672 + 9 Co 1 9.424549 6.720971 0.854480 2.703578 + 10 Co 1 9.304736 7.022494 0.672770 2.282242 + 11 Co 1 9.410720 6.713067 0.876213 2.697653 + 12 Co 1 9.427688 6.719236 0.853076 2.708452 + 13 Co 1 9.396660 6.777733 0.825606 2.618927 + 14 Co 1 9.405927 6.728523 0.865551 2.677404 + 15 Co 1 9.426360 6.732137 0.841503 2.694223 + 16 Co 1 9.357060 6.736457 0.906482 2.620603 + 17 Co 1 9.403421 6.685076 0.911503 2.718345 + 18 Co 1 9.402896 6.674142 0.922962 2.728754 + 19 Co 1 9.407117 6.684262 0.908622 2.722855 + 20 Co 1 9.402282 6.687994 0.909724 2.714288 + 21 Co 2 6.724540 9.421601 0.853859 -2.697060 + 22 Co 2 6.726868 9.432751 0.840381 -2.705883 + 23 Co 2 6.733316 9.426973 0.839711 -2.693657 + 24 Co 2 6.655868 9.385612 0.958520 -2.729745 + 25 Co 2 6.648584 9.394171 0.957244 -2.745587 + 26 Co 2 6.752169 9.419344 0.828487 -2.667175 + 27 Co 2 6.755120 9.431606 0.813273 -2.676486 + 28 Co 2 6.741045 9.432022 0.826933 -2.690977 + 29 Co 2 6.662843 9.397685 0.939472 -2.734842 + 30 Co 2 6.682064 9.399944 0.917991 -2.717880 + 31 Co 2 6.734216 9.432328 0.833456 -2.698112 + 32 Co 2 6.715125 9.426976 0.857900 -2.711851 + 33 Co 2 6.650729 9.385532 0.963739 -2.734803 + 34 Co 2 6.713172 9.417131 0.869697 -2.703959 + 35 Co 2 6.720707 9.414948 0.864345 -2.694240 + 36 Co 2 6.648268 9.379093 0.972640 -2.730825 + 37 Co 2 6.688689 9.411029 0.900282 -2.722340 + 38 Co 2 6.658537 9.379825 0.961638 -2.721287 + 39 Co 2 6.727774 9.431329 0.840897 -2.703555 + 40 Co 2 6.665058 9.396842 0.938100 -2.731784 + 41 H 3 0.430192 0.430290 0.139518 -0.000098 + 42 H 3 0.436930 0.436993 0.126077 -0.000063 + 43 H 3 0.427380 0.428029 0.144591 -0.000649 + 44 H 3 0.421473 0.421490 0.157037 -0.000018 + 45 H 3 0.420323 0.419758 0.159920 0.000565 + 46 H 3 0.410405 0.410563 0.179032 -0.000158 + 47 H 3 0.423748 0.423778 0.152473 -0.000030 + 48 H 3 0.419011 0.419073 0.161916 -0.000062 + 49 H 3 0.439303 0.439945 0.120752 -0.000642 + 50 H 3 0.413015 0.413946 0.173039 -0.000931 + 51 H 3 0.426444 0.426601 0.146954 -0.000157 + 52 H 3 0.416795 0.416962 0.166243 -0.000167 + 53 H 3 0.422427 0.422506 0.155067 -0.000079 + 54 H 3 0.413318 0.413322 0.173360 -0.000004 + 55 H 3 0.439814 0.440557 0.119629 -0.000743 + 56 H 3 0.422839 0.422664 0.154496 0.000175 + 57 H 3 0.432020 0.432024 0.135956 -0.000005 + 58 H 3 0.419923 0.420457 0.159620 -0.000533 + 59 H 3 0.430752 0.430830 0.138418 -0.000077 + 60 H 3 0.405033 0.405215 0.189752 -0.000182 + 61 H 3 0.409945 0.409913 0.180142 0.000032 + 62 H 3 0.434866 0.434996 0.130138 -0.000131 + 63 H 3 0.417525 0.417584 0.164891 -0.000060 + 64 H 3 0.423898 0.424150 0.151952 -0.000252 + 65 H 3 0.427203 0.426430 0.146368 0.000773 + 66 H 3 0.438665 0.439205 0.122130 -0.000539 + 67 H 3 0.417040 0.419040 0.163920 -0.002000 + 68 H 3 0.428079 0.428137 0.143784 -0.000057 + 69 H 3 0.442897 0.443038 0.114065 -0.000140 + 70 H 3 0.434276 0.434680 0.131044 -0.000404 + 71 H 3 0.406934 0.409693 0.183373 -0.002759 + 72 H 3 0.434963 0.435418 0.129620 -0.000455 + 73 H 3 0.437129 0.437206 0.125665 -0.000077 + 74 H 3 0.447798 0.447818 0.104384 -0.000020 + 75 H 3 0.426026 0.426019 0.147955 0.000007 + 76 H 3 0.425707 0.425788 0.148505 -0.000080 + 77 H 3 0.426861 0.426721 0.146419 0.000140 + 78 H 3 0.419445 0.419937 0.160618 -0.000492 + 79 H 3 0.423221 0.424831 0.151948 -0.001609 + 80 H 3 0.426177 0.426246 0.147576 -0.000069 + 81 H 3 0.413711 0.419854 0.166435 -0.006144 + 82 H 3 0.428546 0.430326 0.141128 -0.001780 + 83 H 3 0.442721 0.442701 0.114578 0.000021 + 84 H 3 0.429726 0.429720 0.140554 0.000006 + 85 H 3 0.426930 0.426951 0.146119 -0.000021 + 86 H 3 0.422162 0.422220 0.155618 -0.000059 + 87 H 3 0.426275 0.429523 0.144202 -0.003247 + 88 H 3 0.411754 0.411874 0.176373 -0.000120 + 89 H 3 0.424354 0.424988 0.150658 -0.000633 + 90 H 3 0.425813 0.425883 0.148304 -0.000070 + 91 H 3 0.420083 0.420245 0.159672 -0.000162 + 92 H 3 0.434379 0.435852 0.129769 -0.001473 + 93 H 3 0.432516 0.432483 0.135001 0.000032 + 94 H 3 0.414729 0.415642 0.169629 -0.000912 + 95 H 3 0.427503 0.428332 0.144164 -0.000829 + 96 H 3 0.423030 0.423023 0.153948 0.000007 + 97 H 3 0.426381 0.426372 0.147247 0.000010 + 98 H 3 0.436154 0.435905 0.127941 0.000249 + 99 H 3 0.429088 0.429101 0.141811 -0.000012 + 100 H 3 0.417454 0.420527 0.162019 -0.003073 + 101 H 3 0.429144 0.430951 0.139905 -0.001807 + 102 H 3 0.433691 0.434244 0.132065 -0.000553 + 103 H 3 0.423193 0.423316 0.153491 -0.000123 + 104 H 3 0.433088 0.433235 0.133677 -0.000146 + 105 H 3 0.434759 0.434744 0.130497 0.000015 + 106 H 3 0.425235 0.425773 0.148991 -0.000538 + 107 H 3 0.429980 0.430026 0.139995 -0.000046 + 108 H 3 0.429973 0.435209 0.134818 -0.005236 + 109 H 3 0.442768 0.442699 0.114533 0.000069 + 110 H 3 0.397084 0.399218 0.203697 -0.002134 + 111 H 3 0.439671 0.439680 0.120649 -0.000009 + 112 H 3 0.429562 0.430680 0.139758 -0.001118 + 113 H 3 0.414587 0.414969 0.170444 -0.000382 + 114 H 3 0.439001 0.439007 0.121993 -0.000006 + 115 H 3 0.434457 0.434452 0.131090 0.000005 + 116 H 3 0.420278 0.420255 0.159467 0.000023 + 117 H 3 0.422047 0.422239 0.155714 -0.000193 + 118 H 3 0.422938 0.422959 0.154103 -0.000020 + 119 H 3 0.409784 0.409771 0.180445 0.000013 + 120 H 3 0.422181 0.422173 0.155646 0.000008 + 121 H 3 0.410122 0.411169 0.178709 -0.001047 + 122 H 3 0.418416 0.420043 0.161541 -0.001627 + 123 H 3 0.422637 0.422579 0.154784 0.000058 + 124 H 3 0.420275 0.420472 0.159253 -0.000197 + 125 H 3 0.441383 0.441388 0.117229 -0.000005 + 126 H 3 0.429448 0.429460 0.141092 -0.000013 + 127 H 3 0.413558 0.413602 0.172840 -0.000044 + 128 H 3 0.438521 0.439030 0.122449 -0.000509 + 129 H 3 0.438071 0.439907 0.122022 -0.001836 + 130 H 3 0.432253 0.433680 0.134066 -0.001427 + 131 H 3 0.431662 0.431762 0.136576 -0.000101 + 132 H 3 0.423591 0.423723 0.152685 -0.000132 + 133 H 3 0.422605 0.422556 0.154839 0.000049 + 134 H 3 0.426413 0.427768 0.145819 -0.001355 + 135 H 3 0.419476 0.419472 0.161053 0.000004 + 136 H 3 0.436569 0.436507 0.126924 0.000062 + 137 H 3 0.431204 0.439080 0.129716 -0.007875 + 138 H 3 0.421683 0.421641 0.156676 0.000042 + 139 H 3 0.419550 0.419546 0.160903 0.000004 + 140 H 3 0.411280 0.411260 0.177460 0.000021 + 141 H 3 0.408346 0.409391 0.182263 -0.001045 + 142 H 3 0.439963 0.441146 0.118891 -0.001184 + 143 H 3 0.409306 0.409185 0.181508 0.000121 + 144 H 3 0.431996 0.432010 0.135993 -0.000014 + 145 H 3 0.438689 0.438715 0.122596 -0.000026 + 146 H 3 0.436893 0.438840 0.124267 -0.001947 + 147 H 3 0.408030 0.405683 0.186288 0.002347 + 148 H 3 0.436743 0.432191 0.131066 0.004552 + 149 H 3 0.407318 0.414314 0.178368 -0.006996 + 150 H 3 0.410725 0.410798 0.178477 -0.000072 + 151 H 3 0.437619 0.442076 0.120306 -0.004457 + 152 H 3 0.424409 0.426127 