Dynam units #746

nrnhines · 2020-09-28T17:17:12Z

Closes #599
Closes #324
Closes #519
Linked to neuronsimulator/progref-py#30

Wip: framework only. See comment in src/modlunit/units.c

If variable does not exist or is not 0 or 1, then _nrnunit_use_legacy_ is left at its default value.

pramodk · 2020-10-04T20:27:31Z

@nrnhines : is this ready for review or still any work is pending?

nrnhines · 2020-10-04T22:45:23Z

is this ready for review

Getting very close. Just want to consult with @adamjhn a bit about whether there is a place in rxd that is called by finitialize so it can test whether h.nrnunit_use_legacy() has changed and if so, update things that depended on NA (avogadro's number).

… functions. (#753) * Stop caching constants in rxd and moved calls to constants.NA into functions. This avoids storing constants on import which will be inconsistent if you then switch to using the legacy values. * Check for changes to nrnunit_use_legacy and reinitialize potentially relevant parts of the rxd model.

This reverts commit ec78ca0.

nrnhines · 2020-10-06T23:22:27Z

@pramodk @alexsavulescu This is ready for review. Note: BBP models may need export NRNUNIT_USE_LEGACY=1 to retain quantitative identity with older versions of NEURON and current versions of CoreNEURON

LegacyFR no longer a configure option.

alexsavulescu

LGTM.
Regarding NRN_ENABLE_LEGACY_FR, wouldn't it be more convenient to have it OFF by default?

Modern constants updated to codata2018 values. The units test wasn't activated since it did not begin with 'test_' h.Avogadro_constant available from hoc.

nrnhines · 2020-10-10T00:18:51Z

@ramcdougal @adamjhn To aid in single sourcing the definition of modern physical constants, I went ahead with your original suggestion and introduced h.Avogadro_constant which returns the modern or legacy value (as used in your constants.py for NA). In some ways this obviates constants.py and the change from NA to NA() (since you can recalculate NA = h.Avogadro_constant and others that depend on that whenever you have determined that h.nrnunit_use_legacy() has changed). I'm happy to leave things as they are but leave it up to you to decide whether to simplify your changes relative to this pull request. I should have said "almost single sourcing" as the modern units are also defined in share/lib/nrnunits.lib.in as well as src/oc/nrnunits_modern.h

pramodk · 2020-10-15T21:08:43Z

test/pynrn/test_units.py

+
+def switch_units(legacy):
+  try:
+    h.nrnunit_use_legacy(legacy)


@nrnhines : is this documented somewhere in user docuemtnaiton now?

Yes. https://neuronsimulator.github.io/nrn/py_doc/simctrl/programmatic.html#nrnunit_use_legacy

nrnhines added 5 commits September 27, 2020 09:35

Hoc function nrnunit_use_legacy(0or1) specifies modern or legacy units.

7a18eb7

Wip: framework only. See comment in src/modlunit/units.c

Representation of dynamaic units in translated mod file.

aaf1e07

if NRN_DYNAMIC_UNITS the file used is the raw nrnunits.lib.in

1f8a68a

Make sure .c from .mod depends on the nocmodl sources.

b8774d8

Test legacy units match old version when h.nrnunit_use_legacy(1)

41fc929

nrnhines added this to the Release v8.0a milestone Sep 28, 2020

nrnhines requested review from pramodk and ramcdougal September 28, 2020 17:17

nrnhines added 6 commits September 28, 2020 13:18

Merge branch 'master' into dynam-units

5e23c48

Fix a few, often benign, code mistakes.

7c2c87a

autotools install nrnunits.lib.in

75e44e3

Left out the dynamic handling of creation of new units.

43a6e08

Must copy nrnunits.lib.in to same place as nrnunit.lib

9cf091b

autotools also needs to copy to builddir/share/lib/nrnunits.lib.in

96ea419

nrnhines marked this pull request as draft September 29, 2020 00:50

nrnhines added 4 commits September 29, 2020 10:44

Hoc interpreter dynamic units for R, FARADAY, nernst(), and ghk().

27b82bd

declaration of _nrnunit_use_legacy_ where everyone can find it.

579efb0

constants.py dynamic units for NA() (changed to function).

7d364e7

not all contants.NA converted to function.

79fe10d

nrnhines marked this pull request as ready for review October 1, 2020 23:16

nrnhines added 3 commits October 1, 2020 19:17

Merge branch 'master' into dynam-units

b7933e7

Temporarily turn on _nrnunit_use_legacy_ so rxd tests work.

ec78ca0

NRNUNIT_USE_LEGACY environment variable can be set to 0 or 1

9ae36fe

If variable does not exist or is not 0 or 1, then _nrnunit_use_legacy_ is left at its default value.

pramodk requested a review from alexsavulescu October 4, 2020 20:27

adamjhn and others added 3 commits October 6, 2020 16:04

Merge branch 'master' into dynam-units

974b1ba

Revert "Temporarily turn on _nrnunit_use_legacy_ so rxd tests work."

979ad95

This reverts commit ec78ca0.

NRN_ENABLE_LEGACY_FR no longer a cmake option.

b82f9e9

LegacyFR no longer a configure option.

alexsavulescu reviewed Oct 7, 2020

View reviewed changes

nrnhines added 3 commits October 7, 2020 14:34

Update options.rst

8612389

Single source definition of modern constants.

d4ce883

Modern constants updated to codata2018 values. The units test wasn't activated since it did not begin with 'test_' h.Avogadro_constant available from hoc.

Merge branch 'master' into dynam-units

1533e4d

link to updated pydoc

4690b49

nrnhines mentioned this pull request Oct 12, 2020

dynamic units documentation neuronsimulator/progref-py#30

Merged

nrnhines added 2 commits October 15, 2020 08:25

Merge branch 'master' into dynam-units

7419458

update to current master for py_doc

fb42355

nrnhines merged commit 6aff783 into master Oct 15, 2020

nrnhines deleted the dynam-units branch October 15, 2020 14:15

pramodk reviewed Oct 15, 2020

View reviewed changes

nrnhines mentioned this pull request Oct 25, 2020

modlunit units.c space not allocated. #792

Merged

alexsavulescu mentioned this pull request Dec 8, 2020

build fixes in master that should get cherry-picked into release/7.8.1 #859

Closed

alexsavulescu mentioned this pull request Apr 26, 2021

Create Release Notes for 8.0 releases #1211

Closed

cjayb mentioned this pull request May 5, 2021

[MRG] FIX tests for NEURON v8 jonescompneurolab/hnn-core#324

Merged

olupton mentioned this pull request Mar 22, 2022

Compile NEURON mechanisms as C++ #1597

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olupton added a commit that referenced this pull request Dec 7, 2022

Use hpc/gitlab-pipelines helpers. (#746)

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Dynam units #746

Dynam units #746

nrnhines commented Sep 28, 2020 •

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Dynam units #746

Dynam units #746

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