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kbe.pbe.BE.compute_energy_full is called, but never defined #35

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mcocdawc opened this issue Nov 27, 2024 · 0 comments
Open

kbe.pbe.BE.compute_energy_full is called, but never defined #35

mcocdawc opened this issue Nov 27, 2024 · 0 comments
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bug Something isn't working

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@mcocdawc
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kbe.pbe.BE.compute_energy_full is called, but never defined

the call is in kbe.pbe.BEoneshot and looks like this

        if not calc_frag_energy:
            self.compute_energy_full(approx_cumulant=True, return_rdm=False)

(The problem does not exist in molbe.)

@mcocdawc mcocdawc added the bug Something isn't working label Nov 27, 2024
mcocdawc added a commit that referenced this issue Dec 18, 2024
```
if not calc_frag_energy:
    self.compute_energy_full(approx_cumulant=True, return_rdm=False)
```

issue #35 is related
lweisburn added a commit that referenced this issue Jan 8, 2025
* Untangling eeval and frag_energy energy evaluation options

* small changes for frag_energy consistency

* start changing eeval and ereturn in parallel functions, making serial and parallel consistent

* put if __main__ guard to test

* use h5py contextmanager nearly everywhere

* changed mbe.StoreBE into attrs defined class

* ignore broken link to numpy.float64 in documentation

* fixed a bug from wrong close statement

* testsuite don't wait for analysis

* added types for molbe BE object

* fixed wrong close statements

* fixed scratch-dir for molbe-be

* added typing for molbe.BE.optimize

- this fixed a likely bug in optimize.
previously we had
    J0 = [[J0[-1, -1]]]
now it is
    J0 = [[J0[-1][-1]]]
since it is a list[list[float]]

* renamed _opt.py to opt.py

finished BEOPT attrs refactoring

* pass on solver_kwargs to be_func

* added types to be_func

* added delete multiple_files function

* use the new scratch dir in be_func

* added types to molbe.BE.optimize + call self.scratch_dir.cleanup

call self.scratch_dir.cleanup in both `optimize` and `oneshot`

* moved schmidt_decomposition to prevent circular import

makes much more sense like this

* added type hints to be_func_parallel

* fixed typo

* fixed several small errors in the code

* fixed be_func_parallel calls

* simplified be_func_parallel

* added types to run_solver

* use frag_scratch in be_func_parallel

* use frag_scratch in run_solver

* added typehints to kbe BE class

* simplified a few boolean expressions

* the tests should be working now

* ensure scratch cleanup for kbe

* removed call to self.compute_energy_full (related to #35)

* write nicer Pool statements

- used proper list comprehensions
- use contextmanager for Pool

* fixed naming error

* use more explicit way of freeing memory

(it is still ugly... )

* refactored expression

* use Tuple[int, ...] for numpy shapes :-(

* refactored WorkDir to use atexit.register for cleanup

* added better docstring for config

* require static analysis to be ok for running test suite

* renamed DMRG specific solver kwargs to its proper name

* better naming for DMRG stuff

* added types to block2 DMRG function

* refactor some DMRG arguments

* change behaviour of scratch contextmanager

now it is ensured, that files are deleted even after an exception when
using it as context manager and cleanup_at_end=True

* fixed the deadlock in the test requirements

* added new scratch dir also to ube

* avoid list[list[float]]; use consistently array instead

* Update energy keywords and logic in restricted BE, serial and parallel, oneshot and parallel.

Update and rearrange some documentation for the keywords

TODO: add non-cumulant energy, update unrestricted BE

* Update kbe/pbe and kbe/misc for consistency

* Fix kbe/pbe and kbe/misc to raise error for non-cumulant

* Add non-cumulant energy option for molecular code

* remove mypy attempt from get_energy_frag for now

* fix be2puffin call of oneshot and update ube oneshot default

* Update get_frag_energy function to work for periodic calculations

* Remove double del line

* remove redundant frag_energy keyword

* Update src/quemb/molbe/helper.py, eri_file to be optional

Co-authored-by: Minsik <mscho527@gmail.com>

* Update src/quemb/molbe/mbe.py: ebe_tot readability

Co-authored-by: Minsik <mscho527@gmail.com>

* move use_cumulant to optimize and oneshot, not BE

---------

Co-authored-by: Leah Weisburn <leahw@dhcp-10-29-137-188.dyn.mit.edu>
Co-authored-by: Oskar Weser <oskar.weser@gmail.com>
Co-authored-by: Minsik <mscho527@gmail.com>
ShaunWeatherly added a commit that referenced this issue Jan 14, 2025
* Automatic generation of API documentation (#70)

- Create API reference automatically for all public members of quemb
Before this change one had to manually create rst files and manage them. Now they are recursively created automatically.
The layout of the documentation matches the layout of the namespace

- This change automatically ensures that all (public) docstrings are actually parsed by Sphinx and it is ensured that they are properly written. Had to fix some docstrings

- Type-hinting is now picked up by sphinx.

* H5py use contextmanager (#73)

* put if __main__ guard to test

* use h5py contextmanager nearly everywhere

* fixed a bug from wrong close statement

* Fix parallelization and add parallel tests (#75)

* fix _opt to work with be_parallel

* modify oneshot to work with be_func_parallel

* modify two tests to use nproc > 1

* fix ruff errors

* modify octane test

* Remove CCSD reference from octane test

* Final scratch dir attempt (#74)

# Mayor changes

This PR unifies the use of the ScratchDir. It is now guaranteed, that files are cleaned up if the calculation exits with no error. (If the user passes `WorkDir(cleanup_at_end=False)` the files are retained).
A `WorkDir` is passed from the top of the call stack to the bottom. This allows the user to change the WorkDir if necessary. (Fixes #19)

Got rid of some special cased keyword arguments for DMRG and moved them into an explicit `DMRG_solver_kwargs`.
This way we can catch arguments that are supplied and do nothing.
It is probably a good idea to do the same for SHCI specific keywords @lweisburn .
It is probably a good idea to get rid of the dictionary altogether and to replace it with a dataclass.

# Minor changes

If the `__init__` of a class was just populating the attributes, then I replaced the class definition with `attrs.define`.

On the way I did a lot of type hinting. It is probably a good idea to double check my assumptions in review.

Additionally, I did some refactoring, where explicit open-close pairs where replaced with context managers.
The same was true for multiprocessing Pools.

Here and there I encountered constructs that could be simplified a lot
```python3
veffs = []
[veffs.append(result.get()) for result in results]
# becomes
veffs = [result.get() for result in results]
```
or
```python3
self.frozen_core = False if not fobj.frozen_core else True
# becomes
self.frozen_core = fobj.frozen_core
```
or
```python3
rdm_return = False
if relax_density:
    rdm_return = True
# becomes
rdm_return = relax_density
```

* Update fragment energies (#79)

* Untangling eeval and frag_energy energy evaluation options

* small changes for frag_energy consistency

* start changing eeval and ereturn in parallel functions, making serial and parallel consistent

* put if __main__ guard to test

* use h5py contextmanager nearly everywhere

* changed mbe.StoreBE into attrs defined class

* ignore broken link to numpy.float64 in documentation

* fixed a bug from wrong close statement

* testsuite don't wait for analysis

* added types for molbe BE object

* fixed wrong close statements

* fixed scratch-dir for molbe-be

* added typing for molbe.BE.optimize

- this fixed a likely bug in optimize.
previously we had
    J0 = [[J0[-1, -1]]]
now it is
    J0 = [[J0[-1][-1]]]
since it is a list[list[float]]

* renamed _opt.py to opt.py

finished BEOPT attrs refactoring

* pass on solver_kwargs to be_func

* added types to be_func

* added delete multiple_files function

* use the new scratch dir in be_func

* added types to molbe.BE.optimize + call self.scratch_dir.cleanup

call self.scratch_dir.cleanup in both `optimize` and `oneshot`

* moved schmidt_decomposition to prevent circular import

makes much more sense like this

* added type hints to be_func_parallel

* fixed typo

* fixed several small errors in the code

* fixed be_func_parallel calls

* simplified be_func_parallel

* added types to run_solver

* use frag_scratch in be_func_parallel

* use frag_scratch in run_solver

* added typehints to kbe BE class

* simplified a few boolean expressions

* the tests should be working now

* ensure scratch cleanup for kbe

* removed call to self.compute_energy_full (related to #35)

* write nicer Pool statements

- used proper list comprehensions
- use contextmanager for Pool

* fixed naming error

* use more explicit way of freeing memory

(it is still ugly... )

* refactored expression

* use Tuple[int, ...] for numpy shapes :-(

* refactored WorkDir to use atexit.register for cleanup

* added better docstring for config

* require static analysis to be ok for running test suite

* renamed DMRG specific solver kwargs to its proper name

* better naming for DMRG stuff

* added types to block2 DMRG function

* refactor some DMRG arguments

* change behaviour of scratch contextmanager

now it is ensured, that files are deleted even after an exception when
using it as context manager and cleanup_at_end=True

* fixed the deadlock in the test requirements

* added new scratch dir also to ube

* avoid list[list[float]]; use consistently array instead

* Update energy keywords and logic in restricted BE, serial and parallel, oneshot and parallel.

Update and rearrange some documentation for the keywords

TODO: add non-cumulant energy, update unrestricted BE

* Update kbe/pbe and kbe/misc for consistency

* Fix kbe/pbe and kbe/misc to raise error for non-cumulant

* Add non-cumulant energy option for molecular code

* remove mypy attempt from get_energy_frag for now

* fix be2puffin call of oneshot and update ube oneshot default

* Update get_frag_energy function to work for periodic calculations

* Remove double del line

* remove redundant frag_energy keyword

* Update src/quemb/molbe/helper.py, eri_file to be optional

Co-authored-by: Minsik <mscho527@gmail.com>

* Update src/quemb/molbe/mbe.py: ebe_tot readability

Co-authored-by: Minsik <mscho527@gmail.com>

* move use_cumulant to optimize and oneshot, not BE

---------

Co-authored-by: Leah Weisburn <leahw@dhcp-10-29-137-188.dyn.mit.edu>
Co-authored-by: Oskar Weser <oskar.weser@gmail.com>
Co-authored-by: Minsik <mscho527@gmail.com>

* Adding back veff0 for molecular code, removing the now-unnecessary hf_veff from be_func (#81)

* More type annotations + simpler boolean expressions (#76)

Simplifications in the code

- A couple more type annotations

- simpler boolean expressions

- removed keyword arguments if they are always true in the code

* Dataclass for solver kwargs (#77)

- Introduced a dataclass for solver kwargs. This is makes it much more explicit what arguments are supported by DMRG and SHCI

- Could simplify the interface of BE by removing a couple of arguments

* Simplify init (#82)

- moved the saving operation out of the __init__ method.

- don't redundantly store information from `fobj`, but use `fobj` itself directly.

* Make numpy shorter (#83)

- replacing `np.dot` with `@`
- replacing the `numpy.something` calls with `from numpy import something` if functions appear several times
- replacing the `numpy.something` call with `np.something` if a function appears rarely

---------

Co-authored-by: Oskar Weser <oskar.weser@gmail.com>
Co-authored-by: Leah Weisburn <51750430+lweisburn@users.noreply.github.com>
Co-authored-by: Leah Weisburn <leahw@dhcp-10-29-137-188.dyn.mit.edu>
Co-authored-by: Minsik <mscho527@gmail.com>
ShaunWeatherly added a commit that referenced this issue Jan 22, 2025
* Added default dmrg `settings.py` to `external`, modified workflow,
+ initial testing.

* `ruff` fixes in `dmrgscf_settings`

* `ruff` fixes again.

* Merging and bringing up to date.

* Merge from Main (#87)

* Automatic generation of API documentation (#70)

- Create API reference automatically for all public members of quemb
Before this change one had to manually create rst files and manage them. Now they are recursively created automatically.
The layout of the documentation matches the layout of the namespace

- This change automatically ensures that all (public) docstrings are actually parsed by Sphinx and it is ensured that they are properly written. Had to fix some docstrings

- Type-hinting is now picked up by sphinx.

* H5py use contextmanager (#73)

* put if __main__ guard to test

* use h5py contextmanager nearly everywhere

* fixed a bug from wrong close statement

* Fix parallelization and add parallel tests (#75)

* fix _opt to work with be_parallel

* modify oneshot to work with be_func_parallel

* modify two tests to use nproc > 1

* fix ruff errors

* modify octane test

* Remove CCSD reference from octane test

* Final scratch dir attempt (#74)

# Mayor changes

This PR unifies the use of the ScratchDir. It is now guaranteed, that files are cleaned up if the calculation exits with no error. (If the user passes `WorkDir(cleanup_at_end=False)` the files are retained).
A `WorkDir` is passed from the top of the call stack to the bottom. This allows the user to change the WorkDir if necessary. (Fixes #19)

Got rid of some special cased keyword arguments for DMRG and moved them into an explicit `DMRG_solver_kwargs`.
This way we can catch arguments that are supplied and do nothing.
It is probably a good idea to do the same for SHCI specific keywords @lweisburn .
It is probably a good idea to get rid of the dictionary altogether and to replace it with a dataclass.

# Minor changes

If the `__init__` of a class was just populating the attributes, then I replaced the class definition with `attrs.define`.

On the way I did a lot of type hinting. It is probably a good idea to double check my assumptions in review.

Additionally, I did some refactoring, where explicit open-close pairs where replaced with context managers.
The same was true for multiprocessing Pools.

Here and there I encountered constructs that could be simplified a lot
```python3
veffs = []
[veffs.append(result.get()) for result in results]
# becomes
veffs = [result.get() for result in results]
```
or
```python3
self.frozen_core = False if not fobj.frozen_core else True
# becomes
self.frozen_core = fobj.frozen_core
```
or
```python3
rdm_return = False
if relax_density:
    rdm_return = True
# becomes
rdm_return = relax_density
```

* Update fragment energies (#79)

* Untangling eeval and frag_energy energy evaluation options

* small changes for frag_energy consistency

* start changing eeval and ereturn in parallel functions, making serial and parallel consistent

* put if __main__ guard to test

* use h5py contextmanager nearly everywhere

* changed mbe.StoreBE into attrs defined class

* ignore broken link to numpy.float64 in documentation

* fixed a bug from wrong close statement

* testsuite don't wait for analysis

* added types for molbe BE object

* fixed wrong close statements

* fixed scratch-dir for molbe-be

* added typing for molbe.BE.optimize

- this fixed a likely bug in optimize.
previously we had
    J0 = [[J0[-1, -1]]]
now it is
    J0 = [[J0[-1][-1]]]
since it is a list[list[float]]

* renamed _opt.py to opt.py

finished BEOPT attrs refactoring

* pass on solver_kwargs to be_func

* added types to be_func

* added delete multiple_files function

* use the new scratch dir in be_func

* added types to molbe.BE.optimize + call self.scratch_dir.cleanup

call self.scratch_dir.cleanup in both `optimize` and `oneshot`

* moved schmidt_decomposition to prevent circular import

makes much more sense like this

* added type hints to be_func_parallel

* fixed typo

* fixed several small errors in the code

* fixed be_func_parallel calls

* simplified be_func_parallel

* added types to run_solver

* use frag_scratch in be_func_parallel

* use frag_scratch in run_solver

* added typehints to kbe BE class

* simplified a few boolean expressions

* the tests should be working now

* ensure scratch cleanup for kbe

* removed call to self.compute_energy_full (related to #35)

* write nicer Pool statements

- used proper list comprehensions
- use contextmanager for Pool

* fixed naming error

* use more explicit way of freeing memory

(it is still ugly... )

* refactored expression

* use Tuple[int, ...] for numpy shapes :-(

* refactored WorkDir to use atexit.register for cleanup

* added better docstring for config

* require static analysis to be ok for running test suite

* renamed DMRG specific solver kwargs to its proper name

* better naming for DMRG stuff

* added types to block2 DMRG function

* refactor some DMRG arguments

* change behaviour of scratch contextmanager

now it is ensured, that files are deleted even after an exception when
using it as context manager and cleanup_at_end=True

* fixed the deadlock in the test requirements

* added new scratch dir also to ube

* avoid list[list[float]]; use consistently array instead

* Update energy keywords and logic in restricted BE, serial and parallel, oneshot and parallel.

Update and rearrange some documentation for the keywords

TODO: add non-cumulant energy, update unrestricted BE

* Update kbe/pbe and kbe/misc for consistency

* Fix kbe/pbe and kbe/misc to raise error for non-cumulant

* Add non-cumulant energy option for molecular code

* remove mypy attempt from get_energy_frag for now

* fix be2puffin call of oneshot and update ube oneshot default

* Update get_frag_energy function to work for periodic calculations

* Remove double del line

* remove redundant frag_energy keyword

* Update src/quemb/molbe/helper.py, eri_file to be optional

Co-authored-by: Minsik <mscho527@gmail.com>

* Update src/quemb/molbe/mbe.py: ebe_tot readability

Co-authored-by: Minsik <mscho527@gmail.com>

* move use_cumulant to optimize and oneshot, not BE

---------

Co-authored-by: Leah Weisburn <leahw@dhcp-10-29-137-188.dyn.mit.edu>
Co-authored-by: Oskar Weser <oskar.weser@gmail.com>
Co-authored-by: Minsik <mscho527@gmail.com>

* Adding back veff0 for molecular code, removing the now-unnecessary hf_veff from be_func (#81)

* More type annotations + simpler boolean expressions (#76)

Simplifications in the code

- A couple more type annotations

- simpler boolean expressions

- removed keyword arguments if they are always true in the code

* Dataclass for solver kwargs (#77)

- Introduced a dataclass for solver kwargs. This is makes it much more explicit what arguments are supported by DMRG and SHCI

- Could simplify the interface of BE by removing a couple of arguments

* Simplify init (#82)

- moved the saving operation out of the __init__ method.

- don't redundantly store information from `fobj`, but use `fobj` itself directly.

* Make numpy shorter (#83)

- replacing `np.dot` with `@`
- replacing the `numpy.something` calls with `from numpy import something` if functions appear several times
- replacing the `numpy.something` call with `np.something` if a function appears rarely

---------

Co-authored-by: Oskar Weser <oskar.weser@gmail.com>
Co-authored-by: Leah Weisburn <51750430+lweisburn@users.noreply.github.com>
Co-authored-by: Leah Weisburn <leahw@dhcp-10-29-137-188.dyn.mit.edu>
Co-authored-by: Minsik <mscho527@gmail.com>

* Fixes for scratch management in `solver` and `helper` modules.

* Added `DMRG_ArgsUser` to `TestBE_DMRG`

* Fixed incorrect definition of `ebe_tot` as `rets[0]`, which is only the
correlation energy.

* Make `helper.delete_multiple_files` recursive.

* Make `use_cumulant=True` by default in `solver_block2`.

* Modify `molecular_DMRG_test`

* Redundant fixes for `lo` module.

* Sort imports in `solver`

* Remove extra blank lines.

* Explicit versioning for block2 in `yaml`

* Add `block2` to `test_requirements`

* Reset `frag_type` in `molbe_dmrg...` example script.

* Testing `max_mem`

* Test `LD_PRELOAD`

* try only one of the block2

* cleaned up test environment

* don't wait for analysis

* Test `conda`

* Test `nomkl` via `pip`

* Test `nomkl` via `pip`

* tests `nomkl`

* Tests `nomkl`

* Tests `nomkl`

* Tests `nomkl`

* Test block2 versioning.

* Test block2 versioning.

* Update cache keys.

* Update cache keys.

* Update cache keys

* Update cache keys

* Remove block2 versioning

* Test explicit cache save/restore.

* Fully explicit save/restore for cache

* Block2 `no-binary`

* Test `no-binary`

* Typo

* Explicit block2 versioning

* Move to `test_requirements`

* Edit block2 versioning.

* Force latest `mkl`

* test latest `mkl`

* Separate caching for `block2`

* Test caching

* Test caching

* Fine tune caching

* Further fine-tune caching

* Back to block2 versioning

* Formatting and `ompnum` passing.

* Install quemb in workflows.

* resolve `molecular_DMRG_test` scratch

* Update example script

* Update .gitignore

* update .gitignore

* Enable all unittests

---------

Co-authored-by: Oskar Weser <oskar.weser@gmail.com>
Co-authored-by: Leah Weisburn <51750430+lweisburn@users.noreply.github.com>
Co-authored-by: Leah Weisburn <leahw@dhcp-10-29-137-188.dyn.mit.edu>
Co-authored-by: Minsik <mscho527@gmail.com>
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