Setting up an environment for quantum computing

docker/quantum/Dockerfile

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+FROM python:3.7
+#FROM continuumio/miniconda3:4.8.2 as build
+
+# Switch back to root, set up the environment.
+#USER 0
+#ENV PATH /opt/conda/bin/:$PATH
+
+COPY src/* /app/
+COPY requirements.txt /app/
+
+# Update apt, install blas/lapack for psi4, then Python deps, and then build.
+RUN apt-get update && \
+  apt-get install -y libblas-dev liblapack-dev && \
+  cd /root && \
+  # Needed for projectq
+  pip install pybind11 && \
+  pip install -r /app/requirements.txt && \
+  wget https://github.com/psi4/psi4/archive/v1.3.2.tar.gz && \
+  tar zxvf v1.3.2.tar.gz && \
+  mkdir build && \
+  cd build && \
+  cmake ../psi4-1.3.2 && make -j10 install && \
+  rm -rf /usr/local/psi4/share/psi4/samples && \
+  cd / && rm -rf /root && mkdir /root && \
+  rm -rf /var/lib/apt/lists/*
+
+ENV PYTHONPATH /usr/local/psi4/lib:$PYTHONPATH
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+ENTRYPOINT ["python", "/app/main.py"]

docker/quantum/README.md

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+Running the Qiskit Docker Container
+=================================
+
+In order to run the Qiskit docker container, first build the
+docker image:
+
+```
+docker build -t quantum:1.0 .
+```
+
+Two input files are required: a geometry file and a parameters file.
+The geometry file should be in `xyz` format. The parameters file should be in 
+`json` format. Example input files are provided [here](example). Look in the 
+example parameters file to see the different parameters that may be set.
+
+The following options should be specified in the command line:
+
+*After `docker run`:*
+* `-v`: Mount the input directory into the docker container.
+
+*After the image name:*
+* `-g`: The location of the input geometry in the docker container.
+* `-p`: The location of the parameters file in the docker container.
+* `-o`: The location and name of the output file in the docker container
+        (it should be placed in the mounted directory).
+* `-s`: The location of the scratch directory in the docker container.
+
+A complete example can be seen below:
+
+```
+cd example/
+docker run -v $(pwd):/data quantum:1.0 -g /data/geometry.xyz -p /data/parameters.json -o /data/out.cjson -s /data/scratch
+```
+
+Or to optimize the geometry with Psi4 before running the calculation:
+
+```
+docker run -v $(pwd):/data quantum:1.0 -g /data/geometry.xyz -p /data/optimization_parameters.json -o /data/out.cjson -s /data/scratch
+```
+
+After the docker container finishes, the output file will be located in
+the example directory. The output file is in `cjson` format.
+
+A json description of the image and some of the options may be obtained via:
+```
+docker run quantum:1.0 -d
+```
+
+Register Image to Run Notebook
+=================================
+
+The easiest way:
+- Use the Girder API to register the local image:
+  - Visit http://localhost:8080/api/v1
+  - [GET cluster ID](http://localhost:8080/api/v1#!/clusters/clusters_find)
+  - [Register the local image](http://localhost:8080/api/v1#!/images/images_create)
+    - `type`: <strong>docker</strong>
+    - `repository`: <strong>quantum</strong>
+    - `tag`: <strong>1.0</strong>
+    - `digest`: <strong>123</strong> (can be any value)
+    - `clusterId`: (from GET /clusters)
+    - `size`: <strong>2</strong> (can be any value)

docker/quantum/example/geometry.xyz

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+2
+
+Li      0.00000    0.00000    0.00000
+Li      0.00000    0.00000    2.67298

docker/quantum/example/optimization_parameters.json

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+{
+  "basis": "sto3g",
+  "charge": 0,
+  "multiplicity": 1,
+  "orbital_reduction": [4, 10],
+  "optimization":{
+    "theory": "hf",
+    "basis": "6-31g",
+    "charge": 0,
+    "multiplicity": 1
+  }
+}

docker/quantum/example/parameters.json

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+{
+  "basis": "sto3g",
+  "charge": 0,
+  "multiplicity": 1,
+  "orbital_reduction": [4, 10],
+  "optimization":{
+    "theory": "hf",
+    "basis": "6-31g",
+    "charge": 0,
+    "multiplicity": 1
+  }
+}

