Merge branch 'dev' of github.com:TeamCOMPAS/COMPAS into event-strings

.dictionary.txt

@@ -14,4 +14,3 @@ accrete
 accreted
 YHe
 yhe
-

.github/workflows/compas-compile-ci.yml

@@ -72,4 +72,4 @@ jobs:
         with:
           name: COMPAS-run-artifacts
           path: |
-            py_tests/test_artifacts
+            py_tests/test_artifacts

.github/workflows/precommit-checks.yml

@@ -12,3 +12,5 @@ jobs:
       with:
         python-version: 3.8
     - uses: pre-commit/[email protected]
+
+

compas_python_utils/preprocessing/compasConfigDefault.yaml

@@ -1,5 +1,5 @@
 ##~!!~## COMPAS option values
-##~!!~## File Created Wed Nov  1 11:25:11 2023 by COMPAS v02.40.00
+##~!!~## File Created Tue Oct 31 04:36:43 2023 by COMPAS v02.40.00
 ##~!!~##
 ##~!!~## The default COMPAS YAML file (``compasConfigDefault.yaml``), as distributed, has
 ##~!!~## all COMPAS option entries commented so that the COMPAS default value for the
@@ -47,6 +47,9 @@ booleanChoices:
 #    --common-envelope-lambda-nanjing-use-rejuvenated-mass: False          # Default: False
 #    --revised-energy-formalism-nandez-ivanova: False                      # Default: False
 
+    ### TIDES
+#    --enable-tides: False                                                 # Default: False
+
     ### SUPERNOVAE, KICKS AND REMNANTS
 #    --allow-non-stripped-ECSN: False                                      # Default: False
 #    --pair-instability-supernovae: True                                   # Default: True
@@ -96,7 +99,7 @@ numericalChoices:
 #    --rotational-frequency: 0.000000                                      # Default: 0.000000
 #    --rotational-frequency-1: 0.000000                                    # Default: 0.000000
 #    --rotational-frequency-2: 0.000000                                    # Default: 0.000000
-#    --wolf-rayet-multiplier: 1.000000                                     # Default: 1.000000
+#    --wolf-rayet-multiplier: 0.100000                                     # Default: 0.100000
 
     ### BINARY PROPERTIES
 #    --eccentricity: 0.000000                                              # Default: 0.000000                                                                                                                                                           # eccentricity for BSE
@@ -213,11 +216,7 @@ stringChoices:
 #    --envelope-state-prescription: 'LEGACY'                               # Default: 'LEGACY'                      # Options: ['FIXED_TEMPERATURE','HURLEY','LEGACY']
 #    --initial-mass-function: 'KROUPA'                                     # Default: 'KROUPA'                      # Options: ['KROUPA','UNIFORM','POWERLAW','SALPETER']
 #    --luminous-blue-variable-prescription: 'HURLEY_ADD'                   # Default: 'HURLEY_ADD'                  # Options: ['BELCZYNSKI','HURLEY','HURLEY_ADD','NONE']
-#    --mass-loss-prescription: 'FLEXIBLE2023'                              # Default: 'FLEXIBLE2023'                # Options: ['FLEXIBLE2023','BELCZYNSKI2010','HURLEY','NONE']
-#    --OB-mass-loss: 'VINK2021'                                            # Default: 'VINK2021'                    # Options: ['KRTICKA2018','BJORKLUND2022','VINK2021','VINK2001','NONE']
-#    --RSG-mass-loss: 'DECIN2023'                                          # Default: 'DECIN2023'                   # Options: ['NJ90','KEE2021','YANG2023','DECIN2023','BEASOR2020','VINKSABHAHIT2023','NONE']
-#    --VMS-mass-loss: 'SABHAHIT2023'                                       # Default: 'SABHAHIT2023'                # Options: ['SABHAHIT2023','BESTENLEHNER2020','VINK2011','NONE']
-#    --WR-mass-loss: 'SANDERVINK2023'                                      # Default: 'SANDERVINK2023'              # Options: ['SHENAR2019','SANDERVINK2023','BELCZYNSKI2010']
+#    --mass-loss-prescription: 'VINK'                                      # Default: 'VINK'                        # Options: ['VINK','HURLEY','NONE']
 #    --metallicity-distribution: 'ZSOLAR'                                  # Default: 'ZSOLAR'                      # Options: ['LOGUNIFORM','ZSOLAR']
 #    --pulsational-pair-instability-prescription: 'MARCHANT'               # Default: 'MARCHANT'                    # Options: ['FARMER','MARCHANT','STARTRACK','COMPAS']
 

