Python QEStructure 예제들

예제 #1

파일: qhaformat.py 프로젝트: danse-inelastic/AbInitio

 def read(self, filename = None):
     if filename != None:
         self._filename = filename
     
     self._data =  pickle.load( open(self._filename, 'r') )
     
     from qecalc.qetask.qeparser.qestructure import QEStructure
     
     self._structures = []
     
     for config in self._data['config']:
         stru = QEStructure()
         stru.readStr(config)
         self._structures.append( stru )

예제 #2

파일: qhaformat.py 프로젝트: nityasagarjena/AbInitio

    def read(self, filename=None):
        if filename != None:
            self._filename = filename

        self._data = pickle.load(open(self._filename, 'r'))

        from qecalc.qetask.qeparser.qestructure import QEStructure

        self._structures = []

        for config in self._data['config']:
            stru = QEStructure()
            stru.readStr(config)
            self._structures.append(stru)

예제 #3

파일: testStructure.py 프로젝트: 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 )

예제 #4

파일: pwinput.py 프로젝트: nityasagarjena/AbInitio

    def __init__(self, filename=None, config=None, type = 'pw', setting = None,\
                                                                 parse = True):              
        self._structure = QEStructure(self)
        self.kpoints = PWKpoints(self)
        # Boolean flag, if True, QEInput is updated on change of any property in
        # structure, lattice, or atom
        self.autoUpdate = True

        QESInput.__init__(self,filename, config, type = type, setting = setting,\
                                                                  parse = parse) 

예제 #5

파일: testStructure.py 프로젝트: 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)

예제 #6

파일: testStructure.py 프로젝트: nityasagarjena/AbInitio

    def test_constructor(self):
        from qecalc.qetask.qeparser.qelattice import QELattice
        from qecalc.qetask.qeparser.qestructure import QEStructure
        from qecalc.qetask.qeparser.qeatom import QEAtom

        filename = os.path.join(testdata_dir, 'fev3_pwgeom.out')
        self.input.structure.read(filename, 'pwoutput')

        vmass = 50.94150
        vpot = 'V_potential'
        femass = 55.84700
        fepot = 'Fe_potential'
        at1 = QEAtom('V', [0., 0., 0.], vmass, vpot)
        at2 = QEAtom('V', [0.5, 0., 0.], vmass, vpot)
        at3 = QEAtom('V', [0., 0.5, 0.], vmass, vpot)
        at4 = QEAtom('V', [0., 0., 0.5], vmass, vpot)
        at5 = QEAtom('V', [0.5, 0.5, 0.], vmass, vpot)
        at6 = QEAtom('V', [0., 0.5, 0.5], vmass, vpot)
        at7 = QEAtom('V', [0.5, 0., 0.5], vmass, vpot)
        at8 = QEAtom('V', [0.5, 0.5, 0.5], vmass, vpot)

        at9 = QEAtom('V', [0.25, 0.25, 0.25], vmass, vpot)
        at10 = QEAtom('Fe', [0.75, 0.25, 0.25], femass, fepot)
        at11 = QEAtom('V', [0.75, 0.75, 0.25], vmass, vpot)
        at12 = QEAtom('Fe', [0.25, 0.75, 0.25], femass, fepot)

        at13 = QEAtom('Fe', [0.25, 0.25, 0.75], femass, fepot)
        at14 = QEAtom('V', [0.75, 0.25, 0.75], vmass, vpot)
        at15 = QEAtom('Fe', [0.75, 0.75, 0.75], femass, fepot)
        at16 = QEAtom('V', [0.25, 0.75, 0.75], vmass, vpot)

        lattice = QELattice(lattice=self.input.structure.lattice)
        #print lattice
        new_struct = QEStructure( [ at1, at2, at3, at4, at5, at6, at7, at8, at9, \
                             at10, at11, at12, at13, at14, at15, at16], \
                             lattice = lattice )
        answer = """"Face Centered Cubic" cell:
-5.50788176  0.00000000  5.50788176
 0.00000000  5.50788176  5.50788176
-5.50788176  5.50788176  0.00000000

Atomic positions in crystal coordinates:
V       0.00000000  0.00000000  0.00000000  
V       0.50000000  0.00000000  0.00000000  
V       0.00000000  0.50000000  0.00000000  
V       0.00000000  0.00000000  0.50000000  
V       0.50000000  0.50000000  0.00000000  
V       0.00000000  0.50000000  0.50000000  
V       0.50000000  0.00000000  0.50000000  
V       0.50000000  0.50000000  0.50000000  
V       0.25000000  0.25000000  0.25000000  
Fe      0.75000000  0.25000000  0.25000000  
V       0.75000000  0.75000000  0.25000000  
Fe      0.25000000  0.75000000  0.25000000  
Fe      0.25000000  0.25000000  0.75000000  
V       0.75000000  0.25000000  0.75000000  
Fe      0.75000000  0.75000000  0.75000000  
V       0.25000000  0.75000000  0.75000000  

