Python QEStructure.readの例

コード例 #1

ファイル: testStructure.py プロジェクト: nityasagarjena/AbInitio

    def test_fileInit(self):
        from qecalc.qetask.qeparser.qestructure import QEStructure
        filename = os.path.join(testdata_dir, 'al_pw.in')
        stru = QEStructure(filename=filename)
        answer = """"Face Centered Cubic" cell:
-3.85000000  0.00000000  3.85000000
 0.00000000  3.85000000  3.85000000
-3.85000000  3.85000000  0.00000000

Atomic positions in units of lattice parametr "a":
Al      0.00000000  0.00000000  0.00000000  

Al  26.9800 Al.pz-vbc.UPF
"""

        self.assertEqual(str(stru), answer)

        stru = QEStructure()
        filename = os.path.join(testdata_dir, 'PbTe.cif')
        stru.read(filename=filename, format='cif')

        answer = """&SYSTEM
    ibrav = 0,
    celldm(1) = 1.889725989,
    ntyp = 2,
    nat = 8,
/
ATOMIC_SPECIES
 Pb2+ 0.0000
 Te  0.0000
ATOMIC_POSITIONS (crystal)
 Pb2+     0.50000000  0.50000000  0.50000000
 Pb2+     0.50000000  0.00000000  0.00000000
 Pb2+     0.00000000  0.50000000  0.00000000
 Pb2+     0.00000000  0.00000000  0.50000000
 Te      0.00000000  0.00000000  0.00000000
 Te      0.00000000  0.50000000  0.50000000
 Te      0.50000000  0.00000000  0.50000000
 Te      0.50000000  0.50000000  0.00000000
CELL_PARAMETERS (cubic)
 6.46100000  0.00000000  0.00000000
 0.00000000  6.46100000  0.00000000
 0.00000000  0.00000000  6.46100000
"""
        #print stru.toString( stringConfig )
        self.assertEqual(stru.toString(stringConfig), answer)

コード例 #2

ファイル: testStructure.py プロジェクト: danse-inelastic/AbInitio

    def test_fileInit(self):
        from qecalc.qetask.qeparser.qestructure import QEStructure
        filename = os.path.join(testdata_dir, 'al_pw.in')
        stru = QEStructure(filename = filename)
        answer = """"Face Centered Cubic" cell:
-3.85000000  0.00000000  3.85000000
 0.00000000  3.85000000  3.85000000
-3.85000000  3.85000000  0.00000000

Atomic positions in units of lattice parametr "a":
Al      0.00000000  0.00000000  0.00000000  

Al  26.9800 Al.pz-vbc.UPF
"""
        
        self.assertEqual(str(stru), answer)
        
        stru = QEStructure()
        filename = os.path.join(testdata_dir, 'PbTe.cif')
        stru.read(filename = filename, format = 'cif')
        
        answer ="""&SYSTEM
    ibrav = 0,
    celldm(1) = 1.889725989,
    ntyp = 2,
    nat = 8,
/
ATOMIC_SPECIES
 Pb2+ 0.0000
 Te  0.0000
ATOMIC_POSITIONS (crystal)
 Pb2+     0.50000000  0.50000000  0.50000000
 Pb2+     0.50000000  0.00000000  0.00000000
 Pb2+     0.00000000  0.50000000  0.00000000
 Pb2+     0.00000000  0.00000000  0.50000000
 Te      0.00000000  0.00000000  0.00000000
 Te      0.00000000  0.50000000  0.50000000
 Te      0.50000000  0.00000000  0.50000000
 Te      0.50000000  0.50000000  0.00000000
CELL_PARAMETERS (cubic)
 6.46100000  0.00000000  0.00000000
 0.00000000  6.46100000  0.00000000
 0.00000000  0.00000000  6.46100000
"""
        #print stru.toString( stringConfig )
        self.assertEqual(stru.toString( stringConfig ), answer )

コード例 #3

ファイル: testStructure.py プロジェクト: nityasagarjena/AbInitio

    def test_fileInit(self):
        from qecalc.qetask.qeparser.qestructure import QEStructure
        filename = os.path.join(testdata_dir, 'al_pw.in')
        stru = QEStructure(filename=filename)
        answer = """"Face Centered Cubic" cell:
-3.85000000  0.00000000  3.85000000
 0.00000000  3.85000000  3.85000000
-3.85000000  3.85000000  0.00000000

Atomic positions in units of lattice parametr "a":
Al      0.00000000  0.00000000  0.00000000  