docker/quantum/requirements.txt

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+scipy
+qiskit
+projectq
+avogadro
+click
+jinja2
+cmake
+pint
+pydantic
+deepdiff # Need for psi4
+pyscf

docker/quantum/src/describe.py

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+import json
+import os
+
+def get_description():
+  with open(os.path.join(os.path.dirname(__file__), 'description.json')) as f:
+    return json.load(f)

docker/quantum/src/description.json

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+{
+    "name": "Quantum",
+    "version": "0.22",
+    "input": {
+        "format": "xyz",
+        "parameters": {
+            "basis": {
+                "type": "string",
+                "description": "The basis set.",
+                "default": "sto3g"
+            },
+            "charge": {
+                "type": "number",
+                "description": "The net charge of the system.",
+                "default": 0
+            },
+            "multiplicity": {
+                "type": "number",
+                "description": "The spin multiplicity.",
+                "default": 1
+            },
+            "orbital_reduction": {
+                "type": "array",
+                "description": "Complexity of the calculation",
+                "default": [4, 10]
+            },
+            "optimization": {
+                "theory": {
+                    "type": "string",
+                    "description": "The theory level: hf | dft",
+                    "default": "hf"
+                },
+                "basis": {
+                    "type": "string",
+                    "description": "The basis set.",
+                    "default": "cc-pvdz"
+                },
+                "functional": {
+                    "type": "string",
+                    "description": "The XC functional (if ks theory).",
+                    "default": "b3lyp"
+                },
+                "charge": {
+                    "type": "number",
+                    "description": "The net charge of the system.",
+                    "default": 0
+                },
+                "multiplicity": {
+                    "type": "number",
+                    "description": "The spin multiplicity.",
+                    "default": 1
+                }
+            }
+        }
+    },
+    "output": {
+        "format": "cjson"
+    }
+}

docker/quantum/src/main.py

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+import click
+import sys
+import json
+
+import describe
+import run
+
+def describe_callback(ctx, param, value):
+    if not value:
+        return
+    # Print the description object and stop execution of the container if --describe option is passed
+    description = json.dumps(describe.get_description(), indent=2)
+    click.echo(description, file=sys.stdout)
+    ctx.exit()
+
+@click.command()
+@click.option('--describe', '-d',
+              help='Return an object to std output that describes the expected input and output parameters of this container.',
+              is_flag=True, is_eager=True, expose_value=False, callback=describe_callback)
+@click.option('--geometry', '-g', 'geometry_file', multiple=True,
+              type=click.Path(exists=True, dir_okay=False, resolve_path=True),
+              required=True,
+              help='The path to the file containing the input geometry')
+@click.option('--parameters', '-p', 'parameters_file',
+              type=click.Path(exists=True, dir_okay=False, resolve_path=True),
+              help='The path to the JSON file containing the input input parameters.')
+@click.option('--output', '-o', 'output_file', multiple=True,
+              type=click.Path(exists=False, dir_okay=False, resolve_path=True),
+              required=True,
+              help='The path to the file that will contain the converted calculation output.')
+@click.option('--scratch', '-s', 'scratch_dir',
+              type=click.Path(exists=False, dir_okay=True, file_okay=False, resolve_path=True),
+              help='The path to the directory that will be used as scratch space while running the calculation.')
+def main(geometry_file, parameters_file, output_file, scratch_dir):
+    with open(parameters_file) as f:
+        params = json.load(f)
+
+    for g, o in zip(geometry_file, output_file):
+        run.run_calculation(g, o, params, scratch_dir)
+
+
+if __name__ == '__main__':
+    main()