examples/methods_paper_plots/detailed_evolution/Grid_demo.txt

@@ -0,0 +1,3 @@
+--initial-mass-1 35.0 --initial-mass-2 31.0 --metallicity 0.001 --eccentricity 0.000000e+00 --semi-major-axis 3.5 --kick-magnitude-1 0 --kick-magnitude-2 0 
+--initial-mass-1 35.0 --initial-mass-2 31.0 --metallicity 0.001 --eccentricity 0.000000e+00 --semi-major-axis 3.5 --kick-magnitude-1 0 --kick-magnitude-2 0 
+

src/compasConfigDefault.yaml → examples/methods_paper_plots/detailed_evolution/example_bbh_compas_config.yaml

@@ -1,5 +1,5 @@
 ##~!!~## COMPAS option values
-##~!!~## File Created Wed Nov  1 11:22:29 2023 by COMPAS v02.40.00
+##~!!~## File Created Tue Oct 31 10:11:32 2023 by COMPAS v02.40.00
 ##~!!~##
 ##~!!~## The default COMPAS YAML file (``compasConfigDefault.yaml``), as distributed, has
 ##~!!~## all COMPAS option entries commented so that the COMPAS default value for the
@@ -10,7 +10,7 @@ booleanChoices:
 
     ### LOGISTICS
 #    --debug-to-file: False                                                # Default: False
-#    --detailed-output: False                                              # Default: False                                                                                                                                                              # WARNING! this creates a data heavy file
+     --detailed-output: True                                              # Default: False                                                                                                                                                              # WARNING! this creates a data heavy file
 #    --enable-warnings: False                                              # Default: False                                                                                                                                                              # option to enable/disable warning messages
 #    --errors-to-file: False                                               # Default: False
 #    --evolve-unbound-systems: True                                        # Default: True
@@ -47,6 +47,9 @@ booleanChoices:
 #    --common-envelope-lambda-nanjing-use-rejuvenated-mass: False          # Default: False
 #    --revised-energy-formalism-nandez-ivanova: False                      # Default: False
 
+    ### TIDES
+#    --enable-tides: False                                                 # Default: False
+
     ### SUPERNOVAE, KICKS AND REMNANTS
 #    --allow-non-stripped-ECSN: False                                      # Default: False
 #    --pair-instability-supernovae: True                                   # Default: True
@@ -96,7 +99,7 @@ numericalChoices:
 #    --rotational-frequency: 0.000000                                      # Default: 0.000000
 #    --rotational-frequency-1: 0.000000                                    # Default: 0.000000
 #    --rotational-frequency-2: 0.000000                                    # Default: 0.000000
-#    --wolf-rayet-multiplier: 1.000000                                     # Default: 1.000000
+#    --wolf-rayet-multiplier: 0.100000                                     # Default: 0.100000
 
     ### BINARY PROPERTIES
 #    --eccentricity: 0.000000                                              # Default: 0.000000                                                                                                                                                           # eccentricity for BSE
@@ -202,7 +205,7 @@ stringChoices:
 
