diff --git a/dpdata/ase/__init__.py b/dpdata/ase/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/dpdata/ase/db.py b/dpdata/ase/db.py new file mode 100644 index 00000000..6578cecb --- /dev/null +++ b/dpdata/ase/db.py @@ -0,0 +1,42 @@ +from ase import Atom +from ase.db import connect +import numpy as np + + +def get_frames(fname, begin=0, step=1): + asedb = connect(fname) + num = asedb.count() + at0 = asedb.get(1).toatoms() + + numbers = at0.numbers + nat0 = at0[numbers.argsort()] + chemical_symbols = nat0.get_chemical_symbols() + unique_numbers = np.unique(numbers) + unique_numbers.sort() + atom_names = [Atom(u).symbol for u in unique_numbers] + atom_numbs = [chemical_symbols.count(i) for i in atom_names] + atom_types = np.array([atom_names.index(i) for i in chemical_symbols]) + + all_coords = [] + all_cells = [] + all_energies = [] + all_forces = [] + all_virials = None + + for i in range(begin, num, step): + ati = asedb.get(i+1) + ats_ = ati.toatoms() + numbers = ats_.numbers + sorted_numbers = numbers.argsort() + ats = ats_[sorted_numbers] + data = ati.data + energy = data['energy'] + cell = ats.get_cell().view() + coord = ats.positions + forces = data['forces'][sorted_numbers] + all_coords.append(coord) + all_cells.append(cell) + all_forces.append(forces) + all_energies.append(energy) + + return atom_names, atom_numbs, atom_types, np.array(all_cells), np.array(all_coords), np.array(all_energies), np.array(all_forces), all_virials diff --git a/dpdata/cp2k/.___init__.py b/dpdata/cp2k/.___init__.py new file mode 100644 index 00000000..3def63db Binary files /dev/null and b/dpdata/cp2k/.___init__.py differ diff --git a/dpdata/deepmd/.___init__.py b/dpdata/deepmd/.___init__.py new file mode 100644 index 00000000..16c85526 Binary files /dev/null and b/dpdata/deepmd/.___init__.py differ diff --git a/dpdata/fhi_aims/.___init__.py b/dpdata/fhi_aims/.___init__.py new file mode 100755 index 00000000..f4509a11 Binary files /dev/null and b/dpdata/fhi_aims/.___init__.py differ diff --git a/dpdata/gaussian/.___init__.py b/dpdata/gaussian/.___init__.py new file mode 100644 index 00000000..04034b1f Binary files /dev/null and b/dpdata/gaussian/.___init__.py differ diff --git a/dpdata/gromacs/.___init__.py b/dpdata/gromacs/.___init__.py new file mode 100644 index 00000000..9da9dbe1 Binary files /dev/null and b/dpdata/gromacs/.___init__.py differ diff --git a/dpdata/lammps/.___init__.py b/dpdata/lammps/.___init__.py new file mode 100644 index 00000000..95e2e13b Binary files /dev/null and b/dpdata/lammps/.___init__.py differ diff --git a/dpdata/md/.___init__.py b/dpdata/md/.___init__.py new file mode 100644 index 00000000..fde4b3a9 Binary files /dev/null and b/dpdata/md/.___init__.py differ diff --git a/dpdata/system.py b/dpdata/system.py index 0af60189..133f9745 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -8,6 +8,7 @@ import dpdata.vasp.poscar import dpdata.vasp.xml import dpdata.vasp.outcar +import dpdata.ase.db import dpdata.deepmd.raw import dpdata.deepmd.comp import dpdata.qe.traj @@ -1137,6 +1138,21 @@ def from_vasp_outcar(self, file_name, begin = 0, step = 1) : # rotate the system to lammps convention self.rot_lower_triangular() + @register_from_funcs.register_funcs('db') + @register_from_funcs.register_funcs('ase/db') + def from_ase_db(self, file_name, begin = 0, step = 1) : + self.data['atom_names'], \ + self.data['atom_numbs'], \ + self.data['atom_types'], \ + self.data['cells'], \ + self.data['coords'], \ + self.data['energies'], \ + self.data['forces'], \ + tmp_virial, \ + = dpdata.ase.db.get_frames(file_name, begin = begin, step = step) + + # rotate the system to lammps convention + self.rot_lower_triangular() def affine_map_fv(self, trans, f_idx) : assert(np.linalg.det(trans) != 0) diff --git a/dpdata/vasp/.___init__.py b/dpdata/vasp/.___init__.py new file mode 100644 index 00000000..2eea056c Binary files /dev/null and b/dpdata/vasp/.___init__.py differ diff --git a/setup.py b/setup.py index 8819cda4..fe244982 100644 --- a/setup.py +++ b/setup.py @@ -33,11 +33,13 @@ 'dpdata/siesta', 'dpdata/gaussian', 'dpdata/cp2k', + 'dpdata/ase', 'dpdata/xyz', 'dpdata/pwmat', 'dpdata/amber', 'dpdata/fhi_aims', - 'dpdata/gromacs' + 'dpdata/gromacs', + 'dpdata/ase' ], package_data={'dpdata':['*.json']}, classifiers=[ diff --git a/tags b/tags new file mode 100644 index 00000000..f2a1fd0f --- /dev/null +++ b/tags @@ -0,0 +1,2105 @@ +!_TAG_FILE_FORMAT 2 /extended format; --format=1 will not append ;" to lines/ +!_TAG_FILE_SORTED 1 /0=unsorted, 1=sorted, 2=foldcase/ +!_TAG_PROGRAM_AUTHOR Darren Hiebert /dhiebert@users.sourceforge.net/ +!_TAG_PROGRAM_NAME Exuberant Ctags // +!_TAG_PROGRAM_URL http://ctags.sourceforge.net /official site/ +!_TAG_PROGRAM_VERSION 5.8 // +0 tests/qe.traj/oh-md.for /^ 0.10014992808490E-01 0.10019983634481E-01 0.90694191035741E-02$/;" l file: +0 tests/qe.traj/oh-md.for /^ 0.10220260079288E-01 0.10373723748428E-01 0.95492007700433E-02$/;" l file: +0 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build/lib/dpdata/xyz/quip_gap_xyz.py /^from collections import OrderedDict$/;" i +OrderedDict dpdata/cp2k/cell.py /^from collections import OrderedDict$/;" i +OrderedDict dpdata/cp2k/output.py /^from collections import OrderedDict$/;" i +OrderedDict dpdata/xyz/quip_gap_xyz.py /^from collections import OrderedDict$/;" i +PRETEND_KEY .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/__init__.py /^PRETEND_KEY = "SETUPTOOLS_SCM_PRETEND_VERSION"$/;" v +PY2 .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^PY2 = sys.version_info < (3,)$/;" v +PY3 .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^PY3 = sys.version_info > (3,)$/;" v +Path build/lib/dpdata/periodic_table.py /^from pathlib import Path$/;" i +Path dpdata/periodic_table.py /^from pathlib import Path$/;" i +QuipGapxyzSystems build/lib/dpdata/system.py /^from dpdata.xyz.quip_gap_xyz import QuipGapxyzSystems$/;" i +QuipGapxyzSystems build/lib/dpdata/xyz/quip_gap_xyz.py /^class 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.eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^class ScmVersion(object):$/;" c +SetuptoolsOutdatedWarning .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^class SetuptoolsOutdatedWarning(Warning):$/;" c +Structure build/lib/dpdata/system.py /^ from pymatgen import Structure$/;" i +Structure dpdata/system.py /^ from pymatgen import Structure$/;" i +Structure tests/test_to_pymatgen.py /^ from pymatgen import Structure$/;" i +System build/lib/dpdata/__init__.py /^from .system import System$/;" i +System build/lib/dpdata/system.py /^class System (MSONable) :$/;" c +System dpdata/__init__.py /^from .system import System$/;" i +System dpdata/system.py /^class System (MSONable) :$/;" c +TEMPLATES .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/__init__.py /^TEMPLATES = {$/;" v +TestASE tests/test_to_ase.py /^class TestASE(unittest.TestCase, CompSys, IsPBC):$/;" c +TestAimdSIESTALabeledOutput tests/test_siesta_aiMD_output.py /^class 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TestCellToLowTriangle(unittest.TestCase):$/;" c +TestConverCellDim tests/test_qe_cp_traj.py /^class TestConverCellDim(unittest.TestCase): $/;" c +TestCp2kAimdOutput tests/test_cp2k_aimd_output.py /^class TestCp2kAimdOutput(unittest.TestCase, CompLabeledSys):$/;" c +TestDeepmdCompNoLabels tests/test_deepmd_comp.py /^class TestDeepmdCompNoLabels(unittest.TestCase, CompSys, IsPBC) :$/;" c +TestDeepmdCompNoLabels tests/test_deepmd_raw.py /^class TestDeepmdCompNoLabels(unittest.TestCase, CompSys, IsPBC) :$/;" c +TestDeepmdDumpRaw tests/test_deepmd_raw.py /^class TestDeepmdDumpRaw(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestDeepmdLoadDumpComp tests/test_deepmd_comp.py /^class TestDeepmdLoadDumpComp(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestDeepmdLoadRaw tests/test_deepmd_raw.py /^class TestDeepmdLoadRaw(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestDeepmdLoadRaw tests/test_shuffle.py /^class TestDeepmdLoadRaw(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c 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c +TestFhi_aims_MD tests/test_fhi_md_output.py /^class TestFhi_aims_MD:$/;" c +TestFhi_aims_Output tests/test_fhi_md_multi_elem_output.py /^class TestFhi_aims_Output(unittest.TestCase, TestFhi_aims_MD):$/;" c +TestFhi_aims_Output tests/test_fhi_md_output.py /^class TestFhi_aims_Output(unittest.TestCase, TestFhi_aims_MD):$/;" c +TestGaussianLoadLog tests/test_gaussian_log.py /^class TestGaussianLoadLog(unittest.TestCase, TestGaussianLog):$/;" c +TestGaussianLoadMD tests/test_gaussian_log.py /^class TestGaussianLoadMD(unittest.TestCase, TestGaussianLog):$/;" c +TestGaussianLog tests/test_gaussian_log.py /^class TestGaussianLog :$/;" c +TestGromacsGro tests/test_gromacs_gro.py /^class TestGromacsGro(unittest.TestCase):$/;" c +TestIons tests/test_water_ions.py /^class TestIons(unittest.TestCase):$/;" c +TestJsonLoad tests/test_json.py /^class TestJsonLoad(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestLammpsDumpShiftOrigin tests/test_lammps_dump_shift_origin.py /^class TestLammpsDumpShiftOrigin(unittest.TestCase, CompSys, IsPBC):$/;" c +TestLmp tests/test_lammps_lmp_to_system.py /^class TestLmp(unittest.TestCase, TestPOSCARoh):$/;" c +TestLmpDump tests/test_lammps_lmp_dump.py /^class TestLmpDump(unittest.TestCase, TestPOSCARoh):$/;" c +TestLmpDumpSkip tests/test_lammps_dump_skipload.py /^class TestLmpDumpSkip(unittest.TestCase, CompSys, IsPBC):$/;" c +TestMSD tests/test_msd.py /^class TestMSD (unittest.TestCase) :$/;" c +TestMultiDeepmdDumpComp tests/test_multisystems.py /^class TestMultiDeepmdDumpComp(unittest.TestCase, CompLabeledSys, IsNoPBC):$/;" c +TestMultiDeepmdDumpRaw tests/test_multisystems.py /^class TestMultiDeepmdDumpRaw(unittest.TestCase, CompLabeledSys, IsNoPBC):$/;" c +TestMultiSystems tests/test_multisystems.py /^class TestMultiSystems(unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC):$/;" c +TestMultiSystemsAdd tests/test_multisystems.py /^class TestMultiSystemsAdd(unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC):$/;" c +TestMultiSystemsSorted tests/test_multisystems.py /^class TestMultiSystemsSorted(unittest.TestCase, MultiSystems):$/;" c +TestNonCoveragedGaussianLoadLog tests/test_gaussian_log.py /^class TestNonCoveragedGaussianLoadLog(unittest.TestCase, TestGaussianLog):$/;" c +TestPBC tests/test_system_apply_pbc.py /^class TestPBC(unittest.TestCase) :$/;" c +TestPOSCARCart tests/test_vasp_poscar_to_system.py /^class TestPOSCARCart(unittest.TestCase, TestPOSCARoh):$/;" c +TestPOSCARDirect tests/test_vasp_poscar_to_system.py /^class TestPOSCARDirect(unittest.TestCase, TestPOSCARoh):$/;" c +TestPOSCARDump tests/test_vasp_poscar_dump.py /^class TestPOSCARDump(unittest.TestCase, TestPOSCARoh):$/;" c +TestPOSCARDump1 tests/test_vasp_poscar_dump.py /^class TestPOSCARDump1(unittest.TestCase, TestPOSCARoh):$/;" c +TestPOSCARSkipZeroAtomNumb tests/test_vasp_poscar_dump.py /^class TestPOSCARSkipZeroAtomNumb(unittest.TestCase) :$/;" c +TestPOSCARoh tests/poscars/poscar_ref_oh.py /^class TestPOSCARoh :$/;" c +TestPOSCARoh tests/test_lammps_dump_to_system.py /^from poscars.poscar_ref_oh import TestPOSCARoh $/;" i +TestPOSCARoh tests/test_lammps_lmp_dump.py /^from poscars.poscar_ref_oh import TestPOSCARoh $/;" i +TestPOSCARoh tests/test_lammps_lmp_to_system.py /^from poscars.poscar_ref_oh import TestPOSCARoh $/;" i +TestPOSCARoh tests/test_vasp_poscar_dump.py /^from poscars.poscar_ref_oh import TestPOSCARoh $/;" i +TestPOSCARoh tests/test_vasp_poscar_to_system.py /^from poscars.poscar_ref_oh import TestPOSCARoh$/;" i +TestPWSCFLabeledOutput tests/test_qe_pw_scf.py /^class TestPWSCFLabeledOutput(unittest.TestCase, TestPWSCFSinglePointEnergy):$/;" c +TestPWSCFLabeledOutputListInput tests/test_qe_pw_scf.py /^class TestPWSCFLabeledOutputListInput(unittest.TestCase, TestPWSCFSinglePointEnergy):$/;" c +TestPWSCFLabeledTrajSkip tests/test_qe_cp_traj_skipload.py /^class TestPWSCFLabeledTrajSkip(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestPWSCFSinglePointEnergy tests/test_qe_pw_scf.py /^class TestPWSCFSinglePointEnergy:$/;" c +TestPWSCFTrajSkip tests/test_qe_cp_traj_skipload.py /^class TestPWSCFTrajSkip(unittest.TestCase, CompSys, IsPBC):$/;" c +TestPeriodicTable tests/test_periodic_table.py /^class TestPeriodicTable(unittest.TestCase):$/;" c +TestPerturbConst tests/test_perturb.py /^class TestPerturbConst(unittest.TestCase, CompSys, IsPBC):$/;" c +TestPerturbNormal tests/test_perturb.py /^class TestPerturbNormal(unittest.TestCase, CompSys, IsPBC):$/;" c +TestPerturbUniform tests/test_perturb.py /^class TestPerturbUniform(unittest.TestCase, CompSys, IsPBC):$/;" c +TestPymatgen tests/test_to_pymatgen.py /^class TestPymatgen(unittest.TestCase, CompSys, IsPBC):$/;" c +TestPymatgen tests/test_to_pymatgen_entry.py /^class TestPymatgen(unittest.TestCase):$/;" c +TestQuipGapxyz1 tests/test_quip_gap_xyz.py /^class TestQuipGapxyz1(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestQuipGapxyz2 tests/test_quip_gap_xyz.py /^class TestQuipGapxyz2(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestQuipGapxyzNoVirials tests/test_quip_gap_xyz.py /^class TestQuipGapxyzNoVirials(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestQuipGapxyzfield tests/test_quip_gap_xyz.py /^class TestQuipGapxyzfield(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestQuipGapxyzfield2 tests/test_quip_gap_xyz.py /^class TestQuipGapxyzfield2(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestQuipGapxyzsort1 tests/test_quip_gap_xyz.py /^class TestQuipGapxyzsort1(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestQuipGapxyzsort2 tests/test_quip_gap_xyz.py /^class TestQuipGapxyzsort2(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestRemovePBC tests/test_remove_pbc.py /^class TestRemovePBC(unittest.TestCase):$/;" c +TestReplicate123 tests/test_replicate.py /^class TestReplicate123(unittest.TestCase, CompSys, IsPBC):$/;" c +TestReplicate123_not_change_origin tests/test_replicate.py /^class TestReplicate123_not_change_origin(unittest.TestCase, CompSys, IsPBC):$/;" c +TestSIESTALabeledOutput tests/test_siesta_output.py /^class TestSIESTALabeledOutput(unittest.TestCase, TestSIESTASinglePointEnergy):$/;" c +TestSIESTASinglePointEnergy tests/test_siesta_aiMD_output.py /^class TestSIESTASinglePointEnergy:$/;" c +TestSIESTASinglePointEnergy tests/test_siesta_output.py /^class TestSIESTASinglePointEnergy:$/;" c +TestSetAtomTypes tests/test_system_set_type.py /^class TestSetAtomTypes(unittest.TestCase):$/;" c +TestSingleStep tests/test_pwmat_mlmd.py /^class TestSingleStep(unittest.TestCase):$/;" c +TestSingleStep tests/test_vasp_unconverged_outcar.py /^class TestSingleStep(unittest.TestCase):$/;" c +TestToFunc tests/test_lammps_lmp_dump.py /^class TestToFunc(unittest.TestCase, TestPOSCARoh):$/;" c +TestToList tests/test_to_list.py /^class TestToList(unittest.TestCase, CompLabeledSys, IsPBC):$/;" c +TestTypeMap tests/test_multisystems.py /^class TestTypeMap(unittest.TestCase):$/;" 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build/lib/dpdata/siesta/aiMD_output.py /^ang2ang = 1$/;" v +ang2ang build/lib/dpdata/siesta/output.py /^ang2ang = 1$/;" v +ang2ang dpdata/siesta/aiMD_output.py /^ang2ang = 1$/;" v +ang2ang dpdata/siesta/output.py /^ang2ang = 1$/;" v +append build/lib/dpdata/system.py /^ def append(self, *systems) :$/;" m class:MultiSystems +append build/lib/dpdata/system.py /^ def append(self, system) :$/;" m class:System +append build/lib/dpdata/system.py /^ def append(self, system):$/;" m class:LabeledSystem +append dpdata/system.py /^ def append(self, *systems) :$/;" m class:MultiSystems +append dpdata/system.py /^ def append(self, system) :$/;" m class:System +append dpdata/system.py /^ def append(self, system):$/;" m class:LabeledSystem +apply_pbc build/lib/dpdata/md/pbc.py /^def apply_pbc(system_coords, system_cells) :$/;" f +apply_pbc build/lib/dpdata/system.py /^ def apply_pbc(self) :$/;" m class:System +apply_pbc dpdata/md/pbc.py /^def apply_pbc(system_coords, system_cells) :$/;" f +apply_pbc dpdata/system.py /^ def apply_pbc(self) :$/;" m class:System +apply_type_map build/lib/dpdata/system.py /^ def apply_type_map(self, type_map) :$/;" m class:System +apply_type_map dpdata/system.py /^ def apply_type_map(self, type_map) :$/;" m class:System +archival_to_version .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/hg.py /^def archival_to_version(data, config=None):$/;" f +as_dict build/lib/dpdata/system.py /^ def as_dict(self):$/;" m class:System +as_dict dpdata/system.py /^ def as_dict(self):$/;" m class:System +ase build/lib/dpdata/md/rdf.py /^ import ase.neighborlist $/;" i +ase build/lib/dpdata/md/water.py /^ import ase$/;" i +ase build/lib/dpdata/md/water.py /^ import ase.neighborlist $/;" i +ase build/lib/dpdata/md/water.py /^ import ase.neighborlist $/;" i +ase build/lib/dpdata/system.py /^import dpdata.ase.db$/;" i +ase dpdata/md/rdf.py /^ import ase.neighborlist $/;" i +ase dpdata/md/water.py /^ import ase$/;" i +ase dpdata/md/water.py /^ import ase.neighborlist $/;" i +ase dpdata/md/water.py /^ import ase.neighborlist $/;" i +ase dpdata/system.py /^import dpdata.ase.db$/;" i +ase tests/test_water_ions.py /^ import ase$/;" i +ase tests/test_water_ions.py /^ import ase.neighborlist $/;" i +atomconfig build/lib/dpdata/system.py /^import dpdata.pwmat.atomconfig$/;" i +atomconfig dpdata/system.py /^import dpdata.pwmat.atomconfig$/;" i +author docs/conf.py /^author = 'Han Wang'$/;" v +author setup.py /^ author="Han Wang",$/;" v +author_email setup.py /^ author_email="wang_han@iapcm.ac.cn",$/;" v +avail_patterns build/lib/dpdata/cp2k/output.py /^avail_patterns = []$/;" v +avail_patterns dpdata/cp2k/output.py /^avail_patterns = []$/;" v +bohr2ang build/lib/dpdata/gaussian/log.py /^bohr2ang = 0.52917721067$/;" v +bohr2ang build/lib/dpdata/qe/scf.py /^bohr2ang = 0.52917721067$/;" v +bohr2ang build/lib/dpdata/qe/traj.py /^bohr2ang = 0.52917721067$/;" v +bohr2ang dpdata/gaussian/log.py /^bohr2ang = 0.52917721067$/;" v +bohr2ang dpdata/qe/scf.py /^bohr2ang = 0.52917721067$/;" v +bohr2ang dpdata/qe/traj.py /^bohr2ang = 0.52917721067$/;" v +box2dumpbox build/lib/dpdata/lammps/dump.py /^def box2dumpbox(orig, box) :$/;" f +box2dumpbox dpdata/lammps/dump.py /^def box2dumpbox(orig, box) :$/;" f +box2lmpbox build/lib/dpdata/lammps/lmp.py /^def box2lmpbox(orig, box) :$/;" f +box2lmpbox dpdata/lammps/lmp.py /^def box2lmpbox(orig, box) :$/;" f +builtins .