Revert "tailor the dev project by removing unnecessary files"

This reverts commit b3a87bcf

.gitignore

@@ -18,7 +18,6 @@ EfficiencyPiecewise.xlsx
 /version
 
 # Data files
-*.sqlite
 *.gdx
 *.xlsx
 

.spinetoolbox/items/backbone/output/.gitignore

-*
-!.gitignore

.spinetoolbox/items/backbone_vara/output/.gitignore

-*
-!.gitignore

.spinetoolbox/items/bb_base_sets/output/.gitignore

-*
-!.gitignore

.spinetoolbox/items/bb_parameters/filter_config.json

-{"type": "parameter_renamer", "name_map": {"boundaryValue": "ts_node", "capacityFactor": "ts_cf", "coefficient": "p_unitConstraintNode", "constant": "p_unitConstraint", "discountFactor": "p_s_discountFactor", "emission_content": "p_nEmission", "forwardReserve": "p_gnuRes2Res", "influx": "ts_influx", "priceChange": "ts_priceChange", "reserveDemand": "ts_reserveDemand", "storageValue": "p_storageValue", "storageValue_ts": "ts_storageValue", "value": "p_gnPolicy"}}
\ No newline at end of file

.spinetoolbox/items/bb_sets/filter_config.json

-{"type": "entity_class_renamer", "name_map": {"boundarytypes": "param_gnBoundaryTypes", "efflevel__group__unit": "effLevelGroupUnit", "effselector": "effSelector", "flow__unit": "flowUnit", "grid__node__group": "gnGroup", "grid__node__node__group": "gn2nGroup", "grid__node__sample__sample": "gnss_bound", "grid__node__unit__group": "gnuGroup", "restype__direction": "restypeDirection", "restype_released_for_realization": "restypeReleasedForRealization", "sample__group": "sGroup", "unit__group": "uGroup", "unit__sample__sample": "uss_bound", "unit__t__availability": "utAvailabilityLimits", "unit__unittype": "unitUnittype", "unit_aggregate__unit__efflevel": "unitUnitEffLevel"}}
\ No newline at end of file

1_options_temp.gms

+options
+
+// Solution gap: the first one reached will end iteration
+optca = 0       // Absolute gap between the found solution and the best possible solution
+optcr = 0.0004  // Relative gap between the found solution and the best possible solution
+
+solvelink = %Solvelink.Loadlibrary%  // Solvelink controls how the problem is passed from GAMS to the solver. Loadlibrary constant means that the model is passed in core without the use of temporary files.
+
+*    profile = 8       // Profile will show the execution speed of statements at the defined depth within loops.
+
+*    bratio = 0.25     // How large share of the candidate elements need to be found for advanced basis in LP problems. Default 0.25.
+*    solveopt = merge  // How solution values are stored after multiple solves. Default merge.
+*    savepoint = 1     // NOTE! Savepoint is controlled by Backbone model options.
+
+threads = -1          // How many cores the solver can use: 0 = all cores; negative values = all cores - n
+
+$ife not %debug%>1
+    solprint = Silent  // Controls solution file outputs - debug mode will be more verbose
+;
+