0.149464 -0.001717 + 153 H 3 0.419066 0.414952 0.165983 0.004114 + 154 H 3 0.406920 0.413834 0.179246 -0.006914 + 155 H 3 0.425943 0.423066 0.150991 0.002877 + 156 H 3 0.420110 0.424061 0.155829 -0.003950 + 157 H 3 0.415360 0.407773 0.176867 0.007587 + 158 H 3 0.416556 0.416817 0.166627 -0.000261 + 159 H 3 0.419157 0.417930 0.162913 0.001227 + 160 H 3 0.410066 0.410342 0.179592 -0.000276 + 161 H 3 0.413555 0.412727 0.173719 0.000828 + 162 H 3 0.426354 0.426834 0.146812 -0.000479 + 163 H 3 0.435372 0.438022 0.126607 -0.002650 + 164 H 3 0.414502 0.413901 0.171597 0.000601 + 165 H 3 0.409759 0.411008 0.179232 -0.001249 + 166 H 3 0.429971 0.428155 0.141874 0.001817 + 167 H 3 0.419516 0.417670 0.162814 0.001845 + 168 H 3 0.438438 0.436781 0.124781 0.001657 + 169 H 3 0.430505 0.429528 0.139967 0.000977 + 170 H 3 0.438745 0.435193 0.126063 0.003552 + 171 H 3 0.428007 0.428129 0.143864 -0.000121 + 172 H 3 0.407272 0.403069 0.189660 0.004203 + 173 H 3 0.421787 0.421798 0.156415 -0.000011 + 174 H 3 0.439877 0.439891 0.120232 -0.000015 + 175 H 3 0.408914 0.409227 0.181859 -0.000313 + 176 H 3 0.434649 0.434676 0.130675 -0.000026 + 177 H 3 0.430377 0.430460 0.139164 -0.000083 + 178 H 3 0.420190 0.420431 0.159379 -0.000240 + 179 H 3 0.422123 0.424379 0.153499 -0.002256 + 180 H 3 0.425776 0.421759 0.152465 0.004016 + 181 H 3 0.429778 0.429319 0.140903 0.000459 + 182 H 3 0.427251 0.427264 0.145485 -0.000013 + 183 H 3 0.425468 0.428464 0.146068 -0.002996 + 184 H 3 0.414336 0.416619 0.169045 -0.002282 + 185 H 3 0.427370 0.426337 0.146293 0.001033 + 186 H 3 0.419050 0.419008 0.161941 0.000042 + 187 H 3 0.437546 0.437962 0.124492 -0.000415 + 188 H 3 0.438771 0.439012 0.122217 -0.000241 + 189 O 4 3.415923 3.425831 -0.841754 -0.009908 + 190 O 4 3.449173 3.406438 -0.855611 0.042735 + 191 O 4 3.401428 3.453635 -0.855064 -0.052207 + 192 O 4 3.153496 3.153390 -0.306885 0.000106 + 193 O 4 3.385998 3.449797 -0.835795 -0.063798 + 194 O 4 3.164495 3.164423 -0.328918 0.000072 + 195 O 4 3.125706 3.125732 -0.251438 -0.000026 + 196 O 4 3.434426 3.438914 -0.873339 -0.004488 + 197 O 4 3.428596 3.432788 -0.861384 -0.004191 + 198 O 4 3.443540 3.415413 -0.858953 0.028127 + 199 O 4 3.437403 3.425169 -0.862572 0.012234 + 200 O 4 3.446709 3.416772 -0.863481 0.029936 + 201 O 4 3.450704 3.399104 -0.849808 0.051600 + 202 O 4 3.137579 3.135567 -0.273146 0.002012 + 203 O 4 3.330774 3.339681 -0.670455 -0.008906 + 204 O 4 3.396336 3.457446 -0.853782 -0.061110 + 205 O 4 3.322239 3.325732 -0.647971 -0.003493 + 206 O 4 3.172357 3.172392 -0.344749 -0.000035 + 207 O 4 3.161319 3.106306 -0.267625 0.055012 + 208 O 4 3.407975 3.454244 -0.862219 -0.046269 + 209 O 4 3.418796 3.424797 -0.843593 -0.006001 + 210 O 4 3.370679 3.453755 -0.824433 -0.083076 + 211 O 4 3.419101 3.445631 -0.864733 -0.026530 + 212 O 4 3.163580 3.163208 -0.326787 0.000372 + 213 O 4 3.415803 3.443866 -0.859669 -0.028063 + 214 O 4 3.337891 3.359293 -0.697183 -0.021402 + 215 O 4 3.145726 3.144408 -0.290134 0.001318 + 216 O 4 3.327661 3.343561 -0.671222 -0.015901 + 217 O 4 3.402758 3.454334 -0.857091 -0.051576 + 218 O 4 3.385090 3.443652 -0.828742 -0.058562 + 219 O 4 3.342038 3.349977 -0.692014 -0.007939 + 220 O 4 3.455346 3.376945 -0.832291 0.078401 + 221 O 4 3.128956 3.128977 -0.257934 -0.000021 + 222 O 4 3.329175 3.346333 -0.675508 -0.017158 + 223 O 4 3.342105 3.340358 -0.682463 0.001747 + 224 O 4 3.143238 3.143196 -0.286434 0.000043 + 225 O 4 3.159898 3.151873 -0.311770 0.008025 + 226 O 4 3.180701 3.137379 -0.318081 0.043322 + 227 O 4 3.149464 3.146453 -0.295917 0.003010 + 228 O 4 3.416153 3.448697 -0.864850 -0.032544 + 229 O 4 3.428676 3.415449 -0.844124 0.013227 + 230 O 4 3.157304 3.157450 -0.314754 -0.000146 + 231 O 4 3.430556 3.419187 -0.849742 0.011369 + 232 O 4 3.449616 3.395098 -0.844714 0.054518 + 233 O 4 3.129618 3.130038 -0.259657 -0.000420 + 234 O 4 3.189820 3.093550 -0.283370 0.096271 + 235 O 4 3.430370 3.441198 -0.871567 -0.010828 + 236 O 4 3.398763 3.447058 -0.845821 -0.048295 + 237 O 4 3.427653 3.409049 -0.836702 0.018604 + 238 O 4 3.432488 3.422540 -0.855028 0.009948 + 239 O 4 3.141540 3.137735 -0.279275 0.003805 + 240 O 4 3.441585 3.409975 -0.851559 0.031610 + 241 O 4 3.437305 3.417500 -0.854805 0.019805 + 242 O 4 3.177823 3.177234 -0.355057 0.000589 + 243 O 4 3.179378 3.067544 -0.246922 0.111835 + 244 O 4 3.344924 3.316170 -0.661093 0.028754 + 245 O 4 3.141201 3.140506 -0.281707 0.000696 + 246 O 4 3.153480 3.149938 -0.303418 0.003541 + 247 O 4 3.150130 3.178014 -0.328144 -0.027884 + 248 O 4 3.169573 3.169536 -0.339109 0.000037 + 249 O 4 3.122236 3.131757 -0.253993 -0.009521 + 250 O 4 3.157048 3.155778 -0.312825 0.001270 + 251 O 4 3.336957 3.308485 -0.645442 0.028472 + 252 O 4 3.330360 3.157288 -0.487648 0.173072 + 253 O 4 3.130336 3.130267 -0.260603 0.000069 + 254 O 4 3.311731 3.279106 -0.590837 0.032625 + 255 O 4 3.238506 3.162723 -0.401230 0.075783 + 256 O 4 3.174104 3.190693 -0.364797 -0.016590 + 257 O 4 3.207252 3.201930 -0.409182 0.005322 + 258 O 4 3.136005 3.136160 -0.272166 -0.000155 + 259 O 4 3.139401 3.127342 -0.266743 0.012059 + 260 O 4 3.137214 3.135319 -0.272533 0.001894 + 261 O 4 3.136171 3.135541 -0.271712 0.000630 + 262 O 4 3.134800 3.133794 -0.268594 0.001006 + 263 O 4 3.172592 3.147671 -0.320263 0.024921 + 264 O 4 3.177088 3.081992 -0.259080 0.095096 + 265 O 4 3.133746 3.128080 -0.261826 0.005666 + 266 O 4 3.130722 3.128528 -0.259250 0.002195 + 267 O 4 3.128713 3.128416 -0.257129 0.000298 + 268 O 4 3.149695 3.148741 -0.298436 0.000955 + 269 O 4 3.146607 3.146318 -0.292925 0.000288 + 270 O 4 3.169332 3.164373 -0.333705 0.004959 + 271 O 4 3.129782 3.130119 -0.259901 -0.000337 + 272 O 4 3.162787 3.157540 -0.320327 0.005246 + 273 O 4 3.335846 3.353074 -0.688919 -0.017228 + 274 O 4 3.142651 3.119397 -0.262048 0.023254 + 275 O 4 3.187344 3.176788 -0.364131 0.010556 + 276 O 4 3.314787 3.331166 -0.645953 -0.016379 + 277 O 4 3.336820 3.302889 -0.639709 0.033930 + 278 O 4 3.151704 3.072111 -0.223814 0.079593 + 279 O 4 3.155780 3.154524 -0.310304 0.001256 + 280 O 4 3.352298 3.281571 -0.633870 0.070727 + 281 O 4 3.130764 3.130650 -0.261414 0.000114 + 282 O 4 3.331079 3.275262 -0.606341 0.055818 + 283 O 4 3.157415 3.153211 -0.310626 0.004204 + 284 O 4 3.173500 3.124574 -0.298073 0.048926 + 285 O 4 3.275172 3.319749 -0.594921 -0.044577 + 286 O 4 3.165223 3.165269 -0.330492 -0.000046 + 287 O 4 3.125599 3.161016 -0.286615 -0.035417 + 288 O 4 3.170053 3.170215 -0.340269 -0.000162 + 289 O 4 3.143210 3.143472 -0.286682 -0.000262 + 290 O 4 3.148029 3.169306 -0.317334 -0.021277 + 291 O 4 3.142560 3.140278 -0.282839 0.002282 + 292 O 4 3.174382 3.167003 -0.341384 0.007379 + 293 O 4 3.160291 3.158944 -0.319235 0.001346 + 294 O 4 3.117710 3.087823 -0.205533 0.029887 + 295 O 4 3.329704 3.279460 -0.609163 0.050244 + 296 O 4 3.132458 3.132406 -0.264864 0.000051 + 297 O 4 3.175232 3.153031 -0.328263 0.022201 + 298 O 4 3.146237 3.146225 -0.292462 0.000013 + 299 O 4 3.139241 3.139086 -0.278326 0.000155 + 300 O 4 3.271540 3.332417 -0.603957 -0.060876 + 301 O 4 3.268938 3.313326 -0.582263 -0.044388 + 302 O 4 3.456352 3.397309 -0.853661 0.059043 + # Total charge and spin 756.000000 756.000000 0.000000 0.000000 + + !-----------------------------------------------------------------------------! + + !-----------------------------------------------------------------------------! + Hirshfeld Charges + + #Atom Element Kind Ref Charge Population Spin moment Net charge + 1 Co 1 17.000 10.105 7.509 2.596 -0.614 + 2 Co 1 17.000 10.080 7.469 2.611 -0.549 + 3 Co 1 17.000 10.150 7.555 2.596 -0.705 + 4 Co 1 17.000 10.115 7.515 2.600 -0.631 + 5 Co 1 17.000 10.279 7.670 2.608 -0.949 + 6 Co 1 17.000 10.255 7.648 2.606 -0.903 + 7 Co 1 17.000 10.372 7.779 2.592 -1.151 + 8 Co 1 17.000 10.114 7.517 2.597 -0.631 + 9 Co 1 17.000 10.118 7.520 2.598 -0.637 + 10 Co 1 17.000 9.925 7.742 2.183 -0.667 + 11 Co 1 17.000 10.160 7.573 2.587 -0.733 + 12 Co 1 17.000 10.134 7.534 2.599 -0.668 + 13 Co 1 17.000 10.088 7.567 2.521 -0.654 + 14 Co 1 17.000 10.098 7.520 2.578 -0.619 + 15 Co 1 17.000 10.146 7.558 2.587 -0.704 + 16 Co 1 17.000 10.165 7.631 2.534 -0.796 + 17 Co 1 17.000 10.329 7.709 2.620 -1.039 + 18 Co 1 17.000 10.351 7.724 2.628 -1.075 + 19 Co 1 17.000 10.310 7.683 2.627 -0.993 + 20 Co 1 17.000 10.288 7.674 2.614 -0.961 + 21 Co 2 17.000 7.501 10.089 -2.588 -0.590 + 22 Co 2 17.000 7.495 10.103 -2.608 -0.598 + 23 Co 2 17.000 7.492 10.085 -2.592 -0.577 + 24 Co 2 17.000 7.671 10.295 -2.624 -0.966 + 25 Co 2 17.000 7.583 10.238 -2.654 -0.821 + 26 Co 2 17.000 7.523 10.102 -2.579 -0.625 + 27 Co 2 17.000 7.542 10.127 -2.585 -0.669 + 28 Co 2 17.000 7.542 10.127 -2.585 -0.670 + 29 Co 2 17.000 7.708 10.332 -2.624 -1.040 + 30 Co 2 17.000 7.705 10.324 -2.618 -1.029 + 31 Co 2 17.000 7.548 10.135 -2.587 -0.683 + 32 Co 2 17.000 7.496 10.105 -2.609 -0.601 + 33 Co 2 17.000 7.710 10.344 -2.635 -1.054 + 34 Co 2 17.000 7.505 10.116 -2.611 -0.621 + 35 Co 2 17.000 7.541 10.142 -2.601 -0.683 + 36 Co 2 17.000 7.705 10.339 -2.634 -1.043 + 37 Co 2 17.000 7.429 10.063 -2.635 -0.492 + 38 Co 2 17.000 7.721 10.333 -2.612 -1.054 + 39 Co 2 17.000 7.565 10.161 -2.596 -0.726 + 40 Co 2 17.000 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Trace Determinant + Kinetic Energy Stress 0.12296164 -0.00107828 + Basis Overlap Stress 0.14364039 0.00024813 + ES + XC Stress -5695.42831124 **************** + vdW correction (ff) Stress 0.01588597 0.00000383 + Local Pseudopotential/Core Stress -0.23034553 -0.00983305 + Nonlocal Pseudopotential Stress 0.73049852 0.26198928 + Exact Exchange Stress -0.00000000 -0.00000000 + Sum of Parts Stress -5694.64567025 **************** + Total Stress 1.36842002 2.33519885 + ============================================================================== + + ------------------------------------------------------------------------------- + - - + - DBCSR STATISTICS - + - - + ------------------------------------------------------------------------------- + COUNTER TOTAL BLAS SMM ACC + flops 20 x 20 x 126 12902400 0.0% 100.0% 0.0% + flops 20 x 20 x 134 20582400 0.0% 100.0% 0.0% + flops 20 x 20 x 147 22579200 0.0% 100.0% 0.0% + flops 5 x 20 x 20 37888000 0.0% 100.0% 0.0% + flops 26 x 20 x 20 53248000 0.0% 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3065489129472 0.0% 100.0% 0.0% + flops 96 x 64 x 147 3311404056576 0.0% 100.0% 0.0% + flops 26 x 32 x 13 3985561881600 0.0% 100.0% 0.0% + flops 13 x 32 x 26 3985561881600 0.0% 100.0% 0.0% + flops 26 x 32 x 26 4036012032000 0.0% 100.0% 0.0% + flops 13 x 32 x 13 4188623736960 0.0% 100.0% 0.0% + flops 412 x 64 x 32 4727197663232 0.0% 100.0% 0.0% + flops 407 x 64 x 32 7004743139328 0.0% 100.0% 0.0% + flops inhomo. stacks 13847971430400 100.0% 0.0% 0.0% + flops total 90.998370E+12 15.2% 84.8% 0.0% + flops max/rank 991.438341E+09 15.0% 85.0% 0.0% + matmuls inhomo. stacks 4684800 100.0% 0.0% 0.0% + matmuls total 4736932320 0.1% 99.9% 0.0% + number of processed stacks 125164096 3.7% 96.3% 0.0% + average stack size 1.0 39.3 0.0 + marketing flops 120.210120E+12 + ------------------------------------------------------------------------------- + # multiplications 19037 + max memory usage/rank 369.250304E+06 + # max total images/rank 3 + # max 3D layers 1 + # MPI messages exchanged 78584736 + MPI messages size (bytes): + total size 6.571959E+12 + min size 0.000000E+00 + max size 527.360000E+03 + average size 83.628953E+03 + MPI breakdown and total messages size (bytes): + size <= 128 191232 0 + 128 < size <= 8192 5376 42921984 + 8192 < size <= 32768 29396544 540499309056 + 32768 < size <= 131072 41880480 3681687667392 + 131072 < size <= 4194304 7111104 2350634544544 + 4194304 < size <= 16777216 0 0 + 16777216 < size 0 0 + ------------------------------------------------------------------------------- + + *** WARNING in dbcsr_mm.F:295 :: Using a non-square number of MPI ranks *** + *** might lead to poor performance. Used ranks: 96 Suggested: 100 196 *** + + ------------------------------------------------------------------------------- + - - + - DBCSR MESSAGE PASSING PERFORMANCE - + - - + ------------------------------------------------------------------------------- + ROUTINE CALLS AVE VOLUME [Bytes] + MP_Group 680 + MP_Bcast 131 12. + MP_Allreduce 96794 14. + MP_Alltoall 60012 26130. + MP_Wait 1827552 + MP_ISend 1784598 39828. + MP_IRecv 1770398 39814. + MP_Memory 1585080 + ------------------------------------------------------------------------------- + + MEMORY| Estimated peak process memory [MiB] 353 + + ------------------------------------------------------------------------------- + ---- MULTIGRID INFO ---- + ------------------------------------------------------------------------------- + count for grid 1: 2571518 cutoff [a.u.] 600.00 + count for grid 2: 2498530 cutoff [a.u.] 200.00 + count for grid 3: 1562219 cutoff [a.u.] 66.67 + count for grid 4: 1156713 cutoff [a.u.] 22.22 + total gridlevel count : 7788980 + + ------------------------------------------------------------------------------- + - - + - MESSAGE PASSING PERFORMANCE - + - - + ------------------------------------------------------------------------------- + + ROUTINE CALLS AVE VOLUME [Bytes] + MP_Group 4 + MP_Bcast 33248 23220. + MP_Allreduce 90340 1242. + MP_Sync 4 + MP_Alltoall 26865 9070642. + MP_SendRecv 380 3470. + MP_ISendRecv 456760 52800. + MP_Wait 