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/win_py31_compat.py /^import __builtin__ as builtins$/;" i +calculated_radius build/lib/dpdata/periodic_table.py /^ def calculated_radius(self):$/;" m class:Element +calculated_radius dpdata/periodic_table.py /^ def calculated_radius(self):$/;" m class:Element +callable_or_entrypoint .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^def callable_or_entrypoint(group, callable_or_name):$/;" f +cell_to_low_triangle build/lib/dpdata/cp2k/cell.py /^def cell_to_low_triangle(A,B,C,alpha,beta,gamma):$/;" f +cell_to_low_triangle build/lib/dpdata/cp2k/output.py /^from .cell import cell_to_low_triangle$/;" i +cell_to_low_triangle dpdata/cp2k/cell.py /^def cell_to_low_triangle(A,B,C,alpha,beta,gamma):$/;" f +cell_to_low_triangle dpdata/cp2k/output.py /^from .cell import cell_to_low_triangle$/;" i +cells build/lib/dpdata/qe/traj.py /^ cells = load_data(prefix+'.cel', 3)$/;" v +cells dpdata/qe/traj.py /^ cells = load_data(prefix+'.cel', 3)$/;" v +check_LabeledSystem build/lib/dpdata/system.py /^def check_LabeledSystem(data):$/;" f +check_LabeledSystem dpdata/system.py /^def check_LabeledSystem(data):$/;" f +check_System build/lib/dpdata/system.py /^def check_System(data):$/;" f +check_System dpdata/system.py /^def check_System(data):$/;" f +check_atom_names build/lib/dpdata/system.py /^ def check_atom_names(self, system):$/;" m class:MultiSystems +check_atom_names dpdata/system.py /^ def check_atom_names(self, system):$/;" m class:MultiSystems +check_name build/lib/dpdata/vasp/xml.py /^def check_name(item, name) :$/;" f +check_name dpdata/vasp/xml.py /^def check_name(item, name) :$/;" f +check_type_map build/lib/dpdata/system.py /^ def check_type_map(self, type_map):$/;" m class:System +check_type_map dpdata/system.py /^ def check_type_map(self, type_map):$/;" m class:System +classifiers setup.py /^ classifiers=[$/;" v +code .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/win_py31_compat.py /^ def code(self):$/;" m class:WindowsError +comp build/lib/dpdata/system.py /^import dpdata.deepmd.comp$/;" i +comp dpdata/system.py /^import dpdata.deepmd.comp$/;" i +compat_stat .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/win_py31_compat.py /^def compat_stat(path):$/;" f +compute_bonds build/lib/dpdata/md/water.py /^def compute_bonds (box, $/;" f +compute_bonds dpdata/md/water.py /^def compute_bonds (box, $/;" f +compute_bonds_ase build/lib/dpdata/md/water.py /^def compute_bonds_ase(box, $/;" f +compute_bonds_ase dpdata/md/water.py /^def compute_bonds_ase(box, $/;" f +compute_bonds_naive build/lib/dpdata/md/water.py /^def compute_bonds_naive(box,$/;" f +compute_bonds_naive dpdata/md/water.py /^def compute_bonds_naive(box,$/;" f +compute_rdf build/lib/dpdata/md/rdf.py /^def compute_rdf(box,$/;" f +compute_rdf dpdata/md/rdf.py /^def compute_rdf(box,$/;" f +config .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/__init__.py /^ config = Configuration(**locals())$/;" v +connect build/lib/dpdata/ase/db.py /^from ase.db import connect$/;" i +connect dpdata/ase/db.py /^from ase.db import connect$/;" i +convert_celldm build/lib/dpdata/qe/traj.py /^def convert_celldm(ibrav, celldm) :$/;" f +convert_celldm dpdata/qe/traj.py /^def convert_celldm(ibrav, celldm) :$/;" f +coords build/lib/dpdata/qe/traj.py /^ coords = load_data(prefix+'.pos', np.sum(atom_numbs))$/;" v +coords dpdata/qe/traj.py /^ coords = load_data(prefix+'.pos', np.sum(atom_numbs))$/;" v +copy build/lib/dpdata/system.py /^ def copy(self):$/;" m class:System +copy dpdata/system.py /^ def copy(self):$/;" m class:System +copyright docs/conf.py /^copyright = '2019, Han Wang'$/;" v +count_all_nodes .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/git.py /^ def count_all_nodes(self):$/;" m class:GitWorkdir +covert_dimension build/lib/dpdata/siesta/aiMD_output.py /^def covert_dimension(arr, num):$/;" f +covert_dimension dpdata/siesta/aiMD_output.py /^def covert_dimension(arr, num):$/;" f +cp2k build/lib/dpdata/system.py /^import dpdata.cp2k.output$/;" i +cp2k dpdata/system.py /^import dpdata.cp2k.output$/;" i +cp2k_output tests/cp2k/test.py /^cp2k_output = dpdata.LabeledSystem('cp2k_output', fmt = 'cp2k\/output')$/;" v +ctypes .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/win_py31_compat.py /^import ctypes.wintypes$/;" i +data tests/test_periodic_table.py /^data={"name": "Hydrogen",$/;" v +data_from_mime .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/hacks.py /^from .utils import data_from_mime, trace$/;" i +data_from_mime .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/hg.py /^from .utils import do, trace, data_from_mime, has_command$/;" i +data_from_mime .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^def data_from_mime(path):$/;" f +datetime .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^import datetime$/;" i +datetime .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^import datetime$/;" i +db build/lib/dpdata/system.py /^import dpdata.ase.db$/;" i +db dpdata/system.py /^import dpdata.ase.db$/;" i +debug build/lib/dpdata/fhi_aims/output.py /^debug = False$/;" v +debug dpdata/fhi_aims/output.py /^debug = False$/;" v +decorator build/lib/dpdata/system.py /^ def decorator(func):$/;" f function:Register.register_funcs +decorator dpdata/system.py /^ def decorator(func):$/;" f function:Register.register_funcs +deepcopy build/lib/dpdata/system.py /^from copy import deepcopy$/;" i +deepcopy dpdata/system.py /^from copy import deepcopy$/;" i +deepmd build/lib/dpdata/system.py /^ import deepmd.DeepPot as DeepPot$/;" i +deepmd build/lib/dpdata/system.py /^import dpdata.deepmd.comp$/;" i +deepmd build/lib/dpdata/system.py /^import dpdata.deepmd.raw$/;" i +deepmd dpdata/system.py /^ import deepmd.DeepPot as DeepPot$/;" i +deepmd dpdata/system.py /^import dpdata.deepmd.comp$/;" i +deepmd dpdata/system.py /^import dpdata.deepmd.raw$/;" i +delimiter_p1 build/lib/dpdata/cp2k/output.py /^delimiter_p1 = re.compile(r'^ \\* GO CP2K GO! \\*+')$/;" v +delimiter_p1 dpdata/cp2k/output.py /^delimiter_p1 = re.compile(r'^ \\* GO CP2K GO! \\*+')$/;" v +delimiter_p2 build/lib/dpdata/cp2k/output.py /^delimiter_p2 = re.compile(r'^ \\*+')$/;" v +delimiter_p2 dpdata/cp2k/output.py /^delimiter_p2 = re.compile(r'^ \\*+')$/;" v +delimiter_patterns build/lib/dpdata/cp2k/output.py /^delimiter_patterns=[]$/;" v +delimiter_patterns dpdata/cp2k/output.py /^delimiter_patterns=[]$/;" v +description setup.py /^ description="Manipulating data formats of DeePMD-kit, VASP, QE, PWmat, and LAMMPS, etc.",$/;" v +dir_coord build/lib/dpdata/md/pbc.py /^def dir_coord(coord, box) :$/;" f +dir_coord dpdata/md/pbc.py /^def dir_coord(coord, box) :$/;" f +do .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/hg.py /^from .utils import do, trace, data_from_mime, has_command$/;" i +do .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/integration.py /^from .utils import do, trace_exception$/;" i +do .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^def do(cmd, cwd="."):$/;" f +do_ex .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/git.py /^ def do_ex(self, cmd):$/;" m class:GitWorkdir +do_ex .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/git.py /^from .utils import do_ex, trace, has_command$/;" i +do_ex .