Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
P
parser-dl-poly
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Analytics
Analytics
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Commits
Open sidebar
nomad-lab
parser-dl-poly
Commits
21a53541
Commit
21a53541
authored
Mar 19, 2020
by
Markus Scheidgen
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Added metainfo python code.
parent
de6d49f8
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
208 additions
and
0 deletions
+208
-0
dlpolyparser/metainfo/__init__.py
dlpolyparser/metainfo/__init__.py
+13
-0
dlpolyparser/metainfo/dl_poly.py
dlpolyparser/metainfo/dl_poly.py
+195
-0
No files found.
dlpolyparser/metainfo/__init__.py
0 → 100644
View file @
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
dlpolyparser/metainfo/dl_poly.py
0 → 100644
View file @
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__
()
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment