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nomad-lab
parser-dl-poly
Commits
21a53541
Commit
21a53541
authored
5 years ago
by
Markus Scheidgen
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Added metainfo python code.
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dlpolyparser/metainfo/__init__.py
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-0
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dlpolyparser/metainfo/__init__.py
dlpolyparser/metainfo/dl_poly.py
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195 additions, 0 deletions
dlpolyparser/metainfo/dl_poly.py
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0 deletions
dlpolyparser/metainfo/__init__.py
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+
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21a53541
import
sys
from
nomad.metainfo
import
Environment
from
nomad.metainfo.legacy
import
LegacyMetainfoEnvironment
import
dlpolyparser.metainfo.dl_poly
import
nomad.datamodel.metainfo.common
import
nomad.datamodel.metainfo.public
import
nomad.datamodel.metainfo.general
m_env
=
LegacyMetainfoEnvironment
()
m_env
.
m_add_sub_section
(
Environment
.
packages
,
sys
.
modules
[
'
dlpolyparser.metainfo.dl_poly
'
].
m_package
)
# type: ignore
m_env
.
m_add_sub_section
(
Environment
.
packages
,
sys
.
modules
[
'
nomad.datamodel.metainfo.common
'
].
m_package
)
# type: ignore
m_env
.
m_add_sub_section
(
Environment
.
packages
,
sys
.
modules
[
'
nomad.datamodel.metainfo.public
'
].
m_package
)
# type: ignore
m_env
.
m_add_sub_section
(
Environment
.
packages
,
sys
.
modules
[
'
nomad.datamodel.metainfo.general
'
].
m_package
)
# type: ignore
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dlpolyparser/metainfo/dl_poly.py
0 → 100644
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195
−
0
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21a53541
import
numpy
as
np
# pylint: disable=unused-import
import
typing
# pylint: disable=unused-import
from
nomad.metainfo
import
(
# pylint: disable=unused-import
MSection
,
MCategory
,
Category
,
Package
,
Quantity
,
Section
,
SubSection
,
SectionProxy
,
Reference
)
from
nomad.metainfo.legacy
import
LegacyDefinition
from
nomad.datamodel.metainfo
import
public
m_package
=
Package
(
name
=
'
dl_poly_nomadmetainfo_json
'
,
description
=
'
None
'
,
a_legacy
=
LegacyDefinition
(
name
=
'
dl_poly.nomadmetainfo.json
'
))
class
x_dl_poly_section_md_molecule_type
(
MSection
):
'''
Section to store molecule type information
'''
m_def
=
Section
(
validate
=
False
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_section_md_molecule_type
'
))
x_dl_poly_md_molecule_type_id
=
Quantity
(
type
=
np
.
dtype
(
np
.
int32
),
shape
=
[],
description
=
'''
Molecule type id
'''
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_md_molecule_type_id
'
))
x_dl_poly_md_molecule_type_name
=
Quantity
(
type
=
str
,
shape
=
[],
description
=
'''
Molecule type name
'''
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_md_molecule_type_name
'
))
class
x_dl_poly_section_md_topology
(
MSection
):
'''
Section modelling the MD topology
'''
m_def
=
Section
(
validate
=
False
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_section_md_topology
'
))
x_dl_poly_md_molecular_types
=
Quantity
(
type
=
np
.
dtype
(
np
.
int32
),
shape
=
[],
description
=
'''
Number of molecular types in topology
'''
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_md_molecular_types
'
))
x_dl_poly_section_md_molecule_type
=
SubSection
(
sub_section
=
SectionProxy
(
'
x_dl_poly_section_md_molecule_type
'
),
repeats
=
True
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_section_md_molecule_type
'
))
class
section_sampling_method
(
public
.
section_sampling_method
):
m_def
=
Section
(
validate
=
False
,
extends_base_section
=
True
,
a_legacy
=
LegacyDefinition
(
name
=
'
section_sampling_method
'
))
x_dl_poly_barostat_target_pressure
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
unit
=
'
pascal
'
,
description
=
'''
MD barostat target pressure.