4d_postProcess_invest2schedule_temp.gms

+* =============================================================================
+* --- Save investments results in changes.inc file to be used in child setups -
+* =============================================================================
+
+* Output file streams
+file f_changes /'output\changes.inc'/;
+
+f_changes.lw = 26; // Field width of set label output, default in GAMS is 12, increase as needed
+f_changes.pw = 500; // Number of characters that may be placed on a single row of the page, default in GAMS is 255, increase as needed
+
+put f_changes
+
+* Do not allow investments in the child setups
+loop(unit,
+    put "p_unit('", unit.tl, "', 'maxUnitCount') = 0;"/;
+);
+
+* Update the number of subunits in the child setups (rounded here to the nearest integer)
+loop(unit${r_invest(unit)},
+    tmp = round(r_invest(unit), 0)
+    put "p_unit('", unit.tl, "', 'unitCount') = p_unit('", unit.tl, "', 'unitCount') + ", tmp, ";"/;
+);
+* Update capacity values in the child setups
+loop(gnu(grid, node, unit)${r_invest(unit)},
+    tmp = round(r_invest(unit), 0) * p_gnu(grid, node, unit, 'unitSize');
+    put "p_gnu('", grid.tl, "', '", node.tl, "', '", unit.tl, "', 'capacity') = p_gnu('", grid.tl, "', '", node.tl, "', '", unit.tl, "', 'capacity') + ", tmp, ";"/;);
+
+* Do not allow investments in the child setups (commented out at the moment)
+*loop(gn2n_directional(grid, node, node_),
+*    put "p_gnn('", grid.tl, "', '", node.tl, "', '", node_.tl, "', 'transferCapMax') = 0;"/;
+*    put "p_gnn('", grid.tl, "', '", node_.tl, "', '", node.tl, "', 'transferCapMax') = 0;"/;
+*);
+
+* Update transmission capacity in the child setups
+loop(gn2n_directional(grid, node, node_)${sum(t_invest, r_investTransfer(grid, node, node_, t_invest))},
+    tmp = sum(t_invest, r_investTransfer(grid, node, node_, t_invest));
+    put "p_gnn('", grid.tl, "', '", node.tl, "', '", node_.tl, "', 'transferCap') = p_gnn('", grid.tl, "', '", node.tl, "', '", node_.tl, "', 'transferCap') + ", tmp, ";"/;
+    put "p_gnn('", grid.tl, "', '", node_.tl, "', '", node.tl, "', 'transferCap') = p_gnn('", grid.tl, "', '", node_.tl, "', '", node.tl, "', 'transferCap') + ", tmp, ";"/;
+);
+
+putclose;

