running Madness with QCengine #242

ahurta92 · 2020-04-28T03:06:15Z

Description

This PR creates a new madness directory under programs. The files are the first iterations to setting up madness in qcng. It follows a very similar structure to that of nwchem.

Changelog description

This is the first iteration of setting up qcng to run madness calculations.

Status

Code base linted
Ready to go

Adrian dipole

loriab · 2020-04-30T01:37:39Z

qcengine/programs/madness/runner.py

+    _defaults = {
+        "name": "Madness",
+        "scratch": True,
+        "thread_safe": True,


Sure about this? I can believe it of madness, but thread safety is uncommon among non-trivial programs.

loriab · 2020-04-30T01:37:58Z

qcengine/programs/base.py

@@ -101,6 +102,7 @@ def list_available_programs() -> Set[str]:
 register_program(GAMESSHarness())
 register_program(MolproHarness())
 register_program(NWChemHarness())
+register_program(MadnessHarness())


alphabetize

loriab · 2020-04-30T01:41:07Z

qcengine/programs/madness/runner.py

+
+       """
+        qc = which(
+            "nwchem",


qcengine/programs/madness/runner.py

loriab · 2020-04-30T01:44:14Z

qcengine/programs/madness/runner.py

+
+        # Log the job settings (LORI)  Not sure if i need this
+        logger.debug("JOB_OPTS")
+        logger.debug(pp.pformat(opts))


logging is wild west at this point

loriab · 2020-04-30T01:47:27Z

qcengine/programs/madness/runner.py

+    def execute(
+        self, inputs: Dict[str, Any], *, extra_outfiles=None, extra_commands=None, scratch_name=None, timeout=None
+    ) -> Tuple[bool, Dict]:
+        success, dexe = execute(inputs["command"], inputs["infiles"],)


you'll want scratch_directory=inputs["scratch_directory"], in the execute cmd so that it's user configurable.

loriab · 2020-04-30T01:54:04Z

qcengine/programs/nwchem/harvester.py

+        + r".*\s+.*\s+"
+        + r"ZZ\s+([+-]?\d+[.]\d+)\s+"
+        + r".*\s+.*\s+"
+        + r"XY\s+([+-]?\d+[.]\d+)\s+"


if these are floats, the NUMBER regex def can simplify. also, we're going with the full (redundant) 3x3 quadrupole, rather than 6-element.

loriab · 2020-04-30T01:56:22Z

qcengine/programs/tests/test_standard_suite_hf.py

+    assert "provenance" in res
+    assert res["success"] is True
+
+    # k=7


shouldn't the k=7 be in keywords somewhere? does madness always use k cutoff rather than basis set or just certain methods?

loriab · 2020-04-30T02:09:42Z

qcengine/programs/madness/harvester.py

+    # 2)Calculation converged
+    else:
+        OPTIONS=[r'kinetic',r'nonlocal psp',r'nuclear attraction',r'coulomb',r'PCM',r'exchange-correlation',r'nuclear-repulsion',r'total']
+        PSIVAR=['KINETIC ENERGY','NONLOCAL PSP','NUCLEAR ATTRACTION ENERGY','COULOMB','PCM','EXCHANGE-CORRELATION','NUCLEAR REPULSION ENERGY','TOTAL SCF ENERGY']


maybe collect into AtomicResultProperties directly, since those names will get validated. these aren't "official" psivars/qcvars (but the code that checks names isn't in qcengine).

Update the MADNESS branch

lgtm-com · 2022-06-24T18:36:27Z

This pull request introduces 14 alerts when merging 5e5c8c5 into 113d1e8 - view on LGTM.com

new alerts:

14 for Unused local variable

lgtm-com · 2022-06-27T22:32:21Z

This pull request introduces 14 alerts when merging 68a9193 into dd5eec6 - view on LGTM.com

new alerts:

14 for Unused local variable

lgtm-com · 2022-06-28T17:49:57Z

This pull request introduces 14 alerts when merging 4c74677 into dd5eec6 - view on LGTM.com

new alerts:

14 for Unused local variable

lgtm-com · 2022-06-28T19:50:47Z

This pull request introduces 14 alerts when merging 3feaf7e into dd5eec6 - view on LGTM.com

new alerts:

14 for Unused local variable

lgtm-com · 2022-06-28T20:42:57Z

This pull request introduces 14 alerts when merging 839fb03 into dd5eec6 - view on LGTM.com

new alerts:

14 for Unused local variable

lgtm-com · 2022-06-29T15:21:30Z

This pull request introduces 14 alerts when merging cc192ef into dd5eec6 - view on LGTM.com

new alerts:

14 for Unused local variable

github-advanced-security

CodeQL found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.