     ### LOGISTICS
 #    --add-options-to-sysparms: 'GRID'                                     # Default: 'GRID'                        # Options: ['NEVER','GRID','ALWAYS']
-#    --grid: ''                                                            # Default: ''                                                                                                                                                                 # grid file name (e.g. 'mygrid.txt')
+     --grid: 'Grid_demo.txt'                                               # Default: ''                                                                                                                                                                 # grid file name (e.g. 'mygrid.txt')
 #    --mode: 'BSE'                                                         # Default: 'BSE'                         # Options: ['BSE','SSE']                                                                                                             # evolving single (SSE) or binary stars (BSE)
 #    --notes: { }                                                          # Default: { }
 #    --notes-hdrs: { }                                                     # Default: { }
@@ -213,11 +216,7 @@ stringChoices:
 #    --envelope-state-prescription: 'LEGACY'                               # Default: 'LEGACY'                      # Options: ['FIXED_TEMPERATURE','HURLEY','LEGACY']
 #    --initial-mass-function: 'KROUPA'                                     # Default: 'KROUPA'                      # Options: ['KROUPA','UNIFORM','POWERLAW','SALPETER']
 #    --luminous-blue-variable-prescription: 'HURLEY_ADD'                   # Default: 'HURLEY_ADD'                  # Options: ['BELCZYNSKI','HURLEY','HURLEY_ADD','NONE']
-#    --mass-loss-prescription: 'FLEXIBLE2023'                              # Default: 'FLEXIBLE2023'                # Options: ['FLEXIBLE2023','BELCZYNSKI2010','HURLEY','NONE']
-#    --OB-mass-loss: 'VINK2021'                                            # Default: 'VINK2021'                    # Options: ['KRTICKA2018','BJORKLUND2022','VINK2021','VINK2001','NONE']
-#    --RSG-mass-loss: 'DECIN2023'                                          # Default: 'DECIN2023'                   # Options: ['NJ90','KEE2021','YANG2023','DECIN2023','BEASOR2020','VINKSABHAHIT2023','NONE']
-#    --VMS-mass-loss: 'SABHAHIT2023'                                       # Default: 'SABHAHIT2023'                # Options: ['SABHAHIT2023','BESTENLEHNER2020','VINK2011','NONE']
-#    --WR-mass-loss: 'SANDERVINK2023'                                      # Default: 'SANDERVINK2023'              # Options: ['SHENAR2019','SANDERVINK2023','BELCZYNSKI2010']
+#    --mass-loss-prescription: 'VINK'                                      # Default: 'VINK'                        # Options: ['VINK','HURLEY','NONE']
 #    --metallicity-distribution: 'ZSOLAR'                                  # Default: 'ZSOLAR'                      # Options: ['LOGUNIFORM','ZSOLAR']
 #    --pulsational-pair-instability-prescription: 'MARCHANT'               # Default: 'MARCHANT'                    # Options: ['FARMER','MARCHANT','STARTRACK','COMPAS']
 

online-docs/pages/Getting started/dev-git-workflow.rst

@@ -15,7 +15,7 @@ Contents of this document
 `Day to Day Commands <#day-to-day-commands>`__
 
 
-`Lifetime of a Project <#lifetime-of-a-project>`__
+`Lifetime of a New Feature <#lifetime-of-a-new-feature>`__
 
 
 `COMPAS Git Workflow <#the-compas-git-workflow>`__
@@ -27,7 +27,7 @@ Contents of this document
 
 
 Introduction
-============
+------------
 
 Git & Github for COMPAS developers
 
@@ -117,7 +117,7 @@ which is in common use in industry.
 
 
 Getting Set Up
-==============
+--------------
 
 **Step-by-step directions for how to configure your local and remote git
 repositories**
@@ -215,6 +215,7 @@ homepage <https://compas.science/>`__ for an up-to-date list).
 
 
 Fork the main repo
+------------------
 
 
 As a COMPAS developer, you are highly encouraged to create your own
@@ -262,7 +263,7 @@ The ``<fork-nickname>`` is your choice, but should be informative, e.g
 
 
 Day to Day commands
-===================
+-------------------
 
 Basic commands for navigating local git
 
@@ -461,6 +462,7 @@ preferred text editor.
 
 
 Deleting branches
+-----------------
 
 
 You should become comfortable deleting branches, or else your repos
@@ -607,6 +609,7 @@ which will have an output that looks similar to:
 
 
 git pull
+--------
 
 
 If you have a branch which is "behind" the remote branch it is tracking
@@ -697,7 +700,7 @@ called the "upstream" branch) with:
 
 
 Lifetime of a New Feature
-=========================
+-------------------------
 
 New feature branches
 
@@ -808,7 +811,7 @@ before accepting it, so keep an eye on the pull request conversation.
 
 
 The COMPAS Git Workflow
-=======================
+-----------------------
 
 The above sections go over many of the available git commands that you
 might find useful.
@@ -868,7 +871,7 @@ comparisons of key plots from different papers.
 
 
 Terminology
-===========
+-----------
 
 -  **Commit**: A single commit records a collection of edits to one or
    more files, with an associated commit message.

online-docs/pages/User guide/Program options/program-options-list-defaults.rst

@@ -349,6 +349,10 @@ Default = 0.0
 Multiplication factor for Eddington accretion for NS & BH (i.e. > 1 is super-eddington and 0 is no accretion). |br|
 Default = 1.0
 
+**--enable-tides** |br|
+Enables tides. |br|
+Default = FALSE
+
 **--enable-warnings** |br|
 Display warning messages to stdout. |br|
 Default = FALSE
@@ -935,12 +939,6 @@ Default = 10
 
