m.set_calculator(calculator)
m.get_potential_energy()
cmr_params = {
"db_keywords": [project_id],
# add project_id also as a field to support search across projects
"project_id": project_id,
"formula": formula,
"calculator": calculator.name,
}
write(filename=('reactions_xsimple.%s.db' % formula),
images=m, format='db', cmr_params=cmr_params)
# analyse the results with CMR
from cmr.ui import DirectoryReader
reader = DirectoryReader('.')
# read all compounds in the project calculated with EMT
all = reader.find(name_value_list=[('calculator', 'EMT')],
keyword_list=[project_id])
all.print_table(0, columns=["formula", "ase_potential_energy"])
print
group = cmr.create_group()
group_vars = {"reaction":reaction, "output":"group.db"}
sum = 0.0
for (formula, coef) in reaction:
data = all.get("formula", formula)
if data is None:
print "%s is missing"%formula
"db_keywords": [project_id],
# add project_id also as a field to support search across projects
"project_id": project_id,
"formula": formula,
"calculator": calculator.name,
}
write(filename=('reactions_xsimple.%s.db' % formula),
images=m,
format='db',
cmr_params=cmr_params)
# analyse the results with CMR
from cmr.ui import DirectoryReader
reader = DirectoryReader('.')
# read all compounds in the project calculated with EMT
all = reader.find(name_value_list=[('calculator', 'EMT')],
keyword_list=[project_id])
all.print_table(0, columns=["formula", "ase_potential_energy"])
print
group = cmr.create_group()
group_vars = {"reaction": reaction, "output": "group.db"}
sum = 0.0
for (formula, coef) in reaction:
data = all.get("formula", formula)
if data is None:
print "%s is missing" % formula
# reaction energies on initial, unoptimized geometries
cmr_params = {'geometries': 'initial'}
re.make_reaction_groups(database=False, index=0, cmr_params=cmr_params)
# print
re.print_result(database=False)
# reaction energies on final, optimized geometries
cmr_params = {'geometries': 'final'}
re.make_reaction_groups(database=False, index=-1, cmr_params=cmr_params)
# print
re.print_result(database=False)
reader = DirectoryReader('.')
# retrieve all reactions (groups) with project_id and optimized geometries from the current directory
all = reader.find(name_value_list=[('db_calculator', 'group'),
('geometries', 'final')],
keyword_list=[project_id, 'reaction'])
print 'reaction_id, calc, ref, calc - ref'
# compare with the reference
for r in reactions:
reaction_id = r[-1][1]
res = all.get('reaction_id', reaction_id)
if res is None:
print "Could not find reaction_id %s in reference" % str(reaction_id)
else:
calc = res['reaction_energy']
# reaction energies on initial, unoptimized geometries
cmr_params = {'geometries': 'initial'}
re.make_reaction_groups(database=False, index=0, cmr_params=cmr_params)
# print
re.print_result(database=False)
# reaction energies on final, optimized geometries
cmr_params = {'geometries': 'final'}
re.make_reaction_groups(database=False, index= -1, cmr_params=cmr_params)
# print
re.print_result(database=False)
reader = DirectoryReader('.')