V   50.9415 V_potential
Fe  55.8470 Fe_potential
"""
        self.assertEqual(str(new_struct), answer)

        new_struct = QEStructure(self.input.structure)

        # Check if the constructor messes _qeInput
        self.input.structure.lattice.a = 10
        new_struct.lattice.a = 12
        s1 = self.input.structure.toString()
        s2 = new_struct.toString()
        self.assertNotEqual(s1, s2)

예제 #7

파일: testStructure.py 프로젝트: danse-inelastic/AbInitio

    def test_constructor(self):
        from qecalc.qetask.qeparser.qelattice import QELattice
        from qecalc.qetask.qeparser.qestructure import QEStructure
        from qecalc.qetask.qeparser.qeatom import QEAtom
        
        filename = os.path.join(testdata_dir, 'fev3_pwgeom.out')  
        self.input.structure.read(filename, 'pwoutput')        
        
        vmass = 50.94150
        vpot = 'V_potential'
        femass = 55.84700
        fepot = 'Fe_potential'
        at1 = QEAtom('V', [0., 0., 0.], vmass, vpot)
        at2 = QEAtom('V', [0.5, 0., 0.], vmass, vpot)
        at3 = QEAtom('V', [0., 0.5, 0.], vmass, vpot)
        at4 = QEAtom('V', [0., 0., 0.5], vmass, vpot)
        at5 = QEAtom('V', [0.5, 0.5, 0.], vmass, vpot)
        at6 = QEAtom('V', [0., 0.5, 0.5], vmass, vpot)
        at7 = QEAtom('V', [0.5, 0., 0.5], vmass, vpot)
        at8 = QEAtom('V', [0.5, 0.5, 0.5], vmass, vpot)
    
        at9 = QEAtom('V', [0.25, 0.25, 0.25], vmass, vpot)
        at10 = QEAtom('Fe', [0.75, 0.25, 0.25], femass, fepot)
        at11 = QEAtom('V', [0.75, 0.75, 0.25], vmass, vpot)
        at12 = QEAtom('Fe', [0.25, 0.75, 0.25], femass, fepot)
    
        at13 = QEAtom('Fe', [0.25, 0.25, 0.75], femass, fepot)
        at14 = QEAtom('V', [0.75, 0.25, 0.75], vmass, vpot)
        at15 = QEAtom('Fe', [0.75, 0.75, 0.75], femass, fepot)
        at16 = QEAtom('V', [0.25, 0.75, 0.75], vmass, vpot)
        
        lattice = QELattice(lattice = self.input.structure.lattice)
        #print lattice
        new_struct = QEStructure( [ at1, at2, at3, at4, at5, at6, at7, at8, at9, \
                             at10, at11, at12, at13, at14, at15, at16], \
                             lattice = lattice )
        answer = """"Face Centered Cubic" cell:
-5.50788176  0.00000000  5.50788176
 0.00000000  5.50788176  5.50788176
-5.50788176  5.50788176  0.00000000

Atomic positions in crystal coordinates:
V       0.00000000  0.00000000  0.00000000  
V       0.50000000  0.00000000  0.00000000  
V       0.00000000  0.50000000  0.00000000  
V       0.00000000  0.00000000  0.50000000  
V       0.50000000  0.50000000  0.00000000  
V       0.00000000  0.50000000  0.50000000  
V       0.50000000  0.00000000  0.50000000  
V       0.50000000  0.50000000  0.50000000  
V       0.25000000  0.25000000  0.25000000  
Fe      0.75000000  0.25000000  0.25000000  
V       0.75000000  0.75000000  0.25000000  
Fe      0.25000000  0.75000000  0.25000000  
Fe      0.25000000  0.25000000  0.75000000  
V       0.75000000  0.25000000  0.75000000  
Fe      0.75000000  0.75000000  0.75000000  
V       0.25000000  0.75000000  0.75000000  

V   50.9415 V_potential
Fe  55.8470 Fe_potential
"""
        self.assertEqual(str(new_struct), answer)
        
        new_struct = QEStructure(self.input.structure)
        
        # Check if the constructor messes _qeInput        
        self.input.structure.lattice.a = 10              
        new_struct.lattice.a = 12
        s1 = self.input.structure.toString()
        s2 =  new_struct.toString()
        self.assertNotEqual(s1, s2)

예제 #8

파일: testStructure.py 프로젝트: 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)

예제 #9

    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 )