 :ref:`Back to Top <options-props-top>`
 
-**--OB-mass-loss** |br|
-Main sequence mass loss prescription. |br|
-Options: { NONE, VINK2001, VINK2021, BJORKLUND2022, KRTICKA2018 } |br|
-NONE turns off mass loss for main sequence stars. Also available are Vink (2001, previous default), Vink (2021), Bjorklund (2022), and Krticka (2018).   |br|
-Default = VINK2021
-
 **--orbital-period** |br|
 Initial orbital period for a binary star when evolving in BSE mode (days). |br|
 Used only if the semi-major axis is not specified via ``--semi-major-axis``. |br|
@@ -1107,12 +1105,6 @@ Options: { ZERO, HURLEY, VLTFLAMES } |br|
 ``ZERO`` sets all initial rotational velocities to 0, while ``HURLEY`` and ``VLTFLAMES`` sample them from the Hurley, Pols, Tout (2000) and Ramirez-Agudelo et al. (2013,2015), respectively |br|
 Default = ZERO
 
-**--RSG-mass-loss** |br|
-Red supergiant mass loss prescription. |br|
-Options: { NONE, VINKSABHAHIT2023, BEASOR2020, DECIN2023, YANG2023, KEE2021, NJ90 } |br|
-NONE turns off mass loss for giant (CHeB, FGB, AGB, TPAGB stellar types) stars below the RSG_MAXIMUM_TEMP. Also available are Vink and Sabhahit (2023), Beasor et al. (2020), Decin et al. (2023), Yang et al. (2023), Kee et. al (2021), and Nieuwenhuijzen and de Jager (1990, previous default).   |br|
-Default = DECIN2023
-
 .. _options-props-S:
 
 :ref:`Back to Top <options-props-top>`
@@ -1181,12 +1173,6 @@ Default = TRUE
 **--version [ -v ]** |br|
 Prints COMPAS version string.
 
-**--VMS-mass-loss** |br|
-Very massive main sequence mass loss prescription. |br|
-Options: { NONE, VINK2011, SABHAHIT2023, BESTENLEHNER2020 } |br|
-Applied above the VERY_MASSIVE_MINIMUM_MASS (100 Msol by default). NONE turns off mass loss. Also available are Vink (2011), Bestenlehner (2020), and Sabhahit (2023).   |br|
-Default = SABHAHIT2023
-
 .. _options-props-W:
 
 :ref:`Back to Top <options-props-top>`
@@ -1196,12 +1182,6 @@ Multiplicative constant for Wolf Rayet winds. Note that wind mass loss will also
 ``overall-wind-mass-loss-multiplier``. |br|
 Default = 1.0
 
-**--WR-mass-loss** |br|
-Wolf-Rayet mass loss prescription. |br|
-Options: { BELCZYNSKI2010, SANDERVINK2023, SHENAR2019 } |br|
-Selects between Belczynski (2010), Sander and Vink (2021 updated), and Shenar (2019).   |br|
-Default = SANDERVINK2023
-
 .. _options-props-X:
 .. _options-props-Y:
 
@@ -1259,8 +1239,7 @@ Go to :ref:`the top of this page <options-props-top>` for the full alphabetical
 
 --use-mass-loss, --check-photon-tiring-limit, --cool-wind-mass-loss-multiplier, --luminous-blue-variable-prescription, 
 --luminous-blue-variable-multiplier, --mass-loss-prescription, --overall-wind-mass-loss-multiplier, --wolf-rayet-multiplier, 
---expel-convective-envelope-above-luminosity-threshold, --luminosity-to-mass-threshold,
---OB-mass-loss, --RSG-mass-loss, --VMS-mass-loss, --WR-mass-loss
+--expel-convective-envelope-above-luminosity-threshold, --luminosity-to-mass-threshold
 
 --chemically-homogeneous-evolution
 
@@ -1281,7 +1260,7 @@ Go to :ref:`the top of this page <options-props-top>` for the full alphabetical
 --mass-transfer-rejuvenation-prescription, --mass-transfer-thermal-limit-accretor, --mass-transfer-thermal-limit-C, --retain-core-mass-during-caseA-mass-transfer, 
 --stellar-zeta-prescription, --zeta-adiabatic-arbitrary, --zeta-main-sequence, --zeta-radiative-giant-star 
 
---circulariseBinaryDuringMassTransfer, --angular-momentum-conservation-during-circularisation
+--circulariseBinaryDuringMassTransfer, --angular-momentum-conservation-during-circularisation, --enable-tides
 
 --envelope-state-prescription, --common-envelope-alpha, --common-envelope-alpha-thermal, --common-envelope-formalism,
 --common-envelope-lambda-prescription, --common-envelope-lambda, 

online-docs/pages/User guide/Running COMPAS/running-via-python.rst

@@ -6,7 +6,7 @@ specify the values of the program options.
 