Al  26.9800 Al.pz-vbc.UPF
"""

        self.assertEqual(str(stru), answer)

        stru = QEStructure()
        filename = os.path.join(testdata_dir, 'PbTe.cif')
        stru.read(filename=filename, format='cif')

        answer = """&CONTROL
    calculation = 'scf',
    restart_mode = 'from_scratch',
    tstress = .true.,
    tprnfor = .true.,
    prefix = 'mgalb4',
    pseudo_dir = '/home/user/pslib',
    outdir = '/scratch/user',
/
&SYSTEM
    ibrav = 0,
    nbnd = 21,
    nspin = 1,
    occupations = 'smearing',
    degauss = 0.025,
    smearing = 'methfessel-paxton',
    ecutwfc = 64.0,
    ecutrho = 256.0,
    celldm(1) = 1.889725989,
    ntyp = 2,
    nat = 8,
/
&ELECTRONS
    conv_thr = 1.0d-10,
    mixing_beta = 0.4,
/
ATOMIC_SPECIES
 Pb2+ 0.0000
 Te  0.0000
ATOMIC_POSITIONS (crystal)
 Pb2+     0.50000000  0.50000000  0.50000000
 Pb2+     0.50000000  0.00000000  0.00000000
 Pb2+     0.00000000  0.50000000  0.00000000
 Pb2+     0.00000000  0.00000000  0.50000000
 Te      0.00000000  0.00000000  0.00000000
 Te      0.00000000  0.50000000  0.50000000
 Te      0.50000000  0.00000000  0.50000000
 Te      0.50000000  0.50000000  0.00000000
K_POINTS (automatic)
 32 32 16 0 0 0
CELL_PARAMETERS (cubic)
 6.46100000  0.00000000  0.00000000
 0.00000000  6.46100000  0.00000000
 0.00000000  0.00000000  6.46100000
"""
        #print stru.toString( stringConfig )
        self.assertEqual(stru.toString(stringConfig), answer)

コード例 #4

    def test_fileInit(self):
        from qecalc.qetask.qeparser.qestructure import QEStructure
        filename = os.path.join(testdata_dir, 'al_pw.in')
        stru = QEStructure(filename = filename)
        answer = """"Face Centered Cubic" cell:
-3.85000000  0.00000000  3.85000000
 0.00000000  3.85000000  3.85000000
-3.85000000  3.85000000  0.00000000

Atomic positions in units of lattice parametr "a":
Al      0.00000000  0.00000000  0.00000000  

Al  26.9800 Al.pz-vbc.UPF
"""
        
        self.assertEqual(str(stru), answer)
        
        stru = QEStructure()
        filename = os.path.join(testdata_dir, 'PbTe.cif')
        stru.read(filename = filename, format = 'cif')
        
        answer ="""&CONTROL
    calculation = 'scf',
    restart_mode = 'from_scratch',
    tstress = .true.,
    tprnfor = .true.,
    prefix = 'mgalb4',
    pseudo_dir = '/home/user/pslib',
    outdir = '/scratch/user',
/
&SYSTEM
    ibrav = 0,
    nbnd = 21,
    nspin = 1,
    occupations = 'smearing',
    degauss = 0.025,
    smearing = 'methfessel-paxton',
    ecutwfc = 64.0,
    ecutrho = 256.0,
    celldm(1) = 1.889725989,
    ntyp = 2,
    nat = 8,
/
&ELECTRONS
    conv_thr = 1.0d-10,
    mixing_beta = 0.4,
/
ATOMIC_SPECIES
 Pb2+ 0.0000
 Te  0.0000
ATOMIC_POSITIONS (crystal)
 Pb2+     0.50000000  0.50000000  0.50000000
 Pb2+     0.50000000  0.00000000  0.00000000
 Pb2+     0.00000000  0.50000000  0.00000000
 Pb2+     0.00000000  0.00000000  0.50000000
 Te      0.00000000  0.00000000  0.00000000
 Te      0.00000000  0.50000000  0.50000000
 Te      0.50000000  0.00000000  0.50000000
 Te      0.50000000  0.50000000  0.00000000
K_POINTS (automatic)
 32 32 16 0 0 0
CELL_PARAMETERS (cubic)
 6.46100000  0.00000000  0.00000000
 0.00000000  6.46100000  0.00000000
 0.00000000  0.00000000  6.46100000
"""
        #print stru.toString( stringConfig )
        self.assertEqual(stru.toString( stringConfig ), answer )