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Messages - SMA

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1
Hi
I have tried as per your suggestions but still H2 dissociates. Could you please provide me a  correct input file where H2 does not dissociate.
Thanks in advance

Regards

SMA

2
Hi  experts
Happy New Year to all of you

I was optimizing of H2 molecule using LCAO calculator and DZP basis set. The molecule after optimization  gets dissociated leading to a bond distance of 2.95Angstorm.
The total energy is: -26.96448eV (Is it correct value??).  Could you please help me to find out where is the error.
The input.py is given below.
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Molecule Configuration
# -------------------------------------------------------------

# Define elements
elements = [Hydrogen, Hydrogen]

# Define coordinates
cartesian_coordinates = [[-0.12113621627 ,  0.257571870579,  0.225387244323],
                         [ 0.518863737818,  0.257571870579,  0.225387244323]]*Angstrom

# Set up configuration
molecule_configuration = MoleculeConfiguration(
    elements=elements,
    cartesian_coordinates=cartesian_coordinates
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
    GGABasis.Hydrogen_DoubleZetaPolarized,
    ]

#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = SGGA.PBE

numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=30.0*Hartree,
    )

calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    )

molecule_configuration.setCalculator(calculator)
nlprint(molecule_configuration)
molecule_configuration.update()
nlsave('H2-opt.hdf5', molecule_configuration)

# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------
molecule_configuration = OptimizeGeometry(
    molecule_configuration,
    max_forces=0.05*eV/Ang,
    max_steps=200,
    max_step_length=0.2*Ang,
    trajectory_filename='H2-opt',
    disable_stress=True,
    optimizer_method=LBFGS(),
)
nlsave('H2-opt.hdf5', molecule_configuration)
nlprint(molecule_configuration)
# -------------------------------------------------------------
# Total Energy
# -------------------------------------------------------------
total_energy = TotalEnergy(molecule_configuration)
nlsave('H2-opt.hdf5', total_energy)
nlprint(total_energy)

Regards

SMA

3
Questions and Answers / Re: zero point energy
« on: November 3, 2020, 08:36 »
Thanks. 

4
Questions and Answers / Re: zero point energy
« on: October 27, 2020, 14:01 »
I have a valid license  for 2019.03. Can I get the Q-2020.09 without any additional charge please

5
Questions and Answers / Re: zero point energy
« on: October 26, 2020, 12:20 »
How to update the version of 2019.03 .

6
Questions and Answers / Re: zero point energy
« on: October 20, 2020, 12:22 »
I have followed the tutorial. But the effect of changed mass is not reflected in the vibrational mode. It is showing the mode of H2 molecule only.
Please help to resolve the issue.
# Molecule Configuration
# -------------------------------------------------------------

# Define elements
elements = [Hydrogen, Hydrogen]

# Define coordinates
cartesian_coordinates = [[ 0.  ,  0.  ,  0.  ],
                         [ 0.  ,  0.  ,  0.75]]*Angstrom

# Set up configuration
molecule_configuration = MoleculeConfiguration(
    elements=elements,
    cartesian_coordinates=cartesian_coordinates
    )
# Define a new class where the H atom has mass 2.00
class H2(Hydrogen):
    @staticmethod
    def atomicMass():
        return 2.00*Units.atomic_mass_unit

PeriodicTable.ALL_ELEMENTS.append(H2)

# Replace all atoms tagged "H2" with hydrogen-2
for index in molecule_configuration.indicesFromTags("H2"):
    molecule_configuration.elements()[index] = H2

# Add tags
molecule_configuration.addTags('H2', [0,1])

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=80.0*Hartree,
    )

calculator = LCAOCalculator(
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    )

molecule_configuration.setCalculator(calculator)
nlprint(molecule_configuration)
molecule_configuration.update()
nlsave('D2-vib.hdf5', molecule_configuration)

# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------
molecule_configuration = OptimizeGeometry(
    molecule_configuration,
    max_forces=0.05*eV/Ang,
    max_steps=200,
    max_step_length=0.2*Ang,
    trajectory_filename='D2-dos-vib.hdf',
    disable_stress=True,
    optimizer_method=LBFGS(),
)
nlsave('D2.nc.dos-vib.hdf5', molecule_configuration)
nlprint(molecule_configuration)

# -------------------------------------------------------------
# Dynamical Matrix
# -------------------------------------------------------------
dynamical_matrix = DynamicalMatrix(
    molecule_configuration,
    filename='D2-vib.hdf5',
    object_id='dynamical_matrix',
    repetitions=Automatic,
    atomic_displacement=0.01*Angstrom,
    acoustic_sum_rule=True,
    finite_difference_method=Central,
    force_tolerance=1e-08*Hartree/Bohr**2,
    processes_per_displacement=1,
    log_filename_prefix='forces_displacement_',
    use_wigner_seitz_scheme=False,
    )
dynamical_matrix.update()

# -------------------------------------------------------------
# Phonon Density Of States
# -------------------------------------------------------------
qpoint_grid = MonkhorstPackGrid()

phonon_density_of_states = PhononDensityOfStates(
    configuration=molecule_configuration,
    dynamical_matrix=dynamical_matrix,
    qpoints=qpoint_grid,
    number_of_bands=None,
    )
nlsave('D2.nc.dos-vib.hdf5', phonon_density_of_states)
nlprint(phonon_density_of_states)

# -------------------------------------------------------------
# Vibrational Mode
# -------------------------------------------------------------
vibrational_mode = VibrationalMode(
    configuration=molecule_configuration,
    dynamical_matrix=dynamical_matrix,
    kpoint_fractional=[0, 0, 0],
    mode_indices=None,
    )
nlsave('D2-vib.hdf5', vibrational_mode)

7
Questions and Answers / Re: zero point energy
« on: October 19, 2020, 08:46 »
The version I am using is QuantumATK P-2019.03-SP1.
As per ypur suggestions I used the following input .
#setup H-H geometry
elements = [ Hydrogen2, Hydrogen2]
cartesian_coordinates = [[ 0.0,0.0,0.0],
                         [ 0.0,0.0,0.75]]*Angstrom
molecule_configuration = MoleculeConfiguration(
    elements=elements,
    cartesian_coordinates=cartesian_coordinates
    )

But It is displaying error as given below.

  File "h2-vib.py", line 2, in <module>
    elements = [ Hydrogen2, Hydrogen2]
NameError: name 'Hydrogen2' is not defined
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9

8
Questions and Answers / Re: zero point energy
« on: October 16, 2020, 15:00 »
Thank mlee
I have made one input for D2 molecule. Is it correct
# Define elements
elements = [Hydrogen, Hydrogen]

# Define coordinates
cartesian_coordinates = [[ 0.  ,  0.  ,  0.  ],
                         [ 0.  ,  0.  ,  0.75]]*Angstrom

# Set up configuration
molecule_configuration = MoleculeConfiguration(
    elements=elements,
    cartesian_coordinates=cartesian_coordinates
    )

# Define a new class where the H atom has mass 2.00
class H2(Hydrogen):
    @staticmethod
    def atomicMass():
        return 2.00*Units.atomic_mass_unit

PeriodicTable.ALL_ELEMENTS.append(H2)

# Replace all atoms tagged "H2" with hydrogen-2
for index in molecule_configuration.indicesFromTags("H2"):
    molecule_configuration.elements()[index] = H2

# Add tags
molecule_configuration.addTags('H2', [0,1])

9
Questions and Answers / zero point energy
« on: October 13, 2020, 14:17 »
Hi
How to calculate zero point energy of H2 and D2 molecule

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