974150 + MP_ISend 495734 112980. + MP_IRecv 495734 113105. + MP_Recv 1840 835072. + ------------------------------------------------------------------------------- + + + ------------------------------------------------------------------------------- + - - + - R E F E R E N C E S - + - - + ------------------------------------------------------------------------------- + + CP2K version 7.1, the CP2K developers group (2019). + 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. + https://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. + https://dx.doi.org/10.1016/j.parco.2014.03.012 + + Hutter, J; Iannuzzi, M; Schiffmann, F; VandeVondele, J. + WIREs Comput Mol Sci., 4 (1), 15-25 (2014). + CP2K: atomistic simulations of condensed matter systems. + https://dx.doi.org/10.1002/wcms.1159 + + Marek, A; Blum, V; Johanni, R; Havu, V; Lang, B; Auckenthaler, T; + Heinecke, A; Bungartz, H; Lederer, H. + Journal of Physics: Condensed Matter, 26 (21), (2014). + The ELPA library: scalable parallel eigenvalue solutions for + electronic structure + theory and computational science. + https://dx.doi.org/10.1088/0953-8984/26/21/213201 + + Grimme, S; Ehrlich, S; Goerigk, L. + JOURNAL OF COMPUTATIONAL CHEMISTRY, 32, 1456 (2011). + Effect of the damping function in dispersion corrected density functional theory. + https://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. + https://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. + https://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 + exchange-correlation functionals. + https://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. + https://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. + https://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. + https://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. + https://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. + https://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. + https://dx.doi.org/10.1080/002689797170220 + + 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. + https://dx.doi.org/10.1080/13642819708202343 + + Perdew, JP; Burke, K; Ernzerhof, M. + PHYSICAL REVIEW LETTERS, 77 (18), 3865-3868 (1996). + Generalized gradient approximation made simple. + https://dx.doi.org/10.1103/PhysRevLett.77.3865 + + Goedecker, S; Teter, M; Hutter, J. + PHYSICAL REVIEW B, 54 (3), 1703-1710 (1996). + Separable dual-space Gaussian pseudopotentials. + https://dx.doi.org/10.1103/PhysRevB.54.1703 + + + ------------------------------------------------------------------------------- + - - + - T I M I N G - + - - + ------------------------------------------------------------------------------- + SUBROUTINE CALLS ASD SELF TIME TOTAL TIME + MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM + CP2K 1 1.0 0.092 0.166 2019.026 2019.061 + qs_forces 1 2.0 0.008 0.033 2017.981 2018.020 + qs_energies 1 3.0 0.013 0.040 2014.008 2014.043 + scf_env_do_scf 1 4.0 0.001 0.007 2010.851 2010.890 + scf_env_do_scf_inner_loop 800 5.0 0.034 0.159 1971.799 1971.913 + rebuild_ks_matrix 801 7.0 0.003 0.006 1009.955 1010.318 + qs_ks_build_kohn_sham_matrix 801 8.0 0.087 0.101 1009.952 1010.313 + qs_ks_update_qs_env 816 6.0 0.005 0.006 1007.289 1007.650 + qs_rho_update_rho 801 6.0 0.005 0.009 878.561 878.808 + calculate_rho_elec 1602 7.0 550.991 615.384 878.556 878.803 + pw_transfer 21236 10.5 1.210 1.427 545.966 586.823 + fft_wrap_pw1pw2 19634 11.5 0.212 0.264 541.342 582.636 + fft_wrap_pw1pw2_600 12422 12.9 35.341 42.417 512.794 553.207 + qs_vxc_create 801 9.0 0.015 0.024 541.164 544.381 + fft3d_ps 19634 13.5 200.662 224.648 431.731 503.149 + sum_up_and_integrate 401 9.0 0.874 1.016 424.695 424.741 + integrate_v_rspace 802 10.0 281.172 307.771 423.819 424.289 + xc_rho_set_and_dset_create 801 11.0 5.004 5.502 372.303 389.140 + density_rs2pw 1602 8.0 0.081 0.094 297.136 353.697 + xc_vxc_pw_create 401 10.0 6.103 7.110 347.672 350.888 + mp_alltoall_z22v 19634 15.5 184.021 332.642 184.021 332.642 + rs_pw_transfer 9621 10.0 0.129 0.166 212.814 266.602 + xc_exc_calc 400 10.0 0.499 0.547 193.477 193.481 + x_to_yz 8413 15.2 27.370 36.384 131.582 176.953 + yz_to_x 6413 14.1 14.536 19.261 93.566 171.443 + xc_functional_eval 801 12.0 0.006 0.007 141.414 158.861 + pbe_lsd_eval 801 13.0 141.408 158.855 141.408 158.855 + rs_pw_transfer_RS2PW_600 1604 10.0 27.225 34.160 99.458 155.855 + mp_waitany 495734 12.0 95.444 145.938 95.444 145.938 + qs_scf_new_mos 800 6.0 0.004 0.006 117.821 118.162 + qs_scf_loop_do_ot 800 7.0 0.006 0.007 117.818 118.158 + potential_pw2rs 802 11.0 0.109 0.125 113.364 113.939 + dbcsr_multiply_generic 19037 10.7 0.980 1.029 110.273 112.146 + ot_scf_mini 800 8.0 0.025 0.030 106.208 106.881 + multiply_cannon 19037 11.7 2.979 3.161 70.811 79.658 + mp_sum_d 31066 11.6 17.380 68.438 17.380 68.438 + rs_distribute_matrix 2406 9.0 1.243 2.100 34.572 54.933 + mp_waitall_1 2305968 13.6 44.793 54.794 44.793 54.794 + mp_alltoall_d11v 12391 12.9 32.902 54.453 32.902 54.453 + pw_scatter_p 10017 14.3 40.905 46.466 40.905 46.466 + rs_pw_transfer_PW2RS_600 805 13.0 24.735 28.075 43.848 46.334 + ot_mini 800 9.0 0.008 0.014 43.907 44.192 + multiply_cannon_multrec 456888 12.7 29.184 40.419 29.256 40.493 + ------------------------------------------------------------------------------- + + The number of warnings for this run is : 3 + + ------------------------------------------------------------------------------- + **** **** ****** ** PROGRAM ENDED AT 2021-07-01 18:20:32.755 + ***** ** *** *** ** PROGRAM RAN ON c53-018 + ** **** ****** PROGRAM RAN BY ybzhuang + ***** ** ** ** ** PROGRAM PROCESS ID 394775 + **** ** ******* ** PROGRAM STOPPED IN /data/ybzhuang/workdirs/CoO100-ml/wor + kdirs/fp/52dbdd53-8307-41df-80be-dc25 + da11e058/task.000.000178 diff --git a/tests/cp2k/cp2k_output b/tests/cp2k/cp2k_output index 0aa678f37..a28c7fa27 100644 --- a/tests/cp2k/cp2k_output +++ b/tests/cp2k/cp2k_output @@ -1197,7 +1197,7 @@ Total energy: -1761.41773472839827 - *** WARNING in qs_scf.F:542 :: SCF run NOT converged *** + *** SCF run converged in 47 steps *** Integrated absolute spin density : 58.8663280160 diff --git a/tests/cp2k/restart_aimd/deepmd/energy.raw b/tests/cp2k/restart_aimd/deepmd/energy.raw index 852484ea9..e97cf5960 100644 --- a/tests/cp2k/restart_aimd/deepmd/energy.raw +++ b/tests/cp2k/restart_aimd/deepmd/energy.raw @@ -1,5 +1,5 @@ --2.196387023925781250e+02 --2.196259307861328125e+02 --2.196165771484375000e+02 --2.196100006103515625e+02 --2.196051788330078125e+02 +-2.196387329101562500e+02 +-2.196259460449218750e+02 +-2.196165924072265625e+02 +-2.196100158691406250e+02 +-2.196051940917968750e+02 diff --git a/tests/cp2k/restart_aimd/deepmd/force.raw