def my_error_function(variable_values):
# Get rank from pool
try:
myrank = pool.rank
except:
myrank = 0
# FOR THE RELAXED STRUCTURE
path = str(myrank) + '/relaxed'
relaxed_job = gulp.job(path=path)
ffio.write_forcefield_file(str(myrank) + '/FF',
template,
variable_values,
verbose=False)
relaxed_job.forcefield = str(myrank) + '/FF'
relaxed_job.temporary_forcefield = False
relaxed_job.structure = gt_relaxed_structure
relaxed_job.pbc = True
relaxed_job.options['relax_atoms'] = True
relaxed_job.options['relax_cell'] = True
relaxed_job.options['phonon_dispersion'] = True
# Submit job and read output
relaxed_job.options['phonon_dispersion_from'] = '0 0 0'
relaxed_job.options['phonon_dispersion_to'] = '0.5 0.5 0'
relaxed_job.write_script_file()
relaxed_job.run(command='gulp')
md_relaxed_disp_GS = gulp.read_phonon_dispersion(relaxed_job.path +
'/out.gulp.disp')
phon_error_relax = ezff.error_phonon_dispersion(md_relaxed_disp_GS,
gt_relaxed_disp_GS,
weights='acoustic')
# Calculate errors in lattice constant and elastic modulus
moduli = gulp.read_elastic_moduli(relaxed_job.path + '/' +
relaxed_job.outfile)
lattice = gulp.read_lattice_constant(relaxed_job.path + '/' +
relaxed_job.outfile)
a_latt_error = np.linalg.norm(lattice['err_abc'][0])
b_latt_error = np.linalg.norm(lattice['err_abc'][1])
modulus_error = np.linalg.norm((moduli[0, 0] * lattice['abc'][2] * 2.0 /
13.97) - gt_elastic_modulus)
relaxed_job.cleanup() # FINISH RELAXED JOB
# FOR THE COMPRESSED STRUCTURE
path = str(myrank) + '/compressed'
compressed_job = gulp.job(path=path)
compressed_job.forcefield = str(myrank) + '/FF'
compressed_job.temporary_forcefield = False
compressed_job.structure = gt_compressed_structure
compressed_job.pbc = True
compressed_job.options['relax_atoms'] = True
compressed_job.options['relax_cell'] = False
compressed_job.options['phonon_dispersion'] = True
# Submit job and read output
compressed_job.options['phonon_dispersion_from'] = '0 0 0'
compressed_job.options['phonon_dispersion_to'] = '0.5 0.5 0'
compressed_job.write_script_file()
compressed_job.run(command='gulp')
md_compressed_disp_GS = gulp.read_phonon_dispersion(compressed_job.path +
'/out.gulp.disp')
phon_error_compressed = ezff.error_phonon_dispersion(md_compressed_disp_GS,
gt_compressed_disp_GS,
weights='acoustic')
compressed_job.cleanup() # FINISH COMPRESSED JOB
# FOR THE EXPANDED STRUCTURE
path = str(myrank) + '/expanded'
expanded_job = gulp.job(path=path)
expanded_job.forcefield = str(myrank) + '/FF'
expanded_job.temporary_forcefield = False
expanded_job.structure = gt_expanded_structure
expanded_job.pbc = True
expanded_job.options['relax_atoms'] = True
expanded_job.options['relax_cell'] = False
expanded_job.options['phonon_dispersion'] = True
# Submit job and read output
expanded_job.options['phonon_dispersion_from'] = '0 0 0'
expanded_job.options['phonon_dispersion_to'] = '0.5 0.5 0'
expanded_job.write_script_file()
expanded_job.run(command='gulp')
md_expanded_disp_GS = gulp.read_phonon_dispersion(expanded_job.path +
'/out.gulp.disp')
phon_error_expanded = ezff.error_phonon_dispersion(md_expanded_disp_GS,
gt_expanded_disp_GS,
weights='acoustic')
expanded_job.cleanup() # FINISH EXPANDED JOB
return [
a_latt_error, b_latt_error, modulus_error, phon_error_relax,
phon_error_compressed, phon_error_expanded
]
def my_error_function(variable_values):
# Get rank from pool
try:
myrank = pool.rank
except:
myrank = 0
# FOR THE RELAXED STRUCTURE
path = str(myrank) + '/relaxed'
relaxed_job = gulp.job(path=path)
relaxed_job.structure = gt_relax_structure
relaxed_job.forcefield = ezff.generate_forcefield(template,
variable_values,
FFtype='SW')
relaxed_job.options['pbc'] = True
relaxed_job.options['relax_atoms'] = True
relaxed_job.options['relax_cell'] = True
relaxed_job.options['phonon_dispersion'] = True
relaxed_job.options['phonon_dispersion_from'] = '0 0 0'
relaxed_job.options['phonon_dispersion_to'] = '0.5 0.5 0'
# Submit job and read output
relaxed_job.run()
# Read output from completed GULP job and cleanup job files
md_relax_disp_GS = relaxed_job.read_phonon_dispersion()
md_relaxed_moduli = relaxed_job.read_elastic_moduli()
md_relaxed_structure = relaxed_job.read_structure()
relaxed_job.cleanup() # FINISH RELAXED JOB
# FOR THE COMPRESSED STRUCTURE
path = str(myrank) + '/compressed'
compressed_job = gulp.job(path=path)
compressed_job.structure = gt_compressed_structure
compressed_job.forcefield = ezff.generate_forcefield(template,
variable_values,
FFtype='SW')
compressed_job.options['pbc'] = True
compressed_job.options['relax_atoms'] = True
compressed_job.options['relax_cell'] = False
compressed_job.options['phonon_dispersion'] = True
compressed_job.options['phonon_dispersion_from'] = '0 0 0'
compressed_job.options['phonon_dispersion_to'] = '0.5 0.5 0'
# Submit job and read output
compressed_job.run()
# Read output from completed GULP job and cleanup job files
md_compressed_disp_GS = compressed_job.read_phonon_dispersion()
compressed_job.cleanup() # FINISH COMPRESSED JOB
# FOR THE EXPANDED STRUCTURE
path = str(myrank) + '/expanded'
expanded_job = gulp.job(path=path)
expanded_job.structure = gt_expanded_structure
expanded_job.forcefield = ezff.generate_forcefield(template,
variable_values,
FFtype='SW')
expanded_job.options['pbc'] = True
expanded_job.options['relax_atoms'] = True
expanded_job.options['relax_cell'] = False
expanded_job.options['phonon_dispersion'] = True
expanded_job.options['phonon_dispersion_from'] = '0 0 0'
expanded_job.options['phonon_dispersion_to'] = '0.5 0.5 0'
# Submit job and read output
expanded_job.run()
# Read output from completed GULP job and cleanup job files
md_expanded_disp_GS = expanded_job.read_phonon_dispersion()
expanded_job.cleanup() # FINISH EXPANDED JOB
# Compute 5 errors from the 3 GULP jobs
error_abc, error_ang = ezff.error_lattice_constant(MD=md_relaxed_structure,
GT=gt_relax_structure)
a_lattice_error = np.linalg.norm(
error_abc[0]) # Error in 'a' lattice constant
b_lattice_error = np.linalg.norm(
error_abc[1]) # Error in 'b' lattice constant
md_c11 = md_relaxed_moduli[0][0, 0] * md_relaxed_structure.box[2, 2] * (
2.0 / 13.97
) # Extracting c11 for a bulk-like layered structure from the monolayer GULP calculation
modulus_error = np.linalg.norm(md_c11 - gt_c11)
phon_error_relaxed = ezff.error_phonon_dispersion(MD=md_relax_disp_GS,
GT=gt_relax_disp_GS,
weights='acoustic')
phon_error_expanded = ezff.error_phonon_dispersion(MD=md_expanded_disp_GS,
GT=gt_expanded_disp_GS,
weights='acoustic')
phon_error_compressed = ezff.error_phonon_dispersion(
MD=md_compressed_disp_GS, GT=gt_compressed_disp_GS, weights='acoustic')
return [
a_lattice_error, b_lattice_error, modulus_error, phon_error_relaxed,
phon_error_compressed, phon_error_expanded
]