ogs5py.OGS
- class ogs5py.OGS(task_root=None, task_id='model', output_dir=None)[source]
Bases:
object
Class for an OGS5 model.
In this class everything for an OGS5 model can be specified.
- Parameters:
Notes
- The following Classes are present as attributes
- bcBoundary Condition
Information of the Boundary Conditions for the model.
- cctCommunication Table
Information of the Communication Table for the model.
- fctFunction
Information of the Function definitions for the model.
- gemgeochemical thermodynamic modeling coupling
Information of the geochemical thermodynamic modeling coupling for the model.
- gliGeometry
Information of the Geometry for the model.
- icInitial Condition
Information of the Initial Conditions for the model.
- krcKinetric Reaction
Information of the Kinetric Reaction for the model.
- mcpreactive components for modelling chemical processes
Information of the reactive components for modelling chemical processes for the model.
- mfpFluid Properties
Information of the Fluid Properties for the model.
- mmpMedium Properties
Information of the Medium Properties for the model.
- mshMesh
Information of the Mesh for the model.
- mspSolid Properties
Information of the Solid Properties for the model.
- numSettings for the numerical solver
Information of the numerical solver for the model.
- outOutput Settings
Information of the Output Settings for the model.
- pcsProcess settings
Information of the Process settings for the model.
- pctParticle Definition for Random walk
Information of the Particles defined for Randomwalk setting.
- pqcPhreqqc coupling (not supported yet)
Information of the Boundary Conditions for the model.
- pqcdatPhreqqc coupling (the phreeqc.dat file)
phreeqc.dat file for the model. (just a line-wise file with no comfort)
- reiReaction Interface
Information of the Reaction Interface for the model.
- rfddefinition of time-curves for variing BCs or STs
Information of the time curves for the model.
- stSource Term
Information of the Source Term for the model.
- timTime settings
Information of the Time settings for the model.
- Additional
- mpdDistributed Properties (list of files)
Information of the Distributed Properties for the model.
- gli_extlist for external Geometry definition
External definition of surfaces (TIN) or polylines (POINT_VECTOR)
- rfrlist of restart files
RESTART files as defined in the INITIAL_CONDITION
- gem_initlist of GEMS3K input files (lst file)
given as GEMinit classes
- asclist of ogs ASC files
This file type comes either from .tim .pcs or .gem
- copy_fileslist of path-strings
Files that should be copied to the destiny folder.
- Attributes:
bot_com
Get and set the bottom comment for the ogs files.
has_output_dir
bool
: State if the model has a output directory.output_dir
str
: output directory path of the ogs model.task_id
str
: task_id (name) of the ogs model.task_root
Get and set the task_root path of the ogs model.
top_com
Get and set the top comment for the ogs files.
Methods
add_asc
(asc_file)Method to add a ASC file.
add_copy_file
(path)Method to add an arbitrary file that should be copied.
add_gem_init
(gem_init_file)Method to add a GEMS3K input file.
add_gli_ext
(gli_ext_file)Method to add an external Geometry definition file to the model.
add_mpd
(mpd_file)Method to add an ogs MEDIUM_PROPERTIES_DISTRIBUTED file to the model.
add_rfr
(rfr_file)Method to add an ogs RESTART file to the model.
del_asc
([index])Method to delete a ASC file.
del_copy_file
([index])Method to delete a copy-file.
del_gem_init
([index])Method to delete GEMS3K input file.
del_gli_ext
([index])Method to delete external Geometry file.
del_mpd
([index])Method to delete MEDIUM_PROPERTIES_DISTRIBUTED file.
del_rfr
([index])Method to delete RESTART file.
gen_script
([script_dir, script_name, ...])Generate a python script for the given model.
load_model
(task_root[, task_id, ...])Load an existing OGS5 model.
output_files
([pcs, typ, element, output_dir])Get a list of output file paths.
readpvd
([pcs, output_dir])Read the paraview pvd files of this OGS5 model.
readtec_point
([pcs, output_dir])Collect TECPLOT point output from this OGS5 model.
readtec_polyline
([pcs, trim, output_dir])Collect TECPLOT polyline output from this OGS5 model.
readvtk
([pcs, output_dir])Reader for vtk outputfiles of this OGS5 model.
reset
()Delete every content.
run_model
([ogs_exe, ogs_name, print_log, ...])Run the defined OGS5 model.
Method to call all write_file() methods that are initialized.
- add_copy_file(path)[source]
Method to add an arbitrary file that should be copied.
The base-name of the file will be keept and it will be copied to the task-root when the “write” routine is called.
- add_gem_init(gem_init_file)[source]
Method to add a GEMS3K input file.
This is usually generated by GEM-SELEKTOR.
See ogs5py.GEM and ogs5py.GEMinit for further information
- add_gli_ext(gli_ext_file)[source]
Method to add an external Geometry definition file to the model.
This is used for TIN definition in SURFACE or POINT_VECTOR definition in POLYLINE in the GLI file.
See ogs5py.GLI for further information
- add_mpd(mpd_file)[source]
Method to add an ogs MEDIUM_PROPERTIES_DISTRIBUTED file to the model.
This is used for disributed information in the MMP file.
See ogs5py.MPD for further information
- add_rfr(rfr_file)[source]
Method to add an ogs RESTART file to the model.
This is used for disributed information in the IC file.
See ogs5py.IC for further information
- del_asc(index=None)[source]
Method to delete a ASC file.
- Parameters:
index (int or None, optional) – The index of the ASC file that should be deleted. If None, all ASC files are deleted. Default: None
- del_copy_file(index=None)[source]
Method to delete a copy-file.
- Parameters:
index (int or None, optional) – The index of the copy-file that should be deleted. If None, all copy-files are deleted. Default: None
- del_gem_init(index=None)[source]
Method to delete GEMS3K input file.
- Parameters:
index (int or None, optional) – The index of the GEMS3K file that should be deleted. If None, all GEMS3K files are deleted. Default: None
- del_gli_ext(index=None)[source]
Method to delete external Geometry file.
- Parameters:
index (int or None, optional) – The index of the external gli file that should be deleted. If None, all external gli files are deleted. Default: None
- del_mpd(index=None)[source]
Method to delete MEDIUM_PROPERTIES_DISTRIBUTED file.
- Parameters:
index (int or None, optional) – The index of the mpd-file that should be deleted. If None, all mpd-files are deleted. Default: None
- del_rfr(index=None)[source]
Method to delete RESTART file.
- Parameters:
index (int or None, optional) – The index of the RESTART file that should be deleted. If None, all RESTART files are deleted. Default: None
- gen_script(script_dir='/home/docs/checkouts/readthedocs.org/user_builds/ogs5py/checkouts/latest/docs/source/ogs_script', script_name='model.py', ogs_cls_name='model', task_root=None, task_id=None, output_dir=None, separate_files=None)[source]
Generate a python script for the given model.
- Parameters:
script_dir (str) – target directory for the script
script_name (str) – name for the script file (including .py ending)
ogs_cls_name (str) – name of the model in the script
task_root (str) – used task_root in the script
task_id (str) – used task_id in the script
output_dir (str) – used output_dir in the script
separate_files (list of str or None) – list of files, that should be written to separate files and then loaded from the script
Notes
This will only create BlockFiles from the script. GLI and MSH files as well as every other file are stored separately.
- load_model(task_root, task_id=None, use_task_root=False, use_task_id=False, skip_files=None, skip_ext=None, encoding=None, verbose=False, search_ext=None)[source]
Load an existing OGS5 model.