b/tests/cp2k/restart_aimd/deepmd/force.raw index 2d03f2c87..d08bd63a2 100644 --- a/tests/cp2k/restart_aimd/deepmd/force.raw +++ b/tests/cp2k/restart_aimd/deepmd/force.raw @@ -1,5 +1,5 @@ --2.169162631034851074e-01 3.279730081558227539e-01 6.035397052764892578e-01 7.185621261596679688e-01 1.594181656837463379e-01 4.608764052391052246e-01 -3.765185177326202393e-01 3.857482671737670898e-01 -1.248831078410148621e-01 -6.494076848030090332e-01 1.203697919845581055e-01 -4.328375160694122314e-01 5.217282772064208984e-01 -9.955028891563415527e-01 -5.069978833198547363e-01 --1.989514529705047607e-01 2.921981513500213623e-01 5.636984109878540039e-01 6.776738762855529785e-01 1.945625692605972290e-01 5.051451325416564941e-01 -4.636886715888977051e-01 3.652833104133605957e-01 -1.360401511192321777e-01 -7.025374770164489746e-01 9.427926689386367798e-02 -3.964312076568603516e-01 6.848884224891662598e-01 -9.483894705772399902e-01 -5.365054011344909668e-01 --1.648406237363815308e-01 2.307343930006027222e-01 4.815881848335266113e-01 5.865107774734497070e-01 2.308490723371505737e-01 5.361675620079040527e-01 -5.500597357749938965e-01 3.308701217174530029e-01 -1.434295028448104858e-01 -7.340555787086486816e-01 5.354630947113037109e-02 -3.259690999984741211e-01 8.598077297210693359e-01 -8.481215834617614746e-01 -5.483376383781433105e-01 --1.165429651737213135e-01 1.469107717275619507e-01 3.615300059318542480e-01 4.501595497131347656e-01 2.673597633838653564e-01 5.535713434219360352e-01 -6.303640604019165039e-01 2.890907227993011475e-01 -1.467755436897277832e-01 -7.438977956771850586e-01 -1.830625406000763178e-04 -2.249499261379241943e-01 1.038020730018615723e+00 -7.053260803222656250e-01 -5.432190895080566406e-01 --5.708466097712516785e-02 4.539745301008224487e-02 2.101059257984161377e-01 2.773819267749786377e-01 3.029201626777648926e-01 5.577098131179809570e-01 -6.990006566047668457e-01 2.466197013854980469e-01 -1.458370834589004517e-01 -7.330569624900817871e-01 -6.438967585563659668e-02 -9.865168482065200806e-02 1.209161996841430664e+00 -5.326966047286987305e-01 -5.230426192283630371e-01 +-2.169162780046463013e-01 3.279730379581451416e-01 6.035397648811340332e-01 7.185621857643127441e-01 1.594181805849075317e-01 4.608764648437500000e-01 -3.765185475349426270e-01 3.857482969760894775e-01 -1.248831152915954590e-01 -6.494077444076538086e-01 1.203698068857192993e-01 -4.328375458717346191e-01 5.217282772064208984e-01 -9.955029487609863281e-01 -5.069979429244995117e-01 +-1.989514678716659546e-01 2.921981811523437500e-01 5.636984705924987793e-01 6.776739358901977539e-01 1.945625841617584229e-01 5.051451921463012695e-01 -4.636887311935424805e-01 3.652833402156829834e-01 -1.360401660203933716e-01 -7.025375366210937500e-01 9.427927434444427490e-02 -3.964312374591827393e-01 6.848884820938110352e-01 -9.483895301818847656e-01 -5.365054607391357422e-01 +-1.648406386375427246e-01 2.307344228029251099e-01 4.815882444381713867e-01 5.865108370780944824e-01 2.308490872383117676e-01 5.361676216125488281e-01 -5.500597953796386719e-01 3.308701515197753906e-01 -1.434295177459716797e-01 -7.340556979179382324e-01 5.354631319642066956e-02 -3.259690999984741211e-01 8.598078489303588867e-01 -8.481216430664062500e-01 -5.483376979827880859e-01 +-1.165429726243019104e-01 1.469107866287231445e-01 3.615300357341766357e-01 4.501595795154571533e-01 2.673597931861877441e-01 5.535714030265808105e-01 -6.303641200065612793e-01 2.890907526016235352e-01 -1.467755436897277832e-01 -7.438978552818298340e-01 -1.830625551519915462e-04 -2.249499410390853882e-01 1.038020730018615723e+00 -7.053261399269104004e-01 -5.432191491127014160e-01 +-5.708466470241546631e-02 4.539745673537254333e-02 2.101059406995773315e-01 2.773819565773010254e-01 3.029201924800872803e-01 5.577098727226257324e-01 -6.990007162094116211e-01 2.466197162866592407e-01 -1.458370983600616455e-01 -7.330570816993713379e-01 -6.438968330621719360e-02 -9.865169227123260498e-02 1.209162116050720215e+00 -5.326966047286987305e-01 -5.230426192283630371e-01 diff --git a/tests/poscars/conf_s_su.dump b/tests/poscars/conf_s_su.dump new file mode 100644 index 000000000..8cc97b775 --- /dev/null +++ b/tests/poscars/conf_s_su.dump @@ -0,0 +1,22 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS xy xz yz pp pp pp +0.0 5.0739861 1.2621856 +0.0 2.7916155 1.2874292 +0.0 2.2254033 0.7485898 +ITEM: ATOMS id type xs ys zs +1 1 0.0 0.0 0.0 +2 2 0.2472745002 0.2527254533 0.2477701458 +ITEM: TIMESTEP +1 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS xy xz yz pp pp pp +0.0 5.0739861 1.2621856 +0.0 2.7916155 1.2874292 +0.0 2.2254033 0.7485898 +ITEM: ATOMS id type xsu ysu zsu +1 1 0.0 0.0 0.0 +2 2 1.2472745002 1.2527254533 1.2477701458 diff --git a/tests/poscars/conf_unfold.dump b/tests/poscars/conf_unfold.dump new file mode 100644 index 000000000..3d46a9f44 --- /dev/null +++ b/tests/poscars/conf_unfold.dump @@ -0,0 +1,22 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS xy xz yz pp pp pp +0.0 5.0739861 1.2621856 +0.0 2.7916155 1.2874292 +0.0 2.2254033 0.7485898 +ITEM: ATOMS id type xu yu zu +1 1 5.073986099999999944e+00 2.791615499999999805e+00 2.225403299999999973e+00 +2 2 6.336171700000000406e+00 3.493418300000000087e+00 2.776791800099999818e+00 +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +2 +ITEM: BOX BOUNDS xy xz yz pp pp pp +0.0 5.0739861 1.2621856 +0.0 2.7916155 1.2874292 +1.0 3.2254033 0.7485898 +ITEM: ATOMS id type xu yu zu +1 1 5.073986099999999944e+00 2.791615499999999805e+00 3.225403299999999973e+00 +2 2 6.336171700000000406e+00 3.493418300000000087e+00 3.776791800099999818e+00 diff --git a/tests/poscars/test_lammps_dump_s_su.py b/tests/poscars/test_lammps_dump_s_su.py new file mode 100644 index 000000000..2370cffc4 --- /dev/null +++ b/tests/poscars/test_lammps_dump_s_su.py @@ -0,0 +1,26 @@ +import os +import numpy as np +import unittest +from context import dpdata +from poscars.poscar_ref_oh import TestPOSCARoh + +class TestDump(unittest.TestCase, TestPOSCARoh): + + def setUp(self): + self.system = dpdata.System(os.path.join('poscars', 'conf_s_su.dump'), + type_map = ['O', 'H']) + +class TestDump2(unittest.TestCase, TestPOSCARoh): + + def setUp(self): + self.tmp_system = dpdata.System(os.path.join('poscars', 'conf_s_su.dump'), + type_map = ['O', 'H']) + self.system = self.tmp_system.sub_system([1]) + + def test_nframes (self) : + self.assertEqual(self.tmp_system.get_nframes(), 2) + + +if __name__ == '__main__': + unittest.main() + diff --git a/tests/pymatgen/FA-001.vasp b/tests/pymatgen/FA-001.vasp new file mode 100644 index 000000000..1b267adf9 --- /dev/null +++ b/tests/pymatgen/FA-001.vasp @@ -0,0 +1,16 @@ +C1 H5 N2 +1.0 +2.2504659203492643e+01 0.0000000000000000e+00 0.0000000000000000e+00 +0.0000000000000000e+00 2.2504659203492643e+01 0.0000000000000000e+00 +0.0000000000000000e+00 0.0000000000000000e+00 2.2504659203492643e+01 +C H N +1 5 2 +Cartesian + 11.2523296017 11.9178548890 11.2108422059 + 11.2523296017 11.4836546020 13.4873419539 + 11.2523296017 9.9657546120 12.5961418889 + 11.2523296017 11.5757547460 9.0233422059 + 11.2523296017 9.9209545690 10.0419421929 + 11.2523296017 13.0578542790 11.2108422059 + 11.2523296017 11.0671545110 12.4584418079 + 11.2523296017 11.0296546060 9.9897423529 diff --git a/tests/pymatgen/FA-001.xyz b/tests/pymatgen/FA-001.xyz new file mode 100644 index 000000000..ae5b55695 --- /dev/null +++ b/tests/pymatgen/FA-001.xyz @@ -0,0 +1,10 @@ +8 +Lattice="10 0.0 0.0 0.0 10 0.0 0.0 0.0 10" Properties=species:S:1:pos:R:3:Z:I:1 +C 3.1742845125747904e-16 5.342900276 5.184000015 6 +H 4.568238577398768e-16 4.908699989 7.460499763 1 +N 3.938218942178196e-16 4.492199898 6.431599617 7 +H 4.022535923897687e-16 3.390799999 6.569299698 1 +H 1.834827076007373e-16 5.000800133 2.996500015 1 +N 2.4265764993669136e-16 4.454699993 3.962900162 7 +H 2.4585396828529157e-16 3.345999956 4.015100002 1 +H 3.1742845125747904e-16 6.482899666 5.184000015 1 diff --git a/tests/pymatgen/mol2-new.vasp b/tests/pymatgen/mol2-new.vasp new file mode 100644 index 000000000..22db2fa9a --- /dev/null +++ b/tests/pymatgen/mol2-new.vasp @@ -0,0 +1,16 @@ +H5 C1 N2 +1.0 +10.000000 0.000000 0.000000 +0.000000 10.000000 0.000000 +0.000000 0.000000 10.000000 +H C N +5 1 2 +direct +0.577383 0.631337 0.500367 H +0.440363 0.395639 0.623009 H +0.523296 0.528867 0.297597 H +0.521491 0.528803 0.702604 H +0.441477 0.395690 0.376400 H +0.521985 0.537275 0.500106 C +0.490941 0.484747 0.383775 N +0.489919 0.484705 0.616136 N diff --git a/tests/pymatgen/mol2.vasp b/tests/pymatgen/mol2.vasp new file mode 100644 index 000000000..ea4ec2baf --- /dev/null +++ b/tests/pymatgen/mol2.vasp @@ -0,0 +1,16 @@ +hexagonal-PbI3 + 1.00000000000000 + 8.4261398403369476 -0.0207094818066008 -0.0031014314051307 + -4.2326852079273163 7.4079517949230027 0.0021007606821090 + -0.0033015270376727 0.0018001191064931 7.9750946862221301 + N C H + 2 1 5 +Direct + 0.3230984076298932 0.6454769144393403 0.1041651474646342 + 0.3220267174078323 0.6453279258574751 0.3955245499807875 + 0.3958479883967422 0.7164380537464232 0.2500334235810864 + 0.5257412318253072 0.8435919770693032 0.2503606409552951 + 0.2024793011832460 0.5249247262853158 0.4041424751787161 + 0.3915235842243226 0.7051542887367509 -0.0038936922276933 0.9961063077723067 + 0.3896311952726235 0.7049043576463694 0.5039461714481914 + 0.2036571496859804 0.5250922648687301 0.0949178563751044 diff --git a/tests/test_abacus_md.py b/tests/test_abacus_md.py new file mode 100644 index 000000000..1ce7cf8d0 --- /dev/null +++ b/tests/test_abacus_md.py @@ -0,0 +1,86 @@ +import os +import numpy as np +import unittest +from context import dpdata +from dpdata.unit import LengthConversion + +bohr2ang = LengthConversion("bohr", "angstrom").value() + +class TestABACUSMD: + + def test_atom_names(self) : + self.assertEqual(self.system_Si.data['atom_names'], ['Si']) + #self.assertEqual(self.system_h2o.data['atom_names'], ['O','H']) + + def test_atom_numbs(self) : + self.assertEqual(self.system_Si.data['atom_numbs'], [2]) + #self.assertEqual(self.system_h2o.data['atom_numbs'], [64,128]) + + def test_atom_types(self) : + ref_type = [0, 0] + ref_type = np.array(ref_type) + for ii in range(ref_type.shape[0]) : + self.assertEqual(self.system_Si.data['atom_types'][ii], ref_type[ii]) + + def test_cell(self) : + cell = bohr2ang * 10.2 * np.array([[0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]]) + for idx in range(np.shape(self.system_Si.data['cells'])[0]): + for ii in range(cell.shape[0]) : + for jj in range(cell.shape[1]) : + self.assertAlmostEqual(self.system_Si.data['cells'][idx][ii][jj], cell[ii][jj]) + + def test_coord(self) : + fp = open('abacus.md/Si_coord') + coord = [] + for ii in fp : + coord.append([float(jj) for jj in ii.split()]) + coord = np.array(coord) + coord = coord.reshape([5, 2, 3]) + for ii in range(coord.shape[0]) : + for jj in range(coord.shape[1]) : + for kk in range(coord.shape[2]): + self.assertAlmostEqual(self.system_Si.data['coords'][ii][jj][kk], coord[ii][jj][kk]) + fp.close() + + def test_force(self) : + fp = open('abacus.md/Si_force') + force = [] + for ii in fp : + force.append([float(jj) for jj in ii.split()]) + force = np.array(force) + force = force.reshape([5, 2, 3]) + for ii in range(force.shape[0]) : + for jj in range(force.shape[1]) : + for kk in range(force.shape[2]): + self.assertAlmostEqual(self.system_Si.data['forces'][ii][jj][kk], force[ii][jj][kk]) + fp.close() + + def test_virial(self) : + fp = open('abacus.md/Si_virial') + virial = [] + for ii in fp : + virial.append([float(jj) for jj in ii.split()]) + virial = np.array(virial) + virial = virial.reshape([5, 3, 3]) + for ii in range(virial.shape[0]) : + for jj in range(virial.shape[1]) : + for kk in range(virial.shape[2]) : + self.assertAlmostEqual(self.system_Si.data['virials'][ii][jj][kk], virial[ii][jj][kk]) + fp.close() + + def test_energy(self) : + ref_energy = np.array([-211.77183266, -211.7739761 , -211.77713677, -211.78079673, + -211.78511428]) + for ii in range(5): + self.assertAlmostEqual(self.system_Si.data['energies'][ii], ref_energy[ii]) + + +class TestABACUSMDLabeledOutput(unittest.TestCase, TestABACUSMD): + + def setUp(self): + self.system_Si = dpdata.LabeledSystem('abacus.md',fmt='abacus/md') + # self.system_h2o = dpdata.LabeledSystem('qe.scf/02.out',fmt='qe/pw/scf') + + +if __name__ == '__main__': + unittest.main() \ No newline at end of file diff --git a/tests/test_abacus_pw_scf.py b/tests/test_abacus_pw_scf.py index 8c1dfd29b..3813943f2 100644 --- a/tests/test_abacus_pw_scf.py +++ b/tests/test_abacus_pw_scf.py @@ -2,6 +2,9 @@ import numpy as np import unittest from context import dpdata +from dpdata.unit import LengthConversion + +bohr2ang = LengthConversion("bohr", "angstrom").value() class TestABACUSSinglePointEnergy: @@ -25,7 +28,8 @@ def test_atom_types(self) : # self.assertEqual(self.system_h2o.data['atom_types'][ii], ref_type[ii]) def test_cell(self) : - cell = 5.29177 * np.eye(3) + # cell = 5.29177 * np.eye(3) + cell = bohr2ang * 10 * np.eye(3) for ii in range(cell.shape[0]) : for jj in range(cell.shape[1]) : self.assertAlmostEqual(self.system_ch4.data['cells'][0][ii][jj], cell[ii][jj]) @@ -49,7 +53,7 @@ def test_coord(self) : coord = np.array(coord) for ii in range(coord.shape[0]) : for jj in