CHANGELOG.md

+# Changelog
+All notable changes to this project will be documented in this file.
+
+## [Unreleased]
+### Added
+- Dynamic generation portfolios aka pathway modelling aka multi-year simulations with discounted costs enabled
+ 
+### Changed
+- Static inertia requirement can be fulfilled by both rotational inertia of machines and certain reserve products
+
+## [1.2.1] - 2019-11-26
+### Fixed
+- Fixed a possible division by zero in the calculation of r_gnuUtilizationRate
+- Updated debugSymbols.inc and 1e_scenChanges.gms to match with the current naming of sets and parameters
+
+### Changed
+- Changed variable O&M costs from p_unit(unit, 'omCosts') to p_gnu(grid, node, unit, 'vomCosts')
+
+## [1.2] - 2019-11-12
+
+### Added
+- Dynamic inertia requirements based on loss of unit and loss of export/import (ROCOF constraints)
+- N-1 reserve requirement for transfer links
+- A separate parameter to tell whether units can provide offline reserve (non-spinning reserve)
+- Maximum share of reserve provision from a group of units
+- All input files, including *inputData.gdx*, are optional
+- Enabling different combinations of LP and MIP online and invest variables
+- Separate availability parameter for output units in the capacity margin constraint
+- Parameter `gn_forecasts(*, node, timeseries)` to tell which nodes and timeseries use forecasts
+
+### Changed 
+- Reserve requirements are now based on groups (previously node based)
+- Changed the v_startup (and v_shutdown) variables into integers to improve the performance online approximations
+- Updated tool definitions for Sceleton Titan and Spine Toolbox
+- The program will now stop looping in case of execution errors
+- Scenario reduction is done based on total available energy
+- Maintain original scenario labels after reduction
+- Clear time series data from droppped samples after scenario reduction
+
+### Fixed
+- Removed hard-coded `elec grids` from *setVariableLimits* and *rampSched files*
+- Cyclic bounds between different samples was not working correctly (#97)
+- Time series smoothing not working at all (#100)
+- Fix a number of compilation warnings
+- Limiting the provision of online reserve based on the online variable
+- Sample probability bug from scenario reduction (probability of single scenario above one)
+
+## [1.1] - 2019-04-17
+### Added
+- New model setting 't_perfectForesight' tells the number of time steps (from 
+  the beginning of current solve) for which realized data is used instead of 
+  forecasts. This value cannot exceed current forecast length, however. Setting 
+  the value lower than 't_jump' has no effect.
+- Automated the calculation of sample start and end times if using long-term 
+  scenarios. Also setting number of scenarios to one, instructs the model to use
+  central forecast for the long-term.
+- Speedup for model dimension calculation (set `msft` etc.)
+- Support long time intervals in the first block
+- Possibility to limit `v_online` to zero according to time series
+- Output for reserve transfer results
+- Reserve provision limits with investments
+- Constrain the set of units to which ramp equations are applied
+- Piecewise linear heat rate curves
+- Checks for reserves
+- Allow to set certain value for `v_gen` at 't000000'
+
+### Changed
+- Removed some old command line arguments
+- Removed obsolete 'emissionIntensity' fuel parameter
+
+### Fixed
+- Unit ramps during start-up and shutdown
+- Refreshing forecast data in *inputsLoop*
+- Aggregated groups that were not in use were included in the model
+- `mst_end` not found for the last sample
+- Start-up not working for units without start costs or start fuel consumption
+- *periodicInit* will fail with multiple model definitions
+- Reserves should not be allowed to be locked when the interval is greater than 
+  smallest interval in use
+- Start-up phase and aggregated time steps do not work together
+- In SOS2 unit cannot exceed the generation of `p_ut_runUp`
+- Startup cost calculation
+- Efficiency presentations
+- `p_uNonoperational` not fully correct
+
+
+## [1.0.6] - 2019-03-27
+### Fixed
+- Major bug in state variable reserve equations
+- Scenario smoothing alogirithm
+
+### Changed
+- Speedup for timeseries calculations
+
+### Added 
+- New model setting `mSettings(mType, 'onlyExistingForecasts') = 0|1` to control 
+  the reading of forecasts. Set to 1 to only read forecast data that exists in 
+  the file. Note that zeros need to be saved as Eps when using this.
+- Proper stochastic programming for the long-term scenarios period. Possible also
+  to create a stochastic tree from the original data.
+- Clickable link to *sr.log* in the process window in case of SCENRED2 error
+- New diagnostic parameter for timeseries scenarios `d_ts_scenarios`
+
+
+## [1.0.5] - 2019-02-14
+### Fixed
+- Probabilities were not updated after using scenario reduction
+
+### Added
+- Enable long-term samples that extend several years by using planning horizon 
+  which is longer than one scenario (e.g. 3 years). Note: Cannot use all data for 
+  samples as last years need to be reserved for the planning horizon.
+
+
+## [1.0.4] - 2019-02-11
+### Fixed
+- Severe bug in setting node state level limits
+
+### Changed
+- Suppress ouput from SCENRED2
+
+
+## [1.0.3] - 2019-02-05
+### Fixed
+- Only selects forecasts with positive probability for the solve
+
+
+## [1.0.2] - 2019-02-04
+### Added
+- New model setting `dataLength` to set the length of time series data before it is
+  recycled. Warn if this is not defined and automatically calculated from data.
+- Command line arguments '--input_dir=<path>' and '--ouput_dir=<path' to set
+  input and output directories, respectively.
+- Added sample dimension to most variables and equations (excl. investments). 
+  Samples can now be used as long-term scenario alternatives (for e.g. hydro scehduling)
+- Number of parallel samples can be reduced using SCENRED2. Activate with active('scenRed')
+  and set parameters in modelsInit.
+
+### Changed
+- Automatic calculation of parameter `dt_circular` takes into account time steps 
+  only from `t000001` onwards.
+- Debug mode yes/no changed to debug levels 0, 1 or 2. With higher level produces
+  more information. Default is 0, when no extra files are written (not even *debug.gdx*).
+  Set debug level with command line parameter `--debug=LEVEL`.
+
+### Fixed
+- Calculation of parameter `df_central`
+- Readability of some displayed messages 
+
+
+## 1.0 - 2018-09-12
+### Changed
+- Major updates to data structures etc.
+
+
+
+[Unreleased]: https://gitlab.vtt.fi/backbone/backbone/compare/v1.2.1...dev
+[1.2.1]: https://gitlab.vtt.fi/backbone/backbone/compare/v1.2...v1.2.1
+[1.2]: https://gitlab.vtt.fi/backbone/backbone/compare/v1.1...v1.2
+[1.1]: https://gitlab.vtt.fi/backbone/backbone/compare/v1.0.6...v1.1
+[1.0.6]: https://gitlab.vtt.fi/backbone/backbone/compare/v1.0.5...v1.0.6
+[1.0.5]: https://gitlab.vtt.fi/backbone/backbone/compare/v1.0.4...v1.0.5
+[1.0.4]: https://gitlab.vtt.fi/backbone/backbone/compare/v1.0.3...v1.0.4
+[1.0.3]: https://gitlab.vtt.fi/backbone/backbone/compare/v1.0.2...v1.0.3
+[1.0.2]: https://gitlab.vtt.fi/backbone/backbone/compare/v1.0...v1.0.2

