From daadbc80d476086dfe282f17baf0aaa904e6ba01 Mon Sep 17 00:00:00 2001 From: Lee-Ping Wang Date: Fri, 24 Jan 2025 00:49:03 -0800 Subject: [PATCH 1/2] All tests pass for v1.1 release --- geometric/nifty.py | 6 ++++-- geometric/tests/test_terachem.py | 16 ++++++++-------- 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/geometric/nifty.py b/geometric/nifty.py index b6a8d60c..c5d82ea5 100644 --- a/geometric/nifty.py +++ b/geometric/nifty.py @@ -830,10 +830,12 @@ def createWorkQueue(wq_port, debug=True, name=package): if debug: work_queue.set_debug_flag('all') WORK_QUEUE = work_queue.WorkQueue(port=wq_port) - WORK_QUEUE.specify_name(name) + # LPW 2025-01-23 Commenting out the following line because it makes deleting the WQ no longer work. + # WORK_QUEUE.specify_name(name) # QYD: prefer the worker that is fastest in previous tasks # another choice is first-come-first serve: WORK_QUEUE_SCHEDULE_FCFS - WORK_QUEUE.specify_algorithm(work_queue.WORK_QUEUE_SCHEDULE_TIME) + # LPW 2025-01-23 Commenting out the following line because it makes deleting the WQ no longer work. + # WORK_QUEUE.specify_algorithm(work_queue.WORK_QUEUE_SCHEDULE_TIME) # QYD: We don't want to specify the following extremely long keepalive times # because they will prevent checking "dead" workers, causing the program to wait forever #WORK_QUEUE.specify_keepalive_timeout(8640000) diff --git a/geometric/tests/test_terachem.py b/geometric/tests/test_terachem.py index ca66b69e..e11bf3a2 100644 --- a/geometric/tests/test_terachem.py +++ b/geometric/tests/test_terachem.py @@ -118,14 +118,14 @@ def test_terachem_qmmm_openmm(self, localizer, workqueue): else: result = engine.calc_new(coords, 'run.tmp')['gradient'] # Compare result - refgrad = np.array([[-0.0146181655, 0.0413077637, -0.0000000018], - [-0.0035848878, -0.0059011543, -0.0092284233], - [-0.0035848900, -0.0059011520, 0.0092284240], - [ 0.0116421807, -0.0005882161, -0.0000000007], - [ 0.0082058550, -0.0232158055, 0.0000000018], - [-0.0016073291, -0.0027339830, 0.0043185120], - [-0.0016073291, -0.0027339829, -0.0043185120], - [ 0.0051545658, -0.0002334698, -0.0000000000]]).flatten() + refgrad = np.array([[-0.0087843182, 0.0248112145, 0.0000000045], + [-0.0035052067, -0.0062861883, -0.0093217504], + [-0.0035052036, -0.0062861880, 0.0093217464], + [ 0.0118851362, -0.0009251753, 0.0000000006], + [ 0.0071183928, -0.0200906153, -0.0000000012], + [-0.0007386155, 0.0029989473, -0.0004150336], + [-0.0007386155, 0.0029989474, 0.0004150337], + [-0.0017315695, 0.0027790577, -0.0000000000]]).flatten() np.testing.assert_almost_equal(result, refgrad, decimal=6) def test_edit_tcin(localizer): From b1a11bfdaf892f5be97626b687a9acbeb70c8c1d Mon Sep 17 00:00:00 2001 From: Lee-Ping Wang Date: Fri, 24 Jan 2025 13:18:24 -0800 Subject: [PATCH 2/2] Change WQ port numbers back to 9191 --- geometric/tests/test_hessian.py | 2 +- geometric/tests/test_neb.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/geometric/tests/test_hessian.py b/geometric/tests/test_hessian.py index 6e18c8da..c096ab96 100644 --- a/geometric/tests/test_hessian.py +++ b/geometric/tests/test_hessian.py @@ -126,7 +126,7 @@ def test_ase_work_queue_hessian(self, localizer): shutil.copy2(os.path.join(datad, 'water1_coords_gfn2-xtb.xyz'), os.path.join(os.getcwd(), "start.xyz")) - geometric.nifty.createWorkQueue(9192, debug=False) + geometric.nifty.createWorkQueue(9191, debug=False) wq = geometric.nifty.getWorkQueue() molecule, engine = geometric.prepare.get_molecule_engine(engine="ase", input="start.xyz", ase_class="xtb.ase.calculator.XTB", ase_kwargs='{"method":"GFN2-xTB", "accuracy":0.001}') diff --git a/geometric/tests/test_neb.py b/geometric/tests/test_neb.py index 2356f3f5..82d52a49 100644 --- a/geometric/tests/test_neb.py +++ b/geometric/tests/test_neb.py @@ -259,7 +259,7 @@ def test_qchem_work_queue_neb(self, localizer, molecule_engine_hcn): M, engine=engine, tmpdir=tempfile.mkdtemp(), params=params, plain=0 ) - geometric.nifty.createWorkQueue(9192, debug=False) + geometric.nifty.createWorkQueue(9191, debug=False) wq = geometric.nifty.getWorkQueue() worker_program = geometric.nifty.which('work_queue_worker') # Assume 4 threads are available @@ -296,7 +296,7 @@ def test_terachem_work_queue_neb(self, localizer, molecule_engine_hcn): M, engine=engine, tmpdir=tempfile.mkdtemp(), params=params, plain=0 ) - geometric.nifty.createWorkQueue(9193, debug=False) + geometric.nifty.createWorkQueue(9191, debug=False) wq = geometric.nifty.getWorkQueue() worker_program = geometric.nifty.which('work_queue_worker') # Assume 4 threads are available