From 63f2888c605c860dd67a16ef70baf9d9721dd9ae Mon Sep 17 00:00:00 2001 From: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com> Date: Fri, 8 Sep 2023 04:56:42 +0200 Subject: [PATCH 01/18] Update README.md for recommendation of using cp2kdata (#537) --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1e86a719..67942ac8 100644 --- a/README.md +++ b/README.md @@ -74,8 +74,10 @@ The `System` or `LabeledSystem` can be constructed from the following file forma | gaussian| log | True | True | LabeledSystem | 'gaussian/md' | | siesta | output | False | True | LabeledSystem | 'siesta/output'| | siesta | aimd_output | True | True | LabeledSystem | 'siesta/aimd_output' | -| cp2k | output | False | True | LabeledSystem | 'cp2k/output' | -| cp2k | aimd_output | True | True | LabeledSystem | 'cp2k/aimd_output' | +| cp2k(deprecated in future) | output | False | True | LabeledSystem | 'cp2k/output' | +| cp2k(deprecated in future) | aimd_output | True | True | LabeledSystem | 'cp2k/aimd_output' | +| cp2k([plug-in](https://github.com/robinzyb/cp2kdata#plug-in-for-dpdata)) | stdout | False | True | LabeledSystem | 'cp2kdata/e_f' | +| cp2k([plug-in](https://github.com/robinzyb/cp2kdata#plug-in-for-dpdata)) | stdout | True | True | LabeledSystem | 'cp2kdata/md' | | QE | log | False | True | LabeledSystem | 'qe/pw/scf' | | QE | log | True | False | System | 'qe/cp/traj' | | QE | log | True | True | LabeledSystem | 'qe/cp/traj' | From b45911a90dfee8f507233294fc5f01e6363162c0 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 13 Sep 2023 09:44:49 +0800 Subject: [PATCH 02/18] [pre-commit.ci] pre-commit autoupdate (#539) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 23.7.0 → 23.9.1](https://github.com/psf/black/compare/23.7.0...23.9.1) - [github.com/astral-sh/ruff-pre-commit: v0.0.287 → v0.0.288](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.287...v0.0.288) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index abaa911e..27d6423a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,12 +18,12 @@ repos: - id: check-toml # Python - repo: https://github.com/psf/black - rev: 23.7.0 + rev: 23.9.1 hooks: - id: black-jupyter - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.0.287 + rev: v0.0.288 hooks: - id: ruff args: ["--fix"] From 037c2b8cc5b37890047ac0f8f6012a664e01af17 Mon Sep 17 00:00:00 2001 From: Duo <50307526+iProzd@users.noreply.github.com> Date: Fri, 15 Sep 2023 11:21:06 +0800 Subject: [PATCH 03/18] support assigning 'type_map' for mixed_type (#540) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- dpdata/deepmd/mixed.py | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/dpdata/deepmd/mixed.py b/dpdata/deepmd/mixed.py index e8abce21..0d0ad89d 100644 --- a/dpdata/deepmd/mixed.py +++ b/dpdata/deepmd/mixed.py @@ -46,6 +46,17 @@ def _load_set(folder, nopbc: bool): def to_system_data(folder, type_map=None, labels=True): # data is empty data = load_type(folder) + old_type_map = data["atom_names"].copy() + if type_map is not None: + assert isinstance(type_map, list) + missing_type = [i for i in old_type_map if i not in type_map] + assert ( + not missing_type + ), f"These types are missing in selected type_map: {missing_type} !" + index_map = np.array([type_map.index(i) for i in old_type_map]) + data["atom_names"] = type_map.copy() + else: + index_map = None data["orig"] = np.zeros([3]) if os.path.isfile(os.path.join(folder, "nopbc")): data["nopbc"] = True @@ -63,7 +74,12 @@ def to_system_data(folder, type_map=None, labels=True): nframes = np.reshape(cells, [-1, 3, 3]).shape[0] all_cells.append(np.reshape(cells, [nframes, 3, 3])) all_coords.append(np.reshape(coords, [nframes, -1, 3])) - all_real_atom_types.append(np.reshape(real_atom_types, [nframes, -1])) + if index_map is None: + all_real_atom_types.append(np.reshape(real_atom_types, [nframes, -1])) + else: + all_real_atom_types.append( + np.reshape(index_map[real_atom_types], [nframes, -1]) + ) if eners is not None: eners = np.reshape(eners, [nframes]) if labels: From 9b21f6f07d5ad207c33d6b41d9eadb1f9fe8941d Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Sun, 17 Sep 2023 20:54:15 -0400 Subject: [PATCH 04/18] replace the old data type with the same name and throw warning (#541) When a data type is unexpectedly registered twice, the behavior of some methods will be strange (for example, `append`). For this reason, the old one is replaced, and a warning is thrown. --------- Signed-off-by: Jinzhe Zeng Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- dpdata/system.py | 12 +++++++++++- tests/test_custom_data_type.py | 9 +++++++++ 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/dpdata/system.py b/dpdata/system.py index 8af8e4a5..0748db28 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -1,6 +1,7 @@ # %% import glob import os +import warnings from copy import deepcopy from typing import Any, Dict, Optional, Tuple, Union @@ -963,7 +964,16 @@ def register_data_type(cls, *data_type: Tuple[DataType]): *data_type : tuple[DataType] data type to be regiestered """ - cls.DTYPES = cls.DTYPES + tuple(data_type) + all_dtypes = cls.DTYPES + tuple(data_type) + dtypes_dict = {} + for dt in all_dtypes: + if dt.name in dtypes_dict: + warnings.warn( + f"Data type {dt.name} is registered twice; only the newly registered one will be used.", + UserWarning, + ) + dtypes_dict[dt.name] = dt + cls.DTYPES = tuple(dtypes_dict.values()) def get_cell_perturb_matrix(cell_pert_fraction): diff --git a/tests/test_custom_data_type.py b/tests/test_custom_data_type.py index 5a0e2bab..006d6b01 100644 --- a/tests/test_custom_data_type.py +++ b/tests/test_custom_data_type.py @@ -4,6 +4,7 @@ import numpy as np import dpdata +from dpdata.data_type import Axis, DataType class TestDeepmdLoadDumpComp(unittest.TestCase): @@ -44,6 +45,14 @@ def test_from_deepmd_hdf5(self): x = dpdata.LabeledSystem("data_foo.h5", fmt="deepmd/hdf5") np.testing.assert_allclose(x.data["foo"], self.foo) + def test_duplicated_data_type(self): + dt = DataType("foo", np.ndarray, (Axis.NFRAMES, 2, 4), required=False) + n_dtypes_old = len(dpdata.LabeledSystem.DTYPES) + with self.assertWarns(UserWarning): + dpdata.LabeledSystem.register_data_type(dt) + n_dtypes_new = len(dpdata.LabeledSystem.DTYPES) + self.assertEqual(n_dtypes_old, n_dtypes_new) + class TestDeepmdLoadDumpCompAny(unittest.TestCase): def setUp(self): From 88696bf288d24b0d2717fa72270895007b3713b1 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 20 Sep 2023 10:44:17 +0800 Subject: [PATCH 05/18] [pre-commit.ci] pre-commit autoupdate (#542) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.288 → v0.0.290](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.288...v0.0.290) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 27d6423a..6079b6f5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: - id: black-jupyter - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.0.288 + rev: v0.0.290 hooks: - id: ruff args: ["--fix"] From 93b3addfafb86c811ee09876e0e3751ea3dd4e84 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 27 Sep 2023 09:22:59 +0800 Subject: [PATCH 06/18] [pre-commit.ci] pre-commit autoupdate (#545) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.290 → v0.0.291](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.290...v0.0.291) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6079b6f5..13a96475 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: - id: black-jupyter - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.0.290 + rev: v0.0.291 hooks: - id: ruff args: ["--fix"] From 8c653bab5e84de63a26e48e951c1173d1e114fc2 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 5 Oct 2023 19:07:28 +0800 Subject: [PATCH 07/18] [pre-commit.ci] pre-commit autoupdate (#547) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.291 → v0.0.292](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.291...v0.0.292) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 13a96475..f78930ef 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: - id: black-jupyter - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.0.291 + rev: v0.0.292 hooks: - id: ruff args: ["--fix"] From ee7094208fb0a053857820264c21d61742c7baf7 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 10 Oct 2023 20:30:18 +0800 Subject: [PATCH 08/18] [pre-commit.ci] pre-commit autoupdate (#548) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f78930ef..c461a1e8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ # See https://pre-commit.com/hooks.html for more hooks repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 + rev: v4.5.0 hooks: # there are many log files in tests # TODO: seperate py files and log files From 57c50046ef00dcd805881c2ef731f2aeba751175 Mon Sep 17 00:00:00 2001 From: Peng Xingliang <91927439+pxlxingliang@users.noreply.github.com> Date: Wed, 11 Oct 2023 09:30:24 +0800 Subject: [PATCH 09/18] fix(abacus): fix bug to read the data when relax job not set cal_stress (#549) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- dpdata/abacus/relax.py | 14 +- .../running_cell-relax.log.nostress | 1397 +++++++++++++++++ tests/abacus.relax/STRU.Si | 24 + tests/test_abacus_relax.py | 28 + 4 files changed, 1458 insertions(+), 5 deletions(-) create mode 100644 tests/abacus.relax/OUT.abacus/running_cell-relax.log.nostress create mode 100644 tests/abacus.relax/STRU.Si diff --git a/dpdata/abacus/relax.py b/dpdata/abacus/relax.py index db910fc7..b9cb9905 100644 --- a/dpdata/abacus/relax.py +++ b/dpdata/abacus/relax.py @@ -158,10 +158,13 @@ def get_coords_from_log(loglines, natoms): cells *= bohr2ang coords *= bohr2ang - virial = np.zeros([len(cells), 3, 3]) - for i in range(len(cells)): - volume = np.linalg.det(cells[i, :, :].reshape([3, 3])) - virial[i] = stress[i] * kbar2evperang3 * volume + if len(stress) > 0: + virial = np.zeros([len(cells), 3, 3]) + for i in range(len(cells)): + volume = np.linalg.det(cells[i, :, :].reshape([3, 3])) + virial[i] = stress[i] * kbar2evperang3 * volume + else: + virial = None return energy, cells, coords, force, stress, virial @@ -203,7 +206,8 @@ def get_frame(fname): data["coords"] = coords data["energies"] = energy data["forces"] = force - data["virials"] = virial + if isinstance(virial, np.ndarray): + data["virials"] = virial data["stress"] = stress data["orig"] = np.zeros(3) diff --git a/tests/abacus.relax/OUT.abacus/running_cell-relax.log.nostress b/tests/abacus.relax/OUT.abacus/running_cell-relax.log.nostress new file mode 100644 index 00000000..a77e71aa --- /dev/null +++ b/tests/abacus.relax/OUT.abacus/running_cell-relax.log.nostress @@ -0,0 +1,1397 @@ + + ABACUS v3.3.4 + + Atomic-orbital Based Ab-initio Computation at UStc + + Website: http://abacus.ustc.edu.cn/ + Documentation: https://abacus.deepmodeling.com/ + Repository: https://github.com/abacusmodeling/abacus-develop + https://github.com/deepmodeling/abacus-develop + Commit: e0530a7ae (Tue Sep 19 10:10:45 2023 +0800) + + Start Time is Tue Oct 10 14:36:36 2023 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + DRANK = 1 + DSIZE = 2 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + The esolver type has been set to : ksdft_lcao + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | 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 + lattice constant (Bohr) = 15 + lattice constant (Angstrom) = 7.93766 + + READING ATOM TYPE 1 + atom label = Si + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 2 + + TOTAL ATOM NUMBER = 2 + + CARTESIAN COORDINATES ( UNIT = 15 Bohr ). + atom x y z mag vx vy vz + tauc_Si1 0 0 0 0 0 0 0 + tauc_Si2 0.280000000001 0 0 0 0 0 0 + + + Volume (Bohr^3) = 3375 + Volume (A^3) = 500.122803248 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +1 +0 +0 + +0 +1 +0 + +0 +0 +1 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +1 -0 +0 + -0 +1 -0 + +0 -0 +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.pz-vbc.UPF + pseudopotential type = NC + exchange-correlation functional = PZ + nonlocal core correction = 0 + valence electrons = 4 + lmax = 1 + number of zeta = 2 + number of projectors = 2 + L of projector = 0 + L of projector = 1 + initial pseudo atomic orbital number = 8 + NLOCAL = 26 + + Warning_Memory_Consuming allocated: FFT::grid 5.6953125 MB + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | 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. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + fft grid for charge/potential = [ 72, 72, 72 ] + fft grid division = [ 4, 4, 4 ] + big fft grid for charge/potential = [ 18, 18, 18 ] + nbxx = 2916 + nrxx = 186624 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 161235 + number of sticks = 3577 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 1789 80617 + 2 1788 80618 + --------------- sum ------------------- + 2 3577 161235 + number of |g| = 951 + max |g| = 1139 + min |g| = 0 + + SETUP THE ELECTRONS NUMBER + electron number of element Si = 4 + total electron number of element Si = 8 + AUTOSET number of electrons: = 8 + DONE : SETUP UNITCELL Time : 0.0676418824696 (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 = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0679309559782 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | 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. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + fft grid for wave functions = [ 72, 72, 72 ] + number of plane waves = 20005 + number of sticks = 885 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 443 10003 + 2 442 10002 + --------------- sum ------------------- + 2 885 20005 + DONE : INIT PLANEWAVE Time : 0.0725195150735 (SEC) + + occupied bands = 4 + NLOCAL = 26 + NBANDS = 16 + NBANDS = 16 + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../tests/PP_ORB/./Si_lda_8.0au_50Ry_2s2p1d + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 801 0.01 8 1 1 + 2 0 1 801 0.01 8 1 1 + 3 1 0 801 0.01 8 1 1 + 4 1 1 801 0.01 8 1 1 + 5 2 0 801 0.01 8 1 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 2 + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + global2local_row dimension = 26 + global2local_col dimension = 26 + nloc = 338 + + ------------------------------------------- + STEP OF RELAXATION : 1 + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 8 + longest nonlocal projector rcut (Bohr) = 5.01 + searching radius is (Bohr)) = 16 + searching radius unit is (Bohr)) = 15 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + real space grid = [ 72, 72, 72 ] + big cell numbers in grid = [ 18, 18, 18 ] + meshcell numbers in big cell = [ 4, 4, 4 ] + extended fft grid = [ 10, 10, 10 ] + dimension of extened grid = [ 39, 39, 39 ] + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 26 + lgd_last = 0 + lgd_now = 26 + allocate DM , the dimension is 26 + enter setAlltoallvParameter, nblk = 1 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 26 + nCol_in_proc = 13 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 26 + nCol_in_proc = 13 +receiver_size is 676 ; receiver_size of each process is: +338 338 +sender_size is 676 ; sender_size of each process is: +338 338 + init_chg = atomic + DONE : INIT SCF Time : 0.288423 (SEC) + + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb +--------------AUTO-SET--------------- + Autoset mixing_beta to 0.7 + Autoset mixing_gg0 to 0 +------------------------------------- + + Warning_Memory_Consuming allocated: ChgMix::Rrho 11.3906 MB + + Warning_Memory_Consuming allocated: ChgMix::dRrho 9.9668 MB + + Warning_Memory_Consuming allocated: ChgMix::drho 9.9668 MB + + Density error is 0.180751569625 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2013293385 -206.8246961780 +E_Harris -15.2425400057 -207.3853960707 +E_Fermi -0.3598643762 -4.8962060240 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.156065124268 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2013815120 -206.8254060345 +E_Harris -14.9858718979 -203.8932473090 +E_Fermi -0.2889518174 -3.9313911636 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.126809290852 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2150325554 -207.0111380095 +E_Harris -15.2614471843 -207.6426414320 +E_Fermi -0.2916013792 -3.9674403015 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0297310465632 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2172217249 -207.0409231882 +E_Harris -15.2632171873 -207.6667235583 +E_Fermi -0.2994278914 -4.0739254636 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0204748350332 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2174675539 -207.0442678629 +E_Harris -15.2150578457 -207.0114821006 +E_Fermi -0.2979257327 -4.0534875459 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00358291298089 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175843784 -207.0458573417 +E_Harris -15.2144099768 -207.0026673922 +E_Fermi -0.2980888472 -4.0557068323 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000137852108918 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175868493 -207.0458909609 +E_Harris -15.2179842616 -207.0512980320 +E_Fermi -0.2980849031 -4.0556531704 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000156704082002 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175868470 -207.0458909294 +E_Harris -15.2175271722 -207.0450790117 +E_Fermi -0.2980751674 -4.0555207089 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000113776248293 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175868415 -207.0458908541 +E_Harris -15.2176057193 -207.0461476993 +E_Fermi -0.2980749477 -4.0555177197 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 6.11456847146e-06 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175868445 -207.0458908947 +E_Harris -15.2176033874 -207.0461159728 +E_Fermi -0.2980747991 -4.0555156977 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 3.79671375115e-06 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175868445 -207.0458908949 +E_Harris -15.2175858517 -207.0458773876 +E_Fermi -0.2980747945 -4.0555156356 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 2.1688243861e-09 +---------------------------------------------------------- + Energy Rydberg eV +---------------------------------------------------------- +E_KohnSham -15.2175868445 -207.0458908947 +E_KS(sigma->0) -15.2099423108 -206.9418816778 +E_Harris -15.2175874535 -207.0458991809 +E_band -4.0123371539 -54.5906475901 +E_one_elec -15.2862509583 -207.9801140907 +E_Hartree 8.3645248223 113.8051986462 +E_xc -4.1857282910 -56.9497550371 +E_Ewald -4.0948433501 -55.7132019794 +E_entropy(-TS) -0.0152890674 -0.2080184337 +E_descf 0.0000000000 0.0000000000 +E_exx 0.0000000000 0.0000000000 +E_Fermi -0.2980747965 -4.0555156632 +---------------------------------------------------------- + + charge density convergence is achieved + final etot is -207.04589089 eV + EFERMI = -4.0555156632 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0.0000 0.0000 0.0000 (10003 pws) + 1 -11.4912 2.00000 + 2 -7.60755 2.00000 + 3 -4.11584 1.46935 + 4 -4.08812 1.26533 + 5 -4.08812 1.26533 + 6 -1.05823 0.00000 + 7 -1.05823 0.00000 + 8 3.33208 0.00000 + 9 4.05667 0.00000 + 10 5.18172 0.00000 + 11 6.86533 0.00000 + 12 6.86533 0.00000 + 13 8.35917 0.00000 + 14 8.52401 0.00000 + 15 8.52822 0.00000 + 16 8.81287 0.00000 + + correction force for each atom along direction 1 is 2.15933e-05 + correction force for each atom along direction 2 is 2.27115e-16 + correction force for each atom along direction 3 is -2.17812e-16 + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.29898121 0 0 + Si2 +0.29898121 0 0 + + Relaxation is not converged yet! + + CARTESIAN COORDINATES ( UNIT = 15.000000 Bohr ). + atom x y z mag vx vy vz + tauc_Si1 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + tauc_Si2 0.281883309397 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + + + ------------------------------------------- + STEP OF RELAXATION : 2 + ------------------------------------------- + Find the file, try to read charge from file. + read in fermi energy = 0.00000000000 + NEW-OLD atomic charge density approx. for the potential ! + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 8.00 + longest nonlocal projector rcut (Bohr) = 5.01 + searching radius is (Bohr)) = 16.0 + searching radius unit is (Bohr)) = 15.0 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + real space grid = [ 72, 72, 72 ] + big cell numbers in grid = [ 18, 18, 18 ] + meshcell numbers in big cell = [ 4, 4, 4 ] + extended fft grid = [ 10, 10, 10 ] + dimension of extened grid = [ 39, 39, 39 ] + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 26 + lgd_last = 26 + lgd_now = 26 + allocate DM , the dimension is 26 + enter setAlltoallvParameter, nblk = 1 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 26 + nCol_in_proc = 13 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 26 + nCol_in_proc = 13 +receiver_size is 676 ; receiver_size of each process is: +338 338 +sender_size is 676 ; sender_size of each process is: +338 338 + DONE : INIT SCF Time : 2.74642 (SEC) + + + LCAO ALGORITHM --------------- ION= 2 ELEC= 1-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0168954682260 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175193830 -207.0449730344 +E_Harris -15.2179258264 -207.0505029798 +E_Fermi -0.2961807207 -4.0297454387 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0518353196815 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2172250690 -207.0409686875 +E_Harris -15.2216102024 -207.1006314869 +E_Fermi -0.2971601847 -4.0430717302 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00105868740176 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178444267 -207.0493954808 +E_Harris -15.2054770305 -206.8811284235 +E_Fermi -0.2968921352 -4.0394247300 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00100940956423 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178436236 -207.0493845539 +E_Harris -15.2179619963 -207.0509950967 +E_Fermi -0.2968425171 -4.0387496416 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 5-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000251820456033 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178448391 -207.0494010914 +E_Harris -15.2181672624 -207.0537878854 +E_Fermi -0.2968538269 -4.0389035193 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 6-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 7.94322566771e-05 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178448951 -207.0494018540 +E_Harris -15.2179378285 -207.0506662780 +E_Fermi -0.2968736543 -4.0391732848 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 