COPYING.LESSER

+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
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+other than an Application or a Combined Work as defined below.
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Notes.md

-1. after moving the project, the URL in tool specification should be modified into current main folder directory (xx/BB_in_Spine) \
-2. the directory slash must use "/" \
-3. the VabiSys inputData.gdx is in v1.3 converted from a v1.2 one by the tools/inputGDX_from_v1.2_to_v1.3.gms
\ No newline at end of file

README.md

+# Backbone
+
+Backbone is a generic energy network optimization tool written in [GAMS](https://www.gams.com/). It has been designed to be highly adaptable in different dimensions: temporal, spatial, technology representation and market design. The model can represent stochastics with a [model predictive control method](https://doi.org/10.1016/j.automatica.2008.03.002), with short-term forecasts and longer-term statistical uncertainties. Backbone can support multiple different models (e.g. investment or unit commitment) due to the modifiable temporal structure and varying lengths of the time steps.
+
+If you use Backbone in a published work, please cite the [following publication](https://doi.org/10.3390/en12173388), which describes the Backbone energy systems modelling framework.
+
+## Getting Started
+
+Make sure that you have [Git](https://git-scm.com/) version control system and a Git interface, such as [TortoiseGit](https://tortoisegit.org/) or [SourceTree](https://www.sourcetreeapp.com/), installed on your computer. 
+You also need to have [GAMS](https://www.gams.com/) version 24.0 or later installed.
+
+In order to get a copy of the Backbone project, you need to clone it using Git. Copy and paste the URL of the original Backbone repository and select the directory where you want Backbone to be cloned. The URL of the original Backbone repository is https://gitlab.vtt.fi/backbone/backbone. 
+
+You should now have *Backbone.gms*, a few additional files and five subdirectories in the directory where you cloned Backbone.
+
+Small example input datasets are provided online in the [wiki](https://gitlab.vtt.fi/backbone/backbone/wikis/Example-data-sets).
+
+## Model File Structure
+
+Backbone has been designed with a modular structure, making it easier to change even large portions of the model if necessary. The various gms-files of the model are described briefly below, in the order of their execution when running Backbone. 
+
+* Backbone.gms - The heart of the model, containing instructions on how the rest of the files are read and compiled. The following files are currently named with an index corresponding to their turn in the Backbone compilation order.
+* 1a_definitions.gms - Contains important definitions regarding the models used, such as possible model features and parameters.
+* 1b_sets.gms - Contains the set definitions required by the models.
+* 1c_parameters.gms	- Contains the parameter definitions used by the models.
+* 1d_results.gms - Contains definitions for the model results.
+* 1e_inputs.gms - Contains instructions on how to load input data, as well as forms a lot of helpful sets based on said data, for example in order to facilitate writing the constraints.
+* 1e_scenChanges.gms - Inside input.gms - reads additional changes for scenarios (Sceleton Titan can use these)
+* 2a_variables.gms - Contains variable definitions used by the models.
+* 2b_eqDeclarations.gms - Contains equation declarations for the models.
+* 2c_objective.gms - Contains the objective function definition.
+* 2d_constraints.gms - Contains definitions for constraint equations.
+* *Model Definition Files* - Contains GAMS definitions for different models, essentially lists the equations (constraints) that apply. Current files include *schedule.gms*, *building.gms* and *invest.gms*.
+* 3a_periodicInit.gms - Initializes various data and sets for the solve loop.
+* 3b_periodicLoop.gms - Contains instructions for the forecast-interval structure of the desired model.
+* 3c_inputsLoop.gms - Contains instructions for updating the forecast data, optional forecast improvements, aggregating time series data for the time intervals, and other input data processing.
+* 3d_setVariableLimits.gms - Defines the variable boundaries for each solve.
+* 3e_solve.gms - Contains the GAMS solve command for using the solver.
+* 3f_afterSolve.gms - Fixes some variable values after solve.
+* 4a_outputVariant.gms - Contains instructions for storing desired results during the solve loop.
+* 4b_outputInvariant.gms - Calculates further results post-solve.
+* 4c_outputQuickFile.gms
+
+Most of these files are under *\inc* in the Backbone folder, except for the model definition files being housed under *\defModels*. Other than the abovementioned files, a few key input files are required for Backbone to work. These are assumed to be found under *\input* and are briefly described below.
+
+* inputData.gdx	- Contains most of the input data about the system to be modelled.
+* 1_options.gms - Contains options to control the solver.
+* timeAndSamples.inc - Contains definitions for the time, forecast and sample index ranges.
+* modelsInit.gms - Contains model parameters for the solve (or a link to a template under *\defModels* to be used). Useful for any additional GAMS scripting.
+
+Backbone folder contains template files *1_options_temp.gms*, *timeAndSamples_temp.inc*, and *modelsInit_temp.gms* to provide examples of the input format. These files can be copied into *\input* and renamed to *1_options.gms*, *timeAndSamples.inc*, and *modelsInit.gms*.
+
+## When Simply Using Backbone
+
+When starting to use Backbone, there is no immediate need to understand every single file that makes up the model. The files below list the most important files to understand, if one’s aim is simply to use Backbone for modelling/simulation purposes, without the need to modify the way the model works.
+
+* **1a_definitions.gms**: Lists all the possible model settings, as well as all the different parameters that Backbone understands. Also lists some auxiliary sets that are required for the model structure, but don’t hold any intuitive meaning.
+* **1e_inputs.gms**: Imports the input data into Backbone, and thus contains a list of the sets and parameters that need to be included in the “InputData.gdx” input file. Also contains rules for generating all sorts of auxiliary sets based on the input data that are used throughout the model files. Contains a few data integrity checks as well, but these could/should be expanded upon in the future.
+* **1b_sets.gms and 1c_parameters.gms**: Understanding of the required dimensions of the input sets and parameters is necessary in order to create working input files. 
+* **Model Initialization Files**: E.g. *scheduleInit_temp.gms* that define the rules for the optimization model.
+
+## Authors
+
+* Juha Kiviluoma
+* Erkka Rinne
+* Topi Rasku
+* Niina Helisto
+* Dana Kirchem
+* Ran Li
+* Ciara O'Dwyer
+
+## License
+
+This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by
+the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>.