range(coord.shape[1]) : - self.assertAlmostEqual(self.system_ch4.data['coords'][0][ii][jj], coord[ii][jj]) + self.assertAlmostEqual(self.system_ch4.data['coords'][0][ii][jj], coord[ii][jj], places=5) fp.close() # fp = open('qe.scf/h2o_coord') diff --git a/tests/test_amber_sqm.py b/tests/test_amber_sqm.py index 48342c4cc..dc98a3167 100644 --- a/tests/test_amber_sqm.py +++ b/tests/test_amber_sqm.py @@ -2,20 +2,50 @@ import unittest import shutil from context import dpdata -from comp_sys import CompSys, IsNoPBC +from comp_sys import CompSys, CompLabeledSys, IsNoPBC class TestAmberSqmOut(unittest.TestCase, CompSys, IsNoPBC): def setUp (self) : - self.system_1 = dpdata.System('amber/sqm.out', fmt = 'sqm/out') - self.system_1.to('deepmd/npy','tmp.deepmd.npy') - self.system_2 = dpdata.System('tmp.deepmd.npy', fmt = 'deepmd/npy') + self.system_1 = dpdata.System('amber/sqm_no_forces.out', fmt = 'sqm/out') + self.system_1.to('deepmd/npy','tmp.sqm.noforces') + self.system_2 = dpdata.System('tmp.sqm.noforces', fmt = 'deepmd/npy') self.places = 5 self.e_places = 4 self.f_places = 6 self.v_places = 6 def tearDown(self) : - if os.path.exists('tmp.deepmd.npy'): - shutil.rmtree('tmp.deepmd.npy') + if os.path.exists('tmp.sqm.noforces'): + shutil.rmtree('tmp.sqm.noforces') + +class TestAmberSqmOutLabeled(unittest.TestCase, CompLabeledSys, IsNoPBC): + def setUp(self) : + self.system_1 = dpdata.LabeledSystem('amber/sqm_forces.out', fmt = 'sqm/out') + self.system_1.to('deepmd/npy','tmp.sqm.forces') + self.system_2 = dpdata.LabeledSystem('tmp.sqm.forces', fmt = 'deepmd/npy') + self.places = 5 + self.e_places = 4 + self.f_places = 6 + self.v_places = 6 + + def tearDown(self) : + if os.path.exists('tmp.sqm.forces'): + shutil.rmtree('tmp.sqm.forces') + +class TestAmberSqmIn(unittest.TestCase): + def setUp(self): + self.system = dpdata.BondOrderSystem("amber/methane.mol", fmt='mol', type_map=['H','C']) + with open('amber/sqm.in', 'r') as f: + self.sqm_in = f.read() + + def test_sqm_in(self): + self.system.to("sqm/in", 'amber/sqm_test.in') + with open('amber/sqm_test.in', 'r') as f: + self.sqm_in_test = f.read() + self.assertEqual(self.sqm_in, self.sqm_in_test) + + def tearDown(self): + if os.path.isfile("amber/sqm_test.in"): + os.remove("amber/sqm_test.in") diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py new file mode 100644 index 000000000..43ecaa023 --- /dev/null +++ b/tests/test_ase_traj.py @@ -0,0 +1,32 @@ +import os +import numpy as np +import unittest +from context import dpdata +from comp_sys import CompLabeledSys, IsPBC + +class TestASEtraj1(unittest.TestCase, CompLabeledSys, IsPBC): + def setUp (self) : + self.multi_systems = dpdata.MultiSystems.from_file('ase/HeAlO.traj', fmt='ase/structure') + self.system_1 = self.multi_systems.systems['Al0He4O0'] + self.system_2 = dpdata.LabeledSystem('ase/Al0He4O0', fmt='deepmd') + self.places = 6 + self.e_places = 6 + self.f_places = 6 + self.v_places = 4 + +class TestASEtraj1(unittest.TestCase, CompLabeledSys, IsPBC): + def setUp (self) : + self.system_temp0 = dpdata.MultiSystems.from_file(file_name='ase/HeAlO.traj', fmt='ase/structure') + self.system_1 = self.system_temp0.systems['Al2He1O3'] # .sort_atom_types() + self.system_temp1 = dpdata.LabeledSystem('ase/Al2He1O3', fmt='deepmd') + self.system_temp2 = dpdata.LabeledSystem('ase/Al4He4O6', fmt='deepmd') + self.system_temp3 = dpdata.MultiSystems(self.system_temp2, self.system_temp1) + self.system_2 = self.system_temp3.systems['Al2He1O3'] + self.places = 6 + self.e_places = 6 + self.f_places = 6 + self.v_places = 4 + + +if __name__ == '__main__': + unittest.main() diff --git a/tests/test_bond_order_system.py b/tests/test_bond_order_system.py index c0c97a9a1..06928cde2 100644 --- a/tests/test_bond_order_system.py +++ b/tests/test_bond_order_system.py @@ -6,6 +6,7 @@ from rdkit.Chem import AllChem import shutil import numpy as np +from copy import deepcopy class TestBondOrderSystem(unittest.TestCase): @@ -78,6 +79,16 @@ def test_dump_to_deepmd_npy(self): self.assertEqual(syst['bonds'][bond_idx][ii], bonds[bond_idx][ii]) shutil.rmtree("bond_order/methane") + def test_dump_to_sdf_file(self): + s1 = dpdata.BondOrderSystem("bond_order/methane.sdf", fmt="sdf") + s2 = deepcopy(s1) + s2.data["coords"] += 1.0 + s2.to_sdf_file("bond_order/test.sdf") + + nsyst = dpdata.BondOrderSystem("bond_order/test.sdf", fmt="sdf") + self.assertEqual(nsyst["coords"][0, 0, 0] - s1["coords"][0, 0, 0], 1.0) + os.remove("bond_order/test.sdf") + def test_sanitize_mol_obabel(self): cnt = 0 for sdf_file in glob.glob("bond_order/refined-set-ligands/obabel/*sdf"): diff --git a/tests/test_cp2k_output.py b/tests/test_cp2k_output.py index 2ed548c12..30dae7885 100644 --- a/tests/test_cp2k_output.py +++ b/tests/test_cp2k_output.py @@ -16,14 +16,14 @@ 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]) + self.assertAlmostEqual(self.system.data['cells'][0][ii][jj], cell[ii][jj]) 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]) + self.assertAlmostEqual(self.system.data['coords'][0][ii][jj], coord[ii][jj]) def test_force(self): #eV = 2.72113838565563E+01 @@ -31,18 +31,18 @@ def test_force(self): 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]) + self.assertAlmostEqual(self.system.data['forces'][0][ii][jj], force[ii][jj], places=6) def test_energy(self): #eV = 2.72113838565563E+01 - ref_energy = -48061.44424374075 + ref_energy = -48061.44846401638 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]) + self.assertAlmostEqual(self.system.data['virials'][0][ii][jj], virial[ii][jj], places=6) @@ -52,6 +52,30 @@ class TestCP2KLabeledOutput(unittest.TestCase, TestCP2KSinglePointEnergy): def setUp(self): self.system = dpdata.LabeledSystem('cp2k/cp2k_output', fmt = 'cp2k/output') +class TestNonCoveragedCP2KOutput: + def setUp (self) : + self.system = dpdata.LabeledSystem('cp2k/cp2k_nocon_output', + fmt = 'cp2k/output') + + def test_atom_types(self) : + self.assertEqual(self.system.data['atom_types'], []) + + def test_cells(self) : + self.assertEqual(self.system.data['cells'], []) + + def test_coords(self) : + self.assertEqual(self.system.data['coords'], []) + + def test_energies(self) : + self.assertEqual(self.system.data['energies'], []) + + def test_forces(self) : + self.assertEqual(self.system.data['forces'], []) + + def test_virials(self) : + self.assertFalse('virials' in self.system.data) + + if __name__ == '__main__': unittest.main() diff --git a/tests/test_deepmd_hdf5.py b/tests/test_deepmd_hdf5.py new file mode 100644 index 000000000..3c15b45e8 --- /dev/null +++ b/tests/test_deepmd_hdf5.py @@ -0,0 +1,45 @@ +import os +import numpy as np +import unittest +from context import dpdata +from comp_sys