qcengine/programs/madness/keywords.py

+    # if keyword.upper() == "MEMORY":
+    #    return keyword.lower(), f"{val} byte"


qcengine/programs/madness/harvester.py

+    """
+
+    # Loop over all steps
+    pass_psivar = []


qcengine/programs/madness/harvester.py

+
+    # Loop over all steps
+    pass_psivar = []
+    pass_coord = []


qcengine/programs/madness/harvester.py

+    # Loop over all steps
+    pass_psivar = []
+    pass_coord = []
+    pass_grad = []


qcengine/programs/madness/harvester.py

+    pass_coord = []
+    pass_grad = []
+    # Write now we split at Converge
+    counter = 1


qcengine/programs/madness/runner.py

+        if config.use_mpiexec:
+            which_prog = create_mpi_invocation(which_prog, config)
+        else:
+            command = [which_prog]


qcengine/programs/madness/runner.py

+
+        # Location resolution order config.scratch_dir, /tmp
+        parent = config.scratch_directory
+        scratch_messy = config.scratch_messy


qcengine/programs/madness/runner.py

+        parent = config.scratch_directory
+        scratch_messy = config.scratch_messy
+
+        error_message = None


qcengine/programs/madness/runner.py

+        scratch_messy = config.scratch_messy
+
+        error_message = None
+        compute_success = False


qcengine/programs/madness/runner.py

+
+        output_data = {}
+
+        driver = input_model.driver


qcengine/programs/madness/runner.py

+
+import numpy as np
+
+import qcelemental as qcel


qcengine/programs/madness/runner.py

+import numpy as np
+
+import qcelemental as qcel
+from qcelemental.models import AtomicResult, Provenance, AtomicInput


qcengine/programs/madness/runner.py

+from qcelemental.util import safe_version, which
+from qcengine.config import TaskConfig, get_config
+from qcengine.exceptions import UnknownError
+from qcengine.programs.mrchem import extract_properties


qcengine/programs/madness/runner.py

+from qcengine.config import TaskConfig, get_config
+from qcengine.exceptions import UnknownError
+from qcengine.programs.mrchem import extract_properties
+from .harvester import extract_formatted_properties, tensor_to_numpy


qcengine/programs/madness/runner.py

+                if run_type == "gradient":
+                    opts["dft__derivatives"] = True
+                elif run_type == "hessian":
+                    Pass


ahurta92 added 21 commits January 30, 2020 14:05

Merge pull request #6 from ahurta92/adrian-Dipole

8e34efc

Adrian dipole

Formating and added preceding 0

00de251

Merge branch 'master' of https://github.com/ahurta92/QCEngine

e5f3c63

Merge remote-tracking branch 'upstream/master'

ab8ec4c

add madness dir

f59dbc9

init madness dir

f368814

changin base and test to add madness

8d7ac78

Add madnessHarness to qca

eb0bc38

first attempt at get_version

e695d7d

Got a version of get_version that may work

fb3570a

simple build_input

7d6a24a

simple execuate function

b83169e

add madness pytest dft w/ xc hf

3a00543

updating

61cfa4a

got variables for scf calculation

4a05965

add gopts method to germinate

82352ff

added h20MAD for debuggin I think I can get rid of this

18b721a

pytest passed madness with h20()

43ec24a

split output by Converged! STILL Need to read format stuff

0e7668c

wrote compute, fix mol.keywords, wrote parse_output

98e0f4c

make format

70b0c15

loriab reviewed Apr 30, 2020

View reviewed changes

ahurta92 added 8 commits May 4, 2020 11:38

alphabetize

61bbf8e

which madness and use helium for command

2c28fb6

add scratch_directory to input for execute

b9d24a2

the quadrupole work should have been in a different branch

b1b05fc

added k=7 to keywords of test. k=7 is a default but its okay to define

2e6c2fc

limit to collecting qc vars in results.py

7c4f2d8

return scf_exchange_correlation

0312265

Add none

4eb4a75

ahurta92 added 3 commits June 24, 2022 12:13

Merge branch 'MolSSI:master' into master

4e6e977

formatting

ea814e5

Merge pull request #9 from ahurta92/master

5e5c8c5

Update the MADNESS branch

fix the geometry input for get_version function

68a9193

remove reading scf_info.json

4c74677

first attempt at saving calc_info.json into "native_files"

3feaf7e

ahurta92 added 2 commits June 28, 2022 16:30

save calc_info.json in results.extras[outfiles][calcinfo.json]

2a70856

remove native_files line

839fb03

Merge remote-tracking branch 'upstream/master' into MADNESS

cc192ef

ahurta92 added 5 commits July 13, 2022 16:54

save calc_info json as dictionary into extras

54b09b4

black

3db2391

save calc json and input in native files

c04a005

Merge remote-tracking branch 'upstream/master'

b1b23b0

Merge

170d422

github-advanced-security bot found potential problems Feb 29, 2024

View reviewed changes

ahurta92 added 3 commits March 6, 2024 15:59

typo

cc86262

MADNESS runs

48bffb7

Ran black....was this a mistake?

d14841b

github-advanced-security bot found potential problems Mar 7, 2024

View reviewed changes

ahurta92 added 2 commits March 27, 2024 10:46

Starting new implementation for multiple executables

a1c1b96

A running implementation that can run both moldft and molresponse

fd9fb82

github-advanced-security bot found potential problems Apr 8, 2024

View reviewed changes

ahurta92 added 2 commits April 8, 2024 17:05

format

3de261b

Add some test lines

cbe29d9

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running Madness with QCengine #242

running Madness with QCengine #242

ahurta92 commented Apr 28, 2020

loriab Apr 30, 2020

loriab Apr 30, 2020

loriab Apr 30, 2020

loriab Apr 30, 2020

loriab Apr 30, 2020

loriab Apr 30, 2020

loriab Apr 30, 2020

loriab Apr 30, 2020

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		# if keyword.upper() == "MEMORY":
		# return keyword.lower(), f"{val} byte"

running Madness with QCengine #242

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running Madness with QCengine #242

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ahurta92 commented Apr 28, 2020

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