7-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 1.96701255220e-06 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178448967 -207.0494018751 +E_Harris -15.2178128580 -207.0489659664 +E_Fermi -0.2968701291 -4.0391253214 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 8-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 6.23610651249e-07 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178448967 -207.0494018753 +E_Harris -15.2178453059 -207.0494074433 +E_Fermi -0.2968701680 -4.0391258508 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 9-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 2.92360923727e-08 +---------------------------------------------------------- + Energy Rydberg eV +---------------------------------------------------------- +E_KohnSham -15.2178448967 -207.0494018751 +E_KS(sigma->0) -15.2102395884 -206.9459263474 +E_Harris -15.2178450198 -207.0494035507 +E_band -4.0037521939 -54.4738432173 +E_one_elec -15.2087341393 -206.9254436611 +E_Hartree 8.3269389515 113.2938166390 +E_xc -4.1809665876 -56.8849687391 +E_Ewald -4.1398725048 -56.3258550587 +E_entropy(-TS) -0.0152106166 -0.2069510553 +E_descf 0.0000000000 0.0000000000 +E_exx 0.0000000000 0.0000000000 +E_Fermi -0.2968701786 -4.0391259950 +---------------------------------------------------------- + + charge density convergence is achieved + final etot is -207.04940188 eV + EFERMI = -4.0391259950 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0.0000 0.0000 0.0000 (10003 pws) + 1 -11.4492 2.00000 + 2 -7.62228 2.00000 + 3 -4.10453 1.50341 + 4 -4.06956 1.24829 + 5 -4.06956 1.24829 + 6 -1.08365 0.00000 + 7 -1.08365 0.00000 + 8 3.26511 0.00000 + 9 4.05898 0.00000 + 10 5.18262 0.00000 + 11 6.89860 0.00000 + 12 6.89860 0.00000 + 13 8.35639 0.00000 + 14 8.54894 0.00000 + 15 8.55303 0.00000 + 16 8.78009 0.00000 + + correction force for each atom along direction 1 is 5.02305e-05 + correction force for each atom along direction 2 is -4.05967e-15 + correction force for each atom along direction 3 is -3.16091e-15 + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.16990488 0 0 + Si2 +0.16990488 0 0 + + Relaxation is not converged yet! + + CARTESIAN COORDINATES ( UNIT = 15.000000 Bohr ). + atom x y z mag vx vy vz + tauc_Si1 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + tauc_Si2 0.284362334512 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + + + ------------------------------------------- + STEP OF RELAXATION : 3 + ------------------------------------------- + Find the file, try to read charge from file. + read in fermi energy = 0.00000000000 + first order charge density extrapolation ! + Find the file, try to read charge from file. + read in fermi energy = 0.00000000000 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 8.00 + longest nonlocal projector rcut (Bohr) = 5.01 + searching radius is (Bohr)) = 16.0 + searching radius unit is (Bohr)) = 15.0 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + real space grid = [ 72, 72, 72 ] + big cell numbers in grid = [ 18, 18, 18 ] + meshcell numbers in big cell = [ 4, 4, 4 ] + extended fft grid = [ 10, 10, 10 ] + dimension of extened grid = [ 39, 39, 39 ] + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 26 + lgd_last = 26 + lgd_now = 26 + allocate DM , the dimension is 26 + enter setAlltoallvParameter, nblk = 1 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 26 + nCol_in_proc = 13 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 26 + nCol_in_proc = 13 +receiver_size is 676 ; receiver_size of each process is: +338 338 +sender_size is 676 ; sender_size of each process is: +338 338 + DONE : INIT SCF Time : 4.81331 (SEC) + + + LCAO ALGORITHM --------------- ION= 3 ELEC= 1-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00452318833251 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179529883 -207.0508725373 +E_Harris -15.2179805856 -207.0512480174 +E_Fermi -0.2950793488 -4.0147605064 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0126477900130 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179373427 -207.0506596677 +E_Harris -15.2187956089 -207.0623369786 +E_Fermi -0.2953608067 -4.0185899366 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000229908558519 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179750967 -207.0511733374 +E_Harris -15.2155772307 -207.0185486963 +E_Fermi -0.2952721109 -4.0173831692 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000176918130049 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179750604 -207.0511728440 +E_Harris -15.2179890190 -207.0513627592 +E_Fermi -0.2952608170 -4.0172295074 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 5-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 8.06492625182e-05 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179751029 -207.0511734217 +E_Harris -15.2180437237 -207.0521070555 +E_Fermi -0.2952643859 -4.0172780649 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 6-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 2.15735574673e-05 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179751088 -207.0511735013 +E_Harris -15.2179877529 -207.0513455330 +E_Fermi -0.2952680618 -4.0173280777 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 7-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 7.77502128777e-07 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179751089 -207.0511735026 +E_Harris -15.2179663369 -207.0510541546 +E_Fermi -0.2952667581 -4.0173103395 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 8-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 6.29521796612e-08 +---------------------------------------------------------- + Energy Rydberg eV +---------------------------------------------------------- +E_KohnSham -15.2179751089 -207.0511735028 +E_KS(sigma->0) -15.2104340893 -206.9485726681 +E_Harris -15.2179754378 -207.0511779776 +E_band -3.9924677142 -54.3203099945 +E_one_elec -15.1084358176 -205.5608149869 +E_Hartree 8.2784235056 112.6337301328 +E_xc -4.1748486280 -56.8017296279 +E_Ewald -4.1980321297 -57.1171573515 +E_entropy(-TS) -0.0150820391 -0.2052016694 +E_descf 0.0000000000 0.0000000000 +E_exx 0.0000000000 0.0000000000 +E_Fermi -0.2952667970 -4.0173108700 +---------------------------------------------------------- + + charge density convergence is achieved + final etot is -207.05117350 eV + EFERMI = -4.0173108700 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0.0000 0.0000 0.0000 (10003 pws) + 1 -11.3940 2.00000 + 2 -7.64171 2.00000 + 3 -4.08957 1.54742 + 4 -4.04497 1.22629 + 5 -4.04497 1.22629 + 6 -1.11642 0.00000 + 7 -1.11642 0.00000 + 8 3.17803 0.00000 + 9 4.06227 0.00000 + 10 5.18446 0.00000 + 11 6.94310 0.00000 + 12 6.94310 0.00000 + 13 8.35330 0.00000 + 14 8.58190 0.00000 + 15 8.58585 0.00000 + 16 8.73799 0.00000 + + correction force for each atom along direction 1 is 7.37304e-05 + correction force for each atom along direction 2 is -2.58199e-16 + correction force for each atom along direction 3 is -1.65026e-14 + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.0081614456 0 0 + Si2 +0.0081614456 0 0 + + Relaxation is not converged yet! + + CARTESIAN COORDINATES ( UNIT = 15.000000 Bohr ). + atom x y z mag vx vy vz + tauc_Si1 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + tauc_Si2 0.284487424157 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + + + ------------------------------------------- + STEP OF RELAXATION : 4 + ------------------------------------------- + Find the file, try to read charge from file. + read in fermi energy = 0.00000000000 + first order charge density extrapolation ! + Find the file, try to read charge from file. + read in fermi energy = 0.00000000000 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 8.00 + longest nonlocal projector rcut (Bohr) = 5.01 + searching radius is (Bohr)) = 16.0 + searching radius unit is (Bohr)) = 15.0 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + real space grid = [ 72, 72, 72 ] + big cell numbers in grid = [ 18, 18, 18 ] + meshcell numbers in big cell = [ 4, 4, 4 ] + extended fft grid = [ 10, 10, 10 ] + dimension of extened grid = [ 39, 39, 39 ] + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 26 + lgd_last = 26 + lgd_now = 26 + allocate DM , the dimension is 26 + enter setAlltoallvParameter, nblk = 1 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 26 + nCol_in_proc = 13 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 26 + nCol_in_proc = 13 +receiver_size is 676 ; receiver_size of each process is: +338 338 +sender_size is 676 ; sender_size of each process is: +338 338 + DONE : INIT SCF Time : 6.77403 (SEC) + + + LCAO ALGORITHM --------------- ION= 4 ELEC= 1-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0210093305713 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2174740267 -207.0443559304 +E_Harris -15.2180946308 -207.0527996824 +E_Fermi -0.2959758019 -4.0269573753 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0520812264530 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2173695919 -207.0429350218 +E_Harris -15.2151104840 -207.0121982820 +E_Fermi -0.2944468872 -4.0061554237 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00255897180276 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179722664 -207.0511348291 +E_Harris -15.2285489496 -207.1950379867 +E_Fermi -0.2951521387 -4.0157508630 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00152160816587 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179745476 -207.0511658660 +E_Harris -15.2184116348 -207.0571127427 +E_Fermi -0.2951986701 -4.0163839550 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 5-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000884467080098 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179752767 -207.0511757857 +E_Harris -15.2176581299 -207.0468607828 +E_Fermi -0.2951950382 -4.0163345403 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 6-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000151921968907 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179755488 -207.0511794881 +E_Harris -15.2177962138 -207.0487395102 +E_Fermi -0.2951848623 -4.0161960903 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 7-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 4.87779044592e-06 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179755535 -207.0511795525 +E_Harris -15.2179991669 -207.0515008297 +E_Fermi -0.2951845344 -4.0161916293 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 8-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 5.88489536041e-06 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179755536 -207.0511795533 +E_Harris -15.2179802675 -207.0512436900 +E_Fermi -0.2951854210 -4.0162036916 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 9-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 4.52854000969e-07 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179755536 -207.0511795533 +E_Harris -15.2179745978 -207.0511665498 +E_Fermi -0.2951853571 -4.0162028222 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 10-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 1.19233066338e-08 +---------------------------------------------------------- + Energy Rydberg eV +---------------------------------------------------------- +E_KohnSham -15.2179755536 -207.0511795532 +E_KS(sigma->0) -15.2104381464 -206.9486278675 +E_Harris -15.2179755357 -207.0511793099 +E_band -3.9918990724 -54.3125732252 +E_one_elec -15.1034264128 -205.4926585376 +E_Hartree 8.2760036273 112.6008059995 +E_xc -4.1745441808 -56.7975874122 +E_Ewald -4.2009337729 -57.1566362317 +E_entropy(-TS) -0.0150748143 -0.2051033713 +E_descf 0.0000000000 0.0000000000 +E_exx 0.0000000000 0.0000000000 +E_Fermi -0.2951853570 -4.0162028213 +---------------------------------------------------------- + + charge density convergence is achieved + final etot is -207.05117955 eV + EFERMI = -4.0162028213 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0.0000 0.0000 0.0000 (10003 pws) + 1 -11.3912 2.00000 + 2 -7.64269 2.00000 + 3 -4.08882 1.54961 + 4 -4.04373 1.22520 + 5 -4.04373 1.22520 + 6 -1.11805 0.00000 + 7 -1.11805 0.00000 + 8 3.17367 0.00000 + 9 4.06245 0.00000 + 10 5.18458 0.00000 + 11 6.94536 0.00000 + 12 6.94536 0.00000 + 13 8.35317 0.00000 + 14 8.58357 0.00000 + 15 8.58751 0.00000 + 16 8.73590 0.00000 + + correction force for each atom along direction 1 is 7.39798e-05 + correction force for each atom along direction 2 is 5.71714e-16 + correction force for each atom along direction 3 is -3.36054e-14 + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Si1 -0.00019834712 0 0 + Si2 +0.00019834712 0 0 + + Relaxation is converged! + + + -------------------------------------------- + !FINAL_ETOT_IS -207.0511795531780 eV + -------------------------------------------- + + +TIME STATISTICS +------------------------------------------------------------------------------ + CLASS_NAME NAME TIME(Sec) CALLS AVG(Sec) PER(%) +------------------------------------------------------------------------------ + total 8.66 15 0.58 100.00 +Driver driver_line 8.65 1 8.65 99.90 +Ions opt_ions 8.45 1 8.45 97.62 +ESolver_KS_LCAO Run 7.11 4 1.78 82.19 +ESolver_KS_LCAO beforescf 0.96 4 0.24 11.04 +ESolver_KS_LCAO beforesolver 0.15 4 0.04 1.78 +ESolver_KS_LCAO set_matrix_grid 0.15 4 0.04 1.77 +Grid_Technique init 0.15 4 0.04 1.75 +PW_Basis recip2real 0.14 55 0.00 1.67 +Potential update_from_charge 0.76 43 0.02 8.83 +Potential cal_v_eff 0.75 43 0.02 8.68 +H_Hartree_pw v_hartree 0.37 43 0.01 4.29 +PW_Basis real2recip 0.35 129 0.00 4.06 +PW_Basis gatherp_scatters 0.11 129 0.00 1.32 +PotXC cal_v_eff 0.36 43 0.01 4.12 +XC_Functional v_xc 0.35 43 0.01 4.03 +HSolverLCAO solve 3.80 39 0.10 43.91 +HamiltLCAO updateHk 1.72 39 0.04 19.89 +OperatorLCAO init 1.69 117 0.01 19.54 +Veff contributeHk 1.66 39 0.04 19.21 +Gint_interface cal_gint 4.77 82 0.06 55.10 +Gint_interface cal_gint_vlocal 1.66 39 0.04 19.19 +Gint_Tools cal_psir_ylm 1.40 217776 0.00 16.14 +ElecStateLCAO psiToRho 1.98 39 0.05 22.86 +Gint_interface cal_gint_rho 1.93 39 0.05 22.29 +Charge mix_rho 0.60 35 0.02 6.97 +Charge Pulay_mixing 0.59 35 0.02 6.80 +Force_Stress_LCAO getForceStress 1.33 4 0.33 15.42 +Force_LCAO_gamma ftable_gamma 1.25 4 0.31 14.48 +Force_LCAO_gamma cal_fvl_dphi 1.18 4 0.29 13.62 +Gint_interface cal_gint_force 1.18 4 0.29 13.62 +Gint_Tools cal_dpsir_ylm 0.94 11168 0.00 10.87 +------------------------------------------------------------------------------ + + NAME---------------|MEMORY(MB)-------- + total 99.43 + ChgMix::Rrho 22.78 + ChgMix::dRrho 19.93 + ChgMix::drho 19.93 + FFT::grid 11.39 + Chg::rho 2.848 + Chg::rho_save 2.848 + Chg::rho_core 2.848 + Pot::veff_fix 2.848 + Pot::veff 2.848 + ChgMix::rho_save2 2.848 + SF::strucFac 2.460 + Chg::rhog 1.230 + Chg::rhog_save 1.230 + Chg::rhog_core 1.230 + ------------- < 1.0 MB has been ignored ---------------- + ---------------------------------------------------------- + + Start Time : Tue Oct 10 14:36:36 2023 + Finish Time : Tue Oct 10 14:36:45 2023 + Total Time : 0 h 0 mins 9 secs diff --git a/tests/abacus.relax/STRU.Si b/tests/abacus.relax/STRU.Si new file mode 100644 index 00000000..f2daf9b5 --- /dev/null +++ b/tests/abacus.relax/STRU.Si @@ -0,0 +1,24 @@ +#This is the atom file containing all the information +#about the lattice structure. + +ATOMIC_SPECIES +Si 1.000 Si.pz-vbc.UPF #Element, Mass, Pseudopotential + +NUMERICAL_ORBITAL +./Si_lda_8.0au_50Ry_2s2p1d + +LATTICE_CONSTANT +15 #Lattice constant + +LATTICE_VECTORS +1.0 0.0 0.0 #Lattice vector 1 +0.0 1.0 0.0 #Lattice vector 2 +0.0 0.0 1.0 #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 0 0 0 #x,y,z, move_x, move_y, move_z +0.28 0.00 0.00 1 0 0 diff --git a/tests/test_abacus_relax.py b/tests/test_abacus_relax.py index ed9b77dd..8e8cd225 100644 --- a/tests/test_abacus_relax.py +++ b/tests/test_abacus_relax.py @@ -106,5 +106,33 @@ def tearDown(self): os.remove("abacus.relax/OUT.abacus/running_cell-relax.log") +class TestABACUSRelaxLabeledOutputNoStress(unittest.TestCase): + def setUp(self): + shutil.copy( + "abacus.relax/OUT.abacus/running_cell-relax.log.nostress", + "abacus.relax/OUT.abacus/running_cell-relax.log", + ) + shutil.move( + "abacus.relax/STRU", + "abacus.relax/STRU.bak", + ) + shutil.copy( + "abacus.relax/STRU.Si", + "abacus.relax/STRU", + ) + + def test_result(self): + system = dpdata.LabeledSystem("abacus.relax", fmt="abacus/relax") + self.assertRaises(KeyError, lambda: system.data["virials"]) + + def tearDown(self): + if os.path.isfile("abacus.relax/OUT.abacus/running_cell-relax.log"): + os.remove("abacus.relax/OUT.abacus/running_cell-relax.log") + shutil.move( + "abacus.relax/STRU.bak", + "abacus.relax/STRU", + ) + + if __name__ == "__main__": unittest.main() From 5e8f0ba4cbb1ccdfc39a2d377696cd6170ad6b55 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Thu, 12 Oct 2023 23:57:29 -0400 Subject: [PATCH 10/18] docs: try dpdata online (#552) Signed-off-by: Jinzhe Zeng Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .readthedocs.yaml | 7 +- docs/conf.py | 5 + docs/environment.yml | 11 + docs/index.rst | 1 + docs/nb/OUTCAR | 2491 ++++++++++++++++++++++++++++++++++++++ docs/nb/try_dpdata.ipynb | 73 ++ docs/rtd_environment.yml | 6 + docs/try_dpdata.rst | 4 + dpdata/__init__.py | 13 + dpdata/deepmd/hdf5.py | 14 +- dpdata/plugins/deepmd.py | 24 +- pyproject.toml | 2 + 12 files changed, 2632 insertions(+), 19 deletions(-) create mode 100644 docs/environment.yml create mode 100644 docs/nb/OUTCAR create mode 100644 docs/nb/try_dpdata.ipynb create mode 100644 docs/rtd_environment.yml create mode 100644 docs/try_dpdata.rst diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 87f8c733..83a36032 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -3,10 +3,9 @@ version: 2 build: os: ubuntu-22.04 tools: - python: "3.11" + python: "mambaforge-22.9" +conda: + environment: docs/rtd_environment.yml sphinx: configuration: docs/conf.py formats: all -python: - install: - - requirements: docs/requirements.txt diff --git a/docs/conf.py b/docs/conf.py index e60f18fc..0f9ff097 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -49,6 +49,7 @@ "numpydoc", "m2r2", "sphinxarg.ext", + "jupyterlite_sphinx", ] # Add any paths that contain templates here, relative to this directory. @@ -202,3 +203,7 @@ def setup(app): "monty": ("https://guide.materialsvirtuallab.org/monty/", None), "h5py": ("https://docs.h5py.org/en/stable/", None), } + +# jupyterlite +jupyterlite_contents = "./nb" +jupyterlite_bind_ipynb_suffix = False diff --git a/docs/environment.yml b/docs/environment.yml new file mode 100644 index 00000000..b0a80ffa --- /dev/null +++ b/docs/environment.yml @@ -0,0 +1,11 @@ +name: dpdata +channels: + - https://repo.mamba.pm/emscripten-forge + - https://repo.mamba.pm/conda-forge +dependencies: + - numpy + - scipy + - monty + - wcmatch + - pip: + - .. diff --git a/docs/index.rst b/docs/index.rst index c25592c1..07e381de 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -11,6 +11,7 @@ Welcome to dpdata's documentation! :caption: Contents: Overview + try_dpdata cli formats drivers diff --git a/docs/nb/OUTCAR b/docs/nb/OUTCAR new file mode 100644 index 00000000..15041df5 --- /dev/null +++ b/docs/nb/OUTCAR @@ -0,0 +1,2491 @@ + vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Jan 29 2020 12:26:58) complex + + executed on LinuxIFC date 2020.05.07 01:33:18 + running on 16 total cores + distrk: each k-point on 16 cores, 1 groups + distr: one band on NCORES_PER_BAND= 1 cores, 16 groups + + +-------------------------------------------------------------------------------------------------------- + + + INCAR: + POTCAR: PAW_PBE O_h 06Feb2004 + POTCAR: PAW_PBE H_h 06Feb2004 + + ----------------------------------------------------------------------------- +| | +| W W AA RRRRR N N II N N GGGG !!! | +| W W A A R R NN N II NN N G G !!! | +| W W A A R R N N N II N N N G !!! | +| W WW W AAAAAA RRRRR N N N II N N N G GGG ! | +| WW WW A A R R N NN II N NN G G | +| W W A A R R N N II N N GGGG !!! | +| | +| For optimal performance we recommend to set | +| NCORE= 4 - approx SQRT( number of cores) | +| NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). | +| This setting can greatly improve the performance of VASP for DFT. | +| The default, NCORE=1 might be grossly inefficient | +| on modern multi-core architectures or massively parallel machines. | +| Do your own testing !!!! | +| Unfortunately you need to use the default for GW and RPA calculations. | +| (for HF NCORE is supported but not extensively tested yet) | +| | + ----------------------------------------------------------------------------- + + POTCAR: PAW_PBE O_h 06Feb2004 + VRHFIN =O: s2p4 + LEXCH = PE + EATOM = 432.3788 eV, 31.7789 Ry + + TITEL = PAW_PBE O_h 06Feb2004 + LULTRA = F use ultrasoft PP ? + IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 0.800 partial core radius + POMASS = 16.000; ZVAL = 6.000 mass and valenz + RCORE = 1.100 outmost cutoff radius + RWIGS = 1.400; RWIGS = 0.741 wigner-seitz radius (au A) + ENMAX = 700.000; ENMIN = 500.000 eV + ICORE = 2 local potential + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 888.804 + DEXC = 0.000 + RMAX = 1.128 core radius for proj-oper + RAUG = 1.300 factor for augmentation sphere + RDEP = 1.125 radius for radial grids + RDEPT = 1.088 core radius for aug-charge + + Atomic configuration + 4 entries + n l j E occ. + 1 0 0.50 -514.6923 2.0000 + 2 0 0.50 -23.9615 2.0000 + 2 1 0.50 -9.0305 4.0000 + 3 2 1.50 -9.5241 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -23.9615319 23 1.100 + 0 -25.3221145 23 1.100 + 1 -9.0304911 23 1.100 + 1 -5.4802209 23 1.100 + 2 -9.5240782 7 1.100 + local pseudopotential read in + partial core-charges read in + partial kinetic energy density read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 4 + number of lm-projection operators is LMMAX = 8 + + POTCAR: PAW_PBE H_h 06Feb2004 + VRHFIN =H: ultrasoft test + LEXCH = PE + EATOM = 12.4884 eV, 0.9179 Ry + + TITEL = PAW_PBE H_h 06Feb2004 + LULTRA = F use ultrasoft PP ? + IUNSCR = 0 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 0.000 partial core radius + POMASS = 1.000; ZVAL = 1.000 mass and valenz + RCORE = 0.800 outmost cutoff radius + RWIGS = 0.700; RWIGS = 0.370 wigner-seitz radius (au A) + ENMAX = 700.000; ENMIN = 350.000 eV + RCLOC = 0.701 cutoff for local pot + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 1000.000 + RMAX = 0.819 core radius for proj-oper + RAUG = 1.000 factor for augmentation sphere + RDEP = 0.817 radius for radial grids + RDEPT = 0.817 core radius for aug-charge + + Atomic