docker/quantum/src/run.py

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+import json
+import psi4
+
+from qiskit import BasicAer
+from qiskit.aqua import QuantumInstance
+from qiskit.chemistry.algorithms.ground_state_solvers.minimum_eigensolver_factories import VQEUCCSDFactory
+from qiskit.chemistry.drivers import PySCFDriver, UnitsType, Molecule
+from qiskit.chemistry.transformations import FermionicTransformation, FermionicQubitMappingType
+from qiskit.aqua.algorithms import NumPyMinimumEigensolver, VQE
+from qiskit.chemistry.algorithms.ground_state_solvers import GroundStateEigensolver
+
+
+def optimize_geometry(geometry, params):
+  opt = params.get('optimization', {})
+
+  # Get parameters for optimization
+  # Use qiskit parameters if no optimization values are provided
+  theory = opt.get('theory', params.get('theory', 'hf'))
+  basis = opt.get('basis', params.get('basis', 'cc-pvdz'))
+  functional = opt.get('functional', params.get('functional', 'b3lyp'))
+  charge = opt.get('charge', params.get('charge', 0))
+  multiplicity = opt.get('multiplicity', params.get('multiplicty', 1))
+
+  if theory.lower() == 'dft':
+      _theory = functional
+      reference = 'ks'
+  else:
+      _theory = 'scf'
+      reference = 'hf'
+
+  if multiplicity == 1:
+      reference = 'r' + reference
+  else:
+      reference = 'u' + reference
+
+  # Create molecule
+  geometry.insert(0, f'{charge} {multiplicity}')
+  mol = psi4.geometry(('\n').join(geometry))
+
+  # Optimize geometry
+  psi4.set_options({'reference': reference})
+  psi4.core.be_quiet()
+  energy = psi4.optimize(f'{_theory}/{basis}', molecule=mol)
+  results = mol.to_dict()
+
+  coords = results['geom']
+  geom = []
+  for elem, coord in zip(results['elem'], coords.reshape(-1, 3)):
+    geom.append([elem, coord])
+
+  return list(coords), geom, energy
+
+
+def run_calculation(geometry_file, output_file, params, scratch_dir):
+  # Read in the geometry from the geometry file
+  # This container expects the geometry file to be in .xyz format
+  with open(geometry_file) as f:
+    atoms, comment, *xyz_structure = f.read().splitlines()
+
+  # Warn the user that molecule should have 3 or fewer atoms
+  # TODO: Add warning
+
+  # Optimize geometry if input has been provided
+  if params.get('optimization', {}):
+    coords, geom, psi4_energy = optimize_geometry(xyz_structure, params)
+  else:
+    geom, coords = [], []
+    for atom in xyz_structure:
+      name, vals = atom.split(' ', 1)
+      vals = [val for val in vals.split(' ') if val]
+      coords.extend(vals)
+      geom.append([name, vals])
+
+  # Read the input parameters
+  basis = params.get('basis', 'cc-pvdz')
+  charge = params.get('charge', 0)
+  multiplicity = params.get('multiplicity', 1)
+  range_start, range_end = params.get('orbital_reduction', [4, 10])
+  orbital_reduction = list(range(range_start, range_end))
+
+  # Set up the molcule, here we can feed data from OpenChemistry
+  molecule = Molecule(geometry=geom, charge=charge,
+                      multiplicity=multiplicity)
+
+  # Define the classical quantum chemistry driver to get the molecular integrals
+  # Also gives us the Hartree-Fock energy and orbital energies if desired
+  driver = PySCFDriver(molecule = molecule, unit=UnitsType.ANGSTROM, basis=basis)
+
+  # Generating a small quantum calculation freezing core and throwing away virtuals, 
+  # only keeping 2 electrons in 2 orbitals
+  transformation = FermionicTransformation(qubit_mapping=FermionicQubitMappingType.JORDAN_WIGNER,
+                                           freeze_core=True, orbital_reduction=orbital_reduction)
+
+  # Quantum solver and wave function structure generator (UCCSD)
+  vqe_solver = VQEUCCSDFactory(QuantumInstance(BasicAer.get_backend('qasm_simulator')), 
+                               include_custom=True, method_doubles='succ_full')
+
+  # Run the smallest quantum simulation
+  calc = GroundStateEigensolver(transformation, vqe_solver)
+  res = calc.solve(driver)
+
+  cjson = {
+    'chemicalJson': 1,
+    'atoms': {
+      'coords': {
+        '3d': coords
+      }
+    },
+    'properties': {
+      'ground_state_energy': res.total_energies[0]
+    }
+  }
+
+  if params.get('optimization', {}):
+    cjson['properties']['optimization_energy'] = psi4_energy
+
+  with open(output_file, 'w') as f:
+    json.dump(cjson, f)