# retrieve all reactions (groups) with project_id and optimized geometries from the current directory
all = reader.find(name_value_list=[('db_calculator', 'group'),
('geometries', 'final')
],
keyword_list=[project_id, 'reaction'])
print 'reaction_id, calc, ref, calc - ref'
# compare with the reference
for r in reactions:
reaction_id = r[-1][1]
res = all.get('reaction_id', reaction_id)
if res is None:
print "Could not find reaction_id %s in reference"%str(reaction_id)
else:
data = cmr.read(cmrfile)
data.set_user_variable('xc', xc)
data.write(cmrfile)
# perform PBE calculation on LDA density
ediff = calc2.get_xc_difference('PBE')
# add new results to the cmrfile
data = cmr.read(cmrfile)
data.set_user_variable('PBE', data['ase_potential_energy'] + ediff)
data.write(cmrfile)
# analyze the results with CMR
from cmr.ui import DirectoryReader
reader = DirectoryReader(directory='.', ext='.cmr')
# read all compounds in the project with lcao
all = reader.find(name_value_list=[('mode', 'lcao')],
keyword_list=[project_id])
results = all.get('formula', formula)
print(results['formula'], results['xc'], results['ase_potential_energy'])
# column_length=0 aligns data in the table (-1 : data unaligned is default)
all.print_table(column_length=0,
columns=['formula', 'xc', 'h', 'ase_potential_energy', 'PBE'])
equal(results['PBE'], e + ediff, 1e-6)
if rank == 0:
for file in [formula + '.gpw', formula + '.db', cmrfile]:
data = cmr.read(cmrfile)
data.set_user_variable('xc', xc)
data.write(cmrfile)
# perform PBE calculation on LDA density
ediff = calc2.get_xc_difference('PBE')
# add new results to the cmrfile
data = cmr.read(cmrfile)
data.set_user_variable('PBE', data['ase_potential_energy'] + ediff)
data.write(cmrfile)
# analyze the results with CMR
from cmr.ui import DirectoryReader
reader = DirectoryReader(directory='.', ext='.cmr')
# read all compounds in the project with lcao
all = reader.find(name_value_list=[('mode', 'lcao')],
keyword_list=[project_id])
results = all.get('formula', formula)
print(results['formula'], results['xc'], results['ase_potential_energy'])
# column_length=0 aligns data in the table (-1 : data unaligned is default)
all.print_table(column_length=0,
columns=['formula', 'xc', 'h', 'ase_potential_energy', 'PBE'])
equal(results['PBE'], e + ediff, 1e-6)
if rank == 0:
for file in [formula + '.gpw', formula + '.db', cmrfile]:
data = cmr.read(cmrfile)
data.set_user_variable("xc", xc)
data.write(cmrfile)
# perform PBE calculation on LDA density
ediff = calc2.get_xc_difference("PBE")
# add new results to the cmrfile
data = cmr.read(cmrfile)
data.set_user_variable("PBE", data["ase_potential_energy"] + ediff)
data.write(cmrfile)
# analyze the results with CMR
from cmr.ui import DirectoryReader
reader = DirectoryReader(directory=".", ext=".cmr")
# read all compounds in the project with lcao
all = reader.find(name_value_list=[("mode", "lcao")], keyword_list=[project_id])
results = all.get("formula", formula)
print results["formula"], results["xc"], results["ase_potential_energy"]
# column_length=0 aligns data in the table (-1 : data unaligned is default)
all.print_table(column_length=0, columns=["formula", "xc", "h", "ase_potential_energy", "PBE"])
equal(results["PBE"], e + ediff, 1e-6)
if rank == 0:
for file in [formula + ".gpw", formula + ".db", cmrfile]:
if os.path.exists(file):
os.unlink(file)
cmrfile = formula + '.cmr'
# add new results to the cmrfile
data = cmr.read(cmrfile)
data.set_user_variable('U_potential_energy_PBE', data['U_potential_energy'] + ediff)
data.write(cmrfile)
del calc
if analyse_from_dir:
# analyze the results from cmr files in the local directory
from cmr.ui import DirectoryReader
# read all compounds in the project with lcao and LDA orbitals
reader = DirectoryReader(directory='.', ext='.cmr')
all = reader.find(name_value_list=[('U_mode', 'lcao'), ('U_xc', 'LDA')],
keyword_list=[project_id])
if rank == 0:
print('results from cmr files in the local directory')
# print requested results
# column_length=0 aligns data in the table (-1 : data unaligned is default)
all.print_table(column_length=0,
columns=['U_formula', 'U_vacuum',
'U_xc', 'U_h', 'U_hund',
'U_potential_energy', 'U_potential_energy_PBE',
'ase_temperature'])
# access the results directly and calculate atomization energies
f2 = symbol + '2'
f1 = symbol