configuration + 2 entries + n l j E occ. + 1 0 0.50 -6.4927 1.0000 + 2 1 0.50 -3.4015 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -6.4927493 23 0.800 + 0 6.8029130 23 0.800 + 1 -6.8029130 23 0.800 + local pseudopotential read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 3 + number of lm-projection operators is LMMAX = 5 + + PAW_PBE O_h 06Feb2004 : + energy of atom 1 EATOM= -432.3788 + kinetic energy error for atom= 0.0035 (will be added to EATOM!!) + PAW_PBE H_h 06Feb2004 : + energy of atom 2 EATOM= -12.4884 + kinetic energy error for atom= 0.0001 (will be added to EATOM!!) + + + POSCAR: O2 H4 + positions in cartesian coordinates + No initial velocities read in + exchange correlation table for LEXCH = 8 + RHO(1)= 0.500 N(1) = 2000 + RHO(2)= 100.500 N(2) = 4000 + + + +-------------------------------------------------------------------------------------------------------- + + + ion position nearest neighbor table + 1 0.121 0.105 0.117- 4 1.01 3 1.03 + 2 0.879 0.105 0.117- 6 1.02 5 1.02 + 3 0.132 0.170 0.116- 1 1.03 + 4 0.088 0.111 0.118- 1 1.01 + 5 0.870 0.066 0.171- 2 1.02 + 6 0.870 0.066 0.064- 2 1.02 + + +IMPORTANT INFORMATION: All symmetrisations will be switched off! +NOSYMM: (Re-)initialisation of all symmetry stuff for point group C_1. + + + + +Automatic generation of k-mesh. + generate k-points for: 1 1 1 +Space group operators: + irot det(A) alpha n_x n_y n_z tau_x tau_y tau_z + 1 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + + Subroutine IBZKPT returns following result: + =========================================== + + Found 1 irreducible k-points: + + Following reciprocal coordinates: + Coordinates Weight + 0.000000 0.000000 0.000000 1.000000 + + Following cartesian coordinates: + Coordinates Weight + 0.000000 0.000000 0.000000 1.000000 + + + Subroutine IBZKPT_HF returns following result: + ============================================== + + Found 1 k-points in 1st BZ + the following 1 k-points will be used (e.g. in the exchange kernel) + Following reciprocal coordinates: # in IRBZ + 0.000000 0.000000 0.000000 1.00000000 1 t-inv F + + +-------------------------------------------------------------------------------------------------------- + + + + + Dimension of arrays: + k-points NKPTS = 1 k-points in BZ NKDIM = 1 number of bands NBANDS= 16 + number of dos NEDOS = 301 number of ions NIONS = 6 + non local maximal LDIM = 4 non local SUM 2l+1 LMDIM = 8 + total plane-waves NPLWV = ****** + max r-space proj IRMAX = 1 max aug-charges IRDMAX= 15493 + dimension x,y,z NGX = 384 NGY = 192 NGZ = 192 + dimension x,y,z NGXF= 768 NGYF= 384 NGZF= 384 + support grid NGXF= 768 NGYF= 384 NGZF= 384 + ions per type = 2 4 + NGX,Y,Z is equivalent to a cutoff of 21.28, 21.28, 21.28 a.u. + NGXF,Y,Z is equivalent to a cutoff of 42.56, 42.56, 42.56 a.u. + + SYSTEM = unknown system + POSCAR = O2 H4 + + Startparameter for this run: + NWRITE = 2 write-flag & timer + PREC = a normal or accurate (medium, high low for compatibility) + ISTART = 0 job : 0-new 1-cont 2-samecut + ICHARG = 2 charge: 1-file 2-atom 10-const + ISPIN = 1 spin polarized calculation? + LNONCOLLINEAR = F non collinear calculations + LSORBIT = F spin-orbit coupling + INIWAV = 1 electr: 0-lowe 1-rand 2-diag + LASPH = F aspherical Exc in radial PAW + METAGGA= F non-selfconsistent MetaGGA calc. + + Electronic Relaxation 1 + ENCUT = 1500.0 eV 110.25 Ry 10.50 a.u. 94.74 47.37 47.37*2*pi/ulx,y,z + ENINI = 1500.0 initial cutoff + ENAUG = 1000.0 eV augmentation charge cutoff + NELM = 60; NELMIN= 4; NELMDL= -5 # of ELM steps + EDIFF = 0.1E-07 stopping-criterion for ELM + LREAL = F real-space projection + NLSPLINE = F spline interpolate recip. space projectors + LCOMPAT= F compatible to vasp.4.4 + GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 + LMAXPAW = -100 max onsite density + LMAXMIX = 2 max onsite mixed and CHGCAR + VOSKOWN= 0 Vosko Wilk Nusair interpolation + ROPT = 0.00000 0.00000 + Ionic relaxation + EDIFFG = 0.1E-06 stopping-criterion for IOM + NSW = 0 number of steps for IOM + NBLOCK = 1; KBLOCK = 1 inner block; outer block + IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG + NFREE = 0 steps in history (QN), initial steepest desc. (CG) + ISIF = 2 stress and relaxation + IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb + ISYM = 0 0-nonsym 1-usesym 2-fastsym + LCORR = T Harris-Foulkes like correction to forces + + POTIM = 0.5000 time-step for ionic-motion + TEIN = 0.0 initial temperature + TEBEG = 0.0; TEEND = 0.0 temperature during run + SMASS = -3.00 Nose mass-parameter (am) + estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.206E-25a.u. + SCALEE = 1.0000 scale energy and forces + NPACO = 256; APACO = 16.0 distance and # of slots for P.C. + PSTRESS= 0.0 pullay stress + + Mass of Ions in am + POMASS = 16.00 1.00 + Ionic Valenz + ZVAL = 6.00 1.00 + Atomic Wigner-Seitz radii + RWIGS = -1.00 -1.00 + virtual crystal weights + VCA = 1.00 1.00 + NELECT = 16.0000 total number of electrons + NUPDOWN= -1.0000 fix difference up-down + + DOS related values: + EMIN = 10.00; EMAX =-10.00 energy-range for DOS + EFERMI = 0.00 + ISMEAR = 0; SIGMA = 0.05 broadening in eV -4-tet -1-fermi 0-gaus + + Electronic relaxation 2 (details) + IALGO = 68 algorithm + LDIAG = T sub-space diagonalisation (order eigenvalues) + LSUBROT= F optimize rotation matrix (better conditioning) + TURBO = 0 0=normal 1=particle mesh + IRESTART = 0 0=no restart 2=restart with 2 vectors + NREBOOT = 0 no. of reboots + NMIN = 0 reboot dimension + EREF = 0.00 reference energy to select bands + IMIX = 4 mixing-type and parameters + AMIX = 0.40; BMIX = 1.00 + AMIX_MAG = 1.60; BMIX_MAG = 1.00 + AMIN = 0.10 + WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 + + Intra band minimization: + WEIMIN = 0.0000 energy-eigenvalue tresh-hold + EBREAK = 0.16E-09 absolut break condition + DEPER = 0.30 relativ break condition + + TIME = 0.40 timestep for ELM + + volume/ion in A,a.u. = 1125.00 7591.87 + Fermi-wavevector in a.u.,A,eV,Ry = 0.218280 0.412489 0.648264 0.047646 + Thomas-Fermi vector in A = 0.996232 + + Write flags + LWAVE = F write WAVECAR + LDOWNSAMPLE = F k-point downsampling of WAVECAR + LCHARG = F write CHGCAR + LVTOT = F write LOCPOT, total local potential + LVHAR = F write LOCPOT, Hartree potential only + LELF = F write electronic localiz. function (ELF) + LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes + + + Dipole corrections + LMONO = F monopole corrections only (constant potential shift) + LDIPOL = F correct potential (dipole corrections) + IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions + EPSILON= 1.0000000 bulk dielectric constant + + Exchange correlation treatment: + GGA = -- GGA type + LEXCH = 8 internal setting for exchange type + VOSKOWN= 0 Vosko Wilk Nusair interpolation + LHFCALC = F Hartree Fock is set to + LHFONE = F Hartree Fock one center treatment + AEXX = 0.0000 exact exchange contribution + + Linear response parameters + LEPSILON= F determine dielectric tensor + LRPA = F only Hartree local field effects (RPA) + LNABLA = F use nabla operator in PAW spheres + LVEL = F velocity operator in full k-point grid + LINTERFAST= F fast interpolation + KINTER = 0 interpolate to denser k-point grid + CSHIFT =0.1000 complex shift for real part using Kramers Kronig + OMEGAMAX= -1.0 maximum frequency + DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate + RTIME = -0.100 relaxation time in fs + (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) + DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time + + Orbital magnetization related: + ORBITALMAG= F switch on orbital magnetization + LCHIMAG = F perturbation theory with respect to B field + DQ = 0.001000 dq finite difference perturbation B field + LLRAUG = F two centre corrections for induced B field + + + +-------------------------------------------------------------------------------------------------------- + + + Static calculation + charge density and potential will be updated during run + non-spin polarized calculation + RMM-DIIS sequential band-by-band and + variant of blocked Davidson during initial phase + perform sub-space diagonalisation + before iterative eigenvector-optimisation + modified Broyden-mixing scheme, WC = 100.0 + initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 + Hartree-type preconditioning will be used + using additional bands 8 + reciprocal scheme for non local part + use partial core corrections + calculate Harris-corrections to forces + (improved forces if not selfconsistent) + use gradient corrections + use of overlap-Matrix (Vanderbilt PP) + Gauss-broadening in eV SIGMA = 0.05 + + +-------------------------------------------------------------------------------------------------------- + + + energy-cutoff : 1500.00 + volume of cell : 6750.00 + direct lattice vectors reciprocal lattice vectors + 30.000000000 0.000000000 0.000000000 0.033333333 0.000000000 0.000000000 + 0.000000000 15.000000000 0.000000000 0.000000000 0.066666667 0.000000000 + 0.000000000 0.000000000 15.000000000 0.000000000 0.000000000 0.066666667 + + length of vectors + 30.000000000 15.000000000 15.000000000 0.033333333 0.066666667 0.066666667 + + + + k-points in units of 2pi/SCALE and weight: read from INCAR + 0.00000000 0.00000000 0.00000000 1.000 + + k-points in reciprocal lattice and weights: read from INCAR + 0.00000000 0.00000000 0.00000000 1.000 + + position of ions in fractional coordinates (direct lattice) + 0.12126746 0.10473971 0.11733333 + 0.87873254 0.10473971 0.11733333 + 0.13194264 0.17027479 0.11626154 + 0.08787106 0.11115189 0.11766219 + 0.86972453 0.06627868 0.17073627 + 0.86985000 0.06605326 0.06404818 + + position of ions in cartesian coordinates (Angst): + 3.63802389 1.57109570 1.76000001 + 26.36197611 1.57109570 1.76000001 + 3.95827906 2.55412181 1.74392306 + 2.63613168 1.66727831 1.76493284 + 26.09173582 0.99418024 2.56104402 + 26.09549990 0.99079897 0.96072265 + + + +-------------------------------------------------------------------------------------------------------- + + + k-point 1 : 0.0000 0.0000 0.0000 plane waves: 889965 + + maximum and minimum number of plane-waves per node : 889965 889965 + + maximum number of plane-waves: 889965 + maximum index in each direction: + IXMAX= 94 IYMAX= 47 IZMAX= 47 + IXMIN= -94 IYMIN= -47 IZMIN= -47 + + + serial 3D FFT for wavefunctions + parallel 3D FFT for charge: + minimum data exchange during FFTs selected (reduces bandwidth) + + + total amount of memory used by VASP MPI-rank0 1504469. kBytes +======================================================================= + + base : 30000. kBytes + nonl-proj : 199352. kBytes + fftplans : 295613. kBytes + grid : 965246. kBytes + one-center: 18. kBytes + wavefun : 14240. kBytes + + INWAV: cpu time 0.0000: real time 0.0000 + Broyden mixing: mesh for mixing (old mesh) + NGX =189 NGY = 95 NGZ = 95 + (NGX =768 NGY =384 NGZ =384) + gives a total of ****** points + + initial charge density was supplied: + charge density of overlapping atoms calculated + number of electron 16.0000000 magnetization + keeping initial charge density in first step + + +-------------------------------------------------------------------------------------------------------- + + + Maximum index for augmentation-charges 886 (set IRDMAX) + + +-------------------------------------------------------------------------------------------------------- + + + First call to EWALD: gamma= 0.094 + Maximum number of real-space cells 2x 3x 3 + Maximum number of reciprocal cells 4x 2x 2 + + FEWALD: cpu time 0.0022: real time 0.0022 + + +--------------------------------------- Iteration 1( 1) --------------------------------------- + + + POTLOK: cpu time 7.8125: real time 7.8318 + SETDIJ: cpu time 0.0016: real time 0.0017 + EDDAV: cpu time 7.6793: real time 7.6982 + DOS: cpu time 0.0012: real time 0.0013 + -------------------------------------------- + LOOP: cpu time 15.4947: real time 15.5330 + + eigenvalue-minimisations : 48 + total energy-change (2. order) : 0.1514268E+03 (-0.4031052E+03) + number of electron 16.0000000 magnetization + augmentation part 16.0000000 magnetization + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -972.38151982 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 60.59470546 + PAW double counting = 697.41634940 -699.85762974 + entropy T*S EENTRO = -0.00002531 + eigenvalues EBANDS = -96.53607144 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = 151.42675751 eV + + energy without entropy = 151.42678283 energy(sigma->0) = 151.42677017 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 2) --------------------------------------- + + + EDDAV: cpu time 9.5427: real time 9.5657 + DOS: cpu time 0.0011: real time 0.0011 + -------------------------------------------- + LOOP: cpu time 9.5438: real time 9.5667 + + eigenvalue-minimisations : 64 + total energy-change (2. order) :-0.1039947E+03 (-0.1039945E+03) + number of electron 16.0000000 magnetization + augmentation part 16.0000000 magnetization + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -972.38151982 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 60.59470546 + PAW double counting = 697.41634940 -699.85762974 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -200.53075803 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = 47.43209623 eV + + energy without entropy = 47.43209623 energy(sigma->0) = 47.43209623 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 3) --------------------------------------- + + + EDDAV: cpu time 7.6121: real time 7.6304 + DOS: cpu time 0.0009: real time 0.0009 + -------------------------------------------- + LOOP: cpu time 7.6130: real time 7.6314 + + eigenvalue-minimisations : 48 + total energy-change (2. order) :-0.7308666E+02 (-0.7308666E+02) + number of electron 16.0000000 magnetization + augmentation part 16.0000000 magnetization + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -972.38151982 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 60.59470546 + PAW double counting = 697.41634940 -699.85762974 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -273.61741821 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -25.65456395 eV + + energy without entropy = -25.65456395 energy(sigma->0) = -25.65456395 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 4) --------------------------------------- + + + EDDAV: cpu time 5.6924: real time 5.7061 + DOS: cpu time 0.0010: real time 0.0010 + -------------------------------------------- + LOOP: cpu time 5.6934: real time 5.7071 + + eigenvalue-minimisations : 32 + total energy-change (2. order) :-0.6216357E+01 (-0.6216357E+01) + number of electron 16.0000000 magnetization + augmentation part 16.0000000 magnetization + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -972.38151982 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 60.59470546 + PAW double counting = 697.41634940 -699.85762974 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -279.83377498 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -31.87092072 eV + + energy without entropy = -31.87092072 energy(sigma->0) = -31.87092072 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 5) --------------------------------------- + + + EDDAV: cpu time 9.5565: real time 9.5798 + DOS: cpu time 0.0009: real time 0.0009 + CHARGE: cpu time 1.7681: real time 1.7724 + MIXING: cpu time 0.1715: real time 0.1721 + -------------------------------------------- + LOOP: cpu time 11.4970: real time 11.5251 + + eigenvalue-minimisations : 64 + total energy-change (2. order) :-0.1289698E+00 (-0.1289698E+00) + number of electron 16.0000000 magnetization + augmentation part 0.2051310 magnetization + + Broyden mixing: + rms(total) = 0.18249E+01 rms(broyden)= 0.18249E+01 + rms(prec ) = 0.18540E+01 + weight for this iteration 100.00 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -972.38151982 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 60.59470546 + PAW double counting = 697.41634940 -699.85762974 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -279.96274475 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -31.99989048 eV + + energy without entropy = -31.99989048 energy(sigma->0) = -31.99989048 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 6) --------------------------------------- + + + POTLOK: cpu time 7.6238: real time 7.6421 + SETDIJ: cpu time 0.0014: real time 0.0014 + EDDIAG: cpu time 1.4681: real time 1.4721 + RMM-DIIS: cpu time 10.8174: real time 10.8434 + ORTHCH: cpu time 0.0504: real time 0.0506 + DOS: cpu time 0.0003: real time 0.0003 + CHARGE: cpu time 1.7771: real time 1.7815 + MIXING: cpu time 0.1561: real time 0.1565 + -------------------------------------------- + LOOP: cpu time 21.8947: real time 21.9479 + + eigenvalue-minimisations : 48 + total energy-change (2. order) : 0.3401693E+01 (-0.1284952E+01) + number of electron 16.0000000 magnetization + augmentation part 0.1254852 magnetization + + Broyden mixing: + rms(total) = 0.18033E+01 rms(broyden)= 0.18033E+01 + rms(prec ) = 0.18063E+01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 0.4926 + 0.4926 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1018.21992079 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.07085790 + PAW double counting = 1513.45144763 -1516.49098254 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -232.60054874 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.59819759 eV + + energy without entropy = -28.59819759 energy(sigma->0) = -28.59819759 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 7) --------------------------------------- + + + POTLOK: cpu time 7.6784: real time 7.6969 + SETDIJ: cpu time 0.0013: real time 0.0013 + EDDIAG: cpu time 1.4491: real time 1.4526 + RMM-DIIS: cpu time 11.7565: real time 11.7847 + ORTHCH: cpu time 0.0517: real time 0.0518 + DOS: cpu time 0.0005: real time 0.0005 + CHARGE: cpu time 1.7699: real time 1.7742 + MIXING: cpu time 0.1616: real time 0.1620 + -------------------------------------------- + LOOP: cpu time 22.8690: real time 22.9239 + + eigenvalue-minimisations : 54 + total energy-change (2. order) : 0.4794357E-01 (-0.1172557E+00) + number of electron 16.0000000 magnetization + augmentation part 0.1054543 magnetization + + Broyden mixing: + rms(total) = 0.15927E+01 rms(broyden)= 0.15927E+01 + rms(prec ) = 0.15947E+01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.8963 + 1.7150 2.0777 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1023.40193777 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.35110808 + PAW double counting = 2211.92332504 -2214.95865315 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -227.65504518 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.55025402 eV + + energy without entropy = -28.55025402 energy(sigma->0) = -28.55025402 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 8) --------------------------------------- + + + POTLOK: cpu time 7.6686: real time 7.6873 + SETDIJ: cpu time 0.0013: real time 0.0013 + EDDIAG: cpu time 1.4660: real time 1.4696 + RMM-DIIS: cpu time 10.5114: real time 10.5366 + ORTHCH: cpu time 0.0525: real time 0.0526 + DOS: cpu time 0.0005: real time 0.0005 + CHARGE: cpu time 1.7796: real time 1.7838 + MIXING: cpu time 0.1670: real time 0.1674 + -------------------------------------------- + LOOP: cpu time 21.6468: real time 21.6989 + + eigenvalue-minimisations : 46 + total energy-change (2. order) :-0.8265731E+00 (-0.6778624E+00) + number of electron 16.0000000 magnetization + augmentation part 0.1566603 magnetization + + Broyden mixing: + rms(total) = 0.11958E+01 rms(broyden)= 0.11958E+01 + rms(prec ) = 0.12069E+01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.3893 + 2.2500 0.9590 0.9590 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1009.44372392 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 62.60721834 + PAW double counting = 6839.84251395 -6842.35630999 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -242.21747444 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -29.37682711 eV + + energy without entropy = -29.37682711 energy(sigma->0) = -29.37682711 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 9) --------------------------------------- + + + POTLOK: cpu time 7.6537: real time 7.6720 + SETDIJ: cpu time 0.0015: real time 0.0015 + EDDIAG: cpu time 1.4659: real time 1.4695 + RMM-DIIS: cpu time 10.7640: real time 10.7901 + ORTHCH: cpu time 0.0521: real time 0.0522 + DOS: cpu time 0.0004: real time 0.0004 + CHARGE: cpu time 1.7702: real time 1.7744 + MIXING: cpu time 0.1729: real time 0.1733 + -------------------------------------------- + LOOP: cpu time 21.8807: real time 21.9334 + + eigenvalue-minimisations : 48 + total energy-change (2. order) : 0.1056462E+01 (-0.2351360E+00) + number of electron 16.0000000 magnetization + augmentation part 0.1272037 magnetization + + Broyden mixing: + rms(total) = 0.41679E+00 rms(broyden)= 0.41679E+00 + rms(prec ) = 0.41912E+00 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.0796 + 2.1632 0.8623 0.8623 0.4304 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1029.98144592 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.71854898 + PAW double counting = 5755.03792464 -5757.88626392 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -221.40007737 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.32036463 eV + + energy without entropy = -28.32036463 energy(sigma->0) = -28.32036463 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 10) --------------------------------------- + + + POTLOK: cpu time 7.6539: real time 7.6722 + SETDIJ: cpu time 0.0014: real time 0.0014 + EDDIAG: cpu time 1.4730: real time 1.4765 + RMM-DIIS: cpu time 11.7614: real time 11.7896 + ORTHCH: cpu time 0.0515: real time 0.0517 + DOS: cpu time 0.0006: real time 0.0006 + CHARGE: cpu time 1.7441: real time 1.7485 + MIXING: cpu time 0.1927: real time 0.1932 + -------------------------------------------- + LOOP: cpu time 22.8786: real time 22.9336 + + eigenvalue-minimisations : 54 + total energy-change (2. order) :-0.4627474E-02 (-0.1961741E-01) + number of electron 16.0000000 magnetization + augmentation part 0.1175680 magnetization + + Broyden mixing: + rms(total) = 0.20948E+00 rms(broyden)= 0.20948E+00 + rms(prec ) = 0.21117E+00 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.5721 + 2.5467 2.5467 0.9597 0.9037 0.9037 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1030.92096977 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.76203534 + PAW double counting = 5508.64806262 -5511.51065269 