'''
,
categories
=
[
public
.
settings_molecular_dynamics
,
public
.
settings_barostat
,
public
.
settings_sampling
],
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_barostat_target_pressure
'
))
x_dl_poly_barostat_tau
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
unit
=
'
second
'
,
description
=
'''
MD barostat relaxation time.
'''
,
categories
=
[
public
.
settings_molecular_dynamics
,
public
.
settings_barostat
,
public
.
settings_sampling
],
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_barostat_tau
'
))
x_dl_poly_integrator_dt
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
unit
=
'
second
'
,
description
=
'''
MD integration time step.
'''
,
categories
=
[
public
.
settings_molecular_dynamics
,
public
.
settings_integrator
,
public
.
settings_sampling
],
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_integrator_dt
'
))
x_dl_poly_integrator_type
=
Quantity
(
type
=
str
,
shape
=
[],
description
=
'''
MD integrator type, valid values are defined in the integrator_type wiki page.
'''
,
categories
=
[
public
.
settings_molecular_dynamics
,
public
.
settings_integrator
,
public
.
settings_sampling
],
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_integrator_type
'
))
x_dl_poly_number_of_steps_requested
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
description
=
'''
Number of requested MD integration time steps.
'''
,
categories
=
[
public
.
settings_molecular_dynamics
,
public
.
settings_integrator
,
public
.
settings_sampling
],
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_number_of_steps_requested
'
))
x_dl_poly_thermostat_target_temperature
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
unit
=
'
kelvin
'
,
description
=
'''
MD thermostat target temperature.
'''
,
categories
=
[
public
.
settings_molecular_dynamics
,
public
.
settings_thermostat
,
public
.
settings_sampling
],
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_thermostat_target_temperature
'
))
x_dl_poly_thermostat_tau
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
unit
=
'
second
'
,
description
=
'''
MD thermostat relaxation time.
'''
,
categories
=
[
public
.
settings_molecular_dynamics
,
public
.
settings_thermostat
,
public
.
settings_sampling
],
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_thermostat_tau
'
))
class
section_run
(
public
.
section_run
):
m_def
=
Section
(
validate
=
False
,
extends_base_section
=
True
,
a_legacy
=
LegacyDefinition
(
name
=
'
section_run
'
))
x_dl_poly_program_version_date
=
Quantity
(
type
=
str
,
shape
=
[],
description
=
'''
Program version date
'''
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_program_version_date
'
))
x_dl_poly_system_description
=
Quantity
(
type
=
str
,
shape
=
[],
description
=
'''
Simulation run title
'''
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_system_description
'
))
class
section_system
(
public
.
section_system
):
m_def
=
Section
(
validate
=
False
,
extends_base_section
=
True
,
a_legacy
=
LegacyDefinition
(
name
=
'
section_system
'
))
x_dl_poly_section_md_topology
=
SubSection
(
sub_section
=
SectionProxy
(
'
x_dl_poly_section_md_topology
'
),
repeats
=
True
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_section_md_topology
'
))
class
section_method
(
public
.
section_method
):
m_def
=
Section
(
validate
=
False
,
extends_base_section
=
True
,
a_legacy
=
LegacyDefinition
(
name
=
'
section_method
'
))
x_dl_poly_step_number_equilibration
=
Quantity
(
type
=
np
.
dtype
(
np
.
int32
),
shape
=
[],
description
=
'''
MD equilibration step number
'''
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_step_number_equilibration
'
))
x_dl_poly_step_number
=
Quantity
(
type
=
np
.
dtype
(
np
.
int32
),
shape
=
[],
description
=
'''
MD total step number
'''
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_step_number
'
))
x_dl_poly_thermostat_temperature
=
Quantity
(
type
=
np
.
dtype
(
np
.
float64
),
shape
=
[],
description
=
'''
Thermostat coupling temperature
'''
,
a_legacy
=
LegacyDefinition
(
name
=
'
x_dl_poly_thermostat_temperature
'
))
m_package
.
__init_metainfo__
()
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