Python FaceCenteredCubic.get_stress方法代码示例

# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import get_stress [as 别名]
    def test_stress(self):
        a = FaceCenteredCubic('Au', size=[2,2,2])
        calc = EAM('Au-Grochola-JCP05.eam.alloy')
        a.set_calculator(calc)
        self.assertArrayAlmostEqual(a.get_stress(), calc.calculate_numerical_stress(a), tol=self.tol)

        sx, sy, sz = a.cell.diagonal()
        a.set_cell([sx, 0.9*sy, 1.2*sz], scale_atoms=True)
        self.assertArrayAlmostEqual(a.get_stress(), calc.calculate_numerical_stress(a), tol=self.tol)

        a.set_cell([[sx, 0.1*sx, 0], [0, 0.9*sy, 0], [0, -0.1*sy, 1.2*sz]], scale_atoms=True)
        self.assertArrayAlmostEqual(a.get_stress(), calc.calculate_numerical_stress(a), tol=self.tol)

# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import get_stress [as 别名]
    print "Number of atoms:", atoms.get_number_of_atoms()

    print "Heating to %d K using Langevin" % T_goal
    lgv = Langevin(atoms, 5 * units.fs, temperature=2*T_goal*units.kB, friction=0.05)

    while atoms.get_kinetic_energy() < 1.5 * atoms.get_number_of_atoms() * T_goal * units.kB:
        lgv.run(5)
        T = atoms.get_kinetic_energy() / (1.5 * atoms.get_number_of_atoms() * units.kB)
        print "Temperature is now %.2f K" % (T,)
    print "Desired temperature reached!"

    lgv.set_temperature(T_goal*units.kB)

    for i in range(2):
        lgv.run(20)
        s = atoms.get_stress()
        p = -(s[0] + s[1] + s[2])/3.0 / units.GPa
        T = atoms.get_kinetic_energy() / (1.5 * atoms.get_number_of_atoms() * units.kB)
        print "Pressure is %f GPa, desired pressure is %f GPa (T = %.2f K)" % (p, p_goal, T)
        dv = (p - p_goal) / bulk
        print "Adjusting volume by", dv
        cell = atoms.get_cell()
        atoms.set_cell(cell * (1.0 + dv/3.0))

    T = atoms.get_kinetic_energy() / (1.5 * atoms.get_number_of_atoms() * units.kB)
    print "Temperature is now %.2f K" % (T,)

    stressstate = array([-2, -1, 0, 0, 0, 0])*p_goal*units.GPa
    dyn = NPT(atoms, 5 * units.fs, T_goal*units.kB, stressstate,
              ttime*units.fs, (ptime*units.fs)**2 * bulk * units.GPa)
    traj = PickleTrajectory("NPT-atoms.traj", "w", atoms)

# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import get_stress [as 别名]
#set_verbose(1)

atoms = FaceCenteredCubic(directions=((1,0,0), (0,1,0), (0,0,1)),
                          size=(15,15,15), symbol="Cu", pbc=True)
atoms.set_calculator(EMT())

atoms.get_forces()
atoms.get_forces()
MaxwellBoltzmannDistribution(atoms, 300 * units.kB)
atoms.get_forces()
atoms.get_forces()

atoms = FaceCenteredCubic(directions=((1,0,0), (0,1,0), (0,0,1)),
                          size=(15,15,15), symbol="Cu", pbc=True)
atoms.set_calculator(EMT())
s = atoms.get_stress()
print
print "Stress:", s
s = atoms.get_stress()
print
print "Stress:", s
MaxwellBoltzmannDistribution(atoms, 300 * units.kB)
s = atoms.get_stress()
print
print "Stress:", s
s = atoms.get_stress()
print
print "Stress:", s
MaxwellBoltzmannDistribution(atoms, 300 * units.kB)
s = atoms.get_stress()
print

# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import get_stress [as 别名]
#!/usr/bin/env python
from jasp import *
from ase.lattice.cubic import FaceCenteredCubic
atoms = FaceCenteredCubic(symbol='Al')
with jasp('bulk/Al-bulk',
          xc='PBE',
          kpts=(12, 12, 12),
          encut=350,
          prec='High',
          isif=3,
          nsw=30,
          ibrion=1,
          atoms=atoms) as calc:
    print atoms.get_potential_energy()
    print atoms.get_stress()

# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import get_stress [as 别名]
        emt = EMT()
        emt.set_subtractE0(False)
        atoms_kim.set_calculator(kim)
        atoms_emt.set_calculator(emt)
        ek = atoms_kim.get_potential_energy()
        ee = atoms_emt.get_potential_energy()
        ReportTest(txt+"Total energy", ek, ee, 1e-8)
        ek = atoms_kim.get_potential_energies()
        ee = atoms_emt.get_potential_energies()
        for i in range(0, natoms, step):
            ReportTest(txt+"Energy of atom %i" % (i,), ek[i], ee[i], 1e-8)
        fk = atoms_kim.get_forces()
        fe = atoms_emt.get_forces()
        n = 0
        for i in range(0, natoms, step):
            n = (n + 1) % 3
            ReportTest(txt+"Force(%i) of atom %i" % (n, i), fk[i, n], fe[i, n], 1e-8)
        sk = atoms_kim.get_stress()
        se = atoms_emt.get_stress()
        for i in range(6):
            ReportTest(txt+"Stress(%i)" % (i,), sk[i], se[i], 1e-8)
        sk = atoms_kim.get_stresses()
        se = atoms_emt.get_stresses()
        for i in range(0, natoms, step):
            n = (n + 1) % 6
            # Volume per atom is not defined the same way: greater tolerance needed
            ReportTest(txt+"Stress(%i) of atom %i" % (n, i), sk[i, n], se[i, n], 1e-3)

    
ReportTest.Summary()