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -220.49441655 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.32499210 eV + + energy without entropy = -28.32499210 energy(sigma->0) = -28.32499210 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 11) --------------------------------------- + + + POTLOK: cpu time 7.6712: real time 7.6896 + SETDIJ: cpu time 0.0015: real time 0.0015 + EDDIAG: cpu time 1.4703: real time 1.4739 + RMM-DIIS: cpu time 9.8039: real time 9.8275 + ORTHCH: cpu time 0.0520: real time 0.0521 + DOS: cpu time 0.0002: real time 0.0002 + CHARGE: cpu time 1.7654: real time 1.7697 + MIXING: cpu time 0.1879: real time 0.1884 + -------------------------------------------- + LOOP: cpu time 20.9526: real time 21.0029 + + eigenvalue-minimisations : 41 + total energy-change (2. order) :-0.3396011E-02 (-0.9357442E-03) + number of electron 16.0000000 magnetization + augmentation part 0.1175273 magnetization + + Broyden mixing: + rms(total) = 0.11910E+00 rms(broyden)= 0.11910E+00 + rms(prec ) = 0.12111E+00 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.5111 + 3.0289 2.4604 0.9665 0.9665 0.8220 0.8220 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1032.86725081 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.82823010 + PAW double counting = 5147.75592617 -5150.60791184 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -218.62833069 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.32838812 eV + + energy without entropy = -28.32838812 energy(sigma->0) = -28.32838812 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 12) --------------------------------------- + + + POTLOK: cpu time 7.6888: real time 7.7072 + SETDIJ: cpu time 0.0013: real time 0.0013 + EDDIAG: cpu time 1.4671: real time 1.4708 + RMM-DIIS: cpu time 10.3582: real time 10.3831 + ORTHCH: cpu time 0.0524: real time 0.0526 + DOS: cpu time 0.0003: real time 0.0003 + CHARGE: cpu time 1.7742: real time 1.7785 + MIXING: cpu time 0.2026: real time 0.2031 + -------------------------------------------- + LOOP: cpu time 21.5450: real time 21.5969 + + eigenvalue-minimisations : 45 + total energy-change (2. order) : 0.7972297E-02 (-0.1200521E-01) + number of electron 16.0000000 magnetization + augmentation part 0.1108344 magnetization + + Broyden mixing: + rms(total) = 0.58878E-01 rms(broyden)= 0.58878E-01 + rms(prec ) = 0.59345E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.3822 + 2.6900 2.6900 0.7998 0.7998 0.9841 0.9841 0.7273 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.90921949 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 64.02860913 + PAW double counting = 4915.61293416 -4918.51259087 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.73109770 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.32041582 eV + + energy without entropy = -28.32041582 energy(sigma->0) = -28.32041582 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 13) --------------------------------------- + + + POTLOK: cpu time 7.6648: real time 7.6832 + SETDIJ: cpu time 0.0019: real time 0.0019 + EDDIAG: cpu time 1.4664: real time 1.4699 + RMM-DIIS: cpu time 11.5862: real time 11.6143 + ORTHCH: cpu time 0.0527: real time 0.0529 + DOS: cpu time 0.0001: real time 0.0001 + CHARGE: cpu time 1.7671: real time 1.7714 + MIXING: cpu time 0.2045: real time 0.2050 + -------------------------------------------- + LOOP: cpu time 22.7438: real time 22.7987 + + eigenvalue-minimisations : 53 + total energy-change (2. order) :-0.2817125E-02 (-0.1004256E-02) + number of electron 16.0000000 magnetization + augmentation part 0.1090245 magnetization + + Broyden mixing: + rms(total) = 0.73025E-01 rms(broyden)= 0.73025E-01 + rms(prec ) = 0.73534E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.3706 + 2.7187 2.7187 1.0074 1.0074 0.9318 0.9318 0.8245 0.8245 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.87309953 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 64.02200107 + PAW double counting = 4944.92878187 -4947.82742169 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.76444362 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.32323294 eV + + energy without entropy = -28.32323294 energy(sigma->0) = -28.32323294 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 14) --------------------------------------- + + + POTLOK: cpu time 7.6617: real time 7.6801 + SETDIJ: cpu time 0.0014: real time 0.0014 + EDDIAG: cpu time 1.4692: real time 1.4728 + RMM-DIIS: cpu time 9.6490: real time 9.6722 + ORTHCH: cpu time 0.0540: real time 0.0542 + DOS: cpu time 0.0001: real time 0.0001 + CHARGE: cpu time 1.7674: real time 1.7716 + MIXING: cpu time 0.2142: real time 0.2147 + -------------------------------------------- + LOOP: cpu time 20.8171: real time 20.8671 + + eigenvalue-minimisations : 39 + total energy-change (2. order) :-0.7901685E-02 (-0.3680976E-03) + number of electron 16.0000000 magnetization + augmentation part 0.1080283 magnetization + + Broyden mixing: + rms(total) = 0.78044E-01 rms(broyden)= 0.78044E-01 + rms(prec ) = 0.78650E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.6193 + 4.0671 2.8747 2.3411 0.8187 0.8187 0.9415 0.9415 0.8853 0.8853 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1037.67973570 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 64.04496757 + PAW double counting = 4970.24891255 -4973.15304060 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -213.98318741 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.33113463 eV + + energy without entropy = -28.33113463 energy(sigma->0) = -28.33113463 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 15) --------------------------------------- + + + POTLOK: cpu time 7.6808: real time 7.6994 + SETDIJ: cpu time 0.0013: real time 0.0013 + EDDIAG: cpu time 1.4674: real time 1.4709 + RMM-DIIS: cpu time 9.1159: real time 9.1378 + ORTHCH: cpu time 0.0514: real time 0.0515 + DOS: cpu time 0.0004: real time 0.0004 + CHARGE: cpu time 1.7721: real time 1.7764 + MIXING: cpu time 0.2379: real time 0.2384 + -------------------------------------------- + LOOP: cpu time 20.3271: real time 20.3761 + + eigenvalue-minimisations : 34 + total energy-change (2. order) :-0.2715443E-02 (-0.3426902E-03) + number of electron 16.0000000 magnetization + augmentation part 0.1089825 magnetization + + Broyden mixing: + rms(total) = 0.30925E-01 rms(broyden)= 0.30925E-01 + rms(prec ) = 0.31421E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.5644 + 4.2821 2.5925 2.5925 0.8362 0.8362 0.9712 0.9712 0.8473 0.8571 0.8571 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1037.33486562 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 64.01093561 + PAW double counting = 5060.21957511 -5063.11318511 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.30725901 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.33385007 eV + + energy without entropy = -28.33385007 energy(sigma->0) = -28.33385007 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 16) --------------------------------------- + + + POTLOK: cpu time 7.6492: real time 7.6675 + SETDIJ: cpu time 0.0015: real time 0.0015 + EDDIAG: cpu time 1.4678: real time 1.4713 + RMM-DIIS: cpu time 11.0973: real time 11.1242 + ORTHCH: cpu time 0.0528: real time 0.0529 + DOS: cpu time 0.0002: real time 0.0002 + CHARGE: cpu time 1.7628: real time 1.7670 + MIXING: cpu time 0.2388: real time 0.2393 + -------------------------------------------- + LOOP: cpu time 22.2703: real time 22.3240 + + eigenvalue-minimisations : 50 + total energy-change (2. order) :-0.7488643E-03 (-0.1972646E-03) + number of electron 16.0000000 magnetization + augmentation part 0.1098972 magnetization + + Broyden mixing: + rms(total) = 0.12681E-01 rms(broyden)= 0.12681E-01 + rms(prec ) = 0.13084E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.5914 + 4.3342 2.7215 2.7215 1.4116 1.4116 0.8397 0.8397 0.8249 0.8249 0.7876 + 0.7876 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1037.10399816 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.99572517 + PAW double counting = 5069.76820872 -5072.65677801 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.52870560 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.33459894 eV + + energy without entropy = -28.33459894 energy(sigma->0) = -28.33459894 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 17) --------------------------------------- + + + POTLOK: cpu time 7.6641: real time 7.6825 + SETDIJ: cpu time 0.0014: real time 0.0014 + EDDIAG: cpu time 1.4715: real time 1.4751 + RMM-DIIS: cpu time 7.9624: real time 7.9815 + ORTHCH: cpu time 0.0537: real time 0.0538 + DOS: cpu time 0.0004: real time 0.0004 + CHARGE: cpu time 1.7672: real time 1.7714 + MIXING: cpu time 0.2523: real time 0.2529 + -------------------------------------------- + LOOP: cpu time 19.1729: real time 19.2189 + + eigenvalue-minimisations : 33 + total energy-change (2. order) :-0.3167343E-02 (-0.4434230E-03) + number of electron 16.0000000 magnetization + augmentation part 0.1110904 magnetization + + Broyden mixing: + rms(total) = 0.24794E-01 rms(broyden)= 0.24794E-01 + rms(prec ) = 0.24910E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.6945 + 4.9876 3.0147 3.0147 1.8999 1.4618 0.8327 0.8327 0.8981 0.8981 0.7709 + 0.8611 0.8611 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.58120773 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.95954289 + PAW double counting = 5113.03990271 -5115.91860269 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -215.02835040 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.33776628 eV + + energy without entropy = -28.33776628 energy(sigma->0) = -28.33776628 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 18) --------------------------------------- + + + POTLOK: cpu time 7.6628: real time 7.6815 + SETDIJ: cpu time 0.0013: real time 0.0013 + EDDIAG: cpu time 1.4745: real time 1.4780 + RMM-DIIS: cpu time 9.8757: real time 9.8993 + ORTHCH: cpu time 0.0530: real time 0.0531 + DOS: cpu time 0.0002: real time 0.0002 + CHARGE: cpu time 1.7758: real time 1.7801 + MIXING: cpu time 0.2661: real time 0.2667 + -------------------------------------------- + LOOP: cpu time 21.1093: real time 21.1603 + + eigenvalue-minimisations : 41 + total energy-change (2. order) :-0.1578669E-02 (-0.9871864E-04) + number of electron 16.0000000 magnetization + augmentation part 0.1117241 magnetization + + Broyden mixing: + rms(total) = 0.28035E-01 rms(broyden)= 0.28035E-01 + rms(prec ) = 0.28269E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.8059 + 6.1918 3.3052 2.8921 2.1130 1.3960 1.3960 0.8338 0.8338 1.0096 0.9241 + 0.9241 0.8285 0.8285 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.46619351 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.94830038 + PAW double counting = 5096.98295366 -5099.85999531 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -215.13535913 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.33934495 eV + + energy without entropy = -28.33934495 energy(sigma->0) = -28.33934495 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 19) --------------------------------------- + + + POTLOK: cpu time 7.6500: real time 7.6684 + SETDIJ: cpu time 0.0017: real time 0.0017 + EDDIAG: cpu time 1.4812: real time 1.4848 + RMM-DIIS: cpu time 9.8993: real time 9.9234 + ORTHCH: cpu time 0.0517: real time 0.0519 + DOS: cpu time 0.0005: real time 0.0005 + CHARGE: cpu time 1.7687: real time 1.7729 + MIXING: cpu time 0.2779: real time 0.2786 + -------------------------------------------- + LOOP: cpu time 21.1310: real time 21.1820 + + eigenvalue-minimisations : 41 + total energy-change (2. order) :-0.5446741E-03 (-0.1128610E-03) + number of electron 16.0000000 magnetization + augmentation part 0.1110888 magnetization + + Broyden mixing: + rms(total) = 0.10695E-01 rms(broyden)= 0.10695E-01 + rms(prec ) = 0.10782E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.8664 + 7.3530 3.4623 2.6970 2.5457 1.5606 1.5606 0.8316 0.8316 0.9289 0.9289 + 0.9315 0.9315 0.7834 0.7834 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.83546504 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.96566088 + PAW double counting = 5074.45231031 -5077.33465365 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.77869108 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.33988962 eV + + energy without entropy = -28.33988962 energy(sigma->0) = -28.33988962 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 20) --------------------------------------- + + + POTLOK: cpu time 7.6816: real time 7.7000 + SETDIJ: cpu time 0.0013: real time 0.0013 + EDDIAG: cpu time 1.4711: real time 1.4747 + RMM-DIIS: cpu time 10.7993: real time 10.8255 + ORTHCH: cpu time 0.0525: real time 0.0526 + DOS: cpu time 0.0005: real time 0.0005 + CHARGE: cpu time 1.7435: real time 1.7477 + MIXING: cpu time 0.2951: real time 0.2958 + -------------------------------------------- + LOOP: cpu time 22.0448: real time 22.0980 + + eigenvalue-minimisations : 48 + total energy-change (2. order) :-0.3896540E-03 (-0.4392959E-04) + number of electron 16.0000000 magnetization + augmentation part 0.1106257 magnetization + + Broyden mixing: + rms(total) = 0.91288E-03 rms(broyden)= 0.91284E-03 + rms(prec ) = 0.97027E-03 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.8433 + 7.5249 3.5720 2.6232 2.6232 1.7286 1.7286 0.8324 0.8324 0.9641 0.9641 + 0.9609 0.9609 0.8030 0.8030 0.7279 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.94886690 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97098990 + PAW double counting = 5061.91304487 -5064.79697399 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.66942211 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34027928 eV + + energy without entropy = -28.34027928 energy(sigma->0) = -28.34027928 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 21) --------------------------------------- + + + POTLOK: cpu time 7.6440: real time 7.6623 + SETDIJ: cpu time 0.0016: real time 0.0016 + EDDIAG: cpu time 1.4817: real time 1.4853 + RMM-DIIS: cpu time 9.6796: real time 9.7029 + ORTHCH: cpu time 0.0510: real time 0.0511 + DOS: cpu time 0.0002: real time 0.0002 + CHARGE: cpu time 1.7590: real time 1.7632 + MIXING: cpu time 0.3120: real time 0.3127 + -------------------------------------------- + LOOP: cpu time 20.9290: real time 20.9793 + + eigenvalue-minimisations : 40 + total energy-change (2. order) :-0.2304305E-03 (-0.1690825E-05) + number of electron 16.0000000 magnetization + augmentation part 0.1106527 magnetization + + Broyden mixing: + rms(total) = 0.11007E-02 rms(broyden)= 0.11007E-02 + rms(prec ) = 0.11423E-02 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.9766 + 8.1563 3.5608 3.5608 3.0999 2.2672 1.5556 1.5556 0.8324 0.8324 0.9398 + 0.9398 1.0940 0.7925 0.7925 0.8567 0.7884 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.92222360 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.96938540 + PAW double counting = 5062.03953197 -5064.92302841 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.69512401 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34050971 eV + + energy without entropy = -28.34050971 energy(sigma->0) = -28.34050971 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 22) --------------------------------------- + + + POTLOK: cpu time 7.6715: real time 7.6903 + SETDIJ: cpu time 0.0013: real time 0.0013 + EDDIAG: cpu time 1.4612: real time 1.4647 + RMM-DIIS: cpu time 9.5592: real time 9.5821 + ORTHCH: cpu time 0.0527: real time 0.0528 + DOS: cpu time 0.0006: real time 0.0006 + CHARGE: cpu time 1.7689: real time 1.7731 + MIXING: cpu time 0.3289: real time 0.3296 + -------------------------------------------- + LOOP: cpu time 20.8442: real time 20.8945 + + eigenvalue-minimisations : 39 + total energy-change (2. order) :-0.1835709E-03 (-0.4515843E-05) + number of electron 16.0000000 magnetization + augmentation part 0.1105401 magnetization + + Broyden mixing: + rms(total) = 0.23291E-02 rms(broyden)= 0.23291E-02 + rms(prec ) = 0.23404E-02 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.9358 + 8.5288 4.1348 2.8889 2.8889 2.2825 1.6181 1.6181 0.8326 0.8326 1.2001 + 0.9319 0.9319 0.9169 0.8578 0.8578 0.7936 0.7936 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.99415945 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97309131 + PAW double counting = 5061.88628724 -5064.77078764 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.62607370 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34069328 eV + + energy without entropy = -28.34069328 energy(sigma->0) = -28.34069328 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 23) --------------------------------------- + + + POTLOK: cpu time 7.6847: real time 7.7031 + SETDIJ: cpu time 0.0015: real time 0.0015 + EDDIAG: cpu time 1.4751: real time 1.4786 + RMM-DIIS: cpu time 10.9934: real time 11.0202 + ORTHCH: cpu time 0.0524: real time 0.0525 + DOS: cpu time 0.0006: real time 0.0006 + CHARGE: cpu time 1.7744: real time 1.7787 + MIXING: cpu time 0.3422: real time 0.3431 + -------------------------------------------- + LOOP: cpu time 22.3243: real time 22.3783 + + eigenvalue-minimisations : 49 + total energy-change (2. order) :-0.6534761E-04 (-0.2114694E-05) + number of electron 16.0000000 magnetization + augmentation part 0.1104497 magnetization + + Broyden mixing: + rms(total) = 0.30474E-02 rms(broyden)= 0.30474E-02 + rms(prec ) = 0.30786E-02 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.9913 + 8.8375 4.8274 2.6647 2.6647 2.4899 2.4899 1.5568 1.5568 0.8326 0.8326 + 0.9301 0.9301 1.0541 0.9548 0.8349 0.8349 0.7758 0.7758 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1037.01437174 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97414565 + PAW double counting = 5063.01440221 -5065.89921135 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.60667235 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34075863 eV + + energy without entropy = -28.34075863 energy(sigma->0) = -28.34075863 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 24) --------------------------------------- + + + POTLOK: cpu time 7.6941: real time 7.7125 + SETDIJ: cpu time 0.0016: real time 0.0016 + EDDIAG: cpu time 1.4770: real time 1.4805 + RMM-DIIS: cpu time 9.3615: real time 9.3840 + ORTHCH: cpu time 0.0525: real time 0.0527 + DOS: cpu time 0.0005: real time 0.0005 + CHARGE: cpu time 1.7790: real time 1.7833 + MIXING: cpu time 0.3601: real time 0.3609 + -------------------------------------------- + LOOP: cpu time 20.7263: real time 20.7760 + + eigenvalue-minimisations : 37 + total energy-change (2. order) :-0.3766322E-04 (-0.1162993E-05) + number of electron 16.0000000 magnetization + augmentation part 0.1105096 magnetization + + Broyden mixing: + rms(total) = 0.14979E-02 rms(broyden)= 0.14979E-02 + rms(prec ) = 0.15134E-02 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 2.0035 + 9.1899 5.1470 3.1409 2.5758 2.5758 2.0364 2.0364 1.3098 1.3098 0.8325 + 0.8325 0.9235 0.9235 0.9698 0.9698 0.8381 0.8381 0.8086 0.8086 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.97627491 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97205780 + PAW double counting = 5064.76746833 -5067.65178680 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.64320966 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34079629 eV + + energy without entropy = -28.34079629 energy(sigma->0) = -28.34079629 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 25) --------------------------------------- + + + POTLOK: cpu time 7.6689: real time 7.6876 + SETDIJ: cpu time 0.0014: real time 0.0014 + EDDIAG: cpu time 1.4631: real time 1.4667 + RMM-DIIS: cpu time 10.8421: real time 10.8681 + ORTHCH: cpu time 0.0524: real time 0.0525 + DOS: cpu time 0.0005: real time 0.0005 + CHARGE: cpu time 1.7725: real time 1.7767 + MIXING: cpu time 0.3848: real time 0.3857 + -------------------------------------------- + LOOP: cpu time 22.1857: real time 22.2391 + + eigenvalue-minimisations : 48 + total energy-change (2. order) :-0.1596734E-04 (-0.6312087E-06) + number of electron 16.0000000 magnetization + augmentation part 0.1105646 magnetization + + Broyden mixing: + rms(total) = 0.44451E-03 rms(broyden)= 0.44451E-03 + rms(prec ) = 0.45027E-03 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 2.0446 + 9.2331 5.5481 3.0483 3.0483 2.5706 2.3725 2.3725 1.4898 1.4898 0.8326 + 0.8326 0.9257 0.9257 1.0221 1.0221 0.8965 0.7977 0.7977 0.8331 0.8331 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.96043559 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97118114 + PAW double counting = 5065.35881755 -5068.24291531 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.65840899 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34081226 eV + + energy without entropy = -28.34081226 energy(sigma->0) = -28.34081226 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 26) --------------------------------------- + + + POTLOK: cpu time 7.6901: real time 7.7085 + SETDIJ: cpu time 0.0013: real time 0.0013 + EDDIAG: cpu time 1.4703: real time 1.4742 + RMM-DIIS: cpu time 10.1219: real time 10.1462 + ORTHCH: cpu time 0.0525: real time 0.0527 + DOS: cpu time 0.0004: real time 0.0004 + CHARGE: cpu time 1.7717: real time 1.7760 + MIXING: cpu time 0.3987: real time 0.3997 + -------------------------------------------- + LOOP: cpu time 21.5069: real time 21.5588 + + eigenvalue-minimisations : 43 + total energy-change (2. order) :-0.1249405E-04 (-0.1004617E-06) + number of electron 16.0000000 magnetization + augmentation part 0.1105830 magnetization + + Broyden mixing: + rms(total) = 0.17005E-03 rms(broyden)= 0.17005E-03 + rms(prec ) = 0.17141E-03 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 2.0330 + 9.3115 5.9022 3.2871 2.8646 2.8646 2.2565 2.2565 1.6593 1.6593 0.8326 + 0.8326 0.9109 0.9109 1.0371 1.0371 0.8212 0.8212 0.8490 0.8490 0.8850 + 0.8459 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.95277230 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97074023 + PAW double counting = 5066.04516731 -5068.92918969 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.66571925 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34082475 eV + + energy without entropy = -28.34082475 energy(sigma->0) = -28.34082475 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 27) --------------------------------------- + + + POTLOK: cpu time 7.7511: real time 7.7698 + SETDIJ: cpu time 0.0014: real time 0.0014 + EDDIAG: cpu time 1.4775: real time 1.4810 + RMM-DIIS: cpu time 9.9866: real time 10.0108 + ORTHCH: cpu time 0.0521: real time 0.0523 + DOS: cpu time 0.0003: real