uoi-heavystruct

01-create.py

import mupif as mp
import tqdm

# schemata must be passed at string to HeavyStruct constructor
# they are only needed when creating the container for the first time
# any subsequent access uses schemata stored in the container itself
schemata=open('schemata.json').read()

# schemaName specifies the top-level schema
# to create molecule-only container, say schemaName='gr.uoi.kostis.molecule', as in the second example

# context manger wraps opening/closing the data and is roughly equivalent to this:
#
#   hs=mp.HeavyStruct(...)
#   grains=hs.openData()
#   ...
#   hs.closeData()

with mp.HeavyStruct(h5path='test-grain.h5',mode='overwrite',schemaName='gr.uoi.kostis.grain',schemasJson=schemata) as grains:
    grains.resize(20)
    for ig,g in enumerate(tqdm.tqdm(grains)):
        g.getProperties().setFreeElectrons(100+ig)
        molecules=g.getMolecules()
        molecules.resize(20)
        for m in molecules:
            atoms=m.getAtoms()
            atoms.resize(20)
            for a in atoms:
                a.getGeneralInfo().setElement('H')

with mp.HeavyStruct(h5path='test-molecule.h5',mode='overwrite',schemaName='gr.uoi.kostis.molecule',schemasJson=schemata) as molecules:
    molecules.resize(20)
    for im,m in enumerate(molecules):
        m.getProperties().setHOMO(im*5*mp.U.eV)
        atoms=m.getAtoms()
        atoms.resize(20)
        for a in atoms:
            a.getGeneralInfo().setElement('Si')

02-modify.py

import mupif as mp
import subprocess

# open input data as read-only, extract whatever data is needed
with mp.HeavyStruct(h5path='test-grain.h5',mode='readonly') as grains:
    for ig,g in enumerate(grains): print(f'grain #{ig}: {g.getProperties().getFreeElectrons()} free electrons')
with mp.HeavyStruct(h5path='test-molecule.h5',mode='readonly') as molecules:
    for im,m in enumerate(molecules):
        print(f'molecule #{im}: HOMO is {m.getProperties().getHOMO()}')

# generate files for external code and call it
subprocess.run(['/bin/true','some','other','args','don\'t use os.system(), it stinks'],check=True)

# write back modified copy of the original container
# this is the same as copying the container (h5path) to a temporary and opening it for writing
with (copy:=mp.HeavyStruct(h5path='test-grain.h5',mode='copy-readwrite')) as grains:
    for ig,g in enumerate(grains): g.getProperties().setFreeElectrons(200+ig)

# just to check the temporary contains the updated container
with mp.HeavyStruct(h5path=copy.h5path,mode='readonly') as grains:
    for ig,g in enumerate(grains): print(f'grain #{ig}: {g.getProperties().getFreeElectrons()} free electrons')

schemata.json

[
	{
		"_schema":{
			"name": "gr.uoi.kostis.grain",
			"version": "0.5"
		},
		"_datasetName": "grains",
		"generalInfo":{
			"material":{ "dtype": "a" }
		},
		"computationalInfo":{
			"boundaryCondition": { "dtype": "a" }
		},
		"structure":{
			"cellSize":{ "dtype":"d", "shape":[3],"unit":"m"}
		},
		"link":{
			"other":{ "dtype":"l", "shape": "variable" }
		},
		"properties":{
			"freeElectrons":{ "dtype":"l" },
			"freeHoles":{ "dtype":"l" },
			"reogranizationEnergyExternal":{ "dtype":"d", "unit":"J" }
		},
		"molecules": { "schema":"gr.uoi.kostis.molecule" }
	},
	{
		"_schema":{
			"name": "gr.uoi.kostis.molecule",
			"version": "0.5"
		},
		"_datasetName": "molecules",
		"generalInfo":{
			"chemicalName":{ "dtype":"a" },
			"molecularWeight":{ "dtype":"d", "unit":"g/mol"},
			"type":{ "dtype":"a2"}
		},
		"computationalInfo":{
			"forceFieldType": {"dtype":"l" }
		},
		"structure":{
			"centerOfMass":{ "dtype":"d", "shape": [3], "unit":"m" },
			"nearestNeighbors":{ "dtype":"l", "shape": "variable" },
			"symmetryAxis": { "dtype":"d", "shape": [3] }
		},
		"link":{
			"other":{ "dtype":"l", "shape": "variable" }
		},
		"properties":{
			"HOMO":{ "dtype":"d", "unit": "eV" },
			"LUMO":{ "dtype":"d", "unit": "eV" },
			"polarizability":{
				"neutral": { "dtype":"d", "shape":[3,3], "unit":"AA^2 s^4 kg^-1"},
				"positive":{ "dtype":"d", "shape":[3,3], "unit":"AA^2 s^4 kg^-1"},
				"negative":{ "dtype":"d", "shape":[3,3], "unit":"AA^2 s^4 kg^-1"}
			},
			"reorganizationEnergyInternal":{
				"neutral": { "dtype":"d", "unit":"eV" },
				"anion":   { "dtype":"d", "unit":"eV" },
				"cation":  { "dtype":"d", "unit":"eV" }
			},
			"siteEnergy":{
				"orbital":      { "dtype":"d", "unit":"eV" },
				"electrostatic":{ "dtype":"d", "unit":"eV" },
				"polarization": { "dtype":"d", "unit":"eV" }
			},
			"transferIntegrals":{ "dtype":"d", "shape":"variable" }
			},
		"atoms": { "schema":"gr.uoi.kostis.atom" }
	},
	{
		"_schema":{
			"name": "gr.uoi.kostis.atom",
			"version": "0.5"
		},
		"_datasetName": "atoms",
		"generalInfo":{
			"element":{ "dtype":"a2" },
			"atomicNumber": {
				"dtype": "l",
				"key": "generalInfo.element",
				"lookup": {
					"H": 1,
					"C": 6,
					"N": 7,
					"Na": 11,
					"Cl": 17,
					"Fe": 26
				}
			},
			"atomicMass": {
				"dtype": "f",
				"key": "generalInfo.element",
				"unit": "Dalton",
				"lookup": {
					"H": 1.0079,
					"C": 12.0107,
					"N": 14.0067,
					"Na": 22.9897,
					"Cl": 35.453,
					"Fe": 55.845
				}
			}
		},
		"structure":{
			"bondNeighbors": { "dtype":"l", "shape":"variable" },
			"bondTypes": { "dtype":"l", "shape":"variable" },
			"name": { "dtype":"a10" },
			"type": { "dtype":"l" },
			"position": { "dtype":"d", "shape":[3],"unit":"AA"},
			"velocity": { "dtype":"d", "shape":[3],"unit":"AA/ps"},
			"residueId": {"dtype":"l" }
		},
		"properties":{
			"partialCharge":{
				"neutral": { "dtype":"d", "unit":"e" },
				"anion":   { "dtype":"d", "unit":"e" },
				"cation":  { "dtype":"d", "unit":"e" }
			},
			"polarizability":{
				"neutral": { "dtype":"d", "unit":"AA^2 s^4 kg^-1" },
				"anion":   { "dtype":"d", "unit":"AA^2 s^4 kg^-1" },
				"cation":  { "dtype":"d", "unit":"AA^2 s^4 kg^-1" }
			}
		},
		"link":{
			"other":{ "dtype":"l", "shape": "variable" }
		}
	}
]