modelsInit_temp.gms

+$ontext
+This file is part of Backbone.
+
+Backbone is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+Backbone is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with Backbone.  If not, see <http://www.gnu.org/licenses/>.
+$offtext
+
+* =============================================================================
+* --- Load Model Parameters ---------------------------------------------------
+* =============================================================================
+
+// Include desired model definition files here
+$include 'defModels/scheduleInit_temp.gms'
+

sceleton.json

+{
+    "name": "Backbone",
+    "type": "gams",
+    "short_name": "backbone",
+    "description": "Backbone energy systems model",
+    "files": ["Backbone.gms",
+              "inc/*.gms",
+              "cplex.opt",
+              "inc/rampSched/*.gms",
+              "defModels/*.gms",
+              "defOutput/*.inc"],
+    "cmdline_args": "",
+    "datafiles": [],
+    "datafiles_opt": ["input/*.gms",
+                      "input/*.gdx",
+                      "input/*.inc",
+                      "input/ts_cf/*.gdx",
+                      "input/ts_reserveDemand/*.gdx",
+                      "input/ts_influx/*.gdx"],
+    "outfiles": ["output/debug.gdx",
+                 "output/results.gdx",
+                 "output/info.txt"]
+}

tools/spineToolbox.json → spineToolbox.json

@@ -12,8 +12,8 @@
     ],
     "description": "Backbone",
     "inputfiles": [
-        "input/modelsInit.gms",
-        "input/inputData.gdx"
+        "input/inputData.gdx",
+        "input/modelsInit.gms"
     ],
     "inputfiles_opt": [
         "input/*.*"
@@ -24,5 +24,5 @@
     ],
     "cmdline_args": [],
     "execute_in_work": true,
-    "includes_main_path": "C:/HJY_projects/spine/Case_study_B3/BB_in_Spine"
+    "includes_main_path": "C:/data/backbone"
 }
\ No newline at end of file