time 0.0003 + CHARGE: cpu time 2.0870: real time 2.0920 + MIXING: cpu time 0.4892: real time 0.4904 + -------------------------------------------- + LOOP: cpu time 21.8452: real time 21.8980 + + eigenvalue-minimisations : 42 + total energy-change (2. order) :-0.4542188E-05 (-0.6904532E-07) + number of electron 16.0000000 magnetization + augmentation part 0.1105978 magnetization + + Broyden mixing: + rms(total) = 0.39214E-03 rms(broyden)= 0.39214E-03 + rms(prec ) = 0.39467E-03 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 2.0403 + 9.3674 6.0689 3.7670 2.8401 2.8401 2.5393 2.5393 1.6557 1.6557 0.8326 + 0.8326 0.9238 0.9238 1.0668 0.9729 0.9729 0.9112 0.9112 0.8440 0.8440 + 0.7892 0.7892 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.94457693 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97027781 + PAW double counting = 5066.03676746 -5068.92068946 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.67355713 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34082929 eV + + energy without entropy = -28.34082929 energy(sigma->0) = -28.34082929 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 28) --------------------------------------- + + + POTLOK: cpu time 8.9558: real time 8.9829 + SETDIJ: cpu time 0.0017: real time 0.0018 + EDDIAG: cpu time 1.7457: real time 1.7499 + RMM-DIIS: cpu time 12.4906: real time 12.5207 + ORTHCH: cpu time 0.0531: real time 0.0532 + DOS: cpu time 0.0003: real time 0.0003 + CHARGE: cpu time 2.2062: real time 2.2119 + MIXING: cpu time 0.5461: real time 0.5474 + -------------------------------------------- + LOOP: cpu time 25.9997: real time 26.0681 + + eigenvalue-minimisations : 42 + total energy-change (2. order) :-0.2690320E-05 (-0.5570044E-08) + number of electron 16.0000000 magnetization + augmentation part 0.1105992 magnetization + + Broyden mixing: + rms(total) = 0.26696E-03 rms(broyden)= 0.26696E-03 + rms(prec ) = 0.27060E-03 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 2.0422 + 9.4431 6.4254 4.3745 2.9914 2.9914 2.5250 1.8991 1.8991 1.5419 1.5419 + 0.8326 0.8326 0.9185 0.9185 1.0226 1.0226 0.9525 0.9525 0.8024 0.8024 + 0.8202 0.8202 0.6410 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.94511102 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97030255 + PAW double counting = 5065.65718800 -5068.54111932 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.67304114 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34083198 eV + + energy without entropy = -28.34083198 energy(sigma->0) = -28.34083198 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 29) --------------------------------------- + + + POTLOK: cpu time 9.3987: real time 9.4269 + SETDIJ: cpu time 0.0015: real time 0.0015 + EDDIAG: cpu time 1.7531: real time 1.7573 + RMM-DIIS: cpu time 10.9870: real time 11.0143 + ORTHCH: cpu time 0.0532: real time 0.0533 + DOS: cpu time 0.0004: real time 0.0004 + CHARGE: cpu time 2.1558: real time 2.1611 + MIXING: cpu time 0.5771: real time 0.5785 + -------------------------------------------- + LOOP: cpu time 24.9266: real time 24.9931 + + eigenvalue-minimisations : 34 + total energy-change (2. order) :-0.9984269E-06 (-0.1780315E-08) + number of electron 16.0000000 magnetization + augmentation part 0.1105978 magnetization + + Broyden mixing: + rms(total) = 0.19719E-03 rms(broyden)= 0.19719E-03 + rms(prec ) = 0.20075E-03 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 2.0237 + 9.4686 6.5653 4.5536 2.9419 2.9419 2.6868 2.2582 1.6878 1.6878 1.3519 + 0.8326 0.8326 0.9069 0.9069 0.9566 0.9566 1.0217 1.0217 0.9058 0.9058 + 0.8140 0.8140 0.7751 0.7751 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.94637307 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97036793 + PAW double counting = 5065.52770425 -5068.41165017 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.67183088 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34083298 eV + + energy without entropy = -28.34083298 energy(sigma->0) = -28.34083298 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 30) --------------------------------------- + + + POTLOK: cpu time 8.9642: real time 8.9860 + SETDIJ: cpu time 0.0015: real time 0.0015 + EDDIAG: cpu time 1.6174: real time 1.6224 + RMM-DIIS: cpu time 11.7490: real time 11.7779 + ORTHCH: cpu time 0.0619: real time 0.0621 + DOS: cpu time 0.0006: real time 0.0006 + CHARGE: cpu time 2.1670: real time 2.1736 + MIXING: cpu time 0.6128: real time 0.6143 + -------------------------------------------- + LOOP: cpu time 25.1744: real time 25.2383 + + eigenvalue-minimisations : 42 + total energy-change (2. order) :-0.4557878E-06 (-0.6069651E-08) + number of electron 16.0000000 magnetization + augmentation part 0.1105934 magnetization + + Broyden mixing: + rms(total) = 0.14046E-03 rms(broyden)= 0.14046E-03 + rms(prec ) = 0.14236E-03 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 2.0432 + 9.4786 6.8086 4.8374 2.9755 2.9755 2.5612 2.2733 2.2733 1.6314 1.6314 + 1.2040 1.2040 0.8326 0.8326 0.9236 0.9236 0.9498 0.9498 0.9065 0.8808 + 0.8808 0.8134 0.8134 0.7591 0.7591 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.94860821 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97048719 + PAW double counting = 5065.57246986 -5068.45644144 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.66968978 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34083344 eV + + energy without entropy = -28.34083344 energy(sigma->0) = -28.34083344 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 31) --------------------------------------- + + + POTLOK: cpu time 9.0231: real time 9.0447 + SETDIJ: cpu time 0.0023: real time 0.0023 + EDDIAG: cpu time 1.8458: real time 1.8510 + RMM-DIIS: cpu time 11.3205: real time 11.3497 + ORTHCH: cpu time 0.0655: real time 0.0656 + DOS: cpu time 0.0004: real time 0.0004 + CHARGE: cpu time 2.1578: real time 2.1631 + MIXING: cpu time 0.6525: real time 0.6540 + -------------------------------------------- + LOOP: cpu time 25.0678: real time 25.1309 + + eigenvalue-minimisations : 39 + total energy-change (2. order) :-0.5099819E-06 (-0.5763795E-08) + number of electron 16.0000000 magnetization + augmentation part 0.1105892 magnetization + + Broyden mixing: + rms(total) = 0.49855E-04 rms(broyden)= 0.49855E-04 + rms(prec ) = 0.50730E-04 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 2.0610 + 9.5062 7.0952 4.9171 2.8109 2.8109 3.0317 2.5806 2.5806 1.6558 1.6558 + 1.2909 1.2909 0.8326 0.8326 0.9175 0.9175 1.0173 1.0173 0.9439 0.9439 + 0.8921 0.8921 0.8001 0.8001 0.7761 0.7761 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.95083535 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97060732 + PAW double counting = 5065.51832384 -5068.40231851 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.66756020 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34083395 eV + + energy without entropy = -28.34083395 energy(sigma->0) = -28.34083395 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 32) --------------------------------------- + + + POTLOK: cpu time 9.4370: real time 9.4610 + SETDIJ: cpu time 0.0014: real time 0.0014 + EDDIAG: cpu time 1.7846: real time 1.7890 + RMM-DIIS: cpu time 10.2647: real time 10.2908 + ORTHCH: cpu time 0.0572: real time 0.0574 + DOS: cpu time 0.0003: real time 0.0003 + CHARGE: cpu time 2.2263: real time 2.2382 + MIXING: cpu time 0.6502: real time 0.6518 + -------------------------------------------- + LOOP: cpu time 24.4217: real time 24.4897 + + eigenvalue-minimisations : 34 + total energy-change (2. order) :-0.3252635E-06 (-0.1585956E-08) + number of electron 16.0000000 magnetization + augmentation part 0.1105879 magnetization + + Broyden mixing: + rms(total) = 0.20063E-04 rms(broyden)= 0.20063E-04 + rms(prec ) = 0.20440E-04 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.9955 + 9.5104 7.0833 4.9415 2.8746 2.8746 2.9148 2.5976 2.5976 1.6371 1.6371 + 1.1962 1.1962 0.8326 0.8326 0.9142 0.9142 0.9920 0.9920 0.9590 0.9590 + 0.9058 0.8575 0.7923 0.7923 0.7626 0.7626 0.5478 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.95185260 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97066329 + PAW double counting = 5065.53060872 -5068.41461353 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.66658910 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34083427 eV + + energy without entropy = -28.34083427 energy(sigma->0) = -28.34083427 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 33) --------------------------------------- + + + POTLOK: cpu time 9.2407: real time 9.2630 + SETDIJ: cpu time 0.0017: real time 0.0017 + EDDIAG: cpu time 1.4769: real time 1.4817 + RMM-DIIS: cpu time 11.3022: real time 11.3307 + ORTHCH: cpu time 0.0631: real time 0.0632 + DOS: cpu time 0.0005: real time 0.0005 + CHARGE: cpu time 2.3118: real time 2.3174 + MIXING: cpu time 0.6911: real time 0.6929 + -------------------------------------------- + LOOP: cpu time 25.0881: real time 25.1512 + + eigenvalue-minimisations : 38 + total energy-change (2. order) :-0.6773371E-07 (-0.1062542E-08) + number of electron 16.0000000 magnetization + augmentation part 0.1105866 magnetization + + Broyden mixing: + rms(total) = 0.91623E-05 rms(broyden)= 0.91622E-05 + rms(prec ) = 0.93300E-05 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 2.0350 + 9.5609 7.3253 5.2812 3.4093 3.0686 3.0686 2.5176 2.5176 1.6549 1.6549 + 1.3593 1.3593 0.8326 0.8326 1.1378 1.1378 0.9187 0.9187 0.9231 0.9231 + 0.9599 0.9599 0.8044 0.8044 0.8670 0.7837 0.7837 0.6135 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.95231133 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97068818 + PAW double counting = 5065.53250092 -5068.41651070 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.66615036 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34083434 eV + + energy without entropy = -28.34083434 energy(sigma->0) = -28.34083434 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 34) --------------------------------------- + + + POTLOK: cpu time 8.9953: real time 9.0236 + SETDIJ: cpu time 0.0013: real time 0.0013 + EDDIAG: cpu time 1.7498: real time 1.7541 + RMM-DIIS: cpu time 10.2017: real time 10.2275 + ORTHCH: cpu time 0.0697: real time 0.0699 + DOS: cpu time 0.0010: real time 0.0010 + CHARGE: cpu time 2.3582: real time 2.3639 + MIXING: cpu time 0.7483: real time 0.7500 + -------------------------------------------- + LOOP: cpu time 24.1252: real time 24.1912 + + eigenvalue-minimisations : 30 + total energy-change (2. order) :-0.1850694E-06 (-0.1083993E-08) + number of electron 16.0000000 magnetization + augmentation part 0.1105855 magnetization + + Broyden mixing: + rms(total) = 0.24782E-04 rms(broyden)= 0.24782E-04 + rms(prec ) = 0.25063E-04 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 2.0617 + 9.6214 7.6279 5.7723 3.9386 3.0939 3.0939 2.4466 2.3085 2.3085 1.6327 + 1.6327 1.2031 1.2031 0.8326 0.8326 0.9145 0.9145 0.9829 0.9829 1.0725 + 1.0725 0.8797 0.8439 0.8439 0.7937 0.7937 0.7513 0.7513 0.6430 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.95290231 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97072072 + PAW double counting = 5065.51687695 -5068.40089356 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.66558527 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34083452 eV + + energy without entropy = -28.34083452 energy(sigma->0) = -28.34083452 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 35) --------------------------------------- + + + POTLOK: cpu time 8.6297: real time 8.6582 + SETDIJ: cpu time 0.0016: real time 0.0016 + EDDIAG: cpu time 1.6518: real time 1.6558 + RMM-DIIS: cpu time 10.4320: real time 10.4580 + ORTHCH: cpu time 0.0607: real time 0.0608 + DOS: cpu time 0.0006: real time 0.0006 + CHARGE: cpu time 1.9045: real time 1.9091 + MIXING: cpu time 0.6194: real time 0.6209 + -------------------------------------------- + LOOP: cpu time 23.3002: real time 23.3650 + + eigenvalue-minimisations : 30 + total energy-change (2. order) :-0.1145991E-06 (-0.9243699E-09) + number of electron 16.0000000 magnetization + augmentation part 0.1105845 magnetization + + Broyden mixing: + rms(total) = 0.45365E-04 rms(broyden)= 0.45365E-04 + rms(prec ) = 0.45860E-04 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 2.0554 + 9.6712 7.9403 5.8112 4.2777 3.1164 3.1164 2.4899 2.2563 2.2563 1.7099 + 1.7099 1.1221 1.1221 0.8326 0.8326 1.0892 1.0892 0.9200 0.9200 1.0619 + 0.9253 0.9253 0.8041 0.8041 0.8891 0.8891 0.8492 0.8492 0.6905 0.6905 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.95334531 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97074540 + PAW double counting = 5065.50118967 -5068.38521272 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.66516064 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34083464 eV + + energy without entropy = -28.34083464 energy(sigma->0) = -28.34083464 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 36) --------------------------------------- + + + POTLOK: cpu time 8.5828: real time 8.6041 + SETDIJ: cpu time 0.0014: real time 0.0014 + EDDIAG: cpu time 1.6693: real time 1.6733 + RMM-DIIS: cpu time 10.6530: real time 10.6839 + ORTHCH: cpu time 0.0590: real time 0.0592 + DOS: cpu time 0.0007: real time 0.0007 + CHARGE: cpu time 1.8482: real time 1.8527 + MIXING: cpu time 0.6495: real time 0.6511 + -------------------------------------------- + LOOP: cpu time 23.4638: real time 23.5263 + + eigenvalue-minimisations : 32 + total energy-change (2. order) :-0.3223522E-07 (-0.2489422E-09) + number of electron 16.0000000 magnetization + augmentation part 0.1105843 magnetization + + Broyden mixing: + rms(total) = 0.32658E-04 rms(broyden)= 0.32658E-04 + rms(prec ) = 0.33131E-04 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.9959 + 9.6676 7.9536 5.7782 4.2761 3.1497 3.1497 2.4817 2.3720 1.8707 1.8707 + 1.6817 1.1331 1.1331 0.8326 0.8326 1.0821 1.0821 0.9215 0.9215 1.1164 + 0.9019 0.9019 0.8046 0.8046 0.9055 0.9055 0.8548 0.8548 0.2562 0.6878 + 0.6878 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.95291144 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97072221 + PAW double counting = 5065.51919258 -5068.40321087 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.66557610 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34083467 eV + + energy without entropy = -28.34083467 energy(sigma->0) = -28.34083467 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 37) --------------------------------------- + + + POTLOK: cpu time 8.5484: real time 8.5704 + SETDIJ: cpu time 0.0016: real time 0.0016 + EDDIAG: cpu time 1.6819: real time 1.6859 + RMM-DIIS: cpu time 11.5559: real time 11.5900 + ORTHCH: cpu time 0.0610: real time 0.0611 + DOS: cpu time 0.0006: real time 0.0006 + -------------------------------------------- + LOOP: cpu time 21.8493: real time 21.9095 + + eigenvalue-minimisations : 35 + total energy-change (2. order) :-0.5719812E-08 (-0.5881873E-10) + number of electron 16.0000000 magnetization + augmentation part 0.1105843 magnetization + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 0.09670462 + Ewald energy TEWEN = 247.39057564 + -Hartree energ DENC = -1036.95274706 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 63.97071319 + PAW double counting = 5065.51950922 -5068.40352550 + entropy T*S EENTRO = -0.00000000 + eigenvalues EBANDS = -214.66573348 + atomic energy EATOM = 914.70366869 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -28.34083468 eV + + energy without entropy = -28.34083468 energy(sigma->0) = -28.34083468 + + +-------------------------------------------------------------------------------------------------------- + + + + + average (electrostatic) potential at core + the test charge radii are 0.5955 0.4325 + (the norm of the test charge is 1.0000) + 1-119.5768 2-119.7330 3 -46.9125 4 -47.1157 5 -47.1365 + 6 -47.1399 + + + + E-fermi : -6.7437 XC(G=0): -0.1760 alpha+bet : -0.0402 + + + k-point 1 : 0.0000 0.0000 0.0000 + band No. band energies occupation + 1 -24.7993 2.00000 + 2 -24.6817 2.00000 + 3 -12.6088 2.00000 + 4 -12.4638 2.00000 + 5 -9.3687 2.00000 + 6 -9.2323 2.00000 + 7 -7.1633 2.00000 + 8 -7.0149 2.00000 + 9 -1.2206 0.00000 + 10 -1.0215 0.00000 + 11 0.0535 0.00000 + 12 0.2161 0.00000 + 13 0.2366 0.00000 + 14 0.2520 0.00000 + 15 0.3607 0.00000 + 16 0.5197 0.00000 + + +-------------------------------------------------------------------------------------------------------- + + + soft charge-density along one line, spin component 1 + 0 1 2 3 4 5 6 7 8 9 + total charge-density along one line + + pseudopotential strength for first ion, spin component: 1 + 26.736 32.699 0.059 -0.001 -0.040 0.078 -0.001 -0.053 + 32.699 39.992 0.072 -0.001 -0.049 0.095 -0.001 -0.064 + 0.059 0.072 -9.436 0.001 -0.010 -12.552 0.001 -0.013 + -0.001 -0.001 0.001 -9.391 0.000 0.001 -12.491 0.001 + -0.040 -0.049 -0.010 0.000 -9.444 -0.013 0.001 -12.563 + 0.078 0.095 -12.552 0.001 -0.013 -16.684 0.001 -0.017 + -0.001 -0.001 0.001 -12.491 0.001 0.001 -16.602 0.001 + -0.053 -0.064 -0.013 0.001 -12.563 -0.017 0.001 -16.699 + total augmentation occupancy for first ion, spin component: 1 + 16.309 -14.437 -9.031 0.089 6.355 4.024 -0.039 -2.880 +-14.437 13.923 7.645 -0.075 -5.410 -3.600 0.035 2.589 + -9.031 7.645 8.123 -0.065 0.954 -3.668 0.042 -0.623 + 0.089 -0.075 -0.065 3.991 -0.047 0.042 -1.006 0.031 + 6.355 -5.410 0.954 -0.047 9.349 -0.624 0.031 -4.435 + 4.024 -3.600 -3.668 0.042 -0.624 1.693 -0.023 0.350 + -0.039 0.035 0.042 -1.006 0.031 -0.023 0.254 -0.017 + -2.880 2.589 -0.623 0.031 -4.435 0.350 -0.017 2.124 + + +------------------------ aborting loop because EDIFF is reached ---------------------------------------- + + + CHARGE: cpu time 2.3607: real time 2.3666 + FORLOC: cpu time 0.3467: real time 0.3476 + FORNL : cpu time 0.4188: real time 0.4200 + STRESS: cpu time 6.8955: real time 6.9122 + FORCOR: cpu time 8.2739: real time 8.2938 + FORHAR: cpu time 2.4135: real time 2.4198 + MIXING: cpu time 0.8330: real time 0.8350 + OFIELD: cpu time 0.0001: real time 0.0001 + + FORCE on cell =-STRESS in cart. coord. units (eV): + Direction XX YY ZZ XY YZ ZX + -------------------------------------------------------------------------------------- + Alpha Z 0.09670 0.09670 0.09670 + Ewald 44.43709 111.97467 90.97875 48.57095 -1.05568 -1.20702 + Hartree 312.66211 364.44836 359.83992 10.84590 -0.21030 -0.23663 + E(xc) -72.99191 -72.83952 -72.99285 0.22421 -0.00560 -0.00579 + Local -643.16263 -754.02351 -737.27158 -44.88721 0.91799 1.06557 + n-local -42.68001 -41.36498 -42.37574 2.48098 -0.05873 -0.06449 + augment 1.32366 1.05934 1.33191 -0.32385 0.00853 0.00826 + Kinetic 398.16527 386.91763 397.59899 -18.18450 0.44415 0.47116 + Fock 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + ------------------------------------------------------------------------------------- + Total -2.14971 -3.73130 -2.79389 -1.27352 0.04036 0.03106 + in kB -0.51025 -0.88566 -0.66316 -0.30228 0.00958 0.00737 + external pressure = -0.69 kB Pullay stress = 0.00 kB + + + VOLUME and BASIS-vectors are now : + ----------------------------------------------------------------------------- + energy-cutoff : 1500.00 + volume of cell : 6750.00 + direct lattice vectors reciprocal lattice vectors + 30.000000000 0.000000000 0.000000000 0.033333333 0.000000000 0.000000000 + 0.000000000 15.000000000 0.000000000 0.000000000 0.066666667 0.000000000 + 0.000000000 0.000000000 15.000000000 0.000000000 0.000000000 0.066666667 + + length of vectors + 30.000000000 15.000000000 15.000000000 0.033333333 0.066666667 0.066666667 + + + FORCES acting on ions + electron-ion (+dipol) ewald-force non-local-force convergence-correction + ----------------------------------------------------------------------------------------------- + -.468E+02 0.442E+02 -.434E+00 0.746E+02 -.847E+02 0.837E+00 -.285E+02 0.429E+02 -.435E+00 0.128E-03 -.208E-03 0.192E-05 + -.741E+01 -.487E+02 0.190E-01 0.279E+02 0.930E+02 -.552E-01 -.216E+02 -.467E+02 0.512E-01 0.918E-04 0.193E-03 -.298E-06 + -.305E+02 -.762E+02 0.127E+01 0.320E+02 0.800E+02 -.133E+01 -.228E+01 -.620E+01 0.103E+00 -.133E-04 -.819E-04 0.125E-05 + 0.808E+02 -.472E+01 -.462E+00 -.865E+02 0.507E+01 0.494E+00 0.728E+01 -.451E+00 -.394E-01 0.816E-04 -.217E-04 -.209E-06 + 0.230E+02 0.440E+02 -.664E+02 -.242E+02 -.465E+02 0.702E+02 0.173E+01 0.369E+01 -.552E+01 0.231E-04 0.490E-04 -.494E-04 + 0.227E+02 0.443E+02 0.663E+02 -.239E+02 -.469E+02 -.701E+02 0.171E+01 0.372E+01 0.552E+01 0.229E-04 0.492E-04 0.493E-04 + ----------------------------------------------------------------------------------------------- + 0.417E+02 0.301E+01 0.320E+00 0.000E+00 0.213E-13 -.142E-13 -.417E+02 -.301E+01 -.320E+00 0.334E-03 -.211E-04 0.257E-05 + + + POSITION TOTAL-FORCE (eV/Angst) + ----------------------------------------------------------------------------------- + 3.63802 1.57110 1.76000 -0.719072 2.472756 -0.030872 + 26.36198 1.57110 1.76000 -1.075376 -2.334989 0.015085 + 3.95828 2.55412 1.74392 -0.810143 -2.365156 0.038942 + 2.63613 1.66728 1.76493 1.525263 -0.107359 -0.008087 + 26.09174 0.99418 2.56104 0.545647 1.167904 -1.728483 + 26.09550 0.99080 0.96072 0.533680 1.166843 1.713414 + ----------------------------------------------------------------------------------- + total drift: 0.000060 -0.000041 -0.000020 + + +-------------------------------------------------------------------------------------------------------- + + + + FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) + --------------------------------------------------- + free energy TOTEN = -28.34083468 eV + + energy without entropy= -28.34083468 energy(sigma->0) = -28.34083468 + + + +-------------------------------------------------------------------------------------------------------- + + + POTLOK: cpu time 9.0386: real time 9.0662 + + +-------------------------------------------------------------------------------------------------------- + + + LOOP+: cpu time 859.2600: real time 861.4263 + 4ORBIT: cpu time 0.0000: real time 0.0000 + + total amount of memory used by VASP MPI-rank0 1504469. kBytes +======================================================================= + + base : 30000. kBytes + nonl-proj : 199352. kBytes + fftplans : 295613. kBytes + grid : 965246. kBytes + one-center: 18. kBytes + wavefun : 14240. kBytes + + + + General timing and accounting informations for this job: + ======================================================== + + Total CPU time used (sec): 877.816 + User time (sec): 847.517 + System time (sec): 30.300 + Elapsed time (sec): 880.605 + + Maximum memory used (kb): 3453896. + Average memory used (kb): 0. + + Minor page faults: 702128 + Major page faults: 7 + Voluntary context switches: 10645 diff --git a/docs/nb/try_dpdata.ipynb b/docs/nb/try_dpdata.ipynb new file mode 100644 index 00000000..7dc225b4 --- /dev/null +++ b/docs/nb/try_dpdata.ipynb @@ -0,0 +1,73 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Try dpdata online" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import dpdata" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "system = dpdata.LabeledSystem(\"OUTCAR\", fmt=\"vasp/outcar\", type_map=[\"O\", \"H\"])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "system[\"energies\"]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "system[\"forces\"]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "system.to(\"lammps/lmp\", \"conf.lmp\", frame_idx=0)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "with open(\"conf.lmp\") as f:\n", + " print(f.read())" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/docs/rtd_environment.yml b/docs/rtd_environment.yml new file mode 100644 index 00000000..2752fc1c --- /dev/null +++ b/docs/rtd_environment.yml @@ -0,0 +1,6 @@ +name: dpdata +channels: + - https://repo.mamba.pm/conda-forge +dependencies: + - pip: + - ..