コード例 #1
0
ファイル: reactions_xsimple.py プロジェクト: PHOTOX/fuase
    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
コード例 #2
0
        "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
コード例 #3
0
ファイル: reactions_test.py プロジェクト: lqcata/ase
# 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']
コード例 #4
0
ファイル: reactions_test.py プロジェクト: JConwayAWT/PGSS14CC
# 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:
コード例 #5
0
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]:
コード例 #6
0
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]:
コード例 #7
0
ファイル: cmr_append.py プロジェクト: eojons/gpaw-scme
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)
コード例 #8
0
    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