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^def do_ex(cmd, cwd="."):$/;" f +dpdata build/lib/dpdata/md/rdf.py /^ import dpdata$/;" i +dpdata build/lib/dpdata/qe/traj.py /^import dpdata,warnings$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.amber.md$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.ase.db$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.cp2k.output$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.deepmd.comp$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.deepmd.raw$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.fhi_aims.output$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.gaussian.log$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.gromacs.gro$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.lammps.dump$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.lammps.lmp$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.md.pbc$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.pwmat.atomconfig$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.pwmat.movement$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.qe.scf$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.qe.traj$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.siesta.aiMD_output$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.siesta.output$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.vasp.outcar$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.vasp.poscar$/;" i +dpdata build/lib/dpdata/system.py /^import dpdata.vasp.xml$/;" i +dpdata dpdata/md/rdf.py /^ import dpdata$/;" i +dpdata dpdata/qe/traj.py /^import dpdata,warnings$/;" i +dpdata dpdata/system.py /^import dpdata.amber.md$/;" i +dpdata dpdata/system.py /^import dpdata.ase.db$/;" i +dpdata dpdata/system.py /^import dpdata.cp2k.output$/;" i +dpdata dpdata/system.py /^import dpdata.deepmd.comp$/;" i +dpdata dpdata/system.py /^import dpdata.deepmd.raw$/;" i +dpdata dpdata/system.py /^import dpdata.fhi_aims.output$/;" i +dpdata dpdata/system.py /^import dpdata.gaussian.log$/;" i +dpdata dpdata/system.py /^import dpdata.gromacs.gro$/;" i +dpdata dpdata/system.py /^import dpdata.lammps.dump$/;" i +dpdata dpdata/system.py /^import dpdata.lammps.lmp$/;" i +dpdata dpdata/system.py /^import dpdata.md.pbc$/;" i +dpdata dpdata/system.py /^import dpdata.pwmat.atomconfig$/;" i +dpdata dpdata/system.py /^import dpdata.pwmat.movement$/;" i +dpdata dpdata/system.py /^import dpdata.qe.scf$/;" i +dpdata dpdata/system.py /^import dpdata.qe.traj$/;" i +dpdata dpdata/system.py /^import dpdata.siesta.aiMD_output$/;" i +dpdata dpdata/system.py /^import dpdata.siesta.output$/;" i +dpdata dpdata/system.py /^import dpdata.vasp.outcar$/;" i +dpdata dpdata/system.py /^import dpdata.vasp.poscar$/;" i +dpdata dpdata/system.py /^import dpdata.vasp.xml$/;" i +dpdata tests/context.py /^import dpdata$/;" i +dpdata tests/context.py /^import dpdata.md.msd$/;" i +dpdata tests/context.py /^import dpdata.md.water$/;" i +dpdata tests/cp2k/test.py /^import dpdata$/;" i +dpdata tests/test_amber_md.py /^from context import dpdata$/;" i +dpdata tests/test_cell_to_low_triangle.py /^from context import dpdata$/;" i +dpdata tests/test_cp2k_aimd_output.py /^from context import dpdata$/;" i +dpdata tests/test_cp2k_output.py /^from context import dpdata$/;" i +dpdata tests/test_deepmd_comp.py /^from context import dpdata$/;" i +dpdata tests/test_deepmd_raw.py /^from context import dpdata$/;" i +dpdata tests/test_empty.py /^from context import dpdata$/;" i +dpdata tests/test_fhi_md_multi_elem_output.py /^from context import dpdata$/;" i +dpdata tests/test_fhi_md_output.py /^from context import dpdata$/;" i +dpdata tests/test_fhi_output.py /^from context import dpdata$/;" i +dpdata tests/test_gaussian_log.py /^from context import dpdata$/;" i +dpdata tests/test_gromacs_gro.py /^from context import dpdata$/;" i +dpdata tests/test_json.py /^from context import dpdata$/;" i +dpdata tests/test_lammps_dump_shift_origin.py /^from context import dpdata$/;" i +dpdata tests/test_lammps_dump_skipload.py /^from context import dpdata$/;" i +dpdata tests/test_lammps_dump_to_system.py /^from context import dpdata$/;" i +dpdata tests/test_lammps_lmp_dump.py /^from context import dpdata$/;" i +dpdata tests/test_lammps_lmp_to_system.py /^from context import dpdata$/;" i +dpdata tests/test_msd.py /^from context import dpdata$/;" i +dpdata tests/test_multisystems.py /^from context import dpdata$/;" i +dpdata tests/test_periodic_table.py /^from context import dpdata$/;" i +dpdata tests/test_perturb.py /^from context import dpdata$/;" i +dpdata tests/test_pwmat_config_dump.py /^import dpdata$/;" i +dpdata tests/test_pwmat_config_to_system.py /^import dpdata$/;" i +dpdata tests/test_pwmat_mlmd.py /^import dpdata$/;" i +dpdata tests/test_pwmat_movement.py /^import dpdata$/;" i +dpdata tests/test_qe_cp_traj.py /^from context import dpdata$/;" i +dpdata tests/test_qe_cp_traj_skipload.py /^from context import dpdata$/;" i +dpdata tests/test_qe_pw_scf.py /^from context import dpdata$/;" i +dpdata tests/test_quip_gap_xyz.py /^from context import dpdata$/;" i +dpdata tests/test_remove_pbc.py /^from context import dpdata$/;" i +dpdata tests/test_replicate.py /^from context import dpdata$/;" i +dpdata tests/test_shuffle.py /^from context import dpdata$/;" i +dpdata tests/test_siesta_aiMD_output.py /^from context import dpdata$/;" i +dpdata tests/test_siesta_output.py /^from context import dpdata$/;" i +dpdata tests/test_system_append.py /^from context import dpdata$/;" i +dpdata tests/test_system_apply_pbc.py /^from context import dpdata$/;" i +dpdata tests/test_system_set_type.py /^from context import dpdata$/;" i +dpdata tests/test_to_ase.py /^from context import dpdata$/;" i +dpdata tests/test_to_list.py /^from context import dpdata$/;" i +dpdata tests/test_to_pymatgen.py /^from context import dpdata$/;" i +dpdata tests/test_to_pymatgen_entry.py /^from context import dpdata$/;" i +dpdata tests/test_type_map.py /^from context import dpdata$/;" i +dpdata tests/test_vasp_outcar.py /^from context import dpdata$/;" i +dpdata tests/test_vasp_poscar_dump.py /^from context import dpdata$/;" i +dpdata tests/test_vasp_poscar_to_system.py /^from context import dpdata$/;" i +dpdata tests/test_vasp_unconverged_outcar.py /^from context import dpdata$/;" i +dpdata tests/test_vasp_xml.py /^from context import dpdata$/;" i +dpdata tests/test_water_ions.py /^from context import dpdata$/;" i +dst .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^ def dst(self, dt):$/;" m class:UTC +dump build/lib/dpdata/deepmd/comp.py /^def dump(folder, $/;" f +dump build/lib/dpdata/deepmd/raw.py /^def dump (folder, data) :$/;" f +dump build/lib/dpdata/system.py /^ def dump(self,filename,indent=4):$/;" m class:System +dump build/lib/dpdata/system.py /^import dpdata.lammps.dump$/;" i +dump dpdata/deepmd/comp.py /^def dump(folder, $/;" f +dump dpdata/deepmd/raw.py /^def dump (folder, data) :$/;" f +dump dpdata/system.py /^ def dump(self,filename,indent=4):$/;" m class:System +dump dpdata/system.py /^import dpdata.lammps.dump$/;" i +dump_version .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/__init__.py /^def dump_version(root, version, write_to, template=None):$/;" f +dumpbox2box build/lib/dpdata/lammps/dump.py /^def dumpbox2box(bounds, tilt) :$/;" f +dumpbox2box dpdata/lammps/dump.py /^def dumpbox2box(bounds, tilt) :$/;" f +dumpfn build/lib/dpdata/periodic_table.py /^from monty.serialization import loadfn,dumpfn$/;" i +dumpfn build/lib/dpdata/system.py /^from monty.serialization import loadfn,dumpfn$/;" i +dumpfn dpdata/periodic_table.py /^from monty.serialization import loadfn,dumpfn$/;" i +dumpfn dpdata/system.py /^from monty.serialization import loadfn,dumpfn$/;" i +elements_index_map build/lib/dpdata/system.py /^def elements_index_map(elements,standard=False,inverse=False):$/;" f +elements_index_map dpdata/system.py /^def elements_index_map(elements,standard=False,inverse=False):$/;" f +elements_index_map tests/test_elements_index.py /^from dpdata.system import 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/^pos_patt_first="\\|\\s+[0-9]{1,}[:]\\s\\w+\\s(\\w+)(\\s.*[-]?[0-9]{1,}[.][0-9]*)(\\s+[-]?[0-9]{1,}[.][0-9]*)(\\s+[-]?[0-9]{1,}[.][0-9]*)"$/;" v +pos_patt_first dpdata/fhi_aims/output.py /^pos_patt_first="\\|\\s+[0-9]{1,}[:]\\s\\w+\\s(\\w+)(\\s.*[-]?[0-9]{1,}[.][0-9]*)(\\s+[-]?[0-9]{1,}[.][0-9]*)(\\s+[-]?[0-9]{1,}[.][0-9]*)"$/;" v +pos_patt_other build/lib/dpdata/fhi_aims/output.py /^pos_patt_other="\\s+[a][t][o][m]\\s+([-]?[0-9]{1,}[.][0-9]*)\\s+([-]?[0-9]{1,}[.][0-9]*)\\s+([-]?[0-9]{1,}[.][0-9]*)\\s+(\\w{1,2})"$/;" v +pos_patt_other dpdata/fhi_aims/output.py /^pos_patt_other="\\s+[a][t][o][m]\\s+([-]?[0-9]{1,}[.][0-9]*)\\s+([-]?[0-9]{1,}[.][0-9]*)\\s+([-]?[0-9]{1,}[.][0-9]*)\\s+(\\w{1,2})"$/;" v +poscar build/lib/dpdata/system.py /^import dpdata.vasp.poscar$/;" i +poscar dpdata/system.py /^import dpdata.vasp.poscar$/;" i +posi_diff build/lib/dpdata/md/pbc.py /^def posi_diff(box, r0, r1) :$/;" f +posi_diff build/lib/dpdata/md/water.py /^from .pbc import posi_diff$/;" i +posi_diff 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/^from __future__ import print_function$/;" i +print_function .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/config.py /^from __future__ import print_function, unicode_literals$/;" i +print_function .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^from __future__ import print_function, unicode_literals$/;" i +print_function .