[docs] diff --git a/docs/try_dpdata.rst b/docs/try_dpdata.rst new file mode 100644 index 00000000..fba69153 --- /dev/null +++ b/docs/try_dpdata.rst @@ -0,0 +1,4 @@ +Try dpdata online +================= + +.. retrolite:: nb/try_dpdata.ipynb diff --git a/dpdata/__init__.py b/dpdata/__init__.py index 036643c0..dd853697 100644 --- a/dpdata/__init__.py +++ b/dpdata/__init__.py @@ -1,3 +1,16 @@ +# monty needs lzma +# See https://github.com/pandas-dev/pandas/pull/27882 +try: + import lzma # noqa: F401 +except ImportError: + + class fakemodule: + pass + + import sys + + sys.modules["lzma"] = fakemodule + from . import lammps, md, vasp from .system import LabeledSystem, MultiSystems, System diff --git a/dpdata/deepmd/hdf5.py b/dpdata/deepmd/hdf5.py index f2ee9c8a..0bae0694 100644 --- a/dpdata/deepmd/hdf5.py +++ b/dpdata/deepmd/hdf5.py @@ -1,8 +1,12 @@ """Utils for deepmd/hdf5 format.""" +from __future__ import annotations + import warnings -from typing import Optional, Union -import h5py +try: + import h5py +except ImportError: + pass import numpy as np from wcmatch.glob import globfilter @@ -12,9 +16,9 @@ def to_system_data( - f: Union[h5py.File, h5py.Group], + f: h5py.File | h5py.Group, folder: str, - type_map: Optional[list] = None, + type_map: list | None = None, labels: bool = True, ): """Load a HDF5 file. @@ -151,7 +155,7 @@ def to_system_data( def dump( - f: Union[h5py.File, h5py.Group], + f: h5py.File | h5py.Group, folder: str, data: dict, set_size=5000, diff --git a/dpdata/plugins/deepmd.py b/dpdata/plugins/deepmd.py index 6953aba5..9daadcf3 100644 --- a/dpdata/plugins/deepmd.py +++ b/dpdata/plugins/deepmd.py @@ -1,7 +1,11 @@ +from __future__ import annotations + import os -from typing import List, Optional, Union -import h5py +try: + import h5py +except ImportError: + pass import numpy as np import dpdata @@ -170,8 +174,8 @@ class DeePMDHDF5Format(Format): def _from_system( self, - file_name: Union[str, h5py.Group, h5py.File], - type_map: List[str], + file_name: str | (h5py.Group | h5py.File), + type_map: list[str], labels: bool, ): """Convert HDF5 file to System or LabeledSystem data. @@ -214,8 +218,8 @@ def _from_system( def from_system( self, - file_name: Union[str, h5py.Group, h5py.File], - type_map: Optional[List[str]] = None, + file_name: str | (h5py.Group | h5py.File), + type_map: list[str] | None = None, **kwargs, ) -> dict: """Convert HDF5 file to System data. @@ -244,8 +248,8 @@ def from_system( def from_labeled_system( self, - file_name: Union[str, h5py.Group, h5py.File], - type_map: Optional[List[str]] = None, + file_name: str | (h5py.Group | h5py.File), + type_map: list[str] | None = None, **kwargs, ) -> dict: """Convert HDF5 file to LabeledSystem data. @@ -275,7 +279,7 @@ def from_labeled_system( def to_system( self, data: dict, - file_name: Union[str, h5py.Group, h5py.File], + file_name: str | (h5py.Group | h5py.File), set_size: int = 5000, comp_prec: np.dtype = np.float64, **kwargs, @@ -331,7 +335,7 @@ def from_multi_systems(self, directory: str, **kwargs) -> h5py.Group: yield f[ff] def to_multi_systems( - self, formulas: List[str], directory: str, **kwargs + self, formulas: list[str], directory: str, **kwargs ) -> h5py.Group: """Generate HDF5 groups, which will be passed to `to_system`. diff --git a/pyproject.toml b/pyproject.toml index 087d6ff9..bca3e2d3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,6 +55,8 @@ docs = [ 'deepmodeling-sphinx>=0.1.1', 'sphinx-argparse', 'rdkit', + 'jupyterlite-sphinx', + 'jupyterlite-xeus-python', ] [tool.setuptools.packages.find] From e73531bb178d489fa82bf2e60d5a2739e4cb5646 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Sun, 15 Oct 2023 10:53:44 -0400 Subject: [PATCH 11/18] limit the filename length dumped by MultiSystems (#554) Fix #553. --------- Signed-off-by: Jinzhe Zeng Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- dpdata/system.py | 49 ++++++++++++++++++++++++++++++++++++-- dpdata/utils.py | 5 ++++ tests/test_multisystems.py | 34 ++++++++++++++++++++++++++ 3 files changed, 86 insertions(+), 2 deletions(-) diff --git a/dpdata/system.py b/dpdata/system.py index 0748db28..f1273104 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -1,5 +1,6 @@ # %% import glob +import hashlib import os import warnings from copy import deepcopy @@ -19,7 +20,13 @@ from dpdata.driver import Driver, Minimizer from dpdata.format import Format from dpdata.plugin import Plugin -from dpdata.utils import add_atom_names, elements_index_map, remove_pbc, sort_atom_names +from dpdata.utils import ( + add_atom_names, + elements_index_map, + remove_pbc, + sort_atom_names, + utf8len, +) def load_format(fmt): @@ -562,6 +569,42 @@ def uniq_formula(self): ] ) + @property + def short_formula(self) -> str: + """Return the short formula of this system. Elements with zero number + will be removed. + """ + return "".join( + [ + f"{symbol}{numb}" + for symbol, numb in zip( + self.data["atom_names"], self.data["atom_numbs"] + ) + if numb + ] + ) + + @property + def formula_hash(self) -> str: + """Return the hash of the formula of this system.""" + return hashlib.sha256(self.formula.encode("utf-8")).hexdigest() + + @property + def short_name(self) -> str: + """Return the short name of this system (no more than 255 bytes), in + the following order: + - formula + - short_formula + - formula_hash. + """ + formula = self.formula + if utf8len(formula) <= 255: + return formula + short_formula = self.short_formula + if utf8len(short_formula) <= 255: + return short_formula + return self.formula_hash + def extend(self, systems): """Extend a system list to this system. @@ -1247,7 +1290,9 @@ def from_fmt_obj(self, fmtobj, directory, labeled=True, **kwargs): def to_fmt_obj(self, fmtobj, directory, *args, **kwargs): if not isinstance(fmtobj, dpdata.plugins.deepmd.DeePMDMixedFormat): for fn, ss in zip( - fmtobj.to_multi_systems(self.systems.keys(), directory, **kwargs), + fmtobj.to_multi_systems( + [ss.short_name for ss in self.systems.values()], directory, **kwargs + ), self.systems.values(), ): ss.to_fmt_obj(fmtobj, fn, *args, **kwargs) diff --git a/dpdata/utils.py b/dpdata/utils.py index da726179..cf4a109e 100644 --- a/dpdata/utils.py +++ b/dpdata/utils.py @@ -99,3 +99,8 @@ def uniq_atom_names(data): sum(ii == data["atom_types"]) for ii in range(len(data["atom_names"])) ] return data + + +def utf8len(s: str) -> int: + """Return the byte length of a string.""" + return len(s.encode("utf-8")) diff --git a/tests/test_multisystems.py b/tests/test_multisystems.py index 172c2ad4..2bda13a9 100644 --- a/tests/test_multisystems.py +++ b/tests/test_multisystems.py @@ -1,7 +1,9 @@ import os +import tempfile import unittest from itertools import permutations +import numpy as np from comp_sys import CompLabeledSys, IsNoPBC, MultiSystems from context import dpdata @@ -200,5 +202,37 @@ def setUp(self): self.atom_names = ["C", "H", "O"] +class TestLongFilename(unittest.TestCase): + def test_long_filename1(self): + system = dpdata.System( + data={ + "atom_names": [f"TYPE{ii}" for ii in range(200)], + "atom_numbs": [1] + [0 for _ in range(199)], + "atom_types": np.arange(1), + "coords": np.zeros((1, 1, 3)), + "orig": np.zeros(3), + "cells": np.zeros((1, 3, 3)), + } + ) + ms = dpdata.MultiSystems(system) + with tempfile.TemporaryDirectory() as tmpdir: + ms.to_deepmd_npy(tmpdir) + + def test_long_filename2(self): + system = dpdata.System( + data={ + "atom_names": [f"TYPE{ii}" for ii in range(200)], + "atom_numbs": [1 for _ in range(200)], + "atom_types": np.arange(200), + "coords": np.zeros((1, 200, 3)), + "orig": np.zeros(3), + "cells": np.zeros((1, 3, 3)), + } + ) + ms = dpdata.MultiSystems(system) + with tempfile.TemporaryDirectory() as tmpdir: + ms.to_deepmd_npy(tmpdir) + + if __name__ == "__main__": unittest.main() From 3f35ac6870e6263032f222c07f35483b22e464b7 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Sun, 15 Oct 2023 10:54:15 -0400 Subject: [PATCH 12/18] fix SciPy DeprecationWarning (#551) --- dpdata/amber/md.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dpdata/amber/md.py b/dpdata/amber/md.py index ef058828..279ce55e 100644 --- a/dpdata/amber/md.py +++ b/dpdata/amber/md.py @@ -2,7 +2,7 @@ import re import numpy as np -from scipy.io import netcdf +from scipy.io import netcdf_file from dpdata.amber.mask import pick_by_amber_mask from dpdata.unit import EnergyConversion @@ -77,7 +77,7 @@ def read_amber_traj( for ii in use_element_symbols: amber_types[ii] = symbols[atomic_number[ii]] - with netcdf.netcdf_file(nc_file, "r") as f: + with netcdf_file(nc_file, "r") as f: coords = np.array(f.variables["coordinates"][:]) cell_lengths = np.array(f.variables["cell_lengths"][:]) cell_angles = np.array(f.variables["cell_angles"][:]) @@ -92,7 +92,7 @@ def read_amber_traj( raise RuntimeError("Unsupported cells") if labeled: - with netcdf.netcdf_file(mdfrc_file, "r") as f: + with netcdf_file(mdfrc_file, "r") as f: forces = np.array(f.variables["forces"][:]) # load energy from mden_file or mdout_file From dbe2bc9377f8cf08647d0ac28064fd45aea1121e Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Thu, 19 Oct 2023 21:05:05 -0400 Subject: [PATCH 13/18] update issue templates (#557) Copied from DeePMD-kit with minor changes, which I think is good enough. --- .github/ISSUE_TEMPLATE/bug_report.md | 25 ----------- .github/ISSUE_TEMPLATE/bug_report.yml | 49 ++++++++++++++++++++++ .github/ISSUE_TEMPLATE/config.yml | 5 +++ .github/ISSUE_TEMPLATE/feature_request.md | 21 ---------- .github/ISSUE_TEMPLATE/feature_request.yml | 33 +++++++++++++++ .github/ISSUE_TEMPLATE/generic-issue.md | 17 -------- .github/ISSUE_TEMPLATE/generic-issue.yml | 39 +++++++++++++++++ .github/ISSUE_TEMPLATE/request-for-help.md | 21 ---------- 8 files changed, 126 insertions(+), 84 deletions(-) delete mode 100644 .github/ISSUE_TEMPLATE/bug_report.md create mode 100644 .github/ISSUE_TEMPLATE/bug_report.yml create mode 100644 .github/ISSUE_TEMPLATE/config.yml delete mode 100644 .github/ISSUE_TEMPLATE/feature_request.md create mode 100644 .github/ISSUE_TEMPLATE/feature_request.yml delete mode 100644 .github/ISSUE_TEMPLATE/generic-issue.md create mode 100644 .github/ISSUE_TEMPLATE/generic-issue.yml delete mode 100644 .github/ISSUE_TEMPLATE/request-for-help.md diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md deleted file mode 100644 index b9591ad0..00000000 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ /dev/null @@ -1,25 +0,0 @@ ---- -name: Bug report -about: Create a bug report to help us eliminate issues and improve dpdata. If this - doesn’t look right, [choose a different type](https://github.com/deepmodeling/dpdata/issues/new/choose). -title: "[BUG] _Replace With Suitable Title_" -labels: bug -assignees: '' - ---- - -**Summary** - - - - - - - -**Steps to Reproduce** - - - -**Further Information, Files, and Links** - - diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml new file mode 100644 index 00000000..f25c32d3 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -0,0 +1,49 @@ +name: Bug report +description: Create a bug report to help us eliminate issues and improve deepmd-kit. +title: "[BUG] " +labels: bug +assignees: [] +body: + - type: textarea + id: summary + attributes: + label: Bug summary + description: Please provide a clear and concise description of what the bug is. + placeholder: + value: + validations: + required: true + - type: input + id: version + attributes: + label: dpdata Version + description: "`dpdata --version`" + validations: + required: true + - type: textarea + id: log + attributes: + label: Input Files, Running Commands, Error Log, etc. + description: "Please provide necessary information including input file, running commands, error log , etc., AS DETAILED AS POSSIBLE to help locate and reproduce your problem. WARNING: Do not use image to show error log! Paste texts in a code block instead." + placeholder: + value: + validations: + required: true + - type: textarea + id: reproduce + attributes: + label: Steps to Reproduce + description: "Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem." + placeholder: + value: + validations: + required: true + - type: textarea + id: further + attributes: + label: Further Information, Files, and Links + description: Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications + placeholder: + value: + validations: + required: false diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 00000000..9c8e4e88 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,5 @@ +blank_issues_enabled: false +contact_links: + - name: Request for Help + url: https://github.com/deepmodeling/dpdata/discussions/new?category=q-a + about: If you have an usage question diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md deleted file mode 100644 index 0af5c953..00000000 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ /dev/null @@ -1,21 +0,0 @@ ---- -name: Feature request -about: Suggest an idea for this project. If this doesn’t work right, [choose a different - type]( https://github.com/deepmodeling/dpdata/issues/new/choose). -title: "[Feature Request] _Replace with Title_" -labels: enhancement -assignees: '' - ---- - -**Summary** - - - -**Detailed Description** - - - -**Further Information, Files, and Links** - - diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml new file mode 100644 index 00000000..18781a84 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -0,0 +1,33 @@ +name: Feature request +description: Suggest an idea for this project. +title: "[Feature Request] " +labels: enhancement +assignees: [] +body: + - type: textarea + id: summary + attributes: + label: Summary + description: "Please provide a brief and concise description of the suggested feature or change" + placeholder: + value: + validations: + required: true + - type: textarea + id: details + attributes: + label: Detailed Description + description: "Please explain how you would like to see deepmd-kit enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address." + placeholder: + value: + validations: + required: true + - type: textarea + id: further + attributes: + label: Further Information, Files, and Links + description: Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications + placeholder: + value: + validations: + required: false diff --git a/.github/ISSUE_TEMPLATE/generic-issue.md b/.github/ISSUE_TEMPLATE/generic-issue.md deleted file mode 100644 index 8ae84e1c..00000000 --- a/.github/ISSUE_TEMPLATE/generic-issue.md +++ /dev/null @@ -1,17 +0,0 @@ ---- -name: Generic issue -about: For issues that do not fit any of the other categories. If this doesn’t work - right, [choose a different type]( https://github.com/deepmodeling/dpdata/issues/new/choose). -title: '' -labels: wontfix -assignees: '' - ---- - -**Summary** - - - -**Details** - - diff --git a/.github/ISSUE_TEMPLATE/generic-issue.yml b/.github/ISSUE_TEMPLATE/generic-issue.yml new file mode 100644 index 00000000..fbc5bca8 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/generic-issue.yml @@ -0,0 +1,39 @@ +name: Generic issue +description: For issues that do not fit any of the other categories. +labels: wontfix +assignees: [] +body: + - type: textarea + id: summary + attributes: + label: Summary + description: "Please provide a clear and concise description of what the question is." + placeholder: + value: + validations: + required: true + - type: input + id: version + attributes: + label: dpdata Version + description: "`dpdata --version`" + validations: + required: true + - type: textarea + id: other-version + attributes: + label: Platform, Python Version, etc + description: "If applicable, specify what platform you are running on." + placeholder: + value: + validations: + required: false + - type: textarea + id: details + attributes: + label: Details + description: "Please explain the issue in detail here." + placeholder: + value: + validations: + required: true diff --git a/.github/ISSUE_TEMPLATE/request-for-help.md b/.github/ISSUE_TEMPLATE/request-for-help.md deleted file mode 100644 index ad05a34d..00000000 --- a/.github/ISSUE_TEMPLATE/request-for-help.md +++ /dev/null @@ -1,21 +0,0 @@ ---- -name: Request for Help -about: Don't post help requests here, go to [discussions](https://github.com/deepmodeling/dpdata/discussions) - instead. If this doesn’t look right, choose a different type. -title: '' -labels: '' -assignees: '' - ---- - -Before asking questions, you can - -search the previous issues or discussions -check the [README](https://github.com/deepmodeling/dpdata/#readme). - -Please **do not** post requests for help (e.g. with installing or using dpdata) here. -Instead go to [discussions](https://github.com/deepmodeling/dpdata/discussions). - -This issue tracker is for tracking dpdata development related issues only. - -Thanks for your cooperation. From 36d1e2ec033cfee939dd52946a52ca38a652bdfa Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 24 Oct 2023 10:19:39 +0800 Subject: [PATCH 14/18] [pre-commit.ci] pre-commit autoupdate (#559) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 23.9.1 → 23.10.0](https://github.com/psf/black/compare/23.9.1...23.10.0) - [github.com/astral-sh/ruff-pre-commit: v0.0.292 → v0.1.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.292...v0.1.1) --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 4 ++-- dpdata/system.py | 6 +----- 2 files changed, 3 insertions(+), 7 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c461a1e8..ca94baf5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,12 +18,12 @@ repos: - id: check-toml # Python - repo: https://github.com/psf/black - rev: 23.9.1 + rev: 23.10.0 hooks: - id: black-jupyter - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.0.292 + rev: v0.1.1 hooks: - id: ruff args: ["--fix"] diff --git a/dpdata/system.py b/dpdata/system.py index f1273104..a75e0e88 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -752,11 +752,7 @@ def replace(self, initial_atom_type, end_atom_type, replace_num): if replace_num > max_replace_num: raise RuntimeError( - "not enough {initial_atom_type} atom, only {max_replace_num} available, less than {replace_num}.Please check.".format( - initial_atom_type=initial_atom_type, - max_replace_num=max_replace_num, - replace_num=replace_num, - ) + f"not enough {initial_atom_type} atom, only {max_replace_num} available, less than {replace_num}.Please check." ) may_replace_indices = [ From 1b55e6cf2362a4d22a26a0cf87b97e59eb694a43 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 24 Oct 2023 10:19:52 +0800 Subject: [PATCH 15/18] [pre-commit.ci] pre-commit autoupdate (#559) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 23.9.1 → 23.10.0](https://github.com/psf/black/compare/23.9.1...23.10.0) - [github.com/astral-sh/ruff-pre-commit: v0.0.292 → v0.1.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.292...v0.1.1) --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> From 7fb45d88452886572edba7f48269c79fb84fb22e Mon Sep 17 00:00:00 2001 From: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com> Date: Mon, 30 Oct 2023 17:12:13 -0400 Subject: [PATCH 16/18] add decrecaption warning when dpdata throws errors while parsing cp2k (#558) Squashed commit of the following: commit dfb6191a4c468482105e4720feb9bb8e625cb070 Merge: 1b55e6c 5028af6 Author: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com> Date: Mon Oct 30 22:02:15 2023 +0100 add decrecaption warning when dpdata throws errors while parsing cp2k (#558) commit 5028af6961f82ed368655730e0bbaa6ed0704672 Author: robinzyb <38876805+robinzyb@users.noreply.github.com> Date: Mon Oct 30 21:28:21 2023 +0100 raise PendingDeprecationWarning commit 3ee373dd80adb9e471026c6956afc661461e37fa Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon Oct 30 19:51:57 2023 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit cec3fc26a079f976601fe74dc83178f885502ae1 Author: robinzyb <38876805+robinzyb@users.noreply.github.com> Date: Mon Oct 30 20:51:26 2023 +0100 add exact except for the cp2k plugin. commit 7a09854a85505460cb7ed1cb330264fa17c4ebb0 Author: robinzyb <38876805+robinzyb@users.noreply.github.com> Date: Mon Oct 30 20:38:23 2023 +0100 fixed typo in checking cp2k pattern match. commit 1a4b98522a462eaf08dff222cca438760561b44b Author: robinzyb <38876805+robinzyb@users.noreply.github.com> Date: Mon Oct 30 14:34:50 2023 +0100 update error for cp2k aimdoutput if none pattern is matched commit a1a171a98ed315cc58814f7cede239e44a5ab28c Merge: 621d686 1b55e6c Author: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com> Date: Mon Oct 30 13:59:10 2023 +0100 Merge branch 'deepmodeling:devel' into devel commit 621d686ac4f1df8423ea21594584cf5f0748b932 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri Oct 20 22:53:54 2023 +0000 [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci commit 03cc010a9ae73b11471b7872870482ef4b6d7345 Author: robinzyb <38876805+robinzyb@users.noreply.github.com> Date: Sat Oct 21 00:50:51 2023 +0200 add decrecaption warning when dpdata throws errors while parsing cp2k commit 0576449a57ba244ab5b37ebdf242933002a3921e Merge: 4840bbc dbe2bc9 Author: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com> Date: Sat Oct 21 00:30:18 2023 +0200 Merge branch 'deepmodeling:devel' into devel commit 4840bbcb575de3659e4b582dfef097aa63af53f8 Author: robinzyb <38876805+robinzyb@users.noreply.github.com> Date: Thu Sep 7 14:12:19 2023 +0200 Update README.md for recommendation of using cp2kdata --- dpdata/cp2k/output.py | 8 +++++++ dpdata/plugins/cp2k.py | 49 +++++++++++++++++++++++++++++------------- 2 files changed, 42 insertions(+), 15 deletions(-) diff --git a/dpdata/cp2k/output.py b/dpdata/cp2k/output.py index 0b08c51e..0c8df6d7 100644 --- a/dpdata/cp2k/output.py +++ b/dpdata/cp2k/output.py @@ -76,12 +76,14 @@ def __next__(self): def get_log_block_generator(self): lines = [] delimiter_flag = False + yield_flag = False while True: line = self.log_file_object.readline() if line: lines.append(line) if any(p.match(line) for p in delimiter_patterns): if delimiter_flag is True: + yield_flag = True yield lines lines = [] delimiter_flag = False @@ -91,17 +93,23 @@ def get_log_block_generator(self): if any(p.match(line) for p in avail_patterns): delimiter_flag = True else: + if not yield_flag: + raise StopIteration("None of the delimiter patterns are matched") break if delimiter_flag is True: raise RuntimeError("This file lacks some content, please check") def get_xyz_block_generator(self): p3 = re.compile(r"^\s*(\d+)\s*") + yield_flag = False while True: line = self.xyz_file_object.readline() if not line: + if not yield_flag: + raise StopIteration("None of the xyz patterns are matched") break if p3.match(line): + yield_flag = True atom_num = int(p3.match(line).group(1)) lines = [] lines.append(line) diff --git a/dpdata/plugins/cp2k.py b/dpdata/plugins/cp2k.py index 1f09adae..162098f7 100644 --- a/dpdata/plugins/cp2k.py +++ b/dpdata/plugins/cp2k.py @@ -4,29 +4,48 @@ from dpdata.cp2k.output import Cp2kSystems from dpdata.format import Format +string_warning = """ +Hi, you got an error from dpdata, +please check if your cp2k files include full information, +otherwise its version is not supported by dpdata. +Try use dpdata plugin from cp2kdata package, +for details, please refer to +https://robinzyb.github.io/cp2kdata/ +""" + @Format.register("cp2k/aimd_output") class CP2KAIMDOutputFormat(Format): def from_labeled_system(self, file_name, restart=False, **kwargs): xyz_file = sorted(glob.glob(f"{file_name}/*pos*.xyz"))[0] log_file = sorted(glob.glob(f"{file_name}/*.log"))[0] - return tuple(Cp2kSystems(log_file, xyz_file, restart)) + try: + return tuple(Cp2kSystems(log_file, xyz_file, restart)) + except (StopIteration, RuntimeError) as e: + # StopIteration is raised when pattern match is failed + raise PendingDeprecationWarning(string_warning) from e @Format.register("cp2k/output") class CP2KOutputFormat(Format): def from_labeled_system(self, file_name, restart=False, **kwargs): - data = {} - ( - data["atom_names"], - data["atom_numbs"], - data["atom_types"], - data["cells"], - data["coords"], - data["energies"], - data["forces"], - tmp_virial, - ) = dpdata.cp2k.output.get_frames(file_name) - if tmp_virial is not None: - data["virials"] = tmp_virial - return data + try: + data = {} + ( + data["atom_names"], + data["atom_numbs"], + data["atom_types"], + data["cells"], + data["coords"], + data["energies"], + data["forces"], + tmp_virial, + ) = dpdata.cp2k.output.get_frames(file_name) + if tmp_virial is not None: + data["virials"] = tmp_virial + return data + # TODO: in the future, we should add exact error type here + # TODO: when pattern match is failed + # TODO: For now just use RuntimeError as a placeholder. + except RuntimeError as e: + raise PendingDeprecationWarning(string_warning) from e From a9374617da8799dff81f07192602cbf071c222ed Mon Sep 17 00:00:00 2001 From: Peng Xingliang <91927439+pxlxingliang@users.noreply.github.com> Date: Tue, 31 Oct 2023 08:53:39 +0800 Subject: [PATCH 17/18] abacus: update the read of stress and force for ABACUS v3.4.1 (#560) Signed-off-by: Peng Xingliang <91927439+pxlxingliang@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- dpdata/abacus/relax.py | 26 +- dpdata/abacus/scf.py | 85 +- .../OUT.abacus/running_cell-relax.log.v341 | 1450 +++++++++++++++++ tests/abacus.relax/force.v341.ref | 8 + tests/abacus.relax/stress.v341.ref | 12 + tests/test_abacus_relax.py | 52 + 6 files changed, 1599 insertions(+), 34 deletions(-) create mode 100644 tests/abacus.relax/OUT.abacus/running_cell-relax.log.v341 create mode 100644 tests/abacus.relax/force.v341.ref create mode 100644 tests/abacus.relax/stress.v341.ref diff --git a/dpdata/abacus/relax.py b/dpdata/abacus/relax.py index b9cb9905..346120c4 100644 --- a/dpdata/abacus/relax.py +++ b/dpdata/abacus/relax.py @@ -2,7 +2,15 @@ import numpy as np -from .scf import bohr2ang, get_cell, get_coords, get_geometry_in, kbar2evperang3 +from .scf import ( + bohr2ang, + collect_force, + collect_stress, + get_cell, + get_coords, + get_geometry_in, + kbar2evperang3, +) # Read in geometries from an ABACUS RELAX(CELL-RELAX) trajectory in OUT.XXXX/runnning_relax/cell-relax.log. @@ -40,8 +48,6 @@ def get_coords_from_log(loglines, natoms): energy = [] cells = [] coords = [] - force = [] - stress = [] coord_direct = [] # if the coordinate is direct type or not for i in range(len(loglines)): @@ -91,18 +97,8 @@ def get_coords_from_log(loglines, natoms): # get the energy of current structure energy.append(float(line.split()[-2])) - elif line[4:15] == "TOTAL-FORCE": - force.append([]) - for j in range(5, 5 + natoms): - force[-1].append( - list(map(lambda x: float(x), loglines[i + j].split()[1:4])) - ) - elif line[1:13] == "TOTAL-STRESS": - stress.append([]) - for j in range(4, 7): - stress[-1].append( - list(map(lambda x: float(x), loglines[i + j].split()[0:3])) - ) + force = collect_force(loglines) + stress = collect_stress(loglines) # delete last structures which has no energy while len(energy) < len(coords): diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py index fbd658b4..11f8e411 100644 --- a/dpdata/abacus/scf.py +++ b/dpdata/abacus/scf.py @@ -1,5 +1,6 @@ import os import re +import warnings import numpy as np @@ -123,33 +124,79 @@ def get_energy(outlines): return Etot, False -def get_force(outlines, natoms): +def collect_force(outlines): force = [] - force_inlines = get_block( - outlines, "TOTAL-FORCE (eV/Angstrom)", skip=4, nlines=np.sum(natoms) - ) - if force_inlines is None: - print( - "TOTAL-FORCE (eV/Angstrom) is not found in OUT.XXX/running_scf.log. May be you haven't set 'cal_force 1' in the INPUT." - ) + for i, line in enumerate(outlines): + if "TOTAL-FORCE (eV/Angstrom)" in line: + value_pattern = re.compile( + r"^\s*[A-Z][a-z]?[1-9][0-9]*\s+[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s+[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s+[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s*$" + ) + j = i + # find the first line of force + noforce = False + while not value_pattern.match(outlines[j]): + j += 1 + if ( + j >= i + 10 + ): # if can not find the first line of force in 10 lines, then stop + warnings.warn("Warning: can not find the first line of force") + noforce = True + break + if noforce: + break + + force.append([]) + while value_pattern.match(outlines[j]): + force[-1].append([float(ii) for ii in outlines[j].split()[1:4]]) + j += 1 + return force # only return the last force + + +def get_force(outlines, natoms): + force = collect_force(outlines) + if len(force) == 0: return [[]] - for line in force_inlines: - force.append([float(f) for f in line.split()[1:4]]) - force = np.array(force) - return force + else: + return np.array(force[-1]) # only return the last force -def get_stress(outlines): +def collect_stress(outlines): stress = [] - stress_inlines = get_block(outlines, "TOTAL-STRESS (KBAR)", skip=3, nlines=3) - if stress_inlines is None: - return None - for line in stress_inlines: - stress.append([float(f) for f in line.split()]) - stress = np.array(stress) * kbar2evperang3 + for i, line in enumerate(outlines): + if "TOTAL-STRESS (KBAR)" in line: + value_pattern = re.compile( + r"^\s*[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s+[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s+[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s*$" + ) + j = i + nostress = False + while not value_pattern.match(outlines[j]): + j += 1 + if ( + j >= i + 10 + ): # if can not find the first line of stress in 10 lines, then stop + warnings.warn("Warning: can not find the first line of stress") + nostress = True + break + if nostress: + break + + stress.append([]) + while value_pattern.match(outlines[j]): + stress[-1].append( + list(map(lambda x: float(x), outlines[j].split()[0:3])) + ) + j += 1 return stress +def get_stress(outlines): + stress = collect_stress(outlines) + if len(stress) == 0: + return None + else: + return np.array(stress[-1]) * kbar2evperang3 # only return the last stress + + def get_frame(fname): data = { "atom_names": [], diff --git a/tests/abacus.relax/OUT.abacus/running_cell-relax.log.v341 b/tests/abacus.relax/OUT.abacus/running_cell-relax.log.v341 new file mode 100644 index 00000000..b5af2a8a --- /dev/null +++ b/tests/abacus.relax/OUT.abacus/running_cell-relax.log.v341 @@ -0,0 +1,1450 @@ + + ABACUS v3.4.0 + + Atomic-orbital Based Ab-initio Computation at UStc + + Website: http://abacus.ustc.edu.cn/ + Documentation: https://abacus.deepmodeling.com/ + Repository: https://github.com/abacusmodeling/abacus-develop + https://github.com/deepmodeling/abacus-develop + Commit: b1ac4a406 (Mon Oct 23 11:34:46 2023 +0000) + + Start Time is Fri Oct 27 16:46:11 2023 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + DRANK = 1 + DSIZE = 1 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + The esolver type has been set to : ksdft_lcao + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | 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 + lattice constant (Bohr) = 15 + lattice constant (Angstrom) = 7.93766 + + READING ATOM TYPE 1 + atom label = Si + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 2 + + TOTAL ATOM NUMBER = 2 + + CARTESIAN COORDINATES ( UNIT = 15 Bohr ). + atom x y z mag vx vy vz + tauc_Si1 0 0 0 0 0 0 0 + tauc_Si2 0.280000000001 0 0 0 0 0 0 + + + Volume (Bohr^3) = 3375 + Volume (A^3) = 500.122803248 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +1 +0 +0 + +0 +1 +0 + +0 +0 +1 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +1 -0 +0 + -0 +1 -0 + +0 -0 +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.pz-vbc.UPF + pseudopotential type = NC + exchange-correlation functional = PZ + nonlocal core correction = 0 + valence electrons = 4 + lmax = 1 + number of zeta = 2 + number of projectors = 2 + L of projector = 0 + L of projector = 1 + initial pseudo atomic orbital number = 8 + NLOCAL = 26 + + Warning_Memory_Consuming allocated: FFT::grid 11.390625 MB + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | 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. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + fft grid for charge/potential = [ 72, 72, 72 ] + fft grid division = [ 4, 4, 4 ] + big fft grid for charge/potential = [ 18, 18, 18 ] + nbxx = 5832 + nrxx = 373248 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 161235 + number of sticks = 3577 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3577 161235 + --------------- sum ------------------- + 1 3577 161235 + number of |g| = 952 + max |g| = 1139 + min |g| = 0 + + SETUP THE ELECTRONS NUMBER + electron number of element Si = 4 + total electron number of element Si = 8 + AUTOSET number of electrons: = 8 + DONE : SETUP UNITCELL Time : 0.0486588095191 (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 = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.048920802732 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of wave functions: | + | 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. The number of plane wave of | + | each k-point is 'npwk[ik]' in each processor | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + energy cutoff for wavefunc (unit:Ry) = 50 + fft grid for wave functions = [ 72, 72, 72 ] + number of plane waves = 20005 + number of sticks = 885 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(POT) PW + 1 885 20005 + --------------- sum ------------------- + 1 885 20005 + DONE : INIT PLANEWAVE Time : 0.0542848928781 (SEC) + + occupied bands = 4 + NLOCAL = 26 + NBANDS = 16 + NBANDS = 16 + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../tests/PP_ORB/./Si_lda_8.0au_50Ry_2s2p1d + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 801 0.01 8 1 1 + 2 0 1 801 0.01 8 1 1 + 3 1 0 801 0.01 8 1 1 + 4 1 1 801 0.01 8 1 1 + 5 2 0 801 0.01 8 1 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 2 + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + global2local_row dimension = 26 + global2local_col dimension = 26 + nloc = 676 + + ------------------------------------------- + STEP OF RELAXATION : 1 + ------------------------------------------- + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 8 + longest nonlocal projector rcut (Bohr) = 5.01 + searching radius is (Bohr)) = 16 + searching radius unit is (Bohr)) = 15 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + real space grid = [ 72, 72, 72 ] + big cell numbers in grid = [ 18, 18, 18 ] + meshcell numbers in big cell = [ 4, 4, 4 ] + extended fft grid = [ 10, 10, 10 ] + dimension of extened grid = [ 39, 39, 39 ] + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 26 + lgd_last = 0 + lgd_now = 26 + allocate DM , the dimension is 26 + enter setAlltoallvParameter, nblk = 1 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 26 + nCol_in_proc = 26 +receiver_size is 676 ; receiver_size of each process is: +676 +sender_size is 676 ; sender_size of each process is: +676 + init_chg = atomic + DONE : INIT SCF Time : 0.279638 (SEC) + + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb +--------------AUTO-SET--------------- + Autoset mixing_beta to 0.7 + Autoset mixing_gg0 to 0 +------------------------------------- + + Density error is 0.180751569625 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2013293385 -206.8246961780 +E_Harris -15.2425400057 -207.3853960707 +E_Fermi -0.3598643762 -4.8962060240 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.156065124267 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2013815120 -206.8254060345 +E_Harris -14.9858718979 -203.8932473090 +E_Fermi -0.2889518174 -3.9313911636 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.126809290852 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2150325554 -207.0111380095 +E_Harris -15.2614471843 -207.6426414320 +E_Fermi -0.2916013792 -3.9674403015 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0297310465631 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2172217249 -207.0409231883 +E_Harris -15.2632171873 -207.6667235584 +E_Fermi -0.2994278914 -4.0739254636 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0204748350331 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2174675539 -207.0442678628 +E_Harris -15.2150578457 -207.0114821006 +E_Fermi -0.2979257327 -4.0534875459 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00358291297937 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175843784 -207.0458573418 +E_Harris -15.2144099768 -207.0026673923 +E_Fermi -0.2980888472 -4.0557068323 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000137852112476 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175868493 -207.0458909609 +E_Harris -15.2179842616 -207.0512980320 +E_Fermi -0.2980849031 -4.0556531704 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000156704081621 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175868470 -207.0458909294 +E_Harris -15.2175271722 -207.0450790117 +E_Fermi -0.2980751674 -4.0555207089 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000113776247889 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175868406 -207.0458908424 +E_Harris -15.2176057193 -207.0461476993 +E_Fermi -0.2980749477 -4.0555177197 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 2.48976074747e-05 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175868443 -207.0458908926 +E_Harris -15.2176039592 -207.0461237527 +E_Fermi -0.2980747535 -4.0555150779 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 2.80280522713e-06 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175868445 -207.0458908952 +E_Harris -15.2175833005 -207.0458426764 +E_Fermi -0.2980747918 -4.0555155986 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 8.04650129094e-08 +---------------------------------------------------------- + Energy Rydberg eV +---------------------------------------------------------- +E_KohnSham -15.2175868445 -207.0458908945 +E_KS(sigma->0) -15.2099423104 -206.9418816723 +E_Harris -15.2175873168 -207.0458973209 +E_band -4.0123371487 -54.5906475198 +E_one_elec -15.2862509698 -207.9801142474 +E_Hartree 8.3645248125 113.8051985122 +E_xc -4.1857282688 -56.9497547355 +E_Ewald -4.0948433501 -55.7132019794 +E_entropy(-TS) -0.0152890682 -0.2080184444 +E_descf 0.0000000000 0.0000000000 +E_exx 0.0000000000 0.0000000000 +E_Fermi -0.2980747966 -4.0555156635 +---------------------------------------------------------- + + charge density convergence is achieved + final etot is -207.04589089 eV + EFERMI = -4.0555156635 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0.0000 0.0000 0.0000 (20005 pws) + 1 -11.4912 2.00000 + 2 -7.60755 2.00000 + 3 -4.11584 1.46934 + 4 -4.08812 1.26533 + 5 -4.08812 1.26533 + 6 -1.05823 0.00000 + 7 -1.05823 0.00000 + 8 3.33208 0.00000 + 9 4.05667 0.00000 + 10 5.18172 0.00000 + 11 6.86533 0.00000 + 12 6.86533 0.00000 + 13 8.35917 0.00000 + 14 8.52401 0.00000 + 15 8.52822 0.00000 + 16 8.81287 0.00000 + + correction force for each atom along direction 1 is 2.15932e-05 + correction force for each atom along direction 2 is -6.31203e-16 + correction force for each atom along direction 3 is -9.43934e-16 +TOTAL-FORCE (eV/Angstrom) +--------------------------------------------------------------------- +atom x y z +--------------------------------------------------------------------- + Si1 -0.2989839750 0.0000000000 0.0000000000 + Si2 0.2989839750 0.0000000000 0.0000000000 +--------------------------------------------------------------------- +---------------------------------------------------------------- +TOTAL-STRESS (KBAR) +---------------------------------------------------------------- + -1.5384243115 0.0000000000 0.0000000000 + 0.0000000000 1.2876244979 -0.0000000000 + 0.0000000000 -0.0000000000 1.2876244979 +---------------------------------------------------------------- + + Relaxation is not converged yet! + + CARTESIAN COORDINATES ( UNIT = 15.0000 Bohr ). + atom x y z mag vx vy vz + tauc_Si1 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + tauc_Si2 0.281883326846 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + + + ------------------------------------------- + STEP OF RELAXATION : 2 + ------------------------------------------- + Find the file, try to read charge from file. + read in fermi energy = 0.00000000000 + NEW-OLD atomic charge density approx. for the potential ! + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 8.00 + longest nonlocal projector rcut (Bohr) = 5.01 + searching radius is (Bohr)) = 16.0 + searching radius unit is (Bohr)) = 15.0 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + real space grid = [ 72, 72, 72 ] + big cell numbers in grid = [ 18, 18, 18 ] + meshcell numbers in big cell = [ 4, 4, 4 ] + extended fft grid = [ 10, 10, 10 ] + dimension of extened grid = [ 39, 39, 39 ] + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 26 + lgd_last = 26 + lgd_now = 26 + allocate DM , the dimension is 26 + enter setAlltoallvParameter, nblk = 1 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 26 + nCol_in_proc = 26 +receiver_size is 676 ; receiver_size of each process is: +676 +sender_size is 676 ; sender_size of each process is: +676 + DONE : INIT SCF Time : 1.79228 (SEC) + + + LCAO ALGORITHM --------------- ION= 2 ELEC= 1-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0168959452664 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2175193665 -207.0449728097 +E_Harris -15.2179258329 -207.0505030683 +E_Fermi -0.2961807006 -4.0297451654 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0518368215481 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2172250346 -207.0409682193 +E_Harris -15.2216102864 -207.1006326303 +E_Fermi -0.2971601774 -4.0430716311 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00105872951512 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178444285 -207.0493955048 +E_Harris -15.2054766907 -206.8811238002 +E_Fermi -0.2968921234 -4.0394245689 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00100941289269 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178436253 -207.0493845772 +E_Harris -15.2179620084 -207.0509952623 +E_Fermi -0.2968425058 -4.0387494881 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 5-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000251823216620 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178448408 -207.0494011151 +E_Harris -15.2181672626 -207.0537878884 +E_Fermi -0.2968538157 -4.0389033672 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 6-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 7.94344885985e-05 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178448969 -207.0494018779 +E_Harris -15.2179378279 -207.0506662690 +E_Fermi -0.2968736432 -4.0391731331 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 7-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 1.96702636175e-06 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178448984 -207.0494018988 +E_Harris -15.2178128589 -207.0489659785 +E_Fermi -0.2968701179 -4.0391251688 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 8-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 6.23634943039e-07 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2178448985 -207.0494018993 +E_Harris -15.2178453077 -207.0494074674 +E_Fermi -0.2968701568 -4.0391256982 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 2 ELEC= 9-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 2.92350762196e-08 +---------------------------------------------------------- + Energy Rydberg eV +---------------------------------------------------------- +E_KohnSham -15.2178448984 -207.0494018988 +E_KS(sigma->0) -15.2102395905 -206.9459263766 +E_Harris -15.2178450216 -207.0494035745 +E_band -4.0037521144 -54.4738421357 +E_one_elec -15.2087334264 -206.9254339622 +E_Hartree 8.3269386063 113.2938119414 +E_xc -4.1809665440 -56.8849681452 +E_Ewald -4.1398729186 -56.3258606885 +E_entropy(-TS) -0.0152106158 -0.2069510443 +E_descf 0.0000000000 0.0000000000 +E_exx 