- Parameters:
task_root (str) – Path to the destiny folder.
task_id (str or None, optional) – Task ID of the model to load. If None is given, it will be determind by the found files. If multiple possible task_ids were found, the first one in alphabetic order will be used. Default: None
use_task_root (Bool, optional) – State if the given task_root should be used for this model. Default: False
use_task_id (Bool, optional) – State if the given task_id should be used for this model. Default: False
skip_files (list or None, optional) – List of file-names, that should not be read. Default: None
skip_ext (list or None, optional) – List of file-extensions, that should not be read. Default: None
encoding (str or None, optional) – encoding of the given files. If
None
is given, the system standard is used. Default:None
verbose (bool, optional) – Print information of the reading process. Default: False
search_ext (str) – OGS extension that should be searched for. Default: “.pcs”
Notes
This method will search for all known OGS5 file-extensions in the given path (task_root). Additional files from:
GLI (POINT_VECTOR + TIN)
MMP (distributed media properties)
IC (RESTART)
GEM (GEM3SK init file)
will be read automatically.
If you get an
UnicodeDecodeError
try loading with:encoding="ISO-8859-15"
- output_files(pcs=None, typ='VTK', element=None, output_dir=None)[source]
Get a list of output file paths.
- Parameters:
pcs (string or None, optional) – specify the PCS type that should be collected Possible values are:
None/”” (no PCS_TYPE specified in *.out)
“NO_PCS”
“GROUNDWATER_FLOW”
“LIQUID_FLOW”
“RICHARDS_FLOW”
“AIR_FLOW”
“MULTI_PHASE_FLOW”
“PS_GLOBAL”
“HEAT_TRANSPORT”
“DEFORMATION”
“MASS_TRANSPORT”
“OVERLAND_FLOW”
“FLUID_MOMENTUM”
“RANDOM_WALK”
Default : None
typ (string, optional) – Type of the output (“VTK”, “PVD”, “TEC_POINT” or “TEC_POLYLINE”). Default : “VTK”
element (string or None, optional) – For tecplot output you can specify the name of the output element. (Point-name of Line-name from GLI file) Default: None
- readpvd(pcs='ALL', output_dir=None)[source]
Read the paraview pvd files of this OGS5 model.
All concerned files are converted to a dictionary containing their data
- Parameters:
pcs (string or None, optional) – specify the PCS type that should be collected Possible values are:
None/”” (no PCS_TYPE specified in *.out)
“NO_PCS”
“GROUNDWATER_FLOW”
“LIQUID_FLOW”
“RICHARDS_FLOW”
“AIR_FLOW”
“MULTI_PHASE_FLOW”
“PS_GLOBAL”
“HEAT_TRANSPORT”
“DEFORMATION”
“MASS_TRANSPORT”
“OVERLAND_FLOW”
“FLUID_MOMENTUM”
“RANDOM_WALK”
You can get a list with all known PCS-types by setting PCS=”ALL” Default : “ALL”
output_dir (:any:’None’ or :class:’str’, optional) – Sometimes OGS5 doesn’t put the output in the right directory. You can specify a separate output directory here in this case. Default: :any:’None’
- Returns:
result – keys are the point names and the items are the data from the corresponding files if pcs=”ALL”, the output is a dictionary with the PCS-types as keys
- Return type:
- readtec_point(pcs='ALL', output_dir=None)[source]
Collect TECPLOT point output from this OGS5 model.
- Parameters:
pcs (string or None, optional) – specify the PCS type that should be collected Possible values are:
None/”” (no PCS_TYPE specified in *.out)
“NO_PCS”
“GROUNDWATER_FLOW”
“LIQUID_FLOW”
“RICHARDS_FLOW”
“AIR_FLOW”
“MULTI_PHASE_FLOW”
“PS_GLOBAL”
“HEAT_TRANSPORT”
“DEFORMATION”
“MASS_TRANSPORT”
“OVERLAND_FLOW”
“FLUID_MOMENTUM”
“RANDOM_WALK”
You can get a list with all known PCS-types by setting PCS=”ALL” Default : “ALL”
output_dir (:any:’None’ or :class:’str’, optional) – Sometimes OGS5 doesn’t put the output in the right directory. You can specify a separate output directory here in this case. Default: :any:’None’
- Returns:
result – Keys are the point names and the items are the data from the corresponding files. If pcs=”ALL”, the output is a dictionary with the PCS-types as keys.