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^from __future__ import print_function$/;" i +project docs/conf.py /^project = 'dpdata'$/;" v +ptr_float_fmt build/lib/dpdata/lammps/lmp.py /^ptr_float_fmt = '%15.10f'$/;" v +ptr_float_fmt dpdata/lammps/lmp.py /^ptr_float_fmt = '%15.10f'$/;" v +ptr_int_fmt build/lib/dpdata/lammps/lmp.py /^ptr_int_fmt = '%6d'$/;" v +ptr_int_fmt dpdata/lammps/lmp.py /^ptr_int_fmt = '%6d'$/;" v +ptr_key_fmt build/lib/dpdata/lammps/lmp.py /^ptr_key_fmt = '%15s'$/;" v +ptr_key_fmt dpdata/lammps/lmp.py /^ptr_key_fmt = '%15s'$/;" v +pwmat build/lib/dpdata/system.py /^import dpdata.pwmat.atomconfig$/;" i 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dpdata/xyz/quip_gap_xyz.py /^import re $/;" i +read_amber_traj build/lib/dpdata/amber/md.py /^def read_amber_traj(parm7_file, nc_file, mdfrc_file, mden_file):$/;" f +read_amber_traj dpdata/amber/md.py /^def read_amber_traj(parm7_file, nc_file, mdfrc_file, mden_file):$/;" f +readme setup.py /^ readme = f.read()$/;" v +readme setup.py /^ readme = parse_from_file(readme_file)$/;" v +readme_file setup.py /^readme_file = path.join(path.dirname(path.abspath(__file__)), 'README.md')$/;" v +register_from_funcs build/lib/dpdata/system.py /^ register_from_funcs = Register()$/;" v class:LabeledSystem +register_from_funcs build/lib/dpdata/system.py /^ register_from_funcs = Register()$/;" v class:System +register_from_funcs dpdata/system.py /^ register_from_funcs = Register()$/;" v class:LabeledSystem +register_from_funcs dpdata/system.py /^ register_from_funcs = Register()$/;" v class:System +register_funcs build/lib/dpdata/system.py /^ def register_funcs(self, fmt):$/;" m class:Register 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tests/test_vasp_xml.py /^ def setUp (self) :$/;" m class:TestVaspXmlSkip +setUp tests/test_water_ions.py /^ def setUp(self): $/;" m class:TestIons +setUp tests/test_water_ions.py /^ def setUp(self):$/;" m class:TestAseComputeBond +setup_requires setup.py /^ setup_requires=['setuptools_scm'],$/;" v +setuptools setup.py /^import setuptools$/;" i +shlex .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^import shlex$/;" i +shuffle build/lib/dpdata/system.py /^ def shuffle(self):$/;" m class:LabeledSystem +shuffle build/lib/dpdata/system.py /^ def shuffle(self):$/;" m class:System +shuffle dpdata/system.py /^ def shuffle(self):$/;" m class:LabeledSystem +shuffle dpdata/system.py /^ def shuffle(self):$/;" m class:System +shutil build/lib/dpdata/deepmd/comp.py /^import os,glob,shutil$/;" i +shutil dpdata/deepmd/comp.py /^import os,glob,shutil$/;" i +shutil tests/test_amber_md.py /^import shutil$/;" i +shutil tests/test_deepmd_comp.py /^import os,shutil$/;" i +shutil tests/test_deepmd_raw.py /^import os,shutil$/;" i +siesta build/lib/dpdata/system.py /^import dpdata.siesta.aiMD_output$/;" i +siesta build/lib/dpdata/system.py /^import dpdata.siesta.output$/;" i +siesta dpdata/system.py /^import dpdata.siesta.aiMD_output$/;" i +siesta dpdata/system.py /^import dpdata.siesta.output$/;" i +simplified_semver_version .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^def simplified_semver_version(version):$/;" f +sort_atom_names build/lib/dpdata/system.py /^ def sort_atom_names(self, type_map=None):$/;" m class:System +sort_atom_names dpdata/system.py /^ def sort_atom_names(self, type_map=None):$/;" m class:System +sort_atom_types build/lib/dpdata/system.py /^ def sort_atom_types(self):$/;" m class:LabeledSystem +sort_atom_types build/lib/dpdata/system.py /^ def sort_atom_types(self):$/;" m class:System +sort_atom_types dpdata/system.py /^ def sort_atom_types(self):$/;" m class:LabeledSystem +sort_atom_types dpdata/system.py /^ def sort_atom_types(self):$/;" m class:System +source_suffix docs/conf.py /^source_suffix = ['.rst', '.md']$/;" v +split_traj build/lib/dpdata/lammps/dump.py /^def split_traj(dump_lines) :$/;" f +split_traj dpdata/lammps/dump.py /^def split_traj(dump_lines) :$/;" f +string_types .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/__init__.py /^from .utils import function_has_arg, string_types$/;" i +string_types .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^string_types = (str,) if PY3 else (str, unicode) # noqa$/;" v +string_types .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^from .utils import trace, string_types, utc$/;" i +sub_system build/lib/dpdata/system.py /^ def sub_system(self, f_idx) :$/;" m class:LabeledSystem +sub_system build/lib/dpdata/system.py /^ def sub_system(self, f_idx) :$/;" m class:System +sub_system dpdata/system.py /^ def sub_system(self, f_idx) :$/;" m class:LabeledSystem +sub_system dpdata/system.py /^ def sub_system(self, f_idx) :$/;" m class:System +subprocess .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/file_finder_git.py /^import subprocess$/;" i +subprocess .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/file_finder_hg.py /^import subprocess$/;" i +subprocess .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^import subprocess$/;" i +symbols build/lib/dpdata/gaussian/log.py /^symbols = ['X', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og']$/;" v +symbols dpdata/gaussian/log.py /^symbols = ['X', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og']$/;" v +sys .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/__main__.py /^import sys$/;" i +sys .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^import sys$/;" i +sys .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/win_py31_compat.py /^import sys$/;" i +sys build/lib/dpdata/fhi_aims/output.py /^ import sys$/;" i +sys build/lib/dpdata/lammps/dump.py /^import os, sys$/;" i +sys build/lib/dpdata/md/rdf.py /^ sys = dpdata.System('out.lmp')$/;" v +sys build/lib/dpdata/qe/scf.py /^import os,sys$/;" i +sys docs/conf.py /^import sys$/;" i +sys dpdata/fhi_aims/output.py /^ import sys$/;" i +sys dpdata/lammps/dump.py /^import os, sys$/;" i +sys dpdata/md/rdf.py /^ sys = dpdata.System('out.lmp')$/;" v +sys dpdata/qe/scf.py /^import os,sys$/;" i +sys tests/context.py /^import sys,os$/;" i +system_data build/lib/dpdata/lammps/dump.py /^def system_data(lines, type_map = None, type_idx_zero = True) :$/;" f +system_data build/lib/dpdata/lammps/lmp.py /^def system_data(lines, type_map = None, type_idx_zero = True) :$/;" f +system_data dpdata/lammps/dump.py /^def system_data(lines, type_map = None, type_idx_zero = True) :$/;" f +system_data dpdata/lammps/lmp.py /^def system_data(lines, type_map = None, type_idx_zero = True) :$/;" f +system_info build/lib/dpdata/pwmat/movement.py /^def system_info (lines, type_idx_zero = False) :$/;" f +system_info build/lib/dpdata/vasp/outcar.py /^def system_info (lines, type_idx_zero = False) :$/;" f +system_info dpdata/pwmat/movement.py /^def system_info (lines, type_idx_zero = False) :$/;" f +system_info dpdata/vasp/outcar.py /^def system_info (lines, type_idx_zero = False) :$/;" f +system_pbc_shift build/lib/dpdata/md/msd.py /^from .pbc import system_pbc_shift$/;" i +system_pbc_shift build/lib/dpdata/md/pbc.py /^def system_pbc_shift(system) :$/;" f +system_pbc_shift dpdata/md/msd.py /^from .pbc import system_pbc_shift$/;" i +system_pbc_shift dpdata/md/pbc.py /^def system_pbc_shift(system) :$/;" f +tag_regex .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/config.py /^ def tag_regex(self):$/;" m class:Configuration +tag_regex .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/config.py /^ def tag_regex(self, value):$/;" m class:Configuration +tag_to_version .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/hacks.py /^from .version import tag_to_version, meta$/;" i +tag_to_version .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^def tag_to_version(tag, config=None):$/;" f +tags_to_versions .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/hg.py /^from .version import meta, tags_to_versions$/;" i +tags_to_versions .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^def tags_to_versions(tags, config=None):$/;" f +tarfile .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/file_finder_git.py /^import tarfile$/;" i +tearDown tests/test_amber_md.py /^ def tearDown(self) :$/;" m class:TestAmberMD +tearDown tests/test_deepmd_comp.py /^ def tearDown(self) :$/;" m class:TestDeepmdCompNoLabels +tearDown tests/test_deepmd_comp.py /^ def tearDown(self) :$/;" m class:TestDeepmdLoadDumpComp +tearDown tests/test_deepmd_raw.py /^ def tearDown(self) :$/;" m class:TestDeepmdCompNoLabels +tearDown tests/test_deepmd_raw.py /^ def tearDown(self) :$/;" m class:TestDeepmdDumpRaw +tearDown tests/test_deepmd_raw.py /^ def tearDown(self) :$/;" m class:TestDeepmdRawNoLabels +tearDown tests/test_deepmd_raw.py /^ def tearDown(self) :$/;" m class:TestDeepmdTypeMap +tearDown tests/test_pwmat_config_dump.py /^ def tearDown(self):$/;" m class:TestatomconfigSkipZeroAtomNumb +tearDown tests/test_vasp_poscar_dump.py /^ def tearDown(self):$/;" m class:TestPOSCARSkipZeroAtomNumb +templates_path docs/conf.py /^templates_path = ['_templates']$/;" v +test tests/test_to_pymatgen_entry.py /^ def test(self): $/;" m class:TestPymatgen +test_H tests/test_periodic_table.py /^ def test_H(self):$/;" m class:TestPeriodicTable +test_add_func tests/comp_sys.py /^ def test_add_func(self):$/;" m class:CompSys +test_atom_names tests/comp_sys.py /^ def test_atom_names(self):$/;" m class:CompSys +test_atom_names tests/poscars/poscar_ref_oh.py /^ def test_atom_names(self):$/;" m class:TestPOSCARoh +test_atom_names tests/pwmat/config_ref_ch4.py /^ def test_atom_names(self):$/;" m class:Testconfigch4 +test_atom_names tests/pwmat/config_ref_oh.py /^ def test_atom_names(self):$/;" m class:Testconfigoh +test_atom_names tests/test_cp2k_output.py /^ def test_atom_names(self) :$/;" m class:TestCP2KSinglePointEnergy +test_atom_names tests/test_fhi_md_multi_elem_output.py /^ def test_atom_names(self):$/;" m