0.0000000000 0.0000000000 +E_Fermi -0.2968701674 -4.0391258425 +---------------------------------------------------------- + + charge density convergence is achieved + final etot is -207.04940190 eV + EFERMI = -4.0391258425 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0.0000 0.0000 0.0000 (20005 pws) + 1 -11.4492 2.00000 + 2 -7.62228 2.00000 + 3 -4.10453 1.50341 + 4 -4.06956 1.24829 + 5 -4.06956 1.24829 + 6 -1.08365 0.00000 + 7 -1.08365 0.00000 + 8 3.26511 0.00000 + 9 4.05898 0.00000 + 10 5.18262 0.00000 + 11 6.89861 0.00000 + 12 6.89861 0.00000 + 13 8.35639 0.00000 + 14 8.54894 0.00000 + 15 8.55303 0.00000 + 16 8.78009 0.00000 + + correction force for each atom along direction 1 is 5.02307e-05 + correction force for each atom along direction 2 is -1.83070e-15 + correction force for each atom along direction 3 is 1.04952e-15 +TOTAL-FORCE (eV/Angstrom) +--------------------------------------------------------------------- +atom x y z +--------------------------------------------------------------------- + Si1 -0.1699037102 0.0000000000 0.0000000000 + Si2 0.1699037102 0.0000000000 0.0000000000 +--------------------------------------------------------------------- +---------------------------------------------------------------- +TOTAL-STRESS (KBAR) +---------------------------------------------------------------- + -2.7115205254 0.0000000000 0.0000000000 + 0.0000000000 1.3189389796 -0.0000000000 + 0.0000000000 -0.0000000000 1.3189389796 +---------------------------------------------------------------- + + Relaxation is not converged yet! + + CARTESIAN COORDINATES ( UNIT = 15.0000 Bohr ). + atom x y z mag vx vy vz + tauc_Si1 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + tauc_Si2 0.284362282238 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + + + ------------------------------------------- + STEP OF RELAXATION : 3 + ------------------------------------------- + Find the file, try to read charge from file. + read in fermi energy = 0.00000000000 + first order charge density extrapolation ! + Find the file, try to read charge from file. + read in fermi energy = 0.00000000000 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 8.00 + longest nonlocal projector rcut (Bohr) = 5.01 + searching radius is (Bohr)) = 16.0 + searching radius unit is (Bohr)) = 15.0 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + real space grid = [ 72, 72, 72 ] + big cell numbers in grid = [ 18, 18, 18 ] + meshcell numbers in big cell = [ 4, 4, 4 ] + extended fft grid = [ 10, 10, 10 ] + dimension of extened grid = [ 39, 39, 39 ] + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 26 + lgd_last = 26 + lgd_now = 26 + allocate DM , the dimension is 26 + enter setAlltoallvParameter, nblk = 1 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 26 + nCol_in_proc = 26 +receiver_size is 676 ; receiver_size of each process is: +676 +sender_size is 676 ; sender_size of each process is: +676 + DONE : INIT SCF Time : 3.19119 (SEC) + + + LCAO ALGORITHM --------------- ION= 3 ELEC= 1-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00452212112666 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179529987 -207.0508726785 +E_Harris -15.2179805826 -207.0512479763 +E_Fermi -0.2950794152 -4.0147614098 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0126446908755 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179373608 -207.0506599138 +E_Harris -15.2187954433 -207.0623347249 +E_Fermi -0.2953608204 -4.0185901236 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000229871859222 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179750964 -207.0511733331 +E_Harris -15.2155778055 -207.0185565175 +E_Fermi -0.2952721438 -4.0173836165 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000176872107358 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179750602 -207.0511728399 +E_Harris -15.2179890170 -207.0513627329 +E_Fermi -0.2952608524 -4.0172299887 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 5-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 8.06397474901e-05 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179751026 -207.0511734175 +E_Harris -15.2180437080 -207.0521068422 +E_Fermi -0.2952644207 -4.0172785387 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 6-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 2.15700937431e-05 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179751084 -207.0511734970 +E_Harris -15.2179877479 -207.0513454651 +E_Fermi -0.2952680956 -4.0173285384 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 7-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 7.77406230596e-07 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179751085 -207.0511734981 +E_Harris -15.2179663378 -207.0510541662 +E_Fermi -0.2952667921 -4.0173108024 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 3 ELEC= 8-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 6.29333378635e-08 +---------------------------------------------------------- + Energy Rydberg eV +---------------------------------------------------------- +E_KohnSham -15.2179751086 -207.0511734985 +E_KS(sigma->0) -15.2104340875 -206.9485726434 +E_Harris -15.2179754374 -207.0511779730 +E_band -3.9924679519 -54.3203132277 +E_one_elec -15.1084379120 -205.5608434825 +E_Hartree 8.2784245173 112.6337438987 +E_xc -4.1748487553 -56.8017313598 +E_Ewald -4.1980309165 -57.1171408446 +E_entropy(-TS) -0.0150820421 -0.2052017103 +E_descf 0.0000000000 0.0000000000 +E_exx 0.0000000000 0.0000000000 +E_Fermi -0.2952668311 -4.0173113329 +---------------------------------------------------------- + + charge density convergence is achieved + final etot is -207.05117350 eV + EFERMI = -4.0173113329 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0.0000 0.0000 0.0000 (20005 pws) + 1 -11.3940 2.00000 + 2 -7.64170 2.00000 + 3 -4.08957 1.54741 + 4 -4.04497 1.22629 + 5 -4.04497 1.22629 + 6 -1.11642 0.00000 + 7 -1.11642 0.00000 + 8 3.17804 0.00000 + 9 4.06227 0.00000 + 10 5.18446 0.00000 + 11 6.94310 0.00000 + 12 6.94310 0.00000 + 13 8.35330 0.00000 + 14 8.58190 0.00000 + 15 8.58585 0.00000 + 16 8.73799 0.00000 + + correction force for each atom along direction 1 is 7.37303e-05 + correction force for each atom along direction 2 is 2.78766e-16 + correction force for each atom along direction 3 is -8.53040e-16 +TOTAL-FORCE (eV/Angstrom) +--------------------------------------------------------------------- +atom x y z +--------------------------------------------------------------------- + Si1 -0.0081647776 0.0000000000 0.0000000000 + Si2 0.0081647776 0.0000000000 0.0000000000 +--------------------------------------------------------------------- +---------------------------------------------------------------- +TOTAL-STRESS (KBAR) +---------------------------------------------------------------- + -4.2035731352 0.0000000000 0.0000000000 + 0.0000000000 1.3563557575 -0.0000000000 + 0.0000000000 -0.0000000000 1.3563557575 +---------------------------------------------------------------- + + Relaxation is not converged yet! + + CARTESIAN COORDINATES ( UNIT = 15.0000 Bohr ). + atom x y z mag vx vy vz + tauc_Si1 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + tauc_Si2 0.284487422914 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 + + + ------------------------------------------- + STEP OF RELAXATION : 4 + ------------------------------------------- + Find the file, try to read charge from file. + read in fermi energy = 0.00000000000 + first order charge density extrapolation ! + Find the file, try to read charge from file. + read in fermi energy = 0.00000000000 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Search adjacent atoms: | + | Set the adjacent atoms for each atom and set the periodic boundary | + | condition for the atoms on real space FFT grid. For k-dependent | + | algorithm, we also need to set the sparse H and S matrix element | + | for each atom. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP SEARCHING RADIUS FOR PROGRAM TO SEARCH ADJACENT ATOMS + longest orb rcut (Bohr) = 8.00 + longest nonlocal projector rcut (Bohr) = 5.01 + searching radius is (Bohr)) = 16.0 + searching radius unit is (Bohr)) = 15.0 + + SETUP EXTENDED REAL SPACE GRID FOR GRID INTEGRATION + real space grid = [ 72, 72, 72 ] + big cell numbers in grid = [ 18, 18, 18 ] + meshcell numbers in big cell = [ 4, 4, 4 ] + extended fft grid = [ 10, 10, 10 ] + dimension of extened grid = [ 39, 39, 39 ] + UnitCellTotal = 27 + Atom number in sub-FFT-grid = 2 + Local orbitals number in sub-FFT-grid = 26 + lgd_last = 26 + lgd_now = 26 + allocate DM , the dimension is 26 + enter setAlltoallvParameter, nblk = 1 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 26 + nCol_in_proc = 26 +receiver_size is 676 ; receiver_size of each process is: +676 +sender_size is 676 ; sender_size of each process is: +676 + DONE : INIT SCF Time : 4.85934 (SEC) + + + LCAO ALGORITHM --------------- ION= 4 ELEC= 1-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0210082427297 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2174740788 -207.0443566384 +E_Harris -15.2180946187 -207.0527995176 +E_Fermi -0.2959757638 -4.0269568577 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.0520789344922 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2173696431 -207.0429357185 +E_Harris -15.2151105959 -207.0121998044 +E_Fermi -0.2944469394 -4.0061561343 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00255871214300 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179722670 -207.0511348371 +E_Harris -15.2285484249 -207.1950308480 +E_Fermi -0.2951521403 -4.0157508848 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00152147537902 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179745476 -207.0511658668 +E_Harris -15.2184115890 -207.0571121202 +E_Fermi -0.2951986723 -4.0163839857 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 5-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000884383077030 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179752767 -207.0511757864 +E_Harris -15.2176581335 -207.0468608322 +E_Fermi -0.2951950395 -4.0163345586 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 6-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000151906335795 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179755487 -207.0511794875 +E_Harris -15.2177962263 -207.0487396801 +E_Fermi -0.2951848624 -4.0161960916 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 7-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 4.86089191230e-06 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179755535 -207.0511795529 +E_Harris -15.2179991687 -207.0515008539 +E_Fermi -0.2951845354 -4.0161916430 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 8-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 5.88385975986e-06 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179755536 -207.0511795531 +E_Harris -15.2179802643 -207.0512436461 +E_Fermi -0.2951854218 -4.0162037027 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 9-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 4.52790187506e-07 +------------------------------------------------------ + Energy Rydberg eV +------------------------------------------------------ +E_KohnSham -15.2179755536 -207.0511795534 +E_Harris -15.2179745979 -207.0511665509 +E_Fermi -0.2951853579 -4.0162028332 +------------------------------------------------------ + + LCAO ALGORITHM --------------- ION= 4 ELEC= 10-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 9.13422382836e-09 +---------------------------------------------------------- + Energy Rydberg eV +---------------------------------------------------------- +E_KohnSham -15.2179755536 -207.0511795530 +E_KS(sigma->0) -15.2104381464 -206.9486278673 +E_Harris -15.2179755357 -207.0511793098 +E_band -3.9918990782 -54.3125733044 +E_one_elec -15.1034264625 -205.4926592142 +E_Hartree 8.2760036522 112.6008063391 +E_xc -4.1745441849 -56.7975874668 +E_Ewald -4.2009337440 -57.1566358395 +E_entropy(-TS) -0.0150748144 -0.2051033715 +E_descf 0.0000000000 0.0000000000 +E_exx 0.0000000000 0.0000000000 +E_Fermi -0.2951853578 -4.0162028320 +---------------------------------------------------------- + + charge density convergence is achieved + final etot is -207.05117955 eV + EFERMI = -4.0162028320 eV + + STATE ENERGY(eV) AND OCCUPATIONS NSPIN == 1 + 1/1 kpoint (Cartesian) = 0.0000 0.0000 0.0000 (20005 pws) + 1 -11.3912 2.00000 + 2 -7.64269 2.00000 + 3 -4.08882 1.54961 + 4 -4.04373 1.22520 + 5 -4.04373 1.22520 + 6 -1.11805 0.00000 + 7 -1.11805 0.00000 + 8 3.17367 0.00000 + 9 4.06245 0.00000 + 10 5.18458 0.00000 + 11 6.94536 0.00000 + 12 6.94536 0.00000 + 13 8.35317 0.00000 + 14 8.58357 0.00000 + 15 8.58751 0.00000 + 16 8.73590 0.00000 + + correction force for each atom along direction 1 is 7.39754e-05 + correction force for each atom along direction 2 is -1.43245e-15 + correction force for each atom along direction 3 is 1.88401e-15 +TOTAL-FORCE (eV/Angstrom) +--------------------------------------------------------------------- +atom x y z +--------------------------------------------------------------------- + Si1 -0.0001983233 0.0000000000 0.0000000000 + Si2 0.0001983233 0.0000000000 0.0000000000 +--------------------------------------------------------------------- +---------------------------------------------------------------- +TOTAL-STRESS (KBAR) +---------------------------------------------------------------- + -4.2771700273 -0.0000000000 -0.0000000000 + -0.0000000000 1.3581284090 -0.0000000000 + -0.0000000000 -0.0000000000 1.3581284090 +---------------------------------------------------------------- + + Relaxation is converged! + + + -------------------------------------------- + !FINAL_ETOT_IS -207.0511795530416 eV + -------------------------------------------- + + +TIME STATISTICS +------------------------------------------------------------------------------------ + CLASS_NAME NAME TIME(Sec) CALLS AVG(Sec) PER(%) +------------------------------------------------------------------------------------ + total 5.87 15 0.39 100.00 +Driver reading 0.01 1 0.01 0.09 +Input Init 0.00 1 0.00 0.06 +Input_Conv Convert 0.00 1 0.00 0.00 +Driver driver_line 5.86 1 5.86 99.91 +UnitCell check_tau 0.00 1 0.00 0.00 +PW_Basis setuptransform 0.01 1 0.01 0.10 +PW_Basis distributeg 0.00 1 0.00 0.05 +mymath heapsort 0.02 3 0.01 0.28 +PW_Basis_K setuptransform 0.00 1 0.00 0.05 +PW_Basis_K distributeg 0.00 1 0.00 0.04 +PW_Basis setup_struc_factor 0.01 4 0.00 0.11 +ORB_control read_orb_first 0.06 1 0.06 1.02 +LCAO_Orbitals Read_Orbitals 0.06 1 0.06 1.01 +NOrbital_Lm extra_uniform 0.02 5 0.00 0.29 +Mathzone_Add1 SplineD2 0.00 5 0.00 0.00 +Mathzone_Add1 Cubic_Spline_Interpolation 0.00 5 0.00 0.00 +Mathzone_Add1 Uni_Deriv_Phi 0.02 5 0.00 0.27 +Sphbes Spherical_Bessel 0.01 1422 0.00 0.20 +ppcell_vl init_vloc 0.00 1 0.00 0.01 +Ions opt_ions 5.70 1 5.70 97.04 +ESolver_KS_LCAO Run 4.98 4 1.24 84.83 +ESolver_KS_LCAO beforescf 1.33 4 0.33 22.58 +ESolver_KS_LCAO beforesolver 0.24 4 0.06 4.06 +ESolver_KS_LCAO set_matrix_grid 0.23 4 0.06 4.00 +atom_arrange search 0.00 4 0.00 0.01 +Grid_Technique init 0.23 4 0.06 3.94 +Grid_BigCell grid_expansion_index 0.01 8 0.00 0.19 +Record_adj for_2d 0.00 4 0.00 0.01 +Grid_Driver Find_atom 0.00 56 0.00 0.00 +LCAO_Hamilt grid_prepare 0.00 4 0.00 0.00 +OverlapNew initialize_SR 0.00 4 0.00 0.00 +EkineticNew initialize_HR 0.00 4 0.00 0.00 +NonlocalNew initialize_HR 0.00 4 0.00 0.00 +Veff initialize_HR 0.00 4 0.00 0.00 +LOC Alltoall 0.00 4 0.00 0.04 +Charge set_rho_core 0.00 4 0.00 0.03 +Charge atomic_rho 0.07 8 0.01 1.20 +PW_Basis recip2real 0.21 55 0.00 3.59 +PW_Basis gathers_scatterp 0.02 55 0.00 0.41 +Potential init_pot 0.07 4 0.02 1.21 +Potential update_from_charge 0.62 43 0.01 10.55 +Potential cal_fixed_v 0.02 4 0.00 0.33 +PotLocal cal_fixed_v 0.02 4 0.00 0.31 +Potential cal_v_eff 0.60 43 0.01 10.22 +H_Hartree_pw v_hartree 0.46 43 0.01 7.81 +PW_Basis real2recip 0.22 59 0.00 3.81 +PW_Basis gatherp_scatters 0.01 59 0.00 0.14 +PotXC cal_v_eff 0.10 43 0.00 1.74 +XC_Functional v_xc 0.09 43 0.00 1.50 +H_Ewald_pw compute_ewald 0.05 4 0.01 0.80 +HSolverLCAO solve 1.35 39 0.03 23.04 +HamiltLCAO updateHk 0.58 39 0.01 9.82 +OperatorLCAO init 0.52 117 0.00 8.92 +OverlapNew calculate_SR 0.02 4 0.01 0.42 +OverlapNew contributeHk 0.00 4 0.00 0.00 +EkineticNew contributeHR 0.05 39 0.00 0.78 +EkineticNew calculate_HR 0.05 4 0.01 0.78 +NonlocalNew contributeHR 0.01 39 0.00 0.12 +NonlocalNew calculate_HR 0.01 4 0.00 0.12 +Veff contributeHR 3.05 20 0.15 51.89 +Gint_interface cal_gint 1.46 82 0.02 24.88 +Gint_interface cal_gint_vlocal 0.47 39 0.01 8.01 +Gint_Tools cal_psir_ylm 0.34 27456 0.00 5.84 +Gint_Gamma transfer_pvpR 0.00 39 0.00 0.01 +OperatorLCAO contributeHk 0.01 39 0.00 0.25 +HSolverLCAO hamiltSolvePsiK 0.05 39 0.00 0.93 +OperatorLCAO get_hs_pointers 0.00 43 0.00 0.00 +DiagoElpa elpa_solve 0.03 39 0.00 0.44 +ElecStateLCAO psiToRho 0.72 39 0.02 12.28 +ElecStateLCAO cal_dm_2d 0.00 39 0.00 0.03 +elecstate cal_dm 0.00 43 0.00 0.03 +psiMulPsiMpi pdgemm 0.00 43 0.00 0.01 +DensityMatrix cal_DMR 0.00 39 0.00 0.01 +Gint transfer_DMR 0.02 39 0.00 0.32 +Gint_interface cal_gint_rho 0.60 39 0.02 10.16 +Charge_Mixing get_drho 0.02 39 0.00 0.30 +Charge mix_rho 0.19 35 0.01 3.26 +Charge Broyden_mixing 0.04 35 0.00 0.73 +Force_Stress_LCAO getForceStress 0.70 4 0.17 11.91 +Forces cal_force_loc 0.05 4 0.01 0.91 +Forces cal_force_ew 0.04 4 0.01 0.64 +Forces cal_force_cc 0.00 4 0.00 0.00 +Forces cal_force_scc 0.02 4 0.01 0.35 +Stress_Func stress_loc 0.03 4 0.01 0.48 +Stress_Func stress_har 0.02 4 0.00 0.31 +Stress_Func stress_ewa 0.01 4 0.00 0.15 +Stress_Func stress_cc 0.00 4 0.00 0.00 +Stress_Func stress_gga 0.00 4 0.00 0.00 +Force_LCAO_gamma ftable_gamma 0.53 4 0.13 9.04 +Force_LCAO_gamma allocate_gamma 0.12 4 0.03 2.04 +LCAO_gen_fixedH b_NL_mu_new 0.01 4 0.00 0.12 +Force_LCAO_gamma cal_foverlap 0.00 4 0.00 0.01 +Force_LCAO_gamma cal_edm_2d 0.00 4 0.00 0.00 +Force_LCAO_gamma cal_ftvnl_dphi 0.00 4 0.00 0.00 +Force_LCAO_gamma cal_fvnl_dbeta_new 0.02 4 0.00 0.28 +Force_LCAO_gamma cal_fvl_dphi 0.39 4 0.10 6.71 +Gint_interface cal_gint_force 0.39 4 0.10 6.71 +Gint_Tools cal_dpsir_ylm 0.27 1408 0.00 4.58 +Gint_Tools cal_dpsirr_ylm 0.02 1408 0.00 0.32 +ModuleIO write_istate_info 0.00 1 0.00 0.05 +------------------------------------------------------------------------------------ + + NAME---------------|MEMORY(MB)-------- + total 34.46 + FFT::grid 11.39 + Chg::rho 2.848 + Chg::rho_save 2.848 + Chg::rho_core 2.848 + Pot::veff_fix 2.848 + Pot::veff 2.848 + SF::strucFac 2.460 + Chg::rhog 1.230 + Chg::rhog_save 1.230 + Chg::rhog_core 1.230 + ------------- < 1.0 MB has been ignored ---------------- + ---------------------------------------------------------- + + Start Time : Fri Oct 27 16:46:11 2023 + Finish Time : Fri Oct 27 16:46:17 2023 + Total Time : 0 h 0 mins 6 secs diff --git a/tests/abacus.relax/force.v341.ref b/tests/abacus.relax/force.v341.ref new file mode 100644 index 00000000..221d3922 --- /dev/null +++ b/tests/abacus.relax/force.v341.ref @@ -0,0 +1,8 @@ +-0.298984 0.000000 0.000000 +0.298984 0.000000 0.000000 +-0.169904 0.000000 0.000000 +0.169904 0.000000 0.000000 +-0.008165 0.000000 0.000000 +0.008165 0.000000 0.000000 +-0.000198 0.000000 0.000000 +0.000198 0.000000 0.000000 diff --git a/tests/abacus.relax/stress.v341.ref b/tests/abacus.relax/stress.v341.ref new file mode 100644 index 00000000..40b6c5fe --- /dev/null +++ b/tests/abacus.relax/stress.v341.ref @@ -0,0 +1,12 @@ +-1.538424 0.000000 0.000000 +0.000000 1.287624 -0.000000 +0.000000 -0.000000 1.287624 +-2.711521 0.000000 0.000000 +0.000000 1.318939 -0.000000 +0.000000 -0.000000 1.318939 +-4.203573 0.000000 0.000000 +0.000000 1.356356 -0.000000 +0.000000 -0.000000 1.356356 +-4.277170 -0.000000 -0.000000 +-0.000000 1.358128 -0.000000 +-0.000000 -0.000000 1.358128 diff --git a/tests/test_abacus_relax.py b/tests/test_abacus_relax.py index 8e8cd225..65d73e53 100644 --- a/tests/test_abacus_relax.py +++ b/tests/test_abacus_relax.py @@ -134,5 +134,57 @@ def tearDown(self): ) +class TestABACUSRelaxLabeledOutputV341(unittest.TestCase): + # Since ABACUS v3.4.1, the output format of force and stress has been changed. + def setUp(self): + shutil.copy( + "abacus.relax/OUT.abacus/running_cell-relax.log.v341", + "abacus.relax/OUT.abacus/running_cell-relax.log", + ) + shutil.move( + "abacus.relax/STRU", + "abacus.relax/STRU.bak", + ) + shutil.copy( + "abacus.relax/STRU.Si", + "abacus.relax/STRU", + ) + self.system = dpdata.LabeledSystem("abacus.relax", fmt="abacus/relax") + + def test_force(self): + # with open("abacus.relax/force.v341.ref","w") as fp: + # for i in self.system.data["forces"]: + # for j in i: + # fp.write("%f %f %f\n" % tuple(j.tolist())) + with open("abacus.relax/force.v341.ref") as fp: + ref = [] + for ii in fp: + ref.append([float(jj) for jj in ii.split()]) + ref = np.array(ref) + ref = ref.reshape([4, 2, 3]) + np.testing.assert_almost_equal(self.system.data["forces"], ref, decimal=5) + + def test_stress(self): + # with open("abacus.relax/stress.v341.ref","w") as fp: + # for i in self.system.data["stress"]: + # for j in i: + # fp.write("%f %f %f\n" % tuple(j.tolist())) + with open("abacus.relax/stress.v341.ref") as fp: + ref = [] + for ii in fp: + ref.append([float(jj) for jj in ii.split()]) + ref = np.array(ref) + ref = ref.reshape([4, 3, 3]) + np.testing.assert_almost_equal(self.system.data["stress"], ref, decimal=5) + + def tearDown(self): + if os.path.isfile("abacus.relax/OUT.abacus/running_cell-relax.log"): + os.remove("abacus.relax/OUT.abacus/running_cell-relax.log") + shutil.move( + "abacus.relax/STRU.bak", + "abacus.relax/STRU", + ) + + if __name__ == "__main__": unittest.main() From 0a3bbab789c139e03851c87a6ebfd68a2d6f337c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 31 Oct 2023 08:54:47 +0800 Subject: [PATCH 18/18] [pre-commit.ci] pre-commit autoupdate (#561) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 23.10.0 → 23.10.1](https://github.com/psf/black/compare/23.10.0...23.10.1) - [github.com/astral-sh/ruff-pre-commit: v0.1.1 → v0.1.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.1...v0.1.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ca94baf5..23f19ed8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,12 +18,12 @@ repos: - id: check-toml # Python - repo: https://github.com/psf/black - rev: 23.10.0 + rev: 23.10.1 hooks: - id: black-jupyter - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.1.1 + rev: v0.1.3 hooks: - id: ruff args: ["--fix"]