 An example Python script is provided in the COMPAS suite on github: ``runSubmit.py``. Additionally, the default COMPAS options are specified on ``compasConfigDefault.yaml``. Users should copy the ``runSubmit.py`` and ``runSubmit.py`` scripts and modify the ``compasConfigDefault.yaml`` copy to match their experimental requirements. Refer to the :doc:`Getting started guide <../../Getting started/getting-started>` for more details.
 
-To run COMPAS via Python using the ``runSubmit.py`` script provided, set the shell environment variable ``COMPAS-ROOT-DIR``
+To run COMPAS via Python using the ``runSubmit.py`` script provided, set the shell environment variable ``COMPAS_ROOT_DIR``
 to the parent directory of the directory in which the COMPAS executable resides, then type `python /path-to-runSubmit/runSubmit.py`. 
 For example, for Ubuntu Linux, type::
 

online-docs/pages/whats-new.rst

@@ -6,6 +6,11 @@ Following is a brief list of important updates to the COMPAS code.  A complete r
 
 **LATEST RELEASE** |br|
 
+**02.41.00 Nov 02, 2023**
+
+* Added a naive tides implementation.
+* Added program option ``enable-tides`` to enable the tides implementation (default is ``false``).
+
 **02.40.00 Oct 20, 2023**
 
 * Added ``FLEXIBLE2023`` as a new default, and ``BELCZYNSKI2010`` as a replacement for the previous ``VINK`` mass loss prescription. The following new sub-wrappers are overridden when selecting ``BELCZYNSKI2010``:

py_tests/conftest.py

@@ -1,16 +1,15 @@
 import os
 from typing import Any, Dict
 
+import subprocess
 import h5py
 import pytest
 from compas_python_utils.cosmic_integration.binned_cosmic_integrator.bbh_population import \
     generate_mock_bbh_population_file
 
 HERE = os.path.dirname(__file__)
-DETAILED_EVOLUTION_PATH = os.path.join(
-    HERE, "../misc/examples/methods_paper_plots/detailed_evolution"
-)
-
+TEST_CONFIG_DIR = os.path.join(HERE, "test_data")
+TEST_CONFIG_FNAME = os.path.join(TEST_CONFIG_DIR, "fiducial_bbh_config.yaml")
 TEST_ARCHIVE_DIR = os.path.join(HERE, "test_artifacts")
 
 
@@ -21,16 +20,20 @@ def example_compas_output_path(clean=False):
     (This is a fixture so it can passed as a parameter to other tests)
     """
     compas_data_path = os.path.join(
-        DETAILED_EVOLUTION_PATH, "COMPAS_Output/COMPAS_Output.h5"
+        TEST_CONFIG_DIR, "COMPAS_Output/COMPAS_Output.h5"
     )
 
     if not os.path.exists(compas_data_path) or clean:  # Check if path exists
         curr_dir = os.getcwd()
-        os.chdir(DETAILED_EVOLUTION_PATH)
-        os.system("python runSubmitDemo.py")
+        os.chdir(TEST_CONFIG_DIR)
+        cmd = f"compas_run_submit {TEST_CONFIG_FNAME}"
+        # run the command in shell "compas_run_submit {TEST_CONFIG_FNAME}" with subprocess
+        subprocess.run(cmd, shell=True, check=True)
+
         os.chdir(curr_dir)
         print("Generated COMPAS test data")
 
+
     return compas_data_path
 
 

py_tests/test_data/README.md

@@ -1,8 +1,12 @@
 # Test Data
 
-This folder contains all the COMPAS test data generated manually by running:
+This folder contains COMPAS configs used for testing. 
+COMPAS is run from within the pytest environment and the output is cached for the remainder of the tests.
+
+The pytest runs the following command:
 ```bash
-bash generate_test_data.sh
+compas_run_submit fiducial_bbh_configs.yaml
 ```
 
-These files may need to be periodically updated if the COMPAS code changes.
+The pytest cache is _not_ cleared locally (but will be cleared on the CI server).
+Hence, this may need to be rerun locally if changes are made to COMPAS.