class:TestFhi_aims_MD +test_atom_names tests/test_fhi_md_output.py /^ def test_atom_names(self):$/;" m class:TestFhi_aims_MD +test_atom_names tests/test_fhi_output.py /^ def test_atom_names(self) :$/;" m class:TestFhi_aims +test_atom_names tests/test_gaussian_log.py /^ def test_atom_names(self) :$/;" m class:TestGaussianLog +test_atom_names tests/test_multisystems.py /^ def test_atom_names(self):$/;" m class:MultiSystems +test_atom_names tests/test_pwmat_movement.py /^ def test_atom_names(self) :$/;" m class:TestpwmatSinglePointEnergy +test_atom_names tests/test_qe_cp_traj.py /^ def test_atom_names(self) :$/;" m class:TestCPTRAJProps +test_atom_names tests/test_qe_pw_scf.py /^ def test_atom_names(self) :$/;" m class:TestPWSCFSinglePointEnergy +test_atom_names tests/test_siesta_aiMD_output.py /^ def test_atom_names(self):$/;" m class:TestSIESTASinglePointEnergy +test_atom_names tests/test_siesta_output.py /^ def test_atom_names(self) :$/;" m class:TestSIESTASinglePointEnergy +test_atom_numbs tests/comp_sys.py /^ def test_atom_numbs(self):$/;" m class:CompSys +test_atom_numbs tests/poscars/poscar_ref_oh.py /^ def test_atom_numbs(self):$/;" m class:TestPOSCARoh +test_atom_numbs tests/pwmat/config_ref_ch4.py /^ def test_atom_numbs(self):$/;" m class:Testconfigch4 +test_atom_numbs tests/pwmat/config_ref_oh.py /^ def test_atom_numbs(self):$/;" m class:Testconfigoh +test_atom_numbs tests/test_cp2k_output.py /^ def test_atom_numbs(self) :$/;" m class:TestCP2KSinglePointEnergy +test_atom_numbs tests/test_fhi_md_multi_elem_output.py /^ def test_atom_numbs(self):$/;" m class:TestFhi_aims_MD +test_atom_numbs tests/test_fhi_md_output.py /^ def test_atom_numbs(self):$/;" m class:TestFhi_aims_MD +test_atom_numbs tests/test_fhi_output.py /^ def test_atom_numbs(self) :$/;" m class:TestFhi_aims +test_atom_numbs tests/test_gaussian_log.py /^ def test_atom_numbs(self) :$/;" m class:TestGaussianLog +test_atom_numbs tests/test_pwmat_movement.py /^ def test_atom_numbs(self) :$/;" m class:TestpwmatSinglePointEnergy +test_atom_numbs tests/test_qe_cp_traj.py /^ def test_atom_numbs(self) :$/;" m class:TestCPTRAJProps +test_atom_numbs tests/test_qe_pw_scf.py /^ def test_atom_numbs(self) :$/;" m class:TestPWSCFSinglePointEnergy +test_atom_numbs tests/test_siesta_aiMD_output.py /^ def test_atom_numbs(self):$/;" m class:TestSIESTASinglePointEnergy +test_atom_numbs tests/test_siesta_output.py /^ def test_atom_numbs(self) :$/;" m class:TestSIESTASinglePointEnergy +test_atom_types tests/comp_sys.py /^ def test_atom_types(self):$/;" m class:CompSys +test_atom_types tests/poscars/poscar_ref_oh.py /^ def test_atom_types(self):$/;" m class:TestPOSCARoh +test_atom_types tests/pwmat/config_ref_ch4.py /^ def test_atom_types(self):$/;" m class:Testconfigch4 +test_atom_types tests/pwmat/config_ref_oh.py /^ def test_atom_types(self):$/;" m class:Testconfigoh +test_atom_types tests/test_cp2k_output.py /^ def test_atom_types(self) :$/;" m class:TestCP2KSinglePointEnergy +test_atom_types tests/test_fhi_md_multi_elem_output.py /^ def test_atom_types(self):$/;" m class:TestFhi_aims_MD +test_atom_types tests/test_fhi_md_output.py /^ def test_atom_types(self):$/;" m class:TestFhi_aims_MD +test_atom_types tests/test_fhi_output.py /^ def test_atom_types(self) :$/;" m class:TestFhi_aims +test_atom_types tests/test_gaussian_log.py /^ def test_atom_types(self) :$/;" m class:TestGaussianLog +test_atom_types tests/test_gaussian_log.py /^ def test_atom_types(self) :$/;" m class:TestNonCoveragedGaussianLoadLog +test_atom_types tests/test_pwmat_movement.py /^ def test_atom_types(self) :$/;" m class:TestpwmatSinglePointEnergy +test_atom_types tests/test_qe_cp_traj.py /^ def test_atom_types(self) :$/;" m class:TestCPTRAJProps +test_atom_types tests/test_qe_pw_scf.py /^ def test_atom_types(self) :$/;" m class:TestPWSCFSinglePointEnergy +test_atom_types tests/test_siesta_aiMD_output.py /^ def test_atom_types(self):$/;" m class:TestSIESTASinglePointEnergy +test_atom_types tests/test_siesta_output.py /^ def test_atom_types(self) :$/;" m class:TestSIESTASinglePointEnergy +test_bond_identity tests/test_water_ions.py /^ def test_bond_identity(self):$/;" m class:TestAseComputeBond +test_case_null tests/test_qe_cp_traj.py /^ def test_case_null(self):$/;" m class:TestConverCellDim +test_cell tests/comp_sys.py /^ def test_cell(self):$/;" m class:CompSys +test_cell tests/poscars/poscar_ref_oh.py /^ def test_cell(self):$/;" m class:TestPOSCARoh +test_cell tests/pwmat/config_ref_ch4.py /^ def test_cell(self):$/;" m class:Testconfigch4 +test_cell tests/pwmat/config_ref_oh.py /^ def test_cell(self):$/;" m class:Testconfigoh +test_cell tests/test_cp2k_output.py /^ def test_cell(self) :$/;" m class:TestCP2KSinglePointEnergy +test_cell tests/test_fhi_md_multi_elem_output.py /^ def test_cell(self):$/;" m class:TestFhi_aims_MD +test_cell tests/test_fhi_md_output.py /^ def test_cell(self):$/;" m class:TestFhi_aims_MD +test_cell tests/test_fhi_output.py /^ def test_cell(self) :$/;" m class:TestFhi_aims +test_cell tests/test_pwmat_mlmd.py /^ def test_cell(self) :$/;" m class:TestSingleStep +test_cell tests/test_pwmat_movement.py /^ def test_cell(self) :$/;" m class:TestpwmatSinglePointEnergy +test_cell tests/test_qe_cp_traj.py /^ def test_cell(self) :$/;" m class:TestCPTRAJProps +test_cell tests/test_qe_cp_traj_skipload.py /^ def test_cell(self):$/;" m class:TestPWSCFLabeledTrajSkip +test_cell tests/test_qe_pw_scf.py /^ def test_cell(self) :$/;" m class:TestPWSCFSinglePointEnergy +test_cell tests/test_siesta_aiMD_output.py /^ def test_cell(self):$/;" m class:TestSIESTASinglePointEnergy +test_cell tests/test_siesta_output.py /^ def test_cell(self) :$/;" m class:TestSIESTASinglePointEnergy +test_cells tests/test_gaussian_log.py /^ def test_cells(self) :$/;" m class:TestNonCoveragedGaussianLoadLog +test_check_type_map tests/test_type_map.py /^ def test_check_type_map(self):$/;" m class:TestTypeMap +test_coord tests/comp_sys.py /^ def test_coord(self): $/;" m class:CompSys +test_coord tests/test_cp2k_output.py /^ def test_coord(self) :$/;" m class:TestCP2KSinglePointEnergy +test_coord tests/test_fhi_md_multi_elem_output.py /^ def test_coord(self):$/;" m class:TestFhi_aims_MD +test_coord tests/test_fhi_md_output.py /^ def test_coord(self):$/;" m class:TestFhi_aims_MD +test_coord tests/test_fhi_output.py /^ def test_coord(self) :$/;" m class:TestFhi_aims +test_coord tests/test_pwmat_mlmd.py /^ def test_coord(self) :$/;" m class:TestSingleStep +test_coord tests/test_pwmat_movement.py /^ def test_coord(self) :$/;" m class:TestpwmatSinglePointEnergy +test_coord tests/test_qe_cp_traj.py /^ def test_coord(self) : $/;" m class:TestCPTRAJProps +test_coord tests/test_qe_pw_scf.py /^ def test_coord(self) :$/;" m class:TestPWSCFSinglePointEnergy +test_coord tests/test_siesta_aiMD_output.py /^ def test_coord(self):$/;" m class:TestSIESTASinglePointEnergy +test_coord tests/test_siesta_output.py /^ def test_coord(self) :$/;" m class:TestSIESTASinglePointEnergy +test_coords tests/test_gaussian_log.py /^ def test_coords(self) :$/;" m class:TestNonCoveragedGaussianLoadLog +test_data_empty tests/test_empty.py /^ def test_data_empty(self):$/;" m class:TestEmptySystem +test_dump_pwmat_type_map tests/test_pwmat_config_dump.py /^ def test_dump_pwmat_type_map(self):$/;" m class:TestatomconfigSkipZeroAtomNumb +test_dump_vasp_type_map tests/test_vasp_poscar_dump.py /^ def test_dump_vasp_type_map(self):$/;" m class:TestPOSCARSkipZeroAtomNumb +test_empty tests/test_empty.py /^ def test_empty(self):$/;" m class:TestEmptySystem +test_energies tests/test_gaussian_log.py /^ def test_energies(self) :$/;" m class:TestNonCoveragedGaussianLoadLog +test_energy tests/comp_sys.py /^ def test_energy(self) :$/;" m class:CompLabeledSys +test_energy tests/test_cp2k_output.py /^ def test_energy(self) :$/;" m class:TestCP2KSinglePointEnergy +test_energy tests/test_fhi_md_multi_elem_output.py /^ def test_energy(self):$/;" m class:TestFhi_aims_MD +test_energy tests/test_fhi_md_output.py /^ def test_energy(self):$/;" m class:TestFhi_aims_MD +test_energy tests/test_fhi_output.py /^ def test_energy(self) :$/;" m class:TestFhi_aims +test_energy tests/test_pwmat_movement.py /^ def test_energy(self) :$/;" m class:TestpwmatSinglePointEnergy +test_energy tests/test_qe_pw_scf.py /^ def test_energy(self) :$/;" m class:TestPWSCFSinglePointEnergy +test_energy tests/test_siesta_aiMD_output.py /^ def test_energy(self):$/;" m class:TestSIESTASinglePointEnergy +test_energy tests/test_siesta_output.py /^ def test_energy(self) :$/;" m class:TestSIESTASinglePointEnergy +test_failed_append tests/test_system_append.py /^ def test_failed_append(self):$/;" m class:TestFailedAppend +test_force tests/comp_sys.py /^ def test_force(self) :$/;" m class:CompLabeledSys +test_force tests/test_cp2k_output.py /^ def test_force(self) :$/;" m class:TestCP2KSinglePointEnergy +test_force tests/test_fhi_md_multi_elem_output.py /^ def test_force(self):$/;" m class:TestFhi_aims_MD +test_force tests/test_fhi_md_output.py /^ def test_force(self):$/;" m class:TestFhi_aims_MD +test_force tests/test_fhi_output.py /^ def test_force(self) :$/;" m class:TestFhi_aims +test_force tests/test_pwmat_mlmd.py /^ def test_force(self) :$/;" m class:TestSingleStep +test_force tests/test_pwmat_movement.py /^ def test_force(self) :$/;" m class:TestpwmatSinglePointEnergy +test_force tests/test_qe_pw_scf.py /^ def test_force(self) :$/;" m class:TestPWSCFSinglePointEnergy +test_force tests/test_siesta_aiMD_output.py /^ def test_force(self):$/;" m class:TestSIESTASinglePointEnergy +test_force tests/test_siesta_output.py /^ def test_force(self) :$/;" m class:TestSIESTASinglePointEnergy +test_forces tests/test_gaussian_log.py /^ def test_forces(self) :$/;" m class:TestNonCoveragedGaussianLoadLog +test_frame tests/poscars/poscar_ref_oh.py /^ def test_frame(self): $/;" m class:TestPOSCARoh +test_frame tests/pwmat/config_ref_ch4.py /^ def test_frame(self): $/;" m class:Testconfigch4 +test_frame tests/pwmat/config_ref_oh.py /^ def test_frame(self): $/;" m class:Testconfigoh +test_func1 tests/test_cell_to_low_triangle.py /^ def test_func1(self):$/;" m class:TestCellToLowTriangle +test_func1 tests/test_elements_index.py /^ def test_func1(self):$/;" m class:ElementIndexMap +test_func2 tests/test_cell_to_low_triangle.py /^ def test_func2(self):$/;" m class:TestCellToLowTriangle +test_func2 tests/test_elements_index.py /^ def test_func2(self):$/;" m class:ElementIndexMap +test_func3 tests/test_cell_to_low_triangle.py /^ def test_func3(self):$/;" m class:TestCellToLowTriangle +test_func3 tests/test_elements_index.py /^ def test_func3(self):$/;" m class:ElementIndexMap +test_func4 tests/test_cell_to_low_triangle.py /^ def test_func4(self):$/;" m class:TestCellToLowTriangle +test_func4 tests/test_elements_index.py /^ def test_func4(self):$/;" m class:ElementIndexMap +test_func5 tests/test_cell_to_low_triangle.py /^ def test_func5(self):$/;" m class:TestCellToLowTriangle +test_func6 tests/test_cell_to_low_triangle.py /^ def test_func6(self):$/;" m class:TestCellToLowTriangle +test_ions_count tests/test_water_ions.py /^ def test_ions_count(self) :$/;" m class:TestIons +test_is_nopbc tests/comp_sys.py /^ def test_is_nopbc(self):$/;" m class:IsNoPBC +test_is_pbc tests/comp_sys.py /^ def test_is_pbc(self):$/;" m class:IsPBC +test_len_func tests/comp_sys.py /^ def test_len_func(self):$/;" m class:CompSys +test_mlmd tests/test_pwmat_mlmd.py /^ def test_mlmd(self) :$/;" m class:TestSingleStep +test_msd tests/test_msd.py /^ def test_msd(self) :$/;" m class:TestMSD +test_nframes tests/test_gaussian_log.py /^ def test_nframes(self):$/;" m class:TestGaussianLog +test_nframes tests/test_lammps_dump_to_system.py /^ def test_nframes (self) :$/;" m class:TestDump2 +test_nframs tests/comp_sys.py /^ def test_nframs(self):$/;" m class:CompSys +test_nopbc tests/comp_sys.py /^ def test_nopbc(self):$/;" m class:CompSys +test_nopbc tests/test_gaussian_log.py /^ def test_nopbc(self):$/;" m class:TestGaussianLog +test_npy_type_map tests/test_deepmd_raw.py /^ def test_npy_type_map (self) :$/;" m class:TestDeepmdTypeMap +test_npy_type_map_enforce tests/test_deepmd_raw.py /^ def test_npy_type_map_enforce (self) :$/;" m class:TestDeepmdTypeMap +test_npy_type_map_load tests/test_deepmd_raw.py /^ def test_npy_type_map_load (self) :$/;" m class:TestDeepmdTypeMap +test_orig tests/comp_sys.py /^ def test_orig(self):$/;" m class:CompSys +test_orig tests/poscars/poscar_ref_oh.py /^ def test_orig(self):$/;" m class:TestPOSCARoh +test_orig tests/pwmat/config_ref_ch4.py /^ def test_orig(self):$/;" m class:Testconfigch4 +test_orig tests/pwmat/config_ref_oh.py /^ def test_orig(self):$/;" m class:Testconfigoh +test_pbc tests/test_system_apply_pbc.py /^ def test_pbc(self) :$/;" m class:TestPBC +test_read_file tests/test_gromacs_gro.py /^ def test_read_file(self):$/;" m class:TestGromacsGro +test_read_file_tri tests/test_gromacs_gro.py /^ def test_read_file_tri(self):$/;" m class:TestGromacsGro +test_remove tests/test_remove_pbc.py /^ def test_remove(self):$/;" m class:TestRemovePBC +test_single_step tests/test_vasp_unconverged_outcar.py /^ def test_single_step(self) :$/;" m class:TestSingleStep +test_systems_name tests/test_multisystems.py /^ def test_systems_name(self):$/;" m class:MultiSystems +test_systems_size tests/test_multisystems.py /^ def test_systems_size(self):$/;" m class:MultiSystems +test_type_map tests/test_deepmd_raw.py /^ def test_type_map (self) :$/;" m class:TestDeepmdTypeMap +test_type_map tests/test_multisystems.py /^ def test_type_map(self):$/;" m class:TestTypeMap +test_type_map_enforce tests/test_deepmd_raw.py /^ def test_type_map_enforce (self) :$/;" m class:TestDeepmdTypeMap +test_type_map_is_superset tests/test_type_map.py /^ def test_type_map_is_superset(self):$/;" m class:TestTypeMap +test_type_map_load tests/test_deepmd_raw.py /^ def test_type_map_load (self) :$/;" m class:TestDeepmdTypeMap +test_types_func_1 tests/test_system_set_type.py /^ def test_types_func_1(self):$/;" m class:TestSetAtomTypes +test_types_func_2 tests/test_system_set_type.py /^ def test_types_func_2(self):$/;" m class:TestSetAtomTypes +test_unconverged tests/test_vasp_unconverged_outcar.py /^ def test_unconverged(self) :$/;" m class:TestSingleStep +test_virial tests/comp_sys.py /^ def test_virial(self) :$/;" m class:CompLabeledSys +test_virial tests/test_qe_pw_scf.py /^ def test_virial(self) :$/;" m class:TestPWSCFSinglePointEnergy +test_viriale tests/test_siesta_aiMD_output.py /^ def test_viriale(self):$/;" m class:TestSIESTASinglePointEnergy +test_viriale tests/test_siesta_output.py /^ def test_viriale(self) :$/;" m class:TestSIESTASinglePointEnergy +test_virials tests/test_gaussian_log.py /^ def test_virials(self) :$/;" m class:TestNonCoveragedGaussianLoadLog +texinfo_documents docs/conf.py /^texinfo_documents = [$/;" v +to build/lib/dpdata/system.py /^ def to(self, fmt, *args, **kwargs):$/;" m class:System +to dpdata/system.py /^ def to(self, fmt, *args, **kwargs):$/;" m class:System +to_ase_structure build/lib/dpdata/system.py /^ def to_ase_structure(self):$/;" m class:System +to_ase_structure dpdata/system.py /^ def to_ase_structure(self):$/;" m class:System +to_deepmd_npy build/lib/dpdata/system.py /^ def to_deepmd_npy(self, folder, set_size = 5000, prec=np.float32) :$/;" m class:MultiSystems +to_deepmd_npy build/lib/dpdata/system.py /^ def to_deepmd_npy(self, folder, set_size = 5000, prec=np.float32) :$/;" m class:System +to_deepmd_npy dpdata/system.py /^ def to_deepmd_npy(self, folder, set_size = 5000, prec=np.float32) :$/;" m class:MultiSystems +to_deepmd_npy dpdata/system.py /^ def to_deepmd_npy(self, folder, set_size = 5000, prec=np.float32) :$/;" m class:System +to_deepmd_raw build/lib/dpdata/system.py /^ def to_deepmd_raw(self, folder) :$/;" m class:MultiSystems +to_deepmd_raw build/lib/dpdata/system.py /^ def to_deepmd_raw(self, folder) :$/;" m class:System +to_deepmd_raw dpdata/system.py /^ def to_deepmd_raw(self, folder) :$/;" m class:MultiSystems +to_deepmd_raw dpdata/system.py /^ def to_deepmd_raw(self, folder) :$/;" m class:System +to_lammps_lmp build/lib/dpdata/system.py /^ def to_lammps_lmp(self, file_name, frame_idx = 0) :$/;" m class:System +to_lammps_lmp dpdata/system.py /^ def to_lammps_lmp(self, file_name, frame_idx = 0) :$/;" m class:System +to_list build/lib/dpdata/system.py /^ def to_list(self):$/;" m class:System +to_list dpdata/system.py /^ def to_list(self):$/;" m class:System +to_pwmat_atomconfig build/lib/dpdata/system.py /^ def to_pwmat_atomconfig(self, file_name, frame_idx = 0) :$/;" m class:System +to_pwmat_atomconfig dpdata/system.py /^ def to_pwmat_atomconfig(self, file_name, frame_idx = 0) :$/;" m class:System +to_pymatgen_ComputedStructureEntry build/lib/dpdata/system.py /^ def to_pymatgen_ComputedStructureEntry(self):$/;" m class:LabeledSystem +to_pymatgen_ComputedStructureEntry dpdata/system.py /^ def to_pymatgen_ComputedStructureEntry(self):$/;" m class:LabeledSystem +to_pymatgen_structure build/lib/dpdata/system.py /^ def to_pymatgen_structure(self):$/;" m class:System +to_pymatgen_structure dpdata/system.py /^ def to_pymatgen_structure(self):$/;" m class:System +to_system_data build/lib/dpdata/deepmd/comp.py /^def to_system_data(folder, $/;" f +to_system_data build/lib/dpdata/deepmd/raw.py /^def to_system_data(folder, type_map = None, labels = True) :$/;" f +to_system_data build/lib/dpdata/gaussian/log.py /^def to_system_data(file_name, md=False):$/;" f +to_system_data build/lib/dpdata/lammps/lmp.py /^def to_system_data(lines, type_map = None, type_idx_zero = True) :$/;" f +to_system_data build/lib/dpdata/pwmat/atomconfig.py /^def to_system_data(lines) :$/;" f +to_system_data build/lib/dpdata/qe/traj.py /^def to_system_data(input_name, prefix, begin = 0, step = 1) :$/;" f +to_system_data build/lib/dpdata/vasp/poscar.py /^def to_system_data(lines) :$/;" f +to_system_data dpdata/deepmd/comp.py /^def to_system_data(folder, $/;" f +to_system_data dpdata/deepmd/raw.py /^def to_system_data(folder, type_map = None, labels = True) :$/;" f +to_system_data dpdata/gaussian/log.py /^def to_system_data(file_name, md=False):$/;" f +to_system_data dpdata/lammps/lmp.py /^def to_system_data(lines, type_map = None, type_idx_zero = True) :$/;" f +to_system_data dpdata/pwmat/atomconfig.py /^def to_system_data(lines) :$/;" f +to_system_data dpdata/qe/traj.py /^def to_system_data(input_name, prefix, begin = 0, step = 1) :$/;" f +to_system_data dpdata/vasp/poscar.py /^def to_system_data(lines) :$/;" f +to_system_label build/lib/dpdata/qe/traj.py /^def to_system_label(input_name, prefix, begin = 0, step = 1) :$/;" f +to_system_label dpdata/qe/traj.py /^def to_system_label(input_name, prefix, begin = 0, step = 1) :$/;" f +to_vasp_poscar build/lib/dpdata/system.py /^ def to_vasp_poscar(self, file_name, frame_idx = 0) :$/;" m class:System +to_vasp_poscar dpdata/system.py /^ def to_vasp_poscar(self, file_name, frame_idx = 0) :$/;" m class:System +to_vasp_string build/lib/dpdata/system.py /^ def to_vasp_string(self, frame_idx=0):$/;" m class:System +to_vasp_string dpdata/system.py /^ def to_vasp_string(self, frame_idx=0):$/;" m class:System +trace .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/config.py /^from .utils import trace$/;" i +trace .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/discover.py /^from .utils import trace$/;" i +trace .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/file_finder_git.py /^from .utils import trace$/;" i +trace .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/git.py /^from .utils import do_ex, trace, has_command$/;" i +trace .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/hacks.py /^from .utils import data_from_mime, trace$/;" i +trace .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/hg.py /^from .utils import do, trace, data_from_mime, has_command$/;" i +trace .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^def trace(*k):$/;" f +trace .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^from .utils import trace, string_types, utc$/;" i +trace_exception .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/integration.py /^from .utils import do, trace_exception$/;" i +trace_exception .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^def trace_exception():$/;" f +traceback .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^import traceback$/;" i +traj build/lib/dpdata/system.py /^import dpdata.qe.traj$/;" i +traj dpdata/system.py /^import dpdata.qe.traj$/;" i +tzname .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^ def tzname(self, dt):$/;" m class:UTC +unicode_literals .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/config.py /^from __future__ import print_function, unicode_literals$/;" i +unicode_literals .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^from __future__ import print_function, unicode_literals$/;" i +uniq_formula build/lib/dpdata/system.py /^ def uniq_formula(self):$/;" m class:System +uniq_formula dpdata/system.py /^ def uniq_formula(self):$/;" m class:System +unittest tests/test_amber_md.py /^import unittest$/;" i +unittest tests/test_cell_to_low_triangle.py /^import unittest$/;" i +unittest tests/test_cp2k_aimd_output.py /^import unittest$/;" i +unittest tests/test_cp2k_output.py /^import unittest$/;" i +unittest tests/test_deepmd_comp.py /^import unittest$/;" i +unittest tests/test_deepmd_raw.py /^import unittest$/;" i +unittest tests/test_elements_index.py /^import unittest$/;" i +unittest tests/test_empty.py /^import unittest$/;" i +unittest tests/test_fhi_md_multi_elem_output.py /^import unittest$/;" i +unittest tests/test_fhi_md_output.py /^import unittest$/;" i +unittest tests/test_fhi_output.py /^import unittest$/;" i +unittest tests/test_gaussian_log.py /^import unittest$/;" i +unittest tests/test_gromacs_gro.py /^import unittest$/;" i +unittest tests/test_json.py /^import unittest$/;" i +unittest tests/test_lammps_dump_shift_origin.py /^import unittest$/;" i +unittest tests/test_lammps_dump_skipload.py /^import unittest$/;" i +unittest tests/test_lammps_dump_to_system.py /^import unittest$/;" i +unittest tests/test_lammps_lmp_dump.py /^import unittest$/;" i +unittest tests/test_lammps_lmp_to_system.py /^import unittest$/;" i +unittest tests/test_msd.py /^import unittest$/;" i +unittest tests/test_multisystems.py /^import unittest$/;" i +unittest tests/test_periodic_table.py /^import unittest$/;" i +unittest tests/test_perturb.py /^import unittest$/;" i +unittest tests/test_pwmat_config_dump.py /^import unittest$/;" i +unittest tests/test_pwmat_config_to_system.py /^import unittest$/;" i +unittest tests/test_pwmat_mlmd.py /^import unittest$/;" i +unittest tests/test_pwmat_movement.py /^import unittest$/;" i +unittest tests/test_qe_cp_traj.py /^import unittest$/;" i +unittest tests/test_qe_cp_traj_skipload.py /^import unittest$/;" i +unittest tests/test_qe_pw_scf.py /^import unittest$/;" i +unittest tests/test_quip_gap_xyz.py /^import unittest$/;" i +unittest tests/test_remove_pbc.py /^import unittest$/;" i +unittest tests/test_replicate.py /^import unittest$/;" i +unittest tests/test_shuffle.py /^import unittest$/;" i +unittest tests/test_siesta_aiMD_output.py /^import unittest$/;" i +unittest tests/test_siesta_output.py /^import unittest$/;" i +unittest tests/test_system_append.py /^import unittest$/;" i +unittest tests/test_system_apply_pbc.py /^import unittest$/;" i +unittest tests/test_system_set_type.py /^import unittest$/;" i +unittest tests/test_to_ase.py /^import unittest$/;" i +unittest tests/test_to_list.py /^import unittest$/;" i +unittest tests/test_to_pymatgen.py /^import unittest$/;" i +unittest tests/test_to_pymatgen_entry.py /^import unittest$/;" i +unittest tests/test_type_map.py /^import unittest$/;" i +unittest tests/test_vasp_outcar.py /^import unittest$/;" i +unittest tests/test_vasp_poscar_dump.py /^import unittest$/;" i +unittest tests/test_vasp_poscar_to_system.py /^import unittest$/;" i +unittest tests/test_vasp_unconverged_outcar.py /^import unittest$/;" i +unittest tests/test_vasp_xml.py /^import unittest$/;" i +unittest tests/test_water_ions.py /^import unittest$/;" i +url setup.py /^ url="https:\/\/github.com\/deepmodeling\/dpdata",$/;" v +use_scm_version setup.py /^ use_scm_version={'write_to': 'dpdata\/_version.py'},$/;" v +utc .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^utc = UTC()$/;" v +utc .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^from .utils import trace, string_types, utc$/;" i +utcoffset .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^ def utcoffset(self, dt):$/;" m class:UTC +vasp build/lib/dpdata/__init__.py /^from . import vasp$/;" i +vasp build/lib/dpdata/system.py /^import dpdata.vasp.outcar$/;" i +vasp build/lib/dpdata/system.py /^import dpdata.vasp.poscar$/;" i +vasp build/lib/dpdata/system.py /^import dpdata.vasp.xml$/;" i +vasp dpdata/__init__.py /^from . import vasp$/;" i +vasp dpdata/system.py /^import dpdata.vasp.outcar$/;" i +vasp dpdata/system.py /^import dpdata.vasp.poscar$/;" i +vasp dpdata/system.py /^import dpdata.vasp.xml$/;" i +version build/lib/dpdata/_version.py /^version = '0.1.20.dev0+gf150dd1.d20200909'$/;" v +version docs/conf.py /^version = '0.0'$/;" v +version dpdata/_version.py /^version = '0.1.20.dev0+gf150dd1.d20200909'$/;" v +version_from_scm .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/__init__.py /^def version_from_scm(root):$/;" f +version_keyword .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/integration.py /^def version_keyword(dist, keyword, value):$/;" f +warn_on_shallow .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/git.py /^def warn_on_shallow(wd):$/;" f +warnings .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/__init__.py /^import warnings$/;" i +warnings .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/config.py /^import warnings$/;" i +warnings .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/git.py /^import warnings$/;" i +warnings .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/utils.py /^import warnings$/;" i +warnings .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/version.py /^import warnings$/;" i +warnings build/lib/dpdata/qe/traj.py /^import dpdata,warnings$/;" i +warnings dpdata/qe/traj.py /^import dpdata,warnings$/;" i +water tests/context.py /^import dpdata.md.water$/;" i +wintypes .eggs/setuptools_scm-4.1.2-py3.7.egg/setuptools_scm/win_py31_compat.py /^import ctypes.wintypes$/;" i +write tests/test_to_ase.py /^ from ase.io import write$/;" i +xml build/lib/dpdata/system.py /^import dpdata.vasp.xml$/;" i +xml build/lib/dpdata/vasp/xml.py /^import xml.etree.ElementTree as ET$/;" i +xml dpdata/system.py /^import dpdata.vasp.xml$/;" i +xml dpdata/vasp/xml.py /^import xml.etree.ElementTree as ET$/;" i diff --git a/tests/ase/CuO.db b/tests/ase/CuO.db new file mode 100644 index 00000000..b5b6bcd3 Binary files /dev/null and b/tests/ase/CuO.db differ diff --git a/tests/test_ase_db.py b/tests/test_ase_db.py new file mode 100644 index 00000000..e69de29b