import CompLabeledSys, CompSys, IsPBC + +class TestDeepmdLoadDumpComp(unittest.TestCase, CompLabeledSys, IsPBC): + def setUp (self) : + self.system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md', + fmt = 'vasp/outcar') + self.system_1.to_deepmd_hdf5('tmp.deepmd.hdf5', + prec = np.float64, + set_size = 2) + + self.system_2 = dpdata.LabeledSystem('tmp.deepmd.hdf5', + fmt = 'deepmd/hdf5', + type_map = ['O', 'H']) + self.places = 6 + self.e_places = 6 + self.f_places = 6 + self.v_places = 6 + + def tearDown(self) : + if os.path.exists('tmp.deepmd.hdf5'): + os.remove('tmp.deepmd.hdf5') + + +class TestDeepmdCompNoLabels(unittest.TestCase, CompSys, IsPBC) : + def setUp (self) : + self.system_1 = dpdata.System('poscars/POSCAR.h2o.md', + fmt = 'vasp/poscar') + self.system_1.to_deepmd_hdf5('tmp.deepmd.hdf5', + prec = np.float64, + set_size = 2) + self.system_2 = dpdata.System('tmp.deepmd.hdf5', + fmt = 'deepmd/hdf5', + type_map = ['O', 'H']) + self.places = 6 + self.e_places = 6 + self.f_places = 6 + self.v_places = 6 + + def tearDown(self) : + if os.path.exists('tmp.deepmd.hdf5'): + os.remove('tmp.deepmd.hdf5') diff --git a/tests/test_lammps_dump_unfold.py b/tests/test_lammps_dump_unfold.py new file mode 100644 index 000000000..4ffd5f730 --- /dev/null +++ b/tests/test_lammps_dump_unfold.py @@ -0,0 +1,26 @@ +import os +import numpy as np +import unittest +from context import dpdata +from poscars.poscar_ref_oh import TestPOSCARoh + +class TestDump(unittest.TestCase, TestPOSCARoh): + + def setUp(self): + self.system = dpdata.System(os.path.join('poscars', 'conf_unfold.dump'), + type_map = ['O', 'H']) + +class TestDump2(unittest.TestCase, TestPOSCARoh): + + def setUp(self): + self.tmp_system = dpdata.System(os.path.join('poscars', 'conf_unfold.dump'), + type_map = ['O', 'H']) + self.system = self.tmp_system.sub_system([1]) + + def test_nframes (self) : + self.assertEqual(self.tmp_system.get_nframes(), 2) + + +if __name__ == '__main__': + unittest.main() + diff --git a/tests/test_multisystems.py b/tests/test_multisystems.py index df8d318b6..6e05861b3 100644 --- a/tests/test_multisystems.py +++ b/tests/test_multisystems.py @@ -30,6 +30,15 @@ def setUp(self): self.system_sizes = {'C1H4':2, 'C1H3':1} self.atom_names = ['C', 'H'] + def test_len(self): + self.assertEqual(len(self.systems), 2) + + def test_get_nframes(self): + self.assertEqual(self.systems.get_nframes(), 3) + + def test_str(self): + self.assertEqual(str(self.systems), "MultiSystems (2 systems containing 3 frames)") + class TestMultiSystemsAdd(unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC): def setUp(self): @@ -117,5 +126,18 @@ def test_type_map(self): self.assertEqual(type_map, systems.atom_names) +class TestMultiSystemsTo(unittest.TestCase, MultiSystems): + def setUp(self): + # CH4 and O2 + system_1 = dpdata.LabeledSystem('gaussian/methane.gaussianlog', fmt='gaussian/log') + system_2 = dpdata.LabeledSystem('gaussian/oxygen.gaussianlog', fmt='gaussian/log') + systems1 = dpdata.MultiSystems(system_1, system_2) + systems1.to_deepmd_npy("tmp.multi.to") + self.systems = dpdata.MultiSystems().from_deepmd_npy("tmp.multi.to") + + self.system_names = ['C1H4O0', 'C0H0O2'] + self.system_sizes = {'C1H4O0':1, 'C0H0O2':1} + self.atom_names = ['C', 'H', 'O'] + if __name__ == '__main__': unittest.main() diff --git a/tests/test_pymatgen_molecule.py b/tests/test_pymatgen_molecule.py new file mode 100644 index 000000000..4a1eb0291 --- /dev/null +++ b/tests/test_pymatgen_molecule.py @@ -0,0 +1,31 @@ +import os +import numpy as np +import unittest +from context import dpdata + +class TestPOSCARCart(unittest.TestCase): + + def setUp(self): + self.system = dpdata.System() + self.system.from_pymatgen_molecule(os.path.join('pymatgen', 'FA-001.xyz')) + self.assertEqual(list(self.system["atom_types"]), [0, 1, 2, 1, 1, 2, 1, 1]) + + def test_poscar_to_molecule(self): + tmp_system = dpdata.System() + tmp_system.from_vasp_poscar(os.path.join('pymatgen', 'mol2.vasp')) + natoms = len(tmp_system['coords'][0]) + tmpcoord = tmp_system['coords'][0] + cog = np.average(tmpcoord, axis = 0) + dist = tmpcoord - np.tile(cog, [natoms, 1]) + max_dist_0 = np.max(np.linalg.norm(dist, axis = 1)) + + mols = tmp_system.to("pymatgen/molecule") + cog = np.average(mols[-1].cart_coords, axis = 0) + dist = mols[-1].cart_coords - np.tile(cog, [natoms, 1]) + max_dist_1 = np.max(np.linalg.norm(dist, axis = 1)) + self.assertAlmostEqual(max_dist_0, max_dist_1) + + + +if __name__ == '__main__': + unittest.main() diff --git a/tests/test_qe_cp_traj.py b/tests/test_qe_cp_traj.py index b98a47a4f..cad93fa6c 100644 --- a/tests/test_qe_cp_traj.py +++ b/tests/test_qe_cp_traj.py @@ -3,6 +3,7 @@ import unittest from context import dpdata +bohr2ang = dpdata.unit.LengthConversion("bohr", "angstrom").value() class TestCPTRAJProps : def test_atom_names(self) : @@ -18,7 +19,7 @@ def test_atom_types(self) : self.assertEqual(self.system.data['atom_types'][ii], 1) def test_cell(self) : - ref = 0.52917721067 * 23.5170 * np.eye(3) + ref = bohr2ang * 23.5170 * np.eye(3) self.assertEqual(self.system.get_nframes(), 2) for ff in range(self.system.get_nframes()) : for ii in range(3) : @@ -32,7 +33,6 @@ def test_coord(self) : coords = [] for ii in lines : coords.append([float(jj) for jj in ii.split()]) - bohr2ang = 0.52917721067 coords = bohr2ang * np.array(coords) celll = bohr2ang * 23.5170 for ii in range(coords.shape[0]) : diff --git a/tests/test_qe_cp_traj_skipload.py b/tests/test_qe_cp_traj_skipload.py index c87baa314..b0d92e9d0 100644 --- a/tests/test_qe_cp_traj_skipload.py +++ b/tests/test_qe_cp_traj_skipload.py @@ -6,6 +6,8 @@ from comp_sys import CompLabeledSys from comp_sys import IsPBC +bohr2ang = dpdata.unit.LengthConversion("bohr", "angstrom").value() + class TestPWSCFTrajSkip(unittest.TestCase, CompSys, IsPBC): def setUp(self): self.system_1 = dpdata.System(os.path.join('qe.traj', 'traj6'), @@ -42,7 +44,7 @@ def test_cell(self): ref_cell = [5.359985500701728967e+00, 0, 0, 3.585941820098031974e-01, 5.317218997480877896e+00, 0, 7.606780476053129902e-01, 7.811107228901693622e-01, 5.715864930517207121e+00 ] - ref_cell = 0.52917721067 * np.array(ref_cell).reshape(3,3) + ref_cell = bohr2ang * np.array(ref_cell).reshape(3,3) for ii in range(3) : for jj in range(3) : @@ -51,7 +53,7 @@ def test_cell(self): ref_cell = [5.308510801020571712e+00, 0, 0, 3.076052782312116429e-01, 5.279388982187173340e+00, 0, 4.321921336152507731e-01, 8.121110815096156399e-01, 5.301664983741235737e+00] - ref_cell = 0.52917721067 * np.array(ref_cell).reshape(3,3) + ref_cell = bohr2ang * np.array(ref_cell).reshape(3,3) for ii in range(3) : for jj in range(3) :