- Return type:
- readtec_polyline(pcs='ALL', trim=True, output_dir=None)[source]
Collect TECPLOT polyline output from this OGS5 model.
- Parameters:
pcs (string or None, optional) – specify the PCS type that should be collected Possible values are:
None/”” (no PCS_TYPE specified in *.out)
“NO_PCS”
“GROUNDWATER_FLOW”
“LIQUID_FLOW”
“RICHARDS_FLOW”
“AIR_FLOW”
“MULTI_PHASE_FLOW”
“PS_GLOBAL”
“HEAT_TRANSPORT”
“DEFORMATION”
“MASS_TRANSPORT”
“OVERLAND_FLOW”
“FLUID_MOMENTUM”
“RANDOM_WALK”
You can get a list with all known PCS-types by setting pcs=”ALL” Default : “ALL”
output_dir (:any:’None’ or :class:’str’, optional) – Sometimes OGS5 doesn’t put the output in the right directory. You can specify a separate output directory here in this case. Default: :any:’None’
trim (Bool, optional) – if the ply_ids are not continuous, there will be “None” values in the output list. If trim is “True” these values will be eliminated. If there is just one output for a polyline, the list will be eliminated and the output will be the single dict. Default : True
- Returns:
result – keys are the Polyline names and the items are lists sorted by the ply_id (it is assumed, that the ply_ids are continuous, if not, the corresponding list entries are “None”) if pcs=”ALL”, the output is a dictionary with the PCS-types as keys
- Return type:
- readvtk(pcs='ALL', output_dir=None)[source]
Reader for vtk outputfiles of this OGS5 model.
- Parameters:
pcs (string or None, optional) – specify the PCS type that should be collected Possible values are:
None/”” (no PCS_TYPE specified in *.out)
“NO_PCS”
“GROUNDWATER_FLOW”
“LIQUID_FLOW”
“RICHARDS_FLOW”
“AIR_FLOW”
“MULTI_PHASE_FLOW”
“PS_GLOBAL”
“HEAT_TRANSPORT”
“DEFORMATION”
“MASS_TRANSPORT”
“OVERLAND_FLOW”
“FLUID_MOMENTUM”
“RANDOM_WALK”
You can get a list with all known PCS-types by setting PCS=”ALL” Default : None
output_dir (:any:’None’ or :class:’str’, optional) – Sometimes OGS5 doesn’t put the output in the right directory. You can specify a separate output directory here in this case. Default: :any:’None’
- Returns:
result – keys are the point names and the items are the data from the corresponding files if pcs=”ALL”, the output is a dictionary with the PCS-types as keys
- Return type:
- run_model(ogs_exe=None, ogs_name='ogs', print_log=True, save_log=True, log_path=None, log_name=None, timeout=None)[source]
Run the defined OGS5 model.
- Parameters:
ogs_exe (str or None, optional) – path to the ogs executable. If
None
is given, the default sys path will be searched withwhich
. Can be a folder containing the exe with basename: ogs_name. It will first look in theOGS5PY_CONFIG
folder. Default: Noneogs_name (str or None, optional) – Name of to the ogs executable to search for. Just used if ,ogs_exe is
None
. Default:"ogs"
print_log (bool, optional) – state if the ogs output should be displayed in the terminal. Default: True
save_log (bool, optional) – state if the ogs output should be saved to a file. Default: True
log_path (str or None, optional) – Path, where the log file should be saved. Default: None (the defined output directory or the task_root directory)
log_name (str or None, optional) – Name of the log file. Default: None (task_id+time+”_log.txt”)
timeout (int or None, optional) – Time to wait for OGS5 to finish in seconds. Default: None
- Returns:
success – State if OGS5 terminated ‘normally’. (Allways true on Windows.)
- Return type:
- property bot_com
Get and set the bottom comment for the ogs files.
- property task_root
Get and set the task_root path of the ogs model.